[adios] 01/05: new upstream release 1.12.0
Alastair McKinstry
mckinstry at moszumanska.debian.org
Wed Jul 19 08:49:27 UTC 2017
This is an automated email from the git hooks/post-receive script.
mckinstry pushed a commit to branch debian/master
in repository adios.
commit c0f5b6de3e75d836689b4272c92b64e2aae907ed
Author: Alastair McKinstry <mckinstry at debian.org>
Date: Tue Jul 18 13:18:42 2017 +0100
new upstream release 1.12.0
---
CMakeLists.txt | 364 +-
Makefile.in | 13 +-
NEWS | 18 +
aclocal.m4 | 2 +
cmake_init | 321 +-
config.h.cmake | 19 +-
config.h.in | 12 +
config/ac_bzip2.m4 | 4 +-
config/ac_dataspaces.m4 | 50 +-
config/ac_dimes.m4 | 44 +-
config/ac_flexpath.m4 | 63 +-
config/ac_lz4.m4 | 83 +
config/ac_sz.m4 | 73 +
config/ac_zlib.m4 | 4 +-
config/acx_pthread.m4 | 1 +
config/config.guess | 885 +-
config/config.sub | 473 +-
config/libtool.m4 | 27 +-
config/ltmain.sh | 37 +-
configure | 2438 +---
configure.ac | 79 +-
examples/C/Makefile.in | 13 +-
examples/C/arrays/Makefile.in | 13 +-
examples/C/attributes/Makefile.in | 13 +-
examples/C/flexpath_arrays/Makefile.in | 13 +-
.../global_range_select/Makefile.in | 13 +-
.../C/flexpath_arrays/process_select/Makefile.in | 13 +-
examples/C/global-array-time/Makefile.in | 13 +-
examples/C/global-array/Makefile.in | 13 +-
examples/C/global-array/adios_read_chunk.c | 123 +-
examples/C/global-array/adios_read_global.c | 65 +-
examples/C/global-array/adios_read_gpp.c | 21 +-
examples/C/global-array/adios_read_writeblock.c | 82 +-
examples/C/global-array/gread_temperature.ch | 2 +-
examples/C/icee_arrays/Makefile.in | 13 +-
examples/C/icee_arrays/array/Makefile.in | 13 +-
examples/C/manual/Makefile.in | 13 +-
examples/C/query/Makefile.in | 13 +-
examples/C/query/query_table.c | 2 +-
examples/C/query/query_vars.c | 4 +-
examples/C/read_all/Makefile.in | 13 +-
examples/C/scalars/Makefile.in | 13 +-
examples/C/schema/Makefile.in | 13 +-
examples/C/stat/Makefile.in | 13 +-
examples/C/time_aggregation/Makefile.in | 13 +-
examples/C/transforms/Makefile.in | 13 +-
examples/Fortran/Makefile.in | 13 +-
examples/Fortran/arrays/Makefile.in | 13 +-
examples/Fortran/global-array-time/Makefile.in | 13 +-
examples/Fortran/global-array/Makefile.in | 13 +-
examples/Fortran/scalars/Makefile.in | 13 +-
examples/Fortran/schema/Makefile.in | 13 +-
examples/Makefile.in | 13 +-
examples/staging/stage_write/stage_write.c | 2 +-
.../staging/stage_write_varyingsize/stage_write.c | 2 +-
runconf | 580 +-
scripts/FindADIOS.cmake | 13 +-
src/CMakeLists.txt | 501 +-
src/Makefile.am | 7 +-
src/Makefile.in | 89 +-
src/core/adios_bp_v1.c | 46 +-
src/core/adios_clock.h | 3 +
src/core/adios_internals.c | 34 +-
src/core/adios_internals.h | 7 +-
src/core/adios_internals_mxml.c | 12 +-
src/core/adios_subvolume.c | 8 +-
src/core/adios_transform_methods.c | 5 +-
src/core/adiost_callback_internal.c | 185 +
src/core/adiost_callback_internal.h | 85 +
src/core/adiost_default_tool.c | 348 +
src/core/bp_utils.c | 226 +-
src/core/bp_utils.h | 4 +-
src/core/common_adios.c | 2451 ++--
src/core/common_read.c | 25 +-
src/core/flexpath.h | 179 +-
src/core/globals.c | 104 +-
src/core/globals.h | 4 +
src/mxml/Makefile.in | 13 +-
src/public/adios_error.h | 1 +
src/public/adios_version.h | 6 +-
src/public/adiost_callback_api.h | 153 +
src/public/mpidummy.h | 3 +
src/read/read_bp.c | 84 +-
src/read/read_flexpath.c | 2090 ++-
src/transforms/Makefile.plugins | 8 +
src/transforms/adios_transform_lz4_common.h | 18 +
src/transforms/adios_transform_lz4_read.c | 170 +
src/transforms/adios_transform_lz4_write.c | 278 +
src/transforms/adios_transform_sz_read.c | 122 +
src/transforms/adios_transform_sz_write.c | 343 +
src/transforms/transform_plugins.h | 3 +-
src/write/adios_flexpath.c | 2043 ++-
src/write/adios_icee.c | 4 +-
src/write/adios_mpi.c | 6 +
src/write/adios_mpi_amr.c | 5 +
src/write/adios_posix.c | 183 +-
src/zfp/Makefile.in | 13 +-
tests/C/Makefile.in | 13 +-
tests/C/fgr_tests/Makefile.in | 13 +-
tests/C/flexpath_tests/1D_arr_global/Makefile.in | 13 +-
tests/C/flexpath_tests/1D_arr_global/reader.c | 51 +-
tests/C/flexpath_tests/1D_arr_global/writer.c | 24 +-
.../flexpath_tests/1D_arr_global_noxml/Makefile.in | 13 +-
.../C/flexpath_tests/1D_arr_global_noxml/writer.c | 10 +-
tests/C/flexpath_tests/CMakeLists.txt | 1 -
tests/C/flexpath_tests/Makefile.am | 2 +-
tests/C/flexpath_tests/Makefile.in | 15 +-
tests/C/flexpath_tests/README | 5 +-
tests/C/flexpath_tests/common/utils.c | 12 +-
.../global_range_select/CMakeLists.txt | 12 +-
.../flexpath_tests/global_range_select/Makefile.am | 18 +-
.../flexpath_tests/global_range_select/Makefile.in | 74 +-
.../global_range_select/arrays_read.c | 113 -
.../global_range_select/arrays_write.c | 58 -
.../C/flexpath_tests/global_range_select/reader.c | 132 +
.../{arrays.xml => test_config_flex.xml} | 2 +-
.../C/flexpath_tests/global_range_select/writer.c | 77 +
tests/C/flexpath_tests/include/misc.h | 4 -
tests/C/flexpath_tests/include/test_common.h | 38 +-
tests/C/flexpath_tests/include/utils.h | 2 +-
tests/C/flexpath_tests/local_arrays/Makefile.am | 18 +
.../{maya_append => local_arrays}/Makefile.in | 71 +-
tests/C/flexpath_tests/local_arrays/cfg.h | 15 +
.../{1D_arr_global => local_arrays}/reader.c | 77 +-
.../{1D_arr_global_noxml => local_arrays}/writer.c | 24 +-
tests/C/flexpath_tests/maya_append/CMakeLists.txt | 15 -
tests/C/flexpath_tests/maya_append/Makefile.am | 19 -
tests/C/flexpath_tests/maya_append/cfg.h | 26 -
tests/C/flexpath_tests/maya_append/reader.c | 137 -
tests/C/flexpath_tests/maya_append/readme.txt | 64 -
tests/C/flexpath_tests/maya_append/writer.c | 133 -
tests/C/flexpath_tests/maya_noxml/Makefile.in | 13 +-
tests/C/flexpath_tests/maya_noxml/reader.c | 71 +-
tests/C/flexpath_tests/maya_noxml/writer.c | 118 +-
tests/C/flexpath_tests/scalar/Makefile.in | 13 +-
tests/C/flexpath_tests/scalar/writer.c | 10 +-
tests/C/query/Makefile.in | 13 +-
tests/C/query/alacrity/Makefile.in | 13 +-
tests/C/query/alacrity/adios_alac_query.c | 2 +-
tests/C/query/common/Makefile.in | 13 +-
tests/C/query/fastbit/Makefile.in | 13 +-
tests/Fortran/Makefile.in | 13 +-
tests/Makefile.in | 13 +-
tests/bp_read/Makefile.in | 13 +-
tests/genarray/CMakeLists.txt | 18 +-
tests/genarray/Makefile.am | 18 +-
tests/genarray/Makefile.in | 33 +-
tests/genarray/copyarray.F90 | 60 +-
tests/genarray/genarray.F90 | 53 +-
tests/genarray/genarray.xml | 1 -
tests/genarray/genarray2D.F90 | 10 +-
tests/genarray/genarray3d.xml | 1 -
tests/suite/Makefile.in | 13 +-
tests/suite/programs/CMakeLists.txt | 5 +-
tests/suite/programs/Makefile.am | 8 +-
tests/suite/programs/Makefile.in | 38 +-
tests/suite/programs/adios_amr_write.c | 1 +
tests/suite/programs/adios_amr_write_2vars.c | 1 +
tests/suite/programs/big_file.c | 12 +-
tests/suite/programs/blocks.c | 24 +-
tests/suite/programs/build_standard_dataset.c | 2 +-
tests/suite/programs/examples/CMakeLists.txt | 5 +
tests/suite/programs/examples/Makefile.in | 13 +-
.../programs/examples/attributes/CMakeLists.txt | 10 +-
.../suite/programs/examples/attributes/Makefile.in | 13 +-
.../programs/examples/global_array/CMakeLists.txt | 17 +-
.../programs/examples/global_array/Makefile.in | 13 +-
.../examples/global_array/global_array_read_C.c | 2 +-
.../global_array/global_array_read_byid_noxml_C.c | 2 +-
.../global_array/global_array_read_noxml_C.c | 2 +-
.../examples/global_array_time/CMakeLists.txt | 22 +-
.../examples/global_array_time/Makefile.am | 9 +-
.../examples/global_array_time/Makefile.in | 42 +-
.../global_array_time/global_array_time_aggr_C.xml | 2 +-
.../global_array_time_read_as_file_C.c | 4 +-
.../global_array_time_read_as_stream_C.c | 4 +-
.../global_array_time_write_multifile_C.c | 64 +
.../programs/examples/local_array/CMakeLists.txt | 8 +-
.../programs/examples/local_array/Makefile.in | 13 +-
.../suite/programs/examples/scalars/CMakeLists.txt | 12 +-
tests/suite/programs/examples/scalars/Makefile.in | 13 +-
.../programs/examples/scalars/scalars_read_C.c | 4 +-
tests/suite/programs/many_vars.c | 2 +-
tests/suite/programs/reuse_dim.c | 1 +
tests/suite/programs/selections.c | 1 +
tests/suite/programs/set_path.c | 17 +-
tests/suite/programs/set_path_var.c | 2 +-
tests/suite/programs/steps_read_file.c | 2 +-
tests/suite/programs/steps_read_stream.c | 2 +-
tests/suite/programs/test_singlevalue.c | 350 +
tests/suite/programs/transforms_writeblock_read.c | 2 +-
tests/suite/tests/05_global_array_time.sh | 69 +-
tests/suite/tests/21_test_singlevalue.sh | 37 +
tests/test_src/Makefile.am | 8 +-
tests/test_src/Makefile.in | 69 +-
tests/test_src/query_minmax.c | 8 +-
tests/test_src/read_points_3d.c | 774 +
utils/Makefile.in | 13 +-
utils/adios_lint/Makefile.in | 13 +-
utils/adios_list_methods/Makefile.in | 13 +-
utils/bp2ascii/Makefile.in | 13 +-
utils/bp2bp/Makefile.in | 13 +-
utils/bp2bp/bp2bp.c | 2 +-
utils/bp2h5/Makefile.in | 13 +-
utils/bp2h5/bp2h5.c | 4 +-
utils/bp2ncd/Makefile.in | 13 +-
utils/bpdiff/Makefile.in | 13 +-
utils/bpdump/Makefile.in | 13 +-
utils/bpls/Makefile.in | 13 +-
utils/bpls/bpls.c | 28 +-
utils/bpmeta/Makefile.in | 13 +-
utils/bpmeta/bpmeta.c | 70 +-
utils/bprecover/Makefile.in | 13 +-
utils/bpsplit/Makefile.in | 13 +-
utils/bpsplit/bpappend.c | 2 +
utils/bpsplit/bpsplit.c | 2 +
utils/fastbit/Makefile.in | 13 +-
utils/fastbit/adios_index_fastbit.c | 6 +-
utils/gpp/Makefile.in | 13 +-
utils/gpp/gpp.py | 8 +-
utils/gpp/gpp.py.in | 8 +-
utils/skel/Makefile.in | 13 +-
utils/skel/etc/Makefile.in | 13 +-
utils/skel/etc/templates/source_write_c.tmpl | 2 +-
utils/skel/src/Makefile.in | 13 +-
utils/skeldump/Makefile.in | 13 +-
wrappers/numpy/adios.cpp | 14013 ++++++++++--------
wrappers/numpy/adios.pyx | 90 +-
wrappers/numpy/adios_mpi.cpp | 14269 +++++++++++--------
wrappers/numpy/adios_mpi.pyx | 90 +-
wrappers/numpy/adios_mpi2serial.sed | 2 +
wrappers/numpy/build-and-install.sh | 2 +
wrappers/numpy/doc/source/build.rst | 109 +-
wrappers/numpy/doc/source/conf.py | 4 +-
wrappers/numpy/doc/source/index.rst | 1 +
wrappers/numpy/doc/source/quick.rst | 24 +-
wrappers/numpy/example/staging/adios_read_mpi.py | 7 +-
wrappers/numpy/src/__init__.py | 2 +-
wrappers/numpy/src_mpi/__init__.py | 2 +-
wrappers/numpy/test/test_adios_writer_unittest.py | 47 +-
wrappers/numpy/tests/test_adios_mpi_writer.py | 4 +-
wrappers/numpy/tests/test_adios_writer.py | 3 +-
242 files changed, 29347 insertions(+), 19336 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 30bcb04..a2671aa 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -65,7 +65,7 @@ if(DEFINED ENV{EXTRA_LIBS})
endif()
######## file moved from initial_cache.cmake to indicate external library is used(ON) or not (OFF)######
if(DEFINED ENV{BUILD_WRITE})
- if("$ENV{BUILD_WRITE}" STREQUAL "")
+ if("$ENV{BUILD_WRITE}" STREQUAL "")
set(BUILD_WRITE ON CACHE BOOL "")
else()
set(BUILD_WRITE $ENV{BUILD_WRITE})
@@ -466,7 +466,7 @@ if(GLIB)
else()
set(FGR OFF CACHE BOOL "")
endif()
-
+
if(DEFINED ENV{BZIP2_DIR})
if("$ENV{BZIP2_DIR}" STREQUAL "")
set(BZIP2 OFF CACHE BOOL "")
@@ -483,6 +483,22 @@ elseif(DEFINED ENV{BZIP2})
endif()
endif()
+if(DEFINED ENV{LZ4_DIR})
+ if("$ENV{LZ4_DIR}" STREQUAL "")
+ set(LZ4 OFF CACHE BOOL "")
+ else()
+ set(LZ4 ON CACHE BOOL "")
+ set(LZ4_DIR "$ENV{LZ4_DIR}")
+ endif()
+elseif(DEFINED ENV{LZ4})
+ if("$ENV{LZ4}" STREQUAL "")
+ set(LZ4 OFF CACHE BOOL "")
+ else()
+ set(LZ4 ON CACHE BOOL "")
+ set(LZ4_DIR "$ENV{LZ4}")
+ endif()
+endif()
+
if(DEFINED ENV{SZIP_DIR})
if("$ENV{SZIP_DIR}" STREQUAL "")
set(SZIP OFF CACHE BOOL "")
@@ -567,6 +583,22 @@ else()
set(ZFP_DIR ${PROJECT_SOURCE_DIR}/src/zfp/zfp-0.5.0)
endif()
+if(DEFINED ENV{SZ_DIR})
+ if("$ENV{SZ_DIR}" STREQUAL "")
+ set(SZ OFF CACHE BOOL "")
+ else()
+ set(SZ ON CACHE BOOL "")
+ set(SZ_DIR $ENV{SZ_DIR})
+ endif()
+elseif(DEFINED ENV{SZ})
+ if(NOT "$ENV{SZ}" STREQUAL "")
+ set(SZ OFF CACHE BOOL "")
+ else()
+ set(SZ_DIR $ENV{SZ})
+ set(SZ ON CACHE BOOL "")
+ endif()
+endif()
+
###################### end of external library is used(ON) or not (OFF) ##############################
@@ -603,9 +635,13 @@ CHECK_FUNCTION_EXISTS(gettimeofday HAVE_GETTIMEOFDAY)
# Define to 1 if you have the `clock_gettime' function.
CHECK_FUNCTION_EXISTS(clock_gettime HAVE_CLOCK_GETTIME)
-# Define to 1 if you have the `clock_get_time' function. On OSX.
+# Define to 1 if you have the `clock_get_time' function. On OSX.
CHECK_FUNCTION_EXISTS(clock_get_time HAVE_CLOCK_GET_TIME)
+# Check if clockid_t type exist
+include(CheckTypeSize)
+CHECK_TYPE_SIZE("clockid_t" CLOCKID_T)
+
# Define if you have CRAY_PMI.
set(HAVE_CRAY_PMI 0)
if(CRAY_PMI)
@@ -637,7 +673,7 @@ CHECK_FUNCTION_EXISTS(ibv_alloc_pd HAVE_IBVERBS)
set(HAVE_INFINIBAND 0)
if(HAVE_IBVERBS_H AND HAVE_IBVERBS)
set(HAVE_INFINIBAND 1)
- set(INFINIBAND ON CACHE BOOL "")
+ set(INFINIBAND ON CACHE BOOL "")
set(INFINIBAND_LIBS "-libverbs")
# set(LIBS "${LIBS} ${INFINIBAND_LIBS}")
endif()
@@ -674,10 +710,10 @@ if(PORTALS)
set(PORTALS_CFLAGS "${PORTALS_CFLAGS} ${EXTRA_CFLAGS}")
set(CFLAGS "${CFLAGS} ${PORTALS_CFLAGS}")
set(PORTALS_CPPFLAGS "${PORTALS_CPPFLAGS} ${EXTRA_CPPFLAGS}")
-# set(CPPFLAGS "${CPPFLAGS} ${PORTALS_CPPFLAGS}")
+# set(CPPFLAGS "${CPPFLAGS} ${PORTALS_CPPFLAGS}")
endif()
#else()
-# find_package(TPLPortals)
+# find_package(TPLPortals)
# if(TPLPortals_FOUND)
# set(PORTALS ON CACHE BOOL "" FORCE)
# set(HAVE_PORTALS 1)
@@ -694,7 +730,7 @@ endif()
# Define to 1 if you have the <dataspaces.h> header file.
set(HAVE_DATASPACES_H 0)
if(DATASPACES)
- if(DEFINED DATASPACES_INCDIR)
+ if(DEFINED DATASPACES_INCDIR)
if("${DATASPACES_INCDIR}" STREQUAL "")
set(DATASPACES_INCDIR "$ENV{DATASPACES_DIR}/include")
endif()
@@ -723,10 +759,55 @@ if(HAVE_DATASPACES_H)
else()
set(DATASPACES_LIBDIR "$ENV{DATASPACES_DIR}/lib")
endif()
-
- if(HAVE_INFINIBAND)
- find_library(DATASPACES_LIBS1 NAMES libdspaces.a PATHS ${DATASPACES_LIBDIR})
+
+ # 1.6.2 has a config file
+ set(DATASPACES_BINDIR "$ENV{DATASPACES_DIR}/bin")
+ #message("DATASPACES: look for dspaces_config")
+ find_program (DSPACES_CONFIG NAMES dspaces_config
+ PATHS "$ENV{DATASPACES_DIR}/bin" NO_DEFAULT_PATH)
+
+ if(DSPACES_CONFIG)
+ #message("DATASPACES: run dspaces_config")
+ execute_process(COMMAND ${DSPACES_CONFIG} "-l"
+ OUTPUT_VARIABLE dspaces_config_out
+ RESULT_VARIABLE dspaces_config_ret
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+ )
+ #message("DATASPACES: return value = ${dspaces_config_ret}")
+ #message("DATASPACES: output = ${dspaces_config_out}")
+ if(dspaces_config_ret EQUAL 0)
+ string(REPLACE " " ";" dspaces_config_list ${dspaces_config_out})
+ #message("DATASPACES: list = ${dspaces_config_list}")
+ set(dspaces_libs)
+ set(dspaces_lib_hints)
+ set(dspaces_lib_flags)
+ foreach(OPT IN LISTS dspaces_config_list)
+ if(OPT MATCHES "^-L(.*)")
+ list(APPEND dspaces_lib_hints "${CMAKE_MATCH_1}")
+ elseif(OPT MATCHES "^-l(.*)")
+ list(APPEND dspaces_libs "${CMAKE_MATCH_1}")
+ else()
+ list(APPEND dspaces_lib_flags "${OPT}")
+ endif()
+ endforeach()
+ set(HAVE_DATASPACES 1)
+ endif()
+ #message("DATASPACES: hints = ${dspaces_lib_hints}")
+ #message("DATASPACES: libs = ${dspaces_libs}")
+ #message("DATASPACES: flags = ${dspaces_lib_flags}")
+ set(DATASPACES_LIBS)
+ foreach(lib IN LISTS dspaces_libs)
+ find_library(dspaces_${lib}_LIBRARY NAME ${lib} HINTS ${dspaces_lib_hints})
+ if(dspaces_${lib}_LIBRARY)
+ list(APPEND DATASPACES_LIBS ${dspaces_${lib}_LIBRARY})
+ else()
+ list(APPEND DATASPACES_LIBS ${lib})
+ endif()
+ endforeach()
+
+ elseif(HAVE_INFINIBAND)
set(DATASPACES_LIBS1 "${DATASPACES_LIBS1}" CACHE INTERNAL "Internal variable")
+ find_library(DATASPACES_LIBS1 NAMES libdspaces.a PATHS ${DATASPACES_LIBDIR})
find_library(DATASPACES_LIBS2 NAMES libdscommon.a PATHS ${DATASPACES_LIBDIR})
set(DATASPACES_LIBS2 "${DATASPACES_LIBS2}" CACHE INTERNAL "Internal variable")
find_library(DATASPACES_LIBS3 NAMES libdart.a PATHS ${DATASPACES_LIBDIR})
@@ -778,12 +859,15 @@ endif()
# Define to 1 if you have the <dimes.h> header file.
set(HAVE_DIMES_H 0)
if(HAVE_DATASPACES_H)
- set(HAVE_DIMES_H 1)
+ find_path(DIMES_INCLUDE_DIR NAMES dimes_interface.h PATHS ${DATASPACES_INCDIR})
+ if(DIMES_INCLUDE_DIR)
+ set(HAVE_DIMES_H 1)
+ endif()
endif()
-
+
# Define if you have the DIMES.
set(HAVE_DIMES 0)
-if(HAVE_DATASPACES)
+if(HAVE_DIMES_H)
if(HAVE_INFINIBAND)
set(DIMES OFF CACHE BOOL "" FORCE)
message("DIMES currently NOT supported for Infiniband!")
@@ -814,55 +898,107 @@ set(HAVE_FLEXPATH 0)
set(NO_FLEXPATH 1)
set(HAVE_FLEXPATH_H 0)
if(FLEXPATH)
- if(DEFINED FLEXPATH_INCDIR)
- if("${FLEXPATH_INCDIR}" STREQUAL "")
- set(FLEXPATH_INCDIR "$ENV{FLEXPATH_DIR}/include")
+ # 4.2.1 has a config file
+ set(FLEXPATH_BINDIR "$ENV{FLEXPATH_DIR}/bin")
+ message("FLEXPATH: look for evpath_config")
+ find_program (EVPATH_CONFIG NAMES evpath_config
+ PATHS "$ENV{FLEXPATH_DIR}/bin" NO_DEFAULT_PATH)
+
+ if(EVPATH_CONFIG)
+ message("FLEXPATH: run evpath_config")
+ execute_process(COMMAND ${EVPATH_CONFIG} "-l"
+ OUTPUT_VARIABLE evpath_config_out
+ RESULT_VARIABLE evpath_config_ret
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+ )
+ message("FLEXPATH: return value = ${evpath_config_ret}")
+ message("FLEXPATH: output = ${evpath_config_out}")
+ if(evpath_config_ret EQUAL 0)
+ string(REPLACE " " ";" evpath_config_list ${evpath_config_out})
+ message("FLEXPATH: list = ${evpath_config_list}")
+ set(evpath_libs)
+ set(evpath_lib_hints)
+ set(evpath_lib_flags)
+ foreach(OPT IN LISTS evpath_config_list)
+ if(OPT MATCHES "^-L(.*)")
+ list(APPEND evpath_lib_hints "${CMAKE_MATCH_1}")
+ elseif(OPT MATCHES "^-l(.*)")
+ list(APPEND evpath_libs "${CMAKE_MATCH_1}")
+ else()
+ list(APPEND evpath_libs "${OPT}")
+ endif()
+ endforeach()
+ set(HAVE_FLEXPATH 1)
endif()
- else()
- set(FLEXPATH_INCDIR "$ENV{FLEXPATH_DIR}/include")
- endif()
- find_path(FLEXPATH_INCLUDE_DIR1 NAMES evpath.h PATHS ${FLEXPATH_INCDIR})
- set(FLEXPATH_INCLUDE_DIR1 "${FLEXPATH_INCLUDE_DIR1}" CACHE INTERNAL "Internal variable")
- find_path(FLEXPATH_INCLUDE_DIR2 NAMES ffs.h PATHS ${FLEXPATH_INCDIR})
- set(FLEXPATH_INCLUDE_DIR2 "${FLEXPATH_INCLUDE_DIR2}" CACHE INTERNAL "Internal variable")
- find_path(FLEXPATH_INCLUDE_DIR3 NAMES atl.h PATHS ${FLEXPATH_INCDIR})
- set(FLEXPATH_INCLUDE_DIR3 "${FLEXPATH_INCLUDE_DIR3}" CACHE INTERNAL "Internal variable")
- find_path(FLEXPATH_INCLUDE_DIR4 NAMES dill.h PATHS ${FLEXPATH_INCDIR})
- set(FLEXPATH_INCLUDE_DIR4 "${FLEXPATH_INCLUDE_DIR4}" CACHE INTERNAL "Internal variable")
- find_path(FLEXPATH_INCLUDE_DIR5 NAMES cercs_env.h PATHS ${FLEXPATH_INCDIR})
- set(FLEXPATH_INCLUDE_DIR5 "${FLEXPATH_INCLUDE_DIR5}" CACHE INTERNAL "Internal variable")
- if(FLEXPATH_INCLUDE_DIR1 AND FLEXPATH_INCLUDE_DIR2 AND FLEXPATH_INCLUDE_DIR3 AND FLEXPATH_INCLUDE_DIR4 AND FLEXPATH_INCLUDE_DIR5)
- set(HAVE_FLEXPATH_H 1)
- set(FLEXPATH_INCLUDE_DIR ${FLEXPATH_INCDIR})
- endif()
- if(DEFINED FLEXPATH_LIBDIR)
- if("${FLEXPATH_LIBDIR}" STREQUAL "")
- set(FLEXPATH_LIBDIR "$ENV{FLEXPATH_DIR}/lib")
- endif()
- else()
- set(FLEXPATH_LIBDIR "$ENV{FLEXPATH_DIR}/lib")
- endif()
- find_library(FLEXPATH_LIBS1 NAMES evpath PATHS ${FLEXPATH_LIBDIR})
- set(FLEXPATH_LIBS1 "${FLEXPATH_LIBS1}" CACHE INTERNAL "Internal variable")
- find_library(FLEXPATH_LIBS2 NAMES ffs PATHS ${FLEXPATH_LIBDIR})
- set(FLEXPATH_LIBS2 "${FLEXPATH_LIBS2}" CACHE INTERNAL "Internal variable")
- find_library(FLEXPATH_LIBS3 NAMES atl PATHS ${FLEXPATH_LIBDIR})
- set(FLEXPATH_LIBS3 "${FLEXPATH_LIBS3}" CACHE INTERNAL "Internal variable")
- find_library(FLEXPATH_LIBS4 NAMES dill PATHS ${FLEXPATH_LIBDIR})
- set(FLEXPATH_LIBS4 "${FLEXPATH_LIBS4}" CACHE INTERNAL "Internal variable")
- find_library(FLEXPATH_LIBS5 NAMES cercs_env PATHS ${FLEXPATH_LIBDIR})
- set(FLEXPATH_LIBS5 "${FLEXPATH_LIBS5}" CACHE INTERNAL "Internal variable")
- if(FLEXPATH_LIBS1 AND FLEXPATH_LIBS2 AND FLEXPATH_LIBS3 AND FLEXPATH_LIBS4 AND FLEXPATH_LIBS5 AND HAVE_FLEXPATH_H)
+ message("FLEXPATH: hints = ${evpath_lib_hints}")
+ message("FLEXPATH: libs = ${evpath_libs}")
+ message("FLEXPATH: flags = ${evpath_lib_flags}")
+ set(FP_LIBS)
+ foreach(lib IN LISTS evpath_libs)
+ find_library(evpath_${lib}_LIBRARY NAME ${lib} HINTS ${evpath_lib_hints})
+ if(evpath_${lib}_LIBRARY)
+ list(APPEND FP_LIBS ${evpath_${lib}_LIBRARY})
+ else()
+ list(APPEND FP_LIBS ${lib})
+ endif()
+ endforeach()
set(HAVE_FLEXPATH 1)
set(NO_FLEXPATH 0)
- set(FP_LIBS ${FLEXPATH_LIBS1} ${FLEXPATH_LIBS2} ${FLEXPATH_LIBS3} ${FLEXPATH_LIBS4} ${FLEXPATH_LIBS5})
set(FP_LIBS "${FP_LIBS}" CACHE STRING "")
- set(FP_CPPFLAGS "-I${FLEXPATH_INCLUDE_DIR}")
-# set(FP_CFLAGS ${FP_CPPFLAGS})
-#include_directories(${FLEXPATH_INCLUDE_DIR})
- else()
- set(FLEXPATH OFF CACHE BOOL "do not find supporting library" FORCE)
- endif()
+ set(FP_CPPFLAGS "-I${FLEXPATH_DIR}/include")
+
+ else(EVPATH_CONFIG)
+
+ if(DEFINED FLEXPATH_INCDIR)
+ if("${FLEXPATH_INCDIR}" STREQUAL "")
+ set(FLEXPATH_INCDIR "$ENV{FLEXPATH_DIR}/include")
+ endif()
+ else()
+ set(FLEXPATH_INCDIR "$ENV{FLEXPATH_DIR}/include")
+ endif()
+ find_path(FLEXPATH_INCLUDE_DIR1 NAMES evpath.h PATHS ${FLEXPATH_INCDIR})
+ set(FLEXPATH_INCLUDE_DIR1 "${FLEXPATH_INCLUDE_DIR1}" CACHE INTERNAL "Internal variable")
+ find_path(FLEXPATH_INCLUDE_DIR2 NAMES ffs.h PATHS ${FLEXPATH_INCDIR})
+ set(FLEXPATH_INCLUDE_DIR2 "${FLEXPATH_INCLUDE_DIR2}" CACHE INTERNAL "Internal variable")
+ find_path(FLEXPATH_INCLUDE_DIR3 NAMES atl.h PATHS ${FLEXPATH_INCDIR})
+ set(FLEXPATH_INCLUDE_DIR3 "${FLEXPATH_INCLUDE_DIR3}" CACHE INTERNAL "Internal variable")
+ find_path(FLEXPATH_INCLUDE_DIR4 NAMES dill.h PATHS ${FLEXPATH_INCDIR})
+ set(FLEXPATH_INCLUDE_DIR4 "${FLEXPATH_INCLUDE_DIR4}" CACHE INTERNAL "Internal variable")
+ find_path(FLEXPATH_INCLUDE_DIR5 NAMES cercs_env.h PATHS ${FLEXPATH_INCDIR})
+ set(FLEXPATH_INCLUDE_DIR5 "${FLEXPATH_INCLUDE_DIR5}" CACHE INTERNAL "Internal variable")
+ if(FLEXPATH_INCLUDE_DIR1 AND FLEXPATH_INCLUDE_DIR2 AND FLEXPATH_INCLUDE_DIR3 AND FLEXPATH_INCLUDE_DIR4 AND FLEXPATH_INCLUDE_DIR5)
+ set(HAVE_FLEXPATH_H 1)
+ set(FLEXPATH_INCLUDE_DIR ${FLEXPATH_INCDIR})
+ endif()
+ if(DEFINED FLEXPATH_LIBDIR)
+ if("${FLEXPATH_LIBDIR}" STREQUAL "")
+ set(FLEXPATH_LIBDIR "$ENV{FLEXPATH_DIR}/lib")
+ endif()
+ else()
+ set(FLEXPATH_LIBDIR "$ENV{FLEXPATH_DIR}/lib")
+ endif()
+ find_library(FLEXPATH_LIBS1 NAMES evpath PATHS ${FLEXPATH_LIBDIR})
+ set(FLEXPATH_LIBS1 "${FLEXPATH_LIBS1}" CACHE INTERNAL "Internal variable")
+ find_library(FLEXPATH_LIBS2 NAMES ffs PATHS ${FLEXPATH_LIBDIR})
+ set(FLEXPATH_LIBS2 "${FLEXPATH_LIBS2}" CACHE INTERNAL "Internal variable")
+ find_library(FLEXPATH_LIBS3 NAMES atl PATHS ${FLEXPATH_LIBDIR})
+ set(FLEXPATH_LIBS3 "${FLEXPATH_LIBS3}" CACHE INTERNAL "Internal variable")
+ find_library(FLEXPATH_LIBS4 NAMES dill PATHS ${FLEXPATH_LIBDIR})
+ set(FLEXPATH_LIBS4 "${FLEXPATH_LIBS4}" CACHE INTERNAL "Internal variable")
+ find_library(FLEXPATH_LIBS5 NAMES cercs_env PATHS ${FLEXPATH_LIBDIR})
+ set(FLEXPATH_LIBS5 "${FLEXPATH_LIBS5}" CACHE INTERNAL "Internal variable")
+ if(FLEXPATH_LIBS1 AND FLEXPATH_LIBS2 AND FLEXPATH_LIBS3 AND FLEXPATH_LIBS4 AND FLEXPATH_LIBS5 AND HAVE_FLEXPATH_H)
+ set(HAVE_FLEXPATH 1)
+ set(NO_FLEXPATH 0)
+ set(FP_LIBS ${FLEXPATH_LIBS1} ${FLEXPATH_LIBS2} ${FLEXPATH_LIBS3} ${FLEXPATH_LIBS4} ${FLEXPATH_LIBS5})
+ set(FP_LIBS "${FP_LIBS}" CACHE STRING "")
+ set(FP_CPPFLAGS "-I${FLEXPATH_INCLUDE_DIR}")
+# set(FP_CFLAGS ${FP_CPPFLAGS})
+# include_directories(${FLEXPATH_INCLUDE_DIR})
+ else()
+ set(FLEXPATH OFF CACHE BOOL "do not find supporting library" FORCE)
+ endif()
+ endif(EVPATH_CONFIG)
endif()
if(HAVE_FLEXPATH)
@@ -881,12 +1017,12 @@ if(FASTBIT)
properly installed at the path specified ${FASTBIT_DIR}")
else()
set(HAVE_IAPI_H 1)
- endif()
+ endif()
find_library(FASTBIT_LIB NAMES fastbit PATHS ${FASTBIT_LIBDIR})
if(FASTBIT_INCLUDE_DIR AND FASTBIT_LIB)
set(HAVE_FASTBIT 1)
set(FASTBIT_CPPFLAGS "-I${FASTBIT_INCDIR}")
- set(FASTBIT_LIBS ${FASTBIT_LIB} -lstdc++ CACHE STRING "")
+ set(FASTBIT_LIBS ${FASTBIT_LIB} -lstdc++ CACHE STRING "")
else()
set(FASTBIT OFF CACHE BOOL "" FORCE)
endif()
@@ -908,7 +1044,7 @@ if(BUILD_FORTRAN)
else()
find_package(MPI)
if(MPI_FOUND)
-# if(MPI_LIBRARIES AND MPI_INCLUDE_PATH)
+# if(MPI_LIBRARIES AND MPI_INCLUDE_PATH)
message(STATUS "find MPI")
set (HAVE_MPI 1)
# set(MPILIBS ${MPI_LIBRARIES})
@@ -941,7 +1077,7 @@ endif(HDF5)
# Define to 1 if you have the <inttypes.h> header file.
CHECK_INCLUDE_FILES(inttypes.h HAVE_INTTYPES_H)
-# Define to 1 if you have the `rt' library (-lrt).
+# Define to 1 if you have the `rt' library (-lrt).
set(HAVE_LIBRT 0)
# Define if you have LUSTRE.
@@ -989,7 +1125,7 @@ if (NOT HAVE_MXML)
message(STATUS "MXML will be built for ADIOS in ./src/mxml")
set(HAVE_MXML 1)
set(BUILD_MXML 1)
- set(MXML_LIBS "")
+ set(MXML_LIBS "")
set(MXML_INCLUDE_DIR ${PROJECT_SOURCE_DIR}/src/mxml/mxml-2.9)
message(STATUS "Checking type long long int")
try_compile(HAVE_LONG_LONG ${PROJECT_BINARY_DIR}/src/mxml SOURCES ${PROJECT_SOURCE_DIR}/src/mxml/cmake_try_longlong.c)
@@ -1141,7 +1277,7 @@ set(HAVE_PTHREAD 0)
find_package(Threads)
if(Threads_FOUND)
set(HAVE_PTHREAD 1)
- #INCLUDE_DIRECTORIES(${Threads_INCLUDE_PATH})
+ #INCLUDE_DIRECTORIES(${Threads_INCLUDE_PATH})
endif(Threads_FOUND)
# Define to 1 if you have the `pthread_yield' function.
@@ -1273,6 +1409,19 @@ if(FGR)
endif()
endif()
+set(HAVE_LZ4 0)
+if(LZ4)
+ find_path(LZ4_INCLUDE_DIR NAMES lz4.h PATHS ${LZ4_DIR}/include)
+ if(LZ4_INCLUDE_DIR)
+ set(HAVE_LZ4_H 1)
+ endif()
+ find_library(LZ4_LIBS NAMES lz4 PATHS ${LZ4_DIR}/lib)
+ if(LZ4_INCLUDE_DIR AND LZ4_LIBS)
+ set(HAVE_LZ4 1)
+ set(LZ4_CPPFLAGS "-I${LZ4_INCLUDE_DIR}")
+ endif()
+endif()
+
set(HAVE_BZIP2 0)
if(BZIP2)
find_path(BZIP2_INCLUDE_DIR NAMES bzlib.h PATHS ${BZIP2_DIR}/include)
@@ -1337,7 +1486,7 @@ if(ALACRITY)
if(ALACRITY_INCLUDE_DIR AND ALACRITY_LIB AND RIDCOMPRESS_LIB)
set(HAVE_ALACRITY 1)
set(ALACRITY_CPPFLAGS "-I${ALACRITY_INCLUDE_DIR}")
- set(ALACRITY_LIBS ${ALACRITY_LIB} ${RIDCOMPRESS_LIB} -lstdc++ CACHE STRING "")
+ set(ALACRITY_LIBS ${ALACRITY_LIB} ${RIDCOMPRESS_LIB} -lstdc++ CACHE STRING "")
endif()
endif()
@@ -1363,6 +1512,24 @@ else(ZFP)
message(STATUS "ZFP is turned off")
endif(ZFP)
+set(HAVE_SZ 0)
+set(HAVE_SZ_H 0)
+if(SZ)
+ find_path(SZ_INCLUDE_DIR NAMES sz.h PATHS ${SZ_DIR}/include)
+ if(SZ_INCLUDE_DIR)
+ set(HAVE_SZ_H 1)
+ endif()
+ find_library(SZ_LIB1 NAMES libsz.a PATHS ${SZ_DIR}/lib)
+ find_library(SZ_LIB2 NAMES libzlib.a PATHS ${SZ_DIR}/lib)
+ set(SZ_LIBS ${SZ_LIB1} ${SZ_LIB2} CACHE FILEPATH "SZ libraries")
+ unset(SZ_LIB1 CACHE)
+ unset(SZ_LIB2 CACHE)
+ if(SZ_INCLUDE_DIR AND SZ_LIBS)
+ set(HAVE_SZ 1)
+ set(SZ_CPPFLAGS "-I${SZ_INCLUDE_DIR}")
+ endif()
+endif()
+
# Define to 1 if your C compiler doesn't accept -c and -o together.
# Name of package
@@ -1391,7 +1558,7 @@ set(PACKAGE adios)
set(VERSION_MAJOR 1)
# Minor version number
-set(VERSION_MINOR 10)
+set(VERSION_MINOR 12)
# Micro version number
set(VERSION_MICRO 0)
@@ -1402,6 +1569,12 @@ set(VERSION ${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_MICRO})
# svn revision number
#set(VERSION_SVNREV 2007)
+# Define HAVE_MPI_FALSE because it is used in generating the adios_config script
+if(HAVE_MPI)
+ set(HAVE_MPI_FALSE "#")
+else(HAVE_MPI)
+ set(HAVE_MPI_FALSE "")
+endif(HAVE_MPI)
CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/config.h.cmake ${PROJECT_BINARY_DIR}/config.h)
################################ end of generating config.h ###############################
@@ -1669,6 +1842,24 @@ if(HAVE_ZLIB)
set(ADIOSREADLIB_SEQ_LDADD ${ADIOSREADLIB_SEQ_LDADD} ${ZLIB_LIBS})
endif()
+if(HAVE_LZ4)
+ set(ADIOSLIB_CPPFLAGS "${ADIOSLIB_CPPFLAGS} -DLZ4 ${LZ4_CPPFLAGS}")
+ set(ADIOSLIB_CFLAGS "${ADIOSLIB_CFLAGS} ${LZ4_CFLAGS}")
+ set(ADIOSLIB_LDADD ${ADIOSLIB_LDADD} ${LZ4_LIBS})
+ set(ADIOSLIB_SEQ_CPPFLAGS "${ADIOSLIB_SEQ_CPPFLAGS} -DLZ4 ${LZ4_CPPFLAGS}")
+ set(ADIOSLIB_SEQ_CFLAGS "${ADIOSLIB_SEQ_CFLAGS} ${LZ4_CFLAGS}")
+ set(ADIOSLIB_SEQ_LDADD ${ADIOSLIB_SEQ_LDADD} ${LZ4_LIBS})
+ set(ADIOSLIB_INT_CPPFLAGS "${ADIOSLIB_INT_CPPFLAGS} -DLZ4 ${LZ4_CPPFLAGS}")
+ set(ADIOSLIB_INT_CFLAGS "${ADIOSLIB_INT_CFLAGS} ${LZ4_CFLAGS}")
+ set(ADIOSLIB_INT_LDADD ${ADIOSLIB_INT_LDADD} ${LZ4_LIBS})
+ set(ADIOSREADLIB_CPPFLAGS "${ADIOSREADLIB_CPPFLAGS} -DLZ4 ${LZ4_CPPFLAGS}")
+ set(ADIOSREADLIB_CFLAGS "${ADIOSREADLIB_CFLAGS} ${LZ4_CFLAGS}")
+ set(ADIOSREADLIB_LDADD ${ADIOSREADLIB_LDADD} ${LZ4_LIBS})
+ set(ADIOSREADLIB_SEQ_CPPFLAGS "${ADIOSREADLIB_SEQ_CPPFLAGS} -DLZ4 ${LZ4_CPPFLAGS}")
+ set(ADIOSREADLIB_SEQ_CFLAGS "${ADIOSREADLIB_SEQ_CFLAGS} ${LZ4_CFLAGS}")
+ set(ADIOSREADLIB_SEQ_LDADD ${ADIOSREADLIB_SEQ_LDADD} ${LZ4_LIBS})
+endif()
+
if(HAVE_BZIP2)
set(ADIOSLIB_CPPFLAGS "${ADIOSLIB_CPPFLAGS} -DBZIP2 ${BZIP2_CPPFLAGS}")
set(ADIOSLIB_CFLAGS "${ADIOSLIB_CFLAGS} ${BZIP2_CFLAGS}")
@@ -1772,6 +1963,24 @@ if(HAVE_ZFP)
set(ADIOSREADLIB_SEQ_LDADD ${ADIOSREADLIB_SEQ_LDADD} ${ZFP_LIBS})
endif()
+if(HAVE_SZ)
+ set(ADIOSLIB_CPPFLAGS "${ADIOSLIB_CPPFLAGS} ${SZ_CPPFLAGS}")
+ set(ADIOSLIB_CFLAGS "${ADIOSLIB_CFLAGS} ${SZ_CFLAGS}")
+ set(ADIOSLIB_LDADD ${ADIOSLIB_LDADD} ${SZ_LIBS})
+ set(ADIOSLIB_SEQ_CPPFLAGS "${ADIOSLIB_SEQ_CPPFLAGS} ${SZ_CPPFLAGS}")
+ set(ADIOSLIB_SEQ_CFLAGS "${ADIOSLIB_SEQ_CFLAGS} ${SZ_CFLAGS}")
+ set(ADIOSLIB_SEQ_LDADD ${ADIOSLIB_SEQ_LDADD} ${SZ_LIBS})
+ set(ADIOSLIB_INT_CPPFLAGS "${ADIOSLIB_INT_CPPFLAGS} ${SZ_CPPFLAGS}")
+ set(ADIOSLIB_INT_CFLAGS "${ADIOSLIB_INT_CFLAGS} ${SZ_CFLAGS}")
+ set(ADIOSLIB_INT_LDADD ${ADIOSLIB_INT_LDADD} ${SZ_LIBS})
+ set(ADIOSREADLIB_CPPFLAGS "${ADIOSREADLIB_CPPFLAGS} ${SZ_CPPFLAGS}")
+ set(ADIOSREADLIB_CFLAGS "${ADIOSREADLIB_CFLAGS} ${SZ_CFLAGS}")
+ set(ADIOSREADLIB_LDADD ${ADIOSREADLIB_LDADD} ${SZ_LIBS})
+ set(ADIOSREADLIB_SEQ_CPPFLAGS="${ADIOSREADLIB_SEQ_CPPFLAGS} ${SZ_CPPFLAGS}")
+ set(ADIOSREADLIB_SEQ_CFLAGS="${ADIOSREADLIB_SEQ_CFLAGS} ${SZ_CFLAGS}")
+ set(ADIOSREADLIB_SEQ_LDADD ${ADIOSREADLIB_SEQ_LDADD} ${SZ_LIBS})
+endif()
+
if(HAVE_FASTBIT)
set(ADIOSLIB_CPPFLAGS "${ADIOSLIB_CPPFLAGS} -DFASTBIT ${FASTBIT_CPPFLAGS}")
set(ADIOSLIB_CFLAGS "${ADIOSLIB_CFLAGS} ${FASTBIT_CFLAGS}")
@@ -1800,7 +2009,7 @@ set(ADIOSREADLIB_SEQ_LDADD ${ADIOSREADLIB_SEQ_LDADD} ${M_LIBS})
#install(PROGRAMS adios_config DESTINATION ${bindir})
#if(HAVE_NSSI)
-#install(PROGRAMS scripts/create.nssi.config.sh DESTINATION ${bindir})
+#install(PROGRAMS scripts/create.nssi.config.sh DESTINATION ${bindir})
#install(PROGRAMS scripts/kill.nssi.staging.sh DESTINATION ${bindir})
#install(PROGRAMS scripts/start.nssi.staging.sh DESTINATION ${bindir})
#endif(HAVE_NSSI)
@@ -1828,7 +2037,7 @@ CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/adios_config.makesrc.in ${CMAKE_CURRE
#####################end of processing adios_config.flags.in #####################
install(FILES ${CMAKE_BINARY_DIR}/adios_config.flags DESTINATION ${sysconfdir})
install(PROGRAMS ${CMAKE_BINARY_DIR}/adios_config DESTINATION ${bindir})
-install(FILES ${PROJECT_SOURCE_DIR}/scripts/FindADIOS.cmake DESTINATION ${sysconfdir})
+install(FILES ${PROJECT_SOURCE_DIR}/scripts/FindADIOS.cmake DESTINATION ${sysconfdir})
#install(FILES ${PROJECT_SOURCE_DIR}/adios_git_status DESTINATION ${sysconfdir})
@@ -2057,6 +2266,16 @@ else()
message(" - No ZLIB to build ZLIB transform method")
endif()
+if(HAVE_LZ4)
+ message(" - LZ4")
+ message(" - LZ4_CFLAGS = ${LZ4_CFLAGS}")
+ message(" - LZ4_CPPFLAGS = ${LZ4_CPPFLAGS}")
+ message(" - LZ4_LIBS = ${LZ4_LIBS}")
+ message("")
+else()
+ message(" - No LZ4 to build LZ4 transform method")
+endif()
+
if(HAVE_BZIP2)
message(" - BZIP2")
message(" - BZIP2_CFLAGS = ${BZIP2_CFLAGS}")
@@ -2128,6 +2347,15 @@ else()
message(" - No ZFP to build ZFP transform method")
endif()
+if(HAVE_SZ)
+ message(" - SZ")
+ message(" - SZ_CFLAGS = ${SZ_CFLAGS}")
+ message(" - SZ_CPPFLAGS = ${SZ_CPPFLAGS}")
+ message(" - SZ_LIBS = ${SZ_LIBS}")
+ message("")
+else()
+ message(" - No SZ to build SZ transform method")
+endif()
if(HAVE_BGQ)
message(" - BGQ METHOD is enabled")
diff --git a/Makefile.in b/Makefile.in
index 0b884d9..74b7e96 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -120,7 +120,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -128,8 +128,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -406,6 +406,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -482,6 +486,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/NEWS b/NEWS
index 020f86c..d235660 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,21 @@
+1.12.0 Release June 2017
+ - added LZ4 compression transform by René Widera HZDR, Germany
+ - added SZ compression transform
+ - Support for burst buffer on Summitdev at OLCF, Cori at NERSC
+ - see Chapter 16 in the manual
+ - New Flexpath staging method from Georgia Tech, faster and more reliable
+ - Performance tools interface API by Kevin Huck of the TAU team
+ - fix: cmake build broken since 1.11.0. Also include building
+ the test suite
+ - fix: for >2GB block reads
+ - fix: time-aggregation works with writing multiple files each
+ contaning multiple steps
+ - fix: python interface
+
+1.11.1 Release January 2017
+ - fix: able to read from a BP file when the index itself is > 2GB
+ - fix: bpmeta, bpdump works correctly with index size > 2GB
+
1.11.0 Release November 2016
- Time aggregation (temporal aggregation of an output in memory)
see adios_set_time_aggregation() or the <time-aggregation> element in the XML syntax.
diff --git a/aclocal.m4 b/aclocal.m4
index 84c17eb..6fffe76 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -1437,6 +1437,7 @@ m4_include([config/ac_hdf5.m4])
m4_include([config/ac_infiniband.m4])
m4_include([config/ac_isobar.m4])
m4_include([config/ac_lustre.m4])
+m4_include([config/ac_lz4.m4])
m4_include([config/ac_mxml.m4])
m4_include([config/ac_nc4par.m4])
m4_include([config/ac_netcdf.m4])
@@ -1445,6 +1446,7 @@ m4_include([config/ac_pablo.m4])
m4_include([config/ac_pami.m4])
m4_include([config/ac_phdf5.m4])
m4_include([config/ac_portals.m4])
+m4_include([config/ac_sz.m4])
m4_include([config/ac_szip.m4])
m4_include([config/ac_zfp.m4])
m4_include([config/ac_zlib.m4])
diff --git a/cmake_init b/cmake_init
index 9a0b60c..8185349 100755
--- a/cmake_init
+++ b/cmake_init
@@ -4,117 +4,10 @@
# You can study it to figure out how to configure adios on your system
#
-if [ `hostname | cut -c 1-4` == "sith" ]; then
+SRCDIR=`dirname ${BASH_SOURCE[0]}`
- ########
- # Sith #
- ########
- source /etc/profile.d/modules.sh
- TARGET=`module list 2>&1 | grep "PE"- | sed "s/^.*PE-\([a-z]*\).*/\1/"`
- if [ -z "$TARGET" ]; then
- echo "Cannot determine Programming environment. Exit"
- exit 1
- fi
- echo "Configure on SITH for $TARGET env."
- source /etc/profile.d/modules.sh
- module unload hdf5
- module unload netcdf
- module unload PE-gnu
- module unload PE-pgi
- module unload PE-intel
- module unload PE-pathscale
- module unload pgi gcc intel pathscale
- module unload python
- module load PE-$TARGET
- module load python
- module load szip
- module load bzip2
- export LUSTRE_DIR="/usr/lib64"
-# export FGR_DIR="/ccs/proj/e2e/qliu/tap"
- export GLIB_DIR="/ccs/proj/e2e/qliu/glib"
- export BUILD_WRITE=ON
- export BUILD_FORTRAN=ON
- export adios_timers=ON
- export research_transports=ON
- export CC=mpicc
- export CXX=mpiCC
- export FC=mpif90
- export INSTALL_PREFIX="/ccs/home/jya/ADIOS/sith.$TARGET"
- export APLOD_DIR="/ccs/proj/e2e/ncsu/sith.gnu"
- export ISOBAR_DIR="/ccs/proj/e2e/ncsu/sith.gnu"
- export ALACRITY_DIR="/ccs/proj/e2e/pnorbert/ALACRITY-ADIOS/synced/build.sith/build.gnu"
- export NCSU_TIMER_DIR
- if [ "$TARGET" == "pgi" ]; then
- module load hdf5/1.8.10
- export SEQ_HDF5_DIR=$HDF5_DIR
- export SEQ_HDF5_LIBS="-L/sw/sith/hdf5/1.8.10/rhel6_pgi12.8/lib -L/sw/sith/szip/2.1/rhel6_pgi12.8/lib -lhdf5_hl -lhdf5 -lsz -lz -lm"
- module unload hdf5/1.8.10
- module load hdf5/1.8.10_par
- export PAR_HDF5_DIR=$HDF5_DIR
- export PAR_HDF5_LIBS="-L/sw/sith/hdf5/1.8.10/rhel6_pgi13.4_ompi1.6.3/lib -L/sw/sith/szip/2.1/rhel6_pgi13.4/lib -lhdf5_hl -lhdf5 -lsz -lz -lm"
- module unload hdf5/1.8.10_par
- module load netcdf/4.1.3
- export SEQ_NC_DIR=$NETCDF_DIR
- export SEQ_NC_LIBS="-L/sw/sith/netcdf/4.1.3/rhel6_pgi12.8/lib -L/sw/sith/hdf5/1.8.10/rhel6_pgi12.8/lib -L/sw/sith/szip/2.1/rhel6_pgi12.8/lib -lnetcdf -lcurl -lhdf5_hl -lhdf5 -lsz -lz -lm"
- module unload netcdf/4.1.3
- module load netcdf/4.1.3_par
- export PAR_NC_DIR=$NETCDF_DIR
- export PAR_NC_LIBS="-L/sw/sith/netcdf/4.1.3/rhel6_pgi13.4_ompi1.6.3/lib -L/sw/sith/hdf5/1.8.10/rhel6_pgi13.4_ompi1.6.3/lib -L/sw/sith/szip/2.1/rhel6_pgi13.4/lib -lnetcdf -lcurl -lhdf5_hl -lhdf5 -lsz -lz -lm"
- module unload netcdf/4.1.3_par
-
- export DATASPACES_DIR="/ccs/proj/e2e/dataspaces/sith/$TARGET"
- export FLEXPATH_DIR="/ccs/proj/e2e/chaos/sith/$TARGET"
- export FASTBIT_DIR="/sw/redhat6/fastbit/svn/rhel6_gnu4.8.2"
- elif [ "$TARGET" == "gnu" ]; then
- module load hdf5/1.8.10
- export SEQ_HDF5_DIR=$HDF5_DIR
- export SEQ_HDF5_LIBS="-L/sw/sith/hdf5/1.8.10/rhel6_gnu4.7.1/lib -lhdf5_hl -lhdf5 -L/sw/sith/szip/2.1/rhel6_gnu4.7.1/lib -lsz -lz -lm"
- module unload hdf5/1.8.10
- module load hdf5/1.8.10_par
- export PAR_HDF5_DIR=$HDF5_DIR
- export PAR_HDF5_LIBS="-L/sw/sith/hdf5/1.8.10/rhel6_gnu4.7.1_ompi1.6.3/lib -lhdf5_hl -lhdf5 -L/sw/sith/szip/2.1/rhel6_gnu4.7.1/lib -lsz -lz -lm"
- module unload hdf5/1.8.10_par
- module load netcdf/4.1.3
- export SEQ_NC_DIR=$NETCDF_DIR
- export SEQ_NC_LIBS="-L/sw/sith/netcdf/4.1.3/rhel6_gnu4.7.1/lib -L/sw/sith/hdf5/1.8.10/rhel6_gnu4.7.1/lib -L/sw/sith/szip/2.1/rhel6_gnu4.7.1/lib -lnetcdf -lm -lcurl -lhdf5_hl -lhdf5 -lsz -lz -lm"
- module unload netcdf/4.1.3
-# module load netcdf/4.1.3_par
-# export PAR_NC_DIR=$NETCDF_DIR
-# export PAR_NC_LIBS=""
-# module unload netcdf/4.1.3_par
-# export DATASPACES_DIR="/ccs/proj/e2e/dataspaces/sith/$TARGET"
- export FLEXPATH_DIR="/ccs/proj/e2e/chaos/sith/$TARGET"
- export FASTBIT_DIR="/sw/redhat6/fastbit/svn/rhel6_gnu4.8.2"
- elif [ "$TARGET" == "intel" ]; then
- module load hdf5/1.8.10
- export SEQ_HDF5_DIR=$HDF5_DIR
- export SEQ_HDF5_LIBS="-L/sw/sith/hdf5/1.8.10/rhel6_intel11.1/lib -lhdf5_hl -lhdf5 -L/sw/sith/szip/2.1/rhel6_intel11.1.072/lib -lsz -lz -lm"
- module unload hdf5/1.8.10
- module load hdf5/1.8.10_par
- export PAR_HDF5_DIR=$HDF5_DIR
- export PAR_HDF5_LIBS="-L/sw/sith/hdf5/1.8.10/rhel6_intel11.1_ompi1.6.3/lib -lhdf5_hl -lhdf5 -L/sw/sith/szip/2.1/rhel6_intel11.1.072/lib -lsz -lz -lm"
- module unload hdf5/1.8.10_par
- module load netcdf/4.1.3
- export SEQ_NC_DIR=$NETCDF_DIR
- export SEQ_NC_LIBS="-L/sw/sith/netcdf/4.1.3/rhel6_intel11.1/lib -L/sw/sith/hdf5/1.8.10/rhel6_intel11.1/lib -L/sw/sith/szip/2.1/rhel6_intel11.1.072/lib -lnetcdf -lm -lcurl -lhdf5_hl -lhdf5 -lsz -lz -lm"
- module unload netcdf/4.1.3
-# module load netcdf/4.1.3_par
-# export PAR_NC_DIR=$NETCDF_DIR
-# export PAR_NC_LIBS=""
-# module unload netcdf/4.1.3_par
-# export DATASPACES_DIR="/ccs/proj/e2e/dataspaces/sith/$TARGET"
- export FLEXPATH_DIR=
- else
- echo "TARGET must be pgi or gnu or intel"
- exit 1
- fi
-
- export CPPFLAGS="-DMPICH_IGNORE_CXX_SEEK"
- export CFLAGS="-g -fPIC"
-
-
-elif [ `hostname | cut -c 1-4` == "lens" ]; then
+if [ `hostname | cut -c 1-4` == "rhea" ]; then
source /etc/profile.d/modules.sh
source /etc/profile.d/modules.sh
TARGET=`module list 2>&1 | grep "PE"- | sed "s/^.*PE-\([a-z]*\).*/\1/"`
@@ -123,29 +16,23 @@ elif [ `hostname | cut -c 1-4` == "lens" ]; then
echo "Cannot determine Programming environment. Exit"
exit 1
fi
- echo "Configure on LENS for $TARGET env."
+ echo "Configure on Rhea for $TARGET env. for user ${USER}"
module unload hdf5
module unload netcdf
- module unload PE-gnu
- module unload PE-pgi
- module unload PE-pathscale
- module unload pgi
- module load PE-$TARGET
# Use both seq hdf5 (for utils) and
# parallel hdf5 (for PHDF5 method)
-# module load hdf5/1.8.6
-# export SEQ_HDF5_DIR=$HDF5_DIR
-# export SEQ_HDF5_CLIB=$HDF5_CLIB
-# module unload hdf5
-# module load hdf5/1.8.6_ompi1.4.2
-# export PAR_HDF5_DIR=$HDF5_DIR
-# export PAR_HDF5_CLIB=$HDF5_CLIB
-# module unload hdf5
- # Seq NetCDF 3 for bp2ncd
- module unload netcdf
- module load netcdf/4.1.3
- export SEQ_NC_DIR=$NETCDF_DIR
- module unload netcdf
+ module load hdf5/1.8.11
+ export SEQ_HDF5_DIR=$HDF5_DIR
+ export SEQ_HDF5_CLIB=$HDF5_CLIB
+ module unload hdf5
+ module load hdf5-parallel/1.8.11
+ export PAR_HDF5_DIR=$HDF5_DIR
+ export PAR_HDF5_CLIB=$HDF5_CLIB
+ module unload hdf5
+ # Seq NetCDF 4 for bp2ncd
+# module load netcdf/4.1.3
+# export SEQ_NC_DIR=$NETCDF_DIR
+# module unload netcdf
# module load netcdf/4.1.1_ompi1.3.1
# export PAR_NC_DIR=$NETCDF_DIR
# module unload netcdf
@@ -161,19 +48,24 @@ elif [ `hostname | cut -c 1-4` == "lens" ]; then
# export CC=pgcc
# export CXX=pgCC
# export FC=pgf90
- module switch pgi pgi/10.5
+ export EXTRA_CFLAGS=""
elif [ "$TARGET" == "gnu" ]; then
# export CC=gcc
# export CXX=g++
# export FC=gfortran
- module unload PE-pgi
- module load PE-gnu
+ export EXTRA_CFLAGS=""
+ elif [ "$TARGET" == "intel" ]; then
+# export CC=icc
+# export CXX=icpc
+# export FC=ifort
+ export EXTRA_CFLAGS="-std=c99"
else
echo "TARGET must be pgi or gnu"
exit 1
fi
- export CFLAGS="-g -fPIC"
+ export CFLAGS="-g -fPIC ${EXTRA_CFLAGS}"
+ cmake $SRCDIR
elif [ `hostname | cut -c 1-5` == "titan" ]; then
@@ -278,6 +170,7 @@ elif [ `hostname | cut -c 1-5` == "titan" ]; then
export adios_timers=ON
export INSTALL_PREFIX="/ccs/proj/e2e/pnorbert/ADIOS/titan.cmake.$TARGET"
fi
+ cmake $SRCDIR
elif [ `hostname | cut -c 1-4` == "eos-" ]; then
@@ -323,6 +216,7 @@ elif [ `hostname | cut -c 1-4` == "eos-" ]; then
module load pmi
export CFLAGS="-g -fPIC"
export INSTALL_PREFIX="/ccs/home/jya/ADIOS/eos.$TARGET"
+ cmake $SRCDIR
elif [ `hostname | cut -c 1-7` == "chester" ]; then
@@ -384,7 +278,155 @@ elif [ `hostname | cut -c 1-7` == "chester" ]; then
# WITHDART=""
fi
export CFLAGS="-g -fPIC"
-
+ cmake $SRCDIR
+
+elif [ `hostname -f | cut -c 1-9` == "summitdev" ]; then
+ #####################
+ # SUMMITDEV IBM #
+ #####################
+ MLIST=`module list 2>&1 ` #| grep "PrgEnv"- | sed "s/^.*PrgEnv-\([a-z]*\).*/\1/"`
+ TARGET=`echo $MLIST | grep " xl\/" | sed "s/^.* xl\/.*/xl/"`
+ if [ -z $TARGET ]; then
+ TARGET=`echo $MLIST | grep " pgi\/" | sed "s/^.* pgi\/.*/pgi/"`
+ if [ -z $TARGET ]; then
+ TARGET=`echo $MLIST | grep " gcc\/" | sed "s/^.* gcc\/.*/gcc/"`
+ if [ -z $TARGET ]; then
+ TARGET=`echo $MLIST | grep " clang\/" | sed "s/^.* clang\/.*/clang/"`
+ fi
+ fi
+ fi
+ echo "Configure on Summitdev for $TARGET env."
+
+ export CC=mpicc
+ export CXX=mpic++
+ export FC=mpif90
+ export CFLAGS="-g -O0"
+
+ if [ "$TARGET" == "xl" ]; then
+ #export LIBS="-lrdmacm -libverbs"
+ export DATASPACES_DIR=/ccs/proj/e2e/dataspaces/summitdev/1.6.1/xl
+ elif [ "$TARGET" == "pgi" ]; then
+ export DATASPACES_DIR=/ccs/proj/e2e/dataspaces/summitdev/1.6.1/pgi
+ elif [ "$TARGET" == "gcc" ]; then
+ export DATASPACES_DIR=/ccs/proj/e2e/dataspaces/summitdev/1.6.1/gcc
+ elif [ "$TARGET" == "clang" ]; then
+ export BUILD_FORTRAN=OFF
+ unset DATASPACES_DIR
+ fi
+
+ export INSTALL_PREFIX=/ccs/proj/e2e/pnorbert/ADIOS/summitdev.$TARGET
+ cmake $SRCDIR
+
+elif [ `hostname | cut -c 1-4` == "sith" ]; then
+
+ ########
+ # Sith #
+ ########
+ source /etc/profile.d/modules.sh
+ TARGET=`module list 2>&1 | grep "PE"- | sed "s/^.*PE-\([a-z]*\).*/\1/"`
+
+ if [ -z "$TARGET" ]; then
+ echo "Cannot determine Programming environment. Exit"
+ exit 1
+ fi
+ echo "Configure on SITH for $TARGET env."
+ source /etc/profile.d/modules.sh
+ module unload hdf5
+ module unload netcdf
+ module unload PE-gnu
+ module unload PE-pgi
+ module unload PE-intel
+ module unload PE-pathscale
+ module unload pgi gcc intel pathscale
+ module unload python
+ module load PE-$TARGET
+ module load python
+ module load szip
+ module load bzip2
+ export LUSTRE_DIR="/usr/lib64"
+# export FGR_DIR="/ccs/proj/e2e/qliu/tap"
+ export GLIB_DIR="/ccs/proj/e2e/qliu/glib"
+ export BUILD_WRITE=ON
+ export BUILD_FORTRAN=ON
+ export adios_timers=ON
+ export research_transports=ON
+ export CC=mpicc
+ export CXX=mpiCC
+ export FC=mpif90
+ export INSTALL_PREFIX="/ccs/home/jya/ADIOS/sith.$TARGET"
+ export APLOD_DIR="/ccs/proj/e2e/ncsu/sith.gnu"
+ export ISOBAR_DIR="/ccs/proj/e2e/ncsu/sith.gnu"
+ export ALACRITY_DIR="/ccs/proj/e2e/pnorbert/ALACRITY-ADIOS/synced/build.sith/build.gnu"
+ export NCSU_TIMER_DIR
+ if [ "$TARGET" == "pgi" ]; then
+ module load hdf5/1.8.10
+ export SEQ_HDF5_DIR=$HDF5_DIR
+ export SEQ_HDF5_LIBS="-L/sw/sith/hdf5/1.8.10/rhel6_pgi12.8/lib -L/sw/sith/szip/2.1/rhel6_pgi12.8/lib -lhdf5_hl -lhdf5 -lsz -lz -lm"
+ module unload hdf5/1.8.10
+ module load hdf5/1.8.10_par
+ export PAR_HDF5_DIR=$HDF5_DIR
+ export PAR_HDF5_LIBS="-L/sw/sith/hdf5/1.8.10/rhel6_pgi13.4_ompi1.6.3/lib -L/sw/sith/szip/2.1/rhel6_pgi13.4/lib -lhdf5_hl -lhdf5 -lsz -lz -lm"
+ module unload hdf5/1.8.10_par
+ module load netcdf/4.1.3
+ export SEQ_NC_DIR=$NETCDF_DIR
+ export SEQ_NC_LIBS="-L/sw/sith/netcdf/4.1.3/rhel6_pgi12.8/lib -L/sw/sith/hdf5/1.8.10/rhel6_pgi12.8/lib -L/sw/sith/szip/2.1/rhel6_pgi12.8/lib -lnetcdf -lcurl -lhdf5_hl -lhdf5 -lsz -lz -lm"
+ module unload netcdf/4.1.3
+ module load netcdf/4.1.3_par
+ export PAR_NC_DIR=$NETCDF_DIR
+ export PAR_NC_LIBS="-L/sw/sith/netcdf/4.1.3/rhel6_pgi13.4_ompi1.6.3/lib -L/sw/sith/hdf5/1.8.10/rhel6_pgi13.4_ompi1.6.3/lib -L/sw/sith/szip/2.1/rhel6_pgi13.4/lib -lnetcdf -lcurl -lhdf5_hl -lhdf5 -lsz -lz -lm"
+ module unload netcdf/4.1.3_par
+
+ export DATASPACES_DIR="/ccs/proj/e2e/dataspaces/sith/$TARGET"
+ export FLEXPATH_DIR="/ccs/proj/e2e/chaos/sith/$TARGET"
+ export FASTBIT_DIR="/sw/redhat6/fastbit/svn/rhel6_gnu4.8.2"
+ elif [ "$TARGET" == "gnu" ]; then
+ module load hdf5/1.8.10
+ export SEQ_HDF5_DIR=$HDF5_DIR
+ export SEQ_HDF5_LIBS="-L/sw/sith/hdf5/1.8.10/rhel6_gnu4.7.1/lib -lhdf5_hl -lhdf5 -L/sw/sith/szip/2.1/rhel6_gnu4.7.1/lib -lsz -lz -lm"
+ module unload hdf5/1.8.10
+ module load hdf5/1.8.10_par
+ export PAR_HDF5_DIR=$HDF5_DIR
+ export PAR_HDF5_LIBS="-L/sw/sith/hdf5/1.8.10/rhel6_gnu4.7.1_ompi1.6.3/lib -lhdf5_hl -lhdf5 -L/sw/sith/szip/2.1/rhel6_gnu4.7.1/lib -lsz -lz -lm"
+ module unload hdf5/1.8.10_par
+ module load netcdf/4.1.3
+ export SEQ_NC_DIR=$NETCDF_DIR
+ export SEQ_NC_LIBS="-L/sw/sith/netcdf/4.1.3/rhel6_gnu4.7.1/lib -L/sw/sith/hdf5/1.8.10/rhel6_gnu4.7.1/lib -L/sw/sith/szip/2.1/rhel6_gnu4.7.1/lib -lnetcdf -lm -lcurl -lhdf5_hl -lhdf5 -lsz -lz -lm"
+ module unload netcdf/4.1.3
+# module load netcdf/4.1.3_par
+# export PAR_NC_DIR=$NETCDF_DIR
+# export PAR_NC_LIBS=""
+# module unload netcdf/4.1.3_par
+# export DATASPACES_DIR="/ccs/proj/e2e/dataspaces/sith/$TARGET"
+ export FLEXPATH_DIR="/ccs/proj/e2e/chaos/sith/$TARGET"
+ export FASTBIT_DIR="/sw/redhat6/fastbit/svn/rhel6_gnu4.8.2"
+ elif [ "$TARGET" == "intel" ]; then
+ module load hdf5/1.8.10
+ export SEQ_HDF5_DIR=$HDF5_DIR
+ export SEQ_HDF5_LIBS="-L/sw/sith/hdf5/1.8.10/rhel6_intel11.1/lib -lhdf5_hl -lhdf5 -L/sw/sith/szip/2.1/rhel6_intel11.1.072/lib -lsz -lz -lm"
+ module unload hdf5/1.8.10
+ module load hdf5/1.8.10_par
+ export PAR_HDF5_DIR=$HDF5_DIR
+ export PAR_HDF5_LIBS="-L/sw/sith/hdf5/1.8.10/rhel6_intel11.1_ompi1.6.3/lib -lhdf5_hl -lhdf5 -L/sw/sith/szip/2.1/rhel6_intel11.1.072/lib -lsz -lz -lm"
+ module unload hdf5/1.8.10_par
+ module load netcdf/4.1.3
+ export SEQ_NC_DIR=$NETCDF_DIR
+ export SEQ_NC_LIBS="-L/sw/sith/netcdf/4.1.3/rhel6_intel11.1/lib -L/sw/sith/hdf5/1.8.10/rhel6_intel11.1/lib -L/sw/sith/szip/2.1/rhel6_intel11.1.072/lib -lnetcdf -lm -lcurl -lhdf5_hl -lhdf5 -lsz -lz -lm"
+ module unload netcdf/4.1.3
+# module load netcdf/4.1.3_par
+# export PAR_NC_DIR=$NETCDF_DIR
+# export PAR_NC_LIBS=""
+# module unload netcdf/4.1.3_par
+# export DATASPACES_DIR="/ccs/proj/e2e/dataspaces/sith/$TARGET"
+ export FLEXPATH_DIR=
+ else
+ echo "TARGET must be pgi or gnu or intel"
+ exit 1
+ fi
+
+ export CPPFLAGS="-DMPICH_IGNORE_CXX_SEEK"
+ export CFLAGS="-g -fPIC"
+ cmake $SRCDIR
+
elif [ "x"`hostname -f | cut -c 8-15` == "xintrepid" ]; then
#####################
@@ -396,6 +438,7 @@ elif [ "x"`hostname -f | cut -c 8-15` == "xintrepid" ]; then
export CFLAGS=""
# export FC=xlf90
# export CC=xlc_r
+ cmake $SRCDIR
elif [ `hostname | cut -c 1-4` == "nid0" ]; then
@@ -422,6 +465,7 @@ elif [ `hostname | cut -c 1-4` == "nid0" ]; then
export LDFLAGS="-pgcpplibs"
export CPPFLAGS="-DMPICH_IGNORE_CXX_SEEK"
export CFLAGS="-fPIC"
+ cmake $SRCDIR
elif [ `hostname | cut -c 1-6` == "hopper" ]; then
@@ -456,6 +500,7 @@ elif [ `hostname | cut -c 1-6` == "hopper" ]; then
fi
export CPPFLAGS="-DMPICH_IGNORE_CXX_SEEK"
export CFLAGS="-fPIC"
+ cmake $SRCDIR
elif [ `hostname | cut -c 1-6` == "kraken" ]; then
@@ -498,6 +543,7 @@ elif [ `hostname | cut -c 1-6` == "kraken" ]; then
module load subversion
export CPPFLAGS="-DMPICH_IGNORE_CXX_SEEK"
export CFLAGS="-fPIC -g -O0"
+ cmake $SRCDIR
elif [ `hostname | cut -c 1-4` == "dyn9" -o `hostname | cut -c 1-3` == "pnb" ]; then
@@ -545,6 +591,7 @@ elif [ `hostname | cut -c 1-4` == "dyn9" -o `hostname | cut -c 1-3` == "pnb" ];
unset SEQ_NC_LIBS
unset PAR_NC_DIR
unset PAR_NC_LIBS
+ cmake $SRCDIR
elif [ `hostname | cut -c 1-7` == "ubuntu" ]; then
@@ -554,6 +601,7 @@ elif [ `hostname | cut -c 1-7` == "ubuntu" ]; then
#########################
echo "Configure on UBUNTU"
export CC=mpicc
+ cmake $SRCDIR
elif [ `hostname | cut -c 1-6` == "tomato" ]; then
@@ -563,6 +611,7 @@ elif [ `hostname | cut -c 1-6` == "tomato" ]; then
#########################
echo "Configure on UBUNTU"
export CC=mpicc
+ cmake $SRCDIR
elif [ `hostname | cut -c 1-4` == "qliu" ]; then
@@ -573,6 +622,7 @@ elif [ `hostname | cut -c 1-4` == "qliu" ]; then
echo "Configure on UBUNTU"
export CC=mpicc
export CFLAGS="-g -O0 -fPIC"
+ cmake $SRCDIR
elif [ `hostname | cut -c 1-7` == "esimmon" ]; then
@@ -597,6 +647,7 @@ elif [ `hostname | cut -c 1-7` == "esimmon" ]; then
export SEQ_NC_LIBS="-L/opt/netcdf3/lib -lnetcdf"
export PAR_NC_DIR=/opt/nc4par
export PAR_NC_LIBS="-L/opt/nc4par/lib -lnetcdf"
+ cmake $SRCDIR
elif [ `hostname | cut -c 1-9` == "PC0098504" ]; then
@@ -614,6 +665,7 @@ elif [ `hostname | cut -c 1-9` == "PC0098504" ]; then
export CPPFLAGS="-DMPICH_IGNORE_CXX_SEEK"
export CFLAGS="-g -O0 -fPIC -Wno-int-to-pointer-cast -Wno-pointer-to-int-cast"
export LDFLAGS="-lpthread"
+ cmake $SRCDIR
elif [ `hostname | cut -c 1-7` == "adiosVM" ]; then
@@ -627,7 +679,7 @@ elif [ `hostname | cut -c 1-7` == "adiosVM" ]; then
export CC=mpicc
export CXX=mpicxx
export FC=mpif90
- export INSTALL_PREFIX="/opt/adios/1.11"
+ export INSTALL_PREFIX="/opt/adios/1.12"
export CPPFLAGS="-DMPICH_IGNORE_CXX_SEEK"
export CFLAGS="-g -O0 -fPIC -Wno-int-to-pointer-cast -Wno-pointer-to-int-cast"
export BZIP2_DIR="/usr/lib"
@@ -643,6 +695,7 @@ elif [ `hostname | cut -c 1-7` == "adiosVM" ]; then
export PAR_HDF5_LIBS="-L/opt/hdf5-1.8.17-parallel/lib -lhdf5_hl -lhdf5 -lm"
export SEQ_NC_DIR=/opt/netcdf-4.4.0
export SEQ_NC_LIBS="-L/opt/netcdf-4.4.0/lib -lnetcdf"
+ cmake $SRCDIR
else
echo "Could not determine what machine is this."
echo "This script is for configuring adios on the authors' machines."
diff --git a/config.h.cmake b/config.h.cmake
index 9fb2cfc..0ab0bd6 100644
--- a/config.h.cmake
+++ b/config.h.cmake
@@ -11,7 +11,7 @@
/* Define to a macro mangling the given C identifier (in lower and upper
case), which must not contain underscores, for linking with Fortran. */
-#cmakedefine FC_FUNC ${FC_FUNC}
+#cmakedefine FC_FUNC ${FC_FUNC}
/* As FC_FUNC, but for C identifiers containing underscores. */
#cmakedefine FC_FUNC_ ${FC_FUNC_}
@@ -46,6 +46,9 @@
/* Define to 1 if you have the `clock_get_time' function. */
#cmakedefine HAVE_CLOCK_GET_TIME 1
+/* Define to 1 if the system has the type `clockid_t'. */
+#cmakedefine HAVE_CLOCKID_T 1
+
/* Define if you have CRAY_PMI. */
#cmakedefine HAVE_CRAY_PMI 1
@@ -207,7 +210,7 @@
#cmakedefine HAVE_PTLERRORSTR 1
/* Define to 1 if you have the `PtlEventKindStr' function. */
-#cmakedefine HAVE_PTLEVENTKINDSTR 1
+#cmakedefine HAVE_PTLEVENTKINDSTR 1
/* Define to 1 if you have the `PtlGetJid' function. */
#cmakedefine HAVE_PTLGETJID 1
@@ -276,6 +279,18 @@
/* Define to 1 if you have the <szlib.h> header file. */
#cmakedefine HAVE_SZLIB_H 1
+/* Define if you have SZ. */
+#cmakedefine HAVE_SZ 1
+
+/* Define to 1 if you have the <sz.h> header file. */
+#cmakedefine HAVE_SZ_H 1
+
+/* Define if you have LZ4. */
+#cmakedefine HAVE_LZ4 1
+
+/* Define to 1 if you have the <lz4.h> header file. */
+#cmakedefine HAVE_LZ4_H 1
+
/* Define to 1 if you have the <unistd.h> header file. */
#cmakedefine HAVE_UNISTD_H 1
diff --git a/config.h.in b/config.h.in
index 418eb3d..1bd9164 100644
--- a/config.h.in
+++ b/config.h.in
@@ -149,6 +149,12 @@
/* Define to 1 if you have the <lustre/lustreapi.h> header file. */
#undef HAVE_LUSTRE_LUSTREAPI_H
+/* Define if you have LZ4. */
+#undef HAVE_LZ4
+
+/* Define to 1 if you have the <lz4.h> header file. */
+#undef HAVE_LZ4_H
+
/* Define to 1 if you have the <memory.h> header file. */
#undef HAVE_MEMORY_H
@@ -275,12 +281,18 @@
/* Define to 1 if you have the <sys/types.h> header file. */
#undef HAVE_SYS_TYPES_H
+/* Define if you have SZ. */
+#undef HAVE_SZ
+
/* Define if you have SZIP. */
#undef HAVE_SZIP
/* Define to 1 if you have the <szlib.h> header file. */
#undef HAVE_SZLIB_H
+/* Define to 1 if you have the <sz.h> header file. */
+#undef HAVE_SZ_H
+
/* Define to 1 if you have the <time.h> header file. */
#undef HAVE_TIME_H
diff --git a/config/ac_bzip2.m4 b/config/ac_bzip2.m4
index 9a2267c..54d3465 100644
--- a/config/ac_bzip2.m4
+++ b/config/ac_bzip2.m4
@@ -91,7 +91,9 @@ else
int bzerr = BZ2_bzBuffToBuffCompress (
out, out_len, in, in_len, blocksize100k, 0, 30);
return (bzerr != BZ_OK);],
- [AC_MSG_RESULT(yes)],
+ [AC_MSG_RESULT(yes)
+ AM_CONDITIONAL(HAVE_BZIP2,true)
+ ],
[AM_CONDITIONAL(HAVE_BZIP2,false)
AC_MSG_RESULT(no)
])
diff --git a/config/ac_dataspaces.m4 b/config/ac_dataspaces.m4
index 038c072..2457000 100644
--- a/config/ac_dataspaces.m4
+++ b/config/ac_dataspaces.m4
@@ -26,8 +26,10 @@ AM_CONDITIONAL(HAVE_DATASPACES,true)
AC_ARG_WITH(dataspaces,
[AS_HELP_STRING([--with-dataspaces=DIR],
[Build the DATASPACES transport method. Point to the DATASPACES installation.])],
- [DATASPACES_LDFLAGS="-L$withval/lib";
- DATASPACES_CPPFLAGS="-I$withval/include";],
+ [DATASPACES_LIBS="-L$withval/lib -ldspaces -ldscommon -ldart";
+ DATASPACES_CPPFLAGS="-I$withval/include";
+ DSPACES_CONFIG="$withval/bin/dspaces_config";
+ ],
[with_dataspaces=check])
dnl If --without-dataspaces was given set HAVE_DATASPACES to false and do nothing more
@@ -72,36 +74,29 @@ else
DATASPACES_LIBDIR="${DATASPACES}/lib"
fi
- dnl Add "-I" to DATASPACES_INCDIR.
- if test -n "${DATASPACES_INCDIR}"; then
- DATASPACES_CPPFLAGS="-I${DATASPACES_INCDIR}"
+ dnl 1.6.2 has a config file
+ if test -x "${DSPACES_CONFIG}"; then
+ DATASPACES_LIBS=$(${DSPACES_CONFIG} -l)
+ DATASPACES_CPPFLAGS=$(${DSPACES_CONFIG} -c)
else
- ac_dataspaces_ok=no
- fi
- dnl Add "-L" to DATASPACES_LIBDIR.
- if test -n "${DATASPACES_LIBDIR}"; then
- DATASPACES_LDFLAGS="-L${DATASPACES_LIBDIR}"
- else
- ac_dataspaces_ok=no
+ dnl Add "-I" to DATASPACES_INCDIR.
+ if test -n "${DATASPACES_INCDIR}"; then
+ DATASPACES_CPPFLAGS="-I${DATASPACES_INCDIR}"
+ fi
+
+ dnl Add "-L" to DATASPACES_LIBDIR.
+ if test -n "${DATASPACES_LIBDIR}"; then
+ DATASPACES_LIBS="-L${DATASPACES_LIBDIR} -ldspaces -ldscommon -ldart"
+ fi
fi
save_CC="$CC"
save_CPPFLAGS="$CPPFLAGS"
save_LIBS="$LIBS"
save_LDFLAGS="$LDFLAGS"
- dnl if test "x${ac_infiniband_lib_ok}" == "xyes"; then
- dnl dnl LIBS="$LIBS -ldart -ldataspaces"
- dnl LIBS="$LIBS -ldspaces -ldscommon -ldart"
- dnl elif test "x${ac_portals_lib_ok}" == "xyes"; then
- dnl LIBS="$LIBS -ldart2 -lspaces"
- dnl elif test "x${ac_dmcf_lib_ok}" == "xyes"; then
- dnl LIBS="$LIBS -ldspaces -ldscommon -ldart"
- dnl else
- dnl LIBS="$LIBS -ldspaces -ldscommon -ldart"
- dnl fi
- LIBS="-ldspaces -ldscommon -ldart $LIBS"
- LDFLAGS="$LDFLAGS $DATASPACES_LDFLAGS"
+ dnl LDFLAGS="$LDFLAGS $DATASPACES_LDFLAGS"
+ LIBS="$DATASPACES_LIBS $LIBS"
CPPFLAGS="$CPPFLAGS $DATASPACES_CPPFLAGS"
CC="$MPICC"
@@ -117,14 +112,13 @@ else
dnl if test "x${ac_portals_lib_ok}" == "xyes"; then
dnl elif test "x${ac_infiniband_lib_ok}" == "xyes"; then
dnl elif test -z "${HAVE_CRAY_PMI_TRUE}" -a -z "${HAVE_CRAY_UGNI_TRUE}"; then
- dnl elif test "x${ac_dcmf_lib_ok}" == "xyes"; then
- dnl elif test "x${ac_pami_lib_ok}" == "xyes"; then
+ dnl elif test "x${ac_dcmf_lib_ok}" == "xyes"; then
+ dnl elif test "x${ac_pami_lib_ok}" == "xyes"; then
dnl else
dnl fi
AC_TRY_LINK([#include "dataspaces.h"],
[int err; err = dspaces_init(1,1,0,"");],
- [AC_MSG_RESULT(yes)
- DATASPACES_LIBS="-ldspaces -ldscommon -ldart"],
+ [AC_MSG_RESULT(yes)],
[AC_MSG_RESULT(no)
AM_CONDITIONAL(HAVE_DATASPACES,false)])
fi
diff --git a/config/ac_dimes.m4 b/config/ac_dimes.m4
index 0929822..33d0da0 100644
--- a/config/ac_dimes.m4
+++ b/config/ac_dimes.m4
@@ -23,8 +23,10 @@ AM_CONDITIONAL(HAVE_DIMES,true)
AC_ARG_WITH(dimes,
[AS_HELP_STRING([--with-dimes=DIR],
[Build the DIMES transport method. Point to the DIMES installation.])],
- [DIMES_LDFLAGS="-L$withval/lib";
- DIMES_CPPFLAGS="-I$withval/include";],
+ [DIMES_LIBS="-L$withval/lib -ldspaces -ldscommon -ldart";
+ DIMES_CPPFLAGS="-I$withval/include";
+ DSPACES_CONFIG="$withval/bin/dspaces_config";
+ ],
[with_dimes=check])
dnl If --without-dimes was given set HAVE_DIMES to false and do nothing more
@@ -69,32 +71,29 @@ else
DIMES_LIBDIR="${DIMES}/lib"
fi
- dnl Add "-I" to DIMES_INCDIR.
- if test -n "${DIMES_INCDIR}"; then
- DIMES_CPPFLAGS="-I${DIMES_INCDIR}"
+ dnl 1.6.2 has a config file
+ if test -x "${DSPACES_CONFIG}"; then
+ DIMES_LIBS=$(${DSPACES_CONFIG} -l)
+ DIMES_CPPFLAGS=$(${DSPACES_CONFIG} -c)
else
- ac_dimes_ok=no
- fi
- dnl Add "-L" to DIMES_LIBDIR.
- if test -n "${DIMES_LIBDIR}"; then
- DIMES_LDFLAGS="-L${DIMES_LIBDIR}"
- else
- ac_dimes_ok=no
- fi
+ dnl Add "-I" to DIMES_INCDIR.
+ if test -n "${DIMES_INCDIR}"; then
+ DIMES_CPPFLAGS="-I${DIMES_INCDIR}"
+ fi
+
+ dnl Add "-L" to DIMES_LIBDIR.
+ if test -n "${DIMES_LIBDIR}"; then
+ DIMES_LDFLAGS="-L${DIMES_LIBDIR}"
+ fi
+ fi
save_CC="$CC"
save_CPPFLAGS="$CPPFLAGS"
save_LIBS="$LIBS"
save_LDFLAGS="$LDFLAGS"
- if test "x${ac_portals_lib_ok}" == "xyes"; then
- dnl LIBS="$LIBS -ldart2 -lspaces"
- echo "DIMES currently NOT supported for Cray Portals!"
- AM_CONDITIONAL(HAVE_DIMES, false)
- else
- LIBS="-ldspaces -ldscommon -ldart $LIBS"
- fi
- LDFLAGS="$LDFLAGS $DIMES_LDFLAGS"
+ dnl LDFLAGS="$LDFLAGS $DIMES_LDFLAGS"
+ LIBS="$DIMES_LIBS $LIBS"
CPPFLAGS="$CPPFLAGS $DIMES_CPPFLAGS"
CC="$MPICC"
@@ -113,8 +112,7 @@ else
dnl elif test "x${ac_pami_lib_ok}" == "xyes"; then
AC_TRY_LINK([#include "dimes_interface.h"],
[int err; dimes_put_sync_all();],
- [AC_MSG_RESULT(yes)
- DIMES_LIBS="-ldspaces -ldscommon -ldart"],
+ [AC_MSG_RESULT(yes)],
[AC_MSG_RESULT(no)
AM_CONDITIONAL(HAVE_DIMES,false)])
dnl else
diff --git a/config/ac_flexpath.m4 b/config/ac_flexpath.m4
index a358e1a..1871d5f 100644
--- a/config/ac_flexpath.m4
+++ b/config/ac_flexpath.m4
@@ -36,59 +36,28 @@ if test "x$ac_flexpath_ok" != "xno"; then
flexpath_dir=$withval
datatap_dir=$withval
- CERCS_REQUIRE_PACKAGE(evpath, evpath.h, libevpath.a)
- CERCS_REQUIRE_PACKAGE(ffs, ffs.h,libffs.a)
- CERCS_REQUIRE_PACKAGE(atl, atl.h,libatl.a)
- CERCS_REQUIRE_PACKAGE(dill, dill.h, libdill.a)
- CERCS_REQUIRE_PACKAGE(cercs_env, cercs_env.h, libcercs_env.a)
-
+ CERCS_REQUIRE_PACKAGE(evpath, evpath.h, libevpath.la)
if test -n "$cercs_cv_evpath_link_dir" -a -n "$cercs_cv_evpath_include_arg";then
- FP_LDFLAGS="$FP_LDFLAGS -L$cercs_cv_evpath_link_dir"
- FP_LIBS="$FP_LIBS -levpath"
- FP_CFLAGS="$FP_CFLAGS $cercs_cv_evpath_include_arg"
- FP_CPPFLAGS="$FP_CPPFLAGS $cercs_cv_evpath_include_arg"
+ if (test -x "$withval/bin/evpath_config") ; then
+ FP_CONFIG="$withval/bin/evpath_config"
+ else
+ FP_CONFIG="$cercs_cv_evpath_link_dir/../bin/evpath_config"
+ fi
+ if (test -x "$FP_CONFIG") ; then
+ FP_LIBS=$(${FP_CONFIG} -s)
+ FP_CFLAGS=$(${FP_CONFIG} -c)
+ FP_CPPFLAGS=$(${FP_CONFIG} -c)
+ else
+ FP_LDFLAGS="$FP_LDFLAGS -L$cercs_cv_evpath_link_dir"
+ FP_LIBS="$FP_LIBS -levpath"
+ FP_CFLAGS="$FP_CFLAGS $cercs_cv_evpath_include_arg"
+ FP_CPPFLAGS="$FP_CPPFLAGS $cercs_cv_evpath_include_arg"
+ fi
else
echo "FLEXPATH couldn't find evpath - Not building flexpath"
ac_flexpath_ok=no
fi
- if test -n "$cercs_cv_ffs_link_dir" -a -n "$cercs_cv_ffs_include_arg"; then
- FP_LDFLAGS="$FP_LDFLAGS -L$cercs_cv_ffs_link_dir"
- FP_LIBS="$FP_LIBS -lffs"
- FP_CFLAGS="$FP_CFLAGS $cercs_cv_ffs_include_arg"
- FP_CPPFLAGS="$FP_CPPFLAGS $cercs_cv_ffs_include_arg"
- else
- echo "FLEXPATH couldn't find ffs - Not building flexpath"
- ac_flexpath_ok=no
- fi
- if test -n "$cercs_cv_atl_link_dir" -a -n "$cercs_cv_atl_include_arg"; then
- FP_LDFLAGS="$FP_LDFLAGS -L$cercs_cv_atl_link_dir"
- FP_LIBS="$FP_LIBS -latl"
- FP_CFLAGS="$FP_CFLAGS $cercs_cv_atl_include_arg"
- FP_CPPFLAGS="$FP_CPPFLAGS $cercs_cv_atl_include_arg"
- else
- ac_flexpath_ok=no
- echo "FLEXPATH couldn't find atl - Not building flexpath"
- fi
- if test -n "$cercs_cv_dill_link_dir" -a -n "$cercs_cv_dill_include_arg"; then
- FP_LDFLAGS="$FP_LDFLAGS -L$cercs_cv_dill_link_dir"
- FP_LIBS="$FP_LIBS -ldill"
- FP_CFLAGS="$FP_CFLAGS $cercs_cv_dill_include_arg"
- FP_CPPFLAGS="$FP_CPPFLAGS $cercs_cv_dill_include_arg"
- else
- ac_flexpath_ok=no
- echo "FLEXPATH couldn't find dill - Not building flexpath"
- fi
- if test -n "$cercs_cv_cercs_env_link_dir" -a -n "$cercs_cv_cercs_env_include_arg"; then
- FP_LDFLAGS="$FP_LDFLAGS -L$cercs_cv_cercs_env_link_dir"
- FP_LIBS="$FP_LIBS -lcercs_env"
- FP_CFLAGS="$FP_CFLAGS $cercs_cv_cercs_env_include_arg"
- FP_CPPFLAGS="$FP_CPPFLAGS $cercs_cv_cercs_env_include_arg"
- else
- ac_flexpath_ok=no
- echo "FLEXPATH couldn't find cercs_env - Not building flexpath"
- fi
-
fi
AC_SUBST(FP_LIBS)
diff --git a/config/ac_lz4.m4 b/config/ac_lz4.m4
new file mode 100644
index 0000000..14baf52
--- /dev/null
+++ b/config/ac_lz4.m4
@@ -0,0 +1,83 @@
+#
+#
+# AC_LZ4
+#
+#
+#
+dnl @synopsis AC_LZ4
+dnl
+dnl This macro test if LZ4 is to be used.
+dnl Use in C code:
+dnl #ifdef LZ4
+dnl #include "lz4.h"
+dnl #endif
+dnl
+dnl @version 2.0
+dnl @author Zhenhuan (Steve) Gong
+dnl @author Norbert Podhorszki
+dnl @author Rene Widera
+dnl
+AC_DEFUN([AC_LZ4],[
+
+AC_MSG_NOTICE([=== checking for LZ4 ===])
+
+AM_CONDITIONAL(HAVE_LZ4,true)
+
+AC_ARG_WITH(lz4,
+ [ --with-lz4=DIR Location of LZ4 library],
+ [:], [with_lz4=no])
+
+if test "x$with_lz4" == "xno"; then
+
+ AM_CONDITIONAL(HAVE_LZ4,false)
+
+else
+
+ save_CFLAGS="$CFLAGS"
+ save_LIBS="$LIBS"
+ save_LDFLAGS="$LDFLAGS"
+
+ if test "x$with_lz4" == "xyes"; then
+ dnl No path given
+ LZ4_CFLAGS=""
+ LZ4_CPPFLAGS=""
+ LZ4_LDFLAGS=""
+ LZ4_LIBS="-llz4"
+ else
+ dnl Path given, first try path/lib
+ LZ4_CFLAGS="-I$withval/include"
+ LZ4_CPPFLAGS="-I$withval/include"
+ LZ4_LDFLAGS="-L$withval/lib"
+ LZ4_LIBS="-llz4"
+ fi
+
+ LIBS="$LIBS $LZ4_LIBS"
+ LDFLAGS="$LDFLAGS $LZ4_LDFLAGS"
+ CFLAGS="$CFLAGS $LZ4_CFLAGS"
+ CPPFLAGS="$CPPFLAGS $LZ4_CPPFLAGS"
+
+ dnl Find header file first
+ AC_CHECK_HEADERS(lz4.h,
+ ,
+ [AM_CONDITIONAL(HAVE_LZ4,false)])
+
+ LIBS="$save_LIBS"
+ LDFLAGS="$save_LDFLAGS"
+ CFLAGS="$save_CFLAGS"
+ CPPFLAGS="$save_CPPFLAGS"
+
+ AC_SUBST(LZ4_LIBS)
+ AC_SUBST(LZ4_LDFLAGS)
+ AC_SUBST(LZ4_CFLAGS)
+ AC_SUBST(LZ4_CPPFLAGS)
+
+ # Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND:
+ if test -z "${HAVE_LZ4_TRUE}"; then
+ ifelse([$1],,[AC_DEFINE(HAVE_LZ4,1,[Define if you have LZ4.])],[$1])
+ :
+ else
+ $2
+ :
+ fi
+fi
+])dnl AC_LZ4
diff --git a/config/ac_sz.m4 b/config/ac_sz.m4
new file mode 100644
index 0000000..9b9d144
--- /dev/null
+++ b/config/ac_sz.m4
@@ -0,0 +1,73 @@
+#
+#
+# AC_SZ
+#
+#
+#
+dnl @synopsis AC_SZ
+dnl
+dnl This macro test if SZ is to be used.
+dnl Use in C code:
+dnl #ifdef SZ
+dnl #include "sz.h"
+dnl #endif
+dnl
+dnl @version 1.0
+dnl @author Zhenhuan (Steve) Gong
+dnl
+AC_DEFUN([AC_SZ],[
+
+AC_MSG_NOTICE([=== checking for SZ ===])
+
+AM_CONDITIONAL(HAVE_SZ,true)
+
+AC_ARG_WITH(sz,
+ [ --with-sz=DIR Location of SZ library],
+ [SZ_LDFLAGS="-L$withval/lib";
+ SZ_LIBS="-lsz -lzlib";
+ SZ_CPPFLAGS="-I$withval/include";],
+ [with_sz=no])
+
+if test "x$with_sz" == "xno"; then
+
+ AM_CONDITIONAL(HAVE_SZ,false)
+
+else
+
+ save_CPPFLAGS="$CPPFLAGS"
+ save_LIBS="$LIBS"
+ save_LDFLAGS="$LDFLAGS"
+ LIBS="$LIBS -lsz -lzlib"
+ LDFLAGS="$LDFLAGS $SZ_LDFLAGS"
+ CPPFLAGS="$CPPFLAGS $SZ_CPPFLAGS"
+
+ if test -z "${HAVE_SZ_TRUE}"; then
+ AC_CHECK_HEADERS(sz.h,
+ ,
+ [AM_CONDITIONAL(HAVE_SZ,false)])
+ fi
+
+ # Check for the SZ library and headers
+ dnl AC_TRY_COMPILE([struct obd_uuid {char uuid[40];};int fd, num_ost;struct obd_uuid uuids[1024];],
+ dnl [llapi_lov_get_uuids(fd, uuids, &num_ost);],
+ dnl [SZ_LIBS="-lsz"],
+ dnl [AM_CONDITIONAL(HAVE_SZ,false)])
+
+ LIBS="$save_LIBS"
+ LDFLAGS="$save_LDFLAGS"
+ CPPFLAGS="$save_CPPFLAGS"
+
+ AC_SUBST(SZ_LIBS)
+ AC_SUBST(SZ_LDFLAGS)
+ AC_SUBST(SZ_CPPFLAGS)
+
+ # Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND:
+ if test -z "${HAVE_SZ_TRUE}"; then
+ ifelse([$1],,[AC_DEFINE(HAVE_SZ,1,[Define if you have SZ.])],[$1])
+ :
+ else
+ $2
+ :
+ fi
+fi
+])dnl AC_SZ
diff --git a/config/ac_zlib.m4 b/config/ac_zlib.m4
index 344e6e5..6972808 100644
--- a/config/ac_zlib.m4
+++ b/config/ac_zlib.m4
@@ -88,7 +88,9 @@ else
int level = 5;
int zerr = compress2 (out, out_len, in, in_len, level);
return (zerr != Z_OK);],
- [AC_MSG_RESULT(yes)],
+ [AC_MSG_RESULT(yes)
+ AM_CONDITIONAL(HAVE_ZLIB,true)
+ ]
[AM_CONDITIONAL(HAVE_ZLIB,false)
AC_MSG_RESULT(no)
])
diff --git a/config/acx_pthread.m4 b/config/acx_pthread.m4
index f51bfbc..50c126c 100644
--- a/config/acx_pthread.m4
+++ b/config/acx_pthread.m4
@@ -246,6 +246,7 @@ fi
AC_SUBST(PTHREAD_LIBS)
AC_SUBST(PTHREAD_CFLAGS)
AC_SUBST(PTHREAD_CC)
+AC_MSG_NOTICE([PTHREAD_LIBS=${PTHREAD_LIBS}])
if test x"$acx_pthread_ok" = xyes; then
AC_DEFINE(HAVE_PTHREAD,1,[Define if you have POSIX threads])
diff --git a/config/config.guess b/config/config.guess
index e3ef63f..69ed3e5 100755
--- a/config/config.guess
+++ b/config/config.guess
@@ -1,13 +1,12 @@
#! /bin/sh
# Attempt to guess a canonical system name.
-# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
-# 2000, 2001, 2002, 2003, 2004, 2005 Free Software Foundation, Inc.
+# Copyright 1992-2017 Free Software Foundation, Inc.
-timestamp='2005-12-13'
+timestamp='2017-03-05'
# This file is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2 of the License, or
+# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful, but
@@ -16,26 +15,22 @@ timestamp='2005-12-13'
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
-# 02110-1301, USA.
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
#
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-
-# Originally written by Per Bothner <per at bothner.com>.
-# Please send patches to <config-patches at gnu.org>. Submit a context
-# diff and a properly formatted ChangeLog entry.
+# the same distribution terms that you use for the rest of that
+# program. This Exception is an additional permission under section 7
+# of the GNU General Public License, version 3 ("GPLv3").
#
-# This script attempts to guess a canonical system name similar to
-# config.sub. If it succeeds, it prints the system name on stdout, and
-# exits with 0. Otherwise, it exits with 1.
+# Originally written by Per Bothner; maintained since 2000 by Ben Elliston.
#
-# The plan is that this can be called by configure scripts if you
-# don't specify an explicit build system type.
+# You can get the latest version of this script from:
+# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess
+#
+# Please send patches to <config-patches at gnu.org>.
+
me=`echo "$0" | sed -e 's,.*/,,'`
@@ -55,8 +50,7 @@ version="\
GNU config.guess ($timestamp)
Originally written by Per Bothner.
-Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005
-Free Software Foundation, Inc.
+Copyright 1992-2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
@@ -106,7 +100,7 @@ set_cc_for_build='
trap "exitcode=\$?; (rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null) && exit \$exitcode" 0 ;
trap "rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null; exit 1" 1 2 13 15 ;
: ${TMPDIR=/tmp} ;
- { tmp=`(umask 077 && mktemp -d -q "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||
+ { tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||
{ test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } ||
{ tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir $tmp) && echo "Warning: creating insecure temp directory" >&2 ; } ||
{ echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } ;
@@ -138,12 +132,33 @@ UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown
UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown
UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown
+case "${UNAME_SYSTEM}" in
+Linux|GNU|GNU/*)
+ # If the system lacks a compiler, then just pick glibc.
+ # We could probably try harder.
+ LIBC=gnu
+
+ eval $set_cc_for_build
+ cat <<-EOF > $dummy.c
+ #include <features.h>
+ #if defined(__UCLIBC__)
+ LIBC=uclibc
+ #elif defined(__dietlibc__)
+ LIBC=dietlibc
+ #else
+ LIBC=gnu
+ #endif
+ EOF
+ eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC' | sed 's, ,,g'`
+ ;;
+esac
+
# Note: order is significant - the case branches are not exclusive.
case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
*:NetBSD:*:*)
# NetBSD (nbsd) targets should (where applicable) match one or
- # more of the tupples: *-*-netbsdelf*, *-*-netbsdaout*,
+ # more of the tuples: *-*-netbsdelf*, *-*-netbsdaout*,
# *-*-netbsdecoff* and *-*-netbsd*. For targets that recently
# switched to ELF, *-*-netbsd* would select the old
# object file format. This provides both forward
@@ -153,22 +168,33 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
# Note: NetBSD doesn't particularly care about the vendor
# portion of the name. We always set it to "unknown".
sysctl="sysctl -n hw.machine_arch"
- UNAME_MACHINE_ARCH=`(/sbin/$sysctl 2>/dev/null || \
- /usr/sbin/$sysctl 2>/dev/null || echo unknown)`
+ UNAME_MACHINE_ARCH=`(uname -p 2>/dev/null || \
+ /sbin/$sysctl 2>/dev/null || \
+ /usr/sbin/$sysctl 2>/dev/null || \
+ echo unknown)`
case "${UNAME_MACHINE_ARCH}" in
armeb) machine=armeb-unknown ;;
arm*) machine=arm-unknown ;;
sh3el) machine=shl-unknown ;;
sh3eb) machine=sh-unknown ;;
+ sh5el) machine=sh5le-unknown ;;
+ earmv*)
+ arch=`echo ${UNAME_MACHINE_ARCH} | sed -e 's,^e\(armv[0-9]\).*$,\1,'`
+ endian=`echo ${UNAME_MACHINE_ARCH} | sed -ne 's,^.*\(eb\)$,\1,p'`
+ machine=${arch}${endian}-unknown
+ ;;
*) machine=${UNAME_MACHINE_ARCH}-unknown ;;
esac
# The Operating System including object format, if it has switched
- # to ELF recently, or will in the future.
+ # to ELF recently (or will in the future) and ABI.
case "${UNAME_MACHINE_ARCH}" in
+ earm*)
+ os=netbsdelf
+ ;;
arm*|i386|m68k|ns32k|sh3*|sparc|vax)
eval $set_cc_for_build
if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \
- | grep __ELF__ >/dev/null
+ | grep -q __ELF__
then
# Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout).
# Return netbsd for either. FIX?
@@ -178,7 +204,14 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
fi
;;
*)
- os=netbsd
+ os=netbsd
+ ;;
+ esac
+ # Determine ABI tags.
+ case "${UNAME_MACHINE_ARCH}" in
+ earm*)
+ expr='s/^earmv[0-9]/-eabi/;s/eb$//'
+ abi=`echo ${UNAME_MACHINE_ARCH} | sed -e "$expr"`
;;
esac
# The OS release
@@ -191,34 +224,48 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
release='-gnu'
;;
*)
- release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'`
+ release=`echo ${UNAME_RELEASE} | sed -e 's/[-_].*//' | cut -d. -f1,2`
;;
esac
# Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM:
# contains redundant information, the shorter form:
# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used.
- echo "${machine}-${os}${release}"
+ echo "${machine}-${os}${release}${abi}"
+ exit ;;
+ *:Bitrig:*:*)
+ UNAME_MACHINE_ARCH=`arch | sed 's/Bitrig.//'`
+ echo ${UNAME_MACHINE_ARCH}-unknown-bitrig${UNAME_RELEASE}
exit ;;
*:OpenBSD:*:*)
UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'`
echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE}
exit ;;
+ *:LibertyBSD:*:*)
+ UNAME_MACHINE_ARCH=`arch | sed 's/^.*BSD\.//'`
+ echo ${UNAME_MACHINE_ARCH}-unknown-libertybsd${UNAME_RELEASE}
+ exit ;;
*:ekkoBSD:*:*)
echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE}
exit ;;
+ *:SolidBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-solidbsd${UNAME_RELEASE}
+ exit ;;
macppc:MirBSD:*:*)
- echo powerppc-unknown-mirbsd${UNAME_RELEASE}
+ echo powerpc-unknown-mirbsd${UNAME_RELEASE}
exit ;;
*:MirBSD:*:*)
echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE}
exit ;;
+ *:Sortix:*:*)
+ echo ${UNAME_MACHINE}-unknown-sortix
+ exit ;;
alpha:OSF1:*:*)
case $UNAME_RELEASE in
*4.0)
UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
;;
*5.*)
- UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
+ UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
;;
esac
# According to Compaq, /usr/sbin/psrinfo has been available on
@@ -228,43 +275,46 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1`
case "$ALPHA_CPU_TYPE" in
"EV4 (21064)")
- UNAME_MACHINE="alpha" ;;
+ UNAME_MACHINE=alpha ;;
"EV4.5 (21064)")
- UNAME_MACHINE="alpha" ;;
+ UNAME_MACHINE=alpha ;;
"LCA4 (21066/21068)")
- UNAME_MACHINE="alpha" ;;
+ UNAME_MACHINE=alpha ;;
"EV5 (21164)")
- UNAME_MACHINE="alphaev5" ;;
+ UNAME_MACHINE=alphaev5 ;;
"EV5.6 (21164A)")
- UNAME_MACHINE="alphaev56" ;;
+ UNAME_MACHINE=alphaev56 ;;
"EV5.6 (21164PC)")
- UNAME_MACHINE="alphapca56" ;;
+ UNAME_MACHINE=alphapca56 ;;
"EV5.7 (21164PC)")
- UNAME_MACHINE="alphapca57" ;;
+ UNAME_MACHINE=alphapca57 ;;
"EV6 (21264)")
- UNAME_MACHINE="alphaev6" ;;
+ UNAME_MACHINE=alphaev6 ;;
"EV6.7 (21264A)")
- UNAME_MACHINE="alphaev67" ;;
+ UNAME_MACHINE=alphaev67 ;;
"EV6.8CB (21264C)")
- UNAME_MACHINE="alphaev68" ;;
+ UNAME_MACHINE=alphaev68 ;;
"EV6.8AL (21264B)")
- UNAME_MACHINE="alphaev68" ;;
+ UNAME_MACHINE=alphaev68 ;;
"EV6.8CX (21264D)")
- UNAME_MACHINE="alphaev68" ;;
+ UNAME_MACHINE=alphaev68 ;;
"EV6.9A (21264/EV69A)")
- UNAME_MACHINE="alphaev69" ;;
+ UNAME_MACHINE=alphaev69 ;;
"EV7 (21364)")
- UNAME_MACHINE="alphaev7" ;;
+ UNAME_MACHINE=alphaev7 ;;
"EV7.9 (21364A)")
- UNAME_MACHINE="alphaev79" ;;
+ UNAME_MACHINE=alphaev79 ;;
esac
# A Pn.n version is a patched version.
# A Vn.n version is a released version.
# A Tn.n version is a released field test version.
# A Xn.n version is an unreleased experimental baselevel.
# 1.2 uses "1.2" for uname -r.
- echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
- exit ;;
+ echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz`
+ # Reset EXIT trap before exiting to avoid spurious non-zero exit code.
+ exitcode=$?
+ trap '' 0
+ exit $exitcode ;;
Alpha\ *:Windows_NT*:*)
# How do we know it's Interix rather than the generic POSIX subsystem?
# Should we change UNAME_MACHINE based on the output of uname instead
@@ -290,12 +340,12 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
echo s390-ibm-zvmoe
exit ;;
*:OS400:*:*)
- echo powerpc-ibm-os400
+ echo powerpc-ibm-os400
exit ;;
arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*)
echo arm-acorn-riscix${UNAME_RELEASE}
exit ;;
- arm:riscos:*:*|arm:RISCOS:*:*)
+ arm*:riscos:*:*|arm*:RISCOS:*:*)
echo arm-unknown-riscos
exit ;;
SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*)
@@ -319,14 +369,33 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
case `/usr/bin/uname -p` in
sparc) echo sparc-icl-nx7; exit ;;
esac ;;
+ s390x:SunOS:*:*)
+ echo ${UNAME_MACHINE}-ibm-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
sun4H:SunOS:5.*:*)
echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
exit ;;
sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
exit ;;
- i86pc:SunOS:5.*:*)
- echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*)
+ echo i386-pc-auroraux${UNAME_RELEASE}
+ exit ;;
+ i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*)
+ eval $set_cc_for_build
+ SUN_ARCH=i386
+ # If there is a compiler, see if it is configured for 64-bit objects.
+ # Note that the Sun cc does not turn __LP64__ into 1 like gcc does.
+ # This test works for both compilers.
+ if [ "$CC_FOR_BUILD" != no_compiler_found ]; then
+ if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \
+ (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \
+ grep IS_64BIT_ARCH >/dev/null
+ then
+ SUN_ARCH=x86_64
+ fi
+ fi
+ echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
exit ;;
sun4*:SunOS:6*:*)
# According to config.sub, this is the proper way to canonicalize
@@ -348,7 +417,7 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
exit ;;
sun*:*:4.2BSD:*)
UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
- test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3
+ test "x${UNAME_RELEASE}" = x && UNAME_RELEASE=3
case "`/bin/arch`" in
sun3)
echo m68k-sun-sunos${UNAME_RELEASE}
@@ -370,23 +439,23 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
# MiNT. But MiNT is downward compatible to TOS, so this should
# be no problem.
atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*)
- echo m68k-atari-mint${UNAME_RELEASE}
+ echo m68k-atari-mint${UNAME_RELEASE}
exit ;;
atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*)
echo m68k-atari-mint${UNAME_RELEASE}
- exit ;;
+ exit ;;
*falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*)
- echo m68k-atari-mint${UNAME_RELEASE}
+ echo m68k-atari-mint${UNAME_RELEASE}
exit ;;
milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*)
- echo m68k-milan-mint${UNAME_RELEASE}
- exit ;;
+ echo m68k-milan-mint${UNAME_RELEASE}
+ exit ;;
hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*)
- echo m68k-hades-mint${UNAME_RELEASE}
- exit ;;
+ echo m68k-hades-mint${UNAME_RELEASE}
+ exit ;;
*:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*)
- echo m68k-unknown-mint${UNAME_RELEASE}
- exit ;;
+ echo m68k-unknown-mint${UNAME_RELEASE}
+ exit ;;
m68k:machten:*:*)
echo m68k-apple-machten${UNAME_RELEASE}
exit ;;
@@ -456,8 +525,8 @@ EOF
echo m88k-motorola-sysv3
exit ;;
AViiON:dgux:*:*)
- # DG/UX returns AViiON for all architectures
- UNAME_PROCESSOR=`/usr/bin/uname -p`
+ # DG/UX returns AViiON for all architectures
+ UNAME_PROCESSOR=`/usr/bin/uname -p`
if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ]
then
if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \
@@ -470,7 +539,7 @@ EOF
else
echo i586-dg-dgux${UNAME_RELEASE}
fi
- exit ;;
+ exit ;;
M88*:DolphinOS:*:*) # DolphinOS (SVR3)
echo m88k-dolphin-sysv3
exit ;;
@@ -527,15 +596,16 @@ EOF
echo rs6000-ibm-aix3.2
fi
exit ;;
- *:AIX:*:[45])
+ *:AIX:*:[4567])
IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then
IBM_ARCH=rs6000
else
IBM_ARCH=powerpc
fi
- if [ -x /usr/bin/oslevel ] ; then
- IBM_REV=`/usr/bin/oslevel`
+ if [ -x /usr/bin/lslpp ] ; then
+ IBM_REV=`/usr/bin/lslpp -Lqc bos.rte.libc |
+ awk -F: '{ print $3 }' | sed s/[0-9]*$/0/`
else
IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
fi
@@ -570,58 +640,58 @@ EOF
9000/[678][0-9][0-9])
if [ -x /usr/bin/getconf ]; then
sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null`
- sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
- case "${sc_cpu_version}" in
- 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0
- 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1
- 532) # CPU_PA_RISC2_0
- case "${sc_kernel_bits}" in
- 32) HP_ARCH="hppa2.0n" ;;
- 64) HP_ARCH="hppa2.0w" ;;
- '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20
- esac ;;
- esac
+ sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
+ case "${sc_cpu_version}" in
+ 523) HP_ARCH=hppa1.0 ;; # CPU_PA_RISC1_0
+ 528) HP_ARCH=hppa1.1 ;; # CPU_PA_RISC1_1
+ 532) # CPU_PA_RISC2_0
+ case "${sc_kernel_bits}" in
+ 32) HP_ARCH=hppa2.0n ;;
+ 64) HP_ARCH=hppa2.0w ;;
+ '') HP_ARCH=hppa2.0 ;; # HP-UX 10.20
+ esac ;;
+ esac
fi
if [ "${HP_ARCH}" = "" ]; then
eval $set_cc_for_build
- sed 's/^ //' << EOF >$dummy.c
+ sed 's/^ //' << EOF >$dummy.c
- #define _HPUX_SOURCE
- #include <stdlib.h>
- #include <unistd.h>
+ #define _HPUX_SOURCE
+ #include <stdlib.h>
+ #include <unistd.h>
- int main ()
- {
- #if defined(_SC_KERNEL_BITS)
- long bits = sysconf(_SC_KERNEL_BITS);
- #endif
- long cpu = sysconf (_SC_CPU_VERSION);
+ int main ()
+ {
+ #if defined(_SC_KERNEL_BITS)
+ long bits = sysconf(_SC_KERNEL_BITS);
+ #endif
+ long cpu = sysconf (_SC_CPU_VERSION);
- switch (cpu)
- {
- case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
- case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
- case CPU_PA_RISC2_0:
- #if defined(_SC_KERNEL_BITS)
- switch (bits)
- {
- case 64: puts ("hppa2.0w"); break;
- case 32: puts ("hppa2.0n"); break;
- default: puts ("hppa2.0"); break;
- } break;
- #else /* !defined(_SC_KERNEL_BITS) */
- puts ("hppa2.0"); break;
- #endif
- default: puts ("hppa1.0"); break;
- }
- exit (0);
- }
+ switch (cpu)
+ {
+ case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
+ case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
+ case CPU_PA_RISC2_0:
+ #if defined(_SC_KERNEL_BITS)
+ switch (bits)
+ {
+ case 64: puts ("hppa2.0w"); break;
+ case 32: puts ("hppa2.0n"); break;
+ default: puts ("hppa2.0"); break;
+ } break;
+ #else /* !defined(_SC_KERNEL_BITS) */
+ puts ("hppa2.0"); break;
+ #endif
+ default: puts ("hppa1.0"); break;
+ }
+ exit (0);
+ }
EOF
- (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
+ (CCOPTS="" $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
test -z "$HP_ARCH" && HP_ARCH=hppa
fi ;;
esac
- if [ ${HP_ARCH} = "hppa2.0w" ]
+ if [ ${HP_ARCH} = hppa2.0w ]
then
eval $set_cc_for_build
@@ -634,12 +704,12 @@ EOF
# $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess
# => hppa64-hp-hpux11.23
- if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) |
- grep __LP64__ >/dev/null
+ if echo __LP64__ | (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) |
+ grep -q __LP64__
then
- HP_ARCH="hppa2.0w"
+ HP_ARCH=hppa2.0w
else
- HP_ARCH="hppa64"
+ HP_ARCH=hppa64
fi
fi
echo ${HP_ARCH}-hp-hpux${HPUX_REV}
@@ -706,22 +776,22 @@ EOF
exit ;;
C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*)
echo c1-convex-bsd
- exit ;;
+ exit ;;
C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*)
if getsysinfo -f scalar_acc
then echo c32-convex-bsd
else echo c2-convex-bsd
fi
- exit ;;
+ exit ;;
C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*)
echo c34-convex-bsd
- exit ;;
+ exit ;;
C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*)
echo c38-convex-bsd
- exit ;;
+ exit ;;
C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*)
echo c4-convex-bsd
- exit ;;
+ exit ;;
CRAY*Y-MP:*:*:*)
echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
exit ;;
@@ -744,15 +814,15 @@ EOF
echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
exit ;;
F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*)
- FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
- FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
- FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
- echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
- exit ;;
+ FUJITSU_PROC=`uname -m | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz`
+ FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'`
+ FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
+ echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+ exit ;;
5000:UNIX_System_V:4.*:*)
- FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
- FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'`
- echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+ FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'`
+ FUJITSU_REL=`echo ${UNAME_RELEASE} | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/ /_/'`
+ echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
exit ;;
i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*)
echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE}
@@ -764,27 +834,52 @@ EOF
echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE}
exit ;;
*:FreeBSD:*:*)
- echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
+ UNAME_PROCESSOR=`/usr/bin/uname -p`
+ case ${UNAME_PROCESSOR} in
+ amd64)
+ UNAME_PROCESSOR=x86_64 ;;
+ i386)
+ UNAME_PROCESSOR=i586 ;;
+ esac
+ echo ${UNAME_PROCESSOR}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
exit ;;
i*:CYGWIN*:*)
echo ${UNAME_MACHINE}-pc-cygwin
exit ;;
- i*:MINGW*:*)
+ *:MINGW64*:*)
+ echo ${UNAME_MACHINE}-pc-mingw64
+ exit ;;
+ *:MINGW*:*)
echo ${UNAME_MACHINE}-pc-mingw32
exit ;;
+ *:MSYS*:*)
+ echo ${UNAME_MACHINE}-pc-msys
+ exit ;;
i*:windows32*:*)
- # uname -m includes "-pc" on this system.
- echo ${UNAME_MACHINE}-mingw32
+ # uname -m includes "-pc" on this system.
+ echo ${UNAME_MACHINE}-mingw32
exit ;;
i*:PW*:*)
echo ${UNAME_MACHINE}-pc-pw32
exit ;;
- x86:Interix*:[345]*)
- echo i586-pc-interix${UNAME_RELEASE}|sed -e 's/\..*//'
- exit ;;
+ *:Interix*:*)
+ case ${UNAME_MACHINE} in
+ x86)
+ echo i586-pc-interix${UNAME_RELEASE}
+ exit ;;
+ authenticamd | genuineintel | EM64T)
+ echo x86_64-unknown-interix${UNAME_RELEASE}
+ exit ;;
+ IA64)
+ echo ia64-unknown-interix${UNAME_RELEASE}
+ exit ;;
+ esac ;;
[345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*)
echo i${UNAME_MACHINE}-pc-mks
exit ;;
+ 8664:Windows_NT:*)
+ echo x86_64-pc-mks
+ exit ;;
i*:Windows_NT*:* | Pentium*:Windows_NT*:*)
# How do we know it's Interix rather than the generic POSIX subsystem?
# It also conflicts with pre-2.0 versions of AT&T UWIN. Should we
@@ -805,185 +900,169 @@ EOF
exit ;;
*:GNU:*:*)
# the GNU system
- echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
+ echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-${LIBC}`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
exit ;;
*:GNU/*:*:*)
# other systems with GNU libc and userland
- echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu
+ echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr "[:upper:]" "[:lower:]"``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-${LIBC}
exit ;;
i*86:Minix:*:*)
echo ${UNAME_MACHINE}-pc-minix
exit ;;
+ aarch64:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ exit ;;
+ aarch64_be:Linux:*:*)
+ UNAME_MACHINE=aarch64_be
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ exit ;;
+ alpha:Linux:*:*)
+ case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in
+ EV5) UNAME_MACHINE=alphaev5 ;;
+ EV56) UNAME_MACHINE=alphaev56 ;;
+ PCA56) UNAME_MACHINE=alphapca56 ;;
+ PCA57) UNAME_MACHINE=alphapca56 ;;
+ EV6) UNAME_MACHINE=alphaev6 ;;
+ EV67) UNAME_MACHINE=alphaev67 ;;
+ EV68*) UNAME_MACHINE=alphaev68 ;;
+ esac
+ objdump --private-headers /bin/sh | grep -q ld.so.1
+ if test "$?" = 0 ; then LIBC=gnulibc1 ; fi
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ exit ;;
+ arc:Linux:*:* | arceb:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ exit ;;
arm*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
+ eval $set_cc_for_build
+ if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \
+ | grep -q __ARM_EABI__
+ then
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ else
+ if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \
+ | grep -q __ARM_PCS_VFP
+ then
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}eabi
+ else
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}eabihf
+ fi
+ fi
+ exit ;;
+ avr32*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
cris:Linux:*:*)
- echo cris-axis-linux-gnu
+ echo ${UNAME_MACHINE}-axis-linux-${LIBC}
exit ;;
crisv32:Linux:*:*)
- echo crisv32-axis-linux-gnu
+ echo ${UNAME_MACHINE}-axis-linux-${LIBC}
+ exit ;;
+ e2k:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
frv:Linux:*:*)
- echo frv-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ exit ;;
+ hexagon:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ exit ;;
+ i*86:Linux:*:*)
+ echo ${UNAME_MACHINE}-pc-linux-${LIBC}
exit ;;
ia64:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ exit ;;
+ k1om:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
m32r*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
m68*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
- mips:Linux:*:*)
+ mips:Linux:*:* | mips64:Linux:*:*)
eval $set_cc_for_build
sed 's/^ //' << EOF >$dummy.c
#undef CPU
- #undef mips
- #undef mipsel
+ #undef ${UNAME_MACHINE}
+ #undef ${UNAME_MACHINE}el
#if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
- CPU=mipsel
+ CPU=${UNAME_MACHINE}el
#else
#if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
- CPU=mips
+ CPU=${UNAME_MACHINE}
#else
CPU=
#endif
#endif
EOF
- eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n '/^CPU/{s: ::g;p;}'`"
- test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
+ eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'`
+ test x"${CPU}" != x && { echo "${CPU}-unknown-linux-${LIBC}"; exit; }
;;
- mips64:Linux:*:*)
- eval $set_cc_for_build
- sed 's/^ //' << EOF >$dummy.c
- #undef CPU
- #undef mips64
- #undef mips64el
- #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
- CPU=mips64el
- #else
- #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
- CPU=mips64
- #else
- CPU=
- #endif
- #endif
-EOF
- eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n '/^CPU/{s: ::g;p;}'`"
- test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
- ;;
- or32:Linux:*:*)
- echo or32-unknown-linux-gnu
+ mips64el:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
- ppc:Linux:*:*)
- echo powerpc-unknown-linux-gnu
+ openrisc*:Linux:*:*)
+ echo or1k-unknown-linux-${LIBC}
exit ;;
- ppc64:Linux:*:*)
- echo powerpc64-unknown-linux-gnu
+ or32:Linux:*:* | or1k*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
- alpha:Linux:*:*)
- case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in
- EV5) UNAME_MACHINE=alphaev5 ;;
- EV56) UNAME_MACHINE=alphaev56 ;;
- PCA56) UNAME_MACHINE=alphapca56 ;;
- PCA57) UNAME_MACHINE=alphapca56 ;;
- EV6) UNAME_MACHINE=alphaev6 ;;
- EV67) UNAME_MACHINE=alphaev67 ;;
- EV68*) UNAME_MACHINE=alphaev68 ;;
- esac
- objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null
- if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi
- echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC}
+ padre:Linux:*:*)
+ echo sparc-unknown-linux-${LIBC}
+ exit ;;
+ parisc64:Linux:*:* | hppa64:Linux:*:*)
+ echo hppa64-unknown-linux-${LIBC}
exit ;;
parisc:Linux:*:* | hppa:Linux:*:*)
# Look for CPU level
case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in
- PA7*) echo hppa1.1-unknown-linux-gnu ;;
- PA8*) echo hppa2.0-unknown-linux-gnu ;;
- *) echo hppa-unknown-linux-gnu ;;
+ PA7*) echo hppa1.1-unknown-linux-${LIBC} ;;
+ PA8*) echo hppa2.0-unknown-linux-${LIBC} ;;
+ *) echo hppa-unknown-linux-${LIBC} ;;
esac
exit ;;
- parisc64:Linux:*:* | hppa64:Linux:*:*)
- echo hppa64-unknown-linux-gnu
+ ppc64:Linux:*:*)
+ echo powerpc64-unknown-linux-${LIBC}
+ exit ;;
+ ppc:Linux:*:*)
+ echo powerpc-unknown-linux-${LIBC}
+ exit ;;
+ ppc64le:Linux:*:*)
+ echo powerpc64le-unknown-linux-${LIBC}
+ exit ;;
+ ppcle:Linux:*:*)
+ echo powerpcle-unknown-linux-${LIBC}
+ exit ;;
+ riscv32:Linux:*:* | riscv64:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
s390:Linux:*:* | s390x:Linux:*:*)
- echo ${UNAME_MACHINE}-ibm-linux
+ echo ${UNAME_MACHINE}-ibm-linux-${LIBC}
exit ;;
sh64*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
sh*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
sparc:Linux:*:* | sparc64:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ exit ;;
+ tile*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
vax:Linux:*:*)
- echo ${UNAME_MACHINE}-dec-linux-gnu
+ echo ${UNAME_MACHINE}-dec-linux-${LIBC}
exit ;;
x86_64:Linux:*:*)
- echo x86_64-unknown-linux-gnu
+ echo ${UNAME_MACHINE}-pc-linux-${LIBC}
+ exit ;;
+ xtensa*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
- i*86:Linux:*:*)
- # The BFD linker knows what the default object file format is, so
- # first see if it will tell us. cd to the root directory to prevent
- # problems with other programs or directories called `ld' in the path.
- # Set LC_ALL=C to ensure ld outputs messages in English.
- ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \
- | sed -ne '/supported targets:/!d
- s/[ ][ ]*/ /g
- s/.*supported targets: *//
- s/ .*//
- p'`
- case "$ld_supported_targets" in
- elf32-i386)
- TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu"
- ;;
- a.out-i386-linux)
- echo "${UNAME_MACHINE}-pc-linux-gnuaout"
- exit ;;
- coff-i386)
- echo "${UNAME_MACHINE}-pc-linux-gnucoff"
- exit ;;
- "")
- # Either a pre-BFD a.out linker (linux-gnuoldld) or
- # one that does not give us useful --help.
- echo "${UNAME_MACHINE}-pc-linux-gnuoldld"
- exit ;;
- esac
- # Determine whether the default compiler is a.out or elf
- eval $set_cc_for_build
- sed 's/^ //' << EOF >$dummy.c
- #include <features.h>
- #ifdef __ELF__
- # ifdef __GLIBC__
- # if __GLIBC__ >= 2
- LIBC=gnu
- # else
- LIBC=gnulibc1
- # endif
- # else
- LIBC=gnulibc1
- # endif
- #else
- #if defined(__INTEL_COMPILER) || defined(__PGI)
- LIBC=gnu
- #else
- LIBC=gnuaout
- #endif
- #endif
- #ifdef __dietlibc__
- LIBC=dietlibc
- #endif
-EOF
- eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n '/^LIBC/{s: ::g;p;}'`"
- test x"${LIBC}" != x && {
- echo "${UNAME_MACHINE}-pc-linux-${LIBC}"
- exit
- }
- test x"${TENTATIVE}" != x && { echo "${TENTATIVE}"; exit; }
- ;;
i*86:DYNIX/ptx:4*:*)
# ptx 4.0 does uname -s correctly, with DYNIX/ptx in there.
# earlier versions are messed up and put the nodename in both
@@ -991,11 +1070,11 @@ EOF
echo i386-sequent-sysv4
exit ;;
i*86:UNIX_SV:4.2MP:2.*)
- # Unixware is an offshoot of SVR4, but it has its own version
- # number series starting with 2...
- # I am not positive that other SVR4 systems won't match this,
+ # Unixware is an offshoot of SVR4, but it has its own version
+ # number series starting with 2...
+ # I am not positive that other SVR4 systems won't match this,
# I just have to hope. -- rms.
- # Use sysv4.2uw... so that sysv4* matches it.
+ # Use sysv4.2uw... so that sysv4* matches it.
echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION}
exit ;;
i*86:OS/2:*:*)
@@ -1012,7 +1091,7 @@ EOF
i*86:syllable:*:*)
echo ${UNAME_MACHINE}-pc-syllable
exit ;;
- i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*)
+ i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*)
echo i386-unknown-lynxos${UNAME_RELEASE}
exit ;;
i*86:*DOS:*:*)
@@ -1027,7 +1106,7 @@ EOF
fi
exit ;;
i*86:*:5:[678]*)
- # UnixWare 7.x, OpenUNIX and OpenServer 6.
+ # UnixWare 7.x, OpenUNIX and OpenServer 6.
case `/bin/uname -X | grep "^Machine"` in
*486*) UNAME_MACHINE=i486 ;;
*Pentium) UNAME_MACHINE=i586 ;;
@@ -1055,10 +1134,13 @@ EOF
exit ;;
pc:*:*:*)
# Left here for compatibility:
- # uname -m prints for DJGPP always 'pc', but it prints nothing about
- # the processor, so we play safe by assuming i386.
- echo i386-pc-msdosdjgpp
- exit ;;
+ # uname -m prints for DJGPP always 'pc', but it prints nothing about
+ # the processor, so we play safe by assuming i586.
+ # Note: whatever this is, it MUST be the same as what config.sub
+ # prints for the "djgpp" host, or else GDB configure will decide that
+ # this is a cross-build.
+ echo i586-pc-msdosdjgpp
+ exit ;;
Intel:Mach:3*:*)
echo i386-pc-mach3
exit ;;
@@ -1093,8 +1175,18 @@ EOF
/bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
&& { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
- /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
- && { echo i486-ncr-sysv4; exit; } ;;
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4; exit; } ;;
+ NCR*:*:4.2:* | MPRAS*:*:4.2:*)
+ OS_REL='.3'
+ test -r /etc/.relid \
+ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4.3${OS_REL}; exit; }
+ /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
+ && { echo i586-ncr-sysv4.3${OS_REL}; exit; }
+ /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \
+ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*)
echo m68k-unknown-lynxos${UNAME_RELEASE}
exit ;;
@@ -1107,7 +1199,7 @@ EOF
rs6000:LynxOS:2.*:*)
echo rs6000-unknown-lynxos${UNAME_RELEASE}
exit ;;
- PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*)
+ PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*)
echo powerpc-unknown-lynxos${UNAME_RELEASE}
exit ;;
SM[BE]S:UNIX_SV:*:*)
@@ -1127,10 +1219,10 @@ EOF
echo ns32k-sni-sysv
fi
exit ;;
- PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort
- # says <Richard.M.Bartel at ccMail.Census.GOV>
- echo i586-unisys-sysv4
- exit ;;
+ PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort
+ # says <Richard.M.Bartel at ccMail.Census.GOV>
+ echo i586-unisys-sysv4
+ exit ;;
*:UNIX_System_V:4*:FTX*)
# From Gerald Hewes <hewes at openmarket.com>.
# How about differentiating between stratus architectures? -djm
@@ -1156,11 +1248,11 @@ EOF
exit ;;
R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*)
if [ -d /usr/nec ]; then
- echo mips-nec-sysv${UNAME_RELEASE}
+ echo mips-nec-sysv${UNAME_RELEASE}
else
- echo mips-unknown-sysv${UNAME_RELEASE}
+ echo mips-unknown-sysv${UNAME_RELEASE}
fi
- exit ;;
+ exit ;;
BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only.
echo powerpc-be-beos
exit ;;
@@ -1170,6 +1262,12 @@ EOF
BePC:BeOS:*:*) # BeOS running on Intel PC compatible.
echo i586-pc-beos
exit ;;
+ BePC:Haiku:*:*) # Haiku running on Intel PC compatible.
+ echo i586-pc-haiku
+ exit ;;
+ x86_64:Haiku:*:*)
+ echo x86_64-unknown-haiku
+ exit ;;
SX-4:SUPER-UX:*:*)
echo sx4-nec-superux${UNAME_RELEASE}
exit ;;
@@ -1179,6 +1277,18 @@ EOF
SX-6:SUPER-UX:*:*)
echo sx6-nec-superux${UNAME_RELEASE}
exit ;;
+ SX-7:SUPER-UX:*:*)
+ echo sx7-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-8:SUPER-UX:*:*)
+ echo sx8-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-8R:SUPER-UX:*:*)
+ echo sx8r-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-ACE:SUPER-UX:*:*)
+ echo sxace-nec-superux${UNAME_RELEASE}
+ exit ;;
Power*:Rhapsody:*:*)
echo powerpc-apple-rhapsody${UNAME_RELEASE}
exit ;;
@@ -1187,14 +1297,36 @@ EOF
exit ;;
*:Darwin:*:*)
UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown
- case $UNAME_PROCESSOR in
- unknown) UNAME_PROCESSOR=powerpc ;;
- esac
+ eval $set_cc_for_build
+ if test "$UNAME_PROCESSOR" = unknown ; then
+ UNAME_PROCESSOR=powerpc
+ fi
+ if test `echo "$UNAME_RELEASE" | sed -e 's/\..*//'` -le 10 ; then
+ if [ "$CC_FOR_BUILD" != no_compiler_found ]; then
+ if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \
+ (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \
+ grep IS_64BIT_ARCH >/dev/null
+ then
+ case $UNAME_PROCESSOR in
+ i386) UNAME_PROCESSOR=x86_64 ;;
+ powerpc) UNAME_PROCESSOR=powerpc64 ;;
+ esac
+ fi
+ fi
+ elif test "$UNAME_PROCESSOR" = i386 ; then
+ # Avoid executing cc on OS X 10.9, as it ships with a stub
+ # that puts up a graphical alert prompting to install
+ # developer tools. Any system running Mac OS X 10.7 or
+ # later (Darwin 11 and later) is required to have a 64-bit
+ # processor. This is not true of the ARM version of Darwin
+ # that Apple uses in portable devices.
+ UNAME_PROCESSOR=x86_64
+ fi
echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE}
exit ;;
*:procnto*:*:* | *:QNX:[0123456789]*:*)
UNAME_PROCESSOR=`uname -p`
- if test "$UNAME_PROCESSOR" = "x86"; then
+ if test "$UNAME_PROCESSOR" = x86; then
UNAME_PROCESSOR=i386
UNAME_MACHINE=pc
fi
@@ -1203,12 +1335,18 @@ EOF
*:QNX:*:4*)
echo i386-pc-qnx
exit ;;
- NSE-?:NONSTOP_KERNEL:*:*)
+ NEO-?:NONSTOP_KERNEL:*:*)
+ echo neo-tandem-nsk${UNAME_RELEASE}
+ exit ;;
+ NSE-*:NONSTOP_KERNEL:*:*)
echo nse-tandem-nsk${UNAME_RELEASE}
exit ;;
NSR-?:NONSTOP_KERNEL:*:*)
echo nsr-tandem-nsk${UNAME_RELEASE}
exit ;;
+ NSX-?:NONSTOP_KERNEL:*:*)
+ echo nsx-tandem-nsk${UNAME_RELEASE}
+ exit ;;
*:NonStop-UX:*:*)
echo mips-compaq-nonstopux
exit ;;
@@ -1222,7 +1360,7 @@ EOF
# "uname -m" is not consistent, so use $cputype instead. 386
# is converted to i386 for consistency with other x86
# operating systems.
- if test "$cputype" = "386"; then
+ if test "$cputype" = 386; then
UNAME_MACHINE=i386
else
UNAME_MACHINE="$cputype"
@@ -1248,13 +1386,13 @@ EOF
echo pdp10-unknown-its
exit ;;
SEI:*:*:SEIUX)
- echo mips-sei-seiux${UNAME_RELEASE}
+ echo mips-sei-seiux${UNAME_RELEASE}
exit ;;
*:DragonFly:*:*)
echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
exit ;;
*:*VMS:*:*)
- UNAME_MACHINE=`(uname -p) 2>/dev/null`
+ UNAME_MACHINE=`(uname -p) 2>/dev/null`
case "${UNAME_MACHINE}" in
A*) echo alpha-dec-vms ; exit ;;
I*) echo ia64-dec-vms ; exit ;;
@@ -1264,179 +1402,36 @@ EOF
echo i386-pc-xenix
exit ;;
i*86:skyos:*:*)
- echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//'
+ echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE} | sed -e 's/ .*$//'`
exit ;;
i*86:rdos:*:*)
echo ${UNAME_MACHINE}-pc-rdos
exit ;;
-esac
-
-#echo '(No uname command or uname output not recognized.)' 1>&2
-#echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2
-
-eval $set_cc_for_build
-cat >$dummy.c <<EOF
-#ifdef _SEQUENT_
-# include <sys/types.h>
-# include <sys/utsname.h>
-#endif
-main ()
-{
-#if defined (sony)
-#if defined (MIPSEB)
- /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed,
- I don't know.... */
- printf ("mips-sony-bsd\n"); exit (0);
-#else
-#include <sys/param.h>
- printf ("m68k-sony-newsos%s\n",
-#ifdef NEWSOS4
- "4"
-#else
- ""
-#endif
- ); exit (0);
-#endif
-#endif
-
-#if defined (__arm) && defined (__acorn) && defined (__unix)
- printf ("arm-acorn-riscix\n"); exit (0);
-#endif
-
-#if defined (hp300) && !defined (hpux)
- printf ("m68k-hp-bsd\n"); exit (0);
-#endif
-
-#if defined (NeXT)
-#if !defined (__ARCHITECTURE__)
-#define __ARCHITECTURE__ "m68k"
-#endif
- int version;
- version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`;
- if (version < 4)
- printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version);
- else
- printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version);
- exit (0);
-#endif
-
-#if defined (MULTIMAX) || defined (n16)
-#if defined (UMAXV)
- printf ("ns32k-encore-sysv\n"); exit (0);
-#else
-#if defined (CMU)
- printf ("ns32k-encore-mach\n"); exit (0);
-#else
- printf ("ns32k-encore-bsd\n"); exit (0);
-#endif
-#endif
-#endif
-
-#if defined (__386BSD__)
- printf ("i386-pc-bsd\n"); exit (0);
-#endif
-
-#if defined (sequent)
-#if defined (i386)
- printf ("i386-sequent-dynix\n"); exit (0);
-#endif
-#if defined (ns32000)
- printf ("ns32k-sequent-dynix\n"); exit (0);
-#endif
-#endif
-
-#if defined (_SEQUENT_)
- struct utsname un;
-
- uname(&un);
-
- if (strncmp(un.version, "V2", 2) == 0) {
- printf ("i386-sequent-ptx2\n"); exit (0);
- }
- if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */
- printf ("i386-sequent-ptx1\n"); exit (0);
- }
- printf ("i386-sequent-ptx\n"); exit (0);
-
-#endif
-
-#if defined (vax)
-# if !defined (ultrix)
-# include <sys/param.h>
-# if defined (BSD)
-# if BSD == 43
- printf ("vax-dec-bsd4.3\n"); exit (0);
-# else
-# if BSD == 199006
- printf ("vax-dec-bsd4.3reno\n"); exit (0);
-# else
- printf ("vax-dec-bsd\n"); exit (0);
-# endif
-# endif
-# else
- printf ("vax-dec-bsd\n"); exit (0);
-# endif
-# else
- printf ("vax-dec-ultrix\n"); exit (0);
-# endif
-#endif
-
-#if defined (alliant) && defined (i860)
- printf ("i860-alliant-bsd\n"); exit (0);
-#endif
-
- exit (1);
-}
-EOF
-
-$CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` &&
- { echo "$SYSTEM_NAME"; exit; }
-
-# Apollos put the system type in the environment.
-
-test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; }
-
-# Convex versions that predate uname can use getsysinfo(1)
-
-if [ -x /usr/convex/getsysinfo ]
-then
- case `getsysinfo -f cpu_type` in
- c1*)
- echo c1-convex-bsd
+ i*86:AROS:*:*)
+ echo ${UNAME_MACHINE}-pc-aros
exit ;;
- c2*)
- if getsysinfo -f scalar_acc
- then echo c32-convex-bsd
- else echo c2-convex-bsd
- fi
+ x86_64:VMkernel:*:*)
+ echo ${UNAME_MACHINE}-unknown-esx
exit ;;
- c34*)
- echo c34-convex-bsd
+ amd64:Isilon\ OneFS:*:*)
+ echo x86_64-unknown-onefs
exit ;;
- c38*)
- echo c38-convex-bsd
- exit ;;
- c4*)
- echo c4-convex-bsd
- exit ;;
- esac
-fi
+esac
cat >&2 <<EOF
$0: unable to guess system type
-This script, last modified $timestamp, has failed to recognize
-the operating system you are using. It is advised that you
-download the most up to date version of the config scripts from
+This script (version $timestamp), has failed to recognize the
+operating system you are using. If your script is old, overwrite
+config.guess and config.sub with the latest versions from:
- http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.guess
+ http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess
and
- http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.sub
+ http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub
-If the version you run ($0) is already up to date, please
-send the following data and any information you think might be
-pertinent to <config-patches at gnu.org> in order to provide the needed
-information to handle your system.
+If $0 has already been updated, send the following data and any
+information you think might be pertinent to config-patches at gnu.org to
+provide the necessary information to handle your system.
config.guess timestamp = $timestamp
diff --git a/config/config.sub b/config/config.sub
index 2851647..40ea5df 100755
--- a/config/config.sub
+++ b/config/config.sub
@@ -1,43 +1,40 @@
#! /bin/sh
# Configuration validation subroutine script.
-# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
-# 2000, 2001, 2002, 2003, 2004, 2005 Free Software Foundation, Inc.
+# Copyright 1992-2017 Free Software Foundation, Inc.
-timestamp='2005-12-11'
+timestamp='2017-04-02'
-# This file is (in principle) common to ALL GNU software.
-# The presence of a machine in this file suggests that SOME GNU software
-# can handle that machine. It does not imply ALL GNU software can.
-#
-# This file is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2 of the License, or
+# This file is free software; you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
-# 02110-1301, USA.
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
#
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
+# the same distribution terms that you use for the rest of that
+# program. This Exception is an additional permission under section 7
+# of the GNU General Public License, version 3 ("GPLv3").
-# Please send patches to <config-patches at gnu.org>. Submit a context
-# diff and a properly formatted ChangeLog entry.
+# Please send patches to <config-patches at gnu.org>.
#
# Configuration subroutine to validate and canonicalize a configuration type.
# Supply the specified configuration type as an argument.
# If it is invalid, we print an error message on stderr and exit with code 1.
# Otherwise, we print the canonical config type on stdout and succeed.
+# You can get the latest version of this script from:
+# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub
+
# This file is supposed to be the same for all GNU packages
# and recognize all the CPU types, system types and aliases
# that are meaningful with *any* GNU software.
@@ -56,8 +53,7 @@ timestamp='2005-12-11'
me=`echo "$0" | sed -e 's,.*/,,'`
usage="\
-Usage: $0 [OPTION] CPU-MFR-OPSYS
- $0 [OPTION] ALIAS
+Usage: $0 [OPTION] CPU-MFR-OPSYS or ALIAS
Canonicalize a configuration name.
@@ -71,8 +67,7 @@ Report bugs and patches to <config-patches at gnu.org>."
version="\
GNU config.sub ($timestamp)
-Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005
-Free Software Foundation, Inc.
+Copyright 1992-2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
@@ -119,12 +114,18 @@ esac
# Here we must recognize all the valid KERNEL-OS combinations.
maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
case $maybe_os in
- nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \
- uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \
+ nto-qnx* | linux-gnu* | linux-android* | linux-dietlibc | linux-newlib* | \
+ linux-musl* | linux-uclibc* | uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | \
+ knetbsd*-gnu* | netbsd*-gnu* | netbsd*-eabi* | \
+ kopensolaris*-gnu* | cloudabi*-eabi* | \
storm-chaos* | os2-emx* | rtmk-nova*)
os=-$maybe_os
basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
;;
+ android-linux)
+ os=-linux-android
+ basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`-unknown
+ ;;
*)
basic_machine=`echo $1 | sed 's/-[^-]*$//'`
if [ $basic_machine != $1 ]
@@ -147,10 +148,13 @@ case $os in
-convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\
-c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \
-harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \
- -apple | -axis | -knuth | -cray)
+ -apple | -axis | -knuth | -cray | -microblaze*)
os=
basic_machine=$1
;;
+ -bluegene*)
+ os=-cnk
+ ;;
-sim | -cisco | -oki | -wec | -winbond)
os=
basic_machine=$1
@@ -165,10 +169,10 @@ case $os in
os=-chorusos
basic_machine=$1
;;
- -chorusrdb)
- os=-chorusrdb
+ -chorusrdb)
+ os=-chorusrdb
basic_machine=$1
- ;;
+ ;;
-hiux*)
os=-hiuxwe2
;;
@@ -213,6 +217,12 @@ case $os in
-isc*)
basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
;;
+ -lynx*178)
+ os=-lynxos178
+ ;;
+ -lynx*5)
+ os=-lynxos5
+ ;;
-lynx*)
os=-lynxos
;;
@@ -237,59 +247,93 @@ case $basic_machine in
# Some are omitted here because they have special meanings below.
1750a | 580 \
| a29k \
+ | aarch64 | aarch64_be \
| alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \
| alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \
| am33_2.0 \
- | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr \
+ | arc | arceb \
+ | arm | arm[bl]e | arme[lb] | armv[2-8] | armv[3-8][lb] | armv7[arm] \
+ | avr | avr32 \
+ | ba \
+ | be32 | be64 \
| bfin \
- | c4x | clipper \
+ | c4x | c8051 | clipper \
| d10v | d30v | dlx | dsp16xx \
- | fr30 | frv \
+ | e2k | epiphany \
+ | fido | fr30 | frv | ft32 \
| h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
- | i370 | i860 | i960 | ia64 \
+ | hexagon \
+ | i370 | i860 | i960 | ia16 | ia64 \
| ip2k | iq2000 \
- | m32r | m32rle | m68000 | m68k | m88k | maxq | mcore \
+ | k1om \
+ | le32 | le64 \
+ | lm32 \
+ | m32c | m32r | m32rle | m68000 | m68k | m88k \
+ | maxq | mb | microblaze | microblazeel | mcore | mep | metag \
| mips | mipsbe | mipseb | mipsel | mipsle \
| mips16 \
| mips64 | mips64el \
- | mips64vr | mips64vrel \
+ | mips64octeon | mips64octeonel \
| mips64orion | mips64orionel \
+ | mips64r5900 | mips64r5900el \
+ | mips64vr | mips64vrel \
| mips64vr4100 | mips64vr4100el \
| mips64vr4300 | mips64vr4300el \
| mips64vr5000 | mips64vr5000el \
| mips64vr5900 | mips64vr5900el \
| mipsisa32 | mipsisa32el \
| mipsisa32r2 | mipsisa32r2el \
+ | mipsisa32r6 | mipsisa32r6el \
| mipsisa64 | mipsisa64el \
| mipsisa64r2 | mipsisa64r2el \
+ | mipsisa64r6 | mipsisa64r6el \
| mipsisa64sb1 | mipsisa64sb1el \
| mipsisa64sr71k | mipsisa64sr71kel \
+ | mipsr5900 | mipsr5900el \
| mipstx39 | mipstx39el \
| mn10200 | mn10300 \
+ | moxie \
| mt \
| msp430 \
+ | nds32 | nds32le | nds32be \
+ | nios | nios2 | nios2eb | nios2el \
| ns16k | ns32k \
- | or32 \
+ | open8 | or1k | or1knd | or32 \
| pdp10 | pdp11 | pj | pjl \
- | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \
+ | powerpc | powerpc64 | powerpc64le | powerpcle \
+ | pru \
| pyramid \
- | sh | sh[1234] | sh[24]a | sh[23]e | sh[34]eb | shbe | shle | sh[1234]le | sh3ele \
+ | riscv32 | riscv64 \
+ | rl78 | rx \
+ | score \
+ | sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[234]eb | sheb | shbe | shle | sh[1234]le | sh3ele \
| sh64 | sh64le \
- | sparc | sparc64 | sparc64b | sparc86x | sparclet | sparclite \
- | sparcv8 | sparcv9 | sparcv9b \
- | strongarm \
- | tahoe | thumb | tic4x | tic80 | tron \
- | v850 | v850e \
+ | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \
+ | sparcv8 | sparcv9 | sparcv9b | sparcv9v \
+ | spu \
+ | tahoe | tic4x | tic54x | tic55x | tic6x | tic80 | tron \
+ | ubicom32 \
+ | v850 | v850e | v850e1 | v850e2 | v850es | v850e2v3 \
+ | visium \
+ | wasm32 \
| we32k \
- | x86 | xscale | xscalee[bl] | xstormy16 | xtensa \
- | z8k)
+ | x86 | xc16x | xstormy16 | xtensa \
+ | z8k | z80)
basic_machine=$basic_machine-unknown
;;
- m32c)
- basic_machine=$basic_machine-unknown
+ c54x)
+ basic_machine=tic54x-unknown
+ ;;
+ c55x)
+ basic_machine=tic55x-unknown
+ ;;
+ c6x)
+ basic_machine=tic6x-unknown
;;
- m6811 | m68hc11 | m6812 | m68hc12)
- # Motorola 68HC11/12.
+ leon|leon[3-9])
+ basic_machine=sparc-$basic_machine
+ ;;
+ m6811 | m68hc11 | m6812 | m68hc12 | m68hcs12x | nvptx | picochip)
basic_machine=$basic_machine-unknown
os=-none
;;
@@ -299,6 +343,21 @@ case $basic_machine in
basic_machine=mt-unknown
;;
+ strongarm | thumb | xscale)
+ basic_machine=arm-unknown
+ ;;
+ xgate)
+ basic_machine=$basic_machine-unknown
+ os=-none
+ ;;
+ xscaleeb)
+ basic_machine=armeb-unknown
+ ;;
+
+ xscaleel)
+ basic_machine=armel-unknown
+ ;;
+
# We use `pc' rather than `unknown'
# because (1) that's what they normally are, and
# (2) the word "unknown" tends to confuse beginning users.
@@ -313,65 +372,91 @@ case $basic_machine in
# Recognize the basic CPU types with company name.
580-* \
| a29k-* \
+ | aarch64-* | aarch64_be-* \
| alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \
| alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \
- | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \
+ | alphapca5[67]-* | alpha64pca5[67]-* | arc-* | arceb-* \
| arm-* | armbe-* | armle-* | armeb-* | armv*-* \
- | avr-* \
+ | avr-* | avr32-* \
+ | ba-* \
+ | be32-* | be64-* \
| bfin-* | bs2000-* \
- | c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \
- | clipper-* | craynv-* | cydra-* \
+ | c[123]* | c30-* | [cjt]90-* | c4x-* \
+ | c8051-* | clipper-* | craynv-* | cydra-* \
| d10v-* | d30v-* | dlx-* \
- | elxsi-* \
- | f30[01]-* | f700-* | fr30-* | frv-* | fx80-* \
+ | e2k-* | elxsi-* \
+ | f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \
| h8300-* | h8500-* \
| hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \
- | i*86-* | i860-* | i960-* | ia64-* \
+ | hexagon-* \
+ | i*86-* | i860-* | i960-* | ia16-* | ia64-* \
| ip2k-* | iq2000-* \
- | m32r-* | m32rle-* \
+ | k1om-* \
+ | le32-* | le64-* \
+ | lm32-* \
+ | m32c-* | m32r-* | m32rle-* \
| m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \
- | m88110-* | m88k-* | maxq-* | mcore-* \
+ | m88110-* | m88k-* | maxq-* | mcore-* | metag-* \
+ | microblaze-* | microblazeel-* \
| mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \
| mips16-* \
| mips64-* | mips64el-* \
- | mips64vr-* | mips64vrel-* \
+ | mips64octeon-* | mips64octeonel-* \
| mips64orion-* | mips64orionel-* \
+ | mips64r5900-* | mips64r5900el-* \
+ | mips64vr-* | mips64vrel-* \
| mips64vr4100-* | mips64vr4100el-* \
| mips64vr4300-* | mips64vr4300el-* \
| mips64vr5000-* | mips64vr5000el-* \
| mips64vr5900-* | mips64vr5900el-* \
| mipsisa32-* | mipsisa32el-* \
| mipsisa32r2-* | mipsisa32r2el-* \
+ | mipsisa32r6-* | mipsisa32r6el-* \
| mipsisa64-* | mipsisa64el-* \
| mipsisa64r2-* | mipsisa64r2el-* \
+ | mipsisa64r6-* | mipsisa64r6el-* \
| mipsisa64sb1-* | mipsisa64sb1el-* \
| mipsisa64sr71k-* | mipsisa64sr71kel-* \
+ | mipsr5900-* | mipsr5900el-* \
| mipstx39-* | mipstx39el-* \
| mmix-* \
| mt-* \
| msp430-* \
+ | nds32-* | nds32le-* | nds32be-* \
+ | nios-* | nios2-* | nios2eb-* | nios2el-* \
| none-* | np1-* | ns16k-* | ns32k-* \
+ | open8-* \
+ | or1k*-* \
| orion-* \
| pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \
- | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \
+ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* \
+ | pru-* \
| pyramid-* \
- | romp-* | rs6000-* \
- | sh-* | sh[1234]-* | sh[24]a-* | sh[23]e-* | sh[34]eb-* | shbe-* \
+ | riscv32-* | riscv64-* \
+ | rl78-* | romp-* | rs6000-* | rx-* \
+ | sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \
| shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \
- | sparc-* | sparc64-* | sparc64b-* | sparc86x-* | sparclet-* \
+ | sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \
| sparclite-* \
- | sparcv8-* | sparcv9-* | sparcv9b-* | strongarm-* | sv1-* | sx?-* \
- | tahoe-* | thumb-* \
+ | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | sv1-* | sx*-* \
+ | tahoe-* \
| tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \
+ | tile*-* \
| tron-* \
- | v850-* | v850e-* | vax-* \
+ | ubicom32-* \
+ | v850-* | v850e-* | v850e1-* | v850es-* | v850e2-* | v850e2v3-* \
+ | vax-* \
+ | visium-* \
+ | wasm32-* \
| we32k-* \
- | x86-* | x86_64-* | xps100-* | xscale-* | xscalee[bl]-* \
- | xstormy16-* | xtensa-* \
+ | x86-* | x86_64-* | xc16x-* | xps100-* \
+ | xstormy16-* | xtensa*-* \
| ymp-* \
- | z8k-*)
+ | z8k-* | z80-*)
;;
- m32c-*)
+ # Recognize the basic CPU types without company name, with glob match.
+ xtensa*)
+ basic_machine=$basic_machine-unknown
;;
# Recognize the various machine names and aliases which stand
# for a CPU type and a company and sometimes even an OS.
@@ -389,7 +474,7 @@ case $basic_machine in
basic_machine=a29k-amd
os=-udi
;;
- abacus)
+ abacus)
basic_machine=abacus-unknown
;;
adobe68k)
@@ -435,6 +520,13 @@ case $basic_machine in
basic_machine=m68k-apollo
os=-bsd
;;
+ aros)
+ basic_machine=i386-pc
+ os=-aros
+ ;;
+ asmjs)
+ basic_machine=asmjs-unknown
+ ;;
aux)
basic_machine=m68k-apple
os=-aux
@@ -443,10 +535,35 @@ case $basic_machine in
basic_machine=ns32k-sequent
os=-dynix
;;
+ blackfin)
+ basic_machine=bfin-unknown
+ os=-linux
+ ;;
+ blackfin-*)
+ basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'`
+ os=-linux
+ ;;
+ bluegene*)
+ basic_machine=powerpc-ibm
+ os=-cnk
+ ;;
+ c54x-*)
+ basic_machine=tic54x-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ c55x-*)
+ basic_machine=tic55x-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ c6x-*)
+ basic_machine=tic6x-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
c90)
basic_machine=c90-cray
os=-unicos
;;
+ cegcc)
+ basic_machine=arm-unknown
+ os=-cegcc
+ ;;
convex-c1)
basic_machine=c1-convex
os=-bsd
@@ -475,8 +592,8 @@ case $basic_machine in
basic_machine=craynv-cray
os=-unicosmp
;;
- cr16c)
- basic_machine=cr16c-unknown
+ cr16 | cr16-*)
+ basic_machine=cr16-unknown
os=-elf
;;
crds | unos)
@@ -514,6 +631,10 @@ case $basic_machine in
basic_machine=m88k-motorola
os=-sysv3
;;
+ dicos)
+ basic_machine=i686-pc
+ os=-dicos
+ ;;
djgpp)
basic_machine=i586-pc
os=-msdosdjgpp
@@ -526,6 +647,14 @@ case $basic_machine in
basic_machine=m68k-bull
os=-sysv3
;;
+ e500v[12])
+ basic_machine=powerpc-unknown
+ os=$os"spe"
+ ;;
+ e500v[12]-*)
+ basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
+ os=$os"spe"
+ ;;
ebmon29k)
basic_machine=a29k-amd
os=-ebmon
@@ -629,7 +758,6 @@ case $basic_machine in
i370-ibm* | ibm*)
basic_machine=i370-ibm
;;
-# I'm not sure what "Sysv32" means. Should this be sysv3.2?
i*86v32)
basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
os=-sysv32
@@ -668,6 +796,17 @@ case $basic_machine in
basic_machine=m68k-isi
os=-sysv
;;
+ leon-*|leon[3-9]-*)
+ basic_machine=sparc-`echo $basic_machine | sed 's/-.*//'`
+ ;;
+ m68knommu)
+ basic_machine=m68k-unknown
+ os=-linux
+ ;;
+ m68knommu-*)
+ basic_machine=m68k-`echo $basic_machine | sed 's/^[^-]*-//'`
+ os=-linux
+ ;;
m88k-omron*)
basic_machine=m88k-omron
;;
@@ -679,10 +818,21 @@ case $basic_machine in
basic_machine=ns32k-utek
os=-sysv
;;
+ microblaze*)
+ basic_machine=microblaze-xilinx
+ ;;
+ mingw64)
+ basic_machine=x86_64-pc
+ os=-mingw64
+ ;;
mingw32)
- basic_machine=i386-pc
+ basic_machine=i686-pc
os=-mingw32
;;
+ mingw32ce)
+ basic_machine=arm-unknown
+ os=-mingw32ce
+ ;;
miniframe)
basic_machine=m68000-convergent
;;
@@ -704,6 +854,10 @@ case $basic_machine in
basic_machine=powerpc-unknown
os=-morphos
;;
+ moxiebox)
+ basic_machine=moxie-unknown
+ os=-moxiebox
+ ;;
msdos)
basic_machine=i386-pc
os=-msdos
@@ -711,10 +865,18 @@ case $basic_machine in
ms1-*)
basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'`
;;
+ msys)
+ basic_machine=i686-pc
+ os=-msys
+ ;;
mvs)
basic_machine=i370-ibm
os=-mvs
;;
+ nacl)
+ basic_machine=le32-unknown
+ os=-nacl
+ ;;
ncr3000)
basic_machine=i486-ncr
os=-sysv4
@@ -779,9 +941,18 @@ case $basic_machine in
np1)
basic_machine=np1-gould
;;
+ neo-tandem)
+ basic_machine=neo-tandem
+ ;;
+ nse-tandem)
+ basic_machine=nse-tandem
+ ;;
nsr-tandem)
basic_machine=nsr-tandem
;;
+ nsx-tandem)
+ basic_machine=nsx-tandem
+ ;;
op50n-* | op60c-*)
basic_machine=hppa1.1-oki
os=-proelf
@@ -809,6 +980,14 @@ case $basic_machine in
basic_machine=i860-intel
os=-osf
;;
+ parisc)
+ basic_machine=hppa-unknown
+ os=-linux
+ ;;
+ parisc-*)
+ basic_machine=hppa-`echo $basic_machine | sed 's/^[^-]*-//'`
+ os=-linux
+ ;;
pbd)
basic_machine=sparc-tti
;;
@@ -818,6 +997,12 @@ case $basic_machine in
pc532 | pc532-*)
basic_machine=ns32k-pc532
;;
+ pc98)
+ basic_machine=i386-pc
+ ;;
+ pc98-*)
+ basic_machine=i386-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
pentium | p5 | k5 | k6 | nexgen | viac3)
basic_machine=i586-pc
;;
@@ -847,11 +1032,12 @@ case $basic_machine in
;;
power) basic_machine=power-ibm
;;
- ppc) basic_machine=powerpc-unknown
+ ppc | ppcbe) basic_machine=powerpc-unknown
;;
- ppc-*) basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ppc-* | ppcbe-*)
+ basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
;;
- ppcle | powerpclittle | ppc-le | powerpc-little)
+ ppcle | powerpclittle)
basic_machine=powerpcle-unknown
;;
ppcle-* | powerpclittle-*)
@@ -861,7 +1047,7 @@ case $basic_machine in
;;
ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'`
;;
- ppc64le | powerpc64little | ppc64-le | powerpc64-little)
+ ppc64le | powerpc64little)
basic_machine=powerpc64le-unknown
;;
ppc64le-* | powerpc64little-*)
@@ -874,7 +1060,11 @@ case $basic_machine in
basic_machine=i586-unknown
os=-pw32
;;
- rdos)
+ rdos | rdos64)
+ basic_machine=x86_64-pc
+ os=-rdos
+ ;;
+ rdos32)
basic_machine=i386-pc
os=-rdos
;;
@@ -904,6 +1094,10 @@ case $basic_machine in
sb1el)
basic_machine=mipsisa64sb1el-unknown
;;
+ sde)
+ basic_machine=mipsisa32-sde
+ os=-elf
+ ;;
sei)
basic_machine=mips-sei
os=-seiux
@@ -915,6 +1109,9 @@ case $basic_machine in
basic_machine=sh-hitachi
os=-hms
;;
+ sh5el)
+ basic_machine=sh5le-unknown
+ ;;
sh64)
basic_machine=sh64-unknown
;;
@@ -936,6 +1133,9 @@ case $basic_machine in
basic_machine=i860-stratus
os=-sysv4
;;
+ strongarm-* | thumb-*)
+ basic_machine=arm-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
sun2)
basic_machine=m68000-sun
;;
@@ -992,17 +1192,9 @@ case $basic_machine in
basic_machine=t90-cray
os=-unicos
;;
- tic54x | c54x*)
- basic_machine=tic54x-unknown
- os=-coff
- ;;
- tic55x | c55x*)
- basic_machine=tic55x-unknown
- os=-coff
- ;;
- tic6x | c6x*)
- basic_machine=tic6x-unknown
- os=-coff
+ tile*)
+ basic_machine=$basic_machine-unknown
+ os=-linux-gnu
;;
tx39)
basic_machine=mipstx39-unknown
@@ -1056,6 +1248,9 @@ case $basic_machine in
basic_machine=a29k-wrs
os=-vxworks
;;
+ wasm32)
+ basic_machine=wasm32-unknown
+ ;;
w65*)
basic_machine=w65-wdc
os=-none
@@ -1071,6 +1266,9 @@ case $basic_machine in
xps | xps100)
basic_machine=xps100-honeywell
;;
+ xscale-* | xscalee[bl]-*)
+ basic_machine=`echo $basic_machine | sed 's/^xscale/arm/'`
+ ;;
ymp)
basic_machine=ymp-cray
os=-unicos
@@ -1079,6 +1277,10 @@ case $basic_machine in
basic_machine=z8k-unknown
os=-sim
;;
+ z80-*-coff)
+ basic_machine=z80-unknown
+ os=-sim
+ ;;
none)
basic_machine=none-none
os=-none
@@ -1117,10 +1319,10 @@ case $basic_machine in
we32k)
basic_machine=we32k-att
;;
- sh[1234] | sh[24]a | sh[34]eb | sh[1234]le | sh[23]ele)
+ sh[1234] | sh[24]a | sh[24]aeb | sh[34]eb | sh[1234]le | sh[23]ele)
basic_machine=sh-unknown
;;
- sparc | sparcv8 | sparcv9 | sparcv9b)
+ sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v)
basic_machine=sparc-sun
;;
cydra)
@@ -1164,9 +1366,12 @@ esac
if [ x"$os" != x"" ]
then
case $os in
- # First match some system type aliases
- # that might get confused with valid system types.
+ # First match some system type aliases
+ # that might get confused with valid system types.
# -solaris* is a basic system type, with this one exception.
+ -auroraux)
+ os=-auroraux
+ ;;
-solaris1 | -solaris1.*)
os=`echo $os | sed -e 's|solaris1|sunos4|'`
;;
@@ -1187,28 +1392,32 @@ case $os in
# Each alternative MUST END IN A *, to match a version number.
# -sysv* is not here because it comes later, after sysvr4.
-gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \
- | -*vms* | -sco* | -esix* | -isc* | -aix* | -sunos | -sunos[34]*\
- | -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \
+ | -*vms* | -sco* | -esix* | -isc* | -aix* | -cnk* | -sunos | -sunos[34]*\
+ | -hpux* | -unos* | -osf* | -luna* | -dgux* | -auroraux* | -solaris* \
+ | -sym* | -kopensolaris* | -plan9* \
| -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \
- | -aos* \
+ | -aos* | -aros* | -cloudabi* | -sortix* \
| -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
| -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
- | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* | -openbsd* \
+ | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \
+ | -bitrig* | -openbsd* | -solidbsd* | -libertybsd* \
| -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \
| -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \
| -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
| -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
- | -chorusos* | -chorusrdb* \
- | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
- | -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \
- | -uxpv* | -beos* | -mpeix* | -udk* \
+ | -chorusos* | -chorusrdb* | -cegcc* | -glidix* \
+ | -cygwin* | -msys* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
+ | -midipix* | -mingw32* | -mingw64* | -linux-gnu* | -linux-android* \
+ | -linux-newlib* | -linux-musl* | -linux-uclibc* \
+ | -uxpv* | -beos* | -mpeix* | -udk* | -moxiebox* \
| -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \
| -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \
| -storm-chaos* | -tops10* | -tenex* | -tops20* | -its* \
| -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \
| -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \
| -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \
- | -skyos* | -haiku* | -rdos*)
+ | -skyos* | -haiku* | -rdos* | -toppers* | -drops* | -es* \
+ | -onefs* | -tirtos* | -phoenix* | -fuchsia* | -redox*)
# Remember, each alternative MUST END IN *, to match a version number.
;;
-qnx*)
@@ -1247,7 +1456,7 @@ case $os in
-opened*)
os=-openedition
;;
- -os400*)
+ -os400*)
os=-os400
;;
-wince*)
@@ -1296,7 +1505,7 @@ case $os in
-sinix*)
os=-sysv4
;;
- -tpf*)
+ -tpf*)
os=-tpf
;;
-triton*)
@@ -1332,12 +1541,16 @@ case $os in
-aros*)
os=-aros
;;
- -kaos*)
- os=-kaos
- ;;
-zvmoe)
os=-zvmoe
;;
+ -dicos*)
+ os=-dicos
+ ;;
+ -nacl*)
+ ;;
+ -ios)
+ ;;
-none)
;;
*)
@@ -1360,6 +1573,12 @@ else
# system, and we'll never get to this point.
case $basic_machine in
+ score-*)
+ os=-elf
+ ;;
+ spu-*)
+ os=-elf
+ ;;
*-acorn)
os=-riscix1.2
;;
@@ -1369,9 +1588,24 @@ case $basic_machine in
arm*-semi)
os=-aout
;;
- c4x-* | tic4x-*)
- os=-coff
- ;;
+ c4x-* | tic4x-*)
+ os=-coff
+ ;;
+ c8051-*)
+ os=-elf
+ ;;
+ hexagon-*)
+ os=-elf
+ ;;
+ tic54x-*)
+ os=-coff
+ ;;
+ tic55x-*)
+ os=-coff
+ ;;
+ tic6x-*)
+ os=-coff
+ ;;
# This must come before the *-dec entry.
pdp10-*)
os=-tops20
@@ -1390,13 +1624,13 @@ case $basic_machine in
;;
m68000-sun)
os=-sunos3
- # This also exists in the configure program, but was not the
- # default.
- # os=-sunos4
;;
m68*-cisco)
os=-aout
;;
+ mep-*)
+ os=-elf
+ ;;
mips*-cisco)
os=-elf
;;
@@ -1412,6 +1646,9 @@ case $basic_machine in
sparc-* | *-sun)
os=-sunos4.1.1
;;
+ pru-*)
+ os=-elf
+ ;;
*-be)
os=-beos
;;
@@ -1421,7 +1658,7 @@ case $basic_machine in
*-ibm)
os=-aix
;;
- *-knuth)
+ *-knuth)
os=-mmixware
;;
*-wec)
@@ -1526,7 +1763,7 @@ case $basic_machine in
-sunos*)
vendor=sun
;;
- -aix*)
+ -cnk*|-aix*)
vendor=ibm
;;
-beos*)
diff --git a/config/libtool.m4 b/config/libtool.m4
index a3bc337..10ab284 100644
--- a/config/libtool.m4
+++ b/config/libtool.m4
@@ -2887,6 +2887,18 @@ linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)
dynamic_linker='GNU/Linux ld.so'
;;
+netbsdelf*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='NetBSD ld.elf_so'
+ ;;
+
netbsd*)
version_type=sunos
need_lib_prefix=no
@@ -3546,7 +3558,7 @@ linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)
lt_cv_deplibs_check_method=pass_all
;;
-netbsd*)
+netbsd* | netbsdelf*-gnu)
if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$'
else
@@ -4424,7 +4436,7 @@ m4_if([$1], [CXX], [
;;
esac
;;
- netbsd*)
+ netbsd* | netbsdelf*-gnu)
;;
*qnx* | *nto*)
# QNX uses GNU C++, but need to define -shared option too, otherwise
@@ -4936,6 +4948,9 @@ m4_if([$1], [CXX], [
;;
esac
;;
+ linux* | k*bsd*-gnu | gnu*)
+ _LT_TAGVAR(link_all_deplibs, $1)=no
+ ;;
*)
_LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
;;
@@ -4998,6 +5013,9 @@ dnl Note also adjust exclude_expsyms for C++ above.
openbsd* | bitrig*)
with_gnu_ld=no
;;
+ linux* | k*bsd*-gnu | gnu*)
+ _LT_TAGVAR(link_all_deplibs, $1)=no
+ ;;
esac
_LT_TAGVAR(ld_shlibs, $1)=yes
@@ -5252,7 +5270,7 @@ _LT_EOF
fi
;;
- netbsd*)
+ netbsd* | netbsdelf*-gnu)
if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
_LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib'
wlarc=
@@ -5773,6 +5791,7 @@ _LT_EOF
if test yes = "$lt_cv_irix_exported_symbol"; then
_LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags $wl-soname $wl$soname `test -n "$verstring" && func_echo_all "$wl-set_version $wl$verstring"` $wl-update_registry $wl$output_objdir/so_locations $wl-exports_file $wl$export_symbols -o $lib'
fi
+ _LT_TAGVAR(link_all_deplibs, $1)=no
else
_LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && func_echo_all "-set_version $verstring"` -update_registry $output_objdir/so_locations -o $lib'
_LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && func_echo_all "-set_version $verstring"` -update_registry $output_objdir/so_locations -exports_file $export_symbols -o $lib'
@@ -5794,7 +5813,7 @@ _LT_EOF
esac
;;
- netbsd*)
+ netbsd* | netbsdelf*-gnu)
if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
_LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out
else
diff --git a/config/ltmain.sh b/config/ltmain.sh
index 0f0a2da..147d758 100644
--- a/config/ltmain.sh
+++ b/config/ltmain.sh
@@ -31,7 +31,7 @@
PROGRAM=libtool
PACKAGE=libtool
-VERSION=2.4.6
+VERSION="2.4.6 Debian-2.4.6-0.1"
package_revision=2.4.6
@@ -2073,7 +2073,7 @@ include the following information:
autoconf: `($AUTOCONF --version) 2>/dev/null |$SED 1q`
Report bugs to <bug-libtool at gnu.org>.
-GNU libtool home page: <http://www.gnu.org/software/libtool/>.
+GNU libtool home page: <http://www.gnu.org/s/libtool/>.
General help using GNU software: <http://www.gnu.org/gethelp/>."
exit 0
}
@@ -7272,10 +7272,13 @@ func_mode_link ()
# -tp=* Portland pgcc target processor selection
# --sysroot=* for sysroot support
# -O*, -g*, -flto*, -fwhopr*, -fuse-linker-plugin GCC link-time optimization
+ # -specs=* GCC specs files
# -stdlib=* select c++ std lib with clang
+ # -fsanitize=* Clang/GCC memory and address sanitizer
-64|-mips[0-9]|-r[0-9][0-9]*|-xarch=*|-xtarget=*|+DA*|+DD*|-q*|-m*| \
-t[45]*|-txscale*|-p|-pg|--coverage|-fprofile-*|-F*|@*|-tp=*|--sysroot=*| \
- -O*|-g*|-flto*|-fwhopr*|-fuse-linker-plugin|-fstack-protector*|-stdlib=*)
+ -O*|-g*|-flto*|-fwhopr*|-fuse-linker-plugin|-fstack-protector*|-stdlib=*| \
+ -specs=*|-fsanitize=*)
func_quote_for_eval "$arg"
arg=$func_quote_for_eval_result
func_append compile_command " $arg"
@@ -7568,7 +7571,10 @@ func_mode_link ()
case $pass in
dlopen) libs=$dlfiles ;;
dlpreopen) libs=$dlprefiles ;;
- link) libs="$deplibs %DEPLIBS% $dependency_libs" ;;
+ link)
+ libs="$deplibs %DEPLIBS%"
+ test "X$link_all_deplibs" != Xno && libs="$libs $dependency_libs"
+ ;;
esac
fi
if test lib,dlpreopen = "$linkmode,$pass"; then
@@ -7887,19 +7893,19 @@ func_mode_link ()
# It is a libtool convenience library, so add in its objects.
func_append convenience " $ladir/$objdir/$old_library"
func_append old_convenience " $ladir/$objdir/$old_library"
+ tmp_libs=
+ for deplib in $dependency_libs; do
+ deplibs="$deplib $deplibs"
+ if $opt_preserve_dup_deps; then
+ case "$tmp_libs " in
+ *" $deplib "*) func_append specialdeplibs " $deplib" ;;
+ esac
+ fi
+ func_append tmp_libs " $deplib"
+ done
elif test prog != "$linkmode" && test lib != "$linkmode"; then
func_fatal_error "'$lib' is not a convenience library"
fi
- tmp_libs=
- for deplib in $dependency_libs; do
- deplibs="$deplib $deplibs"
- if $opt_preserve_dup_deps; then
- case "$tmp_libs " in
- *" $deplib "*) func_append specialdeplibs " $deplib" ;;
- esac
- fi
- func_append tmp_libs " $deplib"
- done
continue
fi # $pass = conv
@@ -8823,6 +8829,9 @@ func_mode_link ()
revision=$number_minor
lt_irix_increment=no
;;
+ *)
+ func_fatal_configuration "$modename: unknown library version type '$version_type'"
+ ;;
esac
;;
no)
diff --git a/configure b/configure
index 7046e44..8c753f9 100755
--- a/configure
+++ b/configure
@@ -1,7 +1,7 @@
#! /bin/sh
# From configure.ac Revision.
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for adios 1.11.0.
+# Generated by GNU Autoconf 2.69 for adios 1.12.0.
#
#
# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
@@ -588,8 +588,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='adios'
PACKAGE_TARNAME='adios'
-PACKAGE_VERSION='1.11.0'
-PACKAGE_STRING='adios 1.11.0'
+PACKAGE_VERSION='1.12.0'
+PACKAGE_STRING='adios 1.12.0'
PACKAGE_BUGREPORT=''
PACKAGE_URL=''
@@ -681,6 +681,11 @@ ADIOS_TIMERS_FALSE
ADIOS_TIMERS_TRUE
RESEARCH_TRANSPORTS_FALSE
RESEARCH_TRANSPORTS_TRUE
+SZ_CPPFLAGS
+SZ_LDFLAGS
+SZ_LIBS
+HAVE_SZ_FALSE
+HAVE_SZ_TRUE
ZFP_CPPFLAGS
ZFP_LDFLAGS
ZFP_LIBS
@@ -688,6 +693,12 @@ BUILD_ZFP_FALSE
BUILD_ZFP_TRUE
HAVE_ZFP_FALSE
HAVE_ZFP_TRUE
+LZ4_CPPFLAGS
+LZ4_CFLAGS
+LZ4_LDFLAGS
+LZ4_LIBS
+HAVE_LZ4_FALSE
+HAVE_LZ4_TRUE
HAVE_BGQ_FALSE
HAVE_BGQ_TRUE
FASTBIT_LIBS
@@ -1064,9 +1075,6 @@ with_gen_thread
with_ptlpbio
with_flexpath
with_evpath
-with_atl
-with_dill
-with_cercs_env
with_zlib
with_bzip2
with_szip
@@ -1075,7 +1083,9 @@ with_aplod
with_alacrity
with_fastbit
with_bgq
+with_lz4
with_zfp
+with_sz
enable_research_transports
enable_timers
enable_timer_events
@@ -1640,7 +1650,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures adios 1.11.0 to adapt to many kinds of systems.
+\`configure' configures adios 1.12.0 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1710,7 +1720,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of adios 1.11.0:";;
+ short | recursive ) echo "Configuration of adios 1.12.0:";;
esac
cat <<\_ACEOF
@@ -1808,9 +1818,6 @@ Optional Packages:
--with-ptlpbio=DIR Where to find ptlpbio package
--with-flexpath=DIR Location of FlexPath
--with-evpath=DIR Where to find evpath package
- --with-atl=DIR Where to find atl package
- --with-dill=DIR Where to find dill package
- --with-cercs_env=DIR Where to find cercs_env package
--with-zlib=DIR Location of ZLIB library
--with-bzip2=DIR Location of BZIP2 library
--with-szip=DIR Location of SZIP library
@@ -1819,7 +1826,9 @@ Optional Packages:
--with-alacrity=DIR Location of ALACRITY library
--with-fastbit=DIR Location of the FastBit library
--with-bgq Whether to enable BGQ method or not
+ --with-lz4=DIR Location of LZ4 library
--with-zfp=DIR Location of ZFP library
+ --with-sz=DIR Location of SZ library
Some influential environment variables:
CC C compiler command
@@ -1908,7 +1917,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-adios configure 1.11.0
+adios configure 1.12.0
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2702,7 +2711,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by adios $as_me 1.11.0, which was
+It was created by adios $as_me 1.12.0, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -3571,7 +3580,7 @@ fi
# Define the identity of the package.
PACKAGE='adios'
- VERSION='1.11.0'
+ VERSION='1.12.0'
cat >>confdefs.h <<_ACEOF
@@ -8126,7 +8135,7 @@ linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)
lt_cv_deplibs_check_method=pass_all
;;
-netbsd*)
+netbsd* | netbsdelf*-gnu)
if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$'
else
@@ -11860,6 +11869,9 @@ $as_echo_n "checking whether the $compiler linker ($LD) supports shared librarie
openbsd* | bitrig*)
with_gnu_ld=no
;;
+ linux* | k*bsd*-gnu | gnu*)
+ link_all_deplibs=no
+ ;;
esac
ld_shlibs=yes
@@ -12114,7 +12126,7 @@ _LT_EOF
fi
;;
- netbsd*)
+ netbsd* | netbsdelf*-gnu)
if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
archive_cmds='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib'
wlarc=
@@ -12800,6 +12812,7 @@ $as_echo "$lt_cv_irix_exported_symbol" >&6; }
if test yes = "$lt_cv_irix_exported_symbol"; then
archive_expsym_cmds='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags $wl-soname $wl$soname `test -n "$verstring" && func_echo_all "$wl-set_version $wl$verstring"` $wl-update_registry $wl$output_objdir/so_locations $wl-exports_file $wl$export_symbols -o $lib'
fi
+ link_all_deplibs=no
else
archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && func_echo_all "-set_version $verstring"` -update_registry $output_objdir/so_locations -o $lib'
archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && func_echo_all "-set_version $verstring"` -update_registry $output_objdir/so_locations -exports_file $export_symbols -o $lib'
@@ -12821,7 +12834,7 @@ $as_echo "$lt_cv_irix_exported_symbol" >&6; }
esac
;;
- netbsd*)
+ netbsd* | netbsdelf*-gnu)
if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out
else
@@ -13944,6 +13957,18 @@ fi
dynamic_linker='GNU/Linux ld.so'
;;
+netbsdelf*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='NetBSD ld.elf_so'
+ ;;
+
netbsd*)
version_type=sunos
need_lib_prefix=no
@@ -16894,7 +16919,7 @@ lt_prog_compiler_static_CXX=
;;
esac
;;
- netbsd*)
+ netbsd* | netbsdelf*-gnu)
;;
*qnx* | *nto*)
# QNX uses GNU C++, but need to define -shared option too, otherwise
@@ -17269,6 +17294,9 @@ $as_echo_n "checking whether the $compiler linker ($LD) supports shared librarie
;;
esac
;;
+ linux* | k*bsd*-gnu | gnu*)
+ link_all_deplibs_CXX=no
+ ;;
*)
export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
;;
@@ -17970,6 +17998,18 @@ fi
dynamic_linker='GNU/Linux ld.so'
;;
+netbsdelf*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='NetBSD ld.elf_so'
+ ;;
+
netbsd*)
version_type=sunos
need_lib_prefix=no
@@ -19238,6 +19278,9 @@ $as_echo_n "checking whether the $compiler linker ($LD) supports shared librarie
openbsd* | bitrig*)
with_gnu_ld=no
;;
+ linux* | k*bsd*-gnu | gnu*)
+ link_all_deplibs_FC=no
+ ;;
esac
ld_shlibs_FC=yes
@@ -19492,7 +19535,7 @@ _LT_EOF
fi
;;
- netbsd*)
+ netbsd* | netbsdelf*-gnu)
if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
archive_cmds_FC='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib'
wlarc=
@@ -20112,6 +20155,7 @@ $as_echo "$lt_cv_irix_exported_symbol" >&6; }
if test yes = "$lt_cv_irix_exported_symbol"; then
archive_expsym_cmds_FC='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags $wl-soname $wl$soname `test -n "$verstring" && func_echo_all "$wl-set_version $wl$verstring"` $wl-update_registry $wl$output_objdir/so_locations $wl-exports_file $wl$export_symbols -o $lib'
fi
+ link_all_deplibs_FC=no
else
archive_cmds_FC='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && func_echo_all "-set_version $verstring"` -update_registry $output_objdir/so_locations -o $lib'
archive_expsym_cmds_FC='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && func_echo_all "-set_version $verstring"` -update_registry $output_objdir/so_locations -exports_file $export_symbols -o $lib'
@@ -20133,7 +20177,7 @@ $as_echo "$lt_cv_irix_exported_symbol" >&6; }
esac
;;
- netbsd*)
+ netbsd* | netbsdelf*-gnu)
if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
archive_cmds_FC='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out
else
@@ -21070,6 +21114,18 @@ fi
dynamic_linker='GNU/Linux ld.so'
;;
+netbsdelf*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='NetBSD ld.elf_so'
+ ;;
+
netbsd*)
version_type=sunos
need_lib_prefix=no
@@ -22186,6 +22242,8 @@ fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: PTHREAD_LIBS=${PTHREAD_LIBS}" >&5
+$as_echo "$as_me: PTHREAD_LIBS=${PTHREAD_LIBS}" >&6;}
if test x"$acx_pthread_ok" = xyes; then
@@ -22493,6 +22551,14 @@ fi
fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: PTHREAD_LIBS=${PTHREAD_LIBS}" >&5
+$as_echo "$as_me: PTHREAD_LIBS=${PTHREAD_LIBS}" >&6;}
+if test ! -z "${PTHREAD_LIBS}"; then
+ LIBS="${PTHREAD_LIBS} ${LIBS}"
+fi
+if test ! -z "${PTHREAD_CFLAGS}"; then
+ CFLAGS="$CFLAGS ${PTHREAD_CFLAGS}"
+fi
# Make sure we find Python2
@@ -25482,8 +25548,10 @@ fi
# Check whether --with-dataspaces was given.
if test "${with_dataspaces+set}" = set; then :
- withval=$with_dataspaces; DATASPACES_LDFLAGS="-L$withval/lib";
+ withval=$with_dataspaces; DATASPACES_LIBS="-L$withval/lib -ldspaces -ldscommon -ldart";
DATASPACES_CPPFLAGS="-I$withval/include";
+ DSPACES_CONFIG="$withval/bin/dspaces_config";
+
else
with_dataspaces=check
fi
@@ -25544,24 +25612,25 @@ fi
DATASPACES_LIBDIR="${DATASPACES}/lib"
fi
- if test -n "${DATASPACES_INCDIR}"; then
- DATASPACES_CPPFLAGS="-I${DATASPACES_INCDIR}"
+ if test -x "${DSPACES_CONFIG}"; then
+ DATASPACES_LIBS=$(${DSPACES_CONFIG} -l)
+ DATASPACES_CPPFLAGS=$(${DSPACES_CONFIG} -c)
else
- ac_dataspaces_ok=no
- fi
- if test -n "${DATASPACES_LIBDIR}"; then
- DATASPACES_LDFLAGS="-L${DATASPACES_LIBDIR}"
- else
- ac_dataspaces_ok=no
+ if test -n "${DATASPACES_INCDIR}"; then
+ DATASPACES_CPPFLAGS="-I${DATASPACES_INCDIR}"
+ fi
+
+ if test -n "${DATASPACES_LIBDIR}"; then
+ DATASPACES_LIBS="-L${DATASPACES_LIBDIR} -ldspaces -ldscommon -ldart"
+ fi
fi
save_CC="$CC"
save_CPPFLAGS="$CPPFLAGS"
save_LIBS="$LIBS"
save_LDFLAGS="$LDFLAGS"
- LIBS="-ldspaces -ldscommon -ldart $LIBS"
- LDFLAGS="$LDFLAGS $DATASPACES_LDFLAGS"
+ LIBS="$DATASPACES_LIBS $LIBS"
CPPFLAGS="$CPPFLAGS $DATASPACES_CPPFLAGS"
CC="$MPICC"
@@ -25593,7 +25662,7 @@ done
# Check for the DataSpaces library and headers
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if dataspaces code can be compiled and linked" >&5
$as_echo_n "checking if dataspaces code can be compiled and linked... " >&6; }
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
#include "dataspaces.h"
#ifdef FC_DUMMY_MAIN
@@ -25615,7 +25684,6 @@ _ACEOF
if ac_fn_c_try_link "$LINENO"; then :
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
$as_echo "yes" >&6; }
- DATASPACES_LIBS="-ldspaces -ldscommon -ldart"
else
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
$as_echo "no" >&6; }
@@ -25668,8 +25736,10 @@ fi
# Check whether --with-dimes was given.
if test "${with_dimes+set}" = set; then :
- withval=$with_dimes; DIMES_LDFLAGS="-L$withval/lib";
+ withval=$with_dimes; DIMES_LIBS="-L$withval/lib -ldspaces -ldscommon -ldart";
DIMES_CPPFLAGS="-I$withval/include";
+ DSPACES_CONFIG="$withval/bin/dspaces_config";
+
else
with_dimes=check
fi
@@ -25730,36 +25800,25 @@ fi
DIMES_LIBDIR="${DIMES}/lib"
fi
- if test -n "${DIMES_INCDIR}"; then
- DIMES_CPPFLAGS="-I${DIMES_INCDIR}"
+ if test -x "${DSPACES_CONFIG}"; then
+ DIMES_LIBS=$(${DSPACES_CONFIG} -l)
+ DIMES_CPPFLAGS=$(${DSPACES_CONFIG} -c)
else
- ac_dimes_ok=no
- fi
- if test -n "${DIMES_LIBDIR}"; then
- DIMES_LDFLAGS="-L${DIMES_LIBDIR}"
- else
- ac_dimes_ok=no
- fi
+ if test -n "${DIMES_INCDIR}"; then
+ DIMES_CPPFLAGS="-I${DIMES_INCDIR}"
+ fi
+
+ if test -n "${DIMES_LIBDIR}"; then
+ DIMES_LDFLAGS="-L${DIMES_LIBDIR}"
+ fi
+ fi
save_CC="$CC"
save_CPPFLAGS="$CPPFLAGS"
save_LIBS="$LIBS"
save_LDFLAGS="$LDFLAGS"
- if test "x${ac_portals_lib_ok}" == "xyes"; then
- echo "DIMES currently NOT supported for Cray Portals!"
- if false; then
- HAVE_DIMES_TRUE=
- HAVE_DIMES_FALSE='#'
-else
- HAVE_DIMES_TRUE='#'
- HAVE_DIMES_FALSE=
-fi
-
- else
- LIBS="-ldspaces -ldscommon -ldart $LIBS"
- fi
- LDFLAGS="$LDFLAGS $DIMES_LDFLAGS"
+ LIBS="$DIMES_LIBS $LIBS"
CPPFLAGS="$CPPFLAGS $DIMES_CPPFLAGS"
CC="$MPICC"
@@ -25813,7 +25872,6 @@ _ACEOF
if ac_fn_c_try_link "$LINENO"; then :
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
$as_echo "yes" >&6; }
- DIMES_LIBS="-ldspaces -ldscommon -ldart"
else
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
$as_echo "no" >&6; }
@@ -26696,11 +26754,11 @@ fi
search_list="$datatap_dir/thin_ib.h $datatap_dir/lib/thin_ib.h $datatap_dir/include/thin_ib.h $search_list /usr/include/thin_ib.h /usr/local/include/thin_ib.h /opt/ibpbio/include/thin_ib.h /opt/misc/include/thin_ib.h /opt/misc/include/$cercs_cv_archive/thin_ib.h"
tmp_search_results=""
-echo "configure:26699: searching for $search_list " >&5
+echo "configure:26757: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:26703: first found $tmp_search_results " >&5
+ echo "configure:26761: first found $tmp_search_results " >&5
break
fi
done
@@ -26788,11 +26846,11 @@ fi
search_list="$datatap_dir/libibclient.la $datatap_dir/lib/libibclient.la $datatap_dir/include/libibclient.la $search_list /usr/lib/libibclient.la /usr/local/lib/libibclient.la /opt/ibpbio/lib/libibclient.la /opt/misc/lib/libibclient.la /opt/misc/lib/$cercs_cv_archive/libibclient.la"
tmp_search_results=""
-echo "configure:26791: searching for $search_list " >&5
+echo "configure:26849: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:26795: first found $tmp_search_results " >&5
+ echo "configure:26853: first found $tmp_search_results " >&5
break
fi
done
@@ -26861,11 +26919,11 @@ else
search_list="$PWD/../ibpbio $PWD/../../ibpbio $PWD/../../../ibpbio"
tmp_search_results=""
-echo "configure:26864: searching for $search_list " >&5
+echo "configure:26922: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:26868: first found $tmp_search_results " >&5
+ echo "configure:26926: first found $tmp_search_results " >&5
break
fi
done
@@ -26903,11 +26961,11 @@ else
search_list="$PWD/../ibpbio $PWD/../../ibpbio $PWD/../../../ibpbio"
tmp_search_results=""
-echo "configure:26906: searching for $search_list " >&5
+echo "configure:26964: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:26910: first found $tmp_search_results " >&5
+ echo "configure:26968: first found $tmp_search_results " >&5
break
fi
done
@@ -27031,11 +27089,11 @@ fi
search_list="$datatap_dir/ffs.h $datatap_dir/lib/ffs.h $datatap_dir/include/ffs.h $search_list /usr/include/ffs.h /usr/local/include/ffs.h /opt/ffs/include/ffs.h /opt/misc/include/ffs.h /opt/misc/include/$cercs_cv_archive/ffs.h"
tmp_search_results=""
-echo "configure:27034: searching for $search_list " >&5
+echo "configure:27092: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:27038: first found $tmp_search_results " >&5
+ echo "configure:27096: first found $tmp_search_results " >&5
break
fi
done
@@ -27123,11 +27181,11 @@ fi
search_list="$datatap_dir/libffs.la $datatap_dir/lib/libffs.la $datatap_dir/include/libffs.la $search_list /usr/lib/libffs.la /usr/local/lib/libffs.la /opt/ffs/lib/libffs.la /opt/misc/lib/libffs.la /opt/misc/lib/$cercs_cv_archive/libffs.la"
tmp_search_results=""
-echo "configure:27126: searching for $search_list " >&5
+echo "configure:27184: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:27130: first found $tmp_search_results " >&5
+ echo "configure:27188: first found $tmp_search_results " >&5
break
fi
done
@@ -27196,11 +27254,11 @@ else
search_list="$PWD/../ffs $PWD/../../ffs $PWD/../../../ffs"
tmp_search_results=""
-echo "configure:27199: searching for $search_list " >&5
+echo "configure:27257: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:27203: first found $tmp_search_results " >&5
+ echo "configure:27261: first found $tmp_search_results " >&5
break
fi
done
@@ -27238,11 +27296,11 @@ else
search_list="$PWD/../ffs $PWD/../../ffs $PWD/../../../ffs"
tmp_search_results=""
-echo "configure:27241: searching for $search_list " >&5
+echo "configure:27299: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:27245: first found $tmp_search_results " >&5
+ echo "configure:27303: first found $tmp_search_results " >&5
break
fi
done
@@ -27366,11 +27424,11 @@ fi
search_list="$datatap_dir/gen_thread.h $datatap_dir/lib/gen_thread.h $datatap_dir/include/gen_thread.h $search_list /usr/include/gen_thread.h /usr/local/include/gen_thread.h /opt/gen_thread/include/gen_thread.h /opt/misc/include/gen_thread.h /opt/misc/include/$cercs_cv_archive/gen_thread.h"
tmp_search_results=""
-echo "configure:27369: searching for $search_list " >&5
+echo "configure:27427: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:27373: first found $tmp_search_results " >&5
+ echo "configure:27431: first found $tmp_search_results " >&5
break
fi
done
@@ -27458,11 +27516,11 @@ fi
search_list="$datatap_dir/libgen_thread.la $datatap_dir/lib/libgen_thread.la $datatap_dir/include/libgen_thread.la $search_list /usr/lib/libgen_thread.la /usr/local/lib/libgen_thread.la /opt/gen_thread/lib/libgen_thread.la /opt/misc/lib/libgen_thread.la /opt/misc/lib/$cercs_cv_archive/libgen_thread.la"
tmp_search_results=""
-echo "configure:27461: searching for $search_list " >&5
+echo "configure:27519: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:27465: first found $tmp_search_results " >&5
+ echo "configure:27523: first found $tmp_search_results " >&5
break
fi
done
@@ -27531,11 +27589,11 @@ else
search_list="$PWD/../gen_thread $PWD/../../gen_thread $PWD/../../../gen_thread"
tmp_search_results=""
-echo "configure:27534: searching for $search_list " >&5
+echo "configure:27592: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:27538: first found $tmp_search_results " >&5
+ echo "configure:27596: first found $tmp_search_results " >&5
break
fi
done
@@ -27573,11 +27631,11 @@ else
search_list="$PWD/../gen_thread $PWD/../../gen_thread $PWD/../../../gen_thread"
tmp_search_results=""
-echo "configure:27576: searching for $search_list " >&5
+echo "configure:27634: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:27580: first found $tmp_search_results " >&5
+ echo "configure:27638: first found $tmp_search_results " >&5
break
fi
done
@@ -27724,11 +27782,11 @@ fi
search_list="$datatap_dir/thin_portal.h $datatap_dir/lib/thin_portal.h $datatap_dir/include/thin_portal.h $search_list /usr/include/thin_portal.h /usr/local/include/thin_portal.h /opt/ptlpbio/include/thin_portal.h /opt/misc/include/thin_portal.h /opt/misc/include/$cercs_cv_archive/thin_portal.h"
tmp_search_results=""
-echo "configure:27727: searching for $search_list " >&5
+echo "configure:27785: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:27731: first found $tmp_search_results " >&5
+ echo "configure:27789: first found $tmp_search_results " >&5
break
fi
done
@@ -27816,11 +27874,11 @@ fi
search_list="$datatap_dir/libptlclient.a $datatap_dir/lib/libptlclient.a $datatap_dir/include/libptlclient.a $search_list /usr/lib/libptlclient.a /usr/local/lib/libptlclient.a /opt/ptlpbio/lib/libptlclient.a /opt/misc/lib/libptlclient.a /opt/misc/lib/$cercs_cv_archive/libptlclient.a"
tmp_search_results=""
-echo "configure:27819: searching for $search_list " >&5
+echo "configure:27877: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:27823: first found $tmp_search_results " >&5
+ echo "configure:27881: first found $tmp_search_results " >&5
break
fi
done
@@ -27889,11 +27947,11 @@ else
search_list="$PWD/../ptlpbio $PWD/../../ptlpbio $PWD/../../../ptlpbio"
tmp_search_results=""
-echo "configure:27892: searching for $search_list " >&5
+echo "configure:27950: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:27896: first found $tmp_search_results " >&5
+ echo "configure:27954: first found $tmp_search_results " >&5
break
fi
done
@@ -27931,11 +27989,11 @@ else
search_list="$PWD/../ptlpbio $PWD/../../ptlpbio $PWD/../../../ptlpbio"
tmp_search_results=""
-echo "configure:27934: searching for $search_list " >&5
+echo "configure:27992: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:27938: first found $tmp_search_results " >&5
+ echo "configure:27996: first found $tmp_search_results " >&5
break
fi
done
@@ -28087,11 +28145,11 @@ fi
search_list="$datatap_dir/thin_ib.h $datatap_dir/lib/thin_ib.h $datatap_dir/include/thin_ib.h $search_list /usr/include/thin_ib.h /usr/local/include/thin_ib.h /opt/ibpbio/include/thin_ib.h /opt/misc/include/thin_ib.h /opt/misc/include/$cercs_cv_archive/thin_ib.h"
tmp_search_results=""
-echo "configure:28090: searching for $search_list " >&5
+echo "configure:28148: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:28094: first found $tmp_search_results " >&5
+ echo "configure:28152: first found $tmp_search_results " >&5
break
fi
done
@@ -28179,11 +28237,11 @@ fi
search_list="$datatap_dir/libibclient.la $datatap_dir/lib/libibclient.la $datatap_dir/include/libibclient.la $search_list /usr/lib/libibclient.la /usr/local/lib/libibclient.la /opt/ibpbio/lib/libibclient.la /opt/misc/lib/libibclient.la /opt/misc/lib/$cercs_cv_archive/libibclient.la"
tmp_search_results=""
-echo "configure:28182: searching for $search_list " >&5
+echo "configure:28240: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:28186: first found $tmp_search_results " >&5
+ echo "configure:28244: first found $tmp_search_results " >&5
break
fi
done
@@ -28252,11 +28310,11 @@ else
search_list="$PWD/../ibpbio $PWD/../../ibpbio $PWD/../../../ibpbio"
tmp_search_results=""
-echo "configure:28255: searching for $search_list " >&5
+echo "configure:28313: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:28259: first found $tmp_search_results " >&5
+ echo "configure:28317: first found $tmp_search_results " >&5
break
fi
done
@@ -28294,11 +28352,11 @@ else
search_list="$PWD/../ibpbio $PWD/../../ibpbio $PWD/../../../ibpbio"
tmp_search_results=""
-echo "configure:28297: searching for $search_list " >&5
+echo "configure:28355: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:28301: first found $tmp_search_results " >&5
+ echo "configure:28359: first found $tmp_search_results " >&5
break
fi
done
@@ -28422,11 +28480,11 @@ fi
search_list="$datatap_dir/ffs.h $datatap_dir/lib/ffs.h $datatap_dir/include/ffs.h $search_list /usr/include/ffs.h /usr/local/include/ffs.h /opt/ffs/include/ffs.h /opt/misc/include/ffs.h /opt/misc/include/$cercs_cv_archive/ffs.h"
tmp_search_results=""
-echo "configure:28425: searching for $search_list " >&5
+echo "configure:28483: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:28429: first found $tmp_search_results " >&5
+ echo "configure:28487: first found $tmp_search_results " >&5
break
fi
done
@@ -28514,11 +28572,11 @@ fi
search_list="$datatap_dir/libffs.la $datatap_dir/lib/libffs.la $datatap_dir/include/libffs.la $search_list /usr/lib/libffs.la /usr/local/lib/libffs.la /opt/ffs/lib/libffs.la /opt/misc/lib/libffs.la /opt/misc/lib/$cercs_cv_archive/libffs.la"
tmp_search_results=""
-echo "configure:28517: searching for $search_list " >&5
+echo "configure:28575: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:28521: first found $tmp_search_results " >&5
+ echo "configure:28579: first found $tmp_search_results " >&5
break
fi
done
@@ -28587,11 +28645,11 @@ else
search_list="$PWD/../ffs $PWD/../../ffs $PWD/../../../ffs"
tmp_search_results=""
-echo "configure:28590: searching for $search_list " >&5
+echo "configure:28648: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:28594: first found $tmp_search_results " >&5
+ echo "configure:28652: first found $tmp_search_results " >&5
break
fi
done
@@ -28629,11 +28687,11 @@ else
search_list="$PWD/../ffs $PWD/../../ffs $PWD/../../../ffs"
tmp_search_results=""
-echo "configure:28632: searching for $search_list " >&5
+echo "configure:28690: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:28636: first found $tmp_search_results " >&5
+ echo "configure:28694: first found $tmp_search_results " >&5
break
fi
done
@@ -28757,11 +28815,11 @@ fi
search_list="$datatap_dir/gen_thread.h $datatap_dir/lib/gen_thread.h $datatap_dir/include/gen_thread.h $search_list /usr/include/gen_thread.h /usr/local/include/gen_thread.h /opt/gen_thread/include/gen_thread.h /opt/misc/include/gen_thread.h /opt/misc/include/$cercs_cv_archive/gen_thread.h"
tmp_search_results=""
-echo "configure:28760: searching for $search_list " >&5
+echo "configure:28818: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:28764: first found $tmp_search_results " >&5
+ echo "configure:28822: first found $tmp_search_results " >&5
break
fi
done
@@ -28849,11 +28907,11 @@ fi
search_list="$datatap_dir/libgen_thread.la $datatap_dir/lib/libgen_thread.la $datatap_dir/include/libgen_thread.la $search_list /usr/lib/libgen_thread.la /usr/local/lib/libgen_thread.la /opt/gen_thread/lib/libgen_thread.la /opt/misc/lib/libgen_thread.la /opt/misc/lib/$cercs_cv_archive/libgen_thread.la"
tmp_search_results=""
-echo "configure:28852: searching for $search_list " >&5
+echo "configure:28910: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:28856: first found $tmp_search_results " >&5
+ echo "configure:28914: first found $tmp_search_results " >&5
break
fi
done
@@ -28922,11 +28980,11 @@ else
search_list="$PWD/../gen_thread $PWD/../../gen_thread $PWD/../../../gen_thread"
tmp_search_results=""
-echo "configure:28925: searching for $search_list " >&5
+echo "configure:28983: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:28929: first found $tmp_search_results " >&5
+ echo "configure:28987: first found $tmp_search_results " >&5
break
fi
done
@@ -28964,11 +29022,11 @@ else
search_list="$PWD/../gen_thread $PWD/../../gen_thread $PWD/../../../gen_thread"
tmp_search_results=""
-echo "configure:28967: searching for $search_list " >&5
+echo "configure:29025: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:28971: first found $tmp_search_results " >&5
+ echo "configure:29029: first found $tmp_search_results " >&5
break
fi
done
@@ -29115,11 +29173,11 @@ fi
search_list="$datatap_dir/thin_portal.h $datatap_dir/lib/thin_portal.h $datatap_dir/include/thin_portal.h $search_list /usr/include/thin_portal.h /usr/local/include/thin_portal.h /opt/ptlpbio/include/thin_portal.h /opt/misc/include/thin_portal.h /opt/misc/include/$cercs_cv_archive/thin_portal.h"
tmp_search_results=""
-echo "configure:29118: searching for $search_list " >&5
+echo "configure:29176: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:29122: first found $tmp_search_results " >&5
+ echo "configure:29180: first found $tmp_search_results " >&5
break
fi
done
@@ -29207,11 +29265,11 @@ fi
search_list="$datatap_dir/libptlclient.a $datatap_dir/lib/libptlclient.a $datatap_dir/include/libptlclient.a $search_list /usr/lib/libptlclient.a /usr/local/lib/libptlclient.a /opt/ptlpbio/lib/libptlclient.a /opt/misc/lib/libptlclient.a /opt/misc/lib/$cercs_cv_archive/libptlclient.a"
tmp_search_results=""
-echo "configure:29210: searching for $search_list " >&5
+echo "configure:29268: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:29214: first found $tmp_search_results " >&5
+ echo "configure:29272: first found $tmp_search_results " >&5
break
fi
done
@@ -29280,11 +29338,11 @@ else
search_list="$PWD/../ptlpbio $PWD/../../ptlpbio $PWD/../../../ptlpbio"
tmp_search_results=""
-echo "configure:29283: searching for $search_list " >&5
+echo "configure:29341: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:29287: first found $tmp_search_results " >&5
+ echo "configure:29345: first found $tmp_search_results " >&5
break
fi
done
@@ -29322,11 +29380,11 @@ else
search_list="$PWD/../ptlpbio $PWD/../../ptlpbio $PWD/../../../ptlpbio"
tmp_search_results=""
-echo "configure:29325: searching for $search_list " >&5
+echo "configure:29383: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:29329: first found $tmp_search_results " >&5
+ echo "configure:29387: first found $tmp_search_results " >&5
break
fi
done
@@ -29527,11 +29585,11 @@ fi
search_list="$datatap_dir/evpath.h $datatap_dir/lib/evpath.h $datatap_dir/include/evpath.h $search_list /usr/include/evpath.h /usr/local/include/evpath.h /opt/evpath/include/evpath.h /opt/misc/include/evpath.h /opt/misc/include/$cercs_cv_archive/evpath.h"
tmp_search_results=""
-echo "configure:29530: searching for $search_list " >&5
+echo "configure:29588: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:29534: first found $tmp_search_results " >&5
+ echo "configure:29592: first found $tmp_search_results " >&5
break
fi
done
@@ -29570,7 +29628,7 @@ else
cercs_tmp=""
-search_list="./libevpath.a"
+search_list="./libevpath.la"
CHAOS_HOMEDIR=""
if test -n "$CSH"; then
CHAOS_HOMEDIR=`echo "echo ~chaos" | csh -sf 2>/dev/null | sed 's%/$%%'` || CHAOS_HOMEDIR=""
@@ -29584,46 +29642,46 @@ fi
echo "Datatap = $datatap_dir"
-search_list="$datatap_dir/libevpath.a $datatap_dir/lib/libevpath.a $datatap_dir/include/libevpath.a $search_list $EXPANDED/libevpath.a $EXPANDED/lib/libevpath.a $EXPANDED/share/libevpath.a $EXPANDED/$cercs_cv_archive/libevpath.a $EXPANDED/$cercs_cv_archive/lib/libevpath.a $EXPANDED/evpath/libevpath.a $EXPANDED/evpath/$cercs_cv_archive/libevpath.a $EXPANDED/evpath/lib/libevpath.a $EXPANDED/evpath/lib/$cercs_cv_archive/libevpath.a"
+search_list="$datatap_dir/libevpath.la $datatap_dir/lib/libevpath.la $datatap_dir/include/libevpath.la $search_list $EXPANDED/libevpath.la $EXPANDED/lib/libevpath.la $EXPANDED/share/libevpath.la $EXPANDED/$cercs_cv_archive/libevpath.la $EXPANDED/$cercs_cv_archive/lib/libevpath.la $EXPANDED/evpath/libevpath.la $EXPANDED/evpath/$cercs_cv_archive/libevpath.la $EXPANDED/evpath/lib/libevpath.la $EXPANDED/evpath/lib/$cercs_cv_archive/libevpath.la"
fi
if test -z "$with_installed_specified"; then
-search_list="$search_list `pwd`/../evpath/libevpath.a `pwd`/../lib/libevpath.a `pwd`/../share/libevpath.a"
+search_list="$search_list `pwd`/../evpath/libevpath.la `pwd`/../lib/libevpath.la `pwd`/../share/libevpath.la"
if test "$CHAOS_HOMEDIR" != "$HOME"; then
-search_list="$search_list $HOME/evpath/libevpath.a $HOME/$cercs_cv_archive/lib/libevpath.a $HOME/lib/libevpath.a"
+search_list="$search_list $HOME/evpath/libevpath.la $HOME/$cercs_cv_archive/lib/libevpath.la $HOME/lib/libevpath.la"
fi
fi
if test -n "$CHAOS_HOMEDIR" -a -n "$cercs_cv_archive"; then
-search_list="$search_list $CHAOS_HOMEDIR/$cercs_cv_archive/evpath/lib/libevpath.a $CHAOS_HOMEDIR/$cercs_cv_archive/lib/libevpath.a $CHAOS_HOMEDIR/evpath/$cercs_cv_archive/lib/libevpath.a $CHAOS_HOMEDIR/evpath/lib/libevpath.a $CHAOS_HOMEDIR/lib/libevpath.a"
+search_list="$search_list $CHAOS_HOMEDIR/$cercs_cv_archive/evpath/lib/libevpath.la $CHAOS_HOMEDIR/$cercs_cv_archive/lib/libevpath.la $CHAOS_HOMEDIR/evpath/$cercs_cv_archive/lib/libevpath.la $CHAOS_HOMEDIR/evpath/lib/libevpath.la $CHAOS_HOMEDIR/lib/libevpath.la"
fi
if test "$libdir" != '${exec_prefix}/lib'; then
tmpdir=`echo ${libdir} | sed 's%/$%%'`
-search_list="$tmpdir/libevpath.a $search_list"
+search_list="$tmpdir/libevpath.la $search_list"
fi
if test "$exec_prefix" != "NONE"; then
tmpdir=`echo ${exec_prefix} | sed 's%/$%%'`
-search_list="$tmpdir/lib/libevpath.a $search_list"
+search_list="$tmpdir/lib/libevpath.la $search_list"
fi
if test "$includedir" != '${prefix}/include'; then
tmpdir=`echo ${includedir} | sed 's%/$%%'`
-search_list="$tmpdir/libevpath.a $search_list"
+search_list="$tmpdir/libevpath.la $search_list"
fi
if test "$prefix" != "NONE"; then
tmpdir=`echo ${prefix} | sed 's%/$%%'`
-search_list="$tmpdir/lib/libevpath.a $search_list"
+search_list="$tmpdir/lib/libevpath.la $search_list"
fi
if test "lib" == "lib"; then
for tmp_lib_value in $sys_lib_search_path_spec; do
- search_list="$search_list $tmp_lib_value/libevpath.a"
+ search_list="$search_list $tmp_lib_value/libevpath.la"
done
fi
-search_list="$datatap_dir/libevpath.a $datatap_dir/lib/libevpath.a $datatap_dir/include/libevpath.a $search_list /usr/lib/libevpath.a /usr/local/lib/libevpath.a /opt/evpath/lib/libevpath.a /opt/misc/lib/libevpath.a /opt/misc/lib/$cercs_cv_archive/libevpath.a"
+search_list="$datatap_dir/libevpath.la $datatap_dir/lib/libevpath.la $datatap_dir/include/libevpath.la $search_list /usr/lib/libevpath.la /usr/local/lib/libevpath.la /opt/evpath/lib/libevpath.la /opt/misc/lib/libevpath.la /opt/misc/lib/$cercs_cv_archive/libevpath.la"
tmp_search_results=""
-echo "configure:29622: searching for $search_list " >&5
+echo "configure:29680: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:29626: first found $tmp_search_results " >&5
+ echo "configure:29684: first found $tmp_search_results " >&5
break
fi
done
@@ -29632,8 +29690,8 @@ if test -n "$tmp_search_results"; then
cercs_tmp=$tmp_search_results
fi
-if test -n "$cercs_tmp" -a "$cercs_tmp" != "libevpath.a"; then
-cercs_cv_evpath_link_dir=`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s/.libevpath.a//g"`
+if test -n "$cercs_tmp" -a "$cercs_tmp" != "libevpath.la"; then
+cercs_cv_evpath_link_dir=`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s/.libevpath.la//g"`
else
cercs_cv_evpath_link_dir=""
fi
@@ -29649,7 +29707,7 @@ if test -n "$cercs_cv_evpath_link_arg"; then
arg=$cercs_cv_evpath_link_arg
no_dash_arg=`echo $arg | sed 's/^-//g'`
if test `echo $new_flags | grep -c "$no_dash_arg"` -eq 0; then
-root=`echo libevpath.a | sed 's/\..*//'`
+root=`echo libevpath.la | sed 's/\..*//'`
if test ! -r $cercs_cv_evpath_link_dir/$root.la; then
if eval "test \"\${LIBTOOL+set}\" = set"; then
arg="$cercs_cv_evpath_link_arg "`echo $cercs_cv_evpath_link_dir | sed "/./ s/^/-R/1"`
@@ -29692,11 +29750,11 @@ else
search_list="$PWD/../evpath $PWD/../../evpath $PWD/../../../evpath"
tmp_search_results=""
-echo "configure:29695: searching for $search_list " >&5
+echo "configure:29753: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:29699: first found $tmp_search_results " >&5
+ echo "configure:29757: first found $tmp_search_results " >&5
break
fi
done
@@ -29734,11 +29792,11 @@ else
search_list="$PWD/../evpath $PWD/../../evpath $PWD/../../../evpath"
tmp_search_results=""
-echo "configure:29737: searching for $search_list " >&5
+echo "configure:29795: searching for $search_list " >&5
for tmp_search_value in $search_list; do
if test -r $tmp_search_value; then
tmp_search_results=$tmp_search_value
- echo "configure:29741: first found $tmp_search_results " >&5
+ echo "configure:29799: first found $tmp_search_results " >&5
break
fi
done
@@ -29747,8 +29805,8 @@ if test -n "$tmp_search_results"; then
cercs_tmp=$tmp_search_results
fi
-if test -n "$cercs_tmp" -a "$cercs_tmp" != "libevpath.a"; then
-cercs_cv_evpath_link_dir=`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s/.libevpath.a//g"`
+if test -n "$cercs_tmp" -a "$cercs_tmp" != "libevpath.la"; then
+cercs_cv_evpath_link_dir=`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s/.libevpath.la//g"`
else
cercs_cv_evpath_link_dir=""
fi
@@ -29764,7 +29822,7 @@ if test -n "$cercs_cv_evpath_link_arg"; then
arg=$cercs_cv_evpath_link_arg
no_dash_arg=`echo $arg | sed 's/^-//g'`
if test `echo $new_flags | grep -c "$no_dash_arg"` -eq 0; then
-root=`echo libevpath.a | sed 's/\..*//'`
+root=`echo libevpath.la | sed 's/\..*//'`
if test ! -r $cercs_cv_evpath_link_dir/$root.la; then
if eval "test \"\${LIBTOOL+set}\" = set"; then
arg="$cercs_cv_evpath_link_arg "`echo $cercs_cv_evpath_link_dir | sed "/./ s/^/-R/1"`
@@ -29783,1652 +29841,293 @@ fi
fi
-
-
-if test -z "$with_local_specified"; then
-
-
-
-
-# Check whether --with-ffs was given.
-if test "${with_ffs+set}" = set; then :
- withval=$with_ffs;
+ if test -n "$cercs_cv_evpath_link_dir" -a -n "$cercs_cv_evpath_include_arg";then
+ if (test -x "$withval/bin/evpath_config") ; then
+ FP_CONFIG="$withval/bin/evpath_config"
+ else
+ FP_CONFIG="$cercs_cv_evpath_link_dir/../bin/evpath_config"
+ fi
+ if (test -x "$FP_CONFIG") ; then
+ FP_LIBS=$(${FP_CONFIG} -s)
+ FP_CFLAGS=$(${FP_CONFIG} -c)
+ FP_CPPFLAGS=$(${FP_CONFIG} -c)
+ else
+ FP_LDFLAGS="$FP_LDFLAGS -L$cercs_cv_evpath_link_dir"
+ FP_LIBS="$FP_LIBS -levpath"
+ FP_CFLAGS="$FP_CFLAGS $cercs_cv_evpath_include_arg"
+ FP_CPPFLAGS="$FP_CPPFLAGS $cercs_cv_evpath_include_arg"
+ fi
+ else
+ echo "FLEXPATH couldn't find evpath - Not building flexpath"
+ ac_flexpath_ok=no
+ fi
fi
-if test -n "$with_ffs"; then
-unset cercs_cv_ffs_include_arg
-unset cercs_cv_ffs_link_arg
-if test `echo $with_ffs | sed 's/\(.\).*/\1/g'` != "/"; then
-with_ffs=`pwd`/$with_ffs
-fi
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking needed include args for ffs package" >&5
-$as_echo_n "checking needed include args for ffs package... " >&6; }
-if ${cercs_cv_ffs_include_arg+:} false; then :
- $as_echo_n "(cached) " >&6
-else
-cercs_tmp=""
-search_list="./ffs.h"
-CHAOS_HOMEDIR=""
-if test -n "$CSH"; then
-CHAOS_HOMEDIR=`echo "echo ~chaos" | csh -sf 2>/dev/null | sed 's%/$%%'` || CHAOS_HOMEDIR=""
-fi
-if test -n "$with_ffs"; then
-if test `echo $with_ffs | cut -c1` = "~"; then
-EXPANDED=`echo "echo $with_ffs" | csh -sf 2>/dev/null` || EXPANDED=""
+if test "x$ac_flexpath_ok" = "xyes"; then
+ HAVE_FLEXPATH=1
+ NO_FLEXPATH=0
else
-EXPANDED=$with_ffs
-fi
-
-echo "Datatap = $datatap_dir"
-
-search_list="$datatap_dir/ffs.h $datatap_dir/lib/ffs.h $datatap_dir/include/ffs.h $search_list $EXPANDED/ffs.h $EXPANDED/include/ffs.h $EXPANDED/share/ffs.h $EXPANDED/$cercs_cv_archive/ffs.h $EXPANDED/$cercs_cv_archive/include/ffs.h $EXPANDED/ffs/ffs.h $EXPANDED/ffs/$cercs_cv_archive/ffs.h $EXPANDED/ffs/include/ffs.h $EXPANDED/ffs/include/$cercs_cv_archive/ffs.h"
-fi
-if test -z "$with_installed_specified"; then
-search_list="$search_list `pwd`/../ffs/ffs.h `pwd`/../include/ffs.h `pwd`/../share/ffs.h"
-if test "$CHAOS_HOMEDIR" != "$HOME"; then
-search_list="$search_list $HOME/ffs/ffs.h $HOME/$cercs_cv_archive/include/ffs.h $HOME/include/ffs.h"
-fi
-fi
-if test -n "$CHAOS_HOMEDIR" -a -n "$cercs_cv_archive"; then
-search_list="$search_list $CHAOS_HOMEDIR/$cercs_cv_archive/ffs/include/ffs.h $CHAOS_HOMEDIR/$cercs_cv_archive/include/ffs.h $CHAOS_HOMEDIR/ffs/$cercs_cv_archive/include/ffs.h $CHAOS_HOMEDIR/ffs/include/ffs.h $CHAOS_HOMEDIR/include/ffs.h"
-fi
-if test "$libdir" != '${exec_prefix}/lib'; then
-tmpdir=`echo ${libdir} | sed 's%/$%%'`
-search_list="$tmpdir/ffs.h $search_list"
-fi
-if test "$exec_prefix" != "NONE"; then
-tmpdir=`echo ${exec_prefix} | sed 's%/$%%'`
-search_list="$tmpdir/lib/ffs.h $search_list"
-fi
-if test "$includedir" != '${prefix}/include'; then
-tmpdir=`echo ${includedir} | sed 's%/$%%'`
-search_list="$tmpdir/ffs.h $search_list"
-fi
-if test "$prefix" != "NONE"; then
-tmpdir=`echo ${prefix} | sed 's%/$%%'`
-search_list="$tmpdir/include/ffs.h $search_list"
+ HAVE_FLEXPATH=0
+ NO_FLEXPATH=1
fi
-if test "include" == "lib"; then
- for tmp_lib_value in $sys_lib_search_path_spec; do
- search_list="$search_list $tmp_lib_value/ffs.h"
- done
+ if test "x$ac_flexpath_ok" = "xyes"; then
+ HAVE_FLEXPATH_TRUE=
+ HAVE_FLEXPATH_FALSE='#'
+else
+ HAVE_FLEXPATH_TRUE='#'
+ HAVE_FLEXPATH_FALSE=
fi
-search_list="$datatap_dir/ffs.h $datatap_dir/lib/ffs.h $datatap_dir/include/ffs.h $search_list /usr/include/ffs.h /usr/local/include/ffs.h /opt/ffs/include/ffs.h /opt/misc/include/ffs.h /opt/misc/include/$cercs_cv_archive/ffs.h"
-tmp_search_results=""
-echo "configure:29865: searching for $search_list " >&5
-for tmp_search_value in $search_list; do
- if test -r $tmp_search_value; then
- tmp_search_results=$tmp_search_value
- echo "configure:29869: first found $tmp_search_results " >&5
- break
- fi
-done
-if test -n "$tmp_search_results"; then
-cercs_tmp=$tmp_search_results
-fi
+cat >>confdefs.h <<_ACEOF
+#define NO_FLEXPATH $NO_FLEXPATH
+_ACEOF
-if test -n "$cercs_tmp" -a "$cercs_tmp" != "/usr/include/ffs.h"; then
-cercs_cv_ffs_include_arg=-I`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s#.ffs.h##g"`
-fi
-fi
+cat >>confdefs.h <<_ACEOF
+#define HAVE_FLEXPATH $HAVE_FLEXPATH
+_ACEOF
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cercs_cv_ffs_include_arg" >&5
-$as_echo "$cercs_cv_ffs_include_arg" >&6; }
-if test -n "$cercs_cv_ffs_include_arg"; then
-arg="$cercs_cv_ffs_include_arg"
-no_dash_arg=`echo $arg | sed 's/^-//g'`
-if test `echo $DT_CPPFLAGS | grep -c "$no_dash_arg"` -eq 0; then
-if test `echo $arg | grep -c "ffs"` -eq 0; then
-DT_CPPFLAGS="$DT_CPPFLAGS $arg";
-else
-DT_CPPFLAGS="$arg $DT_CPPFLAGS"
-fi
-fi
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking needed link args for ffs package" >&5
-$as_echo_n "checking needed link args for ffs package... " >&6; }
-if ${cercs_cv_ffs_link_dir+:} false; then :
- $as_echo_n "(cached) " >&6
-else
+{ $as_echo "$as_me:${as_lineno-$LINENO}: === checking for ZLIB ===" >&5
+$as_echo "$as_me: === checking for ZLIB ===" >&6;}
-cercs_tmp=""
-search_list="./libffs.a"
-CHAOS_HOMEDIR=""
-if test -n "$CSH"; then
-CHAOS_HOMEDIR=`echo "echo ~chaos" | csh -sf 2>/dev/null | sed 's%/$%%'` || CHAOS_HOMEDIR=""
-fi
-if test -n "$with_ffs"; then
-if test `echo $with_ffs | cut -c1` = "~"; then
-EXPANDED=`echo "echo $with_ffs" | csh -sf 2>/dev/null` || EXPANDED=""
+ if true; then
+ HAVE_ZLIB_TRUE=
+ HAVE_ZLIB_FALSE='#'
else
-EXPANDED=$with_ffs
-fi
-
-echo "Datatap = $datatap_dir"
-
-search_list="$datatap_dir/libffs.a $datatap_dir/lib/libffs.a $datatap_dir/include/libffs.a $search_list $EXPANDED/libffs.a $EXPANDED/lib/libffs.a $EXPANDED/share/libffs.a $EXPANDED/$cercs_cv_archive/libffs.a $EXPANDED/$cercs_cv_archive/lib/libffs.a $EXPANDED/ffs/libffs.a $EXPANDED/ffs/$cercs_cv_archive/libffs.a $EXPANDED/ffs/lib/libffs.a $EXPANDED/ffs/lib/$cercs_cv_archive/libffs.a"
-fi
-if test -z "$with_installed_specified"; then
-search_list="$search_list `pwd`/../ffs/libffs.a `pwd`/../lib/libffs.a `pwd`/../share/libffs.a"
-if test "$CHAOS_HOMEDIR" != "$HOME"; then
-search_list="$search_list $HOME/ffs/libffs.a $HOME/$cercs_cv_archive/lib/libffs.a $HOME/lib/libffs.a"
-fi
-fi
-if test -n "$CHAOS_HOMEDIR" -a -n "$cercs_cv_archive"; then
-search_list="$search_list $CHAOS_HOMEDIR/$cercs_cv_archive/ffs/lib/libffs.a $CHAOS_HOMEDIR/$cercs_cv_archive/lib/libffs.a $CHAOS_HOMEDIR/ffs/$cercs_cv_archive/lib/libffs.a $CHAOS_HOMEDIR/ffs/lib/libffs.a $CHAOS_HOMEDIR/lib/libffs.a"
-fi
-if test "$libdir" != '${exec_prefix}/lib'; then
-tmpdir=`echo ${libdir} | sed 's%/$%%'`
-search_list="$tmpdir/libffs.a $search_list"
-fi
-if test "$exec_prefix" != "NONE"; then
-tmpdir=`echo ${exec_prefix} | sed 's%/$%%'`
-search_list="$tmpdir/lib/libffs.a $search_list"
-fi
-if test "$includedir" != '${prefix}/include'; then
-tmpdir=`echo ${includedir} | sed 's%/$%%'`
-search_list="$tmpdir/libffs.a $search_list"
-fi
-if test "$prefix" != "NONE"; then
-tmpdir=`echo ${prefix} | sed 's%/$%%'`
-search_list="$tmpdir/lib/libffs.a $search_list"
-fi
-if test "lib" == "lib"; then
- for tmp_lib_value in $sys_lib_search_path_spec; do
- search_list="$search_list $tmp_lib_value/libffs.a"
- done
+ HAVE_ZLIB_TRUE='#'
+ HAVE_ZLIB_FALSE=
fi
-search_list="$datatap_dir/libffs.a $datatap_dir/lib/libffs.a $datatap_dir/include/libffs.a $search_list /usr/lib/libffs.a /usr/local/lib/libffs.a /opt/ffs/lib/libffs.a /opt/misc/lib/libffs.a /opt/misc/lib/$cercs_cv_archive/libffs.a"
-tmp_search_results=""
-echo "configure:29957: searching for $search_list " >&5
-for tmp_search_value in $search_list; do
- if test -r $tmp_search_value; then
- tmp_search_results=$tmp_search_value
- echo "configure:29961: first found $tmp_search_results " >&5
- break
- fi
-done
-if test -n "$tmp_search_results"; then
-cercs_tmp=$tmp_search_results
-fi
-if test -n "$cercs_tmp" -a "$cercs_tmp" != "libffs.a"; then
-cercs_cv_ffs_link_dir=`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s/.libffs.a//g"`
+# Check whether --with-zlib was given.
+if test "${with_zlib+set}" = set; then :
+ withval=$with_zlib; :
else
-cercs_cv_ffs_link_dir=""
+ with_zlib=no
fi
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cercs_cv_ffs_link_dir" >&5
-$as_echo "$cercs_cv_ffs_link_dir" >&6; }
-ld_arg="-L"
-new_flags=$LDFLAGS
-cercs_cv_ffs_link_arg=`echo $cercs_cv_ffs_link_dir | sed "/./ s/^/$ld_arg/1"`
-if test -n "$cercs_cv_ffs_link_arg"; then
-arg=$cercs_cv_ffs_link_arg
-no_dash_arg=`echo $arg | sed 's/^-//g'`
-if test `echo $new_flags | grep -c "$no_dash_arg"` -eq 0; then
-root=`echo libffs.a | sed 's/\..*//'`
-if test ! -r $cercs_cv_ffs_link_dir/$root.la; then
-if eval "test \"\${LIBTOOL+set}\" = set"; then
-arg="$cercs_cv_ffs_link_arg "`echo $cercs_cv_ffs_link_dir | sed "/./ s/^/-R/1"`
-fi
-fi
-if test `echo $arg | grep -c "ffs"` -eq 0; then
-new_flags="$new_flags $arg"
+if test "x$with_zlib" == "xno"; then
+
+ if false; then
+ HAVE_ZLIB_TRUE=
+ HAVE_ZLIB_FALSE='#'
else
-new_flags="$arg $new_flags"
-fi
-fi
-DT_LDFLAGS=$new_flags
+ HAVE_ZLIB_TRUE='#'
+ HAVE_ZLIB_FALSE=
fi
else
+ save_CPPFLAGS="$CPPFLAGS"
+ save_LIBS="$LIBS"
+ save_LDFLAGS="$LDFLAGS"
+ if test "x$with_zlib" == "xyes"; then
+ ZLIB_CPPFLAGS=""
+ ZLIB_LDFLAGS=""
+ ZLIB_LIBS="-lz"
+ else
+ ZLIB_CPPFLAGS="-I$withval/include"
+ ZLIB_LDFLAGS="-L$withval/lib64"
+ ZLIB_LIBS="-lz"
+ fi
+ LIBS="$LIBS $ZLIB_LIBS"
+ LDFLAGS="$LDFLAGS $ZLIB_LDFLAGS"
+ CPPFLAGS="$CPPFLAGS $ZLIB_CPPFLAGS"
-# Check whether --with-ffs was given.
-if test "${with_ffs+set}" = set; then :
- withval=$with_ffs;
-fi
-
+ for ac_header in zlib.h
+do :
+ ac_fn_c_check_header_mongrel "$LINENO" "zlib.h" "ac_cv_header_zlib_h" "$ac_includes_default"
+if test "x$ac_cv_header_zlib_h" = xyes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_ZLIB_H 1
+_ACEOF
-if test -n "$with_ffs"; then
-unset cercs_cv_ffs_include_arg
-unset cercs_cv_ffs_link_arg
-if test `echo $with_ffs | sed 's/\(.\).*/\1/g'` != "/"; then
-with_ffs=`pwd`/$with_ffs
-fi
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking needed include args for ffs package" >&5
-$as_echo_n "checking needed include args for ffs package... " >&6; }
-if ${cercs_cv_ffs_include_arg+:} false; then :
- $as_echo_n "(cached) " >&6
else
-
-
-search_list="$PWD/../ffs $PWD/../../ffs $PWD/../../../ffs"
-tmp_search_results=""
-echo "configure:30030: searching for $search_list " >&5
-for tmp_search_value in $search_list; do
- if test -r $tmp_search_value; then
- tmp_search_results=$tmp_search_value
- echo "configure:30034: first found $tmp_search_results " >&5
- break
- fi
-done
-
-if test -n "$tmp_search_results"; then
-cercs_tmp=$tmp_search_results
+ if false; then
+ HAVE_ZLIB_TRUE=
+ HAVE_ZLIB_FALSE='#'
+else
+ HAVE_ZLIB_TRUE='#'
+ HAVE_ZLIB_FALSE=
fi
-if test -n "$cercs_tmp" -a "$cercs_tmp" != "/usr/include/ffs.h"; then
-cercs_cv_ffs_include_arg=-I`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s#.ffs.h##g"`
fi
-fi
+done
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cercs_cv_ffs_include_arg" >&5
-$as_echo "$cercs_cv_ffs_include_arg" >&6; }
-if test -n "$cercs_cv_ffs_include_arg"; then
-arg="$cercs_cv_ffs_include_arg"
-no_dash_arg=`echo $arg | sed 's/^-//g'`
-if test `echo $DT_CPPFLAGS | grep -c "$no_dash_arg"` -eq 0; then
-if test `echo $arg | grep -c "ffs"` -eq 0; then
-DT_CPPFLAGS="$DT_CPPFLAGS $arg";
-else
-DT_CPPFLAGS="$arg $DT_CPPFLAGS"
-fi
-fi
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking needed link args for ffs package" >&5
-$as_echo_n "checking needed link args for ffs package... " >&6; }
-if ${cercs_cv_ffs_link_dir+:} false; then :
- $as_echo_n "(cached) " >&6
+ if test -z "${HAVE_ZLIB_TRUE}"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if zlib code can be linked with $ZLIB_LDFLAGS" >&5
+$as_echo_n "checking if zlib code can be linked with $ZLIB_LDFLAGS... " >&6; }
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdlib.h>
+ #include "zlib.h"
+#ifdef FC_DUMMY_MAIN
+#ifndef FC_DUMMY_MAIN_EQ_F77
+# ifdef __cplusplus
+ extern "C"
+# endif
+ int FC_DUMMY_MAIN() { return 1; }
+#endif
+#endif
+int
+main ()
+{
+Bytef* in, *out;
+ uLongf in_len, *out_len;
+ int level = 5;
+ int zerr = compress2 (out, out_len, in, in_len, level);
+ return (zerr != Z_OK);
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
else
+ if false; then
+ HAVE_ZLIB_TRUE=
+ HAVE_ZLIB_FALSE='#'
+else
+ HAVE_ZLIB_TRUE='#'
+ HAVE_ZLIB_FALSE=
+fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
-search_list="$PWD/../ffs $PWD/../../ffs $PWD/../../../ffs"
-tmp_search_results=""
-echo "configure:30072: searching for $search_list " >&5
-for tmp_search_value in $search_list; do
- if test -r $tmp_search_value; then
- tmp_search_results=$tmp_search_value
- echo "configure:30076: first found $tmp_search_results " >&5
- break
- fi
-done
-
-if test -n "$tmp_search_results"; then
-cercs_tmp=$tmp_search_results
fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
-if test -n "$cercs_tmp" -a "$cercs_tmp" != "libffs.a"; then
-cercs_cv_ffs_link_dir=`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s/.libffs.a//g"`
+ if test -z "${HAVE_ZLIB_FALSE}"; then
+ if test "x$with_lustre" != "xyes"; then
+ ZLIB_LDFLAGS="-L$withval/lib"
+ LDFLAGS="$LDFLAGS $ZLIB_LDFLAGS"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if zlib code can be linked with $ZLIB_LDFLAGS" >&5
+$as_echo_n "checking if zlib code can be linked with $ZLIB_LDFLAGS... " >&6; }
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdlib.h>
+ #include "zlib.h"
+#ifdef FC_DUMMY_MAIN
+#ifndef FC_DUMMY_MAIN_EQ_F77
+# ifdef __cplusplus
+ extern "C"
+# endif
+ int FC_DUMMY_MAIN() { return 1; }
+#endif
+#endif
+int
+main ()
+{
+Bytef* in, *out;
+ uLongf in_len, *out_len;
+ int level = 5;
+ int zerr = compress2 (out, out_len, in, in_len, level);
+ return (zerr != Z_OK);
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+ if true; then
+ HAVE_ZLIB_TRUE=
+ HAVE_ZLIB_FALSE='#'
else
-cercs_cv_ffs_link_dir=""
+ HAVE_ZLIB_TRUE='#'
+ HAVE_ZLIB_FALSE=
fi
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cercs_cv_ffs_link_dir" >&5
-$as_echo "$cercs_cv_ffs_link_dir" >&6; }
-ld_arg="-L"
-new_flags=$LDFLAGS
-cercs_cv_ffs_link_arg=`echo $cercs_cv_ffs_link_dir | sed "/./ s/^/$ld_arg/1"`
-if test -n "$cercs_cv_ffs_link_arg"; then
-arg=$cercs_cv_ffs_link_arg
-no_dash_arg=`echo $arg | sed 's/^-//g'`
-if test `echo $new_flags | grep -c "$no_dash_arg"` -eq 0; then
-root=`echo libffs.a | sed 's/\..*//'`
-if test ! -r $cercs_cv_ffs_link_dir/$root.la; then
-if eval "test \"\${LIBTOOL+set}\" = set"; then
-arg="$cercs_cv_ffs_link_arg "`echo $cercs_cv_ffs_link_dir | sed "/./ s/^/-R/1"`
-fi
-fi
-if test `echo $arg | grep -c "ffs"` -eq 0; then
-new_flags="$new_flags $arg"
+ if false; then
+ HAVE_ZLIB_TRUE=
+ HAVE_ZLIB_FALSE='#'
else
-new_flags="$arg $new_flags"
-fi
-fi
-DT_LDFLAGS=$new_flags
+ HAVE_ZLIB_TRUE='#'
+ HAVE_ZLIB_FALSE=
fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+ fi
+ fi
+ fi
+ LIBS="$save_LIBS"
+ LDFLAGS="$save_LDFLAGS"
+ CPPFLAGS="$save_CPPFLAGS"
-if test -z "$with_local_specified"; then
-
+ # Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND:
+ if test -z "${HAVE_ZLIB_TRUE}"; then
-# Check whether --with-atl was given.
-if test "${with_atl+set}" = set; then :
- withval=$with_atl;
-fi
+$as_echo "#define HAVE_ZLIB 1" >>confdefs.h
+ :
+ else
-if test -n "$with_atl"; then
-unset cercs_cv_atl_include_arg
-unset cercs_cv_atl_link_arg
-if test `echo $with_atl | sed 's/\(.\).*/\1/g'` != "/"; then
-with_atl=`pwd`/$with_atl
-fi
+ :
+ fi
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking needed include args for atl package" >&5
-$as_echo_n "checking needed include args for atl package... " >&6; }
-if ${cercs_cv_atl_include_arg+:} false; then :
- $as_echo_n "(cached) " >&6
-else
+{ $as_echo "$as_me:${as_lineno-$LINENO}: === checking for BZIP2 ===" >&5
+$as_echo "$as_me: === checking for BZIP2 ===" >&6;}
-cercs_tmp=""
-search_list="./atl.h"
-CHAOS_HOMEDIR=""
-if test -n "$CSH"; then
-CHAOS_HOMEDIR=`echo "echo ~chaos" | csh -sf 2>/dev/null | sed 's%/$%%'` || CHAOS_HOMEDIR=""
-fi
-if test -n "$with_atl"; then
-if test `echo $with_atl | cut -c1` = "~"; then
-EXPANDED=`echo "echo $with_atl" | csh -sf 2>/dev/null` || EXPANDED=""
+ if true; then
+ HAVE_BZIP2_TRUE=
+ HAVE_BZIP2_FALSE='#'
else
-EXPANDED=$with_atl
+ HAVE_BZIP2_TRUE='#'
+ HAVE_BZIP2_FALSE=
fi
-echo "Datatap = $datatap_dir"
-search_list="$datatap_dir/atl.h $datatap_dir/lib/atl.h $datatap_dir/include/atl.h $search_list $EXPANDED/atl.h $EXPANDED/include/atl.h $EXPANDED/share/atl.h $EXPANDED/$cercs_cv_archive/atl.h $EXPANDED/$cercs_cv_archive/include/atl.h $EXPANDED/atl/atl.h $EXPANDED/atl/$cercs_cv_archive/atl.h $EXPANDED/atl/include/atl.h $EXPANDED/atl/include/$cercs_cv_archive/atl.h"
-fi
-if test -z "$with_installed_specified"; then
-search_list="$search_list `pwd`/../atl/atl.h `pwd`/../include/atl.h `pwd`/../share/atl.h"
-if test "$CHAOS_HOMEDIR" != "$HOME"; then
-search_list="$search_list $HOME/atl/atl.h $HOME/$cercs_cv_archive/include/atl.h $HOME/include/atl.h"
-fi
+
+# Check whether --with-bzip2 was given.
+if test "${with_bzip2+set}" = set; then :
+ withval=$with_bzip2; :
+else
+ with_bzip2=no
fi
-if test -n "$CHAOS_HOMEDIR" -a -n "$cercs_cv_archive"; then
-search_list="$search_list $CHAOS_HOMEDIR/$cercs_cv_archive/atl/include/atl.h $CHAOS_HOMEDIR/$cercs_cv_archive/include/atl.h $CHAOS_HOMEDIR/atl/$cercs_cv_archive/include/atl.h $CHAOS_HOMEDIR/atl/include/atl.h $CHAOS_HOMEDIR/include/atl.h"
-fi
-if test "$libdir" != '${exec_prefix}/lib'; then
-tmpdir=`echo ${libdir} | sed 's%/$%%'`
-search_list="$tmpdir/atl.h $search_list"
-fi
-if test "$exec_prefix" != "NONE"; then
-tmpdir=`echo ${exec_prefix} | sed 's%/$%%'`
-search_list="$tmpdir/lib/atl.h $search_list"
-fi
-if test "$includedir" != '${prefix}/include'; then
-tmpdir=`echo ${includedir} | sed 's%/$%%'`
-search_list="$tmpdir/atl.h $search_list"
-fi
-if test "$prefix" != "NONE"; then
-tmpdir=`echo ${prefix} | sed 's%/$%%'`
-search_list="$tmpdir/include/atl.h $search_list"
-fi
-if test "include" == "lib"; then
- for tmp_lib_value in $sys_lib_search_path_spec; do
- search_list="$search_list $tmp_lib_value/atl.h"
- done
-fi
-
-search_list="$datatap_dir/atl.h $datatap_dir/lib/atl.h $datatap_dir/include/atl.h $search_list /usr/include/atl.h /usr/local/include/atl.h /opt/atl/include/atl.h /opt/misc/include/atl.h /opt/misc/include/$cercs_cv_archive/atl.h"
-tmp_search_results=""
-echo "configure:30200: searching for $search_list " >&5
-for tmp_search_value in $search_list; do
- if test -r $tmp_search_value; then
- tmp_search_results=$tmp_search_value
- echo "configure:30204: first found $tmp_search_results " >&5
- break
- fi
-done
-
-if test -n "$tmp_search_results"; then
-cercs_tmp=$tmp_search_results
-fi
-
-if test -n "$cercs_tmp" -a "$cercs_tmp" != "/usr/include/atl.h"; then
-cercs_cv_atl_include_arg=-I`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s#.atl.h##g"`
-fi
-
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cercs_cv_atl_include_arg" >&5
-$as_echo "$cercs_cv_atl_include_arg" >&6; }
-if test -n "$cercs_cv_atl_include_arg"; then
-arg="$cercs_cv_atl_include_arg"
-no_dash_arg=`echo $arg | sed 's/^-//g'`
-if test `echo $DT_CPPFLAGS | grep -c "$no_dash_arg"` -eq 0; then
-if test `echo $arg | grep -c "atl"` -eq 0; then
-DT_CPPFLAGS="$DT_CPPFLAGS $arg";
-else
-DT_CPPFLAGS="$arg $DT_CPPFLAGS"
-fi
-fi
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking needed link args for atl package" >&5
-$as_echo_n "checking needed link args for atl package... " >&6; }
-if ${cercs_cv_atl_link_dir+:} false; then :
- $as_echo_n "(cached) " >&6
-else
-
-
-
-
-cercs_tmp=""
-search_list="./libatl.a"
-CHAOS_HOMEDIR=""
-if test -n "$CSH"; then
-CHAOS_HOMEDIR=`echo "echo ~chaos" | csh -sf 2>/dev/null | sed 's%/$%%'` || CHAOS_HOMEDIR=""
-fi
-if test -n "$with_atl"; then
-if test `echo $with_atl | cut -c1` = "~"; then
-EXPANDED=`echo "echo $with_atl" | csh -sf 2>/dev/null` || EXPANDED=""
-else
-EXPANDED=$with_atl
-fi
-
-echo "Datatap = $datatap_dir"
-
-search_list="$datatap_dir/libatl.a $datatap_dir/lib/libatl.a $datatap_dir/include/libatl.a $search_list $EXPANDED/libatl.a $EXPANDED/lib/libatl.a $EXPANDED/share/libatl.a $EXPANDED/$cercs_cv_archive/libatl.a $EXPANDED/$cercs_cv_archive/lib/libatl.a $EXPANDED/atl/libatl.a $EXPANDED/atl/$cercs_cv_archive/libatl.a $EXPANDED/atl/lib/libatl.a $EXPANDED/atl/lib/$cercs_cv_archive/libatl.a"
-fi
-if test -z "$with_installed_specified"; then
-search_list="$search_list `pwd`/../atl/libatl.a `pwd`/../lib/libatl.a `pwd`/../share/libatl.a"
-if test "$CHAOS_HOMEDIR" != "$HOME"; then
-search_list="$search_list $HOME/atl/libatl.a $HOME/$cercs_cv_archive/lib/libatl.a $HOME/lib/libatl.a"
-fi
-fi
-if test -n "$CHAOS_HOMEDIR" -a -n "$cercs_cv_archive"; then
-search_list="$search_list $CHAOS_HOMEDIR/$cercs_cv_archive/atl/lib/libatl.a $CHAOS_HOMEDIR/$cercs_cv_archive/lib/libatl.a $CHAOS_HOMEDIR/atl/$cercs_cv_archive/lib/libatl.a $CHAOS_HOMEDIR/atl/lib/libatl.a $CHAOS_HOMEDIR/lib/libatl.a"
-fi
-if test "$libdir" != '${exec_prefix}/lib'; then
-tmpdir=`echo ${libdir} | sed 's%/$%%'`
-search_list="$tmpdir/libatl.a $search_list"
-fi
-if test "$exec_prefix" != "NONE"; then
-tmpdir=`echo ${exec_prefix} | sed 's%/$%%'`
-search_list="$tmpdir/lib/libatl.a $search_list"
-fi
-if test "$includedir" != '${prefix}/include'; then
-tmpdir=`echo ${includedir} | sed 's%/$%%'`
-search_list="$tmpdir/libatl.a $search_list"
-fi
-if test "$prefix" != "NONE"; then
-tmpdir=`echo ${prefix} | sed 's%/$%%'`
-search_list="$tmpdir/lib/libatl.a $search_list"
-fi
-if test "lib" == "lib"; then
- for tmp_lib_value in $sys_lib_search_path_spec; do
- search_list="$search_list $tmp_lib_value/libatl.a"
- done
-fi
-
-search_list="$datatap_dir/libatl.a $datatap_dir/lib/libatl.a $datatap_dir/include/libatl.a $search_list /usr/lib/libatl.a /usr/local/lib/libatl.a /opt/atl/lib/libatl.a /opt/misc/lib/libatl.a /opt/misc/lib/$cercs_cv_archive/libatl.a"
-tmp_search_results=""
-echo "configure:30292: searching for $search_list " >&5
-for tmp_search_value in $search_list; do
- if test -r $tmp_search_value; then
- tmp_search_results=$tmp_search_value
- echo "configure:30296: first found $tmp_search_results " >&5
- break
- fi
-done
-
-if test -n "$tmp_search_results"; then
-cercs_tmp=$tmp_search_results
-fi
-
-if test -n "$cercs_tmp" -a "$cercs_tmp" != "libatl.a"; then
-cercs_cv_atl_link_dir=`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s/.libatl.a//g"`
-else
-cercs_cv_atl_link_dir=""
-fi
-
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cercs_cv_atl_link_dir" >&5
-$as_echo "$cercs_cv_atl_link_dir" >&6; }
-ld_arg="-L"
-new_flags=$LDFLAGS
-cercs_cv_atl_link_arg=`echo $cercs_cv_atl_link_dir | sed "/./ s/^/$ld_arg/1"`
-if test -n "$cercs_cv_atl_link_arg"; then
-arg=$cercs_cv_atl_link_arg
-no_dash_arg=`echo $arg | sed 's/^-//g'`
-if test `echo $new_flags | grep -c "$no_dash_arg"` -eq 0; then
-root=`echo libatl.a | sed 's/\..*//'`
-if test ! -r $cercs_cv_atl_link_dir/$root.la; then
-if eval "test \"\${LIBTOOL+set}\" = set"; then
-arg="$cercs_cv_atl_link_arg "`echo $cercs_cv_atl_link_dir | sed "/./ s/^/-R/1"`
-fi
-fi
-if test `echo $arg | grep -c "atl"` -eq 0; then
-new_flags="$new_flags $arg"
-else
-new_flags="$arg $new_flags"
-fi
-fi
-DT_LDFLAGS=$new_flags
-fi
-
-
-else
-
-
-
-
-# Check whether --with-atl was given.
-if test "${with_atl+set}" = set; then :
- withval=$with_atl;
-fi
-
-
-if test -n "$with_atl"; then
-unset cercs_cv_atl_include_arg
-unset cercs_cv_atl_link_arg
-if test `echo $with_atl | sed 's/\(.\).*/\1/g'` != "/"; then
-with_atl=`pwd`/$with_atl
-fi
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking needed include args for atl package" >&5
-$as_echo_n "checking needed include args for atl package... " >&6; }
-if ${cercs_cv_atl_include_arg+:} false; then :
- $as_echo_n "(cached) " >&6
-else
-
-
-search_list="$PWD/../atl $PWD/../../atl $PWD/../../../atl"
-tmp_search_results=""
-echo "configure:30365: searching for $search_list " >&5
-for tmp_search_value in $search_list; do
- if test -r $tmp_search_value; then
- tmp_search_results=$tmp_search_value
- echo "configure:30369: first found $tmp_search_results " >&5
- break
- fi
-done
-
-if test -n "$tmp_search_results"; then
-cercs_tmp=$tmp_search_results
-fi
-
-if test -n "$cercs_tmp" -a "$cercs_tmp" != "/usr/include/atl.h"; then
-cercs_cv_atl_include_arg=-I`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s#.atl.h##g"`
-fi
-
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cercs_cv_atl_include_arg" >&5
-$as_echo "$cercs_cv_atl_include_arg" >&6; }
-if test -n "$cercs_cv_atl_include_arg"; then
-arg="$cercs_cv_atl_include_arg"
-no_dash_arg=`echo $arg | sed 's/^-//g'`
-if test `echo $DT_CPPFLAGS | grep -c "$no_dash_arg"` -eq 0; then
-if test `echo $arg | grep -c "atl"` -eq 0; then
-DT_CPPFLAGS="$DT_CPPFLAGS $arg";
-else
-DT_CPPFLAGS="$arg $DT_CPPFLAGS"
-fi
-fi
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking needed link args for atl package" >&5
-$as_echo_n "checking needed link args for atl package... " >&6; }
-if ${cercs_cv_atl_link_dir+:} false; then :
- $as_echo_n "(cached) " >&6
-else
-
-
-search_list="$PWD/../atl $PWD/../../atl $PWD/../../../atl"
-tmp_search_results=""
-echo "configure:30407: searching for $search_list " >&5
-for tmp_search_value in $search_list; do
- if test -r $tmp_search_value; then
- tmp_search_results=$tmp_search_value
- echo "configure:30411: first found $tmp_search_results " >&5
- break
- fi
-done
-
-if test -n "$tmp_search_results"; then
-cercs_tmp=$tmp_search_results
-fi
-
-if test -n "$cercs_tmp" -a "$cercs_tmp" != "libatl.a"; then
-cercs_cv_atl_link_dir=`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s/.libatl.a//g"`
-else
-cercs_cv_atl_link_dir=""
-fi
-
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cercs_cv_atl_link_dir" >&5
-$as_echo "$cercs_cv_atl_link_dir" >&6; }
-ld_arg="-L"
-new_flags=$LDFLAGS
-cercs_cv_atl_link_arg=`echo $cercs_cv_atl_link_dir | sed "/./ s/^/$ld_arg/1"`
-if test -n "$cercs_cv_atl_link_arg"; then
-arg=$cercs_cv_atl_link_arg
-no_dash_arg=`echo $arg | sed 's/^-//g'`
-if test `echo $new_flags | grep -c "$no_dash_arg"` -eq 0; then
-root=`echo libatl.a | sed 's/\..*//'`
-if test ! -r $cercs_cv_atl_link_dir/$root.la; then
-if eval "test \"\${LIBTOOL+set}\" = set"; then
-arg="$cercs_cv_atl_link_arg "`echo $cercs_cv_atl_link_dir | sed "/./ s/^/-R/1"`
-fi
-fi
-if test `echo $arg | grep -c "atl"` -eq 0; then
-new_flags="$new_flags $arg"
-else
-new_flags="$arg $new_flags"
-fi
-fi
-DT_LDFLAGS=$new_flags
-fi
-
-
-fi
-
-
-
-
-if test -z "$with_local_specified"; then
-
-
-
-
-# Check whether --with-dill was given.
-if test "${with_dill+set}" = set; then :
- withval=$with_dill;
-fi
-
-
-if test -n "$with_dill"; then
-unset cercs_cv_dill_include_arg
-unset cercs_cv_dill_link_arg
-if test `echo $with_dill | sed 's/\(.\).*/\1/g'` != "/"; then
-with_dill=`pwd`/$with_dill
-fi
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking needed include args for dill package" >&5
-$as_echo_n "checking needed include args for dill package... " >&6; }
-if ${cercs_cv_dill_include_arg+:} false; then :
- $as_echo_n "(cached) " >&6
-else
-
-
-
-
-cercs_tmp=""
-search_list="./dill.h"
-CHAOS_HOMEDIR=""
-if test -n "$CSH"; then
-CHAOS_HOMEDIR=`echo "echo ~chaos" | csh -sf 2>/dev/null | sed 's%/$%%'` || CHAOS_HOMEDIR=""
-fi
-if test -n "$with_dill"; then
-if test `echo $with_dill | cut -c1` = "~"; then
-EXPANDED=`echo "echo $with_dill" | csh -sf 2>/dev/null` || EXPANDED=""
-else
-EXPANDED=$with_dill
-fi
-
-echo "Datatap = $datatap_dir"
-
-search_list="$datatap_dir/dill.h $datatap_dir/lib/dill.h $datatap_dir/include/dill.h $search_list $EXPANDED/dill.h $EXPANDED/include/dill.h $EXPANDED/share/dill.h $EXPANDED/$cercs_cv_archive/dill.h $EXPANDED/$cercs_cv_archive/include/dill.h $EXPANDED/dill/dill.h $EXPANDED/dill/$cercs_cv_archive/dill.h $EXPANDED/dill/include/dill.h $EXPANDED/dill/include/$cercs_cv_archive/dill.h"
-fi
-if test -z "$with_installed_specified"; then
-search_list="$search_list `pwd`/../dill/dill.h `pwd`/../include/dill.h `pwd`/../share/dill.h"
-if test "$CHAOS_HOMEDIR" != "$HOME"; then
-search_list="$search_list $HOME/dill/dill.h $HOME/$cercs_cv_archive/include/dill.h $HOME/include/dill.h"
-fi
-fi
-if test -n "$CHAOS_HOMEDIR" -a -n "$cercs_cv_archive"; then
-search_list="$search_list $CHAOS_HOMEDIR/$cercs_cv_archive/dill/include/dill.h $CHAOS_HOMEDIR/$cercs_cv_archive/include/dill.h $CHAOS_HOMEDIR/dill/$cercs_cv_archive/include/dill.h $CHAOS_HOMEDIR/dill/include/dill.h $CHAOS_HOMEDIR/include/dill.h"
-fi
-if test "$libdir" != '${exec_prefix}/lib'; then
-tmpdir=`echo ${libdir} | sed 's%/$%%'`
-search_list="$tmpdir/dill.h $search_list"
-fi
-if test "$exec_prefix" != "NONE"; then
-tmpdir=`echo ${exec_prefix} | sed 's%/$%%'`
-search_list="$tmpdir/lib/dill.h $search_list"
-fi
-if test "$includedir" != '${prefix}/include'; then
-tmpdir=`echo ${includedir} | sed 's%/$%%'`
-search_list="$tmpdir/dill.h $search_list"
-fi
-if test "$prefix" != "NONE"; then
-tmpdir=`echo ${prefix} | sed 's%/$%%'`
-search_list="$tmpdir/include/dill.h $search_list"
-fi
-if test "include" == "lib"; then
- for tmp_lib_value in $sys_lib_search_path_spec; do
- search_list="$search_list $tmp_lib_value/dill.h"
- done
-fi
-
-search_list="$datatap_dir/dill.h $datatap_dir/lib/dill.h $datatap_dir/include/dill.h $search_list /usr/include/dill.h /usr/local/include/dill.h /opt/dill/include/dill.h /opt/misc/include/dill.h /opt/misc/include/$cercs_cv_archive/dill.h"
-tmp_search_results=""
-echo "configure:30535: searching for $search_list " >&5
-for tmp_search_value in $search_list; do
- if test -r $tmp_search_value; then
- tmp_search_results=$tmp_search_value
- echo "configure:30539: first found $tmp_search_results " >&5
- break
- fi
-done
-
-if test -n "$tmp_search_results"; then
-cercs_tmp=$tmp_search_results
-fi
-
-if test -n "$cercs_tmp" -a "$cercs_tmp" != "/usr/include/dill.h"; then
-cercs_cv_dill_include_arg=-I`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s#.dill.h##g"`
-fi
-
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cercs_cv_dill_include_arg" >&5
-$as_echo "$cercs_cv_dill_include_arg" >&6; }
-if test -n "$cercs_cv_dill_include_arg"; then
-arg="$cercs_cv_dill_include_arg"
-no_dash_arg=`echo $arg | sed 's/^-//g'`
-if test `echo $DT_CPPFLAGS | grep -c "$no_dash_arg"` -eq 0; then
-if test `echo $arg | grep -c "dill"` -eq 0; then
-DT_CPPFLAGS="$DT_CPPFLAGS $arg";
-else
-DT_CPPFLAGS="$arg $DT_CPPFLAGS"
-fi
-fi
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking needed link args for dill package" >&5
-$as_echo_n "checking needed link args for dill package... " >&6; }
-if ${cercs_cv_dill_link_dir+:} false; then :
- $as_echo_n "(cached) " >&6
-else
-
-
-
-
-cercs_tmp=""
-search_list="./libdill.a"
-CHAOS_HOMEDIR=""
-if test -n "$CSH"; then
-CHAOS_HOMEDIR=`echo "echo ~chaos" | csh -sf 2>/dev/null | sed 's%/$%%'` || CHAOS_HOMEDIR=""
-fi
-if test -n "$with_dill"; then
-if test `echo $with_dill | cut -c1` = "~"; then
-EXPANDED=`echo "echo $with_dill" | csh -sf 2>/dev/null` || EXPANDED=""
-else
-EXPANDED=$with_dill
-fi
-
-echo "Datatap = $datatap_dir"
-
-search_list="$datatap_dir/libdill.a $datatap_dir/lib/libdill.a $datatap_dir/include/libdill.a $search_list $EXPANDED/libdill.a $EXPANDED/lib/libdill.a $EXPANDED/share/libdill.a $EXPANDED/$cercs_cv_archive/libdill.a $EXPANDED/$cercs_cv_archive/lib/libdill.a $EXPANDED/dill/libdill.a $EXPANDED/dill/$cercs_cv_archive/libdill.a $EXPANDED/dill/lib/libdill.a $EXPANDED/dill/lib/$cercs_cv_archive/libdill.a"
-fi
-if test -z "$with_installed_specified"; then
-search_list="$search_list `pwd`/../dill/libdill.a `pwd`/../lib/libdill.a `pwd`/../share/libdill.a"
-if test "$CHAOS_HOMEDIR" != "$HOME"; then
-search_list="$search_list $HOME/dill/libdill.a $HOME/$cercs_cv_archive/lib/libdill.a $HOME/lib/libdill.a"
-fi
-fi
-if test -n "$CHAOS_HOMEDIR" -a -n "$cercs_cv_archive"; then
-search_list="$search_list $CHAOS_HOMEDIR/$cercs_cv_archive/dill/lib/libdill.a $CHAOS_HOMEDIR/$cercs_cv_archive/lib/libdill.a $CHAOS_HOMEDIR/dill/$cercs_cv_archive/lib/libdill.a $CHAOS_HOMEDIR/dill/lib/libdill.a $CHAOS_HOMEDIR/lib/libdill.a"
-fi
-if test "$libdir" != '${exec_prefix}/lib'; then
-tmpdir=`echo ${libdir} | sed 's%/$%%'`
-search_list="$tmpdir/libdill.a $search_list"
-fi
-if test "$exec_prefix" != "NONE"; then
-tmpdir=`echo ${exec_prefix} | sed 's%/$%%'`
-search_list="$tmpdir/lib/libdill.a $search_list"
-fi
-if test "$includedir" != '${prefix}/include'; then
-tmpdir=`echo ${includedir} | sed 's%/$%%'`
-search_list="$tmpdir/libdill.a $search_list"
-fi
-if test "$prefix" != "NONE"; then
-tmpdir=`echo ${prefix} | sed 's%/$%%'`
-search_list="$tmpdir/lib/libdill.a $search_list"
-fi
-if test "lib" == "lib"; then
- for tmp_lib_value in $sys_lib_search_path_spec; do
- search_list="$search_list $tmp_lib_value/libdill.a"
- done
-fi
-
-search_list="$datatap_dir/libdill.a $datatap_dir/lib/libdill.a $datatap_dir/include/libdill.a $search_list /usr/lib/libdill.a /usr/local/lib/libdill.a /opt/dill/lib/libdill.a /opt/misc/lib/libdill.a /opt/misc/lib/$cercs_cv_archive/libdill.a"
-tmp_search_results=""
-echo "configure:30627: searching for $search_list " >&5
-for tmp_search_value in $search_list; do
- if test -r $tmp_search_value; then
- tmp_search_results=$tmp_search_value
- echo "configure:30631: first found $tmp_search_results " >&5
- break
- fi
-done
-
-if test -n "$tmp_search_results"; then
-cercs_tmp=$tmp_search_results
-fi
-
-if test -n "$cercs_tmp" -a "$cercs_tmp" != "libdill.a"; then
-cercs_cv_dill_link_dir=`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s/.libdill.a//g"`
-else
-cercs_cv_dill_link_dir=""
-fi
-
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cercs_cv_dill_link_dir" >&5
-$as_echo "$cercs_cv_dill_link_dir" >&6; }
-ld_arg="-L"
-new_flags=$LDFLAGS
-cercs_cv_dill_link_arg=`echo $cercs_cv_dill_link_dir | sed "/./ s/^/$ld_arg/1"`
-if test -n "$cercs_cv_dill_link_arg"; then
-arg=$cercs_cv_dill_link_arg
-no_dash_arg=`echo $arg | sed 's/^-//g'`
-if test `echo $new_flags | grep -c "$no_dash_arg"` -eq 0; then
-root=`echo libdill.a | sed 's/\..*//'`
-if test ! -r $cercs_cv_dill_link_dir/$root.la; then
-if eval "test \"\${LIBTOOL+set}\" = set"; then
-arg="$cercs_cv_dill_link_arg "`echo $cercs_cv_dill_link_dir | sed "/./ s/^/-R/1"`
-fi
-fi
-if test `echo $arg | grep -c "dill"` -eq 0; then
-new_flags="$new_flags $arg"
-else
-new_flags="$arg $new_flags"
-fi
-fi
-DT_LDFLAGS=$new_flags
-fi
-
-
-else
-
-
-
-
-# Check whether --with-dill was given.
-if test "${with_dill+set}" = set; then :
- withval=$with_dill;
-fi
-
-
-if test -n "$with_dill"; then
-unset cercs_cv_dill_include_arg
-unset cercs_cv_dill_link_arg
-if test `echo $with_dill | sed 's/\(.\).*/\1/g'` != "/"; then
-with_dill=`pwd`/$with_dill
-fi
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking needed include args for dill package" >&5
-$as_echo_n "checking needed include args for dill package... " >&6; }
-if ${cercs_cv_dill_include_arg+:} false; then :
- $as_echo_n "(cached) " >&6
-else
-
-
-search_list="$PWD/../dill $PWD/../../dill $PWD/../../../dill"
-tmp_search_results=""
-echo "configure:30700: searching for $search_list " >&5
-for tmp_search_value in $search_list; do
- if test -r $tmp_search_value; then
- tmp_search_results=$tmp_search_value
- echo "configure:30704: first found $tmp_search_results " >&5
- break
- fi
-done
-
-if test -n "$tmp_search_results"; then
-cercs_tmp=$tmp_search_results
-fi
-
-if test -n "$cercs_tmp" -a "$cercs_tmp" != "/usr/include/dill.h"; then
-cercs_cv_dill_include_arg=-I`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s#.dill.h##g"`
-fi
-
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cercs_cv_dill_include_arg" >&5
-$as_echo "$cercs_cv_dill_include_arg" >&6; }
-if test -n "$cercs_cv_dill_include_arg"; then
-arg="$cercs_cv_dill_include_arg"
-no_dash_arg=`echo $arg | sed 's/^-//g'`
-if test `echo $DT_CPPFLAGS | grep -c "$no_dash_arg"` -eq 0; then
-if test `echo $arg | grep -c "dill"` -eq 0; then
-DT_CPPFLAGS="$DT_CPPFLAGS $arg";
-else
-DT_CPPFLAGS="$arg $DT_CPPFLAGS"
-fi
-fi
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking needed link args for dill package" >&5
-$as_echo_n "checking needed link args for dill package... " >&6; }
-if ${cercs_cv_dill_link_dir+:} false; then :
- $as_echo_n "(cached) " >&6
-else
-
-
-search_list="$PWD/../dill $PWD/../../dill $PWD/../../../dill"
-tmp_search_results=""
-echo "configure:30742: searching for $search_list " >&5
-for tmp_search_value in $search_list; do
- if test -r $tmp_search_value; then
- tmp_search_results=$tmp_search_value
- echo "configure:30746: first found $tmp_search_results " >&5
- break
- fi
-done
-
-if test -n "$tmp_search_results"; then
-cercs_tmp=$tmp_search_results
-fi
-
-if test -n "$cercs_tmp" -a "$cercs_tmp" != "libdill.a"; then
-cercs_cv_dill_link_dir=`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s/.libdill.a//g"`
-else
-cercs_cv_dill_link_dir=""
-fi
-
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cercs_cv_dill_link_dir" >&5
-$as_echo "$cercs_cv_dill_link_dir" >&6; }
-ld_arg="-L"
-new_flags=$LDFLAGS
-cercs_cv_dill_link_arg=`echo $cercs_cv_dill_link_dir | sed "/./ s/^/$ld_arg/1"`
-if test -n "$cercs_cv_dill_link_arg"; then
-arg=$cercs_cv_dill_link_arg
-no_dash_arg=`echo $arg | sed 's/^-//g'`
-if test `echo $new_flags | grep -c "$no_dash_arg"` -eq 0; then
-root=`echo libdill.a | sed 's/\..*//'`
-if test ! -r $cercs_cv_dill_link_dir/$root.la; then
-if eval "test \"\${LIBTOOL+set}\" = set"; then
-arg="$cercs_cv_dill_link_arg "`echo $cercs_cv_dill_link_dir | sed "/./ s/^/-R/1"`
-fi
-fi
-if test `echo $arg | grep -c "dill"` -eq 0; then
-new_flags="$new_flags $arg"
-else
-new_flags="$arg $new_flags"
-fi
-fi
-DT_LDFLAGS=$new_flags
-fi
-
-
-fi
-
-
-
-
-if test -z "$with_local_specified"; then
-
-
-
-
-# Check whether --with-cercs_env was given.
-if test "${with_cercs_env+set}" = set; then :
- withval=$with_cercs_env;
-fi
-
-
-if test -n "$with_cercs_env"; then
-unset cercs_cv_cercs_env_include_arg
-unset cercs_cv_cercs_env_link_arg
-if test `echo $with_cercs_env | sed 's/\(.\).*/\1/g'` != "/"; then
-with_cercs_env=`pwd`/$with_cercs_env
-fi
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking needed include args for cercs_env package" >&5
-$as_echo_n "checking needed include args for cercs_env package... " >&6; }
-if ${cercs_cv_cercs_env_include_arg+:} false; then :
- $as_echo_n "(cached) " >&6
-else
-
-
-
-
-cercs_tmp=""
-search_list="./cercs_env.h"
-CHAOS_HOMEDIR=""
-if test -n "$CSH"; then
-CHAOS_HOMEDIR=`echo "echo ~chaos" | csh -sf 2>/dev/null | sed 's%/$%%'` || CHAOS_HOMEDIR=""
-fi
-if test -n "$with_cercs_env"; then
-if test `echo $with_cercs_env | cut -c1` = "~"; then
-EXPANDED=`echo "echo $with_cercs_env" | csh -sf 2>/dev/null` || EXPANDED=""
-else
-EXPANDED=$with_cercs_env
-fi
-
-echo "Datatap = $datatap_dir"
-
-search_list="$datatap_dir/cercs_env.h $datatap_dir/lib/cercs_env.h $datatap_dir/include/cercs_env.h $search_list $EXPANDED/cercs_env.h $EXPANDED/include/cercs_env.h $EXPANDED/share/cercs_env.h $EXPANDED/$cercs_cv_archive/cercs_env.h $EXPANDED/$cercs_cv_archive/include/cercs_env.h $EXPANDED/cercs_env/cercs_env.h $EXPANDED/cercs_env/$cercs_cv_archive/cercs_env.h $EXPANDED/cercs_env/include/cercs_env.h $EXPANDED/cercs_env/include/$cercs_cv_archive/cercs_env.h"
-fi
-if test -z "$with_installed_specified"; then
-search_list="$search_list `pwd`/../cercs_env/cercs_env.h `pwd`/../include/cercs_env.h `pwd`/../share/cercs_env.h"
-if test "$CHAOS_HOMEDIR" != "$HOME"; then
-search_list="$search_list $HOME/cercs_env/cercs_env.h $HOME/$cercs_cv_archive/include/cercs_env.h $HOME/include/cercs_env.h"
-fi
-fi
-if test -n "$CHAOS_HOMEDIR" -a -n "$cercs_cv_archive"; then
-search_list="$search_list $CHAOS_HOMEDIR/$cercs_cv_archive/cercs_env/include/cercs_env.h $CHAOS_HOMEDIR/$cercs_cv_archive/include/cercs_env.h $CHAOS_HOMEDIR/cercs_env/$cercs_cv_archive/include/cercs_env.h $CHAOS_HOMEDIR/cercs_env/include/cercs_env.h $CHAOS_HOMEDIR/include/cercs_env.h"
-fi
-if test "$libdir" != '${exec_prefix}/lib'; then
-tmpdir=`echo ${libdir} | sed 's%/$%%'`
-search_list="$tmpdir/cercs_env.h $search_list"
-fi
-if test "$exec_prefix" != "NONE"; then
-tmpdir=`echo ${exec_prefix} | sed 's%/$%%'`
-search_list="$tmpdir/lib/cercs_env.h $search_list"
-fi
-if test "$includedir" != '${prefix}/include'; then
-tmpdir=`echo ${includedir} | sed 's%/$%%'`
-search_list="$tmpdir/cercs_env.h $search_list"
-fi
-if test "$prefix" != "NONE"; then
-tmpdir=`echo ${prefix} | sed 's%/$%%'`
-search_list="$tmpdir/include/cercs_env.h $search_list"
-fi
-if test "include" == "lib"; then
- for tmp_lib_value in $sys_lib_search_path_spec; do
- search_list="$search_list $tmp_lib_value/cercs_env.h"
- done
-fi
-
-search_list="$datatap_dir/cercs_env.h $datatap_dir/lib/cercs_env.h $datatap_dir/include/cercs_env.h $search_list /usr/include/cercs_env.h /usr/local/include/cercs_env.h /opt/cercs_env/include/cercs_env.h /opt/misc/include/cercs_env.h /opt/misc/include/$cercs_cv_archive/cercs_env.h"
-tmp_search_results=""
-echo "configure:30870: searching for $search_list " >&5
-for tmp_search_value in $search_list; do
- if test -r $tmp_search_value; then
- tmp_search_results=$tmp_search_value
- echo "configure:30874: first found $tmp_search_results " >&5
- break
- fi
-done
-
-if test -n "$tmp_search_results"; then
-cercs_tmp=$tmp_search_results
-fi
-
-if test -n "$cercs_tmp" -a "$cercs_tmp" != "/usr/include/cercs_env.h"; then
-cercs_cv_cercs_env_include_arg=-I`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s#.cercs_env.h##g"`
-fi
-
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cercs_cv_cercs_env_include_arg" >&5
-$as_echo "$cercs_cv_cercs_env_include_arg" >&6; }
-if test -n "$cercs_cv_cercs_env_include_arg"; then
-arg="$cercs_cv_cercs_env_include_arg"
-no_dash_arg=`echo $arg | sed 's/^-//g'`
-if test `echo $DT_CPPFLAGS | grep -c "$no_dash_arg"` -eq 0; then
-if test `echo $arg | grep -c "cercs_env"` -eq 0; then
-DT_CPPFLAGS="$DT_CPPFLAGS $arg";
-else
-DT_CPPFLAGS="$arg $DT_CPPFLAGS"
-fi
-fi
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking needed link args for cercs_env package" >&5
-$as_echo_n "checking needed link args for cercs_env package... " >&6; }
-if ${cercs_cv_cercs_env_link_dir+:} false; then :
- $as_echo_n "(cached) " >&6
-else
-
-
-
-
-cercs_tmp=""
-search_list="./libcercs_env.a"
-CHAOS_HOMEDIR=""
-if test -n "$CSH"; then
-CHAOS_HOMEDIR=`echo "echo ~chaos" | csh -sf 2>/dev/null | sed 's%/$%%'` || CHAOS_HOMEDIR=""
-fi
-if test -n "$with_cercs_env"; then
-if test `echo $with_cercs_env | cut -c1` = "~"; then
-EXPANDED=`echo "echo $with_cercs_env" | csh -sf 2>/dev/null` || EXPANDED=""
-else
-EXPANDED=$with_cercs_env
-fi
-
-echo "Datatap = $datatap_dir"
-
-search_list="$datatap_dir/libcercs_env.a $datatap_dir/lib/libcercs_env.a $datatap_dir/include/libcercs_env.a $search_list $EXPANDED/libcercs_env.a $EXPANDED/lib/libcercs_env.a $EXPANDED/share/libcercs_env.a $EXPANDED/$cercs_cv_archive/libcercs_env.a $EXPANDED/$cercs_cv_archive/lib/libcercs_env.a $EXPANDED/cercs_env/libcercs_env.a $EXPANDED/cercs_env/$cercs_cv_archive/libcercs_env.a $EXPANDED/cercs_env/lib/libcercs_env.a $EXPANDED/cercs_env/lib/$cercs_cv_archive/libcercs_env.a"
-fi
-if test -z "$with_installed_specified"; then
-search_list="$search_list `pwd`/../cercs_env/libcercs_env.a `pwd`/../lib/libcercs_env.a `pwd`/../share/libcercs_env.a"
-if test "$CHAOS_HOMEDIR" != "$HOME"; then
-search_list="$search_list $HOME/cercs_env/libcercs_env.a $HOME/$cercs_cv_archive/lib/libcercs_env.a $HOME/lib/libcercs_env.a"
-fi
-fi
-if test -n "$CHAOS_HOMEDIR" -a -n "$cercs_cv_archive"; then
-search_list="$search_list $CHAOS_HOMEDIR/$cercs_cv_archive/cercs_env/lib/libcercs_env.a $CHAOS_HOMEDIR/$cercs_cv_archive/lib/libcercs_env.a $CHAOS_HOMEDIR/cercs_env/$cercs_cv_archive/lib/libcercs_env.a $CHAOS_HOMEDIR/cercs_env/lib/libcercs_env.a $CHAOS_HOMEDIR/lib/libcercs_env.a"
-fi
-if test "$libdir" != '${exec_prefix}/lib'; then
-tmpdir=`echo ${libdir} | sed 's%/$%%'`
-search_list="$tmpdir/libcercs_env.a $search_list"
-fi
-if test "$exec_prefix" != "NONE"; then
-tmpdir=`echo ${exec_prefix} | sed 's%/$%%'`
-search_list="$tmpdir/lib/libcercs_env.a $search_list"
-fi
-if test "$includedir" != '${prefix}/include'; then
-tmpdir=`echo ${includedir} | sed 's%/$%%'`
-search_list="$tmpdir/libcercs_env.a $search_list"
-fi
-if test "$prefix" != "NONE"; then
-tmpdir=`echo ${prefix} | sed 's%/$%%'`
-search_list="$tmpdir/lib/libcercs_env.a $search_list"
-fi
-if test "lib" == "lib"; then
- for tmp_lib_value in $sys_lib_search_path_spec; do
- search_list="$search_list $tmp_lib_value/libcercs_env.a"
- done
-fi
-
-search_list="$datatap_dir/libcercs_env.a $datatap_dir/lib/libcercs_env.a $datatap_dir/include/libcercs_env.a $search_list /usr/lib/libcercs_env.a /usr/local/lib/libcercs_env.a /opt/cercs_env/lib/libcercs_env.a /opt/misc/lib/libcercs_env.a /opt/misc/lib/$cercs_cv_archive/libcercs_env.a"
-tmp_search_results=""
-echo "configure:30962: searching for $search_list " >&5
-for tmp_search_value in $search_list; do
- if test -r $tmp_search_value; then
- tmp_search_results=$tmp_search_value
- echo "configure:30966: first found $tmp_search_results " >&5
- break
- fi
-done
-
-if test -n "$tmp_search_results"; then
-cercs_tmp=$tmp_search_results
-fi
-
-if test -n "$cercs_tmp" -a "$cercs_tmp" != "libcercs_env.a"; then
-cercs_cv_cercs_env_link_dir=`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s/.libcercs_env.a//g"`
-else
-cercs_cv_cercs_env_link_dir=""
-fi
-
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cercs_cv_cercs_env_link_dir" >&5
-$as_echo "$cercs_cv_cercs_env_link_dir" >&6; }
-ld_arg="-L"
-new_flags=$LDFLAGS
-cercs_cv_cercs_env_link_arg=`echo $cercs_cv_cercs_env_link_dir | sed "/./ s/^/$ld_arg/1"`
-if test -n "$cercs_cv_cercs_env_link_arg"; then
-arg=$cercs_cv_cercs_env_link_arg
-no_dash_arg=`echo $arg | sed 's/^-//g'`
-if test `echo $new_flags | grep -c "$no_dash_arg"` -eq 0; then
-root=`echo libcercs_env.a | sed 's/\..*//'`
-if test ! -r $cercs_cv_cercs_env_link_dir/$root.la; then
-if eval "test \"\${LIBTOOL+set}\" = set"; then
-arg="$cercs_cv_cercs_env_link_arg "`echo $cercs_cv_cercs_env_link_dir | sed "/./ s/^/-R/1"`
-fi
-fi
-if test `echo $arg | grep -c "cercs_env"` -eq 0; then
-new_flags="$new_flags $arg"
-else
-new_flags="$arg $new_flags"
-fi
-fi
-DT_LDFLAGS=$new_flags
-fi
-
-
-else
-
-
-
-
-# Check whether --with-cercs_env was given.
-if test "${with_cercs_env+set}" = set; then :
- withval=$with_cercs_env;
-fi
-
-
-if test -n "$with_cercs_env"; then
-unset cercs_cv_cercs_env_include_arg
-unset cercs_cv_cercs_env_link_arg
-if test `echo $with_cercs_env | sed 's/\(.\).*/\1/g'` != "/"; then
-with_cercs_env=`pwd`/$with_cercs_env
-fi
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking needed include args for cercs_env package" >&5
-$as_echo_n "checking needed include args for cercs_env package... " >&6; }
-if ${cercs_cv_cercs_env_include_arg+:} false; then :
- $as_echo_n "(cached) " >&6
-else
-
-
-search_list="$PWD/../cercs_env $PWD/../../cercs_env $PWD/../../../cercs_env"
-tmp_search_results=""
-echo "configure:31035: searching for $search_list " >&5
-for tmp_search_value in $search_list; do
- if test -r $tmp_search_value; then
- tmp_search_results=$tmp_search_value
- echo "configure:31039: first found $tmp_search_results " >&5
- break
- fi
-done
-
-if test -n "$tmp_search_results"; then
-cercs_tmp=$tmp_search_results
-fi
-
-if test -n "$cercs_tmp" -a "$cercs_tmp" != "/usr/include/cercs_env.h"; then
-cercs_cv_cercs_env_include_arg=-I`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s#.cercs_env.h##g"`
-fi
-
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cercs_cv_cercs_env_include_arg" >&5
-$as_echo "$cercs_cv_cercs_env_include_arg" >&6; }
-if test -n "$cercs_cv_cercs_env_include_arg"; then
-arg="$cercs_cv_cercs_env_include_arg"
-no_dash_arg=`echo $arg | sed 's/^-//g'`
-if test `echo $DT_CPPFLAGS | grep -c "$no_dash_arg"` -eq 0; then
-if test `echo $arg | grep -c "cercs_env"` -eq 0; then
-DT_CPPFLAGS="$DT_CPPFLAGS $arg";
-else
-DT_CPPFLAGS="$arg $DT_CPPFLAGS"
-fi
-fi
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking needed link args for cercs_env package" >&5
-$as_echo_n "checking needed link args for cercs_env package... " >&6; }
-if ${cercs_cv_cercs_env_link_dir+:} false; then :
- $as_echo_n "(cached) " >&6
-else
-
-
-search_list="$PWD/../cercs_env $PWD/../../cercs_env $PWD/../../../cercs_env"
-tmp_search_results=""
-echo "configure:31077: searching for $search_list " >&5
-for tmp_search_value in $search_list; do
- if test -r $tmp_search_value; then
- tmp_search_results=$tmp_search_value
- echo "configure:31081: first found $tmp_search_results " >&5
- break
- fi
-done
-
-if test -n "$tmp_search_results"; then
-cercs_tmp=$tmp_search_results
-fi
-
-if test -n "$cercs_tmp" -a "$cercs_tmp" != "libcercs_env.a"; then
-cercs_cv_cercs_env_link_dir=`$PATHPROG $cercs_tmp | sed 's#\\\\#/#g' | sed "s/.libcercs_env.a//g"`
-else
-cercs_cv_cercs_env_link_dir=""
-fi
-
-fi
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cercs_cv_cercs_env_link_dir" >&5
-$as_echo "$cercs_cv_cercs_env_link_dir" >&6; }
-ld_arg="-L"
-new_flags=$LDFLAGS
-cercs_cv_cercs_env_link_arg=`echo $cercs_cv_cercs_env_link_dir | sed "/./ s/^/$ld_arg/1"`
-if test -n "$cercs_cv_cercs_env_link_arg"; then
-arg=$cercs_cv_cercs_env_link_arg
-no_dash_arg=`echo $arg | sed 's/^-//g'`
-if test `echo $new_flags | grep -c "$no_dash_arg"` -eq 0; then
-root=`echo libcercs_env.a | sed 's/\..*//'`
-if test ! -r $cercs_cv_cercs_env_link_dir/$root.la; then
-if eval "test \"\${LIBTOOL+set}\" = set"; then
-arg="$cercs_cv_cercs_env_link_arg "`echo $cercs_cv_cercs_env_link_dir | sed "/./ s/^/-R/1"`
-fi
-fi
-if test `echo $arg | grep -c "cercs_env"` -eq 0; then
-new_flags="$new_flags $arg"
-else
-new_flags="$arg $new_flags"
-fi
-fi
-DT_LDFLAGS=$new_flags
-fi
-
-
-fi
-
-
-
- if test -n "$cercs_cv_evpath_link_dir" -a -n "$cercs_cv_evpath_include_arg";then
- FP_LDFLAGS="$FP_LDFLAGS -L$cercs_cv_evpath_link_dir"
- FP_LIBS="$FP_LIBS -levpath"
- FP_CFLAGS="$FP_CFLAGS $cercs_cv_evpath_include_arg"
- FP_CPPFLAGS="$FP_CPPFLAGS $cercs_cv_evpath_include_arg"
- else
- echo "FLEXPATH couldn't find evpath - Not building flexpath"
- ac_flexpath_ok=no
- fi
- if test -n "$cercs_cv_ffs_link_dir" -a -n "$cercs_cv_ffs_include_arg"; then
- FP_LDFLAGS="$FP_LDFLAGS -L$cercs_cv_ffs_link_dir"
- FP_LIBS="$FP_LIBS -lffs"
- FP_CFLAGS="$FP_CFLAGS $cercs_cv_ffs_include_arg"
- FP_CPPFLAGS="$FP_CPPFLAGS $cercs_cv_ffs_include_arg"
- else
- echo "FLEXPATH couldn't find ffs - Not building flexpath"
- ac_flexpath_ok=no
- fi
- if test -n "$cercs_cv_atl_link_dir" -a -n "$cercs_cv_atl_include_arg"; then
- FP_LDFLAGS="$FP_LDFLAGS -L$cercs_cv_atl_link_dir"
- FP_LIBS="$FP_LIBS -latl"
- FP_CFLAGS="$FP_CFLAGS $cercs_cv_atl_include_arg"
- FP_CPPFLAGS="$FP_CPPFLAGS $cercs_cv_atl_include_arg"
- else
- ac_flexpath_ok=no
- echo "FLEXPATH couldn't find atl - Not building flexpath"
- fi
- if test -n "$cercs_cv_dill_link_dir" -a -n "$cercs_cv_dill_include_arg"; then
- FP_LDFLAGS="$FP_LDFLAGS -L$cercs_cv_dill_link_dir"
- FP_LIBS="$FP_LIBS -ldill"
- FP_CFLAGS="$FP_CFLAGS $cercs_cv_dill_include_arg"
- FP_CPPFLAGS="$FP_CPPFLAGS $cercs_cv_dill_include_arg"
- else
- ac_flexpath_ok=no
- echo "FLEXPATH couldn't find dill - Not building flexpath"
- fi
- if test -n "$cercs_cv_cercs_env_link_dir" -a -n "$cercs_cv_cercs_env_include_arg"; then
- FP_LDFLAGS="$FP_LDFLAGS -L$cercs_cv_cercs_env_link_dir"
- FP_LIBS="$FP_LIBS -lcercs_env"
- FP_CFLAGS="$FP_CFLAGS $cercs_cv_cercs_env_include_arg"
- FP_CPPFLAGS="$FP_CPPFLAGS $cercs_cv_cercs_env_include_arg"
- else
- ac_flexpath_ok=no
- echo "FLEXPATH couldn't find cercs_env - Not building flexpath"
- fi
-
-fi
-
-
-
-
-
-
-if test "x$ac_flexpath_ok" = "xyes"; then
- HAVE_FLEXPATH=1
- NO_FLEXPATH=0
-else
- HAVE_FLEXPATH=0
- NO_FLEXPATH=1
-fi
- if test "x$ac_flexpath_ok" = "xyes"; then
- HAVE_FLEXPATH_TRUE=
- HAVE_FLEXPATH_FALSE='#'
-else
- HAVE_FLEXPATH_TRUE='#'
- HAVE_FLEXPATH_FALSE=
-fi
-
-
-cat >>confdefs.h <<_ACEOF
-#define NO_FLEXPATH $NO_FLEXPATH
-_ACEOF
-
-
-cat >>confdefs.h <<_ACEOF
-#define HAVE_FLEXPATH $HAVE_FLEXPATH
-_ACEOF
-
-
-
-
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: === checking for ZLIB ===" >&5
-$as_echo "$as_me: === checking for ZLIB ===" >&6;}
-
- if true; then
- HAVE_ZLIB_TRUE=
- HAVE_ZLIB_FALSE='#'
-else
- HAVE_ZLIB_TRUE='#'
- HAVE_ZLIB_FALSE=
-fi
-
-
-
-# Check whether --with-zlib was given.
-if test "${with_zlib+set}" = set; then :
- withval=$with_zlib; :
-else
- with_zlib=no
-fi
-
-
-if test "x$with_zlib" == "xno"; then
-
- if false; then
- HAVE_ZLIB_TRUE=
- HAVE_ZLIB_FALSE='#'
-else
- HAVE_ZLIB_TRUE='#'
- HAVE_ZLIB_FALSE=
-fi
-
-
-else
-
- save_CPPFLAGS="$CPPFLAGS"
- save_LIBS="$LIBS"
- save_LDFLAGS="$LDFLAGS"
-
- if test "x$with_zlib" == "xyes"; then
- ZLIB_CPPFLAGS=""
- ZLIB_LDFLAGS=""
- ZLIB_LIBS="-lz"
- else
- ZLIB_CPPFLAGS="-I$withval/include"
- ZLIB_LDFLAGS="-L$withval/lib64"
- ZLIB_LIBS="-lz"
- fi
-
- LIBS="$LIBS $ZLIB_LIBS"
- LDFLAGS="$LDFLAGS $ZLIB_LDFLAGS"
- CPPFLAGS="$CPPFLAGS $ZLIB_CPPFLAGS"
-
- for ac_header in zlib.h
-do :
- ac_fn_c_check_header_mongrel "$LINENO" "zlib.h" "ac_cv_header_zlib_h" "$ac_includes_default"
-if test "x$ac_cv_header_zlib_h" = xyes; then :
- cat >>confdefs.h <<_ACEOF
-#define HAVE_ZLIB_H 1
-_ACEOF
-
-else
- if false; then
- HAVE_ZLIB_TRUE=
- HAVE_ZLIB_FALSE='#'
-else
- HAVE_ZLIB_TRUE='#'
- HAVE_ZLIB_FALSE=
-fi
-
-fi
-
-done
-
-
- if test -z "${HAVE_ZLIB_TRUE}"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking if zlib code can be linked with $ZLIB_LDFLAGS" >&5
-$as_echo_n "checking if zlib code can be linked with $ZLIB_LDFLAGS... " >&6; }
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#include <stdlib.h>
- #include "zlib.h"
-#ifdef FC_DUMMY_MAIN
-#ifndef FC_DUMMY_MAIN_EQ_F77
-# ifdef __cplusplus
- extern "C"
-# endif
- int FC_DUMMY_MAIN() { return 1; }
-#endif
-#endif
-int
-main ()
-{
-Bytef* in, *out;
- uLongf in_len, *out_len;
- int level = 5;
- int zerr = compress2 (out, out_len, in, in_len, level);
- return (zerr != Z_OK);
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-$as_echo "yes" >&6; }
-else
- if false; then
- HAVE_ZLIB_TRUE=
- HAVE_ZLIB_FALSE='#'
-else
- HAVE_ZLIB_TRUE='#'
- HAVE_ZLIB_FALSE=
-fi
-
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }
-
-fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext conftest.$ac_ext
-
- if test -z "${HAVE_ZLIB_FALSE}"; then
- if test "x$with_lustre" != "xyes"; then
- ZLIB_LDFLAGS="-L$withval/lib"
- LDFLAGS="$LDFLAGS $ZLIB_LDFLAGS"
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking if zlib code can be linked with $ZLIB_LDFLAGS" >&5
-$as_echo_n "checking if zlib code can be linked with $ZLIB_LDFLAGS... " >&6; }
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#include <stdlib.h>
- #include "zlib.h"
-#ifdef FC_DUMMY_MAIN
-#ifndef FC_DUMMY_MAIN_EQ_F77
-# ifdef __cplusplus
- extern "C"
-# endif
- int FC_DUMMY_MAIN() { return 1; }
-#endif
-#endif
-int
-main ()
-{
-Bytef* in, *out;
- uLongf in_len, *out_len;
- int level = 5;
- int zerr = compress2 (out, out_len, in, in_len, level);
- return (zerr != Z_OK);
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-$as_echo "yes" >&6; }
-else
- if false; then
- HAVE_ZLIB_TRUE=
- HAVE_ZLIB_FALSE='#'
-else
- HAVE_ZLIB_TRUE='#'
- HAVE_ZLIB_FALSE=
-fi
-
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }
-
-fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext conftest.$ac_ext
- fi
- fi
- fi
-
- LIBS="$save_LIBS"
- LDFLAGS="$save_LDFLAGS"
- CPPFLAGS="$save_CPPFLAGS"
-
-
-
-
-
- # Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND:
- if test -z "${HAVE_ZLIB_TRUE}"; then
-
-$as_echo "#define HAVE_ZLIB 1" >>confdefs.h
-
- :
- else
-
- :
- fi
-fi
-
-
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: === checking for BZIP2 ===" >&5
-$as_echo "$as_me: === checking for BZIP2 ===" >&6;}
-
- if true; then
- HAVE_BZIP2_TRUE=
- HAVE_BZIP2_FALSE='#'
-else
- HAVE_BZIP2_TRUE='#'
- HAVE_BZIP2_FALSE=
-fi
-
-
-
-# Check whether --with-bzip2 was given.
-if test "${with_bzip2+set}" = set; then :
- withval=$with_bzip2; :
-else
- with_bzip2=no
-fi
-
-
-if test "x$with_bzip2" == "xno"; then
-
- if false; then
- HAVE_BZIP2_TRUE=
- HAVE_BZIP2_FALSE='#'
-else
- HAVE_BZIP2_TRUE='#'
- HAVE_BZIP2_FALSE=
+
+
+if test "x$with_bzip2" == "xno"; then
+
+ if false; then
+ HAVE_BZIP2_TRUE=
+ HAVE_BZIP2_FALSE='#'
+else
+ HAVE_BZIP2_TRUE='#'
+ HAVE_BZIP2_FALSE=
fi
@@ -31557,6 +30256,15 @@ _ACEOF
if ac_fn_c_try_link "$LINENO"; then :
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
$as_echo "yes" >&6; }
+ if true; then
+ HAVE_BZIP2_TRUE=
+ HAVE_BZIP2_FALSE='#'
+else
+ HAVE_BZIP2_TRUE='#'
+ HAVE_BZIP2_FALSE=
+fi
+
+
else
if false; then
HAVE_BZIP2_TRUE=
@@ -32084,6 +30792,107 @@ fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: === checking for LZ4 ===" >&5
+$as_echo "$as_me: === checking for LZ4 ===" >&6;}
+
+ if true; then
+ HAVE_LZ4_TRUE=
+ HAVE_LZ4_FALSE='#'
+else
+ HAVE_LZ4_TRUE='#'
+ HAVE_LZ4_FALSE=
+fi
+
+
+
+# Check whether --with-lz4 was given.
+if test "${with_lz4+set}" = set; then :
+ withval=$with_lz4; :
+else
+ with_lz4=no
+fi
+
+
+if test "x$with_lz4" == "xno"; then
+
+ if false; then
+ HAVE_LZ4_TRUE=
+ HAVE_LZ4_FALSE='#'
+else
+ HAVE_LZ4_TRUE='#'
+ HAVE_LZ4_FALSE=
+fi
+
+
+else
+
+ save_CFLAGS="$CFLAGS"
+ save_LIBS="$LIBS"
+ save_LDFLAGS="$LDFLAGS"
+
+ if test "x$with_lz4" == "xyes"; then
+ LZ4_CFLAGS=""
+ LZ4_CPPFLAGS=""
+ LZ4_LDFLAGS=""
+ LZ4_LIBS="-llz4"
+ else
+ LZ4_CFLAGS="-I$withval/include"
+ LZ4_CPPFLAGS="-I$withval/include"
+ LZ4_LDFLAGS="-L$withval/lib"
+ LZ4_LIBS="-llz4"
+ fi
+
+ LIBS="$LIBS $LZ4_LIBS"
+ LDFLAGS="$LDFLAGS $LZ4_LDFLAGS"
+ CFLAGS="$CFLAGS $LZ4_CFLAGS"
+ CPPFLAGS="$CPPFLAGS $LZ4_CPPFLAGS"
+
+ for ac_header in lz4.h
+do :
+ ac_fn_c_check_header_mongrel "$LINENO" "lz4.h" "ac_cv_header_lz4_h" "$ac_includes_default"
+if test "x$ac_cv_header_lz4_h" = xyes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_LZ4_H 1
+_ACEOF
+
+else
+ if false; then
+ HAVE_LZ4_TRUE=
+ HAVE_LZ4_FALSE='#'
+else
+ HAVE_LZ4_TRUE='#'
+ HAVE_LZ4_FALSE=
+fi
+
+fi
+
+done
+
+
+ LIBS="$save_LIBS"
+ LDFLAGS="$save_LDFLAGS"
+ CFLAGS="$save_CFLAGS"
+ CPPFLAGS="$save_CPPFLAGS"
+
+
+
+
+
+
+ # Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND:
+ if test -z "${HAVE_LZ4_TRUE}"; then
+
+$as_echo "#define HAVE_LZ4 1" >>confdefs.h
+
+ :
+ else
+
+ :
+ fi
+fi
+
+
+
{ $as_echo "$as_me:${as_lineno-$LINENO}: === checking for ZFP ===" >&5
@@ -32224,6 +31033,97 @@ fi
fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: === checking for SZ ===" >&5
+$as_echo "$as_me: === checking for SZ ===" >&6;}
+
+ if true; then
+ HAVE_SZ_TRUE=
+ HAVE_SZ_FALSE='#'
+else
+ HAVE_SZ_TRUE='#'
+ HAVE_SZ_FALSE=
+fi
+
+
+
+# Check whether --with-sz was given.
+if test "${with_sz+set}" = set; then :
+ withval=$with_sz; SZ_LDFLAGS="-L$withval/lib";
+ SZ_LIBS="-lsz -lzlib";
+ SZ_CPPFLAGS="-I$withval/include";
+else
+ with_sz=no
+fi
+
+
+if test "x$with_sz" == "xno"; then
+
+ if false; then
+ HAVE_SZ_TRUE=
+ HAVE_SZ_FALSE='#'
+else
+ HAVE_SZ_TRUE='#'
+ HAVE_SZ_FALSE=
+fi
+
+
+else
+
+ save_CPPFLAGS="$CPPFLAGS"
+ save_LIBS="$LIBS"
+ save_LDFLAGS="$LDFLAGS"
+ LIBS="$LIBS -lsz -lzlib"
+ LDFLAGS="$LDFLAGS $SZ_LDFLAGS"
+ CPPFLAGS="$CPPFLAGS $SZ_CPPFLAGS"
+
+ if test -z "${HAVE_SZ_TRUE}"; then
+ for ac_header in sz.h
+do :
+ ac_fn_c_check_header_mongrel "$LINENO" "sz.h" "ac_cv_header_sz_h" "$ac_includes_default"
+if test "x$ac_cv_header_sz_h" = xyes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_SZ_H 1
+_ACEOF
+
+else
+ if false; then
+ HAVE_SZ_TRUE=
+ HAVE_SZ_FALSE='#'
+else
+ HAVE_SZ_TRUE='#'
+ HAVE_SZ_FALSE=
+fi
+
+fi
+
+done
+
+ fi
+
+ # Check for the SZ library and headers
+
+ LIBS="$save_LIBS"
+ LDFLAGS="$save_LDFLAGS"
+ CPPFLAGS="$save_CPPFLAGS"
+
+
+
+
+
+ # Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND:
+ if test -z "${HAVE_SZ_TRUE}"; then
+
+$as_echo "#define HAVE_SZ 1" >>confdefs.h
+
+ :
+ else
+
+ :
+ fi
+fi
+
+
+
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -32801,6 +31701,28 @@ if test -z "${HAVE_SZIP_TRUE}"; then
ADIOSREADLIB_SEQ_LDFLAGS="${ADIOSREADLIB_SEQ_LDFLAGS} ${SZIP_LDFLAGS}"
ADIOSREADLIB_SEQ_LDADD="${ADIOSREADLIB_SEQ_LDADD} ${SZIP_LIBS}"
fi
+if test -z "${HAVE_LZ4_TRUE}"; then
+ ADIOSLIB_CPPFLAGS="${ADIOSLIB_CPPFLAGS} -DLZ4 ${LZ4_CPPFLAGS}"
+ ADIOSLIB_CFLAGS="${ADIOSLIB_CFLAGS} ${LZ4_CFLAGS}"
+ ADIOSLIB_LDFLAGS="${ADIOSLIB_LDFLAGS} ${LZ4_LDFLAGS}"
+ ADIOSLIB_LDADD="${ADIOSLIB_LDADD} ${LZ4_LIBS}"
+ ADIOSLIB_SEQ_CPPFLAGS="${ADIOSLIB_SEQ_CPPFLAGS} -DLZ4 ${LZ4_CPPFLAGS}"
+ ADIOSLIB_SEQ_CFLAGS="${ADIOSLIB_SEQ_CFLAGS} ${LZ4_CFLAGS}"
+ ADIOSLIB_SEQ_LDFLAGS="${ADIOSLIB_SEQ_LDFLAGS} ${LZ4_LDFLAGS}"
+ ADIOSLIB_SEQ_LDADD="${ADIOSLIB_SEQ_LDADD} ${LZ4_LIBS}"
+ ADIOSLIB_INT_CPPFLAGS="${ADIOSLIB_INT_CPPFLAGS} -DLZ4 ${LZ4_CPPFLAGS}"
+ ADIOSLIB_INT_CFLAGS="${ADIOSLIB_INT_CFLAGS} ${LZ4_CFLAGS}"
+ ADIOSLIB_INT_LDFLAGS="${ADIOSLIB_INT_LDFLAGS} ${LZ4_LDFLAGS}"
+ ADIOSLIB_INT_LDADD="${ADIOSLIB_INT_LDADD} ${LZ4_LIBS}"
+ ADIOSREADLIB_CPPFLAGS="${ADIOSREADLIB_CPPFLAGS} -DLZ4 ${LZ4_CPPFLAGS}"
+ ADIOSREADLIB_CFLAGS="${ADIOSREADLIB_CFLAGS} ${LZ4_CFLAGS}"
+ ADIOSREADLIB_LDFLAGS="${ADIOSREADLIB_LDFLAGS} ${LZ4_LDFLAGS}"
+ ADIOSREADLIB_LDADD="${ADIOSREADLIB_LDADD} ${LZ4_LIBS}"
+ ADIOSREADLIB_SEQ_CPPFLAGS="${ADIOSREADLIB_SEQ_CPPFLAGS} -DLZ4 ${LZ4_CPPFLAGS}"
+ ADIOSREADLIB_SEQ_CFLAGS="${ADIOSREADLIB_SEQ_CFLAGS} ${LZ4_CFLAGS}"
+ ADIOSREADLIB_SEQ_LDFLAGS="${ADIOSREADLIB_SEQ_LDFLAGS} ${LZ4_LDFLAGS}"
+ ADIOSREADLIB_SEQ_LDADD="${ADIOSREADLIB_SEQ_LDADD} ${LZ4_LIBS}"
+fi
if test -z "${HAVE_ZFP_TRUE}"; then
ADIOSLIB_LDFLAGS="${ADIOSLIB_LDFLAGS} ${ZFP_LDFLAGS}"
ADIOSLIB_LDADD="${ADIOSLIB_LDADD} ${ZFP_LIBS}"
@@ -32813,6 +31735,28 @@ if test -z "${HAVE_ZFP_TRUE}"; then
ADIOSREADLIB_SEQ_LDFLAGS="${ADIOSREADLIB_SEQ_LDFLAGS} ${ZFP_LDFLAGS}"
ADIOSREADLIB_SEQ_LDADD="${ADIOSREADLIB_SEQ_LDADD} ${ZFP_LIBS}"
fi
+if test -z "${HAVE_SZ_TRUE}"; then
+ ADIOSLIB_CPPFLAGS="${ADIOSLIB_CPPFLAGS} ${SZ_CPPFLAGS}"
+ ADIOSLIB_CFLAGS="${ADIOSLIB_CFLAGS} ${SZ_CFLAGS}"
+ ADIOSLIB_LDFLAGS="${ADIOSLIB_LDFLAGS} ${SZ_LDFLAGS}"
+ ADIOSLIB_LDADD="${ADIOSLIB_LDADD} ${SZ_LIBS}"
+ ADIOSLIB_SEQ_CPPFLAGS="${ADIOSLIB_SEQ_CPPFLAGS} ${SZ_CPPFLAGS}"
+ ADIOSLIB_SEQ_CFLAGS="${ADIOSLIB_SEQ_CFLAGS} ${SZ_CFLAGS}"
+ ADIOSLIB_SEQ_LDFLAGS="${ADIOSLIB_SEQ_LDFLAGS} ${SZ_LDFLAGS}"
+ ADIOSLIB_SEQ_LDADD="${ADIOSLIB_SEQ_LDADD} ${SZ_LIBS}"
+ ADIOSLIB_INT_CPPFLAGS="${ADIOSLIB_INT_CPPFLAGS} ${SZ_CPPFLAGS}"
+ ADIOSLIB_INT_CFLAGS="${ADIOSLIB_INT_CFLAGS} ${SZ_CFLAGS}"
+ ADIOSLIB_INT_LDFLAGS="${ADIOSLIB_INT_LDFLAGS} ${SZ_LDFLAGS}"
+ ADIOSLIB_INT_LDADD="${ADIOSLIB_INT_LDADD} ${SZ_LIBS}"
+ ADIOSREADLIB_CPPFLAGS="${ADIOSREADLIB_CPPFLAGS} ${SZ_CPPFLAGS}"
+ ADIOSREADLIB_CFLAGS="${ADIOSREADLIB_CFLAGS} ${SZ_CFLAGS}"
+ ADIOSREADLIB_LDFLAGS="${ADIOSREADLIB_LDFLAGS} ${SZ_LDFLAGS}"
+ ADIOSREADLIB_LDADD="${ADIOSREADLIB_LDADD} ${SZ_LIBS}"
+ ADIOSREADLIB_SEQ_CPPFLAGS="${ADIOSREADLIB_SEQ_CPPFLAGS} ${SZ_CPPFLAGS}"
+ ADIOSREADLIB_SEQ_CFLAGS="${ADIOSREADLIB_SEQ_CFLAGS} ${SZ_CFLAGS}"
+ ADIOSREADLIB_SEQ_LDFLAGS="${ADIOSREADLIB_SEQ_LDFLAGS} ${SZ_LDFLAGS}"
+ ADIOSREADLIB_SEQ_LDADD="${ADIOSREADLIB_SEQ_LDADD} ${SZ_LIBS}"
+fi
if test -z "${HAVE_ISOBAR_TRUE}"; then
ADIOSLIB_CPPFLAGS="${ADIOSLIB_CPPFLAGS} -DISOBAR ${ISOBAR_CPPFLAGS}"
ADIOSLIB_CFLAGS="${ADIOSLIB_CFLAGS} ${ISOBAR_CFLAGS}"
@@ -32981,7 +31925,7 @@ fi
#fi
#AC_DEFINE_UNQUOTED(VERSION_SVNREV, "${SVNVERSION}", [svn revision number])
-ac_config_files="$ac_config_files Makefile src/Makefile src/zfp/Makefile src/mxml/Makefile tests/Makefile tests/test_src/Makefile tests/C/Makefile tests/C/flexpath_tests/Makefile tests/C/flexpath_tests/1D_arr_global/Makefile tests/C/flexpath_tests/1D_arr_global_noxml/Makefile tests/C/flexpath_tests/global_range_select/Makefile tests/C/flexpath_tests/maya_noxml/Makefile tests/C/flexpath_tests/maya_append/Makefile tests/C/flexpath_tests/scalar/Makefile tests/C/fgr_tests/Makefile tests/C/qu [...]
+ac_config_files="$ac_config_files Makefile src/Makefile src/zfp/Makefile src/mxml/Makefile tests/Makefile tests/test_src/Makefile tests/C/Makefile tests/C/flexpath_tests/Makefile tests/C/flexpath_tests/1D_arr_global/Makefile tests/C/flexpath_tests/1D_arr_global_noxml/Makefile tests/C/flexpath_tests/global_range_select/Makefile tests/C/flexpath_tests/maya_noxml/Makefile tests/C/flexpath_tests/scalar/Makefile tests/C/flexpath_tests/local_arrays/Makefile tests/C/fgr_tests/Makefile tests/C/q [...]
@@ -33418,10 +32362,6 @@ if test -z "${HAVE_DIMES_TRUE}" && test -z "${HAVE_DIMES_FALSE}"; then
as_fn_error $? "conditional \"HAVE_DIMES\" was never defined.
Usually this means the macro was only invoked conditionally." "$LINENO" 5
fi
-if test -z "${HAVE_DIMES_TRUE}" && test -z "${HAVE_DIMES_FALSE}"; then
- as_fn_error $? "conditional \"HAVE_DIMES\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
-fi
if test -z "${HAVE_DMALLOC_TRUE}" && test -z "${HAVE_DMALLOC_FALSE}"; then
as_fn_error $? "conditional \"HAVE_DMALLOC\" was never defined.
Usually this means the macro was only invoked conditionally." "$LINENO" 5
@@ -33526,6 +32466,14 @@ if test -z "${HAVE_ZLIB_TRUE}" && test -z "${HAVE_ZLIB_FALSE}"; then
as_fn_error $? "conditional \"HAVE_ZLIB\" was never defined.
Usually this means the macro was only invoked conditionally." "$LINENO" 5
fi
+if test -z "${HAVE_ZLIB_TRUE}" && test -z "${HAVE_ZLIB_FALSE}"; then
+ as_fn_error $? "conditional \"HAVE_ZLIB\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${HAVE_BZIP2_TRUE}" && test -z "${HAVE_BZIP2_FALSE}"; then
+ as_fn_error $? "conditional \"HAVE_BZIP2\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
if test -z "${HAVE_BZIP2_TRUE}" && test -z "${HAVE_BZIP2_FALSE}"; then
as_fn_error $? "conditional \"HAVE_BZIP2\" was never defined.
Usually this means the macro was only invoked conditionally." "$LINENO" 5
@@ -33610,6 +32558,18 @@ if test -z "${HAVE_BGQ_TRUE}" && test -z "${HAVE_BGQ_FALSE}"; then
as_fn_error $? "conditional \"HAVE_BGQ\" was never defined.
Usually this means the macro was only invoked conditionally." "$LINENO" 5
fi
+if test -z "${HAVE_LZ4_TRUE}" && test -z "${HAVE_LZ4_FALSE}"; then
+ as_fn_error $? "conditional \"HAVE_LZ4\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${HAVE_LZ4_TRUE}" && test -z "${HAVE_LZ4_FALSE}"; then
+ as_fn_error $? "conditional \"HAVE_LZ4\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${HAVE_LZ4_TRUE}" && test -z "${HAVE_LZ4_FALSE}"; then
+ as_fn_error $? "conditional \"HAVE_LZ4\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
if test -z "${HAVE_ZFP_TRUE}" && test -z "${HAVE_ZFP_FALSE}"; then
as_fn_error $? "conditional \"HAVE_ZFP\" was never defined.
Usually this means the macro was only invoked conditionally." "$LINENO" 5
@@ -33634,6 +32594,18 @@ if test -z "${HAVE_ZFP_TRUE}" && test -z "${HAVE_ZFP_FALSE}"; then
as_fn_error $? "conditional \"HAVE_ZFP\" was never defined.
Usually this means the macro was only invoked conditionally." "$LINENO" 5
fi
+if test -z "${HAVE_SZ_TRUE}" && test -z "${HAVE_SZ_FALSE}"; then
+ as_fn_error $? "conditional \"HAVE_SZ\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${HAVE_SZ_TRUE}" && test -z "${HAVE_SZ_FALSE}"; then
+ as_fn_error $? "conditional \"HAVE_SZ\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
+if test -z "${HAVE_SZ_TRUE}" && test -z "${HAVE_SZ_FALSE}"; then
+ as_fn_error $? "conditional \"HAVE_SZ\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
if test -z "${RESEARCH_TRANSPORTS_TRUE}" && test -z "${RESEARCH_TRANSPORTS_FALSE}"; then
as_fn_error $? "conditional \"RESEARCH_TRANSPORTS\" was never defined.
Usually this means the macro was only invoked conditionally." "$LINENO" 5
@@ -34083,7 +33055,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by adios $as_me 1.11.0, which was
+This file was extended by adios $as_me 1.12.0, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -34149,7 +33121,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-adios config.status 1.11.0
+adios config.status 1.12.0
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
@@ -34760,8 +33732,8 @@ do
"tests/C/flexpath_tests/1D_arr_global_noxml/Makefile") CONFIG_FILES="$CONFIG_FILES tests/C/flexpath_tests/1D_arr_global_noxml/Makefile" ;;
"tests/C/flexpath_tests/global_range_select/Makefile") CONFIG_FILES="$CONFIG_FILES tests/C/flexpath_tests/global_range_select/Makefile" ;;
"tests/C/flexpath_tests/maya_noxml/Makefile") CONFIG_FILES="$CONFIG_FILES tests/C/flexpath_tests/maya_noxml/Makefile" ;;
- "tests/C/flexpath_tests/maya_append/Makefile") CONFIG_FILES="$CONFIG_FILES tests/C/flexpath_tests/maya_append/Makefile" ;;
"tests/C/flexpath_tests/scalar/Makefile") CONFIG_FILES="$CONFIG_FILES tests/C/flexpath_tests/scalar/Makefile" ;;
+ "tests/C/flexpath_tests/local_arrays/Makefile") CONFIG_FILES="$CONFIG_FILES tests/C/flexpath_tests/local_arrays/Makefile" ;;
"tests/C/fgr_tests/Makefile") CONFIG_FILES="$CONFIG_FILES tests/C/fgr_tests/Makefile" ;;
"tests/C/query/Makefile") CONFIG_FILES="$CONFIG_FILES tests/C/query/Makefile" ;;
"tests/C/query/common/Makefile") CONFIG_FILES="$CONFIG_FILES tests/C/query/common/Makefile" ;;
@@ -36721,6 +35693,17 @@ else
echo " - No SZIP to build SZIP transform method"
fi
+if test -z "${HAVE_LZ4_TRUE}"; then
+ echo " - LZ4";
+ echo " - LZ4_CFLAGS = $LZ4_CFLAGS";
+ echo " - LZ4_CPPFLAGS = $LZ4_CPPFLAGS";
+ echo " - LZ4_LDFLAGS = $LZ4_LDFLAGS";
+ echo " - LZ4_LIBS = $LZ4_LIBS";
+ echo
+else
+ echo " - No LZ4 to build LZ4 transform method"
+fi
+
if test -z "${BUILD_ZFP_TRUE}"; then
echo " - ZFP is built with ADIOS";
elif test -z "${HAVE_ZFP_TRUE}"; then
@@ -36733,6 +35716,17 @@ else
echo " - No ZFP to build ZFP transform method"
fi
+if test -z "${HAVE_SZ_TRUE}"; then
+ echo " - SZ";
+ echo " - SZ_CFLAGS = $SZ_CFLAGS";
+ echo " - SZ_CPPFLAGS = $SZ_CPPFLAGS";
+ echo " - SZ_LDFLAGS = $SZ_LDFLAGS";
+ echo " - SZ_LIBS = $SZ_LIBS";
+ echo
+else
+ echo " - No SZ to build SZ transform method"
+fi
+
if test -z "${HAVE_ISOBAR_TRUE}"; then
echo " - ISOBAR";
echo " - ISOBAR_CFLAGS = $ISOBAR_CFLAGS";
diff --git a/configure.ac b/configure.ac
index 58d0516..4cd792d 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,4 +1,4 @@
-AC_INIT([adios], [1.11.0])
+AC_INIT([adios], [1.12.0])
AC_CONFIG_SRCDIR([configure.ac])
AC_CONFIG_AUX_DIR(config)
AC_CONFIG_MACRO_DIR(config)
@@ -139,6 +139,13 @@ else
AM_CONDITIONAL(BUILD_MXML,false)
fi
+AC_MSG_NOTICE([PTHREAD_LIBS=${PTHREAD_LIBS}])
+if test ! -z "${PTHREAD_LIBS}"; then
+ LIBS="${PTHREAD_LIBS} ${LIBS}"
+fi
+if test ! -z "${PTHREAD_CFLAGS}"; then
+ CFLAGS="$CFLAGS ${PTHREAD_CFLAGS}"
+fi
# Make sure we find Python2
m4_define_default([_AM_PYTHON_INTERPRETER_LIST],
@@ -179,6 +186,7 @@ AC_APLOD
AC_ALACRITY
AC_FASTBIT
AC_BGQ
+AC_LZ4
AC_ZFP
@@ -196,6 +204,7 @@ if test -z "${BUILD_ZFP_TRUE}"; then
AC_SUBST(ZFP_LIBS)
AC_SUBST(ZFP_LDFLAGS)
fi
+AC_SZ
AC_LANG(C)
@@ -686,6 +695,28 @@ if test -z "${HAVE_SZIP_TRUE}"; then
ADIOSREADLIB_SEQ_LDFLAGS="${ADIOSREADLIB_SEQ_LDFLAGS} ${SZIP_LDFLAGS}"
ADIOSREADLIB_SEQ_LDADD="${ADIOSREADLIB_SEQ_LDADD} ${SZIP_LIBS}"
fi
+if test -z "${HAVE_LZ4_TRUE}"; then
+ ADIOSLIB_CPPFLAGS="${ADIOSLIB_CPPFLAGS} -DLZ4 ${LZ4_CPPFLAGS}"
+ ADIOSLIB_CFLAGS="${ADIOSLIB_CFLAGS} ${LZ4_CFLAGS}"
+ ADIOSLIB_LDFLAGS="${ADIOSLIB_LDFLAGS} ${LZ4_LDFLAGS}"
+ ADIOSLIB_LDADD="${ADIOSLIB_LDADD} ${LZ4_LIBS}"
+ ADIOSLIB_SEQ_CPPFLAGS="${ADIOSLIB_SEQ_CPPFLAGS} -DLZ4 ${LZ4_CPPFLAGS}"
+ ADIOSLIB_SEQ_CFLAGS="${ADIOSLIB_SEQ_CFLAGS} ${LZ4_CFLAGS}"
+ ADIOSLIB_SEQ_LDFLAGS="${ADIOSLIB_SEQ_LDFLAGS} ${LZ4_LDFLAGS}"
+ ADIOSLIB_SEQ_LDADD="${ADIOSLIB_SEQ_LDADD} ${LZ4_LIBS}"
+ ADIOSLIB_INT_CPPFLAGS="${ADIOSLIB_INT_CPPFLAGS} -DLZ4 ${LZ4_CPPFLAGS}"
+ ADIOSLIB_INT_CFLAGS="${ADIOSLIB_INT_CFLAGS} ${LZ4_CFLAGS}"
+ ADIOSLIB_INT_LDFLAGS="${ADIOSLIB_INT_LDFLAGS} ${LZ4_LDFLAGS}"
+ ADIOSLIB_INT_LDADD="${ADIOSLIB_INT_LDADD} ${LZ4_LIBS}"
+ ADIOSREADLIB_CPPFLAGS="${ADIOSREADLIB_CPPFLAGS} -DLZ4 ${LZ4_CPPFLAGS}"
+ ADIOSREADLIB_CFLAGS="${ADIOSREADLIB_CFLAGS} ${LZ4_CFLAGS}"
+ ADIOSREADLIB_LDFLAGS="${ADIOSREADLIB_LDFLAGS} ${LZ4_LDFLAGS}"
+ ADIOSREADLIB_LDADD="${ADIOSREADLIB_LDADD} ${LZ4_LIBS}"
+ ADIOSREADLIB_SEQ_CPPFLAGS="${ADIOSREADLIB_SEQ_CPPFLAGS} -DLZ4 ${LZ4_CPPFLAGS}"
+ ADIOSREADLIB_SEQ_CFLAGS="${ADIOSREADLIB_SEQ_CFLAGS} ${LZ4_CFLAGS}"
+ ADIOSREADLIB_SEQ_LDFLAGS="${ADIOSREADLIB_SEQ_LDFLAGS} ${LZ4_LDFLAGS}"
+ ADIOSREADLIB_SEQ_LDADD="${ADIOSREADLIB_SEQ_LDADD} ${LZ4_LIBS}"
+fi
if test -z "${HAVE_ZFP_TRUE}"; then
ADIOSLIB_LDFLAGS="${ADIOSLIB_LDFLAGS} ${ZFP_LDFLAGS}"
ADIOSLIB_LDADD="${ADIOSLIB_LDADD} ${ZFP_LIBS}"
@@ -698,6 +729,28 @@ if test -z "${HAVE_ZFP_TRUE}"; then
ADIOSREADLIB_SEQ_LDFLAGS="${ADIOSREADLIB_SEQ_LDFLAGS} ${ZFP_LDFLAGS}"
ADIOSREADLIB_SEQ_LDADD="${ADIOSREADLIB_SEQ_LDADD} ${ZFP_LIBS}"
fi
+if test -z "${HAVE_SZ_TRUE}"; then
+ ADIOSLIB_CPPFLAGS="${ADIOSLIB_CPPFLAGS} ${SZ_CPPFLAGS}"
+ ADIOSLIB_CFLAGS="${ADIOSLIB_CFLAGS} ${SZ_CFLAGS}"
+ ADIOSLIB_LDFLAGS="${ADIOSLIB_LDFLAGS} ${SZ_LDFLAGS}"
+ ADIOSLIB_LDADD="${ADIOSLIB_LDADD} ${SZ_LIBS}"
+ ADIOSLIB_SEQ_CPPFLAGS="${ADIOSLIB_SEQ_CPPFLAGS} ${SZ_CPPFLAGS}"
+ ADIOSLIB_SEQ_CFLAGS="${ADIOSLIB_SEQ_CFLAGS} ${SZ_CFLAGS}"
+ ADIOSLIB_SEQ_LDFLAGS="${ADIOSLIB_SEQ_LDFLAGS} ${SZ_LDFLAGS}"
+ ADIOSLIB_SEQ_LDADD="${ADIOSLIB_SEQ_LDADD} ${SZ_LIBS}"
+ ADIOSLIB_INT_CPPFLAGS="${ADIOSLIB_INT_CPPFLAGS} ${SZ_CPPFLAGS}"
+ ADIOSLIB_INT_CFLAGS="${ADIOSLIB_INT_CFLAGS} ${SZ_CFLAGS}"
+ ADIOSLIB_INT_LDFLAGS="${ADIOSLIB_INT_LDFLAGS} ${SZ_LDFLAGS}"
+ ADIOSLIB_INT_LDADD="${ADIOSLIB_INT_LDADD} ${SZ_LIBS}"
+ ADIOSREADLIB_CPPFLAGS="${ADIOSREADLIB_CPPFLAGS} ${SZ_CPPFLAGS}"
+ ADIOSREADLIB_CFLAGS="${ADIOSREADLIB_CFLAGS} ${SZ_CFLAGS}"
+ ADIOSREADLIB_LDFLAGS="${ADIOSREADLIB_LDFLAGS} ${SZ_LDFLAGS}"
+ ADIOSREADLIB_LDADD="${ADIOSREADLIB_LDADD} ${SZ_LIBS}"
+ ADIOSREADLIB_SEQ_CPPFLAGS="${ADIOSREADLIB_SEQ_CPPFLAGS} ${SZ_CPPFLAGS}"
+ ADIOSREADLIB_SEQ_CFLAGS="${ADIOSREADLIB_SEQ_CFLAGS} ${SZ_CFLAGS}"
+ ADIOSREADLIB_SEQ_LDFLAGS="${ADIOSREADLIB_SEQ_LDFLAGS} ${SZ_LDFLAGS}"
+ ADIOSREADLIB_SEQ_LDADD="${ADIOSREADLIB_SEQ_LDADD} ${SZ_LIBS}"
+fi
if test -z "${HAVE_ISOBAR_TRUE}"; then
ADIOSLIB_CPPFLAGS="${ADIOSLIB_CPPFLAGS} -DISOBAR ${ISOBAR_CPPFLAGS}"
ADIOSLIB_CFLAGS="${ADIOSLIB_CFLAGS} ${ISOBAR_CFLAGS}"
@@ -870,8 +923,8 @@ AC_CONFIG_FILES([Makefile
tests/C/flexpath_tests/1D_arr_global_noxml/Makefile
tests/C/flexpath_tests/global_range_select/Makefile
tests/C/flexpath_tests/maya_noxml/Makefile
- tests/C/flexpath_tests/maya_append/Makefile
tests/C/flexpath_tests/scalar/Makefile
+ tests/C/flexpath_tests/local_arrays/Makefile
tests/C/fgr_tests/Makefile
tests/C/query/Makefile
tests/C/query/common/Makefile
@@ -1256,6 +1309,17 @@ else
echo " - No SZIP to build SZIP transform method"
fi
+if test -z "${HAVE_LZ4_TRUE}"; then
+ echo " - LZ4";
+ echo " - LZ4_CFLAGS = $LZ4_CFLAGS";
+ echo " - LZ4_CPPFLAGS = $LZ4_CPPFLAGS";
+ echo " - LZ4_LDFLAGS = $LZ4_LDFLAGS";
+ echo " - LZ4_LIBS = $LZ4_LIBS";
+ echo
+else
+ echo " - No LZ4 to build LZ4 transform method"
+fi
+
if test -z "${BUILD_ZFP_TRUE}"; then
echo " - ZFP is built with ADIOS";
elif test -z "${HAVE_ZFP_TRUE}"; then
@@ -1268,6 +1332,17 @@ else
echo " - No ZFP to build ZFP transform method"
fi
+if test -z "${HAVE_SZ_TRUE}"; then
+ echo " - SZ";
+ echo " - SZ_CFLAGS = $SZ_CFLAGS";
+ echo " - SZ_CPPFLAGS = $SZ_CPPFLAGS";
+ echo " - SZ_LDFLAGS = $SZ_LDFLAGS";
+ echo " - SZ_LIBS = $SZ_LIBS";
+ echo
+else
+ echo " - No SZ to build SZ transform method"
+fi
+
if test -z "${HAVE_ISOBAR_TRUE}"; then
echo " - ISOBAR";
echo " - ISOBAR_CFLAGS = $ISOBAR_CFLAGS";
diff --git a/examples/C/Makefile.in b/examples/C/Makefile.in
index aa15858..b1acbca 100644
--- a/examples/C/Makefile.in
+++ b/examples/C/Makefile.in
@@ -99,7 +99,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -107,8 +107,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -333,6 +333,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -409,6 +413,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/C/arrays/Makefile.in b/examples/C/arrays/Makefile.in
index 38a4f10..ae9c977 100644
--- a/examples/C/arrays/Makefile.in
+++ b/examples/C/arrays/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -334,6 +334,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -410,6 +414,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/C/attributes/Makefile.in b/examples/C/attributes/Makefile.in
index 630593b..12a3eb9 100644
--- a/examples/C/attributes/Makefile.in
+++ b/examples/C/attributes/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -336,6 +336,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -412,6 +416,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/C/flexpath_arrays/Makefile.in b/examples/C/flexpath_arrays/Makefile.in
index 2fbf59c..059f0e2 100644
--- a/examples/C/flexpath_arrays/Makefile.in
+++ b/examples/C/flexpath_arrays/Makefile.in
@@ -99,7 +99,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -107,8 +107,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -333,6 +333,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -409,6 +413,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/C/flexpath_arrays/global_range_select/Makefile.in b/examples/C/flexpath_arrays/global_range_select/Makefile.in
index a546771..293ca32 100644
--- a/examples/C/flexpath_arrays/global_range_select/Makefile.in
+++ b/examples/C/flexpath_arrays/global_range_select/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -334,6 +334,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -410,6 +414,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/C/flexpath_arrays/process_select/Makefile.in b/examples/C/flexpath_arrays/process_select/Makefile.in
index d955394..d0d0f28 100644
--- a/examples/C/flexpath_arrays/process_select/Makefile.in
+++ b/examples/C/flexpath_arrays/process_select/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -334,6 +334,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -410,6 +414,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/C/global-array-time/Makefile.in b/examples/C/global-array-time/Makefile.in
index 831b477..83c58f8 100644
--- a/examples/C/global-array-time/Makefile.in
+++ b/examples/C/global-array-time/Makefile.in
@@ -104,7 +104,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -112,8 +112,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -365,6 +365,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -441,6 +445,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/C/global-array/Makefile.in b/examples/C/global-array/Makefile.in
index 117611d..079f327 100644
--- a/examples/C/global-array/Makefile.in
+++ b/examples/C/global-array/Makefile.in
@@ -106,7 +106,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -114,8 +114,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -428,6 +428,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -504,6 +508,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/C/global-array/adios_read_chunk.c b/examples/C/global-array/adios_read_chunk.c
index da7a3c6..23c3bd8 100644
--- a/examples/C/global-array/adios_read_chunk.c
+++ b/examples/C/global-array/adios_read_chunk.c
@@ -28,7 +28,7 @@ int main (int argc, char ** argv)
int rank, size, i, datasize;
//int j;
MPI_Comm comm = MPI_COMM_WORLD;
- enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP_AGGREGATE;
+ enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP;
ADIOS_SELECTION * sel1;
//ADIOS_SELECTION * sel2;
//ADIOS_VARCHUNK * chunk = 0;
@@ -43,30 +43,32 @@ int main (int argc, char ** argv)
adios_read_init_method (method, comm, "max_chunk_size=4;verbose=3;num_aggregators=2");
ADIOS_FILE * f = adios_read_open_file ("adios_global.bp", method, comm);
- ADIOS_VARINFO * varinfo = adios_inq_var (f, "temperature");
- if (varinfo)
+ if (f != NULL)
{
- printf ("nsteps = %d\n", varinfo->nsteps);
- for (i = 0; i < varinfo->nsteps; i++)
+ ADIOS_VARINFO * varinfo = adios_inq_var (f, "temperature");
+ if (varinfo)
{
- printf ("step: %d has %d", i, varinfo->nblocks[i]);
- }
- printf ("\n");
- printf ("ndim = %d\n", varinfo->ndim);
- printf ("dims = (");
- datasize = 8;
- for (i = 0; i < varinfo->ndim; i++)
- {
- datasize *= varinfo->dims[i];
- printf ("%" PRIu64, varinfo->dims[i]);
- if (i != varinfo->ndim - 1)
+ printf ("nsteps = %d\n", varinfo->nsteps);
+ for (i = 0; i < varinfo->nsteps; i++)
{
- printf (",");
+ printf ("step: %d has %d", i, varinfo->nblocks[i]);
}
- }
- printf (")\n");
- data = malloc (datasize);
-/*
+ printf ("\n");
+ printf ("ndim = %d\n", varinfo->ndim);
+ printf ("dims = (");
+ datasize = 8;
+ for (i = 0; i < varinfo->ndim; i++)
+ {
+ datasize *= varinfo->dims[i];
+ printf ("%" PRIu64, varinfo->dims[i]);
+ if (i != varinfo->ndim - 1)
+ {
+ printf (",");
+ }
+ }
+ printf (")\n");
+ data = malloc (datasize);
+ /*
adios_inq_var_blockinfo (f, varinfo);
for (i = 0; i < varinfo->sum_nblocks; i++)
{
@@ -83,15 +85,15 @@ int main (int argc, char ** argv)
}
printf ("\n");
}
-*/
- for (i = 0; i < varinfo->ndim; i++)
- {
- start[i] = 0;
- count[i] = varinfo->dims[i];
- }
+ */
+ for (i = 0; i < varinfo->ndim; i++)
+ {
+ start[i] = 0;
+ count[i] = varinfo->dims[i];
+ }
- sel1 = adios_selection_boundingbox (varinfo->ndim, start, count);
-/*
+ sel1 = adios_selection_boundingbox (varinfo->ndim, start, count);
+ /*
npoints = 1;
for (i = 0; i < varinfo->ndim; i++)
{
@@ -108,8 +110,8 @@ int main (int argc, char ** argv)
temp = temp/count[j];
}
}
-*/
-/*
+ */
+ /*
for (i = 0; i < npoints; i++)
{
printf ("(");
@@ -121,48 +123,49 @@ int main (int argc, char ** argv)
}
printf ("\n");
-*/
-/*
+ */
+ /*
sel2 = adios_selection_points (varinfo->ndim, npoints, points);
-*/
- adios_schedule_read (f, sel1, "temperature", 0, 1, data);
-/*
+ */
+ adios_schedule_read (f, sel1, "temperature", 0, 1, data);
+ /*
adios_schedule_read (f, sel2, "temperature", 0, 1, data);
-*/
- adios_perform_reads (f, 1);
+ */
+ adios_perform_reads (f, 1);
#if 0
- while (adios_check_reads (f, &chunk) > 0)
- {
- datasize = 1;
- for (i = 0; i < varinfo->ndim; i++)
+ while (adios_check_reads (f, &chunk) > 0)
{
- datasize *= chunk->sel->u.bb.count[i];
- }
- printf ("data:\n");
-/*
+ datasize = 1;
+ for (i = 0; i < varinfo->ndim; i++)
+ {
+ datasize *= chunk->sel->u.bb.count[i];
+ }
+ printf ("data:\n");
+ /*
for (i = 0; i < datasize; i ++)
{
printf ("%7.4f ", * ((double *)chunk->data + i));
}
printf ("\n");
-*/
- for (i = 0; i < 10; i ++)
- {
- printf ("%7.4f ", * ((double *)chunk->data + i));
- }
- printf ("\n");
+ */
+ for (i = 0; i < 10; i ++)
+ {
+ printf ("%7.4f ", * ((double *)chunk->data + i));
+ }
+ printf ("\n");
- adios_free_chunk (chunk);
- }
+ adios_free_chunk (chunk);
+ }
#endif
- adios_selection_delete (sel1);
-/*
+ adios_selection_delete (sel1);
+ /*
adios_selection_delete (sel2);
-*/
- }
+ */
+ }
- adios_free_varinfo (varinfo);
- adios_read_close (f);
+ adios_free_varinfo (varinfo);
+ adios_read_close (f);
+ }
adios_read_finalize_method (ADIOS_READ_METHOD_BP);
MPI_Finalize ();
diff --git a/examples/C/global-array/adios_read_global.c b/examples/C/global-array/adios_read_global.c
index e43c4f0..09abafa 100644
--- a/examples/C/global-array/adios_read_global.c
+++ b/examples/C/global-array/adios_read_global.c
@@ -42,46 +42,47 @@ int main (int argc, char ** argv)
if (f == NULL)
{
printf ("%s\n", adios_errmsg());
- return -1;
}
+ else
+ {
+ ADIOS_VARINFO * v = adios_inq_var (f, "temperature");
- ADIOS_VARINFO * v = adios_inq_var (f, "temperature");
+ /* Using less readers to read the global array back, i.e., non-uniform */
+ uint64_t slice_size = v->dims[0]/size;
+ start[0] = slice_size * rank;
+ if (rank == size-1) /* last rank may read more lines */
+ slice_size = slice_size + v->dims[0]%size;
+ count[0] = slice_size;
- /* Using less readers to read the global array back, i.e., non-uniform */
- uint64_t slice_size = v->dims[0]/size;
- start[0] = slice_size * rank;
- if (rank == size-1) /* last rank may read more lines */
- slice_size = slice_size + v->dims[0]%size;
- count[0] = slice_size;
+ start[1] = 0;
+ count[1] = v->dims[1];
- start[1] = 0;
- count[1] = v->dims[1];
-
- data = malloc (slice_size * v->dims[1] * sizeof (double));
- if (data == NULL)
- {
- fprintf (stderr, "malloc failed.\n");
- return -1;
- }
+ data = malloc (slice_size * v->dims[1] * sizeof (double));
+ if (data == NULL)
+ {
+ fprintf (stderr, "malloc failed.\n");
+ return -1;
+ }
- /* Read a subset of the temperature array */
- sel = adios_selection_boundingbox (v->ndim, start, count);
- adios_schedule_read (f, sel, "temperature", 0, 1, data);
- adios_perform_reads (f, 1);
+ /* Read a subset of the temperature array */
+ sel = adios_selection_boundingbox (v->ndim, start, count);
+ adios_schedule_read (f, sel, "temperature", 0, 1, data);
+ adios_perform_reads (f, 1);
- for (i = 0; i < slice_size; i++) {
- printf ("rank %d: [%" PRIu64 ",%d:%" PRIu64 "]", rank, start[0]+i, 0, slice_size);
- for (j = 0; j < v->dims[1]; j++)
- printf (" %6.6g", * ((double *)data + i * v->dims[1] + j));
- printf ("\n");
- }
+ for (i = 0; i < slice_size; i++) {
+ printf ("rank %d: [%" PRIu64 ",%d:%" PRIu64 "]", rank, start[0]+i, 0, slice_size);
+ for (j = 0; j < v->dims[1]; j++)
+ printf (" %6.6g", * ((double *)data + i * v->dims[1] + j));
+ printf ("\n");
+ }
- free (data);
- adios_selection_delete (sel);
- adios_free_varinfo (v);
- adios_read_close (f);
- MPI_Barrier (comm);
+ free (data);
+ adios_selection_delete (sel);
+ adios_free_varinfo (v);
+ adios_read_close (f);
+ MPI_Barrier (comm);
+ }
adios_read_finalize_method (method);
MPI_Finalize ();
return 0;
diff --git a/examples/C/global-array/adios_read_gpp.c b/examples/C/global-array/adios_read_gpp.c
index 98ebc07..1aefd5b 100644
--- a/examples/C/global-array/adios_read_gpp.c
+++ b/examples/C/global-array/adios_read_gpp.c
@@ -20,7 +20,7 @@ int main (int argc, char ** argv)
{
char filename [256];
int rank, size, i;
- int NX = 4096;
+ int NX = 10;
double t[NX];
MPI_Comm comm = MPI_COMM_WORLD;
@@ -37,19 +37,20 @@ int main (int argc, char ** argv)
//adios_read_init_method (ADIOS_READ_METHOD_BP, comm, "");
fp = adios_read_open_file ("adios_global.bp", ADIOS_READ_METHOD_BP, comm);
+ if (fp != NULL) {
- #include "gread_temperature.ch"
+#include "gread_temperature.ch"
- adios_read_close (fp);
+ adios_read_close (fp);
- // Verify data
- for (i = 0; i < NX; i++)
- if (t[i] != rank*NX + i)
- {
- fprintf (stderr, "Error detected\n");
- }
+ // Verify data
+ for (i = 0; i < NX; i++)
+ if (t[i] != rank*NX + i)
+ {
+ fprintf (stderr, "Error detected\n");
+ }
+ }
-
adios_read_finalize_method (ADIOS_READ_METHOD_BP);
MPI_Finalize ();
diff --git a/examples/C/global-array/adios_read_writeblock.c b/examples/C/global-array/adios_read_writeblock.c
index 1638fd8..8b96090 100644
--- a/examples/C/global-array/adios_read_writeblock.c
+++ b/examples/C/global-array/adios_read_writeblock.c
@@ -38,57 +38,61 @@ int main (int argc, char ** argv)
adios_read_init_method (method, comm, "verbose=4");
ADIOS_FILE * f = adios_read_open_file ("adios_global.bp", method, comm);
- ADIOS_VARINFO * varinfo = adios_inq_var (f, "temperature");
- if (varinfo)
+ if (f != NULL)
{
- printf ("nsteps = %d\n", varinfo->nsteps);
- for (i = 0; i < varinfo->nsteps; i++)
+ printf ("rank %d: Passed adios_read_open_file\n", rank);
+ ADIOS_VARINFO * varinfo = adios_inq_var (f, "temperature");
+ if (varinfo)
{
- printf ("step: %d has %d", i, varinfo->nblocks[i]);
- }
- printf ("\n");
-
- adios_inq_var_blockinfo (f, varinfo);
- for (i = 0; i < varinfo->sum_nblocks; i++)
- {
- printf ("block[%d]: ", i);
- printf ("start=");
- for (j = 0; j < varinfo->ndim; j++)
+ printf ("nsteps = %d\n", varinfo->nsteps);
+ for (i = 0; i < varinfo->nsteps; i++)
{
- printf ("%" PRIu64, varinfo->blockinfo[i].start[j]);
+ printf ("step: %d has %d", i, varinfo->nblocks[i]);
}
- printf ("count=");
- for (j = 0; j < varinfo->ndim; j++)
+ printf ("\n");
+
+ adios_inq_var_blockinfo (f, varinfo);
+ for (i = 0; i < varinfo->sum_nblocks; i++)
{
- printf ("%" PRIu64, varinfo->blockinfo[i].count[j]);
+ printf ("block[%d]: ", i);
+ printf ("start=");
+ for (j = 0; j < varinfo->ndim; j++)
+ {
+ printf ("%" PRIu64, varinfo->blockinfo[i].start[j]);
+ }
+ printf ("count=");
+ for (j = 0; j < varinfo->ndim; j++)
+ {
+ printf ("%" PRIu64, varinfo->blockinfo[i].count[j]);
+ }
+ printf ("\n");
}
- printf ("\n");
- }
- datasize = 8;
- for (i = 0; i < varinfo->ndim; i++)
- {
- datasize *= varinfo->blockinfo[rank].count[i];
- }
+ datasize = 8;
+ for (i = 0; i < varinfo->ndim; i++)
+ {
+ datasize *= varinfo->blockinfo[rank].count[i];
+ }
- data = malloc (datasize);
+ data = malloc (datasize);
- sel = adios_selection_writeblock (rank);
- adios_schedule_read (f, sel, "temperature", 0, 1, data);
- adios_perform_reads (f, 1);
- adios_selection_delete (sel);
- }
+ sel = adios_selection_writeblock (rank);
+ adios_schedule_read (f, sel, "temperature", 0, 1, data);
+ adios_perform_reads (f, 1);
+ adios_selection_delete (sel);
+ }
- adios_free_varinfo (varinfo);
- adios_read_close (f);
+ adios_free_varinfo (varinfo);
+ adios_read_close (f);
- printf ("data:\n");
- for (i = 0; i < datasize/8; i ++)
- {
- printf ("%7.4f ", * ((double *)data + i));
+ printf ("data:\n");
+ for (i = 0; i < datasize/8; i ++)
+ {
+ printf ("%7.4f ", * ((double *)data + i));
+ }
+ printf ("\n");
+ free (data);
}
- printf ("\n");
- free (data);
adios_read_finalize_method (ADIOS_READ_METHOD_BP);
MPI_Finalize ();
return 0;
diff --git a/examples/C/global-array/gread_temperature.ch b/examples/C/global-array/gread_temperature.ch
index 4c16e85..15e2e03 100644
--- a/examples/C/global-array/gread_temperature.ch
+++ b/examples/C/global-array/gread_temperature.ch
@@ -1,4 +1,4 @@
s = adios_selection_writeblock (rank);
-adios_schedule_read (fp, s, "temperature", 1, 1, t);
+adios_schedule_read (fp, s, "temperature", 0, 1, t);
adios_perform_reads (fp, 1);
adios_selection_delete (s);
diff --git a/examples/C/icee_arrays/Makefile.in b/examples/C/icee_arrays/Makefile.in
index da03f1b..bc6959c 100644
--- a/examples/C/icee_arrays/Makefile.in
+++ b/examples/C/icee_arrays/Makefile.in
@@ -99,7 +99,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -107,8 +107,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -333,6 +333,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -409,6 +413,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/C/icee_arrays/array/Makefile.in b/examples/C/icee_arrays/array/Makefile.in
index 7c95530..efb0978 100644
--- a/examples/C/icee_arrays/array/Makefile.in
+++ b/examples/C/icee_arrays/array/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -334,6 +334,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -410,6 +414,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/C/manual/Makefile.in b/examples/C/manual/Makefile.in
index 094fe39..a2fc3c9 100644
--- a/examples/C/manual/Makefile.in
+++ b/examples/C/manual/Makefile.in
@@ -102,7 +102,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -110,8 +110,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -353,6 +353,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -429,6 +433,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/C/query/Makefile.in b/examples/C/query/Makefile.in
index 8dbcb88..22ff16e 100644
--- a/examples/C/query/Makefile.in
+++ b/examples/C/query/Makefile.in
@@ -102,7 +102,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -110,8 +110,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -351,6 +351,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -427,6 +431,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/C/query/query_table.c b/examples/C/query/query_table.c
index 9b06a79..03252cb 100644
--- a/examples/C/query/query_table.c
+++ b/examples/C/query/query_table.c
@@ -137,7 +137,7 @@ void query_columns(ADIOS_FILE* f, enum ADIOS_QUERY_METHOD method, ADIOS_VARINFO
break;
}
- printf("Number of hits returned in batch %d = %lld points in %d containers\n",
+ printf("Number of hits returned in batch %d = %" PRIu64 " points in %d containers\n",
nBatches, result->npoints, result->nselections);
int n;
diff --git a/examples/C/query/query_vars.c b/examples/C/query/query_vars.c
index 1ec8cad..83c9f47 100644
--- a/examples/C/query/query_vars.c
+++ b/examples/C/query/query_vars.c
@@ -48,7 +48,7 @@ void print_block (ADIOS_VARINFO *vi, int blockid, double *P, double *V, double *
int n;
printf (" Block %d of dimensions { ", blockid);
for (n=0; n < vi->ndim; n++) {
- printf ("%lld ", vi->blockinfo[blockid].count[n]);
+ printf ("%" PRIu64 " ", vi->blockinfo[blockid].count[n]);
}
printf ("}\n");
}
@@ -94,7 +94,7 @@ void query_OneBoundBoxForAllVars(ADIOS_FILE* f, enum ADIOS_QUERY_METHOD method)
if (result->selections->type == ADIOS_SELECTION_POINTS)
{
// we have selection(s) and each one contains the points
- printf("Number of hits returned in batch %d = %lld points in %d containers\n",
+ printf("Number of hits returned in batch %d = %" PRIu64 " points in %d containers\n",
nBatches, result->npoints, result->nselections);
for (i=0; i < result->nselections; i++)
diff --git a/examples/C/read_all/Makefile.in b/examples/C/read_all/Makefile.in
index dc80a3f..7e1920c 100644
--- a/examples/C/read_all/Makefile.in
+++ b/examples/C/read_all/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -334,6 +334,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -410,6 +414,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/C/scalars/Makefile.in b/examples/C/scalars/Makefile.in
index 87dded8..5d1c6d1 100644
--- a/examples/C/scalars/Makefile.in
+++ b/examples/C/scalars/Makefile.in
@@ -102,7 +102,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -110,8 +110,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -345,6 +345,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -421,6 +425,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/C/schema/Makefile.in b/examples/C/schema/Makefile.in
index 1da114b..0190052 100644
--- a/examples/C/schema/Makefile.in
+++ b/examples/C/schema/Makefile.in
@@ -104,7 +104,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -112,8 +112,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -395,6 +395,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -471,6 +475,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/C/stat/Makefile.in b/examples/C/stat/Makefile.in
index 88f3573..695de9d 100644
--- a/examples/C/stat/Makefile.in
+++ b/examples/C/stat/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -334,6 +334,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -410,6 +414,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/C/time_aggregation/Makefile.in b/examples/C/time_aggregation/Makefile.in
index 4a32703..e0c5faf 100644
--- a/examples/C/time_aggregation/Makefile.in
+++ b/examples/C/time_aggregation/Makefile.in
@@ -102,7 +102,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -110,8 +110,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -341,6 +341,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -417,6 +421,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/C/transforms/Makefile.in b/examples/C/transforms/Makefile.in
index 8c45625..41697ca 100644
--- a/examples/C/transforms/Makefile.in
+++ b/examples/C/transforms/Makefile.in
@@ -102,7 +102,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -110,8 +110,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -354,6 +354,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -430,6 +434,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/Fortran/Makefile.in b/examples/Fortran/Makefile.in
index 1f966d5..7b7f29e 100644
--- a/examples/Fortran/Makefile.in
+++ b/examples/Fortran/Makefile.in
@@ -99,7 +99,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -107,8 +107,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -333,6 +333,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -409,6 +413,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/Fortran/arrays/Makefile.in b/examples/Fortran/arrays/Makefile.in
index fc96393..bc4537d 100644
--- a/examples/Fortran/arrays/Makefile.in
+++ b/examples/Fortran/arrays/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -331,6 +331,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -407,6 +411,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/Fortran/global-array-time/Makefile.in b/examples/Fortran/global-array-time/Makefile.in
index 9a444da..9db1899 100644
--- a/examples/Fortran/global-array-time/Makefile.in
+++ b/examples/Fortran/global-array-time/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -325,6 +325,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -401,6 +405,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/Fortran/global-array/Makefile.in b/examples/Fortran/global-array/Makefile.in
index a576d12..7a000b0 100644
--- a/examples/Fortran/global-array/Makefile.in
+++ b/examples/Fortran/global-array/Makefile.in
@@ -102,7 +102,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -110,8 +110,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -343,6 +343,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -419,6 +423,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/Fortran/scalars/Makefile.in b/examples/Fortran/scalars/Makefile.in
index 9e8ddf1..53e09b6 100644
--- a/examples/Fortran/scalars/Makefile.in
+++ b/examples/Fortran/scalars/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -331,6 +331,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -407,6 +411,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/Fortran/schema/Makefile.in b/examples/Fortran/schema/Makefile.in
index 795c3d8..a431e6c 100644
--- a/examples/Fortran/schema/Makefile.in
+++ b/examples/Fortran/schema/Makefile.in
@@ -103,7 +103,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -111,8 +111,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -362,6 +362,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -438,6 +442,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/Makefile.in b/examples/Makefile.in
index f1633ca..ea3e779 100644
--- a/examples/Makefile.in
+++ b/examples/Makefile.in
@@ -99,7 +99,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -107,8 +107,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -333,6 +333,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -409,6 +413,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/examples/staging/stage_write/stage_write.c b/examples/staging/stage_write/stage_write.c
index bd6dfd2..326d358 100644
--- a/examples/staging/stage_write/stage_write.c
+++ b/examples/staging/stage_write/stage_write.c
@@ -302,7 +302,7 @@ int process_metadata(int step)
adios_get_grouplist(f, &group_namelist);
group_name = strdup (group_namelist[0]);
print0("Group name is %s\n", group_name);
- adios_declare_group(&gh,group_name,"",adios_flag_yes);
+ adios_declare_group(&gh,group_name,"",adios_stat_default);
varinfo = (VarInfo *) malloc (sizeof(VarInfo) * f->nvars);
diff --git a/examples/staging/stage_write_varyingsize/stage_write.c b/examples/staging/stage_write_varyingsize/stage_write.c
index b35806e..4c0be69 100644
--- a/examples/staging/stage_write_varyingsize/stage_write.c
+++ b/examples/staging/stage_write_varyingsize/stage_write.c
@@ -317,7 +317,7 @@ int process_metadata(int step)
adios_get_grouplist(f, &group_namelist);
group_name = strdup (group_namelist[0]);
print0("Group name is %s\n", group_name);
- adios_declare_group(&gh,group_name,"",adios_flag_yes);
+ adios_declare_group(&gh,group_name,"",adios_stat_default);
}
varinfo = (VarInfo *) malloc (sizeof(VarInfo) * f->nvars);
diff --git a/runconf b/runconf
index 25629a7..74b287d 100755
--- a/runconf
+++ b/runconf
@@ -6,131 +6,7 @@
SRCDIR=`dirname ${BASH_SOURCE[0]}`
-if [ `hostname | cut -c 1-4` == "sith" ]; then
-
- ########
- # Sith #
- ########
- source /etc/profile.d/modules.sh
- TARGET=`module list 2>&1 | grep "PE"- | sed "s/^.*PE-\([a-z]*\).*/\1/"`
-
- if [ -z "$TARGET" ]; then
- echo "Cannot determine Programming environment. Exit"
- exit 1
- fi
- echo "Configure on SITH for $TARGET env. for user ${USER}"
- module unload hdf5
- module unload netcdf
- module unload python
- #module unload PE-gnu
- #module unload PE-pgi
- #module unload PE-intel
- #module unload PE-pathscale
- #module unload pgi gcc intel pathscale
- #module load PE-$TARGET
- module load python
- # Use both seq hdf5 (for utils) and
- # parallel hdf5 (for PHDF5 method)
- module load hdf5/1.8.10
- SEQ_HDF5_DIR=$HDF5_DIR
- SEQ_HDF5_CLIB=$HDF5_CLIB
- module unload hdf5
- module load hdf5/1.8.10_par
- PAR_HDF5_DIR=$HDF5_DIR
- PAR_HDF5_CLIB=$HDF5_CLIB
- module unload hdf5
- # Seq. and Parallel NetCDF 4
- module load netcdf/4.1.3
- SEQ_NC_DIR=$NETCDF_DIR
- SEQ_NC_CLIB=$NETCDF_CLIB
- module unload netcdf
- module load netcdf/4.1.3_par
- PAR_NC_DIR=$NETCDF_DIR
- PAR_NC_CLIB=$NETCDF_CLIB
- module unload netcdf
- #module load szip
- module load bzip2
- module unload dataspaces
- unset DATASPACES_DIR
- module load dataspaces/1.6.0
- export MPICC=mpicc
- export MPICXX=mpiCC
- export MPIFC=mpif90
- export CPPFLAGS="-DMPICH_IGNORE_CXX_SEEK"
- export CFLAGS="-g -O0 -fPIC"
- export CXXFLAGS="-g -O0 -fPIC"
- export FCFLAGS="-g -O0 -fPIC"
- WITHFLEX=""
- WITHFGR=""
- WITHFASTBIT=""
- WITHALACRITY=""
- if [ "$TARGET" == "pgi" ]; then
- export CC=pgcc
- export CXX=pgCC
- export FC=pgf90
- WITHFLEX="--with-flexpath=/ccs/proj/e2e/chaos/sith/$TARGET"
- WITHFGR="--with-fgr=/ccs/proj/e2e/qliu/tap"
- WITHALACRITY="--with-alacrity=/ccs/proj/e2e/ncsu/alacrity/sith/pgi"
- WITHFASTBIT="--with-fastbit=/sw/redhat6/fastbit/svn/rhel6_gnu4.4.7"
- #DATASPACES_DIR="/ccs/proj/e2e/dataspaces/sith-tcp/1.6.pgi"
- #DATASPACES_DIR="/ccs/home/hbui/usr/software/dataspaces-dev"
- elif [ "$TARGET" == "gnu" ]; then
- export CC=gcc
- export CXX=g++
- export FC=gfortran
- #export CFLAGS="$CFLAGS -gdwarf-3"
- #export FCFLAGS="$FCFLAGS -gdwarf-3"
- WITHFLEX="--with-flexpath=/ccs/proj/e2e/chaos/sith/$TARGET"
- WITHALACRITY="--with-alacrity=/ccs/proj/e2e/ncsu/alacrity/sith/gnu"
- WITHFASTBIT="--with-fastbit=/sw/redhat6/fastbit/svn/rhel6_gnu4.8.2"
- #DATASPACES_DIR="/ccs/proj/e2e/dataspaces/sith-tcp/1.6.gnu"
- elif [ "$TARGET" == "intel" ]; then
- export CC=icc
- export CXX=icpc
- export FC=ifort
- WITHALACRITY="--with-alacrity=/ccs/proj/e2e/ncsu/alacrity/sith/intel"
- WITHFASTBIT="--with-fastbit=/sw/redhat6/fastbit/svn/rhel6_gnu4.8.2"
- else
- echo "TARGET must be pgi or gnu or intel"
- exit 1
- fi
-
- $SRCDIR/configure --prefix=/ccs/proj/e2e/${USER}/ADIOS/sith.$TARGET \
- --config-cache \
- --disable-maintainer-mode \
- --enable-dependency-tracking \
- --enable-research-transports \
- --with-lustre \
- --with-hdf5=${SEQ_HDF5_DIR} \
- --with-hdf5-libs="${SEQ_HDF5_CLIB}" \
- --with-zlib \
- --with-bzip2=$BZIP2_DIR \
- --with-dataspaces=$DATASPACES_DIR \
- $WITHFLEX \
- $WITHFASTBIT \
- $WITHALACRITY \
- --with-aplod=/ccs/proj/e2e/ncsu/sith.gnu \
- --with-isobar=/ccs/proj/e2e/ncsu/sith.gnu \
- #$WITHFASTBIT \
- #--with-netcdf=${SEQ_NC_DIR} \
- #--with-netcdf-libs="${SEQ_NC_CLIB}" \
- #--with-dimes=$DATASPACES_DIR \
- #--with-glib=/ccs/proj/e2e/qliu/glib
- #$WITHFGR \
- #--with-szip=$SZIP_DIR \
- #--with-phdf5=${PAR_HDF5_DIR} \
- #--with-phdf5-libs="${PAR_HDF5_CLIB}" \
- #--with-nc4par=${PAR_NC_DIR} \
- #--with-nc4par-libs="${PAR_NC_CLIB}" \
- #--with-dmalloc=/ccs/proj/e2e/qliu/dmalloc.sith.$TARGET
- #--with-dmalloc=/ccs/proj/e2e/pnorbert/dmalloc.$TARGET
- #--enable-shared --disable-static
- #--without-datatap #--without-infiniband
- #--with-dmalloc=/ccs/proj/e2e/pnorbert/dmalloc.$TARGET
- #--with-datatap=/ccs/home/habbasi/work/ewok/
- #--enable-datatap=ib
-
-elif [ `hostname | cut -c 1-4` == "rhea" ]; then
+if [ `hostname | cut -c 1-4` == "rhea" ]; then
########
# Rhea #
@@ -174,13 +50,14 @@ elif [ `hostname | cut -c 1-4` == "rhea" ]; then
#module unload netcdf
#module load szip
#module load bzip2
- module load dataspaces/1.6.1
- module load flexpath/stable
+ module load dataspaces/1.6.2
+ module load flexpath/1.12
module load alacrity/1.0.0
module load fastbit/svn
export MPICC=mpicc
export MPICXX=mpiCC
export MPIFC=mpif90
+ unset EXTRA_CFLAGS
if [ "$TARGET" == "pgi" ]; then
export CC=pgcc
export CXX=pgCC
@@ -193,6 +70,7 @@ elif [ `hostname | cut -c 1-4` == "rhea" ]; then
export CC=icc
export CXX=icpc
export FC=ifort
+ export EXTRA_CFLAGS="-std=c99"
WITHFLEX=""
else
echo "TARGET must be pgi or gnu or intel"
@@ -200,7 +78,7 @@ elif [ `hostname | cut -c 1-4` == "rhea" ]; then
fi
export CPPFLAGS="-DMPICH_IGNORE_CXX_SEEK"
- export CFLAGS="-g -fPIC"
+ export CFLAGS="-g -fPIC ${EXTRA_CFLAGS}"
$SRCDIR/configure --prefix=/ccs/proj/e2e/${USER}/ADIOS/rhea.$TARGET \
--disable-maintainer-mode \
--enable-dependency-tracking \
@@ -212,8 +90,8 @@ elif [ `hostname | cut -c 1-4` == "rhea" ]; then
--with-zlib \
--with-bzip2 \
--with-fastbit=$FASTBIT_DIR \
- #--with-hdf5=${SEQ_HDF5_DIR} \
- #--with-hdf5-libs="${SEQ_HDF5_CLIB}" \
+ --with-hdf5=${SEQ_HDF5_DIR} \
+ --with-hdf5-libs="${SEQ_HDF5_CLIB}" \
#--with-phdf5=${PAR_HDF5_DIR} \
#--with-phdf5-libs="${PAR_HDF5_CLIB}" \
#--with-netcdf=${SEQ_NC_DIR} \
@@ -226,91 +104,6 @@ elif [ `hostname | cut -c 1-4` == "rhea" ]; then
#--with-glib=/ccs/proj/e2e/qliu/glib
#--with-szip=$SZIP_DIR \
-elif [ `hostname | cut -c 1-4` == "yona" ]; then
-
- ########
- # Yona #
- ########
- source /etc/profile.d/modules.sh
- TARGET=`module list 2>&1 | grep "PE"- | sed "s/^.*PE-\([a-z]*\).*/\1/"`
- echo "Configure on Yona for $TARGET env."
- module unload hdf5
- module unload netcdf
- module unload PE-gnu
- module unload PE-pgi
- module unload PE-intel
- module unload PE-pathscale
- module unload pgi gcc intel pathscale
- #module unload python
- module load PE-$TARGET
- #module load python
- # Use both seq hdf5 (for utils) and
- # parallel hdf5 (for PHDF5 method)
- module load hdf5/1.8.5
- SEQ_HDF5_DIR=$HDF5_DIR
- SEQ_HDF5_CLIB=$HDF5_CLIB
- module unload hdf5
- #module load hdf5/1.8.5_par
- #PAR_HDF5_DIR=$HDF5_DIR
- #PAR_HDF5_CLIB=$HDF5_CLIB
- #module unload hdf5
- # Seq. and Parallel NetCDF 4
- module load netcdf/3.6.2
- SEQ_NC_DIR=$NETCDF_DIR
- SEQ_NC_CLIB=$NETCDF_CLIB
- module unload netcdf
- #module load netcdf/4.1.1_par
- #PAR_NC_DIR=$NETCDF_DIR
- #PAR_NC_CLIB=$NETCDF_CLIB
- #module unload netcdf
- export MPICC=mpicc
- export MPICXX=mpiCC
- export MPIFC=mpif90
- if [ "$TARGET" == "pgi" ]; then
- export CC=pgcc
- export CXX=pgCC
- export FC=pgf90
- elif [ "$TARGET" == "gnu" ]; then
- export CC=gcc
- export CXX=g++
- export FC=gfortran
- elif [ "$TARGET" == "intel" ]; then
- export CC=pgcc
- export CXX=pgCC
- export FC=pgf90
- elif [ "$TARGET" == "gnu" ]; then
- export CC=gcc
- export CXX=g++
- export FC=gfortran
- elif [ "$TARGET" == "intel" ]; then
- export CC=icc
- export CXX=icpc
- export FC=ifort
- else
- echo "TARGET must be pgi or gnu or intel"
- exit 1
- fi
-
- export CFLAGS="-g -fPIC"
- ${SRCDIR}/configure --prefix=/ccs/proj/e2e/pnorbert/ADIOS/yona.$TARGET \
- --config-cache \
- --disable-maintainer-mode \
- --enable-dependency-tracking \
- --enable-research-transports \
- --with-hdf5=${SEQ_HDF5_DIR} \
- --with-hdf5-libs="${SEQ_HDF5_CLIB}" \
- --with-netcdf=${SEQ_NC_DIR} \
- --with-netcdf-libs="${SEQ_NC_CLIB}" \
- --with-lustre=/usr \
- --without-datatap --without-infiniband
- #--with-phdf5=${PAR_HDF5_DIR} \
- #--with-phdf5-libs="${PAR_HDF5_CLIB}" \
- #--with-nc4par=${PAR_NC_DIR} \
- #--with-nc4par-libs="${PAR_NC_CLIB}" \
- #--with-dmalloc=/ccs/proj/e2e/pnorbert/dmalloc.$TARGET
- #--with-datatap=/ccs/home/habbasi/work/ewok/
- #--enable-datatap=ib
-
elif [ `hostname | cut -c 1-5` == "titan" ]; then
@@ -334,6 +127,7 @@ elif [ `hostname | cut -c 1-5` == "titan" ]; then
module unload craype-mc8 craype-mc12
module load craype-istanbul
module load dataspaces # /1.6.1
+ module load flexpath # /1.12
unset EXTRA_CFLAGS
unset EXTRA_LIBS
unset LDFLAGS
@@ -348,7 +142,6 @@ elif [ `hostname | cut -c 1-5` == "titan" ]; then
#export EXTRA_LIBS="/opt/gcc/4.9.0/snos/lib64/libstdc++.a"
export EXTRA_CFLAGS="-fast"
#DATASPACES_DIR="/ccs/proj/e2e/dataspaces/titan/$target-cpu"
- module load flexpath/stable
WITHFLEX="--with-flexpath=$FLEXPATH_DIR"
elif [ "$TARGET" == "gnu" ]; then
#export CC=gcc
@@ -360,7 +153,8 @@ elif [ `hostname | cut -c 1-5` == "titan" ]; then
# NSSI/FLEXPATH/FASTBIT needs libstdc++
export LDFLAGS=""
module load fastbit
- WITHFLEX="--with-flexpath=/ccs/proj/e2e/chaos/titan/$TARGET"
+ WITHFLEX="--with-flexpath=$FLEXPATH_DIR"
+ #WITHFLEX="--with-flexpath=/ccs/proj/e2e/chaos/titan/$TARGET"
# FASTBIT needs libstdc++
WITHFASTBIT="--with-fastbit=$FASTBIT_DIR"
#export EXTRA_LIBS="${GCC_PATH}/snos/lib64/libstdc++.a"
@@ -474,7 +268,8 @@ elif [ `hostname | cut -c 1-7` == "chester" ]; then
module unload netcdf-hdf5parallel
module unload hdf5-parallel
module swap craype-interlagos craype-istanbul
- module load dataspaces/1.6.0
+ module load dataspaces # /1.6.2
+ module load flexpath # /1.12
module load fastbit
WITHFASTBIT=""
WITHALACRITY=""
@@ -487,6 +282,7 @@ elif [ `hostname | cut -c 1-7` == "chester" ]; then
export MPICXX=CC
# FASTBIT, ALACRITY need -pgcpplibs flag
WITHALACRITY="--with-alacrity=/ccs/proj/e2e/ncsu/alacrity/xk6/pgi"
+ export FLEXPATH="--with-flexpath=$FLEXPATH_DIR"
export LDFLAGS="-pgc++libs"
unset EXTRA_LIBS
elif [ "$TARGET" == "gnu" ]; then
@@ -502,7 +298,8 @@ elif [ `hostname | cut -c 1-7` == "chester" ]; then
#WITHFASTBIT="--with-fastbit=${FASTBIT_DIR}"
#export LDFLAGS="-static -static-libstdc++"
#export EXTRA_LIBS="${GCC_PATH}/snos/lib64/libstdc++.a"
- export FLEXPATH="--with-flexpath=/ccs/proj/e2e/chaos/titan/gnu"
+ #export FLEXPATH="--with-flexpath=/ccs/proj/e2e/chaos/titan/gnu"
+ export FLEXPATH="--with-flexpath=$FLEXPATH_DIR"
#module swap gcc gcc/4.4.4
elif [ "$TARGET" == "cray" ]; then
export EXTRA_CFLAGS="-h gnu"
@@ -536,6 +333,341 @@ elif [ `hostname | cut -c 1-7` == "chester" ]; then
# --with-cray-ugni-incdir=/opt/cray/gni-headers/2.1-1.0400.4351.3.1.gem/include \
+elif [ `hostname -f | cut -c 1-9` == "summitdev" ]; then
+ #####################
+ # SUMMITDEV IBM #
+ #####################
+ MLIST=`module list 2>&1 ` #| grep "PrgEnv"- | sed "s/^.*PrgEnv-\([a-z]*\).*/\1/"`
+ TARGET=`echo $MLIST | grep " xl\/" | sed "s/^.* xl\/.*/xl/"`
+ if [ -z $TARGET ]; then
+ TARGET=`echo $MLIST | grep " pgi\/" | sed "s/^.* pgi\/.*/pgi/"`
+ if [ -z $TARGET ]; then
+ TARGET=`echo $MLIST | grep " gcc\/" | sed "s/^.* gcc\/.*/gcc/"`
+ if [ -z $TARGET ]; then
+ TARGET=`echo $MLIST | grep " clang\/" | sed "s/^.* clang\/.*/clang/"`
+ fi
+ fi
+ fi
+ echo "Configure on Summitdev for $TARGET env."
+
+ unset WITH_DATASPACES
+ FORTRAN_BUILD="--enable-fortran"
+ if [ "$TARGET" == "xl" ]; then
+ export MPICC=mpicc
+ export MPCXX=mpic++
+ export MPIFC=mpif90
+ export CFLAGS="-g -O0"
+ export FC=xlf90
+ export CC=xlc
+ export CXX=xlC
+ #export LIBS="-lrdmacm -libverbs"
+ DATASPACES_DIR=/ccs/proj/e2e/dataspaces/summitdev/1.6.1/xl
+ #WITH_DATASPACES="--with-dataspaces=$DATASPACES_DIR --with-dimes=$DATASPACES_DIR"
+ elif [ "$TARGET" == "pgi" ]; then
+ export CC=pgcc
+ export FC=pgf90
+ export CXX=pgc++
+ export MPICC=mpicc
+ export MPCXX=mpic++
+ export MPIFC=mpif90
+ export CFLAGS="-g -O0"
+ #DATASPACES_DIR=/ccs/proj/e2e/dataspaces/summitdev/1.6.1/pgi
+ #WITH_DATASPACES="--with-dataspaces=$DATASPACES_DIR --with-dimes=$DATASPACES_DIR"
+ elif [ "$TARGET" == "gcc" ]; then
+ export CC=gcc
+ export FC=gfortran
+ export CXX=g++
+ export MPICC=mpicc
+ export MPCXX=mpic++
+ export MPIFC=mpif90
+ export CFLAGS="-g -O0"
+ DATASPACES_DIR=/ccs/proj/e2e/dataspaces/summitdev/1.6.1/gcc
+ #WITH_DATASPACES="--with-dataspaces=$DATASPACES_DIR --with-dimes=$DATASPACES_DIR"
+ elif [ "$TARGET" == "clang" ]; then
+ export CC=clang
+ export CXX=clang++
+ export MPICC=mpicc
+ export MPCXX=mpic++
+ export CFLAGS="-g -O0"
+ DATASPACES_DIR=/ccs/proj/e2e/dataspaces/summitdev/1.6.1/clang
+ FORTRAN_BUILD="--disable-fortran"
+ #WITH_DATASPACES="--with-dataspaces=$DATASPACES_DIR --with-dimes=$DATASPACES_DIR"
+ fi
+
+ ${SRCDIR}/configure --prefix=/ccs/proj/e2e/pnorbert/ADIOS/summitdev.$TARGET \
+ --disable-maintainer-mode \
+ --enable-dependency-tracking \
+ $FORTRAN_BUILD \
+ --without-datatap \
+ $WITH_DATASPACES
+
+elif [ `hostname | cut -c 1-4` == "sith" ]; then
+
+ ########
+ # Sith #
+ ########
+ #source /etc/profile.d/modules.sh
+ TARGET=`module list 2>&1 | grep "PE"- | sed "s/^.*PE-\([a-z]*\).*/\1/"`
+
+ if [ -z "$TARGET" ]; then
+ echo "Cannot determine Programming environment. Exit"
+ exit 1
+ fi
+ echo "Configure on SITH for $TARGET env. for user ${USER}"
+ module unload hdf5
+ module unload netcdf
+ module unload python
+ #module unload PE-gnu
+ #module unload PE-pgi
+ #module unload PE-intel
+ #module unload PE-pathscale
+ #module unload pgi gcc intel pathscale
+ #module load PE-$TARGET
+ module load python
+ # Use both seq hdf5 (for utils) and
+ # parallel hdf5 (for PHDF5 method)
+ module load hdf5/1.8.10
+ SEQ_HDF5_DIR=$HDF5_DIR
+ SEQ_HDF5_CLIB=$HDF5_CLIB
+ module unload hdf5
+ module load hdf5/1.8.10_par
+ PAR_HDF5_DIR=$HDF5_DIR
+ PAR_HDF5_CLIB=$HDF5_CLIB
+ module unload hdf5
+ # Seq. and Parallel NetCDF 4
+ module load netcdf/4.1.3
+ SEQ_NC_DIR=$NETCDF_DIR
+ SEQ_NC_CLIB=$NETCDF_CLIB
+ module unload netcdf
+ module load netcdf/4.1.3_par
+ PAR_NC_DIR=$NETCDF_DIR
+ PAR_NC_CLIB=$NETCDF_CLIB
+ module unload netcdf
+ #module load szip
+ module load bzip2
+ module unload dataspaces
+ unset DATASPACES_DIR
+ module load dataspaces/1.6.0
+ export MPICC=mpicc
+ export MPICXX=mpiCC
+ export MPIFC=mpif90
+ export CPPFLAGS="-DMPICH_IGNORE_CXX_SEEK"
+ export CFLAGS="-g -O0 -fPIC"
+ export CXXFLAGS="-g -O0 -fPIC"
+ export FCFLAGS="-g -O0 -fPIC"
+ WITHFLEX=""
+ WITHFGR=""
+ WITHFASTBIT=""
+ WITHALACRITY=""
+ if [ "$TARGET" == "pgi" ]; then
+ export CC=pgcc
+ export CXX=pgc++
+ export FC=pgf90
+ WITHFLEX="--with-flexpath=/ccs/proj/e2e/chaos/sith/$TARGET"
+ WITHFGR="--with-fgr=/ccs/proj/e2e/qliu/tap"
+ WITHALACRITY="--with-alacrity=/ccs/proj/e2e/ncsu/alacrity/sith/pgi"
+ WITHFASTBIT="--with-fastbit=/sw/redhat6/fastbit/svn/rhel6_gnu4.4.7"
+ #DATASPACES_DIR="/ccs/proj/e2e/dataspaces/sith-tcp/1.6.pgi"
+ #DATASPACES_DIR="/ccs/home/hbui/usr/software/dataspaces-dev"
+ elif [ "$TARGET" == "gnu" ]; then
+ export CC=gcc
+ export CXX=g++
+ export FC=gfortran
+ #export CFLAGS="$CFLAGS -gdwarf-3"
+ #export FCFLAGS="$FCFLAGS -gdwarf-3"
+ WITHFLEX="--with-flexpath=/ccs/proj/e2e/chaos/sith/$TARGET"
+ WITHALACRITY="--with-alacrity=/ccs/proj/e2e/ncsu/alacrity/sith/gnu"
+ WITHFASTBIT="--with-fastbit=/sw/redhat6/fastbit/svn/rhel6_gnu4.8.2"
+ #DATASPACES_DIR="/ccs/proj/e2e/dataspaces/sith-tcp/1.6.gnu"
+ elif [ "$TARGET" == "intel" ]; then
+ export CC=icc
+ export CXX=icpc
+ export FC=ifort
+ WITHALACRITY="--with-alacrity=/ccs/proj/e2e/ncsu/alacrity/sith/intel"
+ WITHFASTBIT="--with-fastbit=/sw/redhat6/fastbit/svn/rhel6_gnu4.8.2"
+ else
+ echo "TARGET must be pgi or gnu or intel"
+ exit 1
+ fi
+
+ $SRCDIR/configure --prefix=/ccs/proj/e2e/${USER}/ADIOS/sith.$TARGET \
+ --config-cache \
+ --disable-maintainer-mode \
+ --enable-dependency-tracking \
+ --enable-research-transports \
+ --with-lustre \
+ #--with-zlib \
+ #--with-bzip2=$BZIP2_DIR \
+ #--with-dataspaces=$DATASPACES_DIR \
+ #$WITHFLEX \
+ #$WITHFASTBIT \
+ #$WITHALACRITY \
+ #--with-aplod=/ccs/proj/e2e/ncsu/sith.gnu \
+ #--with-isobar=/ccs/proj/e2e/ncsu/sith.gnu \
+ #--with-hdf5=${SEQ_HDF5_DIR} \
+ #--with-hdf5-libs="${SEQ_HDF5_CLIB}" \
+ #--with-netcdf=${SEQ_NC_DIR} \
+ #--with-netcdf-libs="${SEQ_NC_CLIB}" \
+ #--with-dimes=$DATASPACES_DIR \
+ #--with-glib=/ccs/proj/e2e/qliu/glib
+ #$WITHFGR \
+ #--with-szip=$SZIP_DIR \
+ #--with-phdf5=${PAR_HDF5_DIR} \
+ #--with-phdf5-libs="${PAR_HDF5_CLIB}" \
+ #--with-nc4par=${PAR_NC_DIR} \
+ #--with-nc4par-libs="${PAR_NC_CLIB}" \
+ #--with-dmalloc=/ccs/proj/e2e/qliu/dmalloc.sith.$TARGET
+ #--with-dmalloc=/ccs/proj/e2e/pnorbert/dmalloc.$TARGET
+ #--enable-shared --disable-static
+ #--without-datatap #--without-infiniband
+ #--with-dmalloc=/ccs/proj/e2e/pnorbert/dmalloc.$TARGET
+ #--with-datatap=/ccs/home/habbasi/work/ewok/
+ #--enable-datatap=ib
+
+elif [ `hostname | cut -c 1-4` == "yona" ]; then
+
+ ########
+ # Yona #
+ ########
+ source /etc/profile.d/modules.sh
+ TARGET=`module list 2>&1 | grep "PE"- | sed "s/^.*PE-\([a-z]*\).*/\1/"`
+ echo "Configure on Yona for $TARGET env."
+ module unload hdf5
+ module unload netcdf
+ module unload PE-gnu
+ module unload PE-pgi
+ module unload PE-intel
+ module unload PE-pathscale
+ module unload pgi gcc intel pathscale
+ #module unload python
+ module load PE-$TARGET
+ #module load python
+ # Use both seq hdf5 (for utils) and
+ # parallel hdf5 (for PHDF5 method)
+ module load hdf5/1.8.5
+ SEQ_HDF5_DIR=$HDF5_DIR
+ SEQ_HDF5_CLIB=$HDF5_CLIB
+ module unload hdf5
+ #module load hdf5/1.8.5_par
+ #PAR_HDF5_DIR=$HDF5_DIR
+ #PAR_HDF5_CLIB=$HDF5_CLIB
+ #module unload hdf5
+ # Seq. and Parallel NetCDF 4
+ module load netcdf/3.6.2
+ SEQ_NC_DIR=$NETCDF_DIR
+ SEQ_NC_CLIB=$NETCDF_CLIB
+ module unload netcdf
+ #module load netcdf/4.1.1_par
+ #PAR_NC_DIR=$NETCDF_DIR
+ #PAR_NC_CLIB=$NETCDF_CLIB
+ #module unload netcdf
+ export MPICC=mpicc
+ export MPICXX=mpiCC
+ export MPIFC=mpif90
+ if [ "$TARGET" == "pgi" ]; then
+ export CC=pgcc
+ export CXX=pgCC
+ export FC=pgf90
+ elif [ "$TARGET" == "gnu" ]; then
+ export CC=gcc
+ export CXX=g++
+ export FC=gfortran
+ elif [ "$TARGET" == "intel" ]; then
+ export CC=pgcc
+ export CXX=pgCC
+ export FC=pgf90
+ elif [ "$TARGET" == "gnu" ]; then
+ export CC=gcc
+ export CXX=g++
+ export FC=gfortran
+ elif [ "$TARGET" == "intel" ]; then
+ export CC=icc
+ export CXX=icpc
+ export FC=ifort
+ else
+ echo "TARGET must be pgi or gnu or intel"
+ exit 1
+ fi
+
+ export CFLAGS="-g -fPIC"
+ ${SRCDIR}/configure --prefix=/ccs/proj/e2e/pnorbert/ADIOS/yona.$TARGET \
+ --config-cache \
+ --disable-maintainer-mode \
+ --enable-dependency-tracking \
+ --enable-research-transports \
+ --with-hdf5=${SEQ_HDF5_DIR} \
+ --with-hdf5-libs="${SEQ_HDF5_CLIB}" \
+ --with-netcdf=${SEQ_NC_DIR} \
+ --with-netcdf-libs="${SEQ_NC_CLIB}" \
+ --with-lustre=/usr \
+ --without-datatap --without-infiniband
+ #--with-phdf5=${PAR_HDF5_DIR} \
+ #--with-phdf5-libs="${PAR_HDF5_CLIB}" \
+ #--with-nc4par=${PAR_NC_DIR} \
+ #--with-nc4par-libs="${PAR_NC_CLIB}" \
+ #--with-dmalloc=/ccs/proj/e2e/pnorbert/dmalloc.$TARGET
+ #--with-datatap=/ccs/home/habbasi/work/ewok/
+ #--enable-datatap=ib
+
+
+
+elif [ `hostname | cut -c 1-5` == "theta" ]; then
+
+ ##########
+ # THETA #
+ ##########
+ TARGET=`module list 2>&1 | grep "PrgEnv"- | sed "s/^.*PrgEnv-\([a-z]*\).*/\1/"`
+ CPUARCH=`module list 2>&1 | grep -e craype-broadwell -e craype-haswell -e craype-mic-knl -e craype-ivybridge -e craype-sandybridge -e craype-intel-knc | sed -e "s/.*craype-//"`
+ echo "Configure on THETA for $TARGET env. for $CPUARCH CPU"
+ export MPICC=cc
+ export MPICXX=CC
+ export MPIFC=ftn
+ module unload darshan
+ module unload hdf5
+ module unload netcdf
+ module unload hdf5-parallel
+ module unload netcdf-hdf5parallel
+ WITHDART=""
+ if [ "$TARGET" == "pgi" ]; then
+ export CC=pgcc
+ export CXX=pgCC
+ export FC=pgf90
+ export LDFLAGS="-pgc++libs"
+ elif [ "$TARGET" == "gnu" ]; then
+ export CC=gcc
+ export CXX=g++
+ export FC=gfortran
+ export LDFLAGS=""
+ elif [ "$TARGET" == "intel" ]; then
+ export CC=icc
+ export CXX=icpc
+ export FC=ifort
+ export LDFLAGS=""
+ elif [ "$TARGET" == "cray" ]; then
+ export EXTRA_CFLAGS="-h gnu"
+ export CC=cc
+ export CXX=CC
+ export FC=ftn
+ export LDFLAGS=""
+ export EXTRA_CFLAGS="-h gnu"
+ else
+ echo "TARGET must be one of [ pgi | gnu | intel | cray ]"
+ exit 1
+ fi
+
+ export CPPFLAGS="-DMPICH_IGNORE_CXX_SEEK"
+ export CFLAGS="-fPIC ${EXTRA_CFLAGS}"
+ ${SRCDIR}/configure --prefix=/home/pnorbert/sw/adios/1.12/theta/$TARGET.$CPUARCH \
+ --disable-maintainer-mode \
+ --enable-dependency-tracking \
+ --with-cray-pmi-incdir=/opt/cray/pmi/default/include \
+ --with-cray-pmi-libdir=/opt/cray/pmi/default/lib64 \
+ --with-cray-ugni-incdir=/opt/cray/gni-headers/default/include \
+ --with-cray-ugni-libdir=/opt/cray/ugni/default/lib64 \
+ --without-infiniband \
+ --without-hdf5 --without-netcdf
+
+
elif [ `hostname -f | cut -c 1-4` == "mira" ]; then
#####################
# MIRA BlueGene #
@@ -581,7 +713,8 @@ elif [ `hostname | cut -c 1-4` == "cori" ]; then
# CORI #
##########
TARGET=`module list 2>&1 | grep "PrgEnv"- | sed "s/^.*PrgEnv-\([a-z]*\).*/\1/"`
- echo "Configure on CORI for $TARGET env."
+ CPUARCH=`module list 2>&1 | grep -e craype-broadwell -e craype-haswell -e craype-mic-knl -e craype-ivybridge -e craype-intel-knc | sed -e "s/.*craype-//"`
+ echo "Configure on CORI for $TARGET env. for $CPUARCH CPU"
export MPICC=cc
export MPICXX=CC
export MPIFC=ftn
@@ -621,7 +754,7 @@ elif [ `hostname | cut -c 1-4` == "cori" ]; then
export CPPFLAGS="-DMPICH_IGNORE_CXX_SEEK"
export CFLAGS="-fPIC ${EXTRA_CFLAGS}"
- ${SRCDIR}/configure --prefix=/global/homes/p/pnorbert/adios/1.11.0/cori/$TARGET \
+ ${SRCDIR}/configure --prefix=/global/homes/p/pnorbert/adios/1.12/cori/$TARGET.$CPUARCH \
--disable-maintainer-mode \
--enable-dependency-tracking \
--with-lustre=/usr \
@@ -888,14 +1021,15 @@ elif [ `hostname | cut -c 1-7` == "adiosVM" ]; then
export FC=gfortran
export CFLAGS="-g -O0 -fPIC -Wno-int-to-pointer-cast -Wno-pointer-to-int-cast"
- ${SRCDIR}/configure --prefix=/opt/adios/1.11 \
+ ${SRCDIR}/configure --prefix=/opt/adios \
--disable-maintainer-mode \
--enable-dependency-tracking \
--enable-timers \
--disable-timer-events \
--with-zlib \
--with-bzip2 \
- --with-szip=/opt/szip \
+ --with-sz=/opt/SZ \
+ --without-szip \
--with-isobar=/opt/isobar \
--with-flexpath=/opt/chaos \
--with-dataspaces=/opt/dataspaces --without-infiniband \
diff --git a/scripts/FindADIOS.cmake b/scripts/FindADIOS.cmake
index 074cf74..4936daf 100644
--- a/scripts/FindADIOS.cmake
+++ b/scripts/FindADIOS.cmake
@@ -178,10 +178,10 @@ if(ADIOS_FOUND)
endforeach()
# we could append ${CMAKE_PREFIX_PATH} now but that is not really necessary
- #message(STATUS "ADIOS DIRS to look for libs: ${ADIOS_LIBRARY_DIRS}")
+ message(STATUS "ADIOS DIRS to look for libs: ${ADIOS_LIBRARY_DIRS}")
# parse all -lname libraries and find an absolute path for them
- string(REGEX MATCHALL " -l([A-Za-z_0-9\\.-]+)" _ADIOS_LIBS " ${ADIOS_LINKFLAGS}")
+ string(REGEX MATCHALL " -l([A-Za-z_0-9\\.\\-\\+]+)" _ADIOS_LIBS " ${ADIOS_LINKFLAGS}")
foreach(_LIB ${_ADIOS_LIBS})
string(REPLACE " -l" "" _LIB ${_LIB})
@@ -203,8 +203,13 @@ if(ADIOS_FOUND)
endforeach()
#add libraries which are already using cmake format
- string(REGEX MATCHALL "/([A-Za-z_0-9/\\.-]+)\\.([a|so]+)" _ADIOS_LIBS_SUB "${ADIOS_LINKFLAGS}")
- list(APPEND ADIOS_LIBRARIES "${_ADIOS_LIBS_SUB}")
+ string(REGEX MATCHALL "/([A-Za-z_0-9/\\.\\-\\+]+)\\.([a|so]+)" _ADIOS_LIBS_SUB "${ADIOS_LINKFLAGS}")
+ foreach(foo ${_ADIOS_LIBS_SUB})
+ if (EXISTS ${foo})
+ message("Appending: ${foo}")
+ list(APPEND ADIOS_LIBRARIES "${foo}")
+ endif()
+ endforeach(foo)
# add the version string
execute_process(COMMAND ${ADIOS_CONFIG} -v
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 0d797df..0f216b1 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -10,7 +10,7 @@ if (BUILD_MXML)
set(EXTRA_OBJECTS ${EXTRA_OBJECTS} $<TARGET_OBJECTS:mxml>)
endif(BUILD_MXML)
-# Build the zfp library in src/zfp
+# Build the zfp library in src/zfp
if (BUILD_ZFP)
add_subdirectory(zfp)
set(ZFP_BUILDDIR "zfp/zfp-0.5.0")
@@ -29,11 +29,11 @@ link_directories(${PROJECT_BINARY_DIR}/src)
if(HAVE_NSSI)
add_executable(nssi-staging-server nssi/nssi_staging_server.cpp nssi/aggregation.cpp)
- set_target_properties(nssi-staging-server PROPERTIES COMPILE_FLAGS "${ADIOSLIB_CFLAGS} ${ADIOSLIB_EXTRA_CPPFLAGS} ${ADIOSLIB_CPPFLAGS} ${MACRODEFFLAG}PTL_IFACE_CLIENT=CRAY_USER_NAL ${MACRODEFFLAG}PTL_IFACE_SERVER=CRAY_USER_NAL")
+ set_target_properties(nssi-staging-server PROPERTIES COMPILE_FLAGS "${ADIOSLIB_CFLAGS} ${ADIOSLIB_EXTRA_CPPFLAGS} ${ADIOSLIB_CPPFLAGS} ${MACRODEFFLAG}PTL_IFACE_CLIENT=CRAY_USER_NAL ${MACRODEFFLAG}PTL_IFACE_SERVER=CRAY_USER_NAL")
target_link_libraries(nssi-staging-server adios.a ${ADIOSLIB_LDADD} ${NSSI_SERVER_LIBS})
add_executable(nssi-coupling-server nssi/nssi_coupling_server.cpp)
- set_target_properties(nssi-coupling-server PROPERTIES COMPILE_FLAGS "${ADIOSLIB_CFLAGS} ${ADIOSLIB_EXTRA_CPPFLAGS} ${ADIOSLIB_CPPFLAGS} ${MACRODEFFLAG}PTL_IFACE_CLIENT=CRAY_USER_NAL ${MACRODEFFLAG}PTL_IFACE_SERVER=CRAY_USER_NAL")
+ set_target_properties(nssi-coupling-server PROPERTIES COMPILE_FLAGS "${ADIOSLIB_CFLAGS} ${ADIOSLIB_EXTRA_CPPFLAGS} ${ADIOSLIB_CPPFLAGS} ${MACRODEFFLAG}PTL_IFACE_CLIENT=CRAY_USER_NAL ${MACRODEFFLAG}PTL_IFACE_SERVER=CRAY_USER_NAL")
target_link_libraries(nssi-coupling-server adios.a ${ADIOSLIB_LDADD} ${NSSI_SERVER_LIBS})
endif(HAVE_NSSI)
@@ -61,61 +61,63 @@ set(transforms_read_method_SOURCES "")
##
## Core transform framework source files
##
-set (transforms_common_HDRS core/adios_copyspec.h
- core/adios_subvolume.h
- core/adios_selection_util.h
- core/transforms/adios_transforms_common.h
- core/transforms/adios_transforms_hooks.h
- core/transforms/adios_transforms_util.h
+set (transforms_common_HDRS core/adios_copyspec.h
+ core/adios_subvolume.h
+ core/adios_selection_util.h
+ core/transforms/adios_transforms_common.h
+ core/transforms/adios_transforms_hooks.h
+ core/transforms/adios_transforms_util.h
core/adios_subvolume.h
public/adios_transform_methods.h)
-set (transforms_read_HDRS core/transforms/adios_transforms_read.h
- core/transforms/adios_transforms_hooks_read.h
- core/transforms/adios_transforms_reqgroup.h
+set (transforms_read_HDRS core/transforms/adios_transforms_read.h
+ core/transforms/adios_transforms_hooks_read.h
+ core/transforms/adios_transforms_reqgroup.h
core/transforms/adios_transforms_datablock.h
core/transforms/adios_transforms_transinfo.h
core/transforms/adios_patchdata.h)
-set (transforms_write_HDRS core/transforms/adios_transforms_write.h
- core/transforms/adios_transforms_hooks_write.h
+set (transforms_write_HDRS core/transforms/adios_transforms_write.h
+ core/transforms/adios_transforms_hooks_write.h
core/transforms/adios_transforms_specparse.h)
-set (transforms_common_SOURCES ${transforms_common_HDRS}
- core/transforms/adios_transforms_common.c
- core/transforms/adios_transforms_hooks.c
- core/adios_copyspec.c
- core/adios_subvolume.c
- core/transforms/plugindetect/detect_plugin_infos.h
- core/transforms/plugindetect/detect_plugin_types.h
+set (transforms_common_SOURCES ${transforms_common_HDRS}
+ core/transforms/adios_transforms_common.c
+ core/transforms/adios_transforms_hooks.c
+ core/adios_copyspec.c
+ core/adios_subvolume.c
+ core/transforms/plugindetect/detect_plugin_infos.h
+ core/transforms/plugindetect/detect_plugin_types.h
core/transforms/plugindetect/plugin_info_types.h
core/adios_transform_methods.c)
-set (transforms_read_SOURCES ${transforms_read_HDRS}
- core/transforms/adios_transforms_read.c
- core/transforms/adios_transforms_hooks_read.c
- core/transforms/adios_transforms_reqgroup.c
- core/transforms/adios_transforms_datablock.c
- core/transforms/adios_patchdata.c
+set (transforms_read_SOURCES ${transforms_read_HDRS}
+ core/transforms/adios_transforms_read.c
+ core/transforms/adios_transforms_hooks_read.c
+ core/transforms/adios_transforms_reqgroup.c
+ core/transforms/adios_transforms_datablock.c
+ core/transforms/adios_patchdata.c
transforms/adios_transform_alacrity_read.c
transforms/adios_transform_isobar_read.c
transforms/adios_transform_aplod_read.c
- transforms/adios_transform_szip_read.c
+ transforms/adios_transform_szip_read.c
transforms/adios_transform_bzip2_read.c
transforms/adios_transform_identity_read.c
transforms/adios_transform_zlib_read.c
transforms/adios_transform_zfp_read.c
- core/adios_selection_util.c
+ transforms/adios_transform_sz_read.c
+ transforms/adios_transform_lz4_read.c
+ core/adios_selection_util.c
core/transforms/plugindetect/detect_plugin_read_hook_decls.h
core/transforms/plugindetect/detect_plugin_read_hook_reg.h
core/adios_read_ext.c
${transforms_read_method_SOURCES})
-set (transforms_write_SOURCES ${transforms_write_HDRS}
- core/transforms/adios_transforms_write.c
- core/transforms/adios_transforms_hooks_write.c
- core/transforms/adios_transforms_util.c
- core/transforms/adios_transforms_specparse.c
+set (transforms_write_SOURCES ${transforms_write_HDRS}
+ core/transforms/adios_transforms_write.c
+ core/transforms/adios_transforms_hooks_write.c
+ core/transforms/adios_transforms_util.c
+ core/transforms/adios_transforms_specparse.c
transforms/adios_transform_alacrity_write.c
transforms/adios_transform_aplod_write.c
transforms/adios_transform_bzip2_write.c
@@ -124,6 +126,8 @@ set (transforms_write_SOURCES ${transforms_write_HDRS}
transforms/adios_transform_szip_write.c
transforms/adios_transform_zlib_write.c
transforms/adios_transform_zfp_write.c
+ transforms/adios_transform_sz_write.c
+ transforms/adios_transform_lz4_write.c
${transforms_write_method_SOURCES})
#######Query source files
@@ -151,39 +155,41 @@ set(query_F_SOURCES ${query_SOURCES} query/adiosf_query.c)
#start adios.a and adios_nompi.a
if(BUILD_WRITE)
- set(libadios_a_SOURCES core/adios.c
+ set(libadios_a_SOURCES core/adios.c
core/common_adios.c
core/adios_internals.c
- core/adios_internals_mxml.c
- core/buffer.c
- core/adios_bp_v1.c
- core/adios_endianness.c
- core/bp_utils.c
- core/futils.c
- core/adios_error.c
- core/adios_read.c
- core/adios_read_v1.c
- core/common_read.c
+ core/adios_internals_mxml.c
+ core/buffer.c
+ core/adios_bp_v1.c
+ core/adios_endianness.c
+ core/bp_utils.c
+ core/futils.c
+ core/adios_error.c
+ core/adios_read.c
+ core/adios_read_v1.c
+ core/common_read.c
core/adios_infocache.c
core/adios_read_ext.c
- core/globals.c
- core/adios_timing.c
- core/adios_read_hooks.c
- core/adios_transport_hooks.c
- core/adios_socket.c
- core/adios_logger.c
- core/qhashtbl.c
- ${transforms_common_SOURCES}
- ${transforms_read_SOURCES}
- ${transforms_write_SOURCES}
+ core/globals.c
+ core/adios_timing.c
+ core/adios_read_hooks.c
+ core/adios_transport_hooks.c
+ core/adios_socket.c
+ core/adios_logger.c
+ core/qhashtbl.c
+ ${transforms_common_SOURCES}
+ ${transforms_read_SOURCES}
+ ${transforms_write_SOURCES}
${query_C_SOURCES}
- core/util.c
- core/strutil.c
- core/a2sel.c
- core/adios_clock.c
- core/qhashtbl.c
- read/read_bp.c
- read/read_bp_staged.c
+ core/util.c
+ core/strutil.c
+ core/a2sel.c
+ core/adios_clock.c
+ core/qhashtbl.c
+ core/adiost_callback_internal.c
+ core/adiost_default_tool.c
+ read/read_bp.c
+ read/read_bp_staged.c
read/read_bp_staged1.c
write/adios_mpi.c
write/adios_mpi_lustre.c
@@ -195,75 +201,79 @@ if(BUILD_WRITE)
set(libadios_a_SOURCES ${libadios_a_SOURCES} write/adios_mpi_bgq.c)
endif()
- set(libadios_nompi_a_SOURCES core/adios.c
- core/common_adios.c
- core/adios_internals.c
- core/adios_internals_mxml.c
- ${transforms_common_SOURCES}
- ${transforms_read_SOURCES}
- ${transforms_write_SOURCES}
+ set(libadios_nompi_a_SOURCES core/adios.c
+ core/common_adios.c
+ core/adios_internals.c
+ core/adios_internals_mxml.c
+ ${transforms_common_SOURCES}
+ ${transforms_read_SOURCES}
+ ${transforms_write_SOURCES}
${query_C_SOURCES}
- core/buffer.c
- core/adios_bp_v1.c
- core/adios_endianness.c
- core/bp_utils.c
- core/futils.c
- core/adios_error.c
- core/adios_read.c
- core/adios_read_v1.c
- core/common_read.c
+ core/buffer.c
+ core/adios_bp_v1.c
+ core/adios_endianness.c
+ core/bp_utils.c
+ core/futils.c
+ core/adios_error.c
+ core/adios_read.c
+ core/adios_read_v1.c
+ core/common_read.c
core/adios_infocache.c
core/adios_read_ext.c
- core/globals.c
- core/mpidummy.c
- core/adios_timing.c
- core/adios_read_hooks.c
- core/adios_transport_hooks.c
- core/adios_socket.c
- core/adios_logger.c
- core/util.c
- core/strutil.c
- core/a2sel.c
- core/adios_clock.c
- core/qhashtbl.c
- read/read_bp.c
- read/read_bp_staged.c
- read/read_bp_staged1.c
+ core/globals.c
+ core/mpidummy.c
+ core/adios_timing.c
+ core/adios_read_hooks.c
+ core/adios_transport_hooks.c
+ core/adios_socket.c
+ core/adios_logger.c
+ core/util.c
+ core/strutil.c
+ core/a2sel.c
+ core/adios_clock.c
+ core/qhashtbl.c
+ core/adiost_callback_internal.c
+ core/adiost_default_tool.c
+ read/read_bp.c
+ read/read_bp_staged.c
+ read/read_bp_staged1.c
write/adios_posix.c)
#start adiosf.a and adiosf_v1.a
if(BUILD_FORTRAN)
- set(FortranLibSources core/adiosf.c
- core/common_adios.c
- core/adios_internals.c
+ set(FortranLibSources core/adiosf.c
+ core/common_adios.c
+ core/adios_internals.c
core/adios_internals_mxml.c
- ${transforms_common_SOURCES}
- ${transforms_read_SOURCES}
- ${transforms_write_SOURCES}
+ ${transforms_common_SOURCES}
+ ${transforms_read_SOURCES}
+ ${transforms_write_SOURCES}
${query_F_SOURCES}
- core/buffer.c
- core/adios_bp_v1.c
+ core/buffer.c
+ core/adios_bp_v1.c
core/adios_endianness.c
- core/futils.c
- core/adios_error.c
- core/bp_utils.c
- core/common_read.c
+ core/futils.c
+ core/adios_error.c
+ core/bp_utils.c
+ core/common_read.c
core/adios_infocache.c
core/adios_read_ext.c
- core/globals.c
- core/adios_timing.c
- core/adios_read_hooks.c
- core/adios_transport_hooks.c
- core/adios_socket.c
- core/adios_logger.c
- core/util.c
- core/strutil.c
- core/a2sel.c
- core/adios_clock.c
- core/qhashtbl.c
- read/read_bp.c
- read/read_bp_staged.c
- read/read_bp_staged1.c
+ core/globals.c
+ core/adios_timing.c
+ core/adios_read_hooks.c
+ core/adios_transport_hooks.c
+ core/adios_socket.c
+ core/adios_logger.c
+ core/util.c
+ core/strutil.c
+ core/a2sel.c
+ core/adios_clock.c
+ core/qhashtbl.c
+ core/adiost_callback_internal.c
+ core/adiost_default_tool.c
+ read/read_bp.c
+ read/read_bp_staged.c
+ read/read_bp_staged1.c
write/adios_posix.c)
set(FortranLibMPISources write/adios_mpi.c
@@ -278,7 +288,7 @@ if(BUILD_WRITE)
set(libadios_a_CPPFLAGS "${ADIOSLIB_EXTRA_CPPFLAGS} ${ADIOSLIB_CPPFLAGS}")
set(libadios_a_CFLAGS "${ADIOSLIB_CFLAGS}")
- set(libadios_nompi_a_CPPFLAGS "${MACRODEFFLAG}_NOMPI ${ADIOSLIB_EXTRA_CPPFLAGS} ${ADIOSLIB_SEQ_CPPFLAGS}")
+ set(libadios_nompi_a_CPPFLAGS "${MACRODEFFLAG}_NOMPI ${ADIOSLIB_EXTRA_CPPFLAGS} ${ADIOSLIB_SEQ_CPPFLAGS}")
set(libadios_nompi_a_CFLAGS "${MACRODEFFLAG}_NOMPI ${ADIOSLIB_SEQ_CFLAGS}")
set(libadiosf_a_CPPFLAGS "${ADIOSLIB_EXTRA_CPPFLAGS} ${ADIOSLIB_CPPFLAGS}")
set(libadiosf_a_CFLAGS "${ADIOSLIB_CFLAGS}")
@@ -288,15 +298,15 @@ if(BUILD_WRITE)
if(HAVE_DATASPACES)
set(libadios_a_SOURCES ${libadios_a_SOURCES} write/adios_dataspaces.c read/read_dataspaces.c)
set(libadios_nompi_a_SOURCES ${libadios_nompi_a_SOURCES} write/adios_dataspaces.c read/read_dataspaces.c)
- if(BUILD_FORTRAN)
+ if(BUILD_FORTRAN)
set(FortranLibSources ${FortranLibSources} write/adios_dataspaces.c read/read_dataspaces.c)
- endif(BUILD_FORTRAN)
+ endif(BUILD_FORTRAN)
endif(HAVE_DATASPACES)
if(HAVE_DIMES)
set(libadios_a_SOURCES ${libadios_a_SOURCES} write/adios_dimes.c read/read_dimes.c)
set(libadios_nompi_a_SOURCES ${libadios_nompi_a_SOURCES} write/adios_dimes.c read/read_dimes.c)
- if(BUILD_FORTRAN)
+ if(BUILD_FORTRAN)
set(FortranLibSources ${FortranLibSources} write/adios_dimes.c read/read_dimes.c)
endif(BUILD_FORTRAN)
endif(HAVE_DIMES)
@@ -316,7 +326,7 @@ if(BUILD_WRITE)
if(BUILD_FORTRAN)
set(FortranLibMPISources ${FortranLibMPISources} write/adios_phdf5.c)
set(libadiosf_a_CPPFLAGS "${libadiosf_a_CPPFLAGS} ${PHDF5_FLAGS}")
- endif(BUILD_FORTRAN)
+ endif(BUILD_FORTRAN)
endif(HAVE_PHDF5)
if(HAVE_NC4PAR)
@@ -373,7 +383,7 @@ if(BUILD_WRITE)
COMMAND rpcgen -c ${PROJECT_SOURCE_DIR}/src/nssi/adios_nssi_args.x | grep -v "include \"\.\." > adios_nssi_args.c
DEPENDS ${PROJECT_SOURCE_DIR}/src/nssi/adios_nssi_args.h
)
-
+
set(CLEANFILES ${CLEANFILES} adios_nssi_args.c adios_nssi_args.h)
endif(HAVE_NSSI)
@@ -381,12 +391,12 @@ if(BUILD_WRITE)
if(RESEARCH_TRANSPORTS)
# set(libadios_a_SOURCES ${libadios_a_SOURCES}
-# write/adios_mpi_stagger.c
-# write/adios_mpi_aggregate.c
-# write/adios_provenance.c
-# write/adios_mpi_cio.c
-# write/adios_mpi_stripe.c
-# write/adios_mpi_amr1.c
+# write/adios_mpi_stagger.c
+# write/adios_mpi_aggregate.c
+# write/adios_provenance.c
+# write/adios_mpi_cio.c
+# write/adios_mpi_stripe.c
+# write/adios_mpi_amr1.c
# write/adios_adaptive.c)
if(BUILD_FORTRAN)
# set(FortranLibMPISources ${FortranLibMPISources}
@@ -394,8 +404,8 @@ if(BUILD_WRITE)
# write/adios_mpi_aggregate.c
# write/adios_provenance.c
# write/adios_mpi_cio.c
-# write/adios_mpi_stripe.c
-# write/adios_mpi_amr1.c
+# write/adios_mpi_stripe.c
+# write/adios_mpi_amr1.c
# write/adios_adaptive.c)
endif(BUILD_FORTRAN)
else(RESEARCH_TRANSPORTS)
@@ -427,17 +437,17 @@ if(BUILD_WRITE)
set(libadiosf_a_SOURCES ${libadiosf_a_SOURCES}
core/adiosf_defs_mod.f90
- core/adiosf_write_mod.f90
+ core/adiosf_write_mod.f90
core/adiosf_read_mod.f90
query/adios_query_mod.f90)
-
+
set(libadiosf_nompi_a_SOURCES ${libadiosf_nompi_a_SOURCES}
core/adiosf_defs_mod.f90
core/adiosf_write_mod.f90
core/adiosf_read_mod.f90
query/adios_query_mod.f90)
- set(libadiosf_v1_a_SOURCES ${libadiosf_v1_a_SOURCES}
+ set(libadiosf_v1_a_SOURCES ${libadiosf_v1_a_SOURCES}
core/adiosf_defs_mod.f90
core/adiosf_write_mod.f90)
@@ -465,7 +475,7 @@ if(BUILD_WRITE)
DEPENDS adios_defs_mod.o
)
-
+
add_custom_command(
OUTPUT adios_write_mod.mod
DEPENDS adios_defs_mod.o
@@ -483,7 +493,7 @@ if(BUILD_WRITE)
install(FILES ${PROJECT_BINARY_DIR}/src/adios_write_mod.mod ${PROJECT_BINARY_DIR}/src/adios_defs_mod.mod DESTINATION ${includedir})
##add library adiosf and adiosf_v1
add_library(adiosf STATIC ${libadiosf_a_SOURCES} ${EXTRA_OBJECTS})
- add_library(adiosf_v1 STATIC ${libadiosf_v1_a_SOURCES} ${EXTRA_OBJECTS})
+ add_library(adiosf_v1 STATIC ${libadiosf_v1_a_SOURCES} ${EXTRA_OBJECTS})
add_library(adiosf_nompi STATIC ${libadiosf_nompi_a_SOURCES} ${EXTRA_OBJECTS})
add_library(adiosf_nompi_v1 STATIC ${libadiosf_nompi_v1_a_SOURCES} ${EXTRA_OBJECTS})
set_target_properties(adiosf PROPERTIES COMPILE_FLAGS "${libadiosf_a_CPPFLAGS} ${libadiosf_a_CFLAGS}")
@@ -495,49 +505,52 @@ if(BUILD_WRITE)
endif(BUILD_FORTRAN)
endif(BUILD_WRITE)
-
+
#start libadiosread.a
-set(include_HEADERS ${include_HEADERS} public/adios.h
- public/adios_types.h
- public/adios_read.h
+set(include_HEADERS ${include_HEADERS} public/adios.h
+ public/adios_types.h
+ public/adios_read.h
public/adios_error.h
- public/adios_mpi.h
- public/mpidummy.h
- public/adios_read_v1.h
- public/adios_read_v1_defs.h
- public/adios_read_v2.h
- public/adios_read_v2_fwd.h
+ public/adios_mpi.h
+ public/mpidummy.h
+ public/adios_read_v1.h
+ public/adios_read_v1_defs.h
+ public/adios_read_v2.h
+ public/adios_read_v2_fwd.h
public/adios_selection.h
public/adios_schema.h
public/adios_link.h
public/adios_read_ext.h
public/adios_query.h
- public/adios_transform_methods.h)
+ public/adios_transform_methods.h
+ public/adiost_callback_api.h)
set(libadiosread_a_SOURCES core/adios_bp_v1.c
- core/adios_endianness.c
- core/bp_utils.c
- core/futils.c
- core/adios_error.c
- core/adios_read.c
- core/adios_read_v1.c
- core/common_read.c
+ core/adios_endianness.c
+ core/bp_utils.c
+ core/futils.c
+ core/adios_error.c
+ core/adios_read.c
+ core/adios_read_v1.c
+ core/common_read.c
core/adios_infocache.c
core/adios_read_ext.c
- ${transforms_common_SOURCES}
- ${transforms_read_SOURCES}
+ ${transforms_common_SOURCES}
+ ${transforms_read_SOURCES}
${query_C_SOURCES}
- core/globals.c
- core/adios_read_hooks.c
- core/adios_logger.c
- core/util.c
- core/strutil.c
+ core/globals.c
+ core/adios_read_hooks.c
+ core/adios_logger.c
+ core/util.c
+ core/strutil.c
core/a2sel.c
- core/adios_clock.c
- core/qhashtbl.c
- read/read_bp.c
- read/read_bp_staged.c
+ core/adios_clock.c
+ core/qhashtbl.c
+ core/adiost_callback_internal.c
+ core/adiost_default_tool.c
+ read/read_bp.c
+ read/read_bp_staged.c
read/read_bp_staged1.c)
if(HAVE_DMALLOC)
@@ -585,27 +598,29 @@ set_target_properties(adiosread PROPERTIES COMPILE_FLAGS "${libadiosread_a_CPPFL
#start libadiosreadf.a libadiosreadf_v1.a
if(BUILD_FORTRAN)
- set(FortranReadLibSource core/adios_bp_v1.c
- core/adios_endianness.c
- core/bp_utils.c
- core/futils.c
- core/adios_error.c
- core/common_read.c
+ set(FortranReadLibSource core/adios_bp_v1.c
+ core/adios_endianness.c
+ core/bp_utils.c
+ core/futils.c
+ core/adios_error.c
+ core/common_read.c
core/adios_infocache.c
core/adios_read_ext.c
- ${transforms_common_SOURCES}
- ${transforms_read_SOURCES}
+ ${transforms_common_SOURCES}
+ ${transforms_read_SOURCES}
${query_F_SOURCES}
- core/globals.c
- core/adios_read_hooks.c
- core/adios_logger.c
- core/util.c
- core/strutil.c
+ core/globals.c
+ core/adios_read_hooks.c
+ core/adios_logger.c
+ core/util.c
+ core/strutil.c
core/a2sel.c
- core/adios_clock.c
- core/qhashtbl.c
- read/read_bp.c
- read/read_bp_staged.c
+ core/adios_clock.c
+ core/qhashtbl.c
+ core/adiost_callback_internal.c
+ core/adiost_default_tool.c
+ read/read_bp.c
+ read/read_bp_staged.c
read/read_bp_staged1.c)
if(HAVE_DATASPACES)
set(FortranReadLibSource ${FortranReadLibSource} read/read_dataspaces.c)
@@ -622,7 +637,7 @@ if(BUILD_FORTRAN)
if(HAVE_FLEXPATH)
set(FortranReadLibSource ${FortranReadLibSource} read/read_flexpath.c)
endif(HAVE_FLEXPATH)
-
+
if(HAVE_ICEE)
set(FortranReadLibSource ${FortranReadLibSource} read/read_icee.c)
endif()
@@ -642,17 +657,17 @@ if(BUILD_FORTRAN)
set(libadiosreadf_v1_a_CPPFLAGS "${libadiosreadf_a_CPPFLAGS}")
set(libadiosreadf_v1_a_CFLAGS "${libadiosreadf_a_CFLAGS}")
set(libadiosreadf_a_SOURCES ${libadiosreadf_a_SOURCES}
- core/adiosf_defs_mod.f90
+ core/adiosf_defs_mod.f90
core/adiosf_read_mod.f90
query/adios_query_mod.f90)
set(nodist_include_HEADERS ${nodist_include_HEADERS} adios_read_mod.mod adios_defs_mod.mod adios_query_mod.mod)
set(CLEANFILES ${CLEANFILES} adios_read_mod.mod adios_defs_mod.mod adios_query_mod.mod)
-
+
add_custom_command(
OUTPUT adios_read_mod.o
# COMMAND $(FC) -c core/adiosf_read_mod.f90
DEPENDS adios_defs_mod.o
- )
+ )
add_custom_command(
OUTPUT adios_read_mod.mod
DEPENDS adios_read_mod.o
@@ -675,7 +690,7 @@ if(BUILD_FORTRAN)
OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/adios_query_mod.mod
COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_BINARY_DIR}/adios_query_mod.mod ${CMAKE_CURRENT_SOURCE_DIR}
DEPENDS adios_query_mod.mod
- )
+ )
add_custom_command(
OUTPUT adios_defs_mod.mod
@@ -693,7 +708,7 @@ if(BUILD_FORTRAN)
install(FILES ${PROJECT_BINARY_DIR}/src/adios_read_mod.mod ${PROJECT_BINARY_DIR}/src/adios_defs_mod.mod ${PROJECT_BINARY_DIR}/src/adios_query_mod.mod DESTINATION ${includedir})
add_library(adiosreadf ${libadiosreadf_a_SOURCES} ${EXTRA_READ_OBJECTS})
set_target_properties(adiosreadf PROPERTIES COMPILE_FLAGS "${libadiosreadf_a_CPPFLAGS} ${libadiosreadf_a_CFLAGS}")
-
+
# message(STATUS "${nodist_include_HEADERS}")
# message(STATUS "${libadiosreadf_v1_a_SOURCES}")
add_library(adiosreadf_v1 ${libadiosreadf_v1_a_SOURCES} ${EXTRA_READ_OBJECTS})
@@ -704,30 +719,32 @@ endif(BUILD_FORTRAN)
#start libadiosread_nompi.a
set(libadiosread_nompi_a_SOURCES core/mpidummy.c
- core/adios_bp_v1.c
- core/adios_endianness.c
- core/bp_utils.c
- core/futils.c
- core/adios_error.c
- core/adios_read.c
- core/adios_read_v1.c
- core/common_read.c
+ core/adios_bp_v1.c
+ core/adios_endianness.c
+ core/bp_utils.c
+ core/futils.c
+ core/adios_error.c
+ core/adios_read.c
+ core/adios_read_v1.c
+ core/common_read.c
core/adios_infocache.c
core/adios_read_ext.c
- ${transforms_common_SOURCES}
- ${transforms_read_SOURCES}
+ ${transforms_common_SOURCES}
+ ${transforms_read_SOURCES}
${query_C_SOURCES}
-# core/adios_internals.c
- core/adios_logger.c
- core/buffer.c
- core/globals.c
- core/adios_read_hooks.c
-# core/adios_transport_hooks.c
- core/util.c
- core/strutil.c
+# core/adios_internals.c
+ core/adios_logger.c
+ core/buffer.c
+ core/globals.c
+ core/adios_read_hooks.c
+# core/adios_transport_hooks.c
+ core/util.c
+ core/strutil.c
core/a2sel.c
- core/adios_clock.c
- core/qhashtbl.c
+ core/adios_clock.c
+ core/qhashtbl.c
+ core/adiost_callback_internal.c
+ core/adiost_default_tool.c
read/read_bp.c)
if(HAVE_DMALLOC)
@@ -772,25 +789,27 @@ set_target_properties(adiosread_nompi PROPERTIES COMPILE_FLAGS "${libadiosread_n
#start libadiosreadf_nompi.a libadiosreadf_nompi_v1.a
if(BUILD_FORTRAN)
set(FortranReadSeqLibSource core/mpidummy.c
- core/adios_bp_v1.c
- core/adios_endianness.c
- core/bp_utils.c
- core/futils.c
- core/adios_error.c
- core/adios_logger.c
- core/common_read.c
+ core/adios_bp_v1.c
+ core/adios_endianness.c
+ core/bp_utils.c
+ core/futils.c
+ core/adios_error.c
+ core/adios_logger.c
+ core/common_read.c
core/adios_infocache.c
core/adios_read_ext.c
- ${transforms_common_SOURCES}
- ${transforms_read_SOURCES}
+ ${transforms_common_SOURCES}
+ ${transforms_read_SOURCES}
${query_F_SOURCES}
- core/globals.c
- core/adios_read_hooks.c
- core/util.c
- core/strutil.c
+ core/globals.c
+ core/adios_read_hooks.c
+ core/util.c
+ core/strutil.c
core/a2sel.c
- core/adios_clock.c
- core/qhashtbl.c
+ core/adios_clock.c
+ core/qhashtbl.c
+ core/adiost_callback_internal.c
+ core/adiost_default_tool.c
read/read_bp.c)
if(HAVE_DATASPACES)
set(FortranReadSeqLibSource ${FortranReadSeqLibSource} read/read_dataspaces.c)
@@ -839,24 +858,24 @@ endif(BUILD_FORTRAN)
#start libadios_internal_nompi.a
-set(libadios_internal_nompi_a_SOURCES core/mpidummy.c
- core/adios_bp_v1.c
- core/adios_endianness.c
- core/bp_utils.c
- core/adios_internals.c
- ${transforms_common_SOURCES}
- ${transforms_write_SOURCES}
+set(libadios_internal_nompi_a_SOURCES core/mpidummy.c
+ core/adios_bp_v1.c
+ core/adios_endianness.c
+ core/bp_utils.c
+ core/adios_internals.c
+ ${transforms_common_SOURCES}
+ ${transforms_write_SOURCES}
${query_C_SOURCES}
- core/buffer.c
- core/adios_error.c
- core/adios_logger.c
- core/adios_timing.c
- core/util.c
- core/strutil.c
+ core/buffer.c
+ core/adios_error.c
+ core/adios_logger.c
+ core/adios_timing.c
+ core/util.c
+ core/strutil.c
core/a2sel.c
- core/adios_clock.c
- core/qhashtbl.c
- core/futils.c
+ core/adios_clock.c
+ core/qhashtbl.c
+ core/futils.c
core/adios_transport_hooks.c)
if(BUILD_WRITE)
diff --git a/src/Makefile.am b/src/Makefile.am
index 192bf82..6d3af1f 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -177,6 +177,8 @@ libcoreonce_a_SOURCES = core/a2sel.c \
core/strutil.c \
core/util.c \
core/adios_transform_methods.c \
+ core/adiost_callback_internal.c \
+ core/adiost_default_tool.c \
$(transforms_common_SOURCES) \
$(transforms_write_SOURCES) \
$(transforms_read_SOURCES)
@@ -824,7 +826,8 @@ include_HEADERS += public/adios.h \
public/adios_link.h \
public/adios_read_ext.h \
public/adios_query.h \
- public/adios_transform_methods.h
+ public/adios_transform_methods.h \
+ public/adiost_callback_api.h
EXTRA_DIST = core/adios_bp_v1.h core/adios_endianness.h \
core/adios_internals.h core/adios_internals_mxml.h core/adios_logger.h \
@@ -835,6 +838,7 @@ EXTRA_DIST = core/adios_bp_v1.h core/adios_endianness.h \
core/common_read.h core/adios_infocache.h core/futils.h core/globals.h core/ds_metadata.h \
core/types.h core/util.h core/strutil.h core/flexpath.h core/qhashtbl.h \
public/adios_version.h.in core/util_mpi.h \
+ core/adiost_callback_internal.h \
$(transforms_common_HDRS) $(transforms_read_HDRS) $(transforms_write_HDRS) \
$(query_common_HDRS) $(query_method_HDRS) \
transforms/transform_plugins.h \
@@ -844,6 +848,7 @@ EXTRA_DIST = core/adios_bp_v1.h core/adios_endianness.h \
transforms/adios_transform_zfp_common.h \
transforms/adios_transform_template_read.c \
transforms/adios_transform_template_write.c \
+ transforms/adios_transform_lz4_common.h \
query/Makefile.plugins.cmake
# nssi/adios_nssi_config.h nssi/aggregation.h nssi/io_timer.h
diff --git a/src/Makefile.in b/src/Makefile.in
index 0654f85..a311f26 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -332,7 +332,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -340,8 +340,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -1178,7 +1178,9 @@ am__objects_144 = transforms/libcoreonce_a-adios_transform_identity_write.$(OBJE
transforms/libcoreonce_a-adios_transform_isobar_write.$(OBJEXT) \
transforms/libcoreonce_a-adios_transform_aplod_write.$(OBJEXT) \
transforms/libcoreonce_a-adios_transform_alacrity_write.$(OBJEXT) \
- transforms/libcoreonce_a-adios_transform_zfp_write.$(OBJEXT)
+ transforms/libcoreonce_a-adios_transform_zfp_write.$(OBJEXT) \
+ transforms/libcoreonce_a-adios_transform_sz_write.$(OBJEXT) \
+ transforms/libcoreonce_a-adios_transform_lz4_write.$(OBJEXT)
am__objects_145 = $(am__objects_1) \
core/transforms/libcoreonce_a-adios_transforms_write.$(OBJEXT) \
core/transforms/libcoreonce_a-adios_transforms_hooks_write.$(OBJEXT) \
@@ -1192,7 +1194,9 @@ am__objects_146 = transforms/libcoreonce_a-adios_transform_identity_read.$(OBJEX
transforms/libcoreonce_a-adios_transform_isobar_read.$(OBJEXT) \
transforms/libcoreonce_a-adios_transform_aplod_read.$(OBJEXT) \
transforms/libcoreonce_a-adios_transform_alacrity_read.$(OBJEXT) \
- transforms/libcoreonce_a-adios_transform_zfp_read.$(OBJEXT)
+ transforms/libcoreonce_a-adios_transform_zfp_read.$(OBJEXT) \
+ transforms/libcoreonce_a-adios_transform_sz_read.$(OBJEXT) \
+ transforms/libcoreonce_a-adios_transform_lz4_read.$(OBJEXT)
am__objects_147 = $(am__objects_1) \
core/transforms/libcoreonce_a-adios_transforms_read.$(OBJEXT) \
core/transforms/libcoreonce_a-adios_transforms_hooks_read.$(OBJEXT) \
@@ -1216,6 +1220,8 @@ am_libcoreonce_a_OBJECTS = core/libcoreonce_a-a2sel.$(OBJEXT) \
core/libcoreonce_a-strutil.$(OBJEXT) \
core/libcoreonce_a-util.$(OBJEXT) \
core/libcoreonce_a-adios_transform_methods.$(OBJEXT) \
+ core/libcoreonce_a-adiost_callback_internal.$(OBJEXT) \
+ core/libcoreonce_a-adiost_default_tool.$(OBJEXT) \
$(am__objects_143) $(am__objects_145) $(am__objects_147)
libcoreonce_a_OBJECTS = $(am_libcoreonce_a_OBJECTS)
PROGRAMS = $(bin_PROGRAMS)
@@ -1491,6 +1497,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -1567,6 +1577,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
@@ -1717,7 +1730,7 @@ include_HEADERS = public/adios.h public/adios_version.h \
public/adios_read_v2_fwd.h public/adios_selection.h \
public/adios_schema.h public/adios_link.h \
public/adios_read_ext.h public/adios_query.h \
- public/adios_transform_methods.h
+ public/adios_transform_methods.h public/adiost_callback_api.h
nodist_include_HEADERS = $(am__append_43) $(am__append_73)
# End of building Parallel Write libs
@@ -1766,6 +1779,10 @@ libadiosreadf_nompi_a_CFLAGS =
# ALACRITY plugin:
# zfp plugin:
+
+# sz plugin:
+
+# LZ4 plugin:
transforms_write_method_SOURCES = \
transforms/adios_transform_identity_write.c \
transforms/adios_transform_zlib_write.c \
@@ -1774,7 +1791,9 @@ transforms_write_method_SOURCES = \
transforms/adios_transform_isobar_write.c \
transforms/adios_transform_aplod_write.c \
transforms/adios_transform_alacrity_write.c \
- transforms/adios_transform_zfp_write.c
+ transforms/adios_transform_zfp_write.c \
+ transforms/adios_transform_sz_write.c \
+ transforms/adios_transform_lz4_write.c
transforms_read_method_SOURCES = \
transforms/adios_transform_identity_read.c \
transforms/adios_transform_zlib_read.c \
@@ -1783,7 +1802,9 @@ transforms_read_method_SOURCES = \
transforms/adios_transform_isobar_read.c \
transforms/adios_transform_aplod_read.c \
transforms/adios_transform_alacrity_read.c \
- transforms/adios_transform_zfp_read.c
+ transforms/adios_transform_zfp_read.c \
+ transforms/adios_transform_sz_read.c \
+ transforms/adios_transform_lz4_read.c
transforms_common_HDRS = core/adios_copyspec.h \
core/adios_subvolume.h \
core/adios_selection_util.h \
@@ -1877,6 +1898,8 @@ libcoreonce_a_SOURCES = core/a2sel.c \
core/strutil.c \
core/util.c \
core/adios_transform_methods.c \
+ core/adiost_callback_internal.c \
+ core/adiost_default_tool.c \
$(transforms_common_SOURCES) \
$(transforms_write_SOURCES) \
$(transforms_read_SOURCES)
@@ -2095,6 +2118,7 @@ EXTRA_DIST = core/adios_bp_v1.h core/adios_endianness.h \
core/common_read.h core/adios_infocache.h core/futils.h core/globals.h core/ds_metadata.h \
core/types.h core/util.h core/strutil.h core/flexpath.h core/qhashtbl.h \
public/adios_version.h.in core/util_mpi.h \
+ core/adiost_callback_internal.h \
$(transforms_common_HDRS) $(transforms_read_HDRS) $(transforms_write_HDRS) \
$(query_common_HDRS) $(query_method_HDRS) \
transforms/transform_plugins.h \
@@ -2104,6 +2128,7 @@ EXTRA_DIST = core/adios_bp_v1.h core/adios_endianness.h \
transforms/adios_transform_zfp_common.h \
transforms/adios_transform_template_read.c \
transforms/adios_transform_template_write.c \
+ transforms/adios_transform_lz4_common.h \
query/Makefile.plugins.cmake
all: all-recursive
@@ -2755,6 +2780,10 @@ core/libcoreonce_a-strutil.$(OBJEXT): core/$(am__dirstamp)
core/libcoreonce_a-util.$(OBJEXT): core/$(am__dirstamp)
core/libcoreonce_a-adios_transform_methods.$(OBJEXT): \
core/$(am__dirstamp)
+core/libcoreonce_a-adiost_callback_internal.$(OBJEXT): \
+ core/$(am__dirstamp)
+core/libcoreonce_a-adiost_default_tool.$(OBJEXT): \
+ core/$(am__dirstamp)
core/transforms/$(am__dirstamp):
@$(MKDIR_P) core/transforms
@: > core/transforms/$(am__dirstamp)
@@ -2791,6 +2820,10 @@ transforms/libcoreonce_a-adios_transform_alacrity_write.$(OBJEXT): \
transforms/$(am__dirstamp)
transforms/libcoreonce_a-adios_transform_zfp_write.$(OBJEXT): \
transforms/$(am__dirstamp)
+transforms/libcoreonce_a-adios_transform_sz_write.$(OBJEXT): \
+ transforms/$(am__dirstamp)
+transforms/libcoreonce_a-adios_transform_lz4_write.$(OBJEXT): \
+ transforms/$(am__dirstamp)
core/transforms/libcoreonce_a-adios_transforms_read.$(OBJEXT): \
core/transforms/$(am__dirstamp)
core/transforms/libcoreonce_a-adios_transforms_hooks_read.$(OBJEXT): \
@@ -2819,6 +2852,10 @@ transforms/libcoreonce_a-adios_transform_alacrity_read.$(OBJEXT): \
transforms/$(am__dirstamp)
transforms/libcoreonce_a-adios_transform_zfp_read.$(OBJEXT): \
transforms/$(am__dirstamp)
+transforms/libcoreonce_a-adios_transform_sz_read.$(OBJEXT): \
+ transforms/$(am__dirstamp)
+transforms/libcoreonce_a-adios_transform_lz4_read.$(OBJEXT): \
+ transforms/$(am__dirstamp)
libcoreonce.a: $(libcoreonce_a_OBJECTS) $(libcoreonce_a_DEPENDENCIES) $(EXTRA_libcoreonce_a_DEPENDENCIES)
$(AM_V_at)-rm -f libcoreonce.a
@@ -5127,6 +5164,18 @@ core/libcoreonce_a-adios_transform_methods.o: core/adios_transform_methods.c
core/libcoreonce_a-adios_transform_methods.obj: core/adios_transform_methods.c
$(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcoreonce_a_CPPFLAGS) $(CPPFLAGS) $(libcoreonce_a_CFLAGS) $(CFLAGS) -c -o core/libcoreonce_a-adios_transform_methods.obj `if test -f 'core/adios_transform_methods.c'; then $(CYGPATH_W) 'core/adios_transform_methods.c'; else $(CYGPATH_W) '$(srcdir)/core/adios_transform_methods.c'; fi`
+core/libcoreonce_a-adiost_callback_internal.o: core/adiost_callback_internal.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcoreonce_a_CPPFLAGS) $(CPPFLAGS) $(libcoreonce_a_CFLAGS) $(CFLAGS) -c -o core/libcoreonce_a-adiost_callback_internal.o `test -f 'core/adiost_callback_internal.c' || echo '$(srcdir)/'`core/adiost_callback_internal.c
+
+core/libcoreonce_a-adiost_callback_internal.obj: core/adiost_callback_internal.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcoreonce_a_CPPFLAGS) $(CPPFLAGS) $(libcoreonce_a_CFLAGS) $(CFLAGS) -c -o core/libcoreonce_a-adiost_callback_internal.obj `if test -f 'core/adiost_callback_internal.c'; then $(CYGPATH_W) 'core/adiost_callback_internal.c'; else $(CYGPATH_W) '$(srcdir)/core/adiost_callback_internal.c'; fi`
+
+core/libcoreonce_a-adiost_default_tool.o: core/adiost_default_tool.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcoreonce_a_CPPFLAGS) $(CPPFLAGS) $(libcoreonce_a_CFLAGS) $(CFLAGS) -c -o core/libcoreonce_a-adiost_default_tool.o `test -f 'core/adiost_default_tool.c' || echo '$(srcdir)/'`core/adiost_default_tool.c
+
+core/libcoreonce_a-adiost_default_tool.obj: core/adiost_default_tool.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcoreonce_a_CPPFLAGS) $(CPPFLAGS) $(libcoreonce_a_CFLAGS) $(CFLAGS) -c -o core/libcoreonce_a-adiost_default_tool.obj `if test -f 'core/adiost_default_tool.c'; then $(CYGPATH_W) 'core/adiost_default_tool.c'; else $(CYGPATH_W) '$(srcdir)/core/adiost_default_tool.c'; fi`
+
core/transforms/libcoreonce_a-adios_transforms_common.o: core/transforms/adios_transforms_common.c
$(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcoreonce_a_CPPFLAGS) $(CPPFLAGS) $(libcoreonce_a_CFLAGS) $(CFLAGS) -c -o core/transforms/libcoreonce_a-adios_transforms_common.o `test -f 'core/transforms/adios_transforms_common.c' || echo '$(srcdir)/'`core/transforms/adios_transforms_common.c
@@ -5223,6 +5272,18 @@ transforms/libcoreonce_a-adios_transform_zfp_write.o: transforms/adios_transform
transforms/libcoreonce_a-adios_transform_zfp_write.obj: transforms/adios_transform_zfp_write.c
$(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcoreonce_a_CPPFLAGS) $(CPPFLAGS) $(libcoreonce_a_CFLAGS) $(CFLAGS) -c -o transforms/libcoreonce_a-adios_transform_zfp_write.obj `if test -f 'transforms/adios_transform_zfp_write.c'; then $(CYGPATH_W) 'transforms/adios_transform_zfp_write.c'; else $(CYGPATH_W) '$(srcdir)/transforms/adios_transform_zfp_write.c'; fi`
+transforms/libcoreonce_a-adios_transform_sz_write.o: transforms/adios_transform_sz_write.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcoreonce_a_CPPFLAGS) $(CPPFLAGS) $(libcoreonce_a_CFLAGS) $(CFLAGS) -c -o transforms/libcoreonce_a-adios_transform_sz_write.o `test -f 'transforms/adios_transform_sz_write.c' || echo '$(srcdir)/'`transforms/adios_transform_sz_write.c
+
+transforms/libcoreonce_a-adios_transform_sz_write.obj: transforms/adios_transform_sz_write.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcoreonce_a_CPPFLAGS) $(CPPFLAGS) $(libcoreonce_a_CFLAGS) $(CFLAGS) -c -o transforms/libcoreonce_a-adios_transform_sz_write.obj `if test -f 'transforms/adios_transform_sz_write.c'; then $(CYGPATH_W) 'transforms/adios_transform_sz_write.c'; else $(CYGPATH_W) '$(srcdir)/transforms/adios_transform_sz_write.c'; fi`
+
+transforms/libcoreonce_a-adios_transform_lz4_write.o: transforms/adios_transform_lz4_write.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcoreonce_a_CPPFLAGS) $(CPPFLAGS) $(libcoreonce_a_CFLAGS) $(CFLAGS) -c -o transforms/libcoreonce_a-adios_transform_lz4_write.o `test -f 'transforms/adios_transform_lz4_write.c' || echo '$(srcdir)/'`transforms/adios_transform_lz4_write.c
+
+transforms/libcoreonce_a-adios_transform_lz4_write.obj: transforms/adios_transform_lz4_write.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcoreonce_a_CPPFLAGS) $(CPPFLAGS) $(libcoreonce_a_CFLAGS) $(CFLAGS) -c -o transforms/libcoreonce_a-adios_transform_lz4_write.obj `if test -f 'transforms/adios_transform_lz4_write.c'; then $(CYGPATH_W) 'transforms/adios_transform_lz4_write.c'; else $(CYGPATH_W) '$(srcdir)/transforms/adios_transform_lz4_write.c'; fi`
+
core/transforms/libcoreonce_a-adios_transforms_read.o: core/transforms/adios_transforms_read.c
$(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcoreonce_a_CPPFLAGS) $(CPPFLAGS) $(libcoreonce_a_CFLAGS) $(CFLAGS) -c -o core/transforms/libcoreonce_a-adios_transforms_read.o `test -f 'core/transforms/adios_transforms_read.c' || echo '$(srcdir)/'`core/transforms/adios_transforms_read.c
@@ -5307,6 +5368,18 @@ transforms/libcoreonce_a-adios_transform_zfp_read.o: transforms/adios_transform_
transforms/libcoreonce_a-adios_transform_zfp_read.obj: transforms/adios_transform_zfp_read.c
$(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcoreonce_a_CPPFLAGS) $(CPPFLAGS) $(libcoreonce_a_CFLAGS) $(CFLAGS) -c -o transforms/libcoreonce_a-adios_transform_zfp_read.obj `if test -f 'transforms/adios_transform_zfp_read.c'; then $(CYGPATH_W) 'transforms/adios_transform_zfp_read.c'; else $(CYGPATH_W) '$(srcdir)/transforms/adios_transform_zfp_read.c'; fi`
+transforms/libcoreonce_a-adios_transform_sz_read.o: transforms/adios_transform_sz_read.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcoreonce_a_CPPFLAGS) $(CPPFLAGS) $(libcoreonce_a_CFLAGS) $(CFLAGS) -c -o transforms/libcoreonce_a-adios_transform_sz_read.o `test -f 'transforms/adios_transform_sz_read.c' || echo '$(srcdir)/'`transforms/adios_transform_sz_read.c
+
+transforms/libcoreonce_a-adios_transform_sz_read.obj: transforms/adios_transform_sz_read.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcoreonce_a_CPPFLAGS) $(CPPFLAGS) $(libcoreonce_a_CFLAGS) $(CFLAGS) -c -o transforms/libcoreonce_a-adios_transform_sz_read.obj `if test -f 'transforms/adios_transform_sz_read.c'; then $(CYGPATH_W) 'transforms/adios_transform_sz_read.c'; else $(CYGPATH_W) '$(srcdir)/transforms/adios_transform_sz_read.c'; fi`
+
+transforms/libcoreonce_a-adios_transform_lz4_read.o: transforms/adios_transform_lz4_read.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcoreonce_a_CPPFLAGS) $(CPPFLAGS) $(libcoreonce_a_CFLAGS) $(CFLAGS) -c -o transforms/libcoreonce_a-adios_transform_lz4_read.o `test -f 'transforms/adios_transform_lz4_read.c' || echo '$(srcdir)/'`transforms/adios_transform_lz4_read.c
+
+transforms/libcoreonce_a-adios_transform_lz4_read.obj: transforms/adios_transform_lz4_read.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcoreonce_a_CPPFLAGS) $(CPPFLAGS) $(libcoreonce_a_CFLAGS) $(CFLAGS) -c -o transforms/libcoreonce_a-adios_transform_lz4_read.obj `if test -f 'transforms/adios_transform_lz4_read.c'; then $(CYGPATH_W) 'transforms/adios_transform_lz4_read.c'; else $(CYGPATH_W) '$(srcdir)/transforms/adios_transform_lz4_read.c'; fi`
+
.f90.o:
$(AM_V_FC)$(FCCOMPILE) -c -o $@ $<
diff --git a/src/core/adios_bp_v1.c b/src/core/adios_bp_v1.c
index dc01bc3..92d0075 100644
--- a/src/core/adios_bp_v1.c
+++ b/src/core/adios_bp_v1.c
@@ -2238,12 +2238,52 @@ void adios_init_buffer_read_process_group_index (
b->offset = 0;
}
+static uint64_t read64(int f, char *buff, uint64_t readsize)
+{
+ // if we need to read > 2 GB, need to do it in parts
+ // since count is limited to MAX_MPIWRITE_SIZE (signed 32-bit max).
+ uint64_t bytes_read = 0;
+ int32_t to_read = 0;
+ int err = 0;
+ const size_t MAX_READ_SIZE = 0x7ffff000; // = 2,147,479,552
+
+ while (bytes_read < readsize && !err)
+ {
+ if (readsize - bytes_read > MAX_READ_SIZE)
+ {
+ to_read = MAX_READ_SIZE;
+ }
+ else
+ {
+ to_read = readsize - bytes_read;
+ }
+
+ ssize_t actual_read_bytes = read (f, buff+bytes_read, to_read);
+ if (actual_read_bytes == -1)
+ {
+ adios_error (err_file_read_error,
+ "Error while reading from file %d bytes: '%s'\n",
+ to_read, strerror(errno));
+ err = 1;
+ }
+ if (actual_read_bytes != to_read)
+ {
+ adios_error (err_file_read_error,
+ "Error while reading from file tried to read %d bytes but only got %d bytes\n",
+ to_read, actual_read_bytes);
+ err = 1;
+ }
+ bytes_read += actual_read_bytes;
+ }
+ return bytes_read;
+}
+
void adios_posix_read_process_group_index (struct adios_bp_buffer_struct_v1 * b)
{
adios_init_buffer_read_process_group_index (b);
lseek (b->f, b->pg_index_offset, SEEK_SET);
- read (b->f, b->buff, b->pg_size);
+ read64 (b->f, b->buff, b->pg_size);
}
void adios_init_buffer_read_vars_index (struct adios_bp_buffer_struct_v1 * b)
@@ -2259,7 +2299,7 @@ void adios_posix_read_vars_index (struct adios_bp_buffer_struct_v1 * b)
uint64_t r;
lseek (b->f, b->vars_index_offset, SEEK_SET);
- r = read (b->f, b->buff, b->vars_size);
+ r = read64 (b->f, b->buff, b->vars_size);
if (r != b->vars_size)
log_warn("reading vars_index: wanted %" PRIu64 ", read: %" PRIu64 "\n"
@@ -2281,7 +2321,7 @@ void adios_posix_read_attributes_index (struct adios_bp_buffer_struct_v1 * b)
uint64_t r;
lseek (b->f, b->attrs_index_offset, SEEK_SET);
- r = read (b->f, b->buff, b->attrs_size);
+ r = read64 (b->f, b->buff, b->attrs_size);
if (r != b->attrs_size)
log_warn("reading attributess_index: wanted %" PRIu64 ", read: %" PRIu64 "\n",
diff --git a/src/core/adios_clock.h b/src/core/adios_clock.h
index 0a89b2e..53c5e7a 100644
--- a/src/core/adios_clock.h
+++ b/src/core/adios_clock.h
@@ -21,6 +21,9 @@ unsigned long adios_gettime_ms();
#ifndef CLOCK_MONOTONIC
# define CLOCK_MONOTONIC 1
#endif
+#ifndef CLOCK_PROCESS_CPUTIME_ID
+# define CLOCK_PROCESS_CPUTIME_ID 2
+#endif
/* create a timespec variable and pass the pointer here */
int adios_clock_gettime(clockid_t clk_id, struct timespec *ts);
diff --git a/src/core/adios_internals.c b/src/core/adios_internals.c
index 4bafe98..05fe248 100755
--- a/src/core/adios_internals.c
+++ b/src/core/adios_internals.c
@@ -267,6 +267,8 @@ int adios_parse_dimension (const char * dimension
return 0;
}
+ char * end;
+
/* Get the local dimension */
// one of the three fields below will be set, the other two remain 0
dim->dimension.rank = 0;
@@ -383,7 +385,15 @@ int adios_parse_dimension (const char * dimension
}
else
{
- dim->dimension.rank = atoi (dimension);
+ int errno_save = errno;
+ unsigned long long t = strtoull (dimension, &end, 10);
+ if (errno != errno_save || (end != 0 && *end != '\0'))
+ {
+ adios_error (err_invalid_argument,
+ "invalid integer value for local dimension of a variable: '%s'\n",dimension);
+ return 0;
+ }
+ dim->dimension.rank = (uint64_t) t;
}
if (!global_dimension)
@@ -509,7 +519,15 @@ int adios_parse_dimension (const char * dimension
}
else
{
- dim->global_dimension.rank = strtol (global_dimension, NULL, 10);
+ int errno_save = errno;
+ unsigned long long t = strtoull (global_dimension, &end, 10);
+ if (errno != errno_save || (end != 0 && *end != '\0'))
+ {
+ adios_error (err_invalid_argument,
+ "invalid integer value for global dimension of a variable: '%s'\n",global_dimension);
+ return 0;
+ }
+ dim->global_dimension.rank = (uint64_t) t;
}
if (!local_offset)
@@ -635,7 +653,15 @@ int adios_parse_dimension (const char * dimension
}
else
{
- dim->local_offset.rank = strtol (local_offset, NULL, 10);
+ int errno_save = errno;
+ unsigned long long t = strtoull (local_offset, &end, 10);
+ if (errno != errno_save || (end != 0 && *end != '\0'))
+ {
+ adios_error (err_invalid_argument,
+ "invalid integer value for offset of a variable: '%s'\n",local_offset);
+ return 0;
+ }
+ dim->local_offset.rank = (uint64_t) t;
}
return 1;
@@ -1367,7 +1393,7 @@ int adios_common_declare_group (int64_t * id, const char * name
// ADIOS Schema
g->meshs = NULL;
g->mesh_count = 0;
- g->last_buffer_size = 0;
+ g->max_pg_size = 0;
#if defined ADIOS_TIMERS || defined ADIOS_TIMER_EVENTS
g->timing_obj = 0;
diff --git a/src/core/adios_internals.h b/src/core/adios_internals.h
index 09a6d42..49a1eb9 100644
--- a/src/core/adios_internals.h
+++ b/src/core/adios_internals.h
@@ -162,7 +162,8 @@ struct adios_group_struct
enum ADIOS_FLAG all_unique_mesh_names;
int attrid_update_epoch; // ID of special attribute "/__adios__/update_time_epoch" to find it fast
- uint64_t last_buffer_size; // remember how much buffer we used in previous output steps
+ uint64_t max_pg_size; // remember how much buffer we used locally in previous output steps (this is not global maximum)
+ // Note: this variable is not set in time aggregation
#if defined ADIOS_TIMERS || defined ADIOS_TIMER_EVENTS
// Using a "double buffering" approach. Current write cycle stored in timing_obj, while timing info from
@@ -173,8 +174,8 @@ struct adios_group_struct
#endif
int do_ts_aggr; //Yuan: introduced for time steps buffering
struct adios_file_struct *ts_fd; // save and keep open the file struct during time aggr.
- uint64_t ts_buffsize; //Yuan: introduced for time steps buffering
- int ts_to_buffer; //current time steps
+ uint64_t ts_buffsize; //Yuan: introduced for time steps buffering, buffer size specified by user
+ int ts_to_buffer; //how many time steps are left to buffer before flush (counts down from max_ts-1 to 0)
int max_ts; //maximum time steps to buffer
struct adios_index_struct_v1 * index; //the indexes for current written PGs
int built_index; // FIXME: 0 or 1, if index has been built, do not build it during close()
diff --git a/src/core/adios_internals_mxml.c b/src/core/adios_internals_mxml.c
index 4c40a85..6a55612 100644
--- a/src/core/adios_internals_mxml.c
+++ b/src/core/adios_internals_mxml.c
@@ -2032,7 +2032,6 @@ static int parseBuffer (mxml_node_t * node)
else
sizestr = size_MB;
- size = atoi (sizestr);
errno = 0;
size = strtol(sizestr, &end, 10);
if (errno || (end != 0 && *end != '\0')) {
@@ -2076,8 +2075,15 @@ static int parseTimeAggregation (mxml_node_t * node, int rank)
if (!buffersize)
bufsize = 0;
- else
- bufsize = atoi (buffersize);
+ else {
+ char *end;
+ errno = 0;
+ bufsize = strtoull(buffersize, &end, 10);
+ if (errno || (end != 0 && *end != '\0')) {
+ adios_error (err_invalid_buffer_size, "config.xml: time-aggregation buffer size cannot be parsed: %s\n", buffersize);
+ return 0;
+ }
+ }
if (!group)
{
diff --git a/src/core/adios_subvolume.c b/src/core/adios_subvolume.c
index c2340f0..63f9633 100644
--- a/src/core/adios_subvolume.c
+++ b/src/core/adios_subvolume.c
@@ -36,13 +36,13 @@ uint64_t compute_volume(int ndim, const uint64_t *dims) {
int intersect_segments(uint64_t start1, uint64_t len1, uint64_t start2, uint64_t len2,
uint64_t *inter_start, uint64_t *inter_len) {
- int end1, end2;
- int inter_end;
+ uint64_t end1, end2;
+ uint64_t inter_end;
// Swap the segments if segment 1 starts after segment 2, to simplify calculations
if (start1 > start2) {
- int tmps = start1;
- int tmpl = len1;
+ uint64_t tmps = start1;
+ uint64_t tmpl = len1;
start1 = start2;
len1 = len2;
start2 = tmps;
diff --git a/src/core/adios_transform_methods.c b/src/core/adios_transform_methods.c
index 8cd8fe8..a95b8ac 100644
--- a/src/core/adios_transform_methods.c
+++ b/src/core/adios_transform_methods.c
@@ -1,12 +1,15 @@
#include <stdlib.h>
#include <string.h>
#include "public/adios_transform_methods.h"
-#include "core/transforms/adios_transforms_hooks.h"
+#include "core/transforms/adios_transforms_hooks.h"
#include "core/transforms/adios_transforms_hooks_read.h"
#include "core/transforms/adios_transforms_read.h"
ADIOS_AVAILABLE_TRANSFORM_METHODS * adios_available_transform_methods()
{
+ /* Ensure the transforms are initialized before accessing */
+ adios_transform_read_init();
+
int i, n;
n = 0;
for (i = (int)adios_transform_none; i < num_adios_transform_types; i++) {
diff --git a/src/core/adiost_callback_internal.c b/src/core/adiost_callback_internal.c
new file mode 100644
index 0000000..d9e0977
--- /dev/null
+++ b/src/core/adiost_callback_internal.c
@@ -0,0 +1,185 @@
+/*
+ * ADIOS is freely available under the terms of the BSD license described
+ * in the COPYING file in the top level directory of this source distribution.
+ *
+ * Copyright (c) 2008 - 2009. UT-BATTELLE, LLC. All rights reserved.
+ */
+
+#include "adiost_callback_internal.h"
+#include "adios_version.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#define adiost_get_callback_success 1
+#define adiost_get_callback_failure 0
+#define no_tool_present 0
+#define ADIOST_API_ROUTINE static
+
+/* The do { ... } while (0) idiom ensures that the code acts like a statement
+ * (function call). The unconditional use of the code ensures that the compiler
+ * always checks that your debug code is valid — but the optimizer will remove
+ * the code when DEBUG is 0. */
+#define DEBUG 0
+#define debug_print(...) do { \
+ if (DEBUG) { \
+ fprintf(stderr, __VA_ARGS__); \
+ fflush(stderr);\
+ } \
+} while (0)
+
+/* static/global variables for this file */
+adiost_callbacks_t adiost_callbacks;
+static adiost_initialize_t adiost_initialize_fn = NULL;
+static adiost_interface_fn_t adiost_fn_lookup(const char *s);
+int adios_tool_enabled = 0;
+const char adiost_enabled_env_var[] = {"ADIOS_TOOL"};
+
+/* forward declaration of the weak (default) tool */
+
+//extern __attribute__ (( weak )) adiost_initialize_t adiost_tool(void);
+//extern adiost_initialize_t adiost_tool(void);
+extern __attribute__((visibility("default"))) adiost_initialize_t __attribute__((weak)) adiost_tool(void);
+
+/* Pre-initialization. */
+
+void adiost_pre_init(void) {
+ // prevent calling this function more than once
+ static int adiost_pre_initialized = 0;
+ if (adiost_pre_initialized) return;
+ adiost_pre_initialized = 1;
+
+ // check whether we are enabled or disabled
+ char *adiost_env_var = (char *)getenv(adiost_enabled_env_var);
+ adios_tool_setting_t tool_setting = adiost_error;
+
+ // convert the input to our internal enumeration
+ if (adiost_env_var == NULL || strlen(adiost_env_var) == 0) {
+ tool_setting = adiost_unset;
+ } else if (strcmp(adiost_env_var, "disabled") == 0) {
+ tool_setting = adiost_disabled;
+ } else if (strcmp(adiost_env_var, "enabled") == 0) {
+ tool_setting = adiost_enabled;
+ }
+
+ // validate the input
+ debug_print("%s: %s = %d\n", __func__, adiost_enabled_env_var, tool_setting);
+ switch(tool_setting) {
+ case adiost_disabled:
+ break;
+ case adiost_unset:
+ case adiost_enabled:
+ if (adiost_tool) {
+ adiost_initialize_fn = adiost_tool();
+ // if initialization is successful, we are enabled
+ if (adiost_initialize_fn) {
+ adios_tool_enabled = 1;
+ }
+ }
+ break;
+ case adiost_error:
+ fprintf(stderr, "Warning: %s has invalid value '%s'.\n",
+ adiost_enabled_env_var, adiost_env_var);
+ fprintf(stderr, "Legal values are NULL, 'enabled', 'disabled'.\n");
+ break;
+ }
+ debug_print("%s: adiost_enabled = %d\n", __func__, adios_tool_enabled);
+}
+
+/* Post-initialization */
+
+void adiost_post_init(void) {
+ // prevent calling this function more than once
+ static int adiost_post_initialized = 0;
+ if (adiost_post_initialized) return;
+ adiost_post_initialized = 1;
+
+ // initialize the tool if specified
+ if (adios_tool_enabled) {
+ adiost_initialize_fn(adiost_fn_lookup, ADIOS_VERSION, ADIOST_VERSION);
+ }
+}
+
+/* For shutting down the tool support */
+
+void adiost_finalize(void) {
+ if (adios_tool_enabled) {
+ // call the registered shutdown callback function
+ if (adiost_callbacks.adiost_callback(adiost_event_library_shutdown)) {
+ adiost_callbacks.adiost_callback(adiost_event_library_shutdown)();
+ }
+ }
+ // prevent any further callback API attempts
+ adios_tool_enabled = 0;
+}
+
+/*****************************************************************************
+ * interface operations
+ ****************************************************************************/
+
+/*****************************************************************************
+ * callbacks
+ ****************************************************************************/
+
+ADIOST_API_ROUTINE int adiost_set_callback(adiost_event_t evid, adiost_callback_t cb)
+{
+ switch (evid) {
+
+/* Define all callbacks using macro expansion */
+
+#define adiost_event_macro(event_name, callback_type, event_id) \
+ case event_name: \
+ adiost_callbacks.adiost_callback(event_name) = (callback_type) cb; \
+ return adiost_set_result_registration_success;
+
+ FOREACH_ADIOST_EVENT(adiost_event_macro)
+
+#undef adiost_event_macro
+
+ default: return adiost_set_result_registration_error;
+ }
+}
+
+ADIOST_API_ROUTINE int adiost_get_callback(adiost_event_t evid, adiost_callback_t *cb)
+{
+ switch (evid) {
+
+/* Define all callbacks using macro expansion */
+
+#define adiost_event_macro(event_name, callback_type, event_id) \
+ case event_name: \
+ if (1) { \
+ adiost_callback_t mycb = \
+ (adiost_callback_t) adiost_callbacks.adiost_callback(event_name); \
+ if (mycb) { \
+ *cb = mycb; \
+ return adiost_get_callback_success; \
+ } \
+ } \
+ return adiost_get_callback_failure;
+
+ FOREACH_ADIOST_EVENT(adiost_event_macro)
+
+#undef adiost_event_macro
+
+ default: return adiost_get_callback_failure;
+ }
+}
+
+/*****************************************************************************
+ * API inquiry for tool
+ ****************************************************************************/
+
+static adiost_interface_fn_t adiost_fn_lookup(const char *s)
+{
+
+#define adiost_interface_fn(fn) \
+ if (strcmp(s, #fn) == 0) return (adiost_interface_fn_t) fn;
+
+ FOREACH_ADIOST_INQUIRY_FN(adiost_interface_fn)
+
+ //FOREACH_ADIOST_PLACEHOLDER_FN(adiost_interface_fn)
+
+ return (adiost_interface_fn_t) 0;
+}
+
diff --git a/src/core/adiost_callback_internal.h b/src/core/adiost_callback_internal.h
new file mode 100644
index 0000000..a106ebb
--- /dev/null
+++ b/src/core/adiost_callback_internal.h
@@ -0,0 +1,85 @@
+/*
+ * ADIOS is freely available under the terms of the BSD license described
+ * in the COPYING file in the top level directory of this source distribution.
+ *
+ * Copyright (c) 2008 - 2009. UT-BATTELLE, LLC. All rights reserved.
+ */
+
+#ifndef __ADIOST_CALLBACK_INTERNAL_H__
+#define __ADIOST_CALLBACK_INTERNAL_H__
+
+/* ADIOS Event Callback API
+ *
+ * This pair of source files (callback_api.h/c) is used to define a callback
+ * API for any tool that wants to be notified when ADIOS events happen. For
+ * example, a performance tool may want to know when staged writes happen
+ * and be notified how many bytes are transferred, in order to estimate
+ * effective bandwidth.
+ */
+
+#include <stddef.h>
+// we want our implementation of the tool to be weak, and exported.
+#define ADIOST_EXPORT __attribute__((visibility("default")))
+#define ADIOST_WEAK __attribute__ (( weak ))
+#include "public/adiost_callback_api.h"
+
+/* Definitions */
+
+#define ADIOST_VERSION 20170202 // 2017, February 02
+#define ADIOST_EXTERN extern "C"
+extern int adios_tool_enabled;
+
+typedef enum adios_tool_setting_e {
+ adiost_error = 0,
+ adiost_unset,
+ adiost_disabled,
+ adiost_enabled
+} adios_tool_setting_t;
+
+/* management of registered function callbacks */
+#define adiost_callback(e) e ## _callback
+
+typedef struct adiost_callbacks_s {
+#define adiost_event_macro(event, callback, eventid) callback adiost_callback(event);
+
+ FOREACH_ADIOST_EVENT(adiost_event_macro)
+
+ #undef adiost_event_macro
+} adiost_callbacks_t;
+
+
+/* Global variables */
+
+extern adiost_callbacks_t adiost_callbacks;
+
+/* internal callback API functions */
+
+void adiost_pre_init(void);
+void adiost_post_init(void);
+void adiost_finalize(void);
+
+/* These variadic macros save us from having to add 4+ lines of source code
+ * each time that we want to make an event callback. */
+
+#define ADIOST_CALLBACK(__event, __fd, ...) \
+ if (adios_tool_enabled && \
+ adiost_callbacks.adiost_callback(__event)) { \
+ adiost_callbacks.adiost_callback(__event)((int64_t)__fd, \
+ adiost_event, ##__VA_ARGS__); \
+ } \
+
+#define ADIOST_CALLBACK_ENTER(__event, __fd, ...) \
+ if (adios_tool_enabled && \
+ adiost_callbacks.adiost_callback(__event)) { \
+ adiost_callbacks.adiost_callback(__event)((int64_t)__fd, \
+ adiost_event_enter, ##__VA_ARGS__); \
+ } \
+
+#define ADIOST_CALLBACK_EXIT(__event, __fd, ...) \
+ if (adios_tool_enabled && \
+ adiost_callbacks.adiost_callback(__event)) { \
+ adiost_callbacks.adiost_callback(__event)((int64_t)__fd, \
+ adiost_event_exit, ##__VA_ARGS__); \
+ } \
+
+#endif // #ifndef __ADIOST_CALLBACK_INTERNAL_H__
diff --git a/src/core/adiost_default_tool.c b/src/core/adiost_default_tool.c
new file mode 100644
index 0000000..81dd428
--- /dev/null
+++ b/src/core/adiost_default_tool.c
@@ -0,0 +1,348 @@
+/*
+ * ADIOS is freely available under the terms of the BSD license described
+ * in the COPYING file in the top level directory of this source distribution.
+ *
+ * Copyright (c) 2008 - 2009. UT-BATTELLE, LLC. All rights reserved.
+ */
+
+/* ADIOS Event Callback API - Default tool implementation
+ *
+ * This source file is a default implementation of the ADIOS callback API
+ * for tools, or ADIOST. This is a simple tool that will add performance
+ * data to the ADIOS metadata.
+ */
+
+#include "config.h"
+// we want our implementation of the tool to be weak, and exported.
+#define ADIOST_EXPORT __attribute__((visibility("default")))
+#define ADIOST_WEAK __attribute__ (( weak ))
+
+#include "public/adiost_callback_api.h"
+#include <stdint.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <inttypes.h>
+#include <time.h>
+#include "adios_clock.h"
+#define ADIOST_EXTERN
+#define DEBUG_PRINT printf("In %s!\n", __func__); fflush(stdout);
+#define DEBUG_PRINT_FD printf("file_descriptor: %" PRId64 "!\n", file_descriptor); fflush(stdout);
+#define ONE_BILLION 1000000000
+#define ONE_BILLIONF 1000000000.0
+
+#ifndef _GNU_SOURCE
+#define _GNU_SOURCE
+#endif // _GNU_SOURCE
+#include <errno.h> /* to get program name */
+
+/* The do { ... } while (0) idiom ensures that the code acts like a statement
+ * (function call). The unconditional use of the code ensures that the compiler
+ * always checks that your debug code is valid — but the optimizer will remove
+ * the code when DEBUG is 0. */
+#define DEBUG 0
+#define debug_print(...) do { \
+ if (DEBUG) { \
+ fprintf(stderr, __VA_ARGS__); \
+ fflush(stderr);\
+ } \
+} while (0)
+
+/* to get the program name from glibc */
+extern char *program_invocation_name;
+extern char *program_invocation_short_name;
+
+/* Enumeration of timer indices. */
+typedef enum adiost_timer_index {
+ adiost_thread_timer = 0,
+ adiost_open_timer,
+ adiost_close_timer,
+ adiost_open_to_close_timer,
+ adiost_read_timer,
+ adiost_write_timer,
+ adiost_advance_step_timer,
+ adiost_group_size_timer,
+ adiost_transform_timer,
+ adiost_fp_send_read_msg_timer,
+ adiost_fp_send_finalize_msg_timer,
+ adiost_fp_add_var_to_read_msg_timer,
+ adiost_fp_copy_buffer_timer,
+ adiost_last_timer_unused
+} adiost_timer_index_t;
+
+/* Enumeration of counter indices */
+typedef enum adiost_counter_index {
+ adiost_data_bytes_counter = 0,
+ adiost_total_bytes_counter,
+ adiost_last_counter_unused
+} adiost_counter_index_t;
+
+/* Array of timers for all timed events. This is a static
+ * array, limited to the number of events. */
+static uint64_t adiost_timers_accumulated[adiost_last_timer_unused] = {0ULL};
+static uint64_t adiost_timers_count[adiost_last_timer_unused] = {0ULL};
+static struct timespec adiost_timers_start_time[adiost_last_timer_unused];
+static uint64_t adiost_counters_count[adiost_last_counter_unused] = {0ULL};
+static uint64_t adiost_counters_accumulated[adiost_last_counter_unused] = {0ULL};
+
+void __timer_start(adiost_timer_index_t index) {
+ adios_clock_gettime(CLOCK_PROCESS_CPUTIME_ID, &(adiost_timers_start_time[index]));
+}
+
+/* Subtract the ‘struct timeval’ values X and Y,
+ storing the result in RESULT.
+ Return the total difference in nanoseconds. */
+
+uint64_t timespec_subtract (struct timespec *end, struct timespec *start)
+{
+ struct timespec result;
+ /* Perform the carry for the later subtraction by updating start. */
+ if (end->tv_nsec < start->tv_nsec) {
+ uint64_t nsec = (start->tv_nsec - end->tv_nsec) / ONE_BILLION + 1;
+ start->tv_nsec -= ONE_BILLION * nsec;
+ start->tv_sec += nsec;
+ }
+ if (end->tv_nsec - start->tv_nsec > ONE_BILLION) {
+ uint64_t nsec = (end->tv_nsec - start->tv_nsec) / ONE_BILLION;
+ start->tv_nsec += ONE_BILLION * nsec;
+ start->tv_sec -= nsec;
+ }
+
+ /* Compute the time remaining to wait.
+ tv_nsec is certainly positive. */
+ result.tv_sec = end->tv_sec - start->tv_sec;
+ result.tv_nsec = end->tv_nsec - start->tv_nsec;
+ return (result.tv_sec * ONE_BILLION) + result.tv_nsec;
+}
+
+void __timer_stop(adiost_timer_index_t index) {
+ struct timespec end_time;
+ adios_clock_gettime(CLOCK_PROCESS_CPUTIME_ID, &end_time);
+ uint64_t diff = timespec_subtract(&end_time, &(adiost_timers_start_time[index]));
+ adiost_timers_accumulated[index] = adiost_timers_accumulated[index] + diff;
+ adiost_timers_count[index] = adiost_timers_count[index] + 1;
+}
+
+ADIOST_EXTERN void my_thread(int64_t file_descriptor, char * name, adiost_event_type_t type) {
+ DEBUG_PRINT
+ DEBUG_PRINT_FD
+ if (type == adiost_event_enter) {
+ __timer_start(adiost_thread_timer);
+ } else {
+ __timer_stop(adiost_thread_timer);
+ }
+}
+
+ADIOST_EXTERN void my_open ( int64_t file_descriptor, adiost_event_type_t type,
+ const char * group_name, const char * file_name, const char * mode) {
+ DEBUG_PRINT
+ DEBUG_PRINT_FD
+ if (type == adiost_event_enter) {
+ debug_print("group_name: %s!\n", group_name);
+ debug_print("file_name: %s!\n", file_name);
+ debug_print("mode: %s!\n", mode);
+ __timer_start(adiost_open_to_close_timer);
+ __timer_start(adiost_open_timer);
+ } else {
+ __timer_stop(adiost_open_timer);
+ }
+}
+
+ADIOST_EXTERN void my_close(int64_t file_descriptor, adiost_event_type_t type) {
+ DEBUG_PRINT
+ DEBUG_PRINT_FD
+ if (type == adiost_event_enter) {
+ __timer_start(adiost_close_timer);
+ } else {
+ __timer_stop(adiost_close_timer);
+ __timer_stop(adiost_open_to_close_timer);
+ }
+}
+
+ADIOST_EXTERN void my_write( int64_t file_descriptor, adiost_event_type_t type) {
+ DEBUG_PRINT
+ DEBUG_PRINT_FD
+ if (type == adiost_event_enter) {
+ __timer_start(adiost_write_timer);
+ } else {
+ __timer_stop(adiost_write_timer);
+ }
+}
+
+ADIOST_EXTERN void my_read( int64_t file_descriptor, adiost_event_type_t type) {
+ DEBUG_PRINT
+ DEBUG_PRINT_FD
+ if (type == adiost_event_enter) {
+ __timer_start(adiost_read_timer);
+ } else {
+ __timer_stop(adiost_read_timer);
+ }
+}
+
+ADIOST_EXTERN void my_advance_step( int64_t file_descriptor,
+ adiost_event_type_t type) {
+ DEBUG_PRINT
+ DEBUG_PRINT_FD
+ if (type == adiost_event_enter) {
+ __timer_start(adiost_advance_step_timer);
+ } else {
+ __timer_stop(adiost_advance_step_timer);
+ }
+}
+
+ADIOST_EXTERN void my_group_size(int64_t file_descriptor,
+ adiost_event_type_t type, uint64_t data_size, uint64_t total_size) {
+ DEBUG_PRINT
+ DEBUG_PRINT_FD
+ if (type == adiost_event_enter) {
+ __timer_start(adiost_group_size_timer);
+ } else {
+ debug_print("data size: %" PRIu64 "!\n", data_size); fflush(stdout);
+ adiost_counters_accumulated[adiost_data_bytes_counter] =
+ adiost_counters_accumulated[adiost_data_bytes_counter] + data_size;
+ adiost_counters_count[adiost_data_bytes_counter] =
+ adiost_counters_count[adiost_data_bytes_counter] + 1;
+ debug_print("total size: %" PRIu64 "!\n", total_size); fflush(stdout);
+ adiost_counters_accumulated[adiost_total_bytes_counter] =
+ adiost_counters_accumulated[adiost_total_bytes_counter] + total_size;
+ adiost_counters_count[adiost_total_bytes_counter] =
+ adiost_counters_count[adiost_total_bytes_counter] + 1;
+ __timer_stop(adiost_group_size_timer);
+ }
+}
+
+ADIOST_EXTERN void my_transform( int64_t file_descriptor,
+ adiost_event_type_t type) {
+ DEBUG_PRINT
+ DEBUG_PRINT_FD
+ if (type == adiost_event_enter) {
+ __timer_start(adiost_transform_timer);
+ } else {
+ __timer_stop(adiost_transform_timer);
+ }
+}
+
+ADIOST_EXTERN void my_fp_send_read_msg(int64_t file_descriptor,
+ adiost_event_type_t type) {
+ DEBUG_PRINT
+ DEBUG_PRINT_FD
+ if (type == adiost_event_enter) {
+ __timer_start(adiost_fp_send_read_msg_timer);
+ } else {
+ __timer_stop(adiost_fp_send_read_msg_timer);
+ }
+}
+
+ADIOST_EXTERN void my_fp_send_finalize_msg(int64_t file_descriptor,
+ adiost_event_type_t type) {
+ DEBUG_PRINT
+ DEBUG_PRINT_FD
+ if (type == adiost_event_enter) {
+ __timer_start(adiost_fp_send_finalize_msg_timer);
+ } else {
+ __timer_stop(adiost_fp_send_finalize_msg_timer);
+ }
+}
+
+ADIOST_EXTERN void my_fp_add_var_to_read_msg(int64_t file_descriptor,
+ adiost_event_type_t type) {
+ DEBUG_PRINT
+ DEBUG_PRINT_FD
+ if (type == adiost_event_enter) {
+ __timer_start(adiost_fp_add_var_to_read_msg_timer);
+ } else {
+ __timer_stop(adiost_fp_add_var_to_read_msg_timer);
+ }
+}
+
+ADIOST_EXTERN void my_fp_copy_buffer(int64_t file_descriptor,
+ adiost_event_type_t type) {
+ DEBUG_PRINT
+ DEBUG_PRINT_FD
+ if (type == adiost_event_enter) {
+ __timer_start(adiost_fp_copy_buffer_timer);
+ } else {
+ __timer_stop(adiost_fp_copy_buffer_timer);
+ }
+}
+
+/* This function is for printing a timer */
+void print_timer(const char *_name, adiost_timer_index_t index) {
+ if (adiost_timers_count[index] > 0ULL) {
+ debug_print("%s: %s, %" PRIu64 " calls, %3.9f seconds\n",
+ program_invocation_short_name, _name,
+ adiost_timers_count[index],
+ ((double)adiost_timers_accumulated[index])/ONE_BILLIONF);
+ }
+}
+
+/* This function is for printing a counter */
+void print_counter(const char *_name, adiost_counter_index_t index) {
+ if (adiost_counters_count[index] > 0ULL) {
+ debug_print("%s: %s, %" PRIu64 " calls, %" PRIu64 " bytes\n",
+ program_invocation_short_name, _name,
+ adiost_counters_count[index],
+ adiost_counters_accumulated[index]);
+ }
+}
+
+ADIOST_EXTERN void my_finalize(void) {
+ DEBUG_PRINT
+ print_timer("adios_thread", adiost_thread_timer);
+ print_timer("adios_open", adiost_open_timer);
+ print_timer("adios_close", adiost_close_timer);
+ print_timer("adios_open_to_close", adiost_open_to_close_timer);
+ print_timer("adios_group_size", adiost_group_size_timer);
+ print_timer("adios_advance_step", adiost_advance_step_timer);
+ print_timer("adios_transform", adiost_transform_timer);
+ print_timer("adios_read", adiost_read_timer);
+ print_timer("adios_write", adiost_write_timer);
+ print_timer("flexpath send open msg", adiost_fp_send_read_msg_timer);
+ print_timer("flexpath send finalize msg", adiost_fp_send_finalize_msg_timer);
+ print_timer("flexpath send var msg", adiost_fp_add_var_to_read_msg_timer);
+ print_timer("flexpath copy buffer", adiost_fp_copy_buffer_timer);
+ print_counter("adios data written", adiost_data_bytes_counter);
+ print_counter("adios total written", adiost_total_bytes_counter);
+}
+
+// This function is for checking that the function registration worked.
+#define CHECK(EVENT,FUNCTION,NAME) \
+ debug_print("Registering ADIOST callback %s...",NAME); \
+ if (adiost_fn_set_callback(EVENT, (adiost_callback_t)(FUNCTION)) != \
+ adiost_set_result_registration_success) { \
+ debug_print("\n\tFailed to register ADIOST callback %s!\n",NAME); \
+ } else { \
+ debug_print("success.\n"); \
+ } \
+
+ADIOST_EXTERN void default_adiost_initialize (adiost_function_lookup_t adiost_fn_lookup,
+ const char *runtime_version, unsigned int adiost_version) {
+
+ adiost_set_callback_t adiost_fn_set_callback =
+ (adiost_set_callback_t)adiost_fn_lookup("adiost_set_callback");
+
+ if (!getenv("ADIOST")) return;
+ debug_print("Registering ADIOS tool events...\n");
+ CHECK(adiost_event_thread, my_thread, "adios_thread");
+ CHECK(adiost_event_open, my_open, "adios_open");
+ CHECK(adiost_event_close, my_close, "adios_close");
+ CHECK(adiost_event_write, my_write, "adios_write");
+ CHECK(adiost_event_read, my_read, "adios_read");
+ CHECK(adiost_event_advance_step, my_advance_step, "adios_advance_step");
+ CHECK(adiost_event_group_size, my_group_size, "adios_group_size");
+ CHECK(adiost_event_transform, my_transform, "adios_transform");
+ CHECK(adiost_event_fp_send_read_msg,
+ my_fp_send_read_msg, "adios_fp_send_read_msg");
+ CHECK(adiost_event_fp_send_finalize_msg,
+ my_fp_send_finalize_msg, "adios_fp_send_finalize_msg");
+ CHECK(adiost_event_fp_add_var_to_read_msg,
+ my_fp_add_var_to_read_msg, "adiost_fp_add_var_to_read_msg");
+ CHECK(adiost_event_fp_copy_buffer,
+ my_fp_copy_buffer, "adios_fp_copy_buffer");
+ CHECK(adiost_event_library_shutdown, my_finalize, "adios_finalize");
+}
+
+/* Weak function definitions, declarations */
+
+extern adiost_initialize_t adiost_tool(void) { return default_adiost_initialize; }
+
+
diff --git a/src/core/bp_utils.c b/src/core/bp_utils.c
index 1526f9b..6c8f386 100644
--- a/src/core/bp_utils.c
+++ b/src/core/bp_utils.c
@@ -152,6 +152,31 @@ int get_time (struct adios_index_var_struct_v1 * v, int step)
}
+/* Convert 'step' to time, which is used in ADIOS internals.
+ * 'step' should start from 0.
+ */
+int get_time_from_pglist(struct bp_index_pg_struct_v1 * pgs, int step)
+{
+ int i = 0;
+ int prev_ti = 0, counter = 0;
+
+ while (pgs != NULL)
+ {
+ if (pgs->time_index != prev_ti)
+ {
+ counter ++;
+ if (counter == (step + 1))
+ {
+ return pgs->time_index;
+ }
+ prev_ti = pgs->time_index;
+ }
+ pgs = pgs->next;
+ }
+ return -1;
+
+}
+
/* This routine converts "step" to "time", which is an ADIOS internal thing.
* The calculated "time" is needed by other BP routines to figure
* correct piece of var index to process.
@@ -197,7 +222,7 @@ int adios_step_to_time (const ADIOS_FILE * fp, int varid, int from_steps)
return adios_step_to_time_v1 (fp, v, from_steps);
}
-int bp_read_open (const char * filename,
+static int bp_read_open (const char * filename,
MPI_Comm comm,
BP_FILE * fh)
{
@@ -229,6 +254,44 @@ int bp_read_open (const char * filename,
return 0;
}
+static int bp_read_open_rootonly (const char * filename,
+ MPI_Comm comm,
+ BP_FILE * fh)
+{
+ int err;
+ int rank;
+
+ MPI_Comm_rank (comm, &rank);
+
+ // variable definition
+ MPI_Offset file_size = 0;
+
+ if (rank == 0)
+ {
+ // open a file by one processor then broadcast the size and the success
+ err = MPI_File_open (MPI_COMM_SELF, (char *) filename, MPI_MODE_RDONLY,
+ (MPI_Info) MPI_INFO_NULL, &(fh->mpi_fh));
+ if (err == MPI_SUCCESS) {
+ MPI_File_get_size (fh->mpi_fh, &file_size);
+ err = 0;
+ }
+ }
+ MPI_Bcast (&err, 1, MPI_INT, 0, comm);
+ MPI_Bcast (&file_size, 1, MPI_UNSIGNED_LONG_LONG, 0, comm);
+ fh->b->file_size = file_size;
+ fh->mfooter.file_size = file_size;
+ if (err)
+ {
+ char e [MPI_MAX_ERROR_STRING];
+ int len = 0;
+ memset (e, 0, MPI_MAX_ERROR_STRING);
+ MPI_Error_string (err, e, &len);
+ adios_error (err_file_open_error, "MPI open failed for %s: '%s'\n", filename, e);
+ return adios_flag_no;
+ }
+ return err;
+}
+
/* This routine does the parallel bp file open and index parsing.
*/
int bp_open (const char * fname,
@@ -236,13 +299,12 @@ int bp_open (const char * fname,
BP_FILE * fh)
{
int rank;
- uint64_t header_size;
MPI_Comm_rank (comm, &rank);
adios_buffer_struct_init (fh->b);
- if (bp_read_open (fname, comm, fh))
+ if (bp_read_open_rootonly (fname, comm, fh))
{
return -1;
}
@@ -259,22 +321,56 @@ int bp_open (const char * fname,
/* Broadcast to all other processors */
MPI_Bcast (&fh->mfooter, sizeof (struct bp_minifooter), MPI_BYTE, 0, comm);
- header_size = fh->mfooter.file_size-fh->mfooter.pgs_index_offset;
+ if (fh->mfooter.pgs_index_offset > 0)
+ {
+ /* This BP file has data not just metadata. We need to open it
+ * by every reader process.
+ * This check is equivalent to has_subfiles(fh) but this makes it more
+ * secure for future if a metadata+data BP file will ever have subfiles.
+ */
+ if (rank == 0)
+ MPI_File_close(&fh->mpi_fh);
+ if (bp_read_open (fname, comm, fh))
+ {
+ return -1;
+ }
+ }
+
+ uint64_t footer_size = fh->mfooter.file_size-fh->mfooter.pgs_index_offset;
if (rank != 0)
{
if (!fh->b->buff)
{
- bp_alloc_aligned (fh->b, header_size);
+ bp_alloc_aligned (fh->b, footer_size);
assert (fh->b->buff);
- memset (fh->b->buff, 0, header_size);
+ memset (fh->b->buff, 0, footer_size);
fh->b->offset = 0;
}
}
MPI_Barrier (comm);
- MPI_Bcast (fh->b->buff, fh->mfooter.file_size-fh->mfooter.pgs_index_offset, MPI_BYTE, 0, comm);
+ // Broadcast the index which may be bigger than 2GB, so do it in chunks
+ uint64_t bytes_sent = 0;
+ int32_t to_send = 0;
+ int r, err;
+
+ while (bytes_sent < footer_size)
+ {
+ if (footer_size - bytes_sent > MAX_MPIWRITE_SIZE)
+ {
+ to_send = MAX_MPIWRITE_SIZE;
+ }
+ else
+ {
+ to_send = footer_size - bytes_sent;
+ }
+
+ MPI_Bcast (fh->b->buff + bytes_sent, to_send, MPI_BYTE, 0, comm);
+ bytes_sent += to_send;
+ }
+
/* Everyone parses the index on its own */
bp_parse_pgs (fh);
@@ -417,6 +513,7 @@ BP_FILE * BP_FILE_alloc (const char * fname, MPI_Comm comm)
fh->subfile_handles.warning_printed = 0;
fh->subfile_handles.head = NULL;
fh->subfile_handles.tail = NULL;
+ fh->mpi_fh = MPI_FILE_NULL;
return fh;
}
@@ -500,7 +597,7 @@ int bp_close (BP_FILE * fh)
MPI_File mpi_fh = fh->mpi_fh;
adios_errno = 0;
- if (fh->mpi_fh)
+ if (fh->mpi_fh != MPI_FILE_NULL)
MPI_File_close (&mpi_fh);
close_all_BP_subfiles (fh);
@@ -704,7 +801,6 @@ int bp_read_minifooter (BP_FILE * bp_struct)
struct adios_bp_buffer_struct_v1 * b = bp_struct->b;
struct bp_minifooter * mh = &bp_struct->mfooter;
uint64_t attrs_end = b->file_size - MINIFOOTER_SIZE;
- int r;
MPI_Status status;
@@ -727,7 +823,9 @@ int bp_read_minifooter (BP_FILE * bp_struct)
It also sets b->change_endianness */
/* Note that b is not sent over to processes, only the minifooter and then b->buff (the footer) */
b->offset = MINIFOOTER_SIZE - 4;
- adios_parse_version (b, &mh->version);
+ uint32_t v;
+ adios_parse_version (b, &v);
+ mh->version = v;
mh->change_endianness = b->change_endianness;
// validity check
@@ -796,12 +894,56 @@ int bp_read_minifooter (BP_FILE * bp_struct)
uint64_t footer_size = mh->file_size - mh->pgs_index_offset;
bp_realloc_aligned (b, footer_size);
MPI_File_seek (bp_struct->mpi_fh,
- (MPI_Offset) mh->pgs_index_offset,
- MPI_SEEK_SET);
- MPI_File_read (bp_struct->mpi_fh, b->buff, footer_size,
- MPI_BYTE, &status);
+ (MPI_Offset) mh->pgs_index_offset,
+ MPI_SEEK_SET);
+
+ // if we need to read > 2 GB, need to do it in parts
+ // since count is limited to MAX_MPIWRITE_SIZE (signed 32-bit max).
+ uint64_t bytes_read = 0;
+ int32_t to_read = 0;
+ int r, err;
+
+ while (bytes_read < footer_size)
+ {
+ if (footer_size - bytes_read > MAX_MPIWRITE_SIZE)
+ {
+ to_read = MAX_MPIWRITE_SIZE;
+ }
+ else
+ {
+ to_read = footer_size - bytes_read;
+ }
- MPI_Get_count (&status, MPI_BYTE, &r);
+ err = MPI_File_read (bp_struct->mpi_fh, b->buff+bytes_read, to_read, MPI_BYTE, &status);
+ if (err != MPI_SUCCESS)
+ {
+ char e [MPI_MAX_ERROR_STRING];
+ int len = 0;
+ memset (e, 0, MPI_MAX_ERROR_STRING);
+ MPI_Error_string (err, e, &len);
+ adios_error (err_file_open_error,
+ "Error while reading BP index, %" PRIu64 " bytes from file offset %" PRIu64 ": MPI_File_read error: '%s'\n",
+ to_read, mh->pgs_index_offset, e);
+ }
+ err = MPI_Get_count (&status, MPI_BYTE, &r);
+ if (err != MPI_SUCCESS)
+ {
+ char e [MPI_MAX_ERROR_STRING];
+ int len = 0;
+ memset (e, 0, MPI_MAX_ERROR_STRING);
+ MPI_Error_string (err, e, &len);
+ adios_error (err_file_open_error,
+ "Error while reading BP index, %" PRIu64 " bytes from file offset %" PRIu64 ": MPI_Get_count error: '%s'\n",
+ to_read, mh->pgs_index_offset, e);
+ }
+ else if (r != to_read)
+ {
+ adios_error (err_file_open_error,
+ "Error while reading BP index, tried to read %" PRIu64 " bytes from file offset %" PRIu64 " but only got %" PRIu64 " bytes\n",
+ to_read, mh->pgs_index_offset);
+ }
+ bytes_read += to_read;
+ }
// reset the pointer to the beginning of buffer
b->offset = 0;
@@ -826,9 +968,9 @@ int bp_parse_pgs (BP_FILE * fh)
b->change_endianness = (enum ADIOS_FLAG) mh->change_endianness;
BUFREAD64(b, mh->pgs_count)
- BUFREAD64(b, mh->pgs_length)
+ BUFREAD64(b, mh->pgs_length)
- int j;
+ int j;
uint64_t group_count = 0;
char ** namelist;
char fortran_flag;
@@ -1311,6 +1453,53 @@ int bp_parse_attrs (BP_FILE * fh)
return 0;
}
+static const uint64_t JOINEDDIM = 18446744073709551614ULL;
+static void process_joined_array(struct adios_index_var_struct_v1 *v)
+{
+ if (v->characteristics[0].value) // scalar
+ return;
+ if (!is_global_array(&(v->characteristics[0])))
+ return;
+ int ndim = v->characteristics[0].dims.count;
+ int joindim = -1;
+ int i, j;
+ for (i = 0; i < ndim; i++)
+ {
+ if (v->characteristics[0].dims.dims[i*3+1] == JOINEDDIM)
+ {
+ joindim = i;
+ log_debug("Variable %s is a Joined Array in dimension %d\n", v->var_name, i);
+ break;
+ }
+ }
+ if (joindim >= 0)
+ {
+ uint64_t offset = 0;
+ uint32_t timeidx = v->characteristics[0].time_index;
+ log_debug(" Calculate joined array offsets for %" PRIu64 " blocks\n", v->characteristics_count);
+ //log_debug(" Time index start from %d\n", v->characteristics[0].time_index);
+ int startidx = 0; // first characteristics for the current time_index
+ for (i = 0; i < v->characteristics_count; ++i)
+ {
+ if (v->characteristics[i].time_index > timeidx)
+ {
+ //log_debug(" Time index change to %d\n", v->characteristics[i].time_index);
+ // Update global dimensions of all characteristics for this time_index now
+ for (j = startidx; j < i; ++j) {
+ v->characteristics[j].dims.dims[joindim*3+1] = offset;
+ }
+ timeidx = v->characteristics[i].time_index;
+ offset = 0;
+ startidx = i;
+ }
+ //log_debug(" Calculated offset = %" PRIu64 "\n", offset);
+ v->characteristics[i].dims.dims[joindim*3+2] = offset;
+ offset += v->characteristics[i].dims.dims[joindim*3];
+ }
+ }
+}
+
+
/*******************/
/* Parse VARIABLES */
/*******************/
@@ -1428,6 +1617,7 @@ int bp_parse_vars (BP_FILE * fh)
(*root)->characteristics [j].time_index);*/
}
}
+ process_joined_array((*root));
root = &(*root)->next;
}
@@ -1949,7 +2139,7 @@ int bp_seek_to_step (ADIOS_FILE * fp, int tostep, int show_hidden_attrs)
else
{
allstep = 0;
- t = get_time (var_root, tostep);
+ t = get_time_from_pglist (fh->pgs_root, tostep);
}
/* Prepare vars */
diff --git a/src/core/bp_utils.h b/src/core/bp_utils.h
index d7aed08..df45684 100644
--- a/src/core/bp_utils.h
+++ b/src/core/bp_utils.h
@@ -31,9 +31,7 @@ int bp_get_characteristics_data (void ** ptr_data,
int data_size,
enum ADIOS_DATATYPES type);
int bp_read_close (struct adios_bp_buffer_struct_v1 * b);
-int bp_read_open (const char * filename,
- MPI_Comm comm,
- BP_FILE * fh);
+
MPI_File * get_BP_subfile_handle(BP_FILE *fh, uint32_t file_index);
void add_BP_subfile_handle (struct BP_FILE *fh, struct BP_file_handle * n);
void close_all_BP_subfiles (BP_FILE * fh);
diff --git a/src/core/common_adios.c b/src/core/common_adios.c
index 1b90ef1..46510c1 100644
--- a/src/core/common_adios.c
+++ b/src/core/common_adios.c
@@ -7,27 +7,27 @@
#include "config.h"
-#include <stdlib.h>
+#include <assert.h>
#include <math.h>
+#include <stdint.h>
+#include <stdlib.h>
#include <string.h>
+#include <sys/time.h> // gettimeofday
#include <unistd.h>
-#include <stdint.h>
-#include <sys/time.h> // gettimeofday
-#include <assert.h>
// xml parser
#include <mxml.h>
-#include "core/types.h"
+#include "core/adios_bp_v1.h"
#include "core/adios_internals.h"
#include "core/adios_internals_mxml.h"
-#include "core/common_adios.h"
-#include "core/adios_bp_v1.h"
-#include "core/buffer.h"
-#include "core/adios_transport_hooks.h"
#include "core/adios_logger.h"
#include "core/adios_timing.h"
+#include "core/adios_transport_hooks.h"
+#include "core/buffer.h"
+#include "core/common_adios.h"
#include "core/qhashtbl.h"
+#include "core/types.h"
#include "public/adios_error.h"
// NCSU ALACRITY-ADIOS
@@ -43,555 +43,567 @@
#include "dmalloc.h"
#endif
-extern struct adios_transport_struct * adios_transports;
+#include "adiost_callback_internal.h"
+
+extern struct adios_transport_struct *adios_transports;
extern int adios_errno;
///////////////////////////////////////////////////////////////////////////////
-int common_adios_init (const char * config, MPI_Comm comm)
-{
- // parse the config file
- if (comm == MPI_COMM_NULL)
- comm = MPI_COMM_SELF;
- adios_errno = err_no_error;
- adios_parse_config (config, comm);
- return adios_errno;
+int common_adios_init(const char *config, MPI_Comm comm) {
+ // parse the config file
+ if (comm == MPI_COMM_NULL) comm = MPI_COMM_SELF;
+ adios_errno = err_no_error;
+ adiost_pre_init();
+ adios_parse_config(config, comm);
+ adiost_post_init();
+ return adios_errno;
}
///////////////////////////////////////////////////////////////////////////////
// all XML file pieces will be provided by another series of calls
-int common_adios_init_noxml (MPI_Comm comm)
-{
- if (comm == MPI_COMM_NULL)
- comm = MPI_COMM_SELF;
- adios_errno = err_no_error;
- adios_local_config (comm);
- return adios_errno;
+int common_adios_init_noxml(MPI_Comm comm) {
+ if (comm == MPI_COMM_NULL) comm = MPI_COMM_SELF;
+ adios_errno = err_no_error;
+ adiost_pre_init();
+ adios_local_config(comm);
+ adiost_post_init();
+ return adios_errno;
}
-
///////////////////////////////////////////////////////////////////////////////
-int common_adios_finalize (int mype)
-{
- struct adios_method_list_struct * m;
- struct adios_group_list_struct * g;
-
- //Time Aggregation: there may be time steps left in the time aggregated buffer, which
- // needs to be dumped out before finalize
- for (g = adios_get_groups(); g; g = g->next)
- {
- if (TimeAggregationInProgress(g->group)) {
- //log_debug("time buffering enabled and data left in finalize... close file\n");
- /* At this point the buffer of the last step has been closed and
- * the index has been built but it was not yet passed on to the
- * method's close function.
- * do_ts_finalize signals this special case to common_adios_close()
- */
- SetTimeAggregationFlush(g->group, 1);
- // => TimeAggregationIsFlushing => TimeAggregationLastStep
- common_adios_close (g->group->ts_fd); // close file
- SetTimeAggregation(g->group, 0); //turn off ts buffering
- }
+int common_adios_finalize(int mype) {
+ struct adios_method_list_struct *m;
+ struct adios_group_list_struct *g;
+
+ // Time Aggregation: there may be time steps left in the time aggregated
+ // buffer, which
+ // needs to be dumped out before finalize
+ for (g = adios_get_groups(); g; g = g->next) {
+ if (TimeAggregationInProgress(g->group)) {
+ // log_debug("time buffering enabled and data left in finalize... close
+ // file\n");
+ /* At this point the buffer of the last step has been closed and
+ * the index has been built but it was not yet passed on to the
+ * method's close function.
+ * do_ts_finalize signals this special case to common_adios_close()
+ */
+ SetTimeAggregationFlush(g->group, 1);
+ // => TimeAggregationIsFlushing => TimeAggregationLastStep
+ common_adios_close(g->group->ts_fd); // close file
+ SetTimeAggregation(g->group, 0); // turn off ts buffering
}
-
- adios_errno = err_no_error;
- for (m = adios_get_methods (); m; m = m->next)
- {
- if ( m->method->m != ADIOS_METHOD_UNKNOWN
- && m->method->m != ADIOS_METHOD_NULL
- && adios_transports [m->method->m].adios_finalize_fn
- )
- {
- adios_transports [m->method->m].adios_finalize_fn (mype, m->method);
- }
+ }
+
+ adios_errno = err_no_error;
+ for (m = adios_get_methods(); m; m = m->next) {
+ if (m->method->m != ADIOS_METHOD_UNKNOWN &&
+ m->method->m != ADIOS_METHOD_NULL &&
+ adios_transports[m->method->m].adios_finalize_fn) {
+ adios_transports[m->method->m].adios_finalize_fn(mype, m->method);
}
+ }
- adios_cleanup ();
+ adios_cleanup();
#if defined(WITH_NCSU_TIMER) && defined(TIMER_LEVEL) && (TIMER_LEVEL <= 0)
- timer_finalize ();
+ timer_finalize();
#endif
- return adios_errno;
+ adiost_finalize();
+ return adios_errno;
}
///////////////////////////////////////////////////////////////////////////////
-int common_adios_allocate_buffer (enum ADIOS_BUFFER_ALLOC_WHEN adios_buffer_alloc_when
- ,uint64_t buffer_size)
-{
- adios_errno = err_no_error;
- log_warn ("adios_allocate_buffer is not supported anymore. "
- "Use adios_set_max_buffer_size(size_in_MB) to set the maximum allowed "
- "buffer size for each adios_open()...adios_close() operation.\n");
- //adios_buffer_size_requested_set (buffer_size * 1024 * 1024);
- //adios_buffer_alloc_when_set (adios_buffer_alloc_when);
- //adios_set_buffer_size ();
- return adios_errno;
+int common_adios_allocate_buffer(
+ enum ADIOS_BUFFER_ALLOC_WHEN adios_buffer_alloc_when,
+ uint64_t buffer_size) {
+ adios_errno = err_no_error;
+ log_warn(
+ "adios_allocate_buffer is not supported anymore. "
+ "Use adios_set_max_buffer_size(size_in_MB) to set the maximum allowed "
+ "buffer size for each adios_open()...adios_close() operation.\n");
+ // adios_buffer_size_requested_set (buffer_size * 1024 * 1024);
+ // adios_buffer_alloc_when_set (adios_buffer_alloc_when);
+ // adios_set_buffer_size ();
+ return adios_errno;
}
///////////////////////////////////////////////////////////////////////////////
// Drew: used for experiments
static uint32_t pinned_timestep = 0;
-void adios_pin_timestep(uint32_t ts) {
- pinned_timestep = ts;
-}
-
+void adios_pin_timestep(uint32_t ts) { pinned_timestep = ts; }
///////////////////////////////////////////////////////////////////////////////
static const char ADIOS_ATTR_PATH[] = "/__adios__";
-int common_adios_open (int64_t * fd_p, const char * group_name
- ,const char * name, const char * file_mode, MPI_Comm comm
-)
-{
+int common_adios_open(int64_t *fd_p, const char *group_name, const char *name,
+ const char *file_mode, MPI_Comm comm) {
#if defined(WITH_NCSU_TIMER) && defined(TIMER_LEVEL) && (TIMER_LEVEL <= 0)
- timer_start ("adios_open_to_close");
- timer_start ("adios_open");
+ timer_start("adios_open_to_close");
+ timer_start("adios_open");
#endif
+ ADIOST_CALLBACK_ENTER(adiost_event_open, *fd_p, group_name, name, file_mode);
+
+ struct adios_group_struct *g = NULL;
+ struct adios_method_list_struct *methods = NULL;
+ struct adios_file_struct *fd = NULL;
+ enum ADIOS_METHOD_MODE mode;
+
+ // printf("beginning of file open... bytes_written=%llu\n",
+ // fd->bytes_written);
+
+ adios_errno = err_no_error;
+ g = adios_common_get_group(group_name);
+ if (!g) {
+ adios_error(err_invalid_group,
+ "adios_open: try to open file %s with undefined group: %s\n",
+ name, group_name);
+ *fd_p = 0;
+ ADIOST_CALLBACK_EXIT(adiost_event_open, *fd_p, group_name, name, file_mode);
+ return adios_errno;
+ }
+
+ if (!strcasecmp(file_mode, "r"))
+ mode = adios_mode_read;
+ else if (!strcasecmp(file_mode, "w"))
+ mode = adios_mode_write;
+ else if (!strcasecmp(file_mode, "a"))
+ mode = adios_mode_append;
+ else if (!strcasecmp(file_mode, "u"))
+ mode = adios_mode_update;
+ else {
+ adios_error(err_invalid_file_mode,
+ "adios_open: unknown file mode: %s, supported r,w,a,u\n",
+ file_mode);
+
+ *fd_p = 0;
- struct adios_group_struct * g = NULL;
- struct adios_method_list_struct * methods = NULL;
- struct adios_file_struct * fd = NULL;
- enum ADIOS_METHOD_MODE mode;
-
- //printf("beginning of file open... bytes_written=%llu\n", fd->bytes_written);
-
- adios_errno = err_no_error;
- g = adios_common_get_group (group_name);
- if (!g) {
- adios_error(err_invalid_group,
- "adios_open: try to open file %s with undefined group: %s\n",
- name, group_name);
- *fd_p = 0;
- return adios_errno;
- }
-
- if (!strcasecmp (file_mode, "r"))
- mode = adios_mode_read;
+ return adios_errno;
+ }
+
+ // Time Aggregation: if file name suddenly changes for the group
+ // we need to flush the buffer to the old file and start clean
+ if (TimeAggregationInProgress(g) && strcmp(name, g->ts_fd->name)) {
+ log_debug(
+ "TimeAggr: new filename during aggregation. Flush and start buffering "
+ "again\n");
+ SetTimeAggregationFlush(
+ g, 1); // => TimeAggregationIsFlushing => TimeAggregationLastStep
+ common_adios_close(g->ts_fd); // close old file
+ SetTimeAggregationFlush(g, 0); // => NOT TimeAggregationIsFlushing
+ g->ts_fd =
+ NULL; // => TimeAggregationJustBegan AND NOT TimeAggregationInProgress
+ }
+
+ // printf("ts_to buffer=%d max_tx=%d\n", g->ts_to_buffer, g->max_ts);
+ // Time Aggregation: buffering time steps doesn't need to init file open every
+ // time
+ if (TimeAggregationInProgress(g)) {
+ fd = g->ts_fd; // continue writing to the previous file
+ // printf("skip file init... bytes_written=%llu file_handle_addr=%llu\n",
+ // fd->bytes_written, fd);
+ // printf("open: fd->pgs_written->pg_start_in_file=%lld,
+ // fd->current_pg->pg_start_in_file=%lld\n",
+ // fd->pgs_written->pg_start_in_file, fd->current_pg->pg_start_in_file);
+ log_debug("TimeAggr: skip file name and group assignment\n");
+ } else {
+ log_debug("TimeAggr: new open... file struct init\n");
+ fd = (struct adios_file_struct *)malloc(sizeof(struct adios_file_struct));
+ adios_file_struct_init(fd);
+ fd->name = strdup(name);
+ fd->subfile_index = -1; // subfile index is by default -1
+ fd->group = g;
+ fd->mode = mode;
+ if (comm == MPI_COMM_NULL)
+ fd->comm = MPI_COMM_NULL;
+ else if (comm == MPI_COMM_SELF)
+ fd->comm = MPI_COMM_SELF;
else
- if (!strcasecmp (file_mode, "w"))
- mode = adios_mode_write;
- else
- if (!strcasecmp (file_mode, "a"))
- mode = adios_mode_append;
- else
- if (!strcasecmp (file_mode, "u"))
- mode = adios_mode_update;
- else
- {
- adios_error(err_invalid_file_mode,
- "adios_open: unknown file mode: %s, supported r,w,a,u\n",
- file_mode);
-
- *fd_p = 0;
-
- return adios_errno;
- }
-
- //printf("ts_to buffer=%d max_tx=%d\n", g->ts_to_buffer, g->max_ts);
- //Time Aggregation: buffering time steps doesn't need to init file open every time
- if (TimeAggregationInProgress(g)) {
- fd = g->ts_fd; //continue writing to the previous file
- // printf("skip file init... bytes_written=%llu file_handle_addr=%llu\n", fd->bytes_written, fd);
- // printf("open: fd->pgs_written->pg_start_in_file=%lld, fd->current_pg->pg_start_in_file=%lld\n", fd->pgs_written->pg_start_in_file, fd->current_pg->pg_start_in_file);
- log_debug("TimeAggr: skip file name and group assignment\n");
- }
- else {
-
- log_debug("TimeAggr: new open... file struct init\n");
- fd = (struct adios_file_struct *) malloc (sizeof (struct adios_file_struct));
- adios_file_struct_init (fd);
- fd->name = strdup (name);
- fd->subfile_index = -1; // subfile index is by default -1
- fd->group = g;
- fd->mode = mode;
- if (comm == MPI_COMM_NULL)
- fd->comm = MPI_COMM_NULL;
- else if (comm == MPI_COMM_SELF)
- fd->comm = MPI_COMM_SELF;
- else
- MPI_Comm_dup(comm, &fd->comm);
+ MPI_Comm_dup(comm, &fd->comm);
+ }
+
+ methods = g->methods;
+
+ // Time Aggregation: if time aggregation is turned on, only open() at the
+ // first time step
+ if (TimeAggregationInProgress(g)) {
+ *fd_p = (int64_t)fd;
+ // printf("time buffering.... skip open\n");
+ // printf("open: fd->offset=%llu, group_offset=%llu\n", fd->offset,
+ // g->group_offset);
+ } else {
+ while (methods) {
+ if (methods->method->m != ADIOS_METHOD_UNKNOWN &&
+ methods->method->m != ADIOS_METHOD_NULL &&
+ adios_transports[methods->method->m].adios_open_fn) {
+ adios_transports[methods->method->m].adios_open_fn(fd, methods->method,
+ fd->comm);
+ }
+
+ methods = methods->next;
}
- methods = g->methods;
-
- //Time Aggregation: if time aggregation is turned on, only open() at the first time step
- if (TimeAggregationInProgress(g))
- {
- *fd_p=(int64_t)fd;
- //printf("time buffering.... skip open\n");
- //printf("open: fd->offset=%llu, group_offset=%llu\n", fd->offset, g->group_offset);
+ if (!adios_errno) {
+ *fd_p = (int64_t)fd;
+ } else {
+ // free (fd_p);
+ fd_p = 0L;
}
- else
- {
- while (methods)
- {
- if ( methods->method->m != ADIOS_METHOD_UNKNOWN
- && methods->method->m != ADIOS_METHOD_NULL
- && adios_transports [methods->method->m].adios_open_fn
- )
- {
- adios_transports [methods->method->m].adios_open_fn
- (fd, methods->method, fd->comm);
- }
-
- methods = methods->next;
- }
-
- if (!adios_errno)
- {
- *fd_p = (int64_t) fd;
- } else
- {
- //free (fd_p);
- fd_p = 0L;
+ }
+
+ /* Time index
+ * It increases in write/append mode, it does not change in update/read mode.
+ * This piece should be after calling the method's open function, which sets
+ * the time index from the existing file in case of append/update. */
+ if (mode == adios_mode_write || mode == adios_mode_append) {
+ /* Traditionally, time=1 at the first step, and for subsequent file
+ creations, time increases. Although, each file contains one step,
+ the time index indicates that they are in a series.
+ */
+ g->time_index++;
+ }
+ /* time starts from 1 not from 0 in the BP design although it does not have
+ * any meaning */
+ if (g->time_index == 0) g->time_index = 1;
+
+ // Drew: for experiments
+ if (pinned_timestep > 0) g->time_index = pinned_timestep;
+
+ if (!adios_errno && fd->mode != adios_mode_read) {
+ /* Add ADIOS internal attributes now */
+ if ((fd->group->process_id == 0 || fd->subfile_index != -1)) {
+ struct timeval tp;
+ char epoch[16];
+ gettimeofday(&tp, NULL);
+ sprintf(epoch, "%d", (int)tp.tv_sec);
+
+ /* FIXME: this code works fine, it does not duplicate the attribute,
+ but the index will still contain all copies and the read will see
+ only the first one. Thus updating an attribute does not work
+ in practice.
+ */
+
+ if (fd->group->time_index == 1) {
+ log_debug(
+ "Define ADIOS extra attributes, "
+ "time = %d, rank = %d, epoch = %s subfile=%d\n",
+ fd->group->time_index, fd->group->process_id, epoch,
+ fd->subfile_index);
+
+ adios_common_define_attribute((int64_t)fd->group, "version",
+ ADIOS_ATTR_PATH, adios_string, VERSION,
+ NULL);
+
+ adios_common_define_attribute((int64_t)fd->group, "create_time_epoch",
+ ADIOS_ATTR_PATH, adios_integer, epoch,
+ NULL);
+ adios_common_define_attribute((int64_t)fd->group, "update_time_epoch",
+ ADIOS_ATTR_PATH, adios_integer, epoch,
+ NULL);
+ // id of last attribute is fd->group->member_count
+ fd->group->attrid_update_epoch = fd->group->member_count;
+
+ } else {
+ // update attribute of update time (define would duplicate it)
+ struct adios_attribute_struct *attr = adios_find_attribute_by_id(
+ fd->group->attributes, fd->group->attrid_update_epoch);
+ if (attr) {
+ log_debug(
+ "Update ADIOS extra attribute name=%s, "
+ "time = %d, rank = %d, epoch = %s, subfile=%d\n",
+ attr->name, fd->group->time_index, fd->group->process_id, epoch,
+ fd->subfile_index);
+
+ free(attr->value);
+ adios_parse_scalar_string(adios_integer, (void *)epoch, &attr->value);
}
+ }
}
-
- /* Time index
- * It increases in write/append mode, it does not change in update/read mode.
- * This piece should be after calling the method's open function, which sets
- * the time index from the existing file in case of append/update. */
- if (mode == adios_mode_write || mode == adios_mode_append)
- {
- /* Traditionally, time=1 at the first step, and for subsequent file
- creations, time increases. Although, each file contains one step,
- the time index indicates that they are in a series.
- */
- g->time_index++;
+ /* Add first PG to the group */
+ if (NotTimeAggregated(g) || TimeAggregationJustBegan(g)) {
+ assert(!fd->pgs_written); // the start of the PG list
+ assert(!fd->current_pg); // the last of the PG list
}
- /* time starts from 1 not from 0 in the BP design although it does not have any meaning */
- if (g->time_index == 0)
- g->time_index = 1;
-
- // Drew: for experiments
- if (pinned_timestep > 0)
- g->time_index = pinned_timestep;
-
-
-
- if ( !adios_errno && fd->mode != adios_mode_read )
- {
- /* Add ADIOS internal attributes now */
- if ( (fd->group->process_id == 0 || fd->subfile_index != -1) )
- {
- struct timeval tp;
- char epoch[16];
- gettimeofday(&tp, NULL);
- sprintf(epoch, "%d", (int) tp.tv_sec);
-
- /* FIXME: this code works fine, it does not duplicate the attribute,
- but the index will still contain all copies and the read will see
- only the first one. Thus updating an attribute does not work
- in practice.
- */
-
- if (fd->group->time_index == 1)
- {
- log_debug ("Define ADIOS extra attributes, "
- "time = %d, rank = %d, epoch = %s subfile=%d\n",
- fd->group->time_index, fd->group->process_id, epoch, fd->subfile_index);
-
- adios_common_define_attribute ((int64_t)fd->group, "version", ADIOS_ATTR_PATH,
- adios_string, VERSION, NULL);
-
- adios_common_define_attribute ((int64_t)fd->group, "create_time_epoch", ADIOS_ATTR_PATH,
- adios_integer, epoch, NULL);
- adios_common_define_attribute ((int64_t)fd->group, "update_time_epoch", ADIOS_ATTR_PATH,
- adios_integer, epoch, NULL);
- // id of last attribute is fd->group->member_count
- fd->group->attrid_update_epoch = fd->group->member_count;
-
- }
- else
- {
- // update attribute of update time (define would duplicate it)
- struct adios_attribute_struct * attr = adios_find_attribute_by_id
- (fd->group->attributes, fd->group->attrid_update_epoch);
- if (attr) {
- log_debug ("Update ADIOS extra attribute name=%s, "
- "time = %d, rank = %d, epoch = %s, subfile=%d\n",
- attr->name, fd->group->time_index, fd->group->process_id,
- epoch, fd->subfile_index);
-
- free(attr->value);
- adios_parse_scalar_string (adios_integer, (void *) epoch, &attr->value);
- }
- }
- }
-
- /* Add first PG to the group */
- if (NotTimeAggregated(g) || TimeAggregationJustBegan(g))
- {
- assert (!fd->pgs_written); // the start of the PG list
- assert (!fd->current_pg); // the last of the PG list
- }
- //printf("rank %d: fd->bytes-written=%llu\n",fd->group->process_id, fd->bytes_written);
- add_new_pg_written (fd);
- //keep a record of the PG offsets.
- // FIXME: Time Aggregation: Assume every process writes the same amount of data
- if(TimeAggregated(g))
- fd->current_pg->pg_start_in_file=fd->bytes_written;
-
-
+ // printf("rank %d: fd->bytes-written=%llu\n",fd->group->process_id,
+ // fd->bytes_written);
+ add_new_pg_written(fd);
+ // keep a record of the PG offsets.
+ // FIXME: Time Aggregation: Assume every process writes the same amount of
+ // data
+ if (TimeAggregated(g)) fd->current_pg->pg_start_in_file = fd->bytes_written;
#ifdef ADIOS_TIMERS
- /* Add timer variable definitions to this output */
- adios_add_timing_variables (fd);
+ /* Add timer variable definitions to this output */
+ adios_add_timing_variables(fd);
#endif
- /* Now ask the methods if anyone wants common-layer BP formatted buffering */
- methods = g->methods;
-
- if (NotTimeAggregated(g) || TimeAggregationJustBegan(g))
- {
- while (methods)
- {
- enum BUFFERING_STRATEGY bufstrat = no_buffering;
- if ( methods->method->m != ADIOS_METHOD_UNKNOWN
- && methods->method->m != ADIOS_METHOD_NULL
- && adios_transports [methods->method->m].adios_should_buffer_fn
- )
- {
- bufstrat = adios_transports [methods->method->m].
- adios_should_buffer_fn (fd, methods->method);
- }
-
- if (bufstrat != no_buffering) {
- fd->shared_buffer = adios_flag_yes;
- fd->bufstrat = bufstrat;
- /* FIXME: last method determines the value of buffering strategy here. This whole
- buffer overflow thing does not work if there are multiple methods called
- and they want something else (stop vs continue vs continue with new PG
- */
- }
-
- methods = methods->next;
- }
- }
+ /* Now ask the methods if anyone wants common-layer BP formatted buffering
+ */
+ methods = g->methods;
- if (fd->bufstrat != no_buffering)
- {
- /* Allocate BP buffer with remembered size or max size or default size */
- uint64_t bufsize;
-
- if (NotTimeAggregated(g)) {
- if (g->last_buffer_size > 0)
- bufsize = g->last_buffer_size;
- else
- bufsize = adios_databuffer_get_extension_size (fd);
- } else {
- /* Time Aggregation: set the buffer size at the first time step to be buffered.
- ts buffering doesn't need buffer extension,
- only one time allocation at the first time step
- */
- if (TimeAggregationJustBegan(g)) {
- adios_databuffer_set_max_size(g->ts_buffsize);
- bufsize=g->ts_buffsize;
- }
- }
+ if (NotTimeAggregated(g) || TimeAggregationJustBegan(g)) {
+ while (methods) {
+ enum BUFFERING_STRATEGY bufstrat = no_buffering;
+ if (methods->method->m != ADIOS_METHOD_UNKNOWN &&
+ methods->method->m != ADIOS_METHOD_NULL &&
+ adios_transports[methods->method->m].adios_should_buffer_fn) {
+ bufstrat =
+ adios_transports[methods->method->m].adios_should_buffer_fn(
+ fd, methods->method);
+ }
- //printf("==open bufsize=%llu\n", bufsize);
-
- //Time Aggregation: when ts buffering is on, only the first step needs to
- //allocate the buffer
- if (NotTimeAggregated(g) || TimeAggregationJustBegan(g))
- {
- if (adios_databuffer_resize (fd, bufsize))
- {
- fd->bufstate = buffering_stopped;
- adios_error (err_no_memory,
- "Cannot allocate %" PRIu64 " bytes for buffered output "
- "of group %s in adios_open(). Output will fail.\n",
- fd->buffer_size, g->name);
- return adios_errno;
- }
- }
- fd->bufstate = buffering_ongoing;
+ if (bufstrat != no_buffering) {
+ fd->shared_buffer = adios_flag_yes;
+ fd->bufstrat = bufstrat;
+ /* FIXME: last method determines the value of buffering strategy here.
+ This whole
+ buffer overflow thing does not work if there are multiple methods
+ called
+ and they want something else (stop vs continue vs continue with new
+ PG
+ */
+ }
- // write the process group header
- adios_write_open_process_group_header_v1 (fd);
+ methods = methods->next;
+ }
+ }
- // setup for writing vars
- adios_write_open_vars_v1 (fd);
+ if (fd->bufstrat != no_buffering) {
+ /* Allocate BP buffer with remembered size or max size or default size */
+ uint64_t expected_bufsize;
+ if (NotTimeAggregated(g)) {
+ if (g->max_pg_size > 0)
+ expected_bufsize = g->max_pg_size;
+ else
+ expected_bufsize = adios_databuffer_get_extension_size(fd);
+ } else {
+ /* Time Aggregation: set the user given buffer size at the first time
+ * step to be buffered.
+ * Later, check if the calculated number of timesteps knowing the size
+ * encountered so far
+ * would still fit. If not, try to increase the buffer to accommodate
+ * it. The reason for this is
+ * that we must try to avoid buffer overflow in time aggregation, which
+ * situation is not handled.
+ */
+ if (TimeAggregationJustBegan(g)) {
+ adios_databuffer_set_max_size(g->ts_buffsize);
+ expected_bufsize = g->ts_buffsize;
+ } else {
+ // fd->bytes_written is the size of (g->max_ts - g->ts_to_buffer)
+ // steps already buffered
+ expected_bufsize =
+ g->max_ts * fd->bytes_written / (g->max_ts - g->ts_to_buffer);
+ if (expected_bufsize > fd->buffer_size) {
+ adios_databuffer_set_max_size(
+ expected_bufsize); // allow more than what user specified
+ // (g->ts_buffsize)
+ }
}
+ }
+
+ // printf("==open expected_bufsize=%llu\n", expected_bufsize);
+
+ // Time Aggregation: when ts buffering is on, only the first step needs to
+ // allocate the buffer here
+ if (NotTimeAggregated(g) || TimeAggregationJustBegan(g))
+ if (expected_bufsize > fd->buffer_size) {
+ if (adios_databuffer_resize(fd, expected_bufsize)) {
+ fd->bufstate = buffering_stopped;
+ adios_error(err_no_memory,
+ "Cannot allocate %" PRIu64
+ " bytes for buffered output "
+ "of group %s in adios_open(). Output will fail.\n",
+ fd->buffer_size, g->name);
+ return adios_errno;
+ }
+ }
+ fd->bufstate = buffering_ongoing;
- //printf("end of adios_open fd->offset=%llu bytes_written=%llu\n", fd->offset, fd->bytes_written);
+ // write the process group header
+ adios_write_open_process_group_header_v1(fd);
+ // setup for writing vars
+ adios_write_open_vars_v1(fd);
}
+ // printf("end of adios_open fd->offset=%llu bytes_written=%llu\n",
+ // fd->offset, fd->bytes_written);
+ }
+
#if defined(WITH_NCSU_TIMER) && defined(TIMER_LEVEL) && (TIMER_LEVEL <= 0)
- timer_stop ("adios_open");
+ timer_stop("adios_open");
#endif
- return adios_errno;
+ ADIOST_CALLBACK_EXIT(adiost_event_open, *fd_p, group_name, name, file_mode);
+ return adios_errno;
}
///////////////////////////////////////////////////////////////////////////////
-int common_adios_group_size (int64_t fd_p, uint64_t data_size, uint64_t * total_size)
-{
-
+int common_adios_group_size(int64_t fd_p, uint64_t data_size,
+ uint64_t *total_size) {
#if defined(WITH_NCSU_TIMER) && defined(TIMER_LEVEL) && (TIMER_LEVEL <= 0)
- timer_start ("adios_group_size");
+ timer_start("adios_group_size");
#endif
- //printf("enter adios_group_size datasize= %llu\n", data_size);
+ // printf("enter adios_group_size datasize= %llu\n", data_size);
+ ADIOST_CALLBACK_ENTER(adiost_event_group_size, fd_p, data_size, *total_size);
- adios_errno = err_no_error;
- struct adios_file_struct * fd;
- fd = (struct adios_file_struct *) fd_p;
+ adios_errno = err_no_error;
+ struct adios_file_struct *fd;
+ fd = (struct adios_file_struct *)fd_p;
- if (!fd)
- {
- adios_error (err_invalid_file_pointer, "Invalid handle passed to adios_group_size\n");
- return adios_errno;
- }
+ if (!fd) {
+ adios_error(err_invalid_file_pointer,
+ "Invalid handle passed to adios_group_size\n");
+ ADIOST_CALLBACK_EXIT(adiost_event_group_size, fd_p, data_size, *total_size);
+ return adios_errno;
+ }
- struct adios_method_list_struct * m = fd->group->methods;
- if (m && m->next == NULL && m->method->m == ADIOS_METHOD_NULL)
- {
- *total_size = 0;
+ struct adios_method_list_struct *m = fd->group->methods;
+ if (m && m->next == NULL && m->method->m == ADIOS_METHOD_NULL) {
+ *total_size = 0;
#if defined(WITH_NCSU_TIMER) && defined(TIMER_LEVEL) && (TIMER_LEVEL <= 0)
- timer_stop ("adios_group_size");
+ timer_stop("adios_group_size");
#endif
- return err_no_error;
- }
-
- if (fd->buffer_size == 0) {
- *total_size = 0;
- return err_no_error;
- }
+ ADIOST_CALLBACK_EXIT(adiost_event_group_size, fd_p, data_size, *total_size);
+ return err_no_error;
+ }
+ if (fd->buffer_size == 0) {
+ *total_size = 0;
+ ADIOST_CALLBACK_EXIT(adiost_event_group_size, fd_p, data_size, *total_size);
+ return err_no_error;
+ }
#ifdef ADIOS_TIMERS
- data_size += fd->group->tv_size;
+ data_size += fd->group->tv_size;
#endif
-
- uint64_t overhead = adios_calc_overhead_v1 (fd);
- *total_size = data_size + overhead;
-
- // NCSU ALACRITY-ADIOS - Current solution to group_size problem: find
- // the most "expansive" transform method used in the file, and assume
- // all of the data uses that method, for a very rough but safe upper bound.
- //
- // (see the comment in the top of adios_transforms.c, under section
- // 'The "group size" problem,' for more details)
- uint64_t wc_transformed_size = adios_transform_worst_case_transformed_group_size(data_size, fd);
- if (wc_transformed_size > data_size)
- {
- log_debug("Computed worst-case bound on transformed data for a group size of %" PRIu64 " is %" PRIu64 "; increasing group size to match.\n",
- data_size, wc_transformed_size);
-
- *total_size += (wc_transformed_size - data_size);
- }
-
- if (*total_size > fd->buffer_size && fd->bufstate == buffering_ongoing)
- {
- if (adios_databuffer_resize (fd, *total_size))
- {
- log_warn ("Cannot reallocate data buffer to %" PRIu64 " bytes "
- "for group %s in adios_group_size(). Continue buffering "
- "with buffer size %" PRIu64 " MB\n",
- *total_size, fd->group->name, fd->buffer_size/1048576L);
- }
+ uint64_t overhead = adios_calc_overhead_v1(fd);
+ *total_size = data_size + overhead;
+
+ // NCSU ALACRITY-ADIOS - Current solution to group_size problem: find
+ // the most "expansive" transform method used in the file, and assume
+ // all of the data uses that method, for a very rough but safe upper bound.
+ //
+ // (see the comment in the top of adios_transforms.c, under section
+ // 'The "group size" problem,' for more details)
+ uint64_t wc_transformed_size =
+ adios_transform_worst_case_transformed_group_size(data_size, fd);
+ if (wc_transformed_size > data_size) {
+ log_debug(
+ "Computed worst-case bound on transformed data for a group size of "
+ "%" PRIu64 " is %" PRIu64 "; increasing group size to match.\n",
+ data_size, wc_transformed_size);
+
+ *total_size += (wc_transformed_size - data_size);
+ }
+
+ if (*total_size > fd->buffer_size && fd->bufstate == buffering_ongoing) {
+ if (adios_databuffer_resize(fd, *total_size)) {
+ log_warn("Cannot reallocate data buffer to %" PRIu64
+ " bytes "
+ "for group %s in adios_group_size(). Continue buffering "
+ "with buffer size %" PRIu64 " MB\n",
+ *total_size, fd->group->name, fd->buffer_size / 1048576L);
}
-
-
+ }
#if defined(WITH_NCSU_TIMER) && defined(TIMER_LEVEL) && (TIMER_LEVEL <= 0)
- timer_stop ("adios_group_size");
+ timer_stop("adios_group_size");
#endif
- // each var will be added to the buffer by the adios_write calls
- // attributes will be added by adios_close
+ // each var will be added to the buffer by the adios_write calls
+ // attributes will be added by adios_close
- return adios_errno;
+ ADIOST_CALLBACK_EXIT(adiost_event_group_size, fd_p, data_size, *total_size);
+ return adios_errno;
}
+static int common_adios_write_transform_helper(struct adios_file_struct *fd,
+ struct adios_var_struct *v) {
+ int use_shared_buffer = (fd->bufstrat != no_buffering);
+ int wrote_to_shared_buffer = 0;
+
+ if (fd->bufstrat == no_buffering) {
+ int ret = adios_transform_variable_data(fd, v, use_shared_buffer,
+ &wrote_to_shared_buffer);
+ assert(!wrote_to_shared_buffer);
+ assert(v->data);
+ return ret;
+ } else if (fd->bufstate == buffering_ongoing) {
+ // If we are using the shared buffer, transform the data directly into it
+ uint16_t header_size = adios_calc_var_overhead_v1(v);
+ uint64_t header_offset;
+ uint64_t payload_offset;
+ uint64_t end_offset;
+
+ // Reserve space for the variable header (it will need to be written after
+ // the transform to capture updated metadata)
+ header_offset = fd->offset;
+ fd->offset += header_size;
+ payload_offset = fd->offset;
+
+ // This function will either:
+ // a) write to the shared buffer, leave v->data, v->data_size and
+ // v->free_data untouched, and return 1, OR
+ // b) write to v->data, set v->data_size and v->free_data, and return 0
+ //
+ int success = adios_transform_variable_data(fd, v, use_shared_buffer,
+ &wrote_to_shared_buffer);
+ if (!success) {
+ fd->offset = header_offset;
+ return 0;
+ }
-static int common_adios_write_transform_helper(struct adios_file_struct * fd, struct adios_var_struct * v) {
- int use_shared_buffer = (fd->bufstrat != no_buffering);
- int wrote_to_shared_buffer = 0;
-
- if (fd->bufstrat == no_buffering)
- {
- int ret = adios_transform_variable_data(fd, v, use_shared_buffer, &wrote_to_shared_buffer);
- assert(!wrote_to_shared_buffer);
- assert(v->data);
- return ret;
- }
- else if (fd->bufstate == buffering_ongoing)
- {
- // If we are using the shared buffer, transform the data directly into it
- uint16_t header_size = adios_calc_var_overhead_v1(v);
- uint64_t header_offset;
- uint64_t payload_offset;
- uint64_t end_offset;
-
- // Reserve space for the variable header (it will need to be written after
- // the transform to capture updated metadata)
- header_offset = fd->offset;
- fd->offset += header_size;
- payload_offset = fd->offset;
-
- // This function will either:
- // a) write to the shared buffer, leave v->data, v->data_size and
- // v->free_data untouched, and return 1, OR
- // b) write to v->data, set v->data_size and v->free_data, and return 0
- //
- int success = adios_transform_variable_data(fd, v, use_shared_buffer, &wrote_to_shared_buffer);
- if (!success) {
- fd->offset = header_offset;
- return 0;
- }
-
- // Assumption: we don't change the header size, just contents, in
- // adios_transform_variable_data
- assert(adios_calc_var_overhead_v1(v) == header_size);
-
- // Store the ending offset of the payload write (if any)
- end_offset = fd->offset;
-
- // Rewind and write the header back where it should be
- fd->offset = header_offset;
- // var payload sent for sizing information
- adios_write_var_header_v1(fd, v);
-
- assert(fd->offset == payload_offset);
-
- // If the data was stored to the shared buffer, update v->data,
- // v->data_size and v->free_data. Else, write the payload to the shared
- // buffer (the other v->* fields have already been updated)
- if (wrote_to_shared_buffer) {
- v->adata = fd->buffer + payload_offset;
- v->data_size = end_offset - payload_offset;
- v->free_data = adios_flag_no;
- v->data = v->adata;
-
- // Update the buffer back to the end of the header+payload
- fd->offset = end_offset;
- } else {
- /* FIXME: This branch should not happen for memory reasons.
- The buffer either had enough space to store the transformation
- in place, or buffering has stopped.
- However, identity transform does no buffering, so we do it here.
- */
- // either no transformation happened (original data is in v->data), or
- // data was transformed into v->adata
- if (v->adata) {
- v->data = v->adata;
- }
- // write payload
- adios_write_var_payload_v1 (fd, v);
-
- // fd->offset now points to the end of the header+payload
- }
-
- // Success!
- return 1;
+ // Assumption: we don't change the header size, just contents, in
+ // adios_transform_variable_data
+ assert(adios_calc_var_overhead_v1(v) == header_size);
+
+ // Store the ending offset of the payload write (if any)
+ end_offset = fd->offset;
+
+ // Rewind and write the header back where it should be
+ fd->offset = header_offset;
+ // var payload sent for sizing information
+ adios_write_var_header_v1(fd, v);
+
+ assert(fd->offset == payload_offset);
+
+ // If the data was stored to the shared buffer, update v->data,
+ // v->data_size and v->free_data. Else, write the payload to the shared
+ // buffer (the other v->* fields have already been updated)
+ if (wrote_to_shared_buffer) {
+ v->adata = fd->buffer + payload_offset;
+ v->data_size = end_offset - payload_offset;
+ v->free_data = adios_flag_no;
+ v->data = v->adata;
+
+ // Update the buffer back to the end of the header+payload
+ fd->offset = end_offset;
+ } else {
+ /* FIXME: This branch should not happen for memory reasons.
+ The buffer either had enough space to store the transformation
+ in place, or buffering has stopped.
+ However, identity transform does no buffering, so we do it here.
+ */
+ // either no transformation happened (original data is in v->data), or
+ // data was transformed into v->adata
+ if (v->adata) {
+ v->data = v->adata;
+ }
+ // write payload
+ adios_write_var_payload_v1(fd, v);
+
+ // fd->offset now points to the end of the header+payload
}
- /* else: shared buffer but buffering has stopped, nothing needs to be done */
+
+ // Success!
return 1;
+ }
+ /* else: shared buffer but buffering has stopped, nothing needs to be done */
+ return 1;
}
///////////////////////////////////////////////////////////////////////////////
@@ -599,435 +611,415 @@ static int common_adios_write_transform_helper(struct adios_file_struct * fd, st
* structures. This is because C and Fortran implementations of adios_write are
* different for some part and this is the common part.
*/
-int common_adios_write (struct adios_file_struct * fd, struct adios_var_struct * v, const void * var)
-{
+int common_adios_write(struct adios_file_struct *fd, struct adios_var_struct *v,
+ const void *var) {
#if defined(WITH_NCSU_TIMER) && defined(TIMER_LEVEL) && (TIMER_LEVEL <= 0)
- timer_start ("adios_write");
+ timer_start("adios_write");
#endif
- adios_errno = err_no_error;
- struct adios_method_list_struct * m = fd->group->methods;
-
- // First, before doing any transformation, compute variable statistics,
- // as we can't do this after the data is transformed
- adios_generate_var_characteristics_v1 (fd, v);
-
-
- uint64_t vsize = 0;
- if (fd->bufstate == buffering_ongoing)
- {
- // Second, estimate the size needed for buffering and extend buffer when needed
- // and handle the error if buffer cannot be extended
- vsize = adios_transform_worst_case_transformed_var_size(v);
-
- if (fd->buffer_size < fd->offset + vsize)
- {
- // printf("adios_write fd->offset=%llu for variable= %s buffer_size=%llu\n", fd->offset, v->name, fd->buffer_size);
- // printf("max_ts=%d ts_to_buffer=%d\n", fd->group->max_ts, fd->group->ts_to_buffer);
- /* Trouble: this variable does not fit into the current buffer */
- // First, try to realloc the buffer
- uint64_t extrasize = adios_databuffer_get_extension_size (fd);
- if (extrasize < vsize)
- extrasize = vsize;
- if (adios_databuffer_resize (fd, fd->buffer_size + extrasize))
- {
- /* Second, let the method deal with it */
- log_debug ("adios_write(): buffer needs to be dumped before buffering variable %s/%s\n", v->path, v->name);
- // these calls don't extend the buffer but we will get a completed PG here
- adios_write_close_vars_v1 (fd);
- adios_write_close_process_group_header_v1 (fd);
-
- /* Ask the method to do something with the current buffer then we either
- 1. continue buffering from start with a new PG or
- 2. skip buffering variables from now on, then method gets the same buffer again in close()
- */
-
- m = fd->group->methods;
- while (m)
- {
- if ( m->method->m != ADIOS_METHOD_UNKNOWN
- && m->method->m != ADIOS_METHOD_NULL
- && adios_transports [m->method->m].adios_buffer_overflow_fn
- )
- {
- adios_transports [m->method->m].adios_buffer_overflow_fn (fd, m->method);
- }
- m = m->next;
- }
-
- if (fd->bufstrat == continue_with_new_pg)
- {
- // special case: fd->buffer_size is smaller than this single variable, and the extension failed:
- // try to extend it to contain this single variable (plus headers) in the next PG
- if (fd->buffer_size < vsize + 1024)
- {
- if (adios_databuffer_resize (fd, vsize+1024))
- {
- adios_error (err_no_memory, "adios_write(): buffer cannot accommodate variable %s/%s "
- "with its storage size of %" PRIu64 " bytes at all. "
- "No more variables will be written.\n", v->path, v->name, vsize);
- //"This variable won't be written.\n", v->path, v->name, vsize);
- fd->bufstate = buffering_stopped;
- /* FIXME: This stops all writing, not just this variable! */
- /* FIXME: so maybe we should give the method a chance to write this variable directly? */
- }
- }
- /* Start buffering from scratch (a new PG) */
- fd->offset = 0;
- adios_write_open_process_group_header_v1 (fd);
- adios_write_open_vars_v1 (fd);
- add_new_pg_written (fd);
- }
- else if (fd->bufstrat == stop_on_overflow)
- {
- fd->bufstate = buffering_stopped;
- if (!adios_errno)
- {
- // method is expected to throw an error in this case but we can ensure it here
- // to signal error upward to not count this var in index
- adios_errno = err_buffer_overflow;
- }
- }
- }
+ ADIOST_CALLBACK_ENTER(adiost_event_write, fd);
+ adios_errno = err_no_error;
+ struct adios_method_list_struct *m = fd->group->methods;
+
+ // First, before doing any transformation, compute variable statistics,
+ // as we can't do this after the data is transformed
+ adios_generate_var_characteristics_v1(fd, v);
+
+ uint64_t vsize = 0;
+ if (fd->bufstate == buffering_ongoing) {
+ // Second, estimate the size needed for buffering and extend buffer when
+ // needed
+ // and handle the error if buffer cannot be extended
+ vsize = adios_transform_worst_case_transformed_var_size(v);
+
+ if (fd->buffer_size < fd->offset + vsize) {
+ // printf("adios_write fd->offset=%llu for variable= %s
+ // buffer_size=%llu\n", fd->offset, v->name, fd->buffer_size);
+ // printf("max_ts=%d ts_to_buffer=%d\n", fd->group->max_ts,
+ // fd->group->ts_to_buffer);
+ /* Trouble: this variable does not fit into the current buffer */
+ // First, try to realloc the buffer
+ uint64_t extrasize = adios_databuffer_get_extension_size(fd);
+ if (extrasize < vsize) extrasize = vsize;
+ if (adios_databuffer_resize(fd, fd->buffer_size + extrasize)) {
+ /* Second, let the method deal with it */
+ log_debug(
+ "adios_write(): buffer needs to be dumped before buffering "
+ "variable %s/%s\n",
+ v->path, v->name);
+ // these calls don't extend the buffer but we will get a completed PG
+ // here
+ adios_write_close_vars_v1(fd);
+ adios_write_close_process_group_header_v1(fd);
+
+ /* Ask the method to do something with the current buffer then we either
+ 1. continue buffering from start with a new PG or
+ 2. skip buffering variables from now on, then method gets the same
+ buffer again in close()
+ */
+
+ m = fd->group->methods;
+ while (m) {
+ if (m->method->m != ADIOS_METHOD_UNKNOWN &&
+ m->method->m != ADIOS_METHOD_NULL &&
+ adios_transports[m->method->m].adios_buffer_overflow_fn) {
+ adios_transports[m->method->m].adios_buffer_overflow_fn(fd,
+ m->method);
+ }
+ m = m->next;
}
- }
- // If no transform is specified, do the normal thing (write to shared
- // buffer immediately, if one exists)
- if (v->transform_type == adios_transform_none)
- {
- if (fd->bufstate == buffering_ongoing)
- {
- /* Now buffer only if we have the buffer for it */
- if (fd->buffer_size > fd->offset + vsize)
- {
- // var payload sent for sizing information
- adios_write_var_header_v1 (fd, v);
-
- // write payload
- adios_write_var_payload_v1 (fd, v);
+ if (fd->bufstrat == continue_with_new_pg) {
+ // special case: fd->buffer_size is smaller than this single variable,
+ // and the extension failed:
+ // try to extend it to contain this single variable (plus headers) in
+ // the next PG
+ if (fd->buffer_size < vsize + 1024) {
+ if (adios_databuffer_resize(fd, vsize + 1024)) {
+ adios_error(
+ err_no_memory,
+ "adios_write(): buffer cannot accommodate variable %s/%s "
+ "with its storage size of %" PRIu64
+ " bytes at all. "
+ "No more variables will be written.\n",
+ v->path, v->name, vsize);
+ //"This variable won't be written.\n", v->path, v->name, vsize);
+ fd->bufstate = buffering_stopped;
+ /* FIXME: This stops all writing, not just this variable! */
+ /* FIXME: so maybe we should give the method a chance to write
+ * this variable directly? */
}
+ }
+ /* Start buffering from scratch (a new PG) */
+ fd->offset = 0;
+ adios_write_open_process_group_header_v1(fd);
+ adios_write_open_vars_v1(fd);
+ add_new_pg_written(fd);
+ } else if (fd->bufstrat == stop_on_overflow) {
+ fd->bufstate = buffering_stopped;
+ if (!adios_errno) {
+ // method is expected to throw an error in this case but we can
+ // ensure it here
+ // to signal error upward to not count this var in index
+ adios_errno = err_buffer_overflow;
+ }
}
+ }
+ }
+ }
+
+ // If no transform is specified, do the normal thing (write to shared
+ // buffer immediately, if one exists)
+ if (v->transform_type == adios_transform_none) {
+ if (fd->bufstate == buffering_ongoing) {
+ /* Now buffer only if we have the buffer for it */
+ if (fd->buffer_size > fd->offset + vsize) {
+ // var payload sent for sizing information
+ adios_write_var_header_v1(fd, v);
+
+ // write payload
+ adios_write_var_payload_v1(fd, v);
+ }
}
- else // Else, do a transform
- {
+ } else // Else, do a transform
+ {
#if defined(WITH_NCSU_TIMER) && defined(TIMER_LEVEL) && (TIMER_LEVEL <= 0)
- timer_start ("adios_transform");
+ timer_start("adios_transform");
#endif
- int success = common_adios_write_transform_helper(fd, v);
- if (success) {
- // Make it appear as if the user had supplied the transformed data
- var = v->data;
- } else {
- log_error("Error: unable to apply transform %s to variable %s; likely ran out of memory, check previous error messages\n", adios_transform_plugin_primary_xml_alias(v->transform_type), v->name);
- // FIXME: Reverse the transform metadata and write raw data as usual
- }
+ ADIOST_CALLBACK_ENTER(adiost_event_transform, fd);
+ int success = common_adios_write_transform_helper(fd, v);
+ if (success) {
+ // Make it appear as if the user had supplied the transformed data
+ var = v->data;
+ } else {
+ log_error(
+ "Error: unable to apply transform %s to variable %s; likely ran out "
+ "of memory, check previous error messages\n",
+ adios_transform_plugin_primary_xml_alias(v->transform_type), v->name);
+ // FIXME: Reverse the transform metadata and write raw data as usual
+ }
+ ADIOST_CALLBACK_EXIT(adiost_event_transform, fd);
#if defined(WITH_NCSU_TIMER) && defined(TIMER_LEVEL) && (TIMER_LEVEL <= 0)
- timer_stop ("adios_transform");
+ timer_stop("adios_transform");
#endif
+ }
+
+ // now tell each transport attached that it is being written unless buffering
+ // is stopped
+ if (fd->bufstate == buffering_ongoing || fd->bufstrat == no_buffering) {
+ m = fd->group->methods;
+ while (m) {
+ if (m->method->m != ADIOS_METHOD_UNKNOWN &&
+ m->method->m != ADIOS_METHOD_NULL &&
+ adios_transports[m->method->m].adios_write_fn) {
+ adios_transports[m->method->m].adios_write_fn(fd, v, var, m->method);
+ }
+
+ m = m->next;
}
-
- // now tell each transport attached that it is being written unless buffering is stopped
- if (fd->bufstate == buffering_ongoing || fd->bufstrat == no_buffering)
- {
- m = fd->group->methods;
- while (m)
- {
- if ( m->method->m != ADIOS_METHOD_UNKNOWN
- && m->method->m != ADIOS_METHOD_NULL
- && adios_transports [m->method->m].adios_write_fn
- )
- {
- adios_transports [m->method->m].adios_write_fn
- (fd, v, var, m->method);
- }
-
- m = m->next;
- }
- }
- else
- {
- adios_errno = err_buffer_overflow; // signal error but don't print anything anymore
- }
-
- if (v->dimensions)
- {
- // NCSU ALACRITY-ADIOS - Free transform-method-allocated data buffers
- // TODO: Is this correct? Normally v->data is a user buffer, so we
- // can't free it. However, after a transform, we probably do need
- // to free it. We mark this by setting the free_data flag. However,
- // as this flag is hardly ever used, I don't know whether this is
- // using the flag correctly or not. Need verification with
- // Gary/Norbert/someone knowledgable about ADIOS internals.
- if (v->transform_type != adios_transform_none && v->free_data == adios_flag_yes && v->adata)
- {
- free(v->adata);
- }
- v->data = v->adata = 0; // throw away pointers to user data in case of arrays to avoid trying
- // to free them in possible forthcoming adios_write() of the same variable
- }
-
- if (!adios_errno) {
- v->write_count++;
+ } else {
+ adios_errno =
+ err_buffer_overflow; // signal error but don't print anything anymore
+ }
+
+ if (v->dimensions) {
+ // NCSU ALACRITY-ADIOS - Free transform-method-allocated data buffers
+ // TODO: Is this correct? Normally v->data is a user buffer, so we
+ // can't free it. However, after a transform, we probably do need
+ // to free it. We mark this by setting the free_data flag. However,
+ // as this flag is hardly ever used, I don't know whether this is
+ // using the flag correctly or not. Need verification with
+ // Gary/Norbert/someone knowledgable about ADIOS internals.
+ if (v->transform_type != adios_transform_none &&
+ v->free_data == adios_flag_yes && v->adata) {
+ free(v->adata);
}
+ v->data = v->adata = 0; // throw away pointers to user data in case of
+ // arrays to avoid trying
+ // to free them in possible forthcoming adios_write() of the same variable
+ }
+
+ if (!adios_errno) {
+ v->write_count++;
+ }
#if defined(WITH_NCSU_TIMER) && defined(TIMER_LEVEL) && (TIMER_LEVEL <= 0)
- timer_stop ("adios_write");
+ timer_stop("adios_write");
#endif
- // printf ("var: %s written %d\n", v->name, v->write_count);
- return adios_errno;
+ ADIOST_CALLBACK_EXIT(adiost_event_write, fd);
+ // printf ("var: %s written %d\n", v->name, v->write_count);
+ return adios_errno;
}
-
///////////////////////////////////////////////////////////////////////////////
-int common_adios_write_byid (struct adios_file_struct * fd, struct adios_var_struct * v, const void * var)
-{
- struct adios_method_list_struct * m = fd->group->methods;
-
- adios_errno = err_no_error;
- if (m && m->next == NULL && m->method->m == ADIOS_METHOD_NULL)
- {
- return adios_errno;
- }
-
- if (v->adata)
- {
- assert (v->dimensions==NULL); // this must happen only for scalars where we copied the value
- free (v->adata);
- v->adata = 0;
- }
+int common_adios_write_byid(struct adios_file_struct *fd,
+ struct adios_var_struct *v, const void *var) {
+ struct adios_method_list_struct *m = fd->group->methods;
+
+ ADIOST_CALLBACK_ENTER(adiost_event_write, fd);
+ adios_errno = err_no_error;
+ if (m && m->next == NULL && m->method->m == ADIOS_METHOD_NULL) {
+ ADIOST_CALLBACK_EXIT(adiost_event_write, fd);
+ return adios_errno;
+ }
+
+ if (v->adata) {
+ assert(
+ v->dimensions ==
+ NULL); // this must happen only for scalars where we copied the value
+ free(v->adata);
+ v->adata = 0;
+ }
+
+ if (v->dimensions) {
+ v->data = var;
+ } else {
+ uint64_t element_size = adios_get_type_size(v->type, var);
+
+ switch (v->type) {
+ case adios_byte:
+ case adios_short:
+ case adios_integer:
+ case adios_long:
+ case adios_unsigned_byte:
+ case adios_unsigned_short:
+ case adios_unsigned_integer:
+ case adios_unsigned_long:
+ case adios_real:
+ case adios_double:
+ case adios_long_double:
+ case adios_complex:
+ case adios_double_complex:
+ v->adata = malloc(element_size);
+ if (!v->adata) {
+ adios_error(
+ err_no_memory,
+ "In adios_write, cannot allocate %lld bytes to copy scalar %s\n",
+ element_size, v->name);
+ ADIOST_CALLBACK_EXIT(adiost_event_write, fd);
+ return adios_errno;
+ }
- if (v->dimensions)
- {
- v->data = var;
- }
- else
- {
- uint64_t element_size = adios_get_type_size (v->type, var);
-
- switch (v->type)
- {
- case adios_byte:
- case adios_short:
- case adios_integer:
- case adios_long:
- case adios_unsigned_byte:
- case adios_unsigned_short:
- case adios_unsigned_integer:
- case adios_unsigned_long:
- case adios_real:
- case adios_double:
- case adios_long_double:
- case adios_complex:
- case adios_double_complex:
- v->adata = malloc (element_size);
- if (!v->adata)
- {
- adios_error (err_no_memory,
- "In adios_write, cannot allocate %lld bytes to copy scalar %s\n",
- element_size, v->name);
- return adios_errno;
- }
-
- memcpy ((char *) v->adata, var, element_size);
- v->data = v->adata;
- break;
-
- case adios_string:
- v->adata = malloc (element_size + 1);
- if (!v->adata)
- {
- adios_error (err_no_memory,
- "In adios_write, cannot allocate %lld bytes to copy string %s\n",
- element_size, v->name);
- return adios_errno;
- }
- ((char *) v->adata) [element_size] = 0;
- memcpy ((char *) v->adata, var, element_size);
- v->data = v->adata;
- break;
-
- default:
- v->data = 0;
- break;
+ memcpy((char *)v->adata, var, element_size);
+ v->data = v->adata;
+ break;
+
+ case adios_string:
+ v->adata = malloc(element_size + 1);
+ if (!v->adata) {
+ adios_error(
+ err_no_memory,
+ "In adios_write, cannot allocate %lld bytes to copy string %s\n",
+ element_size, v->name);
+ ADIOST_CALLBACK_EXIT(adiost_event_write, fd);
+ return adios_errno;
}
+ ((char *)v->adata)[element_size] = 0;
+ memcpy((char *)v->adata, var, element_size);
+ v->data = v->adata;
+ break;
+
+ default:
+ v->data = 0;
+ break;
}
+ }
- common_adios_write (fd, v, var);
- // v->data is set to NULL in the above call for arrays,
- // but it's pointing to v->adata, which is allocated in ADIOS, for scalars
- // to remember their value if used as dimension in forthcoming writes of arrays.
+ common_adios_write(fd, v, var);
+ // v->data is set to NULL in the above call for arrays,
+ // but it's pointing to v->adata, which is allocated in ADIOS, for scalars
+ // to remember their value if used as dimension in forthcoming writes of
+ // arrays.
- if (!adios_errno && fd->mode != adios_mode_read)
- {
- adios_copy_var_written (fd, v);
- }
+ if (!adios_errno && fd->mode != adios_mode_read) {
+ adios_copy_var_written(fd, v);
+ }
- return adios_errno;
+ ADIOST_CALLBACK_EXIT(adiost_event_write, fd);
+ return adios_errno;
}
///////////////////////////////////////////////////////////////////////////////
-int common_adios_get_write_buffer (int64_t fd_p, const char * name
- ,uint64_t * size
- ,void ** buffer
-)
-{
- struct adios_file_struct * fd = (struct adios_file_struct *) fd_p;
- adios_errno = err_no_error;
- if (!fd)
- {
- adios_error (err_invalid_file_pointer, "Invalid handle passed to adios_group_size\n");
- return adios_errno;
- }
- struct adios_var_struct * v = fd->group->vars;
- struct adios_method_list_struct * m = fd->group->methods;
-
- v = adios_find_var_by_name (fd->group, name);
-
- if (!v)
- {
- adios_error (err_invalid_varname, "Bad var name (ignored): '%s' (%c%c%c)\n",
- name, name[0], name[1], name[2]);
- return adios_errno;
- }
+int common_adios_get_write_buffer(int64_t fd_p, const char *name,
+ uint64_t *size, void **buffer) {
+ struct adios_file_struct *fd = (struct adios_file_struct *)fd_p;
+ adios_errno = err_no_error;
+ if (!fd) {
+ adios_error(err_invalid_file_pointer,
+ "Invalid handle passed to adios_group_size\n");
+ return adios_errno;
+ }
+ struct adios_var_struct *v = fd->group->vars;
+ struct adios_method_list_struct *m = fd->group->methods;
- if (fd->mode == adios_mode_read)
- {
- adios_error (err_invalid_file_mode,
- "write attempted on %s in %s. This was opened for read\n",
- name , fd->name);
- return adios_errno;
- }
+ v = adios_find_var_by_name(fd->group, name);
- // since we are only getting one buffer, get it from the first
- // transport method that can provide it.
- while (m)
- {
- if ( m->method->m != ADIOS_METHOD_UNKNOWN
- && m->method->m != ADIOS_METHOD_NULL
- && adios_transports [m->method->m].adios_get_write_buffer_fn
- )
- {
- adios_transports [m->method->m].adios_get_write_buffer_fn
- (fd, v, size, buffer, m->method);
- m = 0;
- }
- else
- m = m->next;
- }
+ if (!v) {
+ adios_error(err_invalid_varname, "Bad var name (ignored): '%s' (%c%c%c)\n",
+ name, name[0], name[1], name[2]);
+ return adios_errno;
+ }
+ if (fd->mode == adios_mode_read) {
+ adios_error(err_invalid_file_mode,
+ "write attempted on %s in %s. This was opened for read\n", name,
+ fd->name);
return adios_errno;
+ }
+
+ // since we are only getting one buffer, get it from the first
+ // transport method that can provide it.
+ while (m) {
+ if (m->method->m != ADIOS_METHOD_UNKNOWN &&
+ m->method->m != ADIOS_METHOD_NULL &&
+ adios_transports[m->method->m].adios_get_write_buffer_fn) {
+ adios_transports[m->method->m].adios_get_write_buffer_fn(
+ fd, v, size, buffer, m->method);
+ m = 0;
+ } else
+ m = m->next;
+ }
+
+ return adios_errno;
}
///////////////////////////////////////////////////////////////////////////////
-int common_adios_read (int64_t fd_p, const char * name, void * buffer
- ,uint64_t buffer_size
-)
-{
- struct adios_file_struct * fd = (struct adios_file_struct *) fd_p;
- adios_errno = err_no_error;
- if (!fd)
- {
- adios_error (err_invalid_file_pointer, "Invalid handle passed to adios_group_size\n");
-
- return adios_errno;
- }
- struct adios_var_struct * v;
- struct adios_method_list_struct * m = fd->group->methods;
+int common_adios_read(int64_t fd_p, const char *name, void *buffer,
+ uint64_t buffer_size) {
+ ADIOST_CALLBACK_ENTER(adiost_event_read, fd_p);
+ struct adios_file_struct *fd = (struct adios_file_struct *)fd_p;
+ adios_errno = err_no_error;
+ if (!fd) {
+ adios_error(err_invalid_file_pointer,
+ "Invalid handle passed to adios_group_size\n");
+ ADIOST_CALLBACK_EXIT(adiost_event_read, fd_p);
- if (m && m->next == NULL && m->method->m == ADIOS_METHOD_NULL)
- {
- // nothing to do so just return
- return err_no_error;
- }
+ return adios_errno;
+ }
+ struct adios_var_struct *v;
+ struct adios_method_list_struct *m = fd->group->methods;
- if (!(fd->mode == adios_mode_read))
- {
- adios_error (err_invalid_file_mode,
- "read attempted on %s which was opened for write\n",
- fd->name);
+ if (m && m->next == NULL && m->method->m == ADIOS_METHOD_NULL) {
+ // nothing to do so just return
+ ADIOST_CALLBACK_EXIT(adiost_event_read, fd_p);
+ return err_no_error;
+ }
- return adios_errno;
- }
+ if (!(fd->mode == adios_mode_read)) {
+ adios_error(err_invalid_file_mode,
+ "read attempted on %s which was opened for write\n", fd->name);
- v = adios_find_var_by_name (fd->group, name);
- if (v)
- {
- // since can only read from one place into the buffer,
- // read from the first transport method that can
- while (m)
- {
- if ( m->method->m != ADIOS_METHOD_UNKNOWN
- && m->method->m != ADIOS_METHOD_NULL
- && adios_transports [m->method->m].adios_read_fn
- )
- {
- adios_transports [m->method->m].adios_read_fn
- (fd, v, buffer, buffer_size, m->method);
- m = 0;
- }
- else
- m = m->next;
- }
- }
- else
- {
- adios_error (err_invalid_varname, "var %s in file %s not found on read\n",
- name, fd->name);
-
- return adios_errno;
+ ADIOST_CALLBACK_EXIT(adiost_event_read, fd_p);
+ return adios_errno;
+ }
+
+ v = adios_find_var_by_name(fd->group, name);
+ if (v) {
+ // since can only read from one place into the buffer,
+ // read from the first transport method that can
+ while (m) {
+ if (m->method->m != ADIOS_METHOD_UNKNOWN &&
+ m->method->m != ADIOS_METHOD_NULL &&
+ adios_transports[m->method->m].adios_read_fn) {
+ adios_transports[m->method->m].adios_read_fn(fd, v, buffer, buffer_size,
+ m->method);
+ m = 0;
+ } else
+ m = m->next;
}
+ } else {
+ adios_error(err_invalid_varname, "var %s in file %s not found on read\n",
+ name, fd->name);
+ ADIOST_CALLBACK_EXIT(adiost_event_read, fd_p);
return adios_errno;
+ }
+
+ ADIOST_CALLBACK_EXIT(adiost_event_read, fd_p);
+ return adios_errno;
}
///////////////////////////////////////////////////////////////////////////////
// OBSOLETE, kept only for backward compatibility
-int common_adios_set_path (int64_t fd_p, const char * path)
-{
- struct adios_file_struct * fd = (struct adios_file_struct *) fd_p;
- adios_errno = err_no_error;
- if (!fd)
- {
- adios_error (err_invalid_file_pointer, "Invalid handle passed to adios_set_path\n");
-
- return adios_errno;
- }
- struct adios_group_struct * t = fd->group;
- struct adios_var_struct * v = t->vars;
- struct adios_attribute_struct * a = t->attributes;
-
- while (v)
- {
- if (v->path)
- {
- free (v->path);
- }
-
- v->path = strdup (path);
+int common_adios_set_path(int64_t fd_p, const char *path) {
+ struct adios_file_struct *fd = (struct adios_file_struct *)fd_p;
+ adios_errno = err_no_error;
+ if (!fd) {
+ adios_error(err_invalid_file_pointer,
+ "Invalid handle passed to adios_set_path\n");
- v = v->next;
+ return adios_errno;
+ }
+ struct adios_group_struct *t = fd->group;
+ struct adios_var_struct *v = t->vars;
+ struct adios_attribute_struct *a = t->attributes;
+
+ while (v) {
+ if (v->path) {
+ free(v->path);
}
- while (a)
- {
- // skip internal attributes
- if (a->path && strstr (a->path, "__adios__"))
- {
- a = a->next;
- continue;
- }
+ v->path = strdup(path);
- if (a->path)
- {
- free (a->path);
- }
+ v = v->next;
+ }
- a->path = strdup (path);
+ while (a) {
+ // skip internal attributes
+ if (a->path && strstr(a->path, "__adios__")) {
+ a = a->next;
+ continue;
+ }
- a = a->next;
+ if (a->path) {
+ free(a->path);
}
- return adios_errno;
+ a->path = strdup(path);
+
+ a = a->next;
+ }
+
+ return adios_errno;
}
///////////////////////////////////////////////////////////////////////////////
@@ -1035,468 +1027,443 @@ int common_adios_set_path (int64_t fd_p, const char * path)
// Inconsistent behavior with new ADIOS variable naming
// The variable is not replaced with the new path in the hash table here, so
// it is still found using the old path!
-int common_adios_set_path_var (int64_t fd_p, const char * path
- ,const char * name
-)
-{
- struct adios_file_struct * fd = (struct adios_file_struct *) fd_p;
- adios_errno = err_no_error;
- if (!fd)
- {
- adios_error (err_invalid_file_pointer, "Invalid handle passed to adios_set_path_var\n");
-
- return adios_errno;
- }
- struct adios_group_struct * t = fd->group;
- struct adios_var_struct * v = t->vars;
+int common_adios_set_path_var(int64_t fd_p, const char *path,
+ const char *name) {
+ struct adios_file_struct *fd = (struct adios_file_struct *)fd_p;
+ adios_errno = err_no_error;
+ if (!fd) {
+ adios_error(err_invalid_file_pointer,
+ "Invalid handle passed to adios_set_path_var\n");
- // check for vars and then attributes
- v = adios_find_var_by_name (t, name);
+ return adios_errno;
+ }
+ struct adios_group_struct *t = fd->group;
+ struct adios_var_struct *v = t->vars;
- if (v)
- {
- if (v->path)
- {
- free (v->path);
- }
+ // check for vars and then attributes
+ v = adios_find_var_by_name(t, name);
- v->path = strdup (path);
+ if (v) {
+ if (v->path) {
+ free(v->path);
+ }
- /* Possible new behavior: replace the old path with the new path
- * in the hash table so that the variable is found by
- * the new path. Inconsistent with old codes that only used
- * the variable name without the path in adios_write()
- */
- //remove var from hash table by old fullpath...
- //t->hashtbl_vars->remove (t->hashtbl_vars, name);
- // and add it back with new fullpath
- //t->hashtbl_vars->put2 (t->hashtbl_vars, v->path, v->name, v);
+ v->path = strdup(path);
- }
- else
- {
- adios_error (err_invalid_varname,
- "adios_set_path_var (path=%s, var=%s): var not found\n",
- path, name);
+ /* Possible new behavior: replace the old path with the new path
+ * in the hash table so that the variable is found by
+ * the new path. Inconsistent with old codes that only used
+ * the variable name without the path in adios_write()
+ */
+ // remove var from hash table by old fullpath...
+ // t->hashtbl_vars->remove (t->hashtbl_vars, name);
+ // and add it back with new fullpath
+ // t->hashtbl_vars->put2 (t->hashtbl_vars, v->path, v->name, v);
- return adios_errno;
- }
+ } else {
+ adios_error(err_invalid_varname,
+ "adios_set_path_var (path=%s, var=%s): var not found\n", path,
+ name);
return adios_errno;
+ }
+
+ return adios_errno;
}
///////////////////////////////////////////////////////////////////////////////
// hint that we reached the end of an iteration (for asynchronous pacing)
-int common_adios_end_iteration ()
-{
- struct adios_method_list_struct * m;
-
- adios_errno = err_no_error;
- for (m = adios_get_methods (); m; m = m->next)
- {
- if ( m->method->m != ADIOS_METHOD_UNKNOWN
- && m->method->m != ADIOS_METHOD_NULL
- && adios_transports [m->method->m].adios_end_iteration_fn
- )
- {
- adios_transports [m->method->m].adios_end_iteration_fn
- (m->method);
- }
+int common_adios_end_iteration() {
+ struct adios_method_list_struct *m;
+
+ adios_errno = err_no_error;
+ for (m = adios_get_methods(); m; m = m->next) {
+ if (m->method->m != ADIOS_METHOD_UNKNOWN &&
+ m->method->m != ADIOS_METHOD_NULL &&
+ adios_transports[m->method->m].adios_end_iteration_fn) {
+ adios_transports[m->method->m].adios_end_iteration_fn(m->method);
}
+ }
- return adios_errno;
+ return adios_errno;
}
///////////////////////////////////////////////////////////////////////////////
// hint to start communicating
-int common_adios_start_calculation ()
-{
- struct adios_method_list_struct * m;
-
- adios_errno = err_no_error;
- for (m = adios_get_methods (); m; m = m->next)
- {
- if ( m->method->m != ADIOS_METHOD_UNKNOWN
- && m->method->m != ADIOS_METHOD_NULL
- && adios_transports [m->method->m].adios_start_calculation_fn
- )
- {
- adios_transports [m->method->m].adios_start_calculation_fn
- (m->method);
- }
+int common_adios_start_calculation() {
+ struct adios_method_list_struct *m;
+
+ adios_errno = err_no_error;
+ for (m = adios_get_methods(); m; m = m->next) {
+ if (m->method->m != ADIOS_METHOD_UNKNOWN &&
+ m->method->m != ADIOS_METHOD_NULL &&
+ adios_transports[m->method->m].adios_start_calculation_fn) {
+ adios_transports[m->method->m].adios_start_calculation_fn(m->method);
}
+ }
- return adios_errno;
+ return adios_errno;
}
///////////////////////////////////////////////////////////////////////////////
// hint to stop communicating
-int common_adios_stop_calculation ()
-{
- struct adios_method_list_struct * m;
-
- adios_errno = err_no_error;
- for (m = adios_get_methods (); m; m = m->next)
- {
- if ( m->method->m != ADIOS_METHOD_UNKNOWN
- && m->method->m != ADIOS_METHOD_NULL
- && adios_transports [m->method->m].adios_stop_calculation_fn
- )
- {
- adios_transports [m->method->m].adios_stop_calculation_fn
- (m->method);
- }
+int common_adios_stop_calculation() {
+ struct adios_method_list_struct *m;
+
+ adios_errno = err_no_error;
+ for (m = adios_get_methods(); m; m = m->next) {
+ if (m->method->m != ADIOS_METHOD_UNKNOWN &&
+ m->method->m != ADIOS_METHOD_NULL &&
+ adios_transports[m->method->m].adios_stop_calculation_fn) {
+ adios_transports[m->method->m].adios_stop_calculation_fn(m->method);
}
+ }
- return adios_errno;
+ return adios_errno;
}
-
///////////////////////////////////////////////////////////////////////////////
-int common_adios_close (struct adios_file_struct * fd)
-{
+int common_adios_close(struct adios_file_struct *fd) {
#if defined(WITH_NCSU_TIMER) && defined(TIMER_LEVEL) && (TIMER_LEVEL <= 0)
- timer_start ("adios_close");
+ timer_start("adios_close");
#endif
- adios_errno = err_no_error;
+ adios_errno = err_no_error;
- if (!fd)
- {
- adios_error (err_invalid_file_pointer, "Invalid handle passed to adios_close\n");
+ ADIOST_CALLBACK_ENTER(adiost_event_close, fd);
+ if (!fd) {
+ adios_error(err_invalid_file_pointer,
+ "Invalid handle passed to adios_close\n");
- return adios_errno;
- }
+ ADIOST_CALLBACK_EXIT(adiost_event_close, fd);
+ return adios_errno;
+ }
- struct adios_method_list_struct * m = fd->group->methods;
- if (m && m->next == NULL && m->method->m == ADIOS_METHOD_NULL)
- {
- // nothing to do so just return
+ struct adios_method_list_struct *m = fd->group->methods;
+ if (m && m->next == NULL && m->method->m == ADIOS_METHOD_NULL) {
+// nothing to do so just return
#if defined(WITH_NCSU_TIMER) && defined(TIMER_LEVEL) && (TIMER_LEVEL <= 0)
- timer_stop ("adios_close");
- timer_stop ("adios_open_to_close");
+ timer_stop("adios_close");
+ timer_stop("adios_open_to_close");
#endif
- return 0;
- }
+ ADIOST_CALLBACK_EXIT(adiost_event_close, fd);
+ return 0;
+ }
#ifdef ADIOS_TIMERS
- if (fd->mode != adios_mode_read) {
- adios_write_timing_variables (fd);
- }
+ if (fd->mode != adios_mode_read) {
+ adios_write_timing_variables(fd);
+ }
#endif
-
- struct adios_attribute_struct * a = fd->group->attributes;
- struct adios_var_struct * v = fd->group->vars;
-
- if (fd->mode != adios_mode_read && !TimeAggregationIsFlushing(fd->group))
- {
- //printf("=====common_adios_close offset=%llu %llu\n max_ts=%d ts_to_buffer=%d \n", fd->pgs_written->pg_start_in_file, fd->current_pg->pg_start_in_file, fd->group->max_ts, fd->group->ts_to_buffer);
- // fd->current_pg=fd->pgs_written;
- if (fd->bufstate == buffering_ongoing)
- {
- adios_write_close_vars_v1 (fd);
- }
-
- /* Even if buffering has stopped on overflow, let's try to squeeze in the attributes
- to the end of the buffer */
- if (fd->bufstrat != no_buffering)
- {
- /* FIXME: this strategy writes all attributes defined in time step 0
- and thus duplicates them in the PGs and in the attribute index.
- For write mode, where files are new, this is good.
- For append/update it is unnecessary and replicates the attributes
- in the index.
- One should write the newly created attributes only in append mode.
- */
- uint64_t asize = 12; // 12 bytes to store empty attribute list in a PG (the opening bytes)
- if (!fd->group->process_id || fd->subfile_index != -1) {
- // from ADIOS 1.4, only rank 0 writes attributes (or each process to its subfile)
- asize = adios_calc_attrs_overhead_v1(fd); // size of full attribute list
- }
- if (fd->buffer_size < fd->offset + asize)
- {
- /* Trouble, attributes just don't fit into the end of buffer */
- // try to extend the buffer first
- log_debug("Need more space for attributes in close(). "
- "Current buffer usage=%" PRIu64 " Attributes need %" PRIu64 " bytes "
- "var_start offset=%" PRIu64 " and bytes_written=%" PRIu64
- "\n",
- fd->offset, asize, fd->vars_start, fd->bytes_written
- );
-
- if (adios_databuffer_resize (fd, fd->offset + asize))
- {
- /* FIXME: Well, drop them in this case */
- log_error ("adios_close(): There is not enough buffer to write the attributes. "
- "They will be missing from the output\n");
- }
- }
-
- if (fd->buffer_size >= fd->offset + asize)
- {
- adios_write_open_attributes_v1 (fd); // this writes 12 bytes into the buffer
- if (!fd->group->process_id || fd->subfile_index != -1) {
- while (a) {
- adios_write_attribute_v1 (fd, a);
- a = a->next;
- }
- }
- adios_write_close_attributes_v1 (fd);
- }
-
- adios_write_close_process_group_header_v1 (fd);
- }
+ struct adios_attribute_struct *a = fd->group->attributes;
+ struct adios_var_struct *v = fd->group->vars;
+
+ if (fd->mode != adios_mode_read && !TimeAggregationIsFlushing(fd->group)) {
+ // printf("=====common_adios_close offset=%llu %llu\n max_ts=%d
+ // ts_to_buffer=%d \n", fd->pgs_written->pg_start_in_file,
+ // fd->current_pg->pg_start_in_file, fd->group->max_ts,
+ // fd->group->ts_to_buffer);
+ // fd->current_pg=fd->pgs_written;
+ if (fd->bufstate == buffering_ongoing) {
+ adios_write_close_vars_v1(fd);
}
-
- if (TimeAggregationJustBegan(fd->group))
- {
- // first close in time aggregation: we need to figure out how many
- // time steps we can buffer given the buffer size
- if( fd->group->ts_to_buffer > 0 && fd->group->ts_buffsize > 0) {
- fd->group->max_ts = fd->group->ts_buffsize/fd->bytes_written;
- // max_ts may be different on different processes, we need to use the minimum of them
- int min_max_ts;
- MPI_Allreduce(&fd->group->max_ts, &min_max_ts, 1, MPI_INT, MPI_MIN, fd->comm);
- fd->group->max_ts = min_max_ts;
- fd->group->ts_to_buffer = fd->group->max_ts-1; // we already have one in our hand
- // printf("ts_buffsize=%llu bytes_writen=%llu\n", fd->group->ts_buffsize, fd->bytes_written);
- // printf("max_ts=%d ts_to_buffer=%d\n", fd->group->max_ts, fd->group->ts_to_buffer);
+ /* Even if buffering has stopped on overflow, let's try to squeeze in the
+ attributes
+ to the end of the buffer */
+ if (fd->bufstrat != no_buffering) {
+ /* FIXME: this strategy writes all attributes defined in time step 0
+ and thus duplicates them in the PGs and in the attribute index.
+ For write mode, where files are new, this is good.
+ For append/update it is unnecessary and replicates the attributes
+ in the index.
+ One should write the newly created attributes only in append mode.
+ */
+ uint64_t asize = 12; // 12 bytes to store empty attribute list in a PG
+ // (the opening bytes)
+ if (!fd->group->process_id || fd->subfile_index != -1) {
+ // from ADIOS 1.4, only rank 0 writes attributes (or each process to its
+ // subfile)
+ asize +=
+ adios_calc_attrs_overhead_v1(fd); // size of full attribute list
+ }
+ if (fd->buffer_size < fd->offset + asize) {
+ /* Trouble, attributes just don't fit into the end of buffer */
+ // try to extend the buffer first
+ log_debug(
+ "Need more space for attributes in close(). "
+ "Current buffer usage=%" PRIu64 " Attributes need %" PRIu64
+ " bytes "
+ "var_start offset=%" PRIu64 " and bytes_written=%" PRIu64 "\n",
+ fd->offset, asize, fd->vars_start, fd->bytes_written);
+
+ if (adios_databuffer_resize(fd, fd->offset + asize)) {
+ /* FIXME: Well, drop them in this case */
+ log_error(
+ "adios_close(): There is not enough buffer to write the "
+ "attributes. "
+ "They will be missing from the output\n");
+ }
+ }
+
+ if (fd->buffer_size >= fd->offset + asize) {
+ adios_write_open_attributes_v1(
+ fd); // this writes 12 bytes into the buffer
+ if (!fd->group->process_id || fd->subfile_index != -1) {
+ while (a) {
+ adios_write_attribute_v1(fd, a);
+ a = a->next;
+ }
}
- // if we can only have one step in the buffer, now TimeAggregationLastStep() holds.
- // TimeAggregationJustBegan() still holds (fd->group->ts_fd == NULL).
+ adios_write_close_attributes_v1(fd);
+ }
- fd->group->ts_fd = fd;
- // TimeAggregationJustBegan() now moved into TimeAggregationInProgress()
+ adios_write_close_process_group_header_v1(fd);
}
-
- // in order to get the index assembled, we need to do it in the
- // transport once we have collected all of the pieces
-
- // now tell all of the transports to write the buffer during close
- for (;m; m = m->next)
- {
- if ( m->method->m != ADIOS_METHOD_UNKNOWN
- && m->method->m != ADIOS_METHOD_NULL
- && adios_transports [m->method->m].adios_close_fn
- )
- {
-
- if (NotTimeAggregated(fd->group))
- {
- adios_transports [m->method->m].adios_close_fn
- (fd, m->method);
- }
- else
- {
- if (!TimeAggregationIsFlushing(fd->group))
- {
- // Time Aggregation: build index for current step and merge it in to
- // the aggregated index
- struct adios_index_struct_v1 * current_index;
- current_index=adios_alloc_index_v1(1);
- adios_build_index_v1 (fd, current_index);
- //printf("current->index time=%d offset=%llu\n", current_index->vars_root->characteristics[0].time_index, current_index->vars_root->characteristics[0].offset);
- if (fd->group->index == NULL)
- {
- //first time step, we just built the index for the group
- fd->group->index = current_index;
- }
- else
- {
- adios_merge_index_v1 (fd->group->index, current_index->pg_root,
- current_index->vars_root, current_index->attrs_root, 1);
- adios_free_index_v1 (current_index);
- }
- //printf("fd->group->index time=%d offset=%llu\n", fd->group->index->vars_root->characteristics[1].time_index, fd->group->index->vars_root->characteristics[1].offset);
- }
-
- if (TimeAggregationLastStep(fd->group))
- {
- // in last step, move the PG pointer to the first pg
- // to build correct starting offset of this process for all aggregated steps
- fd->current_pg=fd->pgs_written;
- fd->group->built_index=1;
- //printf("bytes-writen=%llu time index=%lu\n", fd->bytes_written, fd->group->index->pg_root->time_index);
-
- adios_transports [m->method->m].adios_close_fn
- (fd, m->method);
-
- /* the method clears the full index data including the one built here.
- * we need to just free the container structure.
- */
- adios_free_index_v1 (fd->group->index);
- fd->group->index = NULL;
- }
- }
- }
+ }
+
+ if (TimeAggregationJustBegan(fd->group)) {
+ // first close in time aggregation: we need to figure out how many
+ // time steps we can buffer given the buffer size
+ if (fd->group->ts_to_buffer > 0 && fd->group->ts_buffsize > 0) {
+ fd->group->max_ts = fd->group->ts_buffsize / fd->bytes_written;
+ // max_ts may be different on different processes, we need to use the
+ // minimum of them
+ int min_max_ts;
+ MPI_Allreduce(&fd->group->max_ts, &min_max_ts, 1, MPI_INT, MPI_MIN,
+ fd->comm);
+ fd->group->max_ts = min_max_ts;
+ fd->group->ts_to_buffer =
+ fd->group->max_ts - 1; // we already have one in our hand
+ // printf("ts_buffsize=%llu bytes_writen=%llu\n",
+ // fd->group->ts_buffsize, fd->bytes_written);
+ // printf("max_ts=%d ts_to_buffer=%d\n", fd->group->max_ts,
+ // fd->group->ts_to_buffer);
}
+ // if we can only have one step in the buffer, now TimeAggregationLastStep()
+ // holds.
+ // TimeAggregationJustBegan() still holds (fd->group->ts_fd == NULL).
+
+ fd->group->ts_fd = fd;
+ // TimeAggregationJustBegan() now moved into TimeAggregationInProgress()
+ }
+
+ // in order to get the index assembled, we need to do it in the
+ // transport once we have collected all of the pieces
+
+ // now tell all of the transports to write the buffer during close
+ for (; m; m = m->next) {
+ if (m->method->m != ADIOS_METHOD_UNKNOWN &&
+ m->method->m != ADIOS_METHOD_NULL &&
+ adios_transports[m->method->m].adios_close_fn) {
+ if (NotTimeAggregated(fd->group)) {
+ adios_transports[m->method->m].adios_close_fn(fd, m->method);
+ } else {
+ if (!TimeAggregationIsFlushing(fd->group)) {
+ // Time Aggregation: build index for current step and merge it in to
+ // the aggregated index
+ struct adios_index_struct_v1 *current_index;
+ current_index = adios_alloc_index_v1(1);
+ adios_build_index_v1(fd, current_index);
+ // printf("current->index time=%d offset=%llu\n",
+ // current_index->vars_root->characteristics[0].time_index,
+ // current_index->vars_root->characteristics[0].offset);
+ if (fd->group->index == NULL) {
+ // first time step, we just built the index for the group
+ fd->group->index = current_index;
+ } else {
+ adios_merge_index_v1(fd->group->index, current_index->pg_root,
+ current_index->vars_root,
+ current_index->attrs_root, 1);
+ adios_free_index_v1(current_index);
+ }
+ // printf("fd->group->index time=%d offset=%llu\n",
+ // fd->group->index->vars_root->characteristics[1].time_index,
+ // fd->group->index->vars_root->characteristics[1].offset);
+ }
-
- /* Synced groups for time-aggregation.
- * Force close on those groups that are time-aggregated and are synced with this group
- */
- if (NotTimeAggregated(fd->group) || TimeAggregationLastStep(fd->group))
- {
- if (TimeAggregationIsaSyncGroup(fd->group))
- {
- struct adios_group_struct ** syncedgroups;
- int ngroups, i;
- TimeAggregationGetSyncedGroups(fd->group, &syncedgroups, &ngroups );
- for (i=0; i<ngroups; i++)
- {
- struct adios_group_struct *sg = syncedgroups[i];
- if (sg->ts_fd != NULL)
- {
- if (fd->group->process_id == 0) {
- log_info ("Sync flush group '%s' because we just wrote group '%s'. "
- "Synced group size is currently %" PRIu64 " bytes holding %d steps\n",
- sg->name, fd->group->name, sg->ts_fd->bytes_written,
- sg->max_ts-sg->ts_to_buffer-1);
- }
- SetTimeAggregationFlush(sg, 1);
- // => TimeAggregationIsFlushing => TimeAggregationLastStep
- common_adios_close (sg->ts_fd); // close file for sync'd group
- SetTimeAggregationFlush(sg, 0);
- }
- }
+ if (TimeAggregationLastStep(fd->group)) {
+ // in last step, move the PG pointer to the first pg
+ // to build correct starting offset of this process for all aggregated
+ // steps
+ fd->current_pg = fd->pgs_written;
+ fd->group->built_index = 1;
+ // printf("bytes-writen=%llu time index=%lu\n", fd->bytes_written,
+ // fd->group->index->pg_root->time_index);
+
+ adios_transports[m->method->m].adios_close_fn(fd, m->method);
+
+ /* the method clears the full index data including the one built here.
+ * we need to just free the container structure.
+ */
+ adios_free_index_v1(fd->group->index);
+ fd->group->index = NULL;
}
+ }
}
-
-
- //Time Aggregation: only free the buffer if 1) we are not buffering time steps;
- //2) we have enough time steps buffered
- //printf("close: do_ts_aggr=%d max_ts=%d ts_to_buffer=%d\n", fd->group->do_ts_aggr, fd->group->max_ts, fd->group->ts_to_buffer);
- if (NotTimeAggregated(fd->group) || TimeAggregationLastStep(fd->group))
- {
- while (v)
- {
- v->write_offset = 0;
- if (v->adata)
- {
- free (v->adata);
- v->data = v->adata = 0;
- }
-
- v = v->next;
+ }
+
+ /* Synced groups for time-aggregation.
+ * Force close on those groups that are time-aggregated and are synced with
+ * this group
+ */
+ if (NotTimeAggregated(fd->group) || TimeAggregationLastStep(fd->group)) {
+ if (TimeAggregationIsaSyncGroup(fd->group)) {
+ struct adios_group_struct **syncedgroups;
+ int ngroups, i;
+ TimeAggregationGetSyncedGroups(fd->group, &syncedgroups, &ngroups);
+ for (i = 0; i < ngroups; i++) {
+ struct adios_group_struct *sg = syncedgroups[i];
+ if (sg->ts_fd != NULL) {
+ if (fd->group->process_id == 0) {
+ log_info(
+ "Sync flush group '%s' because we just wrote group '%s'. "
+ "Synced group size is currently %" PRIu64
+ " bytes holding %d steps\n",
+ sg->name, fd->group->name, sg->ts_fd->bytes_written,
+ sg->max_ts - sg->ts_to_buffer - 1);
+ }
+ SetTimeAggregationFlush(sg, 1);
+ // => TimeAggregationIsFlushing => TimeAggregationLastStep
+ common_adios_close(sg->ts_fd); // close file for sync'd group
+ SetTimeAggregationFlush(sg, 0);
}
+ }
+ }
+ }
+
+ // Time Aggregation: only free the buffer if 1) we are not buffering time
+ // steps;
+ // 2) we have enough time steps buffered
+ // printf("close: do_ts_aggr=%d max_ts=%d ts_to_buffer=%d\n",
+ // fd->group->do_ts_aggr, fd->group->max_ts, fd->group->ts_to_buffer);
+ if (NotTimeAggregated(fd->group) || TimeAggregationLastStep(fd->group)) {
+ while (v) {
+ v->write_offset = 0;
+ if (v->adata) {
+ free(v->adata);
+ v->data = v->adata = 0;
+ }
+
+ v = v->next;
+ }
- /* clean-up all copied variables with statistics and data in all PGs attached to this file */
- adios_free_pglist (fd);
+ /* clean-up all copied variables with statistics and data in all PGs
+ * attached to this file */
+ adios_free_pglist(fd);
- if (fd->name)
- {
- free (fd->name);
- fd->name = 0;
- }
+ if (fd->name) {
+ free(fd->name);
+ fd->name = 0;
+ }
- if (fd->comm != MPI_COMM_NULL && fd->comm != MPI_COMM_SELF) {
- MPI_Comm_free (&fd->comm);
- }
+ if (fd->comm != MPI_COMM_NULL && fd->comm != MPI_COMM_SELF) {
+ MPI_Comm_free(&fd->comm);
}
+ }
#ifdef ADIOS_TIMER_EVENTS
- /* This has to come here before freeing the buffer that zeros out fd->bytes_written */
- char* extension = ".perf";
- int name_len = strlen (fd->name);
- int fn_len = name_len + strlen (extension) + 1;
- char* fn = (char*) malloc (sizeof (char) * fn_len);
+ /* This has to come here before freeing the buffer that zeros out
+ * fd->bytes_written */
+ char *extension = ".perf";
+ int name_len = strlen(fd->name);
+ int fn_len = name_len + strlen(extension) + 1;
+ char *fn = (char *)malloc(sizeof(char) * fn_len);
- sprintf (fn, "%s%s", fd->name, extension);
+ sprintf(fn, "%s%s", fd->name, extension);
- adios_timing_write_xml_common (fd_p, fn);
+ adios_timing_write_xml_common(fd_p, fn);
#endif
-
- //Time Aggregation: add time step aggregation logic
- //ts aggregation will keep the buffer for next time steps
- //only free the buffer when ts aggregation is not required, or it
- //has reached the MAX_TS.
- //printf("close: bytes_written=%llu buffer_siz=%llu fd->group->last_buffer_size=%llu\n", fd->bytes_written, fd->buffer_size, fd->group->last_buffer_size);
- if (fd->bufstrat != no_buffering)
- {
- //printf("rank %d group %s last buffer size = %" PRIu64 " buffer_size = %" PRIu64 "\n",
- // fd->group->process_id, fd->group->name, fd->group->last_buffer_size, fd->buffer_size);
-
- if (fd->group->last_buffer_size < fd->buffer_size) {
- // Remember how much buffer we used for the next cycle.
- // Time Aggregation: with ts buffering, it will be the total amount of data
- // written; however last_buffer_size isn't used anyways
- if(TimeAggregated(fd->group))
- fd->group->last_buffer_size = fd->buffer_size;
- else
- fd->group->last_buffer_size = fd->bytes_written;
- }
- if (NotTimeAggregated(fd->group) || TimeAggregationLastStep(fd->group)) {
- adios_databuffer_free (fd);
- }
+ // Time Aggregation: add time step aggregation logic
+ // ts aggregation will keep the buffer for next time steps
+ // only free the buffer when ts aggregation is not required, or it
+ // has reached the MAX_TS.
+ // printf("close: bytes_written=%llu buffer_siz=%llu
+ // fd->group->max_pg_size=%llu\n", fd->bytes_written, fd->buffer_size,
+ // fd->group->max_pg_size);
+ if (fd->bufstrat != no_buffering) {
+ // printf("rank %d group %s last buffer size = %" PRIu64 " buffer_size = %"
+ // PRIu64 "\n",
+ // fd->group->process_id, fd->group->name, fd->group->max_pg_size,
+ // fd->buffer_size);
+
+ // Remember how much buffer we used for this group for helping buffer
+ // allocation in the next cycle.
+ // This only works for non-time-aggregation. In time aggregation,
+ // bytes_written is the current size of all buffered steps
+ if (NotTimeAggregated(fd->group)) {
+ if (fd->group->max_pg_size < fd->bytes_written) {
+ fd->group->max_pg_size = fd->bytes_written;
+ }
}
-
- if (TimeAggregated(fd->group))
- {
- if (TimeAggregationLastStep(fd->group))
- {
- //Time Aggregation: reset the ts counter when the last ts is in
- //printf("group %s reset ts_to_buffer to %d\n", fd->group->name, fd->group->max_ts);
- fd->group->ts_to_buffer = fd->group->max_ts;
- fd->group->ts_fd = NULL;
- free (fd);
- }
- else
- {
- // fd->group->new_write_offset=fd->current_pg->pg_start_in_file+
- fd->group->ts_to_buffer--;
- // TimeAggregationInProgress() may have moved into
- // TimeAggregationInProgress && TimeAggregationLastStep (i.e. ts_to_buffer==0)
- //printf("didn't free fd, continue buffering addr=%lld\n", fd_p);
- }
+ if (NotTimeAggregated(fd->group) || TimeAggregationLastStep(fd->group)) {
+ adios_databuffer_free(fd);
}
- else
- {
- free (fd);
+ }
+
+ if (TimeAggregated(fd->group)) {
+ if (TimeAggregationLastStep(fd->group)) {
+ // Time Aggregation: reset the ts counter when the last ts is in
+ // printf("group %s reset ts_to_buffer to %d\n", fd->group->name,
+ // fd->group->max_ts);
+ fd->group->ts_to_buffer = fd->group->max_ts;
+ fd->group->ts_fd = NULL;
+ free(fd);
+ } else {
+ // fd->group->new_write_offset=fd->current_pg->pg_start_in_file+
+ fd->group->ts_to_buffer--;
+ // TimeAggregationInProgress() may have moved into
+ // TimeAggregationInProgress && TimeAggregationLastStep (i.e.
+ // ts_to_buffer==0)
+ // printf("didn't free fd, continue buffering addr=%lld\n", fd_p);
}
+ } else {
+ free(fd);
+ }
- //printf("close file==============\n");
- /*
- printf("close: do_ts_aggr=%d max_ts=%d ts_to_buffer=%d\n",
- fd->group->do_ts_aggr, fd->group->max_ts, fd->group->ts_to_buffer);
+// printf("close file==============\n");
+/*
+printf("close: do_ts_aggr=%d max_ts=%d ts_to_buffer=%d\n",
+ fd->group->do_ts_aggr, fd->group->max_ts, fd->group->ts_to_buffer);
- printf("close: fd->offset=%lld, group_offset=%lld\n", fd->offset,
- fd->group->group_offset);
+printf("close: fd->offset=%lld, group_offset=%lld\n", fd->offset,
+ fd->group->group_offset);
- printf("close: fd->pgs_written->pg_start_in_file=%lld, fd->current_pg->pg_start_in_file=%lld\n",
- fd->pgs_written->pg_start_in_file, fd->current_pg->pg_start_in_file);
- */
+printf("close: fd->pgs_written->pg_start_in_file=%lld,
+fd->current_pg->pg_start_in_file=%lld\n",
+ fd->pgs_written->pg_start_in_file, fd->current_pg->pg_start_in_file);
+ */
#if defined(WITH_NCSU_TIMER) && defined(TIMER_LEVEL) && (TIMER_LEVEL <= 0)
- timer_stop ("adios_close");
- timer_stop ("adios_open_to_close");
- // printf ("Timers, ");
- // printf ("%d, ", fd->group->process_id);
- // printf ("%d, ", fd->group->time_index);
- // printf ("%lf, ", timer_get_total_interval ("adios_open" ));
- // printf ("%lf, ", timer_get_total_interval ("adios_group_size"));
- // printf ("%lf, ", timer_get_total_interval ("adios_transform" ));
- // printf ("%lf, ", timer_get_total_interval ("adios_write" ));
- // printf ("%lf\n", timer_get_total_interval ("adios_close" ));
- // timer_reset_timers ();
-
- printf("[TIMERS] Proc: %d Time: %d ", fd->group->process_id, fd->group->time_index);
- int i;
- timer_result_t *results = timer_get_results_sorted();
- for (i = 0; i < timer_get_num_timers(); i++) {
- printf("%s: %0.4lf ", results[i].name, results[i].time);
- }
- printf("\n");
- free(results);
-
- //timer_reset_timers ();
+ timer_stop("adios_close");
+ timer_stop("adios_open_to_close");
+ // printf ("Timers, ");
+ // printf ("%d, ", fd->group->process_id);
+ // printf ("%d, ", fd->group->time_index);
+ // printf ("%lf, ", timer_get_total_interval ("adios_open" ));
+ // printf ("%lf, ", timer_get_total_interval ("adios_group_size"));
+ // printf ("%lf, ", timer_get_total_interval ("adios_transform" ));
+ // printf ("%lf, ", timer_get_total_interval ("adios_write" ));
+ // printf ("%lf\n", timer_get_total_interval ("adios_close" ));
+ // timer_reset_timers ();
+
+ printf("[TIMERS] Proc: %d Time: %d ", fd->group->process_id,
+ fd->group->time_index);
+ int i;
+ timer_result_t *results = timer_get_results_sorted();
+ for (i = 0; i < timer_get_num_timers(); i++) {
+ printf("%s: %0.4lf ", results[i].name, results[i].time);
+ }
+ printf("\n");
+ free(results);
+
+// timer_reset_timers ();
#endif
-
- return adios_errno;
+ ADIOST_CALLBACK_EXIT(adiost_event_close, fd);
+ return adios_errno;
}
-
//////////////////////////////////////////////////////////////////////////////
// Methods normally only called by the XML parser
//////////////////////////////////////////////////////////////////////////////
diff --git a/src/core/common_read.c b/src/core/common_read.c
index ccf8c13..15daa38 100644
--- a/src/core/common_read.c
+++ b/src/core/common_read.c
@@ -34,6 +34,7 @@
#include "dmalloc.h"
#endif
+#include "adiost_callback_internal.h"
/* Note: MATLAB reloads the mex64 files each time, so all static variables get the original value.
Therefore static variables cannot be used to pass info between two Matlab/ADIOS calls */
@@ -83,6 +84,7 @@ int common_read_init_method (enum ADIOS_READ_METHOD method,
int retval;
char *end;
+ adiost_pre_init();
adios_errno = err_no_error;
if ((int)method < 0 || (int)method >= ADIOS_READ_METHOD_COUNT) {
adios_error (err_invalid_read_method,
@@ -170,6 +172,7 @@ int common_read_init_method (enum ADIOS_READ_METHOD method,
// init the query API; may call it multiple times here in multiple read methods' init;
common_query_init();
+ adiost_post_init();
return retval;
}
@@ -203,6 +206,7 @@ int common_read_finalize_method(enum ADIOS_READ_METHOD method)
// finalize the query API; may call it multiple times here in multiple read methods' finalize;
common_query_finalize();
+ adiost_finalize();
return retval;
}
@@ -379,9 +383,12 @@ ADIOS_FILE * common_read_open (const char * fname,
struct common_read_internals_struct * internals;
long i;
+ ADIOST_CALLBACK_ENTER(adiost_event_open, fp, "", "", "");
+
if ((int)method < 0 || (int)method >= ADIOS_READ_METHOD_COUNT) {
adios_error (err_invalid_read_method,
"Invalid read method (=%d) passed to adios_read_open().\n", (int)method);
+ ADIOST_CALLBACK_EXIT(adiost_event_open, fp, "", "", "");
return NULL;
}
@@ -397,6 +404,7 @@ ADIOS_FILE * common_read_open (const char * fname,
adios_error (err_invalid_read_method,
"Read method (=%d) passed to adios_read_open() is not provided "
"by this build of ADIOS.\n", (int)method);
+ ADIOST_CALLBACK_EXIT(adiost_event_open, fp, "", "", "");
return NULL;
}
@@ -410,8 +418,10 @@ ADIOS_FILE * common_read_open (const char * fname,
internals->infocache = adios_infocache_new();
fp = adios_read_hooks[internals->method].adios_read_open_fn (fname, comm, lock_mode, timeout_sec);
- if (!fp)
+ if (!fp) {
+ ADIOST_CALLBACK_EXIT(adiost_event_open, fp, "", "", "");
return fp;
+ }
fp->is_streaming = 1; // Mark file handle as streaming
@@ -439,6 +449,7 @@ ADIOS_FILE * common_read_open (const char * fname,
common_read_link (fp);
+ ADIOST_CALLBACK_EXIT(adiost_event_open, fp, "", "", "");
return fp;
}
@@ -529,6 +540,8 @@ int common_read_close (ADIOS_FILE *fp)
struct common_read_internals_struct * internals;
int retval;
+ ADIOST_CALLBACK_ENTER(adiost_event_close, fp);
+
adios_errno = err_no_error;
if (fp) {
internals = (struct common_read_internals_struct *) fp->internal_data;
@@ -566,6 +579,8 @@ int common_read_close (ADIOS_FILE *fp)
adios_error ( err_invalid_file_pointer, "Invalid file pointer at adios_read_close()\n");
retval = err_invalid_file_pointer;
}
+
+ ADIOST_CALLBACK_EXIT(adiost_event_close, fp);
return retval;
}
@@ -626,6 +641,8 @@ int common_read_advance_step (ADIOS_FILE *fp, int last, float timeout_sec)
int retval;
long i;
+ ADIOST_CALLBACK_ENTER(adiost_event_advance_step, fp);
+
adios_errno = err_no_error;
if (fp) {
if (fp->is_streaming)
@@ -669,6 +686,8 @@ int common_read_advance_step (ADIOS_FILE *fp, int last, float timeout_sec)
adios_error ( err_invalid_file_pointer, "Invalid file pointer at adios_advance_step()\n");
retval = err_invalid_file_pointer;
}
+
+ ADIOST_CALLBACK_EXIT(adiost_event_advance_step, fp);
return retval;
}
@@ -3660,6 +3679,8 @@ int common_read_perform_reads (const ADIOS_FILE *fp, int blocking)
struct common_read_internals_struct * internals;
int retval;
+ ADIOST_CALLBACK_ENTER(adiost_event_read, fp);
+
adios_errno = err_no_error;
if (fp) {
internals = (struct common_read_internals_struct *) fp->internal_data;
@@ -3677,6 +3698,8 @@ int common_read_perform_reads (const ADIOS_FILE *fp, int blocking)
adios_error (err_invalid_file_pointer, "Null pointer passed as file to adios_perform_reads()\n");
retval = err_invalid_file_pointer;
}
+
+ ADIOST_CALLBACK_EXIT(adiost_event_read, fp);
return retval;
}
diff --git a/src/core/flexpath.h b/src/core/flexpath.h
index 3a59441..c41dec3 100644
--- a/src/core/flexpath.h
+++ b/src/core/flexpath.h
@@ -14,6 +14,9 @@
#define FP_DST_ATTR_NAME "fp_dst_rank"
#define FP_DIM_ATTR_NAME "fp_dim"
#define FP_NDIMS_ATTR_NAME "fp_ndims"
+#define FP_TIMESTEP "fp_timestep"
+#define FP_ONLY_SCALARS "fp_only_scalars"
+#define FP_NATTRS "fp_number_of_attrs"
#define CLOSE_MSG 0
#define OPEN_MSG 1
@@ -33,8 +36,8 @@
}
#define fp_verbose(flxp_file, ...) \
if(flxp_file->verbose) { \
- fprintf(stderr, "file %p: %s %d:", flxp_file, FLEXPATH_SIDE, flxp_file->rank); \
- fprintf(stderr, __VA_ARGS__); \
+ fprintf(stdout, "file %p: %s %d:", flxp_file, FLEXPATH_SIDE, flxp_file->rank); \
+ fprintf(stdout, __VA_ARGS__); \
}
@@ -42,18 +45,43 @@
#define CONTACT_STR_LEN 50
-typedef enum {FORMAT, DATA, EVGROUP, STEP } Flush_type;
+typedef struct _finalize_close_msg {
+ int finalize;
+ int close;
+ int final_timestep;
+} finalize_close_msg, * finalize_close_msg_ptr;
-typedef struct _update_step_msg{
- int step;
- int finalized;
- int condition;
-}update_step_msg;
-typedef struct _drop_evgroup{
- int step;
+typedef struct _reader_register_msg {
+ uint64_t writer_file;
+ uint64_t reader_file;
int condition;
-}drop_evgroup_msg;
+ int contact_count;
+ char **contacts;
+} reader_register_msg;
+
+static FMField reader_register_field_list[] =
+{
+ {"writer_file", "integer", sizeof(uint64_t), FMOffset(reader_register_msg*, writer_file)},
+ {"reader_file", "integer", sizeof(uint64_t), FMOffset(reader_register_msg*, reader_file)},
+ {"condition", "integer", sizeof(int), FMOffset(reader_register_msg*, condition)},
+ {"contact_count", "integer", sizeof(int), FMOffset(reader_register_msg*, contact_count)},
+ {"contacts", "string[contact_count]", sizeof(char*), FMOffset(reader_register_msg*, contacts)},
+ {NULL, NULL, 0, 0}
+};
+
+typedef struct _reader_go_msg {
+ uint64_t reader_file;
+ int start_timestep;
+} reader_go_msg;
+
+static FMField reader_go_field_list[] =
+{
+ {"reader_file", "integer", sizeof(uint64_t), FMOffset(reader_go_msg*, reader_file)},
+ {"start_timestep", "integer", sizeof(int), FMOffset(reader_go_msg*, start_timestep)},
+ {NULL, NULL, 0, 0}
+};
+
/*
* Contains the offset information for a variable for all writers.
* offsets_per_rank is == ndims.
@@ -81,27 +109,15 @@ typedef struct _evgroup {
global_var* vars;
} evgroup, *evgroup_ptr;
-typedef struct _op_msg
-{
- int process_id;
- char *file_name;
- int type; //4 = end_of_stream, 3 = init, 2 = ack, 1 = open, 0 = close,
- int step;
- int condition;
-} op_msg, *op_msg_ptr;
-typedef struct flush_msg_ {
- Flush_type type;
- int process_id;
- int condition;
- int id;
-} Flush_msg, *Flush_msg_ptr;
-
-typedef struct var_msg_ {
- char* var_name;
- int process_id;
- int condition;
-} Var_msg, *Var_msg_ptr;
+typedef struct _reader_request_msg {
+ int condition;
+ int timestep_requested;
+ int process_return_id;
+ int current_lamport_min;
+ int var_count;
+ char** var_name_array;
+} read_request_msg, *read_request_msg_ptr;
typedef struct _complex_dummy
{
@@ -115,32 +131,24 @@ typedef struct _double_complex_dummy
double i;
} double_complex_dummy;
-static FMField complex_dummy_field_list[] =
-{
- {"r", "float", sizeof(float), FMOffset(complex_dummy*, r)},
- {"i", "float", sizeof(float), FMOffset(complex_dummy*, i)},
- {NULL, NULL, 0, 0}
-};
-
-static FMField double_complex_dummy_field_list[] =
-{
- {"r", "double", sizeof(double), FMOffset(double_complex_dummy*, r)},
- {"i", "double", sizeof(double), FMOffset(double_complex_dummy*, i)},
- {NULL, NULL, 0, 0}
-};
+typedef struct _queue_size_msg {
+ int queue_size;
+} queue_size_msg, *queue_size_msg_ptr;
-static FMField update_step_msg_field_list[]=
+static FMField queue_size_msg_field_list[]=
{
- {"step", "integer", sizeof(int), FMOffset(update_step_msg*, step)},
- {"finalized", "integer", sizeof(int), FMOffset(update_step_msg*, finalized)},
- {"condition", "integer", sizeof(int), FMOffset(update_step_msg*, condition)},
+ {"size", "integer", sizeof(int), FMOffset(queue_size_msg_ptr, queue_size)},
{NULL, NULL, 0, 0}
};
-static FMField drop_evgroup_msg_field_list[]=
+static FMField read_request_msg_field_list[]=
{
- {"step", "integer", sizeof(int), FMOffset(drop_evgroup_msg*, step)},
- {"condition", "integer", sizeof(int), FMOffset(drop_evgroup_msg*, condition)},
+ {"condition", "integer", sizeof(int), FMOffset(read_request_msg_ptr, condition)},
+ {"timestep_requested", "integer", sizeof(int), FMOffset(read_request_msg_ptr, timestep_requested)},
+ {"process_return_id", "integer", sizeof(int), FMOffset(read_request_msg_ptr, process_return_id)},
+ {"current_lamport_min", "integer", sizeof(int), FMOffset(read_request_msg_ptr, current_lamport_min)},
+ {"var_count", "integer", sizeof(int), FMOffset(read_request_msg_ptr, var_count)},
+ {"var_name_array", "string[var_count]", sizeof(char *), FMOffset(read_request_msg_ptr, var_name_array)},
{NULL, NULL, 0, 0}
};
@@ -162,55 +170,46 @@ static FMField global_var_field_list[]=
{NULL, NULL, 0, 0}
};
-static FMField evgroup_field_list[]=
+static FMField complex_dummy_field_list[] =
{
- {"condition", "integer", sizeof(int), FMOffset(evgroup_ptr, condition)},
- {"num_vars", "integer", sizeof(int), FMOffset(evgroup_ptr, num_vars)},
- {"step", "integer", sizeof(int), FMOffset(evgroup_ptr, step)},
- {"process_id", "integer", sizeof(int), FMOffset(evgroup_ptr, process_id)},
- {"group_name", "string", sizeof(char*), FMOffset(evgroup_ptr, group_name)},
- {"vars", "global_var[num_vars]", sizeof(global_var), FMOffset(evgroup_ptr, vars)},
+ {"r", "float", sizeof(float), FMOffset(complex_dummy*, r)},
+ {"i", "float", sizeof(float), FMOffset(complex_dummy*, i)},
{NULL, NULL, 0, 0}
};
-static FMField flush_field_list[] =
-{
- {"type", "integer", sizeof(Flush_type), FMOffset(Flush_msg_ptr, type)},
- {"process_id", "integer", sizeof(int), FMOffset(Flush_msg_ptr, process_id)},
- {"condition", "integer", sizeof(int), FMOffset(Flush_msg_ptr, condition)},
- {"id", "integer", sizeof(int), FMOffset(Flush_msg_ptr, id)},
+static FMField double_complex_dummy_field_list[] =
+{
+ {"r", "double", sizeof(double), FMOffset(double_complex_dummy*, r)},
+ {"i", "double", sizeof(double), FMOffset(double_complex_dummy*, i)},
{NULL, NULL, 0, 0}
};
-static FMField var_field_list[] =
+static FMField evgroup_field_list[]=
{
- {"var_name", "string", sizeof(char*), FMOffset(Var_msg_ptr, var_name)},
- {"process_id", "integer", sizeof(int), FMOffset(Var_msg_ptr, process_id)},
+ {"condition", "integer", sizeof(int), FMOffset(evgroup_ptr, condition)},
+ {"num_vars", "integer", sizeof(int), FMOffset(evgroup_ptr, num_vars)},
+ {"step", "integer", sizeof(int), FMOffset(evgroup_ptr, step)},
+ {"process_id", "integer", sizeof(int), FMOffset(evgroup_ptr, process_id)},
+ {"group_name", "string", sizeof(char*), FMOffset(evgroup_ptr, group_name)},
+ {"vars", "global_var[num_vars]", sizeof(global_var), FMOffset(evgroup_ptr, vars)},
{NULL, NULL, 0, 0}
};
-static FMField op_file_field_list[] =
+static FMField finalize_close_msg_field_list[] =
{
- {"process_id", "integer", sizeof(int), FMOffset(op_msg_ptr, process_id)},
- {"file_name", "string", sizeof(char*), FMOffset(op_msg_ptr, file_name)},
- {"type", "integer", sizeof(int), FMOffset(op_msg_ptr, type)},
- {"step", "integer", sizeof(int), FMOffset(op_msg_ptr, step)},
- {"condition", "integer", sizeof(int), FMOffset(op_msg_ptr, condition)},
+ {"finalize", "integer", sizeof(int), FMOffset(finalize_close_msg_ptr, finalize)},
+ {"close", "integer", sizeof(int), FMOffset(finalize_close_msg_ptr, close)},
+ {"final_timestep", "integer", sizeof(int), FMOffset(finalize_close_msg_ptr, final_timestep)},
{NULL, NULL, 0, 0}
};
-static FMStructDescRec update_step_msg_format_list[]=
+static FMStructDescRec finalize_close_msg_format_list[]=
{
- {"update_step_msg", update_step_msg_field_list, sizeof(update_step_msg), NULL},
+ {"finalize_close_msg", finalize_close_msg_field_list, sizeof(finalize_close_msg), NULL},
{NULL, NULL, 0, 0}
};
-static FMStructDescRec drop_evgroup_msg_format_list[]=
-{
- {"drop_evgroup_msg", drop_evgroup_msg_field_list, sizeof(drop_evgroup_msg), NULL},
- {NULL, NULL, 0, 0}
-};
static FMStructDescRec offset_struct_format_list[] =
{
@@ -218,6 +217,11 @@ static FMStructDescRec offset_struct_format_list[] =
{NULL, NULL, 0, 0}
};
+static FMStructDescRec read_request_format_list[] =
+{
+ {"read_request", read_request_msg_field_list, sizeof(read_request_msg), NULL},
+ {NULL, NULL, 0, NULL}
+};
static FMStructDescRec evgroup_format_list[] =
{
@@ -227,15 +231,9 @@ static FMStructDescRec evgroup_format_list[] =
{NULL,NULL,0,NULL}
};
-static FMStructDescRec flush_format_list[] =
-{
- {"flush", flush_field_list, sizeof(Flush_msg), NULL},
- {NULL,NULL,0,NULL}
-};
-
-static FMStructDescRec var_format_list[] =
+static FMStructDescRec queue_size_msg_format_list[] =
{
- {"varMsg", var_field_list, sizeof(Var_msg), NULL},
+ {"queue_size_msg", queue_size_msg_field_list, sizeof(queue_size_msg), NULL},
{NULL, NULL, 0, NULL}
};
@@ -245,11 +243,6 @@ static FMStructDescRec data_format_list[] =
{NULL, NULL, 0, NULL}
};
-static FMStructDescRec op_format_list[] =
-{
- {"op_msg", op_file_field_list, sizeof(op_msg), NULL},
- {NULL, NULL, 0, NULL}
-};
static char *getFixedName(char *name);
diff --git a/src/core/globals.c b/src/core/globals.c
index bee3ede..96c4744 100644
--- a/src/core/globals.c
+++ b/src/core/globals.c
@@ -11,7 +11,9 @@
#include "globals.h"
#include <inttypes.h>
-
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
static int globals_adios_appid = -1;
static int globals_adios_was_set = 0;
@@ -341,3 +343,103 @@ void icee_contactinfo_print(const icee_contactinfo_rec_ptr_t cp)
}
#endif
+
+#ifdef HAVE_FLEXPATH
+
+static char ascii_array[128];
+static char reverse_array[128];
+
+static void init_arrays()
+{
+ int i;
+ char translate = 'A';
+ memset(reverse_array, 0, 128);
+ for (i=0; i < sizeof(ascii_array) ; i++) {
+ if (!isprint((char)i)) {
+ ascii_array[i] = 0;
+ } else {
+ /* printable character */
+ if (isalnum((char)i)) {
+ ascii_array[i] = 1;
+ } else {
+ ascii_array[i] = translate;
+ reverse_array[translate] = i;
+ translate++;
+ if (translate == '[') {
+ translate = 'a';
+ }
+ }
+ }
+ }
+}
+
+char*
+flexpath_mangle(const char *name)
+{
+ char *mangle = NULL;
+ const char *tmp = name;
+ int len = 0;
+ int bad = 0;
+ static int first = 1;
+
+ if (first) {
+ first = 0;
+ init_arrays();
+ }
+ if (!name) return NULL;
+ while (*tmp) {
+ if (!isalnum(*tmp) && (*tmp != '_')) {
+ bad++;
+ }
+ tmp++;
+ }
+ if (!bad) {
+ return strdup(name);
+ }
+ mangle = malloc(2*strlen(name) + 4); /* worst case */
+ memset(mangle, 0, 2*strlen(name) + 4);
+ strcpy(mangle, "Z__");
+ int end = strlen(mangle);
+ while (name[0]) {
+ if (ascii_array[name[0]] > 1) {
+ mangle[end++] = '_';
+ mangle[end++] = ascii_array[name[0]];
+ } else {
+ mangle[end++] = name[0];
+ }
+ name++;
+ }
+ return mangle;
+}
+
+char*
+flexpath_unmangle(const char *name)
+{
+ static int first = 1;
+ char *unmangle = NULL;
+ int end = 0;
+
+ if (first) {
+ first = 0;
+ init_arrays();
+ }
+ if (!name) return NULL;
+ if (strncmp(name, "Z__", 3)) {
+ return strdup(name);
+ }
+ unmangle = malloc(strlen(name)); /* worst case */
+ memset(unmangle, 0, strlen(name));
+ name += 3;
+ end = 0;
+ while (name[0]) {
+ if (name[0] == '_') {
+ name++;
+ unmangle[end++] = reverse_array[name[0]];
+ } else {
+ unmangle[end++] = name[0];
+ }
+ name++;
+ }
+ return unmangle;
+}
+#endif
diff --git a/src/core/globals.h b/src/core/globals.h
index ad59519..30579d1 100644
--- a/src/core/globals.h
+++ b/src/core/globals.h
@@ -82,4 +82,8 @@ void icee_fileinfo_print(const void* item);
void icee_contactinfo_print(const icee_contactinfo_rec_ptr_t cp);
#endif
+#ifdef HAVE_FLEXPATH
+extern char *flexpath_unmangle(const char*name);
+extern char *flexpath_mangle(const char*name);
+#endif
#endif /*__GLOBALS_H__*/
diff --git a/src/mxml/Makefile.in b/src/mxml/Makefile.in
index 2796ac5..2ce3c95 100644
--- a/src/mxml/Makefile.in
+++ b/src/mxml/Makefile.in
@@ -100,7 +100,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -108,8 +108,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -337,6 +337,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -413,6 +417,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/src/public/adios_error.h b/src/public/adios_error.h
index c4af3e8..1d1b66e 100644
--- a/src/public/adios_error.h
+++ b/src/public/adios_error.h
@@ -46,6 +46,7 @@ enum ADIOS_ERRCODES {
err_too_many_files = -24, /* some staging methods allow for using only
a fixed number of different filenames */
+ err_file_read_error = -25,
err_unknown_char = -30,
// XML parsing errors
diff --git a/src/public/adios_version.h b/src/public/adios_version.h
index 651f624..37f29cf 100644
--- a/src/public/adios_version.h
+++ b/src/public/adios_version.h
@@ -9,9 +9,9 @@
#define ADIOS_VERSION_H
/* ADIOS Software release version */
-#define ADIOS_VERSION "1.11.0"
+#define ADIOS_VERSION "1.12.0"
#define ADIOS_VERSION_MAJOR 1
-#define ADIOS_VERSION_MINOR 11
+#define ADIOS_VERSION_MINOR 12
#define ADIOS_VERSION_PATCH 0
/* macros for comparing the version */
@@ -27,7 +27,7 @@
/* ADIOS Software release version as strings*/
#define ADIOS_VERSION_MAJOR_STRING "1"
-#define ADIOS_VERSION_MINOR_STRING "11"
+#define ADIOS_VERSION_MINOR_STRING "12"
#define ADIOS_VERSION_PATCH_STRING "0"
/* BP File format version
diff --git a/src/public/adiost_callback_api.h b/src/public/adiost_callback_api.h
new file mode 100644
index 0000000..6a74466
--- /dev/null
+++ b/src/public/adiost_callback_api.h
@@ -0,0 +1,153 @@
+/*
+ * ADIOS is freely available under the terms of the BSD license described
+ * in the COPYING file in the top level directory of this source distribution.
+ *
+ * Copyright (c) 2008 - 2009. UT-BATTELLE, LLC. All rights reserved.
+ */
+
+#ifndef __ADIOST_CALLBACK_API_H__
+#define __ADIOST_CALLBACK_API_H__
+
+/****************************************************************************
+ * System include files
+ ****************************************************************************/
+
+#include <stdint.h>
+#ifndef ADIOST_EXPORT
+#define ADIOST_EXPORT
+#endif
+#ifndef ADIOST_WEAK
+#define ADIOST_WEAK
+#endif
+
+/****************************************************************************
+ * iteration macros - to be expanded by other macros in multiple places
+ ****************************************************************************/
+
+#define FOREACH_ADIOST_INQUIRY_FN(macro) \
+ macro (adiost_set_callback) \
+ macro (adiost_get_callback)
+
+/* For each event, specify the callback type and the enumeration value. */
+#define FOREACH_ADIOST_EVENT(macro) \
+macro(adiost_event_thread, adiost_thread_callback_t, 1) \
+macro(adiost_event_open, adiost_open_callback_t, 3) \
+macro(adiost_event_close, adiost_file_callback_t, 5) \
+macro(adiost_event_write, adiost_file_callback_t, 10) \
+macro(adiost_event_read, adiost_file_callback_t, 12) \
+macro(adiost_event_advance_step, adiost_file_callback_t, 14) \
+macro(adiost_event_group_size, adiost_group_size_callback_t, 51) \
+macro(adiost_event_transform, adiost_file_callback_t, 52) \
+macro(adiost_event_fp_send_finalize_msg, adiost_file_callback_t, 102) \
+macro(adiost_event_fp_send_read_msg, adiost_file_callback_t, 105) \
+macro(adiost_event_fp_add_var_to_read_msg, adiost_file_callback_t, 106) \
+macro(adiost_event_fp_copy_buffer, adiost_file_callback_t, 205) \
+macro(adiost_event_library_shutdown, adiost_callback_t, 999) \
+
+#endif // #ifdef __ADIOST_CALLBACK_API_H__
+
+typedef enum {
+#define adiost_event_macro(event, callback, eventid) event = eventid,
+ FOREACH_ADIOST_EVENT(adiost_event_macro)
+ #undef adiost_event_macro
+} adiost_event_t;
+
+/*---------------------
+ * set callback results
+ *---------------------*/
+typedef enum {
+ adiost_set_result_registration_success = 0,
+ adiost_set_result_registration_error = 1
+} adiost_set_result_t;
+
+typedef enum {
+ adiost_event_enter,
+ adiost_event_exit,
+ adiost_event
+} adiost_event_type_t;
+
+/****************************************************************************
+ * Callback signature types
+ ****************************************************************************/
+
+/* initialization */
+typedef void (*adiost_interface_fn_t)(void);
+
+typedef adiost_interface_fn_t (*adiost_function_lookup_t)(
+ const char * /* entry point to look up */
+);
+
+/* Events: adios_thread */
+typedef void (*adiost_thread_callback_t)(
+ int64_t file_descriptor,
+ adiost_event_type_t type,
+ const char * thread_name
+);
+
+/* Events: adios_open */
+typedef void (*adiost_open_callback_t)(
+ int64_t file_descriptor,
+ adiost_event_type_t type,
+ const char * group_name,
+ const char * file_name,
+ const char * mode
+);
+
+/* Events: adios_close, adios_read_begin...adios_write_end */
+typedef void (*adiost_file_callback_t)(
+ int64_t file_descriptor,
+ adiost_event_type_t type);
+
+/* Events: adios_group_size */
+typedef void (*adiost_group_size_callback_t)(
+ int64_t file_descriptor,
+ adiost_event_type_t type,
+ uint64_t data_size,
+ uint64_t total_size
+);
+
+/* Events: adiost_event_library_shutdown */
+typedef void (*adiost_callback_t)(void);
+
+/****************************************************************************
+ * ADIOST API
+ ****************************************************************************/
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#define ADIOST_API_FNTYPE(fn) fn##_t
+
+#define ADIOST_API_FUNCTION(return_type, fn, args) \
+ typedef return_type (*ADIOST_API_FNTYPE(fn)) args
+
+/****************************************************************************
+ * Initialization functions
+ ****************************************************************************/
+
+ADIOST_API_FUNCTION(void, adiost_initialize, (
+ adiost_function_lookup_t adiost_fn_lookup,
+ const char *runtime_version,
+ unsigned int adiost_version
+));
+
+/* initialization interface - to be defined by tool */
+ADIOST_EXPORT adiost_initialize_t ADIOST_WEAK adiost_tool(void);
+
+/* Registering a callback function */
+ADIOST_API_FUNCTION(int, adiost_set_callback, (
+ adiost_event_t event,
+ adiost_callback_t callback
+));
+
+/* Getting a callback function */
+ADIOST_API_FUNCTION(int, adiost_get_callback, (
+ adiost_event_t event,
+ adiost_callback_t *callback
+));
+
+#ifdef __cplusplus
+}
+#endif
+
diff --git a/src/public/mpidummy.h b/src/public/mpidummy.h
index 72bdc3d..6310462 100644
--- a/src/public/mpidummy.h
+++ b/src/public/mpidummy.h
@@ -56,10 +56,13 @@ typedef enum mpi_operation MPI_Op;
#define MPI_INT 1
#define MPI_CHAR 2
#define MPI_DOUBLE 3
+#define MPI_UINT64_T 4
+#define MPI_UNSIGNED_LONG_LONG 8
#define MPI_ANY_SOURCE 0
#define MPI_ANY_TAG 0
+#define MPI_FILE_NULL 0
#define MPI_MAX_PROCESSOR_NAME 32
int MPI_Init(int *argc, char ***argv);
diff --git a/src/read/read_bp.c b/src/read/read_bp.c
index 982d7ba..3cde677 100644
--- a/src/read/read_bp.c
+++ b/src/read/read_bp.c
@@ -18,6 +18,7 @@
#include "public/adios_read.h"
#include "public/adios_error.h"
#include "public/adios_types.h"
+#include "core/adios_internals.h"
#include "core/util.h"
#include "core/bp_utils.h"
#include "core/bp_types.h"
@@ -66,6 +67,37 @@ static int adios_wbidx_to_pgidx (const ADIOS_FILE * fp, read_request * r, int st
}\
}\
+/* emulate MPI_File_read with support for data >2GiB */
+#define MPI_FILE_READ64(fh, buff, size, type, status) \
+ { \
+ int read_len = 0; \
+ uint64_t total_read = 0; \
+ uint64_t to_read = size; \
+ int count; \
+ while (to_read > 0) \
+ { \
+ read_len = (to_read > MAX_MPIWRITE_SIZE) ? MAX_MPIWRITE_SIZE : to_read; \
+ MPI_File_read (fh \
+ ,(char*)buff + total_read \
+ ,read_len \
+ ,type \
+ ,status \
+ ); \
+ MPI_Get_count (status, type, &count); \
+ int err; \
+ if (count != read_len) \
+ { \
+ log_error ("Need to do multi-read (tried: " \
+ "%d read: %d) errno %d\n", \
+ read_len, count, errno); \
+ err = count; \
+ break; \
+ } \
+ total_read += count; \
+ to_read -= count; \
+ } \
+ }
+
#define MPI_FILE_READ_OPS1 \
bp_realloc_aligned(fh->b, slice_size); \
fh->b->offset = 0; \
@@ -74,13 +106,12 @@ static int adios_wbidx_to_pgidx (const ADIOS_FILE * fp, read_request * r, int st
,(MPI_Offset)slice_offset \
,MPI_SEEK_SET \
); \
- \
- MPI_File_read (fh->mpi_fh \
- ,fh->b->buff \
- ,slice_size \
- ,MPI_BYTE \
- ,&status \
- ); \
+ MPI_FILE_READ64 (fh->mpi_fh \
+ ,fh->b->buff \
+ ,slice_size \
+ ,MPI_BYTE \
+ ,&status \
+ ); \
fh->b->offset = 0; \
// To read subfiles
@@ -135,12 +166,12 @@ static int adios_wbidx_to_pgidx (const ADIOS_FILE * fp, read_request * r, int st
,(MPI_Offset)slice_offset \
,MPI_SEEK_SET \
); \
- MPI_File_read (*sfh \
- ,fh->b->buff \
- ,slice_size \
- ,MPI_BYTE \
- ,&status \
- ); \
+ MPI_FILE_READ64 (*sfh \
+ ,fh->b->buff \
+ ,slice_size \
+ ,MPI_BYTE \
+ ,&status \
+ ); \
fh->b->offset = 0; \
//We also need to be able to read old .bp which doesn't have 'payload_offset'
@@ -157,7 +188,7 @@ static int adios_wbidx_to_pgidx (const ADIOS_FILE * fp, read_request * r, int st
MPI_File_seek (fh->mpi_fh \
,(MPI_Offset) (v->characteristics[start_idx + idx].offset) \
,MPI_SEEK_SET); \
- MPI_File_read (fh->mpi_fh, fh->b->buff, tmpcount + 8, MPI_BYTE, &status); \
+ MPI_FILE_READ64 (fh->mpi_fh, fh->b->buff, tmpcount + 8, MPI_BYTE, &status); \
fh->b->offset = 0; \
adios_parse_var_data_header_v1 (fh->b, &var_header); \
@@ -168,13 +199,12 @@ static int adios_wbidx_to_pgidx (const ADIOS_FILE * fp, read_request * r, int st
,(MPI_Offset)slice_offset \
,MPI_SEEK_SET \
); \
- \
- MPI_File_read (fh->mpi_fh \
- ,(buf) \
- ,slice_size \
- ,MPI_BYTE \
- ,&status \
- );
+ MPI_FILE_READ64 (fh->mpi_fh \
+ ,(buf) \
+ ,slice_size \
+ ,MPI_BYTE \
+ ,&status \
+ );
// To read subfiles
#define MPI_FILE_READ_OPS2_BUF(buf) \
@@ -225,12 +255,12 @@ static int adios_wbidx_to_pgidx (const ADIOS_FILE * fp, read_request * r, int st
,(MPI_Offset)slice_offset \
,MPI_SEEK_SET \
); \
- MPI_File_read (*sfh \
- ,(buf) \
- ,slice_size \
- ,MPI_BYTE \
- ,&status \
- );
+ MPI_FILE_READ64 (*sfh \
+ ,(buf) \
+ ,slice_size \
+ ,MPI_BYTE \
+ ,&status \
+ );
/* This routine release one step. It only frees the var/attr namelist. */
diff --git a/src/read/read_flexpath.c b/src/read/read_flexpath.c
index 360a1de..ce921dd 100644
--- a/src/read/read_flexpath.c
+++ b/src/read/read_flexpath.c
@@ -1,9 +1,3 @@
-/*
- read_flexpath.c
- Goal: to create evpath io connection layer in conjunction with
- write/adios_flexpath.c
-
-*/
// system libraries
#include <stdio.h>
#include <stdlib.h>
@@ -20,6 +14,7 @@
#include <ctype.h>
#include <pthread.h>
#include <unistd.h>
+#include <stdlib.h>
// evpath libraries
#include <ffs.h>
@@ -44,6 +39,8 @@
#define FLEXPATH_SIDE "READER"
#include "core/flexpath.h"
#include "core/futils.h"
+#include "core/globals.h"
+#include "core/adiost_callback_internal.h"
#include "core/transforms/adios_transforms_common.h" // NCSU ALACRITY-ADIOS
@@ -52,18 +49,26 @@
#include "dmalloc.h"
#endif
-#define FP_BATCH_SIZE 4
+#define FP_BATCH_SIZE 100
#define MAX(x, y) (((x) > (y)) ? (x) : (y))
#define MIN(x, y) (((x) < (y)) ? (x) : (y))
+//This is a linked list for the linked list of fp_vars
+//This is necessary to support push based gloabl metadata updates
+
+typedef struct _global_metadata
+{
+ evgroup * metadata;
+ struct _global_metadata * next;
+} global_metadata, * global_metadata_ptr;
+
typedef struct _bridge_info
{
EVstone bridge_stone;
- EVsource flush_source;
- EVsource var_source;
- EVsource op_source;
- int their_num;
+ EVsource read_source;
+ EVsource finalize_source;
+ int remote_stone_ID;
char *contact;
int created;
int opened;
@@ -73,7 +78,6 @@ typedef struct _bridge_info
typedef struct _flexpath_read_request
{
- long pad1, pad2, pad3, pad4, pad5;
int num_pending;
int num_completed;
int condition;
@@ -82,7 +86,6 @@ typedef struct _flexpath_read_request
typedef struct _flexpath_var_chunk
{
int has_data;
- int rank; // the writer's rank this chunk represents. not used or needed right now
void *data;
void *user_buf;
} flexpath_var_chunk;
@@ -101,6 +104,7 @@ typedef struct _array_displ
typedef struct _flexpath_var
{
+ int is_attr;
int id;
char *varname;
char *varpath;
@@ -108,10 +112,9 @@ typedef struct _flexpath_var
enum ADIOS_DATATYPES type;
uint64_t type_size; // type size, not arrays size
- int time_dim; // -1 means it is not a time dimension
int ndims;
uint64_t *global_dims; // ndims size (if ndims>0)
- uint64_t *local_dims; // for local arrays
+ uint64_t *local_dims; // for local arrays
uint64_t array_size; // not relevant for scalars
int num_chunks;
@@ -126,6 +129,15 @@ typedef struct _flexpath_var
struct _flexpath_var *next;
} flexpath_var;
+typedef struct _fp_var_list
+{
+ int timestep;
+ int is_list_filled;
+ flexpath_read_request req_cond;
+ flexpath_var * var_list;
+ struct _fp_var_list * next;
+} timestep_separated_lists;
+
typedef struct _flexpath_reader_file
{
char *file_name;
@@ -134,7 +146,8 @@ typedef struct _flexpath_reader_file
int verbose;
- EVstone stone;
+ EVstone terminal_stone;
+ EVstone feedback_bridge;
MPI_Comm comm;
int rank;
@@ -143,22 +156,26 @@ typedef struct _flexpath_reader_file
int num_bridges;
bridge_info *bridges;
int writer_coordinator;
+ int writer_coordinator_end;
- int num_vars;
- flexpath_var *var_list;
- evgroup *gp;
+ timestep_separated_lists * ts_var_list;
+ global_metadata_ptr global_info;
+ evgroup * current_global_info;
+ //timestep_condition_ptr global_metadata_conditions;
int writer_finalized;
int last_writer_step;
int mystep;
int num_sendees;
int *sendees;
+ read_request_msg *var_read_requests;
+ int go_cond;
+ int num_vars;
uint64_t data_read; // for perf measurements.
double time_in; // for perf measurements.
- flexpath_read_request req;
- pthread_mutex_t data_mutex;
- pthread_cond_t data_condition;
+ pthread_mutex_t queue_mutex;
+ pthread_cond_t queue_condition;
} flexpath_reader_file;
typedef struct _local_read_data
@@ -170,26 +187,286 @@ typedef struct _local_read_data
// EVPath stuff
CManager cm;
- atom_t CM_TRANSPORT;
} flexpath_read_data;
flexpath_read_data* fp_read_data = NULL;
+static atom_t RANK_ATOM = -1;
+static atom_t TIMESTEP_ATOM = -1;
+static atom_t SCALAR_ATOM = -1;
+static atom_t NATTRS = -1;
+static atom_t CM_TRANSPORT = -1;
+
/********** Helper functions. **********/
-static void
-reverse_dims(uint64_t *dims, int len)
+flexpath_var*
+new_flexpath_var(const char *varname, int id, uint64_t type_size)
+{
+ flexpath_var *var = malloc(sizeof(flexpath_var));
+ if (var == NULL) {
+ log_error("Error creating new var: %s\n", varname);
+ return NULL;
+ }
+
+ memset(var, 0, sizeof(flexpath_var));
+ // free this when freeing vars.
+ var->varname = strdup(varname);
+ var->id = id;
+ var->type_size = type_size;
+ var->displ = NULL;
+ return var;
+}
+
+//We need to copy the names and set up the flexpath vars when the data comes in
+flexpath_var*
+pseudo_copy_flexpath_vars(flexpath_var *f)
+{
+ flexpath_var *vars = NULL;
+
+ while (f != NULL) {
+ flexpath_var *curr_var = new_flexpath_var(f->varname, f->id, f->type_size);
+
+ curr_var->num_chunks = 1;
+ curr_var->chunks = malloc(sizeof(flexpath_var_chunk)*curr_var->num_chunks);
+ memset(curr_var->chunks, 0, sizeof(flexpath_var_chunk)*curr_var->num_chunks);
+ curr_var->sel = NULL;
+ curr_var->type = f->type;
+
+ //Make an exact copy of the list if possible
+ if(!vars)
+ vars = curr_var;
+ else
+ {
+ flexpath_var * last_var = vars;
+ while(last_var->next != NULL) last_var = last_var->next;
+ last_var->next = curr_var;
+ }
+
+ f = f->next;
+ }
+ return vars;
+}
+
+static void create_flexpath_var_for_timestep(flexpath_reader_file *fp, int timestep)
+{
+ timestep_separated_lists *curr = fp->ts_var_list;
+ timestep_separated_lists *prev = NULL;
+
+ // Check to see if we have made a mistake and we are trying to create
+ // something that has already
+ // been created
+ while (curr) {
+ if (curr->timestep == timestep) {
+ fp_verbose(fp, "Already created the timestep for timestep:%d\n",
+ timestep);
+ return;
+ }
+ prev = curr;
+ curr = curr->next;
+ }
+
+ // We are the first element in the queue
+ if (!prev) {
+ fp->ts_var_list = calloc(1, sizeof(*fp->ts_var_list));
+ fp->ts_var_list->timestep = timestep;
+ } else {
+ // We are not the first element in the queue
+ prev->next = calloc(1, sizeof(*fp->ts_var_list));
+ prev->next->timestep = timestep;
+ prev->next->var_list =
+ pseudo_copy_flexpath_vars(fp->ts_var_list->var_list);
+ }
+}
+
+static timestep_separated_lists *find_var_list(flexpath_reader_file *fp,
+ int timestep)
+{
+ timestep_separated_lists *temp = fp->ts_var_list;
+ while (temp) {
+ if (temp->timestep == timestep)
+ break;
+
+ temp = temp->next;
+ }
+ return temp;
+}
+
+static evgroup *find_current_global_data(flexpath_reader_file *fp)
+{
+ global_metadata_ptr curr = fp->global_info;
+ int reader_step = fp->mystep;
+ while (curr) {
+ if (curr->metadata->step == reader_step)
+ break;
+
+ curr = curr->next;
+ }
+
+ if (!curr) {
+ fprintf(stderr, "Error: evgroup queue has been messed up!\n");
+ return NULL;
+ }
+
+ return curr->metadata;
+}
+
+flexpath_var *
+find_fp_var(flexpath_var * var_list, const char * varname)
+{
+ while (var_list) {
+ if (!var_list->is_attr && !strcmp(varname, var_list->varname)) {
+ return var_list;
+ }
+ var_list = var_list->next;
+ }
+ return NULL;
+}
+
+flexpath_var *
+find_any_var(flexpath_var * var_list, const char * varname)
+{
+ while (var_list) {
+ if (!strcmp(varname, var_list->varname)) {
+ return var_list;
+ }
+ var_list = var_list->next;
+ }
+ return NULL;
+}
+
+flexpath_var *
+find_fp_attr(flexpath_var * var_list, const char * varname)
+{
+ while (var_list) {
+ if (var_list->is_attr && !strcmp(varname, var_list->varname)) {
+ return var_list;
+ }
+ var_list = var_list->next;
+ }
+ return NULL;
+}
+
+/*Here we are setting the dimensions of the flexpath vars from the
+ global metadata */
+static void share_global_information(flexpath_reader_file *fp)
{
int i;
- for (i = 0; i<(len/2); i++) {
- uint64_t tmp = dims[i];
- int end = len-1-i;
- //printf("%d %d\n", dims[i], dims[end]);
- dims[i] = dims[end];
- dims[end] = tmp;
+ for (i = 0; i < fp->current_global_info->num_vars; i++) {
+ global_var *gblvar = &(fp->current_global_info->vars[i]);
+ timestep_separated_lists *ts_var_list = find_var_list(fp, fp->mystep);
+ if (!ts_var_list) {
+ fprintf(stderr, "Error: could not find var list after it was "
+ "reported that we had it!!\n");
+ fprintf(stderr, "Severe logic error!\n");
+ exit(1);
+ }
+ flexpath_var *fpvar = find_fp_var(ts_var_list->var_list, gblvar->name);
+
+ if (fpvar) {
+ offset_struct *offset = &gblvar->offsets[0];
+ uint64_t *global_dimensions = offset->global_dimensions;
+ fpvar->ndims = offset->offsets_per_rank;
+ fpvar->global_dims = malloc(sizeof(uint64_t) * fpvar->ndims);
+ memcpy(fpvar->global_dims, global_dimensions,
+ sizeof(uint64_t) * fpvar->ndims);
+ } else {
+ adios_error(
+ err_corrupted_variable,
+ "Mismatch between global variables and variables specified %s.",
+ gblvar->name);
+ fprintf(stderr, "Error: Global variable mismatch!!\n");
+ // Not sure what the protocol is here, we will have to figure that
+ // out later
+ // return err_corrupted_variable;
+ }
}
}
+static void dump_timestep_separated_lists(flexpath_reader_file *fp)
+{
+ timestep_separated_lists *curr_list = fp->ts_var_list;
+ int count = 0;
+ fprintf(stderr, "************* Dumping the timestep separated var lists "
+ "*****************\n");
+ while (curr_list) {
+ fprintf(stderr, "List Index: %d\n", count++);
+ fprintf(stderr, "Timestep: %d\n", curr_list->timestep);
+ fprintf(stderr, "Is_List_Filled: %d\n", curr_list->is_list_filled);
+ flexpath_var *curr_var = curr_list->var_list;
+ while (curr_var) {
+ fprintf(stderr, "\t\tFlexpath variable: %s\n", curr_var->varname);
+ curr_var = curr_var->next;
+ }
+
+ curr_list = curr_list->next;
+ fprintf(stderr, "\n");
+ }
+}
+
+static timestep_separated_lists *
+flexpath_get_curr_timestep_list(flexpath_reader_file *fp)
+{
+ pthread_mutex_lock(&(fp->queue_mutex));
+ timestep_separated_lists *curr_var_list = find_var_list(fp, fp->mystep);
+ if (!curr_var_list) {
+ fprintf(stderr,
+ "Severe logic error in flexpath_get_curr_timestep_list!\n");
+ fp_verbose(fp, "Severe logic error in flexpath_get_curr_timestep_list "
+ "for timestep: %d\n",
+ fp->mystep);
+ dump_timestep_separated_lists(fp);
+ exit(1);
+ }
+ pthread_mutex_unlock(&(fp->queue_mutex));
+
+ return curr_var_list;
+}
+
+/* This function will check to see if we have the global metadata and scalar
+ values for the timestep that we specify in the second paramater. It locks
+ and unlocks the pthread queue mutex */
+void flexpath_wait_for_global_metadata(flexpath_reader_file *fp, int timestep)
+{
+
+ fp_verbose(fp, "Checking for global metadata for timestep: %d\n", timestep);
+ pthread_mutex_lock(&(fp->queue_mutex));
+ timestep_separated_lists *ts_var_list = find_var_list(fp, timestep);
+ if (ts_var_list == NULL) {
+ fp_verbose(fp,
+ "Creating the global metadata structures for timestep: %d\n",
+ timestep);
+ create_flexpath_var_for_timestep(fp, timestep);
+ ts_var_list = find_var_list(fp, timestep);
+ }
+
+ // If we don't have the scalar data or if we haven't received a finalized
+ // message, wait
+ while (ts_var_list->is_list_filled == 0 &&
+ fp->mystep != fp->last_writer_step) {
+ fp_verbose(
+ fp, "Waiting for writer to send the global data for timestep: %d\n",
+ timestep);
+ pthread_cond_wait(&(fp->queue_condition), &(fp->queue_mutex));
+ fp_verbose(fp, "Received signal! Last_writer_step:%d\t\tMystep:%d\n",
+ fp->last_writer_step, timestep);
+ }
+
+ // To avoid a deadlock when the writer is slow to send the finalize message
+ if (fp->mystep == fp->last_writer_step) {
+ pthread_mutex_unlock(&(fp->queue_mutex));
+ return;
+ }
+
+ // This is called to marry the metadata with the flexpath vars after we
+ // receive the second message
+ // This is a bad way to do this, it may need to be fixed, ultimately
+ fp->current_global_info = find_current_global_data(fp);
+ share_global_information(fp);
+ pthread_mutex_unlock(&(fp->queue_mutex));
+ fp_verbose(fp, "Finished checking on global data for timestep: %d\n",
+ fp->mystep);
+}
+
void build_bridge(bridge_info* bridge)
{
attr_list contact_list = attr_list_from_string(bridge->contact);
@@ -197,65 +474,290 @@ void build_bridge(bridge_info* bridge)
bridge->bridge_stone =
EVcreate_bridge_action(fp_read_data->cm,
contact_list,
- (EVstone)bridge->their_num);
-
- bridge->flush_source =
- EVcreate_submit_handle(fp_read_data->cm,
- bridge->bridge_stone,
- flush_format_list);
+ (EVstone)bridge->remote_stone_ID);
- bridge->var_source =
- EVcreate_submit_handle(fp_read_data->cm,
- bridge->bridge_stone,
- var_format_list);
+ bridge->read_source =
+ EVcreate_submit_handle(fp_read_data->cm,
+ bridge->bridge_stone,
+ read_request_format_list);
- bridge->op_source =
- EVcreate_submit_handle(fp_read_data->cm,
- bridge->bridge_stone,
- op_format_list);
+ bridge->finalize_source =
+ EVcreate_submit_handle(fp_read_data->cm,
+ bridge->bridge_stone,
+ finalize_close_msg_format_list);
bridge->created = 1;
}
+ free_attr_list(contact_list);
}
-void
-free_displacements(array_displacements *displ, int num)
+
+
+static void
+flexpath_free_displacements(array_displacements **displ, int num)
{
- if (displ) {
+ if (*displ) {
int i;
for (i=0; i<num; i++) {
- free(displ[i].start);
- free(displ[i].count);
+ free((*displ)[i].start);
+ free((*displ)[i].count);
}
- free(displ);
+ free(*displ);
+ *displ = NULL;
}
}
-void
-free_evgroup(evgroup *gp)
+static void
+flexpath_free_read_requests(int num_requests, read_request_msg * read_requests)
+{
+ int i = 0;
+ for(; i < num_requests; i++)
+ {
+ int j = 0;
+ read_request_msg * current_msg = read_requests + i;
+ //Free the inner variable name strings
+ for(; j < current_msg->var_count; j++)
+ {
+ free(current_msg->var_name_array[j]);
+ }
+ current_msg->var_count = 0;
+ //Free the outer array pointing to the strings
+ free(current_msg->var_name_array);
+ }
+ //Free the outer structures
+ free(read_requests);
+}
+
+static void flexpath_free_bridges(int num_bridges,
+ bridge_info *start_of_bridge_array)
+{
+ int i = 0;
+ for (i = 0; i < num_bridges; i++) {
+ if (start_of_bridge_array[i].contact) {
+ free(start_of_bridge_array[i].contact);
+ start_of_bridge_array[i].contact = NULL;
+ }
+
+ if (start_of_bridge_array[i].created) {
+ EVfree_source(start_of_bridge_array[i].read_source);
+ EVfree_source(start_of_bridge_array[i].finalize_source);
+ EVfree_stone(fp_read_data->cm,
+ start_of_bridge_array[i].bridge_stone);
+ }
+ }
+
+ free(start_of_bridge_array);
+}
+
+static void
+flexpath_var_free(flexpath_var * tmpvars)
+{
+ int i;
+ while (tmpvars) {
+
+ if(tmpvars->varname) {
+ free(tmpvars->varname);
+ tmpvars->varname = NULL;
+ }
+
+ if(tmpvars->varpath) {
+ free(tmpvars->varpath);
+ tmpvars->varpath = NULL;
+ }
+
+ if (tmpvars->ndims > 0) {
+ free(tmpvars->global_dims);
+ tmpvars->ndims = 0;
+ }
+ if (tmpvars->displ) {
+ flexpath_free_displacements(&(tmpvars->displ), tmpvars->num_displ);
+ }
+
+ if (tmpvars->sel) {
+ a2sel_free(tmpvars->sel);
+ tmpvars->sel = NULL;
+ }
+
+ tmpvars->sel = NULL;
+ for (i=0; i<tmpvars->num_chunks; i++) {
+ flexpath_var_chunk *chunk = &tmpvars->chunks[i];
+ if (chunk->has_data) {
+ //free(chunk->data);
+ chunk->data = NULL;
+ chunk->has_data = 0;
+ }
+ }
+
+
+
+ flexpath_var * tmp = tmpvars->next;
+ free(tmpvars);
+ tmpvars = tmp;
+ }
+}
+
+static void
+flexpath_free_evgroup(evgroup *gp)
{
EVreturn_event_buffer(fp_read_data->cm, gp);
}
-flexpath_var*
-new_flexpath_var(const char *varname, int id, uint64_t type_size)
+static void flexpath_free_filedata(flexpath_reader_file *fp)
{
- flexpath_var *var = malloc(sizeof(flexpath_var));
- if (var == NULL) {
- log_error("Error creating new var: %s\n", varname);
- return NULL;
+ fp_verbose(fp, "Freeing the flexpath_reader_file metadata structure!\n");
+
+ // Free the stream name
+ if (fp->file_name) {
+ free(fp->file_name);
+ fp->file_name = NULL;
+ }
+
+ // Free the adios group name
+ if (fp->group_name) {
+ free(fp->group_name);
+ fp->file_name = NULL;
+ }
+
+ // Free the bridge data structure by calling the function that does that,
+ // then setting the pointer to NULL
+ if (fp->bridges) {
+ flexpath_free_bridges(fp->num_bridges, fp->bridges);
+ fp->num_bridges = 0;
+ fp->bridges = NULL;
+ }
+
+ // Free the queue, no data should be coming in at this point, but I'm
+ // locking the queue anyway
+ pthread_mutex_lock(&(fp->queue_mutex));
+ timestep_separated_lists *curr = fp->ts_var_list;
+ while (curr) {
+ flexpath_var *v = curr->var_list;
+ flexpath_var_free(v);
+ timestep_separated_lists *temp = curr->next;
+ free(curr);
+ curr = temp;
+ }
+ fp->ts_var_list = NULL;
+ pthread_mutex_unlock(&(fp->queue_mutex));
+
+ // Free the global metadata by calling a function that essentially gives
+ // back the EVpath buffer
+ if (fp->global_info) {
+ while (fp->global_info) {
+ global_metadata_ptr temp = fp->global_info->next;
+ flexpath_free_evgroup(fp->global_info->metadata);
+ free(fp->global_info);
+ fp->global_info = temp;
+ }
}
- memset(var, 0, sizeof(flexpath_var));
- // free this when freeing vars.
- var->varname = strdup(varname);
- var->time_dim = -1;
- var->id = id;
- var->type_size = type_size;
- var->displ = NULL;
- return var;
+ if (fp->sendees) {
+ free(fp->sendees);
+ fp->sendees = NULL;
+ }
+
+ if (fp->var_read_requests) {
+ flexpath_free_read_requests(fp->num_sendees, fp->var_read_requests);
+ fp->var_read_requests = NULL;
+ }
+
+ // Free the mutex and the condition variable...do we need to free
+ // CMCondition?
+ fp_verbose(fp, "FileData is freed, better call open or exit!\n");
+}
+
+
+
+//Return the number of elements removed, don't remove if there's only one in the list
+static int
+cleanup_flexpath_vars(flexpath_reader_file *fp, int timestep)
+{
+ timestep_separated_lists *curr = fp->ts_var_list;
+ timestep_separated_lists *prev = NULL;
+
+ int number_timesteps_in_list = 0;
+ int number_removed = 0;
+ while (curr) {
+ number_timesteps_in_list++;
+ curr = curr->next;
+ }
+
+ curr = fp->ts_var_list;
+ while (number_timesteps_in_list > 1 && curr) {
+ if (curr->timestep <= timestep) {
+ flexpath_var_free(curr->var_list);
+ if (!prev) {
+ fp->ts_var_list = curr->next;
+ free(curr);
+ curr = fp->ts_var_list;
+ } else {
+ prev->next = curr->next;
+ free(curr);
+ curr = prev->next;
+ }
+ number_removed++;
+ number_timesteps_in_list--;
+ continue;
+ }
+
+ prev = curr;
+ curr = curr->next;
+ }
+
+ return number_removed;
+}
+
+//Return the number of elements removed
+static int remove_relevant_global_data(flexpath_reader_file *fp, int timestep)
+{
+ global_metadata_ptr curr = fp->global_info;
+ global_metadata_ptr prev = NULL;
+ int count = 0;
+ while (curr != NULL) {
+ if (timestep >= curr->metadata->step) {
+ global_metadata_ptr temp;
+ if (!prev) // We are at the front of the queue
+ {
+ fp->global_info = curr->next;
+ temp = fp->global_info;
+ } else // We are not at the front of the queue
+ {
+ prev->next = curr->next;
+ temp = prev->next;
+ }
+
+ flexpath_free_evgroup(curr->metadata);
+ free(curr);
+ count++;
+
+ curr = temp;
+ } else {
+ prev = curr;
+ curr = curr->next;
+ }
+ }
+ return count;
}
+
+
+static void
+reverse_dims(uint64_t *dims, int len)
+{
+ int i;
+ for (i = 0; i<(len/2); i++) {
+ uint64_t tmp = dims[i];
+ int end = len-1-i;
+ //printf("%d %d\n", dims[i], dims[end]);
+ dims[i] = dims[end];
+ dims[end] = tmp;
+ }
+}
+
+
+
+
+
flexpath_reader_file*
new_flexpath_reader_file(const char *fname)
{
@@ -268,142 +770,139 @@ new_flexpath_reader_file(const char *fname)
fp->file_name = strdup(fname);
fp->writer_coordinator = -1;
fp->last_writer_step = -1;
- fp->req = (flexpath_read_request) {.pad1 = 0, .pad2 = 0, .pad3 = 0, .pad4 = 0, .pad5=0,.num_pending = 0, .num_completed = 0, .condition = -1};
- pthread_mutex_init(&fp->data_mutex, NULL);
- pthread_cond_init(&fp->data_condition, NULL);
+ fp->go_cond = -1;
+ pthread_mutex_init(&fp->queue_mutex, NULL);
+ pthread_cond_init(&fp->queue_condition, NULL);
return fp;
}
-enum ADIOS_DATATYPES
-ffs_type_to_adios_type(const char *ffs_type, int size)
-
+enum ADIOS_DATATYPES ffs_type_to_adios_type(const char *ffs_type, int size)
{
char *bracket = "[";
size_t posfound = strcspn(ffs_type, bracket);
char *filtered_type = NULL;
+ char *free_pointer;
if (strlen(ffs_type) == strlen(bracket)) {
filtered_type = strdup(ffs_type);
+ } else {
+ filtered_type = malloc(posfound + 1);
+ memset(filtered_type, '\0', posfound + 1);
+ strncpy(filtered_type, ffs_type, posfound);
}
- else {
- filtered_type = malloc(posfound+1);
- memset(filtered_type, '\0', posfound+1);
- filtered_type = strncpy(filtered_type, ffs_type, posfound);
- }
+ free_pointer = filtered_type;
- if (!strcmp("integer", filtered_type)) {
- if (size == sizeof(int)) {
- return adios_integer;
- } else if (size == sizeof(long)) {
- return adios_long;
- }
- }
- else if (!strcmp("unsigned integer", filtered_type)) {
- if (size == sizeof(unsigned int)) {
- return adios_unsigned_integer;
- } else if (size == sizeof(unsigned long)) {
- return adios_unsigned_long;
- }
- }
- else if (!strcmp("float", filtered_type))
- return adios_real;
- else if (!strcmp("string", filtered_type))
- return adios_string;
- else if (!strcmp("double", filtered_type)) {
- if (size == sizeof(double)) {
- return adios_double;
- } else if (size == sizeof(long double)) {
- return adios_long_double;
- }
+ if (filtered_type[0] == '*') {
+ /* skip "*(" at the beginning */
+ filtered_type += 2;
}
- else if (!strcmp("char", filtered_type))
- return adios_byte;
- else if (!strcmp("complex", filtered_type))
- return adios_complex;
- else if (!strcmp("double_complex", filtered_type))
+ if (!strcmp("integer", filtered_type)) {
+ if (size == sizeof(int)) {
+ free(free_pointer);
+ return adios_integer;
+ } else if (size == sizeof(long)) {
+ free(free_pointer);
+ return adios_long;
+ }
+ } else if (!strcmp("unsigned integer", filtered_type)) {
+ if (size == sizeof(unsigned int)) {
+ free(free_pointer);
+ return adios_unsigned_integer;
+ } else if (size == sizeof(unsigned long)) {
+ free(free_pointer);
+ return adios_unsigned_long;
+ }
+ } else if (!strcmp("float", filtered_type)) {
+ free(free_pointer);
+ return adios_real;
+ } else if (!strcmp("string", filtered_type)) {
+ free(free_pointer);
+ return adios_string;
+ } else if (!strcmp("double", filtered_type)) {
+ if (size == sizeof(double)) {
+ free(free_pointer);
+ return adios_double;
+ } else if (size == sizeof(long double)) {
+ free(free_pointer);
+ return adios_long_double;
+ }
+ } else if (!strcmp("char", filtered_type)) {
+ free(free_pointer);
+ return adios_byte;
+ } else if (!strcmp("complex", filtered_type)) {
+ free(free_pointer);
+ return adios_complex;
+ } else if (!strcmp("double_complex", filtered_type)) {
+ free(free_pointer);
return adios_double_complex;
+ }
fprintf(stderr, "returning unknown for: ffs_type: %s\n", ffs_type);
+ free(free_pointer);
return adios_unknown;
}
-ADIOS_VARINFO*
-convert_var_info(flexpath_var * fpvar,
- ADIOS_VARINFO * v,
- const char* varname,
- const ADIOS_FILE *adiosfile)
+ADIOS_VARINFO *convert_var_info(flexpath_var *fpvar, ADIOS_VARINFO *v,
+ const char *varname,
+ const ADIOS_FILE *adiosfile)
{
int i;
- flexpath_reader_file *fp = (flexpath_reader_file*)adiosfile->fh;
+ flexpath_reader_file *fp = (flexpath_reader_file *)adiosfile->fh;
v->type = fpvar->type;
v->ndim = fpvar->ndims;
// needs to change. Has to get information from write.
v->nsteps = 1;
- v->nblocks = malloc(sizeof(int)*v->nsteps);
+ v->nblocks = malloc(sizeof(int) * v->nsteps);
v->sum_nblocks = 1;
v->nblocks[0] = 1;
v->statistics = NULL;
v->blockinfo = NULL;
if (v->ndim == 0) {
- int value_size = fpvar->type_size;
- v->value = malloc(value_size);
- if(!v->value) {
- adios_error(err_no_memory,
- "Cannot allocate buffer in adios_read_flexpath_inq_var()");
- return NULL;
- }
- flexpath_var_chunk * chunk = &fpvar->chunks[0];
- memcpy(v->value, chunk->data, value_size);
- v->global = 0;
+ int value_size = fpvar->type_size;
+ v->value = malloc(value_size);
+ if (!v->value) {
+ adios_error(
+ err_no_memory,
+ "Cannot allocate buffer in adios_read_flexpath_inq_var()");
+ return NULL;
+ }
+ flexpath_var_chunk *chunk = &fpvar->chunks[0];
+ memcpy(v->value, chunk->data, value_size);
+ v->global = 0;
} else { // arrays
- v->dims = (uint64_t*)malloc(v->ndim * sizeof(uint64_t));
- if (!v->dims) {
- adios_error(err_no_memory,
- "Cannot allocate buffer in adios_read_flexpath_inq_var()");
- return NULL;
- }
- // broken. fix. -- why did I put this comment here?
- int cpysize = fpvar->ndims*sizeof(uint64_t);
- if (fpvar->global_dims) {
- v->global = 1;
- memcpy(v->dims, fpvar->global_dims, cpysize);
- }
- else {
- v->global = 0;
- }
+ v->dims = (uint64_t *)malloc(v->ndim * sizeof(uint64_t));
+ if (!v->dims) {
+ adios_error(
+ err_no_memory,
+ "Cannot allocate buffer in adios_read_flexpath_inq_var()");
+ return NULL;
+ }
+ // broken. fix. -- why did I put this comment here?
+ int cpysize = fpvar->ndims * sizeof(uint64_t);
+ if (fpvar->global_dims) {
+ v->global = 1;
+ memcpy(v->dims, fpvar->global_dims, cpysize);
+ } else {
+ v->global = 0;
+ }
}
return v;
}
-flexpath_var *
-find_fp_var(flexpath_var * var_list, const char * varname)
-{
- while (var_list) {
- if (!strcmp(varname, var_list->varname)) {
- return var_list;
- }
- var_list = var_list->next;
- }
- return NULL;
-}
-
-global_var*
-find_gbl_var(global_var *vars, const char *name, int num_vars)
+global_var *find_gbl_var(global_var *vars, const char *name, int num_vars)
{
int i;
- for (i=0; i<num_vars; i++) {
- if (!strcmp(vars[i].name, name))
- return &vars[i];
+ for (i = 0; i < num_vars; i++) {
+ if (!strcmp(vars[i].name, name))
+ return &vars[i];
}
return NULL;
}
-static FMField*
-find_field_by_name (const char *name, const FMFieldList flist)
+static FMField *find_field_by_name(const char *name, const FMFieldList flist)
{
FMField *f = flist;
- while (f->field_name != NULL)
- {
+ while (f->field_name != NULL) {
if (!strcmp(name, f->field_name))
return f;
else
@@ -412,50 +911,6 @@ find_field_by_name (const char *name, const FMFieldList flist)
return NULL;
}
-static uint64_t
-calc_ffspacket_size(FMField *f, attr_list attrs, void *buffer)
-{
- uint64_t size = 0;
- while (f->field_name) {
- char atom_name[200] = "";
-
- strcat(atom_name, FP_NDIMS_ATTR_NAME);
- strcat(atom_name, "_");
- strcat(atom_name, f->field_name);
- int num_dims = 0;
- get_int_attr(attrs, attr_atom_from_string(atom_name), &num_dims);
- if (num_dims == 0) {
- size += (uint64_t)f->field_size;
- }
- else {
- int i;
- uint64_t tmpsize = (uint64_t)f->field_size;
- for (i=0; i<num_dims; i++) {
- char *dim;
- char atom_name[200] ="";
- strcat(atom_name, FP_DIM_ATTR_NAME);
- strcat(atom_name, "_");
- strcat(atom_name, f->field_name);
- strcat(atom_name, "_");
- char dim_num[10] = "";
- sprintf(dim_num, "%d", i+1);
- strcat(atom_name, dim_num);
- get_string_attr(attrs, attr_atom_from_string(atom_name), &dim);
-
- FMField *temp_field = find_field_by_name(dim, f);
- uint64_t *temp_val = get_FMfieldAddr_by_name(temp_field,
- temp_field->field_name,
- buffer);
- uint64_t dimval = *temp_val;
- tmpsize *= dimval;
- }
- size += tmpsize;
- }
- f++;
- }
- return size;
-}
-
void
print_displacement(array_displacements *disp, int myrank)
{
@@ -489,7 +944,6 @@ find_displacement(array_displacements *list, int rank, int num_displ)
return NULL;
}
-
array_displacements*
get_writer_displacements(
int writer_rank,
@@ -519,17 +973,19 @@ get_writer_displacements(
int start = sel->u.bb.start[i] - offsets[pos+i];
displ->start[i] = start;
}
+
+
if ((sel->u.bb.start[i] + sel->u.bb.count[i] - 1) <=
(offsets[pos+i] + local_dims[pos+i] - 1)) {
int count = ((sel->u.bb.start[i] + sel->u.bb.count[i] - 1) -
offsets[pos+i]) - displ->start[i] + 1;
displ->count[i] = count;
-
-
} else {
int count = (local_dims[pos+i] - 1) - displ->start[i] + 1;
displ->count[i] = count;
}
+
+
_size *= displ->count[i];
}
*size = _size;
@@ -550,71 +1006,57 @@ need_writer(
//for each dimension
int i=0;
offset_struct var_offsets = gvar->offsets[0];
+ //if(fp->rank == 1)
+ // printf("Offsets array data********************\n");
+
for (i=0; i< var_offsets.offsets_per_rank; i++) {
int pos = writer*(var_offsets.offsets_per_rank) + i;
+ //if(fp->rank == 1)
+ // printf("Global pos: %d\n", pos);
uint64_t sel_offset = sel->u.bb.start[i];
+ //if(fp->rank == 1)
+ // printf("Select offset: %ld\n", sel_offset);
uint64_t sel_size = sel->u.bb.count[i];
+ //if(fp->rank == 1)
+ // printf("Select size: %ld\n", sel_size);
uint64_t rank_offset = var_offsets.local_offsets[pos];
+ //if(fp->rank == 1)
+ // printf("rank_offset: %ld\n", rank_offset);
uint64_t rank_size = var_offsets.local_dimensions[pos];
+ //if(fp->rank == 1)
+ // printf("rank_size: %ld\n\n", rank_size);
- /* printf("need writer rank: %d writer: %d sel_start: %d sel_count: %d rank_offset: %d rank_size: %d\n", */
- /* fp->rank, writer, (int)sel_offset, (int)sel_size, (int)rank_offset, (int)rank_size); */
+ /* fprintf(stderr, "need writer rank: %d writer: %d sel_start: %d sel_count: %d rank_offset: %d rank_size: %d\n",
+ fp->rank, writer, (int)sel_offset, (int)sel_size, (int)rank_offset, (int)rank_size); */
- if ((rank_offset <= sel_offset) && (rank_offset + rank_size - 1 >=sel_offset)) {
- log_debug("matched overlap type 1\n");
- }
+ if ((rank_size == 0) || (sel_size == 0)) return 0;
- else if ((rank_offset <= sel_offset + sel_size - 1) && \
- (rank_offset+rank_size>=sel_offset+sel_size-1)) {
- } else if ((sel_offset <= rank_offset) && (rank_offset+rank_size<= sel_offset+sel_size-1)) {
- } else {
+ if ((rank_offset < sel_offset && (rank_offset + rank_size) <= sel_offset) || (rank_offset >= sel_offset + sel_size))
+ {
return 0;
}
}
return 1;
}
-void
-free_fmstructdesclist(FMStructDescList struct_list)
-{
- FMField *f = struct_list[0].field_list;
-
- //cant free field_name because it's const.
- /* FMField *temp = f; */
- /* while (temp->field_name) { */
- /* free(temp->field_name); */
- /* temp++; */
- /* } */
- free(f);
- free(struct_list[0].opt_info);
- free(struct_list);
-}
-
-int
-get_ndims_attr(const char *field_name, attr_list attrs)
-{
- char atom_name[200] = "";
- strcat(atom_name, FP_NDIMS_ATTR_NAME);
- strcat(atom_name, "_");
- strcat(atom_name, field_name);
- int num_dims;
- atom_t atm = attr_atom_from_string(atom_name);
- get_int_attr(attrs, atm, &num_dims);
- return num_dims;
-}
-
flexpath_var*
-setup_flexpath_vars(FMField *f, int *num)
+setup_flexpath_vars(FMField *f, int *num, int nattrs)
{
flexpath_var *vars = NULL;
int var_count = 0;
while (f->field_name != NULL) {
- flexpath_var *curr_var = new_flexpath_var(f->field_name,
+ char *unmangle = flexpath_unmangle(f->field_name);
+ flexpath_var *curr_var = new_flexpath_var(unmangle,
var_count,
f->field_size);
+ if (var_count < nattrs) {
+ curr_var->is_attr = 1;
+ } else {
+ curr_var->id -= nattrs;
+ }
curr_var->num_chunks = 1;
curr_var->chunks = malloc(sizeof(flexpath_var_chunk)*curr_var->num_chunks);
memset(curr_var->chunks, 0, sizeof(flexpath_var_chunk)*curr_var->num_chunks);
@@ -623,170 +1065,136 @@ setup_flexpath_vars(FMField *f, int *num)
flexpath_var *temp = vars;
curr_var->next = temp;
vars = curr_var;
- if (strncmp(f->field_name, "FPDIM", 5)) {
+ if (strncmp(unmangle, "FPDIM", 5)) {
var_count++;
}
f++;
+ free(unmangle);
}
*num = var_count;
return vars;
}
+
/*****************Messages to writer procs**********************/
void
-send_open_msg(flexpath_reader_file *fp, int destination)
+send_finalize_msg(flexpath_reader_file *fp)
{
- if (!fp->bridges[destination].created) {
- build_bridge(&(fp->bridges[destination]));
- }
- op_msg msg;
- msg.process_id = fp->rank;
- msg.file_name = fp->file_name;
- msg.step = fp->mystep;
- msg.type = OPEN_MSG;
- int cond = CMCondition_get(fp_read_data->cm, NULL);
- msg.condition = cond;
+ ADIOST_CALLBACK_ENTER(adiost_event_fp_send_finalize_msg, fp);
+ int i;
+ if((fp->rank / fp->num_bridges) == 0)
+ {
+ int num_iterations = (fp->num_bridges / fp->size) + 1;
- fp_verbose(fp, "sending open msg, WAITING on response\n");
- EVsubmit(fp->bridges[destination].op_source, &msg, NULL);
- CMCondition_wait(fp_read_data->cm, cond);
- fp_verbose(fp, "WAIT finished, setting opened to 1, destination %d\n", destination);
- fp->bridges[destination].opened = 1;
-}
+ for(i = 0; i < num_iterations; i++)
+ {
+ int send_to = fp->rank + fp->size * i;
+ if(send_to >= fp->num_bridges)
+ break;
-void
-send_close_msg(flexpath_reader_file *fp, int destination)
-{
- if (!fp->bridges[destination].created) {
- build_bridge(&(fp->bridges[destination]));
- }
- op_msg msg;
- msg.process_id = fp->rank;
- msg.file_name = fp->file_name;
- msg.step = fp->mystep;
- msg.type = CLOSE_MSG;
- //msg.condition = -1;
- int cond = CMCondition_get(fp_read_data->cm, NULL);
- msg.condition = cond;
- EVsubmit(fp->bridges[destination].op_source, &msg, NULL);
- fp_verbose(fp, "sending close msg, setting opened to 0, destination %d, WAITING\n", destination);
- CMCondition_wait(fp_read_data->cm, cond);
- fp_verbose(fp, "Done with WAIT\n");
- fp->bridges[destination].opened = 0;
-}
+ finalize_close_msg msg;
+ msg.finalize = 1;
+ msg.close = 1;
+ msg.final_timestep = fp->last_writer_step;
+ //Create bridge if needed
+ if (!fp->bridges[send_to].created) {
+ build_bridge(&(fp->bridges[send_to]));
+ }
-void
-send_finalize_msg(flexpath_reader_file *fp, int destination)
-{
- if (!fp->bridges[destination].created) {
- build_bridge(&(fp->bridges[destination]));
- }
- op_msg msg;
- msg.process_id = fp->rank;
- msg.file_name = fp->file_name;
- msg.step = fp->mystep;
- msg.type = FINALIZE_MSG;
- //msg.condition = -1;
- int cond = CMCondition_get(fp_read_data->cm, NULL);
- msg.condition = cond;
- EVsubmit(fp->bridges[destination].op_source, &msg, NULL);
- fp_verbose(fp, "sending finalize msg, setting opened to 0, destination %d, WAITING\n", destination);
- CMCondition_wait(fp_read_data->cm, cond);
- fp_verbose(fp, "Done with WAIT\n");
- fp->bridges[destination].opened = 0;
+ EVsubmit(fp->bridges[send_to].finalize_source, &msg, NULL);
+ }
+ }
+ ADIOST_CALLBACK_EXIT(adiost_event_fp_send_finalize_msg, fp);
}
-void
-send_flush_msg(flexpath_reader_file *fp, int destination, Flush_type type, int use_condition)
+static void
+send_read_msg(flexpath_reader_file *fp, int index, int use_condition)
{
- Flush_msg msg;
- msg.type = type;
- msg.process_id = fp->rank;
- msg.id = fp->mystep;
+ ADIOST_CALLBACK_ENTER(adiost_event_fp_send_read_msg, fp);
+ //Initial sanity check
+ if(index >= fp->num_sendees)
+ {
+ fprintf(stderr, "Error: index requested greater than num_sendees\n");
+ exit(1);
+ }
- if (use_condition)
- msg.condition = CMCondition_get(fp_read_data->cm, NULL);
+ read_request_msg_ptr msg = fp->var_read_requests + index;
+ int destination = fp->sendees[index];
+ //Give it a condition if we need to block
+ //and then set the lamport min
+ if(use_condition)
+ msg->condition = CMCondition_get(fp_read_data->cm, NULL);
else
- msg.condition = -1;
- // maybe check to see if the bridge is create first.
- EVsubmit(fp->bridges[destination].flush_source, &msg, NULL);
- if (use_condition) {
- fp_verbose(fp, "WAIT in send_flush_msg\n");
- CMCondition_wait(fp_read_data->cm, msg.condition);
+ msg->condition = -1;
+
+ //TODO: Change this part for the EVstore stuff
+ msg->current_lamport_min = -1;
+ //Basic error checking so we don't break on simple things in the future
+
+
+
+ if(!fp->bridges[destination].opened)
+ {
+ fprintf(stderr, "Error: trying to send to a bridge that is not open yet!\n");
+ exit(1);
+ }
+
+ fp_verbose(fp, "Submitting read request to %d\n", destination);
+ EVsubmit(fp->bridges[destination].read_source, msg, NULL);
+ if(use_condition) {
+ fp_verbose(fp, "WAIT in read_request_msg send\n");
+ CMCondition_wait(fp_read_data->cm, msg->condition);
fp_verbose(fp, "Done with WAIT\n");
}
+ ADIOST_CALLBACK_EXIT(adiost_event_fp_send_read_msg, fp);
}
void
-send_var_message(flexpath_reader_file *fp, int destination, char *varname)
+add_var_to_read_message(flexpath_reader_file *fp, int destination, char *varname)
{
+ ADIOST_CALLBACK_ENTER(adiost_event_fp_add_var_to_read_msg, fp);
int i = 0;
int found = 0;
+ int index = -1;
for (i=0; i<fp->num_sendees; i++) {
if (fp->sendees[i]==destination) {
- found=1;
+ index = i;
break;
}
}
- if (!found) {
+ if (index == -1) {
fp->num_sendees+=1;
fp->sendees=realloc(fp->sendees, fp->num_sendees*sizeof(int));
+ fp->var_read_requests=realloc(fp->var_read_requests, fp->num_sendees*sizeof(read_request_msg));
fp->sendees[fp->num_sendees-1] = destination;
+ memset(&fp->var_read_requests[fp->num_sendees-1], 0, sizeof(read_request_msg));
+ fp->var_read_requests[fp->num_sendees-1].process_return_id = fp->rank;
+ fp->var_read_requests[fp->num_sendees-1].timestep_requested = fp->mystep;
+ fp->var_read_requests[fp->num_sendees-1].current_lamport_min = -1;
+ fp->var_read_requests[fp->num_sendees-1].condition = -1;
+ fp->var_read_requests[fp->num_sendees-1].var_name_array = malloc(sizeof(char*));
+ fp->var_read_requests[fp->num_sendees-1].var_name_array[0] = strdup(varname);
+ fp->var_read_requests[fp->num_sendees-1].var_count = 1;
+ } else {
+ read_request_msg_ptr msg = &(fp->var_read_requests[index]);
+ msg->var_name_array = realloc(msg->var_name_array, sizeof(char*)*(msg->var_count +1));
+ msg->var_name_array[msg->var_count] = strdup(varname);
+ msg->var_count++;
}
if (!fp->bridges[destination].created) {
build_bridge(&(fp->bridges[destination]));
}
+ //TODO: Remove the open nature here
if (!fp->bridges[destination].opened) {
- fp_verbose(fp, "sending open msg in var_message, destination %d, opened was %d\n", destination, fp->bridges[destination].opened);
fp->bridges[destination].opened = 1;
- send_open_msg(fp, destination);
}
- Var_msg var;
- var.process_id = fp->rank;
- var.var_name = varname;
- EVsubmit(fp->bridges[destination].var_source, &var, NULL);
+ ADIOST_CALLBACK_EXIT(adiost_event_fp_add_var_to_read_msg, fp);
}
/********** EVPath Handlers **********/
static int
-update_step_msg_handler(
- CManager cm,
- void *vevent,
- void *client_data,
- attr_list attrs)
-{
- update_step_msg *msg = (update_step_msg*)vevent;
- ADIOS_FILE *adiosfile = (ADIOS_FILE*)client_data;
- flexpath_reader_file *fp = (flexpath_reader_file*)adiosfile->fh;
-
- fp->last_writer_step = msg->step;
- fp->writer_finalized = msg->finalized;
- adiosfile->last_step = msg->step;
- CMCondition_signal(fp_read_data->cm, msg->condition);
- return 0;
-}
-
-static int
-op_msg_handler(CManager cm, void *vevent, void *client_data, attr_list attrs) {
- op_msg* msg = (op_msg*)vevent;
- ADIOS_FILE *adiosfile = (ADIOS_FILE*)client_data;
- flexpath_reader_file *fp = (flexpath_reader_file*)adiosfile->fh;
- if (msg->type==ACK_MSG) {
- if (msg->condition != -1) {
- CMCondition_signal(fp_read_data->cm, msg->condition);
- }
- //ackCondition = CMCondition_get(fp_read_data->cm, NULL);
- }
- if (msg->type == EOS_MSG) {
- adios_errno = err_end_of_stream;
- CMCondition_signal(fp_read_data->cm, msg->condition);
- }
- return 0;
-}
-
-static int
group_msg_handler(CManager cm, void *vevent, void *client_data, attr_list attrs)
{
EVtake_event_buffer(fp_read_data->cm, vevent);
@@ -796,44 +1204,73 @@ group_msg_handler(CManager cm, void *vevent, void *client_data, attr_list attrs)
if (fp->group_name == NULL) {
fp->group_name = strdup(msg->group_name);
}
- fp->gp = msg;
- int i;
- for (i = 0; i<msg->num_vars; i++) {
- global_var *gblvar = &msg->vars[i];
- flexpath_var *fpvar = find_fp_var(fp->var_list, gblvar->name);
- if (fpvar) {
- offset_struct *offset = &gblvar->offsets[0];
- uint64_t *local_dimensions = offset->local_dimensions;
- uint64_t *local_offsets = offset->local_offsets;
- uint64_t *global_dimensions = offset->global_dimensions;
-
- fpvar->ndims = offset->offsets_per_rank;
- fpvar->global_dims = malloc(sizeof(uint64_t)*fpvar->ndims);
- memcpy(fpvar->global_dims, global_dimensions, sizeof(uint64_t)*fpvar->ndims);
- } else {
- adios_error(err_corrupted_variable,
- "Mismatch between global variables and variables specified %s.",
- gblvar->name);
- return err_corrupted_variable;
- }
+
+ pthread_mutex_lock(&(fp->queue_mutex));
+ global_metadata_ptr curr = fp->global_info;
+ while(curr && curr->next)
+ curr = curr->next;
+
+ if(!curr)
+ {
+ fp->global_info = calloc(1, sizeof(global_metadata));
+ curr = fp->global_info;
+ }
+ else
+ {
+ curr->next = calloc(1, sizeof(global_metadata));
+ curr = curr->next;
+ }
+
+ curr->metadata = msg;
+ //Made for debugging purposes, not needed but worked too hard to remove
+ /*if(fp->rank == 1)
+ {
+ printf("Group message_info****************\n");
+ printf("Condition: %d\n", msg->condition);
+ printf("Num_vars: %d\n", msg->num_vars);
+ printf("Step: %d\n", msg->step);
+ printf("Process_id: %d\n", msg->process_id);
+ printf("Group_name: %s\n", msg->group_name);
+ int i;
+ for(i = 0; i < msg->num_vars; i++)
+ {
+ printf("\t\tVariable_name: %s\n", msg->vars->name);
+ printf("\t\tNumber offset_structs: %d\n", msg->vars->noffset_structs);
+ int j;
+ for(j = 0; j < msg->vars->noffset_structs; j++)
+ {
+ printf("\t\t\t\tOffsets_per_rank: %d\n", msg->vars->offsets->offsets_per_rank);
+ printf("\t\t\t\tTotal_offsets: %d\n", msg->vars->offsets->total_offsets);
+ printf("\t\t\t\tLocal_dimensions: ");
+ int k;
+ for(k = 0; k < msg->vars->offsets->total_offsets; k++)
+ printf("%ld ", msg->vars->offsets->local_dimensions[k]);
+
+ printf("\n\t\t\t\tLocal_offsets: ");
+ for(k = 0; k < msg->vars->offsets->total_offsets; k++)
+ printf("%ld ", msg->vars->offsets->local_offsets[k]);
+ printf("\n");
+ }
+ }
}
- CMCondition_signal(fp_read_data->cm, msg->condition);
+*/
+
+ pthread_mutex_unlock(&(fp->queue_mutex));
return 0;
}
-
-int
-increment_index(int64_t ndim, uint64_t *dimen_array, uint64_t *index_array)
+static int
+finalize_msg_handler(CManager cm, void * vevent, void * client_data, attr_list attrs)
{
- ndim--;
- while (ndim >= 0) {
- index_array[ndim]++;
- if (index_array[ndim] < dimen_array[ndim]) {
- return 1;
- }
- index_array[ndim] = 0;
- ndim--;
- }
+ ADIOS_FILE *adiosfile = client_data;
+ flexpath_reader_file * fp = (flexpath_reader_file*)adiosfile->fh;
+ finalize_close_msg_ptr msg = (finalize_close_msg_ptr)vevent;
+ fp_verbose(fp, "Received the finalize message from the writer\n");
+ pthread_mutex_lock(&(fp->queue_mutex));
+ fp->writer_finalized = 1;
+ fp->last_writer_step = msg->final_timestep;
+ pthread_cond_signal(&(fp->queue_condition));
+ pthread_mutex_unlock(&(fp->queue_mutex));
return 0;
}
@@ -941,6 +1378,8 @@ extract_selection_from_partial(int element_size, uint64_t dims, uint64_t *global
free(partial_index);
source_block_start_offset *= element_size;
+ double * temp_doub = (double *) selection;
+
data += source_block_start_offset;
selection += dest_block_start_offset;
int i;
@@ -949,19 +1388,23 @@ extract_selection_from_partial(int element_size, uint64_t dims, uint64_t *global
data += source_block_stride;
selection += dest_block_stride;
}
+ free(first_index);
}
- static int
+static int
raw_handler(CManager cm, void *vevent, int len, void *client_data, attr_list attrs)
{
ADIOS_FILE *adiosfile = client_data;
flexpath_reader_file *fp = (flexpath_reader_file*)adiosfile->fh;
+ fp_verbose(fp, "Received data message!\n");
int writer_rank;
- int flush_id;
- double data_start;
- get_double_attr(attrs, attr_atom_from_string("fp_starttime"), &data_start);
- get_int_attr(attrs, attr_atom_from_string(FP_RANK_ATTR_NAME), &writer_rank);
- get_int_attr(attrs, attr_atom_from_string("fp_flush_id"), &flush_id);
+ int timestep;
+ int only_scalars = 0;
+ int nattrs = 0;
+ get_int_attr(attrs, RANK_ATOM, &writer_rank);
+ get_int_attr(attrs, TIMESTEP_ATOM, ×tep);
+ get_int_attr(attrs, SCALAR_ATOM, &only_scalars);
+ get_int_attr(attrs, NATTRS, &nattrs);
/* fprintf(stderr, "\treader rank:%d:got data from writer:%d:step:%d\n", */
/* fp->rank, writer_rank, fp->mystep); */
FMContext context = CMget_FMcontext(cm);
@@ -969,29 +1412,39 @@ raw_handler(CManager cm, void *vevent, int len, void *client_data, attr_list att
FMFormat format = FMformat_from_ID(context, vevent);
// copy //FMfree_struct_desc_list call
- FMStructDescList struct_list =
- FMcopy_struct_list(format_list_of_FMFormat(format));
+ FMStructDescList struct_list = FMcopy_struct_list(format_list_of_FMFormat(format));
FMField *f = struct_list[0].field_list;
-
-#if 0
- uint64_t packet_size = calc_ffspacket_size(f, attrs, base_data);
- fp->data_read += packet_size;
-#endif
/* setting up initial vars from the format list that comes along with the
message. Message contains both an FFS description and the data. */
if (fp->num_vars == 0) {
+ fp_verbose(fp, "Setting up initial vars!\n");
int var_count = 0;
- fp->var_list = setup_flexpath_vars(f, &var_count);
+
+ pthread_mutex_lock(&(fp->queue_mutex));
+ create_flexpath_var_for_timestep(fp, timestep);
+ timestep_separated_lists * ts_var_list = find_var_list(fp, timestep);
+ ts_var_list->var_list = setup_flexpath_vars(f, &var_count, nattrs);
+ pthread_mutex_unlock(&(fp->queue_mutex));
adiosfile->var_namelist = malloc(var_count * sizeof(char *));
+ adiosfile->attr_namelist = malloc(nattrs * sizeof(char *));
int i = 0;
while (f->field_name != NULL) {
- if (strncmp(f->field_name, "FPDIM", 5)) {
- adiosfile->var_namelist[i++] = strdup(f->field_name);
+ char *unmangle = flexpath_unmangle(f->field_name);
+ if (i < nattrs) {
+ adiosfile->attr_namelist[i++] = unmangle;
+ } else {
+ if (strncmp(unmangle, "FPDIM", 5)) {
+ adiosfile->var_namelist[i - nattrs] = unmangle;
+ i++;
+ } else {
+ free(unmangle);
+ }
}
f++;
}
- adiosfile->nvars = var_count;
+ adiosfile->nvars = var_count - nattrs;
+ adiosfile->nattrs = nattrs;
fp->num_vars = var_count;
}
@@ -1000,7 +1453,20 @@ raw_handler(CManager cm, void *vevent, int len, void *client_data, attr_list att
while (f->field_name) {
char atom_name[200] = "";
- flexpath_var *var = find_fp_var(fp->var_list, f->field_name);
+ char *unmangle = flexpath_unmangle(f->field_name);
+ char *dims[100]; /* more than we should ever need */
+
+ pthread_mutex_lock(&(fp->queue_mutex));
+ timestep_separated_lists * ts_var_list = find_var_list(fp, timestep);
+ if(ts_var_list == NULL)
+ {
+ fp_verbose(fp, "Created timestep in raw handler -- timestep:%d\n", timestep);
+ create_flexpath_var_for_timestep(fp, timestep);
+ ts_var_list = find_var_list(fp, timestep);
+ }
+ flexpath_var * var = find_any_var(ts_var_list->var_list, unmangle);
+ pthread_mutex_unlock(&(fp->queue_mutex));
+ free(unmangle);
if (!var) {
adios_error(err_file_open_error,
@@ -1008,14 +1474,28 @@ raw_handler(CManager cm, void *vevent, int len, void *client_data, attr_list att
return err_file_open_error;
}
- int num_dims = get_ndims_attr(f->field_name, attrs);
+ int num_dims = 0;
+ if (f->field_type) {
+ char *tmp = index(f->field_type, '[');
+ while (tmp != NULL) {
+ int len;
+ tmp++;
+ len = index(tmp, ']') - tmp;
+ dims[num_dims] = calloc(len + 1, 1);
+ strncpy(dims[num_dims], tmp, len);
+ tmp = index(tmp+1, '[');
+ num_dims++;
+ }
+ }
var->ndims = num_dims;
-
flexpath_var_chunk *curr_chunk = &var->chunks[0];
+ int i;
- // has the var been scheduled?
+ // Has the var been scheduled
if (var->sel) {
+ //fp_verbose(fp, "Vars have been scheduled for timestep:%d\n", timestep);
if (var->sel->type == ADIOS_SELECTION_WRITEBLOCK) {
+ //fp_verbose(fp, "Var is type selection_writeblock for scalars!\n");
if (num_dims == 0) { // writeblock selection for scalar
if (var->sel->u.block.index == writer_rank) {
void *tmp_data = get_FMfieldAddr_by_name(f,
@@ -1025,22 +1505,12 @@ raw_handler(CManager cm, void *vevent, int len, void *client_data, attr_list att
}
}
else { // writeblock selection for arrays
+ //fp_verbose(fp, "Var is type selection_writeblock for arrays!\n");
if (var->sel->u.block.index == writer_rank) {
var->array_size = var->type_size;
- int i;
for (i=0; i<num_dims; i++) {
- char *dim;
- atom_name[0] ='\0';
- strcat(atom_name, FP_DIM_ATTR_NAME);
- strcat(atom_name, "_");
- strcat(atom_name, f->field_name);
- strcat(atom_name, "_");
- char dim_num[10] = "";
- sprintf(dim_num, "%d", i+1);
- strcat(atom_name, dim_num);
- get_string_attr(attrs, attr_atom_from_string(atom_name), &dim);
-
- FMField *temp_field = find_field_by_name(dim, f);
+ char *dim = dims[i];
+ FMField *temp_field = find_field_by_name(dim, struct_list[0].field_list);
if (!temp_field) {
adios_error(err_corrupted_variable,
"Could not find fieldname: %s\n",
@@ -1067,18 +1537,21 @@ raw_handler(CManager cm, void *vevent, int len, void *client_data, attr_list att
}
else if (var->sel->type == ADIOS_SELECTION_BOUNDINGBOX) {
+ //fp_verbose(fp, "Var is type selection_boundingbox for arrays!\n");
if (var->ndims > 0) { // arrays
int i;
- global_var *gv = find_gbl_var(fp->gp->vars,
+ global_var *gv = find_gbl_var(fp->current_global_info->vars,
var->varname,
- fp->gp->num_vars);
+ fp->current_global_info->num_vars);
array_displacements *disp = find_displacement(var->displ,
writer_rank,
var->num_displ);
if (disp) { // does this writer hold a chunk we've asked for
+ //fp_verbose(fp, "Var is in the displacement, it should have data that we've asked for!\n");
- //print_displacement(disp, fp->rank);
+ //if(fp->rank == 0)
+ //print_displacement(disp, fp->rank);
uint64_t *global_sel_start = var->sel->u.bb.start;
uint64_t *global_sel_count = var->sel->u.bb.count;
@@ -1093,6 +1566,22 @@ raw_handler(CManager cm, void *vevent, int len, void *client_data, attr_list att
f->field_name,
base_data, 1);
char *reader_array = (char*)var->chunks[0].user_buf;
+ /*if(fp->rank == 0 && writer_rank == 0)
+ {
+ printf("Global_sel_start: %ld, %ld, ...\n", global_sel_start[0], global_sel_start[1]);
+ printf("Global_sel_count: %ld, %ld, ...\n", global_sel_count[0], global_sel_count[1]);
+ printf("Global_dimensions: %ld, %ld, ...\n", global_dimensions[0], global_dimensions[1]);
+ printf("disp->ndims: %ld\n", disp->ndims);
+ printf("offsets_per_rank: %d\n", offsets_per_rank);
+ printf("Writer_sizes: %ld, %ld, ...\n", writer_sizes[0], writer_sizes[1]);
+ printf("Writer_offsets: %ld, %ld, ...\n", writer_offsets[0], writer_offsets[1]);
+ printf("Writer_array: %f, %f, ...\n", ((double *)writer_array)[0],((double *) writer_array)[1]);
+ }
+ */
+
+
+
+ //printf("User_buffer_pointer:%p\n", var->chunks[0].user_buf);
extract_selection_from_partial(f->field_size, disp->ndims, global_dimensions,
writer_offsets, writer_sizes,
@@ -1102,37 +1591,70 @@ raw_handler(CManager cm, void *vevent, int len, void *client_data, attr_list att
}
}
}
- else { //var has not been scheduled;
- if (num_dims == 0) { // only worry about scalars
- flexpath_var_chunk *chunk = &var->chunks[0];
- if (!chunk->has_data) {
+
+ if (num_dims == 0) { // only worry about scalars
+ flexpath_var_chunk *chunk = &var->chunks[0];
+ if (!chunk->has_data) {
+ if (var->type != adios_string) {
void *tmp_data = get_FMfieldAddr_by_name(f, f->field_name, base_data);
chunk->data = malloc(f->field_size);
memcpy(chunk->data, tmp_data, f->field_size);
chunk->has_data = 1;
+ } else {
+ void *xmit_str = get_FMPtrField_by_name(f, f->field_name, base_data, /*encoded (raw)*/1);
+ chunk->data = strdup(xmit_str);
+ chunk->has_data = 1;
}
+
}
}
+ //Clean up the temporary memory
+ for(i = 0; i < num_dims; i++)
+ free(dims[i]);
f++;
}
+ //We need this to differentiate between real data messages and the global metadata hack message that gets sent with every
+ //EVgroup message on the writer side
+ if(!only_scalars)
+ {
+ timestep_separated_lists * curr_var_list = flexpath_get_curr_timestep_list(fp);
+ fp_verbose(fp, "Reporting received data for timestep:%d from writer %d\n", timestep, writer_rank);
+ curr_var_list->req_cond.num_completed++;
+ fp_verbose(fp, "Received data message! (%d of %d)\n", curr_var_list->req_cond.num_completed, curr_var_list->req_cond.num_pending);
+ /* fprintf(stderr, "\t\treader rank:%d:step:%d:num_completed:%d:num_pending:%d\n", */
+ /* fp->rank, fp->mystep, fp->req.num_completed, fp->req.num_pending); */
+ if (curr_var_list->req_cond.num_completed == curr_var_list->req_cond.num_pending) {
+ /* fprintf(stderr, "\t\treader rank:%d:step:%d:signalling_on:%d\n", */
+ /* fp->rank, fp->mystep, fp->req.condition); */
+ CMCondition_signal(fp_read_data->cm, curr_var_list->req_cond.condition);
+ }
- fp->req.num_completed++;
- /* fprintf(stderr, "\t\treader rank:%d:step:%d:num_completed:%d:num_pending:%d\n", */
- /* fp->rank, fp->mystep, fp->req.num_completed, fp->req.num_pending); */
- if (fp->req.num_completed == fp->req.num_pending) {
- /* fprintf(stderr, "\t\treader rank:%d:step:%d:signalling_on:%d\n", */
- /* fp->rank, fp->mystep, fp->req.condition); */
- CMCondition_signal(fp_read_data->cm, fp->req.condition);
+ }
+ else
+ {
+ fp_verbose(fp, "Only scalars message received for timestep:%d from writer %d\n", timestep, writer_rank);
+ pthread_mutex_lock(&(fp->queue_mutex));
+ timestep_separated_lists * ts_var_list = find_var_list(fp, timestep);
+ ts_var_list->is_list_filled = 1;
+ pthread_cond_signal(&(fp->queue_condition));
+ pthread_mutex_unlock(&(fp->queue_mutex));
}
-
- free_fmstructdesclist(struct_list);
+ FMfree_struct_list(struct_list);
return 0;
}
/********** Core ADIOS Read functions. **********/
+extern void
+reader_go_handler(CManager cm, CMConnection conn, void *vmsg, void *client_data, attr_list attrs)
+{
+ reader_go_msg *msg = (reader_go_msg *)vmsg;
+ flexpath_reader_file* fp = (flexpath_reader_file *)msg->reader_file;
+ CMCondition_signal(cm, fp->go_cond);
+}
+
/*
* Gathers basic MPI information; sets up reader CM.
*/
@@ -1140,6 +1662,13 @@ int
adios_read_flexpath_init_method (MPI_Comm comm, PairStruct* params)
{
setenv("CMSelfFormats", "1", 1);
+ // setup ATOMS for attribute lists
+ RANK_ATOM = attr_atom_from_string(FP_RANK_ATTR_NAME);
+ TIMESTEP_ATOM = attr_atom_from_string(FP_TIMESTEP);
+ SCALAR_ATOM = attr_atom_from_string(FP_ONLY_SCALARS);
+ NATTRS = attr_atom_from_string(FP_NATTRS);
+ CM_TRANSPORT = attr_atom_from_string("CM_TRANSPORT");
+
fp_read_data = malloc(sizeof(flexpath_read_data));
if (!fp_read_data) {
adios_error(err_no_memory, "Cannot allocate memory for flexpath.");
@@ -1147,7 +1676,6 @@ adios_read_flexpath_init_method (MPI_Comm comm, PairStruct* params)
}
memset(fp_read_data, 0, sizeof(flexpath_read_data));
- fp_read_data->CM_TRANSPORT = attr_atom_from_string("CM_TRANSPORT");
attr_list listen_list = NULL;
char * transport = NULL;
transport = getenv("CMTransport");
@@ -1170,7 +1698,7 @@ adios_read_flexpath_init_method (MPI_Comm comm, PairStruct* params)
}
} else {
listen_list = create_attr_list();
- add_attr(listen_list, fp_read_data->CM_TRANSPORT, Attr_String,
+ add_attr(listen_list, CM_TRANSPORT, Attr_String,
(attr_value)strdup(transport));
CMlisten_specific(fp_read_data->cm, listen_list);
}
@@ -1179,6 +1707,8 @@ adios_read_flexpath_init_method (MPI_Comm comm, PairStruct* params)
fprintf(stderr, "reader %d failed to fork comm_thread.\n", fp_read_data->rank);
/*log_debug( "forked\n");*/
}
+ CMFormat format = CMregister_simple_format(fp_read_data->cm, "Flexpath reader go", reader_go_field_list, sizeof(reader_go_msg));
+ CMregister_handler(format, reader_go_handler, NULL);
return 0;
}
@@ -1191,6 +1721,34 @@ adios_read_flexpath_open_file(const char * fname, MPI_Comm comm)
return NULL;
}
+char *
+get_writer_contact_info_filesystem(const char *fname, flexpath_reader_file * fp)
+{
+ char writer_info_filename[200];
+
+ sprintf(writer_info_filename, "%s_%s", fname, WRITER_CONTACT_FILE);
+ FILE *fp_in;
+ fp_verbose(fp, "Looking for writer contact in file %s\n", writer_info_filename);
+redo:
+ fp_in = fopen(writer_info_filename, "r");
+ while (!fp_in) {
+ CMusleep(fp_read_data->cm, 500);
+ fp_in = fopen(writer_info_filename, "r");
+ }
+ struct stat buf;
+ fstat(fileno(fp_in), &buf);
+ int size = buf.st_size;
+ if(size == 0) {
+ fp_verbose(fp, "Size of writer contact file is zero, but it shouldn't be! Retrying!\n");
+ goto redo;
+ }
+
+ char *buffer = calloc(1, size + 1);
+ int temp = fread(buffer, size, 1, fp_in);
+ fclose(fp_in);
+ return buffer;
+}
+
/*
* Still have work to do here.
* Change it so that we can support the timeouts and lock_modes.
@@ -1209,6 +1767,7 @@ adios_read_flexpath_open(const char * fname,
enum ADIOS_LOCKMODE lock_mode,
float timeout_sec)
{
+ int i;
ADIOS_FILE *adiosfile = malloc(sizeof(ADIOS_FILE));
if (!adiosfile) {
adios_error (err_no_memory,
@@ -1217,174 +1776,164 @@ adios_read_flexpath_open(const char * fname,
}
flexpath_reader_file *fp = new_flexpath_reader_file(fname);
- fp_verbose(fp, "entering flexpath_open\n");
fp->host_language = futils_is_called_from_fortran();
adios_errno = 0;
- fp->stone = EValloc_stone(fp_read_data->cm);
+ fp->terminal_stone = EValloc_stone(fp_read_data->cm);
+ fp->feedback_bridge = -1;
fp->comm = comm;
+
+ adiosfile->fh = (uint64_t)fp;
+ adiosfile->current_step = 0;
MPI_Comm_size(fp->comm, &(fp->size));
MPI_Comm_rank(fp->comm, &(fp->rank));
- EVassoc_terminal_action(fp_read_data->cm,
- fp->stone,
- op_format_list,
- op_msg_handler,
- adiosfile);
-
- EVassoc_terminal_action(fp_read_data->cm,
- fp->stone,
- update_step_msg_format_list,
- update_step_msg_handler,
- adiosfile);
-
+ fp_verbose(fp, "entering flexpath_open\n");
EVassoc_terminal_action(fp_read_data->cm,
- fp->stone,
+ fp->terminal_stone,
evgroup_format_list,
group_msg_handler,
adiosfile);
+ EVassoc_terminal_action(fp_read_data->cm,
+ fp->terminal_stone,
+ finalize_close_msg_format_list,
+ finalize_msg_handler,
+ adiosfile);
+
EVassoc_raw_terminal_action(fp_read_data->cm,
- fp->stone,
+ fp->terminal_stone,
raw_handler,
adiosfile);
- /* Gather the contact info from the other readers
- and write it to a file. Create a ready file so
- that the writer knows it can parse this file. */
- char writer_ready_filename[200];
- char writer_info_filename[200];
- char reader_ready_filename[200];
- char reader_info_filename[200];
-
- sprintf(reader_ready_filename, "%s_%s", fname, READER_READY_FILE);
- sprintf(reader_info_filename, "%s_%s", fname, READER_CONTACT_FILE);
- sprintf(writer_ready_filename, "%s_%s", fname, WRITER_READY_FILE);
- sprintf(writer_info_filename, "%s_%s", fname, WRITER_CONTACT_FILE);
-
char *string_list;
- char data_contact_info[CONTACT_LENGTH];
+ char data_contact_info[CONTACT_LENGTH] = {0};
string_list = attr_list_to_string(CMget_contact_list(fp_read_data->cm));
- sprintf(&data_contact_info[0], "%d:%s", fp->stone, string_list);
+ sprintf(&data_contact_info[0], "%d:%s", fp->terminal_stone, string_list);
free(string_list);
+ //volatile int qur = 0;
+ //while(qur == 0) { /*Change qur in debugger */ }
+ //MPI_Barrier(MPI_COMM_WORLD);
char * recvbuf;
if (fp->rank == 0) {
+ char *contact_info;
recvbuf = (char*)malloc(sizeof(char)*CONTACT_LENGTH*(fp->size));
- }
-
- MPI_Gather(data_contact_info, CONTACT_LENGTH, MPI_CHAR, recvbuf,
- CONTACT_LENGTH, MPI_CHAR, 0, fp->comm);
-
- if (fp->rank == 0) {
- // print our own contact information
- FILE * fp_out = fopen(reader_info_filename, "w");
- int i;
- if (!fp_out) {
- adios_error(err_file_open_error,
- "File for contact info could not be opened for writing.\n");
- exit(1);
- }
+ fp_verbose(fp, "Running MPI_Gather for reader contact information!\n");
+ MPI_Gather(data_contact_info, CONTACT_LENGTH, MPI_CHAR, recvbuf,
+ CONTACT_LENGTH, MPI_CHAR, 0, fp->comm);
+
+ contact_info = get_writer_contact_info_filesystem(fname, fp);
+
+ char in_contact[CONTACT_LENGTH] = "";
+ int num_bridges = 0;
+ int their_stone;
+ int return_condition;
+
+ char *send_buffer = malloc(CONTACT_LENGTH);
+ void *writer_filedata;
+ char *point = contact_info;
+ //fprintf(stderr, "%s", point);
+ sscanf(point, "%d\n", &return_condition);
+ point = index(point, '\n') + 1;
+ sscanf(point, "%p\n", &writer_filedata);
+ point = index(point, '\n') + 1;
+ while (*point != '\0') {
+ //printf("Point: %s\nInputNewLineAbove\n", point);
+ sscanf(point, "%d:%[^\t\n]", &their_stone, in_contact);
+ point = index(point, '\n'); if (point) point++;
+ fp->bridges = realloc(fp->bridges,
+ sizeof(bridge_info) * (num_bridges+1));
+ send_buffer = realloc(send_buffer, (num_bridges+1)*CONTACT_LENGTH);
+ fp->bridges[num_bridges].remote_stone_ID = their_stone;
+ fp->bridges[num_bridges].contact = strdup(in_contact);
+ sprintf(&send_buffer[num_bridges*CONTACT_LENGTH], "%d:%s", their_stone, in_contact);
+ fp->bridges[num_bridges].created = 0;
+ fp->bridges[num_bridges].step = 0;
+ fp->bridges[num_bridges].opened = 0;
+ fp->bridges[num_bridges].scheduled = 0;
+ num_bridges++;
+ //printf("Num_bridges: %d\n", num_bridges);
+ }
+ fp->num_bridges = num_bridges;
+ free(contact_info);
+
+ // broadcast writer contact info to all reader ranks
+ fp_verbose(fp, "Broadcasting writer data to all ranks!\n");
+ MPI_Bcast(&fp->num_bridges, 1, MPI_INT, 0, MPI_COMM_WORLD);
+
+ MPI_Bcast(send_buffer, fp->num_bridges*CONTACT_LENGTH, MPI_CHAR, 0, MPI_COMM_WORLD);
+
+ // prepare to send all ranks contact info to writer root
+ reader_register_msg reader_register;
+ reader_register.condition = return_condition;
+ reader_register.writer_file = (uint64_t) writer_filedata;
+ reader_register.reader_file = (uint64_t) fp;
+ reader_register.contact_count = fp->size;
+ reader_register.contacts = malloc(fp->size * sizeof(char*));
for (i=0; i<fp->size; i++) {
- fprintf(fp_out,"%s\n", &recvbuf[i*CONTACT_LENGTH]);
+ reader_register.contacts[i] = &recvbuf[i*CONTACT_LENGTH];
}
- fclose(fp_out);
- free(recvbuf);
- FILE * read_ready = fopen(reader_ready_filename, "w");
- fprintf(read_ready, "ready");
- fclose(read_ready);
- }
- fp_verbose(fp, "waiting on First barrier in OPEN\n");
- MPI_Barrier(fp->comm);
- fp_verbose(fp, "done with First barrier in OPEN\n");
+ CMFormat format = CMregister_simple_format(fp_read_data->cm, "Flexpath reader register", reader_register_field_list, sizeof(reader_register_msg));
+ attr_list writer_rank0_contact = attr_list_from_string(fp->bridges[0].contact);
+ CMConnection conn = CMget_conn (fp_read_data->cm, writer_rank0_contact);
+ fp->go_cond = CMCondition_get(fp_read_data->cm, conn);
+ CMwrite(conn, format, &reader_register);
+
+ /* wait for "go" from writer */
+ fp_verbose(fp, "waiting for go message in read_open, WAITING, condition %d\n", fp->go_cond);
+ CMCondition_wait(fp_read_data->cm, fp->go_cond);
+ fp_verbose(fp, "finished wait for go message in read_open\n");
+ //Cleanup
+ free(send_buffer);
+ free(reader_register.contacts);
+ free(recvbuf);
+ free_attr_list(writer_rank0_contact);
- FILE * fp_in = fopen(writer_ready_filename,"r");
- while (!fp_in) {
- //CMsleep(fp_read_data->cm, 1);
- fp_in = fopen(writer_ready_filename, "r");
+ //CMConnection_close(conn);
+ MPI_Barrier(MPI_COMM_WORLD);
+ } else {
+ /* not rank 0 */
+ fp_verbose(fp, "About to run the normal setup for bridges before MPI_Gather operation!\n");
+ char *this_side_contact_buffer;
+ MPI_Gather(data_contact_info, CONTACT_LENGTH, MPI_CHAR, recvbuf,
+ CONTACT_LENGTH, MPI_CHAR, 0, fp->comm);
+ MPI_Bcast(&fp->num_bridges, 1, MPI_INT, 0, MPI_COMM_WORLD);
+ this_side_contact_buffer = malloc(fp->num_bridges*CONTACT_LENGTH);
+ MPI_Bcast(this_side_contact_buffer, fp->num_bridges*CONTACT_LENGTH, MPI_CHAR, 0, MPI_COMM_WORLD);
+ fp->bridges = malloc(sizeof(bridge_info) * fp->num_bridges);
+ for (i = 0; i < fp->num_bridges; i++) {
+ int their_stone;
+ char in_contact[CONTACT_LENGTH];
+ sscanf(&this_side_contact_buffer[i*CONTACT_LENGTH], "%d:%s", &their_stone, in_contact);
+ fp->bridges[i].remote_stone_ID = their_stone;
+ fp->bridges[i].contact = strdup(in_contact);
+ fp->bridges[i].created = 0;
+ fp->bridges[i].step = 0;
+ fp->bridges[i].opened = 0;
+ fp->bridges[i].scheduled = 0;
+ }
+ MPI_Barrier(MPI_COMM_WORLD);
+ fp_verbose(fp, "Past the MPI_Barrier on the non-root side\n");
}
- fclose(fp_in);
- fp_in = fopen(writer_info_filename, "r");
- while (!fp_in) {
- //CMsleep(fp_read_data->cm, 1);
- fp_in = fopen(writer_info_filename, "r");
- }
-
- char in_contact[CONTACT_LENGTH] = "";
- //fp->bridges = malloc(sizeof(bridge_info));
- int num_bridges = 0;
- int their_stone;
-
- // change to read all numbers, dont create stones, turn bridge array into linked list
- while (fscanf(fp_in, "%d:%s", &their_stone, in_contact) != EOF) {
- //fprintf(stderr, "writer contact: %d:%s\n", their_stone, in_contact);
- fp->bridges = realloc(fp->bridges,
- sizeof(bridge_info) * (num_bridges+1));
- fp->bridges[num_bridges].their_num = their_stone;
- fp->bridges[num_bridges].contact = strdup(in_contact);
- fp->bridges[num_bridges].created = 0;
- fp->bridges[num_bridges].step = 0;
- fp->bridges[num_bridges].opened = 0;
- fp->bridges[num_bridges].scheduled = 0;
- num_bridges++;
- }
- fclose(fp_in);
- fp->num_bridges = num_bridges;
- // clean up of writer's files
- fp_verbose(fp, "waiting on second barrier in OPEN\n");
- MPI_Barrier(fp->comm);
- fp_verbose(fp, "done with second barrier in OPEN\n");
- if (fp->rank == 0) {
- unlink(writer_info_filename);
- unlink(writer_ready_filename);
- }
- adiosfile->fh = (uint64_t)fp;
- adiosfile->current_step = 0;
+ //EVstore Setup
- /* Init with a writer to get initial scalar
- data so we can handle inq_var calls and
- also populate the ADIOS_FILE struct. */
- if (fp->size < num_bridges) {
- int mystart = (num_bridges/fp->size) * fp->rank;
- int myend = (num_bridges/fp->size) * (fp->rank+1);
- fp->writer_coordinator = mystart;
- int z;
- for (z=mystart; z<myend; z++) {
- build_bridge(&fp->bridges[z]);
- }
- }
- else {
- int writer_rank = fp->rank % num_bridges;
- build_bridge(&fp->bridges[writer_rank]);
- fp->writer_coordinator = writer_rank;
- }
+ fp_verbose(fp, "About to lock mutex and access timstep_separated_var_list\n");
// requesting initial data.
- fp_verbose(fp, "sending open msg in read_open\n");
- send_open_msg(fp, fp->writer_coordinator);
+
+ fp_verbose(fp, "Waiting on timestep %d\n", fp->mystep);
+ flexpath_wait_for_global_metadata(fp, fp->mystep);
-
- fp->data_read = 0;
- fp->req.condition = CMCondition_get(fp_read_data->cm, NULL);
- fp->req.num_pending = 1;
- fp->req.num_completed = 0;
- send_flush_msg(fp, fp->writer_coordinator, DATA, 0);
- fp_verbose(fp, "sent flush msg in read_open, WAITING\n");
- CMCondition_wait(fp_read_data->cm, fp->req.condition);
- fp_verbose(fp, "done with WAIT in read_open\n");
-
- send_flush_msg(fp, fp->writer_coordinator, EVGROUP, 1);
+ //Fix the last of the info the reader will need
+ fp_verbose(fp, "Reader now has all of the information to begin scheduling reads for the first timestep\n");
+
fp->data_read = 0;
- // this has to change. Writer needs to have some way of
- // taking the attributes out of the xml document
- // and sending them over ffs encoded. Not yet implemented.
- // the rest of this info for adiosfile gets filled in raw_handler.
- adiosfile->nattrs = 0;
- adiosfile->attr_namelist = NULL;
+
// first step is at least one, otherwise raw_handler will not execute.
// in reality, writer might be further along, so we might have to make
// the writer explitly send across messages each time it calls close, to
@@ -1400,8 +1949,34 @@ adios_read_flexpath_open(const char * fname,
return adiosfile;
}
+extern EVsource
+adios_flexpath_create_feedback_source(ADIOS_FILE *adiosfile, FMStructDescList format_list)
+{
+ flexpath_reader_file *fp = (flexpath_reader_file*)adiosfile->fh;
+ static int first = 1;
+ static atom_t global_stone_ID;
+ if (first) {
+ /*
+ * we don't have a means of assigning these truely "globally", so we'll leverage the 32-bit
+ * atom name hashing mechanisms (which we use in ATL and rely upon to hopefully avoid collisions)
+ */
+ global_stone_ID = attr_atom_from_string("flexpath feedback stone");
+ global_stone_ID |= 0x80000000;
+ first = 0;
+ }
+ if (fp->feedback_bridge == -1) {
+ attr_list contact_list = attr_list_from_string(fp->bridges[0].contact);
+ fp->feedback_bridge = EVcreate_bridge_action(fp_read_data->cm, contact_list,
+ global_stone_ID);
+// free(contact_list);
+ }
+ return EVcreate_submit_handle(fp_read_data->cm, fp->feedback_bridge, format_list);
+}
+
int adios_read_flexpath_finalize_method ()
{
+ /* oddly, ADIOS doesn't let us close a single file. Instead, this finalizes all operations. Commented out below is the body that we should have when we can close a file. */
+
/* flexpath_reader_file *fp = (flexpath_reader_file*)adiosfile->fh; */
/* int i; */
/* for (i=0; i<fp->num_bridges; i++) { */
@@ -1410,148 +1985,96 @@ int adios_read_flexpath_finalize_method ()
/* send_finalize_msg(fp, i); */
/* } */
/* } */
- /* return 1; */
+ return 1;
}
+
+//A lot of the complexity of the underlying linked lists is hidden in the functions
void adios_read_flexpath_release_step(ADIOS_FILE *adiosfile) {
int i;
flexpath_reader_file *fp = (flexpath_reader_file*)adiosfile->fh;
- fp_verbose(fp, "waiting at flexpath_release step barrier\n");
- MPI_Barrier(fp->comm);
- fp_verbose(fp, "done with flexpath_release step barrier\n");
- for (i=0; i<fp->num_bridges; i++) {
- if (fp->bridges[i].created && !fp->bridges[i].opened) {
- fp_verbose(fp, "sending open msg in flexpath_release_step\n");
- send_open_msg(fp, i);
- }
- }
- free_evgroup(fp->gp);
- fp->gp = NULL;
-
- flexpath_var *tmpvars = fp->var_list;
- while (tmpvars) {
-
- if (tmpvars->ndims > 0) {
- free(tmpvars->global_dims);
- tmpvars->ndims = 0;
- }
- if (tmpvars->displ) {
- free_displacements(tmpvars->displ, tmpvars->num_displ);
- tmpvars->displ = NULL;
- }
-
- if (tmpvars->sel) {
- a2sel_free(tmpvars->sel);
- tmpvars->sel = NULL;
- }
-
- tmpvars->sel = NULL;
- for (i=0; i<tmpvars->num_chunks; i++) {
- flexpath_var_chunk *chunk = &tmpvars->chunks[i];
- if (chunk->has_data) {
- free(chunk->data);
- chunk->data = NULL;
- chunk->has_data = 0;
- }
- chunk->rank = 0;
- }
- tmpvars = tmpvars->next;
- }
+ //fp_verbose(fp, "waiting at flexpath_release step barrier\n");
+ //MPI_Barrier(fp->comm);
+ //fp_verbose(fp, "done with flexpath_release step barrier\n");
+
+ pthread_mutex_lock(&(fp->queue_mutex));
+ remove_relevant_global_data(fp, fp->mystep);
+ pthread_mutex_unlock(&(fp->queue_mutex));
+ fp->current_global_info = NULL;
+
+ pthread_mutex_lock(&(fp->queue_mutex));
+ cleanup_flexpath_vars(fp, fp->mystep);
+ pthread_mutex_unlock(&(fp->queue_mutex));
}
int
adios_read_flexpath_advance_step(ADIOS_FILE *adiosfile, int last, float timeout_sec)
{
flexpath_reader_file *fp = (flexpath_reader_file*)adiosfile->fh;
- fp_verbose(fp, " waiting on first barrier in flexpath_advance_step:step:%d\n", fp->mystep);
+ fp_verbose(fp, "Entering Flexpath Advance Step!\n");
MPI_Barrier(fp->comm);
- fp_verbose(fp, " wait complete in flexpath_advance_step:step:%d\n", fp->mystep);
- int count = 0; // for perf measurements
- fp_verbose(fp, "advance_step:sending flush step to coordinator:%d:step:%d\n", fp->writer_coordinator,fp->mystep);
- send_flush_msg(fp, fp->writer_coordinator, STEP, 1);
- //fprintf(stderr, "reader_rank:%d:advance_step:advance_step:after sending flush step to:%d:step:%d\n", fp->writer_coordinator,fp->mystep);
- //put this on a timer, so to speak, for timeout_sec
- while (fp->mystep == fp->last_writer_step) {
- if (fp->writer_finalized) {
- adios_errno = err_end_of_stream;
- return err_end_of_stream;
- }
- CMsleep(fp_read_data->cm, 1);
- fp_verbose(fp, "advance_step:while loop sending flush step to coordinator:%d:step:%d\n", fp->writer_coordinator,fp->mystep);
- send_flush_msg(fp, fp->writer_coordinator, STEP, 1);
- //fprintf(stderr, "reader_rank:%d:advance_step:after while loop sending flush step to coordinator:%d:step:%d\n", fp->writer_coordinator,fp->mystep);
+ int count = 0;
+
+ fp->mystep++;
+
+ adiosfile->current_step = fp->mystep;
+ adiosfile->last_step = adiosfile->current_step;
+
+ //Check to see if we have the next steps global metadata
+ fp_verbose(fp, "Waiting for global metadata in timestep:%d\n", fp->mystep);
+ flexpath_wait_for_global_metadata(fp, fp->mystep);
+
+ //If finalized, err_end_of_stream
+ if(fp->last_writer_step == fp->mystep)
+ {
+ fp_verbose(fp, "Received the writer_finalized message! Reader returning err_end_of_stream!\n");
+ adios_errno = err_end_of_stream;
+ return err_end_of_stream;
}
- int i=0;
- for (i=0; i<fp->num_bridges; i++) {
- if (fp->bridges[i].created && fp->bridges[i].opened) {
- count++;
- send_close_msg(fp, i);
- }
+ //Remove obsolete bookeeping information and update current_global_info
+ pthread_mutex_lock(&(fp->queue_mutex));
+
+ int global_data_cleaned = remove_relevant_global_data(fp, fp->mystep - 1);
+ int flexpath_var_cleaned = cleanup_flexpath_vars(fp, fp->mystep - 1);
+ if(!fp->current_global_info)
+ {
+ fprintf(stderr, "Severe logic error!\n");
+ exit(1);
}
- fp_verbose(fp, "waiting on second barrier in flexpath_advance_step:step:%d\n", fp->mystep);
- MPI_Barrier(fp->comm);
- fp_verbose(fp, "done with second barrier in flexpath_advance_step:step:%d\n", fp->mystep);
+ fp_verbose(fp, "Cleaned the global data and the flexpath vars!\n"
+ "Global metadata removed: %d\t\tFlexpath vars removed: %d\n", global_data_cleaned, flexpath_var_cleaned);
+ pthread_mutex_unlock(&(fp->queue_mutex));
- count = 0;
- adiosfile->current_step++;
- fp->mystep = adiosfile->current_step;
+ //Fix the last of the info the reader will need, this locks and unlocks the mutex so that's why we have it out here
+
+ //Wait for all readers to reach this step, this should change in extended version
+ //MPI_Barrier(fp->comm);
- for (i=0; i<fp->num_bridges; i++) {
- if (fp->bridges[i].created && !fp->bridges[i].opened) {
- fp_verbose(fp, "sending open msg in flexpath_advance_step\n");
- send_open_msg(fp, i);
- count++;
- }
- }
- // need to remove selectors from each var now.
- fp->req.num_completed = 0;
- fp->req.num_pending = 1;
- fp->req.condition = CMCondition_get(fp_read_data->cm, NULL);
- fp_verbose(fp, "advance_step: sending flush DATA to coordinator, then WAITING:%d:step:%d\n", fp->writer_coordinator,fp->mystep);
- send_flush_msg(fp, fp->writer_coordinator, DATA, 0);
- CMCondition_wait(fp_read_data->cm, fp->req.condition);
- fp_verbose(fp, "advance_step:Condition wait is complete:%d:step:%d\n", fp->writer_coordinator,fp->mystep);
- // should only happen if there are more steps available.
- // writer should have advanced.
- fp_verbose(fp, "advance_step: sending flush EVGROUP to coordinator:%d:step:%d\n", fp->writer_coordinator,fp->mystep);
- send_flush_msg(fp, fp->writer_coordinator, EVGROUP, 1);
- //fprintf(stderr, "reader_rank:%d:advance_step:while loop after flush EVGROUP to coordinator:%d:step:%d\n", fp->writer_coordinator,fp->mystep);
return 0;
}
int adios_read_flexpath_close(ADIOS_FILE * fp)
{
flexpath_reader_file *file = (flexpath_reader_file*)fp->fh;
- //send to each opened link
- int i;
- for (i = 0; i<file->num_bridges; i++) {
- if (file->bridges[i].created && file->bridges[i].opened) {
- send_close_msg(file, i);
- }
- }
+
+ MPI_Barrier(file->comm);
+
+
+ send_finalize_msg(file);
+
/*
- start to cleanup. Clean up var_lists for now, as the
+ Clean up everything, as the
data has already been copied over to ADIOS_VARINFO structs
that the user maintains a copy of.
*/
- flexpath_var *v = file->var_list;
- while (v) {
- // free chunks; data has already been copied to user
- int i;
- for (i = 0; i<v->num_chunks; i++) {
- flexpath_var_chunk *c = &v->chunks[i];
- if (!c)
- log_error("FLEXPATH: %s This should not happen! line %d\n",__func__,__LINE__);
- //free(c->data);
- c->data = NULL;
- free(c);
- }
- flexpath_var *tmp = v->next;
- free(v);
- v = tmp;
- //v=v->next;
- }
+
+ flexpath_free_filedata(file);
+ CManager_close(fp_read_data->cm);
+
+ //Cleaning the ADIOS FILE
+
+
return 0;
}
@@ -1590,42 +2113,54 @@ int adios_read_flexpath_perform_reads(const ADIOS_FILE *adiosfile, int blocking)
int num_sendees = fp->num_sendees;
int total_sent = 0;
fp->time_in = 0.00;
- fp->req.num_completed = 0;
- fp->req.num_pending = FP_BATCH_SIZE;
- fp->req.condition = CMCondition_get(fp_read_data->cm, NULL);
+
+ timestep_separated_lists * curr_var_list = flexpath_get_curr_timestep_list(fp);
+
+ curr_var_list->req_cond.num_completed = 0;
+ curr_var_list->req_cond.num_pending = num_sendees < FP_BATCH_SIZE ? num_sendees : FP_BATCH_SIZE;
+ curr_var_list->req_cond.condition = CMCondition_get(fp_read_data->cm, NULL);
+
for (i = 0; i<num_sendees; i++) {
- int sendee = fp->sendees[i];
- batchcount++;
- total_sent++;
/* fprintf(stderr, "reader rank:%d:flush_data to writer:%d:of:%d:step:%d:batch:%d:total_sent:%d\n", */
/* fp->rank, sendee, num_sendees, fp->mystep, batchcount, total_sent); */
- send_flush_msg(fp, sendee, DATA, 0);
+ send_read_msg(fp, i, 0);
+ total_sent++;
if ((total_sent % FP_BATCH_SIZE == 0) || (total_sent == num_sendees)) {
- fp->req.num_pending = batchcount;
-
- fp_verbose(fp, "in perform_reads, blocking on:%d:step:%d\n", fp->req.condition, fp->mystep);
- CMCondition_wait(fp_read_data->cm, fp->req.condition);
- fp_verbose(fp, "after blocking:%d:step:%d\n", fp->req.condition, fp->mystep);
- fp->req.num_completed = 0;
- //fp->req.num_pending = 0;
- //total_sent = 0;
- batchcount = 0;
- fp->req.condition = CMCondition_get(fp_read_data->cm, NULL);
+
+ fp_verbose(fp, "in perform_reads, blocking on:%d:step:%d\n", curr_var_list->req_cond.condition, fp->mystep);
+ CMCondition_wait(fp_read_data->cm, curr_var_list->req_cond.condition);
+ fp_verbose(fp, "after blocking:%d:step:%d\n", curr_var_list->req_cond.condition, fp->mystep);
+ curr_var_list->req_cond.num_completed = 0;
+ curr_var_list->req_cond.condition = CMCondition_get(fp_read_data->cm, NULL);
+ int amount_left = num_sendees - total_sent;
+ if (amount_left > 0)
+ {
+ curr_var_list->req_cond.num_pending = amount_left < FP_BATCH_SIZE ? amount_left : FP_BATCH_SIZE;
+ }
}
}
+ //Immediate_cleanup of sendee information
free(fp->sendees);
fp->sendees = NULL;
+
+ //Cleanup read_request_messages!
+ flexpath_free_read_requests(fp->num_sendees, fp->var_read_requests);
+ fp->var_read_requests = NULL;
fp->num_sendees = 0;
- flexpath_var *tmpvars = fp->var_list;
+
+ //Get the current var_list
+ //TODO: call single function instead
+ //timestep_separated_lists * curr_var_list = flexpath_get_curr_timestep_list(fp);
+ flexpath_var *tmpvars = curr_var_list->var_list;
+
while (tmpvars) {
if (tmpvars->displ) {
- free_displacements(tmpvars->displ, tmpvars->num_displ);
- tmpvars->displ = NULL;
+ flexpath_free_displacements(&(tmpvars->displ), tmpvars->num_displ);
}
if (tmpvars->sel) {
@@ -1661,11 +2196,13 @@ adios_read_flexpath_schedule_read_byid(const ADIOS_FILE *adiosfile,
void *data)
{
flexpath_reader_file *fp = (flexpath_reader_file*)adiosfile->fh;
- flexpath_var *fpvar = fp->var_list;
+ fp_verbose(fp, "Entering schedule_read_by_id\n");
+ timestep_separated_lists * curr_var_list = flexpath_get_curr_timestep_list(fp);
+ flexpath_var *fpvar = curr_var_list->var_list;
- fp_verbose(fp, "entering schedule_read_byid\n");
+ fp_verbose(fp, "entering schedule_read_byid, varid %d\n", varid);
while (fpvar) {
- if (fpvar->id == varid)
+ if ((!fpvar->is_attr) && (fpvar->id == varid))
break;
else
fpvar=fpvar->next;
@@ -1676,12 +2213,13 @@ adios_read_flexpath_schedule_read_byid(const ADIOS_FILE *adiosfile,
varid);
return err_invalid_varid;
}
+
//store the user allocated buffer.
flexpath_var_chunk *chunk = &fpvar->chunks[0];
if (nsteps != 1) {
adios_error (err_invalid_timestep,
"Only one step can be read from a stream at a time. "
- "You requested % steps in adios_schedule_read()\n",
+ "You requested %d steps in adios_schedule_read()\n",
nsteps);
return err_invalid_timestep;
}
@@ -1711,19 +2249,25 @@ adios_read_flexpath_schedule_read_byid(const ADIOS_FILE *adiosfile,
chunk->user_buf = data;
fpvar->start_position = 0;
int writer_index = fpvar->sel->u.block.index;
- if (writer_index > fp->num_bridges) {
+ if (writer_index >= fp->num_bridges) {
adios_error(err_out_of_bound,
"No process exists on the writer side matching the index.\n");
return err_out_of_bound;
}
- send_var_message(fp, writer_index, fpvar->varname);
+ fp_verbose(fp, "Adding var to read message for ADIOS_SELECTION_WRITEBLOCK for writer_index: %d\n", writer_index);
+ add_var_to_read_message(fp, writer_index, fpvar->varname);
break;
}
case ADIOS_SELECTION_BOUNDINGBOX:
{
// boundingbox for a scalar; handle it as we do with inq_var
if (fpvar->ndims == 0) {
- memcpy(data, chunk->data, fpvar->type_size);
+ if (chunk->has_data) {
+ memcpy(data, chunk->data, fpvar->type_size);
+ fp_verbose(fp, "Grabbing scalar data immediately, no need for message!\n");
+ } else {
+ printf("Trying to schedule read on scalar %s, no data fpvar %p, chunk %p\n", fpvar->varname, fpvar, chunk);
+ }
} else {
if (fp->host_language == FP_FORTRAN_MODE) {
reverse_dims(sel->u.bb.start, sel->u.bb.ndim);
@@ -1731,20 +2275,20 @@ adios_read_flexpath_schedule_read_byid(const ADIOS_FILE *adiosfile,
}
chunk->user_buf = data;
fpvar->start_position = 0;
- free_displacements(fpvar->displ, fpvar->num_displ);
- fpvar->displ = NULL;
+ flexpath_free_displacements(&(fpvar->displ), fpvar->num_displ);
int j=0;
int need_count = 0;
array_displacements *all_disp = NULL;
uint64_t pos = 0;
for (j=0; j<fp->num_bridges; j++) {
int destination=0;
- if (need_writer(fp, j, fpvar->sel, fp->gp, fpvar->varname)==1) {
- //printf("\t\trank: %d need_writer: %d\n", fp->rank, j);
+ evgroup * the_gp = fp->current_global_info;
+ if (need_writer(fp, j, fpvar->sel, the_gp, fpvar->varname)==1) {
+ /* fprintf(stderr, "\t\trank: %d need_writer: %d\n", fp->rank, j); */
uint64_t _pos = 0;
need_count++;
destination = j;
- global_var *gvar = find_gbl_var(fp->gp->vars, fpvar->varname, fp->gp->num_vars);
+ global_var *gvar = find_gbl_var(the_gp->vars, fpvar->varname, the_gp->num_vars);
// displ is freed in release_step.
array_displacements *displ = get_writer_displacements(j, fpvar->sel, gvar, &_pos);
displ->pos = pos;
@@ -1752,10 +2296,23 @@ adios_read_flexpath_schedule_read_byid(const ADIOS_FILE *adiosfile,
pos += _pos;
all_disp = realloc(all_disp, sizeof(array_displacements)*need_count);
+ //TODO: Figure this out with Greg...
all_disp[need_count-1] = *displ;
- send_var_message(fp, j, fpvar->varname);
+ fp_verbose(fp, "Adding var to read message for ADIOS_SELECTION_BOUNDINGBOX for writer: %d\n", j);
+ add_var_to_read_message(fp, j, fpvar->varname);
+ //free displ
+ if(displ) {
+ //if(displ->start) free(displ->start);
+ //if(displ->count) free(displ->count);
+ free(displ);
+ }
}
}
+ if (all_disp == NULL) {
+ adios_error(err_operation_not_supported,
+ "Selection does not match data written by any writer.");
+ return 1;
+ }
fpvar->displ = all_disp;
fpvar->num_displ = need_count;
}
@@ -1774,7 +2331,7 @@ adios_read_flexpath_schedule_read_byid(const ADIOS_FILE *adiosfile,
break;
}
}
- fp_verbose(fp, "entering schedule_read_byid\n");
+ fp_verbose(fp, "exiting schedule_read_byid\n");
return 0;
}
@@ -1786,23 +2343,46 @@ adios_read_flexpath_schedule_read(const ADIOS_FILE *adiosfile,
int nsteps,
void * data)
{
- fprintf(stderr, "schedule_read is called\n");
- return 0;
+ flexpath_reader_file *fp = (flexpath_reader_file*)adiosfile->fh;
+ fp_verbose(fp, "entering schedule_read, var: %s\n", varname);
+ timestep_separated_lists * curr_var_list = flexpath_get_curr_timestep_list(fp);
+
+ flexpath_var *fpvar = find_fp_var(curr_var_list->var_list, varname);
+
+ if (!fpvar) {
+ adios_error(err_invalid_varid,
+ "Invalid variable id: %s\n",
+ varname);
+ return err_invalid_varid;
+ }
+
+ int id = fpvar->id;
+
+ fp_verbose(fp, "Calling read_by_id, var: %d\n", id);
+ return adios_read_flexpath_schedule_read_byid(adiosfile, sel, id, from_steps, nsteps, data);
}
int
-adios_read_flexpath_get_attr (int *gp, const char *attrname,
+adios_read_flexpath_get_attr (const ADIOS_FILE *adiosfile, const char *attrname,
enum ADIOS_DATATYPES *type,
int *size, void **data)
{
- //log_debug( "debug: adios_read_flexpath_get_attr\n");
- // TODO: borrowed from dimes
- adios_error(err_invalid_read_method,
- "adios_read_flexpath_get_attr is not implemented.");
- *size = 0;
- *type = adios_unknown;
- *data = 0;
- return adios_errno;
+ flexpath_reader_file *fp = (flexpath_reader_file*)adiosfile->fh;
+ timestep_separated_lists * curr_var_list = flexpath_get_curr_timestep_list(fp);
+
+ flexpath_var *fpvar = find_fp_attr(curr_var_list->var_list, attrname);
+
+ if (!fpvar) {
+ adios_error(err_invalid_attrid,
+ "Invalid attribute id: %s\n",
+ attrname);
+ return err_invalid_attrid;
+ }
+
+ *type = fpvar->type;
+ *size = fpvar->type_size;
+ *data = fpvar->chunks[0].data;
+ return 0;
}
int
@@ -1810,14 +2390,17 @@ adios_read_flexpath_get_attr_byid (const ADIOS_FILE *adiosfile, int attrid,
enum ADIOS_DATATYPES *type,
int *size, void **data)
{
-// log_debug( "debug: adios_read_flexpath_get_attr_byid\n");
- // TODO: borrowed from dimes
- adios_error(err_invalid_read_method,
- "adios_read_flexpath_get_attr_byid is not implemented.");
- *size = 0;
- *type = adios_unknown;
- *data = 0;
- return adios_errno;
+ flexpath_reader_file *fp = (flexpath_reader_file*)adiosfile->fh;
+ if (attrid >= 0 && attrid < adiosfile->nattrs) {
+ int ret = adios_read_flexpath_get_attr(adiosfile, adiosfile->attr_namelist[attrid],
+ type, size, data);
+ //fp_verbose(fp, "leaving flexpath_inq_attr_byid\n");
+ return ret;
+ }
+ else {
+ adios_error(err_invalid_attrid, "FLEXPATH method: Cannot find attr %d\n", attrid);
+ return adios_errno;
+ }
}
ADIOS_VARINFO*
@@ -1826,8 +2409,11 @@ adios_read_flexpath_inq_var(const ADIOS_FILE * adiosfile, const char* varname)
flexpath_reader_file *fp = (flexpath_reader_file*)adiosfile->fh;
ADIOS_VARINFO *v = NULL;
- fp_verbose(fp, "entering flexpath_inq_var\n");
- flexpath_var *fpvar = find_fp_var(fp->var_list, varname);
+ fp_verbose(fp, "entering flexpath_inq_var, varname: %s\n", varname);
+
+ timestep_separated_lists * ts_var_list = flexpath_get_curr_timestep_list(fp);
+ flexpath_var *fpvar = find_fp_var(ts_var_list->var_list, varname);
+
if (fpvar) {
v = calloc(1, sizeof(ADIOS_VARINFO));
@@ -1850,10 +2436,10 @@ ADIOS_VARINFO*
adios_read_flexpath_inq_var_byid (const ADIOS_FILE * adiosfile, int varid)
{
flexpath_reader_file *fp = (flexpath_reader_file*)adiosfile->fh;
- fp_verbose(fp, "entering flexpath_inq_var_byid\n");
+ //fp_verbose(fp, "entering flexpath_inq_var_byid, varid: %d\n", varid);
if (varid >= 0 && varid < adiosfile->nvars) {
ADIOS_VARINFO *v = adios_read_flexpath_inq_var(adiosfile, adiosfile->var_namelist[varid]);
- fp_verbose(fp, "leaving flexpath_inq_var_byid\n");
+ //fp_verbose(fp, "leaving flexpath_inq_var_byid\n");
return v;
}
else {
diff --git a/src/transforms/Makefile.plugins b/src/transforms/Makefile.plugins
index 819100c..7d55b8c 100644
--- a/src/transforms/Makefile.plugins
+++ b/src/transforms/Makefile.plugins
@@ -29,3 +29,11 @@ transforms_read_method_SOURCES += transforms/adios_transform_alacrity_read.c
# zfp plugin:
transforms_write_method_SOURCES += transforms/adios_transform_zfp_write.c
transforms_read_method_SOURCES += transforms/adios_transform_zfp_read.c
+
+# sz plugin:
+transforms_write_method_SOURCES += transforms/adios_transform_sz_write.c
+transforms_read_method_SOURCES += transforms/adios_transform_sz_read.c
+
+# LZ4 plugin:
+transforms_write_method_SOURCES += transforms/adios_transform_lz4_write.c
+transforms_read_method_SOURCES += transforms/adios_transform_lz4_read.c
diff --git a/src/transforms/adios_transform_lz4_common.h b/src/transforms/adios_transform_lz4_common.h
new file mode 100644
index 0000000..bb149b7
--- /dev/null
+++ b/src/transforms/adios_transform_lz4_common.h
@@ -0,0 +1,18 @@
+/*
+ * adios_transform_lz4_common.h
+ *
+ * Author: Rene Widera
+ * contact: r.widera at hzdr.de
+ */
+#ifndef ADIOS_TRANSFORM_LZ4_COMMON_H
+#define ADIOS_TRANSFORM_LZ4_COMMON_H
+
+#include "lz4.h"
+
+/** LZ4 type to define sizes */
+typedef int adiosLz4Size_t;
+
+/** largest allowed input size (in byte) for the native LZ4 compression call */
+#define ADIOS_LZ4_MAX_INPUT_SIZE LZ4_MAX_INPUT_SIZE
+
+#endif /* ADIOS_TRANSFORM_LZ4_COMMON_H */
diff --git a/src/transforms/adios_transform_lz4_read.c b/src/transforms/adios_transform_lz4_read.c
new file mode 100644
index 0000000..a0ec051
--- /dev/null
+++ b/src/transforms/adios_transform_lz4_read.c
@@ -0,0 +1,170 @@
+/*
+ * adios_transform_lz4_read.c
+ *
+ * Author: Rene Widera
+ * Contact: r.widera at hzdr.de
+ *
+ * This code based on `adios_transform_zlib_read.c`.
+ */
+
+#include <stdlib.h>
+#include <stdint.h>
+#include <stdio.h>
+#include <assert.h>
+
+#include "core/util.h"
+#include "core/adios_logger.h"
+#include "core/transforms/adios_transforms_hooks_read.h"
+#include "core/transforms/adios_transforms_reqgroup.h"
+#include "core/adios_internals.h" // adios_get_type_size()
+
+#ifdef LZ4
+
+#include "lz4.h"
+#include "adios_transform_lz4_common.h"
+
+int adios_transform_lz4_is_implemented(void)
+{
+ return 1;
+}
+
+/** decompress lz4 compressed data
+ *
+ * @param stream [in|out] LZ4 decode stream object
+ * @param input_data [in] data to decompress
+ * @param input_len size of the input data (in byte)
+ * @param output_data [out] buffer for the decompressed output
+ * @param max_output_len size of the output buffer (in byte)
+ * @param decoded_byte [out] number of decompressed bytes from the input buffer (can be smaller than input_len)
+ * @return zero (0) if something goes wrong else non zero
+ */
+int adios_transform_lz4_decompress(LZ4_streamDecode_t* stream,
+ const char* input_data,
+ const adiosLz4Size_t input_len,
+ char* output_data,
+ const adiosLz4Size_t max_output_len,
+ adiosLz4Size_t* decoded_byte)
+{
+ assert(stream != NULL &&
+ input_data != NULL &&
+ input_len > 0 &&
+ output_data != NULL &&
+ max_output_len > 0);
+
+
+ adiosLz4Size_t result = LZ4_decompress_fast_continue(stream, input_data, output_data, max_output_len);
+
+ *decoded_byte = 0;
+ if (result > 0)
+ {
+ *decoded_byte = result;
+ }
+
+ return result <= 0;
+}
+
+int adios_transform_lz4_generate_read_subrequests(adios_transform_read_request *reqgroup,
+ adios_transform_pg_read_request *pg_reqgroup)
+{
+ void *buf = malloc(pg_reqgroup->raw_var_length);
+ assert(buf);
+ adios_transform_raw_read_request *subreq = adios_transform_raw_read_request_new_whole_pg(pg_reqgroup, buf);
+ adios_transform_raw_read_request_append(pg_reqgroup, subreq);
+ return 0;
+}
+
+/* Do nothing for individual subrequest */
+adios_datablock * adios_transform_lz4_subrequest_completed(adios_transform_read_request *reqgroup,
+ adios_transform_pg_read_request *pg_reqgroup,
+ adios_transform_raw_read_request *completed_subreq)
+{
+ return NULL;
+}
+
+adios_datablock * adios_transform_lz4_pg_reqgroup_completed(adios_transform_read_request *reqgroup,
+ adios_transform_pg_read_request *completed_pg_reqgroup)
+{
+ uint64_t input_size = (uint64_t) completed_pg_reqgroup->raw_var_length;
+ char* input_buff = (char*) (completed_pg_reqgroup->subreqs->data);
+
+ // number of full chunks
+ adiosLz4Size_t num_chunks = *((adiosLz4Size_t*) completed_pg_reqgroup->transform_metadata);
+ // compressed size of the last chunk
+ adiosLz4Size_t compressed_size_last_chunk = *((adiosLz4Size_t*) (completed_pg_reqgroup->transform_metadata + sizeof (adiosLz4Size_t)));
+
+ // flag to mark compressed data (0 means not compressed)
+ int is_compressed = 1;
+ if (num_chunks == 0 && compressed_size_last_chunk == 0)
+ is_compressed = 0;
+
+ /* size of data after compression */
+ uint64_t uncompressed_size = adios_get_type_size(reqgroup->transinfo->orig_type, "");
+ int d = 0;
+ for (d = 0; d < reqgroup->transinfo->orig_ndim; d++)
+ {
+ uncompressed_size *= (uint64_t) (completed_pg_reqgroup->orig_varblock->count[d]);
+ }
+
+ char* output_buff = (char*) malloc(uncompressed_size);
+ if (!output_buff)
+ {
+ log_error("Out of memory allocating %" PRIu64 " bytes in lz4 transform (read)\n", uncompressed_size);
+ return NULL;
+ }
+
+ LZ4_streamDecode_t lz4StreamDecode_body = {0};
+ LZ4_streamDecode_t* lz4StreamDecode = &lz4StreamDecode_body;
+
+ /* offset inside the input buffer */
+ uint64_t input_offset = 0;
+ /* count decompressed data size */
+ uint64_t actual_output_size = 0;
+
+ adiosLz4Size_t chunk = 0;
+ for (; (chunk < num_chunks || input_offset < input_size) && is_compressed; ++chunk)
+ {
+ const char* in_ptr = input_buff + input_offset;
+ char* out_ptr = output_buff + actual_output_size;
+
+ adiosLz4Size_t max_output_size = ADIOS_LZ4_MAX_INPUT_SIZE;
+ // handle the last not full chunk
+ if (chunk >= num_chunks)
+ max_output_size = uncompressed_size - actual_output_size;
+
+ adiosLz4Size_t max_chunk_size = LZ4_compressBound(max_output_size);
+ adiosLz4Size_t decoded_bytes = 0;
+ int rtn = adios_transform_lz4_decompress(lz4StreamDecode, in_ptr, max_chunk_size,
+ out_ptr, max_output_size, &decoded_bytes);
+ /* abort if decompression failed */
+ if (0 != rtn)
+ {
+ return NULL;
+ }
+ actual_output_size += (uint64_t) max_output_size;
+ input_offset += (uint64_t) decoded_bytes;
+ }
+
+ if (is_compressed == 0)
+ {
+ memcpy(output_buff, input_buff, input_size);
+ actual_output_size = input_size;
+ input_offset += input_size;
+ }
+
+ assert(input_offset == input_size);
+ assert(actual_output_size == uncompressed_size);
+
+ return adios_datablock_new_whole_pg(reqgroup, completed_pg_reqgroup, output_buff);
+}
+
+adios_datablock * adios_transform_lz4_reqgroup_completed(adios_transform_read_request *completed_reqgroup)
+{
+ return NULL;
+}
+
+
+#else
+
+DECLARE_TRANSFORM_READ_METHOD_UNIMPL(lz4);
+
+#endif
diff --git a/src/transforms/adios_transform_lz4_write.c b/src/transforms/adios_transform_lz4_write.c
new file mode 100644
index 0000000..e67a0ba
--- /dev/null
+++ b/src/transforms/adios_transform_lz4_write.c
@@ -0,0 +1,278 @@
+/*
+ * adios_transform_lz4_write.c
+ *
+ * Author: Rene Widera
+ * Contact: r.widera at hzdr.de
+ *
+ * This code based on `adios_transform_zlib_write.c`.
+ */
+
+#include <stdint.h>
+#include <inttypes.h>
+#include <assert.h>
+#include <limits.h>
+#include <sys/time.h>
+
+#include "core/adios_logger.h"
+#include "core/transforms/adios_transforms_common.h"
+#include "core/transforms/adios_transforms_write.h"
+#include "core/transforms/adios_transforms_hooks_write.h"
+#include "core/transforms/adios_transforms_util.h"
+
+#ifdef LZ4
+
+#include <lz4.h>
+#include "adios_transform_lz4_common.h"
+
+
+/** compress data with LZ4
+ *
+ * @param stream [in|out] LZ4 stream object
+ * @param input_data [in] data to compress
+ * @param input_len size of the input data (in byte)
+ * @param output_data [out] buffer for the compressed output
+ * @param max_output_len size of the output buffer (in byte)
+ * @param compressed_size [out] number of bytes after compression
+ * @param compress_level LZ4 compression level
+ * @return zero (0) if something goes wrong else non zero
+ */
+static int adios_transform_lz4_compress(LZ4_stream_t* stream,
+ const char* input_data,
+ const adiosLz4Size_t input_len,
+ char* output_data,
+ const adiosLz4Size_t max_output_len,
+ adiosLz4Size_t* compressed_size,
+ int compress_level)
+{
+ assert(stream != NULL &&
+ input_data != NULL &&
+ input_len > 0 &&
+ output_data != NULL &&
+ max_output_len > 0 &&
+ compressed_size != NULL);
+
+
+ adiosLz4Size_t result = LZ4_compress_fast_continue(stream,
+ input_data,
+ output_data,
+ input_len,
+ max_output_len,
+ compress_level);
+ *compressed_size = 0;
+ if (result > 0)
+ {
+ *compressed_size = result;
+ }
+
+ return result <= 0;
+}
+
+uint16_t adios_transform_lz4_get_metadata_size(struct adios_transform_spec *transform_spec)
+{
+ /* number of chunks with max size and compressed size of the last chunk
+ * if both are zero the data are uncompressed
+ */
+ return (sizeof (adiosLz4Size_t) + sizeof (adiosLz4Size_t));
+}
+
+/** calculate the maximum data overhead for non compressible data
+ *
+ * @param input_size data size in byte of the input data
+ * @param n_full_chunks [out] number of full chunks needed to compress the data (NULL is allowed)
+ * @param max_size_last_chunks [out] maximum size in bytes needed to compress the last not full chunk (NULL is allowed)
+ * @return overhead of bytes for non compressible data
+ */
+uint64_t adios_transform_lz4_max_overhead(const uint64_t input_size, uint64_t* n_full_chunks, uint64_t* max_size_last_chunks)
+{
+ const uint64_t max_input_per_chunk = ADIOS_LZ4_MAX_INPUT_SIZE;
+ const uint64_t num_full_chunks = input_size / max_input_per_chunk;
+ const uint64_t size_last_chunk = input_size % max_input_per_chunk;
+
+ const uint64_t max_output_per_chunk = LZ4_compressBound(ADIOS_LZ4_MAX_INPUT_SIZE);
+ const uint64_t max_output_last_chunk = LZ4_compressBound(size_last_chunk);
+
+ if (n_full_chunks)
+ *n_full_chunks = num_full_chunks;
+ if (max_size_last_chunks)
+ *max_size_last_chunks = max_output_last_chunk;
+
+ const uint64_t full_size = max_output_per_chunk * num_full_chunks + max_output_last_chunk;
+ return full_size - input_size;
+}
+
+void adios_transform_lz4_transformed_size_growth(
+ const struct adios_var_struct *var, const struct adios_transform_spec *transform_spec,
+ uint64_t *constant_factor, double *linear_factor, double *capped_linear_factor, uint64_t *capped_linear_cap)
+{
+ struct adios_var_struct *var_no_const = (struct adios_var_struct *) var;
+ const uint64_t input_size = adios_transform_get_pre_transform_var_size(var_no_const);
+
+ const uint64_t max_overhead = adios_transform_lz4_max_overhead(input_size, NULL, NULL);
+
+ *constant_factor = max_overhead;
+}
+
+int adios_transform_lz4_apply(struct adios_file_struct *fd,
+ struct adios_var_struct *var,
+ uint64_t *transformed_len,
+ int use_shared_buffer,
+ int *wrote_to_shared_buffer)
+{
+ // Assume this function is only called for LZ4 transform type
+ assert(var->transform_type == adios_transform_lz4);
+
+ // Get the input data and data length
+ const uint64_t input_size = adios_transform_get_pre_transform_var_size(var);
+ const char *input_buff = (char*) var->data;
+
+ int compress_level = 1;
+ /* input size under this bound (in byte) would not compressed */
+ uint64_t threshold_size = 128;
+
+ int num_param = var->transform_spec->param_count;
+ int p;
+ for (p = 0; p < num_param; ++p)
+ {
+ /* Which zfp mode to use */
+ const struct adios_transform_spec_kv_pair * const param = &var->transform_spec->params[p];
+ if (strcmp(param->key, "lvl") == 0)
+ {
+ compress_level = atoi(param->value);
+ if (compress_level < 1)
+ compress_level = 1;
+ }
+ else if (strcmp(param->key, "threshold") == 0)
+ {
+ threshold_size = atoi(param->value);
+ if (threshold_size < 128)
+ threshold_size = 128;
+ }
+ else
+ {
+ adios_error(err_invalid_argument, "An unknown LZ4 compression mode '%s' was specified for variable %s. "
+ "Available choices are: lvl, threshold.\n",
+ param->key, var->name);
+ return 0;
+ }
+ }
+ // number of full chunks
+ uint64_t num_chunks = 0;
+ // maximum size for the last not full chunk
+ uint64_t max_size_last_chunk = 0;
+ const uint64_t max_overhead = adios_transform_lz4_max_overhead(input_size, &num_chunks, &max_size_last_chunk);
+
+ // maximum size (in byte) for the full output buffer
+ uint64_t output_size = input_size + max_overhead;
+ char* output_buff = NULL;
+
+ if (use_shared_buffer) // If shared buffer is permitted, serialize to there
+ {
+ *wrote_to_shared_buffer = 1;
+ if (!shared_buffer_reserve(fd, output_size))
+ {
+ log_error("Out of memory allocating %" PRIu64 " bytes for %s for lz4 transform\n", output_size, var->name);
+ return 0;
+ }
+
+ // Write directly to the shared buffer
+ output_buff = (char*) (fd->buffer + fd->offset);
+ }
+ else // Else, fall back to var->adata memory allocation
+ {
+ *wrote_to_shared_buffer = 0;
+ output_buff = (char*) malloc(output_size);
+ if (!output_buff)
+ {
+ log_error("Out of memory allocating %" PRIu64 " bytes for %s for lz4 transform\n", output_size, var->name);
+ return 0;
+ }
+ }
+
+ // temporary data for lz4 stream compression
+ LZ4_stream_t lz4Stream_body = {0};
+ LZ4_stream_t* lz4Stream = &lz4Stream_body;
+
+ uint64_t actual_output_size = 0;
+ uint64_t input_offset = 0;
+
+ int disable_compression = 0;
+ if (input_size < threshold_size)
+ {
+ /* disable compression */
+ disable_compression = 1;
+ }
+
+ adiosLz4Size_t compressed_size_last_chunk = 0;
+ uint64_t chunk = 0;
+ for (; (chunk < num_chunks || input_offset < input_size) && !disable_compression; ++chunk)
+ {
+ adiosLz4Size_t max_intput_size = ADIOS_LZ4_MAX_INPUT_SIZE;
+ // handle the last not full chunk
+ if (chunk >= num_chunks)
+ max_intput_size = input_size - input_offset;
+ adiosLz4Size_t max_chunk_size = LZ4_compressBound(max_intput_size);
+
+ const char* in_ptr = input_buff + input_offset;
+ char* out_ptr = output_buff + actual_output_size;
+
+ adiosLz4Size_t compressed_size = 0;
+ disable_compression = adios_transform_lz4_compress(lz4Stream, in_ptr,
+ max_intput_size,
+ out_ptr, max_chunk_size,
+ &compressed_size,
+ compress_level);
+
+ if (chunk >= num_chunks)
+ compressed_size_last_chunk = compressed_size;
+
+ /* add size to written output data */
+ input_offset += (uint64_t) max_intput_size;
+ actual_output_size += (int64_t) compressed_size;
+ }
+
+ if (!disable_compression)
+ assert(input_offset == input_size);
+
+ if (disable_compression)
+ {
+ memcpy(output_buff, input_buff, input_size);
+ actual_output_size = input_size;
+ }
+
+ // Wrap up, depending on buffer mode
+ if (use_shared_buffer)
+ {
+ shared_buffer_mark_written(fd, actual_output_size);
+ }
+ else
+ {
+ var->adata = output_buff;
+ var->data_size = actual_output_size;
+ var->free_data = adios_flag_yes;
+ }
+
+ if (var->transform_metadata && var->transform_metadata_len > 0)
+ {
+ adiosLz4Size_t n_chunks = num_chunks;
+
+ if (disable_compression)
+ {
+ n_chunks = 0;
+ compressed_size_last_chunk = 0;
+ }
+ /* store number of full chunks */
+ memcpy((char*) var->transform_metadata, &n_chunks, sizeof (adiosLz4Size_t));
+ /* size (in byte) of the last not full chunk */
+ memcpy((char*) var->transform_metadata + sizeof (adiosLz4Size_t), &compressed_size_last_chunk, sizeof (adiosLz4Size_t));
+ }
+
+ // return the size of the data buffer
+ *transformed_len = actual_output_size;
+ return 1;
+}
+
+#else
+
+DECLARE_TRANSFORM_WRITE_METHOD_UNIMPL(lz4)
+
+#endif
diff --git a/src/transforms/adios_transform_sz_read.c b/src/transforms/adios_transform_sz_read.c
new file mode 100644
index 0000000..ce67d03
--- /dev/null
+++ b/src/transforms/adios_transform_sz_read.c
@@ -0,0 +1,122 @@
+#include <stdlib.h>
+#include <stdint.h>
+#include <stdio.h>
+#include <assert.h>
+
+#include "util.h"
+#include "adios_logger.h"
+#include "adios_transforms_hooks_read.h"
+#include "adios_transforms_reqgroup.h"
+
+#ifdef HAVE_SZ
+
+#include "sz.h"
+
+int adios_transform_sz_is_implemented (void) {return 1;}
+
+int adios_transform_sz_generate_read_subrequests(adios_transform_read_request *reqgroup,
+ adios_transform_pg_read_request *pg_reqgroup)
+{
+ //log_debug("function: %s\n", __FUNCTION__);
+ void *buf = malloc(pg_reqgroup->raw_var_length);
+ adios_transform_raw_read_request *subreq = adios_transform_raw_read_request_new_whole_pg(pg_reqgroup, buf);
+ adios_transform_raw_read_request_append(pg_reqgroup, subreq);
+ return 0;
+}
+
+// Do nothing for individual subrequest
+adios_datablock * adios_transform_sz_subrequest_completed(adios_transform_read_request *reqgroup,
+ adios_transform_pg_read_request *pg_reqgroup,
+ adios_transform_raw_read_request *completed_subreq)
+{
+ //log_debug("function: %s\n", __FUNCTION__);
+ return NULL;
+}
+
+
+
+adios_datablock * adios_transform_sz_pg_reqgroup_completed(adios_transform_read_request *reqgroup,
+ adios_transform_pg_read_request *completed_pg_reqgroup)
+{
+ //log_debug("function: %s\n", __FUNCTION__);
+ int raw_size = (int) completed_pg_reqgroup->raw_var_length;
+ unsigned char *raw_buff = completed_pg_reqgroup->subreqs->data;
+
+ // Get type info
+ int dtype;
+ switch (reqgroup->transinfo->orig_type)
+ {
+ case adios_double:
+ dtype = SZ_DOUBLE;
+ break;
+ case adios_real:
+ dtype = SZ_FLOAT;
+ break;
+ default:
+ adios_error(err_transform_failure, "No supported data type\n");
+ return NULL;
+ break;
+ }
+
+ // Get dimension info
+ int ndims = reqgroup->transinfo->orig_ndim;
+ if (ndims > 5)
+ {
+ adios_error(err_transform_failure, "No more than 5 dimension is supported.\n");
+ return NULL;
+ }
+
+ int r[5] = {0,0,0,0,0};
+ int i = 0;
+ for(i = 0; i < ndims; i++)
+ {
+ uint64_t dsize = (uint64_t)(completed_pg_reqgroup->orig_varblock->count[i]);
+ r[ndims-i-1] = dsize;
+ }
+
+ void* orig_buff;
+ orig_buff = SZ_decompress(dtype, raw_buff, raw_size, r[4], r[3], r[2], r[1], r[0]);
+
+ if (dtype == SZ_FLOAT)
+ {
+ log_debug("%10s: %g %g %g %g %g ... \n", "out",
+ ((float*)orig_buff)[0], ((float*)orig_buff)[1], ((float*)orig_buff)[2], ((float*)orig_buff)[3], ((float*)orig_buff)[4]);
+ }
+ else if (dtype == SZ_DOUBLE)
+ {
+ log_debug("%10s: %g %g %g %g %g ... \n", "out",
+ ((double*)orig_buff)[0], ((double*)orig_buff)[1], ((double*)orig_buff)[2], ((double*)orig_buff)[3], ((double*)orig_buff)[4]);
+ }
+ //log_debug("=== SZ decompress ===\n");
+ log_debug("%s: %d\n", "SZ dtype", dtype);
+ log_debug("%s: %d\n", "SZ raw_size", raw_size);
+ /*
+ log_debug("%s: %d %d %d %d %d ... %d %d %d %d %d\n", "SZ out_buff",
+ raw_buff[0], raw_buff[1], raw_buff[2], raw_buff[3], raw_buff[4],
+ raw_buff[raw_size-5], raw_buff[raw_size-4], raw_buff[raw_size-3], raw_buff[raw_size-2], raw_buff[raw_size-1]);
+ int sum = 0;
+ for (i=0; i<raw_size; i++)
+ {
+ sum += raw_buff[i];
+ }
+ log_debug("%s: %d\n", "SZ sum", sum);
+ */
+ log_debug("%s: %d %d %d %d %d\n", "SZ dim", r[0], r[1], r[2], r[3], r[4]);
+ //log_debug("=====================\n");
+
+ return adios_datablock_new_whole_pg(reqgroup, completed_pg_reqgroup, orig_buff);
+}
+
+// Do nothing for the full read request complete (typical)
+adios_datablock * adios_transform_sz_reqgroup_completed(adios_transform_read_request *completed_reqgroup)
+{
+ //log_debug("function: %s\n", __FUNCTION__);
+ return NULL;
+}
+
+
+#else
+
+DECLARE_TRANSFORM_READ_METHOD_UNIMPL(sz);
+
+#endif
diff --git a/src/transforms/adios_transform_sz_write.c b/src/transforms/adios_transform_sz_write.c
new file mode 100644
index 0000000..fca49b0
--- /dev/null
+++ b/src/transforms/adios_transform_sz_write.c
@@ -0,0 +1,343 @@
+/*
+ * adios_transform_sz_write.c
+ *
+ * Author: Jong Choi
+ * Contact: choij at ornl.gov
+ */
+
+#include <stdint.h>
+#include <assert.h>
+#include <limits.h>
+#include <sys/time.h>
+
+#include "adios_logger.h"
+#include "adios_transforms_common.h"
+#include "adios_transforms_write.h"
+#include "adios_transforms_hooks_write.h"
+#include "adios_transforms_util.h"
+
+#ifdef HAVE_SZ
+
+#include "sz.h"
+
+typedef unsigned int uint;
+
+typedef struct
+{
+ int r[5];
+} sz_info_t;
+
+uint16_t adios_transform_sz_get_metadata_size(struct adios_transform_spec *transform_spec)
+{
+ //log_debug("function: %s\n", __FUNCTION__);
+ return 0; // Set amount of transform-internal metadata space to allocate
+}
+
+void adios_transform_sz_transformed_size_growth(const struct adios_var_struct *var, const struct adios_transform_spec *transform_spec,
+ uint64_t *constant_factor, double *linear_factor, double *capped_linear_factor, uint64_t *capped_linear_cap)
+{
+ //log_debug("function: %s\n", __FUNCTION__);
+}
+
+int adios_transform_sz_apply(struct adios_file_struct *fd,
+ struct adios_var_struct *var,
+ uint64_t *transformed_len,
+ int use_shared_buffer,
+ int *wrote_to_shared_buffer)
+{
+ //log_debug("function: %s\n", __FUNCTION__);
+ //log_debug("use_shared_buffer: %d\n", use_shared_buffer);
+
+ // Get the input data and data length
+ const uint64_t input_size = adios_transform_get_pre_transform_var_size(var);
+ const void *input_buff = var->data;
+
+ sz_params sz;
+ memset(&sz, 0, sizeof(sz_params));
+ sz.max_quant_intervals = 65536;
+ sz.quantization_intervals = 0;
+ sz.dataEndianType = LITTLE_ENDIAN_DATA;
+ sz.sysEndianType = LITTLE_ENDIAN_DATA;
+ sz.sol_ID = SZ;
+ sz.layers = 1;
+ sz.sampleDistance = 100;
+ sz.predThreshold = 0.99;
+ sz.offset = 0;
+ sz.szMode = SZ_BEST_COMPRESSION; //SZ_BEST_SPEED; //SZ_BEST_COMPRESSION;
+ sz.gzipMode = 1;
+ sz.errorBoundMode = ABS;
+ sz.absErrBound = 1E-4;
+ sz.relBoundRatio = 1E-3;
+ sz.pw_relBoundRatio = 1E-5;
+ sz.segment_size = 32;
+
+ unsigned char *bytes;
+ int outsize;
+ int r[5] = {0,0,0,0,0};
+
+ /* SZ parameters */
+ int use_configfile = 0;
+ char *sz_configfile = NULL;
+ struct adios_transform_spec_kv_pair* param;
+ int i = 0;
+ if (adios_verbose_level>7) log_debug("param_count: %d\n", var->transform_spec->param_count);
+ for (i=0; i<var->transform_spec->param_count; i++)
+ {
+ param = &(var->transform_spec->params[i]);
+ if (adios_verbose_level>7) log_debug("param: %s %s\n", param->key, param->value);
+ if (strcmp(param->key, "init") == 0)
+ {
+ use_configfile = 1;
+ sz_configfile = strdup(param->value);
+ }
+ else if (strcmp(param->key, "max_quant_intervals") == 0)
+ {
+ sz.max_quant_intervals = atoi(param->value);
+ }
+ else if (strcmp(param->key, "quantization_intervals") == 0)
+ {
+ sz.quantization_intervals = atoi(param->value);
+ }
+ else if (strcmp(param->key, "dataEndianType") == 0)
+ {
+ sz.dataEndianType = atoi(param->value);
+ }
+ else if (strcmp(param->key, "sysEndianType") == 0)
+ {
+ sz.sysEndianType = atoi(param->value);
+ }
+ else if (strcmp(param->key, "sol_ID") == 0)
+ {
+ sz.sol_ID = atoi(param->value);
+ }
+ else if (strcmp(param->key, "layers") == 0)
+ {
+ sz.layers = atoi(param->value);
+ }
+ else if (strcmp(param->key, "sampleDistance") == 0)
+ {
+ sz.sampleDistance = atoi(param->value);
+ }
+ else if (strcmp(param->key, "predThreshold") == 0)
+ {
+ sz.predThreshold = atof(param->value);
+ }
+ else if (strcmp(param->key, "offset") == 0)
+ {
+ sz.offset = atoi(param->value);
+ }
+ else if (strcmp(param->key, "szMode") == 0)
+ {
+ int szMode = SZ_BEST_SPEED;
+ if (strcmp(param->value, "SZ_BEST_SPEED") == 0)
+ {
+ szMode = SZ_BEST_SPEED;
+ }
+ else if (strcmp(param->value, "SZ_BEST_COMPRESSION") == 0)
+ {
+ szMode = SZ_BEST_COMPRESSION;
+ }
+ else if (strcmp(param->value, "SZ_DEFAULT_COMPRESSION") == 0)
+ {
+ szMode = SZ_DEFAULT_COMPRESSION;
+ }
+ else
+ {
+ log_warn("An unknown szMode: %s\n", param->value);
+ }
+ sz.szMode = szMode;
+ }
+ else if (strcmp(param->key, "gzipMode") == 0)
+ {
+ sz.gzipMode = atoi(param->value);
+ }
+ else if (strcmp(param->key, "errorBoundMode") == 0)
+ {
+ int errorBoundMode = ABS;
+ if (strcmp(param->value, "ABS") == 0)
+ {
+ errorBoundMode = ABS;
+ }
+ else if (strcmp(param->value, "REL") == 0)
+ {
+ errorBoundMode = REL;
+ }
+ else if (strcmp(param->value, "ABS_AND_REL") == 0)
+ {
+ errorBoundMode = ABS_AND_REL;
+ }
+ else if (strcmp(param->value, "ABS_OR_REL") == 0)
+ {
+ errorBoundMode = ABS_OR_REL;
+ }
+ else if (strcmp(param->value, "PW_REL") == 0)
+ {
+ errorBoundMode = PW_REL;
+ }
+ else
+ {
+ log_warn("An unknown errorBoundMode: %s\n", param->value);
+ }
+ sz.errorBoundMode = errorBoundMode;
+ }
+ else if (strcmp(param->key, "absErrBound") == 0)
+ {
+ sz.absErrBound = atof(param->value);
+ }
+ else if (strcmp(param->key, "relBoundRatio") == 0)
+ {
+ sz.relBoundRatio = atof(param->value);
+ }
+ else if (strcmp(param->key, "pw_relBoundRatio") == 0)
+ {
+ sz.pw_relBoundRatio = atof(param->value);
+ }
+ else if (strcmp(param->key, "segment_size") == 0)
+ {
+ sz.segment_size = atoi(param->value);
+ }
+ else if (!strcmp(param->key, "abs") || !strcmp(param->key, "absolute") || !strcmp(param->key, "accuracy"))
+ {
+ sz.errorBoundMode = ABS;
+ sz.absErrBound = atof(param->value);
+ }
+ else if (!strcmp(param->key, "rel") || !strcmp(param->key, "relative"))
+ {
+ sz.errorBoundMode = REL;
+ sz.relBoundRatio = atof(param->value);
+ }
+ else
+ {
+ log_warn("An unknown SZ parameter: %s\n", param->key);
+ }
+ }
+
+ if (use_configfile)
+ {
+ log_debug("%s: %s\n", "SZ config", sz_configfile);
+ SZ_Init(sz_configfile);
+ free(sz_configfile);
+ }
+ else
+ {
+ if (adios_verbose_level>7)
+ {
+ log_debug("%s: %d\n", "sz.max_quant_intervals", sz.max_quant_intervals);
+ log_debug("%s: %d\n", "sz.quantization_intervals", sz.quantization_intervals);
+ log_debug("%s: %d\n", "sz.dataEndianType", sz.dataEndianType);
+ log_debug("%s: %d\n", "sz.sysEndianType", sz.sysEndianType);
+ log_debug("%s: %d\n", "sz.sol_ID", sz.sol_ID);
+ log_debug("%s: %d\n", "sz.layers", sz.layers);
+ log_debug("%s: %d\n", "sz.sampleDistance", sz.sampleDistance);
+ log_debug("%s: %g\n", "sz.predThreshold", sz.predThreshold);
+ log_debug("%s: %d\n", "sz.offset", sz.offset);
+ log_debug("%s: %d\n", "sz.szMode", sz.szMode);
+ log_debug("%s: %d\n", "sz.gzipMode", sz.gzipMode);
+ log_debug("%s: %d\n", "sz.errorBoundMode", sz.errorBoundMode);
+ log_debug("%s: %g\n", "sz.absErrBound", sz.absErrBound);
+ log_debug("%s: %g\n", "sz.relBoundRatio", sz.relBoundRatio);
+ log_debug("%s: %g\n", "sz.pw_relBoundRatio", sz.pw_relBoundRatio);
+ log_debug("%s: %d\n", "sz.segment_size", sz.segment_size);
+ }
+ SZ_Init_Params(&sz);
+ }
+
+ // Get type info
+ int dtype;
+ switch (var->pre_transform_type)
+ {
+ case adios_double:
+ dtype = SZ_DOUBLE;
+ break;
+ case adios_real:
+ dtype = SZ_FLOAT;
+ break;
+ default:
+ adios_error(err_transform_failure, "No supported data type\n");
+ return -1;
+ break;
+ }
+
+ // Get dimension info
+ struct adios_dimension_struct* d = var->pre_transform_dimensions;
+ int ndims = (uint) count_dimensions(d);
+ //log_debug("ndims: %d\n", ndims);
+ if (ndims > 5)
+ {
+ adios_error(err_transform_failure, "No more than 5 dimension is supported.\n");
+ return -1;
+ }
+
+ // r[0] is the fastest changing dimension and r[4] is the lowest changing dimension
+ // In C, r[0] is the last dimension. In Fortran, r[0] is the first dimension
+ for (i=0; i<ndims; i++)
+ {
+ uint dsize = (uint) adios_get_dim_value(&d->dimension);
+ if (fd->group->adios_host_language_fortran == adios_flag_yes)
+ r[i] = dsize;
+ else
+ r[ndims-i-1] = dsize;
+ d = d->next;
+ }
+
+ bytes = SZ_compress (dtype, (void *) input_buff, &outsize,
+ r[4], r[3], r[2], r[1], r[0]);
+
+ unsigned char *raw_buff = (unsigned char*) bytes;
+
+ int raw_size = outsize;
+ //log_debug("=== SZ compress ===\n");
+ log_debug("%s: %d\n", "SZ dtype", dtype);
+ log_debug("%s: %d\n", "SZ out_size", raw_size);
+ /*
+ log_debug("%s: %d %d %d %d %d ... %d %d %d %d %d\n", "SZ out_buff",
+ raw_buff[0], raw_buff[1], raw_buff[2], raw_buff[3], raw_buff[4],
+ raw_buff[raw_size-5], raw_buff[raw_size-4], raw_buff[raw_size-3], raw_buff[raw_size-2], raw_buff[raw_size-1]);
+ int sum = 0;
+ for (i=0; i<raw_size; i++)
+ {
+ sum += raw_buff[i];
+ }
+ log_debug("%s: %d\n", "SZ sum", sum);
+ */
+ log_debug("%s: %d %d %d %d %d\n", "SZ dim", r[0], r[1], r[2], r[3], r[4]);
+ //log_debug("===================\n");
+
+ // Output
+ uint64_t output_size = outsize/* Compute how much output size we need */;
+ void* output_buff;
+
+ if (use_shared_buffer) {
+ // If shared buffer is permitted, serialize to there
+ assert(shared_buffer_reserve(fd, output_size));
+
+ // Write directly to the shared buffer
+ output_buff = fd->buffer + fd->offset;
+ memcpy(output_buff, bytes, outsize);
+ } else { // Else, fall back to var->adata memory allocation
+ output_buff = bytes;
+ //assert(output_buff);
+ }
+ *wrote_to_shared_buffer = use_shared_buffer;
+
+ // Do transform from input_buff into output_buff, and update output_size to the true output size
+
+ // Wrap up, depending on buffer mode
+ if (*wrote_to_shared_buffer) {
+ shared_buffer_mark_written(fd, output_size);
+ } else {
+ var->adata = output_buff;
+ var->data_size = output_size;
+ var->free_data = adios_flag_yes;
+ }
+
+ *transformed_len = output_size; // Return the size of the data buffer
+ SZ_Finalize();
+ return 1;
+}
+
+#else
+
+DECLARE_TRANSFORM_WRITE_METHOD_UNIMPL(sz)
+
+#endif
diff --git a/src/transforms/transform_plugins.h b/src/transforms/transform_plugins.h
index a0b97d9..d7c7135 100644
--- a/src/transforms/transform_plugins.h
+++ b/src/transforms/transform_plugins.h
@@ -12,4 +12,5 @@ REGISTER_TRANSFORM_PLUGIN(isobar, "isobar", "ncsu-isobar", "ISOBAR compression")
REGISTER_TRANSFORM_PLUGIN(aplod, "aplod", "ncsu-aplod", "APLOD byte-columnar precision-level-of-detail access format")
REGISTER_TRANSFORM_PLUGIN(alacrity, "alacrity", "ncsu-alacrity", "ALACRITY indexing")
REGISTER_TRANSFORM_PLUGIN(zfp, "zfp", "zfp", "zfp compression")
-
+REGISTER_TRANSFORM_PLUGIN(sz, "sz", "sz", "sz compression")
+REGISTER_TRANSFORM_PLUGIN(lz4, "lz4", "lz4", "lz4 compression")
diff --git a/src/write/adios_flexpath.c b/src/write/adios_flexpath.c
index e462074..4e6fa7b 100644
--- a/src/write/adios_flexpath.c
+++ b/src/write/adios_flexpath.c
@@ -12,11 +12,13 @@
#include <math.h>
#include <string.h>
#include <errno.h>
+#include <stdarg.h>
#include <pthread.h>
// xml parser
#include <mxml.h>
+#include <cod.h>
// add by Kimmy 10/15/2012
#include <sys/types.h>
@@ -36,24 +38,25 @@
#include "core/buffer.h"
#include "core/util.h"
#include "core/adios_logger.h"
+#include "core/globals.h"
+#include "core/adiost_callback_internal.h"
#if HAVE_FLEXPATH==1
// // evpath libraries
#include <evpath.h>
-#include <cod.h>
#define FLEXPATH_SIDE "WRITER"
#include "core/flexpath.h"
#include <sys/queue.h>
/************************* Structure and Type Definitions ***********************/
// used for messages in the control queue
-typedef enum {VAR=0, DATA_FLUSH, OPEN, CLOSE, INIT, EVGROUP_FLUSH, DATA_BUFFER, FINALIZE} FlexpathMessageType;
+typedef enum {VAR=0, DATA_FLUSH, OPEN, CLOSE, DATA_BUFFER, FINALIZE} FlexpathMessageType;
// maintains connection information
typedef struct _flexpath_stone {
- int myNum;
- int theirNum;
+ int bridge_stoneID;
+ int reader_stoneID;
int step;
int opened;
int created;
@@ -103,11 +106,35 @@ typedef struct _flexpath_fm_structure {
int size;
unsigned char *buffer;
FMFormat ioFormat;
- attr_list attrList;
+ int nattrs;
LIST_HEAD(tableHead, _flexpath_name_table) nameList;
LIST_HEAD(dims, _flexpath_dim_names) dimList;
} FlexpathFMStructure;
+struct _flexpath_write_file_data;
+
+typedef struct _flexpath_per_subscriber_info {
+ CMConnection reader_0_conn;
+ uint64_t reader_file;
+ //We need to hold the full list somewhere, but this can be freed
+ int total_num_readers;
+ EVstone multiStone;
+ EVstone splitStone;
+ EVstone sinkStone;
+
+ EVsource dataSource;
+ EVsource scalarDataSource;
+ EVsource offsetSource;
+ EVsource finalizeSource;
+
+ int numBridges;
+ FlexpathStone* bridges;
+ int final_condition;
+
+ struct _flexpath_write_file_data *parent_file;
+
+} *subscriber_info;
+
// information used per each flexpath file
typedef struct _flexpath_write_file_data {
// MPI stuff
@@ -115,42 +142,19 @@ typedef struct _flexpath_write_file_data {
int rank;
int size;
int host_language;
- // EVPath stuff
- EVstone multiStone;
- EVstone sinkStone;
-
- EVsource dataSource;
- EVsource offsetSource;
- EVsource dropSource;
- EVsource opSource;
- EVsource stepSource;
- EVaction multi_action;
- FlexpathStone* bridges;
- int numBridges;
- attr_list attrs;
// server state
int maxQueueSize;
- int openCount;
- int readerStep;
+ pthread_mutex_t queue_size_mutex;
+ pthread_cond_t queue_size_condition;
+
int writerStep; // how many times has the writer called closed?
int finalized; // have we finalized?
- int use_ctrl_thread;
FlexpathFMStructure* fm;
- FlexpathVarNode* askedVars;
- FlexpathVarNode* writtenVars;
- FlexpathVarNode* formatVars;
- FlexpathQueueNode* controlQueue;
- FlexpathQueueNode* dataQueue;
- pthread_mutex_t openMutex;
- pthread_mutex_t controlMutex;
- pthread_mutex_t dataMutex;
- pthread_cond_t controlCondition;
- pthread_cond_t dataCondition; //fill
- pthread_t ctrl_thr_id;
+ subscriber_info subscribers;
// global array distribution data
int globalCount;
evgroup *gp;
@@ -158,9 +162,11 @@ typedef struct _flexpath_write_file_data {
// for maintaining open file list
struct _flexpath_write_file_data* next;
char* name;
+ void *adios_file_data;
// general
int verbose;
+ int failed; /* set if all output stones are closed */
} FlexpathWriteFileData;
typedef struct _flexpath_write_data {
@@ -170,16 +176,17 @@ typedef struct _flexpath_write_data {
} FlexpathWriteData;
/************************* Global Variable Declarations *************************/
-// used for sanitizing names
-#define OPLEN 7
-static char opList[OPLEN] = { '+', '-', '*', '/', '.', '>', '<' };
-static char *opRepList[OPLEN] = { "_plus_", "_minus_", "_mult_", "_div_", "_dot_", "_greater_", "_less_" };
+static atom_t RANK_ATOM = -1;
+static atom_t TIMESTEP_ATOM = -1;
+static atom_t SCALAR_ATOM = -1;
+static atom_t CM_TRANSPORT = -1;
+static atom_t QUEUE_SIZE = -1;
+static atom_t NATTRS = -1;
// used for global communication and data structures
FlexpathWriteData flexpathWriteData;
/**************************** Function Definitions *********************************/
-
static void
reverse_dims(uint64_t *dims, int len)
{
@@ -193,14 +200,14 @@ reverse_dims(uint64_t *dims, int len)
}
}
-char*
-resolve_path_name(char *path, char *name)
+static char*
+append_path_name(char *path, char *name)
{
char *fullname = NULL;
if (name) {
if (path) {
if (strcmp(path, "")) {
- fullname = malloc(strlen(path) + strlen(name) + 2);
+ fullname = malloc(strlen(path) + strlen(name) + 8);
strcpy(fullname, path);
strcat(fullname, "/");
strcat(fullname, name);
@@ -214,109 +221,6 @@ resolve_path_name(char *path, char *name)
return NULL;
}
-// add an attr for each dimension to an attr_list
-void
-set_attr_dimensions(char* varName, char* altName, int numDims, attr_list attrs)
-{
- char atomName[200] = "";
- char dimNum[10];
- strcat(atomName, FP_DIM_ATTR_NAME);
- strcat(atomName, "_");
- strcat(atomName, varName);
- strcat(atomName, "_");
- sprintf(dimNum, "%d", numDims);
- strcat(atomName, dimNum);
- atom_t dimAtom = attr_atom_from_string(atomName);
- add_string_attr(attrs, dimAtom, altName);
- atomName[0] = '\0';
- strcat(atomName, FP_NDIMS_ATTR_NAME);
- strcat(atomName, "_");
- strcat(atomName, altName);
-
- atom_t ndimsAtom = attr_atom_from_string(atomName);
- add_int_attr(attrs, ndimsAtom, 0);
-}
-
-
-attr_list
-set_flush_id_atom(attr_list attrs, int value)
-{
- atom_t dst_atom = attr_atom_from_string("fp_flush_id");
- int dst;
- if (!get_int_attr(attrs, dst_atom, &dst)) {
- add_int_attr(attrs, dst_atom, value);
- }
- set_int_attr(attrs, dst_atom, value);
- return attrs;
-}
-
-// sets a size atom
-attr_list
-set_size_atom(attr_list attrs, int value)
-{
- atom_t dst_atom = attr_atom_from_string("fp_size");
- int size;
- if (!get_int_attr(attrs, dst_atom, &size)) {
- add_int_attr(attrs, dst_atom, value);
- }
- set_int_attr(attrs, dst_atom, value);
- return attrs;
-}
-
-// sets a dst rank atom
-attr_list
-set_dst_rank_atom(attr_list attrs, int value)
-{
- atom_t dst_atom = attr_atom_from_string("fp_dst_rank");
- int dst;
- if (!get_int_attr(attrs, dst_atom, &dst)) {
- add_int_attr(attrs, dst_atom, value);
- }
- set_int_attr(attrs, dst_atom, value);
- return attrs;
-}
-
-// sets a dst condition atom
-attr_list
-set_dst_condition_atom(attr_list attrs, int condition)
-{
- atom_t dst_atom = attr_atom_from_string("fp_dst_condition");
- int dst;
- if (!get_int_attr(attrs, dst_atom, &dst)) {
- add_int_attr(attrs, dst_atom, condition);
- }
- set_int_attr(attrs, dst_atom, condition);
- return attrs;
-}
-
-// free format packets once EVPath is finished with them
-
-void
-evgroup_msg_free(void *eventData, void *clientData)
-{
-
- /* evgroup *msg = (evgroup*)eventData; */
- /* int num_vars = msg->num_vars; */
- /* int i; */
- /* for (i=0; i<num_vars; i++) { */
- /* free(msg->vars[i].offsets); */
- /* } */
- /* free(msg); */
-}
-
-void
-drop_evgroup_msg_free(void *eventData, void *clientData)
-{
- free(eventData);
-}
-
-void
-update_step_msg_free(void *eventData, void *clientData)
-{
- update_step_msg *msg = (update_step_msg*)eventData;
- free(msg);
-}
-
// free data packets once EVPath is finished with them
void
data_free(void* eventData, void* clientData)
@@ -326,124 +230,26 @@ data_free(void* eventData, void* clientData)
free(eventData);
}
-// free op packets once EVPath is finished with them
-void
-op_free(void* eventData, void* clientData)
-{
-// fp_write_log("OP", "freeing an op message\n");
- op_msg* op = (op_msg*) eventData;
- if (op->file_name) {
- free(op->file_name);
- }
- free(op);
-}
-// message queue count
-int
-queue_count(FlexpathQueueNode** queue)
-{
- if (*queue==NULL) {
- return 0;
- }
- int count = 1;
- FlexpathQueueNode* current = *queue;
- while (current && current->next) {
- count++;
- current = current->next;
- }
- return count;
-}
-
-// message queue add to head
-void
-threaded_enqueue(
- FlexpathQueueNode **queue,
- void* item,
- FlexpathMessageType type,
- pthread_mutex_t *mutex,
- pthread_cond_t *condition,
- int max_size)
-{
- pthread_mutex_lock(mutex);
- if (max_size > 0) {
- while (queue_count(queue) > max_size) {
- pthread_cond_wait(condition, mutex);
- }
- }
- FlexpathQueueNode* newNode = malloc(sizeof(FlexpathQueueNode));
- newNode->data = item;
- newNode->type = type;
- newNode->next = *queue;
- *queue = newNode;
- pthread_cond_broadcast(condition);
- pthread_mutex_unlock(mutex);
-}
-
-// remove from tail of a message queue
-FlexpathQueueNode*
-threaded_dequeue(
- FlexpathQueueNode **queue,
- pthread_mutex_t *mutex,
- pthread_cond_t *condition,
- int signal_dequeue)
-{
- pthread_mutex_lock(mutex);
- while (queue_count(queue) == 0) {
- pthread_cond_wait(condition, mutex);
- }
- FlexpathQueueNode *tail;
- FlexpathQueueNode *prev = NULL;
- tail = *queue;
- while (tail && tail->next) {
- prev=tail;
- tail=tail->next;
- }
- if (prev) {
- prev->next = NULL;
- } else {
- *queue = NULL;
- }
- pthread_mutex_unlock(mutex);
- if (signal_dequeue==1) {
- pthread_cond_broadcast(condition);
- }
- return tail;
-}
-
-// peek at tail of message queue
-FlexpathQueueNode*
-threaded_peek(FlexpathQueueNode** queue,
- pthread_mutex_t *mutex,
- pthread_cond_t *condition)
-{
- pthread_mutex_lock(mutex);
- int q = queue_count(queue);
- if (q == 0) {
- pthread_cond_wait(condition, mutex);
- }
- FlexpathQueueNode* tail;
- tail = *queue;
- while (tail && tail->next) {
- tail=tail->next;
- }
- pthread_mutex_unlock(mutex);
- return tail;
-}
// add new var to a var list
FlexpathVarNode*
add_var(FlexpathVarNode* queue, char* varName, FlexpathVarNode* dims, int rank)
{
+ FlexpathVarNode *tmp = queue;
+ FlexpathVarNode *new;
+
+ new = (FlexpathVarNode*) malloc(sizeof(FlexpathVarNode));
+ new->varName = strdup(varName);
+ new->dimensions = dims;
+ new->next = NULL;
+ new->rank = rank;
if (queue) {
- queue->next=add_var(queue->next, varName, dims, rank);
+ while (tmp->next != NULL) tmp = tmp->next;
+ tmp->next = new;
return queue;
} else {
- queue = (FlexpathVarNode*) malloc(sizeof(FlexpathVarNode));
- queue->varName = strdup(varName);
- queue->dimensions = dims;
- queue->next = NULL;
- queue->rank = rank;
- return queue;
+ return new;
}
}
@@ -458,40 +264,20 @@ free_vars(FlexpathVarNode* queue)
}
}
-// search a var list
-FlexpathVarNode*
-queue_contains(FlexpathVarNode* queue, const char* name, int rank)
-{
- int compare_rank = 0;
- if (rank >= 0 ) {
- compare_rank = 1;
- }
- FlexpathVarNode* tmp = queue;
- while (tmp) {
- if (strcmp(tmp->varName, name)==0) {
- if (compare_rank) {
- if (tmp->rank == rank) {
- return tmp;
- }
- } else {
- return tmp;
- }
- }
- tmp = tmp->next;
- }
- return NULL;
-}
// returns a name with the dimension prepended
static char*
get_alt_name(char *name, char *dimName)
{
+ /*
+ * Formerly, this created an alternative dimension name for each variable, so that transformation code
+ * might modify it without affecting other vars. This facility is deprecated, so simplifying.
+ * Just return a new copy of the original name.
+ */
+
int len = strlen(name) + strlen(dimName) + strlen("FPDIM_") + 2;
char *newName = malloc(sizeof(char) * len);
- strcpy(newName, "FPDIM_");
- strcat(newName, dimName);
- strcat(newName, "_");
- strcat(newName, name);
+ strcpy(newName, dimName);
return newName;
}
@@ -523,7 +309,7 @@ find_alt_name(FlexpathFMStructure *currentFm, char *dimName, char *varName)
FMField *field = (FMField *) malloc(sizeof(FMField));
a->field = field;
field->field_name = strdup(altName);
- // TO FIX: Should really check datatype (another paramater?)
+ // TO FIX: Should really check datatype (another parameter?)
field->field_type = strdup("integer");
field->field_size = sizeof(int);
field->field_offset = -1;
@@ -531,6 +317,18 @@ find_alt_name(FlexpathFMStructure *currentFm, char *dimName, char *varName)
return a;
}
+static int
+get_dim_count(struct adios_var_struct *v)
+{
+ struct adios_dimension_struct * dim_list = v->dimensions;
+ int ndims = 0;
+ while (dim_list) {
+ ndims++;
+ dim_list = dim_list->next;
+ }
+ return ndims;
+}
+
// populates offsets array
int
get_var_offsets(struct adios_var_struct *v,
@@ -573,62 +371,95 @@ get_var_offsets(struct adios_var_struct *v,
}
// creates multiqueue function to handle ctrl messages for given bridge stones
-char *multiqueue_action = "{\n\
- int found = 0;\n\
- int flush_data_count = 0; \n\
- int my_rank = -1;\n\
- attr_list mine;\n\
- if (EVcount_varMsg()>0) {\n\
- EVdiscard_and_submit_varMsg(0, 0);\n\
- }\n\
- if (EVcount_update_step_msg() > 1) {\n\
- EVdiscard_update_step_msg(0);\n\
- }\n\
- if (EVcount_drop_evgroup_msg()>0) {\n\
- if (EVcount_evgroup()>0) {\n\
- EVdiscard_evgroup(0);\n\
- }\n\
- EVdiscard_and_submit_drop_evgroup_msg(0,0);\n\
- }\n\
- if (EVcount_op_msg()>0) {\n\
- op_msg *msg = EVdata_op_msg(0);\n\
- mine = EVget_attrs_op_msg(0);\n\
- found = attr_ivalue(mine, \"fp_dst_rank\");\n\
- if (found > 0) {\n\
- EVdiscard_and_submit_op_msg(found, 0);\n\
- } else {\n\
- EVdiscard_and_submit_op_msg(0,0);\n\
+/*
+ 1) If reader_request
+ a) Check for data that matches reader timestamp
+ b) If timestamp is lower, discard
+ c) If timestamp matches, submit to request
+
+*/
+
+
+char * multiqueue_action = "{\n\
+ static int lowest_timestamp = 0;\n\
+ attr_list attrs;\n\
+ int old_num_data_in_queue = EVcount_anonymous();\n\
+ if(EVcount_read_request() > 0)\n\
+ {\n\
+ int i = 0;\n\
+ for(i = 0; i < EVcount_read_request(); i++)\n\
+ {\n\
+ read_request *read_msg;\n\
+ int time_req;\n\
+ read_msg = EVdata_read_request(0);\n\
+ time_req = read_msg->timestep_requested;\n\
+ fp_verbose(\"Read request received for timestep %d, from reader %d\\n\", time_req, read_msg->process_return_id);\n \
+ int j;\n\
+ for(j = 0; j < EVcount_anonymous(); j++)\n\
+ {\n\
+ int data_timestep;\n\
+ attrs = EVget_attrs_anonymous(j);\n\
+ data_timestep = attr_ivalue(attrs, \"fp_timestep\");\n\
+ if(data_timestep < time_req)\n\
+ {\n\
+ EVdiscard_anonymous(j);\n\
+ j--;\n\
+ }\n\
+ else if(data_timestep == time_req)\n\
+ {\n\
+ int target;\n\
+ target = read_msg->process_return_id;\n\
+ fp_verbose(\"Data for timestep %d sent to reader %d\\n\", read_msg->timestep_requested, read_msg->process_return_id);\n\
+ EVsubmit_anonymous(target + 1, j);\n\
+ EVdiscard_read_request(i);\n\
+ i--;\n\
+ }\n\
+ }\n\
}\n\
}\n\
- if (EVcount_flush()>0) {\n\
- flush *c = EVdata_flush(0);\n\
- if (c->type == 2) { \n\
- if (EVcount_evgroup()>0) {\n\
- evgroup *g = EVdata_evgroup(0); \n\
- g->condition = c->condition;\n\
- EVsubmit(c->process_id+1, g);\n\
- EVdiscard_flush(0);\n\
- }\n\
- }\n\
- else if (c->type == 3) {\n\
- if (EVcount_update_step_msg()>0) {\n\
- update_step_msg *stepmsg = EVdata_update_step_msg(0);\n\
- stepmsg->condition = c->condition;\n\
- EVsubmit(c->process_id+1, stepmsg);\n\
- EVdiscard_flush(0);\n\
- }\n\
- }\n\
- else {\n\
- EVdiscard_and_submit_flush(0,0);\n\
- flush_data_count++;\n\
- }\n\
+ if(EVcount_finalize_close_msg() > 0)\n\
+ {\n\
+ EVdiscard_and_submit_finalize_close_msg(0, 0);\n\
}\n\
- if (EVcount_anonymous()>0) {\n\
- mine = EVget_attrs_anonymous(0);\n\
- found = attr_ivalue(mine, \"fp_dst_rank\");\n\
- EVdiscard_and_submit_anonymous(found+1,0);\n\
+ int num_data_in_queue = EVcount_anonymous();\n\
+ set_int_attr(stone_attrs, \"queue_size\", num_data_in_queue);\n\
+ if(old_num_data_in_queue > num_data_in_queue)\n\
+ {\n\
+ queue_size_msg new;\n\
+ new.size = num_data_in_queue;\n\
+ EVsubmit(0, new);\n\
}\n\
- }";
+}";
+
+
+static int
+finalize_msg_handler(CManager cm, void *vevent, void *client_data, attr_list attrs)
+{
+ FlexpathWriteFileData * fp = (FlexpathWriteFileData *) client_data;
+ int cond = fp->subscribers->final_condition;
+ fp->subscribers->final_condition = -1;
+ if (cond != -1) {
+ CMCondition_signal(flexpathWriteData.cm, cond);
+ fp_verbose(fp, "Finalize msg handler called and signalled condition %d!", cond);
+ } else {
+ fp_verbose(fp, "Finalize msg handler called and condition already signalled...");
+ }
+
+
+ return 0;
+}
+
+static int
+queue_size_msg_handler(CManager cm, void*vevent, void*client_data, attr_list attrs)
+{
+ FlexpathWriteFileData * fp = (FlexpathWriteFileData *) client_data;
+ fp_verbose(fp, "Sending the condition signal that the queue_size has changed!\n");
+ pthread_mutex_lock(&(fp->queue_size_mutex));
+ pthread_cond_signal(&(fp->queue_size_condition));
+ pthread_mutex_unlock(&(fp->queue_size_mutex));
+ return 0;
+}
+
// sets a field based on data type
void
@@ -668,6 +499,13 @@ set_field(int type, FMFieldList* field_list_ptr, int fieldNo, int* size)
*size += sizeof(unsigned char *);
break;
+ case adios_string_array:
+ field_list[fieldNo].field_type = strdup("string");
+ field_list[fieldNo].field_size = sizeof(char *);
+ field_list[fieldNo].field_offset = *size;
+ *size += sizeof(unsigned char *);
+ break;
+
case adios_double:
field_list[fieldNo].field_type = strdup("double");
field_list[fieldNo].field_size = sizeof(double);
@@ -750,7 +588,7 @@ get_dim_name (struct adios_dimension_item_struct *d)
{
char *vname = NULL;
if (d->var) {
- vname = resolve_path_name(d->var->path, d->var->name);
+ vname = append_path_name(d->var->path, d->var->name);
} else if (d->attr) {
if (d->attr->var)
vname = d->attr->var->name;
@@ -761,6 +599,198 @@ get_dim_name (struct adios_dimension_item_struct *d)
return vname;
}
+static int
+set_field_type(int type, FMFieldList field_list, int fieldNo, char *dims, int all_static, FlexpathFMStructure *currentFm)
+{
+ switch (type) {
+ case adios_unknown:
+ fprintf(stderr, "set_format: Bad Type Error\n");
+ fieldNo--;
+ break;
+
+ case adios_integer:
+ field_list[fieldNo].field_type =
+ (char *) malloc(sizeof(char) * 255);
+ if (all_static) {
+ snprintf((char *) field_list[fieldNo].field_type, 255,
+ "*(integer%s)", dims);
+ } else {
+ snprintf((char *) field_list[fieldNo].field_type, 255,
+ "integer%s", dims);
+ }
+ field_list[fieldNo].field_size = sizeof(int);
+
+ field_list[fieldNo].field_offset = currentFm->size;
+ currentFm->size += sizeof(void *);
+ break;
+
+ case adios_unsigned_integer:
+ field_list[fieldNo].field_type =
+ (char *) malloc(sizeof(char) * 255);
+ if (all_static) {
+ snprintf((char *) field_list[fieldNo].field_type, 255,
+ "*(unsigned integer%s)", dims);
+ } else {
+ snprintf((char *) field_list[fieldNo].field_type, 255,
+ "unsigned integer%s", dims);
+ }
+ field_list[fieldNo].field_size = sizeof(unsigned int);
+
+ field_list[fieldNo].field_offset = currentFm->size;
+ currentFm->size += sizeof(void *);
+ break;
+
+ case adios_real:
+ field_list[fieldNo].field_type =
+ (char *) malloc(sizeof(char) * 255);
+ if (all_static) {
+ snprintf((char *) field_list[fieldNo].field_type, 255,
+ "*(float%s)", dims);
+ } else {
+ snprintf((char *) field_list[fieldNo].field_type, 255,
+ "float%s", dims);
+ }
+ field_list[fieldNo].field_size = sizeof(float);
+ field_list[fieldNo].field_offset = currentFm->size;
+ currentFm->size += sizeof(void *);
+ break;
+
+ case adios_string:
+ field_list[fieldNo].field_type = strdup("string");
+ field_list[fieldNo].field_size = sizeof(char);
+ field_list[fieldNo].field_offset = currentFm->size;
+ currentFm->size += sizeof(void *);
+ break;
+
+ case adios_string_array:
+ field_list[fieldNo].field_type = strdup("string");
+ field_list[fieldNo].field_size = sizeof(char);
+ field_list[fieldNo].field_offset = currentFm->size;
+ currentFm->size += sizeof(void *);
+ break;
+
+ case adios_double:
+ field_list[fieldNo].field_type =
+ (char *) malloc(sizeof(char) * 255);
+ if (all_static) {
+ snprintf((char *) field_list[fieldNo].field_type, 255,
+ "*(double%s)", dims);
+ } else {
+ snprintf((char *) field_list[fieldNo].field_type, 255,
+ "double%s", dims);
+ }
+ field_list[fieldNo].field_size = sizeof(double);
+ field_list[fieldNo].field_offset = currentFm->size;
+ currentFm->size += sizeof(void *);
+ break;
+
+ case adios_long_double:
+ field_list[fieldNo].field_type =
+ (char *) malloc(sizeof(char) * 255);
+ if (all_static) {
+ snprintf((char *) field_list[fieldNo].field_type, 255,
+ "*(double%s)", dims);
+ } else {
+ snprintf((char *) field_list[fieldNo].field_type, 255,
+ "double%s", dims);
+ }
+ field_list[fieldNo].field_size = sizeof(long double);
+ field_list[fieldNo].field_offset = currentFm->size;
+ currentFm->size += sizeof(void *);
+ break;
+
+ case adios_byte:
+ field_list[fieldNo].field_type =
+ (char *) malloc(sizeof(char) * 255);
+ if (all_static) {
+ snprintf((char *) field_list[fieldNo].field_type, 255, "*(char%s)",
+ dims);
+ } else {
+ snprintf((char *) field_list[fieldNo].field_type, 255, "*(char%s)",
+ dims);
+ }
+ field_list[fieldNo].field_size = sizeof(char);
+ field_list[fieldNo].field_offset = currentFm->size;
+ currentFm->size += sizeof(void *);
+ break;
+
+ case adios_long: // needs to be unsigned integer in ffs
+ // to distinguish on reader_side, I have to look at the size also
+ field_list[fieldNo].field_type =
+ (char *) malloc(sizeof(char) * 255);
+ if (all_static) {
+ snprintf((char *) field_list[fieldNo].field_type, 255,
+ "*(integer%s)", dims);
+ } else {
+ snprintf((char *) field_list[fieldNo].field_type, 255,
+ "integer%s", dims);
+ }
+ field_list[fieldNo].field_size = sizeof(long);
+
+ field_list[fieldNo].field_offset = currentFm->size;
+ currentFm->size += sizeof(void *);
+ break;
+
+ case adios_unsigned_long: // needs to be unsigned integer in ffs
+ // to distinguish on reader_side, I have to look at the size also
+ field_list[fieldNo].field_type =
+ (char *) malloc(sizeof(char) * 255);
+ if (all_static) {
+ snprintf((char *) field_list[fieldNo].field_type, 255,
+ "*(unsigned integer%s)", dims);
+ } else {
+ snprintf((char *) field_list[fieldNo].field_type, 255,
+ "unsigned integer%s", dims);
+ }
+ field_list[fieldNo].field_size = sizeof(unsigned long);
+
+ field_list[fieldNo].field_offset = currentFm->size;
+ currentFm->size += sizeof(void *);
+ break;
+
+ case adios_complex:
+ field_list[fieldNo].field_type =
+ (char *) malloc(sizeof(char) * 255);
+ if (all_static) {
+ snprintf((char *) field_list[fieldNo].field_type, 255, "*(complex%s)",
+ dims);
+ } else {
+ snprintf((char *) field_list[fieldNo].field_type, 255, "complex%s",
+ dims);
+ }
+ field_list[fieldNo].field_size = sizeof(complex_dummy);
+ field_list[fieldNo].field_offset = currentFm->size;
+ currentFm->size += sizeof(void *);
+ break;
+
+ case adios_double_complex:
+ field_list[fieldNo].field_type =
+ (char *) malloc(sizeof(char) * 255);
+ if (all_static) {
+ snprintf((char *) field_list[fieldNo].field_type, 255, "*(double_complex%s)",
+ dims);
+ } else {
+ snprintf((char *) field_list[fieldNo].field_type, 255, "double_complex%s",
+ dims);
+ }
+ field_list[fieldNo].field_size = sizeof(double_complex_dummy);
+ field_list[fieldNo].field_offset = currentFm->size;
+ currentFm->size += sizeof(void *);
+ break;
+
+ default:
+ fprintf(stderr, "Rejecting field %d, name %s\n", fieldNo, field_list[fieldNo].field_name);
+ adios_error(err_invalid_group,
+ "set_format: Unknown Type Error %d: name: %s\n",
+ type, field_list[fieldNo].field_name);
+ fieldNo--;
+ return 1;
+ //break;
+ }
+ return 0;
+}
+
+
// construct an fm structure based off the group xml file
FlexpathFMStructure*
set_format(struct adios_group_struct *t,
@@ -779,7 +809,7 @@ set_format(struct adios_group_struct *t,
return NULL;
}
- FMFieldList field_list = malloc(sizeof(FMField) * ((int)t->hashtbl_vars->size(t->hashtbl_vars) + 1));
+ FMFieldList field_list = malloc(sizeof(FMField) * 2);
if (field_list == NULL) {
adios_error(err_invalid_group,
"set_format: Field List Memory Allocation Failed. t->hashtbl_vars->size: %d\n",
@@ -789,17 +819,56 @@ set_format(struct adios_group_struct *t,
int fieldNo = 0;
int altvarcount = 0;
+ int i;
+ currentFm->nattrs = 0;
+
+ struct adios_attribute_struct *attr;
+ for (attr = t->attributes; attr != NULL; attr = attr->next, fieldNo++) {
+ char *fullname = append_path_name(attr->path, attr->name);
+ char *mangle_name = flexpath_mangle(fullname);
+ for (i = 0; i < fieldNo; i++) {
+ if (strcmp(mangle_name, field_list[i].field_name) == 0) {
+ adios_error(err_invalid_group, "set_format: The Flexpath transport does not allow multiple writes using the same name in a single group, variable %s is disallowed\n", fullname);
+ return NULL;
+ }
+ }
+ field_list[fieldNo].field_name = mangle_name;
+ if (!attr->nelems) {
+ // set the field type size and offset approrpriately
+ set_field(attr->type, &field_list, fieldNo, ¤tFm->size);
+ } else {
+ //it's a vector!
+ char dims[100];
+ sprintf(&dims[0], "[%d]", attr->nelems);
+ set_field_type(attr->type, field_list, fieldNo, dims, /* all static */ 1, currentFm);
+ }
+ field_list = (FMFieldList) realloc(field_list, sizeof(FMField) * (fieldNo + 2));
+
+ fp_verbose(fileData, "Attribute %d -> field: %s, %s, %d, %d\n",
+ currentFm->nattrs,
+ field_list[fieldNo].field_name,
+ field_list[fieldNo].field_type,
+ field_list[fieldNo].field_size,
+ field_list[fieldNo].field_offset);
+ currentFm->nattrs++;
+ }
// for each type look through all the fields
struct adios_var_struct *adios_var;
for (adios_var = t->vars; adios_var != NULL; adios_var = adios_var->next, fieldNo++) {
- char *fullname = resolve_path_name(adios_var->path, adios_var->name);
+ char *fullname = append_path_name(adios_var->path, adios_var->name);
+ char *mangle_name = flexpath_mangle(fullname);
+ for (i = 0; i < fieldNo; i++) {
+ if (strcmp(mangle_name, field_list[i].field_name) == 0) {
+ adios_error(err_invalid_group, "set_format: The Flexpath transport does not allow multiple writes using the same name in a single group, variable %s is disallowed\n", fullname);
+ return NULL;
+ }
+ }
// use the mangled name for the field.
- field_list[fieldNo].field_name = fullname;
+ field_list[fieldNo].field_name = mangle_name;
if (fullname!=NULL) {
int num_dims = 0;
- char atom_name[200] = "";
FlexpathVarNode *dims=NULL;
if (adios_var->dimensions) {
struct adios_dimension_struct *adim = adios_var->dimensions;
@@ -813,30 +882,23 @@ set_format(struct adios_group_struct *t,
//printf("vname: %s\n", vname);
//char *name = find_fixed_name(currentFm, vname);
char *aname = get_alt_name(fullname, vname);
+ char *mangle_dim = flexpath_mangle(aname);
//printf("aname: %s\n", aname);
- dims=add_var(dims, strdup(aname), NULL, 0);
- set_attr_dimensions(fullname, aname, num_dims, fileData->attrs);
+ dims=add_var(dims, mangle_dim, NULL, 0);
}
char *gname = get_dim_name(&adim->global_dimension);
if (gname) {
fileData->globalCount++;
//char *name = find_fixed_name(currentFm, gname);
char *aname = get_alt_name(fullname, gname);
- dims=add_var(dims, strdup(aname), NULL, 0);
- set_attr_dimensions(fullname, aname, num_dims, fileData->attrs);
+ char *mangle_dim = flexpath_mangle(aname);
+ dims=add_var(dims, mangle_dim, NULL, 0);
}
if (adim->global_dimension.rank > 0) {
fileData->globalCount++;
}
}
}
- // attach ndims attr
- strcat(atom_name, FP_NDIMS_ATTR_NAME);
- strcat(atom_name, "_");
- strcat(atom_name, fullname);
- atom_t ndims_atom = attr_atom_from_string(strdup(atom_name));
- add_int_attr(fileData->attrs, ndims_atom, num_dims);
- fileData->formatVars = add_var(fileData->formatVars, fullname, dims, 0);
}
// if its a single field
if (!adios_var->dimensions) {
@@ -850,17 +912,17 @@ set_format(struct adios_group_struct *t,
char dims[DIMSIZE] = "";
char el[ELSIZE] = "";
int v_offset=-1;
+ int all_static = 1;
//create the textual representation of the dimensions
for (; d != NULL; d = d->next) {
char *vname = get_dim_name(&d->dimension);
if (vname) {
-
- //char *name = find_fixed_name(currentFm, vname);
- FlexpathAltName *a = find_alt_name(currentFm, vname, (char*)field_list[fieldNo].field_name);
- altvarcount++;
- snprintf(el, ELSIZE, "[%s]", a->name);
+ vname = flexpath_mangle(vname);
+ snprintf(el, ELSIZE, "[%s]", vname);
+ free(vname);
v_offset = 0;
+ all_static = 0;
} else {
snprintf(el, ELSIZE, "[%" PRIu64 "]", d->dimension.rank);
v_offset *= d->dimension.rank;
@@ -873,164 +935,9 @@ set_format(struct adios_group_struct *t,
currentFm->size ++;
}
- switch (adios_var->type) {
- case adios_unknown:
- fprintf(stderr, "set_format: Bad Type Error\n");
- fieldNo--;
- break;
-
- case adios_integer:
- field_list[fieldNo].field_type =
- (char *) malloc(sizeof(char) * 255);
- snprintf((char *) field_list[fieldNo].field_type, 255,
- "integer%s", dims);
- field_list[fieldNo].field_size = sizeof(int);
-
- field_list[fieldNo].field_offset = currentFm->size;
- if (v_offset == 0 ) // pointer to variably sized array
- { currentFm->size += sizeof(void *); }
- else // statically sized array allocated inline
- { currentFm->size += (v_offset * sizeof(int)); }
- break;
-
- case adios_unsigned_integer:
- field_list[fieldNo].field_type =
- (char *) malloc(sizeof(char) * 255);
- snprintf((char *) field_list[fieldNo].field_type, 255,
- "unsigned integer%s", dims);
- field_list[fieldNo].field_size = sizeof(unsigned int);
-
- field_list[fieldNo].field_offset = currentFm->size;
- if (v_offset == 0 ) // pointer to variably sized array
- { currentFm->size += sizeof(void *); }
- else // statically sized array allocated inline
- { currentFm->size += (v_offset * sizeof(unsigned int)); }
- break;
-
- case adios_real:
- field_list[fieldNo].field_type =
- (char *) malloc(sizeof(char) * 255);
- snprintf((char *) field_list[fieldNo].field_type, 255,
- "float%s", dims);
- field_list[fieldNo].field_size = sizeof(float);
- field_list[fieldNo].field_offset = currentFm->size;
- if (v_offset == 0 ) // pointer to variably sized array
- { currentFm->size += sizeof(void *); }
- else // statically sized array allocated inline
- { currentFm->size += (v_offset * sizeof(float)); }
- break;
-
- case adios_string:
- field_list[fieldNo].field_type = strdup("string");
- field_list[fieldNo].field_size = sizeof(char);
- field_list[fieldNo].field_offset = currentFm->size;
- currentFm->size += sizeof(void *);
- break;
-
- case adios_double:
- field_list[fieldNo].field_type =
- (char *) malloc(sizeof(char) * 255);
- snprintf((char *) field_list[fieldNo].field_type, 255,
- "double%s", dims);
- field_list[fieldNo].field_size = sizeof(double);
- field_list[fieldNo].field_offset = currentFm->size;
- if (v_offset == 0 ) // pointer to variably sized array
- { currentFm->size += sizeof(void *); }
- else // statically sized array allocated inline
- { currentFm->size += (v_offset * sizeof(double)); }
- break;
-
- case adios_long_double:
- field_list[fieldNo].field_type =
- (char *) malloc(sizeof(char) * 255);
- snprintf((char *) field_list[fieldNo].field_type, 255,
- "double%s", dims);
- field_list[fieldNo].field_size = sizeof(long double);
- field_list[fieldNo].field_offset = currentFm->size;
- if (v_offset == 0 ) // pointer to variably sized array
- { currentFm->size += sizeof(void *); }
- else // statically sized array allocated inline
- { currentFm->size += (v_offset * sizeof(long double)); }
- break;
-
- case adios_byte:
- field_list[fieldNo].field_type =
- (char *) malloc(sizeof(char) * 255);
- snprintf((char *) field_list[fieldNo].field_type, 255, "char%s",
- dims);
- field_list[fieldNo].field_size = sizeof(char);
- field_list[fieldNo].field_offset = currentFm->size;
- if (v_offset == 0 ) // pointer to variably sized array
- { currentFm->size += sizeof(void *); }
- else // statically sized array allocated inline
- { currentFm->size += (v_offset * sizeof(char)); }
- break;
-
- case adios_long: // needs to be unsigned integer in ffs
- // to distinguish on reader_side, I have to look at the size also
- field_list[fieldNo].field_type =
- (char *) malloc(sizeof(char) * 255);
- snprintf((char *) field_list[fieldNo].field_type, 255,
- "integer%s", dims);
- field_list[fieldNo].field_size = sizeof(long);
-
- field_list[fieldNo].field_offset = currentFm->size;
- if (v_offset == 0 ) // pointer to variably sized array
- { currentFm->size += sizeof(void *); }
- else // statically sized array allocated inline
- { currentFm->size += (v_offset * sizeof(long)); }
- break;
-
- case adios_unsigned_long: // needs to be unsigned integer in ffs
- // to distinguish on reader_side, I have to look at the size also
- field_list[fieldNo].field_type =
- (char *) malloc(sizeof(char) * 255);
- snprintf((char *) field_list[fieldNo].field_type, 255,
- "unsigned integer%s", dims);
- field_list[fieldNo].field_size = sizeof(unsigned long);
-
- field_list[fieldNo].field_offset = currentFm->size;
- if (v_offset == 0 ) // pointer to variably sized array
- { currentFm->size += sizeof(void *); }
- else // statically sized array allocated inline
- { currentFm->size += (v_offset * sizeof(unsigned long)); }
- break;
-
- case adios_complex:
- field_list[fieldNo].field_type =
- (char *) malloc(sizeof(char) * 255);
- snprintf((char *) field_list[fieldNo].field_type, 255, "complex%s",
- dims);
- field_list[fieldNo].field_size = sizeof(complex_dummy);
- field_list[fieldNo].field_offset = currentFm->size;
- if (v_offset == 0 ) // pointer to variably sized array
- { currentFm->size += sizeof(void *); }
- else // statically sized array allocated inline
- { currentFm->size += (v_offset * sizeof(complex_dummy)); }
- break;
-
- case adios_double_complex:
- field_list[fieldNo].field_type =
- (char *) malloc(sizeof(char) * 255);
- snprintf((char *) field_list[fieldNo].field_type, 255, "double_complex%s",
- dims);
- field_list[fieldNo].field_size = sizeof(double_complex_dummy);
- field_list[fieldNo].field_offset = currentFm->size;
- if (v_offset == 0 ) // pointer to variably sized array
- { currentFm->size += sizeof(void *); }
- else // statically sized array allocated inline
- { currentFm->size += (v_offset * sizeof(double_complex_dummy)); }
- break;
-
- default:
- adios_error(err_invalid_group,
- "set_format: Unknown Type Error %d: name: %s\n",
- adios_var->type, field_list[fieldNo].field_name);
- fieldNo--;
- return NULL;
- //break;
- }
- }
+ set_field_type(adios_var->type, field_list, fieldNo, dims, all_static, currentFm);
+ }
+ field_list = (FMFieldList) realloc(field_list, sizeof(FMField) * (fieldNo + 2));
fp_verbose(fileData, "field: %s, %s, %d, %d\n",
field_list[fieldNo].field_name,
@@ -1040,7 +947,7 @@ set_format(struct adios_group_struct *t,
}
FlexpathDimNames *d = NULL;
- field_list = (FMFieldList) realloc(field_list, sizeof(FMField) * (altvarcount + (int)t->hashtbl_vars->size(t->hashtbl_vars) + 1));
+ field_list = (FMFieldList) realloc(field_list, sizeof(FMField) * (altvarcount + fieldNo + 1));
for (d = currentFm->dimList.lh_first; d != NULL; d = d->entries.le_next) {
FlexpathAltName *a = NULL;
@@ -1052,12 +959,11 @@ set_format(struct adios_group_struct *t,
}
}
- for (; fieldNo < (t->hashtbl_vars->size(t->hashtbl_vars) + 1+altvarcount); fieldNo++) {
- field_list[fieldNo].field_type = NULL;
- field_list[fieldNo].field_name = NULL;
- field_list[fieldNo].field_offset = 0;
- field_list[fieldNo].field_size = 0;
- }
+ field_list[fieldNo].field_type = NULL;
+ field_list[fieldNo].field_name = NULL;
+ field_list[fieldNo].field_offset = 0;
+ field_list[fieldNo].field_size = 0;
+
format[0].field_list = field_list;
format[1].format_name = strdup("complex");
@@ -1073,313 +979,24 @@ set_format(struct adios_group_struct *t,
return currentFm;
}
-// copies buffer zeroing out arrays that havent been asked for
-void* copy_buffer(void* buffer, int rank, FlexpathWriteFileData* fileData)
+// copies buffer zeroing out pointers to arrays
+void *copy_buffer_without_array(void *buffer, FlexpathWriteFileData *fileData)
{
- char* temp = (char*)malloc(fileData->fm->size);
+ ADIOST_CALLBACK_ENTER(adiost_event_fp_copy_buffer, fileData);
+ char *temp = (char *)malloc(fileData->fm->size);
memcpy(temp, buffer, fileData->fm->size);
FMField *f = fileData->fm->format[0].field_list;
- while (f->field_name != NULL)
- {
- FlexpathVarNode* a;
- if (!queue_contains(fileData->askedVars, f->field_name, rank)) {
- if ((a=queue_contains(fileData->formatVars, f->field_name, -1))
- &&
- (a->dimensions != NULL)) {
- FlexpathVarNode* dim = a->dimensions;
- while (dim) {
- FMField *f2 = fileData->fm->format[0].field_list;
- while (f2->field_name != NULL) {
- if (strcmp(f2->field_name, dim->varName)==0) {
- break;
- }
- f2++;
- }
- if (f2->field_name != NULL) {
- memset(&temp[f2->field_offset], 0, f2->field_size);
- }
- dim = dim->next;
- }
- memset(&temp[f->field_offset], 0, f->field_size);
- }
- }
+
+ while (f->field_name) {
+ if (index(f->field_type, '[')) {
+ *(void**)&temp[f->field_offset] = NULL;
+ }
f++;
}
+ ADIOST_CALLBACK_EXIT(adiost_event_fp_copy_buffer, fileData);
return temp;
}
-void
-process_data_flush(FlexpathWriteFileData *fileData,
- Flush_msg *flushMsg,
- FlexpathQueueNode *dataNode)
-{
- //fprintf(stderr, "writer:%d:processing flush for reader:%d:reader_step:%d:writer_step:%d\n", fileData->rank, flushMsg->process_id, fileData->readerStep, fileData->writerStep);
- void* temp = copy_buffer(dataNode->data, flushMsg->process_id, fileData);
-
- fileData->attrs = set_dst_rank_atom(fileData->attrs, flushMsg->process_id);
- fileData->attrs = set_flush_id_atom(fileData->attrs, flushMsg->id);
-
- if (!fileData->bridges[flushMsg->process_id].opened) {
- fileData->bridges[flushMsg->process_id].opened=1;
- fileData->openCount++;
- }
- //EVsubmit_general(fileData->dataSource, temp, data_free, fileData->attrs);
- EVsubmit_general(fileData->dataSource, temp, NULL, fileData->attrs);
- //fprintf(stderr, "writer:%d:processed flush for reader:%d:reader_step:%d:writer_step:%d\n", fileData->rank, flushMsg->process_id, fileData->readerStep, fileData->writerStep);
-}
-
-void
-process_var_msg(FlexpathWriteFileData *fileData, Var_msg *varMsg)
-{
- fp_verbose(fileData, "process Var msg for variable \"%s\"\n", varMsg->var_name);
- fileData->askedVars = add_var(fileData->askedVars,
- strdup(varMsg->var_name),
- NULL,
- varMsg->process_id);
-}
-
-void
-drop_queued_data(FlexpathWriteFileData *fileData, int timestep)
-{
- FlexpathQueueNode* node = threaded_dequeue(&fileData->dataQueue,
- &fileData->dataMutex,
- &fileData->dataCondition, 1);
- FMfree_var_rec_elements(fileData->fm->ioFormat, node->data);
-
- drop_evgroup_msg *dropMsg = malloc(sizeof(drop_evgroup_msg));
- dropMsg->step = fileData->readerStep;
- int wait = CMCondition_get(flexpathWriteData.cm, NULL);
- dropMsg->condition = wait;
- fp_verbose(fileData, "******* Triggering drop MSG\n");
- EVsubmit_general(fileData->dropSource, dropMsg, drop_evgroup_msg_free, fileData->attrs);
- //EVsubmit_general(fileData->dropSource, dropMsg, NULL, fileData->attrs);
- // Will have to change when not using ctrl thread.
- CMCondition_wait(flexpathWriteData.cm, wait);
-
- fileData->readerStep++;
-}
-
-void
-process_open_msg(FlexpathWriteFileData *fileData, op_msg *open)
-{
- fp_verbose(fileData, " Process Open msg, bridge %d, timestep %d\n", open->process_id, open->step);
- fileData->bridges[open->process_id].step = open->step;
- fileData->bridges[open->process_id].condition = open->condition;
- if (!fileData->bridges[open->process_id].created) {
- fileData->bridges[open->process_id].created = 1;
- fileData->bridges[open->process_id].myNum =
- EVcreate_bridge_action(
- flexpathWriteData.cm,
- attr_list_from_string(fileData->bridges[open->process_id].contact),
- fileData->bridges[open->process_id].theirNum);
-
- EVaction_set_output(flexpathWriteData.cm,
- fileData->multiStone,
- fileData->multi_action,
- open->process_id+1,
- fileData->bridges[open->process_id].myNum);
- }
-
- if (open->step == fileData->readerStep + 1) {
- drop_queued_data(fileData, fileData->readerStep);
- }
-
- if (open->step == fileData->readerStep) {
- pthread_mutex_lock(&fileData->openMutex);
- fileData->openCount++;
- fileData->bridges[open->process_id].opened = 1;
- pthread_mutex_unlock(&fileData->openMutex);
-
- op_msg *ack = malloc(sizeof(op_msg));
- ack->file_name = strdup(fileData->name);
- ack->process_id = fileData->rank;
- ack->step = fileData->readerStep;
- ack->type = 2;
- ack->condition = open->condition;
- fileData->attrs = set_dst_rank_atom(fileData->attrs, open->process_id+1);
- EVsubmit_general(fileData->opSource, ack, op_free, fileData->attrs);
- }
- else if (open->step < fileData->readerStep) {
- log_error("Flexpath method control_thread: Received Past Step Open\n");
- }
- else {
- fp_verbose(fileData, "received op with future step\n");
- }
-}
-
-void
-process_finalize_msg(FlexpathWriteFileData *fileData, op_msg *finalize)
-{
- fp_verbose(fileData, " Process Finalize msg, bridge %d, timestep %d\n", finalize->process_id, finalize->step);
-
- FlexpathQueueNode* node = threaded_dequeue(&fileData->dataQueue,
- &fileData->dataMutex,
- &fileData->dataCondition, 1);
- FMfree_var_rec_elements(fileData->fm->ioFormat, node->data);
-
- drop_evgroup_msg *dropMsg = malloc(sizeof(drop_evgroup_msg));
- dropMsg->step = fileData->readerStep;
- int wait = CMCondition_get(flexpathWriteData.cm, NULL);
- dropMsg->condition = wait;
- fp_verbose(fileData, "******* Triggering drop MSG\n");
- EVsubmit_general(fileData->dropSource, dropMsg, drop_evgroup_msg_free, fileData->attrs);
- //EVsubmit_general(fileData->dropSource, dropMsg, NULL, fileData->attrs);
- // Will have to change when not using ctrl thread.
- CMCondition_wait(flexpathWriteData.cm, wait);
-}
-
-void
-process_close_msg(FlexpathWriteFileData *fileData, op_msg *close)
-{
-
- fp_verbose(fileData, " process close msg, bridge %d\n", close->process_id);
- pthread_mutex_lock(&fileData->openMutex);
- fileData->openCount--;
- fileData->bridges[close->process_id].opened=0;
- fileData->bridges[close->process_id].condition = close->condition;
- pthread_mutex_unlock(&fileData->openMutex);
-
- /* if (fileData->openCount==0) { */
- /* FlexpathQueueNode* node = threaded_dequeue(&fileData->dataQueue, */
- /* &fileData->dataMutex, */
- /* &fileData->dataCondition, 1); */
- /* FMfree_var_rec_elements(fileData->fm->ioFormat, node->data); */
-
- /* drop_evgroup_msg *dropMsg = malloc(sizeof(drop_evgroup_msg)); */
- /* dropMsg->step = fileData->readerStep; */
- /* int wait = CMCondition_get(flexpathWriteData.cm, NULL); */
- /* dropMsg->condition = wait; */
- /* EVsubmit_general(fileData->dropSource, dropMsg, drop_evgroup_msg_free, fileData->attrs); */
- /* //EVsubmit_general(fileData->dropSource, dropMsg, NULL, fileData->attrs); */
- /* // Will have to change when not using ctrl thread. */
- /* CMCondition_wait(flexpathWriteData.cm, wait); */
-
- /* fileData->readerStep++; */
- /* } */
-
- op_msg *ack = malloc(sizeof(op_msg));
- ack->file_name = strdup(fileData->name);
- ack->process_id = fileData->rank;
- ack->step = fileData->readerStep;
- ack->type = 2;
- ack->condition = close->condition;
- fileData->attrs = set_dst_rank_atom(fileData->attrs, close->process_id + 1);
- EVsubmit_general(fileData->opSource,
- ack,
- op_free,
- fileData->attrs);
-
-}
-
-
-static int
-var_handler(CManager cm, void *vevent, void *client_data, attr_list attrs)
-{
- FlexpathWriteFileData* fileData = (FlexpathWriteFileData*) client_data;
- Var_msg* msg = (Var_msg*) vevent;
- fp_verbose(fileData, " var_msg received and queued\n");
- EVtake_event_buffer(cm, vevent);
- threaded_enqueue(&fileData->controlQueue, msg, VAR,
- &fileData->controlMutex, &fileData->controlCondition, -1);
- return 0;
-}
-
-static int
-flush_handler(CManager cm, void* vevent, void* client_data, attr_list attrs)
-{
- FlexpathWriteFileData* fileData = (FlexpathWriteFileData*) client_data;
- Flush_msg* msg = (Flush_msg*) vevent;
- int err = EVtake_event_buffer(cm, vevent);
- fp_verbose(fileData, "flush_msg received and queued\n");
- threaded_enqueue(&fileData->controlQueue, msg, DATA_FLUSH,
- &fileData->controlMutex, &fileData->controlCondition,
- -1);
- //fprintf(stderr, "writer:%d:enqueued flush for reader:%d:reader_step:%d:writer_step:%d\n", fileData->rank, msg->process_id, fileData->readerStep, fileData->writerStep);
- return 0;
-}
-
-static int
-drop_evgroup_handler(CManager cm, void *vevent, void *client_data, attr_list attrs) {
- FlexpathWriteFileData* fileData = (FlexpathWriteFileData*) client_data;
- drop_evgroup_msg *msg = vevent;
- // will have to change when not using control thread.
- fp_verbose(fileData, "got drop evgroup message, signalling\n");
- CMCondition_signal(cm, msg->condition);
- return 0;
-}
-
-static int
-op_handler(CManager cm, void* vevent, void* client_data, attr_list attrs)
-{
- FlexpathWriteFileData* fileData = (FlexpathWriteFileData*) client_data;
- op_msg* msg = (op_msg*) vevent;
- EVtake_event_buffer(cm, vevent);
- fp_verbose(fileData, " op_msg received, message type %d\n", msg->type);
- if(msg->type == OPEN_MSG) {
- fp_verbose(fileData, " enqueueing open msg, bridge %d, step %d\n", msg->process_id, msg->step);
- threaded_enqueue(&fileData->controlQueue, msg, OPEN,
- &fileData->controlMutex, &fileData->controlCondition, -1);
- } else if(msg->type == CLOSE_MSG) {
- fp_verbose(fileData, " enqueueing close msg, bridge %d, step %d\n", msg->process_id, msg->step);
- threaded_enqueue(&fileData->controlQueue, msg, CLOSE,
- &fileData->controlMutex, &fileData->controlCondition, -1);
- } else if(msg->type == FINALIZE_MSG) {
- fp_verbose(fileData, " enqueueing finalize msg, bridge %d\n", msg->process_id);
- threaded_enqueue(&fileData->controlQueue, msg, FINALIZE,
- &fileData->controlMutex, &fileData->controlCondition, -1);
- }
- return 0;
-}
-
-// processes messages from control queue
-void
-control_thread(void *arg)
-{
- FlexpathWriteFileData *fileData = (FlexpathWriteFileData*)arg;
- int rank = fileData->rank;
- FlexpathQueueNode *controlMsg;
- FlexpathQueueNode *dataNode;
- while (1) {
-// fp_verbose(fileData, " Control thread waiting on msg\n");
- if ((controlMsg = threaded_dequeue(&fileData->controlQueue,
- &fileData->controlMutex, &fileData->controlCondition, 0))) {
-// fp_verbose(fileData, " Control thread got a msg\n");
- if (controlMsg->type==VAR) {
- Var_msg *varMsg = (Var_msg*) controlMsg->data;
- process_var_msg(fileData, varMsg);
- EVreturn_event_buffer(flexpathWriteData.cm,controlMsg->data);
- }
- else if (controlMsg->type==DATA_FLUSH) {
- Flush_msg *flushMsg = (Flush_msg*)controlMsg->data;
- dataNode = threaded_peek(&fileData->dataQueue,
- &fileData->dataMutex,
- &fileData->dataCondition);
- process_data_flush(fileData, flushMsg, dataNode);
-
- }
- else if (controlMsg->type==OPEN) {
- op_msg *open = (op_msg*) controlMsg->data;
- process_open_msg(fileData, open);
- EVreturn_event_buffer(flexpathWriteData.cm, open);
- }
- else if (controlMsg->type==FINALIZE) {
- op_msg *open = (op_msg*) controlMsg->data;
- process_finalize_msg(fileData, open);
- EVreturn_event_buffer(flexpathWriteData.cm, open);
- }
- else if (controlMsg->type==CLOSE) {
- op_msg* close = (op_msg*) controlMsg->data;
- process_close_msg(fileData, close);
- EVreturn_event_buffer(flexpathWriteData.cm, close);
- }
- else {
- log_error("control_thread: Unrecognized Control Message\n");
- }
- }
- }
- return;
-}
-
// adds an open file handle to global open file list
void
add_open_file(FlexpathWriteFileData* newFile)
@@ -1406,42 +1023,115 @@ find_open_file(char* name)
return file;
}
+FlexpathWriteFileData*
+find_flexpath_fileData(void *adios_file_data)
+{
+ FlexpathWriteFileData* file = flexpathWriteData.openFiles;
+ while (file && (file->adios_file_data != adios_file_data)) {
+ file = file->next;
+ }
+ return file;
+}
+
void
stone_close_handler(CManager cm, CMConnection conn, int closed_stone, void *client_data)
{
FlexpathWriteFileData* file = flexpathWriteData.openFiles;
+ fp_verbose(file, "IN STONE CLOSE_HANDLER, closed stone %d\n", closed_stone);
while (file) {
int i;
- for (i=0; i < file->numBridges; i++) {
- if (file->bridges[i].myNum == closed_stone) {
- int j;
- file->bridges[i].opened = 0;
- for (j=0; j< file->numBridges; j++) {
- if (file->bridges[j].opened == 1) {
- /* if any bridge still open, simply return at this point, we're done */
- return;
- }
- }
- /* no bridges in this file still open, drop all data */
- drop_queued_data(file, -1);
+ for (i=0; i < 1; i++) {
+ int j;
+ subscriber_info sub = file->subscribers;
+ for (j=0; j < sub->numBridges; j++) {
+ if (sub->bridges[j].bridge_stoneID == closed_stone) {
+ int cond = sub->final_condition;
+ sub->final_condition = -1;
+ sub->bridges[j].opened = 0;
+ sub->parent_file->failed = 1;
+ if (cond != -1) {
+ /* hearing from one is sufficient for waiting */
+ fp_verbose(file, "IN STONE CLOSE_HANDLER, signaling final condition for File %p, subscriber %p\n", file, sub);
+ CMCondition_signal(cm, cond);
+ }
+ }
}
}
file = file->next;
}
}
+extern void
+reader_register_handler(CManager cm, CMConnection conn, void *vmsg, void *client_data, attr_list attrs)
+{
+ int i;
+ reader_register_msg *msg = (reader_register_msg *)vmsg;
+ FlexpathWriteFileData *fileData = (void*)msg->writer_file;
+ subscriber_info sub = fileData->subscribers;
+ sub->numBridges = msg->contact_count;
+ sub->reader_0_conn = conn;
+ sub->reader_file = msg->reader_file;
+ CMConnection_add_reference(conn);
+ char *recv_buf;
+ char ** recv_buf_ptr = CMCondition_get_client_data(cm, msg->condition);
+ recv_buf = (char *)calloc(sub->numBridges, CONTACT_LENGTH);
+ fp_verbose(fileData, "Reader Register handler called, will signal condition %d!\n", msg->condition);
+ int total_num_readers;
+ sub->total_num_readers = msg->contact_count;
+ for (i = 0; i < msg->contact_count; i++) {
+ strcpy(&recv_buf[i*CONTACT_LENGTH], msg->contacts[i]);
+ //Writer_reader_information, done this way to keep the determining logic in one place (currently on the reader side)
+ }
+
+ *recv_buf_ptr = recv_buf;
+
+
+ CMCondition_signal(cm, msg->condition);
+}
+
+static void
+fp_verbose_wrapper(char *format, ...)
+{
+ static int fp_verbose_set = -1;
+ static int MPI_rank = -1;
+ if (fp_verbose_set == -1) {
+ fp_verbose_set = (getenv("FLEXPATH_VERBOSE") != NULL);
+ MPI_Comm_rank(MPI_COMM_WORLD, &MPI_rank);
+ }
+ if (fp_verbose_set) {
+ va_list args;
+
+ va_start(args, format);
+ fprintf(stdout, "%s %d:", FLEXPATH_SIDE, MPI_rank);
+ vfprintf(stdout, format, args);
+ va_end(args);
+ }
+}
+
// Initializes flexpath write local data structures
extern void
adios_flexpath_init(const PairStruct *params, struct adios_method_struct *method)
{
- setenv("CMSelfFormats", "1", 1);
+ static cod_extern_entry externs[] = { {"fp_verbose", (void*) 0}, {NULL, NULL}};
// global data structure creation
flexpathWriteData.rank = -1;
flexpathWriteData.openFiles = NULL;
-
+
+ // setup ATOMS for attribute lists
+ RANK_ATOM = attr_atom_from_string(FP_RANK_ATTR_NAME);
+ TIMESTEP_ATOM = attr_atom_from_string(FP_TIMESTEP);
+ SCALAR_ATOM = attr_atom_from_string(FP_ONLY_SCALARS);
+ NATTRS = attr_atom_from_string(FP_NATTRS);
+ CM_TRANSPORT = attr_atom_from_string("CM_TRANSPORT");
+ QUEUE_SIZE = attr_atom_from_string("queue_size");
+
+ externs[0].extern_value = fp_verbose_wrapper;
+
// setup CM
+ setenv("CMSelfFormats", "1", 1);
flexpathWriteData.cm = CManager_create();
+ EVadd_standard_routines(flexpathWriteData.cm, "void fp_verbose(string format, ...);", externs);
atom_t CM_TRANSPORT = attr_atom_from_string("CM_TRANSPORT");
char * transport = getenv("CMTransport");
if (transport == NULL) {
@@ -1459,27 +1149,29 @@ adios_flexpath_init(const PairStruct *params, struct adios_method_struct *method
attr_list listen_list = create_attr_list();
add_attr(listen_list, CM_TRANSPORT, Attr_String, (attr_value)strdup(transport));
CMlisten_specific(flexpathWriteData.cm, listen_list);
+ free_attr_list(listen_list);
}
- // configuration setup
- //gen_pthread_init();
- setenv("CMSelfFormats", "1", 1);
-
// fork communications thread
int forked = CMfork_comm_thread(flexpathWriteData.cm);
if (!forked) {
- fprintf(stderr, "Wrtier error forking comm thread\n");
+ fprintf(stderr, "Writer error forking comm thread\n");
}
EVregister_close_handler(flexpathWriteData.cm, stone_close_handler, &flexpathWriteData);
+ CMFormat format = CMregister_simple_format(flexpathWriteData.cm, "Flexpath reader register", reader_register_field_list, sizeof(reader_register_msg));
+ CMregister_handler(format, reader_register_handler, NULL);
}
extern int
-adios_flexpath_open(struct adios_file_struct *fd,
- struct adios_method_struct *method,
- MPI_Comm comm)
-{
- if ( fd == NULL || method == NULL) {
+adios_flexpath_open(struct adios_file_struct *fd,
+ struct adios_method_struct *method,
+ MPI_Comm comm)
+{
+ EVaction split_action;
+ EVaction multi_action;
+ int i;
+ if (fd == NULL || method == NULL) {
perr("open: Bad input parameters\n");
return -1;
}
@@ -1491,191 +1183,203 @@ adios_flexpath_open(struct adios_file_struct *fd,
}
FlexpathWriteFileData *fileData = malloc(sizeof(FlexpathWriteFileData));
+ subscriber_info sub = malloc(sizeof(struct _flexpath_per_subscriber_info));
mem_check(fileData, "fileData");
memset(fileData, 0, sizeof(FlexpathWriteFileData));
fp_verbose_init(fileData);
- fileData->maxQueueSize = 1;
- fileData->use_ctrl_thread = 1;
+ fileData->maxQueueSize = 42;
if (method->parameters) {
- sscanf(method->parameters,"QUEUE_SIZE=%d;", &fileData->maxQueueSize);
+ sscanf(method->parameters, "QUEUE_SIZE=%d;", &fileData->maxQueueSize);
}
-
- // setup step state
- fileData->attrs = create_attr_list();
- fileData->openCount = 0;
- //fileData->readerStep = 0;
-
- pthread_mutex_init(&fileData->controlMutex, NULL);
- pthread_mutex_init(&fileData->dataMutex, NULL);
- pthread_mutex_init(&fileData->openMutex, NULL);
-
- pthread_cond_init(&fileData->controlCondition, NULL);
- pthread_cond_init(&fileData->dataCondition, NULL);
+
+ pthread_mutex_init(&fileData->queue_size_mutex, NULL);
+ pthread_cond_init(&fileData->queue_size_condition, NULL);
// communication channel setup
char writer_info_filename[200];
- char writer_ready_filename[200];
- char reader_info_filename[200];
- char reader_ready_filename[200];
+ char writer_info_tmp[200];
- int i=0;
+ i = 0;
flexpathWriteData.rank = fileData->rank;
fileData->globalCount = 0;
- // mpi setup
+ // mpi setup, why?
MPI_Comm_dup(comm, &fileData->mpiComm);
MPI_Comm_rank((fileData->mpiComm), &fileData->rank);
MPI_Comm_size((fileData->mpiComm), &fileData->size);
char *recv_buff = NULL;
- char sendmsg[CONTACT_LENGTH];
+ char sendmsg[CONTACT_LENGTH] = {0};
if (fileData->rank == 0) {
- recv_buff = (char *) malloc(fileData->size*CONTACT_LENGTH*sizeof(char));
+ recv_buff = (char *)malloc(fileData->size * CONTACT_LENGTH * sizeof(char));
}
-
+
+ fileData->subscribers = sub;
+ sub->parent_file = fileData;
+ sub->multiStone = EValloc_stone(flexpathWriteData.cm);
+ sub->splitStone = EValloc_stone(flexpathWriteData.cm);
+ sub->sinkStone = EValloc_stone(flexpathWriteData.cm);
+
// send out contact string
- char * contact = attr_list_to_string(CMget_contact_list(flexpathWriteData.cm));
- fileData->multiStone = EValloc_stone(flexpathWriteData.cm);
- fileData->sinkStone = EValloc_stone(flexpathWriteData.cm);
- sprintf(&sendmsg[0], "%d:%s", fileData->multiStone, contact);
+ char *contact = attr_list_to_string(CMget_contact_list(flexpathWriteData.cm));
+ sprintf(&sendmsg[0], "%d:%s", sub->multiStone, contact);
MPI_Gather(sendmsg, CONTACT_LENGTH, MPI_CHAR, recv_buff,
- CONTACT_LENGTH, MPI_CHAR, 0, (fileData->mpiComm));
+ CONTACT_LENGTH, MPI_CHAR, 0, (fileData->mpiComm));
+ fp_verbose(fileData, "Gather of writer contact data to rank 0 is complete\n");
+ //TODO: recv_buff has a small memory leak here because of register_reader_handler
// rank 0 prints contact info to file
if (fileData->rank == 0) {
sprintf(writer_info_filename, "%s_%s", fd->name, "writer_info.txt");
- FILE* writer_info = fopen(writer_info_filename,"w");
- for (i=0; i<fileData->size; i++) {
- fprintf(writer_info, "%s\n",&recv_buff[i*CONTACT_LENGTH]);
+ sprintf(writer_info_tmp, "%s_%s", fd->name, "writer_info.tmp");
+ FILE *writer_info = fopen(writer_info_filename, "w");
+ int condition = CMCondition_get(flexpathWriteData.cm, NULL);
+ fp_verbose(fileData, "Setting condition %d\n", condition);
+ CMCondition_set_client_data(flexpathWriteData.cm, condition, &recv_buff);
+ fprintf(writer_info, "%d\n", condition);
+ fprintf(writer_info, "%p\n", fileData);
+ for (i = 0; i < fileData->size; i++) {
+ fprintf(writer_info, "%s\n", &recv_buff[i * CONTACT_LENGTH]);
}
fclose(writer_info);
+ rename(writer_info_tmp, writer_info_filename);
+ free(recv_buff);
+ fp_verbose(fileData, "wrote writer information to writer_info file %s, waiting for condition %d\n", writer_info_filename, condition);
+ /* wait for reader to wake up, tell us he's ready (and provide his contact info) */
+
+ CMCondition_wait(flexpathWriteData.cm, condition);
+ /* recv_buff and fileData->numBridges have been filled in by the reader_register_handler */
+ MPI_Bcast(&sub->numBridges, 1, MPI_INT, 0, MPI_COMM_WORLD);
+ MPI_Bcast(&sub->total_num_readers, 1, MPI_INT, 0, MPI_COMM_WORLD);
+ MPI_Bcast(recv_buff, sub->numBridges * CONTACT_LENGTH, MPI_CHAR, 0, MPI_COMM_WORLD);
+ unlink(writer_info_filename);
+ } else {
+ MPI_Bcast(&sub->numBridges, 1, MPI_INT, 0, MPI_COMM_WORLD);
+ MPI_Bcast(&sub->total_num_readers, 1, MPI_INT, 0, MPI_COMM_WORLD);
+ recv_buff = (char *)malloc(sub->numBridges * CONTACT_LENGTH * sizeof(char));
+ MPI_Bcast(recv_buff, sub->numBridges * CONTACT_LENGTH, MPI_CHAR, 0, MPI_COMM_WORLD);
}
- // poll file - race condition issues
- FILE* reader_ready = NULL;
- sprintf(reader_ready_filename, "%s_%s", fd->name, "reader_ready.txt");
- while (!reader_ready) {
- reader_ready = fopen(reader_ready_filename,"r");
- }
- fclose(reader_ready);
-
- // read contact list
- sprintf(reader_info_filename, "%s_%s", fd->name, "reader_info.txt");
- FILE* reader_info = fopen(reader_info_filename, "r");
- if (!reader_info) {
- reader_info = fopen(reader_info_filename, "r");
- }
- char in_contact[CONTACT_LENGTH] = "";
- int numBridges = 0;
- int stone_num;
// build a bridge per line
- while (fscanf(reader_info, "%d:%s",&stone_num, in_contact)!=EOF) {
- //fprintf(stderr, "reader contact: %d:%s\n", stone_num, in_contact);
- fileData->bridges = realloc(fileData->bridges, sizeof(FlexpathStone) * (numBridges + 1));
+ int numBridges = sub->numBridges;
+ sub->bridges = malloc(sizeof(FlexpathStone) * numBridges);
+ for (i = 0; i < numBridges; i++) {
+ char in_contact[CONTACT_LENGTH];
+ int their_main_stone;
+ int their_sink_stone;
+ sscanf(&recv_buff[i * CONTACT_LENGTH], "%d:%s", &their_main_stone,
+ in_contact);
+ // fprintf(stderr, "reader contact: %d:%s\n", stone_num, in_contact);
attr_list contact_list = attr_list_from_string(in_contact);
- fileData->bridges[numBridges].opened = 0;
- fileData->bridges[numBridges].created = 0;
- fileData->bridges[numBridges].step = 0;
- fileData->bridges[numBridges].theirNum = stone_num;
- fileData->bridges[numBridges].contact = strdup(in_contact);
- numBridges += 1;
+ sub->bridges[i].opened = 1;
+ sub->bridges[i].created = 1;
+ sub->bridges[i].step = 0;
+ sub->bridges[i].reader_stoneID = their_main_stone;
+ sub->bridges[i].contact = strdup(in_contact);
}
- fileData->numBridges = numBridges;
- fclose(reader_info);
MPI_Barrier((fileData->mpiComm));
-
- // cleanup of reader files (writer is done with it).
- if (fileData->rank == 0) {
- unlink(reader_info_filename);
- unlink(reader_ready_filename);
- }
-
- //process group format
+ // process group format
struct adios_group_struct *t = method->group;
if (t == NULL) {
- adios_error(err_invalid_group, "Invalid group.\n");
- return err_invalid_group;
+ adios_error(err_invalid_group, "Invalid group.\n");
+ return err_invalid_group;
}
fileData->host_language = t->adios_host_language_fortran;
struct adios_var_struct *fields = t->vars;
-
+
if (fields == NULL) {
- adios_error(err_invalid_group, "Group has no variables.\n");
- return err_invalid_group;
- }
+ adios_error(err_invalid_group, "Group has no variables.\n");
+ return err_invalid_group;
+ }
fileData->fm = set_format(t, fields, fileData);
-
// attach rank attr and add file to open list
- fileData->name = strdup(method->group->name);
+ fileData->name = strdup(method->group->name);
+ fileData->adios_file_data = fd;
add_open_file(fileData);
- atom_t rank_atom = attr_atom_from_string(FP_RANK_ATTR_NAME);
- add_int_attr(fileData->attrs, rank_atom, fileData->rank);
-
- //generate multiqueue function that sends formats or all data based on flush msg
-
- FMStructDescList queue_list[] = {flush_format_list,
- var_format_list,
- op_format_list,
- evgroup_format_list,
- drop_evgroup_msg_format_list,
- data_format_list,
- update_step_msg_format_list,
- NULL};
- char* q_action_spec = create_multityped_action_spec(queue_list,
- multiqueue_action);
- fileData->multi_action = EVassoc_multi_action(flexpathWriteData.cm,
- fileData->multiStone,
- q_action_spec,
- NULL);
- fileData->dataSource = EVcreate_submit_handle(flexpathWriteData.cm,
- fileData->multiStone,
- fileData->fm->format);
-
- fileData->opSource = EVcreate_submit_handle(flexpathWriteData.cm,
- fileData->multiStone,
- op_format_list);
-
- fileData->offsetSource = EVcreate_submit_handle(flexpathWriteData.cm,
- fileData->multiStone,
- evgroup_format_list);
- fileData->dropSource = EVcreate_submit_handle(flexpathWriteData.cm,
- fileData->multiStone,
- drop_evgroup_msg_format_list);
-
- fileData->stepSource = EVcreate_submit_handle(flexpathWriteData.cm,
- fileData->multiStone,
- update_step_msg_format_list);
-
- EVassoc_terminal_action(flexpathWriteData.cm, fileData->sinkStone,
- var_format_list, var_handler, fileData);
- EVassoc_terminal_action(flexpathWriteData.cm, fileData->sinkStone,
- op_format_list, op_handler, fileData);
- EVassoc_terminal_action(flexpathWriteData.cm, fileData->sinkStone,
- drop_evgroup_msg_format_list, drop_evgroup_handler, fileData);
- EVassoc_terminal_action(flexpathWriteData.cm, fileData->sinkStone,
- flush_format_list, flush_handler, fileData);
-
- //link multiqueue to sink
- EVaction_set_output(flexpathWriteData.cm, fileData->multiStone,
- fileData->multi_action, 0, fileData->sinkStone);
-
+ // Template for all other attrs set here
+
+ //generate multiqueue function that sends formats or all data based on data request msg
+
+ FMStructDescList queue_list[] = {read_request_format_list,
+ finalize_close_msg_format_list,
+ queue_size_msg_format_list,
+ data_format_list,
+ NULL};
+
+ char *q_action_spec = create_multityped_action_spec(queue_list, multiqueue_action);
+
+ multi_action = EVassoc_multi_action(flexpathWriteData.cm, sub->multiStone, q_action_spec, NULL);
+ split_action = EVassoc_split_action(flexpathWriteData.cm, sub->splitStone, NULL);
+
+ EVassoc_terminal_action(flexpathWriteData.cm, sub->sinkStone, finalize_close_msg_format_list,
+ finalize_msg_handler, fileData);
+ EVassoc_terminal_action(flexpathWriteData.cm, sub->sinkStone, queue_size_msg_format_list,
+ queue_size_msg_handler, fileData);
+ //This is just set so the first get_attr doesn't throw an error message
+ attr_list multiqueue_stone_attrs = EVextract_attr_list(flexpathWriteData.cm, sub->multiStone);
+ add_int_attr(multiqueue_stone_attrs, QUEUE_SIZE, 0);
+
+ sub->dataSource = EVcreate_submit_handle(flexpathWriteData.cm, sub->multiStone,
+ fileData->fm->format);
+
+ sub->scalarDataSource = EVcreate_submit_handle(flexpathWriteData.cm, sub->splitStone,
+ fileData->fm->format);
+
+ sub->offsetSource = EVcreate_submit_handle(flexpathWriteData.cm, sub->splitStone,
+ evgroup_format_list);
+
+ sub->finalizeSource = EVcreate_submit_handle(flexpathWriteData.cm, sub->splitStone,
+ finalize_close_msg_format_list);
+
+ // link multiqueue to sink
+
+ EVaction_set_output(flexpathWriteData.cm, sub->multiStone,
+ multi_action, 0, sub->sinkStone);
+
+ // Set each output to the rank + 1 and preserve the 0 output for a sink
+ // stone just in case
+ // we need it for control one day
+ for (i = 0; i < numBridges; i++) {
+ sub->bridges[i].bridge_stoneID = EVcreate_bridge_action(
+ flexpathWriteData.cm,
+ attr_list_from_string(sub->bridges[i].contact),
+ sub->bridges[i].reader_stoneID);
+
+ EVaction_set_output(flexpathWriteData.cm, sub->multiStone,
+ multi_action, i + 1,
+ sub->bridges[i].bridge_stoneID);
+ }
+
+ // Set up split stone to peer'd readers
+ for (i = 0; i < sub->total_num_readers; i++) {
+ if ((i % fileData->size) == fileData->rank) {
+ EVaction_add_split_target(flexpathWriteData.cm,
+ sub->splitStone, split_action,
+ sub->bridges[i].bridge_stoneID);
+ }
+ }
+
FMContext my_context = create_local_FMcontext();
fileData->fm->ioFormat = register_data_format(my_context, fileData->fm->format);
-
- sprintf(writer_ready_filename, "%s_%s", fd->name, "writer_ready.txt");
+
+ // Set this up here so that the reader can close without waiting for the end
+ // of the stream
+ sub->final_condition = CMCondition_get(flexpathWriteData.cm, NULL);
+
if (fileData->rank == 0) {
- FILE* writer_info = fopen(writer_ready_filename, "w");
- fprintf(writer_info, "ready");
- fclose(writer_info);
- }
-
- pthread_create(&fileData->ctrl_thr_id, NULL, (void*)&control_thread, fileData);
- return 0;
+ reader_go_msg go_msg;
+ go_msg.reader_file = sub->reader_file;
+ go_msg.start_timestep = 0;
+ CMFormat format = CMregister_simple_format(flexpathWriteData.cm, "Flexpath reader go", reader_go_field_list, sizeof(reader_go_msg));
+ fp_verbose(fileData, "Writer Rank 0 sending GO message to reader rank 0\n");
+ CMwrite(sub->reader_0_conn, format, &go_msg);
+ }
+ return 0;
}
@@ -1702,8 +1406,9 @@ adios_flexpath_write(
FMFieldList flist = fm->format[0].field_list;
FMField *field = NULL;
- char *fullname = resolve_path_name(f->path, f->name);
- field = internal_find_field(fullname, flist);
+ char *fullname = append_path_name(f->path, f->name);
+ char *mangle_name = flexpath_mangle(fullname);
+ field = internal_find_field(mangle_name, flist);
if (field != NULL) {
//scalar quantity
@@ -1712,7 +1417,8 @@ adios_flexpath_write(
//why wouldn't it have data?
if (f->type == adios_string) {
char *tmpstr = strdup((char*)data);
- set_FMPtrField_by_name(flist, fullname, fm->buffer, tmpstr);
+ if (!set_FMPtrField_by_name(flist, mangle_name, fm->buffer, tmpstr))
+ fprintf(stderr, "Set fmprtfield by name failed, name %s\n", mangle_name);
} else {
memcpy(&fm->buffer[field->field_offset], data, field->field_size);
}
@@ -1729,7 +1435,9 @@ adios_flexpath_write(
for (a = d->altList.lh_first; a != NULL; a = a->entries.le_next) {
if (f->type == adios_string) {
char *tmpstr = strdup((char*)data);
- set_FMPtrField_by_name(flist, fullname, fm->buffer, tmpstr);
+ if (!set_FMPtrField_by_name(flist, mangle_name, fm->buffer, tmpstr))
+ fprintf(stderr, "Set2 fmprtfield by name failed, name %s\n", mangle_name);
+
//(strcpy(&fm->buffer[a->field->field_offset], (char*)data));
} else {
memcpy(&fm->buffer[a->field->field_offset],
@@ -1747,21 +1455,18 @@ adios_flexpath_write(
//vector quantity
if (data) {
struct adios_dimension_struct *dims = f->dimensions;
- int arraysize = 0;
+ int arraysize = field->field_size;
while (dims) {
int size = adios_get_dim_value(&dims->dimension);
- if (arraysize) {
- arraysize *= size;
- }
- else
- arraysize = size;
+ arraysize *= size;
dims = dims->next;
}
- arraysize *= field->field_size;
void *datacpy = malloc(arraysize);
//void *temp = get_FMPtrField_by_name(flist, fullname, fm->buffer, 0);
memcpy(datacpy, data, arraysize);
- set_FMPtrField_by_name(flist, fullname, fm->buffer, datacpy);
+ if (!set_FMPtrField_by_name(flist, mangle_name, fm->buffer, datacpy))
+ fprintf(stderr, "Set3 fmprtfield by name failed, name %s\n", mangle_name);
+
} else {
log_error("adios_flexpath_write: no array data found for var: %s. Bad.\n", f->name);
}
@@ -1769,114 +1474,265 @@ adios_flexpath_write(
}
}
+static void
+exchange_dimension_data(struct adios_file_struct *fd, evgroup *gp, FlexpathWriteFileData *fileData)
+{
+ // process local offsets here
+ struct adios_pg_struct * pg = fd->pgs_written;
+ struct adios_group_struct * g = fd->group;
+ int num_gbl_vars = 0;
+ global_var * gbl_vars = malloc(sizeof(global_var));
+ int num_vars = 0;
+ int myrank = fileData->rank;
+ int commsize = fileData->size;
+ int send_count = 0; /* dimension count, sending size and offset per */
+ uint64_t *send_block = malloc(1);
+
+ while (pg) {
+ struct adios_var_struct * list = pg->vars_written;
+ while (list) {
+ char *fullname = append_path_name(list->path, list->name);
+ //int num_local_offsets = 0;
+ uint64_t *local_offsets = NULL;
+ uint64_t *local_dimensions = NULL;
+ uint64_t *global_dimensions = NULL; // same at each rank.
+ int ndims = get_var_offsets(list, g, &local_offsets,
+ &local_dimensions, &global_dimensions);
+
+ if (ndims == 0) {
+ list=list->next;
+ continue;
+ }
+
+ // flip for fortran here.
+ if (fileData->host_language == FP_FORTRAN_MODE) {
+ reverse_dims(local_offsets, ndims);
+ reverse_dims(local_dimensions, ndims);
+ reverse_dims(global_dimensions, ndims);
+ }
+
+ send_block = realloc(send_block, (send_count + ndims * 2) * sizeof(send_block[0]));
+ memcpy(&send_block[send_count], local_dimensions, ndims * sizeof(send_block[0]));
+ memcpy(&send_block[send_count+ndims], local_offsets, ndims * sizeof(send_block[0]));
+
+
+ offset_struct *ostruct = malloc(sizeof(offset_struct));
+ ostruct->offsets_per_rank = ndims;
+ ostruct->total_offsets = ndims * commsize;
+ ostruct->global_dimensions = global_dimensions;
+
+ num_gbl_vars++;
+ gbl_vars = realloc(gbl_vars, sizeof(global_var) * num_gbl_vars);
+ gbl_vars[num_gbl_vars - 1].name = fullname;
+ gbl_vars[num_gbl_vars - 1].noffset_structs = 1;
+ gbl_vars[num_gbl_vars - 1].offsets = ostruct;
+
+ send_count += ndims * 2;
+ list=list->next;
+ }
+ pg = pg->next;
+ }
+ int buf_size = send_count * commsize * sizeof(uint64_t);
+ uint64_t *comm_block = malloc(buf_size);
+
+ MPI_Allgather(send_block, send_count, MPI_UINT64_T,
+ comm_block, send_count, MPI_UINT64_T,
+ fileData->mpiComm);
+
+ pg = fd->pgs_written;
+ int block_index = 0;
+ int gbl_var_index = 0;
+ while (pg) {
+ struct adios_var_struct * list = pg->vars_written;
+ while (list) {
+ int i, ndims = get_dim_count(list);
+
+ if (ndims == 0) {
+ list=list->next;
+ continue;
+ }
+
+ uint64_t *all_offsets = malloc(ndims*commsize*sizeof(uint64_t));
+ uint64_t *all_local_dims = malloc(ndims*commsize*sizeof(uint64_t));
+
+
+ // extract dimensions for rank i from comm block
+ //block_index = which global variable
+ //i = which MPI rank
+ //send_count = size of the total number of global variables per process * numdimensions * 2
+ for (i = 0; i < commsize; i++) {
+ memcpy(&all_local_dims[i*ndims], &comm_block[i*send_count + block_index], ndims * sizeof(send_block[0]));
+ memcpy(&all_offsets[i*ndims], &comm_block[i*send_count + block_index + ndims], ndims * sizeof(send_block[0]));
+ }
+ gbl_vars[gbl_var_index].offsets->local_offsets = all_offsets;
+ gbl_vars[gbl_var_index].offsets->local_dimensions = all_local_dims;
+
+ gbl_var_index++;
+ block_index += ndims * 2;
+ list=list->next;
+ }
+
+ pg = pg->next;
+ }
+
+ free(comm_block);
+ if (num_gbl_vars == 0) {
+ free(gbl_vars);
+ gbl_vars = NULL;
+ }
+ gp->num_vars = num_gbl_vars;
+ gp->vars = gbl_vars;
+ //fileData->gp = gp;
+}
+
+extern void
+adios_flexpath_feedback_handler(struct adios_file_struct *fd,
+ FMStructDescList format_list,
+ EVSimpleHandlerFunc handler, void *client_data)
+{
+ static int first = 1;
+ static atom_t global_stone_ID;
+ if (first) {
+ /*
+ * we don't have a means of assigning these truely "globally", so we'll leverage the 32-bit
+ * atom name hashing mechanisms (which we use in ATL and rely upon to hopefully avoid collisions)
+ */
+ global_stone_ID = attr_atom_from_string("flexpath feedback stone");
+ global_stone_ID |= 0x80000000;
+ first = 0;
+ }
+ FlexpathWriteFileData* fileData = find_flexpath_fileData(fd);
+ subscriber_info sub = fileData->subscribers;
+ CMadd_stone_to_global_lookup(flexpathWriteData.cm, sub->sinkStone, global_stone_ID);
+ EVassoc_terminal_action(flexpathWriteData.cm, sub->sinkStone, format_list,
+ handler, client_data);
+}
+
+
+
+/* This function is used to free the data when it is no longer needed by EVPath */
+static void
+free_data_buffer(void * event_data, void * client_data)
+{
+ free(event_data);
+}
+
+void
+set_attributes_in_buffer(FlexpathWriteFileData *fileData, struct adios_group_struct *group, char *buffer)
+{
+ struct adios_attribute_struct *attr;
+ FlexpathFMStructure* fm = fileData->fm;
+ FMFieldList flist = fm->format[0].field_list;
+ for (attr = group->attributes; attr != NULL; attr = attr->next) {
+ FMField *field = NULL;
+ char *fullname = append_path_name(attr->path, attr->name);
+ char *mangle_name = flexpath_mangle(fullname);
+ field = internal_find_field(mangle_name, flist);
+
+ if (field != NULL) {
+ void *data = attr->value;
+ if (attr->type == adios_string) {
+ char *tmpstr = strdup((char*)data);
+ if (!set_FMPtrField_by_name(flist, mangle_name, buffer, tmpstr))
+ fp_verbose(fileData, "Set fmprtfield by name failed, name %s\n", mangle_name);
+ } else {
+ memcpy(&buffer[field->field_offset], data, field->field_size);
+ }
+ }
+ }
+}
+
+/*Flexpath_close:
+
+ In this function we send out the global metadata and the scalars to our
+ EVsources that are connected to the split stone for this member of the writer cohort.
+ The split stone is connected in adios_open to the bridge stones of the appropriate reader
+ cohort members. In addition we send all of the available data on this writer cohort to
+ the multiqueue stone, where it is stored and managed.
+
+ There exists a single MPI_ALL_Gather operation in the exchange_dimension_data function in
+ adios_close. This is the synchronization point for the writers and it does not exist in the
+ absence of global variables.
+*/
extern void
adios_flexpath_close(struct adios_file_struct *fd, struct adios_method_struct *method)
{
+ attr_list attrs = create_attr_list();
FlexpathWriteFileData *fileData = find_open_file(method->group->name);
- void *buffer = malloc(fileData->fm->size);
- memcpy(buffer, fileData->fm->buffer, fileData->fm->size);
+ subscriber_info sub = fileData->subscribers;
fp_verbose(fileData, " adios_flexpath_close called\n");
- threaded_enqueue(&fileData->dataQueue, buffer,
- DATA_BUFFER,
- &fileData->dataMutex,
- &fileData->dataCondition,
- fileData->maxQueueSize);
+
+ //Timestep attr needed for raw handler on the reader side to determine which timestep the piece of data is
+ //refering too.
+ add_int_attr(attrs, RANK_ATOM, fileData->rank);
+ add_int_attr(attrs, NATTRS, fileData->fm->nattrs);
+ set_int_attr(attrs, TIMESTEP_ATOM, fileData->writerStep);
+
+ //We create two attr_lists because we reference count them underneath and the two messages that we
+ //send out have got to be different. We want to identify what is the only scalars message on the
+ //reader side to process it differently.
+ attr_list temp_attr_scalars = attr_copy_list(attrs);
+ attr_list temp_attr_noscalars = attr_copy_list(attrs);
// now gather offsets and send them via MPI to root
- struct adios_group_struct * g = fd->group;
- struct adios_pg_struct * pg = fd->pgs_written;
evgroup *gp = malloc(sizeof(evgroup));
+ memset(gp, 0, sizeof(evgroup));
gp->group_name = strdup(method->group->name);
gp->process_id = fileData->rank;
- if (fileData->globalCount == 0 ) {
+ gp->step = fileData->writerStep;
+ set_attributes_in_buffer(fileData, method->group, fileData->fm->buffer);
+
+ if (fileData->globalCount == 0 ) {
gp->num_vars = 0;
- gp->step = fileData->writerStep;
gp->vars = NULL;
- EVsubmit_general(fileData->offsetSource, gp, evgroup_msg_free, fileData->attrs);
- }
-
- else {
- // process local offsets here
- int num_gbl_vars = 0;
- global_var * gbl_vars = NULL;
- int num_vars = 0;
- int myrank = fileData->rank;
- int commsize = fileData->size;
-
- while (pg) {
- struct adios_var_struct * list = pg->vars_written;
- while (list) {
- char *fullname = resolve_path_name(list->path, list->name);
- //int num_local_offsets = 0;
- uint64_t *local_offsets = NULL;
- uint64_t *local_dimensions = NULL;
- uint64_t *global_dimensions = NULL; // same at each rank.
- int num_local_offsets = get_var_offsets(list, g,
- &local_offsets,
- &local_dimensions,
- &global_dimensions);
- // flip for fortran here.
- if (fileData->host_language == FP_FORTRAN_MODE) {
- reverse_dims(local_offsets, num_local_offsets);
- reverse_dims(local_dimensions, num_local_offsets);
- reverse_dims(global_dimensions, num_local_offsets);
- }
-
- if (num_local_offsets > 0) {
- uint64_t *all_offsets = NULL;
- uint64_t *all_local_dims = NULL;
-
- int buf_size = num_local_offsets * commsize * sizeof(uint64_t);
- all_offsets = malloc(buf_size);
- all_local_dims = malloc(buf_size);
+ } else {
+ //Synchronization point due to MPI_All_Gather operation
+ exchange_dimension_data(fd, gp, fileData);
+ }
- int arr_size = num_local_offsets * sizeof(uint64_t);
- MPI_Allgather(local_offsets, arr_size, MPI_BYTE,
- all_offsets, arr_size, MPI_BYTE,
- fileData->mpiComm);
+ //Used to strip out the array data and send only scalar data, array data is stripped out by setting pointer to NULL
+ void* temp = copy_buffer_without_array(fileData->fm->buffer, fileData);
+
+ set_int_attr(temp_attr_scalars, SCALAR_ATOM, 1);
+ set_int_attr(temp_attr_noscalars, SCALAR_ATOM, 0);
- MPI_Allgather(local_dimensions, arr_size, MPI_BYTE,
- all_local_dims, arr_size, MPI_BYTE,
- fileData->mpiComm);
+ //Need to make a copy as we reuse the fileData->fm in every step...
+ void *buffer = malloc(fileData->fm->size);
+ memcpy(buffer, fileData->fm->buffer, fileData->fm->size);
- num_gbl_vars++;
- offset_struct *ostruct = malloc(sizeof(offset_struct));
- ostruct->offsets_per_rank = num_local_offsets;
- ostruct->total_offsets = num_local_offsets * commsize;
- ostruct->local_offsets = all_offsets;
- ostruct->local_dimensions = all_local_dims;
- ostruct->global_dimensions = global_dimensions;
+ //Submit the messages that will get forwarded on immediately to the designated readers through split stone
+ EVsubmit_general(sub->offsetSource, gp, NULL, temp_attr_scalars);
+ EVsubmit_general(sub->scalarDataSource, temp, free_data_buffer, temp_attr_scalars);
- gbl_vars = realloc(gbl_vars, sizeof(global_var) * num_gbl_vars);
- gbl_vars[num_gbl_vars - 1].name = fullname;
- gbl_vars[num_gbl_vars - 1].noffset_structs = 1;
- gbl_vars[num_gbl_vars - 1].offsets = ostruct;
+ //Testing against the maxqueuesize
+ int current_queue_size;
+ attr_list multiqueue_attrs = EVextract_attr_list(flexpathWriteData.cm, sub->multiStone);
+ if(!get_int_attr(multiqueue_attrs, QUEUE_SIZE, ¤t_queue_size)) {
+ fprintf(stderr, "Error: Couldn't find queue_size in multiqueue stone attrs!\n");
+ }
- }
- list=list->next;
- }
+ while(current_queue_size == fileData->maxQueueSize) {
+ pthread_mutex_lock(&(fileData->queue_size_mutex));
+ fp_verbose(fileData, "Waiting for queue to become less full on timestep: %d\n", fileData->writerStep);
+ pthread_cond_wait(&(fileData->queue_size_condition), &(fileData->queue_size_mutex));
+ fp_verbose(fileData, "Received queue_size signal!\n");
+ pthread_mutex_unlock(&(fileData->queue_size_mutex));
- pg = pg->next;
+ if(!get_int_attr(multiqueue_attrs, QUEUE_SIZE, ¤t_queue_size)) {
+ fprintf(stderr, "Error: Couldn't find queue_size in multiqueue stone attrs!\n");
}
-
- gp->num_vars = num_gbl_vars;
- gp->step = fileData->writerStep;
- gp->vars = gbl_vars;
- //fileData->gp = gp;
}
-
- update_step_msg *stepmsg = malloc(sizeof(update_step_msg));
- stepmsg->finalized = 0;
- stepmsg->step = fileData->writerStep;
- stepmsg->condition = -1;
- EVsubmit_general(fileData->stepSource, stepmsg, update_step_msg_free, fileData->attrs);
-
- fileData->attrs = set_size_atom(fileData->attrs, fileData->size);
- EVsubmit_general(fileData->offsetSource, gp, evgroup_msg_free, fileData->attrs);
+
+ //Full data is submitted to multiqueue stone
+ EVsubmit_general(sub->dataSource, buffer, free_data_buffer, temp_attr_noscalars);
+
+ free_attr_list(temp_attr_scalars);
+ free_attr_list(temp_attr_noscalars);
fileData->writerStep++;
+ fp_verbose(fileData, " adios_flexpath_close exit\n");
}
// wait until all open files have finished sending data to shutdown
@@ -1885,24 +1741,39 @@ adios_flexpath_finalize(int mype, struct adios_method_struct *method)
{
FlexpathWriteFileData* fileData = flexpathWriteData.openFiles;
fp_verbose(fileData, "adios_flexpath_finalize called\n");
- while(fileData) {
-
- update_step_msg *stepmsg = malloc(sizeof(update_step_msg));
- stepmsg->finalized = 1;
- stepmsg->step = fileData->writerStep - 1;
- stepmsg->condition = -1;
- EVsubmit_general(fileData->stepSource, stepmsg, update_step_msg_free, fileData->attrs);
-
- pthread_mutex_lock(&fileData->dataMutex);
- while (fileData->dataQueue != NULL) {
- fp_verbose(fileData, " Wait in flexpath finalize\n");
- pthread_cond_wait(&fileData->dataCondition, &fileData->dataMutex);
- }
- pthread_mutex_unlock(&fileData->dataMutex);
+ subscriber_info sub = fileData->subscribers;
+ while(fileData) {
+ attr_list attrs = create_attr_list();
+ finalize_close_msg end_msg;
+ if (fileData->failed) {
+ fp_verbose(fileData, "adios_flexpath_finalize file %p already-failed output stream, rolling on\n", fileData);
+ } else {
+ int cond;
+ end_msg.finalize = 1;
+ end_msg.close = 1;
+ end_msg.final_timestep = fileData->writerStep;
+ add_int_attr(attrs, RANK_ATOM, fileData->rank);
+ EVsubmit_general(sub->finalizeSource, &end_msg, NULL, attrs);
+ free_attr_list(attrs);
+
+ fp_verbose(fileData, "Sent finalize message to readers \n");
+
+ /*TODO:Very Bad!!! This means that our finalization is not going to be able to
+ differentiate between streams...but the API doesn't support that yet, so...*/
+ cond = sub->final_condition;
+ if (cond != -1) {
+ fp_verbose(fileData, "Waiting on condition %d for the reader to be done!\n", cond);
+ CMCondition_wait(flexpathWriteData.cm, cond);
+ }
+ fp_verbose(fileData, "Finished Wait for reader cohort to be finished!\n");
+ }
fileData->finalized = 1;
fileData = fileData->next;
}
+
+ //fp_verbose(fileData, "Finished all waits! Exiting finalize method now!\n");
+
}
// provides unknown functionality
diff --git a/src/write/adios_icee.c b/src/write/adios_icee.c
index 99dca22..0a03f78 100644
--- a/src/write/adios_icee.c
+++ b/src/write/adios_icee.c
@@ -40,7 +40,7 @@
#include "core/util.h"
#include "core/adios_logger.h"
#include "core/adios_clock.h"
-
+#include "core/adiost_callback_internal.h"
#ifdef HAVE_ICEE
@@ -222,6 +222,7 @@ job_cleanup(thr_pool_t *pool)
static void *
worker_thread(void *arg)
{
+ ADIOST_CALLBACK_ENTER(adiost_event_thread, NULL, "ICEE worker thread");
thr_pool_t *pool = (thr_pool_t *)arg;
int timedout;
job_t *job;
@@ -302,6 +303,7 @@ worker_thread(void *arg)
}
}
pthread_cleanup_pop(1); /* worker_cleanup(pool) */
+ ADIOST_CALLBACK_EXIT(adiost_event_thread, NULL, "ICEE worker thread");
return (NULL);
}
diff --git a/src/write/adios_mpi.c b/src/write/adios_mpi.c
index bf0c642..46df727 100644
--- a/src/write/adios_mpi.c
+++ b/src/write/adios_mpi.c
@@ -290,6 +290,12 @@ static void init_mpi_chain(MPI_Comm comm)
{
MPI_Recv (&token, 1, MPI_INT, rank-1, rank-1, comm, &status);
}
+
+ // Wait for Isend to complete before otherwise the request variable may disappear from the stack
+ if (rank < size-1)
+ {
+ MPI_Wait(&req, &status);
+ }
}
void adios_mpi_init (const PairStruct * parameters
diff --git a/src/write/adios_mpi_amr.c b/src/write/adios_mpi_amr.c
index 981b6c2..7f5c740 100644
--- a/src/write/adios_mpi_amr.c
+++ b/src/write/adios_mpi_amr.c
@@ -29,6 +29,7 @@
#include "core/buffer.h"
#include "core/util.h"
#include "core/adios_logger.h"
+#include "core/adiost_callback_internal.h"
#if defined ADIOS_TIMERS || defined ADIOS_TIMER_EVENTS
#include "core/adios_timing.h"
@@ -921,6 +922,7 @@ void * adios_mpi_amr_do_mkdir (char * path)
void * adios_mpi_amr_do_open_thread (void * param)
{
+ ADIOST_CALLBACK_ENTER(adiost_event_thread, NULL, __func__);
struct adios_MPI_thread_data_open * td = (struct adios_MPI_thread_data_open *) param;
int err;
@@ -948,6 +950,7 @@ void * adios_mpi_amr_do_open_thread (void * param)
td->md->subfile_name, e);
}
+ ADIOST_CALLBACK_ENTER(adiost_event_thread, NULL, __func__);
return NULL;
}
@@ -1046,6 +1049,7 @@ void * adios_mpi_amr_do_reopen_thread (void * param)
void * adios_mpi_amr_do_write_thread (void * param)
{
+ ADIOST_CALLBACK_ENTER(adiost_event_thread, NULL, __func__);
struct adios_MPI_thread_data_write * td = (struct adios_MPI_thread_data_write *) param;
uint64_t count = adios_mpi_amr_striping_unit_write(
@@ -1062,6 +1066,7 @@ void * adios_mpi_amr_do_write_thread (void * param)
count, td->total_data_size);
}
+ ADIOST_CALLBACK_EXIT(adiost_event_thread, NULL, __func__);
return NULL;
}
diff --git a/src/write/adios_posix.c b/src/write/adios_posix.c
index 35d6c66..e547e62 100644
--- a/src/write/adios_posix.c
+++ b/src/write/adios_posix.c
@@ -23,6 +23,7 @@
#include <mxml.h>
#include "public/adios_mpi.h" // MPI or dummy MPI for seq. build
+#include "public/adios_error.h"
#include "core/adios_transport_hooks.h"
#include "core/adios_bp_v1.h"
#include "core/adios_internals.h"
@@ -64,8 +65,10 @@ struct adios_POSIX_data_struct
int rank;
int size;
#endif
- int g_have_mdf;
+ int g_have_mdf; // = 1 write global metadata file
+ int local_fs; // = N every N processes are writing to a local file system
int file_is_open; // = 1 if in append mode we leave the file open (close at finalize)
+ char *filename; // remember the currently opened filename to recognize when user suddenly changes to another one
int index_is_in_memory; // = 1 when index is kept in memory, no need to read from file. =1 after first 'append/update' is completed but not after first 'write'.
uint64_t pg_start_next; // remember end of PG data for future append steps
@@ -99,10 +102,46 @@ void adios_posix_init (const PairStruct * parameters
p->size = 0;
#endif
p->g_have_mdf = 1;
+ p->local_fs = 0; // only rank 0 creates the directory for sub-files
p->file_is_open = 0; // = 1 when posix file is open (used in append mode only)
+ p->filename = NULL;
p->index_is_in_memory = 0;
p->pg_start_next = 0;
p->total_bytes_written = 0;
+
+
+ // process user parameters
+ const PairStruct *ps = parameters;
+ while (ps) {
+ if (!strcasecmp (ps->name, "have_metadata_file"))
+ {
+ errno = 0;
+ p->g_have_mdf = strtol(ps->value, NULL, 10);
+ if (!errno) {
+ log_debug ("Parameter 'have_metadata_file' set to %d for POSIX write method\n",
+ p->g_have_mdf);
+ } else {
+ log_error ("Invalid 'have_metadata_file' parameter given to the POSIX write "
+ "method: '%s'\n", ps->value);
+ }
+ }
+ else if (!strcasecmp (ps->name, "local-fs"))
+ {
+ errno = 0;
+ p->local_fs = strtol(ps->value, NULL, 10);
+ if (!errno) {
+ log_debug ("Parameter 'local-fs' set to %d for POSIX write method\n",
+ p->local_fs);
+ } else {
+ log_error ("Invalid 'local-fs' parameter given to the POSIX write "
+ "method: '%s'\n", ps->value);
+ }
+ } else {
+ log_error ("Parameter name %s is not recognized by the POSIX write "
+ "method\n", ps->name);
+ }
+ ps = ps->next;
+ }
}
@@ -128,25 +167,6 @@ int adios_posix_open (struct adios_file_struct * fd
struct adios_POSIX_data_struct * p = (struct adios_POSIX_data_struct *)
method->method_data;
- char *temp_string, *m_size;
-
- temp_string = a2s_trim_spaces (method->parameters);
- if ( (m_size = strstr (temp_string, "have_metadata_file")) )
- {
- char * m = strchr (m_size, '=');
- char * n = strtok (m, ";");
-
- if (!n)
- p->g_have_mdf = atoi (n + 1);
- else
- p->g_have_mdf = atoi (m + 1);
- }
- else
- {
- // by default, write metadata file.
- p->g_have_mdf = 1;
- }
- free (temp_string);
#if defined ADIOS_TIMERS || defined ADIOS_TIMER_EVENTS
int timer_count = 8;
@@ -246,6 +266,27 @@ START_TIMER (ADIOS_TIMER_AD_OPEN);
fd->subfile_index = p->rank; // Only if HAVE_MPI
#endif
+ // if an app writes multiple files with each multiple steps,
+ // i.e. with a w,a,a,a then w to another filename pattern, then
+ // we need to free up stuff kept in memory about the previous file
+ if (!p->filename) {
+ //printf ("ADIOS POSIX Open: First filename %s\n", subfile_name);
+ p->filename = strdup(subfile_name);
+ } else if (strcmp(subfile_name, p->filename)) {
+ //printf ("ADIOS POSIX Open: Change filename %s\n", subfile_name);
+ if (p->file_is_open) {
+ //printf ("ADIOS POSIX Open: Clear up previous file %s\n", p->filename);
+ adios_clear_index_v1 (p->index); // append and update methods never cleared the index and kept file open
+ adios_posix_close_internal (&p->b);
+ p->file_is_open = 0;
+ p->index_is_in_memory = 0;
+ p->b.end_of_pgs = 0;
+ }
+ free (p->filename);
+ p->filename = strdup(subfile_name);
+ }
+
+
p->total_bytes_written = 0; // counts bytes written only in this open()..close() step
switch (fd->mode)
@@ -255,7 +296,7 @@ START_TIMER (ADIOS_TIMER_AD_OPEN);
p->b.f = open (subfile_name, O_RDONLY | O_LARGEFILE);
if (p->b.f == -1)
{
- fprintf (stderr, "ADIOS POSIX: file not found: %s\n", fd->name);
+ log_error("ADIOS POSIX: file not found: %s\n", fd->name);
free (subfile_name);
@@ -275,8 +316,15 @@ START_TIMER (ADIOS_TIMER_AD_OPEN);
// create dir to keep all the subfiles
if (p->group_comm != MPI_COMM_SELF)
{
- if (p->rank == 0)
+ /* p->local_fs controls who creates directories.
+ local_fs = 0 means only rank 0 does
+ local_fs = N means every Nth rank does
+ */
+ if ( (p->local_fs == 0 && p->rank == 0) ||
+ (p->local_fs > 0 && p->rank % p->local_fs == 0)
+ )
{
+ log_debug ("ADIOS POSIX: mkdir by rank %d\n", p->rank);
char * dir_name = malloc (strlen (fd->name) + 4 + 1);
sprintf (dir_name, "%s%s"
, fd->name
@@ -297,7 +345,7 @@ START_TIMER (ADIOS_TIMER_AD_OPEN);
);
if (p->b.f == -1)
{
- fprintf (stderr, "adios_posix_open failed for "
+ log_error("adios_posix_open failed for "
"base_path %s, subfile name %s\n"
,method->base_path, subfile_name
);
@@ -322,7 +370,7 @@ START_TIMER (ADIOS_TIMER_AD_OPEN);
);
if (p->mf == -1)
{
- fprintf (stderr, "adios_posix_open failed for "
+ log_error("adios_posix_open failed for "
"base_path %s, metadata file name %s\n"
,method->base_path, mdfile_name
);
@@ -382,7 +430,7 @@ START_TIMER (ADIOS_TIMER_AD_OPEN);
S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH);
if (p->b.f == -1)
{
- fprintf (stderr, "adios_posix_open failed to create file %s\n" ,subfile_name);
+ log_error("adios_posix_open failed to create file %s\n" ,subfile_name);
free (subfile_name);
free (mdfile_name);
@@ -414,7 +462,7 @@ START_TIMER (ADIOS_TIMER_AD_OPEN);
);
if (p->mf == -1)
{
- fprintf (stderr, "adios_posix_open failed to create file %s\n" ,mdfile_name);
+ log_error("adios_posix_open failed to create file %s\n" ,mdfile_name);
free (subfile_name);
free (mdfile_name);
@@ -482,7 +530,7 @@ START_TIMER (ADIOS_TIMER_AD_OPEN);
break;
default:
- fprintf (stderr, "Unknown bp version: %d. "
+ log_error("Unknown bp version: %d. "
"Cannot append\n"
,version
);
@@ -514,7 +562,7 @@ START_TIMER (ADIOS_TIMER_AD_OPEN);
default:
{
- fprintf (stderr, "Unknown file mode: %d\n", fd->mode);
+ log_error("Unknown file mode: %d\n", fd->mode);
free (subfile_name);
free (mdfile_name);
@@ -600,7 +648,7 @@ void adios_posix_get_write_buffer (struct adios_file_struct * fd
if (!*buffer)
{
adios_method_buffer_free (mem_allowed);
- fprintf (stderr, "Out of memory allocating %" PRIu64 " bytes for %s\n"
+ log_error("Out of memory allocating %" PRIu64 " bytes for %s\n"
,*size, v->name
);
v->got_buffer = adios_flag_no;
@@ -621,7 +669,7 @@ void adios_posix_get_write_buffer (struct adios_file_struct * fd
else
{
adios_method_buffer_free (mem_allowed);
- fprintf (stderr, "OVERFLOW: Cannot allocate requested buffer of %" PRIu64 " "
+ log_error("OVERFLOW: Cannot allocate requested buffer of %" PRIu64 " "
"bytes for %s\n"
,*size
,v->name
@@ -659,6 +707,8 @@ static void adios_posix_write_pg (struct adios_file_struct * fd
off_t offset = fd->current_pg->pg_start_in_file;
/* FIXME: what is this check? Should never happen ? */
+ //printf ("%s: p->b.end_of_pgs = %" PRIu64 " fd->current_pg->pg_start_in_file = %"
+ // PRIu64 "\n", __func__, p->b.end_of_pgs, fd->current_pg->pg_start_in_file);
assert (p->b.end_of_pgs <= fd->current_pg->pg_start_in_file);
if (p->b.end_of_pgs > fd->current_pg->pg_start_in_file)
offset = p->b.end_of_pgs;
@@ -669,30 +719,33 @@ static void adios_posix_write_pg (struct adios_file_struct * fd
lseek (p->b.f, offset, SEEK_SET);
- if (fd->bytes_written > MAX_MPIWRITE_SIZE)
- {
- to_write = MAX_MPIWRITE_SIZE;
- }
- else
- {
- to_write = (int32_t) fd->bytes_written;
- }
-
while (bytes_written < fd->bytes_written)
{
- write (p->b.f, fd->buffer, to_write);
+ if (fd->bytes_written - bytes_written > MAX_MPIWRITE_SIZE)
+ {
+ to_write = MAX_MPIWRITE_SIZE;
+ }
+ else
+ {
+ to_write = fd->bytes_written - bytes_written;
+ }
+
+ ssize_t wrote = write (p->b.f, fd->buffer+bytes_written, to_write);
bytes_written += to_write;
- if (fd->bytes_written > bytes_written)
+
+ if (wrote == -1)
{
- if (fd->bytes_written - bytes_written > MAX_MPIWRITE_SIZE)
- {
- to_write = MAX_MPIWRITE_SIZE;
- }
- else
- {
- to_write = fd->bytes_written - bytes_written;
- }
+ adios_error (err_write_error, "Failure to write data to file %s by rank %d: %s\n",
+ fd->name, p->rank, strerror(errno));
+ break;
}
+ else if (wrote != to_write)
+ {
+ adios_error (err_write_error, "Failure to write data completely to file %s by rank %d: "
+ "Wanted to write %ld bytes to file at once but only %ld was written\n",
+ fd->name, p->rank, to_write, wrote);
+ }
+
}
p->total_bytes_written += bytes_written;
@@ -845,7 +898,7 @@ static void adios_posix_do_read (struct adios_file_struct * fd
}
default:
- fprintf (stderr, "POSIX read: file version unknown: %u\n", version);
+ log_error("POSIX read: file version unknown: %u\n", version);
return;
}
@@ -936,7 +989,7 @@ void adios_posix_close (struct adios_file_struct * fd
recv_buffer = malloc (total_size);
START_TIMER (ADIOS_TIMER_COMM);
- MPI_Gatherv (&size, 0, MPI_BYTE
+ MPI_Gatherv (buffer, 0, MPI_BYTE // 0 == index_sizes[0]
,recv_buffer, index_sizes, index_offsets
,MPI_BYTE, 0, p->group_comm
);
@@ -998,7 +1051,7 @@ void adios_posix_close (struct adios_file_struct * fd
STOP_TIMER (ADIOS_TIMER_IO);
if (s != global_index_buffer_offset)
{
- fprintf (stderr, "POSIX method tried to write %" PRIu64 ", "
+ log_error("POSIX method tried to write %" PRIu64 ", "
"only wrote %" PRId64 ". %s:%d\n"
,fd->bytes_written
,(int64_t)s
@@ -1013,13 +1066,13 @@ void adios_posix_close (struct adios_file_struct * fd
{
START_TIMER (ADIOS_TIMER_COMM);
// Added this explicit cast to avoid truncation of low-order bytes on BGP
- int i_buffer_size = (int) buffer_offset;
- MPI_Gather (&i_buffer_size, 1, MPI_INT
+ int i_buffer_offset = (int) buffer_offset;
+ MPI_Gather (&i_buffer_offset, 1, MPI_INT
,0, 0, MPI_INT
,0, p->group_comm
);
- MPI_Gatherv (buffer, i_buffer_size, MPI_BYTE
+ MPI_Gatherv (buffer, i_buffer_offset, MPI_BYTE
,0, 0, 0, MPI_BYTE
,0, p->group_comm
);
@@ -1094,7 +1147,7 @@ void adios_posix_close (struct adios_file_struct * fd
int * index_offsets = malloc (4 * p->size);
char * recv_buffer = 0;
int i;
- uint32_t size = buffer_size;
+ uint32_t size = buffer_offset;
uint32_t total_size = 0;
// Need to make a temporary copy of p->index and merge
@@ -1121,10 +1174,9 @@ void adios_posix_close (struct adios_file_struct * fd
}
recv_buffer = malloc (total_size);
- memcpy (recv_buffer, buffer, index_sizes[0]);
START_TIMER (ADIOS_TIMER_COMM);
- MPI_Gatherv (&size, 0, MPI_BYTE
+ MPI_Gatherv (buffer, index_sizes[0], MPI_BYTE
,recv_buffer, index_sizes, index_offsets
,MPI_BYTE, 0, p->group_comm
);
@@ -1190,7 +1242,7 @@ void adios_posix_close (struct adios_file_struct * fd
STOP_TIMER (ADIOS_TIMER_IO);
if (s != global_index_buffer_offset)
{
- fprintf (stderr, "POSIX method tried to write %" PRIu64 ", "
+ log_error("POSIX method tried to write %" PRIu64 ", "
"only wrote %" PRId64 ", Mode: a. %s:%d\n"
,global_index_buffer_offset
,(int64_t)s
@@ -1207,12 +1259,14 @@ void adios_posix_close (struct adios_file_struct * fd
else
{
START_TIMER (ADIOS_TIMER_COMM);
- MPI_Gather (&buffer_size, 1, MPI_INT
+ // Added this explicit cast to avoid truncation of low-order bytes on BGP
+ int i_buffer_offset = (int) buffer_offset;
+ MPI_Gather (&i_buffer_offset, 1, MPI_INT
,0, 0, MPI_INT
,0, p->group_comm
);
- MPI_Gatherv (buffer, buffer_size, MPI_BYTE
+ MPI_Gatherv (buffer, i_buffer_offset, MPI_BYTE
,0, 0, 0, MPI_BYTE
,0, p->group_comm
);
@@ -1248,7 +1302,7 @@ void adios_posix_close (struct adios_file_struct * fd
default:
{
- fprintf (stderr, "Unknown file mode: %d\n", fd->mode);
+ log_error("Unknown file mode: %d\n", fd->mode);
return;
}
@@ -1284,6 +1338,11 @@ void adios_posix_finalize (int mype, struct adios_method_struct * method)
adios_free_index_v1 (p->index);
+ if (p->filename) {
+ free (p->filename);
+ p->filename = NULL;
+ }
+
if (adios_posix_initialized)
adios_posix_initialized = 0;
}
diff --git a/src/zfp/Makefile.in b/src/zfp/Makefile.in
index 411d9e0..0cae0c3 100644
--- a/src/zfp/Makefile.in
+++ b/src/zfp/Makefile.in
@@ -100,7 +100,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -108,8 +108,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -341,6 +341,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -417,6 +421,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/C/Makefile.in b/tests/C/Makefile.in
index 6eaa73f..b29204f 100644
--- a/tests/C/Makefile.in
+++ b/tests/C/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -369,6 +369,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -445,6 +449,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/C/fgr_tests/Makefile.in b/tests/C/fgr_tests/Makefile.in
index 8795cf4..be1a734 100644
--- a/tests/C/fgr_tests/Makefile.in
+++ b/tests/C/fgr_tests/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -327,6 +327,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -403,6 +407,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/C/flexpath_tests/1D_arr_global/Makefile.in b/tests/C/flexpath_tests/1D_arr_global/Makefile.in
index 2a55814..497ad66 100644
--- a/tests/C/flexpath_tests/1D_arr_global/Makefile.in
+++ b/tests/C/flexpath_tests/1D_arr_global/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -335,6 +335,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -411,6 +415,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/C/flexpath_tests/1D_arr_global/reader.c b/tests/C/flexpath_tests/1D_arr_global/reader.c
index e67cb0a..0e8a44b 100644
--- a/tests/C/flexpath_tests/1D_arr_global/reader.c
+++ b/tests/C/flexpath_tests/1D_arr_global/reader.c
@@ -28,7 +28,7 @@
int main (int argc, char **argv){
- int rank =0, size =0;
+ int rank =0, writer_size =0;
int NX = 0;
double *t = NULL;
// this is an array we expect as a reference array
@@ -45,6 +45,10 @@ int main (int argc, char **argv){
MPI_Init( &argc, &argv);
MPI_Comm_rank (comm, &rank);
+ /*volatile int qur = 0;
+ while(qur == 0) { Wait for gdb }
+ MPI_Barrier(comm);*/
+
// depending on the method
SET_ERROR_IF_NOT_ZERO(adios_read_init_method(adios_opts.method, comm, adios_opts.adios_options), err.adios);
RET_IF_ERROR(err.adios, rank);
@@ -65,27 +69,20 @@ int main (int argc, char **argv){
// read how many processors wrote that array
avi = adios_inq_var (adios_handle, "size");
if (!avi){
- p_error("rank %d: Quitting ... (%d) %s\n", rank, adios_errno, adios_errmsg());
+ p_error("rank %d: Quitting no inq var for writer size... (%d) %s\n", rank, adios_errno, adios_errmsg());
CLOSE_ADIOS_READER(adios_handle, adios_opts.method);
return DIAG_ERR;
}
- size = *((int*)avi->value);
+ writer_size = *((int*)avi->value);
adios_free_varinfo(avi);
avi = NULL;
- // if I run the more readers than writers; just release
- // the excessive readers
- if (rank >= size){
- p_info("rank %d: I am an excessive rank. Nothing to read ...\n", rank);
- CLOSE_ADIOS_READER(adios_handle, adios_opts.method);
- return DIAG_OK;
- }
- // read the size of the array
+ // read the size of the array per process
avi = adios_inq_var (adios_handle, "NX");
if (!avi){
p_error("rank %d: Quitting ... (%d) %s\n", rank, adios_errno, adios_errmsg());
- CLOSE_ADIOS_READER(adios_handle, adios_opts.method);
+ CLOSE_ADIOS_READER(adios_handle, adios_opts.method)
return DIAG_ERR;
}
@@ -106,11 +103,11 @@ int main (int argc, char **argv){
uint64_t count[2] = {1,0};
count[1] = NX;
uint64_t start[2] = {0,0};
- start[0] = rank;
+ start[0] = rank % writer_size;
sel = adios_selection_boundingbox(2,start, count);
if( !sel ){
- p_error("rank %d: Quitting ... (%d) %s\n", rank, adios_errno, adios_errmsg());
+ p_error("rank %d: Quitting because no sel... (%d) %s\n", rank, adios_errno, adios_errmsg());
diag = DIAG_ERR;
goto close_adios;
}
@@ -119,45 +116,53 @@ int main (int argc, char **argv){
t = calloc(NX, sizeof(double));
if (adios_schedule_read(adios_handle, sel, "var_1d_array",0,1,t) != 0){
- p_error("rank %d: Quitting ...(%d) %s\n", rank, adios_errno, adios_errmsg());
+ p_error("rank %d: Quitting schedule read for var array failed...(%d) %s\n",
+ rank, adios_errno, adios_errmsg());
diag = DIAG_ERR;
goto just_clean;
}
// not sure if this assumption is correct; difficult to find in the ADIOS sources
if (adios_perform_reads(adios_handle, 1) != 0){
- p_error("rank %d: Quitting ...(%d) %s\n", rank, adios_errno, adios_errmsg());
+ p_error("rank %d: Couldn't perform the read...(%d) %s\n", rank, adios_errno, adios_errmsg());
diag = DIAG_ERR;
goto just_clean;
}
// make the reference array with reference values I expect to get
t_ref = calloc(NX, sizeof(double));
- gen_1D_array(t_ref, NX, rank);
+ gen_1D_array(t_ref, NX, (rank % writer_size));
// compare the values what you get with what you expect
int i = 0;
+ if(rank == 0)
+ {
+ printf("Reader received array: ");
+ }
for (i = 0; i < NX; ++i) {
+ if(rank == 0)
+ printf("%f ", t[i]);
if (t[i] != t_ref[i]) {
- p_test_failed("%s: rank %d: for t[%d] (expected %.1f, got %.1f)\n",
- test_result.name, rank, i, t_ref[i], t[i]);
+ test_failed(test_result.name, rank);
test_result.result = TEST_FAILED;
break;
}
}
+ if(rank == 0)
+ printf("\n");
if (TEST_PASSED == test_result.result)
- p_test_passed("%s: rank %d\n", test_result.name, rank);
+ test_passed(test_result.name, rank);
else
- p_test_failed("%s: rank %d\n", test_result.name, rank);
+ test_failed(test_result.name, rank);
adios_release_step(adios_handle);
// 0 - next available step, block for max 30 seconds until the next step
// is available
adios_advance_step(adios_handle, 0, 30);
- if (0 == adios_errno){
- printf("Rank %d: proceeding to the next step ...\n", rank);
+ if (err_end_of_stream == adios_errno){
+ printf("Rank %d: finished the step and moved on appropriately\n", rank);
} else {
printf("ERROR: adios_advance_step(); anyway Quitting ... Rank %d: (%d) %s\n", rank, adios_errno, adios_errmsg());
}
diff --git a/tests/C/flexpath_tests/1D_arr_global/writer.c b/tests/C/flexpath_tests/1D_arr_global/writer.c
index ec04dd6..33ac73d 100644
--- a/tests/C/flexpath_tests/1D_arr_global/writer.c
+++ b/tests/C/flexpath_tests/1D_arr_global/writer.c
@@ -17,9 +17,9 @@
#include "adios.h"
#include "adios_read.h" // for adios_errno
+#include "cfg.h"
#include "misc.h"
#include "utils.h"
-#include "cfg.h"
#include "test_common.h"
#include <stdio.h>
@@ -60,14 +60,27 @@ int main(int argc, char ** argv){
return DIAG_ERR;
}
+ if ((rank == 0) && test_verbose) {
+ printf("Writer side array: ");
+ int j;
+ for(j = 0; j < NX; j++)
+ {
+ printf("%f ", t[j]);
+ }
+ printf("\n");
+ }
+
+
uint64_t adios_groupsize, adios_totalsize;
// open with the group name as specified in the xml file
adios_open( &adios_handle, "temperature", FILE_NAME, "w", comm);
adios_groupsize = 4 + 4 + 4 + 8 * (NX);
retval=adios_group_size (adios_handle, adios_groupsize, &adios_totalsize);
- fprintf(stderr, "Rank=%d adios_group_size(): adios_groupsize=%" PRIu64 ", adios_totalsize=%" PRIu64 ", retval=%d\n",
- rank, adios_groupsize, adios_totalsize, retval);
+ if (test_verbose) {
+ fprintf(stderr, "Rank=%d adios_group_size(): adios_groupsize=%" PRIu64 ", adios_totalsize=%" PRIu64 ", retval=%d\n",
+ rank, adios_groupsize, adios_totalsize, retval);
+ }
// write; don't check errors for simplicity reasons
adios_write(adios_handle, "NX", &NX);
@@ -75,7 +88,9 @@ int main(int argc, char ** argv){
adios_write(adios_handle, "rank", &rank);
adios_write(adios_handle, "var_1d_array", t);
- fprintf(stderr, "Rank=%d committed write\n", rank);
+ if (test_verbose) {
+ fprintf(stderr, "Rank=%d committed write\n", rank);
+ }
adios_close(adios_handle);
@@ -83,6 +98,7 @@ int main(int argc, char ** argv){
adios_finalize(rank);
MPI_Finalize();
+
return DIAG_OK;
}
diff --git a/tests/C/flexpath_tests/1D_arr_global_noxml/Makefile.in b/tests/C/flexpath_tests/1D_arr_global_noxml/Makefile.in
index 8f11e6a..e602c49 100644
--- a/tests/C/flexpath_tests/1D_arr_global_noxml/Makefile.in
+++ b/tests/C/flexpath_tests/1D_arr_global_noxml/Makefile.in
@@ -102,7 +102,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -110,8 +110,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -342,6 +342,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -418,6 +422,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/C/flexpath_tests/1D_arr_global_noxml/writer.c b/tests/C/flexpath_tests/1D_arr_global_noxml/writer.c
index fab08c6..4425cf6 100644
--- a/tests/C/flexpath_tests/1D_arr_global_noxml/writer.c
+++ b/tests/C/flexpath_tests/1D_arr_global_noxml/writer.c
@@ -94,8 +94,10 @@ int main(int argc, char ** argv){
uint64_t adios_totalsize = 0;
retval=adios_group_size (adios_handle, adios_groupsize, &adios_totalsize);
- fprintf(stderr, "Rank=%d adios_group_size(): adios_groupsize=%" PRIu64 ", adios_totalsize=%" PRIu64 ", retval=%d\n",
- rank, adios_groupsize, adios_totalsize, retval);
+ if (test_verbose) {
+ fprintf(stderr, "Rank=%d adios_group_size(): adios_groupsize=%" PRIu64 ", adios_totalsize=%" PRIu64 ", retval=%d\n",
+ rank, adios_groupsize, adios_totalsize, retval);
+ }
// init the array that I will transport over the sea
if (gen_1D_array(t, NX, rank) == DIAG_ERR){
@@ -111,7 +113,9 @@ int main(int argc, char ** argv){
adios_write(adios_handle, "offsets", &offsets);
adios_write(adios_handle, "var_1d_array", t);
- fprintf(stderr, "Rank=%d committed write\n", rank);
+ if (test_verbose) {
+ fprintf(stderr, "Rank=%d committed write\n", rank);
+ }
adios_close(adios_handle);
diff --git a/tests/C/flexpath_tests/CMakeLists.txt b/tests/C/flexpath_tests/CMakeLists.txt
index ae40d2f..859f462 100644
--- a/tests/C/flexpath_tests/CMakeLists.txt
+++ b/tests/C/flexpath_tests/CMakeLists.txt
@@ -2,7 +2,6 @@ add_subdirectory(1D_arr_global)
add_subdirectory(1D_arr_global_noxml)
add_subdirectory(global_range_select)
add_subdirectory(maya_noxml)
-add_subdirectory(maya_append)
add_subdirectory(scalar)
file(COPY README DESTINATION ${PROJECT_BINARY_DIR}/tests/C/flexpath_tests/)
diff --git a/tests/C/flexpath_tests/Makefile.am b/tests/C/flexpath_tests/Makefile.am
index 5a751b4..8d9c6ab 100644
--- a/tests/C/flexpath_tests/Makefile.am
+++ b/tests/C/flexpath_tests/Makefile.am
@@ -1,4 +1,4 @@
-SUBDIRS=1D_arr_global 1D_arr_global_noxml global_range_select maya_noxml maya_append scalar
+SUBDIRS=1D_arr_global 1D_arr_global_noxml global_range_select maya_noxml scalar local_arrays
EXTRA_DIST = include/misc.h include/test_common.h include/utils.h
diff --git a/tests/C/flexpath_tests/Makefile.in b/tests/C/flexpath_tests/Makefile.in
index dddcd69..24bde93 100644
--- a/tests/C/flexpath_tests/Makefile.in
+++ b/tests/C/flexpath_tests/Makefile.in
@@ -99,7 +99,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -107,8 +107,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -333,6 +333,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -409,6 +413,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
@@ -477,7 +484,7 @@ target_alias = @target_alias@
top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
-SUBDIRS = 1D_arr_global 1D_arr_global_noxml global_range_select maya_noxml maya_append scalar
+SUBDIRS = 1D_arr_global 1D_arr_global_noxml global_range_select maya_noxml scalar local_arrays
EXTRA_DIST = include/misc.h include/test_common.h include/utils.h
all: all-recursive
diff --git a/tests/C/flexpath_tests/README b/tests/C/flexpath_tests/README
index 9d27d3d..a19edae 100644
--- a/tests/C/flexpath_tests/README
+++ b/tests/C/flexpath_tests/README
@@ -22,8 +22,6 @@ Existing Directories
* maya_noxml - inspired by maya; same variables written multiple times (doesn't work with Flexpath)
-* maya_append - inspired by maya; testing the append mode (doesn't work with Flexpath)
-
How to build and clean the build
--------------------------------
# build
@@ -74,7 +72,6 @@ TEST_PASSED 1D_arr_global: rank 0
TEST_PASSED 1D_arr_global: rank 1
TEST_PASSED 1D_arr_global_noxml: rank 0
TEST_PASSED 1D_arr_global_noxml: rank 1
-TEST_PASSED maya_append: rank 0
TEST_PASSED maya_noxml: rank 0
FLEXPATH transport (2013-09-04) - my laptop
@@ -86,7 +83,7 @@ TEST_PASSED 1D_arr_global: rank 1
TEST_PASSED 1D_arr_global_noxml: rank 0
TEST_PASSED 1D_arr_global_noxml: rank 1
-maya_append and maya_noxml tests failed
+maya_noxml tests failed
Some tests produced message
diff --git a/tests/C/flexpath_tests/common/utils.c b/tests/C/flexpath_tests/common/utils.c
index c3ac0ef..624b0ae 100644
--- a/tests/C/flexpath_tests/common/utils.c
+++ b/tests/C/flexpath_tests/common/utils.c
@@ -170,7 +170,7 @@ diag_t gen_1D_array_int(int *p_arr, int arr_len, int rank){
* DIAG_ERR if some errors, e.g., the option has not been found
*
*/
-diag_t get_options(struct adios_tsprt_opts * p_tsprt_opts, int argc, char ** argv, int *p_show_help){
+diag_t get_options(struct adios_tsprt_opts * p_tsprt_opts, int argc, char ** argv, int *p_show_help, int *p_verbose){
diag_t diag = DIAG_OK;
int c;
@@ -182,16 +182,16 @@ diag_t get_options(struct adios_tsprt_opts * p_tsprt_opts, int argc, char ** arg
// assume that no showing help
*p_show_help = 0;
- while( (c = getopt(argc, argv, "ht:")) != -1){
+ while( (c = getopt(argc, argv, "hvt:")) != -1){
switch(c){
case 'h':
*p_show_help = 1;
break;
+ case 'v':
+ *p_verbose = 1;
+ break;
case 't':
cvalue = optarg;
- // by default I set adios options to be verbosed
- // TODO might be changed to the actual option
- strcpy(p_tsprt_opts->adios_options, "verbose=4; show hidden_attrs");
if (strcmp(cvalue, "flx") == 0){
p_tsprt_opts->method = ADIOS_READ_METHOD_FLEXPATH;
@@ -311,7 +311,7 @@ diag_t gen_maya_var_name(char *buf, int buf_size, char *maya_var_pfx, int number
}
memset(buf, 0, buf_size);
- sprintf(buf, "%s%d", maya_var_pfx, number);
+ sprintf(buf, "/%s%d", maya_var_pfx, number);
return DIAG_OK;
}
diff --git a/tests/C/flexpath_tests/global_range_select/CMakeLists.txt b/tests/C/flexpath_tests/global_range_select/CMakeLists.txt
index 2f60783..cf89e72 100644
--- a/tests/C/flexpath_tests/global_range_select/CMakeLists.txt
+++ b/tests/C/flexpath_tests/global_range_select/CMakeLists.txt
@@ -1,15 +1,15 @@
include_directories(${PROJECT_SOURCE_DIR}/src/public)
include_directories(${PROJECT_SOURCE_DIR}/src)
-include_directories(${PROJECT_SOURCE_DIR}/test/C/flexpath_tests/include)
+include_directories(${PROJECT_SOURCE_DIR}/tests/C/flexpath_tests/include)
include_directories(${PROJECT_BINARY_DIR}/src/public)
link_directories(${PROJECT_SOURCE_DIR}/src)
link_directories(${PROJECT_BINARY_DIR}/src)
-add_executable(arrays_writer arrays_write.c)
-target_link_libraries(arrays_writer adios ${ADIOSLIB_LDADD} ${MPI_C_LIBRARIES})
+add_executable(writer writer.c ../common/utils.c)
+target_link_libraries(writer adios ${ADIOSLIB_LDADD} ${MPI_C_LIBRARIES})
-add_executable(arrays_reader arrays_read.c)
-target_link_libraries(arrays_reader adios ${ADIOSLIB_LDADD} ${MPI_C_LIBRARIES})
+add_executable(reader reader.c ../common/utils.c)
+target_link_libraries(reader adios ${ADIOSLIB_LDADD} ${MPI_C_LIBRARIES})
-file(COPY arrays.xml DESTINATION ${PROJECT_BINARY_DIR}/tests/C/flexpath_tests/global_range_select)
+file(COPY test_config_flex.xml DESTINATION ${PROJECT_BINARY_DIR}/tests/C/flexpath_tests/global_range_select)
diff --git a/tests/C/flexpath_tests/global_range_select/Makefile.am b/tests/C/flexpath_tests/global_range_select/Makefile.am
index 396fb1d..dbf2578 100644
--- a/tests/C/flexpath_tests/global_range_select/Makefile.am
+++ b/tests/C/flexpath_tests/global_range_select/Makefile.am
@@ -1,21 +1,21 @@
AM_CPPFLAGS = $(all_includes)
AM_CPPFLAGS += -I$(top_builddir)/src/public -I$(top_srcdir)/src -I$(top_srcdir)/src/public -I$(srcdir)/../include
-AUTOMAKE_OPTIONS = no-dependencies
+AUTOMAKE_OPTIONS = no-dependencies subdir-objects
all-local:
test "$(srcdir)" = "$(builddir)" || cp $(srcdir)/*.xml $(builddir)
test "$(srcdir)" = "$(builddir)" || cp $(srcdir)/run_tests.pl $(builddir)
-noinst_PROGRAMS = arrays_write arrays_read
+noinst_PROGRAMS = writer_range reader_range
-arrays_write_SOURCES = arrays_write.c
-arrays_write_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
-arrays_write_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
-arrays_read_SOURCES = arrays_read.c
-arrays_read_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
-arrays_read_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
+writer_range_SOURCES = writer.c ../common/utils.c
+writer_range_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
+writer_range_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
+reader_range_SOURCES = reader.c ../common/utils.c
+reader_range_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
+reader_range_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
CLEANFILES = *.bp
CC=$(MPICC)
-EXTRA_DIST = arrays.xml run_tests.pl
+EXTRA_DIST = test_config_flex.xml run_tests.pl
diff --git a/tests/C/flexpath_tests/global_range_select/Makefile.in b/tests/C/flexpath_tests/global_range_select/Makefile.in
index bcde1a9..b84f58a 100644
--- a/tests/C/flexpath_tests/global_range_select/Makefile.in
+++ b/tests/C/flexpath_tests/global_range_select/Makefile.in
@@ -78,7 +78,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
-noinst_PROGRAMS = arrays_write$(EXEEXT) arrays_read$(EXEEXT)
+noinst_PROGRAMS = writer_range$(EXEEXT) reader_range$(EXEEXT)
subdir = tests/C/flexpath_tests/global_range_select
DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -125,25 +125,26 @@ CONFIG_HEADER = $(top_builddir)/config.h
CONFIG_CLEAN_FILES =
CONFIG_CLEAN_VPATH_FILES =
PROGRAMS = $(noinst_PROGRAMS)
-am_arrays_read_OBJECTS = arrays_read.$(OBJEXT)
-arrays_read_OBJECTS = $(am_arrays_read_OBJECTS)
+am__dirstamp = $(am__leading_dot)dirstamp
+am_reader_range_OBJECTS = reader.$(OBJEXT) ../common/utils.$(OBJEXT)
+reader_range_OBJECTS = $(am_reader_range_OBJECTS)
am__DEPENDENCIES_1 =
-arrays_read_DEPENDENCIES = $(top_builddir)/src/libadios.a \
+reader_range_DEPENDENCIES = $(top_builddir)/src/libadios.a \
$(am__DEPENDENCIES_1)
AM_V_lt = $(am__v_lt_ at AM_V@)
am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
am__v_lt_0 = --silent
am__v_lt_1 =
-arrays_read_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
+reader_range_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
- $(arrays_read_LDFLAGS) $(LDFLAGS) -o $@
-am_arrays_write_OBJECTS = arrays_write.$(OBJEXT)
-arrays_write_OBJECTS = $(am_arrays_write_OBJECTS)
-arrays_write_DEPENDENCIES = $(top_builddir)/src/libadios.a \
+ $(reader_range_LDFLAGS) $(LDFLAGS) -o $@
+am_writer_range_OBJECTS = writer.$(OBJEXT) ../common/utils.$(OBJEXT)
+writer_range_OBJECTS = $(am_writer_range_OBJECTS)
+writer_range_DEPENDENCIES = $(top_builddir)/src/libadios.a \
$(am__DEPENDENCIES_1)
-arrays_write_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
+writer_range_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
- $(arrays_write_LDFLAGS) $(LDFLAGS) -o $@
+ $(writer_range_LDFLAGS) $(LDFLAGS) -o $@
AM_V_P = $(am__v_P_ at AM_V@)
am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
am__v_P_0 = false
@@ -177,8 +178,8 @@ AM_V_CCLD = $(am__v_CCLD_ at AM_V@)
am__v_CCLD_ = $(am__v_CCLD_ at AM_DEFAULT_V@)
am__v_CCLD_0 = @echo " CCLD " $@;
am__v_CCLD_1 =
-SOURCES = $(arrays_read_SOURCES) $(arrays_write_SOURCES)
-DIST_SOURCES = $(arrays_read_SOURCES) $(arrays_write_SOURCES)
+SOURCES = $(reader_range_SOURCES) $(writer_range_SOURCES)
+DIST_SOURCES = $(reader_range_SOURCES) $(writer_range_SOURCES)
am__can_run_installinfo = \
case $$AM_UPDATE_INFO_DIR in \
n|no|NO) false;; \
@@ -334,6 +335,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -410,6 +415,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
@@ -481,15 +489,15 @@ top_srcdir = @top_srcdir@
AM_CPPFLAGS = $(all_includes) -I$(top_builddir)/src/public \
-I$(top_srcdir)/src -I$(top_srcdir)/src/public \
-I$(srcdir)/../include
-AUTOMAKE_OPTIONS = no-dependencies
-arrays_write_SOURCES = arrays_write.c
-arrays_write_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
-arrays_write_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
-arrays_read_SOURCES = arrays_read.c
-arrays_read_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
-arrays_read_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
+AUTOMAKE_OPTIONS = no-dependencies subdir-objects
+writer_range_SOURCES = writer.c ../common/utils.c
+writer_range_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
+writer_range_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
+reader_range_SOURCES = reader.c ../common/utils.c
+reader_range_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
+reader_range_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
CLEANFILES = *.bp
-EXTRA_DIST = arrays.xml run_tests.pl
+EXTRA_DIST = test_config_flex.xml run_tests.pl
all: all-am
.SUFFIXES:
@@ -533,17 +541,22 @@ clean-noinstPROGRAMS:
list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
echo " rm -f" $$list; \
rm -f $$list
+../common/$(am__dirstamp):
+ @$(MKDIR_P) ../common
+ @: > ../common/$(am__dirstamp)
+../common/utils.$(OBJEXT): ../common/$(am__dirstamp)
-arrays_read$(EXEEXT): $(arrays_read_OBJECTS) $(arrays_read_DEPENDENCIES) $(EXTRA_arrays_read_DEPENDENCIES)
- @rm -f arrays_read$(EXEEXT)
- $(AM_V_CCLD)$(arrays_read_LINK) $(arrays_read_OBJECTS) $(arrays_read_LDADD) $(LIBS)
+reader_range$(EXEEXT): $(reader_range_OBJECTS) $(reader_range_DEPENDENCIES) $(EXTRA_reader_range_DEPENDENCIES)
+ @rm -f reader_range$(EXEEXT)
+ $(AM_V_CCLD)$(reader_range_LINK) $(reader_range_OBJECTS) $(reader_range_LDADD) $(LIBS)
-arrays_write$(EXEEXT): $(arrays_write_OBJECTS) $(arrays_write_DEPENDENCIES) $(EXTRA_arrays_write_DEPENDENCIES)
- @rm -f arrays_write$(EXEEXT)
- $(AM_V_CCLD)$(arrays_write_LINK) $(arrays_write_OBJECTS) $(arrays_write_LDADD) $(LIBS)
+writer_range$(EXEEXT): $(writer_range_OBJECTS) $(writer_range_DEPENDENCIES) $(EXTRA_writer_range_DEPENDENCIES)
+ @rm -f writer_range$(EXEEXT)
+ $(AM_V_CCLD)$(writer_range_LINK) $(writer_range_OBJECTS) $(writer_range_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
+ -rm -f ../common/*.$(OBJEXT)
distclean-compile:
-rm -f *.tab.c
@@ -676,6 +689,7 @@ clean-generic:
distclean-generic:
-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+ -rm -f ../common/$(am__dirstamp)
maintainer-clean-generic:
@echo "This command is intended for maintainers to use"
diff --git a/tests/C/flexpath_tests/global_range_select/arrays_read.c b/tests/C/flexpath_tests/global_range_select/arrays_read.c
deleted file mode 100644
index a5c7989..0000000
--- a/tests/C/flexpath_tests/global_range_select/arrays_read.c
+++ /dev/null
@@ -1,113 +0,0 @@
-/*
- * ADIOS is freely available under the terms of the BSD license described
- * in the COPYING file in the top level directory of this source distribution.
- *
- * Copyright (c) 2008 - 2009. UT-BATTELLE, LLC. All rights reserved.
- */
-
-/*************************************************************/
-/* Example of reading arrays in ADIOS */
-/* which were written from the same number of processors */
-/* */
-/* Similar example is manual/2_adios_read.c */
-/*************************************************************/
-#include <stdio.h>
-#include <stdlib.h>
-#include <stdint.h>
-#include <string.h>
-#include "mpi.h"
-#include "adios.h"
-#include "public/adios_read.h"
-
-int main (int argc, char ** argv)
-{
- int rank, j;
- int NX, NY;
- double *t;
- MPI_Comm comm = MPI_COMM_WORLD;
-
- MPI_Init (&argc, &argv);
- MPI_Comm_rank (comm, &rank);
-
- adios_read_init_method(ADIOS_READ_METHOD_FLEXPATH, comm, "");
-
- ADIOS_SELECTION global_range_select;
- //if(rank == 0){
- global_range_select.type=ADIOS_SELECTION_BOUNDINGBOX;
- global_range_select.u.bb.start = malloc(sizeof(uint64_t)*2);
- global_range_select.u.bb.count = malloc(sizeof(uint64_t)*2);
- (global_range_select.u.bb.start)[0] = 0;
- (global_range_select.u.bb.count)[0] = 4;
- (global_range_select.u.bb.start)[1] = 0;
- (global_range_select.u.bb.count)[1] = 40;
- global_range_select.u.bb.ndim = 2;
-
- ADIOS_SELECTION scalar_block_select;
- scalar_block_select.type = ADIOS_SELECTION_WRITEBLOCK;
- scalar_block_select.u.block.index = rank;
- //fprintf(stderr, "app got here\n");
- /* schedule_read of a scalar. */
- int test_scalar = -1;
- ADIOS_FILE* afile = adios_read_open("arrays",
- ADIOS_READ_METHOD_FLEXPATH,
- comm,
- ADIOS_LOCKMODE_NONE, 0.0);
-
- int ii = 0;
- while(adios_errno != err_end_of_stream){
-
- /* get a bounding box - rank 0 for now*/
- ADIOS_VARINFO* nx_info = adios_inq_var( afile, "NX");
- ADIOS_VARINFO* ny_info = adios_inq_var( afile, "NY");
-
- if(nx_info->value) {
- NX = *((int *)nx_info->value);
- }
- if(ny_info->value){
- NY= *((int*)ny_info->value);
- }
-
- //printf("\trank=%d: NX=%d\n", rank, NX);
- //printf("\trank=%d: NY=%d\n", rank, NY);
-
- /* Allocate space for the arrays */
- int nelem = 160;
- int arr_size = sizeof(double) * nelem;
- t = (double *) malloc (arr_size);
- memset(t, 0, arr_size);
- //fprintf(stderr, "t %p\n", t);
-
- /* Read the arrays */
- adios_schedule_read (afile,
- &global_range_select,
- "var_2d_array",
- 0, 1, t);
- adios_schedule_read (afile,
- &scalar_block_select,
- "test_scalar",
- 0, 1, &test_scalar);
-
- adios_perform_reads (afile, 1);
-
- //sleep(20);
-
- printf("Rank=%d: test_scalar: %d step: %d, t[0,5+x] = [%6.2f", rank, test_scalar, ii, t[0]);
- for(j=0; j<nelem; j++) {
- printf(", %6.2f", t[j]);
- }
- printf("]\n");
- adios_release_step(afile);
- adios_advance_step(afile, 0, 30);
- ii++;
- //MPI_Barrier (comm);
- //sleep(1);
- }
- //
- adios_read_close(afile);
-
- adios_read_finalize_method(ADIOS_READ_METHOD_FLEXPATH);
-
- //MPI_Finalize ();
-
- return 0;
-}
diff --git a/tests/C/flexpath_tests/global_range_select/arrays_write.c b/tests/C/flexpath_tests/global_range_select/arrays_write.c
deleted file mode 100644
index 8c74518..0000000
--- a/tests/C/flexpath_tests/global_range_select/arrays_write.c
+++ /dev/null
@@ -1,58 +0,0 @@
-/*
- * ADIOS is freely available under the terms of the BSD license described
- * in the COPYING file in the top level directory of this source distribution.
- *
- * Copyright (c) 2008 - 2009. UT-BATTELLE, LLC. All rights reserved.
- */
-
-#include <stdio.h>
-#include <string.h>
-#include "mpi.h"
-#include "adios.h"
-
-/*************************************************************/
-/* Example of writing arrays in ADIOS */
-/* */
-/* Similar example is manual/2_adios_write.c */
-/*************************************************************/
-int main (int argc, char ** argv)
-{
- char filename [256];
- int rank, size, i;
- int NX = 40;
- int NY = 1;
- double t[NX];
- MPI_Comm comm = MPI_COMM_WORLD;
-
- int64_t adios_handle;
-
- MPI_Init (&argc, &argv);
- MPI_Comm_rank (comm, &rank);
- MPI_Comm_size (comm, &size);
-
- strcpy (filename, "arrays");
- adios_init ("arrays.xml", comm);
-
- int test_scalar = rank * 1000;
- int ii;
- for(ii = 0; ii<20; ii++){
- for (i = 0; i < NX; i++)
- t[i] = rank * NX + i;
-
- adios_open (&adios_handle, "temperature", filename, "w", comm);
-
- adios_write (adios_handle, "NX", &NX);
- adios_write (adios_handle, "NY", &NY);
- adios_write (adios_handle, "test_scalar", &test_scalar);
- adios_write (adios_handle, "size", &size);
- adios_write (adios_handle, "rank", &rank);
- adios_write (adios_handle, "var_2d_array", t);
-
- adios_close (adios_handle);
- fprintf(stderr, "Rank=%d commited write %d\n", rank, ii);
- }
- adios_finalize (rank);
-
- //MPI_Finalize ();
- return 0;
-}
diff --git a/tests/C/flexpath_tests/global_range_select/reader.c b/tests/C/flexpath_tests/global_range_select/reader.c
new file mode 100644
index 0000000..df9b0e5
--- /dev/null
+++ b/tests/C/flexpath_tests/global_range_select/reader.c
@@ -0,0 +1,132 @@
+/*
+ * ADIOS is freely available under the terms of the BSD license described
+ * in the COPYING file in the top level directory of this source distribution.
+ *
+ * Copyright (c) 2008 - 2009. UT-BATTELLE, LLC. All rights reserved.
+ */
+
+/*************************************************************/
+/* Example of reading arrays in ADIOS */
+/* which were written from the same number of processors */
+/* */
+/* Similar example is manual/2_adios_read.c */
+/*************************************************************/
+#include "adios.h"
+#include "mpi.h"
+#include "public/adios_read.h"
+#include <stdint.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+
+#include "misc.h"
+#include "test_common.h"
+#include "utils.h"
+
+int main(int argc, char **argv)
+{
+ int rank, j;
+ int NX, NY;
+ int writer_size;
+ double *t;
+ MPI_Comm comm = MPI_COMM_WORLD;
+ diag_t return_val;
+
+ struct err_counts err = {0, 0};
+ struct adios_tsprt_opts adios_opts;
+ struct test_info test_result = {TEST_PASSED, "global_range_select"};
+
+ GET_ENTRY_OPTIONS(
+ adios_opts,
+ "Runs readers.");
+ MPI_Init(&argc, &argv);
+ MPI_Comm_rank(comm, &rank);
+
+ SET_ERROR_IF_NOT_ZERO(adios_read_init_method(adios_opts.method, comm,
+ adios_opts.adios_options),
+ err.adios);
+ RET_IF_ERROR(err.adios, rank);
+
+ /* schedule_read of a scalar. */
+ int test_scalar = -1;
+ ADIOS_FILE *afile = adios_read_open(FILE_NAME, adios_opts.method, comm,
+ ADIOS_LOCKMODE_NONE, 0.0);
+
+ int ii = 0;
+ while (adios_errno != err_end_of_stream) {
+
+ /* get a bounding box - rank 0 for now*/
+ ADIOS_VARINFO *nx_info = adios_inq_var(afile, "NX");
+ ADIOS_VARINFO *ny_info = adios_inq_var(afile, "NY");
+ ADIOS_VARINFO *writer_size_info = adios_inq_var(afile, "size");
+
+ if (nx_info->value) {
+ NX = *((int *)nx_info->value);
+ } else {
+ test_failed(test_result.name, rank);
+ return_val = DIAG_ERR;
+ }
+
+ if (ny_info->value) {
+ NY = *((int *)ny_info->value);
+ } else {
+ test_failed(test_result.name, rank);
+ return_val = DIAG_ERR;
+ }
+
+ if (writer_size_info->value) {
+ writer_size = *((int *)writer_size_info->value);
+ } else {
+ test_failed(test_result.name, rank);
+ return_val = DIAG_ERR;
+ }
+
+ int sel_index = rank % writer_size;
+ int k;
+
+ /* Allocate space for the arrays */
+ ADIOS_SELECTION *global_range_select;
+ ADIOS_SELECTION *scalar_block_select;
+
+ int nelem = writer_size * NX * NY;
+ size_t arr_size = sizeof(double) * nelem;
+ t = (double *)malloc(arr_size);
+ memset(t, 0, arr_size);
+
+ uint64_t *start_array = malloc(sizeof(uint64_t) * (NY + 1));
+ uint64_t *count_array = malloc(sizeof(uint64_t) * (NY + 1));
+ start_array[0] = 0;
+ count_array[0] = writer_size;
+ for (k = 1; k < (NY + 1); ++k) {
+ start_array[k] = 0;
+ count_array[k] = NX;
+ }
+
+ global_range_select =
+ adios_selection_boundingbox((NY + 1), start_array, count_array);
+ scalar_block_select = adios_selection_writeblock(sel_index);
+
+ /* Read the arrays */
+ adios_schedule_read(afile, global_range_select, "var_2d_array", 0, 1,
+ t);
+ adios_schedule_read(afile, scalar_block_select, "test_scalar", 0, 1,
+ &test_scalar);
+
+ adios_perform_reads(afile, 1);
+
+ adios_release_step(afile);
+ adios_advance_step(afile, 0, 30);
+ ii++;
+ }
+
+just_clean:
+ // clean everything
+ free(t);
+ t = NULL;
+
+close_adios:
+ CLOSE_ADIOS_READER(afile, adios_opts.method);
+
+ return 0;
+}
diff --git a/tests/C/flexpath_tests/global_range_select/arrays.xml b/tests/C/flexpath_tests/global_range_select/test_config_flex.xml
similarity index 88%
rename from tests/C/flexpath_tests/global_range_select/arrays.xml
rename to tests/C/flexpath_tests/global_range_select/test_config_flex.xml
index 2330ab1..f02a154 100644
--- a/tests/C/flexpath_tests/global_range_select/arrays.xml
+++ b/tests/C/flexpath_tests/global_range_select/test_config_flex.xml
@@ -11,7 +11,7 @@
</global-bounds>
</adios-group>
-<method group="temperature" method="FLEXPATH">QUEUE_SIZE=4;</method>
+<method group="temperature" method="FLEXPATH"></method>
<buffer max-size-MB="20"/>
diff --git a/tests/C/flexpath_tests/global_range_select/writer.c b/tests/C/flexpath_tests/global_range_select/writer.c
new file mode 100644
index 0000000..48ddd7c
--- /dev/null
+++ b/tests/C/flexpath_tests/global_range_select/writer.c
@@ -0,0 +1,77 @@
+/*
+ * ADIOS is freely available under the terms of the BSD license described
+ * in the COPYING file in the top level directory of this source distribution.
+ *
+ * Copyright (c) 2008 - 2009. UT-BATTELLE, LLC. All rights reserved.
+ */
+
+#include "adios.h"
+#include "mpi.h"
+#include <stdio.h>
+#include <string.h>
+#include <unistd.h>
+
+#include "misc.h"
+#include "test_common.h"
+#include "utils.h"
+/*************************************************************/
+/* Example of writing arrays in ADIOS */
+/* */
+/* Similar example is manual/2_adios_write.c */
+/*************************************************************/
+int main(int argc, char **argv)
+{
+ char filename[256];
+ int rank, size, i;
+ int NX = 40;
+ int NY = 1;
+ double t[NX];
+ MPI_Comm comm = MPI_COMM_WORLD;
+
+ int64_t adios_handle;
+ struct adios_tsprt_opts adios_opts;
+ int err_count = 0;
+
+ GET_ENTRY_OPTIONS(
+ adios_opts,
+ "Runs writers. It is recommended to run as many writers as readers.");
+
+ MPI_Init(&argc, &argv);
+ MPI_Comm_rank(comm, &rank);
+ MPI_Comm_size(comm, &size);
+
+ SET_ERROR_IF_NOT_ZERO(adios_init(adios_opts.xml_adios_init_filename, comm),
+ err_count);
+ RET_IF_ERROR(err_count, rank);
+
+ int test_scalar = rank * 1000;
+ int group_num;
+ for (group_num = 0; group_num < 20; group_num++) {
+ for (i = 0; i < NX; i++)
+ t[i] = rank * NX + i + 100 * group_num;
+
+ adios_open(&adios_handle, "temperature", FILE_NAME, "w", comm);
+
+ test_scalar++;
+ adios_write(adios_handle, "NX", &NX);
+ adios_write(adios_handle, "NY", &NY);
+ adios_write(adios_handle, "test_scalar", &test_scalar);
+ adios_write(adios_handle, "size", &size);
+ adios_write(adios_handle, "rank", &rank);
+ adios_write(adios_handle, "var_2d_array", t);
+
+ if (test_verbose) {
+ fprintf(stderr,
+ "Writer side Rank=%d: test_scalar: %d step: %d, t[0] = %6.2f\n",
+ rank, test_scalar, group_num, t[0]);
+ }
+
+ adios_close(adios_handle);
+ if (test_verbose)
+ fprintf(stderr, "Rank=%d commited write %d\n", rank, group_num);
+ }
+ adios_finalize(rank);
+
+ MPI_Finalize();
+ return 0;
+}
diff --git a/tests/C/flexpath_tests/include/misc.h b/tests/C/flexpath_tests/include/misc.h
index 7a0d4b5..d85bb1f 100644
--- a/tests/C/flexpath_tests/include/misc.h
+++ b/tests/C/flexpath_tests/include/misc.h
@@ -36,10 +36,6 @@
#define TRANSPORT "MPI"
#endif
-//! options how verbose is ADIOS (see adios_read_init_method)
-//! 0=quiet, ..., 4=debug
-#define ADIOS_OPTIONS "verbose=4; show hidden_attrs"
-
//! defines if the test passed
#define TEST_PASSED 0
//! defines if the test failed
diff --git a/tests/C/flexpath_tests/include/test_common.h b/tests/C/flexpath_tests/include/test_common.h
index 5e0fcd1..fbb8821 100644
--- a/tests/C/flexpath_tests/include/test_common.h
+++ b/tests/C/flexpath_tests/include/test_common.h
@@ -46,23 +46,37 @@
#define p_test_failed(fmt, args...) \
do { \
- printf("%s " fmt, DBG_TEST_FAILED_STR, ##args); \
+ fprintf(stderr, "%s "fmt, DBG_TEST_FAILED_STR, ##args); \
fflush(stdout); \
} while(0)
#define p_test_passed(fmt, args...) \
+ do {if(test_verbose){ \
+ fprintf(stderr, "%s "fmt, DBG_TEST_PASSED_STR, ##args); \
+ fflush(stdout); \
+ }} while(0)
+
+#define test_failed(prog_name, rank) \
do { \
- printf("%s " fmt, DBG_TEST_PASSED_STR, ##args); \
+ fprintf(stdout, "%s\t\tProgram name: %s\tRank: %d\n", DBG_TEST_FAILED_STR, prog_name, rank); \
fflush(stdout); \
} while(0)
+#define test_passed(prog_name, rank) \
+ do { \
+ fprintf(stdout, "%s\t\tProgram name: %s\tRank: %d\n", DBG_TEST_PASSED_STR, prog_name, rank); \
+ fflush(stdout); \
+ } while(0)
+
+
+
//! @todo do something like that but smarter without unnecessary copying
#define p_error(fmt, args...) \
do { \
if((DBG_ERROR) <= DBG_LEVEL) { \
- printf("%s(%d) %s:%s:%d: " fmt, DBG_ERROR_STR, (DBG_ERROR), __FILE__, __FUNCTION__, __LINE__, ##args); \
+ fprintf(stderr, "%s(%d) %s:%s:%d: " fmt, DBG_ERROR_STR, (DBG_ERROR), __FILE__, __FUNCTION__, __LINE__, ##args); \
fflush(stdout); \
} \
} while(0)
@@ -71,7 +85,7 @@
#define p_warn(fmt, args...) \
do { \
if((DBG_WARNING) <= DBG_LEVEL) { \
- printf("%s(%d) %s:%s:%d: " fmt, DBG_WARN_STR, (DBG_ERROR), __FILE__, __FUNCTION__, __LINE__, ##args); \
+ fprintf(stderr, "%s(%d) %s:%s:%d: " fmt, DBG_WARN_STR, (DBG_ERROR), __FILE__, __FUNCTION__, __LINE__, ##args); \
fflush(stdout); \
} \
} while(0)
@@ -79,7 +93,7 @@
#define p_info(fmt, args...) \
do { \
if((DBG_INFO) <= DBG_LEVEL) { \
- printf("%s(%d) %s:%s:%d: " fmt, DBG_INFO_STR, (DBG_ERROR), __FILE__, __FUNCTION__, __LINE__, ##args); \
+ fprintf(stderr, "%s(%d) %s:%s:%d: " fmt, DBG_INFO_STR, (DBG_ERROR), __FILE__, __FUNCTION__, __LINE__, ##args); \
fflush(stdout); \
} \
} while(0)
@@ -87,7 +101,7 @@
#define p_debug(fmt, args...) \
do { \
if((DBG_DEBUG) <= DBG_LEVEL) { \
- printf("%s(%d) %s:%s:%d: " fmt, DBG_DEBUG_STR, (DBG_ERROR), __FILE__, __FUNCTION__, __LINE__, ##args); \
+ fprintf(stderr, "%s(%d) %s:%s:%d: " fmt, DBG_DEBUG_STR, (DBG_ERROR), __FILE__, __FUNCTION__, __LINE__, ##args); \
fflush(stdout); \
} \
} while(0)
@@ -109,14 +123,16 @@
*
* The macro causes to return DIAG_ERR if getting options returned errors
*/
-#define GET_ENTRY_OPTIONS(adios_opts, help_string) \
+static int test_verbose = 0;
+
+#define GET_ENTRY_OPTIONS(adios_opts, help_string) \
if (1 == argc){ \
p_error("See '-h' for options. At least transport param needs to be specified. Quitting ...\n"); \
return DIAG_ERR; \
} \
do { \
int show_help = 0; \
- if( DIAG_OK != get_options(&adios_opts, argc, argv, &show_help) ){ \
+ if( DIAG_OK != get_options(&adios_opts, argc, argv, &show_help, &test_verbose) ){ \
p_error("Got from get_options(). Quitting ...\n."); \
return DIAG_ERR; \
} \
@@ -223,7 +239,7 @@
#define TEST_INT_EQUAL(value_ref, value, err_count, test_res) \
if (value != value_ref ){ \
test_res = TEST_FAILED; \
- p_test_failed("(expected=%d, got=%d)\n", value_ref, value); \
+ p_test_failed("("#value_ref" != "#value" -> expected=%d, got=%d)\n", value_ref, value); \
err_count++; \
}
@@ -238,7 +254,7 @@
#define TEST_LONG_EQUAL(value_ref, value, err_count, test_res) \
if (value != value_ref ){ \
test_res = TEST_FAILED; \
- p_test_failed("(expected=%" PRIu64 ", got=%" PRIu64 ")\n", value_ref, value); \
+ p_test_failed("("#value_ref" != "#value" -> expected=%" PRIu64 ", got=%" PRIu64 ")\n", value_ref, value); \
err_count++; \
}
@@ -253,7 +269,7 @@
#define TEST_DOUBLE_EQUAL(value_ref, value, err_count, test_res) \
if (value != value_ref ){ \
test_res = TEST_FAILED; \
- p_test_failed("(expected=%0.2f, got=%0.2f)\n", value_ref, value); \
+ p_test_failed("("#value_ref" != "#value" -> expected=%g, got=%g)\n", value_ref, value); \
err_count++; \
}
diff --git a/tests/C/flexpath_tests/include/utils.h b/tests/C/flexpath_tests/include/utils.h
index dbd8647..b3f3f60 100644
--- a/tests/C/flexpath_tests/include/utils.h
+++ b/tests/C/flexpath_tests/include/utils.h
@@ -12,7 +12,7 @@ extern diag_t usage(char *program_name, char *program_desc);
extern diag_t gen_1D_array(double *p_arr, int arr_len, int rank);
extern diag_t gen_1D_array2(double *p_arr, int arr_len, int rank);
extern diag_t gen_1D_array_int(int *p_arr, int arr_len, int rank);
-extern diag_t get_options(struct adios_tsprt_opts * p_tsprt_opts, int argc, char ** argv, int *p_show_help);
+extern diag_t get_options(struct adios_tsprt_opts * p_tsprt_opts, int argc, char ** argv, int *p_show_help, int *p_verbose);
extern diag_t set_value(double *p_arr, int arr_len, double value);
extern diag_t get_data_size(int *shape, int shape_elem_count, int* data_size);
diff --git a/tests/C/flexpath_tests/local_arrays/Makefile.am b/tests/C/flexpath_tests/local_arrays/Makefile.am
new file mode 100644
index 0000000..878c2f4
--- /dev/null
+++ b/tests/C/flexpath_tests/local_arrays/Makefile.am
@@ -0,0 +1,18 @@
+AM_CPPFLAGS = $(all_includes)
+AM_CPPFLAGS += -I$(top_builddir)/src/public -I$(top_srcdir)/src -I$(top_srcdir)/src/public -I$(srcdir)/../include
+
+AUTOMAKE_OPTIONS = no-dependencies subdir-objects
+
+noinst_PROGRAMS = writer_local reader_local
+
+writer_local_SOURCES = writer.c ../common/utils.c
+writer_local_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
+writer_local_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
+reader_local_SOURCES = reader.c ../common/utils.c
+reader_local_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
+reader_local_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
+
+CLEANFILES = *.bp
+CC=$(MPICC)
+
+EXTRA_DIST=cfg.h
diff --git a/tests/C/flexpath_tests/maya_append/Makefile.in b/tests/C/flexpath_tests/local_arrays/Makefile.in
similarity index 91%
rename from tests/C/flexpath_tests/maya_append/Makefile.in
rename to tests/C/flexpath_tests/local_arrays/Makefile.in
index 12544b8..fa5ccc5 100644
--- a/tests/C/flexpath_tests/maya_append/Makefile.in
+++ b/tests/C/flexpath_tests/local_arrays/Makefile.in
@@ -78,8 +78,8 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
-noinst_PROGRAMS = writer_maya$(EXEEXT) reader_maya$(EXEEXT)
-subdir = tests/C/flexpath_tests/maya_append
+noinst_PROGRAMS = writer_local$(EXEEXT) reader_local$(EXEEXT)
+subdir = tests/C/flexpath_tests/local_arrays
DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -126,25 +126,25 @@ CONFIG_CLEAN_FILES =
CONFIG_CLEAN_VPATH_FILES =
PROGRAMS = $(noinst_PROGRAMS)
am__dirstamp = $(am__leading_dot)dirstamp
-am_reader_maya_OBJECTS = reader.$(OBJEXT) ../common/utils.$(OBJEXT)
-reader_maya_OBJECTS = $(am_reader_maya_OBJECTS)
+am_reader_local_OBJECTS = reader.$(OBJEXT) ../common/utils.$(OBJEXT)
+reader_local_OBJECTS = $(am_reader_local_OBJECTS)
am__DEPENDENCIES_1 =
-reader_maya_DEPENDENCIES = $(top_builddir)/src/libadios.a \
+reader_local_DEPENDENCIES = $(top_builddir)/src/libadios.a \
$(am__DEPENDENCIES_1)
AM_V_lt = $(am__v_lt_ at AM_V@)
am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
am__v_lt_0 = --silent
am__v_lt_1 =
-reader_maya_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
+reader_local_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
- $(reader_maya_LDFLAGS) $(LDFLAGS) -o $@
-am_writer_maya_OBJECTS = writer.$(OBJEXT) ../common/utils.$(OBJEXT)
-writer_maya_OBJECTS = $(am_writer_maya_OBJECTS)
-writer_maya_DEPENDENCIES = $(top_builddir)/src/libadios.a \
+ $(reader_local_LDFLAGS) $(LDFLAGS) -o $@
+am_writer_local_OBJECTS = writer.$(OBJEXT) ../common/utils.$(OBJEXT)
+writer_local_OBJECTS = $(am_writer_local_OBJECTS)
+writer_local_DEPENDENCIES = $(top_builddir)/src/libadios.a \
$(am__DEPENDENCIES_1)
-writer_maya_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
+writer_local_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
- $(writer_maya_LDFLAGS) $(LDFLAGS) -o $@
+ $(writer_local_LDFLAGS) $(LDFLAGS) -o $@
AM_V_P = $(am__v_P_ at AM_V@)
am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
am__v_P_0 = false
@@ -178,8 +178,8 @@ AM_V_CCLD = $(am__v_CCLD_ at AM_V@)
am__v_CCLD_ = $(am__v_CCLD_ at AM_DEFAULT_V@)
am__v_CCLD_0 = @echo " CCLD " $@;
am__v_CCLD_1 =
-SOURCES = $(reader_maya_SOURCES) $(writer_maya_SOURCES)
-DIST_SOURCES = $(reader_maya_SOURCES) $(writer_maya_SOURCES)
+SOURCES = $(reader_local_SOURCES) $(writer_local_SOURCES)
+DIST_SOURCES = $(reader_local_SOURCES) $(writer_local_SOURCES)
am__can_run_installinfo = \
case $$AM_UPDATE_INFO_DIR in \
n|no|NO) false;; \
@@ -335,6 +335,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -411,6 +415,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
@@ -483,14 +490,14 @@ AM_CPPFLAGS = $(all_includes) -I$(top_builddir)/src/public \
-I$(top_srcdir)/src -I$(top_srcdir)/src/public \
-I$(srcdir)/../include
AUTOMAKE_OPTIONS = no-dependencies subdir-objects
-writer_maya_SOURCES = writer.c ../common/utils.c
-writer_maya_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
-writer_maya_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
-reader_maya_SOURCES = reader.c ../common/utils.c
-reader_maya_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
-reader_maya_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
+writer_local_SOURCES = writer.c ../common/utils.c
+writer_local_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
+writer_local_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
+reader_local_SOURCES = reader.c ../common/utils.c
+reader_local_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
+reader_local_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
CLEANFILES = *.bp
-EXTRA_DIST = cfg.h readme.txt
+EXTRA_DIST = cfg.h
all: all-am
.SUFFIXES:
@@ -504,9 +511,9 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(am__confi
exit 1;; \
esac; \
done; \
- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu tests/C/flexpath_tests/maya_append/Makefile'; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu tests/C/flexpath_tests/local_arrays/Makefile'; \
$(am__cd) $(top_srcdir) && \
- $(AUTOMAKE) --gnu tests/C/flexpath_tests/maya_append/Makefile
+ $(AUTOMAKE) --gnu tests/C/flexpath_tests/local_arrays/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
@@ -539,13 +546,13 @@ clean-noinstPROGRAMS:
@: > ../common/$(am__dirstamp)
../common/utils.$(OBJEXT): ../common/$(am__dirstamp)
-reader_maya$(EXEEXT): $(reader_maya_OBJECTS) $(reader_maya_DEPENDENCIES) $(EXTRA_reader_maya_DEPENDENCIES)
- @rm -f reader_maya$(EXEEXT)
- $(AM_V_CCLD)$(reader_maya_LINK) $(reader_maya_OBJECTS) $(reader_maya_LDADD) $(LIBS)
+reader_local$(EXEEXT): $(reader_local_OBJECTS) $(reader_local_DEPENDENCIES) $(EXTRA_reader_local_DEPENDENCIES)
+ @rm -f reader_local$(EXEEXT)
+ $(AM_V_CCLD)$(reader_local_LINK) $(reader_local_OBJECTS) $(reader_local_LDADD) $(LIBS)
-writer_maya$(EXEEXT): $(writer_maya_OBJECTS) $(writer_maya_DEPENDENCIES) $(EXTRA_writer_maya_DEPENDENCIES)
- @rm -f writer_maya$(EXEEXT)
- $(AM_V_CCLD)$(writer_maya_LINK) $(writer_maya_OBJECTS) $(writer_maya_LDADD) $(LIBS)
+writer_local$(EXEEXT): $(writer_local_OBJECTS) $(writer_local_DEPENDENCIES) $(EXTRA_writer_local_DEPENDENCIES)
+ @rm -f writer_local$(EXEEXT)
+ $(AM_V_CCLD)$(writer_local_LINK) $(writer_local_OBJECTS) $(writer_local_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
diff --git a/tests/C/flexpath_tests/local_arrays/cfg.h b/tests/C/flexpath_tests/local_arrays/cfg.h
new file mode 100644
index 0000000..f8f905d
--- /dev/null
+++ b/tests/C/flexpath_tests/local_arrays/cfg.h
@@ -0,0 +1,15 @@
+/**
+ * cfg.h
+ *
+ * Created on: Sep 4, 2013
+ * Author: Magda Slawinska aka Magic Magg magg dot gatech at gmail.com
+ */
+
+#ifndef CFG_H_
+#define CFG_H_
+
+//! size of the X dimension
+#define NX_DIM 10
+
+
+#endif /* CFG_H_ */
diff --git a/tests/C/flexpath_tests/1D_arr_global/reader.c b/tests/C/flexpath_tests/local_arrays/reader.c
similarity index 70%
copy from tests/C/flexpath_tests/1D_arr_global/reader.c
copy to tests/C/flexpath_tests/local_arrays/reader.c
index e67cb0a..9623345 100644
--- a/tests/C/flexpath_tests/1D_arr_global/reader.c
+++ b/tests/C/flexpath_tests/local_arrays/reader.c
@@ -1,5 +1,5 @@
/**
- * reader.c
+ * arrays_read.c
*
* ADIOS is freely available under the terms of the BSD license described
* in the COPYING file in the top level directory of this source distribution.
@@ -27,6 +27,11 @@
#include <string.h>
+// for printing the values of the variable
+#define STR_BUFFER_SIZE 3000
+
+
+
int main (int argc, char **argv){
int rank =0, size =0;
int NX = 0;
@@ -35,11 +40,11 @@ int main (int argc, char **argv){
double *t_ref = NULL;
MPI_Comm comm = MPI_COMM_WORLD;
diag_t diag = DIAG_OK; // to store the diagnostic information
- struct test_info test_result = { TEST_PASSED, "1D_arr_global" };
+ struct test_info test_result = {TEST_PASSED, "1D_arr_global_noxml"};
struct err_counts err = { 0, 0};
struct adios_tsprt_opts adios_opts;
- GET_ENTRY_OPTIONS(adios_opts, "Runs readers. It is recommended to run as many readers as writers.");
+ GET_ENTRY_OPTIONS(adios_opts, "Runs readers. It is recommended to run as many readers as writers.");
// adios read initialization
MPI_Init( &argc, &argv);
@@ -49,9 +54,10 @@ int main (int argc, char **argv){
SET_ERROR_IF_NOT_ZERO(adios_read_init_method(adios_opts.method, comm, adios_opts.adios_options), err.adios);
RET_IF_ERROR(err.adios, rank);
+
// I will be working with streams so the lock mode is necessary,
// return immediately if the stream unavailable
- ADIOS_FILE *adios_handle = adios_read_open(FILE_NAME,adios_opts.method, comm, ADIOS_LOCKMODE_NONE, 0.0);
+ ADIOS_FILE *adios_handle = adios_read_open(FILE_NAME, adios_opts.method, comm, ADIOS_LOCKMODE_NONE, 0.0);
if ( !adios_handle){
p_error("Quitting ... (%d) %s\n", adios_errno, adios_errmsg());
return DIAG_ERR;
@@ -62,12 +68,17 @@ int main (int argc, char **argv){
ADIOS_VARINFO *avi = NULL;
+ // for storing the variables
+ char buf[STR_BUFFER_SIZE];
+
+ int step = 0;
+
// read how many processors wrote that array
avi = adios_inq_var (adios_handle, "size");
if (!avi){
p_error("rank %d: Quitting ... (%d) %s\n", rank, adios_errno, adios_errmsg());
- CLOSE_ADIOS_READER(adios_handle, adios_opts.method);
- return DIAG_ERR;
+ diag = DIAG_ERR;
+ goto close_adios;
}
size = *((int*)avi->value);
adios_free_varinfo(avi);
@@ -77,16 +88,16 @@ int main (int argc, char **argv){
// the excessive readers
if (rank >= size){
p_info("rank %d: I am an excessive rank. Nothing to read ...\n", rank);
- CLOSE_ADIOS_READER(adios_handle, adios_opts.method);
- return DIAG_OK;
+ diag = DIAG_OK;
+ goto close_adios;
}
// read the size of the array
avi = adios_inq_var (adios_handle, "NX");
if (!avi){
p_error("rank %d: Quitting ... (%d) %s\n", rank, adios_errno, adios_errmsg());
- CLOSE_ADIOS_READER(adios_handle, adios_opts.method);
- return DIAG_ERR;
+ diag = DIAG_ERR;
+ goto close_adios;
}
// I expect a scalar that will tell me the size of an array
@@ -98,23 +109,21 @@ int main (int argc, char **argv){
assert(NX_DIM == NX);
avi = NULL;
-
- // this will define the slice that we want to read; each rank should
- // read its own slice written by a corresponding writer rank
- // the var_1d is a 2-dim ADIOS variable (because we decided to have
- // it as a global array); that's why we need a 2-dim ADIOS variable
- uint64_t count[2] = {1,0};
- count[1] = NX;
- uint64_t start[2] = {0,0};
- start[0] = rank;
-
- sel = adios_selection_boundingbox(2,start, count);
+ sel = adios_selection_writeblock(rank);
if( !sel ){
p_error("rank %d: Quitting ... (%d) %s\n", rank, adios_errno, adios_errmsg());
diag = DIAG_ERR;
goto close_adios;
}
+ // make the reference array with reference values I expect to get
+ t_ref = calloc(NX, sizeof(double));
+ if (gen_1D_array(t_ref, NX, rank) == DIAG_ERR){
+ p_error("Generating 1D array. Quitting ...\n");
+ diag = DIAG_ERR;
+ goto close_adios;
+ }
+
// allocate the memory for the actual array to be read
t = calloc(NX, sizeof(double));
@@ -131,16 +140,12 @@ int main (int argc, char **argv){
goto just_clean;
}
- // make the reference array with reference values I expect to get
- t_ref = calloc(NX, sizeof(double));
- gen_1D_array(t_ref, NX, rank);
+ sprintf(buf, "Rank %d: var_1d_array: step %d: t: ", rank, step);
- // compare the values what you get with what you expect
int i = 0;
- for (i = 0; i < NX; ++i) {
- if (t[i] != t_ref[i]) {
- p_test_failed("%s: rank %d: for t[%d] (expected %.1f, got %.1f)\n",
- test_result.name, rank, i, t_ref[i], t[i]);
+ for(i=0; i < NX; ++i){
+ if( t[i] != t_ref[i] ){
+ p_test_failed("%s: rank %d: for t[%d] (expected %.1f, got %.1f)\n", test_result.name, rank, i, t_ref[i], t[i] );
test_result.result = TEST_FAILED;
break;
}
@@ -148,20 +153,6 @@ int main (int argc, char **argv){
if (TEST_PASSED == test_result.result)
p_test_passed("%s: rank %d\n", test_result.name, rank);
- else
- p_test_failed("%s: rank %d\n", test_result.name, rank);
-
-
- adios_release_step(adios_handle);
- // 0 - next available step, block for max 30 seconds until the next step
- // is available
- adios_advance_step(adios_handle, 0, 30);
- if (0 == adios_errno){
- printf("Rank %d: proceeding to the next step ...\n", rank);
- } else {
- printf("ERROR: adios_advance_step(); anyway Quitting ... Rank %d: (%d) %s\n", rank, adios_errno, adios_errmsg());
- }
-
just_clean:
// clean everything
diff --git a/tests/C/flexpath_tests/1D_arr_global_noxml/writer.c b/tests/C/flexpath_tests/local_arrays/writer.c
similarity index 78%
copy from tests/C/flexpath_tests/1D_arr_global_noxml/writer.c
copy to tests/C/flexpath_tests/local_arrays/writer.c
index fab08c6..c748d59 100644
--- a/tests/C/flexpath_tests/1D_arr_global_noxml/writer.c
+++ b/tests/C/flexpath_tests/local_arrays/writer.c
@@ -72,20 +72,10 @@ int main(int argc, char ** argv){
RET_IF_ERROR(err_count, rank);
- // I am defining here a global array - global bounds is the size
- // of global array for all writers; within that array there is
- // an offset from which each rank has its space
- int global_bounds= NX * size;
- int offsets= NX * rank;
-
-
adios_define_var (adios_grp, "NX", "", adios_integer, 0, 0, 0);
adios_define_var (adios_grp, "size", "", adios_integer, 0, 0, 0);
adios_define_var (adios_grp, "rank", "", adios_integer, 0, 0, 0);
- adios_define_var (adios_grp, "global_bounds", "", adios_integer, 0, 0, 0);
- adios_define_var (adios_grp, "offsets", "", adios_integer, 0, 0, 0);
- // NX - local var dimensions, global_bounds - global dimension, offsets - variable local offsets
- adios_define_var (adios_grp, "var_1d_array", "", adios_double, "NX", "global_bounds", "offsets");
+ adios_define_var (adios_grp, "var_1d_array", "", adios_double, "NX", "", "");
// open our group and transport method associated with it
adios_open (&adios_handle, "temperature", FILE_NAME, "w", comm);
@@ -94,8 +84,10 @@ int main(int argc, char ** argv){
uint64_t adios_totalsize = 0;
retval=adios_group_size (adios_handle, adios_groupsize, &adios_totalsize);
- fprintf(stderr, "Rank=%d adios_group_size(): adios_groupsize=%" PRIu64 ", adios_totalsize=%" PRIu64 ", retval=%d\n",
- rank, adios_groupsize, adios_totalsize, retval);
+ if (test_verbose) {
+ fprintf(stderr, "Rank=%d adios_group_size(): adios_groupsize=%" PRIu64 ", adios_totalsize=%" PRIu64 ", retval=%d\n",
+ rank, adios_groupsize, adios_totalsize, retval);
+ }
// init the array that I will transport over the sea
if (gen_1D_array(t, NX, rank) == DIAG_ERR){
@@ -107,11 +99,11 @@ int main(int argc, char ** argv){
adios_write(adios_handle, "NX", &NX);
adios_write(adios_handle, "size", &size);
adios_write(adios_handle, "rank", &rank);
- adios_write(adios_handle, "global_bounds", &global_bounds);
- adios_write(adios_handle, "offsets", &offsets);
adios_write(adios_handle, "var_1d_array", t);
- fprintf(stderr, "Rank=%d committed write\n", rank);
+ if (test_verbose) {
+ fprintf(stderr, "Rank=%d committed write\n", rank);
+ }
adios_close(adios_handle);
diff --git a/tests/C/flexpath_tests/maya_append/CMakeLists.txt b/tests/C/flexpath_tests/maya_append/CMakeLists.txt
deleted file mode 100644
index 82ccf86..0000000
--- a/tests/C/flexpath_tests/maya_append/CMakeLists.txt
+++ /dev/null
@@ -1,15 +0,0 @@
-include_directories(${PROJECT_SOURCE_DIR}/src/public)
-include_directories(${PROJECT_SOURCE_DIR}/src)
-include_directories(${PROJECT_SOURCE_DIR}/tests/C/flexpath_tests/include)
-include_directories(${PROJECT_BINARY_DIR}/src/public)
-link_directories(${PROJECT_SOURCE_DIR}/src)
-link_directories(${PROJECT_BINARY_DIR}/src)
-
-
-add_executable(writer_maya writer.c ../common/utils.c)
-target_link_libraries(writer_maya adios ${ADIOSLIB_LDADD} ${MPI_C_LIBRARIES})
-
-add_executable(reader_maya reader.c ../common/utils.c)
-target_link_libraries(reader_maya adios ${ADIOSLIB_LDADD} ${MPI_C_LIBRARIES})
-
-file(COPY readme.txt DESTINATION ${PROJECT_BINARY_DIR}/tests/C/flexpath_tests/maya_append)
diff --git a/tests/C/flexpath_tests/maya_append/Makefile.am b/tests/C/flexpath_tests/maya_append/Makefile.am
deleted file mode 100644
index b728f14..0000000
--- a/tests/C/flexpath_tests/maya_append/Makefile.am
+++ /dev/null
@@ -1,19 +0,0 @@
-AM_CPPFLAGS = $(all_includes)
-AM_CPPFLAGS += -I$(top_builddir)/src/public -I$(top_srcdir)/src -I$(top_srcdir)/src/public -I$(srcdir)/../include
-
-AUTOMAKE_OPTIONS = no-dependencies subdir-objects
-
-noinst_PROGRAMS = writer_maya reader_maya
-
-writer_maya_SOURCES = writer.c ../common/utils.c
-writer_maya_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
-writer_maya_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
-reader_maya_SOURCES = reader.c ../common/utils.c
-reader_maya_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
-reader_maya_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
-
-CLEANFILES = *.bp
-CC=$(MPICC)
-
-EXTRA_DIST = cfg.h readme.txt
-
diff --git a/tests/C/flexpath_tests/maya_append/cfg.h b/tests/C/flexpath_tests/maya_append/cfg.h
deleted file mode 100644
index 52ce6d2..0000000
--- a/tests/C/flexpath_tests/maya_append/cfg.h
+++ /dev/null
@@ -1,26 +0,0 @@
-/**
- * cfg.h
- *
- * Created on: Aug 23, 2013
- * Author: Magda Slawinska aka Magic Magg magg dot gatech at gmail.com
- */
-
-#ifndef CFG_H_
-#define CFG_H_
-
-//! params for the method
-#define TRANSPORT_PARAMS ""
-
-//! adios buffer size in MB
-#define ADS_BUFFER_SIZE 50
-
-//! the name of adios group in the file
-#define GRP_NAME "carpet_var"
-
-//! how many loop iterations is in the writer
-#define TIMESTEP_COUNT 10
-
-//! the maya grid function prefix
-#define MAYA_GF_VAR_PFX "maya_gf_var"
-
-#endif /* CFG_H_ */
diff --git a/tests/C/flexpath_tests/maya_append/reader.c b/tests/C/flexpath_tests/maya_append/reader.c
deleted file mode 100644
index 0c96e3d..0000000
--- a/tests/C/flexpath_tests/maya_append/reader.c
+++ /dev/null
@@ -1,137 +0,0 @@
-/**
- * reader.c
- *
- * Created on: Aug 21, 2013
- * Author: Magda Slawinska aka Magic Magg magg dot gatech at gmail.com
- */
-
-#include <string.h>
-#include "mpi.h"
-#include "adios.h"
-#include "adios_read.h"
-
-#include "misc.h"
-#include "utils.h"
-#include "test_common.h"
-#include "cfg.h"
-
-
-/**
- * wrapper for scheduling adios reads; this macro assumes existence of
- * quite a few important variables; please take a look and be careful
- * how to use it
- *
- * @param path_str The path to the variable
- * @param out_buf The output buffer
- */
-#define READ_FULLPATH(attribute, grid_func_name, out_buf) \
- char fullpath[STR_BUFFER_SIZE]; \
- sprintf(fullpath, "%s%s", attribute, grid_func_name); \
- SET_ERROR_IF_NOT_ZERO(adios_schedule_read(adios_handle, sel, fullpath,0,10, out_buf), error_counts.adios);
-
-
-// for printing the values of the variable
-#define STR_BUFFER_SIZE 100
-
-int main (int argc, char **argv){
- int rank =0;
- MPI_Comm comm = MPI_COMM_WORLD;
- struct err_counts err = {0, 0};
- struct test_info test_result = {TEST_PASSED, "maya_append"};
- struct adios_tsprt_opts adios_opts;
-
- GET_ENTRY_OPTIONS(adios_opts, "Runs readers. As many as you want to.");
-
- // adios read initialization
- MPI_Init( &argc, &argv);
- MPI_Comm_rank (comm, &rank);
-
- // depending on the method
- SET_ERROR_IF_NOT_ZERO(adios_read_init_method(adios_opts.method, comm, adios_opts.adios_options), err.adios);
- RET_IF_ERROR(err.adios, rank);
-
-
- // I will be working with streams so the lock mode is necessary,
- // return immediately if the stream unavailable
- ADIOS_FILE *adios_handle = adios_read_open_file(FILE_NAME, adios_opts.method, comm);
- if ( !adios_handle){
- p_error("Quitting ... (%d) %s\n", adios_errno, adios_errmsg());
- return DIAG_ERR;
- }
-
- int i = 0;
- // I will only support reading TIMESTEP_COUNT integers for the level value
- int level[TIMESTEP_COUNT];
- int level_scalar[TIMESTEP_COUNT];
- int cctk_bbox[TIMESTEP_COUNT * 6];
- double *data = malloc(8 * 11* 12*13 * TIMESTEP_COUNT);
-
- memset(level, 0, sizeof(int) * TIMESTEP_COUNT);
- memset(cctk_bbox, 0, sizeof(int) * TIMESTEP_COUNT*6);
- memset(data, 0, sizeof(double) * 11* 12*13 * TIMESTEP_COUNT);
-
- // selection should be NULL or as a single variable
- // just say that you want to take different steps
- adios_schedule_read(adios_handle, NULL, "/level/maya_gf_var",0,10, level);
- adios_schedule_read(adios_handle, NULL, "/scalar/maya_gf_var", 0, 10, level_scalar);
- adios_schedule_read(adios_handle, NULL, "/cctk_bbox/maya_gf_var", 0, 10, cctk_bbox);
-
- // now I will try to read with a single variable but with multiple steps
- ADIOS_SELECTION *sel = NULL;
- uint64_t start_3D[] = {0, 0, 0};
- uint64_t count_3D[] = {11, 12, 13};
- sel = adios_selection_boundingbox(3, start_3D, count_3D );
- adios_schedule_read(adios_handle, sel, "/data/maya_gf_var", 0, 10, data);
- adios_selection_delete(sel);
- sel = NULL;
-
- SET_ERROR_IF_NOT_ZERO(adios_perform_reads(adios_handle, 1), err.adios);
-
- int j = 0;
- if (err.adios){
- test_result.result = TEST_FAILED;
- } else {
- // reference data
- int level_ref[TIMESTEP_COUNT];
- gen_1D_array_int(level_ref, TIMESTEP_COUNT, rank);
-
- int cctk_bbox_ref[6];
- gen_1D_array_int(cctk_bbox_ref, 6, rank);
-
- double * data_ref = (double *)malloc(11*12*13*sizeof(double));
- gen_1D_array2(data_ref, 11*12*13, rank);
-
- // compare with reference values
- for( i = 0; i < TIMESTEP_COUNT; ++i){
- TEST_INT_EQUAL(level_ref[i], level[i], err.test, test_result.result);
- BREAK_IF_ERROR(err.test);
- TEST_INT_EQUAL(level_ref[i], level_scalar[i], err.test, test_result.result);
- BREAK_IF_ERROR(err.test);
-
- for( j = 0; j < 6; ++j){
- TEST_INT_EQUAL(cctk_bbox_ref[j], cctk_bbox[i*6 + j], err.test, test_result.result);
- BREAK_IF_ERROR(err.test);
- }
- BREAK_IF_ERROR(err.test);
-
- for( j = 0; j < 11 * 12 * 13; ++j){
- TEST_DOUBLE_EQUAL(data_ref[j], data[i * 11 * 12 * 13 +j], err.test, test_result.result);
- BREAK_IF_ERROR(err.test);
- }
- BREAK_IF_ERROR(err.test);
- }
-
- free(data_ref);
- data_ref = NULL;
- }
-
- if (TEST_PASSED == test_result.result){
- p_test_passed("%s: rank %d\n", test_result.name, rank);
- }
-
- free(data);
- data = NULL;
- CLOSE_ADIOS_READER(adios_handle, adios_opts.method);
-
- return DIAG_OK;
-}
diff --git a/tests/C/flexpath_tests/maya_append/readme.txt b/tests/C/flexpath_tests/maya_append/readme.txt
deleted file mode 100644
index b385a9f..0000000
--- a/tests/C/flexpath_tests/maya_append/readme.txt
+++ /dev/null
@@ -1,64 +0,0 @@
-# readme.txt
-# Created on: Aug 21, 2013
-# Author: Magda S. aka Magic Magg magg dot gatech at gmail.com
-#
-DESCRIPTION
-===========
-The idea is to test how to write in an appended mode and read from
-that mode. This test is based on the Maya project.
-
-It is designed for two methods (use -t flx or -t mpi)
-
-1. MPI/ADIOS_READ_METHOD_BP
-2. FLEXPATH/ADIOS_READ_METHOD_FLEXPATH
-
-
-RUN
-=====
-# to clean files hanging around after previous runs
-$ make -f Makefile.generic clean_test
-
-# you can run as many writers as you want and as many readers as you want
-# they write and read independently; the default is to run one writer
-# and one reader
-$ ./writer -f mpi
-$ ./reader -f mpi
-
-See Makefile for other options of running the test.
-
-PLAYING WITH TEST CONFIGURATION
-===============================
-To play with the test configuration, you can modify macros in the cfg.h file
-
-TIMESTEP_COUNT seems to be the only reasonable setting to play so far
-
-NOTES
-======
-2013-08-28 Test passes with the MPI method on my laptop; it fails with the FLEXPATH method
-enabled (branch v1.5.1)
-
-$ ./reader
-ERROR: FLEXPATH staging method does not support file mode for reading. Use adios_read_open() to open a staged dataset.
-
-
-
-TROUBLESHOOTING
-================
-
-2013-08-06, ERROR adios_allocate_buffer(): insufficient memory
-
-ERROR: adios_allocate_buffer (): insufficient memory: 5242880000 requested, 860221440 available. Using available.
-
-$ grep ADS_BUFFER_SIZE cfg.h
-#define ADS_BUFFER_SIZE 50
-
-Try changing the ADS_BUFFER_SIZE in cfg.h to a smaller value.
-
-2013-0x-0y, txt files left
-
-There might be text files left; they should be removed for the next run.
-
-# EOF
-
-# EOF
-
diff --git a/tests/C/flexpath_tests/maya_append/writer.c b/tests/C/flexpath_tests/maya_append/writer.c
deleted file mode 100644
index f562c33..0000000
--- a/tests/C/flexpath_tests/maya_append/writer.c
+++ /dev/null
@@ -1,133 +0,0 @@
-/**
- * writer.c
- *
- * Created on: Aug 21, 2013
- * Author: Magda Slawinska aka Magic Magg magg dot gatech at gmail.com
- */
-
-#include "mpi.h"
-#include "adios.h"
-#include "adios_read.h" // for adios_errno
-
-#include "misc.h"
-#include "test_common.h"
-#include "utils.h"
-#include "cfg.h"
-
-#include <string.h>
-
-// for printing the values of the variable
-#define STR_BUFFER_SIZE 100
-
-/**
- * wrapper for writes; this macro assumes existence fullpath
- * quite a few important variables; please take a look and be careful
- * how to use it
- *
- * I simulate Maya var name which consists of the attribute and the
- * grid function
- *
- * @param attribute The attribute (part of adios variable name or path)
- * @param grid_func_name The name of the grid function
- * @param var The var to be written out
- *
- */
-#define WRITE_VAR(attribute, grid_func_name, var) \
- do { \
- sprintf(fullpath, "%s%s", attribute, grid_func_name); \
- adios_write(adios_handle, fullpath, var); \
- } while (0)
-
-
-int main(int argc, char ** argv){
- int rank = 0, size = 0;
- MPI_Comm comm = MPI_COMM_WORLD; // required for ADIOS
- int64_t adios_handle; // the ADIOS file handler
- int retval;
-
- struct adios_tsprt_opts adios_opts;
- int err_count = 0;
-
- GET_ENTRY_OPTIONS(adios_opts, "Runs writers. As many as you want to.");
-
- // ADIOS initialization
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(comm, &rank);
- MPI_Comm_size(comm, &size);
-
- // From sources it just returns 1 (2013-07-16, whatever)
- adios_init_noxml(comm);
-
- // returns 0 (buffer allocated) or 1 (seems everything fine)
- // I guess size of the buffer in MB
- adios_set_max_buffer_size (ADS_BUFFER_SIZE);
-
- // this will hold the group id for all variables defined within this group
- int64_t adios_grp = 0;
-
- // now declare a group and variables you will have in the group
- adios_declare_group(&adios_grp, GRP_NAME, "", adios_stat_default);
-
- uint64_t adios_groupsize = 0;
-
- adios_define_var (adios_grp, MAYA_GF_VAR_PFX, "/level", adios_integer, "1", "1", "0");
- adios_groupsize += 4;
-
- adios_define_var (adios_grp, MAYA_GF_VAR_PFX, "/scalar", adios_integer, "", "", "");
- adios_groupsize += sizeof(uint64_t);
-
- adios_define_var (adios_grp, MAYA_GF_VAR_PFX, "/cctk_bbox", adios_integer, "6", "6", "0" );
- adios_groupsize += (4 * 2 * 3);
-
- adios_define_var (adios_grp, MAYA_GF_VAR_PFX, "/data", adios_double, "11,12,13", "11,12,13", "0,0,0");
- adios_groupsize += (8 * 11 * 12 *13);
-
-
- SET_ERROR_IF_ZERO(adios_select_method(adios_grp, adios_opts.transport, "", ""), err_count);
- RET_IF_ERROR(err_count, rank);
-
-
- int i = 0;
-
- // these are values that will be written
- int level[TIMESTEP_COUNT];
- gen_1D_array_int(level, TIMESTEP_COUNT, rank);
-
- int cctk_bbox[6];
- gen_1D_array_int(cctk_bbox, 6, rank);
-
- double * data = (double *)malloc(11*12*13*sizeof(double));
- gen_1D_array2(data, 11*12*13, rank);
-
-
- // required by WRITE_VAR macro (see the macro)
- char fullpath[STR_BUFFER_SIZE];
-
- // actually adios_write() doesn't write anything; the actual write
- // is performed on or after adios_close() so having
- // adios_open and adios_close out of the for loop will not produce
- // the desired effect i.e., appending to values
- for(i = 0; i < TIMESTEP_COUNT; ++i){
- // open our group and transport method associated with it
- adios_open (&adios_handle, GRP_NAME, FILE_NAME, "a", comm);
-
- uint64_t adios_totalsize = 0;
- retval=adios_group_size (adios_handle, adios_groupsize, &adios_totalsize);
- fprintf(stderr, "Rank=%d adios_group_size(): adios_groupsize=%" PRIu64 ", adios_totalsize=%" PRIu64 ", retval=%d\n",
- rank, adios_groupsize, adios_totalsize, retval);
- WRITE_VAR("/level/", MAYA_GF_VAR_PFX, &level[i]);
- WRITE_VAR("/scalar/", MAYA_GF_VAR_PFX, &level[i]);
- WRITE_VAR("/cctk_bbox/", MAYA_GF_VAR_PFX, cctk_bbox);
- WRITE_VAR("/data/", MAYA_GF_VAR_PFX, data);
-
- fprintf(stderr, "Rank=%d committed write\n", rank);
- adios_close(adios_handle);
- }
-
- free(data);
- data = NULL;
- adios_finalize(rank);
- MPI_Finalize();
-
- return 0;
-}
diff --git a/tests/C/flexpath_tests/maya_noxml/Makefile.in b/tests/C/flexpath_tests/maya_noxml/Makefile.in
index 3ae1812..edfc5af 100644
--- a/tests/C/flexpath_tests/maya_noxml/Makefile.in
+++ b/tests/C/flexpath_tests/maya_noxml/Makefile.in
@@ -102,7 +102,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -110,8 +110,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -341,6 +341,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -417,6 +421,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/C/flexpath_tests/maya_noxml/reader.c b/tests/C/flexpath_tests/maya_noxml/reader.c
index 2464a58..d11c12a 100644
--- a/tests/C/flexpath_tests/maya_noxml/reader.c
+++ b/tests/C/flexpath_tests/maya_noxml/reader.c
@@ -61,7 +61,7 @@
* @param out_buf The output buffer
*/
#define READ_FULLPATH(path_str, out_buf) \
- sprintf(fullpath, "%s%s", path_str, fullname); \
+ sprintf(fullpath, "%s%s", fullname, path_str); \
SET_ERROR_IF_NOT_ZERO(adios_schedule_read(adios_handle, sel, fullpath,0,1, out_buf), error_counts.adios); \
BREAK_IF_ERROR(error_counts.adios);
@@ -135,22 +135,29 @@ int main (int argc, char **argv){
double delta[3];
int32_t iorigin[3];
uint64_t shape[3];
+ char fullpath[STR_BUFFER_SIZE];
// I think these are global variables, so shouldn't be a problem
// first schedule reading of the entire variables (so NULL selection)
// reading the patch_id doesn't make much sense as it seems that only the
// very first value is written out so we will get 0
- SET_ERROR_IF_NOT_ZERO(adios_schedule_read(adios_handle, NULL, "patch_id",0,1, &patch_id), error_counts.adios);
+ gen_maya_var_name(fullname, MAYA_VAR_BUF_SIZE, MAYA_GF_VAR_PFX, 0);
+
+ sprintf(fullpath, "%s%s", fullname, "/patch_id");
+ SET_ERROR_IF_NOT_ZERO(adios_schedule_read(adios_handle, NULL, fullpath, 0,1, &patch_id), error_counts.adios);
RET_AND_CLOSE_ADIOS_READER_IF_ERROR(error_counts.adios, rank, adios_handle, adios_opts.method);
- SET_ERROR_IF_NOT_ZERO(adios_schedule_read(adios_handle, NULL, "shape_dim_x",0,1, &shape_max_dims[0]), error_counts.adios);
+ sprintf(fullpath, "%s%s", fullname, "/shape_dim_x");
+ SET_ERROR_IF_NOT_ZERO(adios_schedule_read(adios_handle, NULL, fullpath, 0,1, &shape_max_dims[0]), error_counts.adios);
RET_AND_CLOSE_ADIOS_READER_IF_ERROR(error_counts.adios, rank, adios_handle, adios_opts.method);
- SET_ERROR_IF_NOT_ZERO(adios_schedule_read(adios_handle, NULL, "shape_dim_y",0,1, &shape_max_dims[1]), error_counts.adios);
+ sprintf(fullpath, "%s%s", fullname, "/shape_dim_y");
+ SET_ERROR_IF_NOT_ZERO(adios_schedule_read(adios_handle, NULL, fullpath, 0,1, &shape_max_dims[1]), error_counts.adios);
RET_AND_CLOSE_ADIOS_READER_IF_ERROR(error_counts.adios, rank, adios_handle, adios_opts.method);
- SET_ERROR_IF_NOT_ZERO(adios_schedule_read(adios_handle, NULL, "shape_dim_z",0,1, &shape_max_dims[2]), error_counts.adios);
+ sprintf(fullpath, "%s%s", fullname, "/shape_dim_z");
+ SET_ERROR_IF_NOT_ZERO(adios_schedule_read(adios_handle, NULL, fullpath, 0,1, &shape_max_dims[2]), error_counts.adios);
RET_AND_CLOSE_ADIOS_READER_IF_ERROR(error_counts.adios, rank, adios_handle, adios_opts.method);
// not sure if this assumption is correct; difficult to find in the ADIOS sources
@@ -196,19 +203,18 @@ int main (int argc, char **argv){
// for storing the name of the variable
- char fullpath[STR_BUFFER_SIZE];
- char * levelpath = "/level/";
- char * datapath = "/data/";
- char * mglevelpath = "/carpet_mglevel/";
- char * timesteppath ="/timestep/";
- char * group_timelevelpath = "/group_timelevel/";
- char * timepath = "/time/";
- char * cbbpath = "/cctk_bbox/";
- char * cngzpath = "/cctk_nghostzones/";
- char * originpath = "/origin/";
- char * deltapath = "/delta/";
- char * ioriginpath = "/iorigin/";
- char * shapepath = "/shape/";
+ char * levelpath = "/level";
+ char * datapath = "/data";
+ char * mglevelpath = "/carpet_mglevel";
+ char * timesteppath ="/timestep";
+ char * group_timelevelpath = "/group_timelevel";
+ char * timepath = "/time";
+ char * cbbpath = "/cctk_bbox";
+ char * cngzpath = "/cctk_nghostzones";
+ char * originpath = "/origin";
+ char * deltapath = "/delta";
+ char * ioriginpath = "/iorigin";
+ char * shapepath = "/shape";
// read all variables with attributes
for(i = 0; i < MAYA_GRID_FUNC_COUNT; ++i){
@@ -289,13 +295,15 @@ int main (int argc, char **argv){
TEST_INT_EQUAL(i, level, error_counts.test, test_result.result);
BREAK_IF_ERROR(error_counts.test);
- TEST_INT_EQUAL(i%2, carpet_mglevel, error_counts.test, test_result.result);
+ int j = i%2;
+ TEST_INT_EQUAL(j, carpet_mglevel, error_counts.test, test_result.result);
BREAK_IF_ERROR(error_counts.test);
TEST_INT_EQUAL(26, timestep, error_counts.test, test_result.result);
BREAK_IF_ERROR(error_counts.test);
- TEST_INT_EQUAL(i%3, grp_tl, error_counts.test, test_result.result);
+ j=i%3;
+ TEST_INT_EQUAL(j, grp_tl, error_counts.test, test_result.result);
BREAK_IF_ERROR(error_counts.test);
TEST_DOUBLE_EQUAL(13.0, time_attr, error_counts.test, test_result.result);
@@ -344,29 +352,36 @@ int main (int argc, char **argv){
// this is assumed that the data are in this patch - we have to know
// how it was written out i-th grid function was outputted in i-th patch
// e.g., bpls -d test.bp -s"1,0,0,0" -c"1,shape[0],shape[1],shape[2] /data/maya_gf_var1 -n 12
- uint64_t start_4D[] = {i, 0, 0, 0};
+ uint64_t start_4D[] = {rank, 0, 0, 0};
sel = adios_selection_boundingbox(4, start_4D, count_4D );
READ_FULLPATH(datapath, data);
adios_selection_delete(sel);
sel = NULL;
+ if( !(ref_data) || (set_value(ref_data, shape_max_dims[0] * shape_max_dims[1] *shape_max_dims[2], (double) 2*i + rank) != DIAG_OK) ){
+ free(data);
+ RET_IF_ERROR(1, rank);
+ }
SET_ERROR_IF_NOT_ZERO(adios_perform_reads(adios_handle, 1), error_counts.adios);
RET_AND_CLOSE_ADIOS_READER_IF_ERROR(error_counts.adios, rank, adios_handle, adios_opts.method);
- // now compare what I got
- for(k = 0 ; k < shape[0] *shape[1] *shape[2]; ++k){
- TEST_DOUBLE_EQUAL(ref_data[k], data[k], error_counts.test, test_result.result);
- BREAK_IF_ERROR(error_counts.test);
- }
+ // We *should* be comparing the incoming "/data" array here. But it isn't really written properly.
+ // We only write slabs corresponding to the number of writers. So lets just skip it.
+
BREAK_IF_ERROR(error_counts.test);
}
+ adios_release_step(adios_handle);
+ adios_advance_step(adios_handle, 0, 30);
adios_free_varinfo(avi);
avi = NULL;
- if (TEST_PASSED == test_result.result)
- p_test_passed("%s: rank %d\n", test_result.name, rank);
+ if (TEST_PASSED == test_result.result) {
+ p_test_passed("%s: rank %d\n", test_result.name, rank);
+ } else {
+ diag = DIAG_ERR;
+ }
CLOSE_ADIOS_READER(adios_handle, adios_opts.method);
diff --git a/tests/C/flexpath_tests/maya_noxml/writer.c b/tests/C/flexpath_tests/maya_noxml/writer.c
index 8e1b990..95e213e 100644
--- a/tests/C/flexpath_tests/maya_noxml/writer.c
+++ b/tests/C/flexpath_tests/maya_noxml/writer.c
@@ -36,8 +36,8 @@
* @param path_str The path to the variable
* @param variable The var to be written out
*/
-#define WRITE_FULLPATH(path_str, var) \
- sprintf(fullpath, "%s%s", path_str, fullname); \
+#define WRITE_FULLPATH(var_name, var) \
+ sprintf(fullpath, "%s%s", fullname, var_name); \
adios_write(adios_handle, fullpath, var);
@@ -102,34 +102,38 @@ int main(int argc, char ** argv){
// first define variable, since I am using no XML api
for(i = 0; i < MAYA_GRID_FUNC_COUNT; ++i ){
// this is common for grid functions and scalars
- adios_define_var (adios_grp, "patch_id", "", adios_unsigned_integer, "", "", "");
+
+ gen_maya_var_name(fullname, MAYA_VAR_BUF_SIZE, MAYA_GF_VAR_PFX, i);
+
+ adios_define_var (adios_grp, "patch_id", fullname, adios_unsigned_integer, "", "", "");
adios_groupsize += sizeof (uint64_t);
- adios_define_var (adios_grp, "shape_dim_x", "", adios_unsigned_integer, "", "", "");
- adios_define_var (adios_grp, "shape_dim_y", "", adios_unsigned_integer, "", "", "");
- adios_define_var (adios_grp, "shape_dim_z", "", adios_unsigned_integer, "", "", "");
+ adios_define_var (adios_grp, "shape_dim_x", fullname, adios_integer, "", "", "");
+ adios_define_var (adios_grp, "shape_dim_y", fullname, adios_integer, "", "", "");
+ adios_define_var (adios_grp, "shape_dim_z", fullname, adios_integer, "", "", "");
adios_groupsize += 3*sizeof (uint64_t); // can be bigger
// I simulate writing grid functions
- char * dimensions="1,shape_dim_x,shape_dim_y,shape_dim_z";
// global dimensions should be, I suppose greater than shap_dim_xxx
// i.e., shape_dim_x <= 48, shape_dim_y <= 89, shape_dim_z <= 116
char * global_dimensions=GLOBAL_DIMENSIONS;
- char * offsets="patch_id,0,0,0";
// the name of maya variable
- memset(fullname, 0, MAYA_VAR_BUF_SIZE);
- sprintf(fullname, MAYA_GF_VAR_PFX "%d", i );
-
+ char *offsets = malloc(strlen(fullname) + strlen("patch_id,0,0,0") + 4);
+ sprintf(offsets, "%d,0,0,0", rank);
+ char *dimensions = malloc(strlen(fullname)*3 + strlen("shape_dim_x,shape_dim_y,shape_dim_z") + 12);
+ sprintf(dimensions, "1,%s/shape_dim_x,%s/shape_dim_y,%s/shape_dim_z", fullname, fullname, fullname);
// I think this is for dataset size for doubles
+ char *single_offset = malloc(strlen(fullname) + strlen("/patch_id") + 1);
+ sprintf(single_offset, "%s/patch_id", fullname);
adios_groupsize += max_data_size;
- adios_define_var (adios_grp, fullname, "/data", adios_double, dimensions, global_dimensions, offsets);
-
- adios_groupsize += (4 + 4 + 4 + 4 + 8);
- adios_define_var (adios_grp, fullname, "/level", adios_integer, "1", "P", "patch_id") ;
- adios_define_var (adios_grp, fullname, "/carpet_mglevel", adios_integer, "1", "P", "patch_id");
- adios_define_var (adios_grp, fullname, "/timestep", adios_integer, "1", "P", "patch_id");
- adios_define_var (adios_grp, fullname, "/group_timelevel", adios_integer, "1", "P", "patch_id");
- adios_define_var (adios_grp, fullname, "/time", adios_double, "1", "P", "patch_id");
+ adios_define_var (adios_grp, "data", fullname, adios_double, dimensions, global_dimensions, offsets);
+
+ adios_groupsize += (4 + 4 + 4 + 4 + 8);
+ adios_define_var (adios_grp, "level", fullname, adios_integer, "1", "P", single_offset) ;
+ adios_define_var (adios_grp, "carpet_mglevel", fullname, adios_integer, "1", "P", single_offset);
+ adios_define_var (adios_grp, "timestep", fullname, adios_integer, "1", "P", single_offset);
+ adios_define_var (adios_grp, "group_timelevel", fullname, adios_integer, "1", "P", single_offset);
+ adios_define_var (adios_grp, "time", fullname, adios_double, "1", "P", single_offset);
char ndim[16];
char global_dims[18];
@@ -138,30 +142,34 @@ int main(int argc, char ** argv){
adios_groupsize += (4 * 2 * dim);
sprintf(ndim, "1,%d", 2 * dim);
sprintf(global_dims, "P,%d", 2 * dim);
- sprintf(local_offsets, "patch_id,0");
- adios_define_var(adios_grp, fullname, "/cctk_bbox", adios_integer, ndim, global_dims, local_offsets);
+ sprintf(local_offsets, "%s/patch_id,0", fullname);
+ adios_define_var(adios_grp, "cctk_bbox", fullname, adios_integer, ndim, global_dims, local_offsets);
adios_groupsize += (4 * dim);
sprintf(ndim, "1,%d", dim);
sprintf(global_dims, "P,%d", dim);
- adios_define_var(adios_grp, fullname, "/cctk_nghostzones",adios_integer, ndim, global_dims, local_offsets);
+ adios_define_var(adios_grp, "cctk_nghostzones", fullname, adios_integer, ndim, global_dims, local_offsets);
adios_groupsize += (8 * dim);
sprintf(ndim, "1,%d", dim);
sprintf(global_dims, "P,%d", dim);
- adios_define_var(adios_grp, fullname, "/origin", adios_double, ndim, global_dims, local_offsets);
+ adios_define_var(adios_grp, "origin", fullname, adios_double, ndim, global_dims, local_offsets);
adios_groupsize += (8 * dim);
- adios_define_var(adios_grp, fullname, "/delta", adios_double, ndim, global_dims, local_offsets);
+ adios_define_var(adios_grp, "delta", fullname, adios_double, ndim, global_dims, local_offsets);
adios_groupsize += (4 * dim);
- adios_define_var(adios_grp, fullname, "/iorigin", adios_integer, ndim, global_dims, local_offsets);
+ adios_define_var(adios_grp, "iorigin", fullname, adios_integer, ndim, global_dims, local_offsets);
adios_groupsize += (sizeof(uint64_t) * dim);
- adios_define_var(adios_grp, fullname, "/shape", adios_unsigned_long,ndim, global_dims, local_offsets);
+ adios_define_var(adios_grp, "shape", fullname, adios_unsigned_long,ndim, global_dims, local_offsets);
+
+ free(dimensions);
+ free(offsets);
+
}
- SET_ERROR_IF_ZERO(adios_select_method(adios_grp, adios_opts.transport, "", ""), err_count);
+ SET_ERROR_IF_NOT_ZERO(adios_select_method(adios_grp, adios_opts.transport, "", ""), err_count);
RET_IF_ERROR(err_count, rank);
// open our group and transport method associated with it
@@ -169,11 +177,12 @@ int main(int argc, char ** argv){
uint64_t adios_totalsize = 0;
retval=adios_group_size (adios_handle, adios_groupsize, &adios_totalsize);
- fprintf(stderr, "Rank=%d adios_group_size(): adios_groupsize=%" PRIu64 ", adios_totalsize=%" PRIu64 ", retval=%d\n",
- rank, adios_groupsize, adios_totalsize, retval);
-
- printf("Writing checkpoint to file %s using the %s method: group size is %" PRIu64 ", total size is %" PRIu64 ". \n", FILE_NAME, adios_opts.transport, adios_groupsize, adios_totalsize);
+ if (test_verbose) {
+ fprintf(stderr, "Rank=%d adios_group_size(): adios_groupsize=%" PRIu64 ", adios_totalsize=%" PRIu64 ", retval=%d\n",
+ rank, adios_groupsize, adios_totalsize, retval);
+ printf("Writing checkpoint to file %s using the %s method: group size is %" PRIu64 ", total size is %" PRIu64 ". \n", FILE_NAME, adios_opts.transport, adios_groupsize, adios_totalsize);
+ }
// arbitrary, but this is what I am getting from Maya
// the number of patches I want to write
@@ -184,18 +193,18 @@ int main(int argc, char ** argv){
// now goes adWRiteGroupVar
char fullpath[STR_BUFFER_SIZE];
- char * levelpath = "/level/";
- char * datapath = "/data/";
- char * mglevelpath = "/carpet_mglevel/";
- char * timesteppath ="/timestep/";
- char * group_timelevelpath = "/group_timelevel/";
- char * timepath = "/time/";
- char * cbbpath = "/cctk_bbox/";
- char * cngzpath = "/cctk_nghostzones/";
- char * originpath = "/origin/";
- char * deltapath = "/delta/";
- char * ioriginpath = "/iorigin/";
- char * shapepath = "/shape/";
+ char * levelpath = "/level";
+ char * datapath = "/data";
+ char * mglevelpath = "/carpet_mglevel";
+ char * timesteppath ="/timestep";
+ char * group_timelevelpath = "/group_timelevel";
+ char * timepath = "/time";
+ char * cbbpath = "/cctk_bbox";
+ char * cngzpath = "/cctk_nghostzones";
+ char * originpath = "/origin";
+ char * deltapath = "/delta";
+ char * ioriginpath = "/iorigin";
+ char * shapepath = "/shape";
assert(shape[0] * shape[1] *shape[2] * 8 == data_size);
assert(max_shape[0] * max_shape[1] * max_shape[2] * 8 == max_data_size);
@@ -216,6 +225,8 @@ int main(int argc, char ** argv){
for(i = 0; i < MAYA_GRID_FUNC_COUNT; ++i){
// generate the name of maya variable
+ memset(fullname, 0, MAYA_VAR_BUF_SIZE);
+
gen_maya_var_name(fullname, MAYA_VAR_BUF_SIZE, MAYA_GF_VAR_PFX, i);
// the purpose of writing this variable is to enable
@@ -230,16 +241,20 @@ int main(int argc, char ** argv){
// you need to have adios_write(patch_id) here; not above the
// for loop
// the idea was to write each variable with a designated different patch
- adios_write (adios_handle, "patch_id", &my_patch_index);
+ WRITE_FULLPATH ("/patch_id", &my_patch_index);
my_patch_index++;
my_patch_index %= global_patch_count;
// these max shape dims; this also tests if we can rewrite the
// same variable over and over; as we did this for the Maya
- adios_write (adios_handle, "shape_dim_x", &max_shape[0]) ;
- adios_write (adios_handle, "shape_dim_y", &max_shape[1]) ;
- adios_write (adios_handle, "shape_dim_z", &max_shape[2]) ;
-
+ WRITE_FULLPATH ("/shape_dim_x", &max_shape[0]) ;
+ WRITE_FULLPATH ("/shape_dim_y", &max_shape[1]) ;
+ WRITE_FULLPATH ("/shape_dim_z", &max_shape[2]) ;
+
+ if( set_value(my_data, max_shape[0] * max_shape[1] *max_shape[2], (double) 2*i+rank) != DIAG_OK ){
+ p_error("with generating data. Quitting\n");
+ return DIAG_ERR;
+ }
// Write the data
WRITE_FULLPATH(datapath, my_data);
@@ -274,8 +289,9 @@ int main(int argc, char ** argv){
WRITE_FULLPATH(shapepath, dim_3_uint64_t);
}
- fprintf(stderr, "Rank=%d committed write\n", rank);
-
+ if (test_verbose) {
+ fprintf(stderr, "Rank=%d committed write\n", rank);
+ }
free(my_data);
my_data = NULL;
@@ -285,8 +301,6 @@ int main(int argc, char ** argv){
adios_finalize(rank);
MPI_Finalize();
- printf("\n");
-
return 0;
}
diff --git a/tests/C/flexpath_tests/scalar/Makefile.in b/tests/C/flexpath_tests/scalar/Makefile.in
index fe81a63..0798a24 100644
--- a/tests/C/flexpath_tests/scalar/Makefile.in
+++ b/tests/C/flexpath_tests/scalar/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -335,6 +335,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -411,6 +415,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/C/flexpath_tests/scalar/writer.c b/tests/C/flexpath_tests/scalar/writer.c
index 17d2e61..76b4306 100644
--- a/tests/C/flexpath_tests/scalar/writer.c
+++ b/tests/C/flexpath_tests/scalar/writer.c
@@ -53,15 +53,19 @@ int main(int argc, char ** argv){
adios_open( &adios_handle, "scalar", FILE_NAME, "w", comm);
adios_groupsize = 4 + 4 + 4;
retval=adios_group_size (adios_handle, adios_groupsize, &adios_totalsize);
- fprintf(stderr, "Rank=%d adios_group_size(): adios_groupsize=%" PRIu64 ", adios_totalsize=%" PRIu64 ", retval=%d\n",
- rank, adios_groupsize, adios_totalsize, retval);
+ if (test_verbose) {
+ fprintf(stderr, "Rank=%d adios_group_size(): adios_groupsize=%" PRIu64 ", adios_totalsize=%" PRIu64 ", retval=%d\n",
+ rank, adios_groupsize, adios_totalsize, retval);
+ }
// write; don't check errors for simplicity reasons
adios_write(adios_handle, "size", &size);
adios_write(adios_handle, "rank", &rank);
adios_write(adios_handle, "lucky_scalar", &rank);
- fprintf(stderr, "Rank=%d committed write\n", rank);
+ if (test_verbose) {
+ fprintf(stderr, "Rank=%d committed write\n", rank);
+ }
// close and finalize the ADIOS and friends
adios_close(adios_handle);
diff --git a/tests/C/query/Makefile.in b/tests/C/query/Makefile.in
index feef088..dba4b3b 100644
--- a/tests/C/query/Makefile.in
+++ b/tests/C/query/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -335,6 +335,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -411,6 +415,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/C/query/alacrity/Makefile.in b/tests/C/query/alacrity/Makefile.in
index f099486..85e3538 100644
--- a/tests/C/query/alacrity/Makefile.in
+++ b/tests/C/query/alacrity/Makefile.in
@@ -105,7 +105,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -113,8 +113,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -379,6 +379,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -455,6 +459,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/C/query/alacrity/adios_alac_query.c b/tests/C/query/alacrity/adios_alac_query.c
index d10060d..c511e3f 100644
--- a/tests/C/query/alacrity/adios_alac_query.c
+++ b/tests/C/query/alacrity/adios_alac_query.c
@@ -57,7 +57,7 @@ int performQuery(ADIOS_QUERY_TEST_INFO *queryInfo, ADIOS_FILE *f)
{
int i = 0, timestep = 0 ;
ADIOS_VARINFO * tempVar = adios_inq_var(f, queryInfo->varName);
- fprintf(stderr,"times steps for variable is: [%d, %d], batch size is %llu\n", queryInfo->fromStep, queryInfo->fromStep + queryInfo->numSteps, queryInfo->batchSize);
+ fprintf(stderr,"times steps for variable is: [%d, %d], batch size is %" PRIu64 "\n", queryInfo->fromStep, queryInfo->fromStep + queryInfo->numSteps, queryInfo->batchSize);
for (timestep = queryInfo->fromStep; timestep < queryInfo->fromStep + queryInfo->numSteps; timestep ++) {
fprintf(stderr,"querying on timestep %d \n", timestep );
diff --git a/tests/C/query/common/Makefile.in b/tests/C/query/common/Makefile.in
index 8dcd42a..0fb099b 100644
--- a/tests/C/query/common/Makefile.in
+++ b/tests/C/query/common/Makefile.in
@@ -103,7 +103,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -111,8 +111,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -359,6 +359,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -435,6 +439,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/C/query/fastbit/Makefile.in b/tests/C/query/fastbit/Makefile.in
index ac21b1e..7a681b0 100644
--- a/tests/C/query/fastbit/Makefile.in
+++ b/tests/C/query/fastbit/Makefile.in
@@ -104,7 +104,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -112,8 +112,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -334,6 +334,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -410,6 +414,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/Fortran/Makefile.in b/tests/Fortran/Makefile.in
index e4d50c8..a85eb70 100644
--- a/tests/Fortran/Makefile.in
+++ b/tests/Fortran/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -324,6 +324,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -400,6 +404,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/Makefile.in b/tests/Makefile.in
index 4fcdd2d..2125ef7 100644
--- a/tests/Makefile.in
+++ b/tests/Makefile.in
@@ -102,7 +102,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -110,8 +110,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -336,6 +336,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -412,6 +416,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/bp_read/Makefile.in b/tests/bp_read/Makefile.in
index 7b4cfef..7838944 100644
--- a/tests/bp_read/Makefile.in
+++ b/tests/bp_read/Makefile.in
@@ -105,7 +105,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -113,8 +113,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -375,6 +375,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -451,6 +455,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/genarray/CMakeLists.txt b/tests/genarray/CMakeLists.txt
index 8a14d86..1d65f4c 100644
--- a/tests/genarray/CMakeLists.txt
+++ b/tests/genarray/CMakeLists.txt
@@ -4,7 +4,7 @@ include_directories(${PROJECT_SOURCE_DIR}/tests/genarray)
include_directories(${PROJECT_BINARY_DIR}/tests/genarray)
link_directories(${PROJECT_BINARY_DIR}/tests/genarray)
-add_executable(genarray genarray.F90 gwrite_genarray.fh)
+add_executable(genarray genarray.F90)
target_link_libraries(genarray adiosf ${ADIOSLIB_LDADD})
set_target_properties(genarray PROPERTIES COMPILE_FLAGS "${ADIOSLIB_CPPFLAGS} ${ADIOSLIB_CFLAGS}")
@@ -12,7 +12,7 @@ add_executable(genarray2D genarray2D.F90)
target_link_libraries(genarray2D adiosf ${ADIOSLIB_LDADD})
set_target_properties(genarray2D PROPERTIES COMPILE_FLAGS "${ADIOSLIB_CPPFLAGS} ${ADIOSLIB_CFLAGS}")
-add_executable(copyarray copyarray.F90 gread_genarray.fh)
+add_executable(copyarray copyarray.F90)
target_link_libraries(copyarray adiosf ${ADIOSLIB_LDADD})
set_target_properties(copyarray PROPERTIES COMPILE_FLAGS "${ADIOSLIB_CPPFLAGS} ${ADIOSLIB_CFLAGS}")
@@ -20,18 +20,4 @@ add_executable(copyarray2D copyarray2D.F90)
target_link_libraries(copyarray2D adiosf ${ADIOSLIB_LDADD})
set_target_properties(copyarray2D PROPERTIES COMPILE_FLAGS "${ADIOSLIB_CPPFLAGS} ${ADIOSLIB_CFLAGS}")
-add_custom_command(
- OUTPUT gwrite_genarray.fh
- COMMAND rm -f gwrite_genarray.fh gread_genarray.fh
- COMMAND ${PROJECT_BINARY_DIR}/utils/gpp/gpp.py ${PROJECT_SOURCE_DIR}/tests/genarray/genarray3d.xml
- DEPENDS genarray3d.xml
- )
-
-add_custom_command(
- OUTPUT gread_genarray.fh
- COMMAND rm -f gwrite_genarray.fh gread_genarray.fh
- COMMAND ${PROJECT_BINARY_DIR}/utils/gpp/gpp.py ${PROJECT_SOURCE_DIR}/tests/genarray/genarray3d.xml
- DEPENDS genarray3d.xml
- )
-
file(COPY genarray.xml genarray3d.xml job.ewok job2D.ewok DESTINATION ${PROJECT_BINARY_DIR}/tests/genarray)
diff --git a/tests/genarray/Makefile.am b/tests/genarray/Makefile.am
index 13c1e8e..161a975 100644
--- a/tests/genarray/Makefile.am
+++ b/tests/genarray/Makefile.am
@@ -31,15 +31,15 @@ copyarray2D_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
FC=$(MPIFC)
-genarray.F90: gwrite_genarray.fh
-copyarray.F90: gwrite_genarray.fh gread_genarray.fh
-
-gwrite_genarray.fh: genarray3d.xml
- rm -f gwrite_genarray.fh gread_genarray.fh
- $(top_builddir)/utils/gpp/gpp.py $(srcdir)/genarray3d.xml
-gread_genarray.fh: genarray3d.xml
- rm -f gwrite_genarray.fh gread_genarray.fh
- $(top_builddir)/utils/gpp/gpp.py $(srcdir)/genarray3d.xml
+#genarray.F90: gwrite_genarray.fh
+#copyarray.F90: gwrite_genarray.fh gread_genarray.fh
+#
+#gwrite_genarray.fh: genarray3d.xml
+# rm -f gwrite_genarray.fh gread_genarray.fh
+# $(top_builddir)/utils/gpp/gpp.py $(srcdir)/genarray3d.xml
+#gread_genarray.fh: genarray3d.xml
+# rm -f gwrite_genarray.fh gread_genarray.fh
+# $(top_builddir)/utils/gpp/gpp.py $(srcdir)/genarray3d.xml
FCLINK = \
$(LIBTOOL) --mode=link --tag F77 $(FC) \
diff --git a/tests/genarray/Makefile.in b/tests/genarray/Makefile.in
index 5a37f21..c73ff42 100644
--- a/tests/genarray/Makefile.in
+++ b/tests/genarray/Makefile.in
@@ -102,7 +102,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -110,8 +110,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -348,6 +348,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -424,6 +428,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
@@ -515,6 +522,16 @@ copyarray2D_CPPFLAGS = $(AM_CPPFLAGS) $(ADIOSLIB_CPPFLAGS)
copyarray2D_CFLAGS = $(ADIOSLIB_CFLAGS)
copyarray2D_LDADD = $(top_builddir)/src/libadiosf.a $(ADIOSLIB_LDADD)
copyarray2D_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
+
+#genarray.F90: gwrite_genarray.fh
+#copyarray.F90: gwrite_genarray.fh gread_genarray.fh
+#
+#gwrite_genarray.fh: genarray3d.xml
+# rm -f gwrite_genarray.fh gread_genarray.fh
+# $(top_builddir)/utils/gpp/gpp.py $(srcdir)/genarray3d.xml
+#gread_genarray.fh: genarray3d.xml
+# rm -f gwrite_genarray.fh gread_genarray.fh
+# $(top_builddir)/utils/gpp/gpp.py $(srcdir)/genarray3d.xml
FCLINK = \
$(LIBTOOL) --mode=link --tag F77 $(FC) \
$(AM_FCFLAGS) $(FCFLAGS) $(LDFLAGS) -o $@
@@ -829,16 +846,6 @@ uninstall-am:
tags tags-am uninstall uninstall-am
-genarray.F90: gwrite_genarray.fh
-copyarray.F90: gwrite_genarray.fh gread_genarray.fh
-
-gwrite_genarray.fh: genarray3d.xml
- rm -f gwrite_genarray.fh gread_genarray.fh
- $(top_builddir)/utils/gpp/gpp.py $(srcdir)/genarray3d.xml
-gread_genarray.fh: genarray3d.xml
- rm -f gwrite_genarray.fh gread_genarray.fh
- $(top_builddir)/utils/gpp/gpp.py $(srcdir)/genarray3d.xml
-
all-local:
test "$(srcdir)" = "$(builddir)" || cp $(srcdir)/genarray3d.xml $(srcdir)/genarray.xml $(builddir)
diff --git a/tests/genarray/copyarray.F90 b/tests/genarray/copyarray.F90
index 364ddf1..bcad40b 100644
--- a/tests/genarray/copyarray.F90
+++ b/tests/genarray/copyarray.F90
@@ -204,7 +204,18 @@ subroutine readArray()
! TODO: Fix this to use the new read API
call adios_open (adios_handle, group, inputfile, "r", group_comm, adios_err)
-#include "gread_genarray.fh"
+ call adios_selection_writeblock (s, rank)
+ call adios_schedule_read (fp, s, "var1", 0, 1, double_xyz, adios_err)
+ call adios_schedule_read (fp, s, "var2", 0, 1, double_xyz, adios_err)
+ call adios_schedule_read (fp, s, "var3", 0, 1, double_xyz, adios_err)
+ call adios_schedule_read (fp, s, "var4", 0, 1, double_xyz, adios_err)
+ call adios_schedule_read (fp, s, "var5", 0, 1, double_xyz, adios_err)
+ call adios_schedule_read (fp, s, "var6", 0, 1, double_xyz, adios_err)
+ call adios_schedule_read (fp, s, "var7", 0, 1, double_xyz, adios_err)
+ call adios_schedule_read (fp, s, "var8", 0, 1, double_xyz, adios_err)
+ call adios_schedule_read (fp, s, "var9", 0, 1, double_xyz, adios_err)
+ call adios_perform_reads (fp, adios_err)
+ call adios_selection_delete (s)
call MPI_BARRIER(MPI_COMM_WORLD,adios_err)
cache_end_time = MPI_WTIME()
cache_total_time = cache_end_time - cache_start_time
@@ -234,7 +245,52 @@ subroutine writeArray()
group = "genarray"
call adios_open (adios_handle, group, outputfile, "w", group_comm, adios_err)
-#include "gwrite_genarray.fh"
+ adios_groupsize = 0
+ adios_groupsize = adios_groupsize + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 8_8 * (ndx) * (ndy) * (ndz) &
+ + 8_8 * (ndx) * (ndy) * (ndz) &
+ + 8_8 * (ndx) * (ndy) * (ndz) &
+ + 8_8 * (ndx) * (ndy) * (ndz) &
+ + 8_8 * (ndx) * (ndy) * (ndz) &
+ + 8_8 * (ndx) * (ndy) * (ndz) &
+ + 8_8 * (ndx) * (ndy) * (ndz) &
+ + 8_8 * (ndx) * (ndy) * (ndz) &
+ + 8_8 * (ndx) * (ndy) * (ndz)
+ call adios_group_size (adios_handle, adios_groupsize, adios_totalsize, adios_err)
+ call adios_write (adios_handle, "/dimensions/gndx", gndx, adios_err)
+ call adios_write (adios_handle, "/dimensions/gndy", gndy, adios_err)
+ call adios_write (adios_handle, "/dimensions/gndz", gndz, adios_err)
+ call adios_write (adios_handle, "/info/nproc", nproc, adios_err)
+ call adios_write (adios_handle, "/info/npx", npx, adios_err)
+ call adios_write (adios_handle, "/info/npy", npy, adios_err)
+ call adios_write (adios_handle, "/info/npz", npz, adios_err)
+ call adios_write (adios_handle, "/aux/offx", offx, adios_err)
+ call adios_write (adios_handle, "/aux/offy", offy, adios_err)
+ call adios_write (adios_handle, "/aux/offz", offz, adios_err)
+ call adios_write (adios_handle, "/aux/ndx", ndx, adios_err)
+ call adios_write (adios_handle, "/aux/ndy", ndy, adios_err)
+ call adios_write (adios_handle, "/aux/ndz", ndz, adios_err)
+ call adios_write (adios_handle, "/var/var1", double_xyz, adios_err)
+ call adios_write (adios_handle, "/var/var2", double_xyz, adios_err)
+ call adios_write (adios_handle, "/var/var3", double_xyz, adios_err)
+ call adios_write (adios_handle, "/var/var4", double_xyz, adios_err)
+ call adios_write (adios_handle, "/var/var5", double_xyz, adios_err)
+ call adios_write (adios_handle, "/var/var6", double_xyz, adios_err)
+ call adios_write (adios_handle, "/var/var7", double_xyz, adios_err)
+ call adios_write (adios_handle, "/var/var8", double_xyz, adios_err)
+ call adios_write (adios_handle, "/var/var9", double_xyz, adios_err)
call MPI_BARRIER(MPI_COMM_WORLD,adios_err)
cache_end_time = MPI_WTIME()
cache_total_time = cache_end_time - cache_start_time
diff --git a/tests/genarray/genarray.F90 b/tests/genarray/genarray.F90
index 6d22f6e..e83169c 100644
--- a/tests/genarray/genarray.F90
+++ b/tests/genarray/genarray.F90
@@ -182,7 +182,52 @@ subroutine writeArray()
group = "genarray"
write (outfilename,'(a,".",i3.3,".bp")') trim(outputfile),tstep
call adios_open (adios_handle, group, outfilename, mode, group_comm, adios_err)
-#include "gwrite_genarray.fh"
+ adios_groupsize = 0
+ adios_groupsize = adios_groupsize + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 4_8 &
+ + 8_8 * (ndx) * (ndy) * (ndz) &
+ + 8_8 * (ndx) * (ndy) * (ndz) &
+ + 8_8 * (ndx) * (ndy) * (ndz) &
+ + 8_8 * (ndx) * (ndy) * (ndz) &
+ + 8_8 * (ndx) * (ndy) * (ndz) &
+ + 8_8 * (ndx) * (ndy) * (ndz) &
+ + 8_8 * (ndx) * (ndy) * (ndz) &
+ + 8_8 * (ndx) * (ndy) * (ndz) &
+ + 8_8 * (ndx) * (ndy) * (ndz)
+ call adios_group_size (adios_handle, adios_groupsize, adios_totalsize, adios_err)
+ call adios_write (adios_handle, "/dimensions/gndx", gndx, adios_err)
+ call adios_write (adios_handle, "/dimensions/gndy", gndy, adios_err)
+ call adios_write (adios_handle, "/dimensions/gndz", gndz, adios_err)
+ call adios_write (adios_handle, "/info/nproc", nproc, adios_err)
+ call adios_write (adios_handle, "/info/npx", npx, adios_err)
+ call adios_write (adios_handle, "/info/npy", npy, adios_err)
+ call adios_write (adios_handle, "/info/npz", npz, adios_err)
+ call adios_write (adios_handle, "/aux/offx", offx, adios_err)
+ call adios_write (adios_handle, "/aux/offy", offy, adios_err)
+ call adios_write (adios_handle, "/aux/offz", offz, adios_err)
+ call adios_write (adios_handle, "/aux/ndx", ndx, adios_err)
+ call adios_write (adios_handle, "/aux/ndy", ndy, adios_err)
+ call adios_write (adios_handle, "/aux/ndz", ndz, adios_err)
+ call adios_write (adios_handle, "/var/var1", double_xyz, adios_err)
+ call adios_write (adios_handle, "/var/var2", double_xyz, adios_err)
+ call adios_write (adios_handle, "/var/var3", double_xyz, adios_err)
+ call adios_write (adios_handle, "/var/var4", double_xyz, adios_err)
+ call adios_write (adios_handle, "/var/var5", double_xyz, adios_err)
+ call adios_write (adios_handle, "/var/var6", double_xyz, adios_err)
+ call adios_write (adios_handle, "/var/var7", double_xyz, adios_err)
+ call adios_write (adios_handle, "/var/var8", double_xyz, adios_err)
+ call adios_write (adios_handle, "/var/var9", double_xyz, adios_err)
call adios_close (adios_handle, adios_err)
call MPI_BARRIER(MPI_COMM_WORLD,ierr)
io_end_time = MPI_WTIME()
@@ -251,9 +296,9 @@ subroutine processArgs()
call getarg(5, ndx_str)
call getarg(6, ndy_str)
call getarg(7, ndz_str)
- read (ndx_str,'(i6)') ndx
- read (ndy_str,'(i6)') ndy
- read (ndz_str,'(i6)') ndz
+ read (ndx_str,'(i12)') ndx
+ read (ndy_str,'(i12)') ndy
+ read (ndz_str,'(i12)') ndz
inputfile=char(0)
common_size = .true.
call getarg(8, time_str)
diff --git a/tests/genarray/genarray.xml b/tests/genarray/genarray.xml
index 66f994d..e02afa8 100644
--- a/tests/genarray/genarray.xml
+++ b/tests/genarray/genarray.xml
@@ -52,6 +52,5 @@
<method group="genarray" method="MPI"></method>
<!--method group="genarray" method="VAR_MERGE">chunk_size=1048576,io_method=MPI_LUSTRE,io_parameters=stripe_count=16,stripe_size=1048576</method-->
- <buffer max-size-MB="400"/>
</adios-config>
diff --git a/tests/genarray/genarray2D.F90 b/tests/genarray/genarray2D.F90
index 87baccb..51792e8 100644
--- a/tests/genarray/genarray2D.F90
+++ b/tests/genarray/genarray2D.F90
@@ -194,9 +194,9 @@ subroutine writeArray()
! Write out data using ADIOS
group = "genarray"
! calculate how much we write from this processor
- group_size = 4 * 9 + & ! X,Y, nproc, all size_ and offs_ integers
- 4 * ndx * ndy + & ! int_xy
- 4 * ndx * ndy ! int_xyt
+ group_size = 4_8 * 9_8 + & ! X,Y, nproc, all size_ and offs_ integers
+ ndx * ndy * 4_8 + & ! int_xy
+ ndx * ndy * 4_8 ! int_xyt
adios_totalsize = group_size
@@ -297,8 +297,8 @@ subroutine processArgs()
call getarg(4, ndx_str)
call getarg(5, ndy_str)
call getarg(6, time_str)
- read (ndx_str,'(i6)') ndx
- read (ndy_str,'(i6)') ndy
+ read (ndx_str,'(i12)') ndx
+ read (ndy_str,'(i12)') ndy
read (time_str,'(i6)') timesteps
inputfile=char(0)
common_size = .true.
diff --git a/tests/genarray/genarray3d.xml b/tests/genarray/genarray3d.xml
index e32b310..275d62e 100644
--- a/tests/genarray/genarray3d.xml
+++ b/tests/genarray/genarray3d.xml
@@ -45,6 +45,5 @@
<method group="genarray" method="MPI"></method>
<!--method group="genarray" method="VAR_MERGE">chunk_size=1048576;io_method=MPI_LUSTRE;io_parameters=stripe_count=16,stripe_size=1048576</method-->
- <buffer max-size-MB="20"/>
</adios-config>
diff --git a/tests/suite/Makefile.in b/tests/suite/Makefile.in
index 241a952..4183688 100644
--- a/tests/suite/Makefile.in
+++ b/tests/suite/Makefile.in
@@ -99,7 +99,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -107,8 +107,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -333,6 +333,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -409,6 +413,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/suite/programs/CMakeLists.txt b/tests/suite/programs/CMakeLists.txt
index 8ee6a89..363dadd 100644
--- a/tests/suite/programs/CMakeLists.txt
+++ b/tests/suite/programs/CMakeLists.txt
@@ -23,7 +23,8 @@ set (WRITE_PROGS1 local_array_time
set_path_var
steps_write
blocks
- build_standard_dataset)
+ build_standard_dataset
+ test_singlevalue)
set(WRITE_PROGS2 adios_staged_read
adios_staged_read_v2
@@ -75,3 +76,5 @@ file(COPY adios_amr_write.xml adios_amr_write_2vars.xml posix_method.xml
path_test.xml adios_transforms.xml set_path.xml set_path_var.xml
two_groups.xml
DESTINATION ${PROJECT_BINARY_DIR}/tests/suite/programs)
+
+add_subdirectory(examples)
diff --git a/tests/suite/programs/Makefile.am b/tests/suite/programs/Makefile.am
index 429bde5..ff4ff5f 100644
--- a/tests/suite/programs/Makefile.am
+++ b/tests/suite/programs/Makefile.am
@@ -33,7 +33,8 @@ check_C=local_array_time \
steps_read_stream \
blocks \
build_standard_dataset \
- transforms_writeblock_read
+ transforms_writeblock_read \
+ test_singlevalue
test_C=
@@ -190,6 +191,11 @@ transforms_writeblock_read_SOURCES = transforms_writeblock_read.c
transforms_writeblock_read_LDADD = $(top_builddir)/src/libadiosread.a $(ADIOSREADLIB_LDADD)
transforms_writeblock_read_LDFLAGS = $(AM_LDFLAGS) $(ADIOSREADLIB_LDFLAGS)
+test_singlevalue_SOURCES=test_singlevalue.c
+test_singlevalue_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
+test_singlevalue_LDFLAGS = $(AM_LDFLAGS) $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
+test_singlevalue.o: test_singlevalue.c
+
#transforms_SOURCES=transforms.c
#transforms_CPPFLAGS = -DADIOS_USE_READ_API_1
#transforms_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
diff --git a/tests/suite/programs/Makefile.in b/tests/suite/programs/Makefile.in
index 4297e96..1e7986c 100644
--- a/tests/suite/programs/Makefile.in
+++ b/tests/suite/programs/Makefile.in
@@ -103,7 +103,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -111,8 +111,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -143,7 +143,8 @@ CONFIG_CLEAN_VPATH_FILES =
@BUILD_WRITE_TRUE@ steps_read_file$(EXEEXT) \
@BUILD_WRITE_TRUE@ steps_read_stream$(EXEEXT) blocks$(EXEEXT) \
@BUILD_WRITE_TRUE@ build_standard_dataset$(EXEEXT) \
- at BUILD_WRITE_TRUE@ transforms_writeblock_read$(EXEEXT)
+ at BUILD_WRITE_TRUE@ transforms_writeblock_read$(EXEEXT) \
+ at BUILD_WRITE_TRUE@ test_singlevalue$(EXEEXT)
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE at am__EXEEXT_2 = \
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@ posix_method$(EXEEXT)
am__EXEEXT_3 =
@@ -316,6 +317,14 @@ steps_write_DEPENDENCIES = $(top_builddir)/src/libadios.a \
steps_write_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
$(steps_write_LDFLAGS) $(LDFLAGS) -o $@
+am_test_singlevalue_OBJECTS = test_singlevalue.$(OBJEXT)
+test_singlevalue_OBJECTS = $(am_test_singlevalue_OBJECTS)
+test_singlevalue_DEPENDENCIES = $(top_builddir)/src/libadios.a \
+ $(am__DEPENDENCIES_1)
+test_singlevalue_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \
+ $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \
+ $(AM_CFLAGS) $(CFLAGS) $(test_singlevalue_LDFLAGS) $(LDFLAGS) \
+ -o $@
am_transforms_writeblock_read_OBJECTS = \
transforms_writeblock_read.$(OBJEXT)
transforms_writeblock_read_OBJECTS = \
@@ -409,6 +418,7 @@ SOURCES = $(adios_amr_write_SOURCES) $(adios_amr_write_2vars_SOURCES) \
$(selections_SOURCES) $(set_path_SOURCES) \
$(set_path_var_SOURCES) $(steps_read_file_SOURCES) \
$(steps_read_stream_SOURCES) $(steps_write_SOURCES) \
+ $(test_singlevalue_SOURCES) \
$(transforms_writeblock_read_SOURCES) $(two_groups_SOURCES) \
$(write_alternate_SOURCES) $(write_read_SOURCES)
DIST_SOURCES = $(adios_amr_write_SOURCES) \
@@ -423,6 +433,7 @@ DIST_SOURCES = $(adios_amr_write_SOURCES) \
$(selections_SOURCES) $(set_path_SOURCES) \
$(set_path_var_SOURCES) $(steps_read_file_SOURCES) \
$(steps_read_stream_SOURCES) $(steps_write_SOURCES) \
+ $(test_singlevalue_SOURCES) \
$(transforms_writeblock_read_SOURCES) $(two_groups_SOURCES) \
$(write_alternate_SOURCES) $(write_read_SOURCES)
RECURSIVE_TARGETS = all-recursive check-recursive cscopelist-recursive \
@@ -823,6 +834,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -899,6 +914,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
@@ -1002,7 +1020,8 @@ check_readonly_C =
@BUILD_WRITE_TRUE@ steps_read_stream \
@BUILD_WRITE_TRUE@ blocks \
@BUILD_WRITE_TRUE@ build_standard_dataset \
- at BUILD_WRITE_TRUE@ transforms_writeblock_read
+ at BUILD_WRITE_TRUE@ transforms_writeblock_read \
+ at BUILD_WRITE_TRUE@ test_singlevalue
@BUILD_WRITE_TRUE at test_C =
@BUILD_WRITE_TRUE at SUBDIRS = examples
@@ -1092,6 +1111,9 @@ build_standard_dataset_LDFLAGS = $(AM_LDFLAGS) $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EX
transforms_writeblock_read_SOURCES = transforms_writeblock_read.c
transforms_writeblock_read_LDADD = $(top_builddir)/src/libadiosread.a $(ADIOSREADLIB_LDADD)
transforms_writeblock_read_LDFLAGS = $(AM_LDFLAGS) $(ADIOSREADLIB_LDFLAGS)
+test_singlevalue_SOURCES = test_singlevalue.c
+test_singlevalue_LDADD = $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
+test_singlevalue_LDFLAGS = $(AM_LDFLAGS) $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
#transforms_SOURCES=transforms.c
#transforms_CPPFLAGS = -DADIOS_USE_READ_API_1
@@ -1237,6 +1259,10 @@ steps_write$(EXEEXT): $(steps_write_OBJECTS) $(steps_write_DEPENDENCIES) $(EXTRA
@rm -f steps_write$(EXEEXT)
$(AM_V_CCLD)$(steps_write_LINK) $(steps_write_OBJECTS) $(steps_write_LDADD) $(LIBS)
+test_singlevalue$(EXEEXT): $(test_singlevalue_OBJECTS) $(test_singlevalue_DEPENDENCIES) $(EXTRA_test_singlevalue_DEPENDENCIES)
+ @rm -f test_singlevalue$(EXEEXT)
+ $(AM_V_CCLD)$(test_singlevalue_LINK) $(test_singlevalue_OBJECTS) $(test_singlevalue_LDADD) $(LIBS)
+
transforms_writeblock_read$(EXEEXT): $(transforms_writeblock_read_OBJECTS) $(transforms_writeblock_read_DEPENDENCIES) $(EXTRA_transforms_writeblock_read_DEPENDENCIES)
@rm -f transforms_writeblock_read$(EXEEXT)
$(AM_V_CCLD)$(transforms_writeblock_read_LINK) $(transforms_writeblock_read_OBJECTS) $(transforms_writeblock_read_LDADD) $(LIBS)
@@ -1279,6 +1305,7 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/steps_read_file.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/steps_read_stream.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/steps_write.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/test_singlevalue.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/transforms_writeblock_read.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/two_groups.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/write_alternate.Po at am__quote@
@@ -1786,6 +1813,7 @@ steps_write.o: steps_write.c
steps_read_file.o: steps_read_file.c
steps_read_stream.o: steps_read_stream.c
blocks.o: blocks.c
+test_singlevalue.o: test_singlevalue.c
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
diff --git a/tests/suite/programs/adios_amr_write.c b/tests/suite/programs/adios_amr_write.c
index a6247b7..74b9c81 100644
--- a/tests/suite/programs/adios_amr_write.c
+++ b/tests/suite/programs/adios_amr_write.c
@@ -14,6 +14,7 @@
*/
#include <stdio.h>
#include <string.h>
+#include <stdlib.h>
#include "adios.h"
int main (int argc, char ** argv)
{
diff --git a/tests/suite/programs/adios_amr_write_2vars.c b/tests/suite/programs/adios_amr_write_2vars.c
index e1d2ec9..2067101 100644
--- a/tests/suite/programs/adios_amr_write_2vars.c
+++ b/tests/suite/programs/adios_amr_write_2vars.c
@@ -14,6 +14,7 @@
*/
#include <stdio.h>
#include <string.h>
+#include <stdlib.h>
#include "adios.h"
int main (int argc, char ** argv)
{
diff --git a/tests/suite/programs/big_file.c b/tests/suite/programs/big_file.c
index 88cde53..a586c2f 100644
--- a/tests/suite/programs/big_file.c
+++ b/tests/suite/programs/big_file.c
@@ -178,13 +178,13 @@ int write_file (int step)
adios_open (&fh, "bigdata", FILENAME, (step ? "a" : "w"), comm);
groupsize = (4 + NBLOCKS*2) * sizeof(int); // dimensions
- log (" groupsize calculated = %llu\n", groupsize);
+ log (" groupsize calculated = %" PRIu64 "\n", groupsize);
groupsize += ldim1 * ldim2 * sizeof(int); // 2D blocks
//groupsize +=1024;
- log (" groupsize calculated = %llu\n", groupsize);
+ log (" groupsize calculated = %" PRIu64 "\n", groupsize);
adios_group_size (fh, groupsize, &totalsize);
- log (" groupsize %llu, totalsize %llu\n", groupsize, totalsize);
+ log (" groupsize %" PRIu64 ", totalsize %" PRIu64 "\n", groupsize, totalsize);
v = VALUE(rank, step);
log (" Write data to %s\n", FILENAME);
@@ -238,7 +238,7 @@ int write_file (int step)
#define CHECK_ARRAY(VARNAME,A,N,VALUE,STEP,i) \
for (i=0;i<N;i++) \
if (A[i] != VALUE) { \
- printE ("%s[%d] step %d: wrote %d but read %d\n",VARNAME,i,STEP,VALUE,A[i]);\
+ printE ("%s[%ld] step %d: wrote %d but read %d\n",VARNAME,(unsigned long int)i,STEP,VALUE,A[i]);\
err = 104; \
/*goto endread;*/\
break; \
@@ -249,7 +249,7 @@ int write_file (int step)
for (i=0;i<DIM1;i++) {\
for (j=0;j<DIM2;j++) {\
if (A[k] != VALUE) { \
- printE ("%s[%d,%d] step %d: wrote %d but read %d\n",VARNAME,i,j,STEP,VALUE,A[k]);\
+ printE ("%s[%ld,%ld] step %d: wrote %d but read %d\n",VARNAME,(unsigned long int)i,(unsigned long int)j,STEP,VALUE,A[k]);\
err = 104; \
/*goto endread;*/\
i=DIM1; /*break to end */\
@@ -310,7 +310,7 @@ int read_file ()
set_offsets();
start[0] = offs1;
start[1] = offs2;
- log (" Step %d bounding box start={%llu,%llu}, count={%llu,%llu}\n",
+ log (" Step %d bounding box start={%" PRIu64 ",%" PRIu64 "}, count={%" PRIu64 ",%" PRIu64 "}\n",
step, start[0], start[1], count[0], count[1]);
sel2 = adios_selection_boundingbox (2, start, count);
diff --git a/tests/suite/programs/blocks.c b/tests/suite/programs/blocks.c
index 5000130..9042b09 100644
--- a/tests/suite/programs/blocks.c
+++ b/tests/suite/programs/blocks.c
@@ -180,10 +180,10 @@ void print_written_info()
printf ("\n------- Information recorded on rank 0 (read will compare to this info) --------\n");
for (s = 0; s < nsteps; s++) {
printf ("Step %d:\n", s);
- printf (" Global dim = %llu\n", gdims[s]);
+ printf (" Global dim = %" PRIu64 "\n", gdims[s]);
for (r = 0; r < size; r++) {
for (b = 0; b < nblocks_per_step; b++) {
- printf (" rank %d: block %d: size=%llu, offset=%llu\n", r, b+1,
+ printf (" rank %d: block %d: size=%" PRIu64 ", offset=%" PRIu64 "\n", r, b+1,
block_count [s*nblocks_per_step*size + nblocks_per_step*r + b],
block_offset [s*nblocks_per_step*size + nblocks_per_step*r + b]
);
@@ -192,7 +192,7 @@ void print_written_info()
}
}
-int print_varinfo (ADIOS_FILE *f, int start_step)
+void print_varinfo (ADIOS_FILE *f, int start_step)
{
ADIOS_VARINFO * v;
int i,j,k;
@@ -202,10 +202,10 @@ int print_varinfo (ADIOS_FILE *f, int start_step)
adios_inq_var_stat (f, v, 0, 1);
printf ("ndim = %d\n", v->ndim);
- printf ("dims[%llu]", v->dims[0]);
+ printf ("dims[%" PRIu64 "]", v->dims[0]);
if (v->dims[0] != gdims[start_step])
{
- printf ("\tERROR: expected [%llu]", gdims[start_step]);
+ printf ("\tERROR: expected [%" PRIu64 "]", gdims[start_step]);
nerrors++;
}
printf("\n");
@@ -215,7 +215,7 @@ int print_varinfo (ADIOS_FILE *f, int start_step)
for (i = 0; i < v->nsteps; i++) {
printf (" nblocks[%d] = %d\n", i, v->nblocks[i]);
for (j = 0; j < v->nblocks[i]; j++) {
- printf(" block %2d: [%llu:%llu]", j,
+ printf(" block %2d: [%" PRIu64 ":%" PRIu64 "]", j,
v->blockinfo[k].start[0],
v->blockinfo[k].start[0] + v->blockinfo[k].count[0]-1);
@@ -223,7 +223,7 @@ int print_varinfo (ADIOS_FILE *f, int start_step)
v->blockinfo[k].count[0] != block_count [(start_step+i)*nblocks_per_step*size + j] )
{
nerrors++;
- printf ("\tERROR: expected [%llu:%llu]",
+ printf ("\tERROR: expected [%" PRIu64 ":%" PRIu64 "]",
block_offset [(start_step+i)*nblocks_per_step*size + j],
block_offset [(start_step+i)*nblocks_per_step*size + j] +
block_count [(start_step+i)*nblocks_per_step*size + j] -1
@@ -315,7 +315,7 @@ int read_stepbystep ()
-int print_scalar (ADIOS_FILE *f, char * name)
+void print_scalar (ADIOS_FILE *f, char * name)
{
ADIOS_VARINFO * v;
int i,j,k;
@@ -359,7 +359,7 @@ int print_scalar (ADIOS_FILE *f, char * name)
nerrors++;
printf ("\tERROR expected = [");
for (j=0; j < v->nsteps; j++) {
- printf ("%llu", block_offset [j*nblocks_per_step*size + i]);
+ printf ("%" PRIu64, block_offset [j*nblocks_per_step*size + i]);
if (j < v->nsteps-1) printf(",");
}
printf("]");
@@ -391,7 +391,7 @@ int print_scalar (ADIOS_FILE *f, char * name)
if (data[0] !=
block_offset [j*nblocks_per_step*size + i])
{
- printf ("\tERROR expected = %llu",
+ printf ("\tERROR expected = %" PRIu64,
block_offset [j*nblocks_per_step*size + i]);
nerrors++;
}
@@ -419,7 +419,7 @@ int print_scalar (ADIOS_FILE *f, char * name)
if (*(int*)stat->blocks->mins[blockid] !=
block_offset [j*nblocks_per_step*size + i])
{
- printf ("\tERROR expected = %llu",
+ printf ("\tERROR expected = %" PRIu64,
block_offset [j*nblocks_per_step*size + i]);
nerrors++;
}
@@ -499,7 +499,7 @@ int read_scalar_stepbystep ()
if (value !=
block_count [f->current_step*nblocks_per_step*size])
{
- printf ("\tERROR expected = %llu",
+ printf ("\tERROR expected = %" PRIu64,
block_count [f->current_step*nblocks_per_step*size]);
nerrors++;
}
diff --git a/tests/suite/programs/build_standard_dataset.c b/tests/suite/programs/build_standard_dataset.c
index 09271f2..42f9bb0 100644
--- a/tests/suite/programs/build_standard_dataset.c
+++ b/tests/suite/programs/build_standard_dataset.c
@@ -120,7 +120,7 @@ static void produce_xml(
fprintf(outfile, VAR_XML, xml_spec->varnames[i], adios_type_to_string_int(xml_spec->vartypes[i]), dimvar_list_buf1, transform_name);
}
- fprintf(outfile, GLOBALBOUNDS_FOOTER_XML);
+ fprintf(outfile, "%s", GLOBALBOUNDS_FOOTER_XML);
fprintf(outfile, FOOTER_XML, xml_spec->group_name, xml_spec->write_transport_method, xml_spec->buffer_size_mb);
}
diff --git a/tests/suite/programs/examples/CMakeLists.txt b/tests/suite/programs/examples/CMakeLists.txt
new file mode 100644
index 0000000..8cdb4d7
--- /dev/null
+++ b/tests/suite/programs/examples/CMakeLists.txt
@@ -0,0 +1,5 @@
+add_subdirectory(attributes)
+add_subdirectory(scalars)
+add_subdirectory(global_array)
+add_subdirectory(global_array_time)
+add_subdirectory(local_array)
diff --git a/tests/suite/programs/examples/Makefile.in b/tests/suite/programs/examples/Makefile.in
index 7d9f693..ddfe030 100644
--- a/tests/suite/programs/examples/Makefile.in
+++ b/tests/suite/programs/examples/Makefile.in
@@ -99,7 +99,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -107,8 +107,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -333,6 +333,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -409,6 +413,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/suite/programs/examples/attributes/CMakeLists.txt b/tests/suite/programs/examples/attributes/CMakeLists.txt
index e0f4e45..24bda23 100644
--- a/tests/suite/programs/examples/attributes/CMakeLists.txt
+++ b/tests/suite/programs/examples/attributes/CMakeLists.txt
@@ -1,11 +1,12 @@
include_directories(${PROJECT_SOURCE_DIR}/src/public)
include_directories(${PROJECT_SOURCE_DIR}/src)
-include_directories(${PROJECT_SOURCE_DIR}/test/suite/programs/examples/attributes)
+include_directories(${PROJECT_SOURCE_DIR}/tests/suite/programs/examples/attributes)
include_directories(${PROJECT_BINARY_DIR}/src)
include_directories(${PROJECT_BINARY_DIR}/src/public)
-link_directories(${PROJECT_BINARY_DIR}/test/suite/programs/examples/attributes)
+include_directories(${PROJECT_BINARY_DIR}/tests/suite/programs/examples/attributes)
+link_directories(${PROJECT_BINARY_DIR}/tests/suite/programs/examples/attributes)
-add_executable(attributes_write_C attributes_write_C.c)
+add_executable(attributes_write_C attributes_write_C.c gwrite_temperature.ch)
if(MPI_COMPILE_FLAGS)
set_target_properties(attributes_write_C PROPERTIES COMPILE_FLAGS "${MPI_C_COMPILE_FLAGS}")
endif()
@@ -30,5 +31,6 @@ endif()
target_link_libraries(attributes_read_C adiosread ${ADIOSREADLIB_LDADD} ${MPI_C_LIBRARIES})
#set_target_properties(attributes_read PROPERTIES COMPILE_FLAGS "-DADIOS_USE_READ_API_1")
-#install(FILES attributes.xml gwrite_temperature.ch gread_temperature.ch DESTINATION ${PROJECT_BINARY_DIR}/examples/C/attributes)
+file(COPY attributes_C.xml
+ DESTINATION ${PROJECT_BINARY_DIR}/tests/suite/programs/examples/attributes)
diff --git a/tests/suite/programs/examples/attributes/Makefile.in b/tests/suite/programs/examples/attributes/Makefile.in
index b775687..d7d46fe 100644
--- a/tests/suite/programs/examples/attributes/Makefile.in
+++ b/tests/suite/programs/examples/attributes/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -336,6 +336,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -412,6 +416,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/suite/programs/examples/global_array/CMakeLists.txt b/tests/suite/programs/examples/global_array/CMakeLists.txt
index 8776a9d..dfecd57 100644
--- a/tests/suite/programs/examples/global_array/CMakeLists.txt
+++ b/tests/suite/programs/examples/global_array/CMakeLists.txt
@@ -1,11 +1,12 @@
include_directories(${PROJECT_SOURCE_DIR}/src/public)
include_directories(${PROJECT_SOURCE_DIR}/src)
-include_directories(${PROJECT_SOURCE_DIR}/test/suite/programs/examples/global_array)
+include_directories(${PROJECT_SOURCE_DIR}/tests/suite/programs/examples/global_array)
include_directories(${PROJECT_BINARY_DIR}/src)
include_directories(${PROJECT_BINARY_DIR}/src/public)
-link_directories(${PROJECT_BINARY_DIR}/test/suite/programs/examples/global_array)
+include_directories(${PROJECT_BINARY_DIR}/tests/suite/programs/examples/global_array)
+link_directories(${PROJECT_BINARY_DIR}/tests/suite/programs/examples/global_array)
-add_executable(global_array_write_C global_array_write_C.c)
+add_executable(global_array_write_C global_array_write_C.c gwrite_temperature.ch)
target_link_libraries(global_array_write_C adios ${ADIOSLIB_LDADD})
add_custom_command(
OUTPUT gwrite_temperature.ch
@@ -46,19 +47,19 @@ foreach (PROG ${PROGS} )
endforeach()
if(BUILD_FORTRAN)
- add_executable(global_array_write_F global_array_write_F.F90)
+ add_executable(global_array_write_F global_array_write_F.F90 gwrite_temperature.fh)
target_link_libraries(global_array_write_F adiosf ${ADIOSLIB_LDADD})
add_custom_command(
OUTPUT gwrite_temperature.fh
- COMMAND ${PROJECT_SOURCE_DIR}/utils/gpp/gpp.py ${PROJECT_SOURCE_DIR}/tests/suite/programs/examples/global_array/global_array_F.xml
+ COMMAND ${PROJECT_BINARY_DIR}/utils/gpp/gpp.py ${PROJECT_SOURCE_DIR}/tests/suite/programs/examples/global_array/global_array_F.xml
DEPENDS global_array_F.xml
)
add_executable(global_array_write_noxml_F global_array_write_noxml_F.F90)
target_link_libraries(global_array_write_noxml_F adiosf ${ADIOSLIB_LDADD})
add_executable(global_array_write_byid_noxml_F global_array_write_byid_noxml_F.F90)
target_link_libraries(global_array_write_byid_noxml_F adiosf ${ADIOSLIB_LDADD})
-endif
+endif()
-
-#install(FILES adios_global.xml gread_temperature.ch gwrite_temperature.ch job.pbs DESTINATION ${PROJECT_BINARY_DIR}/examples/C/global-array)
+file(COPY global_array_C.xml global_array_F.xml
+ DESTINATION ${PROJECT_BINARY_DIR}/tests/suite/programs/examples/global_array)
diff --git a/tests/suite/programs/examples/global_array/Makefile.in b/tests/suite/programs/examples/global_array/Makefile.in
index 72729db..b3bd6e8 100644
--- a/tests/suite/programs/examples/global_array/Makefile.in
+++ b/tests/suite/programs/examples/global_array/Makefile.in
@@ -107,7 +107,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -115,8 +115,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -464,6 +464,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -540,6 +544,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/suite/programs/examples/global_array/global_array_read_C.c b/tests/suite/programs/examples/global_array/global_array_read_C.c
index 321c831..1ce232b 100644
--- a/tests/suite/programs/examples/global_array/global_array_read_C.c
+++ b/tests/suite/programs/examples/global_array/global_array_read_C.c
@@ -73,7 +73,7 @@ int main (int argc, char ** argv)
adios_perform_reads (f, 1);
for (i = 0; i < slice_size; i++) {
- log_test ("rank %d: [%lld,%d:%lld]", rank, start[0]+i, 0, slice_size);
+ log_test ("rank %d: [%" PRIu64 ",%d:%" PRIu64 "]", rank, start[0]+i, 0, slice_size);
for (j = 0; j < v->dims[1]; j++)
log_test (" %6.6g", * ((double *)data + i * v->dims[1] + j));
log_test ("\n");
diff --git a/tests/suite/programs/examples/global_array/global_array_read_byid_noxml_C.c b/tests/suite/programs/examples/global_array/global_array_read_byid_noxml_C.c
index f68fa7a..656ccfb 100644
--- a/tests/suite/programs/examples/global_array/global_array_read_byid_noxml_C.c
+++ b/tests/suite/programs/examples/global_array/global_array_read_byid_noxml_C.c
@@ -78,7 +78,7 @@ int main (int argc, char ** argv)
log_test (" ======== Rank %d ========== \n", rank);
npl = 10;
for (i = 0; i < slice_size; i+=npl) {
- log_test ("[%4.4lld] ", rank*slice_size+i);
+ log_test ("[%4.4" PRIu64 "] ", rank*slice_size+i);
for (j= 0; j < npl; j++) {
log_test (" %6.6g", * ((double *)data + i + j));
}
diff --git a/tests/suite/programs/examples/global_array/global_array_read_noxml_C.c b/tests/suite/programs/examples/global_array/global_array_read_noxml_C.c
index 50afe5d..05002ff 100644
--- a/tests/suite/programs/examples/global_array/global_array_read_noxml_C.c
+++ b/tests/suite/programs/examples/global_array/global_array_read_noxml_C.c
@@ -78,7 +78,7 @@ int main (int argc, char ** argv)
log_test (" ======== Rank %d ========== \n", rank);
npl = 10;
for (i = 0; i < slice_size; i+=npl) {
- log_test ("[%4.4lld] ", rank*slice_size+i);
+ log_test ("[%4.4" PRIu64 "] ", rank*slice_size+i);
for (j= 0; j < npl; j++) {
log_test (" %6.6g", * ((double *)data + i + j));
}
diff --git a/tests/suite/programs/examples/global_array_time/CMakeLists.txt b/tests/suite/programs/examples/global_array_time/CMakeLists.txt
index 531f511..3e03128 100644
--- a/tests/suite/programs/examples/global_array_time/CMakeLists.txt
+++ b/tests/suite/programs/examples/global_array_time/CMakeLists.txt
@@ -1,19 +1,23 @@
include_directories(${PROJECT_SOURCE_DIR}/src/public)
include_directories(${PROJECT_SOURCE_DIR}/src)
-include_directories(${PROJECT_SOURCE_DIR}/test/suite/programs/examples/global_array_time)
+include_directories(${PROJECT_SOURCE_DIR}/tests/suite/programs/examples/global_array_time)
include_directories(${PROJECT_BINARY_DIR}/src)
include_directories(${PROJECT_BINARY_DIR}/src/public)
-link_directories(${PROJECT_BINARY_DIR}/test/suite/programs/examples/global_array_time)
+include_directories(${PROJECT_BINARY_DIR}/tests/suite/programs/examples/global_array_time)
+link_directories(${PROJECT_BINARY_DIR}/tests/suite/programs/examples/global_array_time)
-add_executable(global_array_time_write_C global_array_time_write_C.c)
+add_executable(global_array_time_write_C global_array_time_write_C.c gwrite_restart.ch)
target_link_libraries(global_array_time_write_C adios ${ADIOSLIB_LDADD})
add_custom_command(
OUTPUT gwrite_restart.ch
COMMAND ${PROJECT_BINARY_DIR}/utils/gpp/gpp.py
${PROJECT_SOURCE_DIR}/tests/suite/programs/examples/global_array_time/global_array_time_C.xml
- DEPENDS global_array_C.xml
+ DEPENDS global_array_time_C.xml
)
+add_executable(global_array_time_write_multifile_C global_array_time_write_multifile_C.c gwrite_restart.ch)
+target_link_libraries(global_array_time_write_multifile_C adios ${ADIOSLIB_LDADD})
+
add_executable(global_array_time_read_as_file_C global_array_time_read_as_file_C.c)
target_link_libraries(global_array_time_read_as_file_C adiosread ${ADIOSREADLIB_LDADD})
#set_target_properties(global_array_time_read_as_file_C PROPERTIES COMPILE_FLAGS "-DADIOS_USE_READ_API_1")
@@ -34,14 +38,16 @@ endforeach()
if(BUILD_FORTRAN)
- add_executable(global_array_time_write_F global_array_time_write_F.F90)
+ add_executable(global_array_time_write_F global_array_time_write_F.F90 gwrite_restart.fh)
target_link_libraries(global_array_time_write_F adiosf ${ADIOSLIB_LDADD})
add_custom_command(
OUTPUT gwrite_restart.fh
COMMAND ${PROJECT_BINARY_DIR}/utils/gpp/gpp.py
${PROJECT_SOURCE_DIR}/tests/suite/programs/examples/global_array_time/global_array_time_F.xml
- DEPENDS global_array_F.xml
+ DEPENDS global_array_time_F.xml
)
-endif
+endif()
+
+file(COPY global_array_time_aggr_C.xml global_array_time_C.xml global_array_time_F.xml
+ DESTINATION ${PROJECT_BINARY_DIR}/tests/suite/programs/examples/global_array_time)
-#install(FILES global_array_time_write_C.xml gread_restart.ch gwrite_restart.ch job.pbs DESTINATION ${PROJECT_BINARY_DIR}/examples/C/global-array-time)
diff --git a/tests/suite/programs/examples/global_array_time/Makefile.am b/tests/suite/programs/examples/global_array_time/Makefile.am
index cafa035..4310ed2 100644
--- a/tests/suite/programs/examples/global_array_time/Makefile.am
+++ b/tests/suite/programs/examples/global_array_time/Makefile.am
@@ -6,7 +6,8 @@ AUTOMAKE_OPTIONS = no-dependencies
all-local:
test "$(srcdir)" = "$(builddir)" || cp -p $(srcdir)/*.xml $(builddir)
-check_PROGRAMS = global_array_time_write_C global_array_time_read_as_file_C global_array_time_read_as_stream_C
+check_PROGRAMS = global_array_time_write_C global_array_time_read_as_file_C global_array_time_read_as_stream_C \
+ global_array_time_write_multifile_C
global_array_time_write_C_SOURCES = global_array_time_write_C.c
global_array_time_write_C_LDADD = $(top_builddir)/src/libadios.a
@@ -16,6 +17,12 @@ global_array_time_write_C.o: gwrite_restart.ch
gwrite_restart.ch: global_array_time_C.xml
$(top_builddir)/utils/gpp/gpp.py $(srcdir)/global_array_time_C.xml
+global_array_time_write_multifile_C_SOURCES = global_array_time_write_multifile_C.c
+global_array_time_write_multifile_C_LDADD = $(top_builddir)/src/libadios.a
+global_array_time_write_multifile_C_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
+global_array_time_write_multifile_C_LDADD += $(ADIOSLIB_LDADD)
+global_array_time_write_multifile_C.o: gwrite_restart.ch
+
global_array_time_read_as_file_C_SOURCES = global_array_time_read_as_file_C.c
global_array_time_read_as_file_C_LDADD = $(top_builddir)/src/libadiosread.a
global_array_time_read_as_file_C_LDFLAGS = $(ADIOSREADLIB_LDFLAGS)
diff --git a/tests/suite/programs/examples/global_array_time/Makefile.in b/tests/suite/programs/examples/global_array_time/Makefile.in
index eeec105..f1a0618 100644
--- a/tests/suite/programs/examples/global_array_time/Makefile.in
+++ b/tests/suite/programs/examples/global_array_time/Makefile.in
@@ -79,7 +79,8 @@ build_triplet = @build@
host_triplet = @host@
check_PROGRAMS = global_array_time_write_C$(EXEEXT) \
global_array_time_read_as_file_C$(EXEEXT) \
- global_array_time_read_as_stream_C$(EXEEXT) $(am__EXEEXT_1)
+ global_array_time_read_as_stream_C$(EXEEXT) \
+ global_array_time_write_multifile_C$(EXEEXT) $(am__EXEEXT_1)
@BUILD_FORTRAN_TRUE at am__append_1 = global_array_time_write_F
subdir = tests/suite/programs/examples/global_array_time
DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am
@@ -103,7 +104,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -111,8 +112,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -175,6 +176,17 @@ global_array_time_write_F_LINK = $(LIBTOOL) $(AM_V_lt) --tag=FC \
$(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(FCLD) \
$(AM_FCFLAGS) $(FCFLAGS) $(global_array_time_write_F_LDFLAGS) \
$(LDFLAGS) -o $@
+am_global_array_time_write_multifile_C_OBJECTS = \
+ global_array_time_write_multifile_C.$(OBJEXT)
+global_array_time_write_multifile_C_OBJECTS = \
+ $(am_global_array_time_write_multifile_C_OBJECTS)
+global_array_time_write_multifile_C_DEPENDENCIES = \
+ $(top_builddir)/src/libadios.a $(am__DEPENDENCIES_1)
+global_array_time_write_multifile_C_LINK = $(LIBTOOL) $(AM_V_lt) \
+ --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link \
+ $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
+ $(global_array_time_write_multifile_C_LDFLAGS) $(LDFLAGS) -o \
+ $@
AM_V_P = $(am__v_P_ at AM_V@)
am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
am__v_P_0 = false
@@ -226,11 +238,13 @@ am__v_CCLD_1 =
SOURCES = $(global_array_time_read_as_file_C_SOURCES) \
$(global_array_time_read_as_stream_C_SOURCES) \
$(global_array_time_write_C_SOURCES) \
- $(global_array_time_write_F_SOURCES)
+ $(global_array_time_write_F_SOURCES) \
+ $(global_array_time_write_multifile_C_SOURCES)
DIST_SOURCES = $(global_array_time_read_as_file_C_SOURCES) \
$(global_array_time_read_as_stream_C_SOURCES) \
$(global_array_time_write_C_SOURCES) \
- $(am__global_array_time_write_F_SOURCES_DIST)
+ $(am__global_array_time_write_F_SOURCES_DIST) \
+ $(global_array_time_write_multifile_C_SOURCES)
am__can_run_installinfo = \
case $$AM_UPDATE_INFO_DIR in \
n|no|NO) false;; \
@@ -386,6 +400,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -462,6 +480,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
@@ -538,6 +559,10 @@ global_array_time_write_C_SOURCES = global_array_time_write_C.c
global_array_time_write_C_LDADD = $(top_builddir)/src/libadios.a \
$(ADIOSLIB_LDADD)
global_array_time_write_C_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
+global_array_time_write_multifile_C_SOURCES = global_array_time_write_multifile_C.c
+global_array_time_write_multifile_C_LDADD = \
+ $(top_builddir)/src/libadios.a $(ADIOSLIB_LDADD)
+global_array_time_write_multifile_C_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
global_array_time_read_as_file_C_SOURCES = global_array_time_read_as_file_C.c
global_array_time_read_as_file_C_LDADD = \
$(top_builddir)/src/libadiosread.a $(ADIOSREADLIB_LDADD)
@@ -617,6 +642,10 @@ global_array_time_write_F$(EXEEXT): $(global_array_time_write_F_OBJECTS) $(globa
@rm -f global_array_time_write_F$(EXEEXT)
$(AM_V_FCLD)$(global_array_time_write_F_LINK) $(global_array_time_write_F_OBJECTS) $(global_array_time_write_F_LDADD) $(LIBS)
+global_array_time_write_multifile_C$(EXEEXT): $(global_array_time_write_multifile_C_OBJECTS) $(global_array_time_write_multifile_C_DEPENDENCIES) $(EXTRA_global_array_time_write_multifile_C_DEPENDENCIES)
+ @rm -f global_array_time_write_multifile_C$(EXEEXT)
+ $(AM_V_CCLD)$(global_array_time_write_multifile_C_LINK) $(global_array_time_write_multifile_C_OBJECTS) $(global_array_time_write_multifile_C_LDADD) $(LIBS)
+
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -856,6 +885,7 @@ all-local:
global_array_time_write_C.o: gwrite_restart.ch
gwrite_restart.ch: global_array_time_C.xml
$(top_builddir)/utils/gpp/gpp.py $(srcdir)/global_array_time_C.xml
+global_array_time_write_multifile_C.o: gwrite_restart.ch
@BUILD_FORTRAN_TRUE at global_array_time_write_F.o: gwrite_restart.fh
@BUILD_FORTRAN_TRUE at gwrite_restart.fh: global_array_time_F.xml
@BUILD_FORTRAN_TRUE@ $(top_builddir)/utils/gpp/gpp.py $(srcdir)/global_array_time_F.xml
diff --git a/tests/suite/programs/examples/global_array_time/global_array_time_aggr_C.xml b/tests/suite/programs/examples/global_array_time/global_array_time_aggr_C.xml
index ff4e6a8..ef84ed8 100644
--- a/tests/suite/programs/examples/global_array_time/global_array_time_aggr_C.xml
+++ b/tests/suite/programs/examples/global_array_time/global_array_time_aggr_C.xml
@@ -20,7 +20,7 @@
</adios-group>
<method group="restart" method="MPI"/>
- <time-aggregation group="restart" buffer-size=3000/>
+ <time-aggregation group="restart" buffer-size="3000"/>
<buffer max-size-MB="5"/>
diff --git a/tests/suite/programs/examples/global_array_time/global_array_time_read_as_file_C.c b/tests/suite/programs/examples/global_array_time/global_array_time_read_as_file_C.c
index d86b1e6..6ece8c6 100644
--- a/tests/suite/programs/examples/global_array_time/global_array_time_read_as_file_C.c
+++ b/tests/suite/programs/examples/global_array_time/global_array_time_read_as_file_C.c
@@ -66,7 +66,7 @@ int main (int argc, char ** argv)
adios_perform_reads (f, 1);
if (rank == 0)
- log_test ("Array size of temperature [0:%lld,0:%lld]\n", v->dims[0], v->dims[1]);
+ log_test ("Array size of temperature [0:%" PRIu64 ",0:%" PRIu64 "]\n", v->dims[0], v->dims[1]);
if (rank > 0) {
MPI_Recv (&token, 1, MPI_INT, rank-1, 0, comm, &status);
@@ -75,7 +75,7 @@ int main (int argc, char ** argv)
log_test("------------------------------------------------\n");
log_test("rank=%d: \n", rank);
for (i = 0; i < 2; i++) {
- log_test ("step %lld = [\n", step+i);
+ log_test ("step %" PRIu64 " = [\n", step+i);
for (j = 0; j < v->dims[0]; j++) {
log_test (" [");
for (k = 0; k < v->dims[1]; k++) {
diff --git a/tests/suite/programs/examples/global_array_time/global_array_time_read_as_stream_C.c b/tests/suite/programs/examples/global_array_time/global_array_time_read_as_stream_C.c
index 39b9c4a..59188d7 100644
--- a/tests/suite/programs/examples/global_array_time/global_array_time_read_as_stream_C.c
+++ b/tests/suite/programs/examples/global_array_time/global_array_time_read_as_stream_C.c
@@ -65,7 +65,7 @@ int main (int argc, char ** argv)
log_test ("rank %d: ndim = %d\n", rank, v->ndim);
//log_test ("nsteps = %d\n", v->nsteps);
- log_test ("rank %d: dims[%llu][%llu]\n", rank, v->dims[0], v->dims[1]);
+ log_test ("rank %d: dims[%" PRIu64 "][%" PRIu64 "]\n", rank, v->dims[0], v->dims[1]);
uint64_t slice_size = v->dims[0]/size;
if (rank == size-1)
@@ -86,7 +86,7 @@ int main (int argc, char ** argv)
adios_schedule_read (f, sel, "temperature", 0, 1, data);
adios_perform_reads (f, 1);
- log_test("rank=%d: step %d: [0:%lld,0:%lld] = [", rank, f->current_step, v->dims[0], v->dims[1]);
+ log_test("rank=%d: step %d: [0:%" PRIu64 ",0:%" PRIu64 "] = [", rank, f->current_step, v->dims[0], v->dims[1]);
for (i = 0; i < slice_size; i++) {
log_test (" [");
for (j = 0; j < v->dims[1]; j++) {
diff --git a/tests/suite/programs/examples/global_array_time/global_array_time_write_multifile_C.c b/tests/suite/programs/examples/global_array_time/global_array_time_write_multifile_C.c
new file mode 100644
index 0000000..29e664c
--- /dev/null
+++ b/tests/suite/programs/examples/global_array_time/global_array_time_write_multifile_C.c
@@ -0,0 +1,64 @@
+/*
+ * ADIOS is freely available under the terms of the BSD license described
+ * in the COPYING file in the top level directory of this source distribution.
+ *
+ * Copyright (c) 2008 - 2009. UT-BATTELLE, LLC. All rights reserved.
+ */
+
+#include <stdio.h>
+#include <string.h>
+#include "mpi.h"
+#include "adios.h"
+int main (int argc, char ** argv)
+{
+ char filename [256];
+ int rank, size, i, it, fidx;
+ int NX = 10;
+ // NY = 1 for testing purpose
+ int NY = 1;
+ double t[NX];
+ double p[NY];
+ char mode[2] = "w";
+
+ /* ADIOS variables declarations for matching gwrite_temperature.ch */
+ uint64_t adios_groupsize, adios_totalsize;
+ int64_t adios_handle;
+ MPI_Comm comm=MPI_COMM_WORLD;
+
+ MPI_Init (&argc, &argv);
+ MPI_Comm_rank (MPI_COMM_WORLD, &rank);
+ MPI_Comm_size (comm, &size);
+
+ adios_init ("global_array_time_aggr_C.xml", comm);
+ fidx = 0;
+ for (it = 0; it < 25; it++) {
+
+ for (i = 0; i < NX; i++)
+ t[i] = (it+1)*100.0 + rank*NX + i;
+
+ for (i = 0; i < NY; i++)
+ p[i] = (it+1)*1000.0 + rank*NY + i;
+
+ if (it % 10 == 0) {
+ fidx++; // increases at every 10 steps
+ mode[0] = 'w';
+ //printf ("Reached it=%d, increase file index to %d\n", it, fidx);
+ } else {
+ mode[0] = 'a';
+ }
+ sprintf (filename, "global_array_time_C_%d.bp", fidx);
+ adios_open (&adios_handle, "restart", filename, mode, comm);
+
+# include "gwrite_restart.ch"
+ adios_close (adios_handle);
+ MPI_Barrier (comm);
+ //if (rank==0) printf("Timestep %d written\n", it+1);
+ }
+ MPI_Barrier (comm);
+ //if (rank==0) printf("Finalize adios\n");
+ adios_finalize (rank);
+
+ //if (rank==0) printf("Finalize MPI\n");
+ MPI_Finalize ();
+ return 0;
+}
diff --git a/tests/suite/programs/examples/local_array/CMakeLists.txt b/tests/suite/programs/examples/local_array/CMakeLists.txt
index f6b2da6..1afef5f 100644
--- a/tests/suite/programs/examples/local_array/CMakeLists.txt
+++ b/tests/suite/programs/examples/local_array/CMakeLists.txt
@@ -1,11 +1,12 @@
include_directories(${PROJECT_SOURCE_DIR}/src/public)
include_directories(${PROJECT_SOURCE_DIR}/src)
-include_directories(${PROJECT_SOURCE_DIR}/test/suite/programs/examples/local_array)
+include_directories(${PROJECT_SOURCE_DIR}/tests/suite/programs/examples/local_array)
include_directories(${PROJECT_BINARY_DIR}/src)
include_directories(${PROJECT_BINARY_DIR}/src/public)
+include_directories(${PROJECT_BINARY_DIR}/tests/suite/programs/examples/local_array)
link_directories(${PROJECT_BINARY_DIR}/test/suite/programs/examples/local_array)
-add_executable(local_array_write_C local_array_write_C.c)
+add_executable(local_array_write_C local_array_write_C.c gwrite_arrays.ch)
if(MPI_COMPILE_FLAGS)
set_target_properties(local_array_write_C PROPERTIES COMPILE_FLAGS "${MPI_C_COMPILE_FLAGS}")
endif()
@@ -29,5 +30,6 @@ if(MPI_LINK_FLAGS)
endif()
target_link_libraries(local_array_read_C adiosread ${ADIOSREADLIB_LDADD} ${MPI_C_LIBRARIES})
-#install(FILES arrays.xml gwrite_arrays.ch gread_arrays.ch job.pbs DESTINATION ${PROJECT_BINARY_DIR}/examples/C/arrays)
+file(COPY local_array_C.xml
+ DESTINATION ${PROJECT_BINARY_DIR}/tests/suite/programs/examples/local_array)
diff --git a/tests/suite/programs/examples/local_array/Makefile.in b/tests/suite/programs/examples/local_array/Makefile.in
index 71a4362..f7ec517 100644
--- a/tests/suite/programs/examples/local_array/Makefile.in
+++ b/tests/suite/programs/examples/local_array/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -336,6 +336,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -412,6 +416,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/suite/programs/examples/scalars/CMakeLists.txt b/tests/suite/programs/examples/scalars/CMakeLists.txt
index a9305ea..155af05 100644
--- a/tests/suite/programs/examples/scalars/CMakeLists.txt
+++ b/tests/suite/programs/examples/scalars/CMakeLists.txt
@@ -1,9 +1,10 @@
include_directories(${PROJECT_SOURCE_DIR}/src/public)
include_directories(${PROJECT_SOURCE_DIR}/src)
-include_directories(${PROJECT_SOURCE_DIR}/test/suite/programs/examples/scalars)
+include_directories(${PROJECT_SOURCE_DIR}/tests/suite/programs/examples/scalars)
include_directories(${PROJECT_BINARY_DIR}/src)
include_directories(${PROJECT_BINARY_DIR}/src/public)
-link_directories(${PROJECT_BINARY_DIR}/test/suite/programs/examples/scalars)
+include_directories(${PROJECT_BINARY_DIR}/tests/suite/programs/examples/scalars)
+link_directories(${PROJECT_BINARY_DIR}/tests/suite/programs/examples/scalars)
add_executable(scalars_write_C scalars_write_C.c gwrite_scalars.ch)
if(MPI_COMPILE_FLAGS)
@@ -36,10 +37,9 @@ if(BUILD_FORTRAN)
COMMAND ${PROJECT_BINARY_DIR}/utils/gpp/gpp.py ${PROJECT_SOURCE_DIR}/tests/suite/programs/examples/scalars/scalars_F.xml
DEPENDS scalars_F.xml
)
-
-
add_executable(scalars_read_F scalars_read_F.F90)
target_link_libraries(scalars_read_F adiosreadf ${ADIOSREADLIB_LDADD})
-endif
+endif()
-#install(FILES scalars.xml gwrite_scalars.ch gread_scalars.ch job.pbs DESTINATION ${PROJECT_BINARY_DIR}/examples/C/scalars)
+file(COPY scalars_C.xml scalars_F.xml
+ DESTINATION ${PROJECT_BINARY_DIR}/tests/suite/programs/examples/scalars)
diff --git a/tests/suite/programs/examples/scalars/Makefile.in b/tests/suite/programs/examples/scalars/Makefile.in
index d11ba96..3c81e86 100644
--- a/tests/suite/programs/examples/scalars/Makefile.in
+++ b/tests/suite/programs/examples/scalars/Makefile.in
@@ -102,7 +102,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -110,8 +110,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -378,6 +378,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -454,6 +458,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/tests/suite/programs/examples/scalars/scalars_read_C.c b/tests/suite/programs/examples/scalars/scalars_read_C.c
index 3ae4764..33a252e 100644
--- a/tests/suite/programs/examples/scalars/scalars_read_C.c
+++ b/tests/suite/programs/examples/scalars/scalars_read_C.c
@@ -87,12 +87,12 @@ int main (int argc, char ** argv)
fprintf (outf, "byte v1 = %d\n", v1);
fprintf (outf, "short v2 = %d\n", v2);
fprintf (outf, "integer v3 = %d\n", v3);
- fprintf (outf, "long v4 = %lld\n", v4);
+ fprintf (outf, "long v4 = %" PRId64 "\n", v4);
fprintf (outf, "uns.byte v5 = %u\n", v5);
fprintf (outf, "uns.short v6 = %u\n", v6);
fprintf (outf, "uns.int v7 = %u\n", v7);
- fprintf (outf, "uns.long v8 = %llu\n", v8);
+ fprintf (outf, "uns.long v8 = %" PRIu64 "\n", v8);
fprintf (outf, "float v9 = %g\n", v9);
fprintf (outf, "double v10 = %g\n", v10);
diff --git a/tests/suite/programs/many_vars.c b/tests/suite/programs/many_vars.c
index f8b49c4..d3c949f 100644
--- a/tests/suite/programs/many_vars.c
+++ b/tests/suite/programs/many_vars.c
@@ -244,7 +244,7 @@ int write_file (int step)
//groupsize +=1024;
adios_group_size (fh, groupsize, &totalsize);
- log (" groupsize %lld, totalsize %lld\n", groupsize, totalsize);
+ log (" groupsize %" PRIu64 ", totalsize %" PRIu64 "\n", groupsize, totalsize);
adios_write (fh, "gdim1", &gdim1);
adios_write (fh, "gdim2", &gdim2);
diff --git a/tests/suite/programs/reuse_dim.c b/tests/suite/programs/reuse_dim.c
index f3b2648..6459027 100755
--- a/tests/suite/programs/reuse_dim.c
+++ b/tests/suite/programs/reuse_dim.c
@@ -64,6 +64,7 @@ void fini_vars()
free (r2);
}
+int declare_group ();
int write_file (char *fname);
int read_file (char *fname);
diff --git a/tests/suite/programs/selections.c b/tests/suite/programs/selections.c
index db8ec35..de1f3ac 100644
--- a/tests/suite/programs/selections.c
+++ b/tests/suite/programs/selections.c
@@ -15,6 +15,7 @@
*/
#include <stdio.h>
#include <stdlib.h>
+#include <unistd.h>
#include <stdint.h>
#include <string.h>
#include <errno.h>
diff --git a/tests/suite/programs/set_path.c b/tests/suite/programs/set_path.c
index c2a7c5f..9613464 100644
--- a/tests/suite/programs/set_path.c
+++ b/tests/suite/programs/set_path.c
@@ -136,8 +136,7 @@ int write_file ()
{
int64_t fh;
uint64_t groupsize=0, totalsize;
- char *newpath, *oldpath;
- char varpath[128];
+ char *newpath;
log ("Write to %s\n", FILENAME);
adios_open (&fh, "abc", FILENAME, "w", comm);
@@ -148,7 +147,7 @@ int write_file ()
groupsize += 1000; // add for extra metadata of triplicated variables, which is not expected from the xml itself
adios_group_size (fh, groupsize, &totalsize);
- log ("Group size: data only = %lld, with metadata = %lld\n", groupsize, totalsize);
+ log ("Group size: data only = %" PRIu64 ", with metadata = %" PRIu64 "\n", groupsize, totalsize);
adios_write (fh, "gdim1", &gdim1);
adios_write (fh, "ldim1", &ldim1);
@@ -157,25 +156,25 @@ int write_file ()
newpath = getpath(0);
log (" Change path of all variables to %s\n", newpath);
adios_set_path (fh, newpath);
- log (" Write s0\n", varpath);
+ log (" Write s0\n");
adios_write (fh, "s0", &s0);
- log (" Write a1\n", varpath);
+ log (" Write a1\n");
adios_write (fh, "a1", a0);
newpath = getpath(1);
log (" Change path of all variables to %s\n", newpath);
adios_set_path (fh, newpath);
- log (" Write s0\n", varpath);
+ log (" Write s0\n");
adios_write (fh, "s0", &s1);
- log (" Write a1\n", varpath);
+ log (" Write a1\n");
adios_write (fh, "a1", a1);
newpath = getpath(2);
log (" Change path of all variables to %s\n", newpath);
adios_set_path (fh, newpath);
- log (" Write s0\n", varpath);
+ log (" Write s0\n");
adios_write (fh, "s0", &s2);
- log (" Write a1\n", varpath);
+ log (" Write a1\n");
adios_write (fh, "a1", a2);
adios_close (fh);
diff --git a/tests/suite/programs/set_path_var.c b/tests/suite/programs/set_path_var.c
index 5b6968c..61e9aa7 100644
--- a/tests/suite/programs/set_path_var.c
+++ b/tests/suite/programs/set_path_var.c
@@ -148,7 +148,7 @@ int write_file ()
groupsize += 1000; // add for extra metadata of triplicated variables, which is not expected from the xml itself
adios_group_size (fh, groupsize, &totalsize);
- log ("Group size: data only = %lld, with metadata = %lld\n", groupsize, totalsize);
+ log ("Group size: data only = %" PRIu64 ", with metadata = %" PRIu64 "\n", groupsize, totalsize);
adios_write (fh, "gdim1", &gdim1);
adios_write (fh, "ldim1", &ldim1);
diff --git a/tests/suite/programs/steps_read_file.c b/tests/suite/programs/steps_read_file.c
index ab7e773..57aa366 100644
--- a/tests/suite/programs/steps_read_file.c
+++ b/tests/suite/programs/steps_read_file.c
@@ -153,7 +153,7 @@ int process_metadata()
rank, "record", adios_errmsg());
return 1;
}
- printf ("rank %d: record dims = %llu * %llu \n", rank, varinfo->dims[0], varinfo->dims[1]);
+ printf ("rank %d: record dims = %" PRIu64 " * %" PRIu64 " \n", rank, varinfo->dims[0], varinfo->dims[1]);
printf ("rank %d: total nblocks = %d in %d steps\n",
rank, varinfo->sum_nblocks, varinfo->nsteps);
diff --git a/tests/suite/programs/steps_read_stream.c b/tests/suite/programs/steps_read_stream.c
index 7d78f3b..df51cc5 100644
--- a/tests/suite/programs/steps_read_stream.c
+++ b/tests/suite/programs/steps_read_stream.c
@@ -188,7 +188,7 @@ int process_metadata()
return 1;
}
nblocks = v->nblocks[0];
- printf ("rank %d: record dims = %llu * %llu \n", rank, v->dims[0], v->dims[1]);
+ printf ("rank %d: record dims = %" PRIu64 " * %" PRIu64 " \n", rank, v->dims[0], v->dims[1]);
adios_free_varinfo (v);
printf ("rank %d: nblocks = %d\n", rank, nblocks);
diff --git a/tests/suite/programs/test_singlevalue.c b/tests/suite/programs/test_singlevalue.c
new file mode 100644
index 0000000..4eba360
--- /dev/null
+++ b/tests/suite/programs/test_singlevalue.c
@@ -0,0 +1,350 @@
+/*
+ * ADIOS is freely available under the terms of the BSD license described
+ * in the COPYING file in the top level directory of this source distribution.
+ *
+ * Copyright (c) 2008 - 2009. UT-BATTELLE, LLC. All rights reserved.
+ */
+
+/* ADIOS C test:
+ * Write the first variable only once: one process and one step only.
+ * Then write some other variables over multiple steps.
+ * Then read them all and check if they are correct.
+ *
+ * This situation broke reading step-by-step because bp_utils.c:get_time()
+ * uses the the first variable to find the next timestep for all.
+ *
+ * How to run: mpirun -np <N> test_singlevalue
+ * Output: test_singlevalue.bp
+ *
+ */
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include <string.h>
+#include "adios.h"
+#include "adios_read.h"
+
+#ifdef DMALLOC
+#include "dmalloc.h"
+#endif
+
+#define log(...) fprintf (stderr, "[rank=%3.3d, line %d]: ", rank, __LINE__); fprintf (stderr, __VA_ARGS__); fflush(stderr);
+#define printE(...) fprintf (stderr, "[rank=%3.3d, line %d]: ERROR: ", rank, __LINE__); fprintf (stderr, __VA_ARGS__); fflush(stderr);
+
+static const int NSTEPS = 3;
+static const char FILENAME[] = "test_singlevalue.bp";
+#define VALUE(rank, step) (rank * 100 + step)
+#define VALUE0(step) (step)
+
+/* Variables to write */
+int a0;
+int *a1;
+
+
+/* Variables to read */
+int r0, rt0;
+int *r1, *rt1;
+
+static const int ldim1 = 7;
+int gdim1;
+int offs1;
+
+MPI_Comm comm = MPI_COMM_WORLD;
+int rank;
+int size;
+
+void alloc_vars()
+{
+ int n;
+
+ gdim1 = size*ldim1;
+ offs1 = rank*ldim1;
+ n = ldim1;
+ a1 = (int*) malloc (n * sizeof(int));
+ r1 = (int*) malloc (n * sizeof(int));
+ rt1 = (int*) malloc (n * sizeof(int));
+}
+
+void set_vars(int step)
+{
+ int n, i;
+ int v = VALUE(rank, step);
+
+ a0 = v;
+
+ n = ldim1;
+ for (i=0; i<n; i++) a1[i] = v;
+}
+
+void fini_vars()
+{
+ free (a1);
+ free (r1);
+ free (rt1);
+}
+
+
+int write_file (int step);
+int read_file ();
+int read_stream ();
+
+int main (int argc, char ** argv)
+{
+ int err,i ;
+
+ MPI_Init (&argc, &argv);
+ MPI_Comm_rank (comm, &rank);
+ MPI_Comm_size (comm, &size);
+
+ alloc_vars();
+ adios_init_noxml(comm);
+ err = adios_read_init_method(ADIOS_READ_METHOD_BP, comm, "verbose=2");
+ if (err) {
+ printE ("%s\n", adios_errmsg());
+ }
+
+ int64_t m_adios_group;
+ adios_declare_group (&m_adios_group, "once", "", adios_stat_default);
+ adios_select_method (m_adios_group, "MPI", "", "");
+ adios_define_var (m_adios_group, "once", "", adios_integer, 0, 0, 0);
+ adios_define_var (m_adios_group, "onceperstep", "", adios_integer, 0, 0, 0);
+ adios_define_var (m_adios_group, "scalar", "", adios_integer, 0, 0, 0);
+ char gdimstr[32], ldimstr[32], offsstr[32];
+ sprintf(gdimstr, "%d", gdim1);
+ sprintf(ldimstr, "%d", ldim1);
+ sprintf(offsstr, "%d", offs1);
+ adios_define_var (m_adios_group, "a1", "", adios_integer,
+ ldimstr, gdimstr, offsstr);
+
+ for (i=0; i<NSTEPS; i++) {
+ if (!err) {
+ set_vars (i);
+ err = write_file (i);
+ }
+ }
+
+ if (!err)
+ err = read_file ();
+
+ if (!err)
+ err = read_stream ();
+
+ adios_finalize (rank);
+ fini_vars();
+ MPI_Finalize ();
+ return err;
+}
+
+
+int write_file (int step)
+{
+ int64_t fh;
+ uint64_t groupsize=0, totalsize;
+
+ log ("Write step %d to %s\n", step, FILENAME);
+ adios_open (&fh, "once", FILENAME, (step ? "a" : "w"), comm);
+
+ if (rank == 0) {
+ if (step == 0) {
+ adios_write (fh, "once", &a0);
+ }
+ adios_write (fh, "onceperstep", &a0);
+ }
+ adios_write (fh, "scalar", &a0);
+ adios_write (fh, "a1", a1);
+
+ adios_close (fh);
+ MPI_Barrier (comm);
+ return 0;
+}
+
+
+#define CHECK_VARINFO(VARNAME, NDIM, NSTEPS) \
+ vi = adios_inq_var (f, VARNAME); \
+ if (vi == NULL) { \
+ printE ("No such variable " VARNAME "\n"); \
+ err = 101; \
+ goto endread; \
+ } \
+ if (vi->ndim != NDIM) { \
+ printE ("Variable " VARNAME " has %d dimensions, but expected %d\n", vi->ndim, NDIM); \
+ err = 102; \
+ goto endread; \
+ } \
+ if (vi->nsteps != NSTEPS) { \
+ printE ("Variable " VARNAME " has %d steps, but expected %d\n", vi->nsteps, NSTEPS); \
+ err = 103; \
+ /*goto endread; */\
+ } \
+ adios_free_varinfo (vi);
+
+#define CHECK_SCALAR(VARNAME, VAR, VALUE, STEP) \
+ if (VAR != VALUE) { \
+ printE (#VARNAME " step %d: wrote %d but read %d\n",STEP,VALUE,VAR);\
+ err = 104; \
+ /*goto endread;*/\
+ }
+
+#define CHECK_ARRAY(VARNAME,A,N,VALUE,STEP,i) \
+ for (i=0;i<N;i++) \
+ if (A[i] != VALUE) { \
+ printE (#VARNAME "[%d] step %d: wrote %d but read %d\n",i,STEP,VALUE,A[i]);\
+ err = 104; \
+ /*goto endread;*/\
+ break; \
+ }
+
+void reset_readvars()
+{
+ int n;
+
+ r0 = -1;
+ rt0 = -1;
+
+ n = ldim1;
+ memset (r1, -1, n*sizeof(int));
+ memset (rt1, -1, n*sizeof(int));
+
+}
+
+int read_file ()
+{
+ ADIOS_SELECTION *sel0,*sel1;
+ ADIOS_FILE * f;
+ ADIOS_VARINFO * vi;
+ int err=0,v,v0,i,n;
+ int iMacro; // loop variable in macros
+
+ uint64_t start[1] = {offs1};
+ uint64_t count[1] = {ldim1};
+ uint64_t ndim;
+
+ reset_readvars();
+
+ log ("Read and check data in %s\n", FILENAME);
+ f = adios_read_open_file (FILENAME, ADIOS_READ_METHOD_BP, comm);
+ if (f == NULL) {
+ printE ("Error at opening file: %s\n", adios_errmsg());
+ return 1;
+ }
+
+ sel0 = adios_selection_boundingbox (0, start, count);
+ sel1 = adios_selection_boundingbox (1, start, count);
+
+
+ log (" Check variable definitions... %s\n", FILENAME);
+
+ CHECK_VARINFO("once", 0, 1)
+ CHECK_VARINFO("onceperstep", 0, NSTEPS)
+ CHECK_VARINFO("scalar", 0, NSTEPS)
+ CHECK_VARINFO("a1", 1, NSTEPS)
+
+ log (" Check variable 'once'...\n");
+ v0 = VALUE0(0);
+ adios_schedule_read (f, sel0, "once", 0, 1, &r0);
+ adios_perform_reads (f, 1);
+ CHECK_SCALAR (once, r0, v0, i) // scalar is from writer rank 0, not this rank!
+
+ log (" Check variables 'onceperstep', 'scalar', 'a1', steps=%d...\n",NSTEPS);
+ for (i=0; i<NSTEPS; i++) {
+ v = VALUE(rank,i);
+ v0 = VALUE0(i);
+ log (" Step %d value %d\n", i, v);
+
+ adios_schedule_read (f, sel0, "onceperstep", i, 1, &r0);
+ adios_schedule_read (f, sel0, "scalar", i, 1, &rt0);
+ adios_schedule_read (f, sel1, "a1", i, 1, r1);
+ adios_perform_reads (f, 1);
+
+ CHECK_SCALAR (onceperstep, r0, v0, i) // scalar is from writer rank 0, not this rank!
+ CHECK_SCALAR (scalar, rt0, v0, i) // so value is v0 at step 'i', not v
+ CHECK_ARRAY (a1, r1, ldim1, v, i, iMacro)
+ }
+
+endread:
+
+ adios_selection_delete (sel0);
+ adios_selection_delete (sel1);
+
+ adios_read_close(f);
+ MPI_Barrier (comm);
+ return err;
+}
+
+
+
+
+
+int read_stream ()
+{
+ ADIOS_SELECTION *sel0,*sel1;
+ ADIOS_FILE * f;
+ ADIOS_VARINFO * vi;
+ int err=0,v,v0,i,n;
+ int iMacro; // loop variable in macros
+
+ uint64_t start[3] = {offs1};
+ uint64_t count[3] = {ldim1};
+ uint64_t ndim;
+
+ reset_readvars();
+
+ log ("Read as stream and check data in %s\n", FILENAME);
+ f = adios_read_open (FILENAME, ADIOS_READ_METHOD_BP, comm,
+ ADIOS_LOCKMODE_NONE, 0.0);
+ if (f == NULL) {
+ printE ("Error at opening file as stream: %s\n", adios_errmsg());
+ return 1;
+ }
+
+ sel0 = adios_selection_boundingbox (0, start, count);
+ sel1 = adios_selection_boundingbox (1, start, count);
+
+ n = 0;
+ while (n < NSTEPS && adios_errno != err_end_of_stream) {
+ log (" Step %d\n", n);
+
+ log (" Check variable definitions... %s\n", FILENAME);
+ if (n == 0) {
+ CHECK_VARINFO("once", 0, 1)
+ }
+ CHECK_VARINFO("onceperstep", 0, 1)
+ CHECK_VARINFO("scalar", 0, 1)
+ CHECK_VARINFO("a1", 1, 1)
+
+ v = VALUE(rank,n);
+ v0 = VALUE0(n);
+
+ if (n == 0) {
+ log (" Check variable 'once'...\n");
+ adios_schedule_read (f, sel0, "once", n, 1, &r0);
+ adios_perform_reads (f, 1);
+ CHECK_SCALAR (once, r0, v0, n) // scalar is from writer rank 0, not this rank!
+ }
+
+ log (" Check variables 'onceperstep', 'scalar', 'a1', Step %d value %d\n", n, v);
+
+ adios_schedule_read (f, sel0, "onceperstep", 0, 1, &r0);
+ adios_schedule_read (f, sel0, "scalar", 0, 1, &rt0);
+ adios_schedule_read (f, sel1, "a1", 0, 1, r1);
+ adios_perform_reads (f, 1);
+
+ CHECK_SCALAR (onceperstep, r0, v0, n) // scalar is from writer rank 0, not this rank!
+ CHECK_SCALAR (scalar, rt0, v0, n) // so value is v0 at 'n', not v
+ CHECK_ARRAY (a1, r1, ldim1, v, n, iMacro)
+
+ if (adios_advance_step (f, 0, 0.0) >= 0)
+ n = f->current_step;
+ else
+ n++; //just to end the loop
+ }
+
+endread:
+
+ adios_selection_delete (sel0);
+ adios_selection_delete (sel1);
+
+ adios_read_close(f);
+ MPI_Barrier (comm);
+ return err;
+}
diff --git a/tests/suite/programs/transforms_writeblock_read.c b/tests/suite/programs/transforms_writeblock_read.c
index 9e5d45d..9c785c5 100644
--- a/tests/suite/programs/transforms_writeblock_read.c
+++ b/tests/suite/programs/transforms_writeblock_read.c
@@ -39,7 +39,7 @@ static void test_file_mode_reads_on_var(ADIOS_FILE *fp, const char *bp_filename,
MPI_Assert(COMM, varinfo->blockinfo);
const enum ADIOS_DATATYPES datatype = varinfo->type;
- const int datatypesize = adios_get_type_size(datatype, NULL);
+ const int datatypesize = adios_type_size(datatype, NULL);
int timestep, timestep_blockidx, blockidx = 0;
for (timestep = 0; timestep < varinfo->nsteps; ++timestep) {
diff --git a/tests/suite/tests/05_global_array_time.sh b/tests/suite/tests/05_global_array_time.sh
index 5f1b585..cf894ce 100755
--- a/tests/suite/tests/05_global_array_time.sh
+++ b/tests/suite/tests/05_global_array_time.sh
@@ -24,6 +24,7 @@ cp $SRCDIR/programs/examples/global_array_time/global_array_time_read_as_file_C
cp $SRCDIR/programs/examples/global_array_time/global_array_time_read_as_stream_C .
cp $SRCDIR/programs/examples/global_array_time/global_array_time_C.xml .
cp $SRCDIR/programs/examples/global_array_time/global_array_time_aggr_C.xml .
+cp $SRCDIR/programs/examples/global_array_time/global_array_time_write_multifile_C .
# Insert transform=X if requested by user
add_transform_to_xmls
@@ -94,7 +95,7 @@ $TRUNKDIR/utils/bpls/bpls -la ../global_array_time_C.bp -D -d temperature -n 10
for BUFSIZE in 3000 300000 10000 1000 0 ; do
echo " Run time-aggregation with buffer size = $BUFSIZE"
- cat ../global_array_time_aggr_C.xml | sed -e "s/buffer-size=[0-9]*/buffer-size=$BUFSIZE/" > global_array_time_C.xml
+ cat ../global_array_time_aggr_C.xml | sed -e "s/buffer-size=\"[0-9]*\"/buffer-size=\"$BUFSIZE\"/" > global_array_time_C.xml
$MPIRUN $NP_MPIRUN $PROCS $EXEOPT ../global_array_time_write_C
EX=$?
if [ ! -f global_array_time_C.bp ]; then
@@ -129,6 +130,72 @@ done
popd >/dev/null
+##################################################################################
+# run the time-aggregation test where multiple output files are written over time
+# Check if we have the correct number of steps in each file
+
+echo "Run C global_array_time_write_C with time-aggregation turned on in subdir time_aggr_multifile/ with various buffer sizes:"
+mkdir -p time_aggr_multifile
+pushd time_aggr_multifile >/dev/null
+
+for BUFSIZE in 3000 300000 10000 1000 0 ; do
+
+ echo " Run multi-file time-aggregation with buffer size = $BUFSIZE"
+ cat ../global_array_time_aggr_C.xml | sed -e "s/buffer-size=\"[0-9]*\"/buffer-size=\"$BUFSIZE\"/" > global_array_time_aggr_C.xml
+ $MPIRUN $NP_MPIRUN $PROCS $EXEOPT ../global_array_time_write_multifile_C
+ EX=$?
+ if [ $EX != 0 ]; then
+ echo "ERROR: global_array_time_write_multifile_C failed. Exit code=$EX"
+ exit 1
+ fi
+
+ if [ ! -f global_array_time_C_1.bp ]; then
+ echo "ERROR: global_array_time_write_C failed. global_array_time_C_1.bp file is missing"
+ exit 1
+ fi
+ if [ ! -f global_array_time_C_2.bp ]; then
+ echo "ERROR: global_array_time_write_C failed. global_array_time_C_2.bp file is missing"
+ exit 1
+ fi
+ if [ ! -f global_array_time_C_3.bp ]; then
+ echo "ERROR: global_array_time_write_C failed. global_array_time_C_3.bp file is missing"
+ exit 1
+ fi
+
+ ADIR=bufsize_$BUFSIZE
+ mkdir $ADIR
+ mv global_array_time_aggr_C.xml $ADIR
+ mv global_array_time_C_*.bp $ADIR
+ pushd $ADIR >/dev/null
+
+ echo " Check output with bpls"
+ N1=`$TRUNKDIR/utils/bpls/bpls -l global_array_time_C_1.bp temperature | cut -d 'e' -f 5 | cut -d '*' -f 1`
+ N2=`$TRUNKDIR/utils/bpls/bpls -l global_array_time_C_2.bp temperature | cut -d 'e' -f 5 | cut -d '*' -f 1`
+ N3=`$TRUNKDIR/utils/bpls/bpls -l global_array_time_C_3.bp temperature | cut -d 'e' -f 5 | cut -d '*' -f 1`
+ echo $N1 > steps.txt
+ echo $N2 >> steps.txt
+ echo $N3 >> steps.txt
+
+ if [ "$N1" -ne "10" ]; then
+ echo "ERROR: Expected 10 steps in global_array_time_C_1.bp. Instead got $N1 steps."
+ exit 1
+ fi
+ if [ "$N2" -ne "10" ]; then
+ echo "ERROR: Expected 10 steps in global_array_time_C_2.bp. Instead got $N2 steps."
+ exit 1
+ fi
+ if [ "$N3" -ne "5" ]; then
+ echo "ERROR: Expected 5 steps in global_array_time_C_3.bp. Instead got $N3 steps."
+ exit 1
+ fi
+ popd >/dev/null
+
+done
+
+
+popd >/dev/null
+
+
###################################################
# run the Fortran tests too if available
diff --git a/tests/suite/tests/21_test_singlevalue.sh b/tests/suite/tests/21_test_singlevalue.sh
new file mode 100755
index 0000000..7faabe1
--- /dev/null
+++ b/tests/suite/tests/21_test_singlevalue.sh
@@ -0,0 +1,37 @@
+#!/bin/bash
+#
+# Test if adios can stream back a file where the first variable
+# is written only in the first step. This bug was fixed after 1.11.1
+# Uses ../programs/test_singlevalue
+#
+# Environment variables set by caller:
+# MPIRUN Run command
+# NP_MPIRUN Run commands option to set number of processes
+# MAXPROCS Max number of processes allowed
+# HAVE_FORTRAN yes or no
+# SRCDIR Test source dir (.. of this script)
+# TRUNKDIR ADIOS trunk dir
+
+PROCS=2
+
+if [ $MAXPROCS -lt $PROCS ]; then
+ echo "WARNING: Needs $PROCS processes at least"
+ exit 77 # not failure, just skip
+fi
+
+# copy codes and inputs to .
+cp $SRCDIR/programs/test_singlevalue .
+
+echo "Run test_singlevalue"
+$MPIRUN $NP_MPIRUN $PROCS $EXEOPT ./test_singlevalue
+EX=$?
+if [ ! -f test_singlevalue.bp ]; then
+ echo "ERROR: test_singlevalue failed at creating the BP file, test_singlevalue.bp. Exit code=$EX"
+ exit 1
+fi
+
+if [ $EX != 0 ]; then
+ echo "ERROR: test_singlevalue failed with exit code=$EX"
+ exit 1
+fi
+
diff --git a/tests/test_src/Makefile.am b/tests/test_src/Makefile.am
index 036f227..d2f75c3 100644
--- a/tests/test_src/Makefile.am
+++ b/tests/test_src/Makefile.am
@@ -12,7 +12,7 @@
test_C = hashtest copy_subvolume text_to_pairstruct test_strutil points_1DtoND trim_spaces
if BUILD_WRITE
- test_C += transforms_specparse group_free_test query_minmax read_points_2d array_attribute array_attribute
+ test_C += transforms_specparse group_free_test query_minmax read_points_2d read_points_3d array_attribute array_attribute
endif
if BUILD_FORTRAN
@@ -103,6 +103,12 @@ read_points_2d_LDFLAGS = $(AM_LDFLAGS) $(ADIOSLIB_SEQ_LDFLAGS) $(ADIOSLIB_EXTRA_
read_points_2d_CPPFLAGS = -I$(top_srcdir)/src $(ADIOSLIB_SEQ_CPPFLAGS) -I$(top_builddir)/src/public
read_points_2d.o: read_points_2d.c
+read_points_3d_SOURCES=read_points_3d.c
+read_points_3d_LDADD = $(top_builddir)/src/libadios_nompi.a $(ADIOSLIB_SEQ_LDADD)
+read_points_3d_LDFLAGS = $(AM_LDFLAGS) $(ADIOSLIB_SEQ_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
+read_points_3d_CPPFLAGS = -I$(top_srcdir)/src $(ADIOSLIB_SEQ_CPPFLAGS) -I$(top_builddir)/src/public
+read_points_3d.o: read_points_3d.c
+
array_attribute_SOURCES=array_attribute.c
array_attribute_LDADD = $(top_builddir)/src/libadios_nompi.a $(ADIOSLIB_SEQ_LDADD)
array_attribute_LDFLAGS = $(AM_LDFLAGS) $(ADIOSLIB_SEQ_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
diff --git a/tests/test_src/Makefile.in b/tests/test_src/Makefile.in
index e396bdb..c1419a5 100644
--- a/tests/test_src/Makefile.in
+++ b/tests/test_src/Makefile.in
@@ -88,7 +88,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
- at BUILD_WRITE_TRUE@am__append_1 = transforms_specparse group_free_test query_minmax read_points_2d array_attribute array_attribute
+ at BUILD_WRITE_TRUE@am__append_1 = transforms_specparse group_free_test query_minmax read_points_2d read_points_3d array_attribute array_attribute
check_PROGRAMS = $(am__EXEEXT_2) $(am__EXEEXT_3)
TESTS = $(am__EXEEXT_2) $(am__EXEEXT_3)
subdir = tests/test_src
@@ -114,7 +114,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -122,8 +122,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -141,6 +141,7 @@ CONFIG_CLEAN_VPATH_FILES =
@BUILD_WRITE_TRUE@ group_free_test$(EXEEXT) \
@BUILD_WRITE_TRUE@ query_minmax$(EXEEXT) \
@BUILD_WRITE_TRUE@ read_points_2d$(EXEEXT) \
+ at BUILD_WRITE_TRUE@ read_points_3d$(EXEEXT) \
@BUILD_WRITE_TRUE@ array_attribute$(EXEEXT) \
@BUILD_WRITE_TRUE@ array_attribute$(EXEEXT)
am__EXEEXT_2 = hashtest$(EXEEXT) copy_subvolume$(EXEEXT) \
@@ -207,6 +208,14 @@ read_points_2d_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \
$(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \
$(AM_CFLAGS) $(CFLAGS) $(read_points_2d_LDFLAGS) $(LDFLAGS) -o \
$@
+am_read_points_3d_OBJECTS = read_points_3d-read_points_3d.$(OBJEXT)
+read_points_3d_OBJECTS = $(am_read_points_3d_OBJECTS)
+read_points_3d_DEPENDENCIES = $(top_builddir)/src/libadios_nompi.a \
+ $(am__DEPENDENCIES_1)
+read_points_3d_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \
+ $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \
+ $(AM_CFLAGS) $(CFLAGS) $(read_points_3d_LDFLAGS) $(LDFLAGS) -o \
+ $@
am_selection_api_OBJECTS = selection_api.$(OBJEXT)
selection_api_OBJECTS = $(am_selection_api_OBJECTS)
selection_api_DEPENDENCIES = \
@@ -299,15 +308,17 @@ am__v_CCLD_1 =
SOURCES = $(array_attribute_SOURCES) $(copy_subvolume_SOURCES) \
$(group_free_test_SOURCES) $(hashtest_SOURCES) \
$(points_1DtoND_SOURCES) $(query_minmax_SOURCES) \
- $(read_points_2d_SOURCES) $(selection_api_SOURCES) \
- $(test_strutil_SOURCES) $(text_to_pairstruct_SOURCES) \
- $(transforms_specparse_SOURCES) $(trim_spaces_SOURCES)
+ $(read_points_2d_SOURCES) $(read_points_3d_SOURCES) \
+ $(selection_api_SOURCES) $(test_strutil_SOURCES) \
+ $(text_to_pairstruct_SOURCES) $(transforms_specparse_SOURCES) \
+ $(trim_spaces_SOURCES)
DIST_SOURCES = $(array_attribute_SOURCES) $(copy_subvolume_SOURCES) \
$(group_free_test_SOURCES) $(hashtest_SOURCES) \
$(points_1DtoND_SOURCES) $(query_minmax_SOURCES) \
- $(read_points_2d_SOURCES) $(selection_api_SOURCES) \
- $(test_strutil_SOURCES) $(text_to_pairstruct_SOURCES) \
- $(transforms_specparse_SOURCES) $(trim_spaces_SOURCES)
+ $(read_points_2d_SOURCES) $(read_points_3d_SOURCES) \
+ $(selection_api_SOURCES) $(test_strutil_SOURCES) \
+ $(text_to_pairstruct_SOURCES) $(transforms_specparse_SOURCES) \
+ $(trim_spaces_SOURCES)
am__can_run_installinfo = \
case $$AM_UPDATE_INFO_DIR in \
n|no|NO) false;; \
@@ -671,6 +682,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -747,6 +762,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
@@ -875,6 +893,10 @@ read_points_2d_SOURCES = read_points_2d.c
read_points_2d_LDADD = $(top_builddir)/src/libadios_nompi.a $(ADIOSLIB_SEQ_LDADD)
read_points_2d_LDFLAGS = $(AM_LDFLAGS) $(ADIOSLIB_SEQ_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
read_points_2d_CPPFLAGS = -I$(top_srcdir)/src $(ADIOSLIB_SEQ_CPPFLAGS) -I$(top_builddir)/src/public
+read_points_3d_SOURCES = read_points_3d.c
+read_points_3d_LDADD = $(top_builddir)/src/libadios_nompi.a $(ADIOSLIB_SEQ_LDADD)
+read_points_3d_LDFLAGS = $(AM_LDFLAGS) $(ADIOSLIB_SEQ_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
+read_points_3d_CPPFLAGS = -I$(top_srcdir)/src $(ADIOSLIB_SEQ_CPPFLAGS) -I$(top_builddir)/src/public
array_attribute_SOURCES = array_attribute.c
array_attribute_LDADD = $(top_builddir)/src/libadios_nompi.a $(ADIOSLIB_SEQ_LDADD)
array_attribute_LDFLAGS = $(AM_LDFLAGS) $(ADIOSLIB_SEQ_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
@@ -960,6 +982,10 @@ read_points_2d$(EXEEXT): $(read_points_2d_OBJECTS) $(read_points_2d_DEPENDENCIES
@rm -f read_points_2d$(EXEEXT)
$(AM_V_CCLD)$(read_points_2d_LINK) $(read_points_2d_OBJECTS) $(read_points_2d_LDADD) $(LIBS)
+read_points_3d$(EXEEXT): $(read_points_3d_OBJECTS) $(read_points_3d_DEPENDENCIES) $(EXTRA_read_points_3d_DEPENDENCIES)
+ @rm -f read_points_3d$(EXEEXT)
+ $(AM_V_CCLD)$(read_points_3d_LINK) $(read_points_3d_OBJECTS) $(read_points_3d_LDADD) $(LIBS)
+
selection_api$(EXEEXT): $(selection_api_OBJECTS) $(selection_api_DEPENDENCIES) $(EXTRA_selection_api_DEPENDENCIES)
@rm -f selection_api$(EXEEXT)
$(AM_V_FCLD)$(selection_api_LINK) $(selection_api_OBJECTS) $(selection_api_LDADD) $(LIBS)
@@ -993,6 +1019,7 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/points_1DtoND-points_1DtoND.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/query_minmax-query_minmax.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/read_points_2d-read_points_2d.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/read_points_3d-read_points_3d.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/test_strutil-test_strutil.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/text_to_pairstruct-text_to_pairstruct.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/transforms_specparse-transforms_specparse.Po at am__quote@
@@ -1126,6 +1153,20 @@ read_points_2d-read_points_2d.obj: read_points_2d.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(AM_V_CC at am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(read_points_2d_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) -c -o read_points_2d-read_points_2d.obj `if test -f 'read_points_2d.c'; then $(CYGPATH_W) 'read_points_2d.c'; else $(CYGPATH_W) '$(srcdir)/read_points_2d.c'; fi`
+read_points_3d-read_points_3d.o: read_points_3d.c
+ at am__fastdepCC_TRUE@ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(read_points_3d_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) -MT read_points_3d-read_points_3d.o -MD -MP -MF $(DEPDIR)/read_points_3d-read_points_3d.Tpo -c -o read_points_3d-read_points_3d.o `test -f 'read_points_3d.c' || echo '$(srcdir)/'`read_points_3d.c
+ at am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/read_points_3d-read_points_3d.Tpo $(DEPDIR)/read_points_3d-read_points_3d.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ $(AM_V_CC)source='read_points_3d.c' object='read_points_3d-read_points_3d.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(AM_V_CC at am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(read_points_3d_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) -c -o read_points_3d-read_points_3d.o `test -f 'read_points_3d.c' || echo '$(srcdir)/'`read_points_3d.c
+
+read_points_3d-read_points_3d.obj: read_points_3d.c
+ at am__fastdepCC_TRUE@ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(read_points_3d_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) -MT read_points_3d-read_points_3d.obj -MD -MP -MF $(DEPDIR)/read_points_3d-read_points_3d.Tpo -c -o read_points_3d-read_points_3d.obj `if test -f 'read_points_3d.c'; then $(CYGPATH_W) 'read_points_3d.c'; else $(CYGPATH_W) '$(srcdir)/read_points_3d.c'; fi`
+ at am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/read_points_3d-read_points_3d.Tpo $(DEPDIR)/read_points_3d-read_points_3d.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ $(AM_V_CC)source='read_points_3d.c' object='read_points_3d-read_points_3d.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(AM_V_CC at am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(read_points_3d_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) -c -o read_points_3d-read_points_3d.obj `if test -f 'read_points_3d.c'; then $(CYGPATH_W) 'read_points_3d.c'; else $(CYGPATH_W) '$(srcdir)/read_points_3d.c'; fi`
+
test_strutil-test_strutil.o: test_strutil.c
@am__fastdepCC_TRUE@ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(test_strutil_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) -MT test_strutil-test_strutil.o -MD -MP -MF $(DEPDIR)/test_strutil-test_strutil.Tpo -c -o test_strutil-test_strutil.o `test -f 'test_strutil.c' || echo '$(srcdir)/'`test_strutil.c
@am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/test_strutil-test_strutil.Tpo $(DEPDIR)/test_strutil-test_strutil.Po
@@ -1451,6 +1492,13 @@ read_points_2d.log: read_points_2d$(EXEEXT)
--log-file $$b.log --trs-file $$b.trs \
$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
"$$tst" $(AM_TESTS_FD_REDIRECT)
+read_points_3d.log: read_points_3d$(EXEEXT)
+ @p='read_points_3d$(EXEEXT)'; \
+ b='read_points_3d'; \
+ $(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
+ --log-file $$b.log --trs-file $$b.trs \
+ $(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
+ "$$tst" $(AM_TESTS_FD_REDIRECT)
array_attribute.log: array_attribute$(EXEEXT)
@p='array_attribute$(EXEEXT)'; \
b='array_attribute'; \
@@ -1647,6 +1695,7 @@ transforms_specparse.o: transforms_specparse.c
group_free_test.o: group_free_test.c
query_minmax.o: query_minmax.c
read_points_2d.o: read_points_2d.c
+read_points_3d.o: read_points_3d.c
array_attribute.o: array_attribute.c
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/tests/test_src/query_minmax.c b/tests/test_src/query_minmax.c
index 21ce790..1d34107 100644
--- a/tests/test_src/query_minmax.c
+++ b/tests/test_src/query_minmax.c
@@ -197,12 +197,12 @@ int write_file (int step)
adios_open (&fh, "query_minmax", FILENAME, (step ? "a" : "w"), comm);
groupsize = (4 + nblocks*2) * sizeof(int); // dimensions
- log (" groupsize calculated = %llu\n", groupsize);
+ log (" groupsize calculated = %" PRIu64 "\n", groupsize);
groupsize += nblocks * ldim1 * ldim2 * sizeof(float); // 2D blocks
- log (" groupsize calculated = %llu\n", groupsize);
+ log (" groupsize calculated = %" PRIu64 "\n", groupsize);
adios_group_size (fh, groupsize, &totalsize);
- log (" groupsize %llu, totalsize %llu\n", groupsize, totalsize);
+ log (" groupsize %" PRIu64 ", totalsize %" PRIu64 "\n", groupsize, totalsize);
tb = MPI_Wtime();
for (i=0; i<N; i++) {
@@ -296,7 +296,7 @@ int query_test (ADIOS_FILE *f, ADIOS_SELECTION *boxsel)
// retrieve the whole query result at once
int64_t batchSize = N*N;
- log (" set upper limit to total number of blocks in array = %lld\n", batchSize);
+ log (" set upper limit to total number of blocks in array = %" PRId64 "\n", batchSize);
teb = MPI_Wtime();
ADIOS_QUERY_RESULT *result = adios_query_evaluate(q, boxsel, step, batchSize);
diff --git a/tests/test_src/read_points_3d.c b/tests/test_src/read_points_3d.c
new file mode 100644
index 0000000..84ac6dc
--- /dev/null
+++ b/tests/test_src/read_points_3d.c
@@ -0,0 +1,774 @@
+/*
+ * ADIOS is freely available under the terms of the BSD license described
+ * in the COPYING file in the top level directory of this source distribution.
+ *
+ * Copyright (c) 2008 - 2009. UT-BATTELLE, LLC. All rights reserved.
+ */
+
+/* ADIOS C test:
+ * Write a 3D array of 8 3D blocks, multiple steps. Each block is a 5x5x5 array.
+ * The whole array is 10x10x10 and is patterned like this: 10*step+<blockid>.<row><col><z>
+ *
+ * Front 2D slice of the 3D array:
+ * $ bpls -l read_points_3d.bp -d data -n 10 -f "%6.3f" -s "0,0,0,0" -c "1,10,10,1"
+ real data 2*{10, 10, 10} = 0 / 17.444 / 8.722 / 5.50184
+ slice (0:0, 0:9, 0:9, 0:0)
+ (0,0,0,0) 0.000 0.010 0.020 0.030 0.040 1.000 1.010 1.020 1.030 1.040
+ (0,1,0,0) 0.100 0.110 0.120 0.130 0.140 1.100 1.110 1.120 1.130 1.140
+ (0,2,0,0) 0.200 0.210 0.220 0.230 0.240 1.200 1.210 1.220 1.230 1.240
+ (0,3,0,0) 0.300 0.310 0.320 0.330 0.340 1.300 1.310 1.320 1.330 1.340
+ (0,4,0,0) 0.400 0.410 0.420 0.430 0.440 1.400 1.410 1.420 1.430 1.440
+ (0,5,0,0) 2.000 2.010 2.020 2.030 2.040 3.000 3.010 3.020 3.030 3.040
+ (0,6,0,0) 2.100 2.110 2.120 2.130 2.140 3.100 3.110 3.120 3.130 3.140
+ (0,7,0,0) 2.200 2.210 2.220 2.230 2.240 3.200 3.210 3.220 3.230 3.240
+ (0,8,0,0) 2.300 2.310 2.320 2.330 2.340 3.300 3.310 3.320 3.330 3.340
+ (0,9,0,0) 2.400 2.410 2.420 2.430 2.440 3.400 3.410 3.420 3.430 3.440
+ *
+ * Back 2D slice of the 3D array
+ * $ bpls -l read_points_3d.bp -d data -n 10 -f "%6.3f" -s "0,0,0,-1" -c "1,10,10,1"
+ real data 2*{10, 10, 10} = 0 / 17.444 / 8.722 / 5.50184
+ slice (0:0, 0:9, 0:9, 9:9)
+ (0,0,0,9) 4.004 4.014 4.024 4.034 4.044 5.004 5.014 5.024 5.034 5.044
+ (0,1,0,9) 4.104 4.114 4.124 4.134 4.144 5.104 5.114 5.124 5.134 5.144
+ (0,2,0,9) 4.204 4.214 4.224 4.234 4.244 5.204 5.214 5.224 5.234 5.244
+ (0,3,0,9) 4.304 4.314 4.324 4.334 4.344 5.304 5.314 5.324 5.334 5.344
+ (0,4,0,9) 4.404 4.414 4.424 4.434 4.444 5.404 5.414 5.424 5.434 5.444
+ (0,5,0,9) 6.004 6.014 6.024 6.034 6.044 7.004 7.014 7.024 7.034 7.044
+ (0,6,0,9) 6.104 6.114 6.124 6.134 6.144 7.104 7.114 7.124 7.134 7.144
+ (0,7,0,9) 6.204 6.214 6.224 6.234 6.244 7.204 7.214 7.224 7.234 7.244
+ (0,8,0,9) 6.304 6.314 6.324 6.334 6.344 7.304 7.314 7.324 7.334 7.344
+ (0,9,0,9) 6.404 6.414 6.424 6.434 6.444 7.404 7.414 7.424 7.434 7.444
+
+ * Next slice in Z-coord is similar with all values +0.001
+ * Then test every possible reading of points
+ * with a bounding box container, and without
+ * with a writeblock container
+ * 1D and 3D points (local offset in contiguous space vs N-dim points)
+ * multiple timesteps
+ *
+ * How to run: ./read_points_3d
+ * It writes 5x5x5 3D blocks organized into a 10x10x10 3D array.
+ * Output: read_points.bp
+ *
+ */
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include <string.h>
+#include <errno.h>
+#include <math.h>
+#include <float.h>
+#include "public/adios.h"
+#include "public/adios_read.h"
+#include "public/adios_query.h"
+
+#ifdef DMALLOC
+#include "dmalloc.h"
+#endif
+
+#define log(...) fprintf (stderr, "[rank=%3.3d, line %d]: ", rank, __LINE__); fprintf (stderr, __VA_ARGS__); fflush(stderr);
+#define printE(...) fprintf (stderr, "[rank=%3.3d, line %d]: ERROR: ", rank, __LINE__); fprintf (stderr, __VA_ARGS__); fflush(stderr);
+
+/* user arguments */
+int N = 2; // organize blocks in NxNxN shape
+int NSTEPS = 2; // number of output steps
+
+static const char FILENAME[] = "read_points_3d.bp";
+#define VALUE(rank, step) (step * 1000 + rank + 1)
+
+#define LDIM1 5
+#define LDIM2 5
+#define LDIM3 5
+
+static const int ldim1 = LDIM1;
+static const int ldim2 = LDIM2;
+static const int ldim3 = LDIM3;
+
+int gdim1, gdim2, gdim3;
+int offs1, offs2, offs3;
+
+int64_t m_adios_group;
+
+/* Variables to write */
+float a3[LDIM1*LDIM2*LDIM3];
+
+/* Variables to read */
+float r3[LDIM1*LDIM2*LDIM3];
+
+MPI_Comm comm = MPI_COMM_SELF; // dummy comm for sequential code
+int rank;
+int size;
+
+
+void set_gdim()
+{
+ gdim1 = N*ldim1;
+ gdim2 = N*ldim2;
+ gdim3 = N*ldim3;
+}
+
+void set_offsets (int row, int col, int z)
+{
+ offs1 = row*ldim1;
+ offs2 = col*ldim2;
+ offs3 = z*ldim3;
+}
+
+void fill_block(int step, int row, int col, int z)
+{
+ int n;
+ float v_intpart = 10*step + row*N + col + z*N*N;
+ float v;
+ int i, j, k, idx;
+
+ n = ldim1 * ldim2 * ldim3;
+ //log (" Fill up array of %d elements starting from value %f...\n",n,v_start);
+ idx = 0;
+ for (i=0; i<ldim1; i++) {
+ //v = v_intpart + i*0.1;
+ //log (" row %d starts from value %f... (element %d)\n",i,v,k);
+ for (j=0; j<ldim2; j++) {
+ v = v_intpart + i*0.1 + j*0.01;
+ for (k=0; k<ldim3; k++) {
+ a3[idx] = v;
+ idx++;
+ v += 0.001;
+ }
+ }
+ }
+}
+
+
+void Usage()
+{
+ printf("Usage: read_points <N> <nsteps>\n"
+ " <N>: Number of blocks in each of X and Y direction\n"
+ " <nsteps>: Number of write cycles (to same file)\n");
+}
+
+void define_vars ();
+int write_file (int step);
+int read_points ();
+
+int main (int argc, char ** argv)
+{
+ int err,i ;
+
+ MPI_Init (&argc, &argv);
+ MPI_Comm_rank (comm, &rank);
+ MPI_Comm_size (comm, &size);
+
+ if (argc == 1)
+ {
+ // this case is for the test harness. otherwise this should be calling for Usage();
+ N = 2;
+ NSTEPS = 2;
+ printf("Running read_points <N=%d> <nsteps=%d>\n", N, NSTEPS);
+ }
+ else
+ {
+ if (argc < 3) { Usage(); return 1; }
+
+ errno = 0;
+ i = strtol (argv[1], NULL, 10);
+ if (errno || i < 1) { printf("Invalid 1st argument %s\n", argv[1]); Usage(); return 1;}
+ N = i;
+
+ errno = 0;
+ i = strtol (argv[2], NULL, 10);
+ if (errno || i < 1) { printf("Invalid 2nd argument %s\n", argv[2]); Usage(); return 1;}
+ NSTEPS = i;
+ }
+ adios_init_noxml (comm);
+ err = adios_read_init_method(ADIOS_READ_METHOD_BP, comm, "verbose=2");
+ if (err) {
+ printE ("%s\n", adios_errmsg());
+ }
+
+ adios_declare_group (&m_adios_group, "read_points", "", adios_stat_default);
+ adios_select_method (m_adios_group, "POSIX", "", "");
+
+
+ define_vars();
+ set_gdim();
+
+ for (i=0; i<NSTEPS; i++) {
+ if (!err) {
+ err = write_file (i);
+ }
+ }
+
+ if (!err)
+ err = read_points ();
+
+ adios_read_finalize_method (ADIOS_READ_METHOD_BP);
+ adios_finalize (rank);
+ MPI_Finalize ();
+ return err;
+}
+
+void define_vars ()
+{
+ int i;
+
+ adios_define_var (m_adios_group, "ldim1", "", adios_integer, 0, 0, 0);
+ adios_define_var (m_adios_group, "ldim2", "", adios_integer, 0, 0, 0);
+ adios_define_var (m_adios_group, "ldim3", "", adios_integer, 0, 0, 0);
+ adios_define_var (m_adios_group, "gdim1", "", adios_integer, 0, 0, 0);
+ adios_define_var (m_adios_group, "gdim2", "", adios_integer, 0, 0, 0);
+ adios_define_var (m_adios_group, "gdim3", "", adios_integer, 0, 0, 0);
+ adios_define_var (m_adios_group, "offs1", "", adios_integer, 0, 0, 0);
+ adios_define_var (m_adios_group, "offs2", "", adios_integer, 0, 0, 0);
+ adios_define_var (m_adios_group, "offs3", "", adios_integer, 0, 0, 0);
+
+ for (i=0; i<N*N*N; i++) {
+ adios_define_var (m_adios_group, "data", "", adios_real,
+ "ldim1,ldim2,ldim3",
+ "gdim1,gdim2,gdim3",
+ "offs1,offs2,offs3");
+ }
+}
+
+int write_file (int step)
+{
+ int64_t fh;
+ int i, j, k;
+ double tb, te;
+
+ log ("Write step %d to %s\n", step, FILENAME);
+ adios_open (&fh, "read_points", FILENAME, (step ? "a" : "w"), comm);
+
+ /*
+ groupsize = (4 + nblocks*2) * sizeof(int); // dimensions
+ log (" groupsize calculated = %llu\n", groupsize);
+ groupsize += nblocks * ldim1 * ldim2 * sizeof(float); // 2D blocks
+ log (" groupsize calculated = %llu\n", groupsize);
+
+ adios_group_size (fh, groupsize, &totalsize);
+ log (" groupsize %llu, totalsize %llu\n", groupsize, totalsize);
+ */
+
+ tb = MPI_Wtime();
+ for (i=0; i<N; i++) {
+ for (j=0; j<N; j++) {
+ for (k=0; k<N; k++) {
+ set_offsets (i, j, k);
+ fill_block (step, i, j, k);
+ adios_write (fh, "gdim1", &gdim1);
+ adios_write (fh, "gdim2", &gdim2);
+ adios_write (fh, "gdim3", &gdim3);
+ adios_write (fh, "ldim1", &ldim1);
+ adios_write (fh, "ldim2", &ldim2);
+ adios_write (fh, "ldim3", &ldim3);
+ adios_write (fh, "offs1", &offs1);
+ adios_write (fh, "offs2", &offs2);
+ adios_write (fh, "offs3", &offs3);
+ adios_write (fh, "data", a3);
+ }
+ }
+ }
+ adios_close (fh);
+ te = MPI_Wtime();
+
+ if (rank==0) {
+ log (" Write time for step %d was %6.3lf seconds\n", step, te-tb);
+ }
+ MPI_Barrier (comm);
+ return 0;
+}
+
+#define CHECK_VARINFO(VARNAME, NDIM, NSTEPS) \
+ vi = adios_inq_var (f, VARNAME); \
+ if (vi == NULL) { \
+ printE ("No such variable: %s\n", VARNAME); \
+ err = 101; \
+ goto endread; \
+ } \
+ if (vi->ndim != NDIM) { \
+ printE ("Variable %s has %d dimensions, but expected %d\n", VARNAME, vi->ndim, NDIM); \
+ err = 102; \
+ goto endread; \
+ } \
+ if (vi->nsteps != NSTEPS) { \
+ printE ("Variable %s has %d steps, but expected %d\n", VARNAME, vi->nsteps, NSTEPS); \
+ err = 103; \
+ /*goto endread; */\
+ } \
+ adios_free_varinfo (vi);
+
+
+void reset_readvars()
+{
+ size_t n;
+ n = (size_t)ldim1 * (size_t)ldim2;
+ memset (r3, 0, n*sizeof(float));
+}
+
+int nearlyEqual(float a, float b, float epsilon) {
+ float absA = fabsf(a);
+ float absB = fabsf(b);
+ float diff = fabsf(a - b);
+
+ if (a == b) { // shortcut, handles infinities
+ return 1;
+ } else if (a == 0 || b == 0 || diff < FLT_MIN) {
+ // a or b is zero or both are extremely close to it
+ // relative error is less meaningful here
+ return diff < (epsilon * FLT_MIN);
+ } else { // use relative error
+ return diff / fmin((absA + absB), FLT_MAX) < epsilon;
+ }
+}
+
+int test_read (ADIOS_FILE *f, ADIOS_SELECTION *pts, int from_steps, int nsteps,
+ float *expected)
+{
+ float *data = (float *) malloc (nsteps * pts->u.points.npoints * sizeof(float));
+ adios_schedule_read(f, pts, "data", from_steps, nsteps, data);
+ adios_perform_reads(f, 1);
+ int s, i, idx;
+
+ // print it out just for manual testing's sake
+ for (s = 0; s < nsteps; ++s) {
+ log (" Step %2d: ", s);
+ idx = s * pts->u.points.npoints;
+ for (i = 0; i < pts->u.points.npoints; ++i) {
+ if (nearlyEqual(data[idx], expected[idx], 0.000001)) {
+ printf (" %7.3f ", data[idx]);
+ } else {
+ printf ("**%6.3f* ", data[idx]);
+ }
+ idx++;
+ }
+ printf("\n");
+ }
+
+ for (s = 0; s < nsteps; ++s) {
+ idx = s * pts->u.points.npoints;
+ for (i = 0; i < pts->u.points.npoints; ++i) {
+ if (!nearlyEqual(data[idx], expected[idx], 0.000001))
+ {
+ printE ("Point %d in step %d value = %16.12f but was expected %16.12f\n",
+ i, s, data[idx], expected[idx]);
+ free (data);
+ return 110;
+ }
+ idx++;
+ }
+ }
+
+
+ free (data);
+ return 0;
+}
+
+int read_points ()
+{
+ ADIOS_FILE * f;
+ ADIOS_VARINFO * vi;
+ int err=0;
+
+ reset_readvars();
+
+ log ("Open %s for reading\n", FILENAME);
+ f = adios_read_open_file (FILENAME, ADIOS_READ_METHOD_BP, comm);
+ if (f == NULL) {
+ printE ("Error at opening file: %s\n", adios_errmsg());
+ return 1;
+ }
+
+ log (" Check variable definitions in %s\n", FILENAME);
+ CHECK_VARINFO("data", 3, NSTEPS)
+ MPI_Barrier (comm);
+
+ ADIOS_SELECTION *pts;
+ uint64_t start[100];
+ uint64_t count[100];
+ ADIOS_SELECTION *box;
+ uint64_t boxstart[3];
+ uint64_t boxcount[3];
+ ADIOS_SELECTION *wblock;
+ float expected[32]; // expected values of points
+
+ /*
+ * Points without containers based tests
+ */
+
+ // Test 1
+ // Read a single point with 3D coordinates in global space
+ // middle point of first 5x5x5 block, = 0.22
+ start[0] = 2; start[1] = 2; start[2] = 2;
+ pts = adios_selection_points(3, 1, start);
+ expected[0] = 0.222;
+ log (" Read single 3D global point at one step\n");
+ err = test_read (f, pts, 0, 1, expected);
+ adios_selection_delete(pts);
+ if (err)
+ goto endread;
+
+ /*
+ * Points in BOUNDINGBOX based tests
+ */
+ log (" --------------- Points in Boundinx Boxes ----------------------- \n");
+ // Test 2
+ // Read a single point with 3D coordinates in an 5x5x5 bounding box
+ // middle point of the 5x5x5 block, = 7.00
+ // Limit the query to the bounding box
+ boxstart[0] = 3; boxstart[1] = 3; boxstart[2] = 3;
+ boxcount[0] = 5; boxcount[1] = 5; boxcount[2] = 5;
+ box = adios_selection_boundingbox (3, boxstart, boxcount);
+
+ start[0] = 2; start[1] = 2; start[2] = 2; // 3D point of middle of a 5x5x5 array
+ pts = adios_selection_points(3, 1, start);
+ pts->u.points.container_selection = box;
+ expected[0] = 7.000;
+ log (" Read single 3D point in a 3D bounding box at one step\n");
+ err = test_read (f, pts, 0, 1, expected);
+ adios_selection_delete(pts);
+ //adios_selection_delete (box); // deleted when pts is deleted
+ if (err)
+ goto endread;
+
+
+ // Test 3
+ // Read a single point with 1D offset in an 5x5x5 bounding box
+ // middle point of that 5x5x5 block, = 7.00
+ // Limit the query to the bounding box of the middle of the global array
+ // This is the same actual point as in Test 2
+ boxstart[0] = 3; boxstart[1] = 3; boxstart[2] = 3;
+ boxcount[0] = 5; boxcount[1] = 5; boxcount[2] = 5;
+ box = adios_selection_boundingbox (3, boxstart, boxcount);
+
+ start[0] = 62; // offset of middle of a 5x5x5 array: 2*25 + 2*5 + 2
+ pts = adios_selection_points(1, 1, start);
+ pts->u.points.container_selection = box;
+ expected[0] = 7.000;
+ log (" Read single 1D point in a 3D bounding box at one step\n");
+ err = test_read (f, pts, 0, 1, expected);
+ adios_selection_delete(pts);
+ if (err)
+ goto endread;
+
+
+ // Test 4-5
+ // Read several single points with 3D coordinates in an 5x5x5 bounding box
+ // back diagonal of that 5x5x5 block, = 5.332 5.411 7.000 2.144 2.233
+ // Limit the query to the bounding box of the middle of the global array
+ /* See: $ bpls -l read_points_3d.bp -d data -n 5 -s "0,3,3,3" -c "1,5,5,5" -f "%6.3f "
+ real data 2*{10, 10, 10} = 0 / 17.444 / 8.722 / 5.50184
+ slice (0:0, 3:7, 3:7, 3:7)
+ (0,3,3,3) 0.333 0.334 4.330 4.331 4.332
+ (0,3,4,3) 0.343 0.344 4.340 4.341 4.342
+ (0,3,5,3) 1.303 1.304 5.300 5.301 5.302
+ (0,3,6,3) 1.313 1.314 5.310 5.311 5.312
+ (0,3,7,3) 1.323 1.324 5.320 5.321 [5.322] <-- first point, bottom corner of first 2d slice
+ (0,4,3,3) ...
+ ... v--------------------------------------- last point, top corner
+ (0,7,3,3) [2.233] 2.234 6.230 6.231 6.232
+ (0,7,4,3) 2.243 2.244 6.240 6.241 6.242
+ (0,7,5,3) 3.203 3.204 7.200 7.201 7.202
+ (0,7,6,3) 3.213 3.214 7.210 7.211 7.212
+ (0,7,7,3) 3.223 3.224 7.220 7.221 7.222
+ */
+ boxstart[0] = 3; boxstart[1] = 3; boxstart[2] = 3;
+ boxcount[0] = 5; boxcount[1] = 5; boxcount[2] = 5;
+ box = adios_selection_boundingbox (3, boxstart, boxcount);
+
+ // back diagonal of the 5x5x5 array
+ start[0] = 0; start[1] = 4; start[2] = 4;
+ start[3] = 1; start[4] = 3; start[5] = 3;
+ start[6] = 2; start[7] = 2; start[8] = 2;
+ start[9] = 3; start[10] = 1; start[11] = 1;
+ start[12] = 4; start[13] = 0; start[14] = 0;
+
+ pts = adios_selection_points(3, 5, start);
+ pts->u.points.container_selection = box;
+ expected[0] = 5.322;
+ expected[1] = 5.411;
+ expected[2] = 7.000;
+ expected[3] = 2.144;
+ expected[4] = 2.233;
+ log (" Read back diagonal of box with five 3D points in a 3D bounding box at one step\n");
+ err = test_read (f, pts, 0, 1, expected);
+ if (err) {
+ adios_selection_delete(pts);
+ goto endread;
+ }
+ expected[5] = 15.322;
+ expected[6] = 15.411;
+ expected[7] = 17.000;
+ expected[8] = 12.144;
+ expected[9] = 12.233;
+ log (" Read back diagonal of box with five 3D points in a 3D bounding box at two steps\n");
+ err = test_read (f, pts, 0, 2, expected);
+ adios_selection_delete(pts);
+ if (err)
+ goto endread;
+
+
+ // Test 6-7
+ // Read several single points with 1D offset in an 5x5x5 bounding box
+ // back diagonal of that 5x5x5 block, = 5.332 5.411 7.000 2.144 2.233
+ // Limit the query to the bounding box of the middle of the global array
+ boxstart[0] = 3; boxstart[1] = 3; boxstart[2] = 3;
+ boxcount[0] = 5; boxcount[1] = 5; boxcount[2] = 5;
+ box = adios_selection_boundingbox (3, boxstart, boxcount);
+
+ // back diagonal of the 5x5x5 array
+ start[0] = 4*ldim2 + 4;
+ start[1] = 1*ldim2*ldim3 + 3*ldim2 + 3;
+ start[2] = 2*ldim2*ldim3 + 2*ldim2 + 2;
+ start[3] = 3*ldim2*ldim3 + 1*ldim2 + 1;
+ start[4] = 4*ldim2*ldim3;
+ pts = adios_selection_points(1, 5, start);
+ pts->u.points.container_selection = box;
+ expected[0] = 5.322;
+ expected[1] = 5.411;
+ expected[2] = 7.000;
+ expected[3] = 2.144;
+ expected[4] = 2.233;
+ log (" Read back diagonal of box with five 1D offsets in a 2D bounding box at one step\n");
+ err = test_read (f, pts, 0, 1, expected);
+ if (err) {
+ adios_selection_delete(pts);
+ goto endread;
+ }
+ expected[5] = 15.322;
+ expected[6] = 15.411;
+ expected[7] = 17.000;
+ expected[8] = 12.144;
+ expected[9] = 12.233;
+ log (" Read back diagonal of box with five 1D points in a 2D bounding box at two steps\n");
+ err = test_read (f, pts, 0, 2, expected);
+ adios_selection_delete(pts);
+ if (err)
+ goto endread;
+
+
+ // Test 8
+ // Read "center cross" with 3D offset in an 5x5x5 bounding box
+ // points concentrated in 3x1x3 2D X-Z center plane to test the reduction of reading box size
+ // 5-point center of that 3x1x3 block, = 5.400
+ // 3.004 7.000 7.001
+ // 7.100
+ // The box-reduction should read a 3x3=9 element box instead of
+ // the full 5x5x5=125 elements
+ // (actually read_var_bb then will read more than this because it reads contiguous arrays)
+ // Limit the query to the bounding box of the middle of the global array
+ /*
+ * See the cross in file:
+ $ bpls -l read_points_3d.bp -d data -n 5 -s "0,4,5,5" -c "1,1,1,1" -f "%6.3f " -n 1
+ real data 2*{10, 10, 10} = 0 / 17.444 / 8.722 / 5.50184
+ slice (0:0, 4:4, 5:5, 5:5)
+ (0,4,5,5) 5.400
+
+ $ bpls -l read_points_3d.bp -d data -n 5 -s "0,5,5,4" -c "1,1,1,3" -f "%6.3f " -n 1
+ real data 2*{10, 10, 10} = 0 / 17.444 / 8.722 / 5.50184
+ slice (0:0, 5:5, 5:5, 4:6)
+ (0,5,5,4) 3.004
+ (0,5,5,5) 7.000
+ (0,5,5,6) 7.001
+
+ $ bpls -l read_points_3d.bp -d data -n 5 -s "0,6,5,5" -c "1,1,1,1" -f "%6.3f " -n 1
+ real data 2*{10, 10, 10} = 0 / 17.444 / 8.722 / 5.50184
+ slice (0:0, 6:6, 5:5, 5:5)
+ (0,6,5,5) 7.100
+ */
+ boxstart[0] = 3; boxstart[1] = 3; boxstart[2] = 3;
+ boxcount[0] = 5; boxcount[1] = 5; boxcount[2] = 5;
+ box = adios_selection_boundingbox (3, boxstart, boxcount);
+
+ // 5-point center cross in X-Z plane of the 5x5x5 array
+ start[0] = 1; start[1] = 2; start[2] = 2;
+ start[3] = 2; start[4] = 2; start[5] = 1;
+ start[6] = 2; start[7] = 2; start[8] = 2;
+ start[9] = 2; start[10] = 2; start[11] = 3;
+ start[12] = 3; start[13] = 2; start[14] = 2;
+ pts = adios_selection_points(3, 5, start);
+ pts->u.points.container_selection = box;
+ expected[0] = 5.400;
+ expected[1] = 3.004;
+ expected[2] = 7.000;
+ expected[3] = 7.001;
+ expected[4] = 7.100;
+ log (" Read back center cross in X-Z plane with five 3D points in a 3D bounding box at one step\n");
+ err = test_read (f, pts, 0, 1, expected);
+ adios_selection_delete(pts);
+ if (err)
+ goto endread;
+
+
+ // Test 9
+ // Read "center cross" with 1D offset in an 5x5x5 bounding box
+ // points concentrated in 3x1x3 2D X-Z center plane to test the reduction of reading box size
+ // 5-point center of that 3x1x3 block, = 5.400 3.004 7.000 7.001 7.100
+ // The box-reduction should read a 3x5x5=75 element box instead of
+ // the full 5x5x5=125 elements
+ // Limit the query to the bounding box of the middle of the global array
+ // Same test as Test 8 but with 1D points
+
+ boxstart[0] = 3; boxstart[1] = 3; boxstart[2] = 3;
+ boxcount[0] = 5; boxcount[1] = 5; boxcount[2] = 5;
+ box = adios_selection_boundingbox (3, boxstart, boxcount);
+
+ // 5-point center cross in X-Z plane of the 5x5x5 array
+ start[0] = 1*ldim2*ldim3 + 2*ldim2 + 2;
+ start[1] = 2*ldim2*ldim3 + 2*ldim2 + 1;
+ start[2] = 2*ldim2*ldim3 + 2*ldim2 + 2;
+ start[3] = 2*ldim2*ldim3 + 2*ldim2 + 3;
+ start[4] = 3*ldim2*ldim3 + 2*ldim2 + 2;
+
+ pts = adios_selection_points(1, 5, start);
+ pts->u.points.container_selection = box;
+ expected[0] = 5.400;
+ expected[1] = 3.004;
+ expected[2] = 7.000;
+ expected[3] = 7.001;
+ expected[4] = 7.100;
+ log (" Read back center cross in X-Z plane with five 1D points in a 3D bounding box at one step\n");
+ err = test_read (f, pts, 0, 1, expected);
+ adios_selection_delete(pts);
+ if (err)
+ goto endread;
+
+
+ /*
+ * Points in WRITEBLOCK based tests
+ */
+ log (" --------------- Points in WriteBlocks ----------------------- \n");
+
+ // Test 8
+ // Read a single point with 3D coordinates in writeblock 2 (third block)
+ // block 2: [0:4, 5:9, 0:4] = 1 / 1.444/ 1.222/ 0.142134
+ // middle point of that 5x5x5 block, = 1.222
+ wblock = adios_selection_writeblock(2);
+
+ start[0] = 2; start[1] = 2; start[2] = 2; // 3D point of middle of a 5x5x5 writeblock
+ pts = adios_selection_points(3, 1, start);
+ pts->u.points.container_selection = wblock;
+ expected[0] = 1.222;
+ log (" Read single 3D point in a 3D writeblock at one step\n");
+ err = test_read (f, pts, 0, 1, expected);
+ adios_selection_delete(pts);
+ //adios_selection_delete (wblock); // deleted when pts is deleted
+ if (err)
+ goto endread;
+
+
+ // Test 9
+ // Read a single point with 1D offset in an writeblock 2
+ // middle point of that 5x5x5 block, = 1.222
+ // This is the same actual point as in Test 8
+ wblock = adios_selection_writeblock(2);
+
+ start[0] = 62; // offset of middle of a 5x5x5 array
+ pts = adios_selection_points(1, 1, start);
+ pts->u.points.container_selection = wblock;
+ expected[0] = 1.222;
+ log (" Read single 1D point in a 3D writeblock at one step\n");
+ err = test_read (f, pts, 0, 1, expected);
+ adios_selection_delete(pts);
+ if (err)
+ goto endread;
+
+
+ // Test 10-11
+ // Read several single points with 3D coordinates in writeblock 2
+ // back diagonal of that 5x5x5 block, = 1.044 1.133 1.222 1.311 1.400
+ /* See
+ * $ bpls -l read_points_3d.bp -d data -n 5 -s "0,0,5,0" -c "1,5,5,5" -f "%6.3f "
+ real data 2*{10, 10, 10} = 0 / 17.444 / 8.722 / 5.50184
+ slice (0:0, 0:4, 5:9, 0:4)
+ (0,0,5,0) 1.000 1.001 1.002 1.003 1.004
+ (0,0,6,0) 1.010 1.011 1.012 1.013 1.014
+ (0,0,7,0) 1.020 1.021 1.022 1.023 1.024
+ (0,0,8,0) 1.030 1.031 1.032 1.033 1.034
+ (0,0,9,0) 1.040 1.041 1.042 1.043 [1.044] <-- first point
+ ...
+ v--------------------------------------- last point
+ (0,4,5,0) [1.400] 1.401 1.402 1.403 1.404
+ (0,4,6,0) 1.410 1.411 1.412 1.413 1.414
+ (0,4,7,0) 1.420 1.421 1.422 1.423 1.424
+ (0,4,8,0) 1.430 1.431 1.432 1.433 1.434
+ (0,4,9,0) 1.440 1.441 1.442 1.443 1.444
+ *
+ *
+ */
+
+ wblock = adios_selection_writeblock(2);
+
+ // back diagonal of the 5x5x5 array
+ start[0] = 0; start[1] = 4; start[2] = 4;
+ start[3] = 1; start[4] = 3; start[5] = 3;
+ start[6] = 2; start[7] = 2; start[8] = 2;
+ start[9] = 3; start[10] = 1; start[11] = 1;
+ start[12] = 4; start[13] = 0; start[14] = 0;
+ pts = adios_selection_points(3, 5, start);
+ pts->u.points.container_selection = wblock;
+ expected[0] = 1.044;
+ expected[1] = 1.133;
+ expected[2] = 1.222;
+ expected[3] = 1.311;
+ expected[4] = 1.400;
+ log (" Read back diagonal of box with five 3D points in a 3D writeblock at one step\n");
+ err = test_read (f, pts, 0, 1, expected);
+ if (err) {
+ adios_selection_delete(pts);
+ goto endread;
+ }
+
+ expected[5] = 11.044;
+ expected[6] = 11.133;
+ expected[7] = 11.222;
+ expected[8] = 11.311;
+ expected[9] = 11.400;
+ log (" Read back diagonal of box with five 3D points in a 3D writeblock at two steps\n");
+ err = test_read (f, pts, 0, 2, expected);
+ adios_selection_delete(pts);
+ if (err)
+ goto endread;
+
+
+ // Test 12-13
+ // Read several single points with 1D offset in writeblock 2
+ // back diagonal of that 5x5x5 block, = 1.044 1.133 1.222 1.311 1.400
+ // This is the same actual point as in Test 10-11
+ wblock = adios_selection_writeblock(2);
+
+ // back diagonal of the 5x5x5 array as 1D offsets
+ start[0] = 4*ldim2 + 4;
+ start[1] = 1*ldim2*ldim3 + 3*ldim2 + 3;
+ start[2] = 2*ldim2*ldim3 + 2*ldim2 + 2;
+ start[3] = 3*ldim2*ldim3 + 1*ldim2 + 1;
+ start[4] = 4*ldim2*ldim3;
+ pts = adios_selection_points(1, 5, start);
+ pts->u.points.container_selection = wblock;
+ expected[0] = 1.044;
+ expected[1] = 1.133;
+ expected[2] = 1.222;
+ expected[3] = 1.311;
+ expected[4] = 1.400;
+ log (" Read back diagonal of box with five 1D offsets in a 3D writeblock at one step\n");
+ err = test_read (f, pts, 0, 1, expected);
+ if (err) {
+ adios_selection_delete(pts);
+ goto endread;
+ }
+ expected[5] = 11.044;
+ expected[6] = 11.133;
+ expected[7] = 11.222;
+ expected[8] = 11.311;
+ expected[9] = 11.400;
+ log (" Read back diagonal of box with five 1D points in a 3D writeblock at two steps\n");
+ err = test_read (f, pts, 0, 2, expected);
+ adios_selection_delete(pts);
+ if (err)
+ goto endread;
+
+endread:
+
+ adios_read_close(f);
+ MPI_Barrier (comm);
+ return err;
+}
+
diff --git a/utils/Makefile.in b/utils/Makefile.in
index 7a90f7b..555c747 100644
--- a/utils/Makefile.in
+++ b/utils/Makefile.in
@@ -104,7 +104,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -112,8 +112,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -340,6 +340,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -416,6 +420,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/utils/adios_lint/Makefile.in b/utils/adios_lint/Makefile.in
index d920b0f..2f32432 100644
--- a/utils/adios_lint/Makefile.in
+++ b/utils/adios_lint/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -329,6 +329,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -405,6 +409,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/utils/adios_list_methods/Makefile.in b/utils/adios_list_methods/Makefile.in
index 72ce646..7aa81e2 100644
--- a/utils/adios_list_methods/Makefile.in
+++ b/utils/adios_list_methods/Makefile.in
@@ -109,7 +109,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -117,8 +117,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -380,6 +380,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -456,6 +460,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/utils/bp2ascii/Makefile.in b/utils/bp2ascii/Makefile.in
index 1e1b32a..b430cb5 100644
--- a/utils/bp2ascii/Makefile.in
+++ b/utils/bp2ascii/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -327,6 +327,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -403,6 +407,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/utils/bp2bp/Makefile.in b/utils/bp2bp/Makefile.in
index 7fb309e..4a7e40a 100644
--- a/utils/bp2bp/Makefile.in
+++ b/utils/bp2bp/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -330,6 +330,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -406,6 +410,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/utils/bp2bp/bp2bp.c b/utils/bp2bp/bp2bp.c
index 4060fdf..0848d4b 100644
--- a/utils/bp2bp/bp2bp.c
+++ b/utils/bp2bp/bp2bp.c
@@ -162,7 +162,7 @@ int main (int argc, char ** argv) {
/* First create all of the groups */
// now I need to create this group in the file that will be written
- adios_declare_group(&new_adios_group,f->group_namelist[gidx],"",adios_flag_yes);
+ adios_declare_group(&new_adios_group,f->group_namelist[gidx],"",adios_stat_default);
if(strcmp(argv[5],"MPI_LUSTRE")!=0) //see whether or not the user uses MPI_LUSTRE method
diff --git a/utils/bp2h5/Makefile.in b/utils/bp2h5/Makefile.in
index 5a44569..6ce94d4 100644
--- a/utils/bp2h5/Makefile.in
+++ b/utils/bp2h5/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -332,6 +332,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -408,6 +412,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/utils/bp2h5/bp2h5.c b/utils/bp2h5/bp2h5.c
index fa746bd..c73de90 100644
--- a/utils/bp2h5/bp2h5.c
+++ b/utils/bp2h5/bp2h5.c
@@ -37,7 +37,7 @@
#include "adios_types.h"
#include "hdf5.h"
-//#include "hdf5_hl.h"
+#include "H5LTpublic.h"
#ifdef DMALLOC
#include "dmalloc.h"
@@ -94,7 +94,7 @@ int main (int argc, char ** argv)
{
int gidx, i, j;
MPI_Comm comm_dummy = MPI_COMM_WORLD; /* MPI_Comm is defined through adios_read.h */
- uint64_t count[MAX_DIMS];
+ hsize_t count[MAX_DIMS];
herr_t h5_err;
char h5name[256],aname[256],fname[256];
int h5i, level;
diff --git a/utils/bp2ncd/Makefile.in b/utils/bp2ncd/Makefile.in
index 809e5fb..1c39b01 100644
--- a/utils/bp2ncd/Makefile.in
+++ b/utils/bp2ncd/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -330,6 +330,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -406,6 +410,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/utils/bpdiff/Makefile.in b/utils/bpdiff/Makefile.in
index 4669821..fdc6ff9 100644
--- a/utils/bpdiff/Makefile.in
+++ b/utils/bpdiff/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -329,6 +329,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -405,6 +409,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/utils/bpdump/Makefile.in b/utils/bpdump/Makefile.in
index 06e83ff..63509ee 100644
--- a/utils/bpdump/Makefile.in
+++ b/utils/bpdump/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -328,6 +328,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -404,6 +408,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/utils/bpls/Makefile.in b/utils/bpls/Makefile.in
index 161fa49..66dc32d 100644
--- a/utils/bpls/Makefile.in
+++ b/utils/bpls/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -328,6 +328,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -404,6 +408,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/utils/bpls/bpls.c b/utils/bpls/bpls.c
index 4d22be1..a7748f2 100644
--- a/utils/bpls/bpls.c
+++ b/utils/bpls/bpls.c
@@ -453,7 +453,7 @@ void print_file_size(uint64_t size)
}
if (r > 511)
s++;
- printf (" file size: %" PRId64 " %s\n", s, sm[idx]);
+ printf (" file size: %" PRIu64 " %s\n", s, sm[idx]);
}
@@ -588,9 +588,9 @@ int doList_group (ADIOS_FILE *fp)
if (timed)
fprintf(outf, "%d*", vi->nsteps);
if (vi->ndim > 0) {
- fprintf(outf,"{%" PRId64, vi->dims[0]);
+ fprintf(outf,"{%" PRIu64, vi->dims[0]);
for (j=1; j < vi->ndim; j++) {
- fprintf(outf,", %" PRId64, vi->dims[j]);
+ fprintf(outf,", %" PRIu64, vi->dims[j]);
}
fprintf(outf,"}");
} else {
@@ -763,9 +763,9 @@ int doList_group (ADIOS_FILE *fp)
#define PRINT_ARRAY64(str, ndim, dims, loopvar) \
fprintf(outf,"%s",str); \
if (ndim > 0) { \
- fprintf(outf,"{%" PRId64, dims[0]); \
+ fprintf(outf,"{%" PRIu64, dims[0]); \
for (loopvar=1; loopvar < ndim; loopvar++) { \
- fprintf(outf,", %" PRId64, dims[loopvar]); \
+ fprintf(outf,", %" PRIu64, dims[loopvar]); \
} \
fprintf(outf,"}\n"); \
} else { \
@@ -868,7 +868,7 @@ void printMeshes (ADIOS_FILE *fp)
case ADIOS_MESH_UNSTRUCTURED:
fprintf(outf, "unstructured\n");
if (mi->unstructured->nvar_points <= 1) {
- fprintf(outf, " npoints: %" PRId64 "\n", mi->unstructured->npoints);
+ fprintf(outf, " npoints: %" PRIu64 "\n", mi->unstructured->npoints);
fprintf(outf, " points: single-var: \"%s\"\n",
mi->unstructured->points[0]);
} else {
@@ -1163,7 +1163,7 @@ int getTypeInfo( enum ADIOS_DATATYPES adiosvartype, int* elemsize)
}
#define PRINT_DIMS64(str, v, n, loopvar) printf("%s = { ", str); \
- for (loopvar=0; loopvar<n;loopvar++) printf("%" PRId64 " ", v[loopvar]); \
+ for (loopvar=0; loopvar<n;loopvar++) printf("%" PRIu64 " ", v[loopvar]); \
printf("}")
/** Read data of a variable and print
* Return: 0: ok, != 0 on error
@@ -1285,7 +1285,7 @@ int readVar(ADIOS_FILE *fp, ADIOS_VARINFO *vi, const char * name, bool timed)
sum = sum * (uint64_t) count_t[i];
actualreadn = actualreadn * readn[i];
}
- if (verbose>1) printf(" read %d elements at once, %" PRId64 " in total (nelems=%" PRId64 ")\n", actualreadn, sum, nelems);
+ if (verbose>1) printf(" read %d elements at once, %" PRIu64 " in total (nelems=%" PRIu64 ")\n", actualreadn, sum, nelems);
// init s and c
@@ -1335,8 +1335,6 @@ int readVar(ADIOS_FILE *fp, ADIOS_VARINFO *vi, const char * name, bool timed)
return 11;
}
- //if (verbose>2) printf(" read %" PRId64 " bytes\n", bytes_read);
-
// print slice
print_dataset(data, vi->type, s, c, tdims, ndigits_dims);
@@ -1479,9 +1477,9 @@ void print_slice_info(int ndim, uint64_t *dims, int timed, int nsteps, uint64_t
isaslice = true;
}
if (isaslice) {
- fprintf(outf,"%c slice (%" PRId64 ":%" PRId64, commentchar, s[0], s[0]+c[0]-1);
+ fprintf(outf,"%c slice (%" PRIu64 ":%" PRIu64, commentchar, s[0], s[0]+c[0]-1);
for (i=1; i<tdim; i++) {
- fprintf(outf,", %" PRId64 ":%" PRId64, s[i], s[i]+c[i]-1);
+ fprintf(outf,", %" PRIu64 ":%" PRIu64, s[i], s[i]+c[i]-1);
}
fprintf(outf,")\n");
}
@@ -1746,9 +1744,9 @@ int print_dataset(void *data, enum ADIOS_DATATYPES adiosvartype,
idxstr[0] = '\0'; // empty idx string
if (nextcol == 0) {
if (!noindex && tdims > 0) {
- sprintf(idxstr," (%*" PRId64,ndigits[0], ids[0]);
+ sprintf(idxstr," (%*" PRIu64,ndigits[0], ids[0]);
for (i=1; i<tdims; i++) {
- sprintf(buf,",%*" PRId64,ndigits[i],ids[i]);
+ sprintf(buf,",%*" PRIu64,ndigits[i],ids[i]);
strcat(idxstr, buf);
}
strcat(idxstr,") ");
@@ -1850,7 +1848,7 @@ void print_decomp(ADIOS_VARINFO *vi)
}
for (k=0; k < vi->ndim; k++) {
if (vi->blockinfo[blockid].count[k]) {
- fprintf(outf, "%*" PRId64 ":%*" PRId64,
+ fprintf(outf, "%*" PRIu64 ":%*" PRIu64,
ndigits_dims[k],
vi->blockinfo[blockid].start[k],
ndigits_dims[k],
diff --git a/utils/bpmeta/Makefile.in b/utils/bpmeta/Makefile.in
index 5736f44..ce6cedb 100644
--- a/utils/bpmeta/Makefile.in
+++ b/utils/bpmeta/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -328,6 +328,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -404,6 +408,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/utils/bpmeta/bpmeta.c b/utils/bpmeta/bpmeta.c
index 6656b7b..0fead88 100644
--- a/utils/bpmeta/bpmeta.c
+++ b/utils/bpmeta/bpmeta.c
@@ -283,11 +283,10 @@ int write_index (struct adios_index_struct_v1 * index, char * fname)
uint64_t index_start = 0;
int f;
uint16_t flag = 0;
- ssize_t bytes_written = 0;
+
flag |= ADIOS_VERSION_HAVE_SUBFILE;
- adios_write_index_v1 (&buffer, &buffer_size, &buffer_offset
- ,index_start, index);
+ adios_write_index_v1 (&buffer, &buffer_size, &buffer_offset, index_start, index);
if (verbose>2) {
printf ("buffer=%p size=%" PRId64 " offset=%" PRId64 "\n", buffer, buffer_size, buffer_offset);
}
@@ -297,7 +296,7 @@ int write_index (struct adios_index_struct_v1 * index, char * fname)
printf ("buffer=%p size=%" PRId64 " offset=%" PRId64 "\n", buffer, buffer_size, buffer_offset);
}
- f = open (fname, O_CREAT | O_RDWR, 0644);
+ f = open (fname, O_CREAT | O_WRONLY | O_TRUNC, 0644);
if (f == -1)
{
fprintf (stderr, "Failed to create metadata file %s: %s\n",
@@ -305,17 +304,56 @@ int write_index (struct adios_index_struct_v1 * index, char * fname)
return -1;
}
- bytes_written = write (f, buffer, (size_t)buffer_offset);
- if (bytes_written == -1)
+ uint64_t bytes_written = 0;
+ size_t to_write;
+ const size_t MAX_WRITE_SIZE = 0x7ffff000; // = 2,147,479,552
+
+ if (verbose) {
+ printf ("Total size of metadata to write = %" PRIu64 " bytes\n", buffer_offset);
+ }
+
+ while (bytes_written < buffer_offset)
{
- fprintf (stderr, "Failed to write metadata to file %s: %s\n",
- fname, strerror(errno));
- }
- else if (bytes_written != (ssize_t) buffer_offset)
+ if (buffer_offset - bytes_written > MAX_WRITE_SIZE)
+ {
+ to_write = MAX_WRITE_SIZE;
+ }
+ else
+ {
+ to_write = (size_t) (buffer_offset - bytes_written);
+ }
+
+ if (verbose>2) {
+ printf ("total to write=%" PRIu64 " write now =%ld written so far=%" PRId64 "\n",
+ buffer_offset, to_write, bytes_written);
+ }
+
+ ssize_t wrote = write (f, buffer+bytes_written, to_write);
+ bytes_written += wrote;
+
+ if (verbose>2) {
+ printf ("wrote=%ld bytes to file\n", wrote);
+ }
+
+ if (wrote == -1)
+ {
+ fprintf (stderr, "Failed to write metadata to file %s: %s\n",
+ fname, strerror(errno));
+ break;
+ }
+ else if (wrote != to_write)
+ {
+ fprintf (stderr, "Failed to write (a portion of) metadata of %" PRId64 " bytes to file %s. "
+ "Only wrote %ld bytes\n", buffer_offset, fname, wrote);
+ }
+ }
+
+ if (bytes_written != (ssize_t) buffer_offset)
{
- fprintf (stderr, "Failed to write metadata of %" PRId64 " bytes to file %s. "
+ fprintf (stderr, "Failed to write total metadata of %" PRId64 " bytes to file %s. "
"Only wrote %lld bytes\n", buffer_offset, fname, (long long)bytes_written);
}
+
close(f);
return 0;
}
@@ -383,9 +421,13 @@ int process_subfiles (int tid, int startidx, int endidx)
adios_parse_vars_index_v1 (b[idx], &new_vars_root, NULL, NULL);
print_variable_index (tid, new_vars_root);
- adios_posix_read_attributes_index (b[idx]);
- adios_parse_attributes_index_v1 (b[idx], &new_attrs_root);
- print_attribute_index (tid, new_attrs_root);
+ if (idx == 0)
+ {
+ // only read attributes from the very first file. we don't merge attributes any more
+ adios_posix_read_attributes_index (b[idx]);
+ adios_parse_attributes_index_v1 (b[idx], &new_attrs_root);
+ print_attribute_index (tid, new_attrs_root);
+ }
adios_merge_index_v1 (subindex[tid], new_pg_root, new_vars_root, new_attrs_root, 1);
diff --git a/utils/bprecover/Makefile.in b/utils/bprecover/Makefile.in
index 946020b..a735477 100644
--- a/utils/bprecover/Makefile.in
+++ b/utils/bprecover/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -329,6 +329,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -405,6 +409,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/utils/bpsplit/Makefile.in b/utils/bpsplit/Makefile.in
index 551cb7b..dd15d7f 100644
--- a/utils/bpsplit/Makefile.in
+++ b/utils/bpsplit/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -344,6 +344,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -420,6 +424,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/utils/bpsplit/bpappend.c b/utils/bpsplit/bpappend.c
index 11d31cd..64163fe 100644
--- a/utils/bpsplit/bpappend.c
+++ b/utils/bpsplit/bpappend.c
@@ -353,6 +353,7 @@ void recalc_offsets(void) {
while (vg) {
for (i=0; i < vg->characteristics_count; i++) {
vg->characteristics[i].offset += out_bp->pg_index_offset;
+ vg->characteristics[i].payload_offset += out_bp->pg_index_offset;
}
vg = vg->next;
}
@@ -362,6 +363,7 @@ void recalc_offsets(void) {
while (ag) {
for (i=0; i < ag->characteristics_count; i++) {
ag->characteristics[i].offset += out_bp->pg_index_offset;
+ ag->characteristics[i].payload_offset += out_bp->pg_index_offset;
}
ag = ag->next;
}
diff --git a/utils/bpsplit/bpsplit.c b/utils/bpsplit/bpsplit.c
index 8a20ba9..31b0d28 100644
--- a/utils/bpsplit/bpsplit.c
+++ b/utils/bpsplit/bpsplit.c
@@ -462,6 +462,7 @@ void weed_out_indexes(void) {
vg->characteristics[i].offset <= out_offset_end) {
// recalc offset for output offset
vg->characteristics[i].offset -= out_offset_start;
+ vg->characteristics[i].payload_offset -= out_offset_start;
count++;
} else
break;
@@ -498,6 +499,7 @@ void weed_out_indexes(void) {
ag->characteristics[i].offset <= out_offset_end) {
// recalc offset for output offset
ag->characteristics[i].offset -= out_offset_start;
+ ag->characteristics[i].payload_offset -= out_offset_start;
count++;
} else
break;
diff --git a/utils/fastbit/Makefile.in b/utils/fastbit/Makefile.in
index 1a32496..8de2693 100644
--- a/utils/fastbit/Makefile.in
+++ b/utils/fastbit/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -330,6 +330,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -406,6 +410,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/utils/fastbit/adios_index_fastbit.c b/utils/fastbit/adios_index_fastbit.c
index 127b7ac..3a78925 100644
--- a/utils/fastbit/adios_index_fastbit.c
+++ b/utils/fastbit/adios_index_fastbit.c
@@ -280,7 +280,7 @@ void onSelection(int rank, ADIOS_FILE* f, ADIOS_VARINFO* v, int timestep, char*
sum_nb += nb; sum_nk += nk, sum_no += no;
adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, 500); // +5MB for extra room in buffer
- adios_declare_group (&gAdios_group, gGroupNameFastbitIdx, "", adios_flag_yes);
+ adios_declare_group (&gAdios_group, gGroupNameFastbitIdx, "", adios_stat_default);
adios_select_method (gAdios_group, "MPI", "", "");
adios_open (&gAdios_write_file, gGroupNameFastbitIdx, gIdxFileName, "w", MPI_COMM_WORLD);
@@ -790,14 +790,14 @@ int main (int argc, char** argv)
/*
adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, (f->file_size)*2/1048576 + 5); // +5MB for extra room in buffer
- adios_declare_group (&gAdios_group, gGroupNameFastbitIdx, "", adios_flag_yes);
+ adios_declare_group (&gAdios_group, gGroupNameFastbitIdx, "", adios_stat_default);
adios_select_method (gAdios_group, "MPI", "", "");
*/
gIdxFileName = fastbit_adios_util_getFastbitIndexFileName(argv[1]);
unlink(gIdxFileName);
//adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, 500); // +5MB for extra room in buffer
- adios_declare_group (&gAdios_group, gGroupNameFastbitIdx, "", adios_flag_yes);
+ adios_declare_group (&gAdios_group, gGroupNameFastbitIdx, "", adios_stat_default);
adios_select_method (gAdios_group, "MPI", "", "");
adios_open (&gAdios_write_file, gGroupNameFastbitIdx, gIdxFileName, "w", MPI_COMM_WORLD);
diff --git a/utils/gpp/Makefile.in b/utils/gpp/Makefile.in
index 05e5992..46bb493 100644
--- a/utils/gpp/Makefile.in
+++ b/utils/gpp/Makefile.in
@@ -102,7 +102,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -110,8 +110,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -306,6 +306,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -382,6 +386,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/utils/gpp/gpp.py b/utils/gpp/gpp.py
index 01c9c9c..6b73bab 100755
--- a/utils/gpp/gpp.py
+++ b/utils/gpp/gpp.py
@@ -66,17 +66,17 @@ def get_c_groupsize_code (group):
def get_fortran_groupsize_code (group):
#print('Get Fortran Groupsize code for group "'+group.get_name()+'"')
- groupsize_code_string = ''
- groupsize_code_string += 'adios_groupsize = '
+ groupsize_code_string = 'adios_groupsize = 0\n'
+ groupsize_code_string += 'adios_groupsize = adios_groupsize + '
for v in group.get_vars():
#print(' count variable "'+v.get_fullpath()+'"')
if (v.is_scalar() ):
if v.get_type() != 'string':
- groupsize_code_string += ('%d' % type_mapper.get_size (v.get_type() ) + ' &\n + ')
+ groupsize_code_string += ('%d_8' % type_mapper.get_size (v.get_type() ) + ' &\n + ')
else:
groupsize_code_string += ('len_trim(' + v.get_gwrite() + ')' + ' &\n + ')
else:
- groupsize_code_string += ('%d * ' % type_mapper.get_size (v.get_type() ) )
+ groupsize_code_string += ('%d_8 * ' % type_mapper.get_size (v.get_type() ) )
for d in v.get_dimensions():
#print(' count dim "'+d+'"')
diff --git a/utils/gpp/gpp.py.in b/utils/gpp/gpp.py.in
index cbb0d88..5108952 100755
--- a/utils/gpp/gpp.py.in
+++ b/utils/gpp/gpp.py.in
@@ -66,17 +66,17 @@ def get_c_groupsize_code (group):
def get_fortran_groupsize_code (group):
#print('Get Fortran Groupsize code for group "'+group.get_name()+'"')
- groupsize_code_string = ''
- groupsize_code_string += 'adios_groupsize = '
+ groupsize_code_string = 'adios_groupsize = 0\n'
+ groupsize_code_string += 'adios_groupsize = adios_groupsize + '
for v in group.get_vars():
#print(' count variable "'+v.get_fullpath()+'"')
if (v.is_scalar() ):
if v.get_type() != 'string':
- groupsize_code_string += ('%d' % type_mapper.get_size (v.get_type() ) + ' &\n + ')
+ groupsize_code_string += ('%d_8' % type_mapper.get_size (v.get_type() ) + ' &\n + ')
else:
groupsize_code_string += ('len_trim(' + v.get_gwrite() + ')' + ' &\n + ')
else:
- groupsize_code_string += ('%d * ' % type_mapper.get_size (v.get_type() ) )
+ groupsize_code_string += ('%d_8 * ' % type_mapper.get_size (v.get_type() ) )
for d in v.get_dimensions():
#print(' count dim "'+d+'"')
diff --git a/utils/skel/Makefile.in b/utils/skel/Makefile.in
index aacf829..fc6b93c 100644
--- a/utils/skel/Makefile.in
+++ b/utils/skel/Makefile.in
@@ -104,7 +104,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -112,8 +112,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -369,6 +369,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -445,6 +449,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/utils/skel/etc/Makefile.in b/utils/skel/etc/Makefile.in
index 036e92f..f0d2745 100644
--- a/utils/skel/etc/Makefile.in
+++ b/utils/skel/etc/Makefile.in
@@ -100,7 +100,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -108,8 +108,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -303,6 +303,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -379,6 +383,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/utils/skel/etc/templates/source_write_c.tmpl b/utils/skel/etc/templates/source_write_c.tmpl
index 73eaf5a..48e06da 100644
--- a/utils/skel/etc/templates/source_write_c.tmpl
+++ b/utils/skel/etc/templates/source_write_c.tmpl
@@ -65,7 +65,7 @@ int64_t skel_adios_group;
int color = skel_mpi_rank / 2;
adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, $bpy.get_buf_size_mb());
-adios_declare_group (&skel_adios_group, "${bpy.get_group_name()}", "", adios_flag_no);
+adios_declare_group (&skel_adios_group, "${bpy.get_group_name()}", "", adios_stat_no);
char paramstring[<%= len(self.bpy.get_parameters()) + 64 %>];
//sprintf (paramstring, "color:%i;%s", color, "$bpy.get_parameters()");
diff --git a/utils/skel/src/Makefile.in b/utils/skel/src/Makefile.in
index 8d4cddc..6c8dce8 100644
--- a/utils/skel/src/Makefile.in
+++ b/utils/skel/src/Makefile.in
@@ -103,7 +103,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -111,8 +111,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -363,6 +363,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -439,6 +443,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/utils/skeldump/Makefile.in b/utils/skeldump/Makefile.in
index 5439dbc..01891c1 100644
--- a/utils/skeldump/Makefile.in
+++ b/utils/skeldump/Makefile.in
@@ -101,7 +101,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_infiniband.m4 \
$(top_srcdir)/config/ac_isobar.m4 \
$(top_srcdir)/config/ac_lustre.m4 \
- $(top_srcdir)/config/ac_mxml.m4 \
+ $(top_srcdir)/config/ac_lz4.m4 $(top_srcdir)/config/ac_mxml.m4 \
$(top_srcdir)/config/ac_nc4par.m4 \
$(top_srcdir)/config/ac_netcdf.m4 \
$(top_srcdir)/config/ac_nssi.m4 \
@@ -109,8 +109,8 @@ am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_pami.m4 \
$(top_srcdir)/config/ac_phdf5.m4 \
$(top_srcdir)/config/ac_portals.m4 \
- $(top_srcdir)/config/ac_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
- $(top_srcdir)/config/ac_zlib.m4 \
+ $(top_srcdir)/config/ac_sz.m4 $(top_srcdir)/config/ac_szip.m4 \
+ $(top_srcdir)/config/ac_zfp.m4 $(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
$(top_srcdir)/config/cercs.m4 $(top_srcdir)/config/libtool.m4 \
@@ -328,6 +328,10 @@ LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
LUSTRE_CPPFLAGS = @LUSTRE_CPPFLAGS@
LUSTRE_LDFLAGS = @LUSTRE_LDFLAGS@
LUSTRE_LIBS = @LUSTRE_LIBS@
+LZ4_CFLAGS = @LZ4_CFLAGS@
+LZ4_CPPFLAGS = @LZ4_CPPFLAGS@
+LZ4_LDFLAGS = @LZ4_LDFLAGS@
+LZ4_LIBS = @LZ4_LIBS@
MACRODEFFLAG = @MACRODEFFLAG@
MAINT = @MAINT@
MAKEINFO = @MAKEINFO@
@@ -404,6 +408,9 @@ STRIP = @STRIP@
SZIP_CPPFLAGS = @SZIP_CPPFLAGS@
SZIP_LDFLAGS = @SZIP_LDFLAGS@
SZIP_LIBS = @SZIP_LIBS@
+SZ_CPPFLAGS = @SZ_CPPFLAGS@
+SZ_LDFLAGS = @SZ_LDFLAGS@
+SZ_LIBS = @SZ_LIBS@
VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
diff --git a/wrappers/numpy/adios.cpp b/wrappers/numpy/adios.cpp
index dc001f0..db3944b 100644
--- a/wrappers/numpy/adios.cpp
+++ b/wrappers/numpy/adios.cpp
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.24 */
+/* Generated by Cython 0.25.2 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -7,7 +7,7 @@
#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000)
#error Cython requires Python 2.6+ or Python 3.2+.
#else
-#define CYTHON_ABI "0_24"
+#define CYTHON_ABI "0_25_2"
#include <stddef.h>
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
@@ -29,6 +29,11 @@
#ifndef DL_EXPORT
#define DL_EXPORT(t) t
#endif
+#ifndef HAVE_LONG_LONG
+ #if PY_VERSION_HEX >= 0x03030000 || (PY_MAJOR_VERSION == 2 && PY_VERSION_HEX >= 0x02070000)
+ #define HAVE_LONG_LONG
+ #endif
+#endif
#ifndef PY_LONG_LONG
#define PY_LONG_LONG LONG_LONG
#endif
@@ -37,13 +42,110 @@
#endif
#ifdef PYPY_VERSION
#define CYTHON_COMPILING_IN_PYPY 1
+ #define CYTHON_COMPILING_IN_PYSTON 0
#define CYTHON_COMPILING_IN_CPYTHON 0
+ #undef CYTHON_USE_TYPE_SLOTS
+ #define CYTHON_USE_TYPE_SLOTS 0
+ #undef CYTHON_USE_ASYNC_SLOTS
+ #define CYTHON_USE_ASYNC_SLOTS 0
+ #undef CYTHON_USE_PYLIST_INTERNALS
+ #define CYTHON_USE_PYLIST_INTERNALS 0
+ #undef CYTHON_USE_UNICODE_INTERNALS
+ #define CYTHON_USE_UNICODE_INTERNALS 0
+ #undef CYTHON_USE_UNICODE_WRITER
+ #define CYTHON_USE_UNICODE_WRITER 0
+ #undef CYTHON_USE_PYLONG_INTERNALS
+ #define CYTHON_USE_PYLONG_INTERNALS 0
+ #undef CYTHON_AVOID_BORROWED_REFS
+ #define CYTHON_AVOID_BORROWED_REFS 1
+ #undef CYTHON_ASSUME_SAFE_MACROS
+ #define CYTHON_ASSUME_SAFE_MACROS 0
+ #undef CYTHON_UNPACK_METHODS
+ #define CYTHON_UNPACK_METHODS 0
+ #undef CYTHON_FAST_THREAD_STATE
+ #define CYTHON_FAST_THREAD_STATE 0
+ #undef CYTHON_FAST_PYCALL
+ #define CYTHON_FAST_PYCALL 0
+#elif defined(PYSTON_VERSION)
+ #define CYTHON_COMPILING_IN_PYPY 0
+ #define CYTHON_COMPILING_IN_PYSTON 1
+ #define CYTHON_COMPILING_IN_CPYTHON 0
+ #ifndef CYTHON_USE_TYPE_SLOTS
+ #define CYTHON_USE_TYPE_SLOTS 1
+ #endif
+ #undef CYTHON_USE_ASYNC_SLOTS
+ #define CYTHON_USE_ASYNC_SLOTS 0
+ #undef CYTHON_USE_PYLIST_INTERNALS
+ #define CYTHON_USE_PYLIST_INTERNALS 0
+ #ifndef CYTHON_USE_UNICODE_INTERNALS
+ #define CYTHON_USE_UNICODE_INTERNALS 1
+ #endif
+ #undef CYTHON_USE_UNICODE_WRITER
+ #define CYTHON_USE_UNICODE_WRITER 0
+ #undef CYTHON_USE_PYLONG_INTERNALS
+ #define CYTHON_USE_PYLONG_INTERNALS 0
+ #ifndef CYTHON_AVOID_BORROWED_REFS
+ #define CYTHON_AVOID_BORROWED_REFS 0
+ #endif
+ #ifndef CYTHON_ASSUME_SAFE_MACROS
+ #define CYTHON_ASSUME_SAFE_MACROS 1
+ #endif
+ #ifndef CYTHON_UNPACK_METHODS
+ #define CYTHON_UNPACK_METHODS 1
+ #endif
+ #undef CYTHON_FAST_THREAD_STATE
+ #define CYTHON_FAST_THREAD_STATE 0
+ #undef CYTHON_FAST_PYCALL
+ #define CYTHON_FAST_PYCALL 0
#else
#define CYTHON_COMPILING_IN_PYPY 0
+ #define CYTHON_COMPILING_IN_PYSTON 0
#define CYTHON_COMPILING_IN_CPYTHON 1
+ #ifndef CYTHON_USE_TYPE_SLOTS
+ #define CYTHON_USE_TYPE_SLOTS 1
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ #undef CYTHON_USE_ASYNC_SLOTS
+ #define CYTHON_USE_ASYNC_SLOTS 0
+ #elif !defined(CYTHON_USE_ASYNC_SLOTS)
+ #define CYTHON_USE_ASYNC_SLOTS 1
+ #endif
+ #if PY_VERSION_HEX < 0x02070000
+ #undef CYTHON_USE_PYLONG_INTERNALS
+ #define CYTHON_USE_PYLONG_INTERNALS 0
+ #elif !defined(CYTHON_USE_PYLONG_INTERNALS)
+ #define CYTHON_USE_PYLONG_INTERNALS 1
+ #endif
+ #ifndef CYTHON_USE_PYLIST_INTERNALS
+ #define CYTHON_USE_PYLIST_INTERNALS 1
+ #endif
+ #ifndef CYTHON_USE_UNICODE_INTERNALS
+ #define CYTHON_USE_UNICODE_INTERNALS 1
+ #endif
+ #if PY_VERSION_HEX < 0x030300F0
+ #undef CYTHON_USE_UNICODE_WRITER
+ #define CYTHON_USE_UNICODE_WRITER 0
+ #elif !defined(CYTHON_USE_UNICODE_WRITER)
+ #define CYTHON_USE_UNICODE_WRITER 1
+ #endif
+ #ifndef CYTHON_AVOID_BORROWED_REFS
+ #define CYTHON_AVOID_BORROWED_REFS 0
+ #endif
+ #ifndef CYTHON_ASSUME_SAFE_MACROS
+ #define CYTHON_ASSUME_SAFE_MACROS 1
+ #endif
+ #ifndef CYTHON_UNPACK_METHODS
+ #define CYTHON_UNPACK_METHODS 1
+ #endif
+ #ifndef CYTHON_FAST_THREAD_STATE
+ #define CYTHON_FAST_THREAD_STATE 1
+ #endif
+ #ifndef CYTHON_FAST_PYCALL
+ #define CYTHON_FAST_PYCALL 1
+ #endif
#endif
-#if !defined(CYTHON_USE_PYLONG_INTERNALS) && CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x02070000
- #define CYTHON_USE_PYLONG_INTERNALS 1
+#if !defined(CYTHON_FAST_PYCCALL)
+#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1)
#endif
#if CYTHON_USE_PYLONG_INTERNALS
#include "longintrepr.h"
@@ -79,24 +181,44 @@
#ifndef Py_TPFLAGS_HAVE_FINALIZE
#define Py_TPFLAGS_HAVE_FINALIZE 0
#endif
+#ifndef METH_FASTCALL
+ #define METH_FASTCALL 0x80
+ typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject **args,
+ Py_ssize_t nargs, PyObject *kwnames);
+#else
+ #define __Pyx_PyCFunctionFast _PyCFunctionFast
+#endif
+#if CYTHON_FAST_PYCCALL
+#define __Pyx_PyFastCFunction_Check(func)\
+ ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)))))
+#else
+#define __Pyx_PyFastCFunction_Check(func) 0
+#endif
#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
#define CYTHON_PEP393_ENABLED 1
#define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\
0 : _PyUnicode_Ready((PyObject *)(op)))
#define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
+ #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u)
#define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u)
#define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u)
#define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
+ #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch)
#define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u)))
#else
#define CYTHON_PEP393_ENABLED 0
+ #define PyUnicode_1BYTE_KIND 1
+ #define PyUnicode_2BYTE_KIND 2
+ #define PyUnicode_4BYTE_KIND 4
#define __Pyx_PyUnicode_READY(op) (0)
#define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
+ #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111)
#define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE))
#define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u))
#define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
+ #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch)
#define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u))
#endif
#if CYTHON_COMPILING_IN_PYPY
@@ -110,6 +232,9 @@
#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains)
#define PyUnicode_Contains(u, s) PySequence_Contains(u, s)
#endif
+#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check)
+ #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type)
+#endif
#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format)
#define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt)
#endif
@@ -118,6 +243,13 @@
#define PyObject_Free(p) PyMem_Free(p)
#define PyObject_Realloc(p) PyMem_Realloc(p)
#endif
+#if CYTHON_COMPILING_IN_PYSTON
+ #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co)
+ #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno)
+#else
+ #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0)
+ #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno)
+#endif
#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b))
#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b))
#if PY_MAJOR_VERSION >= 3
@@ -146,6 +278,7 @@
#define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
+#define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception)
#if PY_MAJOR_VERSION >= 3
#define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
@@ -184,18 +317,20 @@
#else
#define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass)
#endif
-#if PY_VERSION_HEX >= 0x030500B1
-#define __Pyx_PyAsyncMethodsStruct PyAsyncMethods
-#define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async)
-#elif CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-typedef struct {
- unaryfunc am_await;
- unaryfunc am_aiter;
- unaryfunc am_anext;
-} __Pyx_PyAsyncMethodsStruct;
-#define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved))
+#if CYTHON_USE_ASYNC_SLOTS
+ #if PY_VERSION_HEX >= 0x030500B1
+ #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods
+ #define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async)
+ #else
+ typedef struct {
+ unaryfunc am_await;
+ unaryfunc am_aiter;
+ unaryfunc am_anext;
+ } __Pyx_PyAsyncMethodsStruct;
+ #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved))
+ #endif
#else
-#define __Pyx_PyType_AsAsync(obj) NULL
+ #define __Pyx_PyType_AsAsync(obj) NULL
#endif
#ifndef CYTHON_RESTRICT
#if defined(__GNUC__)
@@ -208,13 +343,44 @@ typedef struct {
#define CYTHON_RESTRICT
#endif
#endif
+#ifndef CYTHON_UNUSED
+# if defined(__GNUC__)
+# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
+# else
+# define CYTHON_UNUSED
+# endif
+# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
+# else
+# define CYTHON_UNUSED
+# endif
+#endif
+#ifndef CYTHON_MAYBE_UNUSED_VAR
+# if defined(__cplusplus)
+ template<class T> void CYTHON_MAYBE_UNUSED_VAR( const T& ) { }
+# else
+# define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x)
+# endif
+#endif
+#ifndef CYTHON_NCP_UNUSED
+# if CYTHON_COMPILING_IN_CPYTHON
+# define CYTHON_NCP_UNUSED
+# else
+# define CYTHON_NCP_UNUSED CYTHON_UNUSED
+# endif
+#endif
#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None)
#ifndef __cplusplus
#error "Cython files generated with the C++ option must be compiled with a C++ compiler."
#endif
#ifndef CYTHON_INLINE
- #define CYTHON_INLINE inline
+ #if defined(__clang__)
+ #define CYTHON_INLINE __inline__ __attribute__ ((__unused__))
+ #else
+ #define CYTHON_INLINE inline
+ #endif
#endif
template<typename T>
void __Pyx_call_destructor(T& x) {
@@ -226,7 +392,10 @@ class __Pyx_FakeReference {
__Pyx_FakeReference() : ptr(NULL) { }
__Pyx_FakeReference(const T& ref) : ptr(const_cast<T*>(&ref)) { }
T *operator->() { return ptr; }
+ T *operator&() { return ptr; }
operator T&() { return *ptr; }
+ template<typename U> bool operator ==(U other) { return *ptr == other; }
+ template<typename U> bool operator !=(U other) { return *ptr != other; }
private:
T *ptr;
};
@@ -244,6 +413,11 @@ static CYTHON_INLINE float __PYX_NAN() {
return value;
}
#endif
+#if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL)
+#define __Pyx_truncl trunc
+#else
+#define __Pyx_truncl truncl
+#endif
#define __PYX_ERR(f_index, lineno, Ln_error) \
@@ -270,11 +444,12 @@ static CYTHON_INLINE float __PYX_NAN() {
#define __PYX_HAVE__adios
#define __PYX_HAVE_API__adios
#include "string.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "numpy/arrayobject.h"
#include "numpy/ufuncobject.h"
-#include "stdint.h"
+#include <stdint.h>
#include "adios_types.h"
#include "adios.h"
#include "adios_selection.h"
@@ -287,26 +462,6 @@ static CYTHON_INLINE float __PYX_NAN() {
#define CYTHON_WITHOUT_ASSERTIONS
#endif
-#ifndef CYTHON_UNUSED
-# if defined(__GNUC__)
-# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
-# else
-# define CYTHON_UNUSED
-# endif
-# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
-# else
-# define CYTHON_UNUSED
-# endif
-#endif
-#ifndef CYTHON_NCP_UNUSED
-# if CYTHON_COMPILING_IN_CPYTHON
-# define CYTHON_NCP_UNUSED
-# else
-# define CYTHON_NCP_UNUSED CYTHON_UNUSED
-# endif
-#endif
typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding;
const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;
@@ -384,7 +539,7 @@ static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x);
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_ASSUME_SAFE_MACROS
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
#else
#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
@@ -492,7 +647,7 @@ static int __pyx_clineno = 0;
static const char * __pyx_cfilenm= __FILE__;
static const char *__pyx_filename;
-/* None.proto */
+/* Header.proto */
#if !defined(CYTHON_CCOMPLEX)
#if defined(__cplusplus)
#define CYTHON_CCOMPLEX 1
@@ -709,7 +864,7 @@ typedef npy_double __pyx_t_5numpy_double_t;
* ctypedef npy_cfloat cfloat_t
*/
typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
-/* None.proto */
+/* Declarations.proto */
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
typedef ::std::complex< float > __pyx_t_float_complex;
@@ -719,8 +874,9 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
#else
typedef struct { float real, imag; } __pyx_t_float_complex;
#endif
+static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float);
-/* None.proto */
+/* Declarations.proto */
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
typedef ::std::complex< double > __pyx_t_double_complex;
@@ -730,6 +886,7 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
#else
typedef struct { double real, imag; } __pyx_t_double_complex;
#endif
+static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double);
/*--- Type declarations ---*/
@@ -795,7 +952,7 @@ struct __pyx_opt_args_5adios_3var_read_points;
struct __pyx_opt_args_5adios_3var_read_writeblock;
struct __pyx_opt_args_5adios_3var_read;
-/* "adios.pyx":465
+/* "adios.pyx":473
* cdef MPI_Comm read_init_comm
*
* cpdef init(str config, MPI_Comm comm = MPI_COMM_WORLD): # <<<<<<<<<<<<<<
@@ -807,7 +964,7 @@ struct __pyx_opt_args_5adios_init {
MPI_Comm comm;
};
-/* "adios.pyx":470
+/* "adios.pyx":478
* return adios_init(s2b(config), init_comm)
*
* cpdef int64_t open(str group_name, # <<<<<<<<<<<<<<
@@ -819,7 +976,7 @@ struct __pyx_opt_args_5adios_open {
MPI_Comm comm;
};
-/* "adios.pyx":485
+/* "adios.pyx":493
* return total_size
*
* cpdef int write (int64_t fd_p, str name, val, dtype=None): # <<<<<<<<<<<<<<
@@ -831,7 +988,7 @@ struct __pyx_opt_args_5adios_write {
PyObject *dtype;
};
-/* "adios.pyx":525
+/* "adios.pyx":533
* return adios_close(fd_p)
*
* cpdef int finalize(int mype = 0): # <<<<<<<<<<<<<<
@@ -843,7 +1000,7 @@ struct __pyx_opt_args_5adios_finalize {
int mype;
};
-/* "adios.pyx":532
+/* "adios.pyx":540
* ## ====================
*
* cpdef int init_noxml(MPI_Comm comm = MPI_COMM_WORLD): # <<<<<<<<<<<<<<
@@ -855,7 +1012,7 @@ struct __pyx_opt_args_5adios_init_noxml {
MPI_Comm comm;
};
-/* "adios.pyx":542
+/* "adios.pyx":550
* buffer_size)
*
* cpdef int64_t declare_group(str name, # <<<<<<<<<<<<<<
@@ -868,7 +1025,7 @@ struct __pyx_opt_args_5adios_declare_group {
int stats;
};
-/* "adios.pyx":552
+/* "adios.pyx":560
* return id
*
* cpdef int64_t define_var(int64_t group_id, # <<<<<<<<<<<<<<
@@ -882,7 +1039,7 @@ struct __pyx_opt_args_5adios_define_var {
PyObject *local_offsets;
};
-/* "adios.pyx":719
+/* "adios.pyx":727
* <void *> val_.data)
*
* cpdef int select_method (int64_t group, # <<<<<<<<<<<<<<
@@ -895,7 +1052,7 @@ struct __pyx_opt_args_5adios_select_method {
PyObject *base_path;
};
-/* "adios.pyx":746
+/* "adios.pyx":754
* ## ====================
*
* cpdef np.dtype adios2npdtype(ADIOS_DATATYPES t, int strlen = 1): # <<<<<<<<<<<<<<
@@ -907,7 +1064,7 @@ struct __pyx_opt_args_5adios_adios2npdtype {
int strlen;
};
-/* "adios.pyx":875
+/* "adios.pyx":883
*
* """ Call adios_read_init_method """
* cpdef int read_init(str method_name = "BP", # <<<<<<<<<<<<<<
@@ -921,7 +1078,7 @@ struct __pyx_opt_args_5adios_read_init {
PyObject *parameters;
};
-/* "adios.pyx":885
+/* "adios.pyx":893
*
* """ Call adios_read_finalize_method """
* cpdef int read_finalize(str method_name = "BP"): # <<<<<<<<<<<<<<
@@ -933,7 +1090,7 @@ struct __pyx_opt_args_5adios_read_finalize {
PyObject *method_name;
};
-/* "adios.pyx":1062
+/* "adios.pyx":1070
* adios_release_step(self.fp)
*
* cpdef advance(self, int last = 0, float timeout_sec = 0.0): # <<<<<<<<<<<<<<
@@ -946,7 +1103,7 @@ struct __pyx_opt_args_5adios_4file_advance {
float timeout_sec;
};
-/* "adios.pyx":1360
+/* "adios.pyx":1368
* self.nsteps = self.vp.nsteps
*
* cpdef read_points(self, tuple points = (), from_steps = None, nsteps = None): # <<<<<<<<<<<<<<
@@ -960,7 +1117,7 @@ struct __pyx_opt_args_5adios_3var_read_points {
PyObject *nsteps;
};
-/* "adios.pyx":1416
+/* "adios.pyx":1424
* return var
*
* cpdef read_writeblock(self, int rank, from_steps = None, nsteps = None): # <<<<<<<<<<<<<<
@@ -973,7 +1130,7 @@ struct __pyx_opt_args_5adios_3var_read_writeblock {
PyObject *nsteps;
};
-/* "adios.pyx":1457
+/* "adios.pyx":1465
* return var
*
* cpdef read(self, tuple offset = (), tuple count = (), tuple scalar = (), # <<<<<<<<<<<<<<
@@ -991,7 +1148,7 @@ struct __pyx_opt_args_5adios_3var_read {
PyObject *step_scalar;
};
-/* "adios.pyx":890
+/* "adios.pyx":898
*
* ## dict for handling '/' prefix
* cdef class softdict(dict): # <<<<<<<<<<<<<<
@@ -1003,7 +1160,7 @@ struct __pyx_obj_5adios_softdict {
};
-/* "adios.pyx":914
+/* "adios.pyx":922
*
* ## Python class for ADIOS_FILE structure
* cdef class file(dict): # <<<<<<<<<<<<<<
@@ -1030,7 +1187,7 @@ struct __pyx_obj_5adios_file {
};
-/* "adios.pyx":1186
+/* "adios.pyx":1194
* return list(s-set(['']))
*
* cdef class blockinfo(object): # <<<<<<<<<<<<<<
@@ -1046,7 +1203,7 @@ struct __pyx_obj_5adios_blockinfo {
};
-/* "adios.pyx":1221
+/* "adios.pyx":1229
* self.count)
*
* cdef class var(dict): # <<<<<<<<<<<<<<
@@ -1069,7 +1226,7 @@ struct __pyx_obj_5adios_var {
};
-/* "adios.pyx":1686
+/* "adios.pyx":1694
* return self.attrs.keys()
*
* cdef class attr(object): # <<<<<<<<<<<<<<
@@ -1085,7 +1242,7 @@ struct __pyx_obj_5adios_attr {
};
-/* "adios.pyx":1772
+/* "adios.pyx":1780
* (self.name, self.dtype, self.value)
*
* cdef class group(dict): # <<<<<<<<<<<<<<
@@ -1101,7 +1258,7 @@ struct __pyx_obj_5adios_group {
};
-/* "adios.pyx":1884
+/* "adios.pyx":1892
*
* ## Helper dict
* cdef class smartdict(dict): # <<<<<<<<<<<<<<
@@ -1114,7 +1271,7 @@ struct __pyx_obj_5adios_smartdict {
};
-/* "adios.pyx":1896
+/* "adios.pyx":1904
* self.factory(key, value)
*
* cdef class writer(object): # <<<<<<<<<<<<<<
@@ -1131,13 +1288,14 @@ struct __pyx_obj_5adios_writer {
int is_noxml;
PyObject *mode;
MPI_Comm comm;
+ int stats;
PyObject *vars;
PyObject *attrs;
uint64_t timeaggregation_buffersize;
};
-/* "adios.pyx":2150
+/* "adios.pyx":2171
* self.close()
*
* cdef class attrinfo(object): # <<<<<<<<<<<<<<
@@ -1153,7 +1311,7 @@ struct __pyx_obj_5adios_attrinfo {
};
-/* "adios.pyx":2203
+/* "adios.pyx":2224
* self.dtype)
*
* cdef class varinfo(object): # <<<<<<<<<<<<<<
@@ -1172,7 +1330,7 @@ struct __pyx_obj_5adios_varinfo {
-/* "adios.pyx":914
+/* "adios.pyx":922
*
* ## Python class for ADIOS_FILE structure
* cdef class file(dict): # <<<<<<<<<<<<<<
@@ -1189,7 +1347,7 @@ struct __pyx_vtabstruct_5adios_file {
static struct __pyx_vtabstruct_5adios_file *__pyx_vtabptr_5adios_file;
-/* "adios.pyx":1221
+/* "adios.pyx":1229
* self.count)
*
* cdef class var(dict): # <<<<<<<<<<<<<<
@@ -1272,7 +1430,7 @@ static struct __pyx_vtabstruct_5adios_var *__pyx_vtabptr_5adios_var;
#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)
/* PyObjectGetAttrStr.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_USE_TYPE_SLOTS
static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) {
PyTypeObject* tp = Py_TYPE(obj);
if (likely(tp->tp_getattro))
@@ -1290,6 +1448,24 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject
/* GetBuiltinName.proto */
static PyObject *__Pyx_GetBuiltinName(PyObject *name);
+/* PyCFunctionFastCall.proto */
+#if CYTHON_FAST_PYCCALL
+static CYTHON_INLINE PyObject *__Pyx_PyCFunction_FastCall(PyObject *func, PyObject **args, Py_ssize_t nargs);
+#else
+#define __Pyx_PyCFunction_FastCall(func, args, nargs) (assert(0), NULL)
+#endif
+
+/* PyFunctionFastCall.proto */
+#if CYTHON_FAST_PYCALL
+#define __Pyx_PyFunction_FastCall(func, args, nargs)\
+ __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL)
+#if 1 || PY_VERSION_HEX < 0x030600B1
+static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs);
+#else
+#define __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs) _PyFunction_FastCallDict(func, args, nargs, kwargs)
+#endif
+#endif
+
/* PyObjectCall.proto */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw);
@@ -1313,7 +1489,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func);
#endif
/* PyThreadStateGet.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_FAST_THREAD_STATE
#define __Pyx_PyThreadState_declare PyThreadState *__pyx_tstate;
#define __Pyx_PyThreadState_assign __pyx_tstate = PyThreadState_GET();
#else
@@ -1322,7 +1498,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func);
#endif
/* PyErrFetchRestore.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_FAST_THREAD_STATE
#define __Pyx_ErrRestoreWithState(type, value, tb) __Pyx_ErrRestoreInState(PyThreadState_GET(), type, value, tb)
#define __Pyx_ErrFetchWithState(type, value, tb) __Pyx_ErrFetchInState(PyThreadState_GET(), type, value, tb)
#define __Pyx_ErrRestore(type, value, tb) __Pyx_ErrRestoreInState(__pyx_tstate, type, value, tb)
@@ -1374,7 +1550,7 @@ static CYTHON_INLINE int __Pyx_PySequence_ContainsTF(PyObject* item, PyObject* s
}
/* ListAppend.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS
static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
PyListObject* L = (PyListObject*) list;
Py_ssize_t len = Py_SIZE(list);
@@ -1426,7 +1602,7 @@ static CYTHON_INLINE int __Pyx_PyList_Extend(PyObject* L, PyObject* v) {
}
/* PyIntBinop.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
+#if !CYTHON_COMPILING_IN_PYPY
static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace);
#else
#define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace)\
@@ -1434,7 +1610,7 @@ static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval,
#endif
/* PyIntBinop.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
+#if !CYTHON_COMPILING_IN_PYPY
static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, long intval, int inplace);
#else
#define __Pyx_PyInt_SubtractObjC(op1, op2, intval, inplace)\
@@ -1476,7 +1652,7 @@ static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int
#endif
/* PyIntBinop.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
+#if !CYTHON_COMPILING_IN_PYPY
static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, long intval, int inplace);
#else
#define __Pyx_PyInt_EqObjC(op1, op2, intval, inplace)\
@@ -1484,7 +1660,7 @@ static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, long intval, i
#endif
/* ListCompAppend.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS
static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) {
PyListObject* L = (PyListObject*) list;
Py_ssize_t len = Py_SIZE(list);
@@ -1522,7 +1698,9 @@ static PyObject* __Pyx__CallUnboundCMethod0(__Pyx_CachedCFunction* cfunc, PyObje
((likely((cfunc)->func)) ?\
(likely((cfunc)->flag == METH_NOARGS) ? (*((cfunc)->func))(self, NULL) :\
(likely((cfunc)->flag == (METH_VARARGS | METH_KEYWORDS)) ? ((*(PyCFunctionWithKeywords)(cfunc)->func)(self, __pyx_empty_tuple, NULL)) :\
- ((cfunc)->flag == METH_VARARGS ? (*((cfunc)->func))(self, __pyx_empty_tuple) : __Pyx__CallUnboundCMethod0(cfunc, self)))) :\
+ ((cfunc)->flag == METH_VARARGS ? (*((cfunc)->func))(self, __pyx_empty_tuple) :\
+ (PY_VERSION_HEX >= 0x030600B1 && (cfunc)->flag == METH_FASTCALL ? (*(__Pyx_PyCFunctionFast)(cfunc)->func)(self, &PyTuple_GET_ITEM(__pyx_empty_tuple, 0), 0, NULL) :\
+ __Pyx__CallUnboundCMethod0(cfunc, self))))) :\
__Pyx__CallUnboundCMethod0(cfunc, self))
#else
#define __Pyx_CallUnboundCMethod0(cfunc, self) __Pyx__CallUnboundCMethod0(cfunc, self)
@@ -1597,7 +1775,7 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
#endif
/* PyObjectSetAttrStr.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_USE_TYPE_SLOTS
#define __Pyx_PyObject_DelAttrStr(o,n) __Pyx_PyObject_SetAttrStr(o,n,NULL)
static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) {
PyTypeObject* tp = Py_TYPE(obj);
@@ -1636,6 +1814,33 @@ static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* dict_or_iter, Py_ssize_t
/* py_dict_values.proto */
static CYTHON_INLINE PyObject* __Pyx_PyDict_Values(PyObject* d);
+/* SaveResetException.proto */
+#if CYTHON_FAST_THREAD_STATE
+#define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb)
+static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
+#define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb)
+static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb);
+#else
+#define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb)
+#define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb)
+#endif
+
+/* PyErrExceptionMatches.proto */
+#if CYTHON_FAST_THREAD_STATE
+#define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err)
+static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err);
+#else
+#define __Pyx_PyErr_ExceptionMatches(err) PyErr_ExceptionMatches(err)
+#endif
+
+/* GetException.proto */
+#if CYTHON_FAST_THREAD_STATE
+#define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb)
+static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
+#else
+static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb);
+#endif
+
/* SetVTable.proto */
static int __Pyx_SetVtable(PyObject *dict, void *vtable);
@@ -1674,6 +1879,9 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line,
int py_line, const char *filename);
/* CIntToPy.proto */
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ADIOS_STATISTICS_FLAG(ADIOS_STATISTICS_FLAG value);
+
+/* CIntToPy.proto */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);
/* CIntToPy.proto */
@@ -1697,7 +1905,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint32_t(uint32_t value);
/* CIntToPy.proto */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ADIOS_DATATYPES(ADIOS_DATATYPES value);
-/* None.proto */
+/* RealImag.proto */
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
#define __Pyx_CREAL(z) ((z).real())
@@ -1710,7 +1918,8 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ADIOS_DATATYPES(ADIOS_DATATYPES
#define __Pyx_CREAL(z) ((z).real)
#define __Pyx_CIMAG(z) ((z).imag)
#endif
-#if defined(__cplusplus) && CYTHON_CCOMPLEX && (defined(_WIN32) || defined(__clang__) || (defined(__GNUC__) && (__GNUC__ >= 5 || __GNUC__ == 4 && __GNUC_MINOR__ >= 4 )) || __cplusplus >= 201103)
+#if defined(__cplusplus) && CYTHON_CCOMPLEX\
+ && (defined(_WIN32) || defined(__clang__) || (defined(__GNUC__) && (__GNUC__ >= 5 || __GNUC__ == 4 && __GNUC_MINOR__ >= 4 )) || __cplusplus >= 201103)
#define __Pyx_SET_CREAL(z,x) ((z).real(x))
#define __Pyx_SET_CIMAG(z,y) ((z).imag(y))
#else
@@ -1718,85 +1927,79 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ADIOS_DATATYPES(ADIOS_DATATYPES
#define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y)
#endif
-/* None.proto */
-static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float);
-
-/* None.proto */
+/* Arithmetic.proto */
#if CYTHON_CCOMPLEX
- #define __Pyx_c_eqf(a, b) ((a)==(b))
- #define __Pyx_c_sumf(a, b) ((a)+(b))
- #define __Pyx_c_difff(a, b) ((a)-(b))
- #define __Pyx_c_prodf(a, b) ((a)*(b))
- #define __Pyx_c_quotf(a, b) ((a)/(b))
- #define __Pyx_c_negf(a) (-(a))
+ #define __Pyx_c_eq_float(a, b) ((a)==(b))
+ #define __Pyx_c_sum_float(a, b) ((a)+(b))
+ #define __Pyx_c_diff_float(a, b) ((a)-(b))
+ #define __Pyx_c_prod_float(a, b) ((a)*(b))
+ #define __Pyx_c_quot_float(a, b) ((a)/(b))
+ #define __Pyx_c_neg_float(a) (-(a))
#ifdef __cplusplus
- #define __Pyx_c_is_zerof(z) ((z)==(float)0)
- #define __Pyx_c_conjf(z) (::std::conj(z))
+ #define __Pyx_c_is_zero_float(z) ((z)==(float)0)
+ #define __Pyx_c_conj_float(z) (::std::conj(z))
#if 1
- #define __Pyx_c_absf(z) (::std::abs(z))
- #define __Pyx_c_powf(a, b) (::std::pow(a, b))
+ #define __Pyx_c_abs_float(z) (::std::abs(z))
+ #define __Pyx_c_pow_float(a, b) (::std::pow(a, b))
#endif
#else
- #define __Pyx_c_is_zerof(z) ((z)==0)
- #define __Pyx_c_conjf(z) (conjf(z))
+ #define __Pyx_c_is_zero_float(z) ((z)==0)
+ #define __Pyx_c_conj_float(z) (conjf(z))
#if 1
- #define __Pyx_c_absf(z) (cabsf(z))
- #define __Pyx_c_powf(a, b) (cpowf(a, b))
+ #define __Pyx_c_abs_float(z) (cabsf(z))
+ #define __Pyx_c_pow_float(a, b) (cpowf(a, b))
#endif
#endif
#else
- static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex, __pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex, __pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex, __pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex, __pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex, __pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex);
- static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex);
+ static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex);
+ static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex);
#if 1
- static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex, __pyx_t_float_complex);
#endif
#endif
-/* None.proto */
-static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double);
-
-/* None.proto */
+/* Arithmetic.proto */
#if CYTHON_CCOMPLEX
- #define __Pyx_c_eq(a, b) ((a)==(b))
- #define __Pyx_c_sum(a, b) ((a)+(b))
- #define __Pyx_c_diff(a, b) ((a)-(b))
- #define __Pyx_c_prod(a, b) ((a)*(b))
- #define __Pyx_c_quot(a, b) ((a)/(b))
- #define __Pyx_c_neg(a) (-(a))
+ #define __Pyx_c_eq_double(a, b) ((a)==(b))
+ #define __Pyx_c_sum_double(a, b) ((a)+(b))
+ #define __Pyx_c_diff_double(a, b) ((a)-(b))
+ #define __Pyx_c_prod_double(a, b) ((a)*(b))
+ #define __Pyx_c_quot_double(a, b) ((a)/(b))
+ #define __Pyx_c_neg_double(a) (-(a))
#ifdef __cplusplus
- #define __Pyx_c_is_zero(z) ((z)==(double)0)
- #define __Pyx_c_conj(z) (::std::conj(z))
+ #define __Pyx_c_is_zero_double(z) ((z)==(double)0)
+ #define __Pyx_c_conj_double(z) (::std::conj(z))
#if 1
- #define __Pyx_c_abs(z) (::std::abs(z))
- #define __Pyx_c_pow(a, b) (::std::pow(a, b))
+ #define __Pyx_c_abs_double(z) (::std::abs(z))
+ #define __Pyx_c_pow_double(a, b) (::std::pow(a, b))
#endif
#else
- #define __Pyx_c_is_zero(z) ((z)==0)
- #define __Pyx_c_conj(z) (conj(z))
+ #define __Pyx_c_is_zero_double(z) ((z)==0)
+ #define __Pyx_c_conj_double(z) (conj(z))
#if 1
- #define __Pyx_c_abs(z) (cabs(z))
- #define __Pyx_c_pow(a, b) (cpow(a, b))
+ #define __Pyx_c_abs_double(z) (cabs(z))
+ #define __Pyx_c_pow_double(a, b) (cpow(a, b))
#endif
#endif
#else
- static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex, __pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex, __pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex, __pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex, __pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex, __pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex);
- static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex);
+ static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex);
+ static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex);
#if 1
- static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex, __pyx_t_double_complex);
#endif
#endif
@@ -1979,6 +2182,7 @@ static PyObject *__pyx_builtin_enumerate;
static PyObject *__pyx_builtin_NotImplementedError;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_RuntimeError;
+static PyObject *__pyx_builtin_ImportError;
static const char __pyx_k_[] = "/";
static const char __pyx_k_C[] = "C";
static const char __pyx_k_S[] = "S";
@@ -2002,8 +2206,8 @@ static const char __pyx_k_NOW[] = "NOW";
static const char __pyx_k_Var[] = "Var";
static const char __pyx_k_YES[] = "YES";
static const char __pyx_k__10[] = "";
-static const char __pyx_k__63[] = " ";
-static const char __pyx_k__65[] = "(,)";
+static const char __pyx_k__64[] = " ";
+static const char __pyx_k__66[] = "(,)";
static const char __pyx_k_all[] = "all";
static const char __pyx_k_any[] = "any";
static const char __pyx_k_doc[] = "__doc__";
@@ -2015,6 +2219,7 @@ static const char __pyx_k_var[] = "var";
static const char __pyx_k_zip[] = "zip";
static const char __pyx_k_Attr[] = "Attr";
static const char __pyx_k_FLAG[] = "FLAG";
+static const char __pyx_k_FULL[] = "FULL";
static const char __pyx_k_File[] = "File";
static const char __pyx_k_ICEE[] = "ICEE";
static const char __pyx_k_NONE[] = "NONE";
@@ -2090,6 +2295,7 @@ static const char __pyx_k_varid[] = "varid";
static const char __pyx_k_write[] = "write";
static const char __pyx_k_zeros[] = "zeros";
static const char __pyx_k_15s_lu[] = "%15s : %lu";
+static const char __pyx_k_MINMAX[] = "MINMAX";
static const char __pyx_k_POSIX1[] = "POSIX1";
static const char __pyx_k_Writer[] = "Writer";
static const char __pyx_k_config[] = "config";
@@ -2119,6 +2325,7 @@ static const char __pyx_k_values[] = "values";
static const char __pyx_k_var_id[] = "var_id";
static const char __pyx_k_xrange[] = "xrange";
static const char __pyx_k_CURRENT[] = "CURRENT";
+static const char __pyx_k_DEFAULT[] = "DEFAULT";
static const char __pyx_k_Reading[] = "Reading ... ";
static const char __pyx_k_UNKNOWN[] = "UNKNOWN";
static const char __pyx_k_Varinfo[] = "Varinfo";
@@ -2161,6 +2368,7 @@ static const char __pyx_k_meshname[] = "meshname";
static const char __pyx_k_qualname[] = "__qualname__";
static const char __pyx_k_readattr[] = "_readattr";
static const char __pyx_k_string_2[] = "string_";
+static const char __pyx_k_tempfile[] = "tempfile";
static const char __pyx_k_tostring[] = "tostring";
static const char __pyx_k_AdiosFile[] = "=== AdiosFile ===";
static const char __pyx_k_TypeError[] = "TypeError";
@@ -2187,6 +2395,7 @@ static const char __pyx_k_traceback[] = "traceback";
static const char __pyx_k_transform[] = "transform";
static const char __pyx_k_DATASPACES[] = "DATASPACES";
static const char __pyx_k_IndexError[] = "IndexError";
+static const char __pyx_k_STATISTICS[] = "STATISTICS";
static const char __pyx_k_ValueError[] = "ValueError";
static const char __pyx_k_buffersize[] = "buffersize";
static const char __pyx_k_complex128[] = "complex128";
@@ -2203,6 +2412,7 @@ static const char __pyx_k_startswith[] = "startswith";
static const char __pyx_k_time_index[] = "time_index";
static const char __pyx_k_time_steps[] = "time_steps";
static const char __pyx_k_timeseries[] = "timeseries";
+static const char __pyx_k_ImportError[] = "ImportError";
static const char __pyx_k_READ_METHOD[] = "READ_METHOD";
static const char __pyx_k_buffer_size[] = "buffer_size";
static const char __pyx_k_concatenate[] = "concatenate";
@@ -2244,8 +2454,9 @@ static const char __pyx_k_Not_an_open_file[] = "Not an open file";
static const char __pyx_k_unsigned_integer[] = "unsigned_integer";
static const char __pyx_k_BUFFER_ALLOC_WHEN[] = "BUFFER_ALLOC_WHEN";
static const char __pyx_k_global_dimensions[] = "global_dimensions";
+static const char __pyx_k_NamedTemporaryFile[] = "NamedTemporaryFile";
static const char __pyx_k_transform_type_str[] = "transform_type_str";
-static const char __pyx_k_var_read_line_1457[] = "var.read (line 1457)";
+static const char __pyx_k_var_read_line_1465[] = "var.read (line 1465)";
static const char __pyx_k_NotImplementedError[] = "NotImplementedError";
static const char __pyx_k_Not_implemented_yet[] = "Not implemented yet";
static const char __pyx_k_Not_an_open_variable[] = "Not an open variable";
@@ -2253,13 +2464,13 @@ static const char __pyx_k_set_time_aggregation[] = "set_time_aggregation";
static const char __pyx_k_Use_default_BP_method[] = ". Use default BP method";
static const char __pyx_k_AdiosGroup_vars_r_attrs_r[] = "AdiosGroup (vars=%r, attrs=%r)";
static const char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous";
-static const char __pyx_k_writer_define_var_line_2020[] = "writer.define_var (line 2020)";
+static const char __pyx_k_writer_define_var_line_2041[] = "writer.define_var (line 2041)";
static const char __pyx_k_Rank_is_out_of_range_nblock_r[] = "Rank is out of range (nblock=%r)";
static const char __pyx_k_WARN_Invalid_read_method_name[] = "[WARN] Invalid read method name:";
static const char __pyx_k_Data_type_is_not_supported_yet[] = "Data type is not supported yet";
-static const char __pyx_k_Define_a_group_associated_with[] = "\n Define a group associated with the file.\n\n Args:\n gname (str): group name.\n method (str, optional): Adios write method (default: 'POSIX1')\n method_params (str, optional): parameters for the write method (default: '')\n\n Example:\n\n >>> fw.declare_group('group', method='MPI_, method_params='verbose=3')\n\n ";
+static const char __pyx_k_Define_a_group_associated_with[] = "\n Define a group associated with the file.\n\n Args:\n gname (str): group name.\n method (str, optional): Adios write method (default: 'POSIX1')\n method_params (str, optional): parameters for the write method (default: '')\n stats (int, optional): statistics (default: 'DEFAULT')\n\n Example:\n\n >>> fw.declare_group('group', method='MPI_, method_params= [...]
static const char __pyx_k_Perform_read_Read_data_from_an[] = " Perform read.\n\n Read data from an ADIOS BP file. Subset reading is\n supported. Without any options, this will read out a whole\n data.\n\n Args:\n offset (tuple of int, optional): offset (default: ())\n count (tuple of int, optional): count (default: ())\n scalar (tuple of bool, optional): scalar (default: ())\n from_steps (int, optional): starting ste [...]
-static const char __pyx_k_writer_declare_group_line_1983[] = "writer.declare_group (line 1983)";
+static const char __pyx_k_writer_declare_group_line_1996[] = "writer.declare_group (line 1996)";
static const char __pyx_k_AdiosFile_path_r_nvars_r_vars_r[] = "AdiosFile (path=%r, nvars=%r, vars=%r, nattrs=%r, attrs=%r, current_step=%r, last_step=%r, file_size=%r)";
static const char __pyx_k_AdiosVar_varid_r_name_r_dtype_r[] = "AdiosVar (varid=%r, name=%r, dtype=%r, ndim=%r, dims=%r, nsteps=%r, attrs=%r)";
static const char __pyx_k_AdiosVarinfo_name_r_ldim_r_gdim[] = "AdiosVarinfo (name=%r, ldim=%r, gdim=%r, offset=%r, transform=%r, value=%r)";
@@ -2267,6 +2478,8 @@ static const char __pyx_k_Define_a_variable_associated_wi[] = "\n Define
static const char __pyx_k_Step_index_is_out_of_range_from[] = "Step index is out of range: from_steps=%r, nsteps=%r";
static const char __pyx_k_Users_jyc_project_adios_devel_w[] = "/Users/jyc/project/adios-devel/wrappers/numpy/adios.pyx";
static const char __pyx_k_Warning_No_support_yet_s_type_d[] = "Warning: No support yet: %s (type=%d, bytes=%d)";
+static const char __pyx_k_Warning_skipping_defining_var_r[] = "Warning: skipping defining var(%r) with None value";
+static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import";
static const char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)";
static const char __pyx_k_ADIOS_ADIOS_python_module_module[] = "ADIOS: ADIOS python module\n\n.. moduleauthor:: Jong Choi <choij at ornl.gov>\n";
static const char __pyx_k_AdiosAttr_name_r_dtype_r_value_r[] = "AdiosAttr (name=%r, dtype=%r, value=%r)";
@@ -2282,6 +2495,7 @@ static const char __pyx_k_Only_contiguous_arrays_are_suppo[] = "Only contiguous
static const char __pyx_k_Requested_is_larger_than_the_sha[] = "Requested is larger than the shape.";
static const char __pyx_k_Scalar_dimension_mismatch_scalar[] = "Scalar dimension mismatch (scalar dim: %r)";
static const char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous";
+static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import";
static const char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short.";
static PyObject *__pyx_kp_s_;
static PyObject *__pyx_kp_s_15s_d;
@@ -2309,6 +2523,7 @@ static PyObject *__pyx_n_s_CURRENT;
static PyObject *__pyx_kp_s_Count_dimension_mismatch_count_d;
static PyObject *__pyx_n_s_DATASPACES;
static PyObject *__pyx_n_s_DATATYPE;
+static PyObject *__pyx_n_s_DEFAULT;
static PyObject *__pyx_n_s_DIMES;
static PyObject *__pyx_kp_s_Data_type_is_not_supported_yet;
static PyObject *__pyx_kp_u_Define_a_group_associated_with;
@@ -2316,18 +2531,22 @@ static PyObject *__pyx_kp_u_Define_a_variable_associated_wi;
static PyObject *__pyx_n_s_Ellipsis;
static PyObject *__pyx_n_s_FLAG;
static PyObject *__pyx_n_s_FLEXPATH;
+static PyObject *__pyx_n_s_FULL;
static PyObject *__pyx_n_s_FancySelection;
static PyObject *__pyx_n_s_File;
static PyObject *__pyx_kp_u_Format_string_allocated_too_shor;
static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2;
static PyObject *__pyx_n_s_ICEE;
+static PyObject *__pyx_n_s_ImportError;
static PyObject *__pyx_n_s_IndexError;
static PyObject *__pyx_n_s_KeyError;
static PyObject *__pyx_n_s_LATER;
static PyObject *__pyx_n_s_LOCKMODE;
+static PyObject *__pyx_n_s_MINMAX;
static PyObject *__pyx_n_s_NO;
static PyObject *__pyx_n_s_NONE;
static PyObject *__pyx_n_s_NOW;
+static PyObject *__pyx_n_s_NamedTemporaryFile;
static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor;
static PyObject *__pyx_n_s_NotImplementedError;
static PyObject *__pyx_kp_s_Not_a_valid_var;
@@ -2345,6 +2564,7 @@ static PyObject *__pyx_kp_s_Reading;
static PyObject *__pyx_kp_s_Requested_is_larger_than_the_sha;
static PyObject *__pyx_n_s_RuntimeError;
static PyObject *__pyx_n_s_S;
+static PyObject *__pyx_n_s_STATISTICS;
static PyObject *__pyx_kp_s_Scalar_dimension_mismatch_scalar;
static PyObject *__pyx_n_s_SimpleSelection;
static PyObject *__pyx_kp_s_Step_index_is_out_of_range_from;
@@ -2360,11 +2580,12 @@ static PyObject *__pyx_n_s_Var;
static PyObject *__pyx_n_s_Varinfo;
static PyObject *__pyx_kp_s_WARN_Invalid_read_method_name;
static PyObject *__pyx_kp_s_Warning_No_support_yet_s_type_d;
+static PyObject *__pyx_kp_s_Warning_skipping_defining_var_r;
static PyObject *__pyx_n_s_Writer;
static PyObject *__pyx_n_s_YES;
static PyObject *__pyx_kp_s__10;
-static PyObject *__pyx_kp_s__63;
-static PyObject *__pyx_kp_s__65;
+static PyObject *__pyx_kp_s__64;
+static PyObject *__pyx_kp_s__66;
static PyObject *__pyx_n_s_adios;
static PyObject *__pyx_n_s_advance;
static PyObject *__pyx_n_s_all;
@@ -2491,6 +2712,8 @@ static PyObject *__pyx_n_s_npoints;
static PyObject *__pyx_n_s_nspace;
static PyObject *__pyx_n_s_nsteps;
static PyObject *__pyx_n_s_numpy;
+static PyObject *__pyx_kp_s_numpy_core_multiarray_failed_to;
+static PyObject *__pyx_kp_s_numpy_core_umath_failed_to_impor;
static PyObject *__pyx_n_s_nvars;
static PyObject *__pyx_n_s_offset;
static PyObject *__pyx_n_s_order;
@@ -2542,6 +2765,7 @@ static PyObject *__pyx_n_s_strip;
static PyObject *__pyx_n_s_strlen;
static PyObject *__pyx_n_s_syncgroupid;
static PyObject *__pyx_n_s_t;
+static PyObject *__pyx_n_s_tempfile;
static PyObject *__pyx_n_s_test;
static PyObject *__pyx_n_s_time_index;
static PyObject *__pyx_n_s_time_steps;
@@ -2572,7 +2796,7 @@ static PyObject *__pyx_n_s_values;
static PyObject *__pyx_n_s_var;
static PyObject *__pyx_n_s_var_id;
static PyObject *__pyx_n_s_var_namelist;
-static PyObject *__pyx_kp_u_var_read_line_1457;
+static PyObject *__pyx_kp_u_var_read_line_1465;
static PyObject *__pyx_n_s_varid;
static PyObject *__pyx_n_s_varname;
static PyObject *__pyx_n_s_vars;
@@ -2581,8 +2805,8 @@ static PyObject *__pyx_n_s_vp;
static PyObject *__pyx_n_s_w;
static PyObject *__pyx_n_s_when;
static PyObject *__pyx_n_s_write;
-static PyObject *__pyx_kp_u_writer_declare_group_line_1983;
-static PyObject *__pyx_kp_u_writer_define_var_line_2020;
+static PyObject *__pyx_kp_u_writer_declare_group_line_1996;
+static PyObject *__pyx_kp_u_writer_define_var_line_2041;
static PyObject *__pyx_n_s_xrange;
static PyObject *__pyx_n_s_zeros;
static PyObject *__pyx_n_s_zip;
@@ -2730,8 +2954,8 @@ static PyObject *__pyx_pf_5adios_6writer_4mode___get__(struct __pyx_obj_5adios_w
static PyObject *__pyx_pf_5adios_6writer_4vars___get__(struct __pyx_obj_5adios_writer *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_5adios_6writer_5attrs___get__(struct __pyx_obj_5adios_writer *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_5adios_6writer_26timeaggregation_buffersize___get__(struct __pyx_obj_5adios_writer *__pyx_v_self); /* proto */
-static int __pyx_pf_5adios_6writer___init__(struct __pyx_obj_5adios_writer *__pyx_v_self, PyObject *__pyx_v_fname, int __pyx_v_is_noxml, PyObject *__pyx_v_mode, MPI_Comm __pyx_v_comm); /* proto */
-static PyObject *__pyx_pf_5adios_6writer_2declare_group(struct __pyx_obj_5adios_writer *__pyx_v_self, PyObject *__pyx_v_gname, PyObject *__pyx_v_method, PyObject *__pyx_v_method_params); /* proto */
+static int __pyx_pf_5adios_6writer___init__(struct __pyx_obj_5adios_writer *__pyx_v_self, PyObject *__pyx_v_fname, int __pyx_v_is_noxml, PyObject *__pyx_v_mode, int __pyx_v_stats, MPI_Comm __pyx_v_comm, PyObject *__pyx_v_method, PyObject *__pyx_v_method_params); /* proto */
+static PyObject *__pyx_pf_5adios_6writer_2declare_group(struct __pyx_obj_5adios_writer *__pyx_v_self, PyObject *__pyx_v_gname, PyObject *__pyx_v_method, PyObject *__pyx_v_method_params, int __pyx_v_stats); /* proto */
static PyObject *__pyx_pf_5adios_6writer_4set_time_aggregation(struct __pyx_obj_5adios_writer *__pyx_v_self, PyObject *__pyx_v_buffer_size); /* proto */
static PyObject *__pyx_pf_5adios_6writer_6define_var(struct __pyx_obj_5adios_writer *__pyx_v_self, PyObject *__pyx_v_varname, PyObject *__pyx_v_ldim, PyObject *__pyx_v_gdim, PyObject *__pyx_v_offset, PyObject *__pyx_v_transform); /* proto */
static PyObject *__pyx_pf_5adios_6writer_8define_attr(struct __pyx_obj_5adios_writer *__pyx_v_self, PyObject *__pyx_v_attrname); /* proto */
@@ -2809,13 +3033,15 @@ static int __pyx_k__11;
static MPI_Comm __pyx_k__12;
static MPI_Comm __pyx_k__16;
static ADIOS_LOCKMODE __pyx_k__17;
-static MPI_Comm __pyx_k__54;
-static PyObject *__pyx_k__55;
-static PyObject *__pyx_k__56;
+static int __pyx_k__54;
+static MPI_Comm __pyx_k__55;
+static int __pyx_k__56;
static PyObject *__pyx_k__57;
+static PyObject *__pyx_k__58;
static PyObject *__pyx_k__59;
-static PyObject *__pyx_k__60;
static PyObject *__pyx_k__61;
+static PyObject *__pyx_k__62;
+static PyObject *__pyx_k__63;
static PyObject *__pyx_slice__3;
static PyObject *__pyx_slice__4;
static PyObject *__pyx_slice__5;
@@ -2860,10 +3086,8 @@ static PyObject *__pyx_tuple__48;
static PyObject *__pyx_tuple__50;
static PyObject *__pyx_tuple__51;
static PyObject *__pyx_tuple__53;
-static PyObject *__pyx_tuple__58;
-static PyObject *__pyx_tuple__62;
-static PyObject *__pyx_tuple__64;
-static PyObject *__pyx_tuple__66;
+static PyObject *__pyx_tuple__60;
+static PyObject *__pyx_tuple__65;
static PyObject *__pyx_tuple__67;
static PyObject *__pyx_tuple__68;
static PyObject *__pyx_tuple__69;
@@ -2875,13 +3099,17 @@ static PyObject *__pyx_tuple__74;
static PyObject *__pyx_tuple__75;
static PyObject *__pyx_tuple__76;
static PyObject *__pyx_tuple__77;
+static PyObject *__pyx_tuple__78;
static PyObject *__pyx_tuple__79;
+static PyObject *__pyx_tuple__80;
static PyObject *__pyx_tuple__81;
-static PyObject *__pyx_codeobj__78;
-static PyObject *__pyx_codeobj__80;
+static PyObject *__pyx_tuple__83;
+static PyObject *__pyx_tuple__85;
static PyObject *__pyx_codeobj__82;
+static PyObject *__pyx_codeobj__84;
+static PyObject *__pyx_codeobj__86;
-/* "adios.pyx":33
+/* "adios.pyx":35
* ## To convert a string to bytes: "str".encode()
* ## To convert bytes to a String: b"".decode() or str(b"")
* cpdef void test_str(str x): # <<<<<<<<<<<<<<
@@ -2899,17 +3127,17 @@ static void __pyx_f_5adios_test_str(PyObject *__pyx_v_x, CYTHON_UNUSED int __pyx
char const *__pyx_t_4;
__Pyx_RefNannySetupContext("test_str", 0);
- /* "adios.pyx":34
+ /* "adios.pyx":36
* ## To convert bytes to a String: b"".decode() or str(b"")
* cpdef void test_str(str x):
* cdef char * y = strdup(x.encode()) # <<<<<<<<<<<<<<
* print(x, str(y))
*
*/
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_x, __pyx_n_s_encode); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 34, __pyx_L1_error)
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_x, __pyx_n_s_encode); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 36, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = NULL;
- if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_2))) {
+ if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) {
__pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
if (likely(__pyx_t_3)) {
PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
@@ -2919,35 +3147,35 @@ static void __pyx_f_5adios_test_str(PyObject *__pyx_v_x, CYTHON_UNUSED int __pyx
}
}
if (__pyx_t_3) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 34, __pyx_L1_error)
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 36, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 34, __pyx_L1_error)
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 36, __pyx_L1_error)
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_AsString(__pyx_t_1); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) __PYX_ERR(0, 34, __pyx_L1_error)
+ __pyx_t_4 = __Pyx_PyObject_AsString(__pyx_t_1); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) __PYX_ERR(0, 36, __pyx_L1_error)
__pyx_v_y = strdup(__pyx_t_4);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "adios.pyx":35
+ /* "adios.pyx":37
* cpdef void test_str(str x):
* cdef char * y = strdup(x.encode())
* print(x, str(y)) # <<<<<<<<<<<<<<
*
* from cpython.version cimport PY_MAJOR_VERSION
*/
- __pyx_t_1 = __Pyx_PyBytes_FromString(__pyx_v_y); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 35, __pyx_L1_error)
+ __pyx_t_1 = __Pyx_PyBytes_FromString(__pyx_v_y); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 37, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 35, __pyx_L1_error)
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 37, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_2);
__Pyx_GIVEREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(((PyObject *)(&PyString_Type)), __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 35, __pyx_L1_error)
+ __pyx_t_1 = __Pyx_PyObject_Call(((PyObject *)(&PyString_Type)), __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 37, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 35, __pyx_L1_error)
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goto __pyx_L3;
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- /* "adios.pyx":520
+ /* "adios.pyx":528
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__Pyx_RefNannyFinishContext();
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__pyx_t_1 = __pyx_f_5adios_init_noxml(0, &__pyx_t_2);
- __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 532, __pyx_L1_error)
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return __pyx_r;
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goto __pyx_L0;
- /* "adios.pyx":537
+ /* "adios.pyx":545
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else {
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__Pyx_RefNannyFinishContext();
@@ -6281,7 +6509,7 @@ static PyObject *__pyx_pf_5adios_34allocate_buffer(CYTHON_UNUSED PyObject *__pyx
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goto __pyx_L0;
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switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -6453,21 +6681,21 @@ static PyObject *__pyx_pw_5adios_37declare_group(PyObject *__pyx_self, PyObject
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__Pyx_RefNannyFinishContext();
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/* function exit code */
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return __pyx_r;
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}
}
- /* "adios.pyx":560
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__Pyx_GOTREF(__pyx_t_1);
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- /* "adios.pyx":561
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+ __pyx_t_3 = __pyx_f_5adios_s2b(__pyx_v_path, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 569, __pyx_L1_error)
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- __pyx_t_5 = __pyx_f_5adios_s2b(__pyx_v_dimensions, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 563, __pyx_L1_error)
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@@ -8441,7 +8669,7 @@ static PyObject *__pyx_pf_5adios_60define_mesh_timeseriesformat(CYTHON_UNUSED Py
return __pyx_r;
}
-/* "adios.pyx":600
+/* "adios.pyx":608
* return adios_define_mesh_timeseriesformat (s2b(timeseries) , group_id ,s2b(name))
*
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@@ -8467,73 +8695,73 @@ static int __pyx_f_5adios_define_mesh_uniform(PyObject *__pyx_v_dimensions, PyOb
char const *__pyx_t_12;
__Pyx_RefNannySetupContext("define_mesh_uniform", 0);
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* s2b(origin),
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+ __pyx_t_1 = __pyx_f_5adios_s2b(__pyx_v_dimensions, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 616, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_1);
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- /* "adios.pyx":609
+ /* "adios.pyx":617
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* return adios_define_mesh_uniform (s2b(dimensions),
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- __pyx_t_3 = __pyx_f_5adios_s2b(__pyx_v_origin, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 609, __pyx_L1_error)
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- /* "adios.pyx":610
+ /* "adios.pyx":618
* return adios_define_mesh_uniform (s2b(dimensions),
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__Pyx_GOTREF(__pyx_t_5);
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+ __pyx_t_8 = __Pyx_PyObject_AsString(__pyx_t_7); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) __PYX_ERR(0, 619, __pyx_L1_error)
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+ __pyx_t_9 = __pyx_f_5adios_s2b(__pyx_v_nspace, 0); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 620, __pyx_L1_error)
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- /* "adios.pyx":614
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+ __pyx_t_11 = __pyx_f_5adios_s2b(__pyx_v_name, 0); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 622, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_11);
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__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
goto __pyx_L0;
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case 1:
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else {
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else {
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/* function exit code */
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- /* "adios.pyx":627
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__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
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case 1:
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else {
- __Pyx_RaiseArgtupleInvalid("define_mesh_unstructured", 1, 8, 8, 1); __PYX_ERR(0, 643, __pyx_L3_error)
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else {
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else {
- __Pyx_RaiseArgtupleInvalid("define_mesh_unstructured", 1, 8, 8, 3); __PYX_ERR(0, 643, __pyx_L3_error)
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else {
- __Pyx_RaiseArgtupleInvalid("define_mesh_unstructured", 1, 8, 8, 4); __PYX_ERR(0, 643, __pyx_L3_error)
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else {
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* cdef char ** pt2
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@@ -9978,7 +10224,7 @@ static int __pyx_f_5adios_define_attribute_byvalue(int64_t __pyx_v_group, PyObje
goto __pyx_L8;
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- /* "adios.pyx":703
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__pyx_v_pt2 = __pyx_f_5adios_to_cstring_array(__pyx_v_val);
- /* "adios.pyx":705
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+ __pyx_t_5 = __pyx_f_5adios_s2b(__pyx_v_base_path, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 734, __pyx_L1_error)
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+ /* "adios.pyx":806
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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goto __pyx_L3;
}
- /* "adios.pyx":810
+ /* "adios.pyx":818
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goto __pyx_L3;
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goto __pyx_L3;
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- /* "adios.pyx":814
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if (__pyx_t_1) {
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goto __pyx_L3;
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__Pyx_GIVEREF(__pyx_kp_s_WARN_Invalid_read_method_name);
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goto __pyx_L0;
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return __pyx_r;
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goto __pyx_L0;
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/* function exit code */
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PyObject *__pyx_t_13 = NULL;
PyObject *__pyx_t_14 = NULL;
- Py_ssize_t __pyx_t_15;
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__Pyx_DECREF(((PyObject *)__pyx_v_self->file));
__pyx_v_self->file = __pyx_v_file;
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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__pyx_v_self->nsteps = __pyx_t_3;
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goto __pyx_L0;
}
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values[1] = ((PyObject*)__pyx_empty_tuple);
values[2] = ((PyObject*)__pyx_empty_tuple);
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return __pyx_r;
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- /* "adios.pyx":1577
+ /* "adios.pyx":1585
* print ('=== AdiosVariable ===')
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goto __pyx_L5;
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+ case 7: values[6] = PyTuple_GET_ITEM(__pyx_args, 6);
+ case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
+ case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
@@ -30844,15 +32119,33 @@ static int __pyx_pw_5adios_6writer_1__init__(PyObject *__pyx_v_self, PyObject *_
}
case 3:
if (kw_args > 0) {
- PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_comm);
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_stats);
if (value) { values[3] = value; kw_args--; }
}
+ case 4:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_comm);
+ if (value) { values[4] = value; kw_args--; }
+ }
+ case 5:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_method);
+ if (value) { values[5] = value; kw_args--; }
+ }
+ case 6:
+ if (kw_args > 0) {
+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_method_params);
+ if (value) { values[6] = value; kw_args--; }
+ }
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}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
+ case 7: values[6] = PyTuple_GET_ITEM(__pyx_args, 6);
+ case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
+ case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
@@ -30863,38 +32156,47 @@ static int __pyx_pw_5adios_6writer_1__init__(PyObject *__pyx_v_self, PyObject *_
}
__pyx_v_fname = ((PyObject*)values[0]);
if (values[1]) {
- __pyx_v_is_noxml = __Pyx_PyObject_IsTrue(values[1]); if (unlikely((__pyx_v_is_noxml == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 1962, __pyx_L3_error)
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} else {
- /* "adios.pyx":1962
+ /* "adios.pyx":1971
*
* def __init__(self, str fname,
* bint is_noxml = True, # <<<<<<<<<<<<<<
* str mode = "w",
- * MPI_Comm comm = MPI_COMM_WORLD):
+ * int stats = adios_stat_default,
*/
__pyx_v_is_noxml = ((int)1);
}
__pyx_v_mode = ((PyObject*)values[2]);
if (values[3]) {
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+ __pyx_v_stats = __Pyx_PyInt_As_int(values[3]); if (unlikely((__pyx_v_stats == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 1973, __pyx_L3_error)
+ } else {
+ __pyx_v_stats = __pyx_k__54;
+ }
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} else {
- __pyx_v_comm = __pyx_k__54;
+ __pyx_v_comm = __pyx_k__55;
}
+ __pyx_v_method = ((PyObject*)values[5]);
+ __pyx_v_method_params = ((PyObject*)values[6]);
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- __Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 4, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 1961, __pyx_L3_error)
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+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_fname), (&PyString_Type), 1, "fname", 1))) __PYX_ERR(0, 1970, __pyx_L1_error)
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_mode), (&PyString_Type), 1, "mode", 1))) __PYX_ERR(0, 1972, __pyx_L1_error)
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_method), (&PyString_Type), 1, "method", 1))) __PYX_ERR(0, 1975, __pyx_L1_error)
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_method_params), (&PyString_Type), 1, "method_params", 1))) __PYX_ERR(0, 1976, __pyx_L1_error)
+ __pyx_r = __pyx_pf_5adios_6writer___init__(((struct __pyx_obj_5adios_writer *)__pyx_v_self), __pyx_v_fname, __pyx_v_is_noxml, __pyx_v_mode, __pyx_v_stats, __pyx_v_comm, __pyx_v_method, __pyx_v_method_params);
- /* "adios.pyx":1961
+ /* "adios.pyx":1970
* return self.timeaggregation_buffersize
*
* def __init__(self, str fname, # <<<<<<<<<<<<<<
@@ -30911,28 +32213,28 @@ static int __pyx_pw_5adios_6writer_1__init__(PyObject *__pyx_v_self, PyObject *_
return __pyx_r;
}
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+static int __pyx_pf_5adios_6writer___init__(struct __pyx_obj_5adios_writer *__pyx_v_self, PyObject *__pyx_v_fname, int __pyx_v_is_noxml, PyObject *__pyx_v_mode, int __pyx_v_stats, MPI_Comm __pyx_v_comm, PyObject *__pyx_v_method, PyObject *__pyx_v_method_params) {
int __pyx_r;
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struct __pyx_opt_args_5adios_init_noxml __pyx_t_2;
__Pyx_RefNannySetupContext("__init__", 0);
- /* "adios.pyx":1965
- * str mode = "w",
- * MPI_Comm comm = MPI_COMM_WORLD):
+ /* "adios.pyx":1977
+ * str method = "POSIX1",
+ * str method_params = ""):
* self.gid = 0 # <<<<<<<<<<<<<<
* self.fname = fname
- * self.method = ""
+ * self.method = method
*/
__pyx_v_self->gid = 0;
- /* "adios.pyx":1966
- * MPI_Comm comm = MPI_COMM_WORLD):
+ /* "adios.pyx":1978
+ * str method_params = ""):
* self.gid = 0
* self.fname = fname # <<<<<<<<<<<<<<
- * self.method = ""
- * self.method_params = ""
+ * self.method = method
+ * self.method_params = method_params
*/
__Pyx_INCREF(__pyx_v_fname);
__Pyx_GIVEREF(__pyx_v_fname);
@@ -30940,43 +32242,43 @@ static int __pyx_pf_5adios_6writer___init__(struct __pyx_obj_5adios_writer *__py
__Pyx_DECREF(__pyx_v_self->fname);
__pyx_v_self->fname = __pyx_v_fname;
- /* "adios.pyx":1967
+ /* "adios.pyx":1979
* self.gid = 0
* self.fname = fname
- * self.method = "" # <<<<<<<<<<<<<<
- * self.method_params = ""
+ * self.method = method # <<<<<<<<<<<<<<
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*/
- __Pyx_INCREF(__pyx_kp_s__10);
- __Pyx_GIVEREF(__pyx_kp_s__10);
+ __Pyx_INCREF(__pyx_v_method);
+ __Pyx_GIVEREF(__pyx_v_method);
__Pyx_GOTREF(__pyx_v_self->method);
__Pyx_DECREF(__pyx_v_self->method);
- __pyx_v_self->method = __pyx_kp_s__10;
+ __pyx_v_self->method = __pyx_v_method;
- /* "adios.pyx":1968
+ /* "adios.pyx":1980
* self.fname = fname
- * self.method = ""
- * self.method_params = "" # <<<<<<<<<<<<<<
+ * self.method = method
+ * self.method_params = method_params # <<<<<<<<<<<<<<
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* self.mode = mode
*/
- __Pyx_INCREF(__pyx_kp_s__10);
- __Pyx_GIVEREF(__pyx_kp_s__10);
+ __Pyx_INCREF(__pyx_v_method_params);
+ __Pyx_GIVEREF(__pyx_v_method_params);
__Pyx_GOTREF(__pyx_v_self->method_params);
__Pyx_DECREF(__pyx_v_self->method_params);
- __pyx_v_self->method_params = __pyx_kp_s__10;
+ __pyx_v_self->method_params = __pyx_v_method_params;
- /* "adios.pyx":1969
- * self.method = ""
- * self.method_params = ""
+ /* "adios.pyx":1981
+ * self.method = method
+ * self.method_params = method_params
* self.is_noxml = is_noxml # <<<<<<<<<<<<<<
* self.mode = mode
* self.comm = comm
*/
__pyx_v_self->is_noxml = __pyx_v_is_noxml;
- /* "adios.pyx":1970
- * self.method_params = ""
+ /* "adios.pyx":1982
+ * self.method_params = method_params
* self.is_noxml = is_noxml
* self.mode = mode # <<<<<<<<<<<<<<
* self.comm = comm
@@ -30988,7 +32290,7 @@ static int __pyx_pf_5adios_6writer___init__(struct __pyx_obj_5adios_writer *__py
__Pyx_DECREF(__pyx_v_self->mode);
__pyx_v_self->mode = __pyx_v_mode;
- /* "adios.pyx":1971
+ /* "adios.pyx":1983
* self.is_noxml = is_noxml
* self.mode = mode
* self.comm = comm # <<<<<<<<<<<<<<
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*/
__pyx_v_self->comm = __pyx_v_comm;
- /* "adios.pyx":1972
+ /* "adios.pyx":1984
* self.mode = mode
* self.comm = comm
* self.vars = dict() # <<<<<<<<<<<<<<
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* self.timeaggregation_buffersize = 0
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1972, __pyx_L1_error)
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1984, __pyx_L1_error)
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__Pyx_GIVEREF(__pyx_t_1);
__Pyx_GOTREF(__pyx_v_self->vars);
@@ -31012,14 +32314,14 @@ static int __pyx_pf_5adios_6writer___init__(struct __pyx_obj_5adios_writer *__py
__pyx_v_self->vars = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "adios.pyx":1973
+ /* "adios.pyx":1985
* self.comm = comm
* self.vars = dict()
* self.attrs = dict() # <<<<<<<<<<<<<<
* self.timeaggregation_buffersize = 0
- *
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*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1973, __pyx_L1_error)
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__Pyx_GIVEREF(__pyx_t_1);
__Pyx_GOTREF(__pyx_v_self->attrs);
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__pyx_v_self->attrs = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "adios.pyx":1974
+ /* "adios.pyx":1986
* self.vars = dict()
* self.attrs = dict()
* self.timeaggregation_buffersize = 0 # <<<<<<<<<<<<<<
+ * self.stats = stats
*
- * init_noxml(comm)
*/
__pyx_v_self->timeaggregation_buffersize = 0;
- /* "adios.pyx":1976
+ /* "adios.pyx":1987
+ * self.attrs = dict()
* self.timeaggregation_buffersize = 0
+ * self.stats = stats # <<<<<<<<<<<<<<
+ *
+ * init_noxml(comm)
+ */
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+
+ /* "adios.pyx":1989
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*
* init_noxml(comm) # <<<<<<<<<<<<<<
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__pyx_t_2.comm = __pyx_v_comm;
__pyx_f_5adios_init_noxml(0, &__pyx_t_2);
- /* "adios.pyx":1961
+ /* "adios.pyx":1970
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* def __init__(self, str fname, # <<<<<<<<<<<<<<
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return __pyx_r;
}
-/* "adios.pyx":1983
+/* "adios.pyx":1996
* ## print "attr_factory:", name, value
*
* def declare_group(self, str gname = None, # <<<<<<<<<<<<<<
* str method = "POSIX1",
- * str method_params = ""):
+ * str method_params = "",
*/
/* Python wrapper */
static PyObject *__pyx_pw_5adios_6writer_3declare_group(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
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+static char __pyx_doc_5adios_6writer_2declare_group[] = "writer.declare_group(self, str gname=None, str method='POSIX1', str method_params='', int stats=adios_stat_default)\n\n Define a group associated with the file.\n\n Args:\n gname (str): group name.\n method (str, optional): Adios write method (default: 'POSIX1')\n method_params (str, optional): parameters for the write method (default: '')\n stats (int, optional): statistics [...]
static PyObject *__pyx_pw_5adios_6writer_3declare_group(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_gname = 0;
PyObject *__pyx_v_method = 0;
PyObject *__pyx_v_method_params = 0;
+ int __pyx_v_stats;
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("declare_group (wrapper)", 0);
{
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- PyObject* values[3] = {0,0,0};
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_gname,&__pyx_n_s_method,&__pyx_n_s_method_params,&__pyx_n_s_stats,0};
+ PyObject* values[4] = {0,0,0,0};
values[0] = ((PyObject*)Py_None);
values[1] = ((PyObject*)__pyx_n_s_POSIX1);
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@@ -31095,6 +32407,7 @@ static PyObject *__pyx_pw_5adios_6writer_3declare_group(PyObject *__pyx_v_self,
Py_ssize_t kw_args;
const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
switch (pos_args) {
+ case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
@@ -31118,12 +32431,18 @@ static PyObject *__pyx_pw_5adios_6writer_3declare_group(PyObject *__pyx_v_self,
PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_method_params);
if (value) { values[2] = value; kw_args--; }
}
+ case 3:
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+ PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_stats);
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+ }
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if (unlikely(kw_args > 0)) {
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}
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switch (PyTuple_GET_SIZE(__pyx_args)) {
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case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
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__pyx_v_gname = ((PyObject*)values[0]);
__pyx_v_method = ((PyObject*)values[1]);
__pyx_v_method_params = ((PyObject*)values[2]);
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goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("declare_group", 0, 0, 3, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 1983, __pyx_L3_error)
+ __Pyx_RaiseArgtupleInvalid("declare_group", 0, 0, 4, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 1996, __pyx_L3_error)
__pyx_L3_error:;
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__Pyx_RefNannyFinishContext();
return NULL;
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+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_gname), (&PyString_Type), 1, "gname", 1))) __PYX_ERR(0, 1996, __pyx_L1_error)
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_method), (&PyString_Type), 1, "method", 1))) __PYX_ERR(0, 1997, __pyx_L1_error)
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_method_params), (&PyString_Type), 1, "method_params", 1))) __PYX_ERR(0, 1998, __pyx_L1_error)
+ __pyx_r = __pyx_pf_5adios_6writer_2declare_group(((struct __pyx_obj_5adios_writer *)__pyx_v_self), __pyx_v_gname, __pyx_v_method, __pyx_v_method_params, __pyx_v_stats);
/* function exit code */
goto __pyx_L0;
@@ -31157,20 +32481,22 @@ static PyObject *__pyx_pw_5adios_6writer_3declare_group(PyObject *__pyx_v_self,
return __pyx_r;
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+static PyObject *__pyx_pf_5adios_6writer_2declare_group(struct __pyx_obj_5adios_writer *__pyx_v_self, PyObject *__pyx_v_gname, PyObject *__pyx_v_method, PyObject *__pyx_v_method_params, int __pyx_v_stats) {
+ long __pyx_v_rank;
+ PyObject *__pyx_v_ftmp = NULL;
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__Pyx_RefNannyDeclarations
int __pyx_t_1;
int __pyx_t_2;
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- PyObject *__pyx_t_6 = NULL;
- struct __pyx_opt_args_5adios_select_method __pyx_t_7;
- PyObject *__pyx_t_8 = NULL;
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{&__pyx_kp_s_Requested_is_larger_than_the_sha, __pyx_k_Requested_is_larger_than_the_sha, sizeof(__pyx_k_Requested_is_larger_than_the_sha), 0, 0, 1, 0},
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{&__pyx_n_s_S, __pyx_k_S, sizeof(__pyx_k_S), 0, 0, 1, 1},
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{&__pyx_kp_s_Scalar_dimension_mismatch_scalar, __pyx_k_Scalar_dimension_mismatch_scalar, sizeof(__pyx_k_Scalar_dimension_mismatch_scalar), 0, 0, 1, 0},
{&__pyx_n_s_SimpleSelection, __pyx_k_SimpleSelection, sizeof(__pyx_k_SimpleSelection), 0, 0, 1, 1},
{&__pyx_kp_s_Step_index_is_out_of_range_from, __pyx_k_Step_index_is_out_of_range_from, sizeof(__pyx_k_Step_index_is_out_of_range_from), 0, 0, 1, 0},
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{&__pyx_kp_s_WARN_Invalid_read_method_name, __pyx_k_WARN_Invalid_read_method_name, sizeof(__pyx_k_WARN_Invalid_read_method_name), 0, 0, 1, 0},
{&__pyx_kp_s_Warning_No_support_yet_s_type_d, __pyx_k_Warning_No_support_yet_s_type_d, sizeof(__pyx_k_Warning_No_support_yet_s_type_d), 0, 0, 1, 0},
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{&__pyx_n_s_numpy, __pyx_k_numpy, sizeof(__pyx_k_numpy), 0, 0, 1, 1},
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*/
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__Pyx_GIVEREF(__pyx_tuple__31);
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*/
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__Pyx_GIVEREF(__pyx_slice__32);
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+ /* "adios.pyx":1583
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*/
- __pyx_tuple__33 = PyTuple_Pack(1, __pyx_kp_s_AdiosVariable); if (unlikely(!__pyx_tuple__33)) __PYX_ERR(0, 1575, __pyx_L1_error)
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__Pyx_GOTREF(__pyx_tuple__33);
__Pyx_GIVEREF(__pyx_tuple__33);
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__Pyx_GOTREF(__pyx_tuple__34);
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* if key_.startswith('/'): # <<<<<<<<<<<<<<
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*
*/
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__Pyx_GOTREF(__pyx_tuple__35);
__Pyx_GIVEREF(__pyx_tuple__35);
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* if key_.startswith('/'):
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*/
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__Pyx_GOTREF(__pyx_slice__36);
__Pyx_GIVEREF(__pyx_slice__36);
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__Pyx_GIVEREF(__pyx_slice__37);
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__Pyx_GOTREF(__pyx_slice__40);
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*/
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*/
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__Pyx_GIVEREF(__pyx_tuple__50);
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*/
- __pyx_tuple__51 = PyTuple_Pack(1, __pyx_kp_s_); if (unlikely(!__pyx_tuple__51)) __PYX_ERR(0, 1879, __pyx_L1_error)
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__Pyx_GOTREF(__pyx_tuple__51);
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__Pyx_GOTREF(__pyx_slice__52);
__Pyx_GIVEREF(__pyx_slice__52);
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* for k in self.attrs.keys():
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*/
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__Pyx_GOTREF(__pyx_tuple__53);
__Pyx_GIVEREF(__pyx_tuple__53);
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@@ -42074,7 +44271,7 @@ PyMODINIT_FUNC PyInit_adios(void)
*/
__pyx_k__11 = adios_stat_default;
- /* "adios.pyx":542
+ /* "adios.pyx":550
* buffer_size)
*
* cpdef int64_t declare_group(str name, # <<<<<<<<<<<<<<
@@ -42083,7 +44280,7 @@ PyMODINIT_FUNC PyInit_adios(void)
*/
__pyx_k__11 = adios_stat_default;
- /* "adios.pyx":876
+ /* "adios.pyx":884
* """ Call adios_read_init_method """
* cpdef int read_init(str method_name = "BP",
* MPI_Comm comm = MPI_COMM_WORLD, # <<<<<<<<<<<<<<
@@ -42092,7 +44289,7 @@ PyMODINIT_FUNC PyInit_adios(void)
*/
__pyx_k__12 = MPI_COMM_WORLD;
- /* "adios.pyx":875
+ /* "adios.pyx":883
*
* """ Call adios_read_init_method """
* cpdef int read_init(str method_name = "BP", # <<<<<<<<<<<<<<
@@ -42101,7 +44298,7 @@ PyMODINIT_FUNC PyInit_adios(void)
*/
__pyx_k__12 = MPI_COMM_WORLD;
- /* "adios.pyx":997
+ /* "adios.pyx":1005
* def __init__(self, str fname,
* str method_name = "BP",
* MPI_Comm comm = MPI_COMM_WORLD, # <<<<<<<<<<<<<<
@@ -42110,7 +44307,7 @@ PyMODINIT_FUNC PyInit_adios(void)
*/
__pyx_k__16 = MPI_COMM_WORLD;
- /* "adios.pyx":999
+ /* "adios.pyx":1007
* MPI_Comm comm = MPI_COMM_WORLD,
* is_stream = False,
* ADIOS_LOCKMODE lock_mode = ADIOS_LOCKMODE_ALL, # <<<<<<<<<<<<<<
@@ -42119,169 +44316,187 @@ PyMODINIT_FUNC PyInit_adios(void)
*/
__pyx_k__17 = ADIOS_LOCKMODE_ALL;
- /* "adios.pyx":1964
+ /* "adios.pyx":1973
* bint is_noxml = True,
* str mode = "w",
- * MPI_Comm comm = MPI_COMM_WORLD): # <<<<<<<<<<<<<<
- * self.gid = 0
- * self.fname = fname
+ * int stats = adios_stat_default, # <<<<<<<<<<<<<<
+ * MPI_Comm comm = MPI_COMM_WORLD,
+ * str method = "POSIX1",
*/
- __pyx_k__54 = MPI_COMM_WORLD;
+ __pyx_k__54 = adios_stat_default;
- /* "adios.pyx":2021
+ /* "adios.pyx":1974
+ * str mode = "w",
+ * int stats = adios_stat_default,
+ * MPI_Comm comm = MPI_COMM_WORLD, # <<<<<<<<<<<<<<
+ * str method = "POSIX1",
+ * str method_params = ""):
+ */
+ __pyx_k__55 = MPI_COMM_WORLD;
+
+ /* "adios.pyx":1999
+ * str method = "POSIX1",
+ * str method_params = "",
+ * int stats = adios_stat_default): # <<<<<<<<<<<<<<
+ * """
+ * Define a group associated with the file.
+ */
+ __pyx_k__56 = adios_stat_default;
+
+ /* "adios.pyx":2042
*
* def define_var(self, str varname,
* ldim = tuple(), # <<<<<<<<<<<<<<
* gdim = tuple(),
* offset = tuple(),
*/
- __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)(&PyTuple_Type)), __pyx_empty_tuple, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2021, __pyx_L1_error)
+ __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)(&PyTuple_Type)), __pyx_empty_tuple, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2042, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_2);
- __pyx_k__55 = __pyx_t_2;
+ __pyx_k__57 = __pyx_t_2;
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- /* "adios.pyx":2022
+ /* "adios.pyx":2043
* def define_var(self, str varname,
* ldim = tuple(),
* gdim = tuple(), # <<<<<<<<<<<<<<
* offset = tuple(),
* transform = None):
*/
- __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)(&PyTuple_Type)), __pyx_empty_tuple, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2022, __pyx_L1_error)
+ __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)(&PyTuple_Type)), __pyx_empty_tuple, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2043, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_2);
- __pyx_k__56 = __pyx_t_2;
+ __pyx_k__58 = __pyx_t_2;
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- /* "adios.pyx":2023
+ /* "adios.pyx":2044
* ldim = tuple(),
* gdim = tuple(),
* offset = tuple(), # <<<<<<<<<<<<<<
* transform = None):
* """
*/
- __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)(&PyTuple_Type)), __pyx_empty_tuple, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2023, __pyx_L1_error)
+ __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)(&PyTuple_Type)), __pyx_empty_tuple, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2044, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_2);
- __pyx_k__57 = __pyx_t_2;
+ __pyx_k__59 = __pyx_t_2;
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- /* "adios.pyx":2219
+ /* "adios.pyx":2240
*
* def __init__(self, str name,
* ldim = tuple(), # <<<<<<<<<<<<<<
* gdim = tuple(),
* offset = tuple(),
*/
- __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)(&PyTuple_Type)), __pyx_empty_tuple, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2219, __pyx_L1_error)
+ __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)(&PyTuple_Type)), __pyx_empty_tuple, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2240, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_2);
- __pyx_k__59 = __pyx_t_2;
+ __pyx_k__61 = __pyx_t_2;
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- /* "adios.pyx":2220
+ /* "adios.pyx":2241
* def __init__(self, str name,
* ldim = tuple(),
* gdim = tuple(), # <<<<<<<<<<<<<<
* offset = tuple(),
* value = None,
*/
- __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)(&PyTuple_Type)), __pyx_empty_tuple, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2220, __pyx_L1_error)
+ __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)(&PyTuple_Type)), __pyx_empty_tuple, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2241, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_2);
- __pyx_k__60 = __pyx_t_2;
+ __pyx_k__62 = __pyx_t_2;
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- /* "adios.pyx":2221
+ /* "adios.pyx":2242
* ldim = tuple(),
* gdim = tuple(),
* offset = tuple(), # <<<<<<<<<<<<<<
* value = None,
* transform = None):
*/
- __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)(&PyTuple_Type)), __pyx_empty_tuple, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2221, __pyx_L1_error)
+ __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)(&PyTuple_Type)), __pyx_empty_tuple, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2242, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_2);
- __pyx_k__61 = __pyx_t_2;
+ __pyx_k__63 = __pyx_t_2;
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- /* "adios.pyx":2281
+ /* "adios.pyx":2307
*
* ## Aliases
* File = file # <<<<<<<<<<<<<<
* Var = var
* Attr = attr
*/
- if (PyDict_SetItem(__pyx_d, __pyx_n_s_File, ((PyObject *)__pyx_ptype_5adios_file)) < 0) __PYX_ERR(0, 2281, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s_File, ((PyObject *)__pyx_ptype_5adios_file)) < 0) __PYX_ERR(0, 2307, __pyx_L1_error)
- /* "adios.pyx":2282
+ /* "adios.pyx":2308
* ## Aliases
* File = file
* Var = var # <<<<<<<<<<<<<<
* Attr = attr
* Writer = writer
*/
- if (PyDict_SetItem(__pyx_d, __pyx_n_s_Var, ((PyObject *)__pyx_ptype_5adios_var)) < 0) __PYX_ERR(0, 2282, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s_Var, ((PyObject *)__pyx_ptype_5adios_var)) < 0) __PYX_ERR(0, 2308, __pyx_L1_error)
- /* "adios.pyx":2283
+ /* "adios.pyx":2309
* File = file
* Var = var
* Attr = attr # <<<<<<<<<<<<<<
* Writer = writer
* Attrinfo = attrinfo
*/
- if (PyDict_SetItem(__pyx_d, __pyx_n_s_Attr, ((PyObject *)__pyx_ptype_5adios_attr)) < 0) __PYX_ERR(0, 2283, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s_Attr, ((PyObject *)__pyx_ptype_5adios_attr)) < 0) __PYX_ERR(0, 2309, __pyx_L1_error)
- /* "adios.pyx":2284
+ /* "adios.pyx":2310
* Var = var
* Attr = attr
* Writer = writer # <<<<<<<<<<<<<<
* Attrinfo = attrinfo
* Varinfo = varinfo
*/
- if (PyDict_SetItem(__pyx_d, __pyx_n_s_Writer, ((PyObject *)__pyx_ptype_5adios_writer)) < 0) __PYX_ERR(0, 2284, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s_Writer, ((PyObject *)__pyx_ptype_5adios_writer)) < 0) __PYX_ERR(0, 2310, __pyx_L1_error)
- /* "adios.pyx":2285
+ /* "adios.pyx":2311
* Attr = attr
* Writer = writer
* Attrinfo = attrinfo # <<<<<<<<<<<<<<
* Varinfo = varinfo
*
*/
- if (PyDict_SetItem(__pyx_d, __pyx_n_s_Attrinfo, ((PyObject *)__pyx_ptype_5adios_attrinfo)) < 0) __PYX_ERR(0, 2285, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s_Attrinfo, ((PyObject *)__pyx_ptype_5adios_attrinfo)) < 0) __PYX_ERR(0, 2311, __pyx_L1_error)
- /* "adios.pyx":2286
+ /* "adios.pyx":2312
* Writer = writer
* Attrinfo = attrinfo
* Varinfo = varinfo # <<<<<<<<<<<<<<
*
* ## ====================
*/
- if (PyDict_SetItem(__pyx_d, __pyx_n_s_Varinfo, ((PyObject *)__pyx_ptype_5adios_varinfo)) < 0) __PYX_ERR(0, 2286, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s_Varinfo, ((PyObject *)__pyx_ptype_5adios_varinfo)) < 0) __PYX_ERR(0, 2312, __pyx_L1_error)
- /* "adios.pyx":2292
+ /* "adios.pyx":2318
* ## ====================
*
* def readvar(fname, varname): # <<<<<<<<<<<<<<
* """ Retrieve a variable value from an Adios file.
*
*/
- __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_5adios_93readvar, NULL, __pyx_n_s_adios); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2292, __pyx_L1_error)
+ __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_5adios_93readvar, NULL, __pyx_n_s_adios); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2318, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_2);
- if (PyDict_SetItem(__pyx_d, __pyx_n_s_readvar_2, __pyx_t_2) < 0) __PYX_ERR(0, 2292, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s_readvar_2, __pyx_t_2) < 0) __PYX_ERR(0, 2318, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "adios.pyx":2306
+ /* "adios.pyx":2332
* return v.read(from_steps=0, nsteps=v.nsteps)
*
* def bpls(fname): # <<<<<<<<<<<<<<
* """ Return meta data of an Adios file as a Python dictionary object.
*
*/
- __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_5adios_95bpls, NULL, __pyx_n_s_adios); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2306, __pyx_L1_error)
+ __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_5adios_95bpls, NULL, __pyx_n_s_adios); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2332, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_2);
- if (PyDict_SetItem(__pyx_d, __pyx_n_s_bpls, __pyx_t_2) < 0) __PYX_ERR(0, 2306, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s_bpls, __pyx_t_2) < 0) __PYX_ERR(0, 2332, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
/* "adios.pyx":1
@@ -42291,18 +44506,18 @@ PyMODINIT_FUNC PyInit_adios(void)
*/
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- if (PyDict_SetItem(__pyx_t_2, __pyx_kp_u_var_read_line_1457, __pyx_kp_u_Perform_read_Read_data_from_an) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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+ if (PyDict_SetItem(__pyx_t_2, __pyx_kp_u_var_read_line_1465, __pyx_kp_u_Perform_read_Read_data_from_an) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_t_2, __pyx_kp_u_writer_declare_group_line_1996, __pyx_kp_u_Define_a_group_associated_with) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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- * arr.base = baseptr
+ /* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":997
+ * raise ImportError("numpy.core.umath failed to import")
*
- * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<<
- * if arr.base is NULL:
- * return None
+ * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<<
+ * try:
+ * _import_umath()
*/
/*--- Wrapped vars code ---*/
@@ -42360,6 +44575,144 @@ static PyObject *__Pyx_GetBuiltinName(PyObject *name) {
return result;
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+ assert(nargs >= 0);
+ assert(nargs == 0 || args != NULL);
+ /* _PyCFunction_FastCallDict() must not be called with an exception set,
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+ caller loses its exception */
+ assert(!PyErr_Occurred());
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+ PyFrameObject *f;
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject **fastlocals;
+ Py_ssize_t i;
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+ PyObject *result;
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+ goto done;
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+ kwtuple = PyTuple_New(2 * nk);
+ if (kwtuple == NULL) {
+ result = NULL;
+ goto done;
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+ pos = i = 0;
+ while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) {
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+ d = &PyTuple_GET_ITEM(argdefs, 0);
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+ result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL,
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/* PyObjectCall */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) {
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return result;
}
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
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+ if (PyFunction_Check(func)) {
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+ }
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#ifdef __Pyx_CyFunction_USED
if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) {
#else
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#endif
if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) {
return __Pyx_PyObject_CallMethO(func, arg);
+#if CYTHON_FAST_PYCCALL
+ } else if (PyCFunction_GET_FLAGS(func) & METH_FASTCALL) {
+ return __Pyx_PyCFunction_FastCall(func, &arg, 1);
+#endif
}
}
return __Pyx__PyObject_CallOneArg(func, arg);
@@ -42438,6 +44800,11 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObjec
/* PyObjectCallNoArg */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) {
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+#endif
#ifdef __Pyx_CyFunction_USED
if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) {
#else
@@ -42452,7 +44819,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) {
#endif
/* PyErrFetchRestore */
- #if CYTHON_COMPILING_IN_CPYTHON
+ #if CYTHON_FAST_THREAD_STATE
static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) {
PyObject *tmp_type, *tmp_value, *tmp_tb;
tmp_type = tstate->curexc_type;
@@ -42576,7 +44943,7 @@ static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, in
Py_ssize_t cstart, Py_ssize_t cstop,
PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice,
int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) {
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_USE_TYPE_SLOTS
PyMappingMethods* mp;
#if PY_MAJOR_VERSION < 3
PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence;
@@ -42652,7 +45019,7 @@ static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, in
Py_XDECREF(owned_stop);
if (unlikely(!py_slice)) goto bad;
}
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_USE_TYPE_SLOTS
result = mp->mp_subscript(obj, py_slice);
#else
result = PyObject_GetItem(obj, py_slice);
@@ -42679,7 +45046,7 @@ bad:
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
CYTHON_NCP_UNUSED int wraparound,
CYTHON_NCP_UNUSED int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o);
if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
PyObject *r = PyList_GET_ITEM(o, i);
@@ -42694,7 +45061,7 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
CYTHON_NCP_UNUSED int wraparound,
CYTHON_NCP_UNUSED int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o);
if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
PyObject *r = PyTuple_GET_ITEM(o, i);
@@ -42709,7 +45076,7 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list,
CYTHON_NCP_UNUSED int wraparound,
CYTHON_NCP_UNUSED int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS
if (is_list || PyList_CheckExact(o)) {
Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) {
@@ -42750,7 +45117,7 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
}
/* PyIntBinop */
- #if CYTHON_COMPILING_IN_CPYTHON
+ #if !CYTHON_COMPILING_IN_PYPY
static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) {
#if PY_MAJOR_VERSION < 3
if (likely(PyInt_CheckExact(op1))) {
@@ -42763,12 +45130,14 @@ static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED
return PyLong_Type.tp_as_number->nb_add(op1, op2);
}
#endif
- #if CYTHON_USE_PYLONG_INTERNALS && PY_MAJOR_VERSION >= 3
+ #if CYTHON_USE_PYLONG_INTERNALS
if (likely(PyLong_CheckExact(op1))) {
const long b = intval;
long a, x;
+#ifdef HAVE_LONG_LONG
const PY_LONG_LONG llb = intval;
PY_LONG_LONG lla, llx;
+#endif
const digit* digits = ((PyLongObject*)op1)->ob_digit;
const Py_ssize_t size = Py_SIZE(op1);
if (likely(__Pyx_sst_abs(size) <= 1)) {
@@ -42780,58 +45149,74 @@ static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED
if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case 2:
if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case -3:
if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case 3:
if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case -4:
if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case 4:
if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
default: return PyLong_Type.tp_as_number->nb_add(op1, op2);
}
}
x = a + b;
return PyLong_FromLong(x);
+#ifdef HAVE_LONG_LONG
long_long:
llx = lla + llb;
return PyLong_FromLongLong(llx);
+#endif
+
+
}
#endif
if (PyFloat_CheckExact(op1)) {
@@ -42848,7 +45233,7 @@ static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED
#endif
/* PyIntBinop */
- #if CYTHON_COMPILING_IN_CPYTHON
+ #if !CYTHON_COMPILING_IN_PYPY
static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) {
#if PY_MAJOR_VERSION < 3
if (likely(PyInt_CheckExact(op1))) {
@@ -42861,12 +45246,14 @@ static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, CYTHON_U
return PyLong_Type.tp_as_number->nb_subtract(op1, op2);
}
#endif
- #if CYTHON_USE_PYLONG_INTERNALS && PY_MAJOR_VERSION >= 3
+ #if CYTHON_USE_PYLONG_INTERNALS
if (likely(PyLong_CheckExact(op1))) {
const long b = intval;
long a, x;
+#ifdef HAVE_LONG_LONG
const PY_LONG_LONG llb = intval;
PY_LONG_LONG lla, llx;
+#endif
const digit* digits = ((PyLongObject*)op1)->ob_digit;
const Py_ssize_t size = Py_SIZE(op1);
if (likely(__Pyx_sst_abs(size) <= 1)) {
@@ -42878,58 +45265,74 @@ static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, CYTHON_U
if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case 2:
if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case -3:
if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case 3:
if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case -4:
if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case 4:
if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
default: return PyLong_Type.tp_as_number->nb_subtract(op1, op2);
}
}
x = a - b;
return PyLong_FromLong(x);
+#ifdef HAVE_LONG_LONG
long_long:
llx = lla - llb;
return PyLong_FromLongLong(llx);
+#endif
+
+
}
#endif
if (PyFloat_CheckExact(op1)) {
@@ -43103,7 +45506,7 @@ bad:
/* GetModuleGlobalName */
static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) {
PyObject *result;
-#if CYTHON_COMPILING_IN_CPYTHON
+#if !CYTHON_AVOID_BORROWED_REFS
result = PyDict_GetItem(__pyx_d, name);
if (likely(result)) {
Py_INCREF(result);
@@ -43241,7 +45644,7 @@ return_ne:
}
/* PyIntBinop */
- #if CYTHON_COMPILING_IN_CPYTHON
+ #if !CYTHON_COMPILING_IN_PYPY
static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) {
if (op1 == op2) {
Py_RETURN_TRUE;
@@ -43257,7 +45660,7 @@ static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED
}
}
#endif
- #if CYTHON_USE_PYLONG_INTERNALS && PY_MAJOR_VERSION >= 3
+ #if CYTHON_USE_PYLONG_INTERNALS
if (likely(PyLong_CheckExact(op1))) {
const long b = intval;
long a;
@@ -43502,7 +45905,7 @@ bad:
{
PyMethodDescrObject *descr = (PyMethodDescrObject*) method;
target->func = descr->d_method->ml_meth;
- target->flag = descr->d_method->ml_flags & (METH_VARARGS | METH_KEYWORDS | METH_O | METH_NOARGS);
+ target->flag = descr->d_method->ml_flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST);
}
#endif
return 0;
@@ -43512,7 +45915,7 @@ bad:
static PyObject* __Pyx__CallUnboundCMethod0(__Pyx_CachedCFunction* cfunc, PyObject* self) {
PyObject *args, *result = NULL;
if (unlikely(!cfunc->method) && unlikely(__Pyx_TryUnpackUnboundCMethod(cfunc) < 0)) return NULL;
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_ASSUME_SAFE_MACROS
args = PyTuple_New(1);
if (unlikely(!args)) goto bad;
Py_INCREF(self);
@@ -43621,7 +46024,7 @@ static int __Pyx_PyBytes_Tailmatch(PyObject* self, PyObject* substr,
Py_ssize_t i, count = PyTuple_GET_SIZE(substr);
for (i = 0; i < count; i++) {
int result;
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
result = __Pyx_PyBytes_SingleTailmatch(self, PyTuple_GET_ITEM(substr, i),
start, end, direction);
#else
@@ -43646,7 +46049,7 @@ static int __Pyx_PyBytes_Tailmatch(PyObject* self, PyObject* substr,
Py_ssize_t i, count = PyTuple_GET_SIZE(substr);
for (i = 0; i < count; i++) {
Py_ssize_t result;
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
result = PyUnicode_Tailmatch(s, PyTuple_GET_ITEM(substr, i),
start, end, direction);
#else
@@ -43689,7 +46092,7 @@ static int __Pyx_PyBytes_Tailmatch(PyObject* self, PyObject* substr,
/* IterFinish */
static CYTHON_INLINE int __Pyx_IterFinish(void) {
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_FAST_THREAD_STATE
PyThreadState *tstate = PyThreadState_GET();
PyObject* exc_type = tstate->curexc_type;
if (unlikely(exc_type)) {
@@ -43739,7 +46142,7 @@ static int __Pyx_PyBytes_Tailmatch(PyObject* self, PyObject* substr,
Py_ssize_t cstart, Py_ssize_t cstop,
PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice,
int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) {
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_USE_TYPE_SLOTS
PyMappingMethods* mp;
#if PY_MAJOR_VERSION < 3
PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence;
@@ -43815,7 +46218,7 @@ static int __Pyx_PyBytes_Tailmatch(PyObject* self, PyObject* substr,
Py_XDECREF(owned_stop);
if (unlikely(!py_slice)) goto bad;
}
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_USE_TYPE_SLOTS
result = mp->mp_ass_subscript(obj, py_slice, value);
#else
result = value ? PyObject_SetItem(obj, py_slice, value) : PyObject_DelItem(obj, py_slice);
@@ -43845,7 +46248,7 @@ bad:
PyObject *method, *result = NULL;
method = __Pyx_PyObject_GetAttrStr(obj, method_name);
if (unlikely(!method)) goto bad;
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_UNPACK_METHODS
if (likely(PyMethod_Check(method))) {
PyObject *self = PyMethod_GET_SELF(method);
if (likely(self)) {
@@ -44029,8 +46432,103 @@ static CYTHON_INLINE int __Pyx_dict_iter_next(
return PyDict_Values(d);
}
+/* SaveResetException */
+ #if CYTHON_FAST_THREAD_STATE
+static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) {
+ *type = tstate->exc_type;
+ *value = tstate->exc_value;
+ *tb = tstate->exc_traceback;
+ Py_XINCREF(*type);
+ Py_XINCREF(*value);
+ Py_XINCREF(*tb);
+}
+static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) {
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ tmp_type = tstate->exc_type;
+ tmp_value = tstate->exc_value;
+ tmp_tb = tstate->exc_traceback;
+ tstate->exc_type = type;
+ tstate->exc_value = value;
+ tstate->exc_traceback = tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+}
+#endif
+
+/* PyErrExceptionMatches */
+ #if CYTHON_FAST_THREAD_STATE
+static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err) {
+ PyObject *exc_type = tstate->curexc_type;
+ if (exc_type == err) return 1;
+ if (unlikely(!exc_type)) return 0;
+ return PyErr_GivenExceptionMatches(exc_type, err);
+}
+#endif
+
+/* GetException */
+ #if CYTHON_FAST_THREAD_STATE
+static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) {
+#else
+static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
+#endif
+ PyObject *local_type, *local_value, *local_tb;
+#if CYTHON_FAST_THREAD_STATE
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ local_type = tstate->curexc_type;
+ local_value = tstate->curexc_value;
+ local_tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+#else
+ PyErr_Fetch(&local_type, &local_value, &local_tb);
+#endif
+ PyErr_NormalizeException(&local_type, &local_value, &local_tb);
+#if CYTHON_FAST_THREAD_STATE
+ if (unlikely(tstate->curexc_type))
+#else
+ if (unlikely(PyErr_Occurred()))
+#endif
+ goto bad;
+ #if PY_MAJOR_VERSION >= 3
+ if (local_tb) {
+ if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
+ goto bad;
+ }
+ #endif
+ Py_XINCREF(local_tb);
+ Py_XINCREF(local_type);
+ Py_XINCREF(local_value);
+ *type = local_type;
+ *value = local_value;
+ *tb = local_tb;
+#if CYTHON_FAST_THREAD_STATE
+ tmp_type = tstate->exc_type;
+ tmp_value = tstate->exc_value;
+ tmp_tb = tstate->exc_traceback;
+ tstate->exc_type = local_type;
+ tstate->exc_value = local_value;
+ tstate->exc_traceback = local_tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(local_type, local_value, local_tb);
+#endif
+ return 0;
+bad:
+ *type = 0;
+ *value = 0;
+ *tb = 0;
+ Py_XDECREF(local_type);
+ Py_XDECREF(local_value);
+ Py_XDECREF(local_tb);
+ return -1;
+}
+
/* SetVTable */
- static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
+ static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
#if PY_VERSION_HEX >= 0x02070000
PyObject *ob = PyCapsule_New(vtable, 0, 0);
#else
@@ -44048,7 +46546,7 @@ bad:
}
/* Import */
- static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
+ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
PyObject *empty_list = 0;
PyObject *module = 0;
PyObject *global_dict = 0;
@@ -44122,7 +46620,7 @@ bad:
}
/* ImportFrom */
- static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) {
+ static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) {
PyObject* value = __Pyx_PyObject_GetAttrStr(module, name);
if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) {
PyErr_Format(PyExc_ImportError,
@@ -44136,7 +46634,7 @@ bad:
}
/* CalculateMetaclass */
- static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases) {
+ static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases) {
Py_ssize_t i, nbases = PyTuple_GET_SIZE(bases);
for (i=0; i < nbases; i++) {
PyTypeObject *tmptype;
@@ -44175,7 +46673,7 @@ bad:
}
/* Py3ClassCreate */
- static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name,
+ static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name,
PyObject *qualname, PyObject *mkw, PyObject *modname, PyObject *doc) {
PyObject *ns;
if (metaclass) {
@@ -44242,7 +46740,7 @@ static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObj
}
/* CodeObjectCache */
- static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
+ static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
int start = 0, mid = 0, end = count - 1;
if (end >= 0 && code_line > entries[end].code_line) {
return count;
@@ -44322,7 +46820,7 @@ static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
}
/* AddTraceback */
- #include "compile.h"
+ #include "compile.h"
#include "frameobject.h"
#include "traceback.h"
static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
@@ -44395,15 +46893,46 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line,
0 /*PyObject *locals*/
);
if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
+ __Pyx_PyFrame_SetLineNumber(py_frame, py_line);
PyTraceBack_Here(py_frame);
bad:
Py_XDECREF(py_code);
Py_XDECREF(py_frame);
}
+/* CIntToPy */
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ADIOS_STATISTICS_FLAG(ADIOS_STATISTICS_FLAG value) {
+ const ADIOS_STATISTICS_FLAG neg_one = (ADIOS_STATISTICS_FLAG) -1, const_zero = (ADIOS_STATISTICS_FLAG) 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (is_unsigned) {
+ if (sizeof(ADIOS_STATISTICS_FLAG) < sizeof(long)) {
+ return PyInt_FromLong((long) value);
+ } else if (sizeof(ADIOS_STATISTICS_FLAG) <= sizeof(unsigned long)) {
+ return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
+ } else if (sizeof(ADIOS_STATISTICS_FLAG) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
+ }
+ } else {
+ if (sizeof(ADIOS_STATISTICS_FLAG) <= sizeof(long)) {
+ return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
+ } else if (sizeof(ADIOS_STATISTICS_FLAG) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
+ }
+ }
+ {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&value;
+ return _PyLong_FromByteArray(bytes, sizeof(ADIOS_STATISTICS_FLAG),
+ little, !is_unsigned);
+ }
+}
+
/* CIntFromPyVerify */
- #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\
+ #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\
__PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0)
#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\
__PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1)
@@ -44425,7 +46954,7 @@ bad:
}
/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
const int neg_one = (int) -1, const_zero = (int) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
@@ -44433,14 +46962,18 @@ bad:
return PyInt_FromLong((long) value);
} else if (sizeof(int) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) {
return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
}
} else {
if (sizeof(int) <= sizeof(long)) {
return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(int) <= sizeof(PY_LONG_LONG)) {
return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
}
}
{
@@ -44452,7 +46985,7 @@ bad:
}
/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int64_t(int64_t value) {
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int64_t(int64_t value) {
const int64_t neg_one = (int64_t) -1, const_zero = (int64_t) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
@@ -44460,14 +46993,18 @@ bad:
return PyInt_FromLong((long) value);
} else if (sizeof(int64_t) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(int64_t) <= sizeof(unsigned PY_LONG_LONG)) {
return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
}
} else {
if (sizeof(int64_t) <= sizeof(long)) {
return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(int64_t) <= sizeof(PY_LONG_LONG)) {
return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
}
}
{
@@ -44479,7 +47016,7 @@ bad:
}
/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint64_t(uint64_t value) {
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint64_t(uint64_t value) {
const uint64_t neg_one = (uint64_t) -1, const_zero = (uint64_t) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
@@ -44487,14 +47024,18 @@ bad:
return PyInt_FromLong((long) value);
} else if (sizeof(uint64_t) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(uint64_t) <= sizeof(unsigned PY_LONG_LONG)) {
return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
}
} else {
if (sizeof(uint64_t) <= sizeof(long)) {
return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(uint64_t) <= sizeof(PY_LONG_LONG)) {
return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
}
}
{
@@ -44506,7 +47047,7 @@ bad:
}
/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ADIOS_READ_METHOD(ADIOS_READ_METHOD value) {
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ADIOS_READ_METHOD(ADIOS_READ_METHOD value) {
const ADIOS_READ_METHOD neg_one = (ADIOS_READ_METHOD) -1, const_zero = (ADIOS_READ_METHOD) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
@@ -44514,14 +47055,18 @@ bad:
return PyInt_FromLong((long) value);
} else if (sizeof(ADIOS_READ_METHOD) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_READ_METHOD) <= sizeof(unsigned PY_LONG_LONG)) {
return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
}
} else {
if (sizeof(ADIOS_READ_METHOD) <= sizeof(long)) {
return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_READ_METHOD) <= sizeof(PY_LONG_LONG)) {
return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
}
}
{
@@ -44533,7 +47078,7 @@ bad:
}
/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
const long neg_one = (long) -1, const_zero = (long) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
@@ -44541,14 +47086,18 @@ bad:
return PyInt_FromLong((long) value);
} else if (sizeof(long) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) {
return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
}
} else {
if (sizeof(long) <= sizeof(long)) {
return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
}
}
{
@@ -44560,7 +47109,7 @@ bad:
}
/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_long(unsigned long value) {
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_long(unsigned long value) {
const unsigned long neg_one = (unsigned long) -1, const_zero = (unsigned long) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
@@ -44568,14 +47117,18 @@ bad:
return PyInt_FromLong((long) value);
} else if (sizeof(unsigned long) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(unsigned long) <= sizeof(unsigned PY_LONG_LONG)) {
return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
}
} else {
if (sizeof(unsigned long) <= sizeof(long)) {
return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(unsigned long) <= sizeof(PY_LONG_LONG)) {
return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
}
}
{
@@ -44587,7 +47140,7 @@ bad:
}
/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint32_t(uint32_t value) {
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint32_t(uint32_t value) {
const uint32_t neg_one = (uint32_t) -1, const_zero = (uint32_t) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
@@ -44595,14 +47148,18 @@ bad:
return PyInt_FromLong((long) value);
} else if (sizeof(uint32_t) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(uint32_t) <= sizeof(unsigned PY_LONG_LONG)) {
return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
}
} else {
if (sizeof(uint32_t) <= sizeof(long)) {
return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(uint32_t) <= sizeof(PY_LONG_LONG)) {
return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
}
}
{
@@ -44614,7 +47171,7 @@ bad:
}
/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ADIOS_DATATYPES(ADIOS_DATATYPES value) {
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ADIOS_DATATYPES(ADIOS_DATATYPES value) {
const ADIOS_DATATYPES neg_one = (ADIOS_DATATYPES) -1, const_zero = (ADIOS_DATATYPES) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
@@ -44622,14 +47179,18 @@ bad:
return PyInt_FromLong((long) value);
} else if (sizeof(ADIOS_DATATYPES) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_DATATYPES) <= sizeof(unsigned PY_LONG_LONG)) {
return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
}
} else {
if (sizeof(ADIOS_DATATYPES) <= sizeof(long)) {
return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_DATATYPES) <= sizeof(PY_LONG_LONG)) {
return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
}
}
{
@@ -44640,8 +47201,8 @@ bad:
}
}
-/* None */
- #if CYTHON_CCOMPLEX
+/* Declarations */
+ #if CYTHON_CCOMPLEX
#ifdef __cplusplus
static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
return ::std::complex< float >(x, y);
@@ -44660,61 +47221,86 @@ bad:
}
#endif
-/* None */
- #if CYTHON_CCOMPLEX
+/* Arithmetic */
+ #if CYTHON_CCOMPLEX
#else
- static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
return (a.real == b.real) && (a.imag == b.imag);
}
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
__pyx_t_float_complex z;
z.real = a.real + b.real;
z.imag = a.imag + b.imag;
return z;
}
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
__pyx_t_float_complex z;
z.real = a.real - b.real;
z.imag = a.imag - b.imag;
return z;
}
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
__pyx_t_float_complex z;
z.real = a.real * b.real - a.imag * b.imag;
z.imag = a.real * b.imag + a.imag * b.real;
return z;
}
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- float denom = b.real * b.real + b.imag * b.imag;
- z.real = (a.real * b.real + a.imag * b.imag) / denom;
- z.imag = (a.imag * b.real - a.real * b.imag) / denom;
- return z;
+ #if 1
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ if (b.imag == 0) {
+ return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real);
+ } else if (fabsf(b.real) >= fabsf(b.imag)) {
+ if (b.real == 0 && b.imag == 0) {
+ return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag);
+ } else {
+ float r = b.imag / b.real;
+ float s = 1.0 / (b.real + b.imag * r);
+ return __pyx_t_float_complex_from_parts(
+ (a.real + a.imag * r) * s, (a.imag - a.real * r) * s);
+ }
+ } else {
+ float r = b.real / b.imag;
+ float s = 1.0 / (b.imag + b.real * r);
+ return __pyx_t_float_complex_from_parts(
+ (a.real * r + a.imag) * s, (a.imag * r - a.real) * s);
+ }
}
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) {
+ #else
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ if (b.imag == 0) {
+ return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real);
+ } else {
+ float denom = b.real * b.real + b.imag * b.imag;
+ return __pyx_t_float_complex_from_parts(
+ (a.real * b.real + a.imag * b.imag) / denom,
+ (a.imag * b.real - a.real * b.imag) / denom);
+ }
+ }
+ #endif
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) {
__pyx_t_float_complex z;
z.real = -a.real;
z.imag = -a.imag;
return z;
}
- static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) {
+ static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) {
return (a.real == 0) && (a.imag == 0);
}
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) {
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) {
__pyx_t_float_complex z;
z.real = a.real;
z.imag = -a.imag;
return z;
}
#if 1
- static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) {
+ static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) {
#if !defined(HAVE_HYPOT) || defined(_MSC_VER)
return sqrtf(z.real*z.real + z.imag*z.imag);
#else
return hypotf(z.real, z.imag);
#endif
}
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
__pyx_t_float_complex z;
float r, lnr, theta, z_r, z_theta;
if (b.imag == 0 && b.real == (int)b.real) {
@@ -44732,24 +47318,32 @@ bad:
case 1:
return a;
case 2:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(a, a);
+ z = __Pyx_c_prod_float(a, a);
+ return __Pyx_c_prod_float(a, a);
case 3:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(z, a);
+ z = __Pyx_c_prod_float(a, a);
+ return __Pyx_c_prod_float(z, a);
case 4:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(z, z);
+ z = __Pyx_c_prod_float(a, a);
+ return __Pyx_c_prod_float(z, z);
}
}
if (a.imag == 0) {
if (a.real == 0) {
return a;
+ } else if (b.imag == 0) {
+ z.real = powf(a.real, b.real);
+ z.imag = 0;
+ return z;
+ } else if (a.real > 0) {
+ r = a.real;
+ theta = 0;
+ } else {
+ r = -a.real;
+ theta = atan2f(0, -1);
}
- r = a.real;
- theta = 0;
} else {
- r = __Pyx_c_absf(a);
+ r = __Pyx_c_abs_float(a);
theta = atan2f(a.imag, a.real);
}
lnr = logf(r);
@@ -44762,8 +47356,8 @@ bad:
#endif
#endif
-/* None */
- #if CYTHON_CCOMPLEX
+/* Declarations */
+ #if CYTHON_CCOMPLEX
#ifdef __cplusplus
static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
return ::std::complex< double >(x, y);
@@ -44782,61 +47376,86 @@ bad:
}
#endif
-/* None */
- #if CYTHON_CCOMPLEX
+/* Arithmetic */
+ #if CYTHON_CCOMPLEX
#else
- static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
return (a.real == b.real) && (a.imag == b.imag);
}
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
__pyx_t_double_complex z;
z.real = a.real + b.real;
z.imag = a.imag + b.imag;
return z;
}
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
__pyx_t_double_complex z;
z.real = a.real - b.real;
z.imag = a.imag - b.imag;
return z;
}
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
__pyx_t_double_complex z;
z.real = a.real * b.real - a.imag * b.imag;
z.imag = a.real * b.imag + a.imag * b.real;
return z;
}
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- double denom = b.real * b.real + b.imag * b.imag;
- z.real = (a.real * b.real + a.imag * b.imag) / denom;
- z.imag = (a.imag * b.real - a.real * b.imag) / denom;
- return z;
+ #if 1
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ if (b.imag == 0) {
+ return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real);
+ } else if (fabs(b.real) >= fabs(b.imag)) {
+ if (b.real == 0 && b.imag == 0) {
+ return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag);
+ } else {
+ double r = b.imag / b.real;
+ double s = 1.0 / (b.real + b.imag * r);
+ return __pyx_t_double_complex_from_parts(
+ (a.real + a.imag * r) * s, (a.imag - a.real * r) * s);
+ }
+ } else {
+ double r = b.real / b.imag;
+ double s = 1.0 / (b.imag + b.real * r);
+ return __pyx_t_double_complex_from_parts(
+ (a.real * r + a.imag) * s, (a.imag * r - a.real) * s);
+ }
+ }
+ #else
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ if (b.imag == 0) {
+ return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real);
+ } else {
+ double denom = b.real * b.real + b.imag * b.imag;
+ return __pyx_t_double_complex_from_parts(
+ (a.real * b.real + a.imag * b.imag) / denom,
+ (a.imag * b.real - a.real * b.imag) / denom);
+ }
}
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) {
+ #endif
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) {
__pyx_t_double_complex z;
z.real = -a.real;
z.imag = -a.imag;
return z;
}
- static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) {
+ static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) {
return (a.real == 0) && (a.imag == 0);
}
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) {
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) {
__pyx_t_double_complex z;
z.real = a.real;
z.imag = -a.imag;
return z;
}
#if 1
- static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) {
+ static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) {
#if !defined(HAVE_HYPOT) || defined(_MSC_VER)
return sqrt(z.real*z.real + z.imag*z.imag);
#else
return hypot(z.real, z.imag);
#endif
}
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
__pyx_t_double_complex z;
double r, lnr, theta, z_r, z_theta;
if (b.imag == 0 && b.real == (int)b.real) {
@@ -44854,24 +47473,32 @@ bad:
case 1:
return a;
case 2:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(a, a);
+ z = __Pyx_c_prod_double(a, a);
+ return __Pyx_c_prod_double(a, a);
case 3:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(z, a);
+ z = __Pyx_c_prod_double(a, a);
+ return __Pyx_c_prod_double(z, a);
case 4:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(z, z);
+ z = __Pyx_c_prod_double(a, a);
+ return __Pyx_c_prod_double(z, z);
}
}
if (a.imag == 0) {
if (a.real == 0) {
return a;
+ } else if (b.imag == 0) {
+ z.real = pow(a.real, b.real);
+ z.imag = 0;
+ return z;
+ } else if (a.real > 0) {
+ r = a.real;
+ theta = 0;
+ } else {
+ r = -a.real;
+ theta = atan2(0, -1);
}
- r = a.real;
- theta = 0;
} else {
- r = __Pyx_c_abs(a);
+ r = __Pyx_c_abs_double(a);
theta = atan2(a.imag, a.real);
}
lnr = log(r);
@@ -44885,7 +47512,7 @@ bad:
#endif
/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) {
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) {
const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
@@ -44893,14 +47520,18 @@ bad:
return PyInt_FromLong((long) value);
} else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned PY_LONG_LONG)) {
return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
}
} else {
if (sizeof(enum NPY_TYPES) <= sizeof(long)) {
return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(enum NPY_TYPES) <= sizeof(PY_LONG_LONG)) {
return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
}
}
{
@@ -44912,7 +47543,7 @@ bad:
}
/* CIntFromPy */
- static CYTHON_INLINE MPI_Comm __Pyx_PyInt_As_MPI_Comm(PyObject *x) {
+ static CYTHON_INLINE MPI_Comm __Pyx_PyInt_As_MPI_Comm(PyObject *x) {
const MPI_Comm neg_one = (MPI_Comm) -1, const_zero = (MPI_Comm) 0;
const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
@@ -44979,8 +47610,10 @@ bad:
#endif
if (sizeof(MPI_Comm) <= sizeof(unsigned long)) {
__PYX_VERIFY_RETURN_INT_EXC(MPI_Comm, unsigned long, PyLong_AsUnsignedLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(MPI_Comm) <= sizeof(unsigned PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(MPI_Comm, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
+#endif
}
} else {
#if CYTHON_USE_PYLONG_INTERNALS
@@ -45047,8 +47680,10 @@ bad:
#endif
if (sizeof(MPI_Comm) <= sizeof(long)) {
__PYX_VERIFY_RETURN_INT_EXC(MPI_Comm, long, PyLong_AsLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(MPI_Comm) <= sizeof(PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(MPI_Comm, PY_LONG_LONG, PyLong_AsLongLong(x))
+#endif
}
}
{
@@ -45097,7 +47732,7 @@ raise_neg_overflow:
}
/* CIntFromPy */
- static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *x) {
+ static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *x) {
const int64_t neg_one = (int64_t) -1, const_zero = (int64_t) 0;
const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
@@ -45164,8 +47799,10 @@ raise_neg_overflow:
#endif
if (sizeof(int64_t) <= sizeof(unsigned long)) {
__PYX_VERIFY_RETURN_INT_EXC(int64_t, unsigned long, PyLong_AsUnsignedLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(int64_t) <= sizeof(unsigned PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(int64_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
+#endif
}
} else {
#if CYTHON_USE_PYLONG_INTERNALS
@@ -45232,8 +47869,10 @@ raise_neg_overflow:
#endif
if (sizeof(int64_t) <= sizeof(long)) {
__PYX_VERIFY_RETURN_INT_EXC(int64_t, long, PyLong_AsLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(int64_t) <= sizeof(PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(int64_t, PY_LONG_LONG, PyLong_AsLongLong(x))
+#endif
}
}
{
@@ -45282,7 +47921,7 @@ raise_neg_overflow:
}
/* CIntFromPy */
- static CYTHON_INLINE uint64_t __Pyx_PyInt_As_uint64_t(PyObject *x) {
+ static CYTHON_INLINE uint64_t __Pyx_PyInt_As_uint64_t(PyObject *x) {
const uint64_t neg_one = (uint64_t) -1, const_zero = (uint64_t) 0;
const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
@@ -45349,8 +47988,10 @@ raise_neg_overflow:
#endif
if (sizeof(uint64_t) <= sizeof(unsigned long)) {
__PYX_VERIFY_RETURN_INT_EXC(uint64_t, unsigned long, PyLong_AsUnsignedLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(uint64_t) <= sizeof(unsigned PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(uint64_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
+#endif
}
} else {
#if CYTHON_USE_PYLONG_INTERNALS
@@ -45417,8 +48058,10 @@ raise_neg_overflow:
#endif
if (sizeof(uint64_t) <= sizeof(long)) {
__PYX_VERIFY_RETURN_INT_EXC(uint64_t, long, PyLong_AsLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(uint64_t) <= sizeof(PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(uint64_t, PY_LONG_LONG, PyLong_AsLongLong(x))
+#endif
}
}
{
@@ -45467,7 +48110,7 @@ raise_neg_overflow:
}
/* CIntFromPy */
- static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
+ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
const int neg_one = (int) -1, const_zero = (int) 0;
const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
@@ -45534,8 +48177,10 @@ raise_neg_overflow:
#endif
if (sizeof(int) <= sizeof(unsigned long)) {
__PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
+#endif
}
} else {
#if CYTHON_USE_PYLONG_INTERNALS
@@ -45602,8 +48247,10 @@ raise_neg_overflow:
#endif
if (sizeof(int) <= sizeof(long)) {
__PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(int) <= sizeof(PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x))
+#endif
}
}
{
@@ -45652,7 +48299,7 @@ raise_neg_overflow:
}
/* CIntFromPy */
- static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
+ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
const long neg_one = (long) -1, const_zero = (long) 0;
const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
@@ -45719,8 +48366,10 @@ raise_neg_overflow:
#endif
if (sizeof(long) <= sizeof(unsigned long)) {
__PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
+#endif
}
} else {
#if CYTHON_USE_PYLONG_INTERNALS
@@ -45787,8 +48436,10 @@ raise_neg_overflow:
#endif
if (sizeof(long) <= sizeof(long)) {
__PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x))
+#endif
}
}
{
@@ -45837,7 +48488,7 @@ raise_neg_overflow:
}
/* CIntFromPy */
- static CYTHON_INLINE ADIOS_DATATYPES __Pyx_PyInt_As_ADIOS_DATATYPES(PyObject *x) {
+ static CYTHON_INLINE ADIOS_DATATYPES __Pyx_PyInt_As_ADIOS_DATATYPES(PyObject *x) {
const ADIOS_DATATYPES neg_one = (ADIOS_DATATYPES) -1, const_zero = (ADIOS_DATATYPES) 0;
const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
@@ -45904,8 +48555,10 @@ raise_neg_overflow:
#endif
if (sizeof(ADIOS_DATATYPES) <= sizeof(unsigned long)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_DATATYPES, unsigned long, PyLong_AsUnsignedLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_DATATYPES) <= sizeof(unsigned PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_DATATYPES, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
+#endif
}
} else {
#if CYTHON_USE_PYLONG_INTERNALS
@@ -45972,8 +48625,10 @@ raise_neg_overflow:
#endif
if (sizeof(ADIOS_DATATYPES) <= sizeof(long)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_DATATYPES, long, PyLong_AsLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_DATATYPES) <= sizeof(PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_DATATYPES, PY_LONG_LONG, PyLong_AsLongLong(x))
+#endif
}
}
{
@@ -46022,7 +48677,7 @@ raise_neg_overflow:
}
/* CIntFromPy */
- static CYTHON_INLINE ADIOS_LOCKMODE __Pyx_PyInt_As_ADIOS_LOCKMODE(PyObject *x) {
+ static CYTHON_INLINE ADIOS_LOCKMODE __Pyx_PyInt_As_ADIOS_LOCKMODE(PyObject *x) {
const ADIOS_LOCKMODE neg_one = (ADIOS_LOCKMODE) -1, const_zero = (ADIOS_LOCKMODE) 0;
const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
@@ -46089,8 +48744,10 @@ raise_neg_overflow:
#endif
if (sizeof(ADIOS_LOCKMODE) <= sizeof(unsigned long)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_LOCKMODE, unsigned long, PyLong_AsUnsignedLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_LOCKMODE) <= sizeof(unsigned PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_LOCKMODE, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
+#endif
}
} else {
#if CYTHON_USE_PYLONG_INTERNALS
@@ -46157,8 +48814,10 @@ raise_neg_overflow:
#endif
if (sizeof(ADIOS_LOCKMODE) <= sizeof(long)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_LOCKMODE, long, PyLong_AsLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_LOCKMODE) <= sizeof(PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_LOCKMODE, PY_LONG_LONG, PyLong_AsLongLong(x))
+#endif
}
}
{
@@ -46207,7 +48866,7 @@ raise_neg_overflow:
}
/* CIntFromPy */
- static CYTHON_INLINE ADIOS_READ_METHOD __Pyx_PyInt_As_ADIOS_READ_METHOD(PyObject *x) {
+ static CYTHON_INLINE ADIOS_READ_METHOD __Pyx_PyInt_As_ADIOS_READ_METHOD(PyObject *x) {
const ADIOS_READ_METHOD neg_one = (ADIOS_READ_METHOD) -1, const_zero = (ADIOS_READ_METHOD) 0;
const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
@@ -46274,8 +48933,10 @@ raise_neg_overflow:
#endif
if (sizeof(ADIOS_READ_METHOD) <= sizeof(unsigned long)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_READ_METHOD, unsigned long, PyLong_AsUnsignedLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_READ_METHOD) <= sizeof(unsigned PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_READ_METHOD, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
+#endif
}
} else {
#if CYTHON_USE_PYLONG_INTERNALS
@@ -46342,8 +49003,10 @@ raise_neg_overflow:
#endif
if (sizeof(ADIOS_READ_METHOD) <= sizeof(long)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_READ_METHOD, long, PyLong_AsLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_READ_METHOD) <= sizeof(PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_READ_METHOD, PY_LONG_LONG, PyLong_AsLongLong(x))
+#endif
}
}
{
@@ -46392,7 +49055,7 @@ raise_neg_overflow:
}
/* CheckBinaryVersion */
- static int __Pyx_check_binary_version(void) {
+ static int __Pyx_check_binary_version(void) {
char ctversion[4], rtversion[4];
PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
@@ -46408,7 +49071,7 @@ raise_neg_overflow:
}
/* ModuleImport */
- #ifndef __PYX_HAVE_RT_ImportModule
+ #ifndef __PYX_HAVE_RT_ImportModule
#define __PYX_HAVE_RT_ImportModule
static PyObject *__Pyx_ImportModule(const char *name) {
PyObject *py_name = 0;
@@ -46426,7 +49089,7 @@ bad:
#endif
/* TypeImport */
- #ifndef __PYX_HAVE_RT_ImportType
+ #ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
size_t size, int strict)
@@ -46491,7 +49154,7 @@ bad:
#endif
/* InitStrings */
- static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
+ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
while (t->p) {
#if PY_MAJOR_VERSION < 3
if (t->is_unicode) {
@@ -46592,7 +49255,9 @@ static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
else return PyObject_IsTrue(x);
}
static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) {
+#if CYTHON_USE_TYPE_SLOTS
PyNumberMethods *m;
+#endif
const char *name = NULL;
PyObject *res = NULL;
#if PY_MAJOR_VERSION < 3
@@ -46601,8 +49266,9 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) {
if (PyLong_Check(x))
#endif
return __Pyx_NewRef(x);
+#if CYTHON_USE_TYPE_SLOTS
m = Py_TYPE(x)->tp_as_number;
-#if PY_MAJOR_VERSION < 3
+ #if PY_MAJOR_VERSION < 3
if (m && m->nb_int) {
name = "int";
res = PyNumber_Int(x);
@@ -46611,11 +49277,14 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) {
name = "long";
res = PyNumber_Long(x);
}
-#else
+ #else
if (m && m->nb_int) {
name = "int";
res = PyNumber_Long(x);
}
+ #endif
+#else
+ res = PyNumber_Int(x);
#endif
if (res) {
#if PY_MAJOR_VERSION < 3
diff --git a/wrappers/numpy/adios.pyx b/wrappers/numpy/adios.pyx
index fe7226d..cca0642 100644
--- a/wrappers/numpy/adios.pyx
+++ b/wrappers/numpy/adios.pyx
@@ -19,6 +19,8 @@ cimport numpy as np
import cython
cimport cython
+import tempfile
+
from libc.stdlib cimport malloc, free
from cpython.string cimport PyString_AsString
from cpython.bytes cimport PyBytes_AsString, PyBytes_AS_STRING
@@ -178,22 +180,22 @@ cdef extern from "adios.h":
cdef int adios_define_var_timescale (const char * timescale , int64_t group_id ,
const char * name)
-
+
cdef int adios_define_var_timeseriesformat (const char * timeseries , int64_t group_id ,
const char * name)
-
+
cdef int adios_define_var_hyperslab (const char * hyperslab , int64_t group_id ,
const char * name)
-
+
cdef int adios_define_mesh_timevarying (const char * timevarying , int64_t group_id ,
const char * name)
-
+
cdef int adios_define_mesh_timesteps (const char * timesteps , int64_t group_id ,
const char * name)
-
+
cdef int adios_define_mesh_timescale (const char * timescale , int64_t group_id ,
const char * name)
-
+
cdef int adios_define_mesh_timeseriesformat (const char * timeseries , int64_t group_id ,
const char * name)
@@ -205,21 +207,21 @@ cdef extern from "adios.h":
int64_t group_id,
const char * name
)
-
+
cdef int adios_define_mesh_rectilinear (char * dimensions,
char * coordinates,
char * nspace,
int64_t group_id,
const char * name
- )
-
+ )
+
cdef int adios_define_mesh_structured (char * dimensions,
char * points,
char * nspace,
int64_t group_id,
const char * name
)
-
+
cdef int adios_define_mesh_unstructured (char * points,
char * data,
char * count,
@@ -230,7 +232,7 @@ cdef extern from "adios.h":
const char * name
)
- ### Bis hier
+ ### Bis hier
cdef int adios_define_attribute (int64_t group,
char * name,
@@ -430,6 +432,12 @@ class LOCKMODE:
CURRENT = 1
ALL =2
+class STATISTICS:
+ NONE = adios_stat_no
+ MINMAX = adios_stat_minmax
+ FULL = adios_stat_full
+ DEFAULT = adios_stat_default
+
cpdef __parse_index(index, ndim):
# Fix index, handling ellipsis and incomplete slices.
if not isinstance(index, tuple):
@@ -578,25 +586,25 @@ cpdef int define_var_timesteps (str timesteps, int64_t group_id, str name):
cpdef int define_var_timescale (str timescale , int64_t group_id ,str name):
return adios_define_var_timescale (s2b(timescale) , group_id ,s2b(name))
-
+
cpdef int define_var_timeseriesformat (str timeseries , int64_t group_id ,str name):
return adios_define_var_timeseriesformat (s2b(timeseries) , group_id ,s2b(name))
-
+
cpdef int define_var_hyperslab (str hyperslab , int64_t group_id ,str name):
return adios_define_var_hyperslab (s2b(hyperslab) , group_id ,s2b(name))
-
+
cpdef int define_mesh_timevarying (str timevarying , int64_t group_id ,str name):
return adios_define_mesh_timevarying (s2b(timevarying) , group_id ,s2b(name))
-
+
cpdef int define_mesh_timesteps (str timesteps , int64_t group_id ,str name):
return adios_define_mesh_timesteps (s2b(timesteps) , group_id ,s2b(name))
-
+
cpdef int define_mesh_timescale (str timescale , int64_t group_id ,str name):
return adios_define_mesh_timescale (s2b(timescale) , group_id ,s2b(name))
-
+
cpdef int define_mesh_timeseriesformat (str timeseries , int64_t group_id ,str name):
return adios_define_mesh_timeseriesformat (s2b(timeseries) , group_id ,s2b(name))
-
+
cpdef int define_mesh_uniform (str dimensions,
str origin,
str spacing,
@@ -613,20 +621,20 @@ cpdef int define_mesh_uniform (str dimensions,
group_id,
s2b(name)
)
-
+
cpdef int define_mesh_rectilinear (str dimensions,
str coordinates,
str nspace,
int64_t group_id,
str name
- ):
+ ):
return adios_define_mesh_rectilinear (s2b(dimensions),
s2b(coordinates),
s2b(nspace),
group_id,
s2b(name)
- )
-
+ )
+
cpdef int define_mesh_structured (str dimensions,
str points,
str nspace,
@@ -639,7 +647,7 @@ cpdef int define_mesh_structured (str dimensions,
group_id,
s2b(name)
)
-
+
cpdef int define_mesh_unstructured (str points,
str data,
str count,
@@ -1917,6 +1925,7 @@ cdef class writer(object):
cpdef bint is_noxml
cpdef str mode
cpdef MPI_Comm comm
+ cpdef int stats
cpdef dict vars
cpdef dict attrs
@@ -1961,17 +1970,21 @@ cdef class writer(object):
def __init__(self, str fname,
bint is_noxml = True,
str mode = "w",
- MPI_Comm comm = MPI_COMM_WORLD):
+ int stats = adios_stat_default,
+ MPI_Comm comm = MPI_COMM_WORLD,
+ str method = "POSIX1",
+ str method_params = ""):
self.gid = 0
self.fname = fname
- self.method = ""
- self.method_params = ""
+ self.method = method
+ self.method_params = method_params
self.is_noxml = is_noxml
self.mode = mode
self.comm = comm
self.vars = dict()
self.attrs = dict()
self.timeaggregation_buffersize = 0
+ self.stats = stats
init_noxml(comm)
##def __var_factory__(self, name, value):
@@ -1982,7 +1995,8 @@ cdef class writer(object):
def declare_group(self, str gname = None,
str method = "POSIX1",
- str method_params = ""):
+ str method_params = "",
+ int stats = adios_stat_default):
"""
Define a group associated with the file.
@@ -1990,6 +2004,7 @@ cdef class writer(object):
gname (str): group name.
method (str, optional): Adios write method (default: 'POSIX1')
method_params (str, optional): parameters for the write method (default: '')
+ stats (int, optional): statistics (default: 'DEFAULT')
Example:
@@ -2000,9 +2015,15 @@ cdef class writer(object):
self.gname = gname
if self.gname is None:
- self.gname = "group"
+ rank = 0
+ if rank == 0:
+ ftmp = tempfile.NamedTemporaryFile().name
+ else:
+ ftmp = ""
+ ftmp = ftmp
+ self.gname = 'group'+ftmp;
- self.gid = declare_group(self.gname, "", adios_stat_default)
+ self.gid = declare_group(self.gname, "", stats)
self.method = method
self.method_params = method_params
select_method(self.gid, self.method, self.method_params, "")
@@ -2085,9 +2106,9 @@ cdef class writer(object):
Write variables and attributes to a file and close the writer.
"""
if self.gid == 0:
- self.declare_group()
+ self.declare_group(method=self.method, method_params=self.method_params, stats=self.stats)
- fd = open(self.gname, self.fname, self.mode)
+ fd = open(self.gname, self.fname, self.mode, comm=self.comm)
extra_vars = dict()
extra_attrs = dict()
@@ -2230,7 +2251,8 @@ cdef class varinfo(object):
def define(self, int64_t gid):
if self.value is None:
- raise TypeError("Value is none")
+ print ("Warning: skipping defining var(%r) with None value" %(self.name))
+ return
ldim_ = self.ldim
if isinstance(self.ldim, (tuple, list)):
@@ -2268,6 +2290,10 @@ cdef class varinfo(object):
def write(self, int64_t fd):
val_ = self.value
+
+ if val_ is None:
+ return
+
if not isinstance(self.value, (np.ndarray)):
val_ = np.array(self.value)
diff --git a/wrappers/numpy/adios_mpi.cpp b/wrappers/numpy/adios_mpi.cpp
index ca2bd99..b6b702b 100644
--- a/wrappers/numpy/adios_mpi.cpp
+++ b/wrappers/numpy/adios_mpi.cpp
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.24 */
+/* Generated by Cython 0.25.2 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -7,7 +7,7 @@
#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000)
#error Cython requires Python 2.6+ or Python 3.2+.
#else
-#define CYTHON_ABI "0_24"
+#define CYTHON_ABI "0_25_2"
#include <stddef.h>
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
@@ -29,6 +29,11 @@
#ifndef DL_EXPORT
#define DL_EXPORT(t) t
#endif
+#ifndef HAVE_LONG_LONG
+ #if PY_VERSION_HEX >= 0x03030000 || (PY_MAJOR_VERSION == 2 && PY_VERSION_HEX >= 0x02070000)
+ #define HAVE_LONG_LONG
+ #endif
+#endif
#ifndef PY_LONG_LONG
#define PY_LONG_LONG LONG_LONG
#endif
@@ -37,13 +42,110 @@
#endif
#ifdef PYPY_VERSION
#define CYTHON_COMPILING_IN_PYPY 1
+ #define CYTHON_COMPILING_IN_PYSTON 0
#define CYTHON_COMPILING_IN_CPYTHON 0
+ #undef CYTHON_USE_TYPE_SLOTS
+ #define CYTHON_USE_TYPE_SLOTS 0
+ #undef CYTHON_USE_ASYNC_SLOTS
+ #define CYTHON_USE_ASYNC_SLOTS 0
+ #undef CYTHON_USE_PYLIST_INTERNALS
+ #define CYTHON_USE_PYLIST_INTERNALS 0
+ #undef CYTHON_USE_UNICODE_INTERNALS
+ #define CYTHON_USE_UNICODE_INTERNALS 0
+ #undef CYTHON_USE_UNICODE_WRITER
+ #define CYTHON_USE_UNICODE_WRITER 0
+ #undef CYTHON_USE_PYLONG_INTERNALS
+ #define CYTHON_USE_PYLONG_INTERNALS 0
+ #undef CYTHON_AVOID_BORROWED_REFS
+ #define CYTHON_AVOID_BORROWED_REFS 1
+ #undef CYTHON_ASSUME_SAFE_MACROS
+ #define CYTHON_ASSUME_SAFE_MACROS 0
+ #undef CYTHON_UNPACK_METHODS
+ #define CYTHON_UNPACK_METHODS 0
+ #undef CYTHON_FAST_THREAD_STATE
+ #define CYTHON_FAST_THREAD_STATE 0
+ #undef CYTHON_FAST_PYCALL
+ #define CYTHON_FAST_PYCALL 0
+#elif defined(PYSTON_VERSION)
+ #define CYTHON_COMPILING_IN_PYPY 0
+ #define CYTHON_COMPILING_IN_PYSTON 1
+ #define CYTHON_COMPILING_IN_CPYTHON 0
+ #ifndef CYTHON_USE_TYPE_SLOTS
+ #define CYTHON_USE_TYPE_SLOTS 1
+ #endif
+ #undef CYTHON_USE_ASYNC_SLOTS
+ #define CYTHON_USE_ASYNC_SLOTS 0
+ #undef CYTHON_USE_PYLIST_INTERNALS
+ #define CYTHON_USE_PYLIST_INTERNALS 0
+ #ifndef CYTHON_USE_UNICODE_INTERNALS
+ #define CYTHON_USE_UNICODE_INTERNALS 1
+ #endif
+ #undef CYTHON_USE_UNICODE_WRITER
+ #define CYTHON_USE_UNICODE_WRITER 0
+ #undef CYTHON_USE_PYLONG_INTERNALS
+ #define CYTHON_USE_PYLONG_INTERNALS 0
+ #ifndef CYTHON_AVOID_BORROWED_REFS
+ #define CYTHON_AVOID_BORROWED_REFS 0
+ #endif
+ #ifndef CYTHON_ASSUME_SAFE_MACROS
+ #define CYTHON_ASSUME_SAFE_MACROS 1
+ #endif
+ #ifndef CYTHON_UNPACK_METHODS
+ #define CYTHON_UNPACK_METHODS 1
+ #endif
+ #undef CYTHON_FAST_THREAD_STATE
+ #define CYTHON_FAST_THREAD_STATE 0
+ #undef CYTHON_FAST_PYCALL
+ #define CYTHON_FAST_PYCALL 0
#else
#define CYTHON_COMPILING_IN_PYPY 0
+ #define CYTHON_COMPILING_IN_PYSTON 0
#define CYTHON_COMPILING_IN_CPYTHON 1
+ #ifndef CYTHON_USE_TYPE_SLOTS
+ #define CYTHON_USE_TYPE_SLOTS 1
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ #undef CYTHON_USE_ASYNC_SLOTS
+ #define CYTHON_USE_ASYNC_SLOTS 0
+ #elif !defined(CYTHON_USE_ASYNC_SLOTS)
+ #define CYTHON_USE_ASYNC_SLOTS 1
+ #endif
+ #if PY_VERSION_HEX < 0x02070000
+ #undef CYTHON_USE_PYLONG_INTERNALS
+ #define CYTHON_USE_PYLONG_INTERNALS 0
+ #elif !defined(CYTHON_USE_PYLONG_INTERNALS)
+ #define CYTHON_USE_PYLONG_INTERNALS 1
+ #endif
+ #ifndef CYTHON_USE_PYLIST_INTERNALS
+ #define CYTHON_USE_PYLIST_INTERNALS 1
+ #endif
+ #ifndef CYTHON_USE_UNICODE_INTERNALS
+ #define CYTHON_USE_UNICODE_INTERNALS 1
+ #endif
+ #if PY_VERSION_HEX < 0x030300F0
+ #undef CYTHON_USE_UNICODE_WRITER
+ #define CYTHON_USE_UNICODE_WRITER 0
+ #elif !defined(CYTHON_USE_UNICODE_WRITER)
+ #define CYTHON_USE_UNICODE_WRITER 1
+ #endif
+ #ifndef CYTHON_AVOID_BORROWED_REFS
+ #define CYTHON_AVOID_BORROWED_REFS 0
+ #endif
+ #ifndef CYTHON_ASSUME_SAFE_MACROS
+ #define CYTHON_ASSUME_SAFE_MACROS 1
+ #endif
+ #ifndef CYTHON_UNPACK_METHODS
+ #define CYTHON_UNPACK_METHODS 1
+ #endif
+ #ifndef CYTHON_FAST_THREAD_STATE
+ #define CYTHON_FAST_THREAD_STATE 1
+ #endif
+ #ifndef CYTHON_FAST_PYCALL
+ #define CYTHON_FAST_PYCALL 1
+ #endif
#endif
-#if !defined(CYTHON_USE_PYLONG_INTERNALS) && CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x02070000
- #define CYTHON_USE_PYLONG_INTERNALS 1
+#if !defined(CYTHON_FAST_PYCCALL)
+#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1)
#endif
#if CYTHON_USE_PYLONG_INTERNALS
#include "longintrepr.h"
@@ -79,24 +181,44 @@
#ifndef Py_TPFLAGS_HAVE_FINALIZE
#define Py_TPFLAGS_HAVE_FINALIZE 0
#endif
+#ifndef METH_FASTCALL
+ #define METH_FASTCALL 0x80
+ typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject **args,
+ Py_ssize_t nargs, PyObject *kwnames);
+#else
+ #define __Pyx_PyCFunctionFast _PyCFunctionFast
+#endif
+#if CYTHON_FAST_PYCCALL
+#define __Pyx_PyFastCFunction_Check(func)\
+ ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)))))
+#else
+#define __Pyx_PyFastCFunction_Check(func) 0
+#endif
#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
#define CYTHON_PEP393_ENABLED 1
#define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\
0 : _PyUnicode_Ready((PyObject *)(op)))
#define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
+ #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u)
#define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u)
#define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u)
#define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
+ #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch)
#define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u)))
#else
#define CYTHON_PEP393_ENABLED 0
+ #define PyUnicode_1BYTE_KIND 1
+ #define PyUnicode_2BYTE_KIND 2
+ #define PyUnicode_4BYTE_KIND 4
#define __Pyx_PyUnicode_READY(op) (0)
#define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
+ #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111)
#define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE))
#define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u))
#define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
+ #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch)
#define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u))
#endif
#if CYTHON_COMPILING_IN_PYPY
@@ -110,6 +232,9 @@
#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains)
#define PyUnicode_Contains(u, s) PySequence_Contains(u, s)
#endif
+#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check)
+ #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type)
+#endif
#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format)
#define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt)
#endif
@@ -118,6 +243,13 @@
#define PyObject_Free(p) PyMem_Free(p)
#define PyObject_Realloc(p) PyMem_Realloc(p)
#endif
+#if CYTHON_COMPILING_IN_PYSTON
+ #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co)
+ #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno)
+#else
+ #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0)
+ #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno)
+#endif
#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b))
#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b))
#if PY_MAJOR_VERSION >= 3
@@ -146,6 +278,7 @@
#define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
+#define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception)
#if PY_MAJOR_VERSION >= 3
#define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
@@ -184,18 +317,20 @@
#else
#define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass)
#endif
-#if PY_VERSION_HEX >= 0x030500B1
-#define __Pyx_PyAsyncMethodsStruct PyAsyncMethods
-#define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async)
-#elif CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
-typedef struct {
- unaryfunc am_await;
- unaryfunc am_aiter;
- unaryfunc am_anext;
-} __Pyx_PyAsyncMethodsStruct;
-#define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved))
+#if CYTHON_USE_ASYNC_SLOTS
+ #if PY_VERSION_HEX >= 0x030500B1
+ #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods
+ #define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async)
+ #else
+ typedef struct {
+ unaryfunc am_await;
+ unaryfunc am_aiter;
+ unaryfunc am_anext;
+ } __Pyx_PyAsyncMethodsStruct;
+ #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved))
+ #endif
#else
-#define __Pyx_PyType_AsAsync(obj) NULL
+ #define __Pyx_PyType_AsAsync(obj) NULL
#endif
#ifndef CYTHON_RESTRICT
#if defined(__GNUC__)
@@ -208,13 +343,44 @@ typedef struct {
#define CYTHON_RESTRICT
#endif
#endif
+#ifndef CYTHON_UNUSED
+# if defined(__GNUC__)
+# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
+# else
+# define CYTHON_UNUSED
+# endif
+# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
+# else
+# define CYTHON_UNUSED
+# endif
+#endif
+#ifndef CYTHON_MAYBE_UNUSED_VAR
+# if defined(__cplusplus)
+ template<class T> void CYTHON_MAYBE_UNUSED_VAR( const T& ) { }
+# else
+# define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x)
+# endif
+#endif
+#ifndef CYTHON_NCP_UNUSED
+# if CYTHON_COMPILING_IN_CPYTHON
+# define CYTHON_NCP_UNUSED
+# else
+# define CYTHON_NCP_UNUSED CYTHON_UNUSED
+# endif
+#endif
#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None)
#ifndef __cplusplus
#error "Cython files generated with the C++ option must be compiled with a C++ compiler."
#endif
#ifndef CYTHON_INLINE
- #define CYTHON_INLINE inline
+ #if defined(__clang__)
+ #define CYTHON_INLINE __inline__ __attribute__ ((__unused__))
+ #else
+ #define CYTHON_INLINE inline
+ #endif
#endif
template<typename T>
void __Pyx_call_destructor(T& x) {
@@ -226,7 +392,10 @@ class __Pyx_FakeReference {
__Pyx_FakeReference() : ptr(NULL) { }
__Pyx_FakeReference(const T& ref) : ptr(const_cast<T*>(&ref)) { }
T *operator->() { return ptr; }
+ T *operator&() { return ptr; }
operator T&() { return *ptr; }
+ template<typename U> bool operator ==(U other) { return *ptr == other; }
+ template<typename U> bool operator !=(U other) { return *ptr != other; }
private:
T *ptr;
};
@@ -244,6 +413,11 @@ static CYTHON_INLINE float __PYX_NAN() {
return value;
}
#endif
+#if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL)
+#define __Pyx_truncl trunc
+#else
+#define __Pyx_truncl truncl
+#endif
#define __PYX_ERR(f_index, lineno, Ln_error) \
@@ -271,12 +445,13 @@ static CYTHON_INLINE float __PYX_NAN() {
#define __PYX_HAVE_API__adios_mpi
#include "mpi-compat.h"
#include "string.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "numpy/arrayobject.h"
#include "numpy/ufuncobject.h"
#include "mpi.h"
-#include "stdint.h"
+#include <stdint.h>
#include "adios_types.h"
#include "adios.h"
#include "adios_selection.h"
@@ -289,26 +464,6 @@ static CYTHON_INLINE float __PYX_NAN() {
#define CYTHON_WITHOUT_ASSERTIONS
#endif
-#ifndef CYTHON_UNUSED
-# if defined(__GNUC__)
-# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
-# else
-# define CYTHON_UNUSED
-# endif
-# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
-# else
-# define CYTHON_UNUSED
-# endif
-#endif
-#ifndef CYTHON_NCP_UNUSED
-# if CYTHON_COMPILING_IN_CPYTHON
-# define CYTHON_NCP_UNUSED
-# else
-# define CYTHON_NCP_UNUSED CYTHON_UNUSED
-# endif
-#endif
typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding;
const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;
@@ -386,7 +541,7 @@ static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x);
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_ASSUME_SAFE_MACROS
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
#else
#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
@@ -494,7 +649,7 @@ static int __pyx_clineno = 0;
static const char * __pyx_cfilenm= __FILE__;
static const char *__pyx_filename;
-/* None.proto */
+/* Header.proto */
#if !defined(CYTHON_CCOMPLEX)
#if defined(__cplusplus)
#define CYTHON_CCOMPLEX 1
@@ -712,7 +867,7 @@ typedef npy_double __pyx_t_5numpy_double_t;
* ctypedef npy_cfloat cfloat_t
*/
typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
-/* None.proto */
+/* Declarations.proto */
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
typedef ::std::complex< float > __pyx_t_float_complex;
@@ -722,8 +877,9 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
#else
typedef struct { float real, imag; } __pyx_t_float_complex;
#endif
+static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float);
-/* None.proto */
+/* Declarations.proto */
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
typedef ::std::complex< double > __pyx_t_double_complex;
@@ -733,6 +889,7 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
#else
typedef struct { double real, imag; } __pyx_t_double_complex;
#endif
+static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double);
/*--- Type declarations ---*/
@@ -817,7 +974,7 @@ struct __pyx_opt_args_9adios_mpi_3var_read_points;
struct __pyx_opt_args_9adios_mpi_3var_read_writeblock;
struct __pyx_opt_args_9adios_mpi_3var_read;
-/* "adios_mpi.pyx":464
+/* "adios_mpi.pyx":472
* cdef MPI.Comm read_init_comm
*
* cpdef init(str config, MPI.Comm comm = MPI.COMM_WORLD): # <<<<<<<<<<<<<<
@@ -829,7 +986,7 @@ struct __pyx_opt_args_9adios_mpi_init {
struct PyMPICommObject *comm;
};
-/* "adios_mpi.pyx":469
+/* "adios_mpi.pyx":477
* return adios_init(s2b(config), init_comm.ob_mpi)
*
* cpdef int64_t open(str group_name, # <<<<<<<<<<<<<<
@@ -841,7 +998,7 @@ struct __pyx_opt_args_9adios_mpi_open {
struct PyMPICommObject *comm;
};
-/* "adios_mpi.pyx":484
+/* "adios_mpi.pyx":492
* return total_size
*
* cpdef int write (int64_t fd_p, str name, val, dtype=None): # <<<<<<<<<<<<<<
@@ -853,7 +1010,7 @@ struct __pyx_opt_args_9adios_mpi_write {
PyObject *dtype;
};
-/* "adios_mpi.pyx":524
+/* "adios_mpi.pyx":532
* return adios_close(fd_p)
*
* cpdef int finalize(int mype = 0): # <<<<<<<<<<<<<<
@@ -865,7 +1022,7 @@ struct __pyx_opt_args_9adios_mpi_finalize {
int mype;
};
-/* "adios_mpi.pyx":531
+/* "adios_mpi.pyx":539
* ## ====================
*
* cpdef int init_noxml(MPI.Comm comm = MPI.COMM_WORLD): # <<<<<<<<<<<<<<
@@ -877,7 +1034,7 @@ struct __pyx_opt_args_9adios_mpi_init_noxml {
struct PyMPICommObject *comm;
};
-/* "adios_mpi.pyx":541
+/* "adios_mpi.pyx":549
* buffer_size)
*
* cpdef int64_t declare_group(str name, # <<<<<<<<<<<<<<
@@ -890,7 +1047,7 @@ struct __pyx_opt_args_9adios_mpi_declare_group {
int stats;
};
-/* "adios_mpi.pyx":551
+/* "adios_mpi.pyx":559
* return id
*
* cpdef int64_t define_var(int64_t group_id, # <<<<<<<<<<<<<<
@@ -904,7 +1061,7 @@ struct __pyx_opt_args_9adios_mpi_define_var {
PyObject *local_offsets;
};
-/* "adios_mpi.pyx":718
+/* "adios_mpi.pyx":726
* <void *> val_.data)
*
* cpdef int select_method (int64_t group, # <<<<<<<<<<<<<<
@@ -917,7 +1074,7 @@ struct __pyx_opt_args_9adios_mpi_select_method {
PyObject *base_path;
};
-/* "adios_mpi.pyx":745
+/* "adios_mpi.pyx":753
* ## ====================
*
* cpdef np.dtype adios2npdtype(ADIOS_DATATYPES t, int strlen = 1): # <<<<<<<<<<<<<<
@@ -929,7 +1086,7 @@ struct __pyx_opt_args_9adios_mpi_adios2npdtype {
int strlen;
};
-/* "adios_mpi.pyx":874
+/* "adios_mpi.pyx":882
*
* """ Call adios_read_init_method """
* cpdef int read_init(str method_name = "BP", # <<<<<<<<<<<<<<
@@ -943,7 +1100,7 @@ struct __pyx_opt_args_9adios_mpi_read_init {
PyObject *parameters;
};
-/* "adios_mpi.pyx":884
+/* "adios_mpi.pyx":892
*
* """ Call adios_read_finalize_method """
* cpdef int read_finalize(str method_name = "BP"): # <<<<<<<<<<<<<<
@@ -955,7 +1112,7 @@ struct __pyx_opt_args_9adios_mpi_read_finalize {
PyObject *method_name;
};
-/* "adios_mpi.pyx":1061
+/* "adios_mpi.pyx":1069
* adios_release_step(self.fp)
*
* cpdef advance(self, int last = 0, float timeout_sec = 0.0): # <<<<<<<<<<<<<<
@@ -968,7 +1125,7 @@ struct __pyx_opt_args_9adios_mpi_4file_advance {
float timeout_sec;
};
-/* "adios_mpi.pyx":1359
+/* "adios_mpi.pyx":1367
* self.nsteps = self.vp.nsteps
*
* cpdef read_points(self, tuple points = (), from_steps = None, nsteps = None): # <<<<<<<<<<<<<<
@@ -982,7 +1139,7 @@ struct __pyx_opt_args_9adios_mpi_3var_read_points {
PyObject *nsteps;
};
-/* "adios_mpi.pyx":1415
+/* "adios_mpi.pyx":1423
* return var
*
* cpdef read_writeblock(self, int rank, from_steps = None, nsteps = None): # <<<<<<<<<<<<<<
@@ -995,7 +1152,7 @@ struct __pyx_opt_args_9adios_mpi_3var_read_writeblock {
PyObject *nsteps;
};
-/* "adios_mpi.pyx":1456
+/* "adios_mpi.pyx":1464
* return var
*
* cpdef read(self, tuple offset = (), tuple count = (), tuple scalar = (), # <<<<<<<<<<<<<<
@@ -1013,7 +1170,7 @@ struct __pyx_opt_args_9adios_mpi_3var_read {
PyObject *step_scalar;
};
-/* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":28
+/* "../../../../.local/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":28
* ctypedef MPI_Count Count "MPI_Count"
*
* ctypedef public api class Status [ # <<<<<<<<<<<<<<
@@ -1029,7 +1186,7 @@ typedef struct PyMPIStatusObject PyMPIStatusObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPIStatus_Type;
-/* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":35
+/* "../../../../.local/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":35
* cdef unsigned flags
*
* ctypedef public api class Datatype [ # <<<<<<<<<<<<<<
@@ -1045,7 +1202,7 @@ typedef struct PyMPIDatatypeObject PyMPIDatatypeObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPIDatatype_Type;
-/* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":42
+/* "../../../../.local/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":42
* cdef unsigned flags
*
* ctypedef public api class Request [ # <<<<<<<<<<<<<<
@@ -1062,7 +1219,7 @@ typedef struct PyMPIRequestObject PyMPIRequestObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPIRequest_Type;
-/* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":50
+/* "../../../../.local/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":50
* cdef object ob_buf
*
* ctypedef public api class Prequest(Request) [ # <<<<<<<<<<<<<<
@@ -1076,7 +1233,7 @@ typedef struct PyMPIPrequestObject PyMPIPrequestObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPIPrequest_Type;
-/* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":56
+/* "../../../../.local/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":56
* pass
*
* ctypedef public api class Grequest(Request) [ # <<<<<<<<<<<<<<
@@ -1091,7 +1248,7 @@ typedef struct PyMPIGrequestObject PyMPIGrequestObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPIGrequest_Type;
-/* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":62
+/* "../../../../.local/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":62
* cdef MPI_Request ob_grequest
*
* ctypedef public api class Message [ # <<<<<<<<<<<<<<
@@ -1108,7 +1265,7 @@ typedef struct PyMPIMessageObject PyMPIMessageObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPIMessage_Type;
-/* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":70
+/* "../../../../.local/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":70
* cdef object ob_buf
*
* ctypedef public api class Op [ # <<<<<<<<<<<<<<
@@ -1126,7 +1283,7 @@ typedef struct PyMPIOpObject PyMPIOpObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPIOp_Type;
-/* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":79
+/* "../../../../.local/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":79
* cdef int ob_usrid
*
* ctypedef public api class Group [ # <<<<<<<<<<<<<<
@@ -1142,7 +1299,7 @@ typedef struct PyMPIGroupObject PyMPIGroupObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPIGroup_Type;
-/* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":86
+/* "../../../../.local/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":86
* cdef unsigned flags
*
* ctypedef public api class Info [ # <<<<<<<<<<<<<<
@@ -1158,7 +1315,7 @@ typedef struct PyMPIInfoObject PyMPIInfoObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPIInfo_Type;
-/* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":93
+/* "../../../../.local/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":93
* cdef unsigned flags
*
* ctypedef public api class Errhandler [ # <<<<<<<<<<<<<<
@@ -1174,7 +1331,7 @@ typedef struct PyMPIErrhandlerObject PyMPIErrhandlerObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPIErrhandler_Type;
-/* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":100
+/* "../../../../.local/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":100
* cdef unsigned flags
*
* ctypedef public api class Comm [ # <<<<<<<<<<<<<<
@@ -1190,7 +1347,7 @@ typedef struct PyMPICommObject PyMPICommObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPIComm_Type;
-/* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":107
+/* "../../../../.local/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":107
* cdef unsigned flags
*
* ctypedef public api class Intracomm(Comm) [ # <<<<<<<<<<<<<<
@@ -1204,7 +1361,7 @@ typedef struct PyMPIIntracommObject PyMPIIntracommObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPIIntracomm_Type;
-/* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":113
+/* "../../../../.local/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":113
* pass
*
* ctypedef public api class Topocomm(Intracomm) [ # <<<<<<<<<<<<<<
@@ -1218,7 +1375,7 @@ typedef struct PyMPITopocommObject PyMPITopocommObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPITopocomm_Type;
-/* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":119
+/* "../../../../.local/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":119
* pass
*
* ctypedef public api class Cartcomm(Topocomm) [ # <<<<<<<<<<<<<<
@@ -1232,7 +1389,7 @@ typedef struct PyMPICartcommObject PyMPICartcommObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPICartcomm_Type;
-/* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":125
+/* "../../../../.local/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":125
* pass
*
* ctypedef public api class Graphcomm(Topocomm) [ # <<<<<<<<<<<<<<
@@ -1246,7 +1403,7 @@ typedef struct PyMPIGraphcommObject PyMPIGraphcommObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPIGraphcomm_Type;
-/* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":131
+/* "../../../../.local/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":131
* pass
*
* ctypedef public api class Distgraphcomm(Topocomm) [ # <<<<<<<<<<<<<<
@@ -1260,7 +1417,7 @@ typedef struct PyMPIDistgraphcommObject PyMPIDistgraphcommObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPIDistgraphcomm_Type;
-/* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":137
+/* "../../../../.local/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":137
* pass
*
* ctypedef public api class Intercomm(Comm) [ # <<<<<<<<<<<<<<
@@ -1274,7 +1431,7 @@ typedef struct PyMPIIntercommObject PyMPIIntercommObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPIIntercomm_Type;
-/* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":143
+/* "../../../../.local/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":143
* pass
*
* ctypedef public api class Win [ # <<<<<<<<<<<<<<
@@ -1291,7 +1448,7 @@ typedef struct PyMPIWinObject PyMPIWinObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPIWin_Type;
-/* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":151
+/* "../../../../.local/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd":151
* cdef object ob_mem
*
* ctypedef public api class File [ # <<<<<<<<<<<<<<
@@ -1307,7 +1464,7 @@ typedef struct PyMPIFileObject PyMPIFileObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPIFile_Type;
-/* "adios_mpi.pyx":889
+/* "adios_mpi.pyx":897
*
* ## dict for handling '/' prefix
* cdef class softdict(dict): # <<<<<<<<<<<<<<
@@ -1319,7 +1476,7 @@ struct __pyx_obj_9adios_mpi_softdict {
};
-/* "adios_mpi.pyx":913
+/* "adios_mpi.pyx":921
*
* ## Python class for ADIOS_FILE structure
* cdef class file(dict): # <<<<<<<<<<<<<<
@@ -1346,7 +1503,7 @@ struct __pyx_obj_9adios_mpi_file {
};
-/* "adios_mpi.pyx":1185
+/* "adios_mpi.pyx":1193
* return list(s-set(['']))
*
* cdef class blockinfo(object): # <<<<<<<<<<<<<<
@@ -1362,7 +1519,7 @@ struct __pyx_obj_9adios_mpi_blockinfo {
};
-/* "adios_mpi.pyx":1220
+/* "adios_mpi.pyx":1228
* self.count)
*
* cdef class var(dict): # <<<<<<<<<<<<<<
@@ -1385,7 +1542,7 @@ struct __pyx_obj_9adios_mpi_var {
};
-/* "adios_mpi.pyx":1685
+/* "adios_mpi.pyx":1693
* return self.attrs.keys()
*
* cdef class attr(object): # <<<<<<<<<<<<<<
@@ -1401,7 +1558,7 @@ struct __pyx_obj_9adios_mpi_attr {
};
-/* "adios_mpi.pyx":1771
+/* "adios_mpi.pyx":1779
* (self.name, self.dtype, self.value)
*
* cdef class group(dict): # <<<<<<<<<<<<<<
@@ -1417,7 +1574,7 @@ struct __pyx_obj_9adios_mpi_group {
};
-/* "adios_mpi.pyx":1883
+/* "adios_mpi.pyx":1891
*
* ## Helper dict
* cdef class smartdict(dict): # <<<<<<<<<<<<<<
@@ -1430,7 +1587,7 @@ struct __pyx_obj_9adios_mpi_smartdict {
};
-/* "adios_mpi.pyx":1895
+/* "adios_mpi.pyx":1903
* self.factory(key, value)
*
* cdef class writer(object): # <<<<<<<<<<<<<<
@@ -1447,13 +1604,14 @@ struct __pyx_obj_9adios_mpi_writer {
int is_noxml;
PyObject *mode;
struct PyMPICommObject *comm;
+ int stats;
PyObject *vars;
PyObject *attrs;
uint64_t timeaggregation_buffersize;
};
-/* "adios_mpi.pyx":2149
+/* "adios_mpi.pyx":2170
* self.close()
*
* cdef class attrinfo(object): # <<<<<<<<<<<<<<
@@ -1469,7 +1627,7 @@ struct __pyx_obj_9adios_mpi_attrinfo {
};
-/* "adios_mpi.pyx":2202
+/* "adios_mpi.pyx":2223
* self.dtype)
*
* cdef class varinfo(object): # <<<<<<<<<<<<<<
@@ -1488,7 +1646,7 @@ struct __pyx_obj_9adios_mpi_varinfo {
-/* "adios_mpi.pyx":913
+/* "adios_mpi.pyx":921
*
* ## Python class for ADIOS_FILE structure
* cdef class file(dict): # <<<<<<<<<<<<<<
@@ -1505,7 +1663,7 @@ struct __pyx_vtabstruct_9adios_mpi_file {
static struct __pyx_vtabstruct_9adios_mpi_file *__pyx_vtabptr_9adios_mpi_file;
-/* "adios_mpi.pyx":1220
+/* "adios_mpi.pyx":1228
* self.count)
*
* cdef class var(dict): # <<<<<<<<<<<<<<
@@ -1588,7 +1746,7 @@ static struct __pyx_vtabstruct_9adios_mpi_var *__pyx_vtabptr_9adios_mpi_var;
#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)
/* PyObjectGetAttrStr.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_USE_TYPE_SLOTS
static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) {
PyTypeObject* tp = Py_TYPE(obj);
if (likely(tp->tp_getattro))
@@ -1606,6 +1764,24 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject
/* GetBuiltinName.proto */
static PyObject *__Pyx_GetBuiltinName(PyObject *name);
+/* PyCFunctionFastCall.proto */
+#if CYTHON_FAST_PYCCALL
+static CYTHON_INLINE PyObject *__Pyx_PyCFunction_FastCall(PyObject *func, PyObject **args, Py_ssize_t nargs);
+#else
+#define __Pyx_PyCFunction_FastCall(func, args, nargs) (assert(0), NULL)
+#endif
+
+/* PyFunctionFastCall.proto */
+#if CYTHON_FAST_PYCALL
+#define __Pyx_PyFunction_FastCall(func, args, nargs)\
+ __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL)
+#if 1 || PY_VERSION_HEX < 0x030600B1
+static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs);
+#else
+#define __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs) _PyFunction_FastCallDict(func, args, nargs, kwargs)
+#endif
+#endif
+
/* PyObjectCall.proto */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw);
@@ -1629,7 +1805,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func);
#endif
/* PyThreadStateGet.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_FAST_THREAD_STATE
#define __Pyx_PyThreadState_declare PyThreadState *__pyx_tstate;
#define __Pyx_PyThreadState_assign __pyx_tstate = PyThreadState_GET();
#else
@@ -1638,7 +1814,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func);
#endif
/* PyErrFetchRestore.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_FAST_THREAD_STATE
#define __Pyx_ErrRestoreWithState(type, value, tb) __Pyx_ErrRestoreInState(PyThreadState_GET(), type, value, tb)
#define __Pyx_ErrFetchWithState(type, value, tb) __Pyx_ErrFetchInState(PyThreadState_GET(), type, value, tb)
#define __Pyx_ErrRestore(type, value, tb) __Pyx_ErrRestoreInState(__pyx_tstate, type, value, tb)
@@ -1690,7 +1866,7 @@ static CYTHON_INLINE int __Pyx_PySequence_ContainsTF(PyObject* item, PyObject* s
}
/* ListAppend.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS
static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
PyListObject* L = (PyListObject*) list;
Py_ssize_t len = Py_SIZE(list);
@@ -1742,7 +1918,7 @@ static CYTHON_INLINE int __Pyx_PyList_Extend(PyObject* L, PyObject* v) {
}
/* PyIntBinop.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
+#if !CYTHON_COMPILING_IN_PYPY
static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace);
#else
#define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace)\
@@ -1750,7 +1926,7 @@ static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval,
#endif
/* PyIntBinop.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
+#if !CYTHON_COMPILING_IN_PYPY
static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, long intval, int inplace);
#else
#define __Pyx_PyInt_SubtractObjC(op1, op2, intval, inplace)\
@@ -1792,7 +1968,7 @@ static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int
#endif
/* PyIntBinop.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
+#if !CYTHON_COMPILING_IN_PYPY
static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, long intval, int inplace);
#else
#define __Pyx_PyInt_EqObjC(op1, op2, intval, inplace)\
@@ -1800,7 +1976,7 @@ static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, long intval, i
#endif
/* ListCompAppend.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS
static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) {
PyListObject* L = (PyListObject*) list;
Py_ssize_t len = Py_SIZE(list);
@@ -1838,7 +2014,9 @@ static PyObject* __Pyx__CallUnboundCMethod0(__Pyx_CachedCFunction* cfunc, PyObje
((likely((cfunc)->func)) ?\
(likely((cfunc)->flag == METH_NOARGS) ? (*((cfunc)->func))(self, NULL) :\
(likely((cfunc)->flag == (METH_VARARGS | METH_KEYWORDS)) ? ((*(PyCFunctionWithKeywords)(cfunc)->func)(self, __pyx_empty_tuple, NULL)) :\
- ((cfunc)->flag == METH_VARARGS ? (*((cfunc)->func))(self, __pyx_empty_tuple) : __Pyx__CallUnboundCMethod0(cfunc, self)))) :\
+ ((cfunc)->flag == METH_VARARGS ? (*((cfunc)->func))(self, __pyx_empty_tuple) :\
+ (PY_VERSION_HEX >= 0x030600B1 && (cfunc)->flag == METH_FASTCALL ? (*(__Pyx_PyCFunctionFast)(cfunc)->func)(self, &PyTuple_GET_ITEM(__pyx_empty_tuple, 0), 0, NULL) :\
+ __Pyx__CallUnboundCMethod0(cfunc, self))))) :\
__Pyx__CallUnboundCMethod0(cfunc, self))
#else
#define __Pyx_CallUnboundCMethod0(cfunc, self) __Pyx__CallUnboundCMethod0(cfunc, self)
@@ -1913,7 +2091,7 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
#endif
/* PyObjectSetAttrStr.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_USE_TYPE_SLOTS
#define __Pyx_PyObject_DelAttrStr(o,n) __Pyx_PyObject_SetAttrStr(o,n,NULL)
static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) {
PyTypeObject* tp = Py_TYPE(obj);
@@ -1952,6 +2130,33 @@ static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* dict_or_iter, Py_ssize_t
/* py_dict_values.proto */
static CYTHON_INLINE PyObject* __Pyx_PyDict_Values(PyObject* d);
+/* SaveResetException.proto */
+#if CYTHON_FAST_THREAD_STATE
+#define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb)
+static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
+#define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb)
+static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb);
+#else
+#define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb)
+#define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb)
+#endif
+
+/* PyErrExceptionMatches.proto */
+#if CYTHON_FAST_THREAD_STATE
+#define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err)
+static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err);
+#else
+#define __Pyx_PyErr_ExceptionMatches(err) PyErr_ExceptionMatches(err)
+#endif
+
+/* GetException.proto */
+#if CYTHON_FAST_THREAD_STATE
+#define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb)
+static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
+#else
+static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb);
+#endif
+
/* SetVTable.proto */
static int __Pyx_SetVtable(PyObject *dict, void *vtable);
@@ -1990,6 +2195,9 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line,
int py_line, const char *filename);
/* CIntToPy.proto */
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ADIOS_STATISTICS_FLAG(ADIOS_STATISTICS_FLAG value);
+
+/* CIntToPy.proto */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);
/* CIntToPy.proto */
@@ -2013,7 +2221,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint32_t(uint32_t value);
/* CIntToPy.proto */
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ADIOS_DATATYPES(ADIOS_DATATYPES value);
-/* None.proto */
+/* RealImag.proto */
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
#define __Pyx_CREAL(z) ((z).real())
@@ -2026,7 +2234,8 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ADIOS_DATATYPES(ADIOS_DATATYPES
#define __Pyx_CREAL(z) ((z).real)
#define __Pyx_CIMAG(z) ((z).imag)
#endif
-#if defined(__cplusplus) && CYTHON_CCOMPLEX && (defined(_WIN32) || defined(__clang__) || (defined(__GNUC__) && (__GNUC__ >= 5 || __GNUC__ == 4 && __GNUC_MINOR__ >= 4 )) || __cplusplus >= 201103)
+#if defined(__cplusplus) && CYTHON_CCOMPLEX\
+ && (defined(_WIN32) || defined(__clang__) || (defined(__GNUC__) && (__GNUC__ >= 5 || __GNUC__ == 4 && __GNUC_MINOR__ >= 4 )) || __cplusplus >= 201103)
#define __Pyx_SET_CREAL(z,x) ((z).real(x))
#define __Pyx_SET_CIMAG(z,y) ((z).imag(y))
#else
@@ -2034,85 +2243,79 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ADIOS_DATATYPES(ADIOS_DATATYPES
#define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y)
#endif
-/* None.proto */
-static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float);
-
-/* None.proto */
+/* Arithmetic.proto */
#if CYTHON_CCOMPLEX
- #define __Pyx_c_eqf(a, b) ((a)==(b))
- #define __Pyx_c_sumf(a, b) ((a)+(b))
- #define __Pyx_c_difff(a, b) ((a)-(b))
- #define __Pyx_c_prodf(a, b) ((a)*(b))
- #define __Pyx_c_quotf(a, b) ((a)/(b))
- #define __Pyx_c_negf(a) (-(a))
+ #define __Pyx_c_eq_float(a, b) ((a)==(b))
+ #define __Pyx_c_sum_float(a, b) ((a)+(b))
+ #define __Pyx_c_diff_float(a, b) ((a)-(b))
+ #define __Pyx_c_prod_float(a, b) ((a)*(b))
+ #define __Pyx_c_quot_float(a, b) ((a)/(b))
+ #define __Pyx_c_neg_float(a) (-(a))
#ifdef __cplusplus
- #define __Pyx_c_is_zerof(z) ((z)==(float)0)
- #define __Pyx_c_conjf(z) (::std::conj(z))
+ #define __Pyx_c_is_zero_float(z) ((z)==(float)0)
+ #define __Pyx_c_conj_float(z) (::std::conj(z))
#if 1
- #define __Pyx_c_absf(z) (::std::abs(z))
- #define __Pyx_c_powf(a, b) (::std::pow(a, b))
+ #define __Pyx_c_abs_float(z) (::std::abs(z))
+ #define __Pyx_c_pow_float(a, b) (::std::pow(a, b))
#endif
#else
- #define __Pyx_c_is_zerof(z) ((z)==0)
- #define __Pyx_c_conjf(z) (conjf(z))
+ #define __Pyx_c_is_zero_float(z) ((z)==0)
+ #define __Pyx_c_conj_float(z) (conjf(z))
#if 1
- #define __Pyx_c_absf(z) (cabsf(z))
- #define __Pyx_c_powf(a, b) (cpowf(a, b))
+ #define __Pyx_c_abs_float(z) (cabsf(z))
+ #define __Pyx_c_pow_float(a, b) (cpowf(a, b))
#endif
#endif
#else
- static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex, __pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex, __pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex, __pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex, __pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex, __pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex);
- static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex);
+ static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex);
+ static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex);
#if 1
- static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex);
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex, __pyx_t_float_complex);
#endif
#endif
-/* None.proto */
-static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double);
-
-/* None.proto */
+/* Arithmetic.proto */
#if CYTHON_CCOMPLEX
- #define __Pyx_c_eq(a, b) ((a)==(b))
- #define __Pyx_c_sum(a, b) ((a)+(b))
- #define __Pyx_c_diff(a, b) ((a)-(b))
- #define __Pyx_c_prod(a, b) ((a)*(b))
- #define __Pyx_c_quot(a, b) ((a)/(b))
- #define __Pyx_c_neg(a) (-(a))
+ #define __Pyx_c_eq_double(a, b) ((a)==(b))
+ #define __Pyx_c_sum_double(a, b) ((a)+(b))
+ #define __Pyx_c_diff_double(a, b) ((a)-(b))
+ #define __Pyx_c_prod_double(a, b) ((a)*(b))
+ #define __Pyx_c_quot_double(a, b) ((a)/(b))
+ #define __Pyx_c_neg_double(a) (-(a))
#ifdef __cplusplus
- #define __Pyx_c_is_zero(z) ((z)==(double)0)
- #define __Pyx_c_conj(z) (::std::conj(z))
+ #define __Pyx_c_is_zero_double(z) ((z)==(double)0)
+ #define __Pyx_c_conj_double(z) (::std::conj(z))
#if 1
- #define __Pyx_c_abs(z) (::std::abs(z))
- #define __Pyx_c_pow(a, b) (::std::pow(a, b))
+ #define __Pyx_c_abs_double(z) (::std::abs(z))
+ #define __Pyx_c_pow_double(a, b) (::std::pow(a, b))
#endif
#else
- #define __Pyx_c_is_zero(z) ((z)==0)
- #define __Pyx_c_conj(z) (conj(z))
+ #define __Pyx_c_is_zero_double(z) ((z)==0)
+ #define __Pyx_c_conj_double(z) (conj(z))
#if 1
- #define __Pyx_c_abs(z) (cabs(z))
- #define __Pyx_c_pow(a, b) (cpow(a, b))
+ #define __Pyx_c_abs_double(z) (cabs(z))
+ #define __Pyx_c_pow_double(a, b) (cpow(a, b))
#endif
#endif
#else
- static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex, __pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex, __pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex, __pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex, __pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex, __pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex);
- static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex);
+ static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex);
+ static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex);
#if 1
- static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex, __pyx_t_double_complex);
#endif
#endif
@@ -2315,6 +2518,7 @@ static PyObject *__pyx_builtin_enumerate;
static PyObject *__pyx_builtin_NotImplementedError;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_RuntimeError;
+static PyObject *__pyx_builtin_ImportError;
static const char __pyx_k_[] = "/";
static const char __pyx_k_C[] = "C";
static const char __pyx_k_S[] = "S";
@@ -2339,9 +2543,9 @@ static const char __pyx_k_NOW[] = "NOW";
static const char __pyx_k_Var[] = "Var";
static const char __pyx_k_YES[] = "YES";
static const char __pyx_k__10[] = "";
-static const char __pyx_k__63[] = " ";
-static const char __pyx_k__65[] = "(,)";
-static const char __pyx_k__77[] = "*";
+static const char __pyx_k__64[] = " ";
+static const char __pyx_k__66[] = "(,)";
+static const char __pyx_k__81[] = "*";
static const char __pyx_k_all[] = "all";
static const char __pyx_k_any[] = "any";
static const char __pyx_k_doc[] = "__doc__";
@@ -2353,6 +2557,7 @@ static const char __pyx_k_var[] = "var";
static const char __pyx_k_zip[] = "zip";
static const char __pyx_k_Attr[] = "Attr";
static const char __pyx_k_FLAG[] = "FLAG";
+static const char __pyx_k_FULL[] = "FULL";
static const char __pyx_k_File[] = "File";
static const char __pyx_k_ICEE[] = "ICEE";
static const char __pyx_k_NONE[] = "NONE";
@@ -2385,6 +2590,7 @@ static const char __pyx_k_prod[] = "prod";
static const char __pyx_k_rank[] = "rank";
static const char __pyx_k_read[] = "read";
static const char __pyx_k_real[] = "real";
+static const char __pyx_k_root[] = "root";
static const char __pyx_k_size[] = "size";
static const char __pyx_k_test[] = "__test__";
static const char __pyx_k_type[] = "type";
@@ -2398,6 +2604,7 @@ static const char __pyx_k_LATER[] = "LATER";
static const char __pyx_k_array[] = "array";
static const char __pyx_k_attrs[] = "attrs";
static const char __pyx_k_atype[] = "atype";
+static const char __pyx_k_bcast[] = "bcast";
static const char __pyx_k_bytes[] = "(bytes)";
static const char __pyx_k_close[] = "close";
static const char __pyx_k_count[] = "count";
@@ -2428,6 +2635,7 @@ static const char __pyx_k_varid[] = "varid";
static const char __pyx_k_write[] = "write";
static const char __pyx_k_zeros[] = "zeros";
static const char __pyx_k_15s_lu[] = "%15s : %lu";
+static const char __pyx_k_MINMAX[] = "MINMAX";
static const char __pyx_k_POSIX1[] = "POSIX1";
static const char __pyx_k_Writer[] = "Writer";
static const char __pyx_k_config[] = "config";
@@ -2457,6 +2665,7 @@ static const char __pyx_k_values[] = "values";
static const char __pyx_k_var_id[] = "var_id";
static const char __pyx_k_xrange[] = "xrange";
static const char __pyx_k_CURRENT[] = "CURRENT";
+static const char __pyx_k_DEFAULT[] = "DEFAULT";
static const char __pyx_k_Reading[] = "Reading ... ";
static const char __pyx_k_UNKNOWN[] = "UNKNOWN";
static const char __pyx_k_Varinfo[] = "Varinfo";
@@ -2486,6 +2695,7 @@ static const char __pyx_k_Attrinfo[] = "Attrinfo";
static const char __pyx_k_DATATYPE[] = "DATATYPE";
static const char __pyx_k_Ellipsis[] = "Ellipsis";
static const char __pyx_k_FLEXPATH[] = "FLEXPATH";
+static const char __pyx_k_Get_rank[] = "Get_rank";
static const char __pyx_k_KeyError[] = "KeyError";
static const char __pyx_k_LOCKMODE[] = "LOCKMODE";
static const char __pyx_k_asscalar[] = "asscalar";
@@ -2499,6 +2709,7 @@ static const char __pyx_k_meshname[] = "meshname";
static const char __pyx_k_qualname[] = "__qualname__";
static const char __pyx_k_readattr[] = "_readattr";
static const char __pyx_k_string_2[] = "string_";
+static const char __pyx_k_tempfile[] = "tempfile";
static const char __pyx_k_tostring[] = "tostring";
static const char __pyx_k_AdiosFile[] = "=== AdiosFile ===";
static const char __pyx_k_COMM_SELF[] = "COMM_SELF";
@@ -2528,6 +2739,7 @@ static const char __pyx_k_transform[] = "transform";
static const char __pyx_k_COMM_WORLD[] = "COMM_WORLD";
static const char __pyx_k_DATASPACES[] = "DATASPACES";
static const char __pyx_k_IndexError[] = "IndexError";
+static const char __pyx_k_STATISTICS[] = "STATISTICS";
static const char __pyx_k_ValueError[] = "ValueError";
static const char __pyx_k_buffersize[] = "buffersize";
static const char __pyx_k_complex128[] = "complex128";
@@ -2545,6 +2757,7 @@ static const char __pyx_k_startswith[] = "startswith";
static const char __pyx_k_time_index[] = "time_index";
static const char __pyx_k_time_steps[] = "time_steps";
static const char __pyx_k_timeseries[] = "timeseries";
+static const char __pyx_k_ImportError[] = "ImportError";
static const char __pyx_k_READ_METHOD[] = "READ_METHOD";
static const char __pyx_k_buffer_size[] = "buffer_size";
static const char __pyx_k_concatenate[] = "concatenate";
@@ -2586,8 +2799,9 @@ static const char __pyx_k_Not_an_open_file[] = "Not an open file";
static const char __pyx_k_unsigned_integer[] = "unsigned_integer";
static const char __pyx_k_BUFFER_ALLOC_WHEN[] = "BUFFER_ALLOC_WHEN";
static const char __pyx_k_global_dimensions[] = "global_dimensions";
+static const char __pyx_k_NamedTemporaryFile[] = "NamedTemporaryFile";
static const char __pyx_k_transform_type_str[] = "transform_type_str";
-static const char __pyx_k_var_read_line_1456[] = "var.read (line 1456)";
+static const char __pyx_k_var_read_line_1464[] = "var.read (line 1464)";
static const char __pyx_k_NotImplementedError[] = "NotImplementedError";
static const char __pyx_k_Not_implemented_yet[] = "Not implemented yet";
static const char __pyx_k_Not_an_open_variable[] = "Not an open variable";
@@ -2595,13 +2809,13 @@ static const char __pyx_k_set_time_aggregation[] = "set_time_aggregation";
static const char __pyx_k_Use_default_BP_method[] = ". Use default BP method";
static const char __pyx_k_AdiosGroup_vars_r_attrs_r[] = "AdiosGroup (vars=%r, attrs=%r)";
static const char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous";
-static const char __pyx_k_writer_define_var_line_2019[] = "writer.define_var (line 2019)";
+static const char __pyx_k_writer_define_var_line_2040[] = "writer.define_var (line 2040)";
static const char __pyx_k_Rank_is_out_of_range_nblock_r[] = "Rank is out of range (nblock=%r)";
static const char __pyx_k_WARN_Invalid_read_method_name[] = "[WARN] Invalid read method name:";
static const char __pyx_k_Data_type_is_not_supported_yet[] = "Data type is not supported yet";
-static const char __pyx_k_Define_a_group_associated_with[] = "\n Define a group associated with the file.\n\n Args:\n gname (str): group name.\n method (str, optional): Adios write method (default: 'POSIX1')\n method_params (str, optional): parameters for the write method (default: '')\n\n Example:\n\n >>> fw.declare_group('group', method='MPI', method_params='verbose=3')\n\n ";
+static const char __pyx_k_Define_a_group_associated_with[] = "\n Define a group associated with the file.\n\n Args:\n gname (str): group name.\n method (str, optional): Adios write method (default: 'POSIX1')\n method_params (str, optional): parameters for the write method (default: '')\n stats (int, optional): statistics (default: 'DEFAULT')\n\n Example:\n\n >>> fw.declare_group('group', method='MPI', method_params= [...]
static const char __pyx_k_Perform_read_Read_data_from_an[] = " Perform read.\n\n Read data from an ADIOS BP file. Subset reading is\n supported. Without any options, this will read out a whole\n data.\n\n Args:\n offset (tuple of int, optional): offset (default: ())\n count (tuple of int, optional): count (default: ())\n scalar (tuple of bool, optional): scalar (default: ())\n from_steps (int, optional): starting ste [...]
-static const char __pyx_k_writer_declare_group_line_1982[] = "writer.declare_group (line 1982)";
+static const char __pyx_k_writer_declare_group_line_1995[] = "writer.declare_group (line 1995)";
static const char __pyx_k_AdiosFile_path_r_nvars_r_vars_r[] = "AdiosFile (path=%r, nvars=%r, vars=%r, nattrs=%r, attrs=%r, current_step=%r, last_step=%r, file_size=%r)";
static const char __pyx_k_AdiosVar_varid_r_name_r_dtype_r[] = "AdiosVar (varid=%r, name=%r, dtype=%r, ndim=%r, dims=%r, nsteps=%r, attrs=%r)";
static const char __pyx_k_AdiosVarinfo_name_r_ldim_r_gdim[] = "AdiosVarinfo (name=%r, ldim=%r, gdim=%r, offset=%r, transform=%r, value=%r)";
@@ -2609,6 +2823,8 @@ static const char __pyx_k_Define_a_variable_associated_wi[] = "\n Define
static const char __pyx_k_Step_index_is_out_of_range_from[] = "Step index is out of range: from_steps=%r, nsteps=%r";
static const char __pyx_k_Users_jyc_project_adios_devel_w[] = "/Users/jyc/project/adios-devel/wrappers/numpy/adios_mpi.pyx";
static const char __pyx_k_Warning_No_support_yet_s_type_d[] = "Warning: No support yet: %s (type=%d, bytes=%d)";
+static const char __pyx_k_Warning_skipping_defining_var_r[] = "Warning: skipping defining var(%r) with None value";
+static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import";
static const char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)";
static const char __pyx_k_ADIOS_ADIOS_python_module_module[] = "ADIOS: ADIOS python module\n\n.. moduleauthor:: Jong Choi <choij at ornl.gov>\n";
static const char __pyx_k_AdiosAttr_name_r_dtype_r_value_r[] = "AdiosAttr (name=%r, dtype=%r, value=%r)";
@@ -2624,6 +2840,7 @@ static const char __pyx_k_Only_contiguous_arrays_are_suppo[] = "Only contiguous
static const char __pyx_k_Requested_is_larger_than_the_sha[] = "Requested is larger than the shape.";
static const char __pyx_k_Scalar_dimension_mismatch_scalar[] = "Scalar dimension mismatch (scalar dim: %r)";
static const char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous";
+static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import";
static const char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short.";
static PyObject *__pyx_kp_s_;
static PyObject *__pyx_kp_s_15s_d;
@@ -2654,6 +2871,7 @@ static PyObject *__pyx_n_s_Clone;
static PyObject *__pyx_kp_s_Count_dimension_mismatch_count_d;
static PyObject *__pyx_n_s_DATASPACES;
static PyObject *__pyx_n_s_DATATYPE;
+static PyObject *__pyx_n_s_DEFAULT;
static PyObject *__pyx_n_s_DIMES;
static PyObject *__pyx_kp_s_Data_type_is_not_supported_yet;
static PyObject *__pyx_kp_u_Define_a_group_associated_with;
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static PyObject *__pyx_n_s_Ellipsis;
static PyObject *__pyx_n_s_FLAG;
static PyObject *__pyx_n_s_FLEXPATH;
+static PyObject *__pyx_n_s_FULL;
static PyObject *__pyx_n_s_FancySelection;
static PyObject *__pyx_n_s_File;
static PyObject *__pyx_kp_u_Format_string_allocated_too_shor;
static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2;
+static PyObject *__pyx_n_s_Get_rank;
static PyObject *__pyx_n_s_ICEE;
+static PyObject *__pyx_n_s_ImportError;
static PyObject *__pyx_n_s_IndexError;
static PyObject *__pyx_n_s_KeyError;
static PyObject *__pyx_n_s_LATER;
static PyObject *__pyx_n_s_LOCKMODE;
+static PyObject *__pyx_n_s_MINMAX;
static PyObject *__pyx_n_s_MPI;
static PyObject *__pyx_n_s_NO;
static PyObject *__pyx_n_s_NONE;
static PyObject *__pyx_n_s_NOW;
+static PyObject *__pyx_n_s_NamedTemporaryFile;
static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor;
static PyObject *__pyx_n_s_NotImplementedError;
static PyObject *__pyx_kp_s_Not_a_valid_var;
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static PyObject *__pyx_kp_s_Requested_is_larger_than_the_sha;
static PyObject *__pyx_n_s_RuntimeError;
static PyObject *__pyx_n_s_S;
+static PyObject *__pyx_n_s_STATISTICS;
static PyObject *__pyx_kp_s_Scalar_dimension_mismatch_scalar;
static PyObject *__pyx_n_s_SimpleSelection;
static PyObject *__pyx_kp_s_Step_index_is_out_of_range_from;
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static PyObject *__pyx_n_s_Varinfo;
static PyObject *__pyx_kp_s_WARN_Invalid_read_method_name;
static PyObject *__pyx_kp_s_Warning_No_support_yet_s_type_d;
+static PyObject *__pyx_kp_s_Warning_skipping_defining_var_r;
static PyObject *__pyx_n_s_Writer;
static PyObject *__pyx_n_s_YES;
static PyObject *__pyx_kp_s__10;
-static PyObject *__pyx_kp_s__63;
-static PyObject *__pyx_kp_s__65;
-static PyObject *__pyx_n_s__77;
+static PyObject *__pyx_kp_s__64;
+static PyObject *__pyx_kp_s__66;
+static PyObject *__pyx_n_s__81;
static PyObject *__pyx_n_s_adios_mpi;
static PyObject *__pyx_n_s_advance;
static PyObject *__pyx_n_s_all;
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static PyObject *__pyx_n_s_atype;
static PyObject *__pyx_n_s_axis;
static PyObject *__pyx_n_s_base_path;
+static PyObject *__pyx_n_s_bcast;
static PyObject *__pyx_n_s_bool;
static PyObject *__pyx_n_s_bpls;
static PyObject *__pyx_n_s_buffer_size;
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static PyObject *__pyx_n_s_nspace;
static PyObject *__pyx_n_s_nsteps;
static PyObject *__pyx_n_s_numpy;
+static PyObject *__pyx_kp_s_numpy_core_multiarray_failed_to;
+static PyObject *__pyx_kp_s_numpy_core_umath_failed_to_impor;
static PyObject *__pyx_n_s_nvars;
static PyObject *__pyx_n_s_offset;
static PyObject *__pyx_n_s_order;
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static PyObject *__pyx_n_s_release_step;
static PyObject *__pyx_n_s_replace;
static PyObject *__pyx_n_s_reshape;
+static PyObject *__pyx_n_s_root;
static PyObject *__pyx_n_s_rstrip;
static PyObject *__pyx_n_s_scalar;
static PyObject *__pyx_n_s_schema_version;
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static PyObject *__pyx_n_s_strlen;
static PyObject *__pyx_n_s_syncgroupid;
static PyObject *__pyx_n_s_t;
+static PyObject *__pyx_n_s_tempfile;
static PyObject *__pyx_n_s_test;
static PyObject *__pyx_n_s_time_index;
static PyObject *__pyx_n_s_time_steps;
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static PyObject *__pyx_n_s_var;
static PyObject *__pyx_n_s_var_id;
static PyObject *__pyx_n_s_var_namelist;
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+static PyObject *__pyx_kp_u_var_read_line_1464;
static PyObject *__pyx_n_s_varid;
static PyObject *__pyx_n_s_varname;
static PyObject *__pyx_n_s_vars;
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static PyObject *__pyx_n_s_w;
static PyObject *__pyx_n_s_when;
static PyObject *__pyx_n_s_write;
-static PyObject *__pyx_kp_u_writer_declare_group_line_1982;
-static PyObject *__pyx_kp_u_writer_define_var_line_2019;
+static PyObject *__pyx_kp_u_writer_declare_group_line_1995;
+static PyObject *__pyx_kp_u_writer_define_var_line_2040;
static PyObject *__pyx_n_s_xrange;
static PyObject *__pyx_n_s_zeros;
static PyObject *__pyx_n_s_zip;
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static PyObject *__pyx_pf_9adios_mpi_6writer_5attrs___get__(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_9adios_mpi_6writer_26timeaggregation_buffersize___get__(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self); /* proto */
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+static int __pyx_pf_9adios_mpi_6writer___init__(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self, PyObject *__pyx_v_fname, int __pyx_v_is_noxml, PyObject *__pyx_v_mode, int __pyx_v_stats, struct PyMPICommObject *__pyx_v_comm, PyObject *__pyx_v_method, PyObject *__pyx_v_method_params); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_6writer_2declare_group(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self, PyObject *__pyx_v_gname, PyObject *__pyx_v_method, PyObject *__pyx_v_method_params, int __pyx_v_stats); /* proto */
static PyObject *__pyx_pf_9adios_mpi_6writer_4set_time_aggregation(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self, PyObject *__pyx_v_buffer_size); /* proto */
static PyObject *__pyx_pf_9adios_mpi_6writer_6define_var(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self, PyObject *__pyx_v_varname, PyObject *__pyx_v_ldim, PyObject *__pyx_v_gdim, PyObject *__pyx_v_offset, PyObject *__pyx_v_transform); /* proto */
static PyObject *__pyx_pf_9adios_mpi_6writer_8define_attr(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self, PyObject *__pyx_v_attrname); /* proto */
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static struct PyMPICommObject *__pyx_k__16;
static ADIOS_LOCKMODE __pyx_k__17;
static struct PyMPICommObject *__pyx_k__54;
-static PyObject *__pyx_k__55;
-static PyObject *__pyx_k__56;
+static int __pyx_k__55;
+static int __pyx_k__56;
static PyObject *__pyx_k__57;
+static PyObject *__pyx_k__58;
static PyObject *__pyx_k__59;
-static PyObject *__pyx_k__60;
static PyObject *__pyx_k__61;
+static PyObject *__pyx_k__62;
+static PyObject *__pyx_k__63;
static PyObject *__pyx_slice__3;
static PyObject *__pyx_slice__4;
static PyObject *__pyx_slice__5;
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static PyObject *__pyx_tuple__50;
static PyObject *__pyx_tuple__51;
static PyObject *__pyx_tuple__53;
-static PyObject *__pyx_tuple__58;
-static PyObject *__pyx_tuple__62;
-static PyObject *__pyx_tuple__64;
-static PyObject *__pyx_tuple__66;
+static PyObject *__pyx_tuple__60;
+static PyObject *__pyx_tuple__65;
static PyObject *__pyx_tuple__67;
static PyObject *__pyx_tuple__68;
static PyObject *__pyx_tuple__69;
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static PyObject *__pyx_tuple__74;
static PyObject *__pyx_tuple__75;
static PyObject *__pyx_tuple__76;
+static PyObject *__pyx_tuple__77;
static PyObject *__pyx_tuple__78;
+static PyObject *__pyx_tuple__79;
static PyObject *__pyx_tuple__80;
static PyObject *__pyx_tuple__82;
-static PyObject *__pyx_codeobj__79;
-static PyObject *__pyx_codeobj__81;
+static PyObject *__pyx_tuple__84;
+static PyObject *__pyx_tuple__86;
static PyObject *__pyx_codeobj__83;
+static PyObject *__pyx_codeobj__85;
+static PyObject *__pyx_codeobj__87;
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+/* "adios_mpi.pyx":35
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- /* "adios_mpi.pyx":519
+ /* "adios_mpi.pyx":527
* assert val.flags.contiguous, 'Only contiguous arrays are supported.'
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/* function exit code */
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goto __pyx_L4_argument_unpacking_done;
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- __Pyx_RaiseArgtupleInvalid("init_noxml", 0, 0, 1, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 531, __pyx_L3_error)
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__pyx_L3_error:;
__Pyx_AddTraceback("adios_mpi.init_noxml", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
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/* function exit code */
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__pyx_t_1 = __pyx_f_9adios_mpi_init_noxml(0, &__pyx_t_2);
- __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 531, __pyx_L1_error)
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return __pyx_r;
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-/* "adios_mpi.pyx":536
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__Pyx_RefNannySetupContext("allocate_buffer", 0);
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goto __pyx_L0;
- /* "adios_mpi.pyx":536
+ /* "adios_mpi.pyx":544
* return adios_init_noxml(init_comm.ob_mpi)
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else {
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goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("allocate_buffer", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 536, __pyx_L3_error)
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__pyx_L3_error:;
__Pyx_AddTraceback("adios_mpi.allocate_buffer", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -6686,7 +6920,7 @@ static PyObject *__pyx_pf_9adios_mpi_34allocate_buffer(CYTHON_UNUSED PyObject *_
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__Pyx_XDECREF(__pyx_r);
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@@ -6703,7 +6937,7 @@ static PyObject *__pyx_pf_9adios_mpi_34allocate_buffer(CYTHON_UNUSED PyObject *_
return __pyx_r;
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- /* "adios_mpi.pyx":546
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* s2b(time_index),
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+ __pyx_t_1 = __pyx_f_9adios_mpi_s2b(__pyx_v_name, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 554, __pyx_L1_error)
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- __pyx_t_3 = __pyx_f_9adios_mpi_s2b(__pyx_v_time_index, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 547, __pyx_L1_error)
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__Pyx_GOTREF(__pyx_t_3);
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- /* "adios_mpi.pyx":545
+ /* "adios_mpi.pyx":553
* int stats = adios_stat_default):
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* adios_declare_group (&id, # <<<<<<<<<<<<<<
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- /* "adios_mpi.pyx":549
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* s2b(time_index),
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switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -6858,21 +7092,21 @@ static PyObject *__pyx_pw_9adios_mpi_37declare_group(PyObject *__pyx_self, PyObj
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__pyx_L3_error:;
__Pyx_AddTraceback("adios_mpi.declare_group", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
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__pyx_t_2.stats = __pyx_v_stats;
__pyx_t_1 = __pyx_f_9adios_mpi_declare_group(__pyx_v_name, 0, &__pyx_t_2);
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@@ -6913,7 +7147,7 @@ static PyObject *__pyx_pf_9adios_mpi_36declare_group(CYTHON_UNUSED PyObject *__p
return __pyx_r;
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@@ -6951,62 +7185,62 @@ static int64_t __pyx_f_9adios_mpi_define_var(int64_t __pyx_v_group_id, PyObject
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}
- /* "adios_mpi.pyx":559
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* s2b(path),
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- __pyx_t_1 = __pyx_f_9adios_mpi_s2b(__pyx_v_name, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 559, __pyx_L1_error)
+ __pyx_t_1 = __pyx_f_9adios_mpi_s2b(__pyx_v_name, 0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 567, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_AsString(__pyx_t_1); if (unlikely((!__pyx_t_2) && PyErr_Occurred())) __PYX_ERR(0, 559, __pyx_L1_error)
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- /* "adios_mpi.pyx":560
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* return adios_define_var(group_id,
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- __pyx_t_3 = __pyx_f_9adios_mpi_s2b(__pyx_v_path, 0); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 560, __pyx_L1_error)
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- /* "adios_mpi.pyx":562
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* s2b(path),
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- __pyx_t_5 = __pyx_f_9adios_mpi_s2b(__pyx_v_dimensions, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 562, __pyx_L1_error)
+ __pyx_t_5 = __pyx_f_9adios_mpi_s2b(__pyx_v_dimensions, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 570, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_5);
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+ __pyx_t_7 = __pyx_f_9adios_mpi_s2b(__pyx_v_global_dimensions, 0); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 571, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_7);
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__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
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+ __pyx_t_7 = __pyx_f_9adios_mpi_s2b(__pyx_v_cell_type, 0); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 662, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_7);
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- /* "adios_mpi.pyx":655
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+ __pyx_t_11 = __pyx_f_9adios_mpi_s2b(__pyx_v_nspace, 0); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 664, __pyx_L1_error)
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+ __pyx_t_13 = __pyx_f_9adios_mpi_s2b(__pyx_v_name, 0); if (unlikely(!__pyx_t_13)) __PYX_ERR(0, 666, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_13);
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__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
goto __pyx_L0;
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case 1:
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else {
- __Pyx_RaiseArgtupleInvalid("define_mesh_unstructured", 1, 8, 8, 1); __PYX_ERR(0, 642, __pyx_L3_error)
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else {
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if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_cell_type)) != 0)) kw_args--;
else {
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else {
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else {
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else {
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goto __pyx_L8;
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+ /* "adios_mpi.pyx":811
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goto __pyx_L3;
}
- /* "adios_mpi.pyx":805
+ /* "adios_mpi.pyx":813
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goto __pyx_L3;
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goto __pyx_L3;
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+ /* "adios_mpi.pyx":817
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goto __pyx_L3;
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goto __pyx_L3;
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PyObject *__pyx_t_13 = NULL;
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adios_selection_delete(__pyx_v_sel);
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return __pyx_r;
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__Pyx_RefNannySetupContext("__init__", 0);
- /* "adios_mpi.pyx":1964
- * str mode = "w",
- * MPI.Comm comm = MPI.COMM_WORLD):
+ /* "adios_mpi.pyx":1976
+ * str method = "POSIX1",
+ * str method_params = ""):
* self.gid = 0 # <<<<<<<<<<<<<<
* self.fname = fname
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+ * self.method = method
*/
__pyx_v_self->gid = 0;
- /* "adios_mpi.pyx":1965
- * MPI.Comm comm = MPI.COMM_WORLD):
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* self.fname = fname # <<<<<<<<<<<<<<
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__Pyx_DECREF(__pyx_v_self->fname);
__pyx_v_self->fname = __pyx_v_fname;
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- /* "adios_mpi.pyx":1968
- * self.method = ""
- * self.method_params = ""
+ /* "adios_mpi.pyx":1980
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* self.comm = comm
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__pyx_v_self->is_noxml = __pyx_v_is_noxml;
- /* "adios_mpi.pyx":1969
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__pyx_v_self->mode = __pyx_v_mode;
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__pyx_v_self->comm = __pyx_v_comm;
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PyObject *__pyx_v_gname = 0;
PyObject *__pyx_v_method = 0;
PyObject *__pyx_v_method_params = 0;
+ int __pyx_v_stats;
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+ goto __pyx_L1_error;
+ __pyx_L10_try_end:;
+ }
+
+ /* "../../../../sw/anaconda2/4.1.1/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":997
+ * raise ImportError("numpy.core.umath failed to import")
+ *
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+ * try:
+ * _import_umath()
+ */
+
+ /* function exit code */
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_5);
+ __Pyx_XDECREF(__pyx_t_6);
+ __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_t_8);
+ __Pyx_AddTraceback("numpy.import_ufunc", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
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static PyObject *__pyx_tp_new_9adios_mpi_softdict(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = (&PyDict_Type)->tp_new(t, a, k);
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@@ -40376,7 +42510,7 @@ static PyTypeObject __pyx_type_9adios_mpi_writer = {
0, /*tp_setattro*/
0, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- "writer(str fname, bool is_noxml=True, str mode='w', Comm comm=MPI.COMM_WORLD)\n\n writer class for Adios write.\n\n Args:\n fname (str): filename.\n is_noxml (bool, optional): Set True if use noxml APIs (default: True).\n comm (MPI.Comm, optional): MPI comm for parallel read/write (default: MPI.COMM_WORLD).\n\n Example:\n\n >>> import adios as ad\n >>> f = ad.writer('adiosfile.bp')\n\n ", /*tp_doc*/
+ "writer(str fname, bool is_noxml=True, str mode='w', int stats=adios_stat_default, Comm comm=MPI.COMM_WORLD, str method='POSIX1', str method_params='')\n\n writer class for Adios write.\n\n Args:\n fname (str): filename.\n is_noxml (bool, optional): Set True if use noxml APIs (default: True).\n comm (MPI.Comm, optional): MPI comm for parallel read/write (default: MPI.COMM_WORLD).\n\n Example:\n\n >>> import adios as ad\n >>> f = ad.writer('adiosfile. [...]
__pyx_tp_traverse_9adios_mpi_writer, /*tp_traverse*/
__pyx_tp_clear_9adios_mpi_writer, /*tp_clear*/
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{&__pyx_n_s_DATATYPE, __pyx_k_DATATYPE, sizeof(__pyx_k_DATATYPE), 0, 0, 1, 1},
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{&__pyx_n_s_DIMES, __pyx_k_DIMES, sizeof(__pyx_k_DIMES), 0, 0, 1, 1},
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{&__pyx_n_s_FLEXPATH, __pyx_k_FLEXPATH, sizeof(__pyx_k_FLEXPATH), 0, 0, 1, 1},
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{&__pyx_n_s_ICEE, __pyx_k_ICEE, sizeof(__pyx_k_ICEE), 0, 0, 1, 1},
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{&__pyx_n_s_LOCKMODE, __pyx_k_LOCKMODE, sizeof(__pyx_k_LOCKMODE), 0, 0, 1, 1},
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{&__pyx_n_s_MPI, __pyx_k_MPI, sizeof(__pyx_k_MPI), 0, 0, 1, 1},
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{&__pyx_n_s_NOW, __pyx_k_NOW, sizeof(__pyx_k_NOW), 0, 0, 1, 1},
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{&__pyx_n_s_S, __pyx_k_S, sizeof(__pyx_k_S), 0, 0, 1, 1},
+ {&__pyx_n_s_STATISTICS, __pyx_k_STATISTICS, sizeof(__pyx_k_STATISTICS), 0, 0, 1, 1},
{&__pyx_kp_s_Scalar_dimension_mismatch_scalar, __pyx_k_Scalar_dimension_mismatch_scalar, sizeof(__pyx_k_Scalar_dimension_mismatch_scalar), 0, 0, 1, 0},
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{&__pyx_kp_s_Step_index_is_out_of_range_from, __pyx_k_Step_index_is_out_of_range_from, sizeof(__pyx_k_Step_index_is_out_of_range_from), 0, 0, 1, 0},
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{&__pyx_kp_s_WARN_Invalid_read_method_name, __pyx_k_WARN_Invalid_read_method_name, sizeof(__pyx_k_WARN_Invalid_read_method_name), 0, 0, 1, 0},
{&__pyx_kp_s_Warning_No_support_yet_s_type_d, __pyx_k_Warning_No_support_yet_s_type_d, sizeof(__pyx_k_Warning_No_support_yet_s_type_d), 0, 0, 1, 0},
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{&__pyx_n_s_Writer, __pyx_k_Writer, sizeof(__pyx_k_Writer), 0, 0, 1, 1},
{&__pyx_n_s_YES, __pyx_k_YES, sizeof(__pyx_k_YES), 0, 0, 1, 1},
{&__pyx_kp_s__10, __pyx_k__10, sizeof(__pyx_k__10), 0, 0, 1, 0},
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- {&__pyx_n_s__77, __pyx_k__77, sizeof(__pyx_k__77), 0, 0, 1, 1},
+ {&__pyx_kp_s__64, __pyx_k__64, sizeof(__pyx_k__64), 0, 0, 1, 0},
+ {&__pyx_kp_s__66, __pyx_k__66, sizeof(__pyx_k__66), 0, 0, 1, 0},
+ {&__pyx_n_s__81, __pyx_k__81, sizeof(__pyx_k__81), 0, 0, 1, 1},
{&__pyx_n_s_adios_mpi, __pyx_k_adios_mpi, sizeof(__pyx_k_adios_mpi), 0, 0, 1, 1},
{&__pyx_n_s_advance, __pyx_k_advance, sizeof(__pyx_k_advance), 0, 0, 1, 1},
{&__pyx_n_s_all, __pyx_k_all, sizeof(__pyx_k_all), 0, 0, 1, 1},
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{&__pyx_n_s_axis, __pyx_k_axis, sizeof(__pyx_k_axis), 0, 0, 1, 1},
{&__pyx_n_s_base_path, __pyx_k_base_path, sizeof(__pyx_k_base_path), 0, 0, 1, 1},
+ {&__pyx_n_s_bcast, __pyx_k_bcast, sizeof(__pyx_k_bcast), 0, 0, 1, 1},
{&__pyx_n_s_bool, __pyx_k_bool, sizeof(__pyx_k_bool), 0, 0, 1, 1},
{&__pyx_n_s_bpls, __pyx_k_bpls, sizeof(__pyx_k_bpls), 0, 0, 1, 1},
{&__pyx_n_s_buffer_size, __pyx_k_buffer_size, sizeof(__pyx_k_buffer_size), 0, 0, 1, 1},
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{&__pyx_n_s_numpy, __pyx_k_numpy, sizeof(__pyx_k_numpy), 0, 0, 1, 1},
+ {&__pyx_kp_s_numpy_core_multiarray_failed_to, __pyx_k_numpy_core_multiarray_failed_to, sizeof(__pyx_k_numpy_core_multiarray_failed_to), 0, 0, 1, 0},
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{&__pyx_n_s_reshape, __pyx_k_reshape, sizeof(__pyx_k_reshape), 0, 0, 1, 1},
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{&__pyx_n_s_rstrip, __pyx_k_rstrip, sizeof(__pyx_k_rstrip), 0, 0, 1, 1},
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{&__pyx_n_s_t, __pyx_k_t, sizeof(__pyx_k_t), 0, 0, 1, 1},
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{&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1},
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{&__pyx_n_s_varid, __pyx_k_varid, sizeof(__pyx_k_varid), 0, 0, 1, 1},
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__pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) __PYX_ERR(1, 799, __pyx_L1_error)
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__Pyx_GIVEREF(__pyx_slice__24);
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__Pyx_GIVEREF(__pyx_tuple__25);
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*/
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__Pyx_GIVEREF(__pyx_slice__38);
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__Pyx_GIVEREF(__pyx_slice__41);
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+ PyObject **d;
+ Py_ssize_t nd;
+ Py_ssize_t nk;
+ PyObject *result;
+ assert(kwargs == NULL || PyDict_Check(kwargs));
+ nk = kwargs ? PyDict_Size(kwargs) : 0;
+ if (Py_EnterRecursiveCall((char*)" while calling a Python object")) {
+ return NULL;
+ }
+ if (
+#if PY_MAJOR_VERSION >= 3
+ co->co_kwonlyargcount == 0 &&
+#endif
+ likely(kwargs == NULL || nk == 0) &&
+ co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) {
+ if (argdefs == NULL && co->co_argcount == nargs) {
+ result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals);
+ goto done;
+ }
+ else if (nargs == 0 && argdefs != NULL
+ && co->co_argcount == Py_SIZE(argdefs)) {
+ /* function called with no arguments, but all parameters have
+ a default value: use default values as arguments .*/
+ args = &PyTuple_GET_ITEM(argdefs, 0);
+ result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals);
+ goto done;
+ }
+ }
+ if (kwargs != NULL) {
+ Py_ssize_t pos, i;
+ kwtuple = PyTuple_New(2 * nk);
+ if (kwtuple == NULL) {
+ result = NULL;
+ goto done;
+ }
+ k = &PyTuple_GET_ITEM(kwtuple, 0);
+ pos = i = 0;
+ while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) {
+ Py_INCREF(k[i]);
+ Py_INCREF(k[i+1]);
+ i += 2;
+ }
+ nk = i / 2;
+ }
+ else {
+ kwtuple = NULL;
+ k = NULL;
+ }
+ closure = PyFunction_GET_CLOSURE(func);
+#if PY_MAJOR_VERSION >= 3
+ kwdefs = PyFunction_GET_KW_DEFAULTS(func);
+#endif
+ if (argdefs != NULL) {
+ d = &PyTuple_GET_ITEM(argdefs, 0);
+ nd = Py_SIZE(argdefs);
+ }
+ else {
+ d = NULL;
+ nd = 0;
+ }
+#if PY_MAJOR_VERSION >= 3
+ result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL,
+ args, nargs,
+ k, (int)nk,
+ d, (int)nd, kwdefs, closure);
+#else
+ result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL,
+ args, nargs,
+ k, (int)nk,
+ d, (int)nd, closure);
+#endif
+ Py_XDECREF(kwtuple);
+done:
+ Py_LeaveRecursiveCall();
+ return result;
+}
+#endif // CPython < 3.6
+#endif // CYTHON_FAST_PYCALL
+
/* PyObjectCall */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) {
@@ -43001,6 +45408,11 @@ static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) {
return result;
}
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
+#if CYTHON_FAST_PYCALL
+ if (PyFunction_Check(func)) {
+ return __Pyx_PyFunction_FastCall(func, &arg, 1);
+ }
+#endif
#ifdef __Pyx_CyFunction_USED
if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) {
#else
@@ -43008,6 +45420,10 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObjec
#endif
if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) {
return __Pyx_PyObject_CallMethO(func, arg);
+#if CYTHON_FAST_PYCCALL
+ } else if (PyCFunction_GET_FLAGS(func) & METH_FASTCALL) {
+ return __Pyx_PyCFunction_FastCall(func, &arg, 1);
+#endif
}
}
return __Pyx__PyObject_CallOneArg(func, arg);
@@ -43026,6 +45442,11 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObjec
/* PyObjectCallNoArg */
#if CYTHON_COMPILING_IN_CPYTHON
static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) {
+#if CYTHON_FAST_PYCALL
+ if (PyFunction_Check(func)) {
+ return __Pyx_PyFunction_FastCall(func, NULL, 0);
+ }
+#endif
#ifdef __Pyx_CyFunction_USED
if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) {
#else
@@ -43040,7 +45461,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) {
#endif
/* PyErrFetchRestore */
- #if CYTHON_COMPILING_IN_CPYTHON
+ #if CYTHON_FAST_THREAD_STATE
static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) {
PyObject *tmp_type, *tmp_value, *tmp_tb;
tmp_type = tstate->curexc_type;
@@ -43164,7 +45585,7 @@ static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, in
Py_ssize_t cstart, Py_ssize_t cstop,
PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice,
int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) {
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_USE_TYPE_SLOTS
PyMappingMethods* mp;
#if PY_MAJOR_VERSION < 3
PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence;
@@ -43240,7 +45661,7 @@ static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, in
Py_XDECREF(owned_stop);
if (unlikely(!py_slice)) goto bad;
}
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_USE_TYPE_SLOTS
result = mp->mp_subscript(obj, py_slice);
#else
result = PyObject_GetItem(obj, py_slice);
@@ -43267,7 +45688,7 @@ bad:
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
CYTHON_NCP_UNUSED int wraparound,
CYTHON_NCP_UNUSED int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o);
if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
PyObject *r = PyList_GET_ITEM(o, i);
@@ -43282,7 +45703,7 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
CYTHON_NCP_UNUSED int wraparound,
CYTHON_NCP_UNUSED int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o);
if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
PyObject *r = PyTuple_GET_ITEM(o, i);
@@ -43297,7 +45718,7 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list,
CYTHON_NCP_UNUSED int wraparound,
CYTHON_NCP_UNUSED int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS
if (is_list || PyList_CheckExact(o)) {
Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) {
@@ -43338,7 +45759,7 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
}
/* PyIntBinop */
- #if CYTHON_COMPILING_IN_CPYTHON
+ #if !CYTHON_COMPILING_IN_PYPY
static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) {
#if PY_MAJOR_VERSION < 3
if (likely(PyInt_CheckExact(op1))) {
@@ -43351,12 +45772,14 @@ static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED
return PyLong_Type.tp_as_number->nb_add(op1, op2);
}
#endif
- #if CYTHON_USE_PYLONG_INTERNALS && PY_MAJOR_VERSION >= 3
+ #if CYTHON_USE_PYLONG_INTERNALS
if (likely(PyLong_CheckExact(op1))) {
const long b = intval;
long a, x;
+#ifdef HAVE_LONG_LONG
const PY_LONG_LONG llb = intval;
PY_LONG_LONG lla, llx;
+#endif
const digit* digits = ((PyLongObject*)op1)->ob_digit;
const Py_ssize_t size = Py_SIZE(op1);
if (likely(__Pyx_sst_abs(size) <= 1)) {
@@ -43368,58 +45791,74 @@ static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED
if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case 2:
if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case -3:
if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case 3:
if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case -4:
if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case 4:
if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
default: return PyLong_Type.tp_as_number->nb_add(op1, op2);
}
}
x = a + b;
return PyLong_FromLong(x);
+#ifdef HAVE_LONG_LONG
long_long:
llx = lla + llb;
return PyLong_FromLongLong(llx);
+#endif
+
+
}
#endif
if (PyFloat_CheckExact(op1)) {
@@ -43436,7 +45875,7 @@ static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED
#endif
/* PyIntBinop */
- #if CYTHON_COMPILING_IN_CPYTHON
+ #if !CYTHON_COMPILING_IN_PYPY
static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) {
#if PY_MAJOR_VERSION < 3
if (likely(PyInt_CheckExact(op1))) {
@@ -43449,12 +45888,14 @@ static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, CYTHON_U
return PyLong_Type.tp_as_number->nb_subtract(op1, op2);
}
#endif
- #if CYTHON_USE_PYLONG_INTERNALS && PY_MAJOR_VERSION >= 3
+ #if CYTHON_USE_PYLONG_INTERNALS
if (likely(PyLong_CheckExact(op1))) {
const long b = intval;
long a, x;
+#ifdef HAVE_LONG_LONG
const PY_LONG_LONG llb = intval;
PY_LONG_LONG lla, llx;
+#endif
const digit* digits = ((PyLongObject*)op1)->ob_digit;
const Py_ssize_t size = Py_SIZE(op1);
if (likely(__Pyx_sst_abs(size) <= 1)) {
@@ -43466,58 +45907,74 @@ static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, CYTHON_U
if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case 2:
if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) {
a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) {
lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case -3:
if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case 3:
if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) {
a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) {
lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case -4:
if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
case 4:
if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) {
a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]));
break;
+#ifdef HAVE_LONG_LONG
} else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) {
lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0]));
goto long_long;
+#endif
}
default: return PyLong_Type.tp_as_number->nb_subtract(op1, op2);
}
}
x = a - b;
return PyLong_FromLong(x);
+#ifdef HAVE_LONG_LONG
long_long:
llx = lla - llb;
return PyLong_FromLongLong(llx);
+#endif
+
+
}
#endif
if (PyFloat_CheckExact(op1)) {
@@ -43691,7 +46148,7 @@ bad:
/* GetModuleGlobalName */
static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) {
PyObject *result;
-#if CYTHON_COMPILING_IN_CPYTHON
+#if !CYTHON_AVOID_BORROWED_REFS
result = PyDict_GetItem(__pyx_d, name);
if (likely(result)) {
Py_INCREF(result);
@@ -43829,7 +46286,7 @@ return_ne:
}
/* PyIntBinop */
- #if CYTHON_COMPILING_IN_CPYTHON
+ #if !CYTHON_COMPILING_IN_PYPY
static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) {
if (op1 == op2) {
Py_RETURN_TRUE;
@@ -43845,7 +46302,7 @@ static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED
}
}
#endif
- #if CYTHON_USE_PYLONG_INTERNALS && PY_MAJOR_VERSION >= 3
+ #if CYTHON_USE_PYLONG_INTERNALS
if (likely(PyLong_CheckExact(op1))) {
const long b = intval;
long a;
@@ -44090,7 +46547,7 @@ bad:
{
PyMethodDescrObject *descr = (PyMethodDescrObject*) method;
target->func = descr->d_method->ml_meth;
- target->flag = descr->d_method->ml_flags & (METH_VARARGS | METH_KEYWORDS | METH_O | METH_NOARGS);
+ target->flag = descr->d_method->ml_flags & ~(METH_CLASS | METH_STATIC | METH_COEXIST);
}
#endif
return 0;
@@ -44100,7 +46557,7 @@ bad:
static PyObject* __Pyx__CallUnboundCMethod0(__Pyx_CachedCFunction* cfunc, PyObject* self) {
PyObject *args, *result = NULL;
if (unlikely(!cfunc->method) && unlikely(__Pyx_TryUnpackUnboundCMethod(cfunc) < 0)) return NULL;
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_ASSUME_SAFE_MACROS
args = PyTuple_New(1);
if (unlikely(!args)) goto bad;
Py_INCREF(self);
@@ -44209,7 +46666,7 @@ static int __Pyx_PyBytes_Tailmatch(PyObject* self, PyObject* substr,
Py_ssize_t i, count = PyTuple_GET_SIZE(substr);
for (i = 0; i < count; i++) {
int result;
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
result = __Pyx_PyBytes_SingleTailmatch(self, PyTuple_GET_ITEM(substr, i),
start, end, direction);
#else
@@ -44234,7 +46691,7 @@ static int __Pyx_PyBytes_Tailmatch(PyObject* self, PyObject* substr,
Py_ssize_t i, count = PyTuple_GET_SIZE(substr);
for (i = 0; i < count; i++) {
Py_ssize_t result;
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
result = PyUnicode_Tailmatch(s, PyTuple_GET_ITEM(substr, i),
start, end, direction);
#else
@@ -44277,7 +46734,7 @@ static int __Pyx_PyBytes_Tailmatch(PyObject* self, PyObject* substr,
/* IterFinish */
static CYTHON_INLINE int __Pyx_IterFinish(void) {
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_FAST_THREAD_STATE
PyThreadState *tstate = PyThreadState_GET();
PyObject* exc_type = tstate->curexc_type;
if (unlikely(exc_type)) {
@@ -44327,7 +46784,7 @@ static int __Pyx_PyBytes_Tailmatch(PyObject* self, PyObject* substr,
Py_ssize_t cstart, Py_ssize_t cstop,
PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice,
int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) {
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_USE_TYPE_SLOTS
PyMappingMethods* mp;
#if PY_MAJOR_VERSION < 3
PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence;
@@ -44403,7 +46860,7 @@ static int __Pyx_PyBytes_Tailmatch(PyObject* self, PyObject* substr,
Py_XDECREF(owned_stop);
if (unlikely(!py_slice)) goto bad;
}
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_USE_TYPE_SLOTS
result = mp->mp_ass_subscript(obj, py_slice, value);
#else
result = value ? PyObject_SetItem(obj, py_slice, value) : PyObject_DelItem(obj, py_slice);
@@ -44433,7 +46890,7 @@ bad:
PyObject *method, *result = NULL;
method = __Pyx_PyObject_GetAttrStr(obj, method_name);
if (unlikely(!method)) goto bad;
-#if CYTHON_COMPILING_IN_CPYTHON
+#if CYTHON_UNPACK_METHODS
if (likely(PyMethod_Check(method))) {
PyObject *self = PyMethod_GET_SELF(method);
if (likely(self)) {
@@ -44617,8 +47074,103 @@ static CYTHON_INLINE int __Pyx_dict_iter_next(
return PyDict_Values(d);
}
+/* SaveResetException */
+ #if CYTHON_FAST_THREAD_STATE
+static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) {
+ *type = tstate->exc_type;
+ *value = tstate->exc_value;
+ *tb = tstate->exc_traceback;
+ Py_XINCREF(*type);
+ Py_XINCREF(*value);
+ Py_XINCREF(*tb);
+}
+static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) {
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ tmp_type = tstate->exc_type;
+ tmp_value = tstate->exc_value;
+ tmp_tb = tstate->exc_traceback;
+ tstate->exc_type = type;
+ tstate->exc_value = value;
+ tstate->exc_traceback = tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+}
+#endif
+
+/* PyErrExceptionMatches */
+ #if CYTHON_FAST_THREAD_STATE
+static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err) {
+ PyObject *exc_type = tstate->curexc_type;
+ if (exc_type == err) return 1;
+ if (unlikely(!exc_type)) return 0;
+ return PyErr_GivenExceptionMatches(exc_type, err);
+}
+#endif
+
+/* GetException */
+ #if CYTHON_FAST_THREAD_STATE
+static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) {
+#else
+static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
+#endif
+ PyObject *local_type, *local_value, *local_tb;
+#if CYTHON_FAST_THREAD_STATE
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ local_type = tstate->curexc_type;
+ local_value = tstate->curexc_value;
+ local_tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+#else
+ PyErr_Fetch(&local_type, &local_value, &local_tb);
+#endif
+ PyErr_NormalizeException(&local_type, &local_value, &local_tb);
+#if CYTHON_FAST_THREAD_STATE
+ if (unlikely(tstate->curexc_type))
+#else
+ if (unlikely(PyErr_Occurred()))
+#endif
+ goto bad;
+ #if PY_MAJOR_VERSION >= 3
+ if (local_tb) {
+ if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
+ goto bad;
+ }
+ #endif
+ Py_XINCREF(local_tb);
+ Py_XINCREF(local_type);
+ Py_XINCREF(local_value);
+ *type = local_type;
+ *value = local_value;
+ *tb = local_tb;
+#if CYTHON_FAST_THREAD_STATE
+ tmp_type = tstate->exc_type;
+ tmp_value = tstate->exc_value;
+ tmp_tb = tstate->exc_traceback;
+ tstate->exc_type = local_type;
+ tstate->exc_value = local_value;
+ tstate->exc_traceback = local_tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(local_type, local_value, local_tb);
+#endif
+ return 0;
+bad:
+ *type = 0;
+ *value = 0;
+ *tb = 0;
+ Py_XDECREF(local_type);
+ Py_XDECREF(local_value);
+ Py_XDECREF(local_tb);
+ return -1;
+}
+
/* SetVTable */
- static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
+ static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
#if PY_VERSION_HEX >= 0x02070000
PyObject *ob = PyCapsule_New(vtable, 0, 0);
#else
@@ -44636,7 +47188,7 @@ bad:
}
/* Import */
- static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
+ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
PyObject *empty_list = 0;
PyObject *module = 0;
PyObject *global_dict = 0;
@@ -44710,7 +47262,7 @@ bad:
}
/* ImportFrom */
- static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) {
+ static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) {
PyObject* value = __Pyx_PyObject_GetAttrStr(module, name);
if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) {
PyErr_Format(PyExc_ImportError,
@@ -44724,7 +47276,7 @@ bad:
}
/* CalculateMetaclass */
- static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases) {
+ static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases) {
Py_ssize_t i, nbases = PyTuple_GET_SIZE(bases);
for (i=0; i < nbases; i++) {
PyTypeObject *tmptype;
@@ -44763,7 +47315,7 @@ bad:
}
/* Py3ClassCreate */
- static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name,
+ static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name,
PyObject *qualname, PyObject *mkw, PyObject *modname, PyObject *doc) {
PyObject *ns;
if (metaclass) {
@@ -44830,7 +47382,7 @@ static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObj
}
/* CodeObjectCache */
- static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
+ static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
int start = 0, mid = 0, end = count - 1;
if (end >= 0 && code_line > entries[end].code_line) {
return count;
@@ -44910,7 +47462,7 @@ static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
}
/* AddTraceback */
- #include "compile.h"
+ #include "compile.h"
#include "frameobject.h"
#include "traceback.h"
static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
@@ -44983,15 +47535,46 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line,
0 /*PyObject *locals*/
);
if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
+ __Pyx_PyFrame_SetLineNumber(py_frame, py_line);
PyTraceBack_Here(py_frame);
bad:
Py_XDECREF(py_code);
Py_XDECREF(py_frame);
}
+/* CIntToPy */
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ADIOS_STATISTICS_FLAG(ADIOS_STATISTICS_FLAG value) {
+ const ADIOS_STATISTICS_FLAG neg_one = (ADIOS_STATISTICS_FLAG) -1, const_zero = (ADIOS_STATISTICS_FLAG) 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (is_unsigned) {
+ if (sizeof(ADIOS_STATISTICS_FLAG) < sizeof(long)) {
+ return PyInt_FromLong((long) value);
+ } else if (sizeof(ADIOS_STATISTICS_FLAG) <= sizeof(unsigned long)) {
+ return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
+ } else if (sizeof(ADIOS_STATISTICS_FLAG) <= sizeof(unsigned PY_LONG_LONG)) {
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
+ }
+ } else {
+ if (sizeof(ADIOS_STATISTICS_FLAG) <= sizeof(long)) {
+ return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
+ } else if (sizeof(ADIOS_STATISTICS_FLAG) <= sizeof(PY_LONG_LONG)) {
+ return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
+ }
+ }
+ {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&value;
+ return _PyLong_FromByteArray(bytes, sizeof(ADIOS_STATISTICS_FLAG),
+ little, !is_unsigned);
+ }
+}
+
/* CIntFromPyVerify */
- #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\
+ #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\
__PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0)
#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\
__PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1)
@@ -45013,7 +47596,7 @@ bad:
}
/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
const int neg_one = (int) -1, const_zero = (int) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
@@ -45021,14 +47604,18 @@ bad:
return PyInt_FromLong((long) value);
} else if (sizeof(int) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) {
return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
}
} else {
if (sizeof(int) <= sizeof(long)) {
return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(int) <= sizeof(PY_LONG_LONG)) {
return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
}
}
{
@@ -45040,7 +47627,7 @@ bad:
}
/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int64_t(int64_t value) {
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int64_t(int64_t value) {
const int64_t neg_one = (int64_t) -1, const_zero = (int64_t) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
@@ -45048,14 +47635,18 @@ bad:
return PyInt_FromLong((long) value);
} else if (sizeof(int64_t) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(int64_t) <= sizeof(unsigned PY_LONG_LONG)) {
return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
}
} else {
if (sizeof(int64_t) <= sizeof(long)) {
return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(int64_t) <= sizeof(PY_LONG_LONG)) {
return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
}
}
{
@@ -45067,7 +47658,7 @@ bad:
}
/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint64_t(uint64_t value) {
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint64_t(uint64_t value) {
const uint64_t neg_one = (uint64_t) -1, const_zero = (uint64_t) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
@@ -45075,14 +47666,18 @@ bad:
return PyInt_FromLong((long) value);
} else if (sizeof(uint64_t) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(uint64_t) <= sizeof(unsigned PY_LONG_LONG)) {
return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
}
} else {
if (sizeof(uint64_t) <= sizeof(long)) {
return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(uint64_t) <= sizeof(PY_LONG_LONG)) {
return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
}
}
{
@@ -45094,7 +47689,7 @@ bad:
}
/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ADIOS_READ_METHOD(ADIOS_READ_METHOD value) {
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ADIOS_READ_METHOD(ADIOS_READ_METHOD value) {
const ADIOS_READ_METHOD neg_one = (ADIOS_READ_METHOD) -1, const_zero = (ADIOS_READ_METHOD) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
@@ -45102,14 +47697,18 @@ bad:
return PyInt_FromLong((long) value);
} else if (sizeof(ADIOS_READ_METHOD) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_READ_METHOD) <= sizeof(unsigned PY_LONG_LONG)) {
return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
}
} else {
if (sizeof(ADIOS_READ_METHOD) <= sizeof(long)) {
return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_READ_METHOD) <= sizeof(PY_LONG_LONG)) {
return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
}
}
{
@@ -45121,7 +47720,7 @@ bad:
}
/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
const long neg_one = (long) -1, const_zero = (long) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
@@ -45129,14 +47728,18 @@ bad:
return PyInt_FromLong((long) value);
} else if (sizeof(long) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) {
return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
}
} else {
if (sizeof(long) <= sizeof(long)) {
return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
}
}
{
@@ -45148,7 +47751,7 @@ bad:
}
/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_long(unsigned long value) {
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_unsigned_long(unsigned long value) {
const unsigned long neg_one = (unsigned long) -1, const_zero = (unsigned long) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
@@ -45156,14 +47759,18 @@ bad:
return PyInt_FromLong((long) value);
} else if (sizeof(unsigned long) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(unsigned long) <= sizeof(unsigned PY_LONG_LONG)) {
return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
}
} else {
if (sizeof(unsigned long) <= sizeof(long)) {
return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(unsigned long) <= sizeof(PY_LONG_LONG)) {
return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
}
}
{
@@ -45175,7 +47782,7 @@ bad:
}
/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint32_t(uint32_t value) {
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint32_t(uint32_t value) {
const uint32_t neg_one = (uint32_t) -1, const_zero = (uint32_t) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
@@ -45183,14 +47790,18 @@ bad:
return PyInt_FromLong((long) value);
} else if (sizeof(uint32_t) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(uint32_t) <= sizeof(unsigned PY_LONG_LONG)) {
return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
}
} else {
if (sizeof(uint32_t) <= sizeof(long)) {
return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(uint32_t) <= sizeof(PY_LONG_LONG)) {
return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
}
}
{
@@ -45202,7 +47813,7 @@ bad:
}
/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ADIOS_DATATYPES(ADIOS_DATATYPES value) {
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ADIOS_DATATYPES(ADIOS_DATATYPES value) {
const ADIOS_DATATYPES neg_one = (ADIOS_DATATYPES) -1, const_zero = (ADIOS_DATATYPES) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
@@ -45210,14 +47821,18 @@ bad:
return PyInt_FromLong((long) value);
} else if (sizeof(ADIOS_DATATYPES) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_DATATYPES) <= sizeof(unsigned PY_LONG_LONG)) {
return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
}
} else {
if (sizeof(ADIOS_DATATYPES) <= sizeof(long)) {
return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_DATATYPES) <= sizeof(PY_LONG_LONG)) {
return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
}
}
{
@@ -45228,8 +47843,8 @@ bad:
}
}
-/* None */
- #if CYTHON_CCOMPLEX
+/* Declarations */
+ #if CYTHON_CCOMPLEX
#ifdef __cplusplus
static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
return ::std::complex< float >(x, y);
@@ -45248,61 +47863,86 @@ bad:
}
#endif
-/* None */
- #if CYTHON_CCOMPLEX
+/* Arithmetic */
+ #if CYTHON_CCOMPLEX
#else
- static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
return (a.real == b.real) && (a.imag == b.imag);
}
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
__pyx_t_float_complex z;
z.real = a.real + b.real;
z.imag = a.imag + b.imag;
return z;
}
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
__pyx_t_float_complex z;
z.real = a.real - b.real;
z.imag = a.imag - b.imag;
return z;
}
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
__pyx_t_float_complex z;
z.real = a.real * b.real - a.imag * b.imag;
z.imag = a.real * b.imag + a.imag * b.real;
return z;
}
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- float denom = b.real * b.real + b.imag * b.imag;
- z.real = (a.real * b.real + a.imag * b.imag) / denom;
- z.imag = (a.imag * b.real - a.real * b.imag) / denom;
- return z;
+ #if 1
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ if (b.imag == 0) {
+ return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real);
+ } else if (fabsf(b.real) >= fabsf(b.imag)) {
+ if (b.real == 0 && b.imag == 0) {
+ return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag);
+ } else {
+ float r = b.imag / b.real;
+ float s = 1.0 / (b.real + b.imag * r);
+ return __pyx_t_float_complex_from_parts(
+ (a.real + a.imag * r) * s, (a.imag - a.real * r) * s);
+ }
+ } else {
+ float r = b.real / b.imag;
+ float s = 1.0 / (b.imag + b.real * r);
+ return __pyx_t_float_complex_from_parts(
+ (a.real * r + a.imag) * s, (a.imag * r - a.real) * s);
+ }
+ }
+ #else
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ if (b.imag == 0) {
+ return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real);
+ } else {
+ float denom = b.real * b.real + b.imag * b.imag;
+ return __pyx_t_float_complex_from_parts(
+ (a.real * b.real + a.imag * b.imag) / denom,
+ (a.imag * b.real - a.real * b.imag) / denom);
+ }
}
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) {
+ #endif
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) {
__pyx_t_float_complex z;
z.real = -a.real;
z.imag = -a.imag;
return z;
}
- static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) {
+ static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) {
return (a.real == 0) && (a.imag == 0);
}
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) {
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) {
__pyx_t_float_complex z;
z.real = a.real;
z.imag = -a.imag;
return z;
}
#if 1
- static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) {
+ static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) {
#if !defined(HAVE_HYPOT) || defined(_MSC_VER)
return sqrtf(z.real*z.real + z.imag*z.imag);
#else
return hypotf(z.real, z.imag);
#endif
}
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) {
__pyx_t_float_complex z;
float r, lnr, theta, z_r, z_theta;
if (b.imag == 0 && b.real == (int)b.real) {
@@ -45320,24 +47960,32 @@ bad:
case 1:
return a;
case 2:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(a, a);
+ z = __Pyx_c_prod_float(a, a);
+ return __Pyx_c_prod_float(a, a);
case 3:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(z, a);
+ z = __Pyx_c_prod_float(a, a);
+ return __Pyx_c_prod_float(z, a);
case 4:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(z, z);
+ z = __Pyx_c_prod_float(a, a);
+ return __Pyx_c_prod_float(z, z);
}
}
if (a.imag == 0) {
if (a.real == 0) {
return a;
+ } else if (b.imag == 0) {
+ z.real = powf(a.real, b.real);
+ z.imag = 0;
+ return z;
+ } else if (a.real > 0) {
+ r = a.real;
+ theta = 0;
+ } else {
+ r = -a.real;
+ theta = atan2f(0, -1);
}
- r = a.real;
- theta = 0;
} else {
- r = __Pyx_c_absf(a);
+ r = __Pyx_c_abs_float(a);
theta = atan2f(a.imag, a.real);
}
lnr = logf(r);
@@ -45350,8 +47998,8 @@ bad:
#endif
#endif
-/* None */
- #if CYTHON_CCOMPLEX
+/* Declarations */
+ #if CYTHON_CCOMPLEX
#ifdef __cplusplus
static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
return ::std::complex< double >(x, y);
@@ -45370,61 +48018,86 @@ bad:
}
#endif
-/* None */
- #if CYTHON_CCOMPLEX
+/* Arithmetic */
+ #if CYTHON_CCOMPLEX
#else
- static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
return (a.real == b.real) && (a.imag == b.imag);
}
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
__pyx_t_double_complex z;
z.real = a.real + b.real;
z.imag = a.imag + b.imag;
return z;
}
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
__pyx_t_double_complex z;
z.real = a.real - b.real;
z.imag = a.imag - b.imag;
return z;
}
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
__pyx_t_double_complex z;
z.real = a.real * b.real - a.imag * b.imag;
z.imag = a.real * b.imag + a.imag * b.real;
return z;
}
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- double denom = b.real * b.real + b.imag * b.imag;
- z.real = (a.real * b.real + a.imag * b.imag) / denom;
- z.imag = (a.imag * b.real - a.real * b.imag) / denom;
- return z;
+ #if 1
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ if (b.imag == 0) {
+ return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real);
+ } else if (fabs(b.real) >= fabs(b.imag)) {
+ if (b.real == 0 && b.imag == 0) {
+ return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag);
+ } else {
+ double r = b.imag / b.real;
+ double s = 1.0 / (b.real + b.imag * r);
+ return __pyx_t_double_complex_from_parts(
+ (a.real + a.imag * r) * s, (a.imag - a.real * r) * s);
+ }
+ } else {
+ double r = b.real / b.imag;
+ double s = 1.0 / (b.imag + b.real * r);
+ return __pyx_t_double_complex_from_parts(
+ (a.real * r + a.imag) * s, (a.imag * r - a.real) * s);
+ }
}
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) {
+ #else
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ if (b.imag == 0) {
+ return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real);
+ } else {
+ double denom = b.real * b.real + b.imag * b.imag;
+ return __pyx_t_double_complex_from_parts(
+ (a.real * b.real + a.imag * b.imag) / denom,
+ (a.imag * b.real - a.real * b.imag) / denom);
+ }
+ }
+ #endif
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) {
__pyx_t_double_complex z;
z.real = -a.real;
z.imag = -a.imag;
return z;
}
- static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) {
+ static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) {
return (a.real == 0) && (a.imag == 0);
}
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) {
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) {
__pyx_t_double_complex z;
z.real = a.real;
z.imag = -a.imag;
return z;
}
#if 1
- static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) {
+ static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) {
#if !defined(HAVE_HYPOT) || defined(_MSC_VER)
return sqrt(z.real*z.real + z.imag*z.imag);
#else
return hypot(z.real, z.imag);
#endif
}
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) {
__pyx_t_double_complex z;
double r, lnr, theta, z_r, z_theta;
if (b.imag == 0 && b.real == (int)b.real) {
@@ -45442,24 +48115,32 @@ bad:
case 1:
return a;
case 2:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(a, a);
+ z = __Pyx_c_prod_double(a, a);
+ return __Pyx_c_prod_double(a, a);
case 3:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(z, a);
+ z = __Pyx_c_prod_double(a, a);
+ return __Pyx_c_prod_double(z, a);
case 4:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(z, z);
+ z = __Pyx_c_prod_double(a, a);
+ return __Pyx_c_prod_double(z, z);
}
}
if (a.imag == 0) {
if (a.real == 0) {
return a;
+ } else if (b.imag == 0) {
+ z.real = pow(a.real, b.real);
+ z.imag = 0;
+ return z;
+ } else if (a.real > 0) {
+ r = a.real;
+ theta = 0;
+ } else {
+ r = -a.real;
+ theta = atan2(0, -1);
}
- r = a.real;
- theta = 0;
} else {
- r = __Pyx_c_abs(a);
+ r = __Pyx_c_abs_double(a);
theta = atan2(a.imag, a.real);
}
lnr = log(r);
@@ -45473,7 +48154,7 @@ bad:
#endif
/* CIntToPy */
- static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) {
+ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) {
const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0;
const int is_unsigned = neg_one > const_zero;
if (is_unsigned) {
@@ -45481,14 +48162,18 @@ bad:
return PyInt_FromLong((long) value);
} else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned long)) {
return PyLong_FromUnsignedLong((unsigned long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned PY_LONG_LONG)) {
return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value);
+#endif
}
} else {
if (sizeof(enum NPY_TYPES) <= sizeof(long)) {
return PyInt_FromLong((long) value);
+#ifdef HAVE_LONG_LONG
} else if (sizeof(enum NPY_TYPES) <= sizeof(PY_LONG_LONG)) {
return PyLong_FromLongLong((PY_LONG_LONG) value);
+#endif
}
}
{
@@ -45500,7 +48185,7 @@ bad:
}
/* CIntFromPy */
- static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *x) {
+ static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *x) {
const int64_t neg_one = (int64_t) -1, const_zero = (int64_t) 0;
const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
@@ -45567,8 +48252,10 @@ bad:
#endif
if (sizeof(int64_t) <= sizeof(unsigned long)) {
__PYX_VERIFY_RETURN_INT_EXC(int64_t, unsigned long, PyLong_AsUnsignedLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(int64_t) <= sizeof(unsigned PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(int64_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
+#endif
}
} else {
#if CYTHON_USE_PYLONG_INTERNALS
@@ -45635,8 +48322,10 @@ bad:
#endif
if (sizeof(int64_t) <= sizeof(long)) {
__PYX_VERIFY_RETURN_INT_EXC(int64_t, long, PyLong_AsLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(int64_t) <= sizeof(PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(int64_t, PY_LONG_LONG, PyLong_AsLongLong(x))
+#endif
}
}
{
@@ -45685,7 +48374,7 @@ raise_neg_overflow:
}
/* CIntFromPy */
- static CYTHON_INLINE uint64_t __Pyx_PyInt_As_uint64_t(PyObject *x) {
+ static CYTHON_INLINE uint64_t __Pyx_PyInt_As_uint64_t(PyObject *x) {
const uint64_t neg_one = (uint64_t) -1, const_zero = (uint64_t) 0;
const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
@@ -45752,8 +48441,10 @@ raise_neg_overflow:
#endif
if (sizeof(uint64_t) <= sizeof(unsigned long)) {
__PYX_VERIFY_RETURN_INT_EXC(uint64_t, unsigned long, PyLong_AsUnsignedLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(uint64_t) <= sizeof(unsigned PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(uint64_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
+#endif
}
} else {
#if CYTHON_USE_PYLONG_INTERNALS
@@ -45820,8 +48511,10 @@ raise_neg_overflow:
#endif
if (sizeof(uint64_t) <= sizeof(long)) {
__PYX_VERIFY_RETURN_INT_EXC(uint64_t, long, PyLong_AsLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(uint64_t) <= sizeof(PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(uint64_t, PY_LONG_LONG, PyLong_AsLongLong(x))
+#endif
}
}
{
@@ -45870,7 +48563,7 @@ raise_neg_overflow:
}
/* CIntFromPy */
- static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
+ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
const int neg_one = (int) -1, const_zero = (int) 0;
const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
@@ -45937,8 +48630,10 @@ raise_neg_overflow:
#endif
if (sizeof(int) <= sizeof(unsigned long)) {
__PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
+#endif
}
} else {
#if CYTHON_USE_PYLONG_INTERNALS
@@ -46005,8 +48700,10 @@ raise_neg_overflow:
#endif
if (sizeof(int) <= sizeof(long)) {
__PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(int) <= sizeof(PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x))
+#endif
}
}
{
@@ -46055,7 +48752,7 @@ raise_neg_overflow:
}
/* CIntFromPy */
- static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
+ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
const long neg_one = (long) -1, const_zero = (long) 0;
const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
@@ -46122,8 +48819,10 @@ raise_neg_overflow:
#endif
if (sizeof(long) <= sizeof(unsigned long)) {
__PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
+#endif
}
} else {
#if CYTHON_USE_PYLONG_INTERNALS
@@ -46190,8 +48889,10 @@ raise_neg_overflow:
#endif
if (sizeof(long) <= sizeof(long)) {
__PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(long) <= sizeof(PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x))
+#endif
}
}
{
@@ -46240,7 +48941,7 @@ raise_neg_overflow:
}
/* CIntFromPy */
- static CYTHON_INLINE ADIOS_DATATYPES __Pyx_PyInt_As_ADIOS_DATATYPES(PyObject *x) {
+ static CYTHON_INLINE ADIOS_DATATYPES __Pyx_PyInt_As_ADIOS_DATATYPES(PyObject *x) {
const ADIOS_DATATYPES neg_one = (ADIOS_DATATYPES) -1, const_zero = (ADIOS_DATATYPES) 0;
const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
@@ -46307,8 +49008,10 @@ raise_neg_overflow:
#endif
if (sizeof(ADIOS_DATATYPES) <= sizeof(unsigned long)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_DATATYPES, unsigned long, PyLong_AsUnsignedLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_DATATYPES) <= sizeof(unsigned PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_DATATYPES, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
+#endif
}
} else {
#if CYTHON_USE_PYLONG_INTERNALS
@@ -46375,8 +49078,10 @@ raise_neg_overflow:
#endif
if (sizeof(ADIOS_DATATYPES) <= sizeof(long)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_DATATYPES, long, PyLong_AsLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_DATATYPES) <= sizeof(PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_DATATYPES, PY_LONG_LONG, PyLong_AsLongLong(x))
+#endif
}
}
{
@@ -46425,7 +49130,7 @@ raise_neg_overflow:
}
/* CIntFromPy */
- static CYTHON_INLINE ADIOS_LOCKMODE __Pyx_PyInt_As_ADIOS_LOCKMODE(PyObject *x) {
+ static CYTHON_INLINE ADIOS_LOCKMODE __Pyx_PyInt_As_ADIOS_LOCKMODE(PyObject *x) {
const ADIOS_LOCKMODE neg_one = (ADIOS_LOCKMODE) -1, const_zero = (ADIOS_LOCKMODE) 0;
const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
@@ -46492,8 +49197,10 @@ raise_neg_overflow:
#endif
if (sizeof(ADIOS_LOCKMODE) <= sizeof(unsigned long)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_LOCKMODE, unsigned long, PyLong_AsUnsignedLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_LOCKMODE) <= sizeof(unsigned PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_LOCKMODE, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
+#endif
}
} else {
#if CYTHON_USE_PYLONG_INTERNALS
@@ -46560,8 +49267,10 @@ raise_neg_overflow:
#endif
if (sizeof(ADIOS_LOCKMODE) <= sizeof(long)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_LOCKMODE, long, PyLong_AsLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_LOCKMODE) <= sizeof(PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_LOCKMODE, PY_LONG_LONG, PyLong_AsLongLong(x))
+#endif
}
}
{
@@ -46610,7 +49319,7 @@ raise_neg_overflow:
}
/* CIntFromPy */
- static CYTHON_INLINE ADIOS_READ_METHOD __Pyx_PyInt_As_ADIOS_READ_METHOD(PyObject *x) {
+ static CYTHON_INLINE ADIOS_READ_METHOD __Pyx_PyInt_As_ADIOS_READ_METHOD(PyObject *x) {
const ADIOS_READ_METHOD neg_one = (ADIOS_READ_METHOD) -1, const_zero = (ADIOS_READ_METHOD) 0;
const int is_unsigned = neg_one > const_zero;
#if PY_MAJOR_VERSION < 3
@@ -46677,8 +49386,10 @@ raise_neg_overflow:
#endif
if (sizeof(ADIOS_READ_METHOD) <= sizeof(unsigned long)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_READ_METHOD, unsigned long, PyLong_AsUnsignedLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_READ_METHOD) <= sizeof(unsigned PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_READ_METHOD, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x))
+#endif
}
} else {
#if CYTHON_USE_PYLONG_INTERNALS
@@ -46745,8 +49456,10 @@ raise_neg_overflow:
#endif
if (sizeof(ADIOS_READ_METHOD) <= sizeof(long)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_READ_METHOD, long, PyLong_AsLong(x))
+#ifdef HAVE_LONG_LONG
} else if (sizeof(ADIOS_READ_METHOD) <= sizeof(PY_LONG_LONG)) {
__PYX_VERIFY_RETURN_INT_EXC(ADIOS_READ_METHOD, PY_LONG_LONG, PyLong_AsLongLong(x))
+#endif
}
}
{
@@ -46795,7 +49508,7 @@ raise_neg_overflow:
}
/* CheckBinaryVersion */
- static int __Pyx_check_binary_version(void) {
+ static int __Pyx_check_binary_version(void) {
char ctversion[4], rtversion[4];
PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
@@ -46811,7 +49524,7 @@ raise_neg_overflow:
}
/* ModuleImport */
- #ifndef __PYX_HAVE_RT_ImportModule
+ #ifndef __PYX_HAVE_RT_ImportModule
#define __PYX_HAVE_RT_ImportModule
static PyObject *__Pyx_ImportModule(const char *name) {
PyObject *py_name = 0;
@@ -46829,7 +49542,7 @@ bad:
#endif
/* TypeImport */
- #ifndef __PYX_HAVE_RT_ImportType
+ #ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
size_t size, int strict)
@@ -46894,7 +49607,7 @@ bad:
#endif
/* InitStrings */
- static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
+ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
while (t->p) {
#if PY_MAJOR_VERSION < 3
if (t->is_unicode) {
@@ -46995,7 +49708,9 @@ static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
else return PyObject_IsTrue(x);
}
static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) {
+#if CYTHON_USE_TYPE_SLOTS
PyNumberMethods *m;
+#endif
const char *name = NULL;
PyObject *res = NULL;
#if PY_MAJOR_VERSION < 3
@@ -47004,8 +49719,9 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) {
if (PyLong_Check(x))
#endif
return __Pyx_NewRef(x);
+#if CYTHON_USE_TYPE_SLOTS
m = Py_TYPE(x)->tp_as_number;
-#if PY_MAJOR_VERSION < 3
+ #if PY_MAJOR_VERSION < 3
if (m && m->nb_int) {
name = "int";
res = PyNumber_Int(x);
@@ -47014,11 +49730,14 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) {
name = "long";
res = PyNumber_Long(x);
}
-#else
+ #else
if (m && m->nb_int) {
name = "int";
res = PyNumber_Long(x);
}
+ #endif
+#else
+ res = PyNumber_Int(x);
#endif
if (res) {
#if PY_MAJOR_VERSION < 3
diff --git a/wrappers/numpy/adios_mpi.pyx b/wrappers/numpy/adios_mpi.pyx
index b8fb588..60884ec 100644
--- a/wrappers/numpy/adios_mpi.pyx
+++ b/wrappers/numpy/adios_mpi.pyx
@@ -19,6 +19,8 @@ cimport mpi4py.MPI as MPI
import cython
cimport cython
+import tempfile
+
from libc.stdlib cimport malloc, free
from cpython.string cimport PyString_AsString
from cpython.bytes cimport PyBytes_AsString, PyBytes_AS_STRING
@@ -177,22 +179,22 @@ cdef extern from "adios.h":
cdef int adios_define_var_timescale (const char * timescale , int64_t group_id ,
const char * name)
-
+
cdef int adios_define_var_timeseriesformat (const char * timeseries , int64_t group_id ,
const char * name)
-
+
cdef int adios_define_var_hyperslab (const char * hyperslab , int64_t group_id ,
const char * name)
-
+
cdef int adios_define_mesh_timevarying (const char * timevarying , int64_t group_id ,
const char * name)
-
+
cdef int adios_define_mesh_timesteps (const char * timesteps , int64_t group_id ,
const char * name)
-
+
cdef int adios_define_mesh_timescale (const char * timescale , int64_t group_id ,
const char * name)
-
+
cdef int adios_define_mesh_timeseriesformat (const char * timeseries , int64_t group_id ,
const char * name)
@@ -204,21 +206,21 @@ cdef extern from "adios.h":
int64_t group_id,
const char * name
)
-
+
cdef int adios_define_mesh_rectilinear (char * dimensions,
char * coordinates,
char * nspace,
int64_t group_id,
const char * name
- )
-
+ )
+
cdef int adios_define_mesh_structured (char * dimensions,
char * points,
char * nspace,
int64_t group_id,
const char * name
)
-
+
cdef int adios_define_mesh_unstructured (char * points,
char * data,
char * count,
@@ -229,7 +231,7 @@ cdef extern from "adios.h":
const char * name
)
- ### Bis hier
+ ### Bis hier
cdef int adios_define_attribute (int64_t group,
char * name,
@@ -429,6 +431,12 @@ class LOCKMODE:
CURRENT = 1
ALL =2
+class STATISTICS:
+ NONE = adios_stat_no
+ MINMAX = adios_stat_minmax
+ FULL = adios_stat_full
+ DEFAULT = adios_stat_default
+
cpdef __parse_index(index, ndim):
# Fix index, handling ellipsis and incomplete slices.
if not isinstance(index, tuple):
@@ -577,25 +585,25 @@ cpdef int define_var_timesteps (str timesteps, int64_t group_id, str name):
cpdef int define_var_timescale (str timescale , int64_t group_id ,str name):
return adios_define_var_timescale (s2b(timescale) , group_id ,s2b(name))
-
+
cpdef int define_var_timeseriesformat (str timeseries , int64_t group_id ,str name):
return adios_define_var_timeseriesformat (s2b(timeseries) , group_id ,s2b(name))
-
+
cpdef int define_var_hyperslab (str hyperslab , int64_t group_id ,str name):
return adios_define_var_hyperslab (s2b(hyperslab) , group_id ,s2b(name))
-
+
cpdef int define_mesh_timevarying (str timevarying , int64_t group_id ,str name):
return adios_define_mesh_timevarying (s2b(timevarying) , group_id ,s2b(name))
-
+
cpdef int define_mesh_timesteps (str timesteps , int64_t group_id ,str name):
return adios_define_mesh_timesteps (s2b(timesteps) , group_id ,s2b(name))
-
+
cpdef int define_mesh_timescale (str timescale , int64_t group_id ,str name):
return adios_define_mesh_timescale (s2b(timescale) , group_id ,s2b(name))
-
+
cpdef int define_mesh_timeseriesformat (str timeseries , int64_t group_id ,str name):
return adios_define_mesh_timeseriesformat (s2b(timeseries) , group_id ,s2b(name))
-
+
cpdef int define_mesh_uniform (str dimensions,
str origin,
str spacing,
@@ -612,20 +620,20 @@ cpdef int define_mesh_uniform (str dimensions,
group_id,
s2b(name)
)
-
+
cpdef int define_mesh_rectilinear (str dimensions,
str coordinates,
str nspace,
int64_t group_id,
str name
- ):
+ ):
return adios_define_mesh_rectilinear (s2b(dimensions),
s2b(coordinates),
s2b(nspace),
group_id,
s2b(name)
- )
-
+ )
+
cpdef int define_mesh_structured (str dimensions,
str points,
str nspace,
@@ -638,7 +646,7 @@ cpdef int define_mesh_structured (str dimensions,
group_id,
s2b(name)
)
-
+
cpdef int define_mesh_unstructured (str points,
str data,
str count,
@@ -1916,6 +1924,7 @@ cdef class writer(object):
cpdef bint is_noxml
cpdef str mode
cpdef MPI.Comm comm
+ cpdef int stats
cpdef dict vars
cpdef dict attrs
@@ -1960,17 +1969,21 @@ cdef class writer(object):
def __init__(self, str fname,
bint is_noxml = True,
str mode = "w",
- MPI.Comm comm = MPI.COMM_WORLD):
+ int stats = adios_stat_default,
+ MPI.Comm comm = MPI.COMM_WORLD,
+ str method = "POSIX1",
+ str method_params = ""):
self.gid = 0
self.fname = fname
- self.method = ""
- self.method_params = ""
+ self.method = method
+ self.method_params = method_params
self.is_noxml = is_noxml
self.mode = mode
self.comm = comm
self.vars = dict()
self.attrs = dict()
self.timeaggregation_buffersize = 0
+ self.stats = stats
init_noxml(comm)
##def __var_factory__(self, name, value):
@@ -1981,7 +1994,8 @@ cdef class writer(object):
def declare_group(self, str gname = None,
str method = "POSIX1",
- str method_params = ""):
+ str method_params = "",
+ int stats = adios_stat_default):
"""
Define a group associated with the file.
@@ -1989,6 +2003,7 @@ cdef class writer(object):
gname (str): group name.
method (str, optional): Adios write method (default: 'POSIX1')
method_params (str, optional): parameters for the write method (default: '')
+ stats (int, optional): statistics (default: 'DEFAULT')
Example:
@@ -1999,9 +2014,15 @@ cdef class writer(object):
self.gname = gname
if self.gname is None:
- self.gname = "group"
+ rank = self.comm.Get_rank()
+ if rank == 0:
+ ftmp = tempfile.NamedTemporaryFile().name
+ else:
+ ftmp = ""
+ ftmp = self.comm.bcast(ftmp, root=0)
+ self.gname = 'group'+ftmp;
- self.gid = declare_group(self.gname, "", adios_stat_default)
+ self.gid = declare_group(self.gname, "", stats)
self.method = method
self.method_params = method_params
select_method(self.gid, self.method, self.method_params, "")
@@ -2084,9 +2105,9 @@ cdef class writer(object):
Write variables and attributes to a file and close the writer.
"""
if self.gid == 0:
- self.declare_group()
+ self.declare_group(method=self.method, method_params=self.method_params, stats=self.stats)
- fd = open(self.gname, self.fname, self.mode)
+ fd = open(self.gname, self.fname, self.mode, comm=self.comm)
extra_vars = dict()
extra_attrs = dict()
@@ -2229,7 +2250,8 @@ cdef class varinfo(object):
def define(self, int64_t gid):
if self.value is None:
- raise TypeError("Value is none")
+ print ("Warning: skipping defining var(%r) with None value" %(self.name))
+ return
ldim_ = self.ldim
if isinstance(self.ldim, (tuple, list)):
@@ -2267,6 +2289,10 @@ cdef class varinfo(object):
def write(self, int64_t fd):
val_ = self.value
+
+ if val_ is None:
+ return
+
if not isinstance(self.value, (np.ndarray)):
val_ = np.array(self.value)
diff --git a/wrappers/numpy/adios_mpi2serial.sed b/wrappers/numpy/adios_mpi2serial.sed
index 7662b95..c80e0f2 100644
--- a/wrappers/numpy/adios_mpi2serial.sed
+++ b/wrappers/numpy/adios_mpi2serial.sed
@@ -16,3 +16,5 @@ s/comm.Clone()/comm/g
int MPI_COMM_SELF/
}
s/adios_mpi/adios/g
+s/self.comm.Get_rank()/0/g
+s/self.comm.bcast(ftmp, root=0)/ftmp/g
diff --git a/wrappers/numpy/build-and-install.sh b/wrappers/numpy/build-and-install.sh
index 8de14d3..b644dc0 100755
--- a/wrappers/numpy/build-and-install.sh
+++ b/wrappers/numpy/build-and-install.sh
@@ -1,4 +1,6 @@
#!/bin/bash -v
+export MACOSX_DEPLOYMENT_TARGET=10.11
+
rm -rf ./build
sed -f adios_mpi2serial.sed adios_mpi.pyx > adios.pyx
cython -X embedsignature=True --cplus adios.pyx
diff --git a/wrappers/numpy/doc/source/build.rst b/wrappers/numpy/doc/source/build.rst
index 8b4d31b..4a5b878 100644
--- a/wrappers/numpy/doc/source/build.rst
+++ b/wrappers/numpy/doc/source/build.rst
@@ -6,30 +6,52 @@ Installation
Adios Python wrapper requires Adios built with the GNU C compiler with
relocatable codes. Add -fPIC flag to CFLAGS before configuring Adios.
+::
+
+ $ ./configure --prefix=/dir/tp/install \
+ MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 \
+ CC=gcc CXX=g++ FC=gfortran \
+ CFLAGS="-fPIC"
+
+.. note:: Adios provides various functions (such as, staging, compression,
+ hdf5 conversion, etc) which can be turned with proper configure options.
+ Please check 'configure --help' for more options.
+
+::
+
+ $ ./configure --help
+
+
Quick install with pip
----------------------
ADIOS Python wrapper can be installed with pip. Check if pip is
installed already. Otherwise, install pip first
::
-$ wget https://bootstrap.pypa.io/get-pip.py
-$ sudo python get-pip.py
+
+ $ wget https://bootstrap.pypa.io/get-pip.py
+ $ sudo python get-pip.py
+
+
Or,
::
-$ python get-pip.py --user
+
+ $ python get-pip.py --user
to install in a local directory, $HOME/.local
Then, install Adios and Adios-MPI wrapper as follows:
::
-$ pip install adios
-$ pip install adios_mpi
+
+ $ pip install adios
+ $ pip install adios_mpi
If you want to install in a custom directory, use the following:
::
-$ pip install --install-option="--prefix=$PREFIX" adios
-$ pip install --install-option="--prefix=$PREFIX" adios_mpi
+
+ $ pip install --install-option="--prefix=$PREFIX" adios
+ $ pip install --install-option="--prefix=$PREFIX" adios_mpi
Trouble Shooting
@@ -41,8 +63,9 @@ Custom MPICC and MPICXX
If one needs to use a custom MPICC and MPICXX command (e.g., Titan),
then use the following command:
::
-$ pip --global-option=build_ext \
---global-option=--mpicc=cc --global-option=--mpicxx=CC adios
+
+ $ pip --global-option=build_ext \
+ --global-option=--mpicc=cc --global-option=--mpicxx=CC adios
"Could not find any downloads that satisfy the requirement" with pip
@@ -50,6 +73,68 @@ $ pip --global-option=build_ext \
If the error is caused by a certificate error, then, try
::
-$ wget http://curl.haxx.se/ca/cacert.pem
-$ pip --cert cacert.pem search adios
-$ pip --cert cacert.pem install adios
+
+ $ wget http://curl.haxx.se/ca/cacert.pem
+ $ pip --cert cacert.pem search adios
+ $ pip --cert cacert.pem install adios
+
+Custom MPI4py build
+^^^^^^^^^^^^^^^^^^^
+
+You may want to build mpi4py by yourself. The source code is available here[https://bitbucket.org/mpi4py/mpi4py/downloads/mpi4py-2.0.0.tar.gz]
+
+Then, run setup.py as follows:
+::
+ $ python setup.py build_ext --mpicc=cc --mpicxx=CC
+
+Install in a cutom location and set PYTHONPATH env:
+::
+ $ PREFIX=/dir/to/install
+ $ python setup.py install --prefix=$PREFIX
+ $ export PYTHONPATH=$PREFIX/lib/python2.7/site-packages:$PYTHONPATH
+
+
+Build script on Titan
+^^^^^^^^^^^^^^^^^^^^^
+
+The following script is a reference for building Adios python module on Titan:
+::
+ #!/bin/bash -ex
+ module unload PrgEnv-cray
+ module unload PrgEnv-pgi
+ module unload PrgEnv-intel
+ module unload PrgEnv-gnu
+ module unload python
+ module unload python_anaconda
+ module unload python_anaconda_mpi4py
+ module unload python_anaconda_adios
+
+ module load PrgEnv-gnu
+ module load python_anaconda
+ module load python_anaconda_mpi4py
+ module load adios/1.12-devel
+
+ git fetch origin
+ VER=`git describe --always`
+ PVER=1.11.1.post2
+
+ PREFIX=$WORLDWORK_CSC143/sw/python_anaconda_adios/$VER
+ PIP=`which pip`
+
+ [ ! -f cacert.pem ] && wget http://curl.haxx.se/ca/cacert.pem
+
+ $PIP install -I -U \
+ --global-option build_ext \
+ --global-option -lrt --install-option="--prefix=$PREFIX" \
+ --ignore-installed \
+ --cert cacert.pem \
+ adios==$PVER -v
+
+ $PIP install -I -U \
+ --global-option build_ext \
+ --global-option=--mpicc=cc \
+ --global-option=--mpicxx=CC \
+ --global-option -lrt --install-option="--prefix=$PREFIX" \
+ --ignore-installed \
+ --cert cacert.pem \
+ adios_mpi==$PVER -v
diff --git a/wrappers/numpy/doc/source/conf.py b/wrappers/numpy/doc/source/conf.py
index d2e70f2..3906d5e 100644
--- a/wrappers/numpy/doc/source/conf.py
+++ b/wrappers/numpy/doc/source/conf.py
@@ -59,9 +59,9 @@ author = u'Jong Choi (choij at ornl.gov)'
# built documents.
#
# The short X.Y version.
-version = '1.8.0'
+version = '1.11.1'
# The full version, including alpha/beta/rc tags.
-release = '1.8.1b3'
+release = '1.11.1.post1'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
diff --git a/wrappers/numpy/doc/source/index.rst b/wrappers/numpy/doc/source/index.rst
index adfad2c..432bf54 100644
--- a/wrappers/numpy/doc/source/index.rst
+++ b/wrappers/numpy/doc/source/index.rst
@@ -17,6 +17,7 @@ Quick Start Guide
quick
build
+ gallery
ref
Indices and tables
diff --git a/wrappers/numpy/doc/source/quick.rst b/wrappers/numpy/doc/source/quick.rst
index 82f57bb..031542f 100644
--- a/wrappers/numpy/doc/source/quick.rst
+++ b/wrappers/numpy/doc/source/quick.rst
@@ -144,10 +144,9 @@ Then, we initialize Adios:
>>> ad.init_noxml()
-Then, we give a file name to create and specify a group with Adios method:
+Then, we give a file name to create with Adios method:
->>> fw = ad.writer(fname)
->>> fw.declare_group('group', method='POSIX1')
+>>> fw = ad.writer(fname, method='POSIX1')
"POSIX1" is one of many Adios's write methods. Others are "MPI",
"MPI_AGGREGATE", "FLEXPATH", "DATASPACES", etc. More detailed
@@ -166,3 +165,22 @@ To write an attribute, we can do as follows:
Finally, we let Adios to write a file by calling "close"
>>> fw.close()
+
+Transform
+---------
+
+Adios provides transform methods for data reduction and compressions, such as ZFP, SZ, zlib, etc. For the full list, use ```adios_list_methods``` command.
+
+For an example, SZ transform method can be set by the following command:
+
+>>> fw['temperature'].transform = 'SZ'
+
+will compress temperature data with SZ with default parameters.
+
+Method specific parameters can be set like:
+
+>>> fw['temperature'].transform = 'SZ:errorBoundMode=ABS,absErrBound=1E-3'
+
+An example of ZFP is as follows:
+
+>>> fw['temperature'].transform = 'zfp:accuracy=0.001'
diff --git a/wrappers/numpy/example/staging/adios_read_mpi.py b/wrappers/numpy/example/staging/adios_read_mpi.py
index fede8fb..35d9dc3 100644
--- a/wrappers/numpy/example/staging/adios_read_mpi.py
+++ b/wrappers/numpy/example/staging/adios_read_mpi.py
@@ -22,15 +22,16 @@ print ">>> Method:", method, init
ad.read_init(method, parameters=init)
f = ad.file("temp.bp", method, is_stream=True, timeout_sec = 10.0)
-f.printself()
+print f
i = 0
while True:
print ">>> step:", i
v = f.var['temperature']
- v.printself()
+ print v
- val = v.read(nsteps=1)
+ #val = v.read(nsteps=1)
+ val = v[1:2, 1:5]
print val
if (f.advance() < 0):
diff --git a/wrappers/numpy/src/__init__.py b/wrappers/numpy/src/__init__.py
index 415bfcc..59eaace 100644
--- a/wrappers/numpy/src/__init__.py
+++ b/wrappers/numpy/src/__init__.py
@@ -1,2 +1,2 @@
from .adios import *
-__version__ = '1.11.0b1'
+__version__ = '1.11.1.post1'
diff --git a/wrappers/numpy/src_mpi/__init__.py b/wrappers/numpy/src_mpi/__init__.py
index bb65a2d..4c1d0d0 100644
--- a/wrappers/numpy/src_mpi/__init__.py
+++ b/wrappers/numpy/src_mpi/__init__.py
@@ -1,2 +1,2 @@
from .adios_mpi import *
-__version__ = '1.11.0b1'
+__version__ = '1.11.1.post1'
diff --git a/wrappers/numpy/test/test_adios_writer_unittest.py b/wrappers/numpy/test/test_adios_writer_unittest.py
index 5bc17a2..72e9c1e 100644
--- a/wrappers/numpy/test/test_adios_writer_unittest.py
+++ b/wrappers/numpy/test/test_adios_writer_unittest.py
@@ -21,8 +21,7 @@ class AdiosTestCase(ut.TestCase):
val1 = np.array(list(range(NX)), dtype=np.int32)
val2 = np.array(list(range(5)), dtype='f8')
- fw = ad.writer(self.temp.path)
- fw.declare_group("group", method="POSIX1")
+ fw = ad.writer(self.temp.path, method="POSIX1")
fw.define_var("NX")
fw.define_var("val1", "NX")
@@ -54,8 +53,7 @@ class AdiosTestCase(ut.TestCase):
unicode_string = u"unicode"
bytes_string = u"bytes"
- fw = ad.writer(self.temp.path)
- fw.declare_group("group", method="POSIX1")
+ fw = ad.writer(self.temp.path, method="POSIX1")
fw.define_attr("single_string")
fw.define_attr("three_string")
@@ -96,8 +94,7 @@ class AdiosTestCase(ut.TestCase):
val1 = np.array(list(range(NX)), dtype=np.int32)
val2 = np.array(list(range(5)), dtype='f8')
- fw = ad.writer(self.temp.path)
- fw.declare_group("group", method="POSIX1")
+ fw = ad.writer(self.temp.path, method="POSIX1")
fw['NX'] = NX
fw['val1'] = val1
@@ -116,8 +113,7 @@ class AdiosTestCase(ut.TestCase):
val1 = np.array(list(range(NX)), dtype=np.int32)
val2 = np.array(list(range(5)), dtype='f8')
- fw = ad.writer(self.temp.path)
- fw.declare_group("group", method="POSIX1")
+ fw = ad.writer(self.temp.path, method="POSIX1")
fw.vars['NX'] = NX
fw.vars['val1'] = val1
@@ -131,7 +127,7 @@ class AdiosTestCase(ut.TestCase):
def test_writer_default_group(self):
self.temp = TempFile()
- fw = ad.writer(self.temp.path)
+ fw = ad.writer(self.temp.path, method="POSIX1")
fw.close()
f = ad.file(self.temp.path)
@@ -140,8 +136,7 @@ class AdiosTestCase(ut.TestCase):
def test_writer_varname(self):
self.temp = TempFile()
- fw = ad.writer(self.temp.path)
- fw.declare_group("group", method="POSIX1")
+ fw = ad.writer(self.temp.path, method="POSIX1")
NVARS = 99
fw.vars['nvars'] = NVARS
@@ -160,8 +155,7 @@ class AdiosTestCase(ut.TestCase):
val1 = np.array(list(range(NX)), dtype=np.int32)
val2 = np.array(list(range(5)), dtype='f8')
- fw = ad.writer(self.temp.path)
- fw.declare_group("group", method="POSIX1")
+ fw = ad.writer(self.temp.path, method="POSIX1")
fw['NX'] = NX
fw['val1'] = val1
@@ -181,8 +175,7 @@ class AdiosTestCase(ut.TestCase):
val1 = np.array(list(range(NX)), dtype=np.int32)
val2 = np.array(list(range(5)), dtype='f8')
- fw = ad.writer(self.temp.path)
- fw.declare_group("group", method="POSIX1")
+ fw = ad.writer(self.temp.path, method="POSIX1")
fw.set_time_aggregation(3200)
fw['NX'] = NX
@@ -196,5 +189,29 @@ class AdiosTestCase(ut.TestCase):
self.assertTrue((f['val1'][:] == val1).all())
self.assertTrue((f['val2'][:] == val2).all())
+ def test_writer_empty_define_(self):
+ self.temp = TempFile()
+
+ NX = 10
+ val1 = np.array(list(range(NX)), dtype=np.int32)
+ val2 = np.array(list(range(5)), dtype='f8')
+
+ fw = ad.writer(self.temp.path, method="POSIX1")
+
+ fw.define_var("NX")
+ fw.define_var("val1", "NX")
+ fw.define_var("val2", val2.shape)
+ fw.define_var("extra")
+
+ fw['NX'] = NX
+ fw['val1'] = val1
+ fw['val2'] = val2
+ fw.close()
+
+ f = ad.file(self.temp.path)
+ self.assertEqual(f['NX'][...], NX)
+ self.assertTrue((f['val1'][:] == val1).all())
+ self.assertTrue((f['val2'][:] == val2).all())
+
if __name__ == '__main__':
ut.main()
diff --git a/wrappers/numpy/tests/test_adios_mpi_writer.py b/wrappers/numpy/tests/test_adios_mpi_writer.py
index 8f44e0c..d6ff9fe 100644
--- a/wrappers/numpy/tests/test_adios_mpi_writer.py
+++ b/wrappers/numpy/tests/test_adios_mpi_writer.py
@@ -30,8 +30,8 @@ print("\n>>> Writing ... (rank = %d)\n" % rank)
ad.init_noxml()
ad.set_max_buffer_size (100);
-fw = ad.writer(fname, comm=comm)
-fw.declare_group('group', method='MPI')
+fw = ad.writer(fname, comm=comm, method='MPI')
+#fw.declare_group('group', method='MPI', stats=ad.STATISTICS.FULL)
#fw.define_var('temperature', ldim=(1,NX), gdim=gdim, offset=offset, transform='zfp:accuracy=0.0001')
#fw.define_var('temperature', ldim=(1,NX), gdim=gdim, offset=offset, transform='zlib')
fw.define_var('temperature', ldim=ldim, gdim=gdim, offset=offset, transform='none')
diff --git a/wrappers/numpy/tests/test_adios_writer.py b/wrappers/numpy/tests/test_adios_writer.py
index 35be3d9..9185a36 100644
--- a/wrappers/numpy/tests/test_adios_writer.py
+++ b/wrappers/numpy/tests/test_adios_writer.py
@@ -20,8 +20,7 @@ print("\n>>> Writing ...\n")
ad.init_noxml()
ad.set_max_buffer_size (10)
-fw = ad.writer(fname)
-fw.declare_group('group', method='POSIX1')
+fw = ad.writer(fname, method='POSIX1')
fw['NX'] = NX
fw['size'] = size
--
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