[adios] 01/07: Upstream release 1.11.0
Alastair McKinstry
mckinstry at moszumanska.debian.org
Tue Apr 4 12:09:16 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 0c48e5421cc45511653166de865818fb1a3eacbc
Author: Alastair McKinstry <mckinstry at debian.org>
Date: Mon Nov 21 13:09:01 2016 +0000
Upstream release 1.11.0
---
CMakeLists.txt | 73 +
COPYING | 14 +-
Makefile.in | 5 +-
NEWS | 21 +
aclocal.m4 | 1 +
cmake_init | 15 +-
config.h.in | 12 +
config/ac_dataspaces.m4 | 54 +-
config/ac_dimes.m4 | 47 +-
config/ac_zfp.m4 | 83 +
configure | 839 +-
configure.ac | 58 +-
examples/C/CMakeLists.txt | 2 +-
examples/C/Makefile.am | 4 +-
examples/C/Makefile.in | 10 +-
examples/C/arrays/Makefile.in | 5 +-
examples/C/attributes/Makefile.in | 5 +-
examples/C/flexpath_arrays/Makefile.in | 5 +-
.../global_range_select/Makefile.in | 5 +-
.../C/flexpath_arrays/process_select/Makefile.in | 5 +-
examples/C/global-array-time/Makefile.in | 5 +-
examples/C/global-array-time/adios_globaltime.c | 89 +-
examples/C/global-array-time/adios_globaltime.xml | 7 +-
.../C/global-array-time/adios_globaltime_no_xml.c | 4 +-
examples/C/global-array/Makefile.in | 5 +-
.../global-array/adios_global_aggregate_by_color.c | 2 +-
examples/C/global-array/adios_global_no_xml.c | 95 +-
examples/C/global-array/no_xml_write_byid.c | 2 +-
examples/C/icee_arrays/Makefile.in | 5 +-
examples/C/icee_arrays/array/Makefile.in | 5 +-
examples/C/icee_arrays/array/adios_write.c | 2 +-
examples/C/manual/Makefile.in | 5 +-
examples/C/query/Makefile.in | 5 +-
examples/C/query/write_table.c | 2 +-
examples/C/query/write_vars.c | 2 +-
examples/C/read_all/Makefile.in | 5 +-
examples/C/scalars/Makefile.in | 5 +-
examples/C/schema/Makefile.in | 5 +-
examples/C/schema/rectilinear2d_noxml.c | 2 +-
examples/C/schema/structured2d_noxml.c | 2 +-
examples/C/schema/tri2d_noxml.c | 2 +-
examples/C/schema/uniform2d_noxml.c | 2 +-
examples/C/stat/Makefile.in | 5 +-
examples/C/time_aggregation/CMakeLists.txt | 24 +
examples/C/time_aggregation/Makefile.am | 23 +
.../C/{attributes => time_aggregation}/Makefile.in | 72 +-
examples/C/time_aggregation/time_aggregation.c | 111 +
examples/C/time_aggregation/time_aggregation.xml | 45 +
.../C/time_aggregation/time_aggregation_no_xml.c | 158 +
examples/C/transforms/Makefile.in | 5 +-
examples/Fortran/Makefile.in | 5 +-
examples/Fortran/arrays/Makefile.in | 5 +-
examples/Fortran/global-array-time/Makefile.in | 5 +-
examples/Fortran/global-array/Makefile.in | 5 +-
.../Fortran/global-array/adios_global_no_xml.F90 | 3 +-
.../Fortran/global-array/no_xml_write_byid.F90 | 2 +-
examples/Fortran/scalars/Makefile.in | 5 +-
examples/Fortran/schema/Makefile.in | 5 +-
examples/Fortran/schema/rectilinear2d_noxml.F90 | 2 +-
examples/Fortran/schema/structured2d_noxml.F90 | 2 +-
examples/Fortran/schema/tri2d_noxml.F90 | 2 +-
examples/Fortran/schema/tri2d_noxml_seperate.F90 | 4 +-
examples/Fortran/schema/uniform2d_noxml.F90 | 2 +-
examples/Makefile.in | 5 +-
runconf | 50 +-
src/CMakeLists.txt | 69 +-
src/Makefile.am | 69 +-
src/Makefile.in | 383 +-
src/core/adios.c | 77 +-
src/core/adios_bp_v1.c | 1 +
src/core/adios_bp_v1.h | 1 +
src/core/adios_clock.h | 2 +-
src/core/adios_icee.h | 2 +
src/core/adios_internals.c | 741 +-
src/core/adios_internals.h | 116 +-
src/core/adios_internals_mxml.c | 130 +-
src/core/adios_read.c | 3 +-
src/core/adios_transform_methods.c | 59 +
src/core/adiosf.c | 31 +-
src/core/adiosf_defs_mod.f90 | 8 +
src/core/adiosf_write_mod.f90 | 6812 +++++-----
src/core/bp_utils.c | 4 +-
src/core/bp_utils.h | 2 +-
src/core/buffer.c | 12 +
src/core/common_adios.c | 655 +-
src/core/common_adios.h | 2 +-
src/core/common_read.c | 57 +-
src/core/common_read.h | 2 +-
src/core/flexpath.h | 1 +
src/core/mpidummy.c | 22 +
src/mxml/Makefile.am | 2 +-
src/mxml/Makefile.in | 7 +-
src/public/adios.h | 24 +-
src/public/adios_error.h | 1 +
src/public/adios_query.h | 15 +
src/public/adios_read_v2.h | 17 +-
src/public/adios_transform_methods.h | 25 +
src/public/adios_types.h | 9 +
src/public/adios_version.h | 6 +-
src/public/mpidummy.h | 10 +-
src/query/common_query.c | 58 +
src/read/read_flexpath.c | 83 +-
src/read/read_icee.c | 323 +-
src/transforms/Makefile.plugins | 4 +
src/transforms/adios_transform_zfp_common.h | 235 +
src/transforms/adios_transform_zfp_read.c | 223 +
src/transforms/adios_transform_zfp_write.c | 268 +
src/transforms/transform_plugins.h | 1 +
src/write/adios_dataspaces.c | 2 +-
src/write/adios_flexpath.c | 138 +-
src/write/adios_icee.c | 300 +-
src/write/adios_mpi.c | 32 +-
src/write/adios_mpi_amr.c | 89 +-
src/write/adios_mpi_lustre.c | 3 -
src/write/adios_posix.c | 12 +-
src/write/adios_var_merge.c | 7 +-
src/zfp/CMakeLists.txt | 40 +
src/zfp/Makefile.am | 61 +
src/{mxml => zfp}/Makefile.in | 296 +-
src/zfp/zfp-0.5.0/API | 439 +
src/zfp/zfp-0.5.0/Config | 49 +
src/zfp/zfp-0.5.0/FAQ | 371 +
src/zfp/zfp-0.5.0/LICENSE | 57 +
src/zfp/zfp-0.5.0/Makefile | 16 +
src/zfp/zfp-0.5.0/README | 422 +
src/zfp/zfp-0.5.0/VERSIONS | 161 +
src/zfp/zfp-0.5.0/array/cache.h | 224 +
src/zfp/zfp-0.5.0/array/memory.h | 42 +
src/zfp/zfp-0.5.0/array/zfparray.h | 105 +
src/zfp/zfp-0.5.0/array/zfparray1.h | 243 +
src/zfp/zfp-0.5.0/array/zfparray2.h | 273 +
src/zfp/zfp-0.5.0/array/zfparray3.h | 284 +
src/zfp/zfp-0.5.0/array/zfpcodec.h | 17 +
src/zfp/zfp-0.5.0/array/zfpcodecd.h | 149 +
src/zfp/zfp-0.5.0/array/zfpcodecf.h | 149 +
src/zfp/zfp-0.5.0/examples/Makefile | 35 +
src/zfp/zfp-0.5.0/examples/array2d.h | 25 +
src/zfp/zfp-0.5.0/examples/diffusion.cpp | 107 +
src/zfp/zfp-0.5.0/examples/fields.c | 12201 +++++++++++++++++
src/zfp/zfp-0.5.0/examples/fields.h | 20 +
src/zfp/zfp-0.5.0/examples/pgm.c | 112 +
src/zfp/zfp-0.5.0/examples/simple.c | 99 +
src/zfp/zfp-0.5.0/examples/speed.c | 136 +
src/zfp/zfp-0.5.0/examples/testzfp.cpp | 705 +
src/zfp/zfp-0.5.0/examples/zfp.c | 480 +
src/zfp/zfp-0.5.0/inc/bitstream.h | 87 +
src/zfp/zfp-0.5.0/inc/macros.h | 7 +
src/zfp/zfp-0.5.0/inc/system.h | 20 +
src/zfp/zfp-0.5.0/inc/types.h | 30 +
src/zfp/zfp-0.5.0/inc/zfp.h | 549 +
src/zfp/zfp-0.5.0/src/Makefile | 21 +
src/zfp/zfp-0.5.0/src/bitstream.c | 4 +
src/zfp/zfp-0.5.0/src/block1.h | 1 +
src/zfp/zfp-0.5.0/src/block2.h | 1 +
src/zfp/zfp-0.5.0/src/block3.h | 1 +
src/zfp/zfp-0.5.0/src/decode1d.c | 10 +
src/zfp/zfp-0.5.0/src/decode1f.c | 10 +
src/zfp/zfp-0.5.0/src/decode2d.c | 10 +
src/zfp/zfp-0.5.0/src/decode2f.c | 10 +
src/zfp/zfp-0.5.0/src/decode3d.c | 10 +
src/zfp/zfp-0.5.0/src/decode3f.c | 10 +
src/zfp/zfp-0.5.0/src/encode1d.c | 10 +
src/zfp/zfp-0.5.0/src/encode1f.c | 10 +
src/zfp/zfp-0.5.0/src/encode2d.c | 10 +
src/zfp/zfp-0.5.0/src/encode2f.c | 10 +
src/zfp/zfp-0.5.0/src/encode3d.c | 10 +
src/zfp/zfp-0.5.0/src/encode3f.c | 10 +
src/zfp/zfp-0.5.0/src/inline/bitstream.c | 410 +
src/zfp/zfp-0.5.0/src/inline/inline.h | 12 +
src/zfp/zfp-0.5.0/src/template/codec.h | 3 +
src/zfp/zfp-0.5.0/src/template/codec1.c | 11 +
src/zfp/zfp-0.5.0/src/template/codec2.c | 39 +
src/zfp/zfp-0.5.0/src/template/codec3.c | 97 +
src/zfp/zfp-0.5.0/src/template/compress.c | 104 +
src/zfp/zfp-0.5.0/src/template/decode.c | 165 +
src/zfp/zfp-0.5.0/src/template/decode1.c | 55 +
src/zfp/zfp-0.5.0/src/template/decode2.c | 62 +
src/zfp/zfp-0.5.0/src/template/decode3.c | 70 +
src/zfp/zfp-0.5.0/src/template/decompress.c | 104 +
src/zfp/zfp-0.5.0/src/template/encode.c | 216 +
src/zfp/zfp-0.5.0/src/template/encode1.c | 55 +
src/zfp/zfp-0.5.0/src/template/encode2.c | 65 +
src/zfp/zfp-0.5.0/src/template/encode3.c | 77 +
src/zfp/zfp-0.5.0/src/template/template.h | 12 +
src/zfp/zfp-0.5.0/src/traitsd.h | 11 +
src/zfp/zfp-0.5.0/src/traitsf.h | 17 +
src/zfp/zfp-0.5.0/src/zfp.c | 719 +
tests/C/Makefile.in | 5 +-
tests/C/fgr_tests/Makefile.in | 5 +-
tests/C/flexpath_tests/1D_arr_global/Makefile.in | 5 +-
tests/C/flexpath_tests/1D_arr_global/reader.c | 6 +-
.../flexpath_tests/1D_arr_global_noxml/Makefile.in | 5 +-
.../C/flexpath_tests/1D_arr_global_noxml/writer.c | 4 +-
tests/C/flexpath_tests/Makefile.in | 5 +-
.../flexpath_tests/global_range_select/Makefile.in | 5 +-
tests/C/flexpath_tests/maya_append/Makefile.in | 5 +-
tests/C/flexpath_tests/maya_append/writer.c | 2 +-
tests/C/flexpath_tests/maya_noxml/Makefile.in | 5 +-
tests/C/flexpath_tests/maya_noxml/writer.c | 2 +-
tests/C/flexpath_tests/scalar/Makefile.in | 5 +-
tests/C/flexpath_tests/scalar/writer.c | 2 +-
tests/C/query/Makefile.in | 5 +-
tests/C/query/alacrity/Makefile.in | 5 +-
tests/C/query/common/Makefile.in | 5 +-
tests/C/query/fastbit/Makefile.in | 5 +-
tests/Fortran/Makefile.in | 5 +-
tests/Makefile.in | 5 +-
tests/bp_read/Makefile.in | 5 +-
tests/genarray/Makefile.in | 5 +-
tests/suite/Makefile.in | 5 +-
tests/suite/programs/Makefile.in | 5 +-
tests/suite/programs/big_file.c | 2 +-
tests/suite/programs/blocks.c | 2 +-
tests/suite/programs/connect_to_space_subset.c | 2 +-
tests/suite/programs/examples/Makefile.in | 5 +-
.../suite/programs/examples/attributes/Makefile.in | 5 +-
.../programs/examples/global_array/Makefile.in | 5 +-
.../examples/global_array/global_array_F.xml | 2 +-
.../global_array_aggregate_by_color_C.c | 2 +-
.../global_array/global_array_write_byid_noxml_C.c | 2 +-
.../global_array_write_byid_noxml_F.F90 | 2 +-
.../global_array/global_array_write_noxml_C.c | 2 +-
.../global_array/global_array_write_noxml_F.F90 | 2 +-
.../examples/global_array_time/Makefile.am | 2 +-
.../examples/global_array_time/Makefile.in | 7 +-
.../global_array_time/global_array_time_aggr_C.xml | 3 +-
.../global_array_time/global_array_time_write_C.c | 84 +-
.../programs/examples/local_array/Makefile.in | 5 +-
tests/suite/programs/examples/scalars/Makefile.in | 5 +-
.../programs/examples/scalars/scalars_read_C.c | 28 +-
.../programs/examples/scalars/scalars_read_F.F90 | 30 +-
tests/suite/programs/many_vars.c | 2 +-
tests/suite/programs/reuse_dim.c | 2 +-
tests/suite/programs/selections.c | 2 +-
tests/suite/programs/steps_write.c | 2 +-
tests/suite/reference/attributes_bpls.txt | 2 +-
tests/suite/reference/global_array_no_xml_bpls.txt | 2 +-
.../suite/reference/global_array_no_xml_f_bpls.txt | 2 +-
tests/suite/reference/global_array_time_bpls.txt | 4 +-
tests/suite/reference/local_array_C_bpls.txt | 4 +-
tests/suite/reference/no_xml_write_byid_bpls.txt | 2 +-
tests/suite/reference/no_xml_write_byid_f_bpls.txt | 2 +-
tests/suite/test.sh | 17 +-
tests/suite/tests/01_scalars.sh | 4 +-
tests/suite/tests/05_global_array_time.sh | 53 +-
tests/suite/tests/19_query.sh | 9 +-
tests/test_src/CMakeLists.txt | 2 +-
tests/test_src/Makefile.am | 12 +-
tests/test_src/Makefile.in | 105 +-
tests/test_src/array_attribute.c | 327 +
tests/test_src/group_free_test.c | 2 +-
tests/test_src/query_minmax.c | 2 +-
tests/test_src/read_points_2d.c | 2 +-
tests/test_src/read_points_3d.c | 774 --
utils/Makefile.in | 5 +-
utils/adios_lint/Makefile.in | 5 +-
utils/adios_list_methods/Makefile.in | 5 +-
utils/adios_list_methods/adios_list_methods.c | 425 +-
utils/bp2ascii/Makefile.in | 5 +-
utils/bp2bp/Makefile.in | 5 +-
utils/bp2h5/Makefile.in | 5 +-
utils/bp2h5/bp2h5.c | 8 +-
utils/bp2ncd/Makefile.in | 5 +-
utils/bpdiff/Makefile.in | 5 +-
utils/bpdump/Makefile.in | 5 +-
utils/bpls/Makefile.in | 5 +-
utils/bpmeta/Makefile.in | 5 +-
utils/bprecover/Makefile.in | 5 +-
utils/bpsplit/Makefile.in | 5 +-
utils/fastbit/Makefile.in | 5 +-
utils/gpp/CMakeLists.txt | 3 +-
utils/gpp/Makefile.am | 7 +-
utils/gpp/Makefile.in | 62 +-
utils/gpp/gpp.py | 9 +-
utils/gpp/gpp.py.in | 7 +
utils/skel/CMakeLists.txt | 31 +-
utils/skel/Makefile.am | 2 +-
utils/skel/Makefile.in | 7 +-
.../skel/bin/{set_method.sh => skel_set_method.sh} | 0
utils/skel/etc/Makefile.in | 5 +-
utils/skel/etc/templates/Makefile.default.tpl | 2 +-
utils/skel/etc/templates/submit_jaguar.tpl | 2 +-
utils/skel/etc/templates/submit_nautilus.tmpl | 2 +-
utils/skel/etc/templates/submit_nautilus.tpl | 2 +-
utils/skel/etc/templates/submit_sith.tmpl | 2 +-
utils/skel/etc/templates/submit_sith.tpl | 2 +-
utils/skel/src/Makefile.in | 5 +-
utils/skeldump/Makefile.in | 5 +-
utils/skeldump/skeldump.c | 2 +-
wrappers/java/CMakeLists.txt | 6 +-
wrappers/java/gov/ornl/ccs/Adios.java | 8 +-
wrappers/java/gov_ornl_ccs_Adios.cxx | 40 +-
wrappers/java/test/AdiosNoxmlTest.java | 14 +-
wrappers/numpy/adios.cpp | 12949 +++++++++++-------
wrappers/numpy/adios.pyx | 288 +-
wrappers/numpy/adios_mpi.cpp | 13041 ++++++++++++-------
wrappers/numpy/adios_mpi.pyx | 288 +-
wrappers/numpy/build-and-install.sh | 14 +
wrappers/numpy/doc/source/build.rst | 24 +-
wrappers/numpy/src/__init__.py | 2 +-
wrappers/numpy/src_mpi/__init__.py | 2 +-
wrappers/numpy/test/test_adios_writer_unittest.py | 43 +
wrappers/numpy/tests/test_adios_attribute.py | 3 +-
wrappers/numpy/tests/test_adios_mpi_writer.py | 18 +-
wrappers/numpy/tests/test_adios_writer.py | 15 +-
305 files changed, 46943 insertions(+), 15799 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 954d132..30bcb04 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -547,6 +547,26 @@ elseif(DEFINED ENV{ALACRITY})
endif()
endif()
+if(DEFINED ENV{ZFP_DIR})
+ if("$ENV{ZFP_DIR}" STREQUAL "")
+ set(ZFP OFF CACHE BOOL "")
+ else()
+ set(ZFP ON CACHE BOOL "")
+ set(ZFP_DIR "$ENV{ZFP_DIR}")
+ endif()
+elseif(DEFINED ENV{ZFP})
+ if("$ENV{ZFP}" STREQUAL "")
+ set(ZFP OFF CACHE BOOL "")
+ else()
+ set(ZFP ON CACHE BOOL "")
+ set(ZFP_DIR "$ENV{ZFP}")
+ endif()
+else()
+ set(BUILD_ZFP ON CACHE BOOL "")
+ set(ZFP ON CACHE BOOL "")
+ set(ZFP_DIR ${PROJECT_SOURCE_DIR}/src/zfp/zfp-0.5.0)
+endif()
+
###################### end of external library is used(ON) or not (OFF) ##############################
@@ -1321,6 +1341,27 @@ if(ALACRITY)
endif()
endif()
+set(HAVE_ZFP 0)
+if(ZFP)
+ find_path(ZFP_INCLUDE_DIR NAMES zfp.h PATHS ${ZFP_DIR}/inc ${ZFP_DIR}/include)
+ if(ZFP_INCLUDE_DIR)
+ set(HAVE_ZFP_H 1)
+ endif()
+ if (BUILD_ZFP)
+ set(HAVE_ZFP 1)
+ set(ZFP_CPPFLAGS "${MACRODEFFLAG}ZFP -I${ZFP_INCLUDE_DIR}")
+ message(STATUS "ZFP will be built for ADIOS in ./src/zfp")
+ else(BUILD_ZFP)
+ find_library(ZFP_LIBS NAMES zfp PATHS ${ZFP_DIR}/lib)
+ if(ZFP_INCLUDE_DIR AND ZFP_LIBS)
+ set(HAVE_ZFP 1)
+ set(ZFP_CPPFLAGS "${MACRODEFFLAG}ZFP -I${ZFP_INCLUDE_DIR}")
+ endif()
+ message(STATUS "ZFP will be used from ${ZFP_DIR}")
+ endif(BUILD_ZFP)
+else(ZFP)
+ message(STATUS "ZFP is turned off")
+endif(ZFP)
# Define to 1 if your C compiler doesn't accept -c and -o together.
@@ -1718,6 +1759,18 @@ if(HAVE_ALACRITY)
set(ADIOSREADLIB_SEQ_LDADD ${ADIOSREADLIB_SEQ_LDADD} ${ALACRITY_LIBS})
endif()
+if(HAVE_ZFP)
+ set(ADIOSLIB_CPPFLAGS "${ADIOSLIB_CPPFLAGS} ${ZFP_CPPFLAGS}")
+ set(ADIOSLIB_LDADD ${ADIOSLIB_LDADD} ${ZFP_LIBS})
+ set(ADIOSLIB_SEQ_CPPFLAGS "${ADIOSLIB_SEQ_CPPFLAGS} ${ZFP_CPPFLAGS}")
+ set(ADIOSLIB_SEQ_LDADD ${ADIOSLIB_SEQ_LDADD} ${ZFP_LIBS})
+ set(ADIOSLIB_INT_CPPFLAGS "${ADIOSLIB_INT_CPPFLAGS} ${ZFP_CPPFLAGS}")
+ set(ADIOSLIB_INT_LDADD ${ADIOSLIB_INT_LDADD} ${ZFP_LIBS})
+ set(ADIOSREADLIB_CPPFLAGS "${ADIOSREADLIB_CPPFLAGS} ${ZFP_CPPFLAGS}")
+ set(ADIOSREADLIB_LDADD ${ADIOSREADLIB_LDADD} ${ZFP_LIBS})
+ set(ADIOSREADLIB_SEQ_CPPFLAGS "${ADIOSREADLIB_SEQ_CPPFLAGS} ${ZFP_CPPFLAGS}")
+ set(ADIOSREADLIB_SEQ_LDADD ${ADIOSREADLIB_SEQ_LDADD} ${ZFP_LIBS})
+endif()
if(HAVE_FASTBIT)
set(ADIOSLIB_CPPFLAGS "${ADIOSLIB_CPPFLAGS} -DFASTBIT ${FASTBIT_CPPFLAGS}")
@@ -1787,6 +1840,14 @@ if (NOT BUILD_MXML)
set(ADIOSLIB_INT_LDADD ${ADIOSLIB_INT_LDADD} ${MXML_LIBS})
endif()
+if (NOT BUILD_ZFP)
+ set(ADIOSLIB_LDADD ${ADIOSLIB_LDADD} ${ZFP_LIBS})
+ set(ADIOSLIB_SEQ_LDADD ${ADIOSLIB_SEQ_LDADD} ${ZFP_LIBS})
+ set(ADIOSLIB_INT_LDADD ${ADIOSLIB_INT_LDADD} ${ZFP_LIBS})
+ set(ADIOSREADLIB_LDADD ${ADIOSREADLIB_LDADD} ${ZFP_LIBS})
+ set(ADIOSREADLIB_SEQ_LDADD ${ADIOSREADLIB_SEQ_LDADD} ${ZFP_LIBS})
+endif()
+
add_subdirectory(src)
add_subdirectory(utils)
add_subdirectory(tests)
@@ -2056,6 +2117,18 @@ else()
message(" - No ALACRITY to build ALACRITY transform & query method")
endif()
+if(BUILD_ZFP)
+ message(" - ZFP is built with ADIOS")
+elseif (HAVE_ZFP)
+ message(" - ZFP")
+ message(" - ZFP_CPPFLAGS = ${ZFP_CPPFLAGS}")
+ message(" - ZFP_LIBS = ${ZFP_LIBS}")
+ message("")
+else()
+ message(" - No ZFP to build ZFP transform method")
+endif()
+
+
if(HAVE_BGQ)
message(" - BGQ METHOD is enabled")
else()
diff --git a/COPYING b/COPYING
index a827741..d06403d 100644
--- a/COPYING
+++ b/COPYING
@@ -26,9 +26,17 @@ Additional BSD Notice
Note about Mini-XML
===================
-The mxml/mxml-2.9 subdirectory contains the unmodified code of Mini-XML 2.9 which is otherwise freely accessible from
+The src/mxml/mxml-2.9 subdirectory contains the unmodified code of Mini-XML 2.9 which is otherwise freely accessible from
http://www.msweet.org/projects.php/Mini-XML
The author of that open source software is Michael Sweet
-The mxml-2.9 library comes with the LGPL v2 license, see mxml/mxml-2.9/COPYING
-ADIOS can be linked with a pre-installed mxml library otherwise it will build the libmxml.a library from this included source.
+The mxml-2.9 library comes with the LGPL v2 license, see src/mxml/mxml-2.9/COPYING
+ADIOS can be linked with a pre-installed mxml library otherwise it will build mxml from this included source.
+
+Note about ZFP
+===================
+The src/zfp/zfp-0.5.0 subdirectory contains the unmodified code of ZFP which is otherwise freely accessible from
+ http://computation.llnl.gov/projects/floating-point-compression
+The author of that open source software is Peter Lindstrom
+The zfp library comes with a BSD license, see src/zfp/zfp-0.5.0/COPYING
+ADIOS can be linked with a pre-installed zfp library otherwise it will build zfp from this included source.
diff --git a/Makefile.in b/Makefile.in
index 38e526b..0b884d9 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -128,7 +128,7 @@ 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_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 \
@@ -486,6 +486,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/NEWS b/NEWS
index af13359..020f86c 100644
--- a/NEWS
+++ b/NEWS
@@ -1,5 +1,26 @@
+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.
+ - ZFP lossy compression transform method
+ - Python wrapper includes functions for:
+ - Selecting transforms and time aggregation: adios_set_transform()
+ - Time aggregation: adios_set_time_aggregation()
+ - Set maximum buffer size used by any ADIOS group: adios_set_max_buffer_size()
+ - Collect min/max statistics only by default
+ adios_declare_group() last argument type changed to be an option for statistics.
+ Options are: adios_stat_no, adios_stat_minmax, adios_stat_full, and adios_stat_default, which is minmax
+ - Added functions to C API to detect available methods in the ADIOS installation
+ adios.h: adios_available_write_methods()
+ adios_read.h: adios_available_read_methods()
+ adios_transform_methods.h: adios_available_transform_methods()
+ adios_query.h: adios_available_query_methods()
+ - Performance bug in MPI_AGGREGATE method in 1.9/1.10 fixed
+ - fix: bug building with hdf5 1.10
+
1.10.0 Release July 2016
+ - Updated Query API and Minmax, FastBit and Alacrity query methods
- Fortran API for inquiring selections
+ - ADIOS builds without first installing Mini-XML separately
- bprecover utility
- recover a BP file which has a damaged index data
- adios_group_size() optional now
diff --git a/aclocal.m4 b/aclocal.m4
index 877a246..84c17eb 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -1446,6 +1446,7 @@ m4_include([config/ac_pami.m4])
m4_include([config/ac_phdf5.m4])
m4_include([config/ac_portals.m4])
m4_include([config/ac_szip.m4])
+m4_include([config/ac_zfp.m4])
m4_include([config/ac_zlib.m4])
m4_include([config/acx_mpi.m4])
m4_include([config/acx_pthread.m4])
diff --git a/cmake_init b/cmake_init
index 5f77d1c..9a0b60c 100755
--- a/cmake_init
+++ b/cmake_init
@@ -528,16 +528,17 @@ elif [ `hostname | cut -c 1-4` == "dyn9" -o `hostname | cut -c 1-3` == "pnb" ];
echo "Configure using clang"
fi
# The rest is common for all
- export CC=/usr/local/bin/mpicc
- export FC=/usr/local/bin/mpif90
- export CXX=/usr/local/bin/mpicxx
+ # The rest is common for all
+ export CC=mpicc #/usr/local/bin/mpicc
+ export FC=mpif90 #/usr/local/bin/mpif90
+ export CXX=mpicxx #/usr/local/bin/mpicxx
export CFLAGS="-g -Wall -DO_LARGEFILE=0 -fno-common"
export BUILD_WRITE=ON
export BUILD_FORTRAN=ON
export adios_timers=ON
export INSTALL_PREFIX="/opt/adios"
- export PAR_HDF5_DIR=/usr/local
- export PAR_HDF5_LIBS="-L/usr/local/lib -lhdf5_hl -lhdf5 -lm"
+#export PAR_HDF5_DIR=/usr/local
+#export PAR_HDF5_LIBS="-L/usr/local/lib -lhdf5_hl -lhdf5 -lm"
unset SEQ_HDF5_DIR
unset SEQ_HDF5_LIBS
unset SEQ_NC_DIR
@@ -609,7 +610,7 @@ elif [ `hostname | cut -c 1-9` == "PC0098504" ]; then
export CC=mpicc
export CXX=mpicxx
export FC=mpif90
- export INSTALL_PREFIX="/opt/adios/1.10"
+ export INSTALL_PREFIX="/opt/adios"
export CPPFLAGS="-DMPICH_IGNORE_CXX_SEEK"
export CFLAGS="-g -O0 -fPIC -Wno-int-to-pointer-cast -Wno-pointer-to-int-cast"
export LDFLAGS="-lpthread"
@@ -626,7 +627,7 @@ elif [ `hostname | cut -c 1-7` == "adiosVM" ]; then
export CC=mpicc
export CXX=mpicxx
export FC=mpif90
- export INSTALL_PREFIX="/opt/adios/1.10"
+ export INSTALL_PREFIX="/opt/adios/1.11"
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"
diff --git a/config.h.in b/config.h.in
index 1c33776..418eb3d 100644
--- a/config.h.in
+++ b/config.h.in
@@ -44,6 +44,9 @@
/* Define to 1 if you have the <bzlib.h> header file. */
#undef HAVE_BZLIB_H
+/* Define to 1 if the system has the type `clockid_t'. */
+#undef HAVE_CLOCKID_T
+
/* Define to 1 if you have the `clock_gettime' function. */
#undef HAVE_CLOCK_GETTIME
@@ -278,12 +281,21 @@
/* Define to 1 if you have the <szlib.h> header file. */
#undef HAVE_SZLIB_H
+/* Define to 1 if you have the <time.h> header file. */
+#undef HAVE_TIME_H
+
/* Define to 1 if you have the <unistd.h> header file. */
#undef HAVE_UNISTD_H
/* Define to 1 if you have the `vsnprintf' function. */
#undef HAVE_VSNPRINTF
+/* Define if you have ZFP. */
+#undef HAVE_ZFP
+
+/* Define to 1 if you have the <zfp.h> header file. */
+#undef HAVE_ZFP_H
+
/* Define if you have ZLIB. */
#undef HAVE_ZLIB
diff --git a/config/ac_dataspaces.m4 b/config/ac_dataspaces.m4
index 823e304..038c072 100644
--- a/config/ac_dataspaces.m4
+++ b/config/ac_dataspaces.m4
@@ -35,6 +35,11 @@ if test "x$with_dataspaces" == "xno"; then
AM_CONDITIONAL(HAVE_DATASPACES,false)
+elif test -z "${HAVE_MPI_FALSE}"; then
+
+ AC_MSG_NOTICE([ DataSpaces does not build without MPI])
+ AM_CONDITIONAL(HAVE_DATASPACES,false)
+
else
dnl allow args --with-dataspaces incdir and --with-dataspaces-libdir
@@ -81,6 +86,7 @@ else
ac_dataspaces_ok=no
fi
+ save_CC="$CC"
save_CPPFLAGS="$CPPFLAGS"
save_LIBS="$LIBS"
save_LDFLAGS="$LDFLAGS"
@@ -94,9 +100,10 @@ else
dnl else
dnl LIBS="$LIBS -ldspaces -ldscommon -ldart"
dnl fi
- LIBS="$LIBS -ldspaces -ldscommon -ldart"
+ LIBS="-ldspaces -ldscommon -ldart $LIBS"
LDFLAGS="$LDFLAGS $DATASPACES_LDFLAGS"
CPPFLAGS="$CPPFLAGS $DATASPACES_CPPFLAGS"
+ CC="$MPICC"
if test -z "${HAVE_DATASPACES_TRUE}"; then
AC_CHECK_HEADERS(dataspaces.h,
@@ -106,43 +113,26 @@ else
if test -z "${HAVE_DATASPACES_TRUE}"; then
# Check for the DataSpaces library and headers
- if test "x${ac_portals_lib_ok}" == "xyes"; then
- AC_TRY_COMPILE([#include "dataspaces.h"],
- [int err; err = dspaces_init(1,1,0,"");],
- [DATASPACES_LIBS="-ldspaces -ldscommon -ldart"],
- [AM_CONDITIONAL(HAVE_DATASPACES,false)])
- elif test "x${ac_infiniband_lib_ok}" == "xyes"; then
- AC_TRY_COMPILE([#include "dataspaces.h"],
- [int err; err = dspaces_init(1,1,0,"");],
- [DATASPACES_LIBS="-ldspaces -ldscommon -ldart -lrdmacm"],
- [AM_CONDITIONAL(HAVE_DATASPACES,false)])
- elif test -z "${HAVE_CRAY_PMI_TRUE}" -a -z "${HAVE_CRAY_UGNI_TRUE}"; then
- AC_TRY_COMPILE([#include "dataspaces.h"],
+ AC_MSG_CHECKING([if dataspaces code can be compiled and linked])
+ 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 else
+ dnl fi
+ AC_TRY_LINK([#include "dataspaces.h"],
[int err; err = dspaces_init(1,1,0,"");],
- [DATASPACES_LIBS="-ldspaces -ldscommon -ldart"],
- [AM_CONDITIONAL(HAVE_DATASPACES,false)])
- elif test "x${ac_dcmf_lib_ok}" == "xyes"; then
- AC_TRY_COMPILE([#include "dataspaces.h"],
- [int err; err = dspaces_init(1,1,0,"");],
- [DATASPACES_LIBS="-ldspaces -ldscommon -ldart"],
- [AM_CONDITIONAL(HAVE_DATASPACES,false)])
- elif test "x${ac_pami_lib_ok}" == "xyes"; then
- AC_TRY_COMPILE([#include "dataspaces.h"],
- [int err; err = dspaces_init(1,1,0,"");],
- [DATASPACES_LIBS="-ldspaces -ldscommon -ldart"],
- [AM_CONDITIONAL(HAVE_DATASPACES,false)])
- else
- dnl Now TCP is working #AM_CONDITIONAL(HAVE_DATASPACES,false)
- AC_TRY_COMPILE([#include "dataspaces.h"],
- [int err; err = dspaces_init(1,1,0,"");],
- [DATASPACES_LIBS="-ldspaces -ldscommon -ldart"],
- [AM_CONDITIONAL(HAVE_DATASPACES,false)])
- fi
+ [AC_MSG_RESULT(yes)
+ DATASPACES_LIBS="-ldspaces -ldscommon -ldart"],
+ [AC_MSG_RESULT(no)
+ AM_CONDITIONAL(HAVE_DATASPACES,false)])
fi
LIBS="$save_LIBS"
LDFLAGS="$save_LDFLAGS"
CPPFLAGS="$save_CPPFLAGS"
+ CC="$save_CC"
AC_SUBST(DATASPACES_LIBS)
AC_SUBST(DATASPACES_LDFLAGS)
diff --git a/config/ac_dimes.m4 b/config/ac_dimes.m4
index e677dfa..0929822 100644
--- a/config/ac_dimes.m4
+++ b/config/ac_dimes.m4
@@ -32,6 +32,11 @@ if test "x$with_dimes" == "xno"; then
AM_CONDITIONAL(HAVE_DIMES,false)
+elif test -z "${HAVE_MPI_FALSE}"; then
+
+ AC_MSG_NOTICE([ Dimes does not build without MPI])
+ AM_CONDITIONAL(HAVE_DIMES,false)
+
else
dnl allow args --with-dimes incdir and --with-dimes-libdir
@@ -78,6 +83,7 @@ else
ac_dimes_ok=no
fi
+ save_CC="$CC"
save_CPPFLAGS="$CPPFLAGS"
save_LIBS="$LIBS"
save_LDFLAGS="$LDFLAGS"
@@ -85,13 +91,12 @@ else
dnl LIBS="$LIBS -ldart2 -lspaces"
echo "DIMES currently NOT supported for Cray Portals!"
AM_CONDITIONAL(HAVE_DIMES, false)
- elif test "x${ac_dcmf_lib_ok}" == "xyes"; then
- LIBS="$LIBS -ldspaces -ldscommon -ldart"
else
- LIBS="$LIBS -ldspaces -ldscommon -ldart"
+ LIBS="-ldspaces -ldscommon -ldart $LIBS"
fi
LDFLAGS="$LDFLAGS $DIMES_LDFLAGS"
CPPFLAGS="$CPPFLAGS $DIMES_CPPFLAGS"
+ CC="$MPICC"
if test -z "${HAVE_DIMES_TRUE}"; then
AC_CHECK_HEADERS(dimes_interface.h,
@@ -100,35 +105,27 @@ else
fi
if test -z "${HAVE_DIMES_TRUE}"; then
+ AC_MSG_CHECKING([if dimes code can be compiled and linked])
# Check for the DataSpaces/DIMES library and headers
- if test -z "${HAVE_CRAY_PMI_TRUE}" -a -z "${HAVE_CRAY_UGNI_TRUE}"; then
- AC_TRY_LINK([#include "dimes_interface.h"],
- [int err; dimes_put_sync_all();],
- [DIMES_LIBS="-ldspaces -ldscommon -ldart"],
- [AM_CONDITIONAL(HAVE_DIMES,false)])
- elif test "x${ac_infiniband_lib_ok}" == "xyes"; then
- AC_TRY_COMPILE([#include "dimes_interface.h"],
+ dnl if test -z "${HAVE_CRAY_PMI_TRUE}" -a -z "${HAVE_CRAY_UGNI_TRUE}"; then
+ dnl elif test "x${ac_infiniband_lib_ok}" == "xyes"; then
+ dnl elif test "x${ac_dcmf_lib_ok}" == "xyes"; then
+ dnl elif test "x${ac_pami_lib_ok}" == "xyes"; then
+ AC_TRY_LINK([#include "dimes_interface.h"],
[int err; dimes_put_sync_all();],
- [DIMES_LIBS="-ldspaces -ldscommon -ldart"],
- [AM_CONDITIONAL(HAVE_DIMES,false)])
- elif test "x${ac_dcmf_lib_ok}" == "xyes"; then
- AC_TRY_COMPILE([#include "dimes_interface.h"],
- [int err; dimes_put_sync_all();],
- [DIMES_LIBS="-ldspaces -ldscommon -ldart"],
- [AM_CONDITIONAL(HAVE_DIMES,false)])
- elif test "x${ac_pami_lib_ok}" == "xyes"; then
- AC_TRY_COMPILE([#include "dimes_interface.h"],
- [int err; dimes_put_sync_all();],
- [DIMES_LIBS="-ldspaces -ldscommon -ldart"],
- [AM_CONDITIONAL(HAVE_DIMES,false)])
- else
- AM_CONDITIONAL(HAVE_DIMES,false)
- fi
+ [AC_MSG_RESULT(yes)
+ DIMES_LIBS="-ldspaces -ldscommon -ldart"],
+ [AC_MSG_RESULT(no)
+ AM_CONDITIONAL(HAVE_DIMES,false)])
+ dnl else
+ dnl AM_CONDITIONAL(HAVE_DIMES,false)
+ dnl fi
fi
LIBS="$save_LIBS"
LDFLAGS="$save_LDFLAGS"
CPPFLAGS="$save_CPPFLAGS"
+ CC="$save_CC"
AC_SUBST(DIMES_LIBS)
AC_SUBST(DIMES_LDFLAGS)
diff --git a/config/ac_zfp.m4 b/config/ac_zfp.m4
new file mode 100644
index 0000000..13fcff5
--- /dev/null
+++ b/config/ac_zfp.m4
@@ -0,0 +1,83 @@
+#
+#
+# AC_ZFP
+#
+#
+#
+dnl @synopsis AC_ZFP
+dnl
+dnl This macro tests if ZFP is to be used.
+dnl Use in C code:
+dnl #ifdef ZFP
+dnl #include "zfp.h"
+dnl #endif
+dnl
+dnl @version 0.1
+dnl @author Eric Suchyta
+dnl
+
+AC_DEFUN([AC_ZFP],[
+
+AC_MSG_NOTICE([=== checking for ZFP ===])
+AM_CONDITIONAL(HAVE_ZFP,true)
+AM_CONDITIONAL(BUILD_ZFP,false)
+
+
+AC_ARG_WITH(zfp,
+ [ --with-zfp=DIR Location of ZFP library],
+ [],
+ [with_zfp=builtin])
+
+
+if test "x$with_zfp" == "xno"; then
+ AM_CONDITIONAL(HAVE_ZFP,false)
+
+elif test "x$with_zfp" == "xbuiltin"; then
+ AM_CONDITIONAL(BUILD_ZFP,true)
+
+else
+ save_CPPFLAGS="$CPPFLAGS"
+ save_LIBS="$LIBS"
+ save_LDFLAGS="$LDFLAGS"
+
+
+ if test -z "${ZFP_LIBS}"; then
+ ZFP_LIBS="-lzfp"
+ fi
+
+ if test -z "${ZFP_LDFLAGS}"; then
+ ZFP_LDFLAGS="-L$with_zfp/lib"
+ fi
+
+ if test -z "${ZFP_CPPFLAGS}"; then
+ ZFP_CPPFLAGS="-I$with_zfp/inc"
+ fi
+
+
+ LIBS="$LIBS $ZFP_LIBS"
+ LDFLAGS="$LDFLAGS $ZFP_LDFLAGS"
+ CPPFLAGS="$CPPFLAGS $ZFP_CPPFLAGS"
+
+ if test -z "${HAVE_ZFP_TRUE}"; then
+ AC_CHECK_HEADERS(zfp.h, , [AM_CONDITIONAL(HAVE_ZFP,false)])
+ fi
+
+ LIBS="$save_LIBS"
+ LDFLAGS="$save_LDFLAGS"
+ CPPFLAGS="$save_CPPFLAGS"
+
+ AC_SUBST(ZFP_LIBS)
+ AC_SUBST(ZFP_LDFLAGS)
+ AC_SUBST(ZFP_CPPFLAGS)
+
+ # Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND:
+ if test -z "${HAVE_ZFP_TRUE}"; then
+ ifelse([$1], , [AC_DEFINE(HAVE_ZFP,1,[Define if you have ZFP.])], [$1])
+ :
+ else
+ $2
+ :
+ fi
+fi
+])
+dnl AC_ZFP
diff --git a/configure b/configure
index f0ae781..7046e44 100755
--- a/configure
+++ b/configure
@@ -1,7 +1,7 @@
#! /bin/sh
# From configure.ac Revision.
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for adios 1.10.0.
+# Generated by GNU Autoconf 2.69 for adios 1.11.0.
#
#
# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
@@ -588,8 +588,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='adios'
PACKAGE_TARNAME='adios'
-PACKAGE_VERSION='1.10.0'
-PACKAGE_STRING='adios 1.10.0'
+PACKAGE_VERSION='1.11.0'
+PACKAGE_STRING='adios 1.11.0'
PACKAGE_BUGREPORT=''
PACKAGE_URL=''
@@ -681,6 +681,13 @@ ADIOS_TIMERS_FALSE
ADIOS_TIMERS_TRUE
RESEARCH_TRANSPORTS_FALSE
RESEARCH_TRANSPORTS_TRUE
+ZFP_CPPFLAGS
+ZFP_LDFLAGS
+ZFP_LIBS
+BUILD_ZFP_FALSE
+BUILD_ZFP_TRUE
+HAVE_ZFP_FALSE
+HAVE_ZFP_TRUE
HAVE_BGQ_FALSE
HAVE_BGQ_TRUE
FASTBIT_LIBS
@@ -1068,6 +1075,7 @@ with_aplod
with_alacrity
with_fastbit
with_bgq
+with_zfp
enable_research_transports
enable_timers
enable_timer_events
@@ -1632,7 +1640,7 @@ if test "$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 1.10.0 to adapt to many kinds of systems.
+\`configure' configures adios 1.11.0 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1702,7 +1710,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of adios 1.10.0:";;
+ short | recursive ) echo "Configuration of adios 1.11.0:";;
esac
cat <<\_ACEOF
@@ -1811,6 +1819,7 @@ Optional Packages:
--with-alacrity=DIR Location of ALACRITY library
--with-fastbit=DIR Location of the FastBit library
--with-bgq Whether to enable BGQ method or not
+ --with-zfp=DIR Location of ZFP library
Some influential environment variables:
CC C compiler command
@@ -1899,7 +1908,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-adios configure 1.10.0
+adios configure 1.11.0
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2693,7 +2702,7 @@ 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 1.10.0, which was
+It was created by adios $as_me 1.11.0, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -3562,7 +3571,7 @@ fi
# Define the identity of the package.
PACKAGE='adios'
- VERSION='1.10.0'
+ VERSION='1.11.0'
cat >>confdefs.h <<_ACEOF
@@ -21542,6 +21551,30 @@ fi
done
+for ac_header in time.h
+do :
+ ac_fn_c_check_header_mongrel "$LINENO" "time.h" "ac_cv_header_time_h" "$ac_includes_default"
+if test "x$ac_cv_header_time_h" = xyes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_TIME_H 1
+_ACEOF
+
+fi
+
+done
+
+ac_fn_c_check_type "$LINENO" "clockid_t" "ac_cv_type_clockid_t" "#include <time.h>
+"
+if test "x$ac_cv_type_clockid_t" = xyes; then :
+
+cat >>confdefs.h <<_ACEOF
+#define HAVE_CLOCKID_T 1
+_ACEOF
+
+
+fi
+
+
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for preprocessor stringizing operator" >&5
$as_echo_n "checking for preprocessor stringizing operator... " >&6; }
if ${ac_cv_c_stringize+:} false; then :
@@ -25467,6 +25500,19 @@ else
fi
+elif test -z "${HAVE_MPI_FALSE}"; then
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: DataSpaces does not build without MPI" >&5
+$as_echo "$as_me: DataSpaces does not build without MPI" >&6;}
+ if false; then
+ HAVE_DATASPACES_TRUE=
+ HAVE_DATASPACES_FALSE='#'
+else
+ HAVE_DATASPACES_TRUE='#'
+ HAVE_DATASPACES_FALSE=
+fi
+
+
else
@@ -25510,12 +25556,14 @@ fi
ac_dataspaces_ok=no
fi
+ save_CC="$CC"
save_CPPFLAGS="$CPPFLAGS"
save_LIBS="$LIBS"
save_LDFLAGS="$LDFLAGS"
- LIBS="$LIBS -ldspaces -ldscommon -ldart"
+ LIBS="-ldspaces -ldscommon -ldart $LIBS"
LDFLAGS="$LDFLAGS $DATASPACES_LDFLAGS"
CPPFLAGS="$CPPFLAGS $DATASPACES_CPPFLAGS"
+ CC="$MPICC"
if test -z "${HAVE_DATASPACES_TRUE}"; then
for ac_header in dataspaces.h
@@ -25543,140 +25591,9 @@ done
if test -z "${HAVE_DATASPACES_TRUE}"; then
# Check for the DataSpaces library and headers
- if test "x${ac_portals_lib_ok}" == "xyes"; then
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#include "dataspaces.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 ()
-{
-int err; err = dspaces_init(1,1,0,"");
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
- DATASPACES_LIBS="-ldspaces -ldscommon -ldart"
-else
- if false; then
- HAVE_DATASPACES_TRUE=
- HAVE_DATASPACES_FALSE='#'
-else
- HAVE_DATASPACES_TRUE='#'
- HAVE_DATASPACES_FALSE=
-fi
-
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- elif test "x${ac_infiniband_lib_ok}" == "xyes"; then
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#include "dataspaces.h"
-#ifdef FC_DUMMY_MAIN
-#ifndef FC_DUMMY_MAIN_EQ_F77
-# ifdef __cplusplus
- extern "C"
-# endif
- int FC_DUMMY_MAIN() { return 1; }
-#endif
-#endif
-int
-main ()
-{
-int err; err = dspaces_init(1,1,0,"");
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
- DATASPACES_LIBS="-ldspaces -ldscommon -ldart -lrdmacm"
-else
- if false; then
- HAVE_DATASPACES_TRUE=
- HAVE_DATASPACES_FALSE='#'
-else
- HAVE_DATASPACES_TRUE='#'
- HAVE_DATASPACES_FALSE=
-fi
-
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- elif test -z "${HAVE_CRAY_PMI_TRUE}" -a -z "${HAVE_CRAY_UGNI_TRUE}"; then
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#include "dataspaces.h"
-#ifdef FC_DUMMY_MAIN
-#ifndef FC_DUMMY_MAIN_EQ_F77
-# ifdef __cplusplus
- extern "C"
-# endif
- int FC_DUMMY_MAIN() { return 1; }
-#endif
-#endif
-int
-main ()
-{
-int err; err = dspaces_init(1,1,0,"");
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
- DATASPACES_LIBS="-ldspaces -ldscommon -ldart"
-else
- if false; then
- HAVE_DATASPACES_TRUE=
- HAVE_DATASPACES_FALSE='#'
-else
- HAVE_DATASPACES_TRUE='#'
- HAVE_DATASPACES_FALSE=
-fi
-
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- elif test "x${ac_dcmf_lib_ok}" == "xyes"; then
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#include "dataspaces.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 ()
-{
-int err; err = dspaces_init(1,1,0,"");
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
- DATASPACES_LIBS="-ldspaces -ldscommon -ldart"
-else
- if false; then
- HAVE_DATASPACES_TRUE=
- HAVE_DATASPACES_FALSE='#'
-else
- HAVE_DATASPACES_TRUE='#'
- HAVE_DATASPACES_FALSE=
-fi
-
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- elif test "x${ac_pami_lib_ok}" == "xyes"; then
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ { $as_echo "$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
/* end confdefs.h. */
#include "dataspaces.h"
#ifdef FC_DUMMY_MAIN
@@ -25695,43 +25612,14 @@ int err; err = dspaces_init(1,1,0,"");
return 0;
}
_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
- DATASPACES_LIBS="-ldspaces -ldscommon -ldart"
-else
- if false; then
- HAVE_DATASPACES_TRUE=
- HAVE_DATASPACES_FALSE='#'
-else
- HAVE_DATASPACES_TRUE='#'
- HAVE_DATASPACES_FALSE=
-fi
-
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#include "dataspaces.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 ()
-{
-int err; err = dspaces_init(1,1,0,"");
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
- DATASPACES_LIBS="-ldspaces -ldscommon -ldart"
+if ac_fn_c_try_link "$LINENO"; then :
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+ DATASPACES_LIBS="-ldspaces -ldscommon -ldart"
else
- if false; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ if false; then
HAVE_DATASPACES_TRUE=
HAVE_DATASPACES_FALSE='#'
else
@@ -25740,13 +25628,14 @@ else
fi
fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
fi
LIBS="$save_LIBS"
LDFLAGS="$save_LDFLAGS"
CPPFLAGS="$save_CPPFLAGS"
+ CC="$save_CC"
@@ -25797,6 +25686,19 @@ else
fi
+elif test -z "${HAVE_MPI_FALSE}"; then
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: Dimes does not build without MPI" >&5
+$as_echo "$as_me: Dimes does not build without MPI" >&6;}
+ if false; then
+ HAVE_DIMES_TRUE=
+ HAVE_DIMES_FALSE='#'
+else
+ HAVE_DIMES_TRUE='#'
+ HAVE_DIMES_FALSE=
+fi
+
+
else
@@ -25840,6 +25742,7 @@ fi
ac_dimes_ok=no
fi
+ save_CC="$CC"
save_CPPFLAGS="$CPPFLAGS"
save_LIBS="$LIBS"
save_LDFLAGS="$LDFLAGS"
@@ -25853,13 +25756,12 @@ else
HAVE_DIMES_FALSE=
fi
- elif test "x${ac_dcmf_lib_ok}" == "xyes"; then
- LIBS="$LIBS -ldspaces -ldscommon -ldart"
else
- LIBS="$LIBS -ldspaces -ldscommon -ldart"
+ LIBS="-ldspaces -ldscommon -ldart $LIBS"
fi
LDFLAGS="$LDFLAGS $DIMES_LDFLAGS"
CPPFLAGS="$CPPFLAGS $DIMES_CPPFLAGS"
+ CC="$MPICC"
if test -z "${HAVE_DIMES_TRUE}"; then
for ac_header in dimes_interface.h
@@ -25886,9 +25788,10 @@ done
fi
if test -z "${HAVE_DIMES_TRUE}"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if dimes code can be compiled and linked" >&5
+$as_echo_n "checking if dimes code can be compiled and linked... " >&6; }
# Check for the DataSpaces/DIMES library and headers
- if test -z "${HAVE_CRAY_PMI_TRUE}" -a -z "${HAVE_CRAY_UGNI_TRUE}"; then
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
#include "dimes_interface.h"
#ifdef FC_DUMMY_MAIN
@@ -25908,9 +25811,13 @@ int err; dimes_put_sync_all();
}
_ACEOF
if ac_fn_c_try_link "$LINENO"; then :
- DIMES_LIBS="-ldspaces -ldscommon -ldart"
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+ DIMES_LIBS="-ldspaces -ldscommon -ldart"
else
- if false; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ if false; then
HAVE_DIMES_TRUE=
HAVE_DIMES_FALSE='#'
else
@@ -25921,120 +25828,12 @@ fi
fi
rm -f core conftest.err conftest.$ac_objext \
conftest$ac_exeext conftest.$ac_ext
- elif test "x${ac_infiniband_lib_ok}" == "xyes"; then
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#include "dimes_interface.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 ()
-{
-int err; dimes_put_sync_all();
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
- DIMES_LIBS="-ldspaces -ldscommon -ldart"
-else
- if false; then
- HAVE_DIMES_TRUE=
- HAVE_DIMES_FALSE='#'
-else
- HAVE_DIMES_TRUE='#'
- HAVE_DIMES_FALSE=
-fi
-
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- elif test "x${ac_dcmf_lib_ok}" == "xyes"; then
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#include "dimes_interface.h"
-#ifdef FC_DUMMY_MAIN
-#ifndef FC_DUMMY_MAIN_EQ_F77
-# ifdef __cplusplus
- extern "C"
-# endif
- int FC_DUMMY_MAIN() { return 1; }
-#endif
-#endif
-int
-main ()
-{
-int err; dimes_put_sync_all();
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
- DIMES_LIBS="-ldspaces -ldscommon -ldart"
-else
- if false; then
- HAVE_DIMES_TRUE=
- HAVE_DIMES_FALSE='#'
-else
- HAVE_DIMES_TRUE='#'
- HAVE_DIMES_FALSE=
-fi
-
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- elif test "x${ac_pami_lib_ok}" == "xyes"; then
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#include "dimes_interface.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 ()
-{
-int err; dimes_put_sync_all();
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
- DIMES_LIBS="-ldspaces -ldscommon -ldart"
-else
- if false; then
- HAVE_DIMES_TRUE=
- HAVE_DIMES_FALSE='#'
-else
- HAVE_DIMES_TRUE='#'
- HAVE_DIMES_FALSE=
-fi
-
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- else
- if false; then
- HAVE_DIMES_TRUE=
- HAVE_DIMES_FALSE='#'
-else
- HAVE_DIMES_TRUE='#'
- HAVE_DIMES_FALSE=
-fi
-
- fi
- fi
+ fi
LIBS="$save_LIBS"
LDFLAGS="$save_LDFLAGS"
CPPFLAGS="$save_CPPFLAGS"
+ CC="$save_CC"
@@ -26897,11 +26696,11 @@ fi
search_list="$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:26900: searching for $search_list " >&5
+echo "configure:26699: 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:26904: first found $tmp_search_results " >&5
+ echo "configure:26703: first found $tmp_search_results " >&5
break
fi
done
@@ -26989,11 +26788,11 @@ fi
search_list="$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:26992: searching for $search_list " >&5
+echo "configure:26791: 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:26996: first found $tmp_search_results " >&5
+ echo "configure:26795: first found $tmp_search_results " >&5
break
fi
done
@@ -27062,11 +26861,11 @@ else
search_list="$PWD/../ibpbio $PWD/../../ibpbio $PWD/../../../ibpbio"
tmp_search_results=""
-echo "configure:27065: searching for $search_list " >&5
+echo "configure:26864: 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:27069: first found $tmp_search_results " >&5
+ echo "configure:26868: first found $tmp_search_results " >&5
break
fi
done
@@ -27104,11 +26903,11 @@ else
search_list="$PWD/../ibpbio $PWD/../../ibpbio $PWD/../../../ibpbio"
tmp_search_results=""
-echo "configure:27107: searching for $search_list " >&5
+echo "configure:26906: 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:27111: first found $tmp_search_results " >&5
+ echo "configure:26910: first found $tmp_search_results " >&5
break
fi
done
@@ -27232,11 +27031,11 @@ fi
search_list="$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:27235: searching for $search_list " >&5
+echo "configure:27034: 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:27239: first found $tmp_search_results " >&5
+ echo "configure:27038: first found $tmp_search_results " >&5
break
fi
done
@@ -27324,11 +27123,11 @@ fi
search_list="$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:27327: searching for $search_list " >&5
+echo "configure:27126: 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:27331: first found $tmp_search_results " >&5
+ echo "configure:27130: first found $tmp_search_results " >&5
break
fi
done
@@ -27397,11 +27196,11 @@ else
search_list="$PWD/../ffs $PWD/../../ffs $PWD/../../../ffs"
tmp_search_results=""
-echo "configure:27400: searching for $search_list " >&5
+echo "configure:27199: 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:27404: first found $tmp_search_results " >&5
+ echo "configure:27203: first found $tmp_search_results " >&5
break
fi
done
@@ -27439,11 +27238,11 @@ else
search_list="$PWD/../ffs $PWD/../../ffs $PWD/../../../ffs"
tmp_search_results=""
-echo "configure:27442: searching for $search_list " >&5
+echo "configure:27241: 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:27446: first found $tmp_search_results " >&5
+ echo "configure:27245: first found $tmp_search_results " >&5
break
fi
done
@@ -27567,11 +27366,11 @@ fi
search_list="$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:27570: searching for $search_list " >&5
+echo "configure:27369: 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:27574: first found $tmp_search_results " >&5
+ echo "configure:27373: first found $tmp_search_results " >&5
break
fi
done
@@ -27659,11 +27458,11 @@ fi
search_list="$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:27662: searching for $search_list " >&5
+echo "configure:27461: 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:27666: first found $tmp_search_results " >&5
+ echo "configure:27465: first found $tmp_search_results " >&5
break
fi
done
@@ -27732,11 +27531,11 @@ else
search_list="$PWD/../gen_thread $PWD/../../gen_thread $PWD/../../../gen_thread"
tmp_search_results=""
-echo "configure:27735: searching for $search_list " >&5
+echo "configure:27534: 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:27739: first found $tmp_search_results " >&5
+ echo "configure:27538: first found $tmp_search_results " >&5
break
fi
done
@@ -27774,11 +27573,11 @@ else
search_list="$PWD/../gen_thread $PWD/../../gen_thread $PWD/../../../gen_thread"
tmp_search_results=""
-echo "configure:27777: searching for $search_list " >&5
+echo "configure:27576: 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:27781: first found $tmp_search_results " >&5
+ echo "configure:27580: first found $tmp_search_results " >&5
break
fi
done
@@ -27925,11 +27724,11 @@ fi
search_list="$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:27928: searching for $search_list " >&5
+echo "configure:27727: 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:27932: first found $tmp_search_results " >&5
+ echo "configure:27731: first found $tmp_search_results " >&5
break
fi
done
@@ -28017,11 +27816,11 @@ fi
search_list="$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:28020: searching for $search_list " >&5
+echo "configure:27819: 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:28024: first found $tmp_search_results " >&5
+ echo "configure:27823: first found $tmp_search_results " >&5
break
fi
done
@@ -28090,11 +27889,11 @@ else
search_list="$PWD/../ptlpbio $PWD/../../ptlpbio $PWD/../../../ptlpbio"
tmp_search_results=""
-echo "configure:28093: searching for $search_list " >&5
+echo "configure:27892: 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:28097: first found $tmp_search_results " >&5
+ echo "configure:27896: first found $tmp_search_results " >&5
break
fi
done
@@ -28132,11 +27931,11 @@ else
search_list="$PWD/../ptlpbio $PWD/../../ptlpbio $PWD/../../../ptlpbio"
tmp_search_results=""
-echo "configure:28135: searching for $search_list " >&5
+echo "configure:27934: 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:28139: first found $tmp_search_results " >&5
+ echo "configure:27938: first found $tmp_search_results " >&5
break
fi
done
@@ -28288,11 +28087,11 @@ fi
search_list="$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:28291: searching for $search_list " >&5
+echo "configure:28090: 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:28295: first found $tmp_search_results " >&5
+ echo "configure:28094: first found $tmp_search_results " >&5
break
fi
done
@@ -28380,11 +28179,11 @@ fi
search_list="$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:28383: searching for $search_list " >&5
+echo "configure:28182: 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:28387: first found $tmp_search_results " >&5
+ echo "configure:28186: first found $tmp_search_results " >&5
break
fi
done
@@ -28453,11 +28252,11 @@ else
search_list="$PWD/../ibpbio $PWD/../../ibpbio $PWD/../../../ibpbio"
tmp_search_results=""
-echo "configure:28456: searching for $search_list " >&5
+echo "configure:28255: 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:28460: first found $tmp_search_results " >&5
+ echo "configure:28259: first found $tmp_search_results " >&5
break
fi
done
@@ -28495,11 +28294,11 @@ else
search_list="$PWD/../ibpbio $PWD/../../ibpbio $PWD/../../../ibpbio"
tmp_search_results=""
-echo "configure:28498: searching for $search_list " >&5
+echo "configure:28297: 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:28502: first found $tmp_search_results " >&5
+ echo "configure:28301: first found $tmp_search_results " >&5
break
fi
done
@@ -28623,11 +28422,11 @@ fi
search_list="$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:28626: searching for $search_list " >&5
+echo "configure:28425: 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:28630: first found $tmp_search_results " >&5
+ echo "configure:28429: first found $tmp_search_results " >&5
break
fi
done
@@ -28715,11 +28514,11 @@ fi
search_list="$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:28718: searching for $search_list " >&5
+echo "configure:28517: 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:28722: first found $tmp_search_results " >&5
+ echo "configure:28521: first found $tmp_search_results " >&5
break
fi
done
@@ -28788,11 +28587,11 @@ else
search_list="$PWD/../ffs $PWD/../../ffs $PWD/../../../ffs"
tmp_search_results=""
-echo "configure:28791: searching for $search_list " >&5
+echo "configure:28590: 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:28795: first found $tmp_search_results " >&5
+ echo "configure:28594: first found $tmp_search_results " >&5
break
fi
done
@@ -28830,11 +28629,11 @@ else
search_list="$PWD/../ffs $PWD/../../ffs $PWD/../../../ffs"
tmp_search_results=""
-echo "configure:28833: searching for $search_list " >&5
+echo "configure:28632: 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:28837: first found $tmp_search_results " >&5
+ echo "configure:28636: first found $tmp_search_results " >&5
break
fi
done
@@ -28958,11 +28757,11 @@ fi
search_list="$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:28961: searching for $search_list " >&5
+echo "configure:28760: 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:28965: first found $tmp_search_results " >&5
+ echo "configure:28764: first found $tmp_search_results " >&5
break
fi
done
@@ -29050,11 +28849,11 @@ fi
search_list="$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:29053: searching for $search_list " >&5
+echo "configure:28852: 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:29057: first found $tmp_search_results " >&5
+ echo "configure:28856: first found $tmp_search_results " >&5
break
fi
done
@@ -29123,11 +28922,11 @@ else
search_list="$PWD/../gen_thread $PWD/../../gen_thread $PWD/../../../gen_thread"
tmp_search_results=""
-echo "configure:29126: searching for $search_list " >&5
+echo "configure:28925: 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:29130: first found $tmp_search_results " >&5
+ echo "configure:28929: first found $tmp_search_results " >&5
break
fi
done
@@ -29165,11 +28964,11 @@ else
search_list="$PWD/../gen_thread $PWD/../../gen_thread $PWD/../../../gen_thread"
tmp_search_results=""
-echo "configure:29168: searching for $search_list " >&5
+echo "configure:28967: 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:29172: first found $tmp_search_results " >&5
+ echo "configure:28971: first found $tmp_search_results " >&5
break
fi
done
@@ -29316,11 +29115,11 @@ fi
search_list="$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:29319: searching for $search_list " >&5
+echo "configure:29118: 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:29323: first found $tmp_search_results " >&5
+ echo "configure:29122: first found $tmp_search_results " >&5
break
fi
done
@@ -29408,11 +29207,11 @@ fi
search_list="$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:29411: searching for $search_list " >&5
+echo "configure:29210: 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:29415: first found $tmp_search_results " >&5
+ echo "configure:29214: first found $tmp_search_results " >&5
break
fi
done
@@ -29481,11 +29280,11 @@ else
search_list="$PWD/../ptlpbio $PWD/../../ptlpbio $PWD/../../../ptlpbio"
tmp_search_results=""
-echo "configure:29484: searching for $search_list " >&5
+echo "configure:29283: 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:29488: first found $tmp_search_results " >&5
+ echo "configure:29287: first found $tmp_search_results " >&5
break
fi
done
@@ -29523,11 +29322,11 @@ else
search_list="$PWD/../ptlpbio $PWD/../../ptlpbio $PWD/../../../ptlpbio"
tmp_search_results=""
-echo "configure:29526: searching for $search_list " >&5
+echo "configure:29325: 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:29530: first found $tmp_search_results " >&5
+ echo "configure:29329: first found $tmp_search_results " >&5
break
fi
done
@@ -29728,11 +29527,11 @@ fi
search_list="$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:29731: searching for $search_list " >&5
+echo "configure:29530: 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:29735: first found $tmp_search_results " >&5
+ echo "configure:29534: first found $tmp_search_results " >&5
break
fi
done
@@ -29820,11 +29619,11 @@ fi
search_list="$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"
tmp_search_results=""
-echo "configure:29823: searching for $search_list " >&5
+echo "configure:29622: 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:29827: first found $tmp_search_results " >&5
+ echo "configure:29626: first found $tmp_search_results " >&5
break
fi
done
@@ -29893,11 +29692,11 @@ else
search_list="$PWD/../evpath $PWD/../../evpath $PWD/../../../evpath"
tmp_search_results=""
-echo "configure:29896: searching for $search_list " >&5
+echo "configure:29695: 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:29900: first found $tmp_search_results " >&5
+ echo "configure:29699: first found $tmp_search_results " >&5
break
fi
done
@@ -29935,11 +29734,11 @@ else
search_list="$PWD/../evpath $PWD/../../evpath $PWD/../../../evpath"
tmp_search_results=""
-echo "configure:29938: searching for $search_list " >&5
+echo "configure:29737: 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:29942: first found $tmp_search_results " >&5
+ echo "configure:29741: first found $tmp_search_results " >&5
break
fi
done
@@ -30063,11 +29862,11 @@ fi
search_list="$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:30066: searching for $search_list " >&5
+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:30070: first found $tmp_search_results " >&5
+ echo "configure:29869: first found $tmp_search_results " >&5
break
fi
done
@@ -30155,11 +29954,11 @@ fi
search_list="$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:30158: searching for $search_list " >&5
+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:30162: first found $tmp_search_results " >&5
+ echo "configure:29961: first found $tmp_search_results " >&5
break
fi
done
@@ -30228,11 +30027,11 @@ else
search_list="$PWD/../ffs $PWD/../../ffs $PWD/../../../ffs"
tmp_search_results=""
-echo "configure:30231: searching for $search_list " >&5
+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:30235: first found $tmp_search_results " >&5
+ echo "configure:30034: first found $tmp_search_results " >&5
break
fi
done
@@ -30270,11 +30069,11 @@ else
search_list="$PWD/../ffs $PWD/../../ffs $PWD/../../../ffs"
tmp_search_results=""
-echo "configure:30273: searching for $search_list " >&5
+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:30277: first found $tmp_search_results " >&5
+ echo "configure:30076: first found $tmp_search_results " >&5
break
fi
done
@@ -30398,11 +30197,11 @@ fi
search_list="$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:30401: searching for $search_list " >&5
+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:30405: first found $tmp_search_results " >&5
+ echo "configure:30204: first found $tmp_search_results " >&5
break
fi
done
@@ -30490,11 +30289,11 @@ fi
search_list="$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:30493: searching for $search_list " >&5
+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:30497: first found $tmp_search_results " >&5
+ echo "configure:30296: first found $tmp_search_results " >&5
break
fi
done
@@ -30563,11 +30362,11 @@ else
search_list="$PWD/../atl $PWD/../../atl $PWD/../../../atl"
tmp_search_results=""
-echo "configure:30566: searching for $search_list " >&5
+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:30570: first found $tmp_search_results " >&5
+ echo "configure:30369: first found $tmp_search_results " >&5
break
fi
done
@@ -30605,11 +30404,11 @@ else
search_list="$PWD/../atl $PWD/../../atl $PWD/../../../atl"
tmp_search_results=""
-echo "configure:30608: searching for $search_list " >&5
+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:30612: first found $tmp_search_results " >&5
+ echo "configure:30411: first found $tmp_search_results " >&5
break
fi
done
@@ -30733,11 +30532,11 @@ fi
search_list="$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:30736: searching for $search_list " >&5
+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:30740: first found $tmp_search_results " >&5
+ echo "configure:30539: first found $tmp_search_results " >&5
break
fi
done
@@ -30825,11 +30624,11 @@ fi
search_list="$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:30828: searching for $search_list " >&5
+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:30832: first found $tmp_search_results " >&5
+ echo "configure:30631: first found $tmp_search_results " >&5
break
fi
done
@@ -30898,11 +30697,11 @@ else
search_list="$PWD/../dill $PWD/../../dill $PWD/../../../dill"
tmp_search_results=""
-echo "configure:30901: searching for $search_list " >&5
+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:30905: first found $tmp_search_results " >&5
+ echo "configure:30704: first found $tmp_search_results " >&5
break
fi
done
@@ -30940,11 +30739,11 @@ else
search_list="$PWD/../dill $PWD/../../dill $PWD/../../../dill"
tmp_search_results=""
-echo "configure:30943: searching for $search_list " >&5
+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:30947: first found $tmp_search_results " >&5
+ echo "configure:30746: first found $tmp_search_results " >&5
break
fi
done
@@ -31068,11 +30867,11 @@ fi
search_list="$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:31071: searching for $search_list " >&5
+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:31075: first found $tmp_search_results " >&5
+ echo "configure:30874: first found $tmp_search_results " >&5
break
fi
done
@@ -31160,11 +30959,11 @@ fi
search_list="$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:31163: searching for $search_list " >&5
+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:31167: first found $tmp_search_results " >&5
+ echo "configure:30966: first found $tmp_search_results " >&5
break
fi
done
@@ -31233,11 +31032,11 @@ else
search_list="$PWD/../cercs_env $PWD/../../cercs_env $PWD/../../../cercs_env"
tmp_search_results=""
-echo "configure:31236: searching for $search_list " >&5
+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:31240: first found $tmp_search_results " >&5
+ echo "configure:31039: first found $tmp_search_results " >&5
break
fi
done
@@ -31275,11 +31074,11 @@ else
search_list="$PWD/../cercs_env $PWD/../../cercs_env $PWD/../../../cercs_env"
tmp_search_results=""
-echo "configure:31278: searching for $search_list " >&5
+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:31282: first found $tmp_search_results " >&5
+ echo "configure:31081: first found $tmp_search_results " >&5
break
fi
done
@@ -32284,6 +32083,147 @@ $as_echo "#define HAVE_BGQ 1" >>confdefs.h
fi
+
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: === checking for ZFP ===" >&5
+$as_echo "$as_me: === checking for ZFP ===" >&6;}
+ if true; then
+ HAVE_ZFP_TRUE=
+ HAVE_ZFP_FALSE='#'
+else
+ HAVE_ZFP_TRUE='#'
+ HAVE_ZFP_FALSE=
+fi
+
+ if false; then
+ BUILD_ZFP_TRUE=
+ BUILD_ZFP_FALSE='#'
+else
+ BUILD_ZFP_TRUE='#'
+ BUILD_ZFP_FALSE=
+fi
+
+
+
+
+# Check whether --with-zfp was given.
+if test "${with_zfp+set}" = set; then :
+ withval=$with_zfp;
+else
+ with_zfp=builtin
+fi
+
+
+
+if test "x$with_zfp" == "xno"; then
+ if false; then
+ HAVE_ZFP_TRUE=
+ HAVE_ZFP_FALSE='#'
+else
+ HAVE_ZFP_TRUE='#'
+ HAVE_ZFP_FALSE=
+fi
+
+
+elif test "x$with_zfp" == "xbuiltin"; then
+ if true; then
+ BUILD_ZFP_TRUE=
+ BUILD_ZFP_FALSE='#'
+else
+ BUILD_ZFP_TRUE='#'
+ BUILD_ZFP_FALSE=
+fi
+
+
+else
+ save_CPPFLAGS="$CPPFLAGS"
+ save_LIBS="$LIBS"
+ save_LDFLAGS="$LDFLAGS"
+
+
+ if test -z "${ZFP_LIBS}"; then
+ ZFP_LIBS="-lzfp"
+ fi
+
+ if test -z "${ZFP_LDFLAGS}"; then
+ ZFP_LDFLAGS="-L$with_zfp/lib"
+ fi
+
+ if test -z "${ZFP_CPPFLAGS}"; then
+ ZFP_CPPFLAGS="-I$with_zfp/inc"
+ fi
+
+
+ LIBS="$LIBS $ZFP_LIBS"
+ LDFLAGS="$LDFLAGS $ZFP_LDFLAGS"
+ CPPFLAGS="$CPPFLAGS $ZFP_CPPFLAGS"
+
+ if test -z "${HAVE_ZFP_TRUE}"; then
+ for ac_header in zfp.h
+do :
+ ac_fn_c_check_header_mongrel "$LINENO" "zfp.h" "ac_cv_header_zfp_h" "$ac_includes_default"
+if test "x$ac_cv_header_zfp_h" = xyes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_ZFP_H 1
+_ACEOF
+
+else
+ if false; then
+ HAVE_ZFP_TRUE=
+ HAVE_ZFP_FALSE='#'
+else
+ HAVE_ZFP_TRUE='#'
+ HAVE_ZFP_FALSE=
+fi
+
+fi
+
+done
+
+ fi
+
+ LIBS="$save_LIBS"
+ LDFLAGS="$save_LDFLAGS"
+ CPPFLAGS="$save_CPPFLAGS"
+
+
+
+
+
+ # Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND:
+ if test -z "${HAVE_ZFP_TRUE}"; then
+
+$as_echo "#define HAVE_ZFP 1" >>confdefs.h
+
+ :
+ else
+
+ :
+ fi
+fi
+
+if test -z "${BUILD_ZFP_TRUE}"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: Build the included ZFP source. Use --without-zfp to turn this off, --with-zfp=path to use an external library." >&5
+$as_echo "$as_me: Build the included ZFP source. Use --without-zfp to turn this off, --with-zfp=path to use an external library." >&6;}
+ if true; then
+ HAVE_ZFP_TRUE=
+ HAVE_ZFP_FALSE='#'
+else
+ HAVE_ZFP_TRUE='#'
+ HAVE_ZFP_FALSE=
+fi
+
+ ZFP_CPPFLAGS="${CPPFLAGS} -I\$(top_srcdir)/src/zfp/zfp-0.5.0/inc"
+ ZFP_BUILD_LDFLAGS=
+ ZFP_LDFLAGS=
+ ZFP_LIBS=
+
+
+
+fi
+
+
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -32512,6 +32452,10 @@ esac
ADIOSLIB_EXTRA_CPPFLAGS="${MACRODEFFLAG}_FILE_OFFSET_BITS=64 ${MACRODEFFLAG}_LARGEFILE_SOURCE ${MACRODEFFLAG}_LARGEFILE64_SOURCE ${MACRODEFFLAG}_GNU_SOURCE ${MXML_CPPFLAGS}"
ADIOSLIB_EXTRA_LDFLAGS="${MXML_BUILD_LDFLAGS}"
+if test -z "${HAVE_ZFP_TRUE}"; then
+ ADIOSLIB_EXTRA_CPPFLAGS="${ADIOSLIB_EXTRA_CPPFLAGS} ${MACRODEFFLAG}ZFP ${ZFP_CPPFLAGS}"
+ ADIOSLIB_EXTRA_LDFLAGS="${ADIOSLIB_EXTRA_LDFLAGS} ${ZFP_BUILD_LDFLAGS}"
+fi
ADIOSLIB_CPPFLAGS=
ADIOSLIB_CFLAGS=
ADIOSLIB_LDFLAGS="${MXML_LDFLAGS}"
@@ -32857,6 +32801,18 @@ 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_ZFP_TRUE}"; then
+ ADIOSLIB_LDFLAGS="${ADIOSLIB_LDFLAGS} ${ZFP_LDFLAGS}"
+ ADIOSLIB_LDADD="${ADIOSLIB_LDADD} ${ZFP_LIBS}"
+ ADIOSLIB_SEQ_LDFLAGS="${ADIOSLIB_SEQ_LDFLAGS} ${ZFP_LDFLAGS}"
+ ADIOSLIB_SEQ_LDADD="${ADIOSLIB_SEQ_LDADD} ${ZFP_LIBS}"
+ ADIOSLIB_INT_LDFLAGS="${ADIOSLIB_INT_LDFLAGS} ${ZFP_LDFLAGS}"
+ ADIOSLIB_INT_LDADD="${ADIOSLIB_INT_LDADD} ${ZFP_LIBS}"
+ ADIOSREADLIB_LDFLAGS="${ADIOSREADLIB_LDFLAGS} ${ZFP_LDFLAGS}"
+ ADIOSREADLIB_LDADD="${ADIOSREADLIB_LDADD} ${ZFP_LIBS}"
+ ADIOSREADLIB_SEQ_LDFLAGS="${ADIOSREADLIB_SEQ_LDFLAGS} ${ZFP_LDFLAGS}"
+ ADIOSREADLIB_SEQ_LDADD="${ADIOSREADLIB_SEQ_LDADD} ${ZFP_LIBS}"
+fi
if test -z "${HAVE_ISOBAR_TRUE}"; then
ADIOSLIB_CPPFLAGS="${ADIOSLIB_CPPFLAGS} -DISOBAR ${ISOBAR_CPPFLAGS}"
ADIOSLIB_CFLAGS="${ADIOSLIB_CFLAGS} ${ISOBAR_CFLAGS}"
@@ -33025,12 +32981,7 @@ fi
#fi
#AC_DEFINE_UNQUOTED(VERSION_SVNREV, "${SVNVERSION}", [svn revision number])
-
-if test -z "${BUILD_MXML_TRUE}" -a -z "${BUILD_WRITE_TRUE}"; then
- ac_config_files="$ac_config_files src/mxml/Makefile"
-
-fi
-ac_config_files="$ac_config_files Makefile src/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/query/Makefile tests/C/query/common/M [...]
+ac_config_files="$ac_config_files Makefile src/Makefile src/zfp/Makefile src/mxml/Makefile tests/Makefile tests/test_src/Makefile tests/C/Makefile tests/C/flexpath_tests/Makefile tests/C/flexpath_tests/1D_arr_global/Makefile tests/C/flexpath_tests/1D_arr_global_noxml/Makefile tests/C/flexpath_tests/global_range_select/Makefile tests/C/flexpath_tests/maya_noxml/Makefile tests/C/flexpath_tests/maya_append/Makefile tests/C/flexpath_tests/scalar/Makefile tests/C/fgr_tests/Makefile tests/C/qu [...]
@@ -33447,34 +33398,6 @@ if test -z "${HAVE_DATASPACES_TRUE}" && test -z "${HAVE_DATASPACES_FALSE}"; then
as_fn_error $? "conditional \"HAVE_DATASPACES\" was never defined.
Usually this means the macro was only invoked conditionally." "$LINENO" 5
fi
-if test -z "${HAVE_DATASPACES_TRUE}" && test -z "${HAVE_DATASPACES_FALSE}"; then
- as_fn_error $? "conditional \"HAVE_DATASPACES\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
-fi
-if test -z "${HAVE_DATASPACES_TRUE}" && test -z "${HAVE_DATASPACES_FALSE}"; then
- as_fn_error $? "conditional \"HAVE_DATASPACES\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
-fi
-if test -z "${HAVE_DATASPACES_TRUE}" && test -z "${HAVE_DATASPACES_FALSE}"; then
- as_fn_error $? "conditional \"HAVE_DATASPACES\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
-fi
-if test -z "${HAVE_DATASPACES_TRUE}" && test -z "${HAVE_DATASPACES_FALSE}"; then
- as_fn_error $? "conditional \"HAVE_DATASPACES\" was never defined.
-Usually this means the macro was only invoked conditionally." "$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 "${HAVE_DIMES_TRUE}" && test -z "${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 "${HAVE_DIMES_TRUE}" && test -z "${HAVE_DIMES_FALSE}"; then
as_fn_error $? "conditional \"HAVE_DIMES\" was never defined.
Usually this means the macro was only invoked conditionally." "$LINENO" 5
@@ -33687,6 +33610,30 @@ 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 "${HAVE_ZFP_TRUE}" && test -z "${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 "${BUILD_ZFP_TRUE}" && test -z "${BUILD_ZFP_FALSE}"; then
+ as_fn_error $? "conditional \"BUILD_ZFP\" was never defined.
+Usually this means the macro was only invoked conditionally." "$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
+fi
+if test -z "${BUILD_ZFP_TRUE}" && test -z "${BUILD_ZFP_FALSE}"; then
+ as_fn_error $? "conditional \"BUILD_ZFP\" was never defined.
+Usually this means the macro was only invoked conditionally." "$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
+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
+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
@@ -34136,7 +34083,7 @@ 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 1.10.0, which was
+This file was extended by adios $as_me 1.11.0, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -34202,7 +34149,7 @@ _ACEOF
cat >>$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 1.10.0
+adios config.status 1.11.0
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
@@ -34801,9 +34748,10 @@ do
"config.h") CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;;
"depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
"libtool") CONFIG_COMMANDS="$CONFIG_COMMANDS libtool" ;;
- "src/mxml/Makefile") CONFIG_FILES="$CONFIG_FILES src/mxml/Makefile" ;;
"Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
"src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
+ "src/zfp/Makefile") CONFIG_FILES="$CONFIG_FILES src/zfp/Makefile" ;;
+ "src/mxml/Makefile") CONFIG_FILES="$CONFIG_FILES src/mxml/Makefile" ;;
"tests/Makefile") CONFIG_FILES="$CONFIG_FILES tests/Makefile" ;;
"tests/test_src/Makefile") CONFIG_FILES="$CONFIG_FILES tests/test_src/Makefile" ;;
"tests/C/Makefile") CONFIG_FILES="$CONFIG_FILES tests/C/Makefile" ;;
@@ -34869,6 +34817,7 @@ do
"examples/C/schema/Makefile") CONFIG_FILES="$CONFIG_FILES examples/C/schema/Makefile" ;;
"examples/C/transforms/Makefile") CONFIG_FILES="$CONFIG_FILES examples/C/transforms/Makefile" ;;
"examples/C/query/Makefile") CONFIG_FILES="$CONFIG_FILES examples/C/query/Makefile" ;;
+ "examples/C/time_aggregation/Makefile") CONFIG_FILES="$CONFIG_FILES examples/C/time_aggregation/Makefile" ;;
"examples/Fortran/Makefile") CONFIG_FILES="$CONFIG_FILES examples/Fortran/Makefile" ;;
"examples/Fortran/scalars/Makefile") CONFIG_FILES="$CONFIG_FILES examples/Fortran/scalars/Makefile" ;;
"examples/Fortran/arrays/Makefile") CONFIG_FILES="$CONFIG_FILES examples/Fortran/arrays/Makefile" ;;
@@ -36772,6 +36721,18 @@ else
echo " - No SZIP to build SZIP transform method"
fi
+if test -z "${BUILD_ZFP_TRUE}"; then
+ echo " - ZFP is built with ADIOS";
+elif test -z "${HAVE_ZFP_TRUE}"; then
+ echo " - ZFP";
+ echo " - ZFP_CPPFLAGS = $ZFP_CPPFLAGS";
+ echo " - ZFP_LDFLAGS = $ZFP_LDFLAGS";
+ echo " - ZFP_LIBS = $ZFP_LIBS";
+ echo
+else
+ echo " - No ZFP to build ZFP transform method"
+fi
+
if test -z "${HAVE_ISOBAR_TRUE}"; then
echo " - ISOBAR";
echo " - ISOBAR_CFLAGS = $ISOBAR_CFLAGS";
diff --git a/configure.ac b/configure.ac
index 0bccc02..58d0516 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,4 +1,4 @@
-AC_INIT([adios], [1.10.0])
+AC_INIT([adios], [1.11.0])
AC_CONFIG_SRCDIR([configure.ac])
AC_CONFIG_AUX_DIR(config)
AC_CONFIG_MACRO_DIR(config)
@@ -72,6 +72,9 @@ AC_SEARCH_LIBS([nanosleep], [rt])
AC_SEARCH_LIBS([clock_gettime], [rt])
AC_CHECK_FUNCS([nanosleep gettimeofday clock_gettime clock_get_time strncpy strerror])
+AC_CHECK_HEADERS([time.h])
+AC_CHECK_TYPES([clockid_t], [], [], [[#include <time.h>]])
+
AC_C_STRINGIZE
dnl generates HAVE_STRINGIZE
AC_FUNC_STRTOLD
@@ -177,6 +180,24 @@ AC_ALACRITY
AC_FASTBIT
AC_BGQ
+
+AC_ZFP
+dnl ZFP is included in the source, so we build it unless a) explicitely disabled by --without-zfp
+dnl or b) an external zfp lib is provided by --with-zfp=path
+dnl config/ac_zfp.m4 sets BUILD_ZFP if none of the above options were given
+if test -z "${BUILD_ZFP_TRUE}"; then
+ AC_MSG_NOTICE([Build the included ZFP source. Use --without-zfp to turn this off, --with-zfp=path to use an external library.])
+ AM_CONDITIONAL(HAVE_ZFP,true)
+ ZFP_CPPFLAGS="${CPPFLAGS} -I\$(top_srcdir)/src/zfp/zfp-0.5.0/inc"
+ ZFP_BUILD_LDFLAGS=
+ ZFP_LDFLAGS=
+ ZFP_LIBS=
+ AC_SUBST(ZFP_CPPFLAGS)
+ AC_SUBST(ZFP_LIBS)
+ AC_SUBST(ZFP_LDFLAGS)
+fi
+
+
AC_LANG(C)
@@ -300,6 +321,10 @@ dnl adios_config will contain flags for users' code linking based on these flags
dnl EXTRA flags are used for compiling adios stuff, which need not go into adios_config for user codes
ADIOSLIB_EXTRA_CPPFLAGS="${MACRODEFFLAG}_FILE_OFFSET_BITS=64 ${MACRODEFFLAG}_LARGEFILE_SOURCE ${MACRODEFFLAG}_LARGEFILE64_SOURCE ${MACRODEFFLAG}_GNU_SOURCE ${MXML_CPPFLAGS}"
ADIOSLIB_EXTRA_LDFLAGS="${MXML_BUILD_LDFLAGS}"
+if test -z "${HAVE_ZFP_TRUE}"; then
+ ADIOSLIB_EXTRA_CPPFLAGS="${ADIOSLIB_EXTRA_CPPFLAGS} ${MACRODEFFLAG}ZFP ${ZFP_CPPFLAGS}"
+ ADIOSLIB_EXTRA_LDFLAGS="${ADIOSLIB_EXTRA_LDFLAGS} ${ZFP_BUILD_LDFLAGS}"
+fi
ADIOSLIB_CPPFLAGS=
ADIOSLIB_CFLAGS=
ADIOSLIB_LDFLAGS="${MXML_LDFLAGS}"
@@ -661,6 +686,18 @@ 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_ZFP_TRUE}"; then
+ ADIOSLIB_LDFLAGS="${ADIOSLIB_LDFLAGS} ${ZFP_LDFLAGS}"
+ ADIOSLIB_LDADD="${ADIOSLIB_LDADD} ${ZFP_LIBS}"
+ ADIOSLIB_SEQ_LDFLAGS="${ADIOSLIB_SEQ_LDFLAGS} ${ZFP_LDFLAGS}"
+ ADIOSLIB_SEQ_LDADD="${ADIOSLIB_SEQ_LDADD} ${ZFP_LIBS}"
+ ADIOSLIB_INT_LDFLAGS="${ADIOSLIB_INT_LDFLAGS} ${ZFP_LDFLAGS}"
+ ADIOSLIB_INT_LDADD="${ADIOSLIB_INT_LDADD} ${ZFP_LIBS}"
+ ADIOSREADLIB_LDFLAGS="${ADIOSREADLIB_LDFLAGS} ${ZFP_LDFLAGS}"
+ ADIOSREADLIB_LDADD="${ADIOSREADLIB_LDADD} ${ZFP_LIBS}"
+ ADIOSREADLIB_SEQ_LDFLAGS="${ADIOSREADLIB_SEQ_LDFLAGS} ${ZFP_LDFLAGS}"
+ ADIOSREADLIB_SEQ_LDADD="${ADIOSREADLIB_SEQ_LDADD} ${ZFP_LIBS}"
+fi
if test -z "${HAVE_ISOBAR_TRUE}"; then
ADIOSLIB_CPPFLAGS="${ADIOSLIB_CPPFLAGS} -DISOBAR ${ISOBAR_CPPFLAGS}"
ADIOSLIB_CFLAGS="${ADIOSLIB_CFLAGS} ${ISOBAR_CFLAGS}"
@@ -821,12 +858,10 @@ AC_SUBST(VERSION_MICRO)
#fi
#AC_DEFINE_UNQUOTED(VERSION_SVNREV, "${SVNVERSION}", [svn revision number])
-
-if test -z "${BUILD_MXML_TRUE}" -a -z "${BUILD_WRITE_TRUE}"; then
- AC_CONFIG_FILES([src/mxml/Makefile])
-fi
AC_CONFIG_FILES([Makefile
src/Makefile
+ src/zfp/Makefile
+ src/mxml/Makefile
tests/Makefile
tests/test_src/Makefile
tests/C/Makefile
@@ -892,6 +927,7 @@ AC_CONFIG_FILES([Makefile
examples/C/schema/Makefile
examples/C/transforms/Makefile
examples/C/query/Makefile
+ examples/C/time_aggregation/Makefile
examples/Fortran/Makefile
examples/Fortran/scalars/Makefile
examples/Fortran/arrays/Makefile
@@ -1220,6 +1256,18 @@ else
echo " - No SZIP to build SZIP transform method"
fi
+if test -z "${BUILD_ZFP_TRUE}"; then
+ echo " - ZFP is built with ADIOS";
+elif test -z "${HAVE_ZFP_TRUE}"; then
+ echo " - ZFP";
+ echo " - ZFP_CPPFLAGS = $ZFP_CPPFLAGS";
+ echo " - ZFP_LDFLAGS = $ZFP_LDFLAGS";
+ echo " - ZFP_LIBS = $ZFP_LIBS";
+ echo
+else
+ echo " - No ZFP to build ZFP transform method"
+fi
+
if test -z "${HAVE_ISOBAR_TRUE}"; then
echo " - ISOBAR";
echo " - ISOBAR_CFLAGS = $ISOBAR_CFLAGS";
diff --git a/examples/C/CMakeLists.txt b/examples/C/CMakeLists.txt
index 96e0efe..0977110 100644
--- a/examples/C/CMakeLists.txt
+++ b/examples/C/CMakeLists.txt
@@ -11,4 +11,4 @@ add_subdirectory(flexpath_arrays)
add_subdirectory(transforms)
add_subdirectory(query)
add_subdirectory(icee_arrays)
-#SUBDIRS=scalars arrays attributes manual global-array global-array-time read_all stat schema
+add_subdirectory(time_aggregation)
diff --git a/examples/C/Makefile.am b/examples/C/Makefile.am
index 6a1dd28..3c99eb3 100644
--- a/examples/C/Makefile.am
+++ b/examples/C/Makefile.am
@@ -1 +1,3 @@
-SUBDIRS=scalars arrays attributes manual global-array global-array-time read_all stat schema flexpath_arrays transforms query icee_arrays
+SUBDIRS=scalars arrays attributes manual global-array global-array-time \
+ read_all stat schema flexpath_arrays transforms query icee_arrays \
+ time_aggregation
diff --git a/examples/C/Makefile.in b/examples/C/Makefile.in
index 41c1ab6..aa15858 100644
--- a/examples/C/Makefile.in
+++ b/examples/C/Makefile.in
@@ -107,7 +107,7 @@ 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_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 \
@@ -413,6 +413,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
@@ -474,7 +477,10 @@ target_alias = @target_alias@
top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
-SUBDIRS = scalars arrays attributes manual global-array global-array-time read_all stat schema flexpath_arrays transforms query icee_arrays
+SUBDIRS = scalars arrays attributes manual global-array global-array-time \
+ read_all stat schema flexpath_arrays transforms query icee_arrays \
+ time_aggregation
+
all: all-recursive
.SUFFIXES:
diff --git a/examples/C/arrays/Makefile.in b/examples/C/arrays/Makefile.in
index 038632f..38a4f10 100644
--- a/examples/C/arrays/Makefile.in
+++ b/examples/C/arrays/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -414,6 +414,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/C/attributes/Makefile.in b/examples/C/attributes/Makefile.in
index 068dd53..630593b 100644
--- a/examples/C/attributes/Makefile.in
+++ b/examples/C/attributes/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -416,6 +416,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/C/flexpath_arrays/Makefile.in b/examples/C/flexpath_arrays/Makefile.in
index cca5534..2fbf59c 100644
--- a/examples/C/flexpath_arrays/Makefile.in
+++ b/examples/C/flexpath_arrays/Makefile.in
@@ -107,7 +107,7 @@ 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_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 \
@@ -413,6 +413,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/C/flexpath_arrays/global_range_select/Makefile.in b/examples/C/flexpath_arrays/global_range_select/Makefile.in
index dec52ef..a546771 100644
--- a/examples/C/flexpath_arrays/global_range_select/Makefile.in
+++ b/examples/C/flexpath_arrays/global_range_select/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -414,6 +414,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/C/flexpath_arrays/process_select/Makefile.in b/examples/C/flexpath_arrays/process_select/Makefile.in
index ca807e9..d955394 100644
--- a/examples/C/flexpath_arrays/process_select/Makefile.in
+++ b/examples/C/flexpath_arrays/process_select/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -414,6 +414,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/C/global-array-time/Makefile.in b/examples/C/global-array-time/Makefile.in
index 3469949..831b477 100644
--- a/examples/C/global-array-time/Makefile.in
+++ b/examples/C/global-array-time/Makefile.in
@@ -112,7 +112,7 @@ 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_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 \
@@ -445,6 +445,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/C/global-array-time/adios_globaltime.c b/examples/C/global-array-time/adios_globaltime.c
index f9077f0..70782b8 100644
--- a/examples/C/global-array-time/adios_globaltime.c
+++ b/examples/C/global-array-time/adios_globaltime.c
@@ -11,48 +11,49 @@
#include "adios.h"
int main (int argc, char ** argv)
{
- char filename [256];
- int rank, size, i, it;
- int NX = 10;
- // NY = 1 for testing purpose
- int NY = 1;
- double t[NX];
- double p[NY];
-
- /* 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 ("adios_globaltime.xml", comm);
- strcpy (filename, "adios_globaltime.bp");
- for (it =1; it <= 13; it++) {
-
- for (i = 0; i < NX; i++)
- t[i] = it*100.0 + rank*NX + i;
-
- for (i = 0; i < NY; i++)
- p[i] = it*1000.0 + rank*NY + i;
-
- if (it==1)
- adios_open (&adios_handle, "restart", filename, "w", comm);
- else
- adios_open (&adios_handle, "restart", filename, "a", 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;
+ char filename [256], fname[256];
+ int rank, size, i, it;
+ int NX = 10;
+ // NY = 1 for testing purpose
+ int NY = 1;
+ double t[NX];
+ double p[NY];
+
+ /* 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 ("adios_globaltime.xml", comm);
+ strcpy (filename, "adios_globaltime.bp");
+ for (it = 1; it <= 13; it++) {
+
+ for (i = 0; i < NX; i++)
+ t[i] = it*100.0 + rank*NX + i;
+
+ for (i = 0; i < NY; i++)
+ p[i] = it*1000.0 + rank*NY + i;
+
+ if (it==1)
+ adios_open (&adios_handle, "restart", filename, "w", comm);
+ else
+ adios_open (&adios_handle, "restart", filename, "a", comm);
+
+# include "gwrite_restart.ch"
+
+ adios_close (adios_handle);
+ MPI_Barrier (comm);
+ if (rank==0) printf("Timestep %d written\n", it);
+ }
+ 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/examples/C/global-array-time/adios_globaltime.xml b/examples/C/global-array-time/adios_globaltime.xml
index a0d308d..ad737a6 100644
--- a/examples/C/global-array-time/adios_globaltime.xml
+++ b/examples/C/global-array-time/adios_globaltime.xml
@@ -19,7 +19,12 @@
type="string"/>
</adios-group>
- <method group="restart" method="MPI"/>
+ <method group="restart" method="MPI">verbose=3</method>
+ <time-aggregation group="restart" buffer-size=0/>
+
+ <!--
+ <method group="restart" method="MPI_AGGREGATE">num_aggregators=1;num_ost=1</method>
+ -->
<buffer max-size-MB="1"/>
diff --git a/examples/C/global-array-time/adios_globaltime_no_xml.c b/examples/C/global-array-time/adios_globaltime_no_xml.c
index 54cb924..b897292 100644
--- a/examples/C/global-array-time/adios_globaltime_no_xml.c
+++ b/examples/C/global-array-time/adios_globaltime_no_xml.c
@@ -76,10 +76,12 @@ int main (int argc, char ** argv)
int64_t m_adios_group;
int64_t m_adios_file;
- adios_declare_group (&m_adios_group, "restart", "", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "restart", "", adios_stat_default);
adios_select_method (m_adios_group, "MPI", "", "");
//adios_select_method (m_adios_group, "MPI_AGGREGATE", "num_ost=2;num_aggregators=2;aggregation_type=2;verbose=3", "");
+ adios_set_time_aggregation (m_adios_group, 32000, 0);
+
adios_define_var (m_adios_group, "NX"
,"", adios_integer
,0, 0, 0);
diff --git a/examples/C/global-array/Makefile.in b/examples/C/global-array/Makefile.in
index b6a7e0d..117611d 100644
--- a/examples/C/global-array/Makefile.in
+++ b/examples/C/global-array/Makefile.in
@@ -114,7 +114,7 @@ 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_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 \
@@ -508,6 +508,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/C/global-array/adios_global_aggregate_by_color.c b/examples/C/global-array/adios_global_aggregate_by_color.c
index 45a4ded..3408ff2 100644
--- a/examples/C/global-array/adios_global_aggregate_by_color.c
+++ b/examples/C/global-array/adios_global_aggregate_by_color.c
@@ -55,7 +55,7 @@ int main (int argc, char ** argv)
int64_t m_adios_group;
int64_t m_adios_file;
- adios_declare_group (&m_adios_group, "restart", "iter", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "restart", "iter", adios_stat_default);
// split into 2 groups
color = (rank % 2 == 0 ? 0 : 1);
diff --git a/examples/C/global-array/adios_global_no_xml.c b/examples/C/global-array/adios_global_no_xml.c
index 3c6c18e..7f5f37a 100644
--- a/examples/C/global-array/adios_global_no_xml.c
+++ b/examples/C/global-array/adios_global_no_xml.c
@@ -20,6 +20,7 @@
*/
#include <stdio.h>
+#include <stdlib.h>
#include <inttypes.h>
#include <string.h>
#include "mpi.h"
@@ -34,8 +35,8 @@ int main (int argc, char ** argv)
{
char filename [256];
int rank, size, i, block;
- int NX = 100, Global_bounds, Offsets;
- double t[NX];
+ int NX = 10000000, Global_bounds, Offsets;
+ double *t;
int sub_blocks = 3;
int64_t var_ids[sub_blocks];
MPI_Comm comm = MPI_COMM_WORLD;
@@ -47,81 +48,83 @@ int main (int argc, char ** argv)
MPI_Comm_rank (comm, &rank);
MPI_Comm_size (comm, &size);
- Global_bounds = sub_blocks * NX * size;
+ t = (double *) malloc (NX * sizeof(double));
+ Global_bounds = sub_blocks * NX * size;
strcpy (filename, "adios_global_no_xml.bp");
adios_init_noxml (comm);
- adios_set_max_buffer_size (10);
+ adios_set_max_buffer_size (sub_blocks*NX*sizeof(double)/1048576 + 2);
- int64_t m_adios_group;
- int64_t m_adios_file;
+ int64_t m_adios_group;
+ int64_t m_adios_file;
- adios_declare_group (&m_adios_group, "restart", "iter", adios_flag_yes);
- adios_select_method (m_adios_group, "MPI", "", "");
+ adios_declare_group (&m_adios_group, "restart", "iter", adios_stat_default);
+ adios_select_method (m_adios_group, "MPI", "verbose=3", "");
- adios_define_var (m_adios_group, "NX"
+ adios_define_var (m_adios_group, "NX"
,"", adios_integer
,0, 0, 0);
-
+
adios_define_var (m_adios_group, "Global_bounds"
,"", adios_integer
,0, 0, 0);
- for (i=0;i<sub_blocks;i++) {
-
- adios_define_var (m_adios_group, "Offsets"
- ,"", adios_integer
- ,0, 0, 0);
-
- var_ids[i] = adios_define_var (m_adios_group, "temperature"
- ,"", adios_double
- ,"NX", "Global_bounds", "Offsets");
- adios_set_transform (var_ids[i], "identity");
-
- /* This is here just for test and will cause errors.
- * adios_expected_var_size() does not work here because the definition of the variable depends
- * on the "NX" dimension variable and it's value known to adios only after adios_write("NX")
- */
- /*
+ for (i=0;i<sub_blocks;i++) {
+
+ adios_define_var (m_adios_group, "Offsets"
+ ,"", adios_integer
+ ,0, 0, 0);
+
+ var_ids[i] = adios_define_var (m_adios_group, "temperature"
+ ,"", adios_double
+ ,"NX", "Global_bounds", "Offsets");
+ adios_set_transform (var_ids[i], "identity");
+
+ /* This is here just for test and will cause errors.
+ * adios_expected_var_size() does not work here because the definition of the variable depends
+ * on the "NX" dimension variable and it's value known to adios only after adios_write("NX")
+ */
+ /*
uint64_t varsize = adios_expected_var_size(var_ids[i]);
fprintf (stderr, "Temperature block %d is %" PRIu64 " bytes\n", i, varsize);
- */
+ */
+
+ }
- }
-
- adios_open (&m_adios_file, "restart", filename, "w", comm);
+ adios_open (&m_adios_file, "restart", filename, "w", comm);
- adios_groupsize = sub_blocks * (4 + 4 + 4 + NX * 8);
+ adios_groupsize = sub_blocks * (4 + 4 + 4 + NX * 8);
- adios_group_size (m_adios_file, adios_groupsize, &adios_totalsize);
+ adios_group_size (m_adios_file, adios_groupsize, &adios_totalsize);
adios_write(m_adios_file, "NX", (void *) &NX);
adios_write(m_adios_file, "Global_bounds", (void *) &Global_bounds);
-/* now we will write the data for each sub block */
- for (block=0;block<sub_blocks;block++) {
+ /* now we will write the data for each sub block */
+ for (block=0;block<sub_blocks;block++) {
- Offsets = rank * sub_blocks * NX + block*NX;
- adios_write(m_adios_file, "Offsets", (void *) &Offsets);
+ Offsets = rank * sub_blocks * NX + block*NX;
+ adios_write(m_adios_file, "Offsets", (void *) &Offsets);
- for (i = 0; i < NX; i++)
- t[i] = Offsets + i;
+ for (i = 0; i < NX; i++)
+ t[i] = Offsets + i;
- /* This is here just for fun */
- uint64_t varsize = adios_expected_var_size(var_ids[block]);
- /* adios_expected_var_size() works here because NX's value is known by adios at this point */
- fprintf (stderr, "Temperature block %d is %" PRIu64 " bytes\n", block, varsize);
+ /* This is here just for fun */
+ uint64_t varsize = adios_expected_var_size(var_ids[block]);
+ /* adios_expected_var_size() works here because NX's value is known by adios at this point */
+ fprintf (stderr, "Temperature block %d is %" PRIu64 " bytes\n", block, varsize);
- adios_write(m_adios_file, "temperature", t);
- }
+ adios_write(m_adios_file, "temperature", t);
+ }
- adios_close (m_adios_file);
+ adios_close (m_adios_file);
- MPI_Barrier (comm);
+ MPI_Barrier (comm);
adios_finalize (rank);
+ free (t);
MPI_Finalize ();
return 0;
}
diff --git a/examples/C/global-array/no_xml_write_byid.c b/examples/C/global-array/no_xml_write_byid.c
index 7c5c9e3..b036900 100644
--- a/examples/C/global-array/no_xml_write_byid.c
+++ b/examples/C/global-array/no_xml_write_byid.c
@@ -63,7 +63,7 @@ int main (int argc, char ** argv)
int64_t m_adios_file;
int64_t var_ids[nblocks];
- adios_declare_group (&m_adios_group, "restart", "iter", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "restart", "iter", adios_stat_default);
adios_select_method (m_adios_group, "MPI", "", "");
for (i = 0; i < nblocks; i++)
diff --git a/examples/C/icee_arrays/Makefile.in b/examples/C/icee_arrays/Makefile.in
index 4fd096c..da03f1b 100644
--- a/examples/C/icee_arrays/Makefile.in
+++ b/examples/C/icee_arrays/Makefile.in
@@ -107,7 +107,7 @@ 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_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 \
@@ -413,6 +413,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/C/icee_arrays/array/Makefile.in b/examples/C/icee_arrays/array/Makefile.in
index ecb7cf0..7c95530 100644
--- a/examples/C/icee_arrays/array/Makefile.in
+++ b/examples/C/icee_arrays/array/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -414,6 +414,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/C/icee_arrays/array/adios_write.c b/examples/C/icee_arrays/array/adios_write.c
index d5e3999..fd98a20 100644
--- a/examples/C/icee_arrays/array/adios_write.c
+++ b/examples/C/icee_arrays/array/adios_write.c
@@ -135,7 +135,7 @@ int main (int argc, char ** argv)
int64_t m_adios_group;
int64_t m_adios_file;
- adios_declare_group (&m_adios_group, "restart", "", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "restart", "", adios_stat_default);
adios_select_method (m_adios_group, adios_write_method, initstring, "");
adios_define_var (m_adios_group, "NX"
diff --git a/examples/C/manual/Makefile.in b/examples/C/manual/Makefile.in
index b979909..094fe39 100644
--- a/examples/C/manual/Makefile.in
+++ b/examples/C/manual/Makefile.in
@@ -110,7 +110,7 @@ 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_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 \
@@ -433,6 +433,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/C/query/Makefile.in b/examples/C/query/Makefile.in
index 80b2950..8dbcb88 100644
--- a/examples/C/query/Makefile.in
+++ b/examples/C/query/Makefile.in
@@ -110,7 +110,7 @@ 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_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 \
@@ -431,6 +431,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/C/query/write_table.c b/examples/C/query/write_table.c
index beaebba..339cb09 100644
--- a/examples/C/query/write_table.c
+++ b/examples/C/query/write_table.c
@@ -95,7 +95,7 @@ int main (int argc, char ** argv)
adios_init_noxml (comm);
adios_set_max_buffer_size (1);
- adios_declare_group (&g, "table", "", adios_flag_yes);
+ adios_declare_group (&g, "table", "", adios_stat_default);
adios_select_method (g, "POSIX", "", "");
sprintf (dimstr, "%d,%d", NX, NY);
diff --git a/examples/C/query/write_vars.c b/examples/C/query/write_vars.c
index 64b04bd..f49885c 100644
--- a/examples/C/query/write_vars.c
+++ b/examples/C/query/write_vars.c
@@ -74,7 +74,7 @@ int main (int argc, char ** argv)
adios_init_noxml (comm);
adios_set_max_buffer_size (1);
- adios_declare_group (&g, "vars", "", adios_flag_yes);
+ adios_declare_group (&g, "vars", "", adios_stat_default);
adios_select_method (g, "POSIX", "", "");
Tid = adios_define_var (g, "T" ,"", adios_double, dimstr, dimstr, "0,0");
diff --git a/examples/C/read_all/Makefile.in b/examples/C/read_all/Makefile.in
index 101a6fb..dc80a3f 100644
--- a/examples/C/read_all/Makefile.in
+++ b/examples/C/read_all/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -414,6 +414,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/C/scalars/Makefile.in b/examples/C/scalars/Makefile.in
index 638587c..87dded8 100644
--- a/examples/C/scalars/Makefile.in
+++ b/examples/C/scalars/Makefile.in
@@ -110,7 +110,7 @@ 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_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 \
@@ -425,6 +425,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/C/schema/Makefile.in b/examples/C/schema/Makefile.in
index a555630..1da114b 100644
--- a/examples/C/schema/Makefile.in
+++ b/examples/C/schema/Makefile.in
@@ -112,7 +112,7 @@ 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_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 \
@@ -475,6 +475,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/C/schema/rectilinear2d_noxml.c b/examples/C/schema/rectilinear2d_noxml.c
index 057a3ed..22702a9 100644
--- a/examples/C/schema/rectilinear2d_noxml.c
+++ b/examples/C/schema/rectilinear2d_noxml.c
@@ -121,7 +121,7 @@ int main (int argc, char ** argv)
adios_init_noxml (comm);
adios_set_max_buffer_size (50);
- adios_declare_group (&m_adios_group, "rectilinear2d", "", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "rectilinear2d", "", adios_stat_default);
adios_select_method (m_adios_group, "MPI", "", "");
adios_define_var (m_adios_group, "nx_global"
diff --git a/examples/C/schema/structured2d_noxml.c b/examples/C/schema/structured2d_noxml.c
index 0eb03d1..4347cbc 100644
--- a/examples/C/schema/structured2d_noxml.c
+++ b/examples/C/schema/structured2d_noxml.c
@@ -122,7 +122,7 @@ int main (int argc, char ** argv)
adios_init_noxml (comm);
adios_set_max_buffer_size (50);
- adios_declare_group (&m_adios_group, "structured2d", "", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "structured2d", "", adios_stat_default);
adios_select_method (m_adios_group, "MPI", "", "");
adios_define_var (m_adios_group, "nx_global"
diff --git a/examples/C/schema/tri2d_noxml.c b/examples/C/schema/tri2d_noxml.c
index 2bfa37a..568a2c3 100644
--- a/examples/C/schema/tri2d_noxml.c
+++ b/examples/C/schema/tri2d_noxml.c
@@ -244,7 +244,7 @@ int main (int argc, char ** argv)
adios_init_noxml (comm);
adios_set_max_buffer_size (50);
- adios_declare_group (&m_adios_group, "tri2d", "", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "tri2d", "", adios_stat_default);
adios_select_method (m_adios_group, "MPI", "", "");
adios_define_var (m_adios_group, "nx_global"
diff --git a/examples/C/schema/uniform2d_noxml.c b/examples/C/schema/uniform2d_noxml.c
index b8d408d..e90d76a 100644
--- a/examples/C/schema/uniform2d_noxml.c
+++ b/examples/C/schema/uniform2d_noxml.c
@@ -115,7 +115,7 @@ int main (int argc, char ** argv)
adios_init_noxml (comm);
adios_set_max_buffer_size (50);
- adios_declare_group (&m_adios_group, "uniform2d", "", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "uniform2d", "", adios_stat_default);
adios_select_method (m_adios_group, "MPI", "", "");
adios_define_var (m_adios_group, "nx_global"
diff --git a/examples/C/stat/Makefile.in b/examples/C/stat/Makefile.in
index 8587a04..88f3573 100644
--- a/examples/C/stat/Makefile.in
+++ b/examples/C/stat/Makefile.in
@@ -109,7 +109,7 @@ 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_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
$(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
@@ -414,6 +414,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/C/time_aggregation/CMakeLists.txt b/examples/C/time_aggregation/CMakeLists.txt
new file mode 100644
index 0000000..1176b0b
--- /dev/null
+++ b/examples/C/time_aggregation/CMakeLists.txt
@@ -0,0 +1,24 @@
+include_directories(${PROJECT_SOURCE_DIR}/src/public)
+include_directories(${PROJECT_SOURCE_DIR}/src)
+include_directories(${PROJECT_SOURCE_DIR}/examples/C/time_aggregation)
+include_directories(${PROJECT_BINARY_DIR}/src/public)
+link_directories(${PROJECT_BINARY_DIR}/examples/C/time_aggregation)
+
+add_executable(time_aggregation time_aggregation.c)
+target_link_libraries(time_aggregation adios ${ADIOSLIB_LDADD})
+
+add_executable(time_aggregation_no_xml time_aggregation_no_xml.c)
+target_link_libraries(time_aggregation_no_xml adios ${ADIOSLIB_LDADD})
+
+set (PROGS time_aggregation time_aggregation_no_xml)
+foreach (PROG ${PROGS} )
+ if(MPI_COMPILE_FLAGS)
+ set_target_properties(${PROG} PROPERTIES COMPILE_FLAGS "${MPI_C_COMPILE_FLAGS}")
+ endif()
+ if(MPI_LINK_FLAGS)
+ set_target_properties(${PROG} PROPERTIES LINK_FLAGS "${MPI_C_LINK_FLAGS}")
+ endif()
+ target_link_libraries(${PROG} adios ${MPI_C_LIBRARIES})
+endforeach()
+
+file(COPY time_aggregation.xml DESTINATION ${PROJECT_BINARY_DIR}/examples/C/time_aggregation)
diff --git a/examples/C/time_aggregation/Makefile.am b/examples/C/time_aggregation/Makefile.am
new file mode 100644
index 0000000..fb03fef
--- /dev/null
+++ b/examples/C/time_aggregation/Makefile.am
@@ -0,0 +1,23 @@
+AM_CPPFLAGS = $(all_includes)
+AM_CPPFLAGS += -I$(top_builddir)/src/public -I$(top_srcdir)/src -I$(top_srcdir)/src/public
+
+AUTOMAKE_OPTIONS = no-dependencies
+
+all-local:
+ test "$(srcdir)" = "$(builddir)" || cp $(srcdir)/*.xml $(builddir)
+
+noinst_PROGRAMS = time_aggregation time_aggregation_no_xml
+
+time_aggregation_SOURCES = time_aggregation.c
+time_aggregation_LDADD = $(top_builddir)/src/libadios.a
+time_aggregation_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
+time_aggregation_LDADD += $(ADIOSLIB_LDADD)
+
+time_aggregation_no_xml_SOURCES = time_aggregation_no_xml.c
+time_aggregation_no_xml_LDADD = $(top_builddir)/src/libadios.a
+time_aggregation_no_xml_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
+time_aggregation_no_xml_LDADD += $(ADIOSLIB_LDADD)
+
+CLEANFILES = *.bp
+CC=$(MPICC)
+EXTRA_DIST = time_aggregation.xml
diff --git a/examples/C/attributes/Makefile.in b/examples/C/time_aggregation/Makefile.in
similarity index 90%
copy from examples/C/attributes/Makefile.in
copy to examples/C/time_aggregation/Makefile.in
index 068dd53..4a32703 100644
--- a/examples/C/attributes/Makefile.in
+++ b/examples/C/time_aggregation/Makefile.in
@@ -78,8 +78,9 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
-noinst_PROGRAMS = attributes_write$(EXEEXT) attributes_read$(EXEEXT)
-subdir = examples/C/attributes
+noinst_PROGRAMS = time_aggregation$(EXEEXT) \
+ time_aggregation_no_xml$(EXEEXT)
+subdir = examples/C/time_aggregation
DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
@@ -109,7 +110,7 @@ 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_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 \
@@ -125,27 +126,29 @@ CONFIG_HEADER = $(top_builddir)/config.h
CONFIG_CLEAN_FILES =
CONFIG_CLEAN_VPATH_FILES =
PROGRAMS = $(noinst_PROGRAMS)
-am_attributes_read_OBJECTS = attributes_read.$(OBJEXT)
-attributes_read_OBJECTS = $(am_attributes_read_OBJECTS)
+am_time_aggregation_OBJECTS = time_aggregation.$(OBJEXT)
+time_aggregation_OBJECTS = $(am_time_aggregation_OBJECTS)
am__DEPENDENCIES_1 =
-attributes_read_DEPENDENCIES = $(top_builddir)/src/libadiosread.a \
+time_aggregation_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 =
-attributes_read_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \
+time_aggregation_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \
$(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \
- $(AM_CFLAGS) $(CFLAGS) $(attributes_read_LDFLAGS) $(LDFLAGS) \
+ $(AM_CFLAGS) $(CFLAGS) $(time_aggregation_LDFLAGS) $(LDFLAGS) \
-o $@
-am_attributes_write_OBJECTS = attributes_write.$(OBJEXT)
-attributes_write_OBJECTS = $(am_attributes_write_OBJECTS)
-attributes_write_DEPENDENCIES = $(top_builddir)/src/libadios.a \
+am_time_aggregation_no_xml_OBJECTS = \
+ time_aggregation_no_xml.$(OBJEXT)
+time_aggregation_no_xml_OBJECTS = \
+ $(am_time_aggregation_no_xml_OBJECTS)
+time_aggregation_no_xml_DEPENDENCIES = $(top_builddir)/src/libadios.a \
$(am__DEPENDENCIES_1)
-attributes_write_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \
+time_aggregation_no_xml_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \
$(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \
- $(AM_CFLAGS) $(CFLAGS) $(attributes_write_LDFLAGS) $(LDFLAGS) \
- -o $@
+ $(AM_CFLAGS) $(CFLAGS) $(time_aggregation_no_xml_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
@@ -179,8 +182,10 @@ 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 = $(attributes_read_SOURCES) $(attributes_write_SOURCES)
-DIST_SOURCES = $(attributes_read_SOURCES) $(attributes_write_SOURCES)
+SOURCES = $(time_aggregation_SOURCES) \
+ $(time_aggregation_no_xml_SOURCES)
+DIST_SOURCES = $(time_aggregation_SOURCES) \
+ $(time_aggregation_no_xml_SOURCES)
am__can_run_installinfo = \
case $$AM_UPDATE_INFO_DIR in \
n|no|NO) false;; \
@@ -416,6 +421,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
@@ -480,16 +488,16 @@ top_srcdir = @top_srcdir@
AM_CPPFLAGS = $(all_includes) -I$(top_builddir)/src/public \
-I$(top_srcdir)/src -I$(top_srcdir)/src/public
AUTOMAKE_OPTIONS = no-dependencies
-attributes_write_SOURCES = attributes_write.c
-attributes_write_LDADD = $(top_builddir)/src/libadios.a \
+time_aggregation_SOURCES = time_aggregation.c
+time_aggregation_LDADD = $(top_builddir)/src/libadios.a \
+ $(ADIOSLIB_LDADD)
+time_aggregation_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
+time_aggregation_no_xml_SOURCES = time_aggregation_no_xml.c
+time_aggregation_no_xml_LDADD = $(top_builddir)/src/libadios.a \
$(ADIOSLIB_LDADD)
-attributes_write_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
-attributes_read_SOURCES = attributes_read.c
-attributes_read_LDADD = $(top_builddir)/src/libadiosread.a \
- $(ADIOSREADLIB_LDADD)
-attributes_read_LDFLAGS = $(ADIOSREADLIB_LDFLAGS)
+time_aggregation_no_xml_LDFLAGS = $(ADIOSLIB_LDFLAGS) $(ADIOSLIB_EXTRA_LDFLAGS)
CLEANFILES = *.bp
-EXTRA_DIST = attributes.xml gwrite_temperature.ch gread_temperature.ch
+EXTRA_DIST = time_aggregation.xml
all: all-am
.SUFFIXES:
@@ -503,9 +511,9 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(am__confi
exit 1;; \
esac; \
done; \
- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu examples/C/attributes/Makefile'; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu examples/C/time_aggregation/Makefile'; \
$(am__cd) $(top_srcdir) && \
- $(AUTOMAKE) --gnu examples/C/attributes/Makefile
+ $(AUTOMAKE) --gnu examples/C/time_aggregation/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
@@ -534,13 +542,13 @@ clean-noinstPROGRAMS:
echo " rm -f" $$list; \
rm -f $$list
-attributes_read$(EXEEXT): $(attributes_read_OBJECTS) $(attributes_read_DEPENDENCIES) $(EXTRA_attributes_read_DEPENDENCIES)
- @rm -f attributes_read$(EXEEXT)
- $(AM_V_CCLD)$(attributes_read_LINK) $(attributes_read_OBJECTS) $(attributes_read_LDADD) $(LIBS)
+time_aggregation$(EXEEXT): $(time_aggregation_OBJECTS) $(time_aggregation_DEPENDENCIES) $(EXTRA_time_aggregation_DEPENDENCIES)
+ @rm -f time_aggregation$(EXEEXT)
+ $(AM_V_CCLD)$(time_aggregation_LINK) $(time_aggregation_OBJECTS) $(time_aggregation_LDADD) $(LIBS)
-attributes_write$(EXEEXT): $(attributes_write_OBJECTS) $(attributes_write_DEPENDENCIES) $(EXTRA_attributes_write_DEPENDENCIES)
- @rm -f attributes_write$(EXEEXT)
- $(AM_V_CCLD)$(attributes_write_LINK) $(attributes_write_OBJECTS) $(attributes_write_LDADD) $(LIBS)
+time_aggregation_no_xml$(EXEEXT): $(time_aggregation_no_xml_OBJECTS) $(time_aggregation_no_xml_DEPENDENCIES) $(EXTRA_time_aggregation_no_xml_DEPENDENCIES)
+ @rm -f time_aggregation_no_xml$(EXEEXT)
+ $(AM_V_CCLD)$(time_aggregation_no_xml_LINK) $(time_aggregation_no_xml_OBJECTS) $(time_aggregation_no_xml_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
diff --git a/examples/C/time_aggregation/time_aggregation.c b/examples/C/time_aggregation/time_aggregation.c
new file mode 100644
index 0000000..9ea4ccc
--- /dev/null
+++ b/examples/C/time_aggregation/time_aggregation.c
@@ -0,0 +1,111 @@
+/*
+ * 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"
+
+const int NX = 10;
+const int NY = 5;
+const char diagfilename[] = "diag.bp";
+const char diag2filename[] = "diag2.bp";
+const char ckptfilename[] = "ckpt.bp";
+
+const MPI_Comm comm = MPI_COMM_WORLD;
+int rank, size;
+
+void write_diag (int step, double * p)
+{
+ int64_t adios_handle;
+ if (rank==0) printf(" write diagnostics\n");
+
+ if (step==1)
+ adios_open (&adios_handle, "diagnostics", diagfilename, "w", comm);
+ else
+ adios_open (&adios_handle, "diagnostics", diagfilename, "a", comm);
+
+ adios_write (adios_handle, "NY", &NY);
+ adios_write (adios_handle, "size", &size);
+ adios_write (adios_handle, "rank", &rank);
+ adios_write (adios_handle, "pressure", p);
+
+ adios_close (adios_handle);
+}
+
+void write_diag2 (int step, double * t)
+{
+ int64_t adios_handle;
+ if (rank==0) printf(" write diag2\n");
+
+ if (step==1)
+ adios_open (&adios_handle, "diag2", diag2filename, "w", comm);
+ else
+ adios_open (&adios_handle, "diag2", diag2filename, "a", comm);
+
+ adios_write (adios_handle, "size", &size);
+ adios_write (adios_handle, "rank", &rank);
+ adios_write (adios_handle, "t0", t);
+
+ adios_close (adios_handle);
+}
+
+void write_checkpoint (int step, double * p, double *t)
+{
+ int64_t adios_handle;
+ if (rank==0) printf(" Checkpointing at step %d\n", step);
+ adios_open (&adios_handle, "checkpoint", ckptfilename, "w", comm);
+ adios_write (adios_handle, "NX", &NX);
+ adios_write (adios_handle, "NY", &NY);
+ adios_write (adios_handle, "size", &size);
+ adios_write (adios_handle, "rank", &rank);
+ adios_write (adios_handle, "step", &step);
+ adios_write (adios_handle, "temperature", t);
+ adios_write (adios_handle, "pressure", p);
+ adios_close (adios_handle);
+}
+
+int main (int argc, char ** argv)
+{
+
+ int i, it;
+ double t[NX];
+ double p[NY];
+
+ MPI_Init (&argc, &argv);
+ MPI_Comm_rank (comm, &rank);
+ MPI_Comm_size (comm, &size);
+
+ adios_init ("time_aggregation.xml", comm);
+
+
+ for (it = 1; it <= 100; it++)
+ {
+ if (rank==0) printf("Timestep %d...\n", it);
+
+ for (i = 0; i < NX; i++)
+ t[i] = it*1000.0 + rank*NX + i;
+
+ for (i = 0; i < NY; i++)
+ p[i] = it*1000.0 + rank*NY + i;
+
+ write_diag(it, p);
+ write_diag2(it, t);
+
+ if ( it%30 == 0) {
+ write_checkpoint(it, p, t);
+ }
+
+ MPI_Barrier (comm);
+ if (rank==0) printf(" step completed\n");
+ }
+
+ MPI_Barrier (comm);
+ adios_finalize (rank);
+ MPI_Finalize ();
+ return 0;
+}
diff --git a/examples/C/time_aggregation/time_aggregation.xml b/examples/C/time_aggregation/time_aggregation.xml
new file mode 100644
index 0000000..ae994df
--- /dev/null
+++ b/examples/C/time_aggregation/time_aggregation.xml
@@ -0,0 +1,45 @@
+<?xml version="1.0"?>
+<adios-config host-language="C">
+
+ <adios-group name="checkpoint">
+ <var name="NX" type="integer"/>
+ <var name="NY" type="integer"/>
+ <var name="size" type="integer"/>
+ <var name="rank" type="integer"/>
+ <var name="step" type="integer"/>
+
+ <global-bounds dimensions="size,NX" offsets="rank,0">
+ <var name="temperature" gwrite="t" type="double" dimensions="1,NX"/>
+ </global-bounds>
+
+ <global-bounds dimensions="size,NY" offsets="rank,0">
+ <var name="pressure" gwrite="p" type="double" dimensions="1,NY"/>
+ </global-bounds>
+ </adios-group> <!-- checkpoint -->
+
+ <adios-group name="diagnostics">
+ <var name="NY" type="integer"/>
+ <var name="size" type="integer"/>
+ <var name="rank" type="integer"/>
+ <global-bounds dimensions="size,NY" offsets="rank,0">
+ <var name="pressure" gwrite="p" type="double" dimensions="1,NY"/>
+ </global-bounds>
+ </adios-group> <!-- diagnostics -->
+
+ <adios-group name="diag2">
+ <var name="size" type="integer"/>
+ <var name="rank" type="integer"/>
+ <global-bounds dimensions="size,1" offsets="rank,0">
+ <var name="t0" gwrite="temperature[0]" type="double" dimensions="1,1"/>
+ </global-bounds>
+ </adios-group> <!-- diagnostics -->
+
+ <method group="checkpoint" method="MPI">verbose=3</method>
+ <method group="diagnostics" method="MPI">verbose=3</method>
+ <method group="diag2" method="MPI">verbose=3</method>
+
+ <time-aggregation group="diagnostics" buffer-size=12000 sync-with-group="checkpoint"/>
+ <time-aggregation group="diag2" buffer-size=32000 sync-with-group="checkpoint"/>
+
+</adios-config>
+
diff --git a/examples/C/time_aggregation/time_aggregation_no_xml.c b/examples/C/time_aggregation/time_aggregation_no_xml.c
new file mode 100644
index 0000000..c14e854
--- /dev/null
+++ b/examples/C/time_aggregation/time_aggregation_no_xml.c
@@ -0,0 +1,158 @@
+/*
+ * 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"
+
+const int NX = 10;
+const int NY = 5;
+const char diagfilename[] = "diag.bp";
+const char diag2filename[] = "diag2.bp";
+const char ckptfilename[] = "ckpt.bp";
+
+const MPI_Comm comm = MPI_COMM_WORLD;
+int rank, size;
+
+void write_diag (int step, double * p)
+{
+ int64_t adios_handle;
+ if (rank==0) printf(" write diagnostics\n");
+
+ if (step==1)
+ adios_open (&adios_handle, "diagnostics", diagfilename, "w", comm);
+ else
+ adios_open (&adios_handle, "diagnostics", diagfilename, "a", comm);
+
+ adios_write (adios_handle, "NY", &NY);
+ adios_write (adios_handle, "size", &size);
+ adios_write (adios_handle, "rank", &rank);
+ adios_write (adios_handle, "pressure", p);
+
+ adios_close (adios_handle);
+}
+
+void write_diag2 (int step, double * t)
+{
+ int64_t adios_handle;
+ if (rank==0) printf(" write diag2\n");
+
+ if (step==1)
+ adios_open (&adios_handle, "diag2", diag2filename, "w", comm);
+ else
+ adios_open (&adios_handle, "diag2", diag2filename, "a", comm);
+
+ adios_write (adios_handle, "size", &size);
+ adios_write (adios_handle, "rank", &rank);
+ adios_write (adios_handle, "t0", t);
+
+ adios_close (adios_handle);
+}
+
+void write_checkpoint (int step, double * p, double *t)
+{
+ int64_t adios_handle;
+ if (rank==0) printf(" Checkpointing at step %d\n", step);
+ adios_open (&adios_handle, "checkpoint", ckptfilename, "w", comm);
+ adios_write (adios_handle, "NX", &NX);
+ adios_write (adios_handle, "NY", &NY);
+ adios_write (adios_handle, "size", &size);
+ adios_write (adios_handle, "rank", &rank);
+ adios_write (adios_handle, "step", &step);
+ adios_write (adios_handle, "temperature", t);
+ adios_write (adios_handle, "pressure", p);
+ adios_close (adios_handle);
+}
+
+void define_groups ()
+{
+ int64_t g_diag, g_diag2, g_ckpt;
+
+ // Group diagnosis
+ adios_declare_group (&g_diag, "diagnostics", "", adios_stat_default);
+ adios_define_var (g_diag, "NY", "", adios_integer, 0, 0, 0);
+ adios_define_var (g_diag, "size","", adios_integer, 0, 0, 0);
+ adios_define_var (g_diag, "rank","", adios_integer, 0, 0, 0);
+ int64_t var_p = adios_define_var (g_diag, "pressure", "", adios_double,
+ "1,NY", "size,NY", "rank,0");
+ adios_set_transform (var_p, "none");
+
+
+ // Group diag2
+ adios_declare_group (&g_diag2, "diag2", "", adios_stat_default);
+ adios_define_var (g_diag2, "size","", adios_integer, 0, 0, 0);
+ adios_define_var (g_diag2, "rank","", adios_integer, 0, 0, 0);
+ int64_t var_t0 = adios_define_var (g_diag2, "t0", "", adios_double,
+ "1,1", "size,1", "rank,0");
+ adios_set_transform (var_t0, "none");
+
+
+ // Group checkpoint
+ adios_declare_group (&g_ckpt, "checkpoint", "", adios_stat_default);
+ adios_define_var (g_ckpt, "NX", "", adios_integer, 0, 0, 0);
+ adios_define_var (g_ckpt, "NY", "", adios_integer, 0, 0, 0);
+ adios_define_var (g_ckpt, "size","", adios_integer, 0, 0, 0);
+ adios_define_var (g_ckpt, "rank","", adios_integer, 0, 0, 0);
+ adios_define_var (g_ckpt, "step","", adios_integer, 0, 0, 0);
+ adios_define_var (g_ckpt, "temperature", "", adios_double,
+ "1,NX", "size,NX", "rank,0");
+ adios_define_var (g_ckpt, "pressure", "", adios_double,
+ "1,NY", "size,NY", "rank,0");
+
+
+ adios_select_method (g_diag, "MPI", "verbose=3", "");
+ adios_select_method (g_diag2, "MPI", "verbose=3", "");
+ adios_select_method (g_ckpt, "MPI", "verbose=3", "");
+ //adios_select_method (m_ckpt, "MPI_AGGREGATE", "num_ost=2;num_aggregators=2;aggregation_type=2;verbose=3", "");
+
+ adios_set_time_aggregation (g_diag, 12000, g_ckpt);
+ adios_set_time_aggregation (g_diag2, 32000, g_ckpt);
+}
+
+int main (int argc, char ** argv)
+{
+
+ int i, it;
+ double t[NX];
+ double p[NY];
+
+ MPI_Init (&argc, &argv);
+ MPI_Comm_rank (comm, &rank);
+ MPI_Comm_size (comm, &size);
+
+ adios_init_noxml (comm);
+ adios_set_max_buffer_size (10);
+ define_groups();
+
+
+ for (it = 1; it <= 100; it++)
+ {
+ if (rank==0) printf("Timestep %d...\n", it);
+
+ for (i = 0; i < NX; i++)
+ t[i] = it*1000.0 + rank*NX + i;
+
+ for (i = 0; i < NY; i++)
+ p[i] = it*1000.0 + rank*NY + i;
+
+ write_diag(it, p);
+ write_diag2(it, t);
+
+ if ( it%30 == 0) {
+ write_checkpoint(it, p, t);
+ }
+
+ MPI_Barrier (comm);
+ if (rank==0) printf(" step completed\n");
+ }
+
+ MPI_Barrier (comm);
+ adios_finalize (rank);
+ MPI_Finalize ();
+ return 0;
+}
diff --git a/examples/C/transforms/Makefile.in b/examples/C/transforms/Makefile.in
index 646f0b9..8c45625 100644
--- a/examples/C/transforms/Makefile.in
+++ b/examples/C/transforms/Makefile.in
@@ -110,7 +110,7 @@ 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_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 \
@@ -434,6 +434,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/Fortran/Makefile.in b/examples/Fortran/Makefile.in
index f04f53e..1f966d5 100644
--- a/examples/Fortran/Makefile.in
+++ b/examples/Fortran/Makefile.in
@@ -107,7 +107,7 @@ 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_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 \
@@ -413,6 +413,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/Fortran/arrays/Makefile.in b/examples/Fortran/arrays/Makefile.in
index 65c8cb3..fc96393 100644
--- a/examples/Fortran/arrays/Makefile.in
+++ b/examples/Fortran/arrays/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -411,6 +411,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/Fortran/global-array-time/Makefile.in b/examples/Fortran/global-array-time/Makefile.in
index 9ee2fa0..9a444da 100644
--- a/examples/Fortran/global-array-time/Makefile.in
+++ b/examples/Fortran/global-array-time/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -405,6 +405,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/Fortran/global-array/Makefile.in b/examples/Fortran/global-array/Makefile.in
index 979a347..a576d12 100644
--- a/examples/Fortran/global-array/Makefile.in
+++ b/examples/Fortran/global-array/Makefile.in
@@ -110,7 +110,7 @@ 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_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 \
@@ -423,6 +423,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/Fortran/global-array/adios_global_no_xml.F90 b/examples/Fortran/global-array/adios_global_no_xml.F90
index a170488..63e98b8 100644
--- a/examples/Fortran/global-array/adios_global_no_xml.F90
+++ b/examples/Fortran/global-array/adios_global_no_xml.F90
@@ -37,8 +37,9 @@ program adios_global
call adios_init_noxml (comm, adios_err)
call adios_set_max_buffer_size (10)
- call adios_declare_group (m_adios_group, "restart", "iter", 1, adios_err)
+ call adios_declare_group (m_adios_group, "restart", "iter", ADIOS_STAT_DEFAULT, adios_err)
call adios_select_method (m_adios_group, "MPI", "", "", adios_err)
+ call adios_set_time_aggregation (m_adios_group, 32000_8, 0_8, adios_err);
! This example doesn't use varid during writing.
! So we simply put 'varid' everywhere.
diff --git a/examples/Fortran/global-array/no_xml_write_byid.F90 b/examples/Fortran/global-array/no_xml_write_byid.F90
index 485f8d6..ec3789a 100644
--- a/examples/Fortran/global-array/no_xml_write_byid.F90
+++ b/examples/Fortran/global-array/no_xml_write_byid.F90
@@ -43,7 +43,7 @@ program no_xml_write_byid
call adios_init_noxml (comm, adios_err)
call adios_set_max_buffer_size (10)
- call adios_declare_group (m_adios_group, "restart", "iter", 1, adios_err)
+ call adios_declare_group (m_adios_group, "restart", "iter", ADIOS_STAT_DEFAULT, adios_err)
call adios_select_method (m_adios_group, "MPI", "", "", adios_err)
G = 2 * NX * size
diff --git a/examples/Fortran/scalars/Makefile.in b/examples/Fortran/scalars/Makefile.in
index d16e41d..9e8ddf1 100644
--- a/examples/Fortran/scalars/Makefile.in
+++ b/examples/Fortran/scalars/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -411,6 +411,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/Fortran/schema/Makefile.in b/examples/Fortran/schema/Makefile.in
index c7a37bd..795c3d8 100644
--- a/examples/Fortran/schema/Makefile.in
+++ b/examples/Fortran/schema/Makefile.in
@@ -111,7 +111,7 @@ 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_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 \
@@ -442,6 +442,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/examples/Fortran/schema/rectilinear2d_noxml.F90 b/examples/Fortran/schema/rectilinear2d_noxml.F90
index 7bd9da8..55a06fc 100644
--- a/examples/Fortran/schema/rectilinear2d_noxml.F90
+++ b/examples/Fortran/schema/rectilinear2d_noxml.F90
@@ -123,7 +123,7 @@ program rectilinear2d_f_noxml
call adios_init_noxml (comm, adios_err)
call adios_set_max_buffer_size (50)
- call adios_declare_group (m_adios_group, "rectilinear2d", "", 1, adios_err)
+ call adios_declare_group (m_adios_group, "rectilinear2d", "", ADIOS_STAT_DEFAULT, adios_err)
call adios_select_method (m_adios_group, "MPI", "", "", adios_err)
! This example doesn't use varid during writing.
diff --git a/examples/Fortran/schema/structured2d_noxml.F90 b/examples/Fortran/schema/structured2d_noxml.F90
index eb4dc2f..3e0509e 100644
--- a/examples/Fortran/schema/structured2d_noxml.F90
+++ b/examples/Fortran/schema/structured2d_noxml.F90
@@ -128,7 +128,7 @@ program structured2d_f_noxml
call adios_init_noxml (comm, adios_err)
call adios_set_max_buffer_size (50)
- call adios_declare_group (m_adios_group, "structured2d", "", 1, adios_err)
+ call adios_declare_group (m_adios_group, "structured2d", "", ADIOS_STAT_DEFAULT, adios_err)
call adios_select_method (m_adios_group, "MPI", "", "", adios_err)
! This example doesn't use varid during writing.
diff --git a/examples/Fortran/schema/tri2d_noxml.F90 b/examples/Fortran/schema/tri2d_noxml.F90
index d470adc..2d85ebc 100644
--- a/examples/Fortran/schema/tri2d_noxml.F90
+++ b/examples/Fortran/schema/tri2d_noxml.F90
@@ -222,7 +222,7 @@ program tri2d_f_noxml
call adios_init_noxml (comm, adios_err)
call adios_set_max_buffer_size (10)
- call adios_declare_group (m_adios_group, "tri2d", "", 1, adios_err)
+ call adios_declare_group (m_adios_group, "tri2d", "", ADIOS_STAT_DEFAULT, adios_err)
call adios_select_method (m_adios_group, "MPI", "", "", adios_err)
! This example doesn't use varid during writing.
diff --git a/examples/Fortran/schema/tri2d_noxml_seperate.F90 b/examples/Fortran/schema/tri2d_noxml_seperate.F90
index 5806f6e..0e490ba 100644
--- a/examples/Fortran/schema/tri2d_noxml_seperate.F90
+++ b/examples/Fortran/schema/tri2d_noxml_seperate.F90
@@ -229,7 +229,7 @@ program tri2d_f_noxml
!!
!! Define the Data group
!!
- call adios_declare_group (data_group, "tri2d", "", 1, adios_err)
+ call adios_declare_group (data_group, "tri2d", "", ADIOS_STAT_DEFAULT, adios_err)
call adios_select_method (data_group, "MPI", "", "", adios_err)
! This example doesn't use varid during writing.
@@ -299,7 +299,7 @@ program tri2d_f_noxml
!!
!! Define the Mesh group
!!
- call adios_declare_group (mesh_group, "trimesh", "", 1, adios_err)
+ call adios_declare_group (mesh_group, "trimesh", "", ADIOS_STAT_DEFAULT, adios_err)
call adios_select_method (mesh_group, "MPI", "", "", adios_err)
call adios_define_var (mesh_group, "npoints" &
,"", adios_integer &
diff --git a/examples/Fortran/schema/uniform2d_noxml.F90 b/examples/Fortran/schema/uniform2d_noxml.F90
index af0d2d8..50098c5 100644
--- a/examples/Fortran/schema/uniform2d_noxml.F90
+++ b/examples/Fortran/schema/uniform2d_noxml.F90
@@ -117,7 +117,7 @@ program uniform2d_f_noxml
call adios_init_noxml (comm, adios_err)
call adios_set_max_buffer_size (50)
- call adios_declare_group (m_adios_group, "uniform2d", "", 1, adios_err)
+ call adios_declare_group (m_adios_group, "uniform2d", "", ADIOS_STAT_DEFAULT, adios_err)
call adios_select_method (m_adios_group, "MPI", "", "", adios_err)
! This example doesn't use varid during writing.
diff --git a/examples/Makefile.in b/examples/Makefile.in
index 3f495ec..f1633ca 100644
--- a/examples/Makefile.in
+++ b/examples/Makefile.in
@@ -107,7 +107,7 @@ 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_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 \
@@ -413,6 +413,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/runconf b/runconf
index d497636..25629a7 100755
--- a/runconf
+++ b/runconf
@@ -152,7 +152,7 @@ elif [ `hostname | cut -c 1-4` == "rhea" ]; then
module unload pgi gcc intel pathscale
module unload python
module load PE-$TARGET
- module load python
+ #module load python
# Use both seq hdf5 (for utils) and
# parallel hdf5 (for PHDF5 method)
module load hdf5/1.8.11
@@ -174,7 +174,10 @@ elif [ `hostname | cut -c 1-4` == "rhea" ]; then
#module unload netcdf
#module load szip
#module load bzip2
- #module load dataspaces/1.4.0
+ module load dataspaces/1.6.1
+ module load flexpath/stable
+ module load alacrity/1.0.0
+ module load fastbit/svn
export MPICC=mpicc
export MPICXX=mpiCC
export MPIFC=mpif90
@@ -182,12 +185,10 @@ elif [ `hostname | cut -c 1-4` == "rhea" ]; then
export CC=pgcc
export CXX=pgCC
export FC=pgf90
- WITHFLEX="--with-flexpath=/ccs/proj/e2e/chaos/sith/$TARGET"
elif [ "$TARGET" == "gnu" ]; then
export CC=gcc
export CXX=g++
export FC=gfortran
- WITHFLEX="--with-flexpath=/ccs/proj/e2e/chaos/sith/$TARGET"
elif [ "$TARGET" == "intel" ]; then
export CC=icc
export CXX=icpc
@@ -201,11 +202,16 @@ elif [ `hostname | cut -c 1-4` == "rhea" ]; then
export CPPFLAGS="-DMPICH_IGNORE_CXX_SEEK"
export CFLAGS="-g -fPIC"
$SRCDIR/configure --prefix=/ccs/proj/e2e/${USER}/ADIOS/rhea.$TARGET \
- --config-cache \
--disable-maintainer-mode \
--enable-dependency-tracking \
--enable-research-transports \
--with-lustre \
+ --with-dataspaces=$DATASPACES_DIR \
+ --with-flexpath=$FLEXPATH_DIR \
+ --with-alacrity=$ALACRITY_DIR \
+ --with-zlib \
+ --with-bzip2 \
+ --with-fastbit=$FASTBIT_DIR \
#--with-hdf5=${SEQ_HDF5_DIR} \
#--with-hdf5-libs="${SEQ_HDF5_CLIB}" \
#--with-phdf5=${PAR_HDF5_DIR} \
@@ -214,10 +220,6 @@ elif [ `hostname | cut -c 1-4` == "rhea" ]; then
#--with-netcdf-libs="${SEQ_NC_CLIB}" \
#--with-nc4par=${PAR_NC_DIR} \
#--with-nc4par-libs="${PAR_NC_CLIB}" \
- #--with-zlib \
- #--with-bzip2=$BZIP2_DIR \
- #--with-dataspaces=$DATASPACES_DIR \
- #$WITHFLEX \
#--with-aplod=/ccs/proj/e2e/ncsu/sith.gnu \
#--with-isobar=/ccs/proj/e2e/ncsu/sith.gnu \
#--with-fgr=/ccs/proj/e2e/qliu/tap \
@@ -342,9 +344,12 @@ elif [ `hostname | cut -c 1-5` == "titan" ]; then
export CXX=CC
if [ "$TARGET" == "pgi" ]; then
# FASTBIT needs libstdc++ and -pgcpplibs flag
- export LDFLAGS="-pgcpplibs"
+ export LDFLAGS="-pgc++libs"
#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
#export FC=gfortran
@@ -359,6 +364,7 @@ elif [ `hostname | cut -c 1-5` == "titan" ]; then
# FASTBIT needs libstdc++
WITHFASTBIT="--with-fastbit=$FASTBIT_DIR"
#export EXTRA_LIBS="${GCC_PATH}/snos/lib64/libstdc++.a"
+ export EXTRA_CFLAGS="-Ofast"
#DATASPACES_DIR="/ccs/proj/e2e/dataspaces/titan/$TARGET"
elif [ "$TARGET" == "cray" ]; then
export EXTRA_CFLAGS="-h gnu"
@@ -373,7 +379,7 @@ elif [ `hostname | cut -c 1-5` == "titan" ]; then
#export CC=mpicc
#export FC=mpif90
export CPPFLAGS="-DMPICH_IGNORE_CXX_SEEK -DDART_DO_VERSIONING"
- export CFLAGS="-fPIC -g -O2 ${EXTRA_CFLAGS}"
+ export CFLAGS="-fPIC -g ${EXTRA_CFLAGS}"
LIBS="$EXTRA_LIBS" ${SRCDIR}/configure --prefix=/ccs/proj/e2e/${USER}/ADIOS/xk6.$TARGET \
--enable-dependency-tracking \
--disable-maintainer-mode \
@@ -424,8 +430,8 @@ elif [ `hostname | cut -c 1-4` == "eos-" ]; then
module unload papi
module unload pmi
if [ "$TARGET" == "pgi" ]; then
- # NSSI needs -pgcpplibs flag
- export LDFLAGS="-pgcpplibs"
+ # NSSI needs -pgc++libs flag
+ export LDFLAGS="-pgc++libs"
unset EXTRA_LIBS
elif [ "$TARGET" == "gnu" ]; then
# NSSI needs libstdc++
@@ -481,7 +487,7 @@ 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 LDFLAGS="-pgcpplibs"
+ export LDFLAGS="-pgc++libs"
unset EXTRA_LIBS
elif [ "$TARGET" == "gnu" ]; then
export CC=gcc
@@ -615,7 +621,7 @@ 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/1.10.0/cori/$TARGET \
+ ${SRCDIR}/configure --prefix=/global/homes/p/pnorbert/adios/1.11.0/cori/$TARGET \
--disable-maintainer-mode \
--enable-dependency-tracking \
--with-lustre=/usr \
@@ -705,6 +711,7 @@ elif [ `hostname | cut -c 1-4` == "dyn9" -o `hostname | cut -c 1-3` == "pnb" ];
# Installed Homebrew, gcc/gfortran 5.3.0 and OpenMPI 1.10.2 in /usr/local
# But should work with default mpicc and gcc, using --disable-fortran or with Homebrew gfortran
#
+ unset WITHZFP # build from the included zfp source
USE_GCC5=false
if [ $USE_GCC5 == "true" ]; then
# If want to use gcc/gfortran 5.3.0
@@ -716,6 +723,9 @@ elif [ `hostname | cut -c 1-4` == "dyn9" -o `hostname | cut -c 1-3` == "pnb" ];
export OMPI_FC=/usr/local/bin/gfortran
export WITHALACRITY="--with-alacrity=/opt/alacrity/gcc5"
export WITHFASTBIT="--without-fastbit"
+ export WITHFLEXPATH="--without-flexpath"
+ export WITHDATASPACES="--without-dataspaces --without-dimes"
+ #export WITHZFP="--without-zfp"
# ALACRITY, FASTBIT are C++ lib so we need to link with the actual libstdc++
# if the automatically added -lstdc++ does not work
#export LIBS="/usr/local/Cellar/gcc/5.3.0/lib/gcc/5/libstdc++.dylib"
@@ -730,6 +740,9 @@ elif [ `hostname | cut -c 1-4` == "dyn9" -o `hostname | cut -c 1-3` == "pnb" ];
unset OMPI_FC
export WITHALACRITY="--with-alacrity=/opt/alacrity/clang"
export WITHFASTBIT="--with-fastbit=/opt/fastbit"
+ export WITHDATASPACES="--with-dataspaces=/opt/dataspaces --without-dimes"
+ export WITHFLEXPATH="--with-flexpath=/opt/chaos"
+ #export WITHZFP="--with-zfp=/Users/pnb/scratch/zfp-0.5.0"
echo "Configure using clang"
# Problem: test/test_src/selection_api.F90 link will fail because
# gfortran is used which finds the gcc-5 libstdc++ library instead of the system libstdc++
@@ -747,6 +760,9 @@ elif [ `hostname | cut -c 1-4` == "dyn9" -o `hostname | cut -c 1-3` == "pnb" ];
--with-zlib \
${WITHALACRITY} \
${WITHFASTBIT} \
+ ${WITHZFP} \
+ ${WITHDATASPACES} \
+ ${WITHFLEXPATH} \
--with-phdf5=/usr/local
# --disable-mpi --disable-write --disable-fortran \
# --with-netcdf=/opt/netcdf \
@@ -853,7 +869,7 @@ elif [ `hostname | cut -c 1-9` == "PC0098504" ]; then
export CPPFLAGS="-DMPICH_IGNORE_CXX_SEEK"
export LDFLAGS="-lpthread"
export CFLAGS="-g -O0 -fPIC -Wno-int-to-pointer-cast -Wno-pointer-to-int-cast"
- ${SRCDIR}/configure --prefix=/opt/adios/1.10 \
+ ${SRCDIR}/configure --prefix=/opt/adios \
--enable-dependency-tracking \
--enable-timers \
--disable-timer-events
@@ -872,7 +888,7 @@ 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/1.10 \
+ ${SRCDIR}/configure --prefix=/opt/adios/1.11 \
--disable-maintainer-mode \
--enable-dependency-tracking \
--enable-timers \
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index c332765..0d797df 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,18 +1,32 @@
+set(EXTRA_OBJECTS "") # added to libraries that include read+write
+set(EXTRA_READ_OBJECTS "") # added to read-only libraries
# First build the mxml library in src/mxml before setting include directories for src/
# Those source files must find PROJECT_SOURCE_DIR/src/mxml/config.h first, then PROJECT_BIN/DIR/config.h
if (BUILD_MXML)
add_subdirectory(mxml)
set(MXML_BUILDDIR "mxml/mxml-2.9")
set(MXML_LIB=libmxml_a)
+ set(EXTRA_OBJECTS ${EXTRA_OBJECTS} $<TARGET_OBJECTS:mxml>)
endif(BUILD_MXML)
+# Build the zfp library in src/zfp
+if (BUILD_ZFP)
+ add_subdirectory(zfp)
+ set(ZFP_BUILDDIR "zfp/zfp-0.5.0")
+ set(ZFP_LIB=libzfp_a)
+ include_directories(${ZFP_INCLUDE_DIR})
+ set(EXTRA_OBJECTS ${EXTRA_OBJECTS} $<TARGET_OBJECTS:zfp>)
+ set(EXTRA_READ_OBJECTS ${EXTRA_READ_OBJECTS} $<TARGET_OBJECTS:zfp>)
+endif(BUILD_ZFP)
+
include_directories(${PROJECT_BINARY_DIR})
include_directories(${PROJECT_SOURCE_DIR}/src ${PROJECT_SOURCE_DIR}/src/core ${PROJECT_SOURCE_DIR}/src/core/transforms)
include_directories(${PROJECT_BINARY_DIR}/src ${PROJECT_BINARY_DIR}/src/public)
include_directories(${MXML_INCLUDE_DIR})
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")
@@ -53,7 +67,8 @@ set (transforms_common_HDRS core/adios_copyspec.h
core/transforms/adios_transforms_common.h
core/transforms/adios_transforms_hooks.h
core/transforms/adios_transforms_util.h
- core/adios_subvolume.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
@@ -73,7 +88,8 @@ set (transforms_common_SOURCES ${transforms_common_HDRS}
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/transforms/plugindetect/plugin_info_types.h
+ core/adios_transform_methods.c)
set (transforms_read_SOURCES ${transforms_read_HDRS}
core/transforms/adios_transforms_read.c
@@ -88,6 +104,7 @@ set (transforms_read_SOURCES ${transforms_read_HDRS}
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
core/transforms/plugindetect/detect_plugin_read_hook_decls.h
core/transforms/plugindetect/detect_plugin_read_hook_reg.h
@@ -106,6 +123,7 @@ set (transforms_write_SOURCES ${transforms_write_HDRS}
transforms/adios_transform_isobar_write.c
transforms/adios_transform_szip_write.c
transforms/adios_transform_zlib_write.c
+ transforms/adios_transform_zfp_write.c
${transforms_write_method_SOURCES})
#######Query source files
@@ -388,13 +406,8 @@ if(BUILD_WRITE)
endif(RESEARCH_TRANSPORTS)
# add library adios and adios_nompi
- if(BUILD_MXML)
- add_library(adios STATIC ${libadios_a_SOURCES} $<TARGET_OBJECTS:mxml>)
- add_library(adios_nompi STATIC ${libadios_nompi_a_SOURCES} $<TARGET_OBJECTS:mxml>)
- else(BUILD_MXML)
- add_library(adios STATIC ${libadios_a_SOURCES})
- add_library(adios_nompi STATIC ${libadios_nompi_a_SOURCES})
- endif(BUILD_MXML)
+ add_library(adios STATIC ${libadios_a_SOURCES} ${EXTRA_OBJECTS})
+ add_library(adios_nompi STATIC ${libadios_nompi_a_SOURCES} ${EXTRA_OBJECTS})
set_target_properties(adios PROPERTIES COMPILE_FLAGS "${libadios_a_CPPFLAGS} ${libadios_a_CFLAGS}")
set_target_properties(adios_nompi PROPERTIES COMPILE_FLAGS "${libadios_nompi_a_CPPFLAGS} ${libadios_nompi_a_CFLAGS}")
# message(STATUS "${libadios_a_CPPFLAGS}")
@@ -469,17 +482,10 @@ if(BUILD_WRITE)
# install(FILES ${nodist_include_HEADERS} DESTINATION ${includedir})
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
- if(BUILD_MXML)
- add_library(adiosf STATIC ${libadiosf_a_SOURCES} $<TARGET_OBJECTS:mxml>)
- add_library(adiosf_v1 STATIC ${libadiosf_v1_a_SOURCES} $<TARGET_OBJECTS:mxml>)
- add_library(adiosf_nompi STATIC ${libadiosf_nompi_a_SOURCES} $<TARGET_OBJECTS:mxml>)
- add_library(adiosf_nompi_v1 STATIC ${libadiosf_nompi_v1_a_SOURCES} $<TARGET_OBJECTS:mxml>)
- else(BUILD_MXML)
- add_library(adiosf STATIC ${libadiosf_a_SOURCES})
- add_library(adiosf_v1 STATIC ${libadiosf_v1_a_SOURCES})
- add_library(adiosf_nompi STATIC ${libadiosf_nompi_a_SOURCES})
- add_library(adiosf_nompi_v1 STATIC ${libadiosf_nompi_v1_a_SOURCES})
- endif(BUILD_MXML)
+ add_library(adiosf STATIC ${libadiosf_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}")
set_target_properties(adiosf_v1 PROPERTIES COMPILE_FLAGS "${libadiosf_v1_a_CPPFLAGS} ${libadiosf_v1_a_CFLAGS}")
set_target_properties(adiosf_nompi PROPERTIES COMPILE_FLAGS "${libadiosf_nompi_a_CPPFLAGS} ${libadiosf_nompi_a_CFLAGS}")
@@ -506,7 +512,8 @@ set(include_HEADERS ${include_HEADERS} public/adios.h
public/adios_schema.h
public/adios_link.h
public/adios_read_ext.h
- public/adios_query.h)
+ public/adios_query.h
+ public/adios_transform_methods.h)
set(libadiosread_a_SOURCES core/adios_bp_v1.c
core/adios_endianness.c
@@ -573,7 +580,7 @@ set(libadiosread_a_CPPFLAGS "${libadiosread_a_CPPFLAGS} ${ADIOSLIB_EXTRA_CPPFLAG
install(FILES ${include_HEADERS} DESTINATION ${includedir})
# install generated header file adios_version.h
install(FILES ${PROJECT_BINARY_DIR}/src/public/adios_version.h DESTINATION ${includedir})
-add_library(adiosread STATIC ${libadiosread_a_SOURCES})
+add_library(adiosread STATIC ${libadiosread_a_SOURCES} ${EXTRA_READ_OBJECTS})
set_target_properties(adiosread PROPERTIES COMPILE_FLAGS "${libadiosread_a_CPPFLAGS} ${libadiosread_a_CFLAGS}")
#start libadiosreadf.a libadiosreadf_v1.a
@@ -683,13 +690,13 @@ if(BUILD_FORTRAN)
#add library adiosreadf and adiosreadf_v1
#include_directories(${nodist_include_HEADERS})
# install(FILES ${nodist_include_HEADERS} DESTINATION ${includedir})
- install(FILES ${PROJECT_BINARY_DIR}/src/adios_read_mod.mod DESTINATION ${includedir})
- add_library(adiosreadf ${libadiosreadf_a_SOURCES})
+ 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})
+ add_library(adiosreadf_v1 ${libadiosreadf_v1_a_SOURCES} ${EXTRA_READ_OBJECTS})
set_target_properties(adiosreadf_v1 PROPERTIES COMPILE_FLAGS "${libadiosreadf_v1_a_CPPFLAGS} ${libadiosreadf_v1_a_CFLAGS}")
endif(BUILD_FORTRAN)
@@ -758,7 +765,7 @@ endif(HAVE_NSSI)
set(libadiosread_nompi_a_CPPFLAGS "${libadiosread_nompi_a_CPPFLAGS} ${MACRODEFFLAG}_NOMPI ${ADIOSLIB_EXTRA_CPPFLAGS} ${ADIOSREADLIB_CPPFLAGS}")
#add library adiosread_nompi
-add_library(adiosread_nompi ${libadiosread_nompi_a_SOURCES})
+add_library(adiosread_nompi ${libadiosread_nompi_a_SOURCES} ${EXTRA_READ_OBJECTS})
set_target_properties(adiosread_nompi PROPERTIES COMPILE_FLAGS "${libadiosread_nompi_a_CPPFLAGS} ${libadiosread_nompi_a_CFLAGS}")
@@ -822,10 +829,10 @@ if(BUILD_FORTRAN)
set(libadiosreadf_nompi_v1_a_CFLAGS "${libadiosreadf_nompi_a_CFLAGS}")
#add library adiosreadf_nompi and adiosreadf_nompi_v1
- add_library(adiosreadf_nompi ${libadiosreadf_nompi_a_SOURCES})
+ add_library(adiosreadf_nompi ${libadiosreadf_nompi_a_SOURCES} ${EXTRA_READ_OBJECTS})
set_target_properties(adiosreadf_nompi PROPERTIES COMPILE_FLAGS "${libadiosreadf_nompi_a_CPPFLAGS} ${libadiosreadf_nompi_a_CFLAGS}")
- add_library(adiosreadf_nompi_v1 ${libadiosreadf_nompi_v1_a_SOURCES})
+ add_library(adiosreadf_nompi_v1 ${libadiosreadf_nompi_v1_a_SOURCES} ${EXTRA_READ_OBJECTS})
set_target_properties(adiosreadf_nompi_v1 PROPERTIES COMPILE_FLAGS "${libadiosreadf_nompi_v1_a_CPPFLAGS} ${libadiosreadf_nompi_v1_a_CFLAGS}")
endif(BUILD_FORTRAN)
@@ -859,11 +866,7 @@ endif(BUILD_WRITE)
set(libadios_internal_nompi_a_CPPFLAGS "${MACRODEFFLAG}_INTERNAL ${ADIOSLIB_EXTRA_CPPFLAGS} ${ADIOSLIB_INT_CPPFLAGS} ${ADIOSLIB_CPPFLAGS}")
-if(BUILD_MXML)
- add_library(adios_internal_nompi ${libadios_internal_nompi_a_SOURCES} $<TARGET_OBJECTS:mxml>)
-else(BUILD_MXML)
- add_library(adios_internal_nompi ${libadios_internal_nompi_a_SOURCES})
-endif(BUILD_MXML)
+add_library(adios_internal_nompi ${libadios_internal_nompi_a_SOURCES} ${EXTRA_OBJECTS})
set_target_properties(adios_internal_nompi PROPERTIES COMPILE_FLAGS "${libadios_internal_nompi_a_CPPFLAGS}")
add_subdirectory(core)
diff --git a/src/Makefile.am b/src/Makefile.am
index d1bc164..192bf82 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,10 +1,14 @@
AM_CPPFLAGS=-I$(top_builddir)/src/public -I$(top_srcdir) -I$(top_srcdir)/src/core -I$(top_srcdir)/src/core/transforms -I$(top_srcdir)/src/core/query
+AUTOMAKE_OPTIONS = no-dependencies subdir-objects
+METASOURCES=AUTO
+SUBDIRS=
+
if BUILD_MXML
-SUBDIRS = mxml
-MXML_BUILDDIR=mxml/mxml-2.9
-MXML_LIB=libmxml_a
-MXML_OBJECTS = ${MXML_BUILDDIR}/${MXML_LIB}-mxml-attr.${OBJEXT} \
+ SUBDIRS += mxml
+ MXML_BUILDDIR=mxml/mxml-2.9
+ MXML_LIB=libmxml_a
+ MXML_OBJECTS = ${MXML_BUILDDIR}/${MXML_LIB}-mxml-attr.${OBJEXT} \
${MXML_BUILDDIR}/${MXML_LIB}-mxml-get.${OBJEXT} \
${MXML_BUILDDIR}/${MXML_LIB}-mxml-private.${OBJEXT} \
${MXML_BUILDDIR}/${MXML_LIB}-mxml-string.${OBJEXT} \
@@ -16,8 +20,25 @@ MXML_OBJECTS = ${MXML_BUILDDIR}/${MXML_LIB}-mxml-attr.${OBJEXT} \
${MXML_BUILDDIR}/${MXML_LIB}-mxml-set.${OBJEXT}
endif BUILD_MXML
-AUTOMAKE_OPTIONS = no-dependencies subdir-objects
-METASOURCES=AUTO
+if BUILD_ZFP
+ SUBDIRS += zfp
+ ZFP_BUILDDIR=zfp/zfp-0.5.0/src
+ ZFP_LIB=libzfp_a
+ ZFP_OBJECTS = ${ZFP_BUILDDIR}/${ZFP_LIB}-bitstream.${OBJEXT} \
+ ${ZFP_BUILDDIR}/${ZFP_LIB}-decode1f.${OBJEXT} \
+ ${ZFP_BUILDDIR}/${ZFP_LIB}-decode1d.${OBJEXT} \
+ ${ZFP_BUILDDIR}/${ZFP_LIB}-encode1f.${OBJEXT} \
+ ${ZFP_BUILDDIR}/${ZFP_LIB}-encode1d.${OBJEXT} \
+ ${ZFP_BUILDDIR}/${ZFP_LIB}-decode2f.${OBJEXT} \
+ ${ZFP_BUILDDIR}/${ZFP_LIB}-decode2d.${OBJEXT} \
+ ${ZFP_BUILDDIR}/${ZFP_LIB}-encode2f.${OBJEXT} \
+ ${ZFP_BUILDDIR}/${ZFP_LIB}-encode2d.${OBJEXT} \
+ ${ZFP_BUILDDIR}/${ZFP_LIB}-decode3f.${OBJEXT} \
+ ${ZFP_BUILDDIR}/${ZFP_LIB}-decode3d.${OBJEXT} \
+ ${ZFP_BUILDDIR}/${ZFP_LIB}-encode3f.${OBJEXT} \
+ ${ZFP_BUILDDIR}/${ZFP_LIB}-encode3d.${OBJEXT} \
+ ${ZFP_BUILDDIR}/${ZFP_LIB}-zfp.${OBJEXT}
+endif BUILD_ZFP
bin_PROGRAMS=
#if HAVE_NSSI
@@ -155,6 +176,7 @@ libcoreonce_a_SOURCES = core/a2sel.c \
core/qhashtbl.c \
core/strutil.c \
core/util.c \
+ core/adios_transform_methods.c \
$(transforms_common_SOURCES) \
$(transforms_write_SOURCES) \
$(transforms_read_SOURCES)
@@ -344,6 +366,9 @@ libadios_nompi_a_LIBADD = $(libcoreonce_a_OBJECTS)
if BUILD_MXML
libadios_nompi_a_LIBADD += ${MXML_OBJECTS}
endif
+if BUILD_ZFP
+libadios_nompi_a_LIBADD += ${ZFP_OBJECTS}
+endif BUILD_ZFP
# force building the noinst_LIBRARIES first, before libadios_nompi.a
EXTRA_libadios_nompi_a_DEPENDENCIES = libcoreonce.a
if !RESEARCH_TRANSPORTS
@@ -374,6 +399,10 @@ if BUILD_MXML
libadiosf_nompi_a_LIBADD += ${MXML_OBJECTS}
libadiosf_nompi_v1_a_LIBADD += ${MXML_OBJECTS}
endif
+if BUILD_ZFP
+libadiosf_nompi_a_LIBADD += ${ZFP_OBJECTS}
+libadiosf_nompi_v1_a_LIBADD += ${ZFP_OBJECTS}
+endif BUILD_ZFP
EXTRA_libadiosf_nompi_a_DEPENDENCIES = libcoreonce.a
EXTRA_libadiosf_nompi_v1_a_DEPENDENCIES = libcoreonce.a
if !RESEARCH_TRANSPORTS
@@ -405,6 +434,9 @@ libadios_a_LIBADD = $(libcoreonce_a_OBJECTS)
if BUILD_MXML
libadios_a_LIBADD += ${MXML_OBJECTS}
endif
+if BUILD_ZFP
+libadios_a_LIBADD += ${ZFP_OBJECTS}
+endif BUILD_ZFP
# force building the noinst_LIBRARIES first, before libadios.a
EXTRA_libadios_a_DEPENDENCIES = libcoreonce.a
@@ -437,6 +469,10 @@ if BUILD_MXML
libadiosf_a_LIBADD += ${MXML_OBJECTS}
libadiosf_v1_a_LIBADD += ${MXML_OBJECTS}
endif
+if BUILD_ZFP
+libadiosf_a_LIBADD += ${ZFP_OBJECTS}
+libadiosf_v1_a_LIBADD += ${ZFP_OBJECTS}
+endif BUILD_ZFP
EXTRA_libadiosf_a_DEPENDENCIES = libcoreonce.a
EXTRA_libadiosf_v1_a_DEPENDENCIES = libcoreonce.a
@@ -521,6 +557,9 @@ libadiosread_nompi_a_CPPFLAGS += $(MACRODEFFLAG)DMALLOC
endif
libadiosread_nompi_a_CPPFLAGS += $(MACRODEFFLAG)_NOMPI $(ADIOSLIB_EXTRA_CPPFLAGS) $(ADIOSREADLIB_CPPFLAGS)
libadiosread_nompi_a_LIBADD = $(libcoreonce_a_OBJECTS)
+if BUILD_ZFP
+libadiosread_nompi_a_LIBADD += ${ZFP_OBJECTS}
+endif BUILD_ZFP
EXTRA_libadiosread_nompi_a_DEPENDENCIES = libcoreonce.a
if BUILD_FORTRAN
@@ -571,6 +610,10 @@ libadiosreadf_nompi_a_SOURCES += core/adiosf_defs_mod.f90 \
query/adios_query_mod.f90
libadiosreadf_nompi_a_LIBADD = $(libcoreonce_a_OBJECTS)
libadiosreadf_nompi_v1_a_LIBADD = $(libcoreonce_a_OBJECTS)
+if BUILD_ZFP
+libadiosreadf_nompi_a_LIBADD += ${ZFP_OBJECTS}
+libadiosreadf_nompi_v1_a_LIBADD += ${ZFP_OBJECTS}
+endif BUILD_ZFP
EXTRA_libadiosreadf_nompi_a_DEPENDENCIES = libcoreonce.a
EXTRA_libadiosreadf_nompi_v1_a_DEPENDENCIES = libcoreonce.a
@@ -636,6 +679,9 @@ endif
libadiosread_a_CPPFLAGS += $(ADIOSLIB_EXTRA_CPPFLAGS) $(ADIOSREADLIB_CPPFLAGS)
libadiosread_a_LIBADD = $(libcoreonce_a_OBJECTS)
+if BUILD_ZFP
+libadiosread_a_LIBADD += ${ZFP_OBJECTS}
+endif BUILD_ZFP
EXTRA_libadiosread_a_DEPENDENCIES = libcoreonce.a
if BUILD_FORTRAN
@@ -688,6 +734,10 @@ libadiosreadf_a_SOURCES += core/adiosf_defs_mod.f90 \
libadiosreadf_a_LIBADD = $(libcoreonce_a_OBJECTS)
libadiosreadf_v1_a_LIBADD = $(libcoreonce_a_OBJECTS)
+if BUILD_ZFP
+libadiosreadf_a_LIBADD += ${ZFP_OBJECTS}
+libadiosreadf_v1_a_LIBADD += ${ZFP_OBJECTS}
+endif BUILD_ZFP
EXTRA_libadiosreadf_a_DEPENDENCIES = libcoreonce.a
EXTRA_libadiosreadf_v1_a_DEPENDENCIES = libcoreonce.a
@@ -724,6 +774,9 @@ if BUILD_MXML
libadios_internal_nompi_a_LIBADD += ${MXML_OBJECTS}
endif
endif
+if BUILD_ZFP
+libadios_internal_nompi_a_LIBADD += ${ZFP_OBJECTS}
+endif BUILD_ZFP
EXTRA_libadios_internal_nompi_a_DEPENDENCIES = libcoreonce.a
@@ -770,7 +823,8 @@ include_HEADERS += public/adios.h \
public/adios_schema.h \
public/adios_link.h \
public/adios_read_ext.h \
- public/adios_query.h
+ public/adios_query.h \
+ public/adios_transform_methods.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 \
@@ -787,6 +841,7 @@ EXTRA_DIST = core/adios_bp_v1.h core/adios_endianness.h \
transforms/adios_transform_identity_read.h \
transforms/adios_transform_szip.h \
transforms/adios_transform_alacrity_common.h \
+ transforms/adios_transform_zfp_common.h \
transforms/adios_transform_template_read.c \
transforms/adios_transform_template_write.c \
query/Makefile.plugins.cmake
diff --git a/src/Makefile.in b/src/Makefile.in
index a6f14f5..0654f85 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -80,29 +80,31 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
+ at BUILD_MXML_TRUE@am__append_1 = mxml
+ at BUILD_ZFP_TRUE@am__append_2 = zfp
bin_PROGRAMS =
DIST_COMMON = $(srcdir)/transforms/Makefile.plugins \
$(srcdir)/query/Makefile.plugins $(srcdir)/Makefile.in \
$(srcdir)/Makefile.am $(include_HEADERS)
- at HAVE_FASTBIT_TRUE@am__append_1 = query/query_fastbit.c \
+ at HAVE_FASTBIT_TRUE@am__append_3 = query/query_fastbit.c \
@HAVE_FASTBIT_TRUE@ query/fastbit_adios.c
- at HAVE_FASTBIT_TRUE@am__append_2 = query/fastbit_adios.h
- at HAVE_ALACRITY_TRUE@am__append_3 = query/query_alac.c
- at BUILD_WRITE_TRUE@@HAVE_FLEXPATH_TRUE at am__append_4 = write/adios_flexpath.c read/read_flexpath.c
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_FLEXPATH_TRUE at am__append_5 = write/adios_flexpath.c read/read_flexpath.c
- at BUILD_WRITE_TRUE@@HAVE_ICEE_TRUE at am__append_6 = write/adios_icee.c read/read_icee.c
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_ICEE_TRUE at am__append_7 = write/adios_icee.c read/read_icee.c
- at BUILD_WRITE_TRUE@@HAVE_BGQ_TRUE at am__append_8 = write/adios_mpi_bgq.c
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_BGQ_TRUE at am__append_9 = write/adios_mpi_bgq.c
- at BUILD_WRITE_TRUE@@HAVE_DATASPACES_TRUE at am__append_10 = write/adios_dataspaces.c read/read_dataspaces.c
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_DATASPACES_TRUE at am__append_11 = write/adios_dataspaces.c read/read_dataspaces.c
- at BUILD_WRITE_TRUE@@HAVE_DIMES_TRUE at am__append_12 = write/adios_dimes.c read/read_dimes.c
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_DIMES_TRUE at am__append_13 = write/adios_dimes.c read/read_dimes.c
- at BUILD_WRITE_TRUE@@HAVE_PHDF5_TRUE at am__append_14 = write/adios_phdf5.c
- at BUILD_WRITE_TRUE@@HAVE_PHDF5_TRUE at am__append_15 = $(MACRODEFFLAG)PHDF5 $(MACRODEFFLAG)H5_USE_16_API
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_PHDF5_TRUE at am__append_16 = write/adios_phdf5.c
- at BUILD_WRITE_TRUE@@HAVE_NC4PAR_TRUE at am__append_17 = write/adios_nc4.c
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_NC4PAR_TRUE at am__append_18 = write/adios_nc4.c
+ at HAVE_FASTBIT_TRUE@am__append_4 = query/fastbit_adios.h
+ at HAVE_ALACRITY_TRUE@am__append_5 = query/query_alac.c
+ at BUILD_WRITE_TRUE@@HAVE_FLEXPATH_TRUE at am__append_6 = write/adios_flexpath.c read/read_flexpath.c
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_FLEXPATH_TRUE at am__append_7 = write/adios_flexpath.c read/read_flexpath.c
+ at BUILD_WRITE_TRUE@@HAVE_ICEE_TRUE at am__append_8 = write/adios_icee.c read/read_icee.c
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_ICEE_TRUE at am__append_9 = write/adios_icee.c read/read_icee.c
+ at BUILD_WRITE_TRUE@@HAVE_BGQ_TRUE at am__append_10 = write/adios_mpi_bgq.c
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_BGQ_TRUE at am__append_11 = write/adios_mpi_bgq.c
+ at BUILD_WRITE_TRUE@@HAVE_DATASPACES_TRUE at am__append_12 = write/adios_dataspaces.c read/read_dataspaces.c
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_DATASPACES_TRUE at am__append_13 = write/adios_dataspaces.c read/read_dataspaces.c
+ at BUILD_WRITE_TRUE@@HAVE_DIMES_TRUE at am__append_14 = write/adios_dimes.c read/read_dimes.c
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_DIMES_TRUE at am__append_15 = write/adios_dimes.c read/read_dimes.c
+ at BUILD_WRITE_TRUE@@HAVE_PHDF5_TRUE at am__append_16 = write/adios_phdf5.c
+ at BUILD_WRITE_TRUE@@HAVE_PHDF5_TRUE at am__append_17 = $(MACRODEFFLAG)PHDF5 $(MACRODEFFLAG)H5_USE_16_API
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_PHDF5_TRUE at am__append_18 = write/adios_phdf5.c
+ at BUILD_WRITE_TRUE@@HAVE_NC4PAR_TRUE at am__append_19 = write/adios_nc4.c
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_NC4PAR_TRUE at am__append_20 = write/adios_nc4.c
#if HAVE_DATATAP
#CLibSources += write/adios_datatap.c read/read_datatap.c
@@ -110,10 +112,10 @@ DIST_COMMON = $(srcdir)/transforms/Makefile.plugins \
#FortranLibSources += write/adios_datatap.c read/read_datatap.c
#endif
#endif
- at BUILD_WRITE_TRUE@@HAVE_FLEXPATH_TRUE at am__append_19 = write/adios_flexpath.c read/read_flexpath.c
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_FLEXPATH_TRUE at am__append_20 = write/adios_flexpath.c read/read_flexpath.c
- at BUILD_WRITE_TRUE@@HAVE_ICEE_TRUE at am__append_21 = write/adios_icee.c read/read_icee.c
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_ICEE_TRUE at am__append_22 = write/adios_icee.c read/read_icee.c
+ at BUILD_WRITE_TRUE@@HAVE_FLEXPATH_TRUE at am__append_21 = write/adios_flexpath.c read/read_flexpath.c
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_FLEXPATH_TRUE at am__append_22 = write/adios_flexpath.c read/read_flexpath.c
+ at BUILD_WRITE_TRUE@@HAVE_ICEE_TRUE at am__append_23 = write/adios_icee.c read/read_icee.c
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_ICEE_TRUE at am__append_24 = write/adios_icee.c read/read_icee.c
#if HAVE_NSSI
#dist_libadios_a_SOURCES = nssi/adios_nssi_args.x
@@ -156,17 +158,20 @@ DIST_COMMON = $(srcdir)/transforms/Makefile.plugins \
#
# Sequential C write library
#
- at BUILD_WRITE_TRUE@am__append_23 = libadios_nompi.a
- at BUILD_MXML_TRUE@@BUILD_WRITE_TRUE at am__append_24 = ${MXML_OBJECTS}
- at BUILD_WRITE_TRUE@@RESEARCH_TRANSPORTS_FALSE at am__append_25 = $(MACRODEFFLAG)NO_RESEARCH_TRANSPORTS
+ at BUILD_WRITE_TRUE@am__append_25 = libadios_nompi.a
+ at BUILD_MXML_TRUE@@BUILD_WRITE_TRUE at am__append_26 = ${MXML_OBJECTS}
+ at BUILD_WRITE_TRUE@@BUILD_ZFP_TRUE at am__append_27 = ${ZFP_OBJECTS}
+ at BUILD_WRITE_TRUE@@RESEARCH_TRANSPORTS_FALSE at am__append_28 = $(MACRODEFFLAG)NO_RESEARCH_TRANSPORTS
#
# Sequential Fortran write library
#
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE at am__append_26 = libadiosf_nompi.a libadiosf_nompi_v1.a
- at BUILD_FORTRAN_TRUE@@BUILD_MXML_TRUE@@BUILD_WRITE_TRUE at am__append_27 = ${MXML_OBJECTS}
- at BUILD_FORTRAN_TRUE@@BUILD_MXML_TRUE@@BUILD_WRITE_TRUE at am__append_28 = ${MXML_OBJECTS}
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@RESEARCH_TRANSPORTS_FALSE at am__append_29 = $(MACRODEFFLAG)NO_RESEARCH_TRANSPORTS
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE at am__append_29 = libadiosf_nompi.a libadiosf_nompi_v1.a
+ at BUILD_FORTRAN_TRUE@@BUILD_MXML_TRUE@@BUILD_WRITE_TRUE at am__append_30 = ${MXML_OBJECTS}
+ at BUILD_FORTRAN_TRUE@@BUILD_MXML_TRUE@@BUILD_WRITE_TRUE at am__append_31 = ${MXML_OBJECTS}
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@BUILD_ZFP_TRUE at am__append_32 = ${ZFP_OBJECTS}
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@BUILD_ZFP_TRUE at am__append_33 = ${ZFP_OBJECTS}
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@RESEARCH_TRANSPORTS_FALSE at am__append_34 = $(MACRODEFFLAG)NO_RESEARCH_TRANSPORTS
#
# Rules to build Parallel C+Fortran write libraries
@@ -175,20 +180,23 @@ DIST_COMMON = $(srcdir)/transforms/Makefile.plugins \
#
# Parallel C Write library
#
- at BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at am__append_30 = libadios.a
- at BUILD_MXML_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at am__append_31 = ${MXML_OBJECTS}
+ at BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at am__append_35 = libadios.a
+ at BUILD_MXML_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at am__append_36 = ${MXML_OBJECTS}
+ at BUILD_WRITE_TRUE@@BUILD_ZFP_TRUE@@HAVE_MPI_TRUE at am__append_37 = ${ZFP_OBJECTS}
#
# Parallel Fortran Write library
#
# Build two different Fortran libraries, for the two read APIs
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at am__append_32 = libadiosf.a libadiosf_v1.a
- at BUILD_FORTRAN_TRUE@@BUILD_MXML_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at am__append_33 = ${MXML_OBJECTS}
- at BUILD_FORTRAN_TRUE@@BUILD_MXML_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at am__append_34 = ${MXML_OBJECTS}
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at am__append_38 = libadiosf.a libadiosf_v1.a
+ at BUILD_FORTRAN_TRUE@@BUILD_MXML_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at am__append_39 = ${MXML_OBJECTS}
+ at BUILD_FORTRAN_TRUE@@BUILD_MXML_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at am__append_40 = ${MXML_OBJECTS}
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@BUILD_ZFP_TRUE@@HAVE_MPI_TRUE at am__append_41 = ${ZFP_OBJECTS}
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@BUILD_ZFP_TRUE@@HAVE_MPI_TRUE at am__append_42 = ${ZFP_OBJECTS}
#nodist_libadiosreadf_a_SOURCES += adios_write.mod
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at am__append_35 = adios_write_mod.mod
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at am__append_36 = adios_write_mod.mod
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at am__append_43 = adios_write_mod.mod
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at am__append_44 = adios_write_mod.mod
#libadios_a_SOURCES += write/adios_mpi_stagger.c \
# write/adios_mpi_aggregate.c \
@@ -204,14 +212,14 @@ DIST_COMMON = $(srcdir)/transforms/Makefile.plugins \
# write/adios_mpi_stripe.c \
# write/adios_mpi_amr1.c \
# write/adios_adaptive.c
- at BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@@RESEARCH_TRANSPORTS_FALSE at am__append_37 = $(MACRODEFFLAG)NO_RESEARCH_TRANSPORTS
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@@RESEARCH_TRANSPORTS_FALSE at am__append_38 = $(MACRODEFFLAG)NO_RESEARCH_TRANSPORTS
+ at BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@@RESEARCH_TRANSPORTS_FALSE at am__append_45 = $(MACRODEFFLAG)NO_RESEARCH_TRANSPORTS
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@@RESEARCH_TRANSPORTS_FALSE at am__append_46 = $(MACRODEFFLAG)NO_RESEARCH_TRANSPORTS
#if HAVE_DATATAP
#libadiosread_nompi_a_SOURCES += read/read_datatap.c
#endif
- at HAVE_FLEXPATH_TRUE@am__append_39 = read/read_flexpath.c
- at HAVE_ICEE_TRUE@am__append_40 = read/read_icee.c
+ at HAVE_FLEXPATH_TRUE@am__append_47 = read/read_flexpath.c
+ at HAVE_ICEE_TRUE@am__append_48 = read/read_icee.c
#if HAVE_NSSI
#dist_libadiosread_nompi_a_SOURCES = nssi/adios_nssi_args.x
#nodist_libadiosread_nompi_a_SOURCES = adios_nssi_args.c adios_nssi_args.h
@@ -219,12 +227,13 @@ DIST_COMMON = $(srcdir)/transforms/Makefile.plugins \
#libadiosread_nompi_a_CPPFLAGS += $(MACRODEFFLAG)PTL_IFACE_CLIENT=CRAY_USER_NAL $(MACRODEFFLAG)PTL_IFACE_SERVER=CRAY_USER_NAL
#libadiosread_nompi_a_CFLAGS += $(ADIOSLIB_CFLAGS)
#endif
- at HAVE_DMALLOC_TRUE@am__append_41 = $(MACRODEFFLAG)DMALLOC
+ at HAVE_DMALLOC_TRUE@am__append_49 = $(MACRODEFFLAG)DMALLOC
+ at BUILD_ZFP_TRUE@am__append_50 = ${ZFP_OBJECTS}
#
# Sequential Fortran Read libraries
#
- at BUILD_FORTRAN_TRUE@am__append_42 = libadiosreadf_nompi.a libadiosreadf_nompi_v1.a
+ at BUILD_FORTRAN_TRUE@am__append_51 = libadiosreadf_nompi.a libadiosreadf_nompi_v1.a
#if HAVE_DATASPACES
#FortranReadSeqLibSource += read/read_dataspaces.c
#endif
@@ -234,8 +243,8 @@ DIST_COMMON = $(srcdir)/transforms/Makefile.plugins \
#if HAVE_DATATAP
#FortranReadSeqLibSource += read/read_datatap.c
#endif
- at BUILD_FORTRAN_TRUE@@HAVE_FLEXPATH_TRUE at am__append_43 = read/read_flexpath.c
- at BUILD_FORTRAN_TRUE@@HAVE_ICEE_TRUE at am__append_44 = read/read_icee.c
+ at BUILD_FORTRAN_TRUE@@HAVE_FLEXPATH_TRUE at am__append_52 = read/read_flexpath.c
+ at BUILD_FORTRAN_TRUE@@HAVE_ICEE_TRUE at am__append_53 = read/read_icee.c
#if HAVE_NSSI
#dist_libadiosreadf_nompi_a_SOURCES = nssi/adios_nssi_args.x
#nodist_libadiosreadf_nompi_a_SOURCES = adios_nssi_args.c adios_nssi_args.h
@@ -244,7 +253,9 @@ DIST_COMMON = $(srcdir)/transforms/Makefile.plugins \
#libadiosreadf_nompi_a_CPPFLAGS += $(ADIOSLIB_EXTRA_CPPFLAGS) $(ADIOSLIB_CPPFLAGS) # $(MACRODEFFLAG)USE_TIMERS
#libadiosreadf_nompi_a_CFLAGS += $(ADIOSLIB_CFLAGS)
#endif
- at BUILD_FORTRAN_TRUE@am__append_45 = $(MACRODEFFLAG)_NOMPI $(ADIOSLIB_EXTRA_CPPFLAGS) $(ADIOSREADLIB_CPPFLAGS)
+ at BUILD_FORTRAN_TRUE@am__append_54 = $(MACRODEFFLAG)_NOMPI $(ADIOSLIB_EXTRA_CPPFLAGS) $(ADIOSREADLIB_CPPFLAGS)
+ at BUILD_FORTRAN_TRUE@@BUILD_ZFP_TRUE at am__append_55 = ${ZFP_OBJECTS}
+ at BUILD_FORTRAN_TRUE@@BUILD_ZFP_TRUE at am__append_56 = ${ZFP_OBJECTS}
#
# Rules to build Parallel C+Fortran write libraries
@@ -253,14 +264,14 @@ DIST_COMMON = $(srcdir)/transforms/Makefile.plugins \
#
# Parallel C Read library
#
- at HAVE_MPI_TRUE@am__append_46 = libadiosread.a
- at HAVE_DATASPACES_TRUE@@HAVE_MPI_TRUE at am__append_47 = read/read_dataspaces.c
- at HAVE_DIMES_TRUE@@HAVE_MPI_TRUE at am__append_48 = read/read_dimes.c
+ at HAVE_MPI_TRUE@am__append_57 = libadiosread.a
+ at HAVE_DATASPACES_TRUE@@HAVE_MPI_TRUE at am__append_58 = read/read_dataspaces.c
+ at HAVE_DIMES_TRUE@@HAVE_MPI_TRUE at am__append_59 = read/read_dimes.c
#if HAVE_DATATAP
#libadiosread_a_SOURCES += read/read_datatap.c
#endif
- at HAVE_FLEXPATH_TRUE@@HAVE_MPI_TRUE at am__append_49 = read/read_flexpath.c
- at HAVE_ICEE_TRUE@@HAVE_MPI_TRUE at am__append_50 = read/read_icee.c
+ at HAVE_FLEXPATH_TRUE@@HAVE_MPI_TRUE at am__append_60 = read/read_flexpath.c
+ at HAVE_ICEE_TRUE@@HAVE_MPI_TRUE at am__append_61 = read/read_icee.c
#if HAVE_NSSI
#dist_libadiosread_a_SOURCES = nssi/adios_nssi_args.x
#nodist_libadiosread_a_SOURCES = adios_nssi_args.c adios_nssi_args.h
@@ -268,20 +279,21 @@ DIST_COMMON = $(srcdir)/transforms/Makefile.plugins \
#libadiosread_a_CPPFLAGS += $(MACRODEFFLAG)PTL_IFACE_CLIENT=CRAY_USER_NAL $(MACRODEFFLAG)PTL_IFACE_SERVER=CRAY_USER_NAL
#libadiosread_a_CFLAGS += $(ADIOSLIB_CFLAGS)
#endif
- at HAVE_DMALLOC_TRUE@@HAVE_MPI_TRUE at am__append_51 = $(MACRODEFFLAG)DMALLOC
- at HAVE_MPI_TRUE@am__append_52 = $(ADIOSLIB_EXTRA_CPPFLAGS) $(ADIOSREADLIB_CPPFLAGS)
+ at HAVE_DMALLOC_TRUE@@HAVE_MPI_TRUE at am__append_62 = $(MACRODEFFLAG)DMALLOC
+ at HAVE_MPI_TRUE@am__append_63 = $(ADIOSLIB_EXTRA_CPPFLAGS) $(ADIOSREADLIB_CPPFLAGS)
+ at BUILD_ZFP_TRUE@@HAVE_MPI_TRUE at am__append_64 = ${ZFP_OBJECTS}
#
# Parallel Fortran Read libraries
#
- at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at am__append_53 = libadiosreadf.a libadiosreadf_v1.a
- at BUILD_FORTRAN_TRUE@@HAVE_DATASPACES_TRUE@@HAVE_MPI_TRUE at am__append_54 = read/read_dataspaces.c
- at BUILD_FORTRAN_TRUE@@HAVE_DIMES_TRUE@@HAVE_MPI_TRUE at am__append_55 = read/read_dimes.c
+ at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at am__append_65 = libadiosreadf.a libadiosreadf_v1.a
+ at BUILD_FORTRAN_TRUE@@HAVE_DATASPACES_TRUE@@HAVE_MPI_TRUE at am__append_66 = read/read_dataspaces.c
+ at BUILD_FORTRAN_TRUE@@HAVE_DIMES_TRUE@@HAVE_MPI_TRUE at am__append_67 = read/read_dimes.c
#if HAVE_DATATAP
#FortranReadLibSource += read/read_datatap.c
#endif
- at BUILD_FORTRAN_TRUE@@HAVE_FLEXPATH_TRUE@@HAVE_MPI_TRUE at am__append_56 = read/read_flexpath.c
- at BUILD_FORTRAN_TRUE@@HAVE_ICEE_TRUE@@HAVE_MPI_TRUE at am__append_57 = read/read_icee.c
+ at BUILD_FORTRAN_TRUE@@HAVE_FLEXPATH_TRUE@@HAVE_MPI_TRUE at am__append_68 = read/read_flexpath.c
+ at BUILD_FORTRAN_TRUE@@HAVE_ICEE_TRUE@@HAVE_MPI_TRUE at am__append_69 = read/read_icee.c
#if HAVE_NSSI
#dist_libadiosreadf_a_SOURCES = nssi/adios_nssi_args.x
#nodist_libadiosreadf_a_SOURCES = adios_nssi_args.c adios_nssi_args.h
@@ -289,13 +301,16 @@ DIST_COMMON = $(srcdir)/transforms/Makefile.plugins \
#libadiosreadf_a_CPPFLAGS += $(MACRODEFFLAG)PTL_IFACE_CLIENT=CRAY_USER_NAL $(MACRODEFFLAG)PTL_IFACE_SERVER=CRAY_USER_NAL
#libadiosreadf_a_CFLAGS += $(ADIOSLIB_CFLAGS)
#endif
- at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at am__append_58 = $(ADIOSLIB_EXTRA_CPPFLAGS) $(ADIOSREADLIB_CPPFLAGS)
+ at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at am__append_70 = $(ADIOSLIB_EXTRA_CPPFLAGS) $(ADIOSREADLIB_CPPFLAGS)
+ at BUILD_FORTRAN_TRUE@@BUILD_ZFP_TRUE@@HAVE_MPI_TRUE at am__append_71 = ${ZFP_OBJECTS}
+ at BUILD_FORTRAN_TRUE@@BUILD_ZFP_TRUE@@HAVE_MPI_TRUE at am__append_72 = ${ZFP_OBJECTS}
#nodist_libadiosreadf_a_SOURCES += adios_read_mod.mod
- at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at am__append_59 = adios_read_mod.mod adios_defs_mod.mod adios_query_mod.mod
- at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at am__append_60 = adios_read_mod.mod adios_defs_mod.mod adios_query_mod.mod
- at BUILD_WRITE_TRUE@am__append_61 = core/adios_internals_mxml.c
- at BUILD_MXML_TRUE@@BUILD_WRITE_TRUE at am__append_62 = ${MXML_OBJECTS}
+ at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at am__append_73 = adios_read_mod.mod adios_defs_mod.mod adios_query_mod.mod
+ at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at am__append_74 = adios_read_mod.mod adios_defs_mod.mod adios_query_mod.mod
+ at BUILD_WRITE_TRUE@am__append_75 = core/adios_internals_mxml.c
+ at BUILD_MXML_TRUE@@BUILD_WRITE_TRUE at am__append_76 = ${MXML_OBJECTS}
+ at BUILD_ZFP_TRUE@am__append_77 = ${ZFP_OBJECTS}
subdir = src
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
@@ -325,7 +340,7 @@ 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_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 \
@@ -377,8 +392,10 @@ am__v_AR_0 = @echo " AR " $@;
am__v_AR_1 =
libadios_a_AR = $(AR) $(ARFLAGS)
@BUILD_MXML_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at am__DEPENDENCIES_1 = $(MXML_OBJECTS)
+ at BUILD_WRITE_TRUE@@BUILD_ZFP_TRUE@@HAVE_MPI_TRUE at am__DEPENDENCIES_2 = $(ZFP_OBJECTS)
@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at libadios_a_DEPENDENCIES = \
- at BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(am__DEPENDENCIES_1)
+ at BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(am__DEPENDENCIES_1) \
+ at BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(am__DEPENDENCIES_2)
am__libadios_a_SOURCES_DIST = core/adios.c core/common_adios.c \
core/adios_internals.c core/adios_internals_mxml.c \
query/common_query.h query/adios_query_hooks.h \
@@ -460,9 +477,11 @@ am__objects_8 = $(am__objects_7) \
@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(am__objects_17)
libadios_a_OBJECTS = $(am_libadios_a_OBJECTS)
libadios_internal_nompi_a_AR = $(AR) $(ARFLAGS)
- at BUILD_MXML_TRUE@@BUILD_WRITE_TRUE at am__DEPENDENCIES_2 = \
+ at BUILD_MXML_TRUE@@BUILD_WRITE_TRUE at am__DEPENDENCIES_3 = \
@BUILD_MXML_TRUE@@BUILD_WRITE_TRUE@ $(MXML_OBJECTS)
-libadios_internal_nompi_a_DEPENDENCIES = $(am__DEPENDENCIES_2)
+ at BUILD_ZFP_TRUE@am__DEPENDENCIES_4 = $(ZFP_OBJECTS)
+libadios_internal_nompi_a_DEPENDENCIES = $(am__DEPENDENCIES_3) \
+ $(am__DEPENDENCIES_4)
am__libadios_internal_nompi_a_SOURCES_DIST = core/mpidummy.c \
core/bp_utils.c core/adios_internals.c core/util_mpi.c \
query/common_query.h query/adios_query_hooks.h \
@@ -499,8 +518,9 @@ am_libadios_internal_nompi_a_OBJECTS = \
libadios_internal_nompi_a_OBJECTS = \
$(am_libadios_internal_nompi_a_OBJECTS)
libadios_nompi_a_AR = $(AR) $(ARFLAGS)
+ at BUILD_WRITE_TRUE@@BUILD_ZFP_TRUE at am__DEPENDENCIES_5 = $(ZFP_OBJECTS)
@BUILD_WRITE_TRUE at libadios_nompi_a_DEPENDENCIES = \
- at BUILD_WRITE_TRUE@ $(am__DEPENDENCIES_2)
+ at BUILD_WRITE_TRUE@ $(am__DEPENDENCIES_3) $(am__DEPENDENCIES_5)
am__libadios_nompi_a_SOURCES_DIST = core/adios.c core/common_adios.c \
core/adios_internals.c core/adios_internals_mxml.c \
query/common_query.h query/adios_query_hooks.h \
@@ -560,8 +580,10 @@ am__objects_30 = $(am__objects_29) \
@BUILD_WRITE_TRUE@ $(am__objects_34)
libadios_nompi_a_OBJECTS = $(am_libadios_nompi_a_OBJECTS)
libadiosf_a_AR = $(AR) $(ARFLAGS)
- at BUILD_FORTRAN_TRUE@@BUILD_MXML_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at am__DEPENDENCIES_3 = $(MXML_OBJECTS)
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at libadiosf_a_DEPENDENCIES = $(am__DEPENDENCIES_3)
+ at BUILD_FORTRAN_TRUE@@BUILD_MXML_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at am__DEPENDENCIES_6 = $(MXML_OBJECTS)
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@BUILD_ZFP_TRUE@@HAVE_MPI_TRUE at am__DEPENDENCIES_7 = $(ZFP_OBJECTS)
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at libadiosf_a_DEPENDENCIES = $(am__DEPENDENCIES_6) \
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(am__DEPENDENCIES_7)
am__libadiosf_a_SOURCES_DIST = core/adiosf.c core/common_adios.c \
core/adios_internals.c core/adios_internals_mxml.c \
query/common_query.h query/adios_query_hooks.h \
@@ -645,9 +667,11 @@ am__objects_40 = $(am__objects_39) \
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ query/adios_query_mod.$(OBJEXT)
libadiosf_a_OBJECTS = $(am_libadiosf_a_OBJECTS)
libadiosf_nompi_a_AR = $(AR) $(ARFLAGS)
- at BUILD_FORTRAN_TRUE@@BUILD_MXML_TRUE@@BUILD_WRITE_TRUE at am__DEPENDENCIES_4 = $(MXML_OBJECTS)
+ at BUILD_FORTRAN_TRUE@@BUILD_MXML_TRUE@@BUILD_WRITE_TRUE at am__DEPENDENCIES_8 = $(MXML_OBJECTS)
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@BUILD_ZFP_TRUE at am__DEPENDENCIES_9 = $(ZFP_OBJECTS)
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE at libadiosf_nompi_a_DEPENDENCIES = \
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@ $(am__DEPENDENCIES_4)
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@ $(am__DEPENDENCIES_8) \
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@ $(am__DEPENDENCIES_9)
am__libadiosf_nompi_a_SOURCES_DIST = core/adiosf.c core/common_adios.c \
core/adios_internals.c core/adios_internals_mxml.c \
query/common_query.h query/adios_query_hooks.h \
@@ -715,7 +739,8 @@ am__objects_55 = $(am__objects_54) \
libadiosf_nompi_a_OBJECTS = $(am_libadiosf_nompi_a_OBJECTS)
libadiosf_nompi_v1_a_AR = $(AR) $(ARFLAGS)
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE at libadiosf_nompi_v1_a_DEPENDENCIES = \
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@ $(am__DEPENDENCIES_4)
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@ $(am__DEPENDENCIES_8) \
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@ $(am__DEPENDENCIES_9)
am__libadiosf_nompi_v1_a_SOURCES_DIST = core/adiosf.c \
core/common_adios.c core/adios_internals.c \
core/adios_internals_mxml.c query/common_query.h \
@@ -779,7 +804,8 @@ am__objects_65 = $(am__objects_64) \
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@ core/adiosf_write_mod.$(OBJEXT)
libadiosf_nompi_v1_a_OBJECTS = $(am_libadiosf_nompi_v1_a_OBJECTS)
libadiosf_v1_a_AR = $(AR) $(ARFLAGS)
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at libadiosf_v1_a_DEPENDENCIES = $(am__DEPENDENCIES_3)
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at libadiosf_v1_a_DEPENDENCIES = $(am__DEPENDENCIES_6) \
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(am__DEPENDENCIES_7)
am__libadiosf_v1_a_SOURCES_DIST = core/adiosf.c core/common_adios.c \
core/adios_internals.c core/adios_internals_mxml.c \
query/common_query.h query/adios_query_hooks.h \
@@ -860,7 +886,8 @@ am__objects_75 = $(am__objects_74) \
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ core/adiosf_write_mod.$(OBJEXT)
libadiosf_v1_a_OBJECTS = $(am_libadiosf_v1_a_OBJECTS)
libadiosread_a_AR = $(AR) $(ARFLAGS)
-libadiosread_a_DEPENDENCIES =
+ at BUILD_ZFP_TRUE@@HAVE_MPI_TRUE at am__DEPENDENCIES_10 = $(ZFP_OBJECTS)
+ at HAVE_MPI_TRUE@libadiosread_a_DEPENDENCIES = $(am__DEPENDENCIES_10)
am__libadiosread_a_SOURCES_DIST = core/bp_utils.c core/adios_read.c \
core/adios_read_v1.c core/common_read.c core/adios_read_ext.c \
query/common_query.h query/adios_query_hooks.h \
@@ -906,7 +933,7 @@ am__objects_90 = $(am__objects_89) \
@HAVE_MPI_TRUE@ $(am__objects_93) $(am__objects_94)
libadiosread_a_OBJECTS = $(am_libadiosread_a_OBJECTS)
libadiosread_nompi_a_AR = $(AR) $(ARFLAGS)
-libadiosread_nompi_a_DEPENDENCIES =
+libadiosread_nompi_a_DEPENDENCIES = $(am__DEPENDENCIES_4)
am__libadiosread_nompi_a_SOURCES_DIST = core/mpidummy.c \
core/bp_utils.c core/adios_read.c core/adios_read_v1.c \
core/common_read.c core/adios_read_ext.c query/common_query.h \
@@ -947,7 +974,9 @@ am_libadiosread_nompi_a_OBJECTS = \
$(am__objects_102)
libadiosread_nompi_a_OBJECTS = $(am_libadiosread_nompi_a_OBJECTS)
libadiosreadf_a_AR = $(AR) $(ARFLAGS)
-libadiosreadf_a_DEPENDENCIES =
+ at BUILD_FORTRAN_TRUE@@BUILD_ZFP_TRUE@@HAVE_MPI_TRUE at am__DEPENDENCIES_11 = $(ZFP_OBJECTS)
+ at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at libadiosreadf_a_DEPENDENCIES = \
+ at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ $(am__DEPENDENCIES_11)
am__libadiosreadf_a_SOURCES_DIST = core/bp_utils.c core/common_read.c \
core/adios_read_ext.c query/common_query.h \
query/adios_query_hooks.h query/query_utils.h \
@@ -998,7 +1027,10 @@ am__objects_108 = $(am__objects_107) \
@BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ query/adios_query_mod.$(OBJEXT)
libadiosreadf_a_OBJECTS = $(am_libadiosreadf_a_OBJECTS)
libadiosreadf_nompi_a_AR = $(AR) $(ARFLAGS)
-libadiosreadf_nompi_a_DEPENDENCIES =
+ at BUILD_FORTRAN_TRUE@@BUILD_ZFP_TRUE at am__DEPENDENCIES_12 = \
+ at BUILD_FORTRAN_TRUE@@BUILD_ZFP_TRUE@ $(ZFP_OBJECTS)
+ at BUILD_FORTRAN_TRUE@libadiosreadf_nompi_a_DEPENDENCIES = \
+ at BUILD_FORTRAN_TRUE@ $(am__DEPENDENCIES_12)
am__libadiosreadf_nompi_a_SOURCES_DIST = core/mpidummy.c \
core/bp_utils.c core/common_read.c core/adios_read_ext.c \
query/common_query.h query/adios_query_hooks.h \
@@ -1042,7 +1074,8 @@ am__objects_119 = $(am__objects_118) \
@BUILD_FORTRAN_TRUE@ query/adios_query_mod.$(OBJEXT)
libadiosreadf_nompi_a_OBJECTS = $(am_libadiosreadf_nompi_a_OBJECTS)
libadiosreadf_nompi_v1_a_AR = $(AR) $(ARFLAGS)
-libadiosreadf_nompi_v1_a_DEPENDENCIES =
+ at BUILD_FORTRAN_TRUE@libadiosreadf_nompi_v1_a_DEPENDENCIES = \
+ at BUILD_FORTRAN_TRUE@ $(am__DEPENDENCIES_12)
am__libadiosreadf_nompi_v1_a_SOURCES_DIST = core/mpidummy.c \
core/bp_utils.c core/common_read.c core/adios_read_ext.c \
query/common_query.h query/adios_query_hooks.h \
@@ -1084,7 +1117,8 @@ am__objects_128 = $(am__objects_127) \
libadiosreadf_nompi_v1_a_OBJECTS = \
$(am_libadiosreadf_nompi_v1_a_OBJECTS)
libadiosreadf_v1_a_AR = $(AR) $(ARFLAGS)
-libadiosreadf_v1_a_DEPENDENCIES =
+ at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at libadiosreadf_v1_a_DEPENDENCIES = \
+ at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ $(am__DEPENDENCIES_11)
am__libadiosreadf_v1_a_SOURCES_DIST = core/bp_utils.c \
core/common_read.c core/adios_read_ext.c query/common_query.h \
query/adios_query_hooks.h query/query_utils.h \
@@ -1143,7 +1177,8 @@ am__objects_144 = transforms/libcoreonce_a-adios_transform_identity_write.$(OBJE
transforms/libcoreonce_a-adios_transform_szip_write.$(OBJEXT) \
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_alacrity_write.$(OBJEXT) \
+ transforms/libcoreonce_a-adios_transform_zfp_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) \
@@ -1156,7 +1191,8 @@ am__objects_146 = transforms/libcoreonce_a-adios_transform_identity_read.$(OBJEX
transforms/libcoreonce_a-adios_transform_szip_read.$(OBJEXT) \
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_alacrity_read.$(OBJEXT) \
+ transforms/libcoreonce_a-adios_transform_zfp_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) \
@@ -1178,8 +1214,9 @@ am_libcoreonce_a_OBJECTS = core/libcoreonce_a-a2sel.$(OBJEXT) \
core/libcoreonce_a-globals.$(OBJEXT) \
core/libcoreonce_a-qhashtbl.$(OBJEXT) \
core/libcoreonce_a-strutil.$(OBJEXT) \
- core/libcoreonce_a-util.$(OBJEXT) $(am__objects_143) \
- $(am__objects_145) $(am__objects_147)
+ core/libcoreonce_a-util.$(OBJEXT) \
+ core/libcoreonce_a-adios_transform_methods.$(OBJEXT) \
+ $(am__objects_143) $(am__objects_145) $(am__objects_147)
libcoreonce_a_OBJECTS = $(am_libcoreonce_a_OBJECTS)
PROGRAMS = $(bin_PROGRAMS)
AM_V_P = $(am__v_P_ at AM_V@)
@@ -1297,7 +1334,7 @@ am__define_uniq_tagged_files = \
done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
-DIST_SUBDIRS = mxml
+DIST_SUBDIRS = mxml zfp
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
am__relativize = \
dir0=`pwd`; \
@@ -1534,6 +1571,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
@@ -1596,7 +1636,9 @@ top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
AM_CPPFLAGS = -I$(top_builddir)/src/public -I$(top_srcdir) -I$(top_srcdir)/src/core -I$(top_srcdir)/src/core/transforms -I$(top_srcdir)/src/core/query
- at BUILD_MXML_TRUE@SUBDIRS = mxml
+AUTOMAKE_OPTIONS = no-dependencies subdir-objects
+METASOURCES = AUTO
+SUBDIRS = $(am__append_1) $(am__append_2)
@BUILD_MXML_TRUE at MXML_BUILDDIR = mxml/mxml-2.9
@BUILD_MXML_TRUE at MXML_LIB = libmxml_a
@BUILD_MXML_TRUE at MXML_OBJECTS = ${MXML_BUILDDIR}/${MXML_LIB}-mxml-attr.${OBJEXT} \
@@ -1610,8 +1652,23 @@ AM_CPPFLAGS = -I$(top_builddir)/src/public -I$(top_srcdir) -I$(top_srcdir)/src/c
@BUILD_MXML_TRUE@ ${MXML_BUILDDIR}/${MXML_LIB}-mxml-node.${OBJEXT} \
@BUILD_MXML_TRUE@ ${MXML_BUILDDIR}/${MXML_LIB}-mxml-set.${OBJEXT}
-AUTOMAKE_OPTIONS = no-dependencies subdir-objects
-METASOURCES = AUTO
+ at BUILD_ZFP_TRUE@ZFP_BUILDDIR = zfp/zfp-0.5.0/src
+ at BUILD_ZFP_TRUE@ZFP_LIB = libzfp_a
+ at BUILD_ZFP_TRUE@ZFP_OBJECTS = ${ZFP_BUILDDIR}/${ZFP_LIB}-bitstream.${OBJEXT} \
+ at BUILD_ZFP_TRUE@ ${ZFP_BUILDDIR}/${ZFP_LIB}-decode1f.${OBJEXT} \
+ at BUILD_ZFP_TRUE@ ${ZFP_BUILDDIR}/${ZFP_LIB}-decode1d.${OBJEXT} \
+ at BUILD_ZFP_TRUE@ ${ZFP_BUILDDIR}/${ZFP_LIB}-encode1f.${OBJEXT} \
+ at BUILD_ZFP_TRUE@ ${ZFP_BUILDDIR}/${ZFP_LIB}-encode1d.${OBJEXT} \
+ at BUILD_ZFP_TRUE@ ${ZFP_BUILDDIR}/${ZFP_LIB}-decode2f.${OBJEXT} \
+ at BUILD_ZFP_TRUE@ ${ZFP_BUILDDIR}/${ZFP_LIB}-decode2d.${OBJEXT} \
+ at BUILD_ZFP_TRUE@ ${ZFP_BUILDDIR}/${ZFP_LIB}-encode2f.${OBJEXT} \
+ at BUILD_ZFP_TRUE@ ${ZFP_BUILDDIR}/${ZFP_LIB}-encode2d.${OBJEXT} \
+ at BUILD_ZFP_TRUE@ ${ZFP_BUILDDIR}/${ZFP_LIB}-decode3f.${OBJEXT} \
+ at BUILD_ZFP_TRUE@ ${ZFP_BUILDDIR}/${ZFP_LIB}-decode3d.${OBJEXT} \
+ at BUILD_ZFP_TRUE@ ${ZFP_BUILDDIR}/${ZFP_LIB}-encode3f.${OBJEXT} \
+ at BUILD_ZFP_TRUE@ ${ZFP_BUILDDIR}/${ZFP_LIB}-encode3d.${OBJEXT} \
+ at BUILD_ZFP_TRUE@ ${ZFP_BUILDDIR}/${ZFP_LIB}-zfp.${OBJEXT}
+
#if HAVE_NSSI
#
#bin_PROGRAMS+=nssi-staging-server
@@ -1633,7 +1690,7 @@ METASOURCES = AUTO
#nssi_coupling_server_LDADD += $(ADIOSLIB_LDADD) $(NSSI_SERVER_LIBS)
#
#endif # HAVE_NSSI
-CLEANFILES = $(am__append_36) $(am__append_60)
+CLEANFILES = $(am__append_44) $(am__append_74)
#bin_PROGRAMS+=adios_flags
#nodist_adios_flags_SOURCES = adios_flags.h
@@ -1659,8 +1716,9 @@ include_HEADERS = public/adios.h public/adios_version.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
-nodist_include_HEADERS = $(am__append_35) $(am__append_59)
+ public/adios_read_ext.h public/adios_query.h \
+ public/adios_transform_methods.h
+nodist_include_HEADERS = $(am__append_43) $(am__append_73)
# End of building Parallel Write libs
@@ -1677,17 +1735,17 @@ nodist_include_HEADERS = $(am__append_35) $(am__append_59)
#
# Sequential C Read library
#
-lib_LIBRARIES = $(am__append_23) $(am__append_26) $(am__append_30) \
- $(am__append_32) libadiosread_nompi.a $(am__append_42) \
- $(am__append_46) $(am__append_53)
-EXTRA_DEPENDENCY_CPPFLAGS = $(am__append_15)
-libadiosread_a_CPPFLAGS = $(AM_CPPFLAGS) $(am__append_51) \
- $(am__append_52)
-libadiosreadf_a_CPPFLAGS = $(AM_CPPFLAGS) $(am__append_58)
-libadiosread_nompi_a_CPPFLAGS = $(AM_CPPFLAGS) $(am__append_41) \
+lib_LIBRARIES = $(am__append_25) $(am__append_29) $(am__append_35) \
+ $(am__append_38) libadiosread_nompi.a $(am__append_51) \
+ $(am__append_57) $(am__append_65)
+EXTRA_DEPENDENCY_CPPFLAGS = $(am__append_17)
+libadiosread_a_CPPFLAGS = $(AM_CPPFLAGS) $(am__append_62) \
+ $(am__append_63)
+libadiosreadf_a_CPPFLAGS = $(AM_CPPFLAGS) $(am__append_70)
+libadiosread_nompi_a_CPPFLAGS = $(AM_CPPFLAGS) $(am__append_49) \
$(MACRODEFFLAG)_NOMPI $(ADIOSLIB_EXTRA_CPPFLAGS) \
$(ADIOSREADLIB_CPPFLAGS)
-libadiosreadf_nompi_a_CPPFLAGS = $(AM_CPPFLAGS) $(am__append_45)
+libadiosreadf_nompi_a_CPPFLAGS = $(AM_CPPFLAGS) $(am__append_54)
libadiosread_a_CFLAGS =
libadiosreadf_a_CFLAGS =
libadiosread_nompi_a_CFLAGS =
@@ -1706,6 +1764,8 @@ libadiosreadf_nompi_a_CFLAGS =
# APLOD plugin:
# ALACRITY plugin:
+
+# zfp plugin:
transforms_write_method_SOURCES = \
transforms/adios_transform_identity_write.c \
transforms/adios_transform_zlib_write.c \
@@ -1713,7 +1773,8 @@ transforms_write_method_SOURCES = \
transforms/adios_transform_szip_write.c \
transforms/adios_transform_isobar_write.c \
transforms/adios_transform_aplod_write.c \
- transforms/adios_transform_alacrity_write.c
+ transforms/adios_transform_alacrity_write.c \
+ transforms/adios_transform_zfp_write.c
transforms_read_method_SOURCES = \
transforms/adios_transform_identity_read.c \
transforms/adios_transform_zlib_read.c \
@@ -1721,7 +1782,8 @@ transforms_read_method_SOURCES = \
transforms/adios_transform_szip_read.c \
transforms/adios_transform_isobar_read.c \
transforms/adios_transform_aplod_read.c \
- transforms/adios_transform_alacrity_read.c
+ transforms/adios_transform_alacrity_read.c \
+ transforms/adios_transform_zfp_read.c
transforms_common_HDRS = core/adios_copyspec.h \
core/adios_subvolume.h \
core/adios_selection_util.h \
@@ -1780,9 +1842,9 @@ query_common_SOURCES = $(query_common_HDRS) \
# Include source files that are specific to each query plugin
-query_method_HDRS = $(am__append_2)
-query_method_SOURCES = query/query_minmax.c $(am__append_1) \
- $(am__append_3) $(query_method_HDRS)
+query_method_HDRS = $(am__append_4)
+query_method_SOURCES = query/query_minmax.c $(am__append_3) \
+ $(am__append_5) $(query_method_HDRS)
query_SOURCES = $(query_common_SOURCES) \
$(query_method_SOURCES)
@@ -1814,6 +1876,7 @@ libcoreonce_a_SOURCES = core/a2sel.c \
core/qhashtbl.c \
core/strutil.c \
core/util.c \
+ core/adios_transform_methods.c \
$(transforms_common_SOURCES) \
$(transforms_write_SOURCES) \
$(transforms_read_SOURCES)
@@ -1834,14 +1897,14 @@ libcoreonce_a_CFLAGS = $(ADIOSLIB_CFLAGS)
@BUILD_WRITE_TRUE@ core/adios_transport_hooks.c core/util_mpi.c \
@BUILD_WRITE_TRUE@ read/read_bp.c read/read_bp_staged.c \
@BUILD_WRITE_TRUE@ read/read_bp_staged1.c write/adios_posix.c \
- at BUILD_WRITE_TRUE@ $(am__append_4) $(am__append_6) \
- at BUILD_WRITE_TRUE@ $(am__append_19) $(am__append_21)
+ at BUILD_WRITE_TRUE@ $(am__append_6) $(am__append_8) \
+ at BUILD_WRITE_TRUE@ $(am__append_21) $(am__append_23)
@BUILD_WRITE_TRUE at CLibParallelSources = write/adios_mpi.c \
@BUILD_WRITE_TRUE@ write/adios_mpi_lustre.c \
@BUILD_WRITE_TRUE@ write/adios_mpi_amr.c \
- at BUILD_WRITE_TRUE@ write/adios_var_merge.c $(am__append_8) \
- at BUILD_WRITE_TRUE@ $(am__append_10) $(am__append_12) \
- at BUILD_WRITE_TRUE@ $(am__append_14) $(am__append_17)
+ at BUILD_WRITE_TRUE@ write/adios_var_merge.c $(am__append_10) \
+ at BUILD_WRITE_TRUE@ $(am__append_12) $(am__append_14) \
+ at BUILD_WRITE_TRUE@ $(am__append_16) $(am__append_19)
@BUILD_WRITE_TRUE at CLibSEQSources = core/mpidummy.c
@BUILD_WRITE_TRUE at FortranLibSources = core/adiosf.c \
@BUILD_WRITE_TRUE@ core/common_adios.c core/adios_internals.c \
@@ -1853,23 +1916,23 @@ libcoreonce_a_CFLAGS = $(ADIOSLIB_CFLAGS)
@BUILD_WRITE_TRUE@ core/adios_transport_hooks.c core/util_mpi.c \
@BUILD_WRITE_TRUE@ read/read_bp.c read/read_bp_staged.c \
@BUILD_WRITE_TRUE@ read/read_bp_staged1.c write/adios_posix.c \
- at BUILD_WRITE_TRUE@ $(am__append_5) $(am__append_7) \
- at BUILD_WRITE_TRUE@ $(am__append_20) $(am__append_22)
+ at BUILD_WRITE_TRUE@ $(am__append_7) $(am__append_9) \
+ at BUILD_WRITE_TRUE@ $(am__append_22) $(am__append_24)
@BUILD_WRITE_TRUE at FortranLibParallelSources = write/adios_mpi.c \
@BUILD_WRITE_TRUE@ write/adios_mpi_lustre.c \
@BUILD_WRITE_TRUE@ write/adios_mpi_amr.c \
- at BUILD_WRITE_TRUE@ write/adios_var_merge.c $(am__append_9) \
- at BUILD_WRITE_TRUE@ $(am__append_11) $(am__append_13) \
- at BUILD_WRITE_TRUE@ $(am__append_16) $(am__append_18)
+ at BUILD_WRITE_TRUE@ write/adios_var_merge.c $(am__append_11) \
+ at BUILD_WRITE_TRUE@ $(am__append_13) $(am__append_15) \
+ at BUILD_WRITE_TRUE@ $(am__append_18) $(am__append_20)
@BUILD_WRITE_TRUE at FortranLibSEQSources = core/mpidummy.c
@BUILD_WRITE_TRUE at libadios_nompi_a_SOURCES = $(CLibSources) $(CLibSEQSources)
@BUILD_WRITE_TRUE at libadios_nompi_a_CPPFLAGS = $(AM_CPPFLAGS) \
@BUILD_WRITE_TRUE@ $(MACRODEFFLAG)_NOMPI \
@BUILD_WRITE_TRUE@ $(ADIOSLIB_EXTRA_CPPFLAGS) \
- at BUILD_WRITE_TRUE@ $(ADIOSLIB_SEQ_CPPFLAGS) $(am__append_25)
+ at BUILD_WRITE_TRUE@ $(ADIOSLIB_SEQ_CPPFLAGS) $(am__append_28)
@BUILD_WRITE_TRUE at libadios_nompi_a_CFLAGS = $(MACRODEFFLAG)_NOMPI $(ADIOSLIB_SEQ_CFLAGS)
@BUILD_WRITE_TRUE at libadios_nompi_a_LIBADD = $(libcoreonce_a_OBJECTS) \
- at BUILD_WRITE_TRUE@ $(am__append_24)
+ at BUILD_WRITE_TRUE@ $(am__append_26) $(am__append_27)
# force building the noinst_LIBRARIES first, before libadios_nompi.a
@BUILD_WRITE_TRUE at EXTRA_libadios_nompi_a_DEPENDENCIES = libcoreonce.a
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE at libadiosf_nompi_a_SOURCES = \
@@ -1891,14 +1954,16 @@ libcoreonce_a_CFLAGS = $(ADIOSLIB_CFLAGS)
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@ $(MACRODEFFLAG)_NOMPI \
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@ $(ADIOSLIB_EXTRA_CPPFLAGS) \
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@ $(ADIOSLIB_SEQ_CPPFLAGS) \
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@ $(am__append_29)
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@ $(am__append_34)
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE at libadiosf_nompi_v1_a_CPPFLAGS = $(libadiosf_nompi_a_CPPFLAGS)
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE at libadiosf_nompi_a_CFLAGS = $(MACRODEFFLAG)_NOMPI $(ADIOSLIB_SEQ_CFLAGS)
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE at libadiosf_nompi_v1_a_CFLAGS = $(libadiosf_nompi_a_CFLAGS)
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE at libadiosf_nompi_a_LIBADD = $(libcoreonce_a_OBJECTS) \
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@ $(am__append_27)
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@ $(am__append_30) \
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@ $(am__append_32)
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE at libadiosf_nompi_v1_a_LIBADD = $(libcoreonce_a_OBJECTS) \
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@ $(am__append_28)
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@ $(am__append_31) \
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@ $(am__append_33)
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE at EXTRA_libadiosf_nompi_a_DEPENDENCIES = libcoreonce.a
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE at EXTRA_libadiosf_nompi_v1_a_DEPENDENCIES = libcoreonce.a
@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at libadios_a_SOURCES = $(CLibSources) $(CLibParallelSources)
@@ -1906,11 +1971,12 @@ libcoreonce_a_CFLAGS = $(ADIOSLIB_CFLAGS)
@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(ADIOSLIB_EXTRA_CPPFLAGS) \
@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(ADIOSLIB_CPPFLAGS) \
@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(EXTRA_DEPENDENCY_CPPFLAGS) \
- at BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(am__append_37)
+ at BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(am__append_45)
@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at libadios_a_CFLAGS = $(ADIOSLIB_CFLAGS)
@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at libadios_a_LIBADD = \
@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(libcoreonce_a_OBJECTS) \
- at BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(am__append_31)
+ at BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(am__append_36) \
+ at BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(am__append_37)
# force building the noinst_LIBRARIES first, before libadios.a
@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at EXTRA_libadios_a_DEPENDENCIES = libcoreonce.a
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at libadiosf_a_SOURCES = $(FortranLibSources) \
@@ -1929,29 +1995,32 @@ libcoreonce_a_CFLAGS = $(ADIOSLIB_CFLAGS)
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(ADIOSLIB_EXTRA_CPPFLAGS) \
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(ADIOSLIB_CPPFLAGS) \
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(EXTRA_DEPENDENCY_CPPFLAGS) \
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(am__append_38)
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(am__append_46)
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at libadiosf_v1_a_CPPFLAGS = $(libadiosf_a_CPPFLAGS)
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at libadiosf_a_CFLAGS = $(ADIOSLIB_CFLAGS)
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at libadiosf_v1_a_CFLAGS = $(libadiosf_a_CFLAGS)
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at libadiosf_a_LIBADD = $(libcoreonce_a_OBJECTS) \
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(am__append_33)
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(am__append_39) \
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(am__append_41)
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at libadiosf_v1_a_LIBADD = $(libcoreonce_a_OBJECTS) \
- at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(am__append_34)
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(am__append_40) \
+ at BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE@ $(am__append_42)
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at EXTRA_libadiosf_a_DEPENDENCIES = libcoreonce.a
@BUILD_FORTRAN_TRUE@@BUILD_WRITE_TRUE@@HAVE_MPI_TRUE at EXTRA_libadiosf_v1_a_DEPENDENCIES = libcoreonce.a
libadiosread_nompi_a_SOURCES = core/mpidummy.c core/bp_utils.c \
core/adios_read.c core/adios_read_v1.c core/common_read.c \
core/adios_read_ext.c $(query_C_SOURCES) \
core/adios_read_hooks.c core/util_mpi.c read/read_bp.c \
- $(am__append_39) $(am__append_40)
-libadiosread_nompi_a_LIBADD = $(libcoreonce_a_OBJECTS)
+ $(am__append_47) $(am__append_48)
+libadiosread_nompi_a_LIBADD = $(libcoreonce_a_OBJECTS) \
+ $(am__append_50)
EXTRA_libadiosread_nompi_a_DEPENDENCIES = libcoreonce.a
@BUILD_FORTRAN_TRUE at FortranReadSeqLibSource = core/mpidummy.c \
@BUILD_FORTRAN_TRUE@ core/bp_utils.c core/common_read.c \
@BUILD_FORTRAN_TRUE@ core/adios_read_ext.c $(query_F_SOURCES) \
@BUILD_FORTRAN_TRUE@ core/adios_read_hooks.c core/util_mpi.c \
- at BUILD_FORTRAN_TRUE@ read/read_bp.c $(am__append_43) \
- at BUILD_FORTRAN_TRUE@ $(am__append_44)
+ at BUILD_FORTRAN_TRUE@ read/read_bp.c $(am__append_52) \
+ at BUILD_FORTRAN_TRUE@ $(am__append_53)
@BUILD_FORTRAN_TRUE at libadiosreadf_nompi_a_SOURCES = \
@BUILD_FORTRAN_TRUE@ $(FortranReadSeqLibSource) \
@BUILD_FORTRAN_TRUE@ core/adiosf_read.c \
@@ -1961,8 +2030,10 @@ EXTRA_libadiosread_nompi_a_DEPENDENCIES = libcoreonce.a
@BUILD_FORTRAN_TRUE at libadiosreadf_nompi_v1_a_SOURCES = $(FortranReadSeqLibSource) core/adiosf_read_v1.c
@BUILD_FORTRAN_TRUE at libadiosreadf_nompi_v1_a_CPPFLAGS = $(libadiosreadf_nompi_a_CPPFLAGS)
@BUILD_FORTRAN_TRUE at libadiosreadf_nompi_v1_a_CFLAGS = $(libadiosreadf_nompi_a_CFLAGS)
- at BUILD_FORTRAN_TRUE@libadiosreadf_nompi_a_LIBADD = $(libcoreonce_a_OBJECTS)
- at BUILD_FORTRAN_TRUE@libadiosreadf_nompi_v1_a_LIBADD = $(libcoreonce_a_OBJECTS)
+ at BUILD_FORTRAN_TRUE@libadiosreadf_nompi_a_LIBADD = \
+ at BUILD_FORTRAN_TRUE@ $(libcoreonce_a_OBJECTS) $(am__append_55)
+ at BUILD_FORTRAN_TRUE@libadiosreadf_nompi_v1_a_LIBADD = \
+ at BUILD_FORTRAN_TRUE@ $(libcoreonce_a_OBJECTS) $(am__append_56)
@BUILD_FORTRAN_TRUE at EXTRA_libadiosreadf_nompi_a_DEPENDENCIES = libcoreonce.a
@BUILD_FORTRAN_TRUE at EXTRA_libadiosreadf_nompi_v1_a_DEPENDENCIES = libcoreonce.a
@HAVE_MPI_TRUE at libadiosread_a_SOURCES = core/bp_utils.c \
@@ -1971,9 +2042,10 @@ EXTRA_libadiosread_nompi_a_DEPENDENCIES = libcoreonce.a
@HAVE_MPI_TRUE@ $(query_C_SOURCES) core/adios_read_hooks.c \
@HAVE_MPI_TRUE@ core/util_mpi.c read/read_bp.c \
@HAVE_MPI_TRUE@ read/read_bp_staged.c read/read_bp_staged1.c \
- at HAVE_MPI_TRUE@ $(am__append_47) $(am__append_48) \
- at HAVE_MPI_TRUE@ $(am__append_49) $(am__append_50)
- at HAVE_MPI_TRUE@libadiosread_a_LIBADD = $(libcoreonce_a_OBJECTS)
+ at HAVE_MPI_TRUE@ $(am__append_58) $(am__append_59) \
+ at HAVE_MPI_TRUE@ $(am__append_60) $(am__append_61)
+ at HAVE_MPI_TRUE@libadiosread_a_LIBADD = $(libcoreonce_a_OBJECTS) \
+ at HAVE_MPI_TRUE@ $(am__append_64)
@HAVE_MPI_TRUE at EXTRA_libadiosread_a_DEPENDENCIES = libcoreonce.a
@BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at FortranReadLibSource = \
@BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ core/bp_utils.c \
@@ -1985,10 +2057,10 @@ EXTRA_libadiosread_nompi_a_DEPENDENCIES = libcoreonce.a
@BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ read/read_bp.c \
@BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ read/read_bp_staged.c \
@BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ read/read_bp_staged1.c \
- at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ $(am__append_54) \
- at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ $(am__append_55) \
- at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ $(am__append_56) \
- at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ $(am__append_57)
+ at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ $(am__append_66) \
+ at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ $(am__append_67) \
+ at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ $(am__append_68) \
+ at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ $(am__append_69)
@BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at libadiosreadf_a_SOURCES = \
@BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ $(FortranReadLibSource) \
@BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ core/adiosf_read.c \
@@ -1998,16 +2070,20 @@ EXTRA_libadiosread_nompi_a_DEPENDENCIES = libcoreonce.a
@BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at libadiosreadf_v1_a_SOURCES = $(FortranReadLibSource) core/adiosf_read_v1.c
@BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at libadiosreadf_v1_a_CPPFLAGS = $(libadiosreadf_a_CPPFLAGS)
@BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at libadiosreadf_v1_a_CFLAGS = $(libadiosreadf_a_CFLAGS)
- at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at libadiosreadf_a_LIBADD = $(libcoreonce_a_OBJECTS)
- at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at libadiosreadf_v1_a_LIBADD = $(libcoreonce_a_OBJECTS)
+ at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at libadiosreadf_a_LIBADD = \
+ at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ $(libcoreonce_a_OBJECTS) \
+ at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ $(am__append_71)
+ at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at libadiosreadf_v1_a_LIBADD = \
+ at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ $(libcoreonce_a_OBJECTS) \
+ at BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE@ $(am__append_72)
@BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at EXTRA_libadiosreadf_a_DEPENDENCIES = libcoreonce.a
@BUILD_FORTRAN_TRUE@@HAVE_MPI_TRUE at EXTRA_libadiosreadf_v1_a_DEPENDENCIES = libcoreonce.a
libadios_internal_nompi_a_SOURCES = core/mpidummy.c core/bp_utils.c \
core/adios_internals.c core/util_mpi.c $(query_C_SOURCES) \
core/adios_timing.c core/adios_transport_hooks.c \
- $(am__append_61)
+ $(am__append_75)
libadios_internal_nompi_a_LIBADD = $(libcoreonce_a_OBJECTS) \
- $(am__append_62)
+ $(am__append_76) $(am__append_77)
EXTRA_libadios_internal_nompi_a_DEPENDENCIES = libcoreonce.a
libadios_internal_nompi_a_CPPFLAGS = $(AM_CPPFLAGS) $(MACRODEFFLAG)_INTERNAL $(ADIOSLIB_EXTRA_CPPFLAGS) $(ADIOSLIB_INT_CPPFLAGS) $(ADIOSLIB_CPPFLAGS)
EXTRA_DIST = core/adios_bp_v1.h core/adios_endianness.h \
@@ -2025,6 +2101,7 @@ EXTRA_DIST = core/adios_bp_v1.h core/adios_endianness.h \
transforms/adios_transform_identity_read.h \
transforms/adios_transform_szip.h \
transforms/adios_transform_alacrity_common.h \
+ transforms/adios_transform_zfp_common.h \
transforms/adios_transform_template_read.c \
transforms/adios_transform_template_write.c \
query/Makefile.plugins.cmake
@@ -2676,6 +2753,8 @@ core/libcoreonce_a-globals.$(OBJEXT): core/$(am__dirstamp)
core/libcoreonce_a-qhashtbl.$(OBJEXT): core/$(am__dirstamp)
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/transforms/$(am__dirstamp):
@$(MKDIR_P) core/transforms
@: > core/transforms/$(am__dirstamp)
@@ -2710,6 +2789,8 @@ transforms/libcoreonce_a-adios_transform_aplod_write.$(OBJEXT): \
transforms/$(am__dirstamp)
transforms/libcoreonce_a-adios_transform_alacrity_write.$(OBJEXT): \
transforms/$(am__dirstamp)
+transforms/libcoreonce_a-adios_transform_zfp_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): \
@@ -2736,6 +2817,8 @@ transforms/libcoreonce_a-adios_transform_aplod_read.$(OBJEXT): \
transforms/$(am__dirstamp)
transforms/libcoreonce_a-adios_transform_alacrity_read.$(OBJEXT): \
transforms/$(am__dirstamp)
+transforms/libcoreonce_a-adios_transform_zfp_read.$(OBJEXT): \
+ transforms/$(am__dirstamp)
libcoreonce.a: $(libcoreonce_a_OBJECTS) $(libcoreonce_a_DEPENDENCIES) $(EXTRA_libcoreonce_a_DEPENDENCIES)
$(AM_V_at)-rm -f libcoreonce.a
@@ -5038,6 +5121,12 @@ core/libcoreonce_a-util.o: core/util.c
core/libcoreonce_a-util.obj: core/util.c
$(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libcoreonce_a_CPPFLAGS) $(CPPFLAGS) $(libcoreonce_a_CFLAGS) $(CFLAGS) -c -o core/libcoreonce_a-util.obj `if test -f 'core/util.c'; then $(CYGPATH_W) 'core/util.c'; else $(CYGPATH_W) '$(srcdir)/core/util.c'; fi`
+core/libcoreonce_a-adios_transform_methods.o: 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.o `test -f 'core/adios_transform_methods.c' || echo '$(srcdir)/'`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/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
@@ -5128,6 +5217,12 @@ transforms/libcoreonce_a-adios_transform_alacrity_write.o: transforms/adios_tran
transforms/libcoreonce_a-adios_transform_alacrity_write.obj: transforms/adios_transform_alacrity_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_alacrity_write.obj `if test -f 'transforms/adios_transform_alacrity_write.c'; then $(CYGPATH_W) 'transforms/adios_transform_alacrity_write.c'; else $(CYGPATH_W) '$(srcdir)/transforms/adios_transform_alacrity_write.c'; fi`
+transforms/libcoreonce_a-adios_transform_zfp_write.o: 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.o `test -f 'transforms/adios_transform_zfp_write.c' || echo '$(srcdir)/'`transforms/adios_transform_zfp_write.c
+
+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`
+
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
@@ -5206,6 +5301,12 @@ transforms/libcoreonce_a-adios_transform_alacrity_read.o: transforms/adios_trans
transforms/libcoreonce_a-adios_transform_alacrity_read.obj: transforms/adios_transform_alacrity_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_alacrity_read.obj `if test -f 'transforms/adios_transform_alacrity_read.c'; then $(CYGPATH_W) 'transforms/adios_transform_alacrity_read.c'; else $(CYGPATH_W) '$(srcdir)/transforms/adios_transform_alacrity_read.c'; fi`
+transforms/libcoreonce_a-adios_transform_zfp_read.o: 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.o `test -f 'transforms/adios_transform_zfp_read.c' || echo '$(srcdir)/'`transforms/adios_transform_zfp_read.c
+
+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`
+
.f90.o:
$(AM_V_FC)$(FCCOMPILE) -c -o $@ $<
diff --git a/src/core/adios.c b/src/core/adios.c
index 0a14555..71b833a 100644
--- a/src/core/adios.c
+++ b/src/core/adios.c
@@ -203,7 +203,7 @@ int adios_close (int64_t fd_p)
}
struct adios_var_struct * v = fd->group->vars;
- retval = common_adios_close (fd_p);
+ retval = common_adios_close (fd);
// Q.L. 10-2010. To fix a memory leak problem.
while (v) {
@@ -263,7 +263,7 @@ int adios_close (int64_t fd_p)
// group a list of vars into a composite group
int adios_declare_group (int64_t * id, const char * name
,const char * time_index
- ,enum ADIOS_FLAG stats
+ ,enum ADIOS_STATISTICS_FLAG stats
)
{
int ret;
@@ -272,7 +272,7 @@ int adios_declare_group (int64_t * id, const char * name
,""
,""
,time_index
- ,stats
+ ,(stats != adios_stat_no_do_not_use_this ? stats : adios_stat_no)
);
if (ret == 1) {
struct adios_group_struct * g = (struct adios_group_struct *) *id;
@@ -288,6 +288,27 @@ int adios_free_group (int64_t id)
return adios_errno;
}
+
+
+int adios_set_time_aggregation(int64_t groupid,
+ uint64_t buffersize,
+ int64_t syncgroupid
+ )
+{
+ adios_errno = err_no_error;
+ if (groupid == 0) {
+ adios_error (err_invalid_group, "adios_set_time_aggregation() called with 0 argument\n");
+ }
+ struct adios_group_struct * g = (struct adios_group_struct *) groupid;
+ struct adios_group_struct * sg = NULL;
+ if (syncgroupid != 0)
+ sg = (struct adios_group_struct *) syncgroupid;
+
+ adios_common_set_time_aggregation(g, buffersize, sg);
+ return adios_errno;
+}
+
+
///////////////////////////////////////////////////////////////////////////////
// adios_common_define_var is in adios_internals.c
@@ -577,3 +598,53 @@ int adios_define_mesh_unstructured (char * points,
return adios_common_define_mesh_unstructured (points, data, count, cell_type, nspace, npoints, name, group_id);
}
+ADIOS_AVAILABLE_WRITE_METHODS * adios_available_write_methods()
+{
+ int i, n;
+ n = 0;
+ for (i = 0; i < ADIOS_METHOD_COUNT; i++) {
+ if (adios_transports[i].method_name) {
+ n++;
+ }
+ }
+
+ if (n == 0)
+ return NULL;
+
+ ADIOS_AVAILABLE_WRITE_METHODS * m = (ADIOS_AVAILABLE_WRITE_METHODS *) malloc (sizeof(ADIOS_AVAILABLE_WRITE_METHODS));
+ if (!m)
+ return NULL;
+
+ m->name = (char**) malloc (n*sizeof(char*));
+ m->nmethods = n;
+
+ n = 0;
+ for (i = 0; i < ADIOS_METHOD_COUNT; i++) {
+ if (adios_transports[i].method_name) {
+ m->name[n] = strdup (adios_transports[i].method_name);
+ n++;
+ }
+ }
+ return m;
+}
+
+void adios_available_write_methods_free (ADIOS_AVAILABLE_WRITE_METHODS * m)
+{
+ int i;
+ if (m)
+ {
+ if (m->name)
+ {
+ for (i=0; i < m->nmethods; i++)
+ {
+ if (m->name[i]) {
+ free (m->name[i]);
+ m->name[i] = NULL;
+ }
+ }
+ free (m->name);
+ m->name = NULL;
+ }
+ free (m);
+ }
+}
diff --git a/src/core/adios_bp_v1.c b/src/core/adios_bp_v1.c
index 1a1c57b..dc01bc3 100644
--- a/src/core/adios_bp_v1.c
+++ b/src/core/adios_bp_v1.c
@@ -232,6 +232,7 @@ int adios_parse_process_group_index_v1 (struct adios_bp_buffer_struct_v1 * b,
{
*root = (struct adios_index_process_group_struct_v1 *)
malloc (sizeof(struct adios_index_process_group_struct_v1));
+ (*root)->is_time_aggregated = 0;
(*root)->next = 0;
}
uint16_t length_of_name;
diff --git a/src/core/adios_bp_v1.h b/src/core/adios_bp_v1.h
index 2ed623e..3469746 100644
--- a/src/core/adios_bp_v1.h
+++ b/src/core/adios_bp_v1.h
@@ -85,6 +85,7 @@ struct adios_index_process_group_struct_v1
char * time_index_name;
uint32_t time_index;
uint64_t offset_in_file;
+ int is_time_aggregated;
struct adios_index_process_group_struct_v1 * next;
};
diff --git a/src/core/adios_clock.h b/src/core/adios_clock.h
index 10882b7..0a89b2e 100644
--- a/src/core/adios_clock.h
+++ b/src/core/adios_clock.h
@@ -12,7 +12,7 @@ double adios_gettime_double();
/* get current time in milliseconds as unsigned long */
unsigned long adios_gettime_ms();
-#ifndef clockid_t
+#ifndef HAVE_CLOCKID_T
typedef int clockid_t;
#endif
#ifndef CLOCK_REALTIME
diff --git a/src/core/adios_icee.h b/src/core/adios_icee.h
index 1d75d01..c89948f 100644
--- a/src/core/adios_icee.h
+++ b/src/core/adios_icee.h
@@ -54,6 +54,7 @@ typedef struct icee_fileinfo_rec {
int timestep;
struct icee_varinfo_rec * varinfo;
struct icee_fileinfo_rec * next;
+ double timestamp;
} icee_fileinfo_rec_t, *icee_fileinfo_rec_ptr_t;
static FMField icee_fileinfo_field_list[] =
@@ -67,6 +68,7 @@ static FMField icee_fileinfo_field_list[] =
{"timestep", "integer", sizeof(int), FMOffset(icee_fileinfo_rec_ptr_t, timestep)},
{"varinfo", "*icee_varinfo", sizeof(struct icee_varinfo_rec ), FMOffset(icee_fileinfo_rec_ptr_t, varinfo)},
{"next", "*icee_fileinfo", sizeof(struct icee_fileinfo_rec ), FMOffset(icee_fileinfo_rec_ptr_t, next)},
+ {"timestamp", "float", sizeof(double), FMOffset(icee_fileinfo_rec_ptr_t, timestamp)},
{NULL, NULL, 0, 0}
};
diff --git a/src/core/adios_internals.c b/src/core/adios_internals.c
old mode 100644
new mode 100755
index ea033f7..4bafe98
--- a/src/core/adios_internals.c
+++ b/src/core/adios_internals.c
@@ -670,65 +670,64 @@ int adios_parse_scalar_string (enum ADIOS_DATATYPES type, char * value, void **
"value: '%s' not valid integer\n",value);
return 0;
}
- else
+
+ switch (type)
{
- switch (type)
- {
- case adios_byte:
- if (t < SCHAR_MIN || t > SCHAR_MAX)
- {
- adios_error (err_out_of_bound,
- "type is %s, value "
- "is out of range: '%s'\n",
- adios_type_to_string_int (type),
- value);
- return 0;
- }
- else
- {
- *out = malloc (1);
- *((int8_t *) *out) = t;
+ case adios_byte:
+ if (t < SCHAR_MIN || t > SCHAR_MAX)
+ {
+ adios_error (err_out_of_bound,
+ "type is %s, value "
+ "is out of range: '%s'\n",
+ adios_type_to_string_int (type),
+ value);
+ return 0;
+ }
+ else
+ {
+ *out = malloc (1);
+ *((int8_t *) *out) = t;
- return 1;
- }
- case adios_short:
- if (t < SHRT_MIN || t > SHRT_MAX)
- {
- adios_error (err_out_of_bound,
- "type is %s, value "
- "is out of range: '%s'\n",
- adios_type_to_string_int (type),
- value);
- return 0;
- }
- else
- {
- *out = malloc (2);
- *((int16_t *) *out) = t;
+ return 1;
+ }
+ case adios_short:
+ if (t < SHRT_MIN || t > SHRT_MAX)
+ {
+ adios_error (err_out_of_bound,
+ "type is %s, value "
+ "is out of range: '%s'\n",
+ adios_type_to_string_int (type),
+ value);
+ return 0;
+ }
+ else
+ {
+ *out = malloc (2);
+ *((int16_t *) *out) = t;
- return 1;
- }
- case adios_integer:
- if (t < INT_MIN || t > INT_MAX)
- {
- adios_error (err_out_of_bound,
- "type is %s, value "
- "is out of range: '%s'\n",
- adios_type_to_string_int (type),
- value);
- return 0;
- }
- else
- {
- *out = malloc (4);
- *((int32_t *) *out) = t;
+ return 1;
+ }
+ case adios_integer:
+ if (t < INT_MIN || t > INT_MAX)
+ {
+ adios_error (err_out_of_bound,
+ "type is %s, value "
+ "is out of range: '%s'\n",
+ adios_type_to_string_int (type),
+ value);
+ return 0;
+ }
+ else
+ {
+ *out = malloc (4);
+ *((int32_t *) *out) = t;
- return 1;
- }
- default:
- return 1;
- }
+ return 1;
+ }
+ default:
+ return 1;
}
+ break; // just to make eclipse happy
}
case adios_long:
{
@@ -763,65 +762,63 @@ int adios_parse_scalar_string (enum ADIOS_DATATYPES type, char * value, void **
"value: '%s' not valid integer\n", value);
return 0;
}
- else
+ switch (type)
{
- switch (type)
- {
- case adios_unsigned_byte:
- if (t > UCHAR_MAX)
- {
- adios_error (err_out_of_bound,
- "type is %s, value "
- "is out of range: '%s'\n",
- adios_type_to_string_int (type),
- value);
- return 0;
- }
- else
- {
- *out = malloc (1);
- *((uint8_t *) *out) = t;
+ case adios_unsigned_byte:
+ if (t > UCHAR_MAX)
+ {
+ adios_error (err_out_of_bound,
+ "type is %s, value "
+ "is out of range: '%s'\n",
+ adios_type_to_string_int (type),
+ value);
+ return 0;
+ }
+ else
+ {
+ *out = malloc (1);
+ *((uint8_t *) *out) = t;
- return 1;
- }
- case adios_unsigned_short:
- if (t > USHRT_MAX)
- {
- adios_error (err_out_of_bound,
- "type is %s, value "
- "is out of range: '%s'\n",
- adios_type_to_string_int (type),
- value);
- return 0;
- }
- else
- {
- *out = malloc (2);
- *((uint16_t *) *out) = t;
+ return 1;
+ }
+ case adios_unsigned_short:
+ if (t > USHRT_MAX)
+ {
+ adios_error (err_out_of_bound,
+ "type is %s, value "
+ "is out of range: '%s'\n",
+ adios_type_to_string_int (type),
+ value);
+ return 0;
+ }
+ else
+ {
+ *out = malloc (2);
+ *((uint16_t *) *out) = t;
- return 1;
- }
- case adios_unsigned_integer:
- if (t > UINT_MAX)
- {
- adios_error (err_out_of_bound,
- "type is %s, value "
- "is out of range: '%s'\n",
- adios_type_to_string_int (type),
- value);
- return 0;
- }
- else
- {
- *out = malloc (4);
- *((uint32_t *) *out) = t;
+ return 1;
+ }
+ case adios_unsigned_integer:
+ if (t > UINT_MAX)
+ {
+ adios_error (err_out_of_bound,
+ "type is %s, value "
+ "is out of range: '%s'\n",
+ adios_type_to_string_int (type),
+ value);
+ return 0;
+ }
+ else
+ {
+ *out = malloc (4);
+ *((uint32_t *) *out) = t;
- return 1;
- }
- default:
- return 1;
- }
+ return 1;
+ }
+ default:
+ return 1;
}
+ break; // just to make eclipse happy
}
case adios_unsigned_long:
{
@@ -903,6 +900,7 @@ int adios_parse_scalar_string (enum ADIOS_DATATYPES type, char * value, void **
{
*out = malloc (16);
*((long double *) *out) = t;
+ return 1;
}
}
case adios_string:
@@ -1342,7 +1340,7 @@ int adios_common_declare_group (int64_t * id, const char * name
,const char * coordination_comm
,const char * coordination_var
,const char * time_index_name
- ,enum ADIOS_FLAG stats
+ ,enum ADIOS_STATISTICS_FLAG stats
)
{
struct adios_group_struct * g = (struct adios_group_struct *)
@@ -1363,7 +1361,7 @@ int adios_common_declare_group (int64_t * id, const char * name
g->group_comm = (coordination_comm ? strdup (coordination_comm) : 0L);
g->time_index_name = (time_index_name ? strdup (time_index_name) : 0L);
g->time_index = 0;
- g->stats_on = stats;
+ g->stats_flag = stats;
g->process_id = 0;
g->methods = NULL;
// ADIOS Schema
@@ -1377,6 +1375,19 @@ int adios_common_declare_group (int64_t * id, const char * name
g->tv_size = 0;
#endif
+ //Yuan: added for time steps buffering
+ g->do_ts_aggr=0;
+ g->ts_fd = NULL;
+ g->ts_buffsize=0;
+ g->max_ts=1;
+ g->ts_to_buffer=1;
+ g->index=NULL;
+ g->built_index=0;
+ g->do_ts_flush=0;
+ g->synced_groups=NULL;
+ g->synced_groups_size=0;
+ g->synced_groups_capacity=0;
+
*id = (int64_t) g;
adios_append_group (g);
@@ -1384,6 +1395,35 @@ int adios_common_declare_group (int64_t * id, const char * name
return 1;
}
+
+int adios_common_set_time_aggregation(struct adios_group_struct * group,
+ uint64_t buffersize,
+ struct adios_group_struct * syncgroup
+)
+{
+ if (buffersize > 0) {
+ SetTimeAggregation(group, 1);
+ log_debug ("Time aggregation set for group '%s' with buffer size %" PRIu64 " bytes\n",
+ group->name, buffersize);
+ }
+ else
+ {
+ SetTimeAggregation(group, 0); // zero size turns off time-aggregation
+ log_debug ("Time aggregation turned off for group '%s' because buffer size is set to %" PRIu64 " bytes\n",
+ group->name, buffersize);
+ }
+ group->ts_buffsize = buffersize;
+ if (syncgroup)
+ {
+ log_debug ("Group '%s' will be forced to flush whenever group '%s' is written\n",
+ group->name, syncgroup->name);
+ SetTimeAggregationSyncGroup(syncgroup, group);
+ }
+ // FIXME: add sync group
+
+ return 1;
+}
+
struct adios_pg_struct * add_new_pg_written (struct adios_file_struct * fd)
{
struct adios_pg_struct * pg = (struct adios_pg_struct *)
@@ -1394,6 +1434,7 @@ struct adios_pg_struct * add_new_pg_written (struct adios_file_struct * fd)
pg->vars_written = NULL;
pg->vars_written_tail = NULL;
pg->next = NULL;
+ pg->has_index=0; //Yuan: for ts buffering
if (!fd->pgs_written)
{
fd->pgs_written = pg;
@@ -1594,6 +1635,11 @@ void adios_common_free_groupstruct (struct adios_group_struct * g)
adios_timing_destroy(g->timing_obj);
adios_timing_destroy(g->prev_timing_obj);
#endif
+ if (g->synced_groups)
+ {
+ free (g->synced_groups);
+ g->synced_groups = NULL;
+ }
free (g);
}
@@ -1849,14 +1895,22 @@ int64_t adios_common_define_var (int64_t group_id, const char * name
adios_transform_init_transform_var(v);
// Q.L. - Check whether stats are disabled or not
- if (t->stats_on == adios_flag_yes)
+ if (t->stats_flag != adios_stat_no)
{
- // '1' at the bit location of stat id in adios_bp_v1.h, enables calculation of statistic.
- for (i = 0; i < ADIOS_STAT_LENGTH; i++)
- v->bitmap |= (1 << i);
-
- // Default values for histogram not yet implemented. Disabling it.
- v->bitmap ^= (1 << adios_statistic_hist);
+ if (t->stats_flag == adios_stat_minmax)
+ {
+ v->bitmap |= (1 << adios_statistic_min);
+ v->bitmap |= (1 << adios_statistic_max);
+ v->bitmap |= (1 << adios_statistic_finite);
+ }
+ else // if (t->stats_flag == adios_stat_full)
+ {
+ // '1' at the bit location of stat id in adios_bp_v1.h, enables calculation of statistic.
+ for (i = 0; i < ADIOS_STAT_LENGTH; i++)
+ v->bitmap |= (1 << i);
+ // Default values for histogram not yet implemented. Disabling it.
+ v->bitmap ^= (1 << adios_statistic_hist);
+ }
// For complex numbers, the set of statistics occur thrice: stat[0] - magnitude, stat[1] - real, stat[2] - imaginary
if (v->type == adios_complex || v->type == adios_double_complex)
@@ -1977,27 +2031,19 @@ int adios_common_set_transform (int64_t var_id, const char *transform_type_str)
}
-void adios_common_get_group (int64_t * group_id, const char * name)
+struct adios_group_struct * adios_common_get_group (const char * name)
{
struct adios_group_list_struct * g = adios_get_groups ();
-
- *group_id = 0;
-
while (g)
{
if (!strcasecmp (g->group->name, name))
{
- *group_id = (int64_t) g->group;
-
- return;
+ return g->group;
}
-
g = g->next;
}
-
- adios_error (err_invalid_group,
- "adios-group '%s' not found in configuration file\n",
- name);
+ adios_error (err_invalid_group, "adios group '%s' does not exist\n", name);
+ return NULL;
}
// *****************************************************************************
@@ -2441,6 +2487,7 @@ void index_append_var_v1 (
} else {
// existing variable, add this item to its characteristics
log_debug (" Append to existing variable\n");
+ //printf(" Append to existing variable\n");
/* NOTE: old append made sure the variable mathes
* name + path + group name + type
@@ -2464,6 +2511,7 @@ void index_append_var_v1 (
log_debug (" ----------- Append index with merging --------------\n");
struct adios_index_characteristic_struct_v1 * c;
int count = olditem->characteristics_count + item->characteristics_count;
+// printf("new variable index has %d\n", count);
c = malloc ( count * sizeof (struct adios_index_characteristic_struct_v1));
if (!c)
{
@@ -2529,6 +2577,7 @@ void index_append_var_v1 (
}
else
{
+ //printf("else in mergeing var index\n");
if ( olditem->characteristics_count
+ item->characteristics_count
> olditem->characteristics_allocated
@@ -2655,6 +2704,16 @@ void adios_merge_index_v1 (
{
// this will just add it on to the end and all should work fine
index_append_process_group_v1 (main_index, new_pg_root);
+ log_debug("merge index on rank %u with sorting %s pg_root time aggregated %s new pg_root time aggregated %s\n",
+ main_index->pg_root->process_id,
+ (needs_sorting ? "ON" : "OFF"),
+ (main_index->pg_root->is_time_aggregated ? "YES" : "NO"),
+ (new_pg_root->is_time_aggregated ? "YES" : "NO"));
+ if (main_index->pg_root->is_time_aggregated || new_pg_root->is_time_aggregated)
+ {
+ // variable characteristics need to be sorted if time steps are buffered
+ needs_sorting = 1;
+ }
// need to do vars attrs one at a time to merge them properly
struct adios_index_var_struct_v1 * v = new_vars_root;
@@ -2667,6 +2726,7 @@ void adios_merge_index_v1 (
v_temp = v->next;
v->next = 0;
log_debug ("merge index var %s/%s\n", v->var_path, v->var_name);
+
index_append_var_v1 (main_index, v, needs_sorting);
v = v_temp;
}
@@ -2934,12 +2994,13 @@ static void adios_clear_vars_index_v1 (struct adios_index_var_struct_v1 * root)
// NCSU ALACRITY-ADIOS - Clear the transform metadata
adios_transform_clear_transform_characteristic(&root->characteristics[i].transform);
- /*if (root->characteristics [i].value) {
+ if (root->characteristics [i].value) {
if (root->type == adios_string_array)
- free_string_array (root->characteristics [i].value, root->nelems);
+ a2s_free_string_array (root->characteristics [i].value, root->nelems);
else
free (root->characteristics [i].value);
- }*/
+ root->characteristics [i].value = NULL;
+ }
}
if (root->characteristics)
@@ -3284,6 +3345,8 @@ void adios_copy_var_written (struct adios_file_struct * fd, struct adios_var_str
{
adios_error (err_unspecified, "String arrays are not supported for variables %s:%s:%d\n",
__FILE__,__func__, __LINE__);
+
+ break;
}
default:
{
@@ -3501,8 +3564,83 @@ void adios_build_index_v1 (struct adios_file_struct * fd,
struct adios_pg_struct * pg = fd->pgs_written;
int pgid = 0;
+// printf("%d: ============build index, pg_start_in_file=%llu\n",fd->group->process_id, pg->pg_start_in_file);
+
+ /* Yuan: if index has been built during time-aggregation,
+ * update the offsets and append the already built time-aggregation index
+ * (fd->group->index) to the 'index' that comes from the method and
+ * which may contain the indices from previous steps from a file (in append mode)
+ */
+ if (fd->group->built_index==1) {
+ log_debug("TimeAggr: index already built in time-aggregation, merge it in and move on\n");
+ struct adios_index_process_group_struct_v1 *g_item = g->index->pg_root;
+ while (g_item) {
+ g_item->offset_in_file += pg->pg_start_in_file;
+ g_item->is_time_aggregated = TimeAggregated(g); // yes
+ g_item= g_item->next;
+ }
+ /* When we later merge indexes, it may still be the case that both index and new index
+ * indicates no time aggregation. e.g. index is from parsing index from file at append,
+ * while new index is coming from other processes. Both index is created by parse_index
+ * which does not have info on time aggregation.
+ * We fix this issue here by updating the main index.
+ */
+ if (index && index->pg_root) {
+ struct adios_index_process_group_struct_v1 *pg = index->pg_root;
+ while (pg) {
+ pg->is_time_aggregated |= TimeAggregated(g);
+ pg = pg->next;
+ }
+ }
+ // append whole PG list at once
+ index_append_process_group_v1 (index, g->index->pg_root);
+
+ struct adios_index_var_struct_v1 * v_index = g->index->vars_root;
+ struct adios_index_var_struct_v1 * v_next;
+ while (v_index) {
+ int i;
+ for (i=0; i < v_index->characteristics_count; i++)
+ {
+ //printf("old var offset = %llu payload_offset=%llu\n", v_index->characteristics [cnt].offset, v_index->characteristics[cnt].payload_offset);
+ v_index->characteristics [i].offset += pg->pg_start_in_file;
+ v_index->characteristics [i].payload_offset += pg->pg_start_in_file;
+ //printf("var time index=%d\n",v_index->characteristics[cnt].time_index);
+ //printf("var offset = %llu payload_offset=%llu\n", v_index->characteristics [cnt].offset, v_index->characteristics[cnt].payload_offset);
+ }
+ v_next = v_index->next;
+ v_index->next = NULL;
+ index_append_var_v1 (index, v_index, 0);
+ v_index = v_next;
+ }
+
+
+ struct adios_index_attribute_struct_v1 * a_index = g->index->attrs_root;
+ struct adios_index_attribute_struct_v1 * a_next;
+ while (a_index)
+ {
+ a_index->characteristics [0].offset += pg->pg_start_in_file;
+ a_index->characteristics [0].payload_offset += pg->pg_start_in_file;
+ // printf("attr time index=%d offset=%llu\n", a->characteristics[cnt].time_index, a->characteristics [cnt].offset);
+ a_next = a_index->next;
+ a_index->next = NULL; // separate head from tail, to insert a single attribute here
+ index_append_attribute_v1(&index->attrs_root, a_index);
+ a_index = a_next;
+ }
+
+ fd->group->built_index=0;
+ return;
+ }
+
+ log_debug("TimeAggr: build index now and merge it in\n");
+
while (pg)
{
+ if(pg->has_index==1) {
+ pg=pg->next;
+ continue;
+ }
+
+
/* Create a PG entry in index */
struct adios_index_process_group_struct_v1 * g_item;
g_item = (struct adios_index_process_group_struct_v1 *)
@@ -3512,16 +3650,28 @@ void adios_build_index_v1 (struct adios_file_struct * fd,
g_item->process_id = g->process_id;
g_item->time_index_name = (g->time_index_name ? strdup (g->time_index_name) : 0L);
g_item->time_index = g->time_index;
+ g_item->is_time_aggregated = TimeAggregated(fd->group);
+
+ //printf("adios_build_index_v1 g->time_index=%d, start_in_file=%llu\n", g->time_index, pg->pg_start_in_file);
g_item->offset_in_file = pg->pg_start_in_file;
g_item->next = 0;
// build the groups and vars index
index_append_process_group_v1 (index, g_item);
+ //Yuan: if time buffering is on, all the offsets are relative to the
+ //current buffer, they will be updated in the end after
+ //pg_start_in_file is established correctly
+ if (TimeAggregated(fd->group))
+ pg->pg_start_in_file=0;
+
+ //printf("after clearing... adios_build_index_v1 g->time_index=%d, start_in_file=%llu\n", g->time_index, pg->pg_start_in_file);
+
/* For each written variable, create a variable entry in the index */
struct adios_var_struct * v = pg->vars_written;
while (v)
{
+ //printf("in the variable loop varname=%s pg->pg_start_in_file=%llu\n",v->name, pg->pg_start_in_file);
// only add items that were written to the index
assert (v->write_offset > 0); // v is vars_written, so yes it was written actually
//if (v->write_offset != 0)
@@ -3539,7 +3689,9 @@ void adios_build_index_v1 (struct adios_file_struct * fd,
v_index->type = v->type;
v_index->characteristics_count = 1;
v_index->characteristics_allocated = 1;
+ //printf("var=%s v_offset=%llu start_in_file=%llu\n", v->name, v->write_offset, pg->pg_start_in_file);
v_index->characteristics [0].offset = v->write_offset + pg->pg_start_in_file;
+ //printf("var=%s characteristic offset=%llu\n", v->name, v_index->characteristics [0].offset);
// Find the old var in g->vars.
// We need this to calculate the correct payload_offset, because that
// holds the variable references in the dimensions, while v-> contains
@@ -3562,6 +3714,7 @@ void adios_build_index_v1 (struct adios_file_struct * fd,
adios_transform_init_transform_characteristic(&v_index->characteristics[0].transform);
//v_index->characteristics [0].transform_type = adios_transform_none;
+// printf("offset=%llu payload_offset=%llu\n", v_index->characteristics [0].offset, v_index->characteristics [0].payload_offset);
uint64_t size = adios_get_type_size (v->type, v->data);
switch (v->type)
{
@@ -3690,6 +3843,8 @@ void adios_build_index_v1 (struct adios_file_struct * fd,
{
adios_error (err_unspecified, "String arrays are not supported for variables %s:%s:%d\n",
__FILE__,__func__, __LINE__);
+
+ break;
}
default:
{
@@ -3707,6 +3862,7 @@ void adios_build_index_v1 (struct adios_file_struct * fd,
v = v->next;
}
+ pg->has_index=1;
pg = pg->next;
pgid++;
}
@@ -3731,7 +3887,7 @@ void adios_build_index_v1 (struct adios_file_struct * fd,
a_index->nelems = a->nelems;
a_index->characteristics_count = 1;
a_index->characteristics_allocated = 1;
- //uint64_t size = a_index->nelems * adios_get_type_size (a->type, a->value);
+ uint64_t size = a_index->nelems * adios_get_type_size (a->type, a->value);
// pg_file_offsets [pgid] is now the last PG's start offset, which is the base
// offset for attributes
@@ -3750,24 +3906,41 @@ void adios_build_index_v1 (struct adios_file_struct * fd,
adios_transform_init_transform_characteristic(&a_index->characteristics[0].transform);
//a_index->characteristics[0].transform_type = adios_transform_none;
- a_index->characteristics [0].value = a->value;
+
/* Do not copy the attributes to index, since they don't change */
- /*
+ /* a_index->characteristics [0].value = a->value;*/
+ /* Actually, let's copy, so we can free all attribute indices, both these ones created from attributes and
+ * those that get read in from file or other processors and merged into the index. The latter ones are
+ * always allocated, not linked to an existing attribute's value.
+ */
+
if (a->value)
{
- if (a->type == adios_string)
- size++;
- a_index->characteristics [0].value = malloc (size);
- if (a->type == adios_string)
- ((char *) (a_index->characteristics [0].value)) [size] = 0;
- memcpy (a_index->characteristics [0].value, a->value, size);
+ if (a->type == adios_string_array)
+ {
+ char ** sa = (char**) malloc (a->nelems*sizeof(char*));
+ a_index->characteristics [0].value = sa;
+ int i;
+ for (i=0; i<a->nelems; i++) {
+ sa[i] = strdup ( ((char**)a->value)[i]);
+ }
+ }
+ else if (a->type == adios_string)
+ {
+ a_index->characteristics [0].value = strdup(a->value);
+ }
+ else
+ {
+ a_index->characteristics [0].value = malloc (size);
+ memcpy (a_index->characteristics [0].value, a->value, size);
+ }
}
else
{
a_index->characteristics [0].value = 0;
}
- */
+
if (a_index->nelems > 1) {
// for array attributes, save nelems as a dimension characteristic
@@ -3795,6 +3968,12 @@ void adios_build_index_v1 (struct adios_file_struct * fd,
a = a->next;
}
+
+ //Yuan: at the end of close, save current index
+ // if(fd->group->do_ts_aggr==1 && fd->group->ts_to_buffer>1) {
+ // printf("store the index\n");
+ // fd->group->index=index;
+ // }
}
int adios_write_index_v1 (char ** buffer
@@ -3879,6 +4058,7 @@ int adios_write_index_v1 (char ** buffer
index_size += len;
group_size += len;
+ //printf("write index time=%lu\n", pg_root->time_index);
buffer_write (buffer, buffer_size, buffer_offset
,&pg_root->time_index, 4
);
@@ -3961,6 +4141,7 @@ int adios_write_index_v1 (char ** buffer
index_size += 8;
var_size += 8;
+ //printf("name=%s vars_root->characteristics_count=%d\n",vars_root->var_name, vars_root->characteristics_count);
for (i = 0; i < vars_root->characteristics_count; i++)
{
uint64_t size;
@@ -5042,7 +5223,8 @@ uint16_t adios_write_var_characteristics_v1 (struct adios_file_struct * fd
int adios_generate_var_characteristics_v1 (struct adios_file_struct * fd, struct adios_var_struct * var)
{
uint64_t total_size = 0;
- uint64_t size = 0;
+ uint64_t n = 0;
+ uint64_t total_n = 0;
enum ADIOS_DATATYPES original_var_type = adios_transform_get_var_original_type_var(var);
if (var->transform_type != adios_transform_none) {
@@ -5054,6 +5236,7 @@ int adios_generate_var_characteristics_v1 (struct adios_file_struct * fd, struct
if (var->bitmap == 0)
return 0;
+ enum ADIOS_STATISTICS_FLAG stat_flag = fd->group->stats_flag;
int32_t map[32];
memset (map, -1, sizeof(map));
@@ -5087,10 +5270,12 @@ int adios_generate_var_characteristics_v1 (struct adios_file_struct * fd, struct
-# define CHECK_FLOAT() (isnan (data [size]) || !isfinite (data [size]))
+# define CHECK_FLOAT() (isnan (data [n]) || !isfinite (data [n]))
# define CHECK_INT() (0)
+# define CHECK_FLOAT_NAN() (isnan (data [n]))
+# define CHECK_INT_NAN() (0)
-#define ADIOS_STATISTICS(a,b,NON_FINITE_CHECK) \
+#define ADIOS_STATISTICS_FULL(a,b,NON_FINITE_CHECK) \
{\
a * data = (a *) var->data; \
int i, j; \
@@ -5122,41 +5307,87 @@ int adios_generate_var_characteristics_v1 (struct adios_file_struct * fd, struct
hist->frequencies = calloc ((hist->num_breaks + 1), adios_get_type_size(adios_unsigned_integer, "")); \
} \
int have_finite_value = 0; \
- size = 0; \
- while ((size * b) < total_size) \
+ n = 0; \
+ while ((n * b) < total_size) \
{ \
if (NON_FINITE_CHECK()) {\
- size ++; \
+ n ++; \
continue; \
}\
if (!have_finite_value) { \
- *min = data [size]; \
- *max = data [size]; \
- *sum = data [size]; \
- *sum_square = (data [size] * data [size]) ; \
+ *min = data [n]; \
+ *max = data [n]; \
+ *sum = data [n]; \
+ *sum_square = (data [n] * data [n]) ; \
*cnt = *cnt + 1; \
if (map[adios_statistic_hist] != -1) \
- HIST(data [size]); \
+ HIST(data [n]); \
have_finite_value = 1; \
- size ++; \
+ n ++; \
continue; \
} \
- if (data [size] < *min) \
- *min = data [size]; \
- if (data [size] > *max) \
- *max = data [size]; \
- *sum += data [size]; \
- *sum_square += (data [size] * data [size]) ; \
+ if (data [n] < *min) \
+ *min = data [n]; \
+ if (data [n] > *max) \
+ *max = data [n]; \
+ *sum += data [n]; \
+ *sum_square += (data [n] * data [n]) ; \
*cnt = *cnt + 1; \
if (map[adios_statistic_hist] != -1) \
- HIST(data [size]); \
- size++; \
+ HIST(data [n]); \
+ n++; \
} \
if (map[adios_statistic_finite] != -1) \
* ((uint8_t * ) stats[map[adios_statistic_finite]].data) = have_finite_value; \
return 0; \
}
+#define ADIOS_STATISTICS_MINMAX(a,b,NAN_CHECK) \
+{\
+ a * data = (a *) var->data; \
+ struct adios_stat_struct * stats = var->stats[0]; \
+ map[adios_statistic_min] = 0; \
+ map[adios_statistic_max] = 1; \
+ map[adios_statistic_finite] = 2; \
+ stats[0].data = malloc(adios_get_stat_size(NULL, original_var_type, adios_statistic_min)); \
+ stats[1].data = malloc(adios_get_stat_size(NULL, original_var_type, adios_statistic_max)); \
+ stats[2].data = malloc(adios_get_stat_size(NULL, original_var_type, adios_statistic_finite)); \
+ a *min = (a *) stats[map[adios_statistic_min]].data; \
+ a *max = (a *) stats[map[adios_statistic_max]].data; \
+ int have_finite_value = 0; \
+ total_n = total_size / b; \
+ n = 0; \
+ while (n < total_n && NAN_CHECK()) \
+ { \
+ n++; \
+ } \
+ if (n < total_n) { \
+ *min = *data; \
+ *max = *data; \
+ have_finite_value = 1; \
+ data++; \
+ n++; \
+ }\
+ while (n < total_n) \
+ { \
+ if (*data < *min) \
+ *min = *data; \
+ if (*data > *max) \
+ *max = *data; \
+ n++; \
+ data++; \
+ } \
+ * ((uint8_t * ) stats[map[adios_statistic_finite]].data) = have_finite_value; \
+ return 0; \
+}
+
+#define ADIOS_STATISTICS(a,b,NON_FINITE_CHECK,NAN_CHECK) \
+ if (stat_flag == adios_stat_minmax) \
+ ADIOS_STATISTICS_MINMAX(a,b,NAN_CHECK) \
+ else \
+ ADIOS_STATISTICS_FULL(a,b,NON_FINITE_CHECK)
+
+
#define MIN_MAX(a,b)\
{\
a * data = (a *) var->data; \
@@ -5173,37 +5404,37 @@ int adios_generate_var_characteristics_v1 (struct adios_file_struct * fd, struct
switch (original_var_type)
{
case adios_byte:
- ADIOS_STATISTICS(int8_t,1,CHECK_INT)
+ ADIOS_STATISTICS(int8_t,1,CHECK_INT,CHECK_INT_NAN)
case adios_unsigned_byte:
- ADIOS_STATISTICS(uint8_t,1,CHECK_INT)
+ ADIOS_STATISTICS(uint8_t,1,CHECK_INT,CHECK_INT_NAN)
case adios_short:
- ADIOS_STATISTICS(int16_t,2,CHECK_INT)
+ ADIOS_STATISTICS(int16_t,2,CHECK_INT,CHECK_INT_NAN)
case adios_unsigned_short:
- ADIOS_STATISTICS(uint16_t,2,CHECK_INT)
+ ADIOS_STATISTICS(uint16_t,2,CHECK_INT,CHECK_INT_NAN)
case adios_integer:
- ADIOS_STATISTICS(int32_t,4,CHECK_INT)
+ ADIOS_STATISTICS(int32_t,4,CHECK_INT,CHECK_INT_NAN)
case adios_unsigned_integer:
- ADIOS_STATISTICS(uint32_t,4,CHECK_INT)
+ ADIOS_STATISTICS(uint32_t,4,CHECK_INT,CHECK_INT_NAN)
case adios_long:
- ADIOS_STATISTICS(int64_t,8,CHECK_INT)
+ ADIOS_STATISTICS(int64_t,8,CHECK_INT,CHECK_INT_NAN)
case adios_unsigned_long:
- ADIOS_STATISTICS(uint64_t,8,CHECK_INT)
+ ADIOS_STATISTICS(uint64_t,8,CHECK_INT,CHECK_INT_NAN)
case adios_real:
- ADIOS_STATISTICS(float,4,CHECK_FLOAT)
+ ADIOS_STATISTICS(float,4,CHECK_FLOAT,CHECK_FLOAT_NAN)
case adios_double:
- ADIOS_STATISTICS(double,8,CHECK_FLOAT)
+ ADIOS_STATISTICS(double,8,CHECK_FLOAT,CHECK_FLOAT_NAN)
case adios_long_double:
- ADIOS_STATISTICS(long double,16,CHECK_FLOAT)
+ ADIOS_STATISTICS(long double,16,CHECK_FLOAT,CHECK_FLOAT_NAN)
case adios_complex:
{
@@ -5265,66 +5496,71 @@ int adios_generate_var_characteristics_v1 (struct adios_file_struct * fd, struct
}
*/
- *cnt_r = *cnt_i = *cnt_m = 0;
*min_r = *min_i = *min_m = HUGE_VAL;
*max_r = *max_i = *max_m = -HUGE_VAL;
- *sum_r = *sum_i = *sum_m = 0;
- *sum_square_r = *sum_square_i = *sum_square_m = 0;
+ if (stat_flag == adios_stat_full)
+ {
+ *cnt_r = *cnt_i = *cnt_m = 0;
+ *sum_r = *sum_i = *sum_m = 0;
+ *sum_square_r = *sum_square_i = *sum_square_m = 0;
+ }
- while ((size * sizeof(float)) < total_size) {
+ while ((n * sizeof(float)) < total_size) {
- magnitude = sqrt((double) data [size] * data [size] + (double) data[size + 1] * data[size + 1]);
+ magnitude = sqrt((double) data [n] * data [n] + (double) data[n + 1] * data[n + 1]);
// Both real and imaginary parts have to be finite, else skip calculating the characteristic
- if ( isnan(data [size]) || !isfinite(data [size]) || isnan(data[size + 1]) || !isfinite(data[size + 1]) ) {
- size += 2;
+ if ( isnan(data [n]) || !isfinite(data [n]) || isnan(data[n + 1]) || !isfinite(data[n + 1]) ) {
+ n += 2;
continue;
}
finite = 1;
// Updating the characteristic values
- if (data [size] < *min_r)
- *min_r = data [size];
- if (data [size + 1] < *min_i)
- *min_i = data [size + 1];
+ if (data [n] < *min_r)
+ *min_r = data [n];
+ if (data [n + 1] < *min_i)
+ *min_i = data [n + 1];
if (magnitude < *min_m)
*min_m = magnitude;
- if (data [size] > *max_r)
- *max_r = data [size];
- if (data [size + 1] > *max_i)
- *max_i = data [size + 1];
+ if (data [n] > *max_r)
+ *max_r = data [n];
+ if (data [n + 1] > *max_i)
+ *max_i = data [n + 1];
if (magnitude > *max_m)
*max_m = magnitude;
- *sum_r += data [size];
- *sum_i += data [size + 1];
- *sum_m += magnitude;
-
- *sum_square_r += (double) data [size] * data [size];
- *sum_square_i += (double) data [size + 1] * data [size + 1];
- *sum_square_m += magnitude * magnitude;
-
- *cnt_r = *cnt_r + 1;
- *cnt_i = *cnt_i + 1;
- *cnt_m = *cnt_m + 1;
- // Histogram not available yet
- /*
- if (map[adios_statistic_hist] != -1)
+ if (stat_flag == adios_stat_full)
{
- hist = hist_r;
- HIST (data[size]);
+ *sum_r += data [n];
+ *sum_i += data [n + 1];
+ *sum_m += magnitude;
+
+ *sum_square_r += (double) data [n] * data [n];
+ *sum_square_i += (double) data [n + 1] * data [n + 1];
+ *sum_square_m += magnitude * magnitude;
+
+ *cnt_r = *cnt_r + 1;
+ *cnt_i = *cnt_i + 1;
+ *cnt_m = *cnt_m + 1;
+ // Histogram not available yet
+ /*
+ if (map[adios_statistic_hist] != -1)
+ {
+ hist = hist_r;
+ HIST (data[size]);
- hist = hist_i;
- HIST (data[size + 1]);
+ hist = hist_i;
+ HIST (data[size + 1]);
- hist = hist_m;
- HIST (magnitude);
+ hist = hist_m;
+ HIST (magnitude);
+ }
+ */
}
- */
-
- size += 2;
+ n += 2;
}
if (map[adios_statistic_finite] != -1)
@@ -5395,67 +5631,72 @@ int adios_generate_var_characteristics_v1 (struct adios_file_struct * fd, struct
cnt_r = (uint32_t *) stats[1][map[adios_statistic_cnt]].data;
cnt_i = (uint32_t *) stats[2][map[adios_statistic_cnt]].data;
- *cnt_r = *cnt_i = *cnt_m = 0;
*min_r = *min_i = *min_m = HUGE_VAL;
*max_r = *max_i = *max_m = -HUGE_VAL;
- *sum_r = *sum_i = *sum_m = 0;
- *sum_square_r = *sum_square_i = *sum_square_m = 0;
+ if (stat_flag == adios_stat_full)
+ {
+ *cnt_r = *cnt_i = *cnt_m = 0;
+ *sum_r = *sum_i = *sum_m = 0;
+ *sum_square_r = *sum_square_i = *sum_square_m = 0;
+ }
- while ((size * sizeof(double)) < total_size)
+ while ((n * sizeof(double)) < total_size)
{
- magnitude = sqrt((long double) data [size] * data [size] +
- (long double) data[size + 1] * data[size + 1]);
+ magnitude = sqrt((long double) data [n] * data [n] +
+ (long double) data[n + 1] * data[n + 1]);
// Both real and imaginary parts have to be finite, else skip calculating the characteristic
- if ( isnan(data [size]) || !isfinite(data [size]) || isnan(data[size + 1]) || !isfinite(data[size + 1]) ) {
- size += 2;
+ if ( isnan(data [n]) || !isfinite(data [n]) || isnan(data[n + 1]) || !isfinite(data[n + 1]) ) {
+ n += 2;
continue;
}
finite = 1;
- if (data [size] < *min_r)
- *min_r = data [size];
- if (data [size + 1] < *min_i)
- *min_i = data [size + 1];
+ if (data [n] < *min_r)
+ *min_r = data [n];
+ if (data [n + 1] < *min_i)
+ *min_i = data [n + 1];
if (magnitude < *min_m)
*min_m = magnitude;
- if (data [size] > *max_r)
- *max_r = data [size];
- if (data [size + 1] > *max_i)
- *max_i = data [size + 1];
+ if (data [n] > *max_r)
+ *max_r = data [n];
+ if (data [n + 1] > *max_i)
+ *max_i = data [n + 1];
if (magnitude > *max_m)
*max_m = magnitude;
- *sum_r += data [size];
- *sum_i += data [size + 1];
- *sum_m += magnitude;
-
- *sum_square_r += (long double) data [size] * data [size];
- *sum_square_i += (long double) data [size + 1] * data [size + 1];
- *sum_square_m += magnitude * magnitude;
-
- // Histgram has not available for complex yet
- /*
- if (map[adios_statistic_hist] != -1)
+ if (stat_flag == adios_stat_full)
{
- hist = hist_r;
- HIST (data[size]);
+ *sum_r += data [n];
+ *sum_i += data [n + 1];
+ *sum_m += magnitude;
- hist = hist_i;
- HIST (data[size + 1]);
+ *sum_square_r += (long double) data [n] * data [n];
+ *sum_square_i += (long double) data [n + 1] * data [n + 1];
+ *sum_square_m += magnitude * magnitude;
- hist = hist_m;
- HIST (magnitude);
- }
- */
+ // Histgram has not available for complex yet
+ /*
+ if (map[adios_statistic_hist] != -1)
+ {
+ hist = hist_r;
+ HIST (data[size]);
- *cnt_r = *cnt_r + 1;
- *cnt_i = *cnt_i + 1;
- *cnt_m = *cnt_m + 1;
+ hist = hist_i;
+ HIST (data[size + 1]);
- size += 2;
+ hist = hist_m;
+ HIST (magnitude);
+ }
+ */
+
+ *cnt_r = *cnt_r + 1;
+ *cnt_i = *cnt_i + 1;
+ *cnt_m = *cnt_m + 1;
+ }
+ n += 2;
}
if (map[adios_statistic_finite] != -1)
diff --git a/src/core/adios_internals.h b/src/core/adios_internals.h
index a2f51c0..09a6d42 100644
--- a/src/core/adios_internals.h
+++ b/src/core/adios_internals.h
@@ -152,7 +152,7 @@ struct adios_group_struct
char * group_by;
char * time_index_name;
uint32_t time_index;
- enum ADIOS_FLAG stats_on;
+ enum ADIOS_STATISTICS_FLAG stats_flag;
uint32_t process_id;
struct adios_method_list_struct * methods;
@@ -171,8 +171,109 @@ struct adios_group_struct
struct adios_timing_struct * prev_timing_obj;
uint64_t tv_size; // the additional data size used by timing variables
#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
+ 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()
+ int do_ts_flush; // 1 if we need close during finalize/group-sync, otherwise always 0
+ struct adios_group_struct **synced_groups;
+ int synced_groups_size; // > 0 if this group forces time-aggregated groups to be flushed
+ int synced_groups_capacity; // synced_groups is a Vector
};
+static inline void SetTimeAggregation (struct adios_group_struct * g, int flag)
+{
+ g->do_ts_aggr = (flag != 0);
+}
+
+
+static inline int TimeAggregated (struct adios_group_struct * g)
+{
+ return (g->do_ts_aggr != 0);
+}
+
+static inline int NotTimeAggregated (struct adios_group_struct * g)
+{
+ return (g->do_ts_aggr == 0);
+}
+
+static inline int TimeAggregationJustBegan (struct adios_group_struct * g)
+{
+ return (g->do_ts_aggr
+ && g->ts_fd == NULL
+ //&& g->ts_to_buffer == g->max_ts
+ );
+}
+
+static inline int TimeAggregationInProgress (struct adios_group_struct * g)
+{
+ return (g->do_ts_aggr
+ && g->ts_fd != NULL
+ //&& g->ts_to_buffer < g->max_ts
+ );
+}
+// TimeAggregationAggregationInProgress => TimeAggregated AND NOT TimeAggreationJustBegan
+// TimeAggregationAggregationJustBegan => TimeAggregated AND NOT TimeAggreationInProgress
+
+static inline int TimeAggregationLastStep (struct adios_group_struct * g)
+{
+ return (g->do_ts_aggr && g->ts_to_buffer == 0);
+}
+// TimeAggregationAggregationLastStep => TimeAggregated AND TimeAggreationInProgress
+
+static inline void SetTimeAggregationFlush (struct adios_group_struct * g, int do_flush)
+{
+ g->do_ts_flush = (do_flush != 0); // => TimeAggregationIsFlushing
+ if (g->do_ts_flush)
+ g->ts_to_buffer = 0; // => TimeAggregationLastStep
+}
+
+// TimeAggregationIsFlushing => TimeAggregated AND TimeAggreationInProgress AND TimeAggregationLastStep
+static inline int TimeAggregationIsFlushing (struct adios_group_struct * g)
+{
+ return (g->do_ts_flush != 0);
+}
+
+static inline void SetTimeAggregationSyncGroup (struct adios_group_struct * g,
+ struct adios_group_struct * synced_group)
+{
+ if (g->synced_groups_capacity <= g->synced_groups_size) // first synced group
+ {
+ struct adios_group_struct ** newg = (struct adios_group_struct **)
+ realloc (g->synced_groups, g->synced_groups_size+5);
+ if (newg != NULL)
+ {
+ g->synced_groups_capacity = g->synced_groups_size + 5;
+ g->synced_groups = newg;
+ }
+ /*else
+ {
+ adios_error(err_no_memory, "Could not (re)allocate small memory for synchronized groups. "
+ "Keep the current list of %d groups synchronized with group %s\n",
+ g->synced_groups_capacity, g->name);
+ }*/
+ }
+
+ g->synced_groups[g->synced_groups_size] = synced_group;
+ g->synced_groups_size++; // => TimeAggregationIsaSyncGroup
+}
+
+static inline int TimeAggregationIsaSyncGroup (struct adios_group_struct * g)
+{
+ return (g->synced_groups_size != 0);
+}
+
+static inline void TimeAggregationGetSyncedGroups (struct adios_group_struct * g,
+ struct adios_group_struct *** synced_groups,
+ int *ngroups)
+{
+ *synced_groups = g->synced_groups;
+ *ngroups = g->synced_groups_size;
+}
+
struct adios_group_list_struct
{
struct adios_group_struct * group;
@@ -187,6 +288,7 @@ struct adios_group_list_struct
struct adios_pg_struct
{
uint64_t pg_start_in_file; // where this pg start in file, handled by methods!
+ uint64_t has_index; // Yuan: 0 or 1, if the index has been built for this PG
struct adios_var_struct * vars_written;
struct adios_var_struct * vars_written_tail; // last variable in 'vars_written'
struct adios_pg_struct * next;
@@ -205,6 +307,7 @@ struct adios_file_struct
struct adios_pg_struct * pgs_written;
struct adios_pg_struct * current_pg; // points to last PG in the list, which is being created in buffer
+ struct adios_pg_struct * first_pg_written; // Yuan: points to first PG in the list
char * allocated_bufptr; // actual allocated buffer before alignment
char * buffer; // buffer we use for building the output (aligned, made from allocated_bufptr)
@@ -493,8 +596,13 @@ int adios_common_declare_group (int64_t * id, const char * name
,const char * coordination_comm
,const char * coordination_var
,const char * time_index_name
- ,enum ADIOS_FLAG stats
- );
+ ,enum ADIOS_STATISTICS_FLAG stats
+);
+
+int adios_common_set_time_aggregation(struct adios_group_struct * group,
+ uint64_t buffersize,
+ struct adios_group_struct * syncgroup
+);
int64_t adios_common_define_var (int64_t group_id, const char * name
,const char * path, enum ADIOS_DATATYPES type
@@ -514,7 +622,7 @@ int adios_common_define_var_characteristics (struct adios_group_struct * g
,const char * bin_count
);
-void adios_common_get_group (int64_t * group_id, const char * name);
+struct adios_group_struct * adios_common_get_group (const char * name);
int adios_common_delete_attrdefs (struct adios_group_struct * g);
int adios_common_delete_vardefs (struct adios_group_struct * g);
void adios_common_free_groupstruct (struct adios_group_struct * g);
diff --git a/src/core/adios_internals_mxml.c b/src/core/adios_internals_mxml.c
index 62e04fc..4c40a85 100644
--- a/src/core/adios_internals_mxml.c
+++ b/src/core/adios_internals_mxml.c
@@ -1052,7 +1052,8 @@ static int parseGroup (mxml_node_t * node, char * schema_version)
int64_t ptr_new_group;
struct adios_group_struct * new_group;
- enum ADIOS_FLAG host_language_fortran = adios_flag_yes, enable_stats = adios_flag_yes;
+ enum ADIOS_FLAG host_language_fortran = adios_flag_yes;
+ enum ADIOS_STATISTICS_FLAG enable_stats = adios_stat_default;
int i;
for (i = 0; i < node->value.element.num_attrs; i++)
@@ -1110,25 +1111,28 @@ static int parseGroup (mxml_node_t * node, char * schema_version)
}
}
- if (!stats)
+ if (!stats || !strcasecmp (stats, "default") || !strcasecmp (stats, "minmax"))
{
- enable_stats = adios_flag_yes;
+ enable_stats = adios_stat_default;
}
else
{
- if (!strcasecmp (stats, "On"))
+ if (!strcasecmp (stats, "minmax"))
{
- enable_stats = adios_flag_yes;
+ enable_stats = adios_stat_minmax;
}
- else if (!strcasecmp (stats, "Off"))
+ else if (!strcasecmp (stats, "on") || !strcasecmp(stats, "full"))
{
- enable_stats = adios_flag_no;
+ enable_stats = adios_stat_full;
+ }
+ else if (!strcasecmp (stats, "off") || !strcasecmp(stats, "no"))
+ {
+ enable_stats = adios_stat_no;
}
else
{
- log_error ("config.xml, invalid stats %s"
- ,stats
- );
+ log_error ("config.xml: invalid statistics flag %s. "
+ "Valid options are [off|on|default|minmax].\n", stats);
return 0;
}
}
@@ -1883,9 +1887,7 @@ static int parseAnalysis (mxml_node_t * node)
return 0;
}
- adios_common_get_group (&group_id, group);
- g = (struct adios_group_struct *) group_id;
-
+ g = adios_common_get_group (group);
if (!g)
{
log_warn ("config.xml: Didn't find group %s for analysis\n", group);
@@ -2047,6 +2049,75 @@ static int parseBuffer (mxml_node_t * node)
}
+static int parseTimeAggregation (mxml_node_t * node, int rank)
+{
+ mxml_node_t * n;
+
+ const char * buffersize = 0;
+ const char * syncgroup = 0;
+ const char * group = 0;
+ uint64_t bufsize;
+ int i;
+
+
+ for (i = 0; i < node->value.element.num_attrs; i++)
+ {
+ mxml_attr_t * attr = &node->value.element.attrs [i];
+
+ GET_ATTR("buffer-size",attr,buffersize,"method")
+ GET_ATTR("sync-with-group",attr,syncgroup,"method")
+ GET_ATTR("group",attr,group,"method")
+ log_warn ("config.xml: unknown attribute '%s' on %s "
+ "(ignored)\n"
+ ,attr->name
+ ,"method"
+ );
+ }
+
+ if (!buffersize)
+ bufsize = 0;
+ else
+ bufsize = atoi (buffersize);
+
+ if (!group)
+ {
+ adios_error (err_no_group_defined, "config.xml: time-aggregation requires a group\n");
+ return 0;
+ }
+
+ struct adios_group_struct *g = adios_common_get_group (group);
+ if (!g)
+ {
+ log_warn ("config.xml: Didn't find group %s for time-aggregation\n", group);
+ return 0;
+ }
+
+ struct adios_group_struct *sg = NULL;
+ if (syncgroup) {
+ sg = adios_common_get_group (syncgroup);
+ if (!sg)
+ {
+ log_warn ("config.xml: Didn't find sync group %s for time-aggregation of group %s\n",
+ syncgroup, group);
+ }
+ }
+
+ if (rank == 0)
+ {
+ if (sg) {
+ log_info ("Set time aggregation for group '%s' with buffer size %" PRIu64 " bytes and "
+ "synchronizing flushes with group '%s'\n",
+ group, bufsize, syncgroup);
+ } else {
+ log_info ("Set time aggregation for group '%s' with buffer size %" PRIu64 " bytes\n",
+ group, bufsize);
+ }
+ }
+ int ret = adios_common_set_time_aggregation(g, bufsize, sg);
+ return ret;
+}
+
+
void PRINT_MXML_NODE (mxml_node_t *root)
{
@@ -2071,6 +2142,8 @@ void PRINT_MXML_NODE (mxml_node_t *root)
}
}
+static const char * config_file_name; // hold the name of config to allow for error messages
+
int adios_parse_config (const char * config, MPI_Comm comm)
{
FILE * fp = 0;
@@ -2175,11 +2248,12 @@ int adios_parse_config (const char * config, MPI_Comm comm)
PRINT_MXML_NODE(root);
}
-
+ config_file_name = config;
if (!root || !root->value.element.name || strcasecmp (root->value.element.name, "adios-config"))
{
adios_error (err_invalid_xml_doc, "config.xml: did not find adios-config xml element\n");
mxmlRelease (doc);
+ config_file_name = NULL;
return 0;
}
else
@@ -2226,6 +2300,7 @@ int adios_parse_config (const char * config, MPI_Comm comm)
);
mxmlRelease (doc);
+ config_file_name = NULL;
return 0;
}
@@ -2274,17 +2349,25 @@ int adios_parse_config (const char * config, MPI_Comm comm)
}
else
{
- if (!strncmp (node->value.element.name, "!--", 3))
+ if (!strcasecmp (node->value.element.name, "time-aggregation"))
{
- continue;
+ if (!parseTimeAggregation(node, rank))
+ break;
}
else
{
- log_warn ("config.xml: invalid element: %s\n"
- ,node->value.element.name
- );
-
- break;
+ if (!strncmp (node->value.element.name, "!--", 3))
+ {
+ continue;
+ }
+ else
+ {
+ log_warn ("config.xml: invalid element: %s\n"
+ ,node->value.element.name
+ );
+
+ break;
+ }
}
}
}
@@ -2293,6 +2376,7 @@ int adios_parse_config (const char * config, MPI_Comm comm)
}
mxmlRelease (doc);
+ config_file_name = NULL;
if (!saw_datagroup)
{
@@ -2416,7 +2500,6 @@ int adios_common_select_method (int priority, const char * method
,const char * base_path, int iters
)
{
- int64_t group_id;
struct adios_group_struct * g;
struct adios_method_struct * new_method;
int requires_group_comm = 0;
@@ -2461,8 +2544,7 @@ int adios_common_select_method (int priority, const char * method
return 0;
}
- adios_common_get_group (&group_id, group);
- g = (struct adios_group_struct *) group_id;
+ g = adios_common_get_group (group);
if (!g)
{
adios_error (err_missing_invalid_group, "config.xml: Didn't find group: %s for transport: %s\n"
diff --git a/src/core/adios_read.c b/src/core/adios_read.c
index 3805e53..5d28bb5 100644
--- a/src/core/adios_read.c
+++ b/src/core/adios_read.c
@@ -192,7 +192,7 @@ const char * adios_type_to_string (enum ADIOS_DATATYPES type)
return common_read_type_to_string (type);
}
-int adios_type_size(enum ADIOS_DATATYPES type, void *data)
+int adios_type_size(enum ADIOS_DATATYPES type, const void *data)
{
return common_read_type_size(type, data);
}
@@ -212,7 +212,6 @@ void adios_print_fileinfo (ADIOS_FILE *fp)
common_read_print_fileinfo(fp);
}
-
ADIOS_SELECTION * adios_selection_boundingbox (int ndim, const uint64_t *start, const uint64_t *count)
{
return a2sel_boundingbox (ndim, start, count);
diff --git a/src/core/adios_transform_methods.c b/src/core/adios_transform_methods.c
new file mode 100644
index 0000000..8cd8fe8
--- /dev/null
+++ b/src/core/adios_transform_methods.c
@@ -0,0 +1,59 @@
+#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_read.h"
+#include "core/transforms/adios_transforms_read.h"
+
+ADIOS_AVAILABLE_TRANSFORM_METHODS * adios_available_transform_methods()
+{
+ int i, n;
+ n = 0;
+ for (i = (int)adios_transform_none; i < num_adios_transform_types; i++) {
+ if (adios_transform_is_implemented((enum ADIOS_TRANSFORM_TYPE)i)) {
+ n++;
+ }
+ }
+
+ if (n == 0)
+ return NULL;
+
+ ADIOS_AVAILABLE_TRANSFORM_METHODS * t = (ADIOS_AVAILABLE_TRANSFORM_METHODS *) malloc (sizeof(ADIOS_AVAILABLE_TRANSFORM_METHODS));
+ if (!t)
+ return NULL;
+
+ t->name = (char**) malloc (n*sizeof(char*));
+ t->description = (char**) malloc (n*sizeof(char*));
+ t->ntransforms = n;
+
+ n = 0;
+ for (i = (int)adios_transform_none; i < num_adios_transform_types; i++) {
+ if (adios_transform_is_implemented((enum ADIOS_TRANSFORM_TYPE)i)) {
+ t->name[n] = strdup (adios_transform_plugin_primary_xml_alias((enum ADIOS_TRANSFORM_TYPE)i));
+ t->description[n] = strdup (adios_transform_plugin_desc((enum ADIOS_TRANSFORM_TYPE)i));
+ n++;
+ }
+ }
+ return t;
+}
+
+void adios_available_transform_methods_free (ADIOS_AVAILABLE_TRANSFORM_METHODS *t)
+{
+ int i;
+ if (t)
+ {
+ for (i=0; i < t->ntransforms; i++)
+ {
+ if (t->name[i]) {
+ free (t->name[i]);
+ t->name[i] = NULL;
+ }
+ if (t->description[i]) {
+ free (t->description[i]);
+ t->description[i] = NULL;
+ }
+ }
+ free (t);
+ }
+}
+
diff --git a/src/core/adiosf.c b/src/core/adiosf.c
index 4cdf778..785c3b4 100644
--- a/src/core/adiosf.c
+++ b/src/core/adiosf.c
@@ -477,7 +477,8 @@ void FC_FUNC_(adios_stop_calculation, ADIOS_STOP_CALCULATION) (int * err)
///////////////////////////////////////////////////////////////////////////////
void FC_FUNC_(adios_close, ADIOS_CLOSE) (int64_t * fd_p, int * err)
{
- *err = common_adios_close (*fd_p);
+ struct adios_file_struct * fd = (struct adios_file_struct *) *fd_p;
+ *err = common_adios_close (fd);
}
///////////////////////////////////////////////////////////////////////////////
@@ -502,7 +503,7 @@ void FC_FUNC_(adios_timing_write_xml, ADIOS_TIMING_WRITE_XML) (int64_t * fd_p, c
// group a list of vars into a composite group
void FC_FUNC_(adios_declare_group, ADIOS_DECLARE_GROUP)
(int64_t * id, const char * name
- ,const char * time_index, enum ADIOS_FLAG *stats
+ ,const char * time_index, enum ADIOS_STATISTICS_FLAG *stats
,int * err, int name_size, int time_index_size
)
{
@@ -513,8 +514,12 @@ void FC_FUNC_(adios_declare_group, ADIOS_DECLARE_GROUP)
buf1 = futils_fstr_to_cstr (name, name_size);
buf2 = futils_fstr_to_cstr (time_index, time_index_size);
+ enum ADIOS_STATISTICS_FLAG stat_flag = *stats;
+ if (stat_flag == adios_stat_no_do_not_use_this)
+ stat_flag = adios_stat_no;
+
if (buf1 != 0 && buf2 != 0) {
- int ret = adios_common_declare_group (id, buf1, adios_flag_yes, "", "", buf2, *stats);
+ int ret = adios_common_declare_group (id, buf1, adios_flag_yes, "", "", buf2, stat_flag);
free (buf1);
free (buf2);
if (ret == 1) {
@@ -525,6 +530,26 @@ void FC_FUNC_(adios_declare_group, ADIOS_DECLARE_GROUP)
*err = adios_errno;
}
+int FC_FUNC_(adios_set_time_aggregation, ADIOS_SET_TIME_AGGREGATION)
+ (int64_t * group_id, int64_t * buffersize, int64_t * sync_group_id, int * err)
+{
+ adios_errno = err_no_error;
+ if (*group_id == 0) {
+ adios_error (err_invalid_group, "adios_set_time_aggregation() called with 0 argument\n");
+ }
+ else
+ {
+ struct adios_group_struct * g = (struct adios_group_struct *) *group_id;
+ struct adios_group_struct * sg = NULL;
+ if (*sync_group_id != 0)
+ sg = (struct adios_group_struct *) *sync_group_id;
+ uint64_t bufsize = (uint64_t) *buffersize;
+
+ adios_common_set_time_aggregation(g, bufsize, sg);
+ }
+ *err = adios_errno;
+}
+
///////////////////////////////////////////////////////////////////////////////
// adios_common_define_var is in adios_internals.c
// declare a single var as an entry in a group
diff --git a/src/core/adiosf_defs_mod.f90 b/src/core/adiosf_defs_mod.f90
index 2f6d826..3b626ea 100644
--- a/src/core/adiosf_defs_mod.f90
+++ b/src/core/adiosf_defs_mod.f90
@@ -64,6 +64,14 @@ module adios_defs_mod
integer, parameter :: ADIOS_SELECTION_TYPE_AUTO = 3
!
+ ! Statistics option in adios_declare_group()
+ !
+ integer, parameter :: ADIOS_STAT_NO = -1 ! turn off statistics generation
+ integer, parameter :: ADIOS_STAT_DEFAULT = 0 ! min + max only
+ integer, parameter :: ADIOS_STAT_FULL = 1 ! all statistics turned on
+
+
+ !
! ADIOS error codes
!
integer, parameter :: err_no_error = 0
diff --git a/src/core/adiosf_write_mod.f90 b/src/core/adiosf_write_mod.f90
index 231b29f..195d9f3 100644
--- a/src/core/adiosf_write_mod.f90
+++ b/src/core/adiosf_write_mod.f90
@@ -113,6 +113,14 @@ module adios_write_mod
integer, intent(out) :: err
end subroutine
+ subroutine adios_set_time_aggregation (group_id, buffersize, sync_group_id, err)
+ implicit none
+ integer*8, intent(in) :: group_id
+ integer*8, intent(in) :: buffersize
+ integer*8, intent(in) :: sync_group_id
+ integer, intent(out) :: err
+ end subroutine
+
subroutine adios_define_var (group_id, varname, path, vartype, dimensions, global_dimensions, local_offsets, id)
implicit none
integer*8, intent(in) :: group_id
@@ -645,7 +653,7 @@ module adios_write_mod
end interface
- contains
+contains
!
! ADIOS_WRITE generic interface
@@ -653,3210 +661,3210 @@ module adios_write_mod
! Usage: call adios_write (fd, varname, data, err)
!
!
- !
- ! scalars
- !
-
- ! INTEGER*1 scalar
- subroutine adios_write_int1_d0 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*1, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! INTEGER*2 scalar
- subroutine adios_write_int2_d0 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*2, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! INTEGER*4 scalar
- subroutine adios_write_int4_d0 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*4, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! INTEGER*8 scalar
- subroutine adios_write_int8_d0 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*8, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! REAL*4 scalar
- subroutine adios_write_real4_d0 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*4, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! REAL*8 scalar
- subroutine adios_write_real8_d0 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*8, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! COMPLEX (*8) scalar
- subroutine adios_write_complex8_d0 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! DOUBLE-COMPLEX scalar
- subroutine adios_write_complex16_d0 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex*16, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! CHARACTER scalar (Same as 1D?)
- !subroutine adios_write_char_d0 (fd, varname, data, err)
- ! implicit none
- ! integer*8, intent(in) :: fd
- ! character(*), intent(in) :: varname
- ! character(*), intent(inout) :: data
- ! integer, intent(in) :: err
- !
- ! call adios_write_f2c (fd, varname, data, err)
- !end subroutine
-
- ! LOGICAL*1 scalar
- subroutine adios_write_logical1_d0 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*1, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! LOGICAL*2 scalar
- subroutine adios_write_logical2_d0 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*2, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! LOGICAL*4 scalar
- subroutine adios_write_logical4_d0 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*4, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! LOGICAL*8 scalar
- subroutine adios_write_logical8_d0 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*8, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
-
- !
- ! 1D data
- !
-
- ! INTEGER*1 array
- subroutine adios_write_int1_d1 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*1, dimension(*), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ !
+ ! scalars
+ !
- ! INTEGER*2 array
- subroutine adios_write_int2_d1 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*2, dimension(*), intent(in) :: data
- integer, intent(in) :: err
+ ! INTEGER*1 scalar
+ subroutine adios_write_int1_d0 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*1, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*2 scalar
+ subroutine adios_write_int2_d0 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*2, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*4 scalar
+ subroutine adios_write_int4_d0 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*4, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*8 scalar
+ subroutine adios_write_int8_d0 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*8, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! REAL*4 scalar
+ subroutine adios_write_real4_d0 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*4, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! REAL*8 scalar
+ subroutine adios_write_real8_d0 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*8, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! COMPLEX (*8) scalar
+ subroutine adios_write_complex8_d0 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX scalar
+ subroutine adios_write_complex16_d0 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex*16, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! CHARACTER scalar (Same as 1D?)
+ !subroutine adios_write_char_d0 (fd, varname, data, err)
+ ! implicit none
+ ! integer*8, intent(in) :: fd
+ ! character(*), intent(in) :: varname
+ ! character(*), intent(inout) :: data
+ ! integer, intent(in) :: err
+ !
+ ! call adios_write_f2c (fd, varname, data, err)
+ !end subroutine
+
+ ! LOGICAL*1 scalar
+ subroutine adios_write_logical1_d0 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*1, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*2 scalar
+ subroutine adios_write_logical2_d0 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*2, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*4 scalar
+ subroutine adios_write_logical4_d0 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*4, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*8 scalar
+ subroutine adios_write_logical8_d0 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*8, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
- ! INTEGER*4 array
- subroutine adios_write_int4_d1 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*4, dimension(*), intent(in) :: data
- integer, intent(in) :: err
+ !
+ ! 1D data
+ !
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ ! INTEGER*1 array
+ subroutine adios_write_int1_d1 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*1, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*2 array
+ subroutine adios_write_int2_d1 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*2, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*4 array
+ subroutine adios_write_int4_d1 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*4, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*8 array
+ subroutine adios_write_int8_d1 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*8, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! REAL*4 array
+ subroutine adios_write_real4_d1 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*4, dimension(*), intent(out) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! REAL*8 array
+ subroutine adios_write_real8_d1 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*8, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! COMPLEX (*8) array
+ subroutine adios_write_complex8_d1 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX array
+ subroutine adios_write_complex16_d1 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex*16,dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! CHARACTER array
+ subroutine adios_write_char_d1 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ character(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*1 array
+ subroutine adios_write_logical1_d1 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*1, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*2 array
+ subroutine adios_write_logical2_d1 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*2, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*4 array
+ subroutine adios_write_logical4_d1 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*4, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*8 array
+ subroutine adios_write_logical8_d1 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*8, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
- ! INTEGER*8 array
- subroutine adios_write_int8_d1 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*8, dimension(*), intent(in) :: data
- integer, intent(in) :: err
+ !
+ ! 2D data
+ !
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ ! INTEGER*1 array
+ subroutine adios_write_int1_d2 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*1, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*2 array
+ subroutine adios_write_int2_d2 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*2, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*4 array
+ subroutine adios_write_int4_d2 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*4, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*8 array
+ subroutine adios_write_int8_d2 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*8, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! REAL*4 array
+ subroutine adios_write_real4_d2 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*4, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! REAL*8 array
+ subroutine adios_write_real8_d2 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*8, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! COMPLEX (*8) array
+ subroutine adios_write_complex8_d2 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX array
+ subroutine adios_write_complex16_d2 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex*16,dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! CHARACTER array
+ subroutine adios_write_char_d2 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ character(*),dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*1 array
+ subroutine adios_write_logical1_d2 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*1, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*2 array
+ subroutine adios_write_logical2_d2 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*2, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*4 array
+ subroutine adios_write_logical4_d2 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*4, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*8 array
+ subroutine adios_write_logical8_d2 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*8, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
- ! REAL*4 array
- subroutine adios_write_real4_d1 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*4, dimension(*), intent(out) :: data
- integer, intent(in) :: err
+ !
+ ! 3D data
+ !
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ ! INTEGER*1 array
+ subroutine adios_write_int1_d3 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*1, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*2 array
+ subroutine adios_write_int2_d3 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*2, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*4 array
+ subroutine adios_write_int4_d3 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*4, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*8 array
+ subroutine adios_write_int8_d3 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*8, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! REAL*4 array
+ subroutine adios_write_real4_d3 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*4, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! REAL*8 array
+ subroutine adios_write_real8_d3 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*8, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! COMPLEX (*8) array
+ subroutine adios_write_complex8_d3 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX array
+ subroutine adios_write_complex16_d3 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex*16,dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! CHARACTER array
+ subroutine adios_write_char_d3 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ character(*),dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*1 array
+ subroutine adios_write_logical1_d3 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*1, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*2 array
+ subroutine adios_write_logical2_d3 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*2, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*4 array
+ subroutine adios_write_logical4_d3 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*4, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*8 array
+ subroutine adios_write_logical8_d3 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*8, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
- ! REAL*8 array
- subroutine adios_write_real8_d1 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*8, dimension(*), intent(in) :: data
- integer, intent(in) :: err
+ !
+ ! 4D data
+ !
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ ! INTEGER*1 array
+ subroutine adios_write_int1_d4 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*1, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*2 array
+ subroutine adios_write_int2_d4 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*2, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*4 array
+ subroutine adios_write_int4_d4 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*4, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*8 array
+ subroutine adios_write_int8_d4 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*8, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! REAL*4 array
+ subroutine adios_write_real4_d4 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*4, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! REAL*8 array
+ subroutine adios_write_real8_d4 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*8, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! COMPLEX (*8) array
+ subroutine adios_write_complex8_d4 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX array
+ subroutine adios_write_complex16_d4 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex*16,dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! CHARACTER array
+ subroutine adios_write_char_d4 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ character(*),dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*1 array
+ subroutine adios_write_logical1_d4 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*1, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*2 array
+ subroutine adios_write_logical2_d4 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*2, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*4 array
+ subroutine adios_write_logical4_d4 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*4, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*8 array
+ subroutine adios_write_logical8_d4 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*8, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
- ! COMPLEX (*8) array
- subroutine adios_write_complex8_d1 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex, dimension(*), intent(in) :: data
- integer, intent(in) :: err
+ !
+ ! 5D data
+ !
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ ! INTEGER*1 array
+ subroutine adios_write_int1_d5 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*1, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*2 array
+ subroutine adios_write_int2_d5 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*2, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*4 array
+ subroutine adios_write_int4_d5 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*4, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*8 array
+ subroutine adios_write_int8_d5 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*8, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! REAL*4 array
+ subroutine adios_write_real4_d5 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*4, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! REAL*8 array
+ subroutine adios_write_real8_d5 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*8, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! COMPLEX (*8) array
+ subroutine adios_write_complex8_d5 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX array
+ subroutine adios_write_complex16_d5 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex*16,dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! CHARACTER array
+ subroutine adios_write_char_d5 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ character(*),dimension(:,:,:,:),intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*1 array
+ subroutine adios_write_logical1_d5 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*1, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*2 array
+ subroutine adios_write_logical2_d5 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*2, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*4 array
+ subroutine adios_write_logical4_d5 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*4, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*8 array
+ subroutine adios_write_logical8_d5 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*8, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
- ! DOUBLE-COMPLEX array
- subroutine adios_write_complex16_d1 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex*16,dimension(*), intent(in) :: data
- integer, intent(in) :: err
+ !
+ ! 6D data
+ !
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ ! INTEGER*1 array
+ subroutine adios_write_int1_d6 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*1, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*2 array
+ subroutine adios_write_int2_d6 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*2, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*4 array
+ subroutine adios_write_int4_d6 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*4, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! INTEGER*8 array
+ subroutine adios_write_int8_d6 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*8, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! REAL*4 array
+ subroutine adios_write_real4_d6 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*4, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! REAL*8 array
+ subroutine adios_write_real8_d6 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*8, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! COMPLEX (*8) array
+ subroutine adios_write_complex8_d6 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX array
+ subroutine adios_write_complex16_d6 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex*16,dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! CHARACTER array
+ subroutine adios_write_char_d6 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ character(*),dimension(:,:,:,:,:),intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*1 array
+ subroutine adios_write_logical1_d6 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*1, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*2 array
+ subroutine adios_write_logical2_d6 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*2, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*4 array
+ subroutine adios_write_logical4_d6 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*4, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
+
+ ! LOGICAL*8 array
+ subroutine adios_write_logical8_d6 (fd, varname, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*8, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_f2c (fd, varname, data, err)
+ end subroutine
- ! CHARACTER array
- subroutine adios_write_char_d1 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- character(*), intent(in) :: data
- integer, intent(in) :: err
+ ! end of ADIOS_WRITE functions
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
- ! LOGICAL*1 array
- subroutine adios_write_logical1_d1 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*1, dimension(*), intent(in) :: data
- integer, intent(in) :: err
+ !
+ !
+ ! ADIOS_WRITE_BYID generic interface
+ !
+ ! Usage: call adios_write_byid (fd, varid, data, err)
+ !
+ !
+ !
+ ! scalars
+ !
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ ! INTEGER*1 scalar
+ subroutine adios_write_byid_int1_d0 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*1, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*2 scalar
+ subroutine adios_write_byid_int2_d0 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*2, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*4 scalar
+ subroutine adios_write_byid_int4_d0 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*4, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*8 scalar
+ subroutine adios_write_byid_int8_d0 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*8, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! REAL*4 scalar
+ subroutine adios_write_byid_real4_d0 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ real*4, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! REAL*8 scalar
+ subroutine adios_write_byid_real8_d0 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ real*8, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! COMPLEX (*8) scalar
+ subroutine adios_write_byid_complex8_d0 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ complex, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX scalar
+ subroutine adios_write_byid_complex16_d0 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ complex*16, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! CHARACTER scalar (Same as 1D?)
+ !subroutine adios_write_byid_char_d0 (fd, varid, data, err)
+ ! implicit none
+ ! integer*8, intent(in) :: fd
+ ! integer*8, intent(in) :: varid
+ ! character(*), intent(inout) :: data
+ ! integer, intent(in) :: err
+ !
+ ! call adios_write_byid_f2c (fd, varid, data, err)
+ !end subroutine
+
+ ! LOGICAL*1 scalar
+ subroutine adios_write_byid_logical1_d0 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*1, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*2 scalar
+ subroutine adios_write_byid_logical2_d0 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*2, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*4 scalar
+ subroutine adios_write_byid_logical4_d0 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*4, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*8 scalar
+ subroutine adios_write_byid_logical8_d0 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*8, intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
- ! LOGICAL*2 array
- subroutine adios_write_logical2_d1 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*2, dimension(*), intent(in) :: data
- integer, intent(in) :: err
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ !
+ ! 1D data
+ !
- ! LOGICAL*4 array
- subroutine adios_write_logical4_d1 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*4, dimension(*), intent(in) :: data
- integer, intent(in) :: err
+ ! INTEGER*1 array
+ subroutine adios_write_byid_int1_d1 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*1, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*2 array
+ subroutine adios_write_byid_int2_d1 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*2, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*4 array
+ subroutine adios_write_byid_int4_d1 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*4, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*8 array
+ subroutine adios_write_byid_int8_d1 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*8, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! REAL*4 array
+ subroutine adios_write_byid_real4_d1 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ real*4, dimension(*), intent(out) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! REAL*8 array
+ subroutine adios_write_byid_real8_d1 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ real*8, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! COMPLEX (*8) array
+ subroutine adios_write_byid_complex8_d1 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ complex, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX array
+ subroutine adios_write_byid_complex16_d1 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ complex*16,dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! CHARACTER array
+ subroutine adios_write_byid_char_d1 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ character(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*1 array
+ subroutine adios_write_byid_logical1_d1 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*1, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*2 array
+ subroutine adios_write_byid_logical2_d1 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*2, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*4 array
+ subroutine adios_write_byid_logical4_d1 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*4, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*8 array
+ subroutine adios_write_byid_logical8_d1 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*8, dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ !
+ ! 2D data
+ !
- ! LOGICAL*8 array
- subroutine adios_write_logical8_d1 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*8, dimension(*), intent(in) :: data
- integer, intent(in) :: err
+ ! INTEGER*1 array
+ subroutine adios_write_byid_int1_d2 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*1, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*2 array
+ subroutine adios_write_byid_int2_d2 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*2, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*4 array
+ subroutine adios_write_byid_int4_d2 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*4, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*8 array
+ subroutine adios_write_byid_int8_d2 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*8, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! REAL*4 array
+ subroutine adios_write_byid_real4_d2 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ real*4, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! REAL*8 array
+ subroutine adios_write_byid_real8_d2 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ real*8, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! COMPLEX (*8) array
+ subroutine adios_write_byid_complex8_d2 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ complex, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX array
+ subroutine adios_write_byid_complex16_d2 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ complex*16,dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! CHARACTER array
+ subroutine adios_write_byid_char_d2 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ character(*),dimension(*), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*1 array
+ subroutine adios_write_byid_logical1_d2 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*1, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*2 array
+ subroutine adios_write_byid_logical2_d2 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*2, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*4 array
+ subroutine adios_write_byid_logical4_d2 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*4, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*8 array
+ subroutine adios_write_byid_logical8_d2 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*8, dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ !
+ ! 3D data
+ !
- !
- ! 2D data
- !
+ ! INTEGER*1 array
+ subroutine adios_write_byid_int1_d3 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*1, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*2 array
+ subroutine adios_write_byid_int2_d3 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*2, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*4 array
+ subroutine adios_write_byid_int4_d3 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*4, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*8 array
+ subroutine adios_write_byid_int8_d3 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*8, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! REAL*4 array
+ subroutine adios_write_byid_real4_d3 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ real*4, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! REAL*8 array
+ subroutine adios_write_byid_real8_d3 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ real*8, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! COMPLEX (*8) array
+ subroutine adios_write_byid_complex8_d3 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ complex, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX array
+ subroutine adios_write_byid_complex16_d3 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ complex*16,dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! CHARACTER array
+ subroutine adios_write_byid_char_d3 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ character(*),dimension(:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*1 array
+ subroutine adios_write_byid_logical1_d3 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*1, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*2 array
+ subroutine adios_write_byid_logical2_d3 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*2, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*4 array
+ subroutine adios_write_byid_logical4_d3 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*4, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*8 array
+ subroutine adios_write_byid_logical8_d3 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*8, dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
- ! INTEGER*1 array
- subroutine adios_write_int1_d2 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*1, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
+ !
+ ! 4D data
+ !
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ ! INTEGER*1 array
+ subroutine adios_write_byid_int1_d4 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*1, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*2 array
+ subroutine adios_write_byid_int2_d4 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*2, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*4 array
+ subroutine adios_write_byid_int4_d4 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*4, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*8 array
+ subroutine adios_write_byid_int8_d4 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*8, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! REAL*4 array
+ subroutine adios_write_byid_real4_d4 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ real*4, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! REAL*8 array
+ subroutine adios_write_byid_real8_d4 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ real*8, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! COMPLEX (*8) array
+ subroutine adios_write_byid_complex8_d4 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ complex, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX array
+ subroutine adios_write_byid_complex16_d4 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ complex*16,dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! CHARACTER array
+ subroutine adios_write_byid_char_d4 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ character(*),dimension(:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*1 array
+ subroutine adios_write_byid_logical1_d4 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*1, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*2 array
+ subroutine adios_write_byid_logical2_d4 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*2, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*4 array
+ subroutine adios_write_byid_logical4_d4 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*4, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*8 array
+ subroutine adios_write_byid_logical8_d4 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*8, dimension(:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
- ! INTEGER*2 array
- subroutine adios_write_int2_d2 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*2, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
+ !
+ ! 5D data
+ !
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ ! INTEGER*1 array
+ subroutine adios_write_byid_int1_d5 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*1, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*2 array
+ subroutine adios_write_byid_int2_d5 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*2, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*4 array
+ subroutine adios_write_byid_int4_d5 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*4, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*8 array
+ subroutine adios_write_byid_int8_d5 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*8, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! REAL*4 array
+ subroutine adios_write_byid_real4_d5 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ real*4, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! REAL*8 array
+ subroutine adios_write_byid_real8_d5 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ real*8, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! COMPLEX (*8) array
+ subroutine adios_write_byid_complex8_d5 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ complex, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX array
+ subroutine adios_write_byid_complex16_d5 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ complex*16,dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! CHARACTER array
+ subroutine adios_write_byid_char_d5 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ character(*),dimension(:,:,:,:),intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*1 array
+ subroutine adios_write_byid_logical1_d5 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*1, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*2 array
+ subroutine adios_write_byid_logical2_d5 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*2, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*4 array
+ subroutine adios_write_byid_logical4_d5 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*4, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*8 array
+ subroutine adios_write_byid_logical8_d5 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*8, dimension(:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
- ! INTEGER*4 array
- subroutine adios_write_int4_d2 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*4, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
+ !
+ ! 6D data
+ !
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ ! INTEGER*1 array
+ subroutine adios_write_byid_int1_d6 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*1, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*2 array
+ subroutine adios_write_byid_int2_d6 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*2, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*4 array
+ subroutine adios_write_byid_int4_d6 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*4, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! INTEGER*8 array
+ subroutine adios_write_byid_int8_d6 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ integer*8, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! REAL*4 array
+ subroutine adios_write_byid_real4_d6 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ real*4, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! REAL*8 array
+ subroutine adios_write_byid_real8_d6 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ real*8, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! COMPLEX (*8) array
+ subroutine adios_write_byid_complex8_d6 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ complex, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX array
+ subroutine adios_write_byid_complex16_d6 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ complex*16,dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! CHARACTER array
+ subroutine adios_write_byid_char_d6 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ character(*),dimension(:,:,:,:,:),intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*1 array
+ subroutine adios_write_byid_logical1_d6 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*1, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*2 array
+ subroutine adios_write_byid_logical2_d6 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*2, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*4 array
+ subroutine adios_write_byid_logical4_d6 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*4, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
+
+ ! LOGICAL*8 array
+ subroutine adios_write_byid_logical8_d6 (fd, varid, data, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ integer*8, intent(in) :: varid
+ logical*8, dimension(:,:,:,:,:,:), intent(in) :: data
+ integer, intent(in) :: err
+
+ call adios_write_byid_f2c (fd, varid, data, err)
+ end subroutine
- ! INTEGER*8 array
- subroutine adios_write_int8_d2 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*8, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
+ ! end of ADIOS_WRITE functions
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
- ! REAL*4 array
- subroutine adios_write_real4_d2 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*4, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
- ! REAL*8 array
- subroutine adios_write_real8_d2 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*8, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
+ !
+ !
+ ! ADIOS_READ generic interface
+ !
+ ! Usage: call adios_read (fd, varname, buffer, buffer_size, err)
+ !
+ !
+ !
+ ! scalar data
+ !
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ ! INTEGER*1 scalar
+ subroutine adios_read_int1_d0 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*1, intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*2 scalar
+ subroutine adios_read_int2_d0 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*2, intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*4 scalar
+ subroutine adios_read_int4_d0 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*4, intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*8 scalar
+ subroutine adios_read_int8_d0 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*8, intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! REAL*4 scalar
+ subroutine adios_read_real4_d0 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*4, intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! REAL*8 scalar
+ subroutine adios_read_real8_d0 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*8, intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! COMPLEX (*8) scalar
+ subroutine adios_read_complex8_d0 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex, intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX scalar
+ subroutine adios_read_complex16_d0 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex*16, intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! CHARACTER scalar
+ !subroutine adios_read_char_d0 (fd, varname, buffer, buffer_size, err)
+ ! implicit none
+ ! integer*8, intent(in) :: fd
+ ! character(*), intent(in) :: varname
+ ! character(*), intent(out) :: buffer
+ ! integer*8, intent(in) :: buffer_size
+ ! integer, intent(in) :: err
+ !
+ ! call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ !end subroutine
+
+ ! LOGICAL*1 scalar
+ subroutine adios_read_logical1_d0 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*1, intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*2 scalar
+ subroutine adios_read_logical2_d0 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*2, intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*4 scalar
+ subroutine adios_read_logical4_d0 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*4, intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*8 scalar
+ subroutine adios_read_logical8_d0 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*8, intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
- ! COMPLEX (*8) array
- subroutine adios_write_complex8_d2 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ !
+ ! 1D data
+ !
- ! DOUBLE-COMPLEX array
- subroutine adios_write_complex16_d2 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex*16,dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
+ ! INTEGER*1 array
+ subroutine adios_read_int1_d1 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*1, dimension(*), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*2 array
+ subroutine adios_read_int2_d1 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*2, dimension(*), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*4 array
+ subroutine adios_read_int4_d1 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*4, dimension(*), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*8 array
+ subroutine adios_read_int8_d1 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*8, dimension(*), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! REAL*4 array
+ subroutine adios_read_real4_d1 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*4, dimension(*), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! REAL*8 array
+ subroutine adios_read_real8_d1 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*8, dimension(*), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! COMPLEX (*8) array
+ subroutine adios_read_complex8_d1 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex, dimension(*), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX array
+ subroutine adios_read_complex16_d1 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex*16,dimension(*), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! CHARACTER array
+ subroutine adios_read_char_d1 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ character(*), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*1 array
+ subroutine adios_read_logical1_d1 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*1, dimension(*), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*2 array
+ subroutine adios_read_logical2_d1 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*2, dimension(*), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*4 array
+ subroutine adios_read_logical4_d1 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*4, dimension(*), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*8 array
+ subroutine adios_read_logical8_d1 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*8, dimension(*), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ !
+ ! 2D buffer
+ !
- ! CHARACTER array
- subroutine adios_write_char_d2 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- character(*),dimension(*), intent(in) :: data
- integer, intent(in) :: err
+ ! INTEGER*1 array
+ subroutine adios_read_int1_d2 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*1, dimension(:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*2 array
+ subroutine adios_read_int2_d2 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*2, dimension(:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*4 array
+ subroutine adios_read_int4_d2 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*4, dimension(:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*8 array
+ subroutine adios_read_int8_d2 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*8, dimension(:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! REAL*4 array
+ subroutine adios_read_real4_d2 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*4, dimension(:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! REAL*8 array
+ subroutine adios_read_real8_d2 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*8, dimension(:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! COMPLEX (*8) array
+ subroutine adios_read_complex8_d2 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex, dimension(:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX array
+ subroutine adios_read_complex16_d2 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex*16,dimension(:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! CHARACTER array
+ subroutine adios_read_char_d2 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ character(*),dimension(*), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*1 array
+ subroutine adios_read_logical1_d2 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*1, dimension(:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*2 array
+ subroutine adios_read_logical2_d2 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*2, dimension(:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*4 array
+ subroutine adios_read_logical4_d2 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*4, dimension(:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*8 array
+ subroutine adios_read_logical8_d2 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*8, dimension(:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ !
+ ! 3D buffer
+ !
- ! LOGICAL*1 array
- subroutine adios_write_logical1_d2 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*1, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
+ ! INTEGER*1 array
+ subroutine adios_read_int1_d3 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*1, dimension(:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*2 array
+ subroutine adios_read_int2_d3 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*2, dimension(:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*4 array
+ subroutine adios_read_int4_d3 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*4, dimension(:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*8 array
+ subroutine adios_read_int8_d3 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*8, dimension(:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! REAL*4 array
+ subroutine adios_read_real4_d3 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*4, dimension(:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! REAL*8 array
+ subroutine adios_read_real8_d3 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*8, dimension(:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! COMPLEX (*8) array
+ subroutine adios_read_complex8_d3 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex, dimension(:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX array
+ subroutine adios_read_complex16_d3 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex*16,dimension(:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! CHARACTER array
+ subroutine adios_read_char_d3 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ character(*),dimension(:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*1 array
+ subroutine adios_read_logical1_d3 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*1, dimension(:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*2 array
+ subroutine adios_read_logical2_d3 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*2, dimension(:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*4 array
+ subroutine adios_read_logical4_d3 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*4, dimension(:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*8 array
+ subroutine adios_read_logical8_d3 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*8, dimension(:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ !
+ ! 4D buffer
+ !
- ! LOGICAL*2 array
- subroutine adios_write_logical2_d2 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*2, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
+ ! INTEGER*1 array
+ subroutine adios_read_int1_d4 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*1, dimension(:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*2 array
+ subroutine adios_read_int2_d4 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*2, dimension(:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*4 array
+ subroutine adios_read_int4_d4 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*4, dimension(:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*8 array
+ subroutine adios_read_int8_d4 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*8, dimension(:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! REAL*4 array
+ subroutine adios_read_real4_d4 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*4, dimension(:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! REAL*8 array
+ subroutine adios_read_real8_d4 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*8, dimension(:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! COMPLEX (*8) array
+ subroutine adios_read_complex8_d4 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex, dimension(:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX array
+ subroutine adios_read_complex16_d4 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex*16,dimension(:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! CHARACTER array
+ subroutine adios_read_char_d4 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ character(*),dimension(:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*1 array
+ subroutine adios_read_logical1_d4 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*1, dimension(:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*2 array
+ subroutine adios_read_logical2_d4 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*2, dimension(:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*4 array
+ subroutine adios_read_logical4_d4 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*4, dimension(:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*8 array
+ subroutine adios_read_logical8_d4 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*8, dimension(:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ !
+ ! 5D buffer
+ !
- ! LOGICAL*4 array
- subroutine adios_write_logical4_d2 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*4, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
+ ! INTEGER*1 array
+ subroutine adios_read_int1_d5 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*1, dimension(:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*2 array
+ subroutine adios_read_int2_d5 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*2, dimension(:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*4 array
+ subroutine adios_read_int4_d5 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*4, dimension(:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*8 array
+ subroutine adios_read_int8_d5 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*8, dimension(:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! REAL*4 array
+ subroutine adios_read_real4_d5 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*4, dimension(:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! REAL*8 array
+ subroutine adios_read_real8_d5 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*8, dimension(:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! COMPLEX (*8) array
+ subroutine adios_read_complex8_d5 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex, dimension(:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX array
+ subroutine adios_read_complex16_d5 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex*16,dimension(:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! CHARACTER array
+ subroutine adios_read_char_d5 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ character(*),dimension(:,:,:,:),intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*1 array
+ subroutine adios_read_logical1_d5 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*1, dimension(:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*2 array
+ subroutine adios_read_logical2_d5 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*2, dimension(:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*4 array
+ subroutine adios_read_logical4_d5 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*4, dimension(:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*8 array
+ subroutine adios_read_logical8_d5 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*8, dimension(:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
+ !
+ ! 6D buffer
+ !
- ! LOGICAL*8 array
- subroutine adios_write_logical8_d2 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*8, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
+ ! INTEGER*1 array
+ subroutine adios_read_int1_d6 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*1, dimension(:,:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*2 array
+ subroutine adios_read_int2_d6 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*2, dimension(:,:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*4 array
+ subroutine adios_read_int4_d6 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*4, dimension(:,:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! INTEGER*8 array
+ subroutine adios_read_int8_d6 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ integer*8, dimension(:,:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! REAL*4 array
+ subroutine adios_read_real4_d6 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*4, dimension(:,:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! REAL*8 array
+ subroutine adios_read_real8_d6 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ real*8, dimension(:,:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! COMPLEX (*8) array
+ subroutine adios_read_complex8_d6 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex, dimension(:,:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! DOUBLE-COMPLEX array
+ subroutine adios_read_complex16_d6 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ complex*16,dimension(:,:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! CHARACTER array
+ subroutine adios_read_char_d6 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ character(*),dimension(:,:,:,:,:),intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*1 array
+ subroutine adios_read_logical1_d6 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*1, dimension(:,:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*2 array
+ subroutine adios_read_logical2_d6 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*2, dimension(:,:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*4 array
+ subroutine adios_read_logical4_d6 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*4, dimension(:,:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
+
+ ! LOGICAL*8 array
+ subroutine adios_read_logical8_d6 (fd, varname, buffer, buffer_size, err)
+ implicit none
+ integer*8, intent(in) :: fd
+ character(*), intent(in) :: varname
+ logical*8, dimension(:,:,:,:,:,:), intent(out) :: buffer
+ integer*8, intent(in) :: buffer_size
+ integer, intent(in) :: err
+
+ call adios_read_f2c (fd, varname, buffer, buffer_size, err)
+ end subroutine
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- !
- ! 3D data
- !
-
- ! INTEGER*1 array
- subroutine adios_write_int1_d3 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*1, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! INTEGER*2 array
- subroutine adios_write_int2_d3 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*2, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! INTEGER*4 array
- subroutine adios_write_int4_d3 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*4, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! INTEGER*8 array
- subroutine adios_write_int8_d3 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*8, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! REAL*4 array
- subroutine adios_write_real4_d3 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*4, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! REAL*8 array
- subroutine adios_write_real8_d3 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*8, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! COMPLEX (*8) array
- subroutine adios_write_complex8_d3 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! DOUBLE-COMPLEX array
- subroutine adios_write_complex16_d3 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex*16,dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! CHARACTER array
- subroutine adios_write_char_d3 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- character(*),dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! LOGICAL*1 array
- subroutine adios_write_logical1_d3 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*1, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! LOGICAL*2 array
- subroutine adios_write_logical2_d3 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*2, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! LOGICAL*4 array
- subroutine adios_write_logical4_d3 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*4, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! LOGICAL*8 array
- subroutine adios_write_logical8_d3 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*8, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- !
- ! 4D data
- !
-
- ! INTEGER*1 array
- subroutine adios_write_int1_d4 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*1, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! INTEGER*2 array
- subroutine adios_write_int2_d4 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*2, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! INTEGER*4 array
- subroutine adios_write_int4_d4 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*4, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! INTEGER*8 array
- subroutine adios_write_int8_d4 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*8, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! REAL*4 array
- subroutine adios_write_real4_d4 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*4, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! REAL*8 array
- subroutine adios_write_real8_d4 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*8, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! COMPLEX (*8) array
- subroutine adios_write_complex8_d4 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! DOUBLE-COMPLEX array
- subroutine adios_write_complex16_d4 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex*16,dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! CHARACTER array
- subroutine adios_write_char_d4 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- character(*),dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! LOGICAL*1 array
- subroutine adios_write_logical1_d4 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*1, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! LOGICAL*2 array
- subroutine adios_write_logical2_d4 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*2, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! LOGICAL*4 array
- subroutine adios_write_logical4_d4 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*4, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! LOGICAL*8 array
- subroutine adios_write_logical8_d4 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*8, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- !
- ! 5D data
- !
-
- ! INTEGER*1 array
- subroutine adios_write_int1_d5 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*1, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! INTEGER*2 array
- subroutine adios_write_int2_d5 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*2, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! INTEGER*4 array
- subroutine adios_write_int4_d5 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*4, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! INTEGER*8 array
- subroutine adios_write_int8_d5 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*8, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! REAL*4 array
- subroutine adios_write_real4_d5 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*4, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! REAL*8 array
- subroutine adios_write_real8_d5 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*8, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! COMPLEX (*8) array
- subroutine adios_write_complex8_d5 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! DOUBLE-COMPLEX array
- subroutine adios_write_complex16_d5 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex*16,dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! CHARACTER array
- subroutine adios_write_char_d5 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- character(*),dimension(:,:,:,:),intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! LOGICAL*1 array
- subroutine adios_write_logical1_d5 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*1, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! LOGICAL*2 array
- subroutine adios_write_logical2_d5 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*2, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! LOGICAL*4 array
- subroutine adios_write_logical4_d5 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*4, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! LOGICAL*8 array
- subroutine adios_write_logical8_d5 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*8, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- !
- ! 6D data
- !
-
- ! INTEGER*1 array
- subroutine adios_write_int1_d6 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*1, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! INTEGER*2 array
- subroutine adios_write_int2_d6 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*2, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! INTEGER*4 array
- subroutine adios_write_int4_d6 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*4, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! INTEGER*8 array
- subroutine adios_write_int8_d6 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*8, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! REAL*4 array
- subroutine adios_write_real4_d6 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*4, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! REAL*8 array
- subroutine adios_write_real8_d6 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*8, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! COMPLEX (*8) array
- subroutine adios_write_complex8_d6 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! DOUBLE-COMPLEX array
- subroutine adios_write_complex16_d6 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex*16,dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! CHARACTER array
- subroutine adios_write_char_d6 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- character(*),dimension(:,:,:,:,:),intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! LOGICAL*1 array
- subroutine adios_write_logical1_d6 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*1, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! LOGICAL*2 array
- subroutine adios_write_logical2_d6 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*2, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! LOGICAL*4 array
- subroutine adios_write_logical4_d6 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*4, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! LOGICAL*8 array
- subroutine adios_write_logical8_d6 (fd, varname, data, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*8, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_f2c (fd, varname, data, err)
- end subroutine
-
- ! end of ADIOS_WRITE functions
-
-
- !
- !
- ! ADIOS_WRITE_BYID generic interface
- !
- ! Usage: call adios_write_byid (fd, varid, data, err)
- !
- !
- !
- ! scalars
- !
-
- ! INTEGER*1 scalar
- subroutine adios_write_byid_int1_d0 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*1, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*2 scalar
- subroutine adios_write_byid_int2_d0 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*2, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*4 scalar
- subroutine adios_write_byid_int4_d0 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*4, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*8 scalar
- subroutine adios_write_byid_int8_d0 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*8, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! REAL*4 scalar
- subroutine adios_write_byid_real4_d0 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- real*4, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! REAL*8 scalar
- subroutine adios_write_byid_real8_d0 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- real*8, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! COMPLEX (*8) scalar
- subroutine adios_write_byid_complex8_d0 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- complex, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! DOUBLE-COMPLEX scalar
- subroutine adios_write_byid_complex16_d0 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- complex*16, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! CHARACTER scalar (Same as 1D?)
- !subroutine adios_write_byid_char_d0 (fd, varid, data, err)
- ! implicit none
- ! integer*8, intent(in) :: fd
- ! integer*8, intent(in) :: varid
- ! character(*), intent(inout) :: data
- ! integer, intent(in) :: err
- !
- ! call adios_write_byid_f2c (fd, varid, data, err)
- !end subroutine
-
- ! LOGICAL*1 scalar
- subroutine adios_write_byid_logical1_d0 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*1, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*2 scalar
- subroutine adios_write_byid_logical2_d0 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*2, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*4 scalar
- subroutine adios_write_byid_logical4_d0 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*4, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*8 scalar
- subroutine adios_write_byid_logical8_d0 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*8, intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
-
- !
- ! 1D data
- !
-
- ! INTEGER*1 array
- subroutine adios_write_byid_int1_d1 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*1, dimension(*), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*2 array
- subroutine adios_write_byid_int2_d1 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*2, dimension(*), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*4 array
- subroutine adios_write_byid_int4_d1 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*4, dimension(*), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*8 array
- subroutine adios_write_byid_int8_d1 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*8, dimension(*), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! REAL*4 array
- subroutine adios_write_byid_real4_d1 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- real*4, dimension(*), intent(out) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! REAL*8 array
- subroutine adios_write_byid_real8_d1 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- real*8, dimension(*), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! COMPLEX (*8) array
- subroutine adios_write_byid_complex8_d1 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- complex, dimension(*), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! DOUBLE-COMPLEX array
- subroutine adios_write_byid_complex16_d1 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- complex*16,dimension(*), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! CHARACTER array
- subroutine adios_write_byid_char_d1 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- character(*), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*1 array
- subroutine adios_write_byid_logical1_d1 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*1, dimension(*), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*2 array
- subroutine adios_write_byid_logical2_d1 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*2, dimension(*), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*4 array
- subroutine adios_write_byid_logical4_d1 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*4, dimension(*), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*8 array
- subroutine adios_write_byid_logical8_d1 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*8, dimension(*), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- !
- ! 2D data
- !
-
- ! INTEGER*1 array
- subroutine adios_write_byid_int1_d2 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*1, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*2 array
- subroutine adios_write_byid_int2_d2 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*2, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*4 array
- subroutine adios_write_byid_int4_d2 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*4, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*8 array
- subroutine adios_write_byid_int8_d2 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*8, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! REAL*4 array
- subroutine adios_write_byid_real4_d2 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- real*4, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! REAL*8 array
- subroutine adios_write_byid_real8_d2 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- real*8, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! COMPLEX (*8) array
- subroutine adios_write_byid_complex8_d2 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- complex, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! DOUBLE-COMPLEX array
- subroutine adios_write_byid_complex16_d2 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- complex*16,dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! CHARACTER array
- subroutine adios_write_byid_char_d2 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- character(*),dimension(*), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*1 array
- subroutine adios_write_byid_logical1_d2 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*1, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*2 array
- subroutine adios_write_byid_logical2_d2 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*2, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*4 array
- subroutine adios_write_byid_logical4_d2 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*4, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*8 array
- subroutine adios_write_byid_logical8_d2 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*8, dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- !
- ! 3D data
- !
-
- ! INTEGER*1 array
- subroutine adios_write_byid_int1_d3 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*1, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*2 array
- subroutine adios_write_byid_int2_d3 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*2, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*4 array
- subroutine adios_write_byid_int4_d3 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*4, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*8 array
- subroutine adios_write_byid_int8_d3 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*8, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! REAL*4 array
- subroutine adios_write_byid_real4_d3 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- real*4, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! REAL*8 array
- subroutine adios_write_byid_real8_d3 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- real*8, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! COMPLEX (*8) array
- subroutine adios_write_byid_complex8_d3 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- complex, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! DOUBLE-COMPLEX array
- subroutine adios_write_byid_complex16_d3 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- complex*16,dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! CHARACTER array
- subroutine adios_write_byid_char_d3 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- character(*),dimension(:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*1 array
- subroutine adios_write_byid_logical1_d3 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*1, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*2 array
- subroutine adios_write_byid_logical2_d3 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*2, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*4 array
- subroutine adios_write_byid_logical4_d3 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*4, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*8 array
- subroutine adios_write_byid_logical8_d3 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*8, dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- !
- ! 4D data
- !
-
- ! INTEGER*1 array
- subroutine adios_write_byid_int1_d4 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*1, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*2 array
- subroutine adios_write_byid_int2_d4 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*2, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*4 array
- subroutine adios_write_byid_int4_d4 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*4, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*8 array
- subroutine adios_write_byid_int8_d4 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*8, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! REAL*4 array
- subroutine adios_write_byid_real4_d4 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- real*4, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! REAL*8 array
- subroutine adios_write_byid_real8_d4 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- real*8, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! COMPLEX (*8) array
- subroutine adios_write_byid_complex8_d4 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- complex, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! DOUBLE-COMPLEX array
- subroutine adios_write_byid_complex16_d4 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- complex*16,dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! CHARACTER array
- subroutine adios_write_byid_char_d4 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- character(*),dimension(:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*1 array
- subroutine adios_write_byid_logical1_d4 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*1, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*2 array
- subroutine adios_write_byid_logical2_d4 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*2, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*4 array
- subroutine adios_write_byid_logical4_d4 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*4, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*8 array
- subroutine adios_write_byid_logical8_d4 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*8, dimension(:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- !
- ! 5D data
- !
-
- ! INTEGER*1 array
- subroutine adios_write_byid_int1_d5 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*1, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*2 array
- subroutine adios_write_byid_int2_d5 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*2, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*4 array
- subroutine adios_write_byid_int4_d5 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*4, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*8 array
- subroutine adios_write_byid_int8_d5 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*8, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! REAL*4 array
- subroutine adios_write_byid_real4_d5 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- real*4, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! REAL*8 array
- subroutine adios_write_byid_real8_d5 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- real*8, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! COMPLEX (*8) array
- subroutine adios_write_byid_complex8_d5 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- complex, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! DOUBLE-COMPLEX array
- subroutine adios_write_byid_complex16_d5 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- complex*16,dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! CHARACTER array
- subroutine adios_write_byid_char_d5 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- character(*),dimension(:,:,:,:),intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*1 array
- subroutine adios_write_byid_logical1_d5 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*1, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*2 array
- subroutine adios_write_byid_logical2_d5 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*2, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*4 array
- subroutine adios_write_byid_logical4_d5 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*4, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*8 array
- subroutine adios_write_byid_logical8_d5 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*8, dimension(:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- !
- ! 6D data
- !
-
- ! INTEGER*1 array
- subroutine adios_write_byid_int1_d6 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*1, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*2 array
- subroutine adios_write_byid_int2_d6 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*2, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*4 array
- subroutine adios_write_byid_int4_d6 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*4, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! INTEGER*8 array
- subroutine adios_write_byid_int8_d6 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- integer*8, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! REAL*4 array
- subroutine adios_write_byid_real4_d6 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- real*4, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! REAL*8 array
- subroutine adios_write_byid_real8_d6 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- real*8, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! COMPLEX (*8) array
- subroutine adios_write_byid_complex8_d6 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- complex, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! DOUBLE-COMPLEX array
- subroutine adios_write_byid_complex16_d6 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- complex*16,dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! CHARACTER array
- subroutine adios_write_byid_char_d6 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- character(*),dimension(:,:,:,:,:),intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*1 array
- subroutine adios_write_byid_logical1_d6 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*1, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*2 array
- subroutine adios_write_byid_logical2_d6 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*2, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*4 array
- subroutine adios_write_byid_logical4_d6 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*4, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! LOGICAL*8 array
- subroutine adios_write_byid_logical8_d6 (fd, varid, data, err)
- implicit none
- integer*8, intent(in) :: fd
- integer*8, intent(in) :: varid
- logical*8, dimension(:,:,:,:,:,:), intent(in) :: data
- integer, intent(in) :: err
-
- call adios_write_byid_f2c (fd, varid, data, err)
- end subroutine
-
- ! end of ADIOS_WRITE functions
-
-
-
-
- !
- !
- ! ADIOS_READ generic interface
- !
- ! Usage: call adios_read (fd, varname, buffer, buffer_size, err)
- !
- !
- !
- ! scalar data
- !
-
- ! INTEGER*1 scalar
- subroutine adios_read_int1_d0 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*1, intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*2 scalar
- subroutine adios_read_int2_d0 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*2, intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*4 scalar
- subroutine adios_read_int4_d0 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*4, intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*8 scalar
- subroutine adios_read_int8_d0 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*8, intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! REAL*4 scalar
- subroutine adios_read_real4_d0 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*4, intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! REAL*8 scalar
- subroutine adios_read_real8_d0 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*8, intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! COMPLEX (*8) scalar
- subroutine adios_read_complex8_d0 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex, intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! DOUBLE-COMPLEX scalar
- subroutine adios_read_complex16_d0 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex*16, intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! CHARACTER scalar
- !subroutine adios_read_char_d0 (fd, varname, buffer, buffer_size, err)
- ! implicit none
- ! integer*8, intent(in) :: fd
- ! character(*), intent(in) :: varname
- ! character(*), intent(out) :: buffer
- ! integer*8, intent(in) :: buffer_size
- ! integer, intent(in) :: err
- !
- ! call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- !end subroutine
-
- ! LOGICAL*1 scalar
- subroutine adios_read_logical1_d0 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*1, intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*2 scalar
- subroutine adios_read_logical2_d0 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*2, intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*4 scalar
- subroutine adios_read_logical4_d0 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*4, intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*8 scalar
- subroutine adios_read_logical8_d0 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*8, intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
-
- !
- ! 1D data
- !
-
- ! INTEGER*1 array
- subroutine adios_read_int1_d1 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*1, dimension(*), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*2 array
- subroutine adios_read_int2_d1 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*2, dimension(*), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*4 array
- subroutine adios_read_int4_d1 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*4, dimension(*), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*8 array
- subroutine adios_read_int8_d1 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*8, dimension(*), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! REAL*4 array
- subroutine adios_read_real4_d1 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*4, dimension(*), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! REAL*8 array
- subroutine adios_read_real8_d1 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*8, dimension(*), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! COMPLEX (*8) array
- subroutine adios_read_complex8_d1 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex, dimension(*), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! DOUBLE-COMPLEX array
- subroutine adios_read_complex16_d1 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex*16,dimension(*), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! CHARACTER array
- subroutine adios_read_char_d1 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- character(*), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*1 array
- subroutine adios_read_logical1_d1 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*1, dimension(*), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*2 array
- subroutine adios_read_logical2_d1 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*2, dimension(*), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*4 array
- subroutine adios_read_logical4_d1 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*4, dimension(*), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*8 array
- subroutine adios_read_logical8_d1 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*8, dimension(*), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- !
- ! 2D buffer
- !
-
- ! INTEGER*1 array
- subroutine adios_read_int1_d2 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*1, dimension(:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*2 array
- subroutine adios_read_int2_d2 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*2, dimension(:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*4 array
- subroutine adios_read_int4_d2 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*4, dimension(:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*8 array
- subroutine adios_read_int8_d2 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*8, dimension(:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! REAL*4 array
- subroutine adios_read_real4_d2 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*4, dimension(:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! REAL*8 array
- subroutine adios_read_real8_d2 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*8, dimension(:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! COMPLEX (*8) array
- subroutine adios_read_complex8_d2 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex, dimension(:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! DOUBLE-COMPLEX array
- subroutine adios_read_complex16_d2 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex*16,dimension(:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! CHARACTER array
- subroutine adios_read_char_d2 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- character(*),dimension(*), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*1 array
- subroutine adios_read_logical1_d2 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*1, dimension(:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*2 array
- subroutine adios_read_logical2_d2 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*2, dimension(:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*4 array
- subroutine adios_read_logical4_d2 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*4, dimension(:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*8 array
- subroutine adios_read_logical8_d2 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*8, dimension(:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- !
- ! 3D buffer
- !
-
- ! INTEGER*1 array
- subroutine adios_read_int1_d3 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*1, dimension(:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*2 array
- subroutine adios_read_int2_d3 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*2, dimension(:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*4 array
- subroutine adios_read_int4_d3 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*4, dimension(:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*8 array
- subroutine adios_read_int8_d3 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*8, dimension(:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! REAL*4 array
- subroutine adios_read_real4_d3 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*4, dimension(:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! REAL*8 array
- subroutine adios_read_real8_d3 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*8, dimension(:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! COMPLEX (*8) array
- subroutine adios_read_complex8_d3 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex, dimension(:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! DOUBLE-COMPLEX array
- subroutine adios_read_complex16_d3 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex*16,dimension(:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! CHARACTER array
- subroutine adios_read_char_d3 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- character(*),dimension(:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*1 array
- subroutine adios_read_logical1_d3 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*1, dimension(:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*2 array
- subroutine adios_read_logical2_d3 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*2, dimension(:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*4 array
- subroutine adios_read_logical4_d3 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*4, dimension(:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*8 array
- subroutine adios_read_logical8_d3 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*8, dimension(:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- !
- ! 4D buffer
- !
-
- ! INTEGER*1 array
- subroutine adios_read_int1_d4 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*1, dimension(:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*2 array
- subroutine adios_read_int2_d4 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*2, dimension(:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*4 array
- subroutine adios_read_int4_d4 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*4, dimension(:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*8 array
- subroutine adios_read_int8_d4 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*8, dimension(:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! REAL*4 array
- subroutine adios_read_real4_d4 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*4, dimension(:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! REAL*8 array
- subroutine adios_read_real8_d4 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*8, dimension(:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! COMPLEX (*8) array
- subroutine adios_read_complex8_d4 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex, dimension(:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! DOUBLE-COMPLEX array
- subroutine adios_read_complex16_d4 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex*16,dimension(:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! CHARACTER array
- subroutine adios_read_char_d4 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- character(*),dimension(:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*1 array
- subroutine adios_read_logical1_d4 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*1, dimension(:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*2 array
- subroutine adios_read_logical2_d4 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*2, dimension(:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*4 array
- subroutine adios_read_logical4_d4 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*4, dimension(:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*8 array
- subroutine adios_read_logical8_d4 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*8, dimension(:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- !
- ! 5D buffer
- !
-
- ! INTEGER*1 array
- subroutine adios_read_int1_d5 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*1, dimension(:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*2 array
- subroutine adios_read_int2_d5 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*2, dimension(:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*4 array
- subroutine adios_read_int4_d5 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*4, dimension(:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*8 array
- subroutine adios_read_int8_d5 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*8, dimension(:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! REAL*4 array
- subroutine adios_read_real4_d5 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*4, dimension(:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! REAL*8 array
- subroutine adios_read_real8_d5 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*8, dimension(:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! COMPLEX (*8) array
- subroutine adios_read_complex8_d5 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex, dimension(:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! DOUBLE-COMPLEX array
- subroutine adios_read_complex16_d5 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex*16,dimension(:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! CHARACTER array
- subroutine adios_read_char_d5 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- character(*),dimension(:,:,:,:),intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*1 array
- subroutine adios_read_logical1_d5 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*1, dimension(:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*2 array
- subroutine adios_read_logical2_d5 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*2, dimension(:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*4 array
- subroutine adios_read_logical4_d5 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*4, dimension(:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*8 array
- subroutine adios_read_logical8_d5 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*8, dimension(:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- !
- ! 6D buffer
- !
-
- ! INTEGER*1 array
- subroutine adios_read_int1_d6 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*1, dimension(:,:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*2 array
- subroutine adios_read_int2_d6 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*2, dimension(:,:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*4 array
- subroutine adios_read_int4_d6 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*4, dimension(:,:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! INTEGER*8 array
- subroutine adios_read_int8_d6 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- integer*8, dimension(:,:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! REAL*4 array
- subroutine adios_read_real4_d6 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*4, dimension(:,:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! REAL*8 array
- subroutine adios_read_real8_d6 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- real*8, dimension(:,:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! COMPLEX (*8) array
- subroutine adios_read_complex8_d6 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex, dimension(:,:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! DOUBLE-COMPLEX array
- subroutine adios_read_complex16_d6 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- complex*16,dimension(:,:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! CHARACTER array
- subroutine adios_read_char_d6 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- character(*),dimension(:,:,:,:,:),intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*1 array
- subroutine adios_read_logical1_d6 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*1, dimension(:,:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*2 array
- subroutine adios_read_logical2_d6 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*2, dimension(:,:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*4 array
- subroutine adios_read_logical4_d6 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*4, dimension(:,:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! LOGICAL*8 array
- subroutine adios_read_logical8_d6 (fd, varname, buffer, buffer_size, err)
- implicit none
- integer*8, intent(in) :: fd
- character(*), intent(in) :: varname
- logical*8, dimension(:,:,:,:,:,:), intent(out) :: buffer
- integer*8, intent(in) :: buffer_size
- integer, intent(in) :: err
-
- call adios_read_f2c (fd, varname, buffer, buffer_size, err)
- end subroutine
-
- ! end of ADIOS_READ functions
+ ! end of ADIOS_READ functions
!
!
@@ -3865,254 +3873,254 @@ module adios_write_mod
! Usage: call adios_define_attrribute_byvalue (group_id, attrname, path, nelems, values, err)
!
!
- ! Special case: CHARACTER*1 array
- ! This calls a different function to keep the string length information within
- subroutine adios_define_attribute_byvalue_char_d1 (group_id, attrname, path, nelems, values, err)
- implicit none
- integer*8, intent(in) :: group_id
- character(*), intent(in) :: attrname
- character(*), intent(in) :: path
- integer, intent(in) :: nelems
- character(*), intent(in) :: values
- integer, intent(out) :: err
-
- call adios_define_attribute_byvalue_string (group_id, attrname, path, nelems, values, err)
- end subroutine
-
- ! Special case: CHARACTER*2 array
- ! This calls a different function to keep the string length information within
- subroutine adios_define_attribute_byvalue_char_d2 (group_id, attrname, path, nelems, values, err)
- implicit none
- integer*8, intent(in) :: group_id
- character(*), intent(in) :: attrname
- character(*), intent(in) :: path
- integer, intent(in) :: nelems
- character(*), dimension(:), intent(in) :: values
- integer, intent(out) :: err
-
- !character(*) :: v1
- !v1 = values(1)
-
- if (nelems <= size(values)) then
- !write (*,'("String Array: dims = ",i4, "string size=",i4)') size(values,1), len(values)
- !write (*,*) shape(values)
- call adios_define_attribute_byvalue_string_array (group_id, attrname, path, nelems, &
- values, len(values), err)
- else
- write (*,'("ADIOS Attribute definition error: ",a,"/",a," string array size =",i4," nelems = ",i4)') &
- path, attrname, size(values), nelems
- endif
- end subroutine
-
- ! INTEGER*1 scalar
- subroutine adios_define_attribute_byvalue_int1_d0 (group_id, attrname, path, nelems, values, err)
- implicit none
- integer*8, intent(in) :: group_id
- character(*), intent(in) :: attrname
- character(*), intent(in) :: path
- integer, intent(in) :: nelems
- integer*1, intent(in) :: values
- integer, intent(out) :: err
-
- call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_double_complex, adios_byte, values, err)
- end subroutine
-
- ! INTEGER*2 scalar
- subroutine adios_define_attribute_byvalue_int2_d0 (group_id, attrname, path, nelems, values, err)
- implicit none
- integer*8, intent(in) :: group_id
- character(*), intent(in) :: attrname
- character(*), intent(in) :: path
- integer, intent(in) :: nelems
- integer*2, intent(in) :: values
- integer, intent(out) :: err
-
- call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_short, nelems, values, err)
- end subroutine
-
-
- ! INTEGER*4 scalar
- subroutine adios_define_attribute_byvalue_int4_d0 (group_id, attrname, path, nelems, values, err)
- implicit none
- integer*8, intent(in) :: group_id
- character(*), intent(in) :: attrname
- character(*), intent(in) :: path
- integer, intent(in) :: nelems
- integer*4, intent(in) :: values
- integer, intent(out) :: err
-
- call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_integer, nelems, values, err)
- end subroutine
-
- ! INTEGER*8 scalar
- subroutine adios_define_attribute_byvalue_int8_d0 (group_id, attrname, path, nelems, values, err)
- implicit none
- integer*8, intent(in) :: group_id
- character(*), intent(in) :: attrname
- character(*), intent(in) :: path
- integer, intent(in) :: nelems
- integer*8, intent(in) :: values
- integer, intent(out) :: err
-
- call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_long, nelems, values, err)
- end subroutine
-
- ! REAL*4 scalar
- subroutine adios_define_attribute_byvalue_real4_d0 (group_id, attrname, path, nelems, values, err)
- implicit none
- integer*8, intent(in) :: group_id
- character(*), intent(in) :: attrname
- character(*), intent(in) :: path
- integer, intent(in) :: nelems
- real*4, intent(in) :: values
- integer, intent(out) :: err
-
- call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_real, nelems, values, err)
- end subroutine
-
- ! REAL*8 scalar
- subroutine adios_define_attribute_byvalue_real8_d0 (group_id, attrname, path, nelems, values, err)
- implicit none
- integer*8, intent(in) :: group_id
- character(*), intent(in) :: attrname
- character(*), intent(in) :: path
- integer, intent(in) :: nelems
- real*8, intent(in) :: values
- integer, intent(out) :: err
-
- call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_double, nelems, values, err)
- end subroutine
-
- ! COMPLEX*8 scalar
- subroutine adios_define_attribute_byvalue_complex8_d0 (group_id, attrname, path, nelems, values, err)
- implicit none
- integer*8, intent(in) :: group_id
- character(*), intent(in) :: attrname
- character(*), intent(in) :: path
- integer, intent(in) :: nelems
- complex*8, intent(in) :: values
- integer, intent(out) :: err
-
- call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_complex, nelems, values, err)
- end subroutine
-
- ! COMPLEX*16 scalar
- subroutine adios_define_attribute_byvalue_complex16_d0 (group_id, attrname, path, nelems, values, err)
- implicit none
- integer*8, intent(in) :: group_id
- character(*), intent(in) :: attrname
- character(*), intent(in) :: path
- integer, intent(in) :: nelems
- complex*16, intent(in) :: values
- integer, intent(out) :: err
-
- call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_double_complex, nelems, values, err)
- end subroutine
-
-
- ! INTEGER*1 array
- subroutine adios_define_attribute_byvalue_int1_d1 (group_id, attrname, path, nelems, values, err)
- implicit none
- integer*8, intent(in) :: group_id
- character(*), intent(in) :: attrname
- character(*), intent(in) :: path
- integer, intent(in) :: nelems
- integer*1, dimension(:), intent(in) :: values
- integer, intent(out) :: err
-
- call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_byte, nelems, values, err)
- end subroutine
-
- ! INTEGER*2 array
- subroutine adios_define_attribute_byvalue_int2_d1 (group_id, attrname, path, nelems, values, err)
- implicit none
- integer*8, intent(in) :: group_id
- character(*), intent(in) :: attrname
- character(*), intent(in) :: path
- integer, intent(in) :: nelems
- integer*2, dimension(:), intent(in) :: values
- integer, intent(out) :: err
-
- call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_short, nelems, values, err)
- end subroutine
-
- ! INTEGER*4 array
- subroutine adios_define_attribute_byvalue_int4_d1 (group_id, attrname, path, nelems, values, err)
- implicit none
- integer*8, intent(in) :: group_id
- character(*), intent(in) :: attrname
- character(*), intent(in) :: path
- integer, intent(in) :: nelems
- integer*4, dimension(:), intent(in) :: values
- integer, intent(out) :: err
-
- call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_integer, nelems, values, err)
- end subroutine
-
- ! INTEGER*8 array
- subroutine adios_define_attribute_byvalue_int8_d1 (group_id, attrname, path, nelems, values, err)
- implicit none
- integer*8, intent(in) :: group_id
- character(*), intent(in) :: attrname
- character(*), intent(in) :: path
- integer, intent(in) :: nelems
- integer*8, dimension(:), intent(in) :: values
- integer, intent(out) :: err
-
- call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_long, nelems, values, err)
- end subroutine
-
- ! REAL*4 array
- subroutine adios_define_attribute_byvalue_real4_d1 (group_id, attrname, path, nelems, values, err)
- implicit none
- integer*8, intent(in) :: group_id
- character(*), intent(in) :: attrname
- character(*), intent(in) :: path
- integer, intent(in) :: nelems
- real*4, dimension(:), intent(in) :: values
- integer, intent(out) :: err
-
- call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_real, nelems, values, err)
- end subroutine
-
- ! REAL*8 array
- subroutine adios_define_attribute_byvalue_real8_d1 (group_id, attrname, path, nelems, values, err)
- implicit none
- integer*8, intent(in) :: group_id
- character(*), intent(in) :: attrname
- character(*), intent(in) :: path
- integer, intent(in) :: nelems
- real*8, dimension(:), intent(in) :: values
- integer, intent(out) :: err
-
- call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_double, nelems, values, err)
- end subroutine
-
- ! COMPLEX*8 array
- subroutine adios_define_attribute_byvalue_complex8_d1 (group_id, attrname, path, nelems, values, err)
- implicit none
- integer*8, intent(in) :: group_id
- character(*), intent(in) :: attrname
- character(*), intent(in) :: path
- integer, intent(in) :: nelems
- complex*8, dimension(:), intent(in) :: values
- integer, intent(out) :: err
-
- call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_complex, nelems, values, err)
- end subroutine
-
- ! COMPLEX*16 array
- subroutine adios_define_attribute_byvalue_complex16_d1 (group_id, attrname, path, nelems, values, err)
- implicit none
- integer*8, intent(in) :: group_id
- character(*), intent(in) :: attrname
- character(*), intent(in) :: path
- integer, intent(in) :: nelems
- complex*16, dimension(:), intent(in) :: values
- integer, intent(out) :: err
-
- call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_double_complex, nelems, values, err)
- end subroutine
+ ! Special case: CHARACTER*1 array
+ ! This calls a different function to keep the string length information within
+ subroutine adios_define_attribute_byvalue_char_d1 (group_id, attrname, path, nelems, values, err)
+ implicit none
+ integer*8, intent(in) :: group_id
+ character(*), intent(in) :: attrname
+ character(*), intent(in) :: path
+ integer, intent(in) :: nelems
+ character(*), intent(in) :: values
+ integer, intent(out) :: err
+
+ call adios_define_attribute_byvalue_string (group_id, attrname, path, nelems, values, err)
+ end subroutine
+
+ ! Special case: CHARACTER*2 array
+ ! This calls a different function to keep the string length information within
+ subroutine adios_define_attribute_byvalue_char_d2 (group_id, attrname, path, nelems, values, err)
+ implicit none
+ integer*8, intent(in) :: group_id
+ character(*), intent(in) :: attrname
+ character(*), intent(in) :: path
+ integer, intent(in) :: nelems
+ character(*), dimension(:), intent(in) :: values
+ integer, intent(out) :: err
+
+ !character(*) :: v1
+ !v1 = values(1)
+
+ if (nelems <= size(values)) then
+ !write (*,'("String Array: dims = ",i4, "string size=",i4)') size(values,1), len(values)
+ !write (*,*) shape(values)
+ call adios_define_attribute_byvalue_string_array (group_id, attrname, path, nelems, &
+ values, len(values), err)
+ else
+ write (*,'("ADIOS Attribute definition error: ",a,"/",a," string array size =",i4," nelems = ",i4)') &
+ path, attrname, size(values), nelems
+ endif
+ end subroutine
+
+ ! INTEGER*1 scalar
+ subroutine adios_define_attribute_byvalue_int1_d0 (group_id, attrname, path, nelems, values, err)
+ implicit none
+ integer*8, intent(in) :: group_id
+ character(*), intent(in) :: attrname
+ character(*), intent(in) :: path
+ integer, intent(in) :: nelems
+ integer*1, intent(in) :: values
+ integer, intent(out) :: err
+
+ call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_double_complex, adios_byte, values, err)
+ end subroutine
+
+ ! INTEGER*2 scalar
+ subroutine adios_define_attribute_byvalue_int2_d0 (group_id, attrname, path, nelems, values, err)
+ implicit none
+ integer*8, intent(in) :: group_id
+ character(*), intent(in) :: attrname
+ character(*), intent(in) :: path
+ integer, intent(in) :: nelems
+ integer*2, intent(in) :: values
+ integer, intent(out) :: err
+
+ call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_short, nelems, values, err)
+ end subroutine
+
+
+ ! INTEGER*4 scalar
+ subroutine adios_define_attribute_byvalue_int4_d0 (group_id, attrname, path, nelems, values, err)
+ implicit none
+ integer*8, intent(in) :: group_id
+ character(*), intent(in) :: attrname
+ character(*), intent(in) :: path
+ integer, intent(in) :: nelems
+ integer*4, intent(in) :: values
+ integer, intent(out) :: err
+
+ call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_integer, nelems, values, err)
+ end subroutine
+
+ ! INTEGER*8 scalar
+ subroutine adios_define_attribute_byvalue_int8_d0 (group_id, attrname, path, nelems, values, err)
+ implicit none
+ integer*8, intent(in) :: group_id
+ character(*), intent(in) :: attrname
+ character(*), intent(in) :: path
+ integer, intent(in) :: nelems
+ integer*8, intent(in) :: values
+ integer, intent(out) :: err
+
+ call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_long, nelems, values, err)
+ end subroutine
+
+ ! REAL*4 scalar
+ subroutine adios_define_attribute_byvalue_real4_d0 (group_id, attrname, path, nelems, values, err)
+ implicit none
+ integer*8, intent(in) :: group_id
+ character(*), intent(in) :: attrname
+ character(*), intent(in) :: path
+ integer, intent(in) :: nelems
+ real*4, intent(in) :: values
+ integer, intent(out) :: err
+
+ call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_real, nelems, values, err)
+ end subroutine
+
+ ! REAL*8 scalar
+ subroutine adios_define_attribute_byvalue_real8_d0 (group_id, attrname, path, nelems, values, err)
+ implicit none
+ integer*8, intent(in) :: group_id
+ character(*), intent(in) :: attrname
+ character(*), intent(in) :: path
+ integer, intent(in) :: nelems
+ real*8, intent(in) :: values
+ integer, intent(out) :: err
+
+ call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_double, nelems, values, err)
+ end subroutine
+
+ ! COMPLEX*8 scalar
+ subroutine adios_define_attribute_byvalue_complex8_d0 (group_id, attrname, path, nelems, values, err)
+ implicit none
+ integer*8, intent(in) :: group_id
+ character(*), intent(in) :: attrname
+ character(*), intent(in) :: path
+ integer, intent(in) :: nelems
+ complex*8, intent(in) :: values
+ integer, intent(out) :: err
+
+ call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_complex, nelems, values, err)
+ end subroutine
+
+ ! COMPLEX*16 scalar
+ subroutine adios_define_attribute_byvalue_complex16_d0 (group_id, attrname, path, nelems, values, err)
+ implicit none
+ integer*8, intent(in) :: group_id
+ character(*), intent(in) :: attrname
+ character(*), intent(in) :: path
+ integer, intent(in) :: nelems
+ complex*16, intent(in) :: values
+ integer, intent(out) :: err
+
+ call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_double_complex, nelems, values, err)
+ end subroutine
+
+
+ ! INTEGER*1 array
+ subroutine adios_define_attribute_byvalue_int1_d1 (group_id, attrname, path, nelems, values, err)
+ implicit none
+ integer*8, intent(in) :: group_id
+ character(*), intent(in) :: attrname
+ character(*), intent(in) :: path
+ integer, intent(in) :: nelems
+ integer*1, dimension(:), intent(in) :: values
+ integer, intent(out) :: err
+
+ call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_byte, nelems, values, err)
+ end subroutine
+
+ ! INTEGER*2 array
+ subroutine adios_define_attribute_byvalue_int2_d1 (group_id, attrname, path, nelems, values, err)
+ implicit none
+ integer*8, intent(in) :: group_id
+ character(*), intent(in) :: attrname
+ character(*), intent(in) :: path
+ integer, intent(in) :: nelems
+ integer*2, dimension(:), intent(in) :: values
+ integer, intent(out) :: err
+
+ call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_short, nelems, values, err)
+ end subroutine
+
+ ! INTEGER*4 array
+ subroutine adios_define_attribute_byvalue_int4_d1 (group_id, attrname, path, nelems, values, err)
+ implicit none
+ integer*8, intent(in) :: group_id
+ character(*), intent(in) :: attrname
+ character(*), intent(in) :: path
+ integer, intent(in) :: nelems
+ integer*4, dimension(:), intent(in) :: values
+ integer, intent(out) :: err
+
+ call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_integer, nelems, values, err)
+ end subroutine
+
+ ! INTEGER*8 array
+ subroutine adios_define_attribute_byvalue_int8_d1 (group_id, attrname, path, nelems, values, err)
+ implicit none
+ integer*8, intent(in) :: group_id
+ character(*), intent(in) :: attrname
+ character(*), intent(in) :: path
+ integer, intent(in) :: nelems
+ integer*8, dimension(:), intent(in) :: values
+ integer, intent(out) :: err
+
+ call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_long, nelems, values, err)
+ end subroutine
+
+ ! REAL*4 array
+ subroutine adios_define_attribute_byvalue_real4_d1 (group_id, attrname, path, nelems, values, err)
+ implicit none
+ integer*8, intent(in) :: group_id
+ character(*), intent(in) :: attrname
+ character(*), intent(in) :: path
+ integer, intent(in) :: nelems
+ real*4, dimension(:), intent(in) :: values
+ integer, intent(out) :: err
+
+ call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_real, nelems, values, err)
+ end subroutine
+
+ ! REAL*8 array
+ subroutine adios_define_attribute_byvalue_real8_d1 (group_id, attrname, path, nelems, values, err)
+ implicit none
+ integer*8, intent(in) :: group_id
+ character(*), intent(in) :: attrname
+ character(*), intent(in) :: path
+ integer, intent(in) :: nelems
+ real*8, dimension(:), intent(in) :: values
+ integer, intent(out) :: err
+
+ call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_double, nelems, values, err)
+ end subroutine
+
+ ! COMPLEX*8 array
+ subroutine adios_define_attribute_byvalue_complex8_d1 (group_id, attrname, path, nelems, values, err)
+ implicit none
+ integer*8, intent(in) :: group_id
+ character(*), intent(in) :: attrname
+ character(*), intent(in) :: path
+ integer, intent(in) :: nelems
+ complex*8, dimension(:), intent(in) :: values
+ integer, intent(out) :: err
+
+ call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_complex, nelems, values, err)
+ end subroutine
+
+ ! COMPLEX*16 array
+ subroutine adios_define_attribute_byvalue_complex16_d1 (group_id, attrname, path, nelems, values, err)
+ implicit none
+ integer*8, intent(in) :: group_id
+ character(*), intent(in) :: attrname
+ character(*), intent(in) :: path
+ integer, intent(in) :: nelems
+ complex*16, dimension(:), intent(in) :: values
+ integer, intent(out) :: err
+
+ call adios_define_attribute_byvalue_f2c (group_id, attrname, path, adios_double_complex, nelems, values, err)
+ end subroutine
! end of ADIOS_DEFINE_ATTRIBUTE_BYVALUE functions
diff --git a/src/core/bp_utils.c b/src/core/bp_utils.c
index 524423c..1526f9b 100644
--- a/src/core/bp_utils.c
+++ b/src/core/bp_utils.c
@@ -3143,7 +3143,7 @@ int is_global_array_generic (const struct adios_index_characteristic_dims_struct
* Note that adios_internals:adios_get_type_size returns
* strlen(var) for strings.
*/
-int bp_get_type_size (enum ADIOS_DATATYPES type, void * var)
+int bp_get_type_size (enum ADIOS_DATATYPES type, const void * var)
{
switch (type)
{
@@ -3155,7 +3155,7 @@ int bp_get_type_size (enum ADIOS_DATATYPES type, void * var)
if (!var)
return 1;
else
- return strlen ((char *) var) + 1;
+ return strlen ((const char *) var) + 1;
case adios_string_array:
return sizeof(char*);
diff --git a/src/core/bp_utils.h b/src/core/bp_utils.h
index f5fa920..d7aed08 100644
--- a/src/core/bp_utils.h
+++ b/src/core/bp_utils.h
@@ -52,7 +52,7 @@ int64_t get_var_start_index (struct adios_index_var_struct_v1 * v, int t);
int64_t get_var_stop_index (struct adios_index_var_struct_v1 * v, int t);
const char * bp_value_to_string (enum ADIOS_DATATYPES type, void * data);
-int bp_get_type_size (enum ADIOS_DATATYPES type, void * var);
+int bp_get_type_size (enum ADIOS_DATATYPES type, const void * var);
int bp_get_dimension_generic(const struct adios_index_characteristic_dims_struct_v1 *dims,
uint64_t *ldims, uint64_t *gdims, uint64_t *offsets);
int bp_get_dimension_characteristics(struct adios_index_characteristic_struct_v1 *ch,
diff --git a/src/core/buffer.c b/src/core/buffer.c
index e6f0435..fcb6d44 100644
--- a/src/core/buffer.c
+++ b/src/core/buffer.c
@@ -86,6 +86,18 @@ int adios_databuffer_resize (struct adios_file_struct *fd, uint64_t size)
else
{
retval = 1;
+ // try to alloc/realloc a buffer to max allowed size
+ // align usable buffer to BYTE_ALIGN bytes
+ void * b = realloc (fd->allocated_bufptr, max_size + BYTE_ALIGN - 1);
+ if (b)
+ {
+ fd->allocated_bufptr = b;
+ uint64_t p = (uint64_t) fd->allocated_bufptr;
+ fd->buffer = (char *) ((p + BYTE_ALIGN - 1) & ~(BYTE_ALIGN - 1));
+ log_debug ("Data buffer extended from %" PRIu64 " to %" PRIu64 " bytes\n", fd->buffer_size, size);
+ fd->buffer_size = max_size;
+
+ }
log_warn ("Cannot allocate %" PRIu64 " bytes for buffered output of group %s "
" because max allowed is %" PRIu64 " bytes. "
"Continue buffering with buffer size %" PRIu64 " MB\n",
diff --git a/src/core/common_adios.c b/src/core/common_adios.c
index 4357621..1b90ef1 100644
--- a/src/core/common_adios.c
+++ b/src/core/common_adios.c
@@ -68,18 +68,38 @@ int common_adios_init_noxml (MPI_Comm comm)
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
+ }
+ }
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
- )
+ && 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);
}
@@ -96,12 +116,12 @@ int common_adios_finalize (int mype)
///////////////////////////////////////////////////////////////////////////////
int common_adios_allocate_buffer (enum ADIOS_BUFFER_ALLOC_WHEN adios_buffer_alloc_when
- ,uint64_t buffer_size)
+ ,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");
+ "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 ();
@@ -112,36 +132,35 @@ int common_adios_allocate_buffer (enum ADIOS_BUFFER_ALLOC_WHEN adios_buffer_allo
// Drew: used for experiments
static uint32_t pinned_timestep = 0;
void adios_pin_timestep(uint32_t ts) {
- pinned_timestep = 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
- )
+ ,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");
#endif
- int64_t group_id = 0;
- struct adios_file_struct * fd = (struct adios_file_struct *)
- malloc (sizeof (struct adios_file_struct));
- struct adios_group_struct * g = 0;
- struct adios_method_list_struct * methods = 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;
- adios_file_struct_init (fd);
- adios_common_get_group (&group_id, group_name);
- g = (struct adios_group_struct *) group_id;
+ 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);
+ "adios_open: try to open file %s with undefined group: %s\n",
+ name, group_name);
*fd_p = 0;
return adios_errno;
}
@@ -160,88 +179,96 @@ int common_adios_open (int64_t * fd_p, const char * group_name
else
{
adios_error(err_invalid_file_mode,
- "adios_open: unknown file mode: %s, supported r,w,a,u\n",
- file_mode);
+ "adios_open: unknown file mode: %s, supported r,w,a,u\n",
+ file_mode);
*fd_p = 0;
return adios_errno;
}
- 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;
+ //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);
+ }
+
+ 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
- MPI_Comm_dup(comm, &fd->comm);
+ {
+ 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;
+ }
+ }
-#if 1
- /* Time index magic done here */
- if (mode == adios_mode_write)
+ /* 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++;
- }
- /* FIXME: the time_index is updated in the actual method in case of append/update
- so this code below is useless */
-# if 0
- else if (mode == adios_mode_append)
- {
+ */
g->time_index++;
}
- else if (mode == adios_mode_update && g->time_index > 0)
- {
- /* Update from Append differs only in the time index. All methods had
- code for Append, now for Update we decrease the counter by one,
- for all methods. (But do not go below 1).
- */
- g->time_index--;
- }
-# endif
- /* time starts from 1 not from 0 (traditionally; now no one cares */
+ /* 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;
-#else
- /* old way pre-1.4*/
- if (mode != adios_mode_read)
- g->time_index++;
-#endif
// Drew: for experiments
if (pinned_timestep > 0)
g->time_index = pinned_timestep;
- methods = g->methods;
- 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;
- }
if ( !adios_errno && fd->mode != adios_mode_read )
{
@@ -253,37 +280,34 @@ int common_adios_open (int64_t * fd_p, const char * group_name
gettimeofday(&tp, NULL);
sprintf(epoch, "%d", (int) tp.tv_sec);
- int def_adios_init_attrs = 1;
- // if we append/update, define these attributes only at the first step
- if (fd->mode != adios_mode_write && fd->group->time_index > 1)
- def_adios_init_attrs = 0;
+ /* 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 (def_adios_init_attrs) {
+ 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_string, VERSION, NULL);
adios_common_define_attribute ((int64_t)fd->group, "create_time_epoch", ADIOS_ATTR_PATH,
- adios_integer, epoch, NULL);
+ adios_integer, epoch, NULL);
adios_common_define_attribute ((int64_t)fd->group, "update_time_epoch", ADIOS_ATTR_PATH,
- adios_integer, epoch, NULL);
+ adios_integer, epoch, NULL);
// id of last attribute is fd->group->member_count
fd->group->attrid_update_epoch = fd->group->member_count;
}
- /* 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.
- */
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);
+ (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",
@@ -297,9 +321,18 @@ int common_adios_open (int64_t * fd_p, const char * group_name
}
/* Add first PG to the group */
- assert (!fd->pgs_written);
- assert (!fd->current_pg);
+ 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;
+
#ifdef ADIOS_TIMERS
@@ -309,61 +342,83 @@ int common_adios_open (int64_t * fd_p, const char * group_name
/* Now ask the methods if anyone wants common-layer BP formatted buffering */
methods = g->methods;
- while (methods)
+
+ if (NotTimeAggregated(g) || TimeAggregationJustBegan(g))
{
- 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
- )
+ while (methods)
{
- bufstrat = adios_transports [methods->method->m].
- adios_should_buffer_fn (fd, methods->method);
- }
+ 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
- */
- }
+ 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;
+ methods = methods->next;
+ }
}
-
if (fd->bufstrat != no_buffering)
{
/* Allocate BP buffer with remembered size or max size or default size */
uint64_t bufsize;
- if (g->last_buffer_size > 0)
- bufsize = g->last_buffer_size;
- else
- bufsize = adios_databuffer_get_extension_size (fd);
- if (!adios_databuffer_resize (fd, bufsize))
- {
- fd->bufstate = buffering_ongoing;
+ 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;
+ }
+ }
- // write the process group header
- adios_write_open_process_group_header_v1 (fd);
+ //printf("==open bufsize=%llu\n", bufsize);
- // setup for writing vars
- adios_write_open_vars_v1 (fd);
- }
- else
+ //Time Aggregation: when ts buffering is on, only the first step needs to
+ //allocate the buffer
+ if (NotTimeAggregated(g) || TimeAggregationJustBegan(g))
{
- 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;
+ 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;
+
+ // 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)
@@ -380,9 +435,12 @@ int common_adios_group_size (int64_t fd_p, uint64_t data_size, uint64_t * total_
#if defined(WITH_NCSU_TIMER) && defined(TIMER_LEVEL) && (TIMER_LEVEL <= 0)
timer_start ("adios_group_size");
#endif
+ //printf("enter adios_group_size datasize= %llu\n", data_size);
adios_errno = err_no_error;
- struct adios_file_struct * fd = (struct adios_file_struct *) fd_p;
+ 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");
@@ -394,7 +452,7 @@ int common_adios_group_size (int64_t fd_p, uint64_t data_size, uint64_t * total_
{
*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;
}
@@ -409,6 +467,7 @@ int common_adios_group_size (int64_t fd_p, uint64_t data_size, uint64_t * total_
data_size += fd->group->tv_size;
#endif
+
uint64_t overhead = adios_calc_overhead_v1 (fd);
*total_size = data_size + overhead;
@@ -432,9 +491,9 @@ int common_adios_group_size (int64_t fd_p, uint64_t data_size, uint64_t * total_
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);
+ "for group %s in adios_group_size(). Continue buffering "
+ "with buffer size %" PRIu64 " MB\n",
+ *total_size, fd->group->name, fd->buffer_size/1048576L);
}
}
@@ -552,6 +611,7 @@ int common_adios_write (struct adios_file_struct * fd, struct adios_var_struct *
// 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)
{
@@ -561,6 +621,8 @@ int common_adios_write (struct adios_file_struct * fd, struct adios_var_struct *
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);
@@ -585,7 +647,7 @@ int common_adios_write (struct adios_file_struct * fd, struct adios_var_struct *
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);
}
@@ -601,9 +663,9 @@ int common_adios_write (struct adios_file_struct * fd, struct adios_var_struct *
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);
+ "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? */
@@ -649,7 +711,7 @@ int common_adios_write (struct adios_file_struct * fd, struct adios_var_struct *
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) {
@@ -660,7 +722,7 @@ int common_adios_write (struct adios_file_struct * fd, struct adios_var_struct *
// FIXME: Reverse the transform metadata and write raw data as usual
}
#if defined(WITH_NCSU_TIMER) && defined(TIMER_LEVEL) && (TIMER_LEVEL <= 0)
- timer_stop ("adios_transform");
+ timer_stop ("adios_transform");
#endif
}
@@ -673,10 +735,10 @@ int common_adios_write (struct adios_file_struct * fd, struct adios_var_struct *
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);
+ (fd, v, var, m->method);
}
m = m->next;
@@ -701,7 +763,7 @@ int common_adios_write (struct adios_file_struct * fd, struct adios_var_struct *
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
+ // to free them in possible forthcoming adios_write() of the same variable
}
if (!adios_errno) {
@@ -804,9 +866,9 @@ int common_adios_write_byid (struct adios_file_struct * fd, struct adios_var_str
///////////////////////////////////////////////////////////////////////////////
int common_adios_get_write_buffer (int64_t fd_p, const char * name
- ,uint64_t * size
- ,void ** buffer
- )
+ ,uint64_t * size
+ ,void ** buffer
+)
{
struct adios_file_struct * fd = (struct adios_file_struct *) fd_p;
adios_errno = err_no_error;
@@ -840,12 +902,12 @@ int common_adios_get_write_buffer (int64_t fd_p, const char * name
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
- )
+ && 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);
+ (fd, v, size, buffer, m->method);
m = 0;
}
else
@@ -858,8 +920,8 @@ int common_adios_get_write_buffer (int64_t fd_p, const char * name
///////////////////////////////////////////////////////////////////////////////
int common_adios_read (int64_t fd_p, const char * name, void * buffer
- ,uint64_t buffer_size
- )
+ ,uint64_t buffer_size
+)
{
struct adios_file_struct * fd = (struct adios_file_struct *) fd_p;
adios_errno = err_no_error;
@@ -895,17 +957,17 @@ int common_adios_read (int64_t fd_p, const char * name, void * buffer
while (m)
{
if ( m->method->m != ADIOS_METHOD_UNKNOWN
- && m->method->m != ADIOS_METHOD_NULL
- && adios_transports [m->method->m].adios_read_fn
- )
+ && 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);
+ (fd, v, buffer, buffer_size, m->method);
m = 0;
}
else
m = m->next;
- }
+ }
}
else
{
@@ -974,8 +1036,8 @@ int common_adios_set_path (int64_t fd_p, const char * path)
// 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
- )
+ ,const char * name
+)
{
struct adios_file_struct * fd = (struct adios_file_struct *) fd_p;
adios_errno = err_no_error;
@@ -1033,12 +1095,12 @@ int common_adios_end_iteration ()
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
- )
+ && 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);
+ (m->method);
}
}
@@ -1055,12 +1117,12 @@ int common_adios_start_calculation ()
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
- )
+ && 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);
+ (m->method);
}
}
@@ -1077,27 +1139,27 @@ int common_adios_stop_calculation ()
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
- )
+ && 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);
+ (m->method);
}
}
return adios_errno;
}
+
///////////////////////////////////////////////////////////////////////////////
-int common_adios_close (int64_t fd_p)
+int common_adios_close (struct adios_file_struct * fd)
{
#if defined(WITH_NCSU_TIMER) && defined(TIMER_LEVEL) && (TIMER_LEVEL <= 0)
timer_start ("adios_close");
#endif
adios_errno = err_no_error;
- struct adios_file_struct * fd = (struct adios_file_struct *) fd_p;
if (!fd)
{
adios_error (err_invalid_file_pointer, "Invalid handle passed to adios_close\n");
@@ -1110,8 +1172,8 @@ int common_adios_close (int64_t fd_p)
{
// 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;
}
@@ -1126,8 +1188,10 @@ int common_adios_close (int64_t fd_p)
struct adios_attribute_struct * a = fd->group->attributes;
struct adios_var_struct * v = fd->group->vars;
- if (fd->mode != adios_mode_read )
+ 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);
@@ -1153,7 +1217,14 @@ int common_adios_close (int64_t fd_p)
{
/* Trouble, attributes just don't fit into the end of buffer */
// try to extend the buffer first
- if (adios_databuffer_resize (fd, fd->buffer_size + asize))
+ 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. "
@@ -1177,6 +1248,28 @@ int common_adios_close (int64_t fd_p)
}
}
+
+ 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
@@ -1184,38 +1277,122 @@ int common_adios_close (int64_t fd_p)
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
- )
+ && m->method->m != ADIOS_METHOD_NULL
+ && adios_transports [m->method->m].adios_close_fn
+ )
{
- adios_transports [m->method->m].adios_close_fn
- (fd, m->method);
+
+ 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;
+ }
+ }
}
}
- while (v)
+
+ /* 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))
{
- v->write_offset = 0;
- if (v->adata)
+ if (TimeAggregationIsaSyncGroup(fd->group))
{
- free (v->adata);
- v->data = v->adata = 0;
+ 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);
+ }
+ }
}
-
- v = v->next;
}
- /* clean-up all copied variables with statistics and data in all PGs attached to this file */
- adios_free_pglist (fd);
- if (fd->name)
+ //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))
{
- free (fd->name);
- fd->name = 0;
- }
+ 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);
+
+ 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
@@ -1224,36 +1401,84 @@ int common_adios_close (int64_t fd_p)
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);
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
- 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);
}
- adios_databuffer_free (fd);
}
- 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: 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);
+ */
#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, ");
+ // 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;
@@ -1267,9 +1492,11 @@ int common_adios_close (int64_t fd_p)
//timer_reset_timers ();
#endif
+
return adios_errno;
}
+
//////////////////////////////////////////////////////////////////////////////
// Methods normally only called by the XML parser
//////////////////////////////////////////////////////////////////////////////
diff --git a/src/core/common_adios.h b/src/core/common_adios.h
index b36276f..e9ff44e 100644
--- a/src/core/common_adios.h
+++ b/src/core/common_adios.h
@@ -62,6 +62,6 @@ int common_adios_start_calculation (void);
int common_adios_stop_calculation (void);
-int common_adios_close (int64_t fd_p);
+int common_adios_close (struct adios_file_struct * fd );
#endif
diff --git a/src/core/common_read.c b/src/core/common_read.c
index e7b44f1..ccf8c13 100644
--- a/src/core/common_read.c
+++ b/src/core/common_read.c
@@ -3818,7 +3818,7 @@ const char * common_read_type_to_string (enum ADIOS_DATATYPES type)
}
-int common_read_type_size(enum ADIOS_DATATYPES type, void *data)
+int common_read_type_size(enum ADIOS_DATATYPES type, const void *data)
{
return bp_get_type_size(type, data);
}
@@ -3966,5 +3966,60 @@ void common_read_print_fileinfo (const ADIOS_FILE *fp)
}
+ADIOS_AVAILABLE_READ_METHODS * adios_available_read_methods()
+{
+ int i, n;
+ n = 0;
+ for (i = 0; i < ADIOS_READ_METHOD_COUNT; i++) {
+ if (adios_read_hooks[i].method_name) {
+ n++;
+ }
+ }
+
+ if (n == 0)
+ return NULL;
+
+ ADIOS_AVAILABLE_READ_METHODS * m = (ADIOS_AVAILABLE_READ_METHODS *) malloc (sizeof(ADIOS_AVAILABLE_READ_METHODS));
+ if (!m)
+ return NULL;
+
+ m->name = (char**) malloc (n*sizeof(char*));
+ m->methodID = (enum ADIOS_READ_METHOD *) malloc (n*sizeof(enum ADIOS_READ_METHOD));
+ m->nmethods = n;
+
+ n = 0;
+ for (i = 0; i < ADIOS_READ_METHOD_COUNT; i++) {
+ if (adios_read_hooks[i].method_name) {
+ m->name[n] = strdup (adios_read_hooks[i].method_name);
+ m->methodID[n] = (enum ADIOS_READ_METHOD) i;
+ n++;
+ }
+ }
+ return m;
+}
+void adios_available_read_methods_free (ADIOS_AVAILABLE_READ_METHODS *m)
+{
+ int i;
+ if (m)
+ {
+ if (m->name)
+ {
+ for (i=0; i < m->nmethods; i++)
+ {
+ if (m->name[i]) {
+ free (m->name[i]);
+ m->name[i] = NULL;
+ }
+ }
+ free (m->name);
+ m->name = NULL;
+ }
+ if (m->methodID) {
+ free (m->methodID);
+ m->methodID = NULL;
+ }
+ free (m);
+ }
+}
diff --git a/src/core/common_read.h b/src/core/common_read.h
index 233a369..8d17416 100644
--- a/src/core/common_read.h
+++ b/src/core/common_read.h
@@ -102,7 +102,7 @@ int common_read_get_attr_byid (const ADIOS_FILE * fp, int attrid, enum ADIOS_DA
int * size, void ** data);
const char * common_read_type_to_string (enum ADIOS_DATATYPES type);
-int common_read_type_size(enum ADIOS_DATATYPES type, void *data);
+int common_read_type_size(enum ADIOS_DATATYPES type, const void *data);
int common_read_get_grouplist (const ADIOS_FILE *fp, char ***group_namelist);
diff --git a/src/core/flexpath.h b/src/core/flexpath.h
index 03bbef1..3a59441 100644
--- a/src/core/flexpath.h
+++ b/src/core/flexpath.h
@@ -20,6 +20,7 @@
#define ACK_MSG 2
#define INIT_MSG 3
#define EOS_MSG 4
+#define FINALIZE_MSG 5
#define FP_FORTRAN_MODE 1
#define FP_C_MODE 0
diff --git a/src/core/mpidummy.c b/src/core/mpidummy.c
index ea763ba..57ad081 100644
--- a/src/core/mpidummy.c
+++ b/src/core/mpidummy.c
@@ -156,6 +156,28 @@ int MPI_Scatterv( void *sendbuf, int *sendcnts, int *displs,
return ier ;
}
+int MPI_Allreduce(const void *sendbuf, void *recvbuf, int count,
+ MPI_Datatype datatype, MPI_Op op, MPI_Comm comm)
+{
+ int ier = MPI_SUCCESS;
+ size_t elemsize=0, nbytes=0;
+ if( !sendbuf || !recvbuf ) ier = MPI_ERR_BUFFER ;
+
+ switch( datatype )
+ {
+ case MPI_INT : elemsize = sizeof( int ) ;
+ break;
+ default : return MPI_ERR_TYPE ;
+ }
+ nbytes = elemsize * count ;
+
+ if( nbytes <= 0 ) ier = MPI_ERR_COUNT ;
+
+ if( ier == MPI_SUCCESS ) memcpy( recvbuf, sendbuf, nbytes );
+ else snprintf(mpierrmsg, ier, "could not allreduce data\n" );
+
+ return ier ;
+}
int MPI_File_open(MPI_Comm comm, char *filename, int amode, MPI_Info info, MPI_File *fh)
{
diff --git a/src/mxml/Makefile.am b/src/mxml/Makefile.am
index bcc0913..dda7f32 100644
--- a/src/mxml/Makefile.am
+++ b/src/mxml/Makefile.am
@@ -1,6 +1,6 @@
MXML_SRCDIR=mxml-2.9
-AM_CPPFLAGS=-I$(top_srcdir)/mxml/${MXML_SRCDIR}
+AM_CPPFLAGS=-I$(srcdir)/${MXML_SRCDIR}
AUTOMAKE_OPTIONS = no-dependencies subdir-objects
METASOURCES=AUTO
diff --git a/src/mxml/Makefile.in b/src/mxml/Makefile.in
index 9bede00..2796ac5 100644
--- a/src/mxml/Makefile.in
+++ b/src/mxml/Makefile.in
@@ -108,7 +108,7 @@ 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_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 \
@@ -417,6 +417,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
@@ -479,7 +482,7 @@ top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
MXML_SRCDIR = mxml-2.9
-AM_CPPFLAGS = -I$(top_srcdir)/mxml/${MXML_SRCDIR}
+AM_CPPFLAGS = -I$(srcdir)/${MXML_SRCDIR}
AUTOMAKE_OPTIONS = no-dependencies subdir-objects
METASOURCES = AUTO
CLEANFILES =
diff --git a/src/public/adios.h b/src/public/adios.h
index 87ccc44..6fe36a3 100644
--- a/src/public/adios.h
+++ b/src/public/adios.h
@@ -98,12 +98,19 @@ void adios_set_max_buffer_size (uint64_t max_buffer_size_MB);
int adios_declare_group (int64_t * id,
const char * name,
const char * time_index,
- enum ADIOS_FLAG stats
+ enum ADIOS_STATISTICS_FLAG stats
);
// To free a ADIOS group
int adios_free_group (int64_t id);
+// To set time aggregation of a group output in a certain buffer size but
+// flush whenever the synced group is being output
+int adios_set_time_aggregation(int64_t groupid,
+ uint64_t buffersize,
+ int64_t syncgroupid
+ );
+
// To select a I/O method for a ADIOS group
int adios_select_method (int64_t group,
const char * method,
@@ -264,6 +271,21 @@ int adios_define_mesh_unstructured (char * points,
char * nspace,
int64_t group_id,
const char * name);
+
+
+typedef struct
+{
+ int nmethods; // number of available methods
+ char ** name; // array of transport method names
+} ADIOS_AVAILABLE_WRITE_METHODS;
+
+/* Provide the names of transport methods available in the running application
+ */
+ADIOS_AVAILABLE_WRITE_METHODS * adios_available_write_methods();
+
+void adios_available_write_methods_free (ADIOS_AVAILABLE_WRITE_METHODS *);
+
+
#ifdef __cplusplus
}
#endif
diff --git a/src/public/adios_error.h b/src/public/adios_error.h
index 9f49ddd..c4af3e8 100644
--- a/src/public/adios_error.h
+++ b/src/public/adios_error.h
@@ -148,6 +148,7 @@ enum ADIOS_ERRCODES {
// Transform layer errors
err_invalid_transform_type = -300, // unknown transform is requested
+ err_transform_failure = -301, // the execution of transform failed
// Query errors
err_unsupported_selection = -401, // unsupported selection
diff --git a/src/public/adios_query.h b/src/public/adios_query.h
index 875386c..343e4f1 100644
--- a/src/public/adios_query.h
+++ b/src/public/adios_query.h
@@ -208,6 +208,21 @@ void adios_query_free(ADIOS_QUERY* q);
/* conversion from string to query operation enum type */
enum ADIOS_PREDICATE_MODE adios_query_getOp(const char* opStr);
+
+typedef struct
+{
+ int nmethods; // number of available query methods
+ char ** name; // array of query method names
+ enum ADIOS_QUERY_METHOD * methodID; // enum ID of the method in source code
+} ADIOS_AVAILABLE_QUERY_METHODS;
+
+/* Provide the names of query methods available in the running application
+ */
+ADIOS_AVAILABLE_QUERY_METHODS * adios_available_query_methods();
+
+void adios_available_query_methods_free (ADIOS_AVAILABLE_QUERY_METHODS *);
+
+
#endif /* __INCLUDED_FROM_FORTRAN_API__ */
#ifdef __cplusplus
diff --git a/src/public/adios_read_v2.h b/src/public/adios_read_v2.h
index 8359997..802093d 100644
--- a/src/public/adios_read_v2.h
+++ b/src/public/adios_read_v2.h
@@ -542,7 +542,7 @@ const char * adios_type_to_string (enum ADIOS_DATATYPES type);
* For other types, it does not care about data and returns
* the size occupied by one element.
*/
-int adios_type_size(enum ADIOS_DATATYPES type, void *data);
+int adios_type_size(enum ADIOS_DATATYPES type, const void *data);
@@ -591,6 +591,21 @@ void adios_reset_dimension_order (ADIOS_FILE *fp, int is_fortran);
/** Test function to print basic info about the file to stdout */
void adios_print_fileinfo (ADIOS_FILE *fp);
+
+typedef struct
+{
+ int nmethods; // number of available read methods
+ char ** name; // array of read method names
+ enum ADIOS_READ_METHOD * methodID; // enum ID of the method in source code
+} ADIOS_AVAILABLE_READ_METHODS;
+
+/* Provide the names of read methods available in the running application
+ */
+ADIOS_AVAILABLE_READ_METHODS * adios_available_read_methods();
+
+void adios_available_read_methods_free (ADIOS_AVAILABLE_READ_METHODS *);
+
+
#endif /*__INCLUDED_FROM_FORTRAN_API__*/
#ifdef __cplusplus
diff --git a/src/public/adios_transform_methods.h b/src/public/adios_transform_methods.h
new file mode 100644
index 0000000..2d72bfc
--- /dev/null
+++ b/src/public/adios_transform_methods.h
@@ -0,0 +1,25 @@
+#ifndef ADIOS_TRANSFORM_METHODS_H
+#define ADIOS_TRANSFORM_METHODS_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+typedef struct
+{
+ int ntransforms; // number of transformations
+ char ** name; // array of transform names
+ char ** description; // array of descriptions
+} ADIOS_AVAILABLE_TRANSFORM_METHODS;
+
+/* Provide the names of transformations available in the running application
+ */
+ADIOS_AVAILABLE_TRANSFORM_METHODS * adios_available_transform_methods();
+
+void adios_available_transform_methods_free (ADIOS_AVAILABLE_TRANSFORM_METHODS *);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/src/public/adios_types.h b/src/public/adios_types.h
index 3ebc079..111867e 100644
--- a/src/public/adios_types.h
+++ b/src/public/adios_types.h
@@ -43,6 +43,15 @@ enum ADIOS_FLAG {adios_flag_unknown = 0
,adios_flag_no = 2
};
+enum ADIOS_STATISTICS_FLAG {
+ adios_stat_no = -1, /* turn off statistics generation */
+ adios_stat_minmax = 0, /* min + max only */
+ adios_stat_full = 1, /* all statistics turned on */
+
+ adios_stat_default = adios_stat_minmax,
+ adios_stat_no_do_not_use_this = 2 /* keep it for historic reason (== adios_flag_no) */
+};
+
enum ADIOS_BUFFER_ALLOC_WHEN {ADIOS_BUFFER_ALLOC_UNKNOWN
,ADIOS_BUFFER_ALLOC_NOW
,ADIOS_BUFFER_ALLOC_LATER
diff --git a/src/public/adios_version.h b/src/public/adios_version.h
index f059aa9..651f624 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 "1.10.0"
+#define ADIOS_VERSION "1.11.0"
#define ADIOS_VERSION_MAJOR 1
-#define ADIOS_VERSION_MINOR 10
+#define ADIOS_VERSION_MINOR 11
#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 "10"
+#define ADIOS_VERSION_MINOR_STRING "11"
#define ADIOS_VERSION_PATCH_STRING "0"
/* BP File format version
diff --git a/src/public/mpidummy.h b/src/public/mpidummy.h
index ae0cbaf..72bdc3d 100644
--- a/src/public/mpidummy.h
+++ b/src/public/mpidummy.h
@@ -21,6 +21,9 @@
extern "C" {
#endif
+/* This dummy MPI only supports functions what is included in both the parallel and
+ * sequential ADIOS library */
+
typedef int MPI_Comm;
typedef uint64_t MPI_Status;
typedef int MPI_File;
@@ -29,6 +32,9 @@ typedef int MPI_Datatype; /* Store the byte size of a type in such vars */
typedef uint64_t MPI_Offset;
typedef int MPI_Fint;
+enum mpi_operation { MPI_MIN, MPI_SUM };
+typedef enum mpi_operation MPI_Op;
+
#define MPI_SUCCESS 0
#define MPI_ERR_BUFFER 1 /* Invalid buffer pointer */
#define MPI_ERR_COUNT 2 /* Invalid count argument */
@@ -54,7 +60,6 @@ typedef int MPI_Fint;
#define MPI_ANY_SOURCE 0
#define MPI_ANY_TAG 0
-#define MPI_SUM 0
#define MPI_MAX_PROCESSOR_NAME 32
int MPI_Init(int *argc, char ***argv);
@@ -79,7 +84,8 @@ int MPI_Allgather(void *sendbuf, int sendcount, MPI_Datatype sendtype,
int MPI_Scatter(void *sendbuf, int sendcnt, MPI_Datatype sendtype, void *recvbuf, int recvcnt, MPI_Datatype recvtype, int root, MPI_Comm comm);
int MPI_Scatterv(void *sendbuf, int *sendcnts, int *displs, MPI_Datatype sendtype, void *recvbuf, int recvcnt, MPI_Datatype recvtype, int root, MPI_Comm comm);
-
+int MPI_Allreduce(const void *sendbuf, void *recvbuf, int count,
+ MPI_Datatype datatype, MPI_Op op, MPI_Comm comm);
int MPI_File_open(MPI_Comm comm, char *filename, int amode, MPI_Info info, MPI_File *fh);
int MPI_File_close(MPI_File *fh);
diff --git a/src/query/common_query.c b/src/query/common_query.c
index 5b8ffed..ca9f6dd 100644
--- a/src/query/common_query.c
+++ b/src/query/common_query.c
@@ -890,3 +890,61 @@ enum ADIOS_PREDICATE_MODE adios_query_getOp(const char* opStr)
return ADIOS_NE;
}
}
+
+
+ADIOS_AVAILABLE_QUERY_METHODS * adios_available_query_methods()
+{
+ int i, n;
+ n = 0;
+ for (i = 0; i < ADIOS_QUERY_METHOD_COUNT; i++) {
+ if (query_hooks[i].method_name) {
+ n++;
+ }
+ }
+
+ if (n == 0)
+ return NULL;
+
+ ADIOS_AVAILABLE_QUERY_METHODS * m = (ADIOS_AVAILABLE_QUERY_METHODS *) malloc (sizeof(ADIOS_AVAILABLE_QUERY_METHODS));
+ if (!m)
+ return NULL;
+
+ m->name = (char**) malloc (n*sizeof(char*));
+ m->methodID = (enum ADIOS_QUERY_METHOD *) malloc (n*sizeof(enum ADIOS_QUERY_METHOD));
+ m->nmethods = n;
+
+ n = 0;
+ for (i = 0; i < ADIOS_QUERY_METHOD_COUNT; i++) {
+ if (query_hooks[i].method_name) {
+ m->name[n] = strdup (query_hooks[i].method_name);
+ m->methodID[n] = (enum ADIOS_QUERY_METHOD)i;
+ n++;
+ }
+ }
+ return m;
+}
+
+void adios_available_query_methods_free (ADIOS_AVAILABLE_QUERY_METHODS *m)
+{
+ int i;
+ if (m)
+ {
+ if (m->name)
+ {
+ for (i=0; i < m->nmethods; i++)
+ {
+ if (m->name[i]) {
+ free (m->name[i]);
+ m->name[i] = NULL;
+ }
+ }
+ free (m->name);
+ m->name = NULL;
+ }
+ if (m->methodID) {
+ free (m->methodID);
+ m->methodID = NULL;
+ }
+ free (m);
+ }
+}
diff --git a/src/read/read_flexpath.c b/src/read/read_flexpath.c
index f4a69b5..360a1de 100644
--- a/src/read/read_flexpath.c
+++ b/src/read/read_flexpath.c
@@ -321,10 +321,9 @@ ffs_type_to_adios_type(const char *ffs_type, int size)
return adios_complex;
else if (!strcmp("double_complex", filtered_type))
return adios_double_complex;
- else {
- fprintf(stderr, "returning unknown for: ffs_type: %s\n", ffs_type);
- return adios_unknown;
- }
+
+ fprintf(stderr, "returning unknown for: ffs_type: %s\n", ffs_type);
+ return adios_unknown;
}
ADIOS_VARINFO*
@@ -649,8 +648,10 @@ send_open_msg(flexpath_reader_file *fp, int destination)
int cond = CMCondition_get(fp_read_data->cm, NULL);
msg.condition = cond;
+ 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;
}
@@ -669,7 +670,30 @@ send_close_msg(flexpath_reader_file *fp, int destination)
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;
+}
+
+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;
}
@@ -688,7 +712,9 @@ send_flush_msg(flexpath_reader_file *fp, int destination, Flush_type type, int u
// 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);
+ fp_verbose(fp, "Done with WAIT\n");
}
}
@@ -712,6 +738,7 @@ send_var_message(flexpath_reader_file *fp, int destination, char *varname)
build_bridge(&(fp->bridges[destination]));
}
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);
}
@@ -1269,7 +1296,9 @@ adios_read_flexpath_open(const char * fname,
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");
FILE * fp_in = fopen(writer_ready_filename,"r");
while (!fp_in) {
@@ -1305,7 +1334,9 @@ adios_read_flexpath_open(const char * fname,
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);
@@ -1333,6 +1364,7 @@ adios_read_flexpath_open(const char * fname,
}
// requesting initial data.
+ fp_verbose(fp, "sending open msg in read_open\n");
send_open_msg(fp, fp->writer_coordinator);
@@ -1341,7 +1373,9 @@ adios_read_flexpath_open(const char * fname,
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);
fp->data_read = 0;
@@ -1368,15 +1402,26 @@ adios_read_flexpath_open(const char * fname,
int adios_read_flexpath_finalize_method ()
{
- return 0;
+ /* flexpath_reader_file *fp = (flexpath_reader_file*)adiosfile->fh; */
+ /* int i; */
+ /* 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_finalize_msg(fp, i); */
+ /* } */
+ /* } */
+ /* return 1; */
}
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);
}
}
@@ -1418,12 +1463,13 @@ int
adios_read_flexpath_advance_step(ADIOS_FILE *adiosfile, int last, float timeout_sec)
{
flexpath_reader_file *fp = (flexpath_reader_file*)adiosfile->fh;
- //fprintf(stderr, "reader_rank:%d:calling advance_step:step:%d\n", fp->rank, fp->mystep);
+ fp_verbose(fp, " waiting on first barrier in flexpath_advance_step:step:%d\n", fp->mystep);
MPI_Barrier(fp->comm);
+ fp_verbose(fp, " wait complete in flexpath_advance_step:step:%d\n", fp->mystep);
int count = 0; // for perf measurements
- //fprintf(stderr, "reader_rank:%d:advance_step:sending flush step to coordinator:%d:step:%d\n", fp->rank, fp->writer_coordinator,fp->mystep);
+ 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->rank, fp->writer_coordinator,fp->mystep);
+ //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) {
@@ -1431,9 +1477,9 @@ adios_read_flexpath_advance_step(ADIOS_FILE *adiosfile, int last, float timeout_
return err_end_of_stream;
}
CMsleep(fp_read_data->cm, 1);
- //fprintf(stderr, "reader_rank:%d:advance_step:while loop sending flush step to coordinator:%d:step:%d\n", fp->rank, fp->writer_coordinator,fp->mystep);
+ 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->rank, fp->writer_coordinator,fp->mystep);
+ //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 i=0;
@@ -1443,7 +1489,9 @@ adios_read_flexpath_advance_step(ADIOS_FILE *adiosfile, int last, float timeout_
send_close_msg(fp, i);
}
}
+ 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);
count = 0;
adiosfile->current_step++;
@@ -1451,6 +1499,7 @@ adios_read_flexpath_advance_step(ADIOS_FILE *adiosfile, int last, float timeout_
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++;
}
@@ -1459,15 +1508,15 @@ adios_read_flexpath_advance_step(ADIOS_FILE *adiosfile, int last, float timeout_
fp->req.num_completed = 0;
fp->req.num_pending = 1;
fp->req.condition = CMCondition_get(fp_read_data->cm, NULL);
- //fprintf(stderr, "reader_rank:%d:advance_step:while loop sending flush DATA to coordinator:%d:step:%d\n", fp->rank, fp->writer_coordinator,fp->mystep);
+ 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);
- //fprintf(stderr, "reader_rank:%d:advance_step:while loop after flush DATA to coordinator:%d:step:%d\n", fp->rank, fp->writer_coordinator,fp->mystep);
+ 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.
- //fprintf(stderr, "reader_rank:%d:advance_step:while loop sending flush EVGROUP to coordinator:%d:step:%d\n", fp->rank, fp->writer_coordinator,fp->mystep);
+ 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->rank, fp->writer_coordinator,fp->mystep);
+ //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;
}
@@ -1556,11 +1605,9 @@ int adios_read_flexpath_perform_reads(const ADIOS_FILE *adiosfile, int blocking)
if ((total_sent % FP_BATCH_SIZE == 0) || (total_sent == num_sendees)) {
fp->req.num_pending = batchcount;
- /* fprintf(stderr, "\t\treader rank:%d:blocking on:%d:step:%d\n", */
- /* fp->rank, fp->req.condition, fp->mystep); */
+ 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);
- /* fprintf(stderr, "\t\treader rank:%d:after blocking:%d:step:%d\n", */
- /* fp->rank, fp->req.condition, fp->mystep); */
+ 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;
diff --git a/src/read/read_icee.c b/src/read/read_icee.c
index 413948a..15b496b 100644
--- a/src/read/read_icee.c
+++ b/src/read/read_icee.c
@@ -1,6 +1,6 @@
/*
- read_icee.c
- Goal: to create evpath io connection layer in conjunction with
+ read_icee.c
+ Goal: to create evpath io connection layer in conjunction with
write/adios_icee.c
*/
// system libraries
@@ -74,12 +74,12 @@
///////////////////////////
#include "core/globals.h"
-#define DUMP(fmt, ...) fprintf(stderr, ">>> "fmt"\n", ## __VA_ARGS__);
+#define DUMP(fmt, ...) fprintf(stderr, ">>> "fmt"\n", ## __VA_ARGS__);
/* Data Structure
+ fileinfo 1.1 - fileinfo 1.2 - ...
- | + var 1.1 + var 1.2
+ | + var 1.1 + var 1.2
| + var 2.1 + var 2.2
| + ... + ...
+ fileinfo 2.1 - fileinfo 2.2 - ...
@@ -101,7 +101,7 @@ icee_llist_create(void* item)
icee_llist_ptr_t node = malloc(sizeof(icee_llist_t));
node->item = item;
node->next = NULL;
-
+
return node;
}
@@ -109,16 +109,16 @@ icee_llist_ptr_t
icee_llist_append(const icee_llist_ptr_t root, void* item)
{
assert(root != NULL);
-
+
icee_llist_ptr_t p = root;
-
+
while (p->next != NULL)
p = p->next;
icee_llist_ptr_t node = malloc(sizeof(icee_llist_t));
node->item = item;
node->next = NULL;
-
+
p->next = node;
return node;
@@ -128,7 +128,7 @@ icee_llist_ptr_t
icee_llist_search(const icee_llist_ptr_t root, int (*fp)(const void*, const void*), const void* arg)
{
icee_llist_ptr_t p = root;
-
+
while (p != NULL)
{
if ((*fp)(p->item, arg)) break;
@@ -142,7 +142,7 @@ void
icee_llist_map(const icee_llist_ptr_t root, void (*fp)(const void*))
{
icee_llist_ptr_t p = root;
-
+
while (p != NULL)
{
(*fp)(p->item);
@@ -165,18 +165,18 @@ pthread_mutex_t fileinfo_lock;
void icee_fileinfo_append(const icee_fileinfo_rec_ptr_t root, icee_fileinfo_rec_ptr_t fp)
{
assert(root != NULL);
-
+
icee_fileinfo_rec_ptr_t p = root;
while ((p->timestep != fp->timestep) && (p->next != NULL))
{
- p = p->next;
+ p = p->next;
}
if (p->timestep == fp->timestep)
{
icee_varinfo_rec_ptr_t v = p->varinfo;
-
+
while (v->next != NULL)
v = v->next;
@@ -227,7 +227,7 @@ void icee_fileinfo_free(icee_fileinfo_rec_ptr_t fp)
}
free(fp);
- fp = NULL;
+ fp = NULL;
}
icee_varinfo_rec_ptr_t
@@ -259,7 +259,7 @@ void icee_varinfo_copy(icee_varinfo_rec_ptr_t dest, const icee_varinfo_rec_ptr_t
memcpy(dest->gdims, src->gdims, dimsize);
memcpy(dest->ldims, src->ldims, dimsize);
memcpy(dest->offsets, src->offsets, dimsize);
-
+
dest->data = malloc(src->varlen);
memcpy(dest->data, src->data, src->varlen);
@@ -300,6 +300,10 @@ void icee_sel_bb_print(const ADIOS_SELECTION *sel)
}
}
+static double sum_deltat = 0;
+static int cnt_deltat = 0;
+static int use_read_probe = 0;
+
static int
icee_fileinfo_handler(CManager cm, void *vevent, void *client_data, attr_list attrs)
{
@@ -309,6 +313,44 @@ icee_fileinfo_handler(CManager cm, void *vevent, void *client_data, attr_list at
icee_fileinfo_rec_ptr_t lfp = malloc(sizeof(icee_fileinfo_rec_t));
icee_fileinfo_copy(lfp, event);
lfp->merge_count = 1;
+
+ double deltat = MPI_Wtime() - lfp->timestamp;
+ if (strcmp(lfp->fname, "_icee_.probe") == 0)
+ {
+ cnt_deltat++;
+ if (cnt_deltat > 1) // discard the first deltat
+ {
+ sum_deltat += deltat;
+ }
+ log_debug("deltat: %g (sum: %g, count: %d)\n", deltat, sum_deltat, cnt_deltat);
+ return 1;
+ }
+
+ if (cnt_deltat > 1)
+ {
+ uint64_t dsize = 0;
+ icee_varinfo_rec_ptr_t vp = lfp->varinfo;
+ while (vp != NULL)
+ {
+ dsize += vp->varlen;
+ vp = vp->next;
+ }
+ double adjustedt = deltat - sum_deltat/(cnt_deltat-1);
+ log_debug("received, deltat, adjusted, throughput = %g (MB), %g (sec), %g (sec), %g (MB/sec)\n",
+ (double)dsize/1024/1024, deltat, adjustedt, (double)dsize/adjustedt/1024/1024);
+
+
+ {
+ icee_varinfo_rec_ptr_t vp = NULL;
+ vp = icee_varinfo_search_byname(lfp->varinfo, "__icee_deltat__");
+
+ if (vp != NULL)
+ {
+ *((double*)vp->data) = adjustedt;
+ }
+ }
+
+ }
icee_varinfo_rec_ptr_t eventvp = event->varinfo;
icee_varinfo_rec_ptr_t *lvpp = &lfp->varinfo;
@@ -318,7 +360,7 @@ icee_fileinfo_handler(CManager cm, void *vevent, void *client_data, attr_list at
*lvpp = malloc(sizeof(icee_varinfo_rec_t));
icee_varinfo_copy(*lvpp, eventvp);
if (adios_verbose_level > 5) DUMP("id,name = %d,%s", (*lvpp)->varid, (*lvpp)->varname);
-
+
lvpp = &(*lvpp)->next;
eventvp = eventvp->next;
}
@@ -382,8 +424,8 @@ typedef struct {
icee_matrix_t* mat;
} icee_matrix_view_t;
-void
-mat_init (icee_matrix_t *m,
+void
+mat_init (icee_matrix_t *m,
int typesize,
int ndims,
const uint64_t *dims,
@@ -405,7 +447,7 @@ mat_init (icee_matrix_t *m,
m->data = data;
}
-void
+void
view_init (icee_matrix_view_t *v,
icee_matrix_t *m,
const int64_t *vdims,
@@ -429,7 +471,7 @@ void
view_copy (icee_matrix_view_t *dest, icee_matrix_view_t *src)
{
assert(dest->mat->ndims == src->mat->ndims);
-
+
int i;
for (i=0; i<dest->mat->ndims; i++)
assert(dest->vdims[i] == src->vdims[i]);
@@ -440,13 +482,13 @@ view_copy (icee_matrix_view_t *dest, icee_matrix_view_t *src)
int s, d;
d = dest->offsets[0] * dest->mat->accumdims[0];
s = src->offsets[0] * src->mat->accumdims[0];
- memcpy(dest->mat->data + d * dest->mat->typesize,
- src->mat->data + s * dest->mat->typesize,
+ memcpy(dest->mat->data + d * dest->mat->typesize,
+ src->mat->data + s * dest->mat->typesize,
dest->vdims[0] * dest->mat->accumdims[0] * dest->mat->typesize);
return;
}
-
+
// Non-contiguous merging
switch (dest->mat->ndims)
{
@@ -455,8 +497,8 @@ view_copy (icee_matrix_view_t *dest, icee_matrix_view_t *src)
int s, d;
d = dest->offsets[0];
s = src->offsets[0];
- memcpy(dest->mat->data + d * dest->mat->typesize,
- src->mat->data + s * dest->mat->typesize,
+ memcpy(dest->mat->data + d * dest->mat->typesize,
+ src->mat->data + s * dest->mat->typesize,
dest->vdims[0] * dest->mat->typesize);
break;
}
@@ -465,12 +507,12 @@ view_copy (icee_matrix_view_t *dest, icee_matrix_view_t *src)
int i, s, d;
for (i=0; i<dest->vdims[0]; i++)
{
- d = (i + dest->offsets[0]) * dest->mat->accumdims[0]
+ d = (i + dest->offsets[0]) * dest->mat->accumdims[0]
+ dest->offsets[1];
- s = (i + src->offsets[0]) * src->mat->accumdims[0]
+ s = (i + src->offsets[0]) * src->mat->accumdims[0]
+ src->offsets[1];
- memcpy(dest->mat->data + d * dest->mat->typesize,
- src->mat->data + s * dest->mat->typesize,
+ memcpy(dest->mat->data + d * dest->mat->typesize,
+ src->mat->data + s * dest->mat->typesize,
dest->vdims[1] * dest->mat->typesize);
}
break;
@@ -482,14 +524,14 @@ view_copy (icee_matrix_view_t *dest, icee_matrix_view_t *src)
{
for (j=0; j<dest->vdims[1]; j++)
{
- d = (i + dest->offsets[0]) * dest->mat->accumdims[0]
+ d = (i + dest->offsets[0]) * dest->mat->accumdims[0]
+ (j + dest->offsets[1]) * dest->mat->accumdims[1]
+ dest->offsets[2];
- s = (i + src->offsets[0]) * src->mat->accumdims[0]
- + (j + src->offsets[1]) * src->mat->accumdims[1]
+ s = (i + src->offsets[0]) * src->mat->accumdims[0]
+ + (j + src->offsets[1]) * src->mat->accumdims[1]
+ src->offsets[2];
- memcpy(dest->mat->data + d * dest->mat->typesize,
- src->mat->data + s * dest->mat->typesize,
+ memcpy(dest->mat->data + d * dest->mat->typesize,
+ src->mat->data + s * dest->mat->typesize,
dest->vdims[2] * dest->mat->typesize);
}
}
@@ -503,58 +545,58 @@ view_copy (icee_matrix_view_t *dest, icee_matrix_view_t *src)
}
}
-void
-set_contact_list (attr_list contact_list,
- const icee_transport_t icee_transport,
+void
+set_contact_list (attr_list contact_list,
+ const icee_transport_t icee_transport,
char *host, int port)
{
switch (icee_transport)
{
case ENET:
- add_string_attr(contact_list,
- attr_atom_from_string("CM_TRANSPORT"),
+ add_string_attr(contact_list,
+ attr_atom_from_string("CM_TRANSPORT"),
"enet");
- add_string_attr(contact_list,
- attr_atom_from_string("CM_ENET_HOST"),
+ add_string_attr(contact_list,
+ attr_atom_from_string("CM_ENET_HOST"),
host);
- add_int_attr(contact_list,
- attr_atom_from_string("CM_ENET_PORT"),
+ add_int_attr(contact_list,
+ attr_atom_from_string("CM_ENET_PORT"),
port);
break;
case NNTI:
- add_string_attr(contact_list,
- attr_atom_from_string("CM_TRANSPORT"),
+ add_string_attr(contact_list,
+ attr_atom_from_string("CM_TRANSPORT"),
"nnti");
- add_string_attr(contact_list,
- attr_atom_from_string("IP_HOST"),
+ add_string_attr(contact_list,
+ attr_atom_from_string("IP_HOST"),
host);
- add_int_attr(contact_list,
- attr_atom_from_string("NNTI_PORT"),
+ add_int_attr(contact_list,
+ attr_atom_from_string("NNTI_PORT"),
port);
- add_string_attr(contact_list,
- attr_atom_from_string("CM_NNTI_TRANSPORT"),
+ add_string_attr(contact_list,
+ attr_atom_from_string("CM_NNTI_TRANSPORT"),
"ib");
break;
case IB:
- add_string_attr(contact_list,
- attr_atom_from_string("CM_TRANSPORT"),
+ add_string_attr(contact_list,
+ attr_atom_from_string("CM_TRANSPORT"),
"ib");
- add_string_attr(contact_list,
- attr_atom_from_string("IP_HOST"),
+ add_string_attr(contact_list,
+ attr_atom_from_string("IP_HOST"),
host);
- add_int_attr(contact_list,
- attr_atom_from_string("IP_PORT"),
+ add_int_attr(contact_list,
+ attr_atom_from_string("IP_PORT"),
port);
break;
default:
- add_string_attr(contact_list,
- attr_atom_from_string("IP_HOST"),
+ add_string_attr(contact_list,
+ attr_atom_from_string("IP_HOST"),
host);
- add_int_attr(contact_list,
- attr_atom_from_string("IP_PORT"),
+ add_int_attr(contact_list,
+ attr_atom_from_string("IP_PORT"),
port);
break;
-
+
}
}
@@ -562,7 +604,7 @@ set_contact_list (attr_list contact_list,
int
adios_read_icee_init_method (MPI_Comm comm, PairStruct* params)
-{
+{
log_debug ("%s\n", __FUNCTION__);
int cm_port = 59997;
@@ -657,6 +699,10 @@ adios_read_icee_init_method (MPI_Comm comm, PairStruct* params)
{
use_native_contact = atoi(p->value);
}
+ else if (!strcasecmp (p->name, "use_probe"))
+ {
+ use_read_probe = atoi(p->value);
+ }
p = p->next;
}
@@ -719,7 +765,7 @@ adios_read_icee_init_method (MPI_Comm comm, PairStruct* params)
p = malloc(sizeof(icee_contactinfo_rec_t));
attr_list contact_list;
-
+
contact_list = create_attr_list();
set_contact_list(contact_list, icee_transport_init, host, port);
p->contact_string = attr_list_to_string(contact_list);
@@ -754,7 +800,7 @@ adios_read_icee_init_method (MPI_Comm comm, PairStruct* params)
p = malloc(sizeof(icee_contactinfo_rec_t));
attr_list contact_list;
-
+
p->stone_id = remote_stone;
p->contact_string = strdup(string_list);
p->next = NULL;
@@ -782,7 +828,7 @@ adios_read_icee_init_method (MPI_Comm comm, PairStruct* params)
log_info ("cm_host : %s\n", cm_host);
log_info ("cm_port : %d\n", cm_port);
- for (i = 0; i < num_remote_server; i++)
+ for (i = 0; i < num_remote_server; i++)
{
log_info ("remote_list : %s:%d\n", remote_server[i].client_host, remote_server[i].client_port);
}
@@ -826,7 +872,7 @@ adios_read_icee_init_method (MPI_Comm comm, PairStruct* params)
sleep(2);
conn = CMinitiate_conn(pcm[i], contact_list);
-
+
if (n > 5) break;
n++;
}
@@ -834,7 +880,7 @@ adios_read_icee_init_method (MPI_Comm comm, PairStruct* params)
if (conn == NULL)
{
log_error ("Initializing passive connection failed (%d)\n", i);
-
+
}
CMFormat fm_checkin, fm_fileinfo;
@@ -875,12 +921,12 @@ adios_read_icee_init_method (MPI_Comm comm, PairStruct* params)
if (CMlisten_specific(icee_read_cm[i], contact[i]) == 0)
printf("Error: unable to initialize connection manager[%d].\n", i);
-
- if (!CMfork_comm_thread(icee_read_cm[i]))
+
+ if (!CMfork_comm_thread(icee_read_cm[i]))
printf("Fork of communication thread[%d] failed.\n", i);
stone[i] = EValloc_stone(icee_read_cm[i]);
- if (adios_verbose_level > 5)
+ if (adios_verbose_level > 5)
{
log_debug("Reader contact: \"%d:%s\"\n", stone[i], attr_list_to_string(CMget_contact_list(icee_read_cm[i])));
dump_attr_list(CMget_contact_list(icee_read_cm[i]));
@@ -894,27 +940,27 @@ adios_read_icee_init_method (MPI_Comm comm, PairStruct* params)
contact_list = CMget_contact_list(icee_read_cm[i]);
else
contact_list = contact[i];
-
+
contact_msg[i].contact_string = attr_list_to_string(contact_list);
contact_msg[i].next = NULL;
if (i>0)
contact_msg[i-1].next = &contact_msg[i];
}
-
+
EVstone split_stone;
EVaction split_action;
split_stone = EValloc_stone(icee_read_cm[0]);
split_action = EVassoc_split_action(icee_read_cm[0], split_stone, NULL);
icee_contactinfo_rec_t *prev;
- for (i = 0; i < num_remote_server; i++)
+ for (i = 0; i < num_remote_server; i++)
{
attr_list contact_list;
EVstone remote_stone, output_stone;
output_stone = EValloc_stone(icee_read_cm[0]);
icee_contactinfo_rec_t *p = (i == 0)? remote_contact : prev->next;
-
+
remote_stone = p->stone_id;
contact_list = attr_list_from_string(p->contact_string);
@@ -926,10 +972,10 @@ adios_read_icee_init_method (MPI_Comm comm, PairStruct* params)
{
log_error ("Connection failed (%d). Try again ...\n", i);
dump_attr_list(contact_list);
-
+
sleep(2);
action = EVassoc_bridge_action(icee_read_cm[0], output_stone, contact_list, remote_stone);
-
+
if (n > 5) break;
n++;
}
@@ -944,9 +990,9 @@ adios_read_icee_init_method (MPI_Comm comm, PairStruct* params)
}
source = EVcreate_submit_handle(icee_read_cm[0], split_stone, icee_contactinfo_format_list);
-
+
//if (adios_verbose_level > 5) icee_contactinfo_print(contact_msg);
-
+
EVsubmit(source, contact_msg, NULL);
done:
@@ -975,10 +1021,10 @@ adios_read_icee_open(const char * fname,
icee_llist_ptr_t head = NULL;
- float waited_sec = 0.0;
+ float waited_sec = 0.0;
while (waited_sec <= timeout_sec)
{
- head = icee_llist_search(icee_filelist, icee_fileinfo_checkname,
+ head = icee_llist_search(icee_filelist, icee_fileinfo_checkname,
(const void*) fname);
if (head != NULL)
break;
@@ -986,19 +1032,19 @@ adios_read_icee_open(const char * fname,
usleep(0.1*1E6);
waited_sec += 0.1;
}
-
+
if (head == NULL)
{
log_error ("No data yet\n");
return NULL;
}
-
+
icee_fileinfo_rec_ptr_t fp = (icee_fileinfo_rec_ptr_t)head->item;
-
+
while (fp->merge_count != fp->nchunks)
{
log_debug("Waiting the rest of blocks (%d/%d)\n", fp->merge_count, fp->nchunks);
-
+
usleep(0.1*1E6);
}
@@ -1009,7 +1055,7 @@ adios_read_icee_open(const char * fname,
#if 0
int hashsize = 10;
qhashtbl_t *tbl = qhashtbl(hashsize);
-
+
icee_varinfo_rec_ptr_t vp = fp->varinfo;
while (vp != NULL)
{
@@ -1057,6 +1103,7 @@ adios_read_icee_open(const char * fname,
for (i = 0; i < fp->nvars; i++)
{
adiosfile->var_namelist[i] = strdup(vp->varname);
+ adiosfile->file_size += vp->varlen + sizeof(icee_varinfo_rec_t);
vp = vp->next;
}
@@ -1069,13 +1116,13 @@ adios_read_icee_open(const char * fname,
adiosfile->path = strdup(fname);
adiosfile->version = -1;
- adiosfile->file_size = 0;
- adios_errno = err_no_error;
+ //adiosfile->file_size = 0;
+ adios_errno = err_no_error;
return adiosfile;
}
-int
+int
adios_read_icee_finalize_method ()
{
log_debug("%s\n", __FUNCTION__);
@@ -1084,7 +1131,7 @@ adios_read_icee_finalize_method ()
{
int i;
if (is_read_cm_passive == 1)
- for (i = 0; i < num_remote_server; i++)
+ for (i = 0; i < num_remote_server; i++)
CManager_close(pcm[i]);
else
for (i=0; i<icee_read_num_parallel; i++)
@@ -1096,14 +1143,14 @@ adios_read_icee_finalize_method ()
return 0;
}
-void
-adios_read_icee_release_step(ADIOS_FILE *adiosfile)
+void
+adios_read_icee_release_step(ADIOS_FILE *adiosfile)
{
log_debug("%s\n", __FUNCTION__);
}
-int
-adios_read_icee_advance_step(ADIOS_FILE *adiosfile, int last, float timeout_sec)
+int
+adios_read_icee_advance_step(ADIOS_FILE *adiosfile, int last, float timeout_sec)
{
log_debug("%s\n", __FUNCTION__);
adios_errno = 0;
@@ -1122,11 +1169,11 @@ adios_read_icee_advance_step(ADIOS_FILE *adiosfile, int last, float timeout_sec)
usleep(0.1*1E6);
waited_sec += 0.1;
}
-
+
if (next != NULL)
{
icee_llist_ptr_t head = NULL;
- head = icee_llist_search(icee_filelist, icee_fileinfo_checkname,
+ head = icee_llist_search(icee_filelist, icee_fileinfo_checkname,
(const void*) fp->fname);
assert(head != NULL);
@@ -1136,13 +1183,13 @@ adios_read_icee_advance_step(ADIOS_FILE *adiosfile, int last, float timeout_sec)
icee_fileinfo_free(fp);
}
else
- adios_error (err_step_notready,
+ adios_error (err_step_notready,
"No more data yet\n");
return adios_errno;
}
-int
+int
adios_read_icee_close(ADIOS_FILE * fp)
{
log_debug("%s\n", __FUNCTION__);
@@ -1151,21 +1198,21 @@ adios_read_icee_close(ADIOS_FILE * fp)
}
ADIOS_FILE *
-adios_read_icee_fopen(const char *fname, MPI_Comm comm)
+adios_read_icee_fopen(const char *fname, MPI_Comm comm)
{
log_error("No support yet: %s\n", __FUNCTION__);
return NULL;
}
-int
-adios_read_icee_is_var_timed(const ADIOS_FILE* fp, int varid)
-{
+int
+adios_read_icee_is_var_timed(const ADIOS_FILE* fp, int varid)
+{
log_error("No support yet: %s\n", __FUNCTION__);
- return 0;
+ return 0;
}
-void
-adios_read_icee_get_groupinfo(const ADIOS_FILE *fp, int *ngroups, char ***group_namelist, uint32_t **nvars_per_group, uint32_t **nattrs_per_group)
+void
+adios_read_icee_get_groupinfo(const ADIOS_FILE *fp, int *ngroups, char ***group_namelist, uint32_t **nvars_per_group, uint32_t **nattrs_per_group)
{
log_debug("%s\n", __FUNCTION__);
@@ -1177,15 +1224,15 @@ adios_read_icee_get_groupinfo(const ADIOS_FILE *fp, int *ngroups, char ***group_
*group_namelist = (char **) malloc (sizeof (char*));
*group_namelist[0] = strdup ("noname");
}
-
+
return;
}
-int
-adios_read_icee_check_reads(const ADIOS_FILE* fp, ADIOS_VARCHUNK** chunk)
-{
+int
+adios_read_icee_check_reads(const ADIOS_FILE* fp, ADIOS_VARCHUNK** chunk)
+{
log_error("No support yet: %s\n", __FUNCTION__);
- return 0;
+ return 0;
}
int adios_read_icee_perform_reads(const ADIOS_FILE *adiosfile, int blocking)
@@ -1199,7 +1246,7 @@ adios_read_icee_inq_var_blockinfo(const ADIOS_FILE* fp,
ADIOS_VARINFO* varinfo)
{
log_error("No support yet: %s\n", __FUNCTION__);
- return 0;
+ return 0;
}
int
@@ -1209,18 +1256,18 @@ adios_read_icee_inq_var_stat(const ADIOS_FILE* fp,
int per_block_stat)
{
log_error("No support yet: %s\n", __FUNCTION__);
- return 0;
+ return 0;
}
-int
+int
adios_read_icee_schedule_read_byid(const ADIOS_FILE *adiosfile,
const ADIOS_SELECTION *sel,
int varid,
int from_steps,
int nsteps,
void *data)
-{
+{
int i;
icee_fileinfo_rec_ptr_t fp = (icee_fileinfo_rec_ptr_t) adiosfile->fh;
log_debug("%s (%d:%s)\n", __FUNCTION__, varid, fp->fname);
@@ -1230,11 +1277,11 @@ adios_read_icee_schedule_read_byid(const ADIOS_FILE *adiosfile,
{
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 % steps in adios_schedule_read()\n",
nsteps);
return err_invalid_timestep;
}
-
+
icee_varinfo_rec_ptr_t vp = NULL;
vp = icee_varinfo_search_byname(fp->varinfo, adiosfile->var_namelist[varid]);
if (adios_verbose_level > 5) icee_varinfo_print(vp);
@@ -1248,7 +1295,7 @@ adios_read_icee_schedule_read_byid(const ADIOS_FILE *adiosfile,
while (fp->merge_count != fp->nchunks)
{
log_debug("Waiting the rest of blocks (%d/%d)\n", fp->merge_count, fp->nchunks);
-
+
usleep(0.1*1E6);
}
@@ -1292,7 +1339,7 @@ adios_read_icee_schedule_read_byid(const ADIOS_FILE *adiosfile,
int i;
if (adios_verbose_level > 5) icee_varinfo_print(vp);
-
+
mat_init(&m_sel, vp->typesize, vp->ndims, sel->u.bb.count, data);
mat_init(&m_var, vp->typesize, vp->ndims, vp->ldims, vp->data);
@@ -1301,11 +1348,11 @@ adios_read_icee_schedule_read_byid(const ADIOS_FILE *adiosfile,
for (i=0; i<vp->ndims; i++)
{
- count[i] =
+ count[i] =
MYMIN(sel->u.bb.start[i]+sel->u.bb.count[i],
vp->offsets[i]+vp->ldims[i]) - start[i];
}
-
+
for (i=0; i<vp->ndims; i++)
{
if (count[i] <= 0)
@@ -1324,7 +1371,7 @@ adios_read_icee_schedule_read_byid(const ADIOS_FILE *adiosfile,
view_init (&v_sel, &m_sel, count, s_offsets);
view_init (&v_var, &m_var, count, v_offsets);
view_copy (&v_sel, &v_var);
-
+
next:
vp = icee_varinfo_search_byname(vp->next, adiosfile->var_namelist[varid]);
}
@@ -1347,7 +1394,7 @@ adios_read_icee_schedule_read_byid(const ADIOS_FILE *adiosfile,
return adios_errno;
}
-int
+int
adios_read_icee_schedule_read(const ADIOS_FILE *adiosfile,
const ADIOS_SELECTION * sel,
const char * varname,
@@ -1359,7 +1406,7 @@ adios_read_icee_schedule_read(const ADIOS_FILE *adiosfile,
return 0;
}
-int
+int
adios_read_icee_get_attr (int *gp, const char *attrname,
enum ADIOS_DATATYPES *type,
int *size, void **data)
@@ -1368,7 +1415,7 @@ adios_read_icee_get_attr (int *gp, const char *attrname,
return 0;
}
-int
+int
adios_read_icee_get_attr_byid (const ADIOS_FILE *adiosfile, int attrid,
enum ADIOS_DATATYPES *type,
int *size, void **data)
@@ -1377,7 +1424,7 @@ adios_read_icee_get_attr_byid (const ADIOS_FILE *adiosfile, int attrid,
return 0;
}
-ADIOS_VARINFO*
+ADIOS_VARINFO*
adios_read_icee_inq_var(const ADIOS_FILE * adiosfile, const char* varname)
{
log_debug("%s (%s)\n", __FUNCTION__, varname);
@@ -1385,7 +1432,7 @@ adios_read_icee_inq_var(const ADIOS_FILE * adiosfile, const char* varname)
return NULL;
}
-ADIOS_VARINFO*
+ADIOS_VARINFO*
adios_read_icee_inq_var_byid (const ADIOS_FILE * adiosfile, int varid)
{
log_debug("%s (%d)\n", __FUNCTION__, varid);
@@ -1394,7 +1441,7 @@ adios_read_icee_inq_var_byid (const ADIOS_FILE * adiosfile, int varid)
//assert((varid < fp->nvars) || (fp->nvars == 0));
ADIOS_VARINFO *a = calloc(1, sizeof(ADIOS_VARINFO));
-
+
icee_varinfo_rec_ptr_t vp = NULL;
vp = icee_varinfo_search_byname(fp->varinfo, adiosfile->var_namelist[varid]);
//icee_varinfo_print(vp);
@@ -1405,7 +1452,7 @@ adios_read_icee_inq_var_byid (const ADIOS_FILE * adiosfile, int varid)
a->type = vp->type;
a->ndim = vp->ndims;
a->nsteps = 1;
-
+
if (vp->ndims == 0)
{
a->value = malloc(vp->typesize);
@@ -1417,13 +1464,13 @@ adios_read_icee_inq_var_byid (const ADIOS_FILE * adiosfile, int varid)
a->dims = malloc(dimsize);
memcpy(a->dims, vp->gdims, dimsize);
a->global = 1;
-
+
if (a->dims[0] == 0)
{
a->global = 0;
memcpy(a->dims, vp->ldims, dimsize);
}
-
+
a->value = NULL;
}
}
@@ -1431,7 +1478,7 @@ adios_read_icee_inq_var_byid (const ADIOS_FILE * adiosfile, int varid)
return a;
}
-void
+void
adios_read_icee_free_varinfo (ADIOS_VARINFO *adiosvar)
{
log_debug("%s\n", __FUNCTION__);
@@ -1440,10 +1487,10 @@ adios_read_icee_free_varinfo (ADIOS_VARINFO *adiosvar)
}
-ADIOS_TRANSINFO*
-adios_read_icee_inq_var_transinfo(const ADIOS_FILE *gp,
+ADIOS_TRANSINFO*
+adios_read_icee_inq_var_transinfo(const ADIOS_FILE *gp,
const ADIOS_VARINFO *vi)
-{
+{
log_debug("%s\n", __FUNCTION__);
ADIOS_TRANSINFO *trans = malloc(sizeof(ADIOS_TRANSINFO));
memset(trans, 0, sizeof(ADIOS_TRANSINFO));
@@ -1452,9 +1499,9 @@ adios_read_icee_inq_var_transinfo(const ADIOS_FILE *gp,
}
-int
-adios_read_icee_inq_var_trans_blockinfo(const ADIOS_FILE *gp,
- const ADIOS_VARINFO *vi,
+int
+adios_read_icee_inq_var_trans_blockinfo(const ADIOS_FILE *gp,
+ const ADIOS_VARINFO *vi,
ADIOS_TRANSINFO *ti)
{
log_error("No support yet: %s\n", __FUNCTION__);
@@ -1469,7 +1516,7 @@ adios_read_icee_get_dimension_order (const ADIOS_FILE *adiosfile)
}
void
-adios_read_icee_reset_dimension_order (const ADIOS_FILE *adiosfile,
+adios_read_icee_reset_dimension_order (const ADIOS_FILE *adiosfile,
int is_fortran)
{
log_error("No support yet: %s\n", __FUNCTION__);
diff --git a/src/transforms/Makefile.plugins b/src/transforms/Makefile.plugins
index 1a7db30..819100c 100644
--- a/src/transforms/Makefile.plugins
+++ b/src/transforms/Makefile.plugins
@@ -25,3 +25,7 @@ transforms_read_method_SOURCES += transforms/adios_transform_aplod_read.c
# ALACRITY plugin:
transforms_write_method_SOURCES += transforms/adios_transform_alacrity_write.c
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
diff --git a/src/transforms/adios_transform_zfp_common.h b/src/transforms/adios_transform_zfp_common.h
new file mode 100644
index 0000000..e453d07
--- /dev/null
+++ b/src/transforms/adios_transform_zfp_common.h
@@ -0,0 +1,235 @@
+/*
+ * adios_transform_zfp_common.h
+ *
+ * Author: Eric Suchyta
+ * contact: eric.d.suchyta at gmail.com
+ *
+ */
+
+#ifndef ADIOS_TRANSFORM_ZFP_COMMON_H_
+#define ADIOS_TRANSFORM_ZFP_COMMON_H_
+
+
+/* general C stuff */
+#include <stdint.h> // uint64_t
+#include <stdio.h> // NULL, sprintf, sscanf
+#include <stdlib.h> // NULL, malloc, free
+#include <string.h> // memcpy, strcmp, strlen
+
+
+/* Were in the template included from ADIOS. Not necessarily sure if they're all strictly needed. */
+#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"
+#include "core/transforms/adios_transforms_hooks_read.h"
+#include "core/transforms/adios_transforms_reqgroup.h"
+
+
+/* Extra ADIOS headers that weren't added in the template */
+#include "adios_logger.h" // log_warn()
+#include "public/adios_error.h" // adios_error
+#include "public/adios_types.h" // adios datatypes
+
+
+/* Sort of a hack to deal with ADIOS and ZFP both using TYPES_H */
+#ifdef TYPES_H
+#undef TYPES_H
+#endif
+
+
+/* ZFP specific */
+#include "zfp.h"
+#define ZFP_STRSIZE 256 // size for string variables
+
+
+/* Transform metadata */
+struct zfp_metadata
+{
+ uint64_t usize; // uncompressed size;
+ uint64_t csize; // compressed size
+ uint cmode; // compression mode
+ char ctol[ZFP_STRSIZE]; // string of "tolerance"
+ char name[ZFP_STRSIZE]; // variable name
+};
+
+
+/* Attributes related to ZFP's operation */
+struct zfp_buffer
+{
+ bool error; // true if error
+
+ char name[ZFP_STRSIZE]; // Name of variable
+ zfp_type type; // data type
+ uint mode; // 0 = accuracy, 1 = precsion, 2 = rate
+ char ctol[ZFP_STRSIZE]; // string for "tolerance"
+ uint ndims; // number of dimensions
+ uint* dims; // array of dimension sizes
+
+ zfp_field* field; // Point to the array that zfp will compress
+ zfp_stream* zstream; // Connect field to this as input and to bitstream as output
+ bitstream* bstream; // Stores the "sorted" bits. Send this into the output ADIOS buffer
+ size_t buffsize; // Output bufffer size
+};
+
+
+/* Set a few defaults */
+static void init_zfp_buffer(struct zfp_buffer* zbuff, char* name)
+{
+ strcpy(zbuff->name, name);
+ zbuff->error = false;
+ return;
+}
+
+
+/* adios to zfp datatype */
+static int zfp_get_datatype(struct zfp_buffer* zbuff, enum ADIOS_DATATYPES type)
+{
+ if (type == adios_double)
+ {
+ zbuff->type = zfp_type_double;
+ }
+ else if (type == adios_real)
+ {
+ zbuff->type = zfp_type_float;
+ }
+ else
+ {
+ adios_error(err_unspecified, "ZFP does not handle the type of variable %s. "
+ "Supported types are adios_double, adios_real.\n",
+ zbuff->name);
+ zbuff->error = true;
+ return 0;
+ }
+ return 1;
+}
+
+
+/* Configure ZFP according to the user's specified mode and tolerance */
+static void zfp_initialize(void* array, struct zfp_buffer* zbuff)
+{
+ zbuff->zstream = zfp_stream_open(NULL);
+
+ /* set up the field dimensionality */
+ if (zbuff->ndims == 1)
+ {
+ zbuff->field = zfp_field_1d(array, zbuff->type, zbuff->dims[0]);
+ }
+ else if (zbuff->ndims == 2)
+ {
+ zbuff->field = zfp_field_2d(array, zbuff->type, zbuff->dims[0], zbuff->dims[1]);
+ }
+ else if (zbuff->ndims == 3)
+ {
+ zbuff->field = zfp_field_3d(array, zbuff->type, zbuff->dims[0], zbuff->dims[1], zbuff->dims[2]);
+ }
+ else
+ {
+ adios_error(err_invalid_dimension, "ZFP does not handle the %u dimensional variable %s. "
+ "Only 1, 2, and 3 dimensions are handled.\n",
+ zbuff->ndims, zbuff->name);
+ zbuff->error = true;
+ return;
+ }
+
+
+ /* Which mode to use. Alrady checked that the mode is okay upstream. */
+ if (zbuff->mode == 0) // accuracy
+ {
+ double tol;
+ int success = sscanf(zbuff->ctol, "%lf", &tol);
+ if (success != 1)
+ {
+ adios_error(err_invalid_argument, "Error in accuracy specification for variable %s: %s. "
+ "Provide a double value.\n",
+ zbuff->name, zbuff->ctol);
+ zbuff->error = true;
+ return;
+ }
+ zfp_stream_set_accuracy(zbuff->zstream, tol, zbuff->type);
+ }
+ else if (zbuff->mode == 1) // precision
+ {
+ uint tol;
+ long int ct;
+ char* end;
+ ct = strtol(zbuff->ctol, &end, 10);
+ if (ct == 0)
+ {
+ adios_error(err_invalid_argument, "Error in precision specification for variable %s: %s. "
+ "Provide an integer value.\n",
+ zbuff->name, zbuff->ctol);
+ zbuff->error = true;
+ return;
+ }
+
+ if (*end != '\0')
+ {
+ log_warn("A float was given for ZFP precision for variable %s: %s "
+ "-- the value was cast to an integer. ZFP accepts integer precisions.",
+ zbuff->name, zbuff->ctol);
+ }
+ tol = (uint) ct;
+
+
+ zfp_stream_set_precision(zbuff->zstream, tol, zbuff->type);
+ }
+ else if (zbuff->mode == 2) // rate
+ {
+ double tol;
+ int success = sscanf(zbuff->ctol, "%lf", &tol);
+ if (success != 1)
+ {
+ adios_error(err_invalid_argument, "Error in rate specification for variable %s: %s. "
+ "Provide a double value.\n",
+ zbuff->name, zbuff->ctol);
+ zbuff->error = true;
+ return;
+ }
+ zfp_stream_set_rate(zbuff->zstream, tol, zbuff->type, zbuff->ndims, 0); // I don't know what the 0 is.
+ }
+
+ zbuff->buffsize = zfp_stream_maximum_size(zbuff->zstream, zbuff->field);
+}
+
+
+/* Do the bit streaming */
+static void zfp_streaming(struct zfp_buffer* zbuff, void* abuff, bool decompress, uint64_t* finalsize)
+{
+
+ /* associate bit stream with allocated buffer */
+ zbuff->bstream = stream_open(abuff, zbuff->buffsize);
+ zfp_stream_set_bit_stream(zbuff->zstream, zbuff->bstream);
+ zfp_stream_rewind(zbuff->zstream);
+
+ /* (de)compress array */
+ if (decompress)
+ {
+ int success = zfp_decompress(zbuff->zstream, zbuff->field);
+ if (!success)
+ {
+ adios_error(err_transform_failure, "ZFP decompression failed for variable %s\n", zbuff->name);
+ zbuff->error = true;
+ return;
+ }
+ }
+ else
+ {
+ *finalsize = (uint64_t) zfp_compress(zbuff->zstream, zbuff->field);
+ if (! *finalsize)
+ {
+ adios_error(err_transform_failure, "ZFP compression failed for variable %s\n", zbuff->name);
+ zbuff->error = true;
+ return;
+ }
+ }
+
+ /* clean up */
+ zfp_field_free(zbuff->field);
+ zfp_stream_close(zbuff->zstream);
+ stream_close(zbuff->bstream);
+ free(zbuff->dims);
+}
+
+
+#endif /* ADIOS_TRANSFORM_ZFP_COMMON_H_ */
diff --git a/src/transforms/adios_transform_zfp_read.c b/src/transforms/adios_transform_zfp_read.c
new file mode 100755
index 0000000..e63f753
--- /dev/null
+++ b/src/transforms/adios_transform_zfp_read.c
@@ -0,0 +1,223 @@
+/*
+ * adios_transform_zfp_read.c
+ *
+ * Author: Eric Suchyta
+ * Contact: eric.d.suchyta at gmail.com
+ */
+
+#include "core/transforms/adios_transforms_hooks_read.h"
+
+#ifdef ZFP
+
+/* general C stuff */
+#include <stdint.h> // uint64_t
+#include <stdio.h> // NULL, sprintf
+#include <stdlib.h> // NULL, malloc, free
+#include <string.h> // memcpy, strcmp, strlen
+#include <assert.h>
+
+
+/* Were in the template included from ADIOS. Not necessarily sure if they're all strictly needed. */
+#include "util.h"
+#include "core/transforms/adios_transforms_reqgroup.h"
+
+
+/* Extra ADIOS headers that weren't added in the template */
+#include "core/adios_internals.h" // adios_get_type_size()
+
+
+/* ZFP specific */
+#include "adios_transform_zfp_common.h"
+#include "zfp.h"
+
+
+
+/* Basically giving an address and a size */
+static void* zfp_read_metadata_var(const void* pos, size_t size, size_t* offset)
+{
+ *offset += size;
+ return ((void*) pos + *offset - size);
+}
+
+
+/* Read string by iterating over byes */
+static void read_metastring(char s[ZFP_STRSIZE], const void* pos, size_t* offset)
+{
+ int i;
+ for (i=0; i<ZFP_STRSIZE; i++)
+ {
+ s[i] = *((char*)zfp_read_metadata_var(pos, 1, offset));
+ }
+ return;
+}
+
+
+/* Read each memory location and cast to the correct type */
+static struct zfp_metadata* zfp_read_metadata(struct zfp_metadata* metadata, adios_transform_pg_read_request *completed_pg_reqgroup)
+{
+ const void* pos = completed_pg_reqgroup->transform_metadata;
+ size_t offset = 0;
+
+ metadata->usize = *((uint64_t*)zfp_read_metadata_var(pos, sizeof(uint64_t), &offset));
+ metadata->csize = *((uint64_t*)zfp_read_metadata_var(pos, sizeof(uint64_t), &offset));
+ metadata->cmode = *((uint*)zfp_read_metadata_var(pos, sizeof(uint), &offset));
+ read_metastring(metadata->ctol, pos, &offset);
+ read_metastring(metadata->name, pos, &offset);
+
+ return metadata;
+}
+
+
+
+/* This is called in the main transform-level function.
+ * In a nutshell: decompress array, using (undoing) the settings in the other args. Connect to the ADIOS buffer.
+ */
+static int zfp_decompression(struct zfp_buffer* zbuff, void* uarray, void* carray)
+{
+ zfp_initialize(uarray, zbuff);
+ if (zbuff->error)
+ {
+ return 0;
+ }
+
+
+ zfp_streaming(zbuff, carray, 1, NULL);
+ if (zbuff->error)
+ {
+ return 0;
+ }
+ /* Possibly add a check for output size later, if it matches what ADIOS though it should be.
+ if (zusize != usize)
+ {
+ log_warn("ZFP thinks uncompressed size is %u" \
+ "bytes. ADIOS thinks uncompressed size is %" PRIu64 \
+ "bytes. Likely corruption.\n", zusize, usize);
+ }
+ */
+
+ return 1;
+}
+
+
+/* ZFP is installed */
+int adios_transform_zfp_is_implemented (void) {return 1;}
+
+
+/* Kept the default. I think this is piecing together how to read a "block" from smaller subrequests*/
+int adios_transform_zfp_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;
+}
+
+
+/* Kept the default. Template says "Do nothing for individual subrequest" */
+adios_datablock * adios_transform_zfp_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_zfp_pg_reqgroup_completed(adios_transform_read_request *reqgroup,
+ adios_transform_pg_read_request *completed_pg_reqgroup)
+{
+
+ int i;
+ int success; // was (a piece of) the decompression okay
+
+
+ /* Get the transform metadata */
+ struct zfp_metadata* metadata = (struct zfp_metadata*) malloc(sizeof(struct zfp_metadata)); // allocate metadata
+ metadata = zfp_read_metadata(metadata, completed_pg_reqgroup);
+
+
+ /* Set up ZFP */
+ void* cdata = completed_pg_reqgroup->subreqs->data; // get the compressed data
+ struct zfp_buffer* zbuff = (struct zfp_buffer*) malloc(sizeof(struct zfp_buffer)); // Handle zfp streaming
+ init_zfp_buffer(zbuff, metadata->name);
+
+
+ /* Get the data native to ADIOS (as opposed to the metadata which only the tranform plugin knows about) */
+ uint64_t csize = (uint64_t)completed_pg_reqgroup->raw_var_length;
+ uint64_t usize = adios_get_type_size(reqgroup->transinfo->orig_type, "");
+
+ zbuff->ndims = (uint) reqgroup->transinfo->orig_ndim;
+ zbuff->dims = malloc(zbuff->ndims*sizeof(uint));
+ for(i=0; i<zbuff->ndims; i++)
+ {
+ usize *= completed_pg_reqgroup->orig_varblock->count[i];
+ zbuff->dims[i] = (uint) completed_pg_reqgroup->orig_varblock->count[i];
+ }
+
+
+ /* Do the metadata and ADIOS agree? */
+ if (metadata->csize != csize)
+ {
+ log_warn("zfp processing variable %s: Metadata thinks compressed size is %" PRIu64 \
+ "bytes. ADIOS thinks compressed size is %" PRIu64 \
+ "bytes. Likely corruption.\n", zbuff->name, metadata->csize, csize);
+ }
+
+ if (metadata->usize != usize)
+ {
+ log_warn("zfp processing variable %s: Metadata thinks uncompressed size is %" PRIu64 \
+ "bytes. ADIOS thinks uncompressed size is %" PRIu64 \
+ "bytes. Likely corruption.\n", zbuff->name, metadata->usize, usize);
+ }
+
+
+ /* zfp datatype */
+ success = zfp_get_datatype(zbuff, reqgroup->transinfo->orig_type);
+ if (!success)
+ {
+ return NULL;
+ }
+
+
+ /* mode */
+ zbuff->mode = metadata->cmode;
+ strcpy(zbuff->ctol, metadata->ctol);
+
+
+ /* Allocate the array we'll store the uncompressed data in */
+ void* udata;
+ udata = malloc(usize);
+ if(!udata)
+ {
+ adios_error(err_no_memory, "Ran out of memory allocating uncompressed "
+ "buffer for ZFP transformation.\n");
+ return NULL;
+ }
+
+
+ /* possibly add check for successful decompression eventually */
+ success = zfp_decompression(zbuff, udata, cdata);
+ if(!success)
+ {
+ return NULL;
+ }
+
+ free(zbuff);
+ free(metadata);
+
+ return adios_datablock_new_whole_pg(reqgroup, completed_pg_reqgroup, udata);
+}
+
+
+/* Kept the default. Template says "Do nothing for the full read request complete (typical)" */
+adios_datablock * adios_transform_zfp_reqgroup_completed(adios_transform_read_request *completed_reqgroup)
+{
+ return NULL;
+}
+
+
+#else
+
+DECLARE_TRANSFORM_READ_METHOD_UNIMPL(zfp);
+
+#endif
+
diff --git a/src/transforms/adios_transform_zfp_write.c b/src/transforms/adios_transform_zfp_write.c
new file mode 100755
index 0000000..b4e6412
--- /dev/null
+++ b/src/transforms/adios_transform_zfp_write.c
@@ -0,0 +1,268 @@
+/*
+ * adios_transform_zfp_write.c
+ *
+ * Author: Eric Suchyta
+ * Contact: eric.d.suchyta at gmail.com
+ */
+
+#include "core/transforms/adios_transforms_hooks_write.h"
+
+#ifdef ZFP
+
+/* general C stuff */
+#include <stdint.h> // uint64_t
+#include <stdio.h> // NULL, sprintf
+#include <stdlib.h> // NULL, malloc, free
+#include <string.h> // memcpy, strcmp, strlen
+
+
+/* Were in the template included from ADIOS. Not necessarily sure if they're all strictly needed. */
+#include "core/transforms/adios_transforms_common.h"
+#include "core/transforms/adios_transforms_write.h"
+#include "core/transforms/adios_transforms_util.h"
+
+
+/* Extra ADIOS headers that weren't added in the template */
+//#include "core/adios_internals.h" // count_dimensions
+
+
+/* ZFP specific */
+#include "adios_transform_zfp_common.h"
+#include "zfp.h"
+
+
+/* Basically giving an address and a size */
+static void zfp_write_metadata_var(char* pos, void* towrite, size_t size, size_t* offset)
+{
+ memcpy(pos + *offset, towrite, size);
+ *offset += size;
+ return;
+}
+
+
+/* This is called in the main transform-level function.
+ * In a nutshell: compress array, using the settings in the other args to configure the compression. Connect to the ADIOS output buffer.
+ */
+static int zfp_compression(struct zfp_buffer* zbuff, const void* array, void** abuff, uint64_t* asize, int sharedbuffer, struct adios_file_struct* fd)
+{
+ zfp_initialize((void*) array, zbuff);
+ if (zbuff->error)
+ {
+ return 0;
+ }
+
+
+ if (sharedbuffer)
+ {
+ if (!shared_buffer_reserve(fd, zbuff->buffsize))
+ {
+ adios_error(err_no_memory, "Cannot allocate shared buffer of %zu bytes for ZFP transform for variable %s\n",
+ zbuff->buffsize, zbuff->name);
+ zbuff->error = true;
+
+ return 0;
+ }
+ *abuff = fd->offset + fd->buffer;
+ }
+ else
+ {
+ *abuff = malloc(zbuff->buffsize);
+ if (! *abuff)
+ {
+ adios_error(err_no_memory, "Cannot allocate buffer of %zu bytes for ZFP transform for variable %s\n",
+ zbuff->buffsize, zbuff->name);
+ zbuff->error = true;
+ return 0;
+ }
+ }
+
+
+ zfp_streaming(zbuff, *abuff, 0, asize);
+ if (zbuff->error)
+ {
+ return 0;
+ }
+
+
+ return 1;
+}
+
+
+
+/* see zfp_metadata in adios_transform_zfp_common.h */
+uint16_t adios_transform_zfp_get_metadata_size(struct adios_transform_spec *transform_spec)
+{
+ return (2*sizeof(uint64_t) + sizeof(uint) + 2*ZFP_STRSIZE);
+}
+
+
+/* Template says: 'Doing nothing defaults to "no transform effect on data size"'.
+ * I think this means a blank function equates to I don't need to grow the array to do transform */
+void adios_transform_zfp_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)
+{
+ return;
+}
+
+
+/* Get the length of each dimension. ZFP needs to know this. */
+static void get_dims(const struct adios_dimension_struct* d, struct zfp_buffer* zbuff, struct adios_var_struct* var, struct adios_file_struct *fd)
+{
+ uint zdim;
+ int i, ii;
+ struct adios_dimension_struct *ddim = (struct adios_dimension_struct *) d;
+
+ zbuff->ndims = (uint) count_dimensions(d);
+ zbuff->dims = malloc(zbuff->ndims*sizeof(uint));
+
+ for (i=0; i<zbuff->ndims; i++)
+ {
+ zdim = (uint) adios_get_dim_value(&ddim->dimension);
+ if (fd->group->adios_host_language_fortran == adios_flag_yes) ii = zbuff->ndims - 1 - i;
+ else ii = i;
+ zbuff->dims[ii] = zdim;
+ ddim = ddim->next;
+ }
+
+ return;
+}
+
+
+/* Does the main compression work */
+int adios_transform_zfp_apply(struct adios_file_struct *fd, struct adios_var_struct *var,
+ uint64_t *transformed_len, int use_shared_buffer, int *wrote_to_shared_buffer)
+{
+
+ int success; // Did (some part of) compression succeed?
+ void* outbuffer = NULL; // What to send to ADIOS
+ uint64_t outsize; // size of output buffer
+
+ uint64_t insize = adios_transform_get_pre_transform_var_size(var); // size of input buffer
+ struct zfp_buffer* zbuff = (struct zfp_buffer*) malloc(sizeof(struct zfp_buffer)); // Handle zfp streaming
+ init_zfp_buffer(zbuff, var->name);
+
+
+ /* adios to zfp datatype */
+ success = zfp_get_datatype(zbuff, var->pre_transform_type);
+ if (!success)
+ {
+ return 0;
+ }
+
+
+ /* dimensionality */
+ struct adios_dimension_struct* d = var->pre_transform_dimensions;
+ get_dims(d, zbuff, var, fd);
+
+
+ /* make sure the user only gives the sensible number of key:values -- 1. */
+ if (var->transform_spec->param_count == 0)
+ {
+ adios_error(err_invalid_argument, "No ZFP compression mode specified for variable %s. "
+ "Choose from: accuracy, precision, rate\n", zbuff->name);
+ zbuff->error = true;
+ return 0;
+ }
+ else if (var->transform_spec->param_count > 1)
+ {
+ adios_error(err_invalid_argument, "Too many ZFP parameters specified for variable %s. "
+ "You can only give one key:value, the compression mode and it's tolerance.\n",
+ zbuff->name);
+ zbuff->error = true;
+ return 0;
+ }
+ else if (var->transform_spec->param_count < 0)
+ {
+ adios_error(err_invalid_argument, "Negative number of ZFP parameters for variable %s indicates corruption.\n",
+ zbuff->name);
+ zbuff->error = true;
+ return 0;
+ }
+
+
+ /* Which zfp mode to use */
+ const struct adios_transform_spec_kv_pair* const param = &var->transform_spec->params[0];
+ if (strcmp(param->key, "accuracy") == 0)
+ {
+ zbuff->mode = 0;
+ }
+ else if (strcmp(param->key, "precision") == 0)
+ {
+ zbuff->mode = 1;
+ }
+ else if (strcmp(param->key, "rate") == 0)
+ {
+ zbuff->mode = 2;
+ }
+ else
+ {
+ adios_error(err_invalid_argument, "An unknown ZFP compression mode '%s' was specified for variable %s. "
+ "Available choices are: accuracy, precision, rate.\n",
+ param->key, zbuff->name);
+ zbuff->error = true;
+ return 0;
+ }
+
+ if (param->value == NULL)
+ {
+ adios_error(err_invalid_argument, "ZFP compression type %s must be given a value "
+ "to set the output storage parameter for variable %s.\n",
+ param->key, zbuff->name);
+ zbuff->error = true;
+ return 0;
+ }
+ strcpy(zbuff->ctol, param->value);
+
+
+ /* do compression */
+ success = zfp_compression(zbuff, var->data, &outbuffer, &outsize, use_shared_buffer, fd);
+
+
+ /* What do do if compresssion fails. For now, just give up. Maybe eventually use raw data. */
+ if(!success)
+ {
+ return 0;
+ }
+
+
+ /* Write the data */
+ *wrote_to_shared_buffer = use_shared_buffer;
+ if (*wrote_to_shared_buffer)
+ {
+ shared_buffer_mark_written(fd, outsize);
+ }
+ else
+ {
+ var->adata = outbuffer;
+ var->data_size = outsize;
+ var->free_data = adios_flag_yes;
+ }
+
+
+ /* Write the transform metadata */
+ char* pos = (char*)var->transform_metadata;
+ size_t offset = 0;
+
+ if(var->transform_metadata && var->transform_metadata_len > 0)
+ {
+ zfp_write_metadata_var(pos, &insize, sizeof(uint64_t), &offset);
+ zfp_write_metadata_var(pos, &outsize, sizeof(uint64_t), &offset);
+ zfp_write_metadata_var(pos, &zbuff->mode, sizeof(uint), &offset);
+ zfp_write_metadata_var(pos, zbuff->ctol, ZFP_STRSIZE, &offset);
+ zfp_write_metadata_var(pos, zbuff->name, ZFP_STRSIZE, &offset);
+ }
+
+
+ /* clean up */
+ free(zbuff);
+
+ *transformed_len = outsize; // Return the size of the data buffer
+ return 1;
+}
+
+#else
+
+DECLARE_TRANSFORM_WRITE_METHOD_UNIMPL(zfp)
+
+#endif
+
diff --git a/src/transforms/transform_plugins.h b/src/transforms/transform_plugins.h
index 0ee1938..a0b97d9 100644
--- a/src/transforms/transform_plugins.h
+++ b/src/transforms/transform_plugins.h
@@ -11,4 +11,5 @@ REGISTER_TRANSFORM_PLUGIN(szip, "szip", "szip", "szip compression")
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")
diff --git a/src/write/adios_dataspaces.c b/src/write/adios_dataspaces.c
index 5066aad..15d5952 100644
--- a/src/write/adios_dataspaces.c
+++ b/src/write/adios_dataspaces.c
@@ -1015,7 +1015,7 @@ void adios_dataspaces_finalize (int mype, struct adios_method_struct * method)
}
}
- free_dspaces_stream_info(md);
+ free_dspaces_stream_info();
log_info("%s: Disconnect from DATASPACES server now, rank=%d ...\n", __func__, mype);
// disconnect from dataspaces if we are connected from writer but not anymore from reader
diff --git a/src/write/adios_flexpath.c b/src/write/adios_flexpath.c
index 4ef7963..e462074 100644
--- a/src/write/adios_flexpath.c
+++ b/src/write/adios_flexpath.c
@@ -48,7 +48,7 @@
/************************* Structure and Type Definitions ***********************/
// used for messages in the control queue
-typedef enum {VAR=0, DATA_FLUSH, OPEN, CLOSE, INIT, EVGROUP_FLUSH, DATA_BUFFER} FlexpathMessageType;
+typedef enum {VAR=0, DATA_FLUSH, OPEN, CLOSE, INIT, EVGROUP_FLUSH, DATA_BUFFER, FINALIZE} FlexpathMessageType;
// maintains connection information
typedef struct _flexpath_stone {
@@ -1131,6 +1131,7 @@ process_data_flush(FlexpathWriteFileData *fileData,
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,
@@ -1138,8 +1139,30 @@ process_var_msg(FlexpathWriteFileData *fileData, Var_msg *varMsg)
}
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) {
@@ -1157,6 +1180,10 @@ process_open_msg(FlexpathWriteFileData *fileData, op_msg *open)
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++;
@@ -1181,32 +1208,54 @@ process_open_msg(FlexpathWriteFileData *fileData, op_msg *open)
}
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);
+ /* 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++;
- }
+ /* fileData->readerStep++; */
+ /* } */
op_msg *ack = malloc(sizeof(op_msg));
ack->file_name = strdup(fileData->name);
@@ -1228,6 +1277,7 @@ 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);
@@ -1240,7 +1290,7 @@ 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);
- //fprintf(stderr, "writer:%d:got_flush for reader:%d:reader_step:%d:writer_step:%d\n", fileData->rank, msg->process_id, fileData->readerStep, fileData->writerStep);
+ fp_verbose(fileData, "flush_msg received and queued\n");
threaded_enqueue(&fileData->controlQueue, msg, DATA_FLUSH,
&fileData->controlMutex, &fileData->controlCondition,
-1);
@@ -1250,8 +1300,10 @@ flush_handler(CManager cm, void* vevent, void* client_data, attr_list attrs)
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;
}
@@ -1262,12 +1314,19 @@ 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);
- if (msg->type == OPEN_MSG) {
+ 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) {
+ } 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;
}
@@ -1281,8 +1340,10 @@ control_thread(void *arg)
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);
@@ -1301,6 +1362,11 @@ control_thread(void *arg)
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);
@@ -1341,6 +1407,30 @@ find_open_file(char* name)
}
+void
+stone_close_handler(CManager cm, CMConnection conn, int closed_stone, void *client_data)
+{
+ FlexpathWriteFileData* file = flexpathWriteData.openFiles;
+ 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);
+ }
+ }
+ file = file->next;
+ }
+}
+
// Initializes flexpath write local data structures
extern void
adios_flexpath_init(const PairStruct *params, struct adios_method_struct *method)
@@ -1380,6 +1470,8 @@ adios_flexpath_init(const PairStruct *params, struct adios_method_struct *method
if (!forked) {
fprintf(stderr, "Wrtier error forking comm thread\n");
}
+
+ EVregister_close_handler(flexpathWriteData.cm, stone_close_handler, &flexpathWriteData);
}
extern int
@@ -1600,6 +1692,7 @@ adios_flexpath_write(
FlexpathWriteFileData* fileData = find_open_file(method->group->name);
FlexpathFMStructure* fm = fileData->fm;
+ fp_verbose(fileData, " adios_flexpath_write called\n");
if (fm == NULL)
{
log_error("adios_flexpath_write: something has gone wrong with format registration: %s\n",
@@ -1683,6 +1776,7 @@ adios_flexpath_close(struct adios_file_struct *fd, struct adios_method_struct *m
void *buffer = malloc(fileData->fm->size);
memcpy(buffer, fileData->fm->buffer, fileData->fm->size);
+ fp_verbose(fileData, " adios_flexpath_close called\n");
threaded_enqueue(&fileData->dataQueue, buffer,
DATA_BUFFER,
&fileData->dataMutex,
@@ -1790,7 +1884,8 @@ extern void
adios_flexpath_finalize(int mype, struct adios_method_struct *method)
{
FlexpathWriteFileData* fileData = flexpathWriteData.openFiles;
- while (fileData) {
+ fp_verbose(fileData, "adios_flexpath_finalize called\n");
+ while(fileData) {
update_step_msg *stepmsg = malloc(sizeof(update_step_msg));
stepmsg->finalized = 1;
@@ -1800,6 +1895,7 @@ adios_flexpath_finalize(int mype, struct adios_method_struct *method)
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);
diff --git a/src/write/adios_icee.c b/src/write/adios_icee.c
index b3d7e1e..99dca22 100644
--- a/src/write/adios_icee.c
+++ b/src/write/adios_icee.c
@@ -54,7 +54,7 @@
///////////////////////////
#include "core/globals.h"
-#define DUMP(fmt, ...) fprintf(stderr, ">>> "fmt"\n", ## __VA_ARGS__);
+#define DUMP(fmt, ...) fprintf(stderr, ">>> "fmt"\n", ## __VA_ARGS__);
#define MYMALLOC(var, size) { \
var = malloc(size); \
@@ -82,6 +82,7 @@ EVsource (*source)[ICEE_MAX_PARALLEL];
static int n_client = 0;
static int max_client = 1;
static int is_cm_passive = 0;
+static int use_probe = 0;
static icee_fileinfo_rec_ptr_t fp = NULL;
static int reverse_dim = 0;
@@ -516,11 +517,11 @@ icee_contactinfo_handler(CManager cm, void *vevent, void *client_data, attr_list
log_debug ("%s\n", __FUNCTION__);
icee_contactinfo_rec_ptr_t event = vevent;
- if (adios_verbose_level > 5)
+ if (adios_verbose_level > 5)
icee_contactinfo_print(event);
icee_contactinfo_rec_ptr_t prev = NULL;
- int num_parallel = 0;
+ int num_parallel = 0;
while (event != NULL)
{
icee_contactinfo_rec_t *c = malloc(sizeof(icee_contactinfo_rec_t));
@@ -546,10 +547,10 @@ icee_contactinfo_handler(CManager cm, void *vevent, void *client_data, attr_list
return 1;
}
-void *dosubmit(icee_fileinfo_rec_t *fp)
+void *dosubmit(icee_fileinfo_rec_t *fp)
{
- if (adios_verbose_level > 5)
- DUMP("threadid is %lu, submitting %d(%s)",
+ if (adios_verbose_level > 5)
+ DUMP("threadid is %lu, submitting %d(%s)",
(unsigned long)pthread_self(), fp->varinfo->varid, fp->varinfo->varname);
int i;
@@ -559,18 +560,18 @@ void *dosubmit(icee_fileinfo_rec_t *fp)
EVsubmit(source[i][k], fp, NULL);
}
-
+
icee_varinfo_rec_ptr_t vp = fp->varinfo;
free(vp->varname);
free(vp->gdims);
free(vp->ldims);
free(vp->offsets);
free(fp);
-
- return NULL;
-}
-void
+ return NULL;
+}
+
+void
on_icee_passivecheckin_request (CManager cm, CMConnection conn, icee_passivecheckin_rec_t *m)
{
log_debug("%s\n", __FUNCTION__);
@@ -581,9 +582,39 @@ on_icee_passivecheckin_request (CManager cm, CMConnection conn, icee_passivechec
return;
}
+void
+send_probe (int nprobe)
+{
+ icee_fileinfo_rec_ptr_t f;
+ MYCALLOC(f, 1, sizeof(icee_fileinfo_rec_t));
+
+ f->fname = "_icee_.probe";
+ f->next = NULL;
+
+ int i;
+ for (i=0; i<nprobe; i++)
+ {
+ f->timestamp = MPI_Wtime();
+
+ if (!is_cm_passive)
+ EVsubmit(icee_write_source, f, NULL);
+ else
+ {
+ CMFormat fm = CMlookup_format(icee_write_cm, icee_fileinfo_format_list);
+ int i;
+ for (i=0; i<n_client; i++)
+ if (CMwrite(icee_write_cm_conn[i], fm, (void*)f) != 1)
+ log_error ("Sending fileinfo failed\n");
+ }
+ usleep(0.1*1E7);
+ }
+
+ free(f);
+}
+
// Initializes icee write local data structures
-extern void
-adios_icee_init(const PairStruct *params, struct adios_method_struct *method)
+extern void
+adios_icee_init(const PairStruct *params, struct adios_method_struct *method)
{
log_debug ("%s\n", __FUNCTION__);
@@ -595,7 +626,7 @@ adios_icee_init(const PairStruct *params, struct adios_method_struct *method)
int rank;
MPI_Comm_rank(method->init_comm, &rank);
log_debug ("rank : %d\n", rank);
-
+
const PairStruct * p = params;
@@ -622,7 +653,7 @@ adios_icee_init(const PairStruct *params, struct adios_method_struct *method)
char* token = strtok(p->value, ",");
int len = 0;
- while (token)
+ while (token)
{
plist[len] = token;
@@ -681,6 +712,10 @@ adios_icee_init(const PairStruct *params, struct adios_method_struct *method)
{
is_cm_passive = atoi(p->value);
}
+ else if (!strcasecmp (p->name, "use_probe"))
+ {
+ use_probe = atoi(p->value);
+ }
p = p->next;
}
@@ -697,10 +732,10 @@ adios_icee_init(const PairStruct *params, struct adios_method_struct *method)
// Init parallel
if (icee_num_parallel > 1)
{
- pthread_attr_t attr;
- pthread_attr_init(&attr);
- pthread_attr_setdetachstate(&attr,PTHREAD_CREATE_DETACHED);
- icee_pool = thr_pool_create(icee_num_parallel,icee_num_parallel,10,NULL);
+ pthread_attr_t attr;
+ pthread_attr_init(&attr);
+ pthread_attr_setdetachstate(&attr,PTHREAD_CREATE_DETACHED);
+ icee_pool = thr_pool_create(icee_num_parallel,icee_num_parallel,10,NULL);
}
EVstone stone, remote_stone;
@@ -719,7 +754,7 @@ adios_icee_init(const PairStruct *params, struct adios_method_struct *method)
CMlisten_specific(wpcm, attr);
DUMP("Passive mode at port %d.", cm_passive_port);
-
+
CMFormat fm = CMregister_format(wpcm, icee_passivecheckin_format_list);
CMregister_handler(fm, icee_passivecheckin_request_handler, on_icee_passivecheckin_request);
@@ -735,57 +770,57 @@ adios_icee_init(const PairStruct *params, struct adios_method_struct *method)
goto done;
}
#endif
-
+
contact_list = create_attr_list();
switch (icee_transport)
{
case ENET:
- add_string_attr(contact_list,
- attr_atom_from_string("CM_TRANSPORT"),
+ add_string_attr(contact_list,
+ attr_atom_from_string("CM_TRANSPORT"),
"enet");
- add_int_attr(contact_list,
- attr_atom_from_string("CM_ENET_PORT"),
+ add_int_attr(contact_list,
+ attr_atom_from_string("CM_ENET_PORT"),
cm_port);
- add_string_attr(contact_list,
- attr_atom_from_string("CM_ENET_HOST"),
+ add_string_attr(contact_list,
+ attr_atom_from_string("CM_ENET_HOST"),
cm_host);
break;
case NNTI:
- add_string_attr(contact_list,
- attr_atom_from_string("CM_TRANSPORT"),
+ add_string_attr(contact_list,
+ attr_atom_from_string("CM_TRANSPORT"),
"nnti");
- add_int_attr(contact_list,
- attr_atom_from_string("NNTI_PORT"),
+ add_int_attr(contact_list,
+ attr_atom_from_string("NNTI_PORT"),
cm_port);
- add_string_attr(contact_list,
- attr_atom_from_string("CM_NNTI_TRANSPORT"),
+ add_string_attr(contact_list,
+ attr_atom_from_string("CM_NNTI_TRANSPORT"),
"ib");
- add_string_attr(contact_list,
- attr_atom_from_string("IP_HOST"),
+ add_string_attr(contact_list,
+ attr_atom_from_string("IP_HOST"),
cm_host);
break;
case IB:
- add_string_attr(contact_list,
- attr_atom_from_string("CM_TRANSPORT"),
+ add_string_attr(contact_list,
+ attr_atom_from_string("CM_TRANSPORT"),
"ib");
- add_int_attr(contact_list,
- attr_atom_from_string("IP_PORT"),
+ add_int_attr(contact_list,
+ attr_atom_from_string("IP_PORT"),
cm_port);
- add_string_attr(contact_list,
- attr_atom_from_string("IP_HOST"),
+ add_string_attr(contact_list,
+ attr_atom_from_string("IP_HOST"),
cm_host);
break;
default:
- add_int_attr(contact_list,
- attr_atom_from_string("IP_PORT"),
+ add_int_attr(contact_list,
+ attr_atom_from_string("IP_PORT"),
cm_port);
- add_string_attr(contact_list,
- attr_atom_from_string("IP_HOST"),
+ add_string_attr(contact_list,
+ attr_atom_from_string("IP_HOST"),
cm_host);
break;
}
- if (CMlisten_specific(icee_write_cm, contact_list) == 0)
+ if (CMlisten_specific(icee_write_cm, contact_list) == 0)
{
fprintf(stderr, "error: unable to initialize connection manager.\n");
exit(-1);
@@ -805,7 +840,7 @@ adios_icee_init(const PairStruct *params, struct adios_method_struct *method)
EVassoc_terminal_action(icee_write_cm, stone, icee_contactinfo_format_list, icee_contactinfo_handler, NULL);
MYCALLOC(remote_info, max_client, sizeof(icee_remoteinfo_rec_t));
-
+
if (is_cm_passive == 1)
{
CMFormat fm;
@@ -843,7 +878,7 @@ adios_icee_init(const PairStruct *params, struct adios_method_struct *method)
contact_list = attr_list_from_string(cinfo->contact_string);
EVaction evaction;
- evaction = EVassoc_bridge_action(icee_write_cm, stone,
+ evaction = EVassoc_bridge_action(icee_write_cm, stone,
contact_list, remote_stone);
if (evaction == -1)
{
@@ -880,7 +915,7 @@ adios_icee_init(const PairStruct *params, struct adios_method_struct *method)
stone = EValloc_stone(cm[i][k]);
remote_stone = cinfo->stone_id;
contact_list = attr_list_from_string(cinfo->contact_string);
-
+
EVassoc_bridge_action(cm[i][k], stone, contact_list, remote_stone);
source[i][k] = EVcreate_submit_handle(cm[i][k], stone, icee_fileinfo_format_list);
@@ -892,14 +927,17 @@ adios_icee_init(const PairStruct *params, struct adios_method_struct *method)
}
done:
adios_icee_initialized = 1;
+
+ if (use_probe)
+ send_probe(10);
}
}
-extern int
-adios_icee_open(struct adios_file_struct *fd,
- struct adios_method_struct *method,
- MPI_Comm comm)
-{
+extern int
+adios_icee_open(struct adios_file_struct *fd,
+ struct adios_method_struct *method,
+ MPI_Comm comm)
+{
log_debug ("%s\n", __FUNCTION__);
if( fd == NULL || method == NULL) {
@@ -909,7 +947,7 @@ adios_icee_open(struct adios_file_struct *fd,
if (fp == NULL)
MYCALLOC(fp, 1, sizeof(icee_fileinfo_rec_t));
-
+
fp->fname = fd->name;
MPI_Comm_size(comm, &(fp->comm_size));
MPI_Comm_rank(comm, &(fp->comm_rank));
@@ -921,10 +959,10 @@ adios_icee_open(struct adios_file_struct *fd,
// writes data to multiqueue
extern void
adios_icee_write(
- struct adios_file_struct *fd,
- struct adios_var_struct *f,
- const void *data,
- struct adios_method_struct *method)
+ struct adios_file_struct *fd,
+ struct adios_var_struct *f,
+ const void *data,
+ struct adios_method_struct *method)
{
log_debug ("%s\n", __FUNCTION__);
@@ -959,7 +997,7 @@ adios_icee_write(
vp->varid = f->id;
vp->type = f->type;
- vp->typesize = adios_get_type_size(f->type, "");
+ vp->typesize = adios_get_type_size(f->type, "");
vp->ndims = count_dimensions(f->dimensions);
@@ -969,9 +1007,9 @@ adios_icee_write(
vp->gdims = calloc(vp->ndims, sizeof(uint64_t));
vp->ldims = calloc(vp->ndims, sizeof(uint64_t));
vp->offsets = calloc(vp->ndims, sizeof(uint64_t));
-
+
struct adios_dimension_struct *d = f->dimensions;
- // Default: Fortran.
+ // Default: Fortran.
if (reverse_dim)
{
int i;
@@ -980,9 +1018,9 @@ adios_icee_write(
vp->gdims[i] = adios_get_dim_value(&d->global_dimension);
vp->ldims[i] = adios_get_dim_value(&d->dimension);
vp->offsets[i] = adios_get_dim_value(&d->local_offset);
-
+
vp->varlen *= vp->ldims[i];
-
+
d = d->next;
}
}
@@ -994,24 +1032,61 @@ adios_icee_write(
vp->gdims[i] = adios_get_dim_value(&d->global_dimension);
vp->ldims[i] = adios_get_dim_value(&d->dimension);
vp->offsets[i] = adios_get_dim_value(&d->local_offset);
-
+
vp->varlen *= vp->ldims[i];
-
+
d = d->next;
}
}
}
-
+
vp->data = (char*)f->data;
if (adios_verbose_level > 5) icee_varinfo_print(vp);
fp->nvars++;
}
-extern void
-adios_icee_close(struct adios_file_struct *fd, struct adios_method_struct *method)
+extern void
+adios_icee_close(struct adios_file_struct *fd, struct adios_method_struct *method)
{
log_debug ("%s\n", __FUNCTION__);
+ double timestamp = MPI_Wtime();
+ fp->timestamp = timestamp;
+
+ if (use_probe)
+ {
+ icee_varinfo_rec_ptr_t v;
+ MYCALLOC(v, 1, sizeof(icee_varinfo_rec_t));
+
+ int max_varid = 0;
+ icee_varinfo_rec_ptr_t vp = fp->varinfo;
+ if (vp == NULL)
+ {
+ fp->varinfo = v;
+ }
+ else
+ {
+ if (max_varid < vp->varid)
+ max_varid = vp->varid + 1;
+ while (vp->next != NULL)
+ {
+ vp = vp->next;
+ if (max_varid < vp->varid)
+ max_varid = vp->varid + 1;
+ }
+ vp->next = v;
+ }
+
+ fp->nvars++;
+ v->varname = strdup("__icee_deltat__");
+ v->varid = max_varid;
+ v->type = adios_double;
+ v->typesize = sizeof(double);
+ v->varlen = sizeof(double);
+ v->data = (char*) ×tamp;
+ v->next = NULL;
+
+ }
if( fd == NULL || method == NULL) {
perror("open: Bad input parameters\n");
@@ -1068,10 +1143,10 @@ adios_icee_close(struct adios_file_struct *fd, struct adios_method_struct *metho
free(vp->gdims);
free(vp->ldims);
free(vp->offsets);
-
+
icee_varinfo_rec_ptr_t prev = vp;
vp = vp->next;
-
+
free(prev);
}
}
@@ -1082,8 +1157,8 @@ done:
}
// wait until all open files have finished sending data to shutdown
-extern void
-adios_icee_finalize(int mype, struct adios_method_struct *method)
+extern void
+adios_icee_finalize(int mype, struct adios_method_struct *method)
{
log_debug ("%s\n", __FUNCTION__);
@@ -1097,7 +1172,7 @@ adios_icee_finalize(int mype, struct adios_method_struct *method)
for (i=0; i<max_client; i++)
for (k=0; k<remote_info[i].num_parallel; k++)
CManager_close(cm[i][k]);
-
+
free(cm);
free(source);
}
@@ -1106,89 +1181,88 @@ adios_icee_finalize(int mype, struct adios_method_struct *method)
}
// provides unknown functionality
-extern enum BUFFERING_STRATEGY
-adios_icee_should_buffer (struct adios_file_struct * fd,struct adios_method_struct * method)
+extern enum BUFFERING_STRATEGY
+adios_icee_should_buffer (struct adios_file_struct * fd,struct adios_method_struct * method)
{
return no_buffering;
}
-extern void
+extern void
adios_icee_buffer_overflow (struct adios_file_struct * fd,
struct adios_method_struct * method)
{
}
// provides unknown functionality
-extern void
-adios_icee_end_iteration(struct adios_method_struct *method)
+extern void
+adios_icee_end_iteration(struct adios_method_struct *method)
{
}
// provides unknown functionality
-extern void
-adios_icee_start_calculation(struct adios_method_struct *method)
+extern void
+adios_icee_start_calculation(struct adios_method_struct *method)
{
}
// provides unknown functionality
-extern void
-adios_icee_stop_calculation(struct adios_method_struct *method)
+extern void
+adios_icee_stop_calculation(struct adios_method_struct *method)
{
}
// provides unknown functionality
-extern void
-adios_icee_get_write_buffer(struct adios_file_struct *fd,
- struct adios_var_struct *v,
- uint64_t *size,
- void **buffer,
- struct adios_method_struct *method)
+extern void
+adios_icee_get_write_buffer(struct adios_file_struct *fd,
+ struct adios_var_struct *v,
+ uint64_t *size,
+ void **buffer,
+ struct adios_method_struct *method)
{
}
// should not be called from write, reason for inclusion here unknown
-void
-adios_icee_read(struct adios_file_struct *fd,
- struct adios_var_struct *f,
- void *buffer,
- uint64_t buffer_size,
- struct adios_method_struct *method)
+void
+adios_icee_read(struct adios_file_struct *fd,
+ struct adios_var_struct *f,
+ void *buffer,
+ uint64_t buffer_size,
+ struct adios_method_struct *method)
{
}
#else // print empty version of all functions (if HAVE_ICEE == 0)
-void
-adios_icee_read(struct adios_file_struct *fd,
- struct adios_var_struct *f,
- void *buffer,
- struct adios_method_struct *method)
+void
+adios_icee_read(struct adios_file_struct *fd,
+ struct adios_var_struct *f,
+ void *buffer,
+ struct adios_method_struct *method)
{
}
-extern void
-adios_icee_get_write_buffer(struct adios_file_struct *fd,
- struct adios_var_struct *f,
- unsigned long long *size,
- void **buffer,
- struct adios_method_struct *method)
+extern void
+adios_icee_get_write_buffer(struct adios_file_struct *fd,
+ struct adios_var_struct *f,
+ unsigned long long *size,
+ void **buffer,
+ struct adios_method_struct *method)
{
}
-extern void
-adios_icee_stop_calculation(struct adios_method_struct *method)
+extern void
+adios_icee_stop_calculation(struct adios_method_struct *method)
{
}
-extern void
-adios_icee_start_calculation(struct adios_method_struct *method)
+extern void
+adios_icee_start_calculation(struct adios_method_struct *method)
{
}
-extern void
-adios_icee_end_iteration(struct adios_method_struct *method)
+extern void
+adios_icee_end_iteration(struct adios_method_struct *method)
{
}
#endif
-
diff --git a/src/write/adios_mpi.c b/src/write/adios_mpi.c
index 2867958..bf0c642 100644
--- a/src/write/adios_mpi.c
+++ b/src/write/adios_mpi.c
@@ -263,6 +263,34 @@ static void print_metric (FILE * f, struct timing_metrics * t, int iteration, in
}
#endif
+/** Set up a simple MPI communication chain from ranks 0,...,size-1
+ * This chain is used in the cascaded open, which is faster if
+ * this chain is already set up by MPI.
+ */
+
+static void init_mpi_chain(MPI_Comm comm)
+{
+ int rank, size;
+ int token=1;
+ MPI_Request req;
+ MPI_Status status;
+ MPI_Comm_rank(comm, &rank);
+ MPI_Comm_size(comm, &size);
+
+ //if (rank == 0)
+ // log_info ("Initialize MPI chain between ranks 0..%d\n", size-1);
+
+ // Send a message to next process and receive from previous to
+ if (rank < size-1)
+ {
+ MPI_Isend (&token, 1, MPI_INT, rank+1, rank, comm, &req);
+ }
+
+ if (rank > 0)
+ {
+ MPI_Recv (&token, 1, MPI_INT, rank-1, rank-1, comm, &status);
+ }
+}
void adios_mpi_init (const PairStruct * parameters
,struct adios_method_struct * method
@@ -289,6 +317,7 @@ void adios_mpi_init (const PairStruct * parameters
md->index = adios_alloc_index_v1(1); // with hashtables
adios_buffer_struct_init (&md->b);
+ init_mpi_chain (md->group_comm);
#if COLLECT_METRICS
// init the pointer for the first go around avoiding the bad free in open
timing.t24 = 0;
@@ -683,9 +712,6 @@ int adios_mpi_open (struct adios_file_struct * fd
max_time_index = p->time_index;
p = p->next;
}
- if (fd->mode == adios_mode_append) {
- ++max_time_index;
- }
fd->group->time_index = max_time_index;
MPI_Bcast (&fd->group->time_index, 1, MPI_INT, 0
,md->group_comm
diff --git a/src/write/adios_mpi_amr.c b/src/write/adios_mpi_amr.c
index d714d1e..981b6c2 100644
--- a/src/write/adios_mpi_amr.c
+++ b/src/write/adios_mpi_amr.c
@@ -995,7 +995,7 @@ void * adios_mpi_amr_do_reopen_thread (void * param)
max_time_index = p->time_index;
p = p->next;
}
- fd->group->time_index = ++max_time_index;
+ fd->group->time_index = max_time_index;
adios_init_buffer_read_vars_index (&md->b);
MPI_File_seek (md->fh, md->b.vars_index_offset, MPI_SEEK_SET);
@@ -1584,6 +1584,32 @@ int adios_MPI_Recv(void *buf, uint64_t count, int source,
}
+/* Help routine to receive data size greater than 2 GB non-blocking
+ * Returns the number of MPI_Irecv requests made.
+ * requests should be pre-allocated before calling.
+ */
+int adios_MPI_Irecv(void *buf, uint64_t count, int source,
+ int tag, MPI_Comm comm, MPI_Request *requests)
+{
+ int n = 0;
+ while (count > INT32_MAX)
+ {
+ MPI_Irecv (buf, INT32_MAX, MPI_BYTE, source, tag, comm, requests+n);
+ count -= INT32_MAX;
+ buf += INT32_MAX;
+ n++;
+ }
+
+ if (count)
+ {
+ int temp_count = (int) count;
+ MPI_Irecv (buf, temp_count, MPI_BYTE, source, tag, comm, requests+n);
+ }
+ n++;
+
+ return n;
+}
+
void adios_mpi_amr_bg_close (struct adios_file_struct * fd
,struct adios_method_struct * method
)
@@ -1630,7 +1656,6 @@ void adios_mpi_amr_bg_close (struct adios_file_struct * fd
{
//printf ("do not merge pg\n");
uint64_t pg_size;
- MPI_Status status;
pg_size = fd->bytes_written;
pg_sizes = (uint64_t *) malloc (new_group_size * 8);
@@ -1657,6 +1682,10 @@ void adios_mpi_amr_bg_close (struct adios_file_struct * fd
max_data_size = (pg_sizes[i] > max_data_size) ? pg_sizes[i] : max_data_size;
}
+ int nMPIrequests = max_data_size / UINT32_MAX + 1;
+ MPI_Request *requests = (MPI_Request *) malloc (nMPIrequests * sizeof (MPI_Request));
+ MPI_Status *statuses = (MPI_Status *) malloc (nMPIrequests * sizeof (MPI_Status));
+
if (is_aggregator (md->rank))
{
aggr_buff = malloc (max_data_size);
@@ -1702,8 +1731,8 @@ void adios_mpi_amr_bg_close (struct adios_file_struct * fd
if (i + 1 < new_group_size)
{
START_TIMER (ADIOS_TIMER_COMM);
- adios_MPI_Recv (recv_buff, pg_sizes[i + 1], new_rank + 1
- ,0, md->g_comm1, &status);
+ nMPIrequests = adios_MPI_Irecv (recv_buff, pg_sizes[i + 1], new_rank + 1
+ ,0, md->g_comm1, requests);
STOP_TIMER (ADIOS_TIMER_COMM);
}
@@ -1724,7 +1753,14 @@ void adios_mpi_amr_bg_close (struct adios_file_struct * fd
if (i + 1 < new_group_size)
{
- memcpy (aggr_buff, recv_buff, pg_sizes[i + 1]);
+ START_TIMER (ADIOS_TIMER_COMM);
+ MPI_Waitall (nMPIrequests, requests, statuses);
+ STOP_TIMER (ADIOS_TIMER_COMM);
+ // swap receive and aggregate buffers, so we can write out the just received PG while getting another one
+ void *tmp = aggr_buff;
+ aggr_buff = recv_buff;
+ recv_buff = tmp;
+ //memcpy (aggr_buff, recv_buff, pg_sizes[i + 1]);
}
}
}
@@ -1743,15 +1779,15 @@ void adios_mpi_amr_bg_close (struct adios_file_struct * fd
{
START_TIMER (ADIOS_TIMER_COMM);
// Recv data from upstream rank
- adios_MPI_Recv (recv_buff, pg_sizes[i], new_rank + 1
- ,0, md->g_comm1, &status);
+ nMPIrequests = adios_MPI_Irecv (recv_buff, pg_sizes[i], new_rank + 1
+ ,0, md->g_comm1, requests);
if (i == new_rank + 1)
// Send my data to downstream rank
adios_MPI_Send (fd->buffer, pg_size, new_rank - 1
,0, md->g_comm1);
- //MPI_Wait (&request, &status);
+ MPI_Waitall(nMPIrequests, requests, statuses);
// Send it to downstream rank
adios_MPI_Send (recv_buff, pg_sizes[i], new_rank - 1
,0, md->g_comm1);
@@ -1762,6 +1798,8 @@ void adios_mpi_amr_bg_close (struct adios_file_struct * fd
FREE (aggr_buff);
FREE (recv_buff);
+ FREE (requests);
+ FREE (statuses);
}
else
{
@@ -1833,9 +1871,10 @@ void adios_mpi_amr_bg_close (struct adios_file_struct * fd
adios_parse_process_group_index_v1 (&md->b, &new_pg_root, NULL);
adios_parse_vars_index_v1 (&md->b, &new_vars_root, NULL, NULL);
- adios_parse_attributes_index_v1 (&md->b
+ // do not merge attributes from other processes from 1.4
+ /*adios_parse_attributes_index_v1 (&md->b
,&new_attrs_root
- );
+ );*/
if (md->g_merging_pgs)
new_pg_root = 0;
@@ -1861,10 +1900,11 @@ void adios_mpi_amr_bg_close (struct adios_file_struct * fd
,0, md->index);
START_TIMER (ADIOS_TIMER_COMM);
- MPI_Gather (&buffer_size, 1, MPI_INT, 0, 0, MPI_INT
+ uint32_t index_size = (uint32_t) buffer_offset;
+ MPI_Gather (&index_size, 1, MPI_INT, 0, 0, MPI_INT
,0, md->g_comm1
);
- MPI_Gatherv (buffer, buffer_size, MPI_BYTE
+ MPI_Gatherv (buffer, index_size, MPI_BYTE
,0, 0, 0, MPI_BYTE
,0, md->g_comm1
);
@@ -1967,9 +2007,10 @@ void adios_mpi_amr_bg_close (struct adios_file_struct * fd
adios_parse_process_group_index_v1 (&md->b, &new_pg_root, NULL);
adios_parse_vars_index_v1 (&md->b, &new_vars_root, NULL, NULL);
- adios_parse_attributes_index_v1 (&md->b
+ // do not merge attributes from other processes from 1.4
+ /*adios_parse_attributes_index_v1 (&md->b
,&new_attrs_root
- );
+ );*/
// global index would become unsorted on main aggregator during merging
// so sort timesteps if appending
@@ -1999,11 +2040,12 @@ void adios_mpi_amr_bg_close (struct adios_file_struct * fd
,0, md->index);
START_TIMER (ADIOS_TIMER_COMM);
- MPI_Gather (&buffer_size2, 1, MPI_INT
+ uint32_t index_size = (uint32_t) buffer_offset2;
+ MPI_Gather (&index_size, 1, MPI_INT
,0, 0, MPI_INT
,0, md->g_comm2
);
- MPI_Gatherv (buffer2, buffer_size2, MPI_BYTE
+ MPI_Gatherv (buffer2, index_size, MPI_BYTE
,0, 0, 0, MPI_BYTE
,0, md->g_comm2
);
@@ -2327,9 +2369,10 @@ void adios_mpi_amr_ag_close (struct adios_file_struct * fd
adios_parse_process_group_index_v1 (&md->b, &new_pg_root, NULL);
adios_parse_vars_index_v1 (&md->b, &new_vars_root, NULL, NULL);
- adios_parse_attributes_index_v1 (&md->b
+ // do not merge attributes from other processes from 1.4
+ /*adios_parse_attributes_index_v1 (&md->b
,&new_attrs_root
- );
+ );*/
if (md->g_merging_pgs)
new_pg_root = 0;
@@ -2490,9 +2533,10 @@ void adios_mpi_amr_ag_close (struct adios_file_struct * fd
adios_parse_process_group_index_v1 (&md->b, &new_pg_root, NULL);
adios_parse_vars_index_v1 (&md->b, &new_vars_root, NULL, NULL);
- adios_parse_attributes_index_v1 (&md->b
+ // do not merge attributes from other processes from 1.4
+ /*adios_parse_attributes_index_v1 (&md->b
,&new_attrs_root
- );
+ );*/
// global index would become unsorted on main aggregator during merging
// so sort timesteps if appending
@@ -2522,11 +2566,12 @@ void adios_mpi_amr_ag_close (struct adios_file_struct * fd
,0, md->index);
START_TIMER (ADIOS_TIMER_COMM);
- MPI_Gather (&buffer_size2, 1, MPI_INT
+ uint32_t index_size = (uint32_t) buffer_offset2;
+ MPI_Gather (&index_size, 1, MPI_INT
,0, 0, MPI_INT
,0, md->g_comm2
);
- MPI_Gatherv (buffer2, buffer_size2, MPI_BYTE
+ MPI_Gatherv (buffer2, index_size, MPI_BYTE
,0, 0, 0, MPI_BYTE
,0, md->g_comm2
);
diff --git a/src/write/adios_mpi_lustre.c b/src/write/adios_mpi_lustre.c
index e65c267..b12109e 100644
--- a/src/write/adios_mpi_lustre.c
+++ b/src/write/adios_mpi_lustre.c
@@ -947,9 +947,6 @@ int adios_mpi_lustre_open (struct adios_file_struct * fd
max_time_index = p->time_index;
p = p->next;
}
- if (fd->mode == adios_mode_append) {
- ++max_time_index;
- }
fd->group->time_index = max_time_index;
MPI_Bcast (&fd->group->time_index, 1, MPI_INT, 0
,md->group_comm
diff --git a/src/write/adios_posix.c b/src/write/adios_posix.c
index e9da157..35d6c66 100644
--- a/src/write/adios_posix.c
+++ b/src/write/adios_posix.c
@@ -466,9 +466,6 @@ START_TIMER (ADIOS_TIMER_AD_OPEN);
max_time_index = pg->time_index;
pg = pg->next;
}
- if (fd->mode == adios_mode_append) {
- ++max_time_index;
- }
fd->group->time_index = max_time_index;
adios_posix_read_vars_index (&p->b);
@@ -498,10 +495,7 @@ START_TIMER (ADIOS_TIMER_AD_OPEN);
}
else
{
- // index is in memory, update time index and offsets
- if (fd->mode == adios_mode_append) {
- fd->group->time_index++;
- }
+ // index is in memory, right now there is nothing to do here
}
}
else
@@ -1019,13 +1013,13 @@ 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_size;
+ int i_buffer_size = (int) buffer_offset;
MPI_Gather (&i_buffer_size, 1, MPI_INT
,0, 0, MPI_INT
,0, p->group_comm
);
- MPI_Gatherv (buffer, buffer_size, MPI_BYTE
+ MPI_Gatherv (buffer, i_buffer_size, MPI_BYTE
,0, 0, 0, MPI_BYTE
,0, p->group_comm
);
diff --git a/src/write/adios_var_merge.c b/src/write/adios_var_merge.c
index 7a20f43..41ca100 100644
--- a/src/write/adios_var_merge.c
+++ b/src/write/adios_var_merge.c
@@ -650,7 +650,7 @@ static int do_write (int64_t fd_p, const char * name, void * var)
// temporary solution for compiling error
static int declare_group (int64_t * id, const char * name
,const char * time_index
- ,enum ADIOS_FLAG stats
+ ,enum ADIOS_STATISTICS_FLAG stats
)
{
int ret;
@@ -745,7 +745,8 @@ static void output_vars(struct aggr_var_struct *vars, int varcnt, struct
vars=vars->next;
}
//close the file
- common_adios_close(md->fpr);
+ struct adios_file_struct * mdf = (struct adios_file_struct *) md->fpr;
+ common_adios_close(mdf);
}
@@ -758,7 +759,7 @@ static void define_iogroup(char *group_name)
grp_name=(char *)malloc(len);
memset(grp_name, 0x00, len);
sprintf(grp_name, "agg_%s",group_name);
- declare_group (&grp,grp_name, "", adios_flag_yes);
+ declare_group (&grp,grp_name, "", adios_stat_default);
select_method (grp, io_method,io_parameters,"");
grpflag=1;
}
diff --git a/src/zfp/CMakeLists.txt b/src/zfp/CMakeLists.txt
new file mode 100644
index 0000000..8d2b424
--- /dev/null
+++ b/src/zfp/CMakeLists.txt
@@ -0,0 +1,40 @@
+set(ZFP_SRCDIR "zfp-0.5.0")
+include_directories(${PROJECT_SOURCE_DIR}/src/zfp/${ZFP_SRCDIR}/inc)
+include_directories(${PROJECT_SOURCE_DIR}/src/zfp/${ZFP_SRCDIR})
+include_directories(${PROJECT_BINARY_DIR}/src/zfp)
+link_directories(${PROJECT_BINARY_DIR}/src/zfp)
+
+
+set(CLEANFILES "")
+set(include_HEADERS "")
+set(nodist_include_HEADERS "")
+set(lib_LIBRARIES "")
+
+if(BUILD_ZFP)
+ set(libzfp_a_SOURCES
+ ${ZFP_SRCDIR}/src/bitstream.c
+ ${ZFP_SRCDIR}/src/decode1f.c
+ ${ZFP_SRCDIR}/src/decode1d.c
+ ${ZFP_SRCDIR}/src/encode1f.c
+ ${ZFP_SRCDIR}/src/encode1d.c
+ ${ZFP_SRCDIR}/src/decode2f.c
+ ${ZFP_SRCDIR}/src/decode2d.c
+ ${ZFP_SRCDIR}/src/encode2f.c
+ ${ZFP_SRCDIR}/src/encode2d.c
+ ${ZFP_SRCDIR}/src/decode3f.c
+ ${ZFP_SRCDIR}/src/decode3d.c
+ ${ZFP_SRCDIR}/src/encode3f.c
+ ${ZFP_SRCDIR}/src/encode3d.c
+ ${ZFP_SRCDIR}/src/zfp.c
+ )
+ set(libzfp_a_CPPFLAGS "${AM_CPPFLAGS}")
+ set(libzfp_a_CFLAGS "${AM_CFLAGS}")
+
+ add_library(zfp OBJECT ${libzfp_a_SOURCES})
+ #set_target_properties(zfp PROPERTIES COMPILE_FLAGS "")
+
+## Do not install libzfp.a, adios does not need it
+#install(FILES ${PROJECT_BINARY_DIR}/zfp/libzfp.a
+# DESTINATION ${libdir})
+
+endif(BUILD_ZFP)
diff --git a/src/zfp/Makefile.am b/src/zfp/Makefile.am
new file mode 100644
index 0000000..549c729
--- /dev/null
+++ b/src/zfp/Makefile.am
@@ -0,0 +1,61 @@
+ZFP_SRCDIR=zfp-0.5.0
+
+AM_CPPFLAGS=-I${srcdir}/${ZFP_SRCDIR}/inc -I${srcdir}/${ZFP_SRCDIR}/src
+
+AUTOMAKE_OPTIONS = no-dependencies subdir-objects
+METASOURCES=AUTO
+
+CLEANFILES=
+
+noinst_LIBRARIES = libzfp.a
+libzfp_a_SOURCES = ${ZFP_SRCDIR}/src/bitstream.c \
+ ${ZFP_SRCDIR}/src/decode1f.c \
+ ${ZFP_SRCDIR}/src/decode1d.c \
+ ${ZFP_SRCDIR}/src/encode1f.c \
+ ${ZFP_SRCDIR}/src/encode1d.c \
+ ${ZFP_SRCDIR}/src/decode2f.c \
+ ${ZFP_SRCDIR}/src/decode2d.c \
+ ${ZFP_SRCDIR}/src/encode2f.c \
+ ${ZFP_SRCDIR}/src/encode2d.c \
+ ${ZFP_SRCDIR}/src/decode3f.c \
+ ${ZFP_SRCDIR}/src/decode3d.c \
+ ${ZFP_SRCDIR}/src/encode3f.c \
+ ${ZFP_SRCDIR}/src/encode3d.c \
+ ${ZFP_SRCDIR}/src/zfp.c
+
+
+libzfp_a_CPPFLAGS=$(AM_CPPFLAGS)
+libzfp_a_CFLAGS=
+
+
+
+EXTRA_DIST = ${ZFP_SRCDIR}/src/block1.h \
+ ${ZFP_SRCDIR}/src/block2.h \
+ ${ZFP_SRCDIR}/src/block3.h \
+ ${ZFP_SRCDIR}/src/traitsd.h \
+ ${ZFP_SRCDIR}/src/traitsf.h \
+ ${ZFP_SRCDIR}/src/Makefile \
+ ${ZFP_SRCDIR}/src/inline \
+ ${ZFP_SRCDIR}/src/template/codec.h \
+ ${ZFP_SRCDIR}/src/template/codec1.c \
+ ${ZFP_SRCDIR}/src/template/codec2.c \
+ ${ZFP_SRCDIR}/src/template/codec3.c \
+ ${ZFP_SRCDIR}/src/template/compress.c \
+ ${ZFP_SRCDIR}/src/template/decode.c \
+ ${ZFP_SRCDIR}/src/template/decode1.c \
+ ${ZFP_SRCDIR}/src/template/decode2.c \
+ ${ZFP_SRCDIR}/src/template/decode3.c \
+ ${ZFP_SRCDIR}/src/template/decompress.c \
+ ${ZFP_SRCDIR}/src/template/encode.c \
+ ${ZFP_SRCDIR}/src/template/encode1.c \
+ ${ZFP_SRCDIR}/src/template/encode2.c \
+ ${ZFP_SRCDIR}/src/template/encode3.c \
+ ${ZFP_SRCDIR}/src/template/template.h \
+ ${ZFP_SRCDIR}/inc/bitstream.h \
+ ${ZFP_SRCDIR}/inc/macros.h \
+ ${ZFP_SRCDIR}/inc/system.h \
+ ${ZFP_SRCDIR}/inc/types.h \
+ ${ZFP_SRCDIR}/inc/zfp.h \
+ ${ZFP_SRCDIR}/API ${ZFP_SRCDIR}/Config ${ZFP_SRCDIR}/FAQ ${ZFP_SRCDIR}/LICENSE \
+ ${ZFP_SRCDIR}/Makefile ${ZFP_SRCDIR}/README ${ZFP_SRCDIR}/VERSIONS \
+ ${ZFP_SRCDIR}/array ${ZFP_SRCDIR}/examples
diff --git a/src/mxml/Makefile.in b/src/zfp/Makefile.in
similarity index 58%
copy from src/mxml/Makefile.in
copy to src/zfp/Makefile.in
index 9bede00..411d9e0 100644
--- a/src/mxml/Makefile.in
+++ b/src/zfp/Makefile.in
@@ -78,7 +78,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
-subdir = src/mxml
+subdir = src/zfp
DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
@@ -108,7 +108,7 @@ 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_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 \
@@ -129,20 +129,24 @@ AM_V_AR = $(am__v_AR_ at AM_V@)
am__v_AR_ = $(am__v_AR_ at AM_DEFAULT_V@)
am__v_AR_0 = @echo " AR " $@;
am__v_AR_1 =
-libmxml_a_AR = $(AR) $(ARFLAGS)
-libmxml_a_LIBADD =
+libzfp_a_AR = $(AR) $(ARFLAGS)
+libzfp_a_LIBADD =
am__dirstamp = $(am__leading_dot)dirstamp
-am_libmxml_a_OBJECTS = ${MXML_SRCDIR}/libmxml_a-mxml-attr.$(OBJEXT) \
- ${MXML_SRCDIR}/libmxml_a-mxml-get.$(OBJEXT) \
- ${MXML_SRCDIR}/libmxml_a-mxml-private.$(OBJEXT) \
- ${MXML_SRCDIR}/libmxml_a-mxml-string.$(OBJEXT) \
- ${MXML_SRCDIR}/libmxml_a-mxml-entity.$(OBJEXT) \
- ${MXML_SRCDIR}/libmxml_a-mxml-index.$(OBJEXT) \
- ${MXML_SRCDIR}/libmxml_a-mxml-search.$(OBJEXT) \
- ${MXML_SRCDIR}/libmxml_a-mxml-file.$(OBJEXT) \
- ${MXML_SRCDIR}/libmxml_a-mxml-node.$(OBJEXT) \
- ${MXML_SRCDIR}/libmxml_a-mxml-set.$(OBJEXT)
-libmxml_a_OBJECTS = $(am_libmxml_a_OBJECTS)
+am_libzfp_a_OBJECTS = ${ZFP_SRCDIR}/src/libzfp_a-bitstream.$(OBJEXT) \
+ ${ZFP_SRCDIR}/src/libzfp_a-decode1f.$(OBJEXT) \
+ ${ZFP_SRCDIR}/src/libzfp_a-decode1d.$(OBJEXT) \
+ ${ZFP_SRCDIR}/src/libzfp_a-encode1f.$(OBJEXT) \
+ ${ZFP_SRCDIR}/src/libzfp_a-encode1d.$(OBJEXT) \
+ ${ZFP_SRCDIR}/src/libzfp_a-decode2f.$(OBJEXT) \
+ ${ZFP_SRCDIR}/src/libzfp_a-decode2d.$(OBJEXT) \
+ ${ZFP_SRCDIR}/src/libzfp_a-encode2f.$(OBJEXT) \
+ ${ZFP_SRCDIR}/src/libzfp_a-encode2d.$(OBJEXT) \
+ ${ZFP_SRCDIR}/src/libzfp_a-decode3f.$(OBJEXT) \
+ ${ZFP_SRCDIR}/src/libzfp_a-decode3d.$(OBJEXT) \
+ ${ZFP_SRCDIR}/src/libzfp_a-encode3f.$(OBJEXT) \
+ ${ZFP_SRCDIR}/src/libzfp_a-encode3d.$(OBJEXT) \
+ ${ZFP_SRCDIR}/src/libzfp_a-zfp.$(OBJEXT)
+libzfp_a_OBJECTS = $(am_libzfp_a_OBJECTS)
AM_V_P = $(am__v_P_ at AM_V@)
am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
am__v_P_0 = false
@@ -180,8 +184,8 @@ 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 = $(libmxml_a_SOURCES)
-DIST_SOURCES = $(libmxml_a_SOURCES)
+SOURCES = $(libzfp_a_SOURCES)
+DIST_SOURCES = $(libzfp_a_SOURCES)
am__can_run_installinfo = \
case $$AM_UPDATE_INFO_DIR in \
n|no|NO) false;; \
@@ -417,6 +421,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
@@ -478,38 +485,59 @@ target_alias = @target_alias@
top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
-MXML_SRCDIR = mxml-2.9
-AM_CPPFLAGS = -I$(top_srcdir)/mxml/${MXML_SRCDIR}
+ZFP_SRCDIR = zfp-0.5.0
+AM_CPPFLAGS = -I${srcdir}/${ZFP_SRCDIR}/inc -I${srcdir}/${ZFP_SRCDIR}/src
AUTOMAKE_OPTIONS = no-dependencies subdir-objects
METASOURCES = AUTO
CLEANFILES =
-noinst_LIBRARIES = libmxml.a
-libmxml_a_SOURCES = ${MXML_SRCDIR}/mxml-attr.c \
- ${MXML_SRCDIR}/mxml-get.c \
- ${MXML_SRCDIR}/mxml-private.c \
- ${MXML_SRCDIR}/mxml-string.c \
- ${MXML_SRCDIR}/mxml-entity.c \
- ${MXML_SRCDIR}/mxml-index.c \
- ${MXML_SRCDIR}/mxml-search.c \
- ${MXML_SRCDIR}/mxml-file.c \
- ${MXML_SRCDIR}/mxml-node.c \
- ${MXML_SRCDIR}/mxml-set.c
-
-libmxml_a_CPPFLAGS = $(AM_CPPFLAGS)
-libmxml_a_CFLAGS =
-EXTRA_DIST = config.h CMakeLists.txt \
- ${MXML_SRCDIR}/ANNOUNCEMENT ${MXML_SRCDIR}/CHANGES \
- ${MXML_SRCDIR}/COPYING ${MXML_SRCDIR}/Makefile.in \
- ${MXML_SRCDIR}/README ${MXML_SRCDIR}/config.h.in \
- ${MXML_SRCDIR}/configure ${MXML_SRCDIR}/configure.in \
- ${MXML_SRCDIR}/install-sh ${MXML_SRCDIR}/mxml.list.in \
- ${MXML_SRCDIR}/mxml.pc.in ${MXML_SRCDIR}/mxml.spec \
- ${MXML_SRCDIR}/mxml.xml ${MXML_SRCDIR}/mxmldoc.c \
- ${MXML_SRCDIR}/test.xml ${MXML_SRCDIR}/testmxml.c \
- ${MXML_SRCDIR}/mxml-private.h ${MXML_SRCDIR}/mxml.h \
- ${MXML_SRCDIR}/doc \
- ${MXML_SRCDIR}/test \
- ${MXML_SRCDIR}/vcnet
+noinst_LIBRARIES = libzfp.a
+libzfp_a_SOURCES = ${ZFP_SRCDIR}/src/bitstream.c \
+ ${ZFP_SRCDIR}/src/decode1f.c \
+ ${ZFP_SRCDIR}/src/decode1d.c \
+ ${ZFP_SRCDIR}/src/encode1f.c \
+ ${ZFP_SRCDIR}/src/encode1d.c \
+ ${ZFP_SRCDIR}/src/decode2f.c \
+ ${ZFP_SRCDIR}/src/decode2d.c \
+ ${ZFP_SRCDIR}/src/encode2f.c \
+ ${ZFP_SRCDIR}/src/encode2d.c \
+ ${ZFP_SRCDIR}/src/decode3f.c \
+ ${ZFP_SRCDIR}/src/decode3d.c \
+ ${ZFP_SRCDIR}/src/encode3f.c \
+ ${ZFP_SRCDIR}/src/encode3d.c \
+ ${ZFP_SRCDIR}/src/zfp.c
+
+libzfp_a_CPPFLAGS = $(AM_CPPFLAGS)
+libzfp_a_CFLAGS =
+EXTRA_DIST = ${ZFP_SRCDIR}/src/block1.h \
+ ${ZFP_SRCDIR}/src/block2.h \
+ ${ZFP_SRCDIR}/src/block3.h \
+ ${ZFP_SRCDIR}/src/traitsd.h \
+ ${ZFP_SRCDIR}/src/traitsf.h \
+ ${ZFP_SRCDIR}/src/Makefile \
+ ${ZFP_SRCDIR}/src/inline \
+ ${ZFP_SRCDIR}/src/template/codec.h \
+ ${ZFP_SRCDIR}/src/template/codec1.c \
+ ${ZFP_SRCDIR}/src/template/codec2.c \
+ ${ZFP_SRCDIR}/src/template/codec3.c \
+ ${ZFP_SRCDIR}/src/template/compress.c \
+ ${ZFP_SRCDIR}/src/template/decode.c \
+ ${ZFP_SRCDIR}/src/template/decode1.c \
+ ${ZFP_SRCDIR}/src/template/decode2.c \
+ ${ZFP_SRCDIR}/src/template/decode3.c \
+ ${ZFP_SRCDIR}/src/template/decompress.c \
+ ${ZFP_SRCDIR}/src/template/encode.c \
+ ${ZFP_SRCDIR}/src/template/encode1.c \
+ ${ZFP_SRCDIR}/src/template/encode2.c \
+ ${ZFP_SRCDIR}/src/template/encode3.c \
+ ${ZFP_SRCDIR}/src/template/template.h \
+ ${ZFP_SRCDIR}/inc/bitstream.h \
+ ${ZFP_SRCDIR}/inc/macros.h \
+ ${ZFP_SRCDIR}/inc/system.h \
+ ${ZFP_SRCDIR}/inc/types.h \
+ ${ZFP_SRCDIR}/inc/zfp.h \
+ ${ZFP_SRCDIR}/API ${ZFP_SRCDIR}/Config ${ZFP_SRCDIR}/FAQ ${ZFP_SRCDIR}/LICENSE \
+ ${ZFP_SRCDIR}/Makefile ${ZFP_SRCDIR}/README ${ZFP_SRCDIR}/VERSIONS \
+ ${ZFP_SRCDIR}/array ${ZFP_SRCDIR}/examples
all: all-am
@@ -524,9 +552,9 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(am__confi
exit 1;; \
esac; \
done; \
- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/mxml/Makefile'; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/zfp/Makefile'; \
$(am__cd) $(top_srcdir) && \
- $(AUTOMAKE) --gnu src/mxml/Makefile
+ $(AUTOMAKE) --gnu src/zfp/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
@@ -548,38 +576,46 @@ $(am__aclocal_m4_deps):
clean-noinstLIBRARIES:
-test -z "$(noinst_LIBRARIES)" || rm -f $(noinst_LIBRARIES)
-${MXML_SRCDIR}/$(am__dirstamp):
- @$(MKDIR_P) ${MXML_SRCDIR}
- @: > ${MXML_SRCDIR}/$(am__dirstamp)
-${MXML_SRCDIR}/libmxml_a-mxml-attr.$(OBJEXT): \
- ${MXML_SRCDIR}/$(am__dirstamp)
-${MXML_SRCDIR}/libmxml_a-mxml-get.$(OBJEXT): \
- ${MXML_SRCDIR}/$(am__dirstamp)
-${MXML_SRCDIR}/libmxml_a-mxml-private.$(OBJEXT): \
- ${MXML_SRCDIR}/$(am__dirstamp)
-${MXML_SRCDIR}/libmxml_a-mxml-string.$(OBJEXT): \
- ${MXML_SRCDIR}/$(am__dirstamp)
-${MXML_SRCDIR}/libmxml_a-mxml-entity.$(OBJEXT): \
- ${MXML_SRCDIR}/$(am__dirstamp)
-${MXML_SRCDIR}/libmxml_a-mxml-index.$(OBJEXT): \
- ${MXML_SRCDIR}/$(am__dirstamp)
-${MXML_SRCDIR}/libmxml_a-mxml-search.$(OBJEXT): \
- ${MXML_SRCDIR}/$(am__dirstamp)
-${MXML_SRCDIR}/libmxml_a-mxml-file.$(OBJEXT): \
- ${MXML_SRCDIR}/$(am__dirstamp)
-${MXML_SRCDIR}/libmxml_a-mxml-node.$(OBJEXT): \
- ${MXML_SRCDIR}/$(am__dirstamp)
-${MXML_SRCDIR}/libmxml_a-mxml-set.$(OBJEXT): \
- ${MXML_SRCDIR}/$(am__dirstamp)
-
-libmxml.a: $(libmxml_a_OBJECTS) $(libmxml_a_DEPENDENCIES) $(EXTRA_libmxml_a_DEPENDENCIES)
- $(AM_V_at)-rm -f libmxml.a
- $(AM_V_AR)$(libmxml_a_AR) libmxml.a $(libmxml_a_OBJECTS) $(libmxml_a_LIBADD)
- $(AM_V_at)$(RANLIB) libmxml.a
+${ZFP_SRCDIR}/src/$(am__dirstamp):
+ @$(MKDIR_P) ${ZFP_SRCDIR}/src
+ @: > ${ZFP_SRCDIR}/src/$(am__dirstamp)
+${ZFP_SRCDIR}/src/libzfp_a-bitstream.$(OBJEXT): \
+ ${ZFP_SRCDIR}/src/$(am__dirstamp)
+${ZFP_SRCDIR}/src/libzfp_a-decode1f.$(OBJEXT): \
+ ${ZFP_SRCDIR}/src/$(am__dirstamp)
+${ZFP_SRCDIR}/src/libzfp_a-decode1d.$(OBJEXT): \
+ ${ZFP_SRCDIR}/src/$(am__dirstamp)
+${ZFP_SRCDIR}/src/libzfp_a-encode1f.$(OBJEXT): \
+ ${ZFP_SRCDIR}/src/$(am__dirstamp)
+${ZFP_SRCDIR}/src/libzfp_a-encode1d.$(OBJEXT): \
+ ${ZFP_SRCDIR}/src/$(am__dirstamp)
+${ZFP_SRCDIR}/src/libzfp_a-decode2f.$(OBJEXT): \
+ ${ZFP_SRCDIR}/src/$(am__dirstamp)
+${ZFP_SRCDIR}/src/libzfp_a-decode2d.$(OBJEXT): \
+ ${ZFP_SRCDIR}/src/$(am__dirstamp)
+${ZFP_SRCDIR}/src/libzfp_a-encode2f.$(OBJEXT): \
+ ${ZFP_SRCDIR}/src/$(am__dirstamp)
+${ZFP_SRCDIR}/src/libzfp_a-encode2d.$(OBJEXT): \
+ ${ZFP_SRCDIR}/src/$(am__dirstamp)
+${ZFP_SRCDIR}/src/libzfp_a-decode3f.$(OBJEXT): \
+ ${ZFP_SRCDIR}/src/$(am__dirstamp)
+${ZFP_SRCDIR}/src/libzfp_a-decode3d.$(OBJEXT): \
+ ${ZFP_SRCDIR}/src/$(am__dirstamp)
+${ZFP_SRCDIR}/src/libzfp_a-encode3f.$(OBJEXT): \
+ ${ZFP_SRCDIR}/src/$(am__dirstamp)
+${ZFP_SRCDIR}/src/libzfp_a-encode3d.$(OBJEXT): \
+ ${ZFP_SRCDIR}/src/$(am__dirstamp)
+${ZFP_SRCDIR}/src/libzfp_a-zfp.$(OBJEXT): \
+ ${ZFP_SRCDIR}/src/$(am__dirstamp)
+
+libzfp.a: $(libzfp_a_OBJECTS) $(libzfp_a_DEPENDENCIES) $(EXTRA_libzfp_a_DEPENDENCIES)
+ $(AM_V_at)-rm -f libzfp.a
+ $(AM_V_AR)$(libzfp_a_AR) libzfp.a $(libzfp_a_OBJECTS) $(libzfp_a_LIBADD)
+ $(AM_V_at)$(RANLIB) libzfp.a
mostlyclean-compile:
-rm -f *.$(OBJEXT)
- -rm -f ${MXML_SRCDIR}/*.$(OBJEXT)
+ -rm -f ${ZFP_SRCDIR}/src/*.$(OBJEXT)
distclean-compile:
-rm -f *.tab.c
@@ -593,65 +629,89 @@ distclean-compile:
.c.lo:
$(AM_V_CC)$(LTCOMPILE) -c -o $@ $<
-${MXML_SRCDIR}/libmxml_a-mxml-attr.o: ${MXML_SRCDIR}/mxml-attr.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-attr.o `test -f '${MXML_SRCDIR}/mxml-attr.c' || echo '$(srcdir)/'`${MXML_SRCDIR}/mxml-attr.c
+${ZFP_SRCDIR}/src/libzfp_a-bitstream.o: ${ZFP_SRCDIR}/src/bitstream.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-bitstream.o `test -f '${ZFP_SRCDIR}/src/bitstream.c' || echo '$(srcdir)/'`${ZFP_SRCDIR}/src/bitstream.c
-${MXML_SRCDIR}/libmxml_a-mxml-attr.obj: ${MXML_SRCDIR}/mxml-attr.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-attr.obj `if test -f '${MXML_SRCDIR}/mxml-attr.c'; then $(CYGPATH_W) '${MXML_SRCDIR}/mxml-attr.c'; else $(CYGPATH_W) '$(srcdir)/${MXML_SRCDIR}/mxml-attr.c'; fi`
+${ZFP_SRCDIR}/src/libzfp_a-bitstream.obj: ${ZFP_SRCDIR}/src/bitstream.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-bitstream.obj `if test -f '${ZFP_SRCDIR}/src/bitstream.c'; then $(CYGPATH_W) '${ZFP_SRCDIR}/src/bitstream.c'; else $(CYGPATH_W) '$(srcdir)/${ZFP_SRCDIR}/src/bitstream.c'; fi`
-${MXML_SRCDIR}/libmxml_a-mxml-get.o: ${MXML_SRCDIR}/mxml-get.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-get.o `test -f '${MXML_SRCDIR}/mxml-get.c' || echo '$(srcdir)/'`${MXML_SRCDIR}/mxml-get.c
+${ZFP_SRCDIR}/src/libzfp_a-decode1f.o: ${ZFP_SRCDIR}/src/decode1f.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-decode1f.o `test -f '${ZFP_SRCDIR}/src/decode1f.c' || echo '$(srcdir)/'`${ZFP_SRCDIR}/src/decode1f.c
-${MXML_SRCDIR}/libmxml_a-mxml-get.obj: ${MXML_SRCDIR}/mxml-get.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-get.obj `if test -f '${MXML_SRCDIR}/mxml-get.c'; then $(CYGPATH_W) '${MXML_SRCDIR}/mxml-get.c'; else $(CYGPATH_W) '$(srcdir)/${MXML_SRCDIR}/mxml-get.c'; fi`
+${ZFP_SRCDIR}/src/libzfp_a-decode1f.obj: ${ZFP_SRCDIR}/src/decode1f.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-decode1f.obj `if test -f '${ZFP_SRCDIR}/src/decode1f.c'; then $(CYGPATH_W) '${ZFP_SRCDIR}/src/decode1f.c'; else $(CYGPATH_W) '$(srcdir)/${ZFP_SRCDIR}/src/decode1f.c'; fi`
-${MXML_SRCDIR}/libmxml_a-mxml-private.o: ${MXML_SRCDIR}/mxml-private.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-private.o `test -f '${MXML_SRCDIR}/mxml-private.c' || echo '$(srcdir)/'`${MXML_SRCDIR}/mxml-private.c
+${ZFP_SRCDIR}/src/libzfp_a-decode1d.o: ${ZFP_SRCDIR}/src/decode1d.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-decode1d.o `test -f '${ZFP_SRCDIR}/src/decode1d.c' || echo '$(srcdir)/'`${ZFP_SRCDIR}/src/decode1d.c
-${MXML_SRCDIR}/libmxml_a-mxml-private.obj: ${MXML_SRCDIR}/mxml-private.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-private.obj `if test -f '${MXML_SRCDIR}/mxml-private.c'; then $(CYGPATH_W) '${MXML_SRCDIR}/mxml-private.c'; else $(CYGPATH_W) '$(srcdir)/${MXML_SRCDIR}/mxml-private.c'; fi`
+${ZFP_SRCDIR}/src/libzfp_a-decode1d.obj: ${ZFP_SRCDIR}/src/decode1d.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-decode1d.obj `if test -f '${ZFP_SRCDIR}/src/decode1d.c'; then $(CYGPATH_W) '${ZFP_SRCDIR}/src/decode1d.c'; else $(CYGPATH_W) '$(srcdir)/${ZFP_SRCDIR}/src/decode1d.c'; fi`
-${MXML_SRCDIR}/libmxml_a-mxml-string.o: ${MXML_SRCDIR}/mxml-string.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-string.o `test -f '${MXML_SRCDIR}/mxml-string.c' || echo '$(srcdir)/'`${MXML_SRCDIR}/mxml-string.c
+${ZFP_SRCDIR}/src/libzfp_a-encode1f.o: ${ZFP_SRCDIR}/src/encode1f.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-encode1f.o `test -f '${ZFP_SRCDIR}/src/encode1f.c' || echo '$(srcdir)/'`${ZFP_SRCDIR}/src/encode1f.c
-${MXML_SRCDIR}/libmxml_a-mxml-string.obj: ${MXML_SRCDIR}/mxml-string.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-string.obj `if test -f '${MXML_SRCDIR}/mxml-string.c'; then $(CYGPATH_W) '${MXML_SRCDIR}/mxml-string.c'; else $(CYGPATH_W) '$(srcdir)/${MXML_SRCDIR}/mxml-string.c'; fi`
+${ZFP_SRCDIR}/src/libzfp_a-encode1f.obj: ${ZFP_SRCDIR}/src/encode1f.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-encode1f.obj `if test -f '${ZFP_SRCDIR}/src/encode1f.c'; then $(CYGPATH_W) '${ZFP_SRCDIR}/src/encode1f.c'; else $(CYGPATH_W) '$(srcdir)/${ZFP_SRCDIR}/src/encode1f.c'; fi`
-${MXML_SRCDIR}/libmxml_a-mxml-entity.o: ${MXML_SRCDIR}/mxml-entity.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-entity.o `test -f '${MXML_SRCDIR}/mxml-entity.c' || echo '$(srcdir)/'`${MXML_SRCDIR}/mxml-entity.c
+${ZFP_SRCDIR}/src/libzfp_a-encode1d.o: ${ZFP_SRCDIR}/src/encode1d.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-encode1d.o `test -f '${ZFP_SRCDIR}/src/encode1d.c' || echo '$(srcdir)/'`${ZFP_SRCDIR}/src/encode1d.c
-${MXML_SRCDIR}/libmxml_a-mxml-entity.obj: ${MXML_SRCDIR}/mxml-entity.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-entity.obj `if test -f '${MXML_SRCDIR}/mxml-entity.c'; then $(CYGPATH_W) '${MXML_SRCDIR}/mxml-entity.c'; else $(CYGPATH_W) '$(srcdir)/${MXML_SRCDIR}/mxml-entity.c'; fi`
+${ZFP_SRCDIR}/src/libzfp_a-encode1d.obj: ${ZFP_SRCDIR}/src/encode1d.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-encode1d.obj `if test -f '${ZFP_SRCDIR}/src/encode1d.c'; then $(CYGPATH_W) '${ZFP_SRCDIR}/src/encode1d.c'; else $(CYGPATH_W) '$(srcdir)/${ZFP_SRCDIR}/src/encode1d.c'; fi`
-${MXML_SRCDIR}/libmxml_a-mxml-index.o: ${MXML_SRCDIR}/mxml-index.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-index.o `test -f '${MXML_SRCDIR}/mxml-index.c' || echo '$(srcdir)/'`${MXML_SRCDIR}/mxml-index.c
+${ZFP_SRCDIR}/src/libzfp_a-decode2f.o: ${ZFP_SRCDIR}/src/decode2f.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-decode2f.o `test -f '${ZFP_SRCDIR}/src/decode2f.c' || echo '$(srcdir)/'`${ZFP_SRCDIR}/src/decode2f.c
-${MXML_SRCDIR}/libmxml_a-mxml-index.obj: ${MXML_SRCDIR}/mxml-index.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-index.obj `if test -f '${MXML_SRCDIR}/mxml-index.c'; then $(CYGPATH_W) '${MXML_SRCDIR}/mxml-index.c'; else $(CYGPATH_W) '$(srcdir)/${MXML_SRCDIR}/mxml-index.c'; fi`
+${ZFP_SRCDIR}/src/libzfp_a-decode2f.obj: ${ZFP_SRCDIR}/src/decode2f.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-decode2f.obj `if test -f '${ZFP_SRCDIR}/src/decode2f.c'; then $(CYGPATH_W) '${ZFP_SRCDIR}/src/decode2f.c'; else $(CYGPATH_W) '$(srcdir)/${ZFP_SRCDIR}/src/decode2f.c'; fi`
-${MXML_SRCDIR}/libmxml_a-mxml-search.o: ${MXML_SRCDIR}/mxml-search.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-search.o `test -f '${MXML_SRCDIR}/mxml-search.c' || echo '$(srcdir)/'`${MXML_SRCDIR}/mxml-search.c
+${ZFP_SRCDIR}/src/libzfp_a-decode2d.o: ${ZFP_SRCDIR}/src/decode2d.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-decode2d.o `test -f '${ZFP_SRCDIR}/src/decode2d.c' || echo '$(srcdir)/'`${ZFP_SRCDIR}/src/decode2d.c
-${MXML_SRCDIR}/libmxml_a-mxml-search.obj: ${MXML_SRCDIR}/mxml-search.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-search.obj `if test -f '${MXML_SRCDIR}/mxml-search.c'; then $(CYGPATH_W) '${MXML_SRCDIR}/mxml-search.c'; else $(CYGPATH_W) '$(srcdir)/${MXML_SRCDIR}/mxml-search.c'; fi`
+${ZFP_SRCDIR}/src/libzfp_a-decode2d.obj: ${ZFP_SRCDIR}/src/decode2d.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-decode2d.obj `if test -f '${ZFP_SRCDIR}/src/decode2d.c'; then $(CYGPATH_W) '${ZFP_SRCDIR}/src/decode2d.c'; else $(CYGPATH_W) '$(srcdir)/${ZFP_SRCDIR}/src/decode2d.c'; fi`
-${MXML_SRCDIR}/libmxml_a-mxml-file.o: ${MXML_SRCDIR}/mxml-file.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-file.o `test -f '${MXML_SRCDIR}/mxml-file.c' || echo '$(srcdir)/'`${MXML_SRCDIR}/mxml-file.c
+${ZFP_SRCDIR}/src/libzfp_a-encode2f.o: ${ZFP_SRCDIR}/src/encode2f.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-encode2f.o `test -f '${ZFP_SRCDIR}/src/encode2f.c' || echo '$(srcdir)/'`${ZFP_SRCDIR}/src/encode2f.c
-${MXML_SRCDIR}/libmxml_a-mxml-file.obj: ${MXML_SRCDIR}/mxml-file.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-file.obj `if test -f '${MXML_SRCDIR}/mxml-file.c'; then $(CYGPATH_W) '${MXML_SRCDIR}/mxml-file.c'; else $(CYGPATH_W) '$(srcdir)/${MXML_SRCDIR}/mxml-file.c'; fi`
+${ZFP_SRCDIR}/src/libzfp_a-encode2f.obj: ${ZFP_SRCDIR}/src/encode2f.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-encode2f.obj `if test -f '${ZFP_SRCDIR}/src/encode2f.c'; then $(CYGPATH_W) '${ZFP_SRCDIR}/src/encode2f.c'; else $(CYGPATH_W) '$(srcdir)/${ZFP_SRCDIR}/src/encode2f.c'; fi`
-${MXML_SRCDIR}/libmxml_a-mxml-node.o: ${MXML_SRCDIR}/mxml-node.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-node.o `test -f '${MXML_SRCDIR}/mxml-node.c' || echo '$(srcdir)/'`${MXML_SRCDIR}/mxml-node.c
+${ZFP_SRCDIR}/src/libzfp_a-encode2d.o: ${ZFP_SRCDIR}/src/encode2d.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-encode2d.o `test -f '${ZFP_SRCDIR}/src/encode2d.c' || echo '$(srcdir)/'`${ZFP_SRCDIR}/src/encode2d.c
-${MXML_SRCDIR}/libmxml_a-mxml-node.obj: ${MXML_SRCDIR}/mxml-node.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-node.obj `if test -f '${MXML_SRCDIR}/mxml-node.c'; then $(CYGPATH_W) '${MXML_SRCDIR}/mxml-node.c'; else $(CYGPATH_W) '$(srcdir)/${MXML_SRCDIR}/mxml-node.c'; fi`
+${ZFP_SRCDIR}/src/libzfp_a-encode2d.obj: ${ZFP_SRCDIR}/src/encode2d.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-encode2d.obj `if test -f '${ZFP_SRCDIR}/src/encode2d.c'; then $(CYGPATH_W) '${ZFP_SRCDIR}/src/encode2d.c'; else $(CYGPATH_W) '$(srcdir)/${ZFP_SRCDIR}/src/encode2d.c'; fi`
-${MXML_SRCDIR}/libmxml_a-mxml-set.o: ${MXML_SRCDIR}/mxml-set.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-set.o `test -f '${MXML_SRCDIR}/mxml-set.c' || echo '$(srcdir)/'`${MXML_SRCDIR}/mxml-set.c
+${ZFP_SRCDIR}/src/libzfp_a-decode3f.o: ${ZFP_SRCDIR}/src/decode3f.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-decode3f.o `test -f '${ZFP_SRCDIR}/src/decode3f.c' || echo '$(srcdir)/'`${ZFP_SRCDIR}/src/decode3f.c
-${MXML_SRCDIR}/libmxml_a-mxml-set.obj: ${MXML_SRCDIR}/mxml-set.c
- $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libmxml_a_CPPFLAGS) $(CPPFLAGS) $(libmxml_a_CFLAGS) $(CFLAGS) -c -o ${MXML_SRCDIR}/libmxml_a-mxml-set.obj `if test -f '${MXML_SRCDIR}/mxml-set.c'; then $(CYGPATH_W) '${MXML_SRCDIR}/mxml-set.c'; else $(CYGPATH_W) '$(srcdir)/${MXML_SRCDIR}/mxml-set.c'; fi`
+${ZFP_SRCDIR}/src/libzfp_a-decode3f.obj: ${ZFP_SRCDIR}/src/decode3f.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-decode3f.obj `if test -f '${ZFP_SRCDIR}/src/decode3f.c'; then $(CYGPATH_W) '${ZFP_SRCDIR}/src/decode3f.c'; else $(CYGPATH_W) '$(srcdir)/${ZFP_SRCDIR}/src/decode3f.c'; fi`
+
+${ZFP_SRCDIR}/src/libzfp_a-decode3d.o: ${ZFP_SRCDIR}/src/decode3d.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-decode3d.o `test -f '${ZFP_SRCDIR}/src/decode3d.c' || echo '$(srcdir)/'`${ZFP_SRCDIR}/src/decode3d.c
+
+${ZFP_SRCDIR}/src/libzfp_a-decode3d.obj: ${ZFP_SRCDIR}/src/decode3d.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-decode3d.obj `if test -f '${ZFP_SRCDIR}/src/decode3d.c'; then $(CYGPATH_W) '${ZFP_SRCDIR}/src/decode3d.c'; else $(CYGPATH_W) '$(srcdir)/${ZFP_SRCDIR}/src/decode3d.c'; fi`
+
+${ZFP_SRCDIR}/src/libzfp_a-encode3f.o: ${ZFP_SRCDIR}/src/encode3f.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-encode3f.o `test -f '${ZFP_SRCDIR}/src/encode3f.c' || echo '$(srcdir)/'`${ZFP_SRCDIR}/src/encode3f.c
+
+${ZFP_SRCDIR}/src/libzfp_a-encode3f.obj: ${ZFP_SRCDIR}/src/encode3f.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-encode3f.obj `if test -f '${ZFP_SRCDIR}/src/encode3f.c'; then $(CYGPATH_W) '${ZFP_SRCDIR}/src/encode3f.c'; else $(CYGPATH_W) '$(srcdir)/${ZFP_SRCDIR}/src/encode3f.c'; fi`
+
+${ZFP_SRCDIR}/src/libzfp_a-encode3d.o: ${ZFP_SRCDIR}/src/encode3d.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-encode3d.o `test -f '${ZFP_SRCDIR}/src/encode3d.c' || echo '$(srcdir)/'`${ZFP_SRCDIR}/src/encode3d.c
+
+${ZFP_SRCDIR}/src/libzfp_a-encode3d.obj: ${ZFP_SRCDIR}/src/encode3d.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-encode3d.obj `if test -f '${ZFP_SRCDIR}/src/encode3d.c'; then $(CYGPATH_W) '${ZFP_SRCDIR}/src/encode3d.c'; else $(CYGPATH_W) '$(srcdir)/${ZFP_SRCDIR}/src/encode3d.c'; fi`
+
+${ZFP_SRCDIR}/src/libzfp_a-zfp.o: ${ZFP_SRCDIR}/src/zfp.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-zfp.o `test -f '${ZFP_SRCDIR}/src/zfp.c' || echo '$(srcdir)/'`${ZFP_SRCDIR}/src/zfp.c
+
+${ZFP_SRCDIR}/src/libzfp_a-zfp.obj: ${ZFP_SRCDIR}/src/zfp.c
+ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libzfp_a_CPPFLAGS) $(CPPFLAGS) $(libzfp_a_CFLAGS) $(CFLAGS) -c -o ${ZFP_SRCDIR}/src/libzfp_a-zfp.obj `if test -f '${ZFP_SRCDIR}/src/zfp.c'; then $(CYGPATH_W) '${ZFP_SRCDIR}/src/zfp.c'; else $(CYGPATH_W) '$(srcdir)/${ZFP_SRCDIR}/src/zfp.c'; fi`
mostlyclean-libtool:
-rm -f *.lo
@@ -772,7 +832,7 @@ clean-generic:
distclean-generic:
-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
- -rm -f ${MXML_SRCDIR}/$(am__dirstamp)
+ -rm -f ${ZFP_SRCDIR}/src/$(am__dirstamp)
maintainer-clean-generic:
@echo "This command is intended for maintainers to use"
diff --git a/src/zfp/zfp-0.5.0/API b/src/zfp/zfp-0.5.0/API
new file mode 100644
index 0000000..381e310
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/API
@@ -0,0 +1,439 @@
+OVERVIEW
+
+zfp consists of three distinct components: (1) a set of low-level C codecs
+for compressing and decompressing block subsets of one-, two-, and three-
+dimensional single- and double-precision arrays; (2) a set of corresponding
+C++ compressed array classes that support random access; and (3) a high-level
+C interface for compressing and decompressing entire floating-point arrays.
+
+The compression codecs operate on individual d-dimensional blocks of size
+4^d, e.g. 4 values in 1D, 4x4 = 16 values in 2D, and 4x4x4 = 64 values in
+3D. The block being compressed need not be stored contiguously but can
+be processed by specifying regular strides in each dimension. This is
+useful if the block is initially stored uncompressed as part of a larger
+array.
+
+The array classes represent an entire array of floating-point values as
+a collection of compressed blocks, each whose compressed size in number
+of bits is fixed and specified by the user. The array classes cache
+uncompressed blocks to reduce the number of compression and decompression
+calls. Whenever an array value is read, the corresponding block is first
+looked up in the cache, and if found the uncompressed value is returned.
+Otherwise the block is first decompressed and stored in the cache.
+Whenever an array element is written (whether actually modified or not),
+a "dirty bit" is set with its cached block to indicate that the block
+must be compressed back to persistent storage when evicted from the cache.
+
+The libzfp C interface is useful for quickly compressing and archiving
+large floating-point arrays of arbitrary dimensions without having to
+understand the technical details of the compression algorithm and codec.
+This library comes with utility functions for specifying the compression
+rate, precision, or accuracy of the compressed data.
+
+All code examples below are for 3D arrays of doubles, but it should be
+clear how to modify the function calls for single precision and for 1D
+or 2D arrays.
+
+
+GENERAL DESIGN AND LIMITATIONS
+
+The zfp API has been designed to facilitate integration with existing
+applications. After initial array declaration, a zfp array can often
+be used in place of a regular C/C++ array or STL vector, e.g. using flat
+indexing via a[index] or using multidimensional indexing via a(i),
+a(i, j), or a(i, j, k). There are, however, some important differences.
+For instance, it is not possible to take the address of an array element,
+i.e. constructions like &a[i] and a + i are not allowed. Moreover, the
+operators [] and () do not return regular C++ references. Instead, a
+proxy reference class is used (similar to how STL bit vectors are
+implemented). These proxy references can, however, safely be passed to
+functions and used where regular references can.
+
+zfp does not support special floating-point values like infinities and
+NaNs, although denormalized numbers are handled correctly. Similarly,
+because the compressor assumes that the array values vary smoothly,
+using finite but large values like HUGE_VAL in place of infinities is
+not advised, as this will introduce large errors in smaller values
+within the same block. Future extensions will provide support for a
+bit mask to mark the presence of non-values.
+
+The zfp C++ classes are implemented entirely as header files and make
+extensive use of C++ templates to reduce code redundancy. Most classes
+are wrapped in the 'zfp' namespace.
+
+
+API OVERVIEW
+
+The documentation is divided into three parts: the high-level libzfp
+library; the low-level compression codecs; and the compressed array
+classes (in that order). Users interested only in the compressed arrays,
+which do not directly expose anything related to compression other than
+compression rate control, may safely skip the next two sections.
+
+
+ZFP HIGH-LEVEL C INTERFACE
+
+Users concerned only with storing their floating-point data compressed may
+use zfp as a black box that maps a possibly non-contiguous floating-point
+array to a compressed bit stream. The intent of libzfp is to provide both
+a high- and low-level interface to the compressor that can be called from
+both C and C++ (and possibly other languages). libzfp supports strided
+access, e.g. for compressing vector fields one scalar at a time, or for
+compressing arrays of structs.
+
+Consider compressing the 3D C/C++ array
+
+ // define an uncompressed array
+ double a[nz][ny][nx];
+
+where nx, ny, and nz can be any positive dimensions. To invoke the libzfp
+compressor, the dimensions and type must first be specified in a zfp_field
+parameter object that encapsulates the type, size, and memory layout of the
+array:
+
+ // allocate metadata for the 3D array a[nz][ny][nx]
+ uint dims = 3;
+ zfp_type type = zfp_type_double;
+ zfp_field* field = zfp_field_3d(&a[0][0][0], type, nx, ny, nz);
+
+For single-precision data, use zfp_type_float. Note that the high-level
+API does not support integer arrays (zfp_type_int32 and zfp_type_int64).
+Such arrays must be compressed via the low-level interface.
+
+Functions similar to zfp_field_3d exist for declaring 1D and 2D arrays.
+If the dimensionality of the array is unknown at this point, then a generic
+zfp_field_alloc() call can be made to just allocate a zfp_field struct,
+which can be filled in later using the zfp_field_set_* functions. If the
+array is non-contiguous, then zfp_field_set_stride_3d should be called.
+
+The zfp_field parameter object holds information about the uncompressed
+array. To specify the compressed array, a zfp_stream object must be
+allocated:
+
+ // allocate metadata for a compressed stream
+ zfp_stream* zfp = zfp_stream_open(NULL);
+
+We may now specify the rate, precision, or accuracy (see the README file
+for more details on the meaning of these parameters):
+
+ // set compression mode and parameters
+ zfp_stream_set_rate(zfp, rate, type, dims, 0);
+ zfp_stream_set_precision(zfp, precision, type);
+ zfp_stream_set_accuracy(zfp, tolerance, type);
+
+Note that only one of these three functions should be called. The return
+value from these functions gives the actual rate, precision, or tolerance,
+and may differ slightly from the argument passed due to constraints imposed
+by the compressor, e.g. each block must be stored using a whole number of
+bits at least as large as the number of bits in the floating-point exponent;
+the precision cannot exceed the number of bits in a floating-point value
+(i.e. 32 for single and 64 for double precision); and the tolerance must
+be a (possibly negative) power of two.
+
+The compression parameters have now been specified, but before compression
+can occur a buffer large enough to hold the compressed bit stream must be
+allocated. Another utility function exists for estimating how many bytes
+are needed:
+
+ // allocate buffer for compressed data
+ size_t bufsize = zfp_stream_maximum_size(zfp, field);
+ uchar* buffer = new uchar[bufsize];
+
+Note that zfp_stream_maximum_size returns the smallest buffer size
+necessary to safely compress the data--the actual compressed size may be
+smaller. If the members of zfp and field are for whatever reason not
+initialized correctly, then zfp_stream_maximum_size returns 0.
+
+Before compression can commence, we must associate the allocated buffer
+with a bit stream used by the compressor to read and write bits:
+
+ // associate bit stream with allocated buffer
+ bitstream* stream = stream_open(buffer, bufsize);
+ zfp_stream_set_bit_stream(zfp, stream);
+
+Finally, the array is compressed as follows:
+
+ // compress entire array
+ size_t size = zfp_compress(zfp, field);
+
+The return value is the actual number of bytes of compressed storage, and
+as already mentioned, size <= bufsize. If size = 0, then the compressor
+failed. Since zfp 0.5.0, the compressor does not rewind the bit stream
+before compressing, which allows multiple fields to be compressed one
+after the other. The return value from zfp_compress is always the total
+number of bytes of compressed storage so far relative to the memory
+location pointed to by 'buffer'.
+
+To decompress the data, the field and compression parameters must be
+initialized with the same values as used for compression, either via
+the same sequence of function calls as above, or by recording these
+fields and setting them directly. Metadata such as array dimensions and
+compression parameters are by default not stored in the compressed stream.
+It is up to the caller to store this information, either separately from
+the compressed data, or via the zfp_write_header and zfp_read_header calls.
+These calls allow the user to specify what information to store in the
+header, including a 'magic' format identifier, the field type and
+dimensions, and the compression parameters (see the ZFP_HEADER_* macros).
+
+In addition to this initialization, the bit stream has to be rewound to
+the beginning:
+
+ // rewind compressed stream and decompress array
+ zfp_stream_rewind(zfp);
+ int success = zfp_decompress(zfp, field);
+
+The return value is zero if the decompressor failed.
+
+
+ZFP LOW-LEVEL COMPRESSION AND DECOMPRESSION CODEC
+
+For applications that wish to compress or decompress portions of an array
+on demand, a low-level interface is available. Since this API is useful
+primarily for supporting random access, the user also needs to manipulate
+the bit stream (see inc/bitstream.h), e.g. to position the bit pointer
+to where data is to be read or written. Please be advised that the bit
+stream functions have been optimized for speed, and do not check for
+buffer overruns or other types of programmer error.
+
+Like the high-level API, the low-level API also makes use of the zfp_stream
+parameter object (see section above) to specify compression parameters and
+storage, but does not encapsulate array metadata in a zfp_field object.
+Functions exists for encoding and decoding complete or partial blocks, with
+or without strided access. In non-strided mode, the uncompressed block to
+be encoded or decoded is assumed to be stored contiguously. For example,
+
+ // compress a single contiguous block
+ double block[4 * 4 * 4] = { /* some set of values */ };
+ uint bits = zfp_encode_block_double_3(zfp, block);
+
+The return value is the number of bits of compressed storage for the block.
+For fixed-rate streams, if random access is desired, then the stream should
+also be flushed after each block is encoded:
+
+ // flush any buffered bits
+ zfp_stream_flush(zfp);
+
+This flushing should be done only after the last block has been compressed in
+fixed-precision and fixed-accuracy mode, or when random access is not needed
+in fixed-rate mode.
+
+The block above could also have been compressed as follows using strides:
+
+ // compress a single contiguous block using strides
+ double block[4][4][4] = { /* some set of values */ };
+ int sx = &block[0][0][1] - &block[0][0][0]; // x stride = 1
+ int sy = &block[0][1][0] - &block[0][0][0]; // y stride = 4
+ int sz = &block[1][0][0] - &block[0][0][0]; // z stride = 16
+ uint bits = zfp_encode_block_strided_double_3(zfp, block, sx, sy, sz);
+
+The strides are measured in number of scalars, not in bytes.
+
+For partial blocks, e.g. near the boundaries of arrays whose dimensions
+are not multiples of four, there are corresponding functions that accept
+parameters (nx, ny, nz) to specify the actual block dimensions, with
+1 <= nx, ny, nz <= 4. Corresponding functions exist for decompression.
+
+To position a bit stream for reading (decompression), use
+
+ // position the stream at given bit offset for reading
+ stream_rseek(stream, offset);
+
+where the offset is measured in number of bits from the beginning of the
+stream. For writing (compression), a corresponding call exists:
+
+ // position the stream at given bit offset for writing
+ stream_wseek(stream, offset);
+
+Note that it is possible to decompress fewer bits than are stored with a
+compressed block to quickly obtain an approximation. This is done by
+setting zfp->maxbits to fewer bits than used during compression, e.g. to
+decompress only the first 256 bits of each block:
+
+ // modify decompression parameters to decode 256 bits per block
+ uint maxbits;
+ uint maxprec;
+ int minexp;
+ zfp_stream_params(zfp, NULL, &maxbits, &maxprec, &minexp);
+ assert(maxbits >= 256);
+ zfp_stream_set_params(zfp, 256, 256, maxprec, minexp);
+
+This feature may be combined with progressive decompression, as discussed
+further in the FAQ.
+
+
+COMPRESSED ARRAYS
+
+Currently there are six array classes for 1D, 2D, and 3D arrays, each of
+which can represent single- or double-precision values. Although these
+arrays store values in a form different from conventional single- and
+double-precision floating point, the user interacts with the arrays via
+floats and doubles.
+
+The description below is for 3D arrays of doubles--the necessary changes
+for other array types should be obvious. To declare and zero initialize
+an array, use
+
+ // declare nx * ny * nz array of compressed doubles
+ zfp::array3<double> a(nx, ny, nz, rate);
+
+This declaration is conceptually equivalent to
+
+ double a[nz][ny][nx] = {};
+
+or
+
+ std::vector<double> a(nx * ny * nz, 0.0);
+
+but with the user specifying the amount of storage used. (A predefined type
+array3d also exists, while the suffix 'f' is used for floats.) Note that
+the array dimensions can be arbitrary, and need not be multiples of four
+(see above for a discussion of incomplete blocks). The 'rate' argument
+specifies how many bits per value (amortized) to store in the compressed
+representation. By default the block size is restricted to a multiple of
+64 bits, and therefore the rate argument can be specified in increments of
+64 / 4^d bits in d dimensions, i.e.
+
+ 1D arrays: 16-bit granularity
+ 2D arrays: 4-bit granularity
+ 3D arrays: 1-bit granularity
+
+For finer granularity, the BITSTREAM_WORD_TYPE macro needs to be set to a
+type narrower than 64 bits, e.g. if set to uint8 the rate granularity
+becomes 8 / 4^d bits in d dimensions, or
+
+ 1D arrays: 2-bit granularity
+ 2D arrays: 1/2-bit granularity
+ 3D arrays: 1/8-bit granularity
+
+Note that finer granularity implies lower performance. Also note that
+because the arrays are stored compressed, their effective precision is
+likely to be higher than the user-specified rate.
+
+The array can also optionally be initialized from an existing contiguous
+floating-point array stored at 'pointer' with an x stride of 1, y stride
+of nx, and z stride of nx * ny:
+
+ // declare and initialize 3D array of doubles
+ zfp::array3d a(nx, ny, nz, precision, pointer, cache_size);
+
+The 'cache_size' argument specifies the minimum number of bytes to allocate
+for the cache of uncompressed blocks (see the section on Caching below for
+more details).
+
+If not already initialized, a function set() can be used to copy uncompressed
+data to the compressed array:
+
+ const double* pointer; // pointer to uncompressed, initialized data
+ a.set(pointer); // initialize compressed array with floating-point data
+
+Similarly, a get() function exists for retrieving uncompressed data:
+
+ double* pointer; // pointer to where to write uncompressed data
+ a.get(pointer); // decompress and store the array at pointer
+
+The compressed representation of an array can also be queried or initialized
+directly without having to convert to/from its floating-point representation:
+
+ size_t bytes = compressed_size(); // number of bytes of compressed storage
+ uchar* compressed_data(); // pointer to compressed data
+
+The array can through this pointer be initialized from offline compressed
+storage, but only after its dimensions and rate have been specified (see
+above). For this to work properly, the cache must first be emptied via a
+clear_cache() call (see below).
+
+Through operator overloading, the array can be accessed in one of two ways.
+For read accesses, use
+
+ double value = a[index]; // fetch value with given flat array index
+ double value = a(i, j, k); // fetch value with 3D index (i, j, k)
+
+These access the same value if and only if index = i + nx * (j + ny * k).
+Note that 0 <= i < nx, 0 <= j < ny, and 0 <= k < nz, and i varies faster
+than j, which varies faster than k.
+
+Array values may be written and updated using the usual set of C++ assignment
+and compound assignment operators. For example:
+
+ a[index] = value; // set value at flat array index
+ a(i, j, k) += value; // increment value with 3D index (i, j, k)
+
+Whereas one might expect these operators to return a (non-const) reference
+to an array element, this would allow seating a reference to a value that
+currently is cached but is transient, which could be unsafe. Moreover,
+this would preclude detecting when an array element is modified. Therefore,
+the return type of both operators [] and () is a proxy reference class,
+similar to std::vector<bool>::reference from the STL library. Because
+read accesses to a mutable object cannot call the const-qualified accessor,
+a proxy reference may be returned even for read calls, e.g. in
+
+ a[i - 1] = a[i];
+
+the array a clearly must be mutable to allow assignment to a[i - 1], and
+therefore the read access a[i] returns type zfp::array3d::reference. The
+value associated with the read access is obtained via an implicit conversion.
+
+Array dimensions (nx, ny, nz) can be queried using these functions:
+
+ size_t size(); // total number of elements nx * ny * nz
+ uint size_x(); // nx
+ uint size_y(); // ny
+ uint size_z(); // nz
+
+The array dimensions can also be changed dynamically, e.g. if not known
+at declaration time, using
+
+ void resize(uint nx, uint ny, uint nz, bool clear = true);
+
+When clear = true, the array is explicitly zeroed. In either case, all
+previous contents of the array are lost. If nx = ny = nz = 0, all storage
+is freed.
+
+Finally, the rate supported by the array may be queried via
+
+ double rate(); // number of compressed bits per value
+
+and changed using
+
+ void set_rate(rate); // change rate
+
+This also destroys prior contents.
+
+
+CACHING
+
+As mentioned above, the array class maintains a software write-back cache
+of at least one uncompressed block. When a block in this cache is evicted
+(e.g. due to a conflict), it is compressed back to permanent storage only
+if it has previously been modified.
+
+The size cache to use is specified by the user, and is an important
+parameter that needs careful consideration in order to balance the extra
+memory usage, performance, and quality (recall that data loss is incurred
+only when a block is evicted from the cache and compressed). Although the
+best choice varies from one application to another, we suggest allocating
+at least two layers of blocks (2 * (nx / 4) * (ny / 4) blocks) for
+applications that stream through the array and perform stencil computations
+such as gathering data from neighboring elements. This allows limiting the
+cache misses to compulsory ones. If the cache_size parameter is set to
+zero bytes, then this default of two layers is used.
+
+The cache size can be set during construction, or can be set at a later
+time via
+
+ void set_cache_size(bytes); // change cache size
+
+Note that if bytes = 0, then the array dimensions must have already been
+specified for the default size to be computed correctly. When the cache
+is resized, it is first flushed if not already empty. The cache can
+also be flushed explicitly if desired by calling
+
+ void flush_cache(); // empty cache by first compressing any modified blocks
+
+To empty the cache without compressing any cached data, call
+
+ void clear_cache(); // empty cache without compression
+
+To query the byte size of the cache, use
+
+ size_t cache_size(); // actual cache size in bytes
diff --git a/src/zfp/zfp-0.5.0/Config b/src/zfp/zfp-0.5.0/Config
new file mode 100644
index 0000000..663804c
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/Config
@@ -0,0 +1,49 @@
+# compiler settings -----------------------------------------------------------
+
+# GNU compiler
+CC = gcc
+CXX = g++
+FLAGS = -O3 -fPIC -Wall -I../inc $(DEFS)
+CFLAGS = $(FLAGS) -std=c89 -Wno-unused-function
+#CFLAGS = $(FLAGS) -std=c99
+CXXFLAGS = $(FLAGS) -std=c++98
+
+# IBM compiler
+# CC = xlc
+# CXX = xlc++
+# CFLAGS = -O2 -qmaxmem=-1 -qpic=large -I../inc $(DEFS)
+# CXXFLAGS= $(CFLAGS)
+
+# optional compiler macros ----------------------------------------------------
+
+# use smaller bit stream word type for finer rate granularity
+# DEFS += -DBIT_STREAM_WORD_TYPE=uint8
+# DEFS += -DBIT_STREAM_WORD_TYPE=uint16
+# DEFS += -DBIT_STREAM_WORD_TYPE=uint32
+
+# enable strided access for progressive zfp streams
+# DEFS += -DBIT_STREAM_STRIDED
+
+# run regression test with medium sized arrays
+# DEFS += -DTESTZFP_MEDIUM_ARRAYS
+
+# run regression test with large arrays
+# DEFS += -DTESTZFP_LARGE_ARRAYS
+
+# run diffusion without compression
+# DEFS += -DWITHOUT_COMPRESSION
+
+# use aligned memory allocation
+# DEFS += -DALIGNED_ALLOC
+
+# use two-way skew-associative cache
+# DEFS += -DCACHE_TWOWAY
+
+# use faster but more collision prone hash function
+# DEFS += -DCACHE_FAST_HASH
+
+# count cache misses
+# DEFS += -DCACHE_PROFILE
+
+# for recent versions of MSVC
+# DEFS += -DHAVE_C99_MATH
diff --git a/src/zfp/zfp-0.5.0/FAQ b/src/zfp/zfp-0.5.0/FAQ
new file mode 100644
index 0000000..c822231
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/FAQ
@@ -0,0 +1,371 @@
+The following is a list of answers to frequently asked questions. For
+questions not answered here or elsewhere in the documentation, please
+e-mail the author at pl at llnl.gov.
+
+Questions answered in this FAQ:
+
+ Q1: Can zfp compress vector fields?
+ Q2: Should I declare a 2D array as zfp::array1d a(nx * ny, rate)?
+ Q3: How can I initialize a zfp compressed array from disk?
+ Q4: Can I use zfp to represent dense matrices?
+ Q5: Can zfp compress logically regular but geometrically irregular data?
+ Q6: Does zfp handle infinities, NaNs, and denormal floating-point numbers?
+ Q7: Can zfp handle data with some missing values?
+ Q8: Can I use zfp to store integer data?
+ Q9: Can I compress 32-bit integers using zfp?
+Q10: Why does zfp corrupt memory if my allocated buffer is too small?
+Q11: Are zfp compressed streams portable across platforms?
+Q12: How can I achieve finer rate granularity?
+Q13: Can I generate progressive zfp streams?
+Q14: How do I initialize the decompressor?
+Q15: Must I use the same parameters during compression and decompression?
+Q16: Do strides have to match during compression and decompression?
+Q17: Why does zfp sometimes not respect my error tolerance?
+
+-------------------------------------------------------------------------------
+
+Q1: I have a 2D vector field
+
+ double velocity[ny][nx][2];
+
+of dimensions nx * ny. Can I use a 3D zfp array to store this as
+
+ array3d velocity(2, nx, ny, rate);
+
+A: Although this could be done, zfp assumes that consecutive values are
+related. The two velocity components (vx, vy) are almost suredly independent,
+and would not exhibit smoothness. This will severely hurt the compression
+rate or quality. Instead, consider storing vx and vy as two separate 2D
+scalar arrays
+
+ array2d vx(nx, ny, rate);
+ array2d vy(nx, ny, rate);
+
+or as
+
+ array2d velocity[2] = {array2d(nx, ny, rate), array2d(nx, ny, rate)};
+
+-------------------------------------------------------------------------------
+
+Q2: I have a 2D scalar field of dimensions nx * ny that I allocate as
+
+ double* a = new double[nx * ny];
+
+and index as
+
+ a[x + nx * y]
+
+Should I use a corresponding zfp array
+
+ array1d a(nx * ny, rate);
+
+to store my data in compressed form?
+
+A: Although this is certainly possible, if the scalar field exhibits
+coherence in both spatial dimensions, then far better results can be
+achieved by using a 2D array
+
+ array2d a(nx, ny, rate);
+
+Although both compressed arrays can be indexed as above, the 2D array can
+exploit smoothness in both dimensions and improve the quality dramatically
+for the same rate.
+
+-------------------------------------------------------------------------------
+
+Q3: I have a large, uncompressed, 3D data set
+
+ double a[nz][ny][nx];
+
+stored on disk that I would like to read into a compressed array. This data
+set will not fit in memory uncompressed. What is the best way of doing this?
+
+A: Using a zfp array
+
+ array3d a(nx, ny, nz, rate);
+
+the most straightforward way is to read one floating-point value at a time
+and copy it into the array:
+
+ for (uint z = 0; z < nz; z++)
+ for (uint y = 0; y < ny; y++)
+ for (uint x = 0; x < nx; x++) {
+ double f;
+ if (fread(&f, sizeof(f), 1, file) == 1)
+ a(x, y, z) = f;
+ else
+ // handle I/O error
+ }
+
+Note, however, that if the array cache is not large enough, then this may
+compress blocks before they have been completely filled. Therefore it is
+recommended that the cache holds at least one complete layer of blocks,
+i.e. (nx / 4) * (ny / 4) blocks in the example above.
+
+-------------------------------------------------------------------------------
+
+Q4: Can I use zfp to represent dense matrices?
+
+A: Yes, but your mileage may vary. Dense matrices, unlike smooth scalar
+fields, rarely exhibit correlation between adjacent rows and columns. Thus,
+the quality or compression ratio may suffer.
+
+-------------------------------------------------------------------------------
+
+Q5: My data is logically structured but irregularly sampled, e.g. it is
+rectilinear, curvilinear, or Lagrangian, or uses an irregular spacing of
+quadrature points. Can I still use zfp to compress it?
+
+A: Yes, as long as the data is (or can be) represented as a logical
+multidimensional array, though your mileage may vary. zfp has been designed
+for uniformly sampled data, and compression will in general suffer the more
+irregular the sampling is.
+
+-------------------------------------------------------------------------------
+
+Q6: Does zfp handle infinities and NaNs? What about denormal floating-point
+numbers?
+
+A: No, only finite, valid floating-point values are supported. If a block
+contains a NaN or an infinity, undefined behavior is invoked due to the
+C math function frexp being undefined for non-numbers. Denorms are, however,
+handled correctly.
+
+-------------------------------------------------------------------------------
+
+Q7: My data has some missing values that are flagged by very large numbers,
+e.g. 1e30. Is that OK?
+
+A: Although all finite numbers are "correctly" handled, such large sentinel
+values are likely to pollute nearby values, because all values within a block
+are expressed with respect to a common largest exponent. The presence of
+very large values may result in complete loss of precision of nearby, valid
+numbers. Currently no solution to this problem is available, but future
+versions of zfp will likely support a bit mask to tag values that should be
+excluded from compression.
+
+-------------------------------------------------------------------------------
+
+Q8: Can I use zfp to store integer data such as 8-bit quantized images or
+16-bit digital elevation models?
+
+A: Yes (as of version 0.4.0), but the data has to be promoted to 32-bit signed
+integers first. This should be done one block at a time using an appropriate
+zfp_promote_*_to_int32 function call (see zfp.h). Note that these functions
+shift the low-precision integers into the most significant bits of 31-bit (not
+32-bit) integers and also convert unsigned to signed integers. Do use these
+functions rather than simply casting 8-bit integers to 32 bits to avoid wasting
+compressed bits to encode leading zeros. Moreover, in fixed-precision mode,
+set the precision relative to the precision of the source data.
+
+-------------------------------------------------------------------------------
+
+Q9: I have some 32-bit integer data. Can I compress it using zfp's 32-bit
+integer support?
+
+A: Maybe. zfp compression of 32-bit and 64-bit integers requires that each
+integer f have magnitude |f| < 2^30 and |f| < 2^62, respectively. To handle
+signed integers that span the entire range -2^31 <= x < 2^31, or unsigned
+integers 0 <= x < 2^32, the data has to be promoted to 64 bits first.
+
+-------------------------------------------------------------------------------
+
+Q10: Why does zfp corrupt memory rather than return an error code if not enough
+memory is allocated for the compressed data?
+
+A: This is for performance reasons. zfp was primarily designed for fast
+random access to fixed-rate compressed arrays, where checking for buffer
+overruns is unnecessary. Adding a test for every compressed byte output
+would significantly compromise performance.
+
+One way around this problem (when not in fixed-rate mode) is to use the
+maxbits parameter in conjunction with the maximum precision or maximum
+absolute error parameters to limit the size of compressed blocks. Finally,
+the function zfp_stream_maximum_size returns a conservative buffer size
+that is guaranteed to be large enough to hold the compressed data and the
+optional header.
+
+-------------------------------------------------------------------------------
+
+Q11: Are zfp compressed streams portable across platforms? Are there, for
+example, endianness issues?
+
+A: To ensure portability across different endian platforms, the bit stream
+must be written in increments of single bytes on big endian processors (e.g.
+PowerPC, SPARC), which is achieved by compiling zfp with
+
+ -DBITSTREAM_WORD_TYPE=uint8
+
+See the Config file. Note that on little endian processors (e.g. Intel
+x86-64 and AMD64), the word size does not affect the bit stream produced,
+and thus the default word size may be used. By default, zfp uses a word
+size of 64 bits, which results in the coarsest rate granularity but fastest
+(de)compression. If cross-platform portability is not needed, then the
+maximum word size is recommended (but see also the next question).
+
+Furthermore, zfp assumes that the floating-point format conforms to IEEE 754.
+Issues may arise on architectures that do not support IEEE floating point.
+
+-------------------------------------------------------------------------------
+
+Q12: How can I achieve finer rate granularity?
+
+A: For d-dimensional arrays, zfp supports a granularity of 8 / 4^d bits, i.e.
+the rate can be specified in increments of a fraction of a bit for 2D and 3D
+arrays. Such fine rate selection is always available for sequential
+compression (e.g. when calling zfp_compress).
+
+Unlike in sequential compression, zfp's compressed arrays require random
+access writes, which are supported only at the granularity of whole words.
+By default, a word is 64 bits, which gives a rate granularity of 64 / 4^d
+in d dimensions, i.e. 16 bits in 1D, 4 bits in 2D, and 1 bit in 3D.
+
+To achieve finer granularity, recompile zfp with a smaller (but as large as
+possible) stream word size, e.g.
+
+ -DBITSTREAM_WORD_TYPE=uint8
+
+gives the finest possible granularity, but at the expense of (de)compression
+speed. See the Config file.
+
+-------------------------------------------------------------------------------
+
+Q13: Can I generate progressive zfp streams?
+
+A: Yes, but it requires some coding effort. There is no high-level support
+for progressive zfp streams. To implement progressive fixed-rate streams,
+the fixed-length bit streams should be interleaved among the blocks that
+make up an array. For instance, if a 3D array uses 1024 bits per block,
+then those 1024 bits could be broken down into, say, 16 pieces of 64 bits
+each, resulting in 16 discrete quality settings. By storing the blocks
+interleaved such that the first 64 bits of all blocks are contiguous,
+followed by the next 64 bits of all blocks, etc., one can achieve progressive
+decompression by setting the maxbits parameter (see zfp_stream_set_params)
+to the number of bits per block received so far.
+
+To enable interleaving of blocks, zfp must first be compiled with
+
+ -DBIT_STREAM_STRIDED
+
+to enable strided bit stream access. In the example above, if the stream
+word size is 64 bits and there are n blocks, then
+
+ stream_set_stride(stream, m, n);
+
+implies that after every m 64-bit words have been decoded, the bit stream
+is advanced by m * n words to the next set of m 64-bit words associated
+with the block.
+
+-------------------------------------------------------------------------------
+
+Q14: How do I initialize the decompressor?
+
+A: The zfp_stream and zfp_field objects usually need to be initialized with
+the same values as they had during compression (but see Q15 for exceptions).
+These objects hold the compression mode and parameters, and field data like
+the scalar type and dimensions. By default, these parameters are not stored
+with the compressed stream (the "codestream") and prior to zfp 0.5.0 had to
+be maintained separately by the application.
+
+Since version 0.5.0, functions exist for reading and writing a 12- to 19-byte
+header that encodes compression and field parameters. For applications that
+wish to embed only the compression parameters, e.g. when the field dimensions
+are already known, there are separate functions that encode and decode this
+information independently.
+
+-------------------------------------------------------------------------------
+
+Q15: Must I use the same parameters during compression and decompression?
+
+A: Not necessarily. It is possible to use more tightly constrained zfp_stream
+parameters during decompression than were used during compression. For
+instance, one may use a larger minbits, smaller maxbits, smaller maxprec, or
+larger minexp during decompression to process fewer compressed bits than are
+stored, and to decompress the array more quickly at a lower precision. This
+may be useful in situations where the precision and accuracy requirements are
+not known a priori, thus forcing conservative settings during compression, or
+when the compressed stream is used for multiple purposes. For instance,
+visualization usually has less stringent precision requirements than
+quantitative data analysis. This feature of decompressing to a lower precision
+is particularly useful when the stream is stored progressively (see Q13).
+
+Note that one may not use less constrained parameters during decompression,
+e.g. one cannot ask for more than maxprec bits of precision when decompressing.
+
+-------------------------------------------------------------------------------
+
+Q16: Do strides have to match during compression and decompression?
+
+A: No. For instance, a 2D vector field
+
+ float in[ny][nx][2];
+
+could be compressed as two scalar fields with strides sx = 2, sy = 2 * nx,
+and with pointers &in[0][0][0] and &in[0][0][1] to the first value of each
+scalar field. These two scalar fields can later be decompressed as
+non-interleaved fields
+
+ float out[2][ny][nx];
+
+using strides sx = 1, sy = nx and pointers &out[0][0][0] and &out[1][0][0].
+
+-------------------------------------------------------------------------------
+
+Q17: Why does zfp sometimes not respect my error tolerance?
+
+A: zfp does not store each floating-point value independently, but represents
+a group of values (4, 16, or 64 values, depending on dimensionality) as linear
+combinations like averages by evaluating arithmetic expressions. Just like in
+uncompressed IEEE floating-point arithmetic, both representation error and
+roundoff error in the least significant bit(s) often occur.
+
+To illustrate this, consider compressing the following 1D array of four floats
+
+ float f[4] = { 1, 1e-1, 1e-2, 1e-3 };
+
+using the zfp command-line tool:
+
+ zfp -f -a 0 4 0 0 input.dat output.dat
+
+In spite of an error tolerance of zero, the reconstructed values are
+
+ float g[4] = { 1, 1e-1, 9.999998e-03, 9.999946e-04 };
+
+with a (computed) maximum error of 5.472e-9. Because f[3] = 1e-3 can only
+be approximately represented in radix-2 floating-point, the actual error
+is even smaller: 5.424e-9. This reconstruction error is primarily due to zfp's
+block-floating-point representation, which expresses the four values relative
+to a single, common binary exponent. Such exponent alignment occurs also in
+regular IEEE floating-point operations like addition. For instance,
+
+ float x = (f[0] + f[3]) - 1;
+
+should of course result in x = f[3] = 1e-3, but due to exponent alignment
+a few of the least significant bits of f[3] are lost in the addition, giving
+a result of x = 1.0000467e-3 and a roundoff error of 4.668e-8. Similarly,
+
+ float sum = f[0] + f[1] + f[2] + f[3];
+
+should return sum = 1.111, but is computed as 1.1110000610. Moreover, the
+value 1.111 cannot even be represented exactly in (radix-2) floating-point;
+the closest float is 1.1109999. Thus the computed error
+
+ float error = sum - 1.111f;
+
+which itself has some roundoff error, is 1.192e-7.
+
+Phew! Note how the error introduced by zfp (5.472e-9) is in fact one to two
+orders of magnitude smaller than the roundoff errors (4.668e-8 and 1.192e-7)
+introduced by IEEE floating-point in these computations. This lower error
+is in part due to zfp's use of 30-bit significands compared to IEEE's 24-bit
+single-precision significands. Note that data sets with a large dynamic
+range, e.g. where adjacent values differ a lot in magnitude, are more
+susceptible to representation errors.
+
+The moral of the story is that error tolerances smaller than machine epsilon
+(relative to the data range) cannot always be satisfied by zfp. Nor are such
+tolerances necessarily meaningful for representing floating-point data that
+originated in floating-point arithmetic expressions, since accumulated
+roundoff errors are likely to swamp compression errors. Because such roundoff
+errors occur frequently in floating-point arithmetic, insisting on lossless
+compression on the grounds of accuracy is tenuous at best.
diff --git a/src/zfp/zfp-0.5.0/LICENSE b/src/zfp/zfp-0.5.0/LICENSE
new file mode 100644
index 0000000..b8275dc
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/LICENSE
@@ -0,0 +1,57 @@
+Copyright (c) 2014-2016, Lawrence Livermore National Security, LLC.
+Produced at the Lawrence Livermore National Laboratory.
+Written by Peter Lindstrom.
+LLNL-CODE-663824.
+All rights reserved.
+
+This file is part of the zfp library.
+For details, see http://computation.llnl.gov/casc/zfp/.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+this list of conditions and the disclaimer below.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the disclaimer (as noted below) in the
+documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the LLNS/LLNL nor the names of its contributors may
+be used to endorse or promote products derived from this software without
+specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL LAWRENCE LIVERMORE NATIONAL SECURITY,
+LLC, THE U.S. DEPARTMENT OF ENERGY OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
+THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+Additional BSD Notice
+
+1. This notice is required to be provided under our contract with the U.S.
+Department of Energy (DOE). This work was produced at Lawrence Livermore
+National Laboratory under Contract No. DE-AC52-07NA27344 with the DOE.
+
+2. Neither the United States Government nor Lawrence Livermore National
+Security, LLC nor any of their employees, makes any warranty, express or
+implied, or assumes any liability or responsibility for the accuracy,
+completeness, or usefulness of any information, apparatus, product, or
+process disclosed, or represents that its use would not infringe
+privately-owned rights.
+
+3. Also, reference herein to any specific commercial products, process, or
+services by trade name, trademark, manufacturer or otherwise does not
+necessarily constitute or imply its endorsement, recommendation, or
+favoring by the United States Government or Lawrence Livermore National
+Security, LLC. The views and opinions of authors expressed herein do not
+necessarily state or reflect those of the United States Government or
+Lawrence Livermore National Security, LLC, and shall not be used for
+advertising or product endorsement purposes.
diff --git a/src/zfp/zfp-0.5.0/Makefile b/src/zfp/zfp-0.5.0/Makefile
new file mode 100644
index 0000000..ddaa91d
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/Makefile
@@ -0,0 +1,16 @@
+MAKEFLAGS += --no-print-directory
+
+all:
+ @cd src; $(MAKE) clean static
+ @cd examples; $(MAKE) clean all
+
+shared:
+ @cd src; $(MAKE) shared
+
+test:
+ @cd examples; $(MAKE) test
+
+clean:
+ @cd src; $(MAKE) clean
+ @cd examples; $(MAKE) clean
+
diff --git a/src/zfp/zfp-0.5.0/README b/src/zfp/zfp-0.5.0/README
new file mode 100644
index 0000000..9f50d39
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/README
@@ -0,0 +1,422 @@
+INTRODUCTION
+
+ This is zfp 0.5.0, an open source C/C++ library for compressed numerical
+ arrays that support high throughput read and write random access. zfp was
+ written by Peter Lindstrom at Lawrence Livermore National Laboratory, and
+ is loosely based on the algorithm described in the following paper:
+
+ Peter Lindstrom
+ "Fixed-Rate Compressed Floating-Point Arrays"
+ IEEE Transactions on Visualization and Computer Graphics,
+ 20(12):2674-2683, December 2014
+ doi:10.1109/TVCG.2014.2346458
+
+ zfp was originally designed for floating-point data only, but has been
+ extended to also support integer data, and could for instance be used to
+ compress images and quantized volumetric data. To achieve high compression
+ ratios, zfp uses lossy but optionally error-bounded compression. Although
+ bit-for-bit lossless compression of floating-point data is not always
+ possible, zfp is usually accurate to within machine epsilon in near-lossless
+ mode.
+
+ zfp works best for 2D and 3D arrays that exhibit spatial coherence, such
+ as smooth fields from physics simulations, images, regularly sampled terrain
+ surfaces, etc. Although zfp also provides a 1D array class that can be used
+ for 1D signals such as audio, or even unstructured floating-point streams,
+ the compression scheme has not been well optimized for this use case, and
+ rate and quality may not be competitive with floating-point compressors
+ designed specifically for 1D streams.
+
+ zfp is freely available as open source under a BSD license, as outlined in
+ the file 'LICENSE'. For information on the API and general usage, please
+ see the file 'API' in this directory.
+
+
+INSTALLATION
+
+ zfp consists of three distinct parts: a compression library written in C;
+ a set of C++ header files that implement compressed arrays; and a set of
+ C and C++ examples. The main compression codec is written in C and should
+ conform to both the ISO C89 and C99 standards. The C++ array classes are
+ implemented entirely in header files and can be included as is, but since
+ they call the compression library applications must link with libzfp.
+
+ To compile libzfp and all example programs (see below for more details)
+ on Linux or OS X, type
+
+ make
+
+ from this directory. This compiles libzfp as a static library and the
+ example programs. To optionally create a shared library, type
+
+ make shared
+
+ and set LD_LIBRARY_PATH to point to ./lib. To test the compressor, type
+
+ make test
+
+ If the compilation or regression tests fail, it is possible that some of
+ the macros in the file 'Config' have to be adjusted. Also, the tests may
+ fail due to minute differences in the computed floating-point fields
+ being compressed (as indicated by checksum errors). It is surprisingly
+ difficult to portably generate a floating-point array that agrees
+ bit-for-bit across platforms. If most tests succeed and the failures
+ result in byte sizes and error values reasonably close to the expected
+ values, then it is likely that the compressor is working correctly.
+
+ NOTE: zfp requires 64-bit compiler and operating system support.
+
+ zfp has successfully been built and tested using these compilers:
+
+ gcc versions 4.4.7, 4.7.2, 4.8.2, 4.9.2, 5.1.0
+ icc versions 12.0.5, 12.1.5, 15.0.4, 16.0.1
+ clang versions 3.4.2, 3.6.0
+ xlc version 12.1
+ mingw32-gcc version 4.8.1
+
+
+ALGORITHM OVERVIEW
+
+ The zfp lossy compression scheme is based on the idea of breaking a
+ d-dimensional array into independent blocks of 4^d values, e.g. 4x4x4
+ values in three dimensions. Each block is compressed/decompressed
+ entirely independently from all other blocks. In this sense, zfp is
+ similar to current hardware texture compression schemes for image
+ coding implemented on graphics cards and mobile devices.
+
+ The compression scheme implemented in this version of zfp has evolved
+ from the method described in the paper cited above, and can conceptually
+ be thought of as consisting of eight sequential steps (in practice some
+ steps are consolidated or exist only for illustrative purposes):
+
+ (1) The d-dimensional array is partitioned into blocks of dimensions 4^d.
+ If the array dimensions are not multiples of four, then blocks near the
+ boundary are padded to the next multiple of four. This padding is
+ invisible to the application.
+
+ (2) The independent floating-point values in a block are converted to what
+ is known as a block-floating-point representation, which uses a single,
+ common floating-point exponent for all 4^d values. The effect of this
+ conversion is to turn each floating-point value into a 31- or 63-bit
+ signed integer. Note that this step is not performed if the input data
+ already consists of integers.
+
+ (3) The integers are decorrelated using a custom, high-speed, near
+ orthogonal transform similar to the discrete cosine transform used in
+ JPEG image coding. The transform exploits separability and is implemented
+ efficiently in-place using the lifting scheme, requiring only 2.5*d
+ integer additions and 1.5*d bit shifts by one per integer in d dimensions.
+ If the data is "smooth," then this transform will turn most integers into
+ small signed values clustered around zero.
+
+ (4) The two's complement signed integers are converted to their negabinary
+ (base negative two) representation using one addition and one bit-wise
+ exclusive or per integer. Because negabinary has no dedicated single sign
+ bit, these integers are subsequently treated as unsigned.
+
+ (5) The unsigned integer coefficients are reordered in a manner similar to
+ JPEG zig-zag ordering so that statistically they appear in a roughly
+ monotonically decreasing order. Coefficients corresponding to low
+ frequencies tend to have larger magnitude, and are listed first. In 3D,
+ coefficients corresponding to frequencies i, j, k in the three dimensions
+ are ordered by i + j + k first, and then by i^2 + j^2 + k^2.
+
+ (6) The bits that represent the list of 4^d integers are now ordered by
+ coefficient. These bits are transposed so that they are instead ordered
+ by bit plane, from most to least significant bit. Viewing each bit plane
+ as an integer, with the lowest bit corresponding to the lowest frequency
+ coefficient, the anticipation is that the first several of these transposed
+ integers are small, because the coefficients are assumed to be ordered by
+ magnitude.
+
+ (7) The transform coefficients are compressed losslessly using embedded
+ coding by exploiting the property that the coefficients tend to have many
+ leading zeros that need not be encoded explicitly. Each bit plane is
+ encoded in two parts, from lowest to highest bit. First the n lowest bits
+ are emitted verbatim, where n depends on previous bit planes and is
+ initially zero. Then a variable-length representation, x, of the
+ remaining 4^d - n bits is encoded. For such an integer x, a single bit is
+ emitted to indicate if x = 0, in which case we are done with the current
+ bit plane. If not, then bits of x are emitted, starting from the lowest
+ bit, until a one bit is emitted. This triggers another test whether this
+ is the highest set bit of x, and the result of this test is output as a
+ single bit. If not, then the procedure repeats until all n of x's value
+ bits have been output, where 2^(n-1) <= x < 2^n. This can be thought of
+ as a run-length encoding of the zeros of x, where the run lengths are
+ expressed in unary. The current value of n is then passed on to the next
+ bit plane, which is encoded by first emitting its n lowest bits. The
+ assumption is that these bits correspond to n coefficients whose most
+ significant bits have already been output, i.e. these n bits are
+ essentially random and not compressible. Following this, the remaining
+ 4^d - n bits of the bit plane are run-length encoded as described above,
+ which potentially results in n being increased.
+
+ (8) The embedded coder emits one bit at a time, with each successive bit
+ potentially improving the quality of the reconstructed signal. The early
+ bits are most important and have the greatest impact on signal quality,
+ with the last few bits providing very small changes. The resulting
+ compressed bit stream can be truncated at any point and still allow for a
+ valid approximate reconstruction of the original signal. The final step
+ truncates the bit stream in one of three ways: to a fixed number of bits
+ (the fixed-rate mode); after some fixed number of bit planes have been
+ encoded (the fixed-precision mode); or until a lowest bit plane number has
+ been encoded, as expressed in relation to the common floating-point
+ exponent within the block (the fixed-accuracy mode).
+
+ Various parameters are exposed for controlling the quality and compressed
+ size of a block, and can be specified by the user at a very fine
+ granularity. These parameters are discussed below.
+
+
+CODE EXAMPLES
+
+ The 'examples' directory includes six programs that make use of the
+ compressor.
+
+ The 'simple' program is a minimal example that shows how to call the
+ compressor and decompressor on a double-precision 3D array. Without
+ the '-d' option, it will compress the array and write the compressed
+ stream to standard output. With the '-d' option, it will instead
+ read the compressed stream from standard input and decompress the
+ array:
+
+ simple > compressed.zfp
+ simple -d < compressed.zfp
+
+ For a more elaborate use of the compressor, see the 'zfp' example.
+
+ The 'diffusion' example is a simple forward Euler solver for the heat
+ equation on a 2D regular grid, and is intended to show how to declare
+ and work with zfp's compressed arrays, as well as give an idea of how
+ changing the compression rate affects the error in the solution. The
+ usage is:
+
+ diffusion-zfp [rate] [nx] [ny] [nt]
+
+ where 'rate' specifies the exact number of compressed bits to store per
+ double-precision floating-point value (default = 64); 'nx' and 'ny'
+ specify the grid size (default = 100x100); and 'nt' specifies the number
+ of time steps to run (the default is to run until time t = 1).
+
+ Running diffusion with the following arguments
+
+ diffusion-zfp 8
+ diffusion-zfp 12
+ diffusion-zfp 20
+ diffusion-zfp 64
+
+ should result in this output
+
+ rate=8 sum=0.996442 error=4.813938e-07
+ rate=12 sum=0.998338 error=1.967777e-07
+ rate=20 sum=0.998326 error=1.967952e-07
+ rate=64 sum=0.998326 error=1.967957e-07
+
+ For speed and quality comparison, diffusion-raw solves the same problem
+ using uncompressed double-precision arrays.
+
+ The 'zfp' program is primarily intended for evaluating the rate-distortion
+ (compression ratio and quality) provided by the compressor, but since
+ version 0.5.0 also allows reading and writing compressed data sets. zfp
+ takes as input a raw, binary array of floats or doubles, and optionally
+ outputs a compressed or reconstructed array obtained after lossy
+ compression followed by decompression. Various statistics on compression
+ rate and error are also displayed.
+
+ zfp requires a set of command-line options, the most important being the
+ -i option that specifies that the input is uncompressed. When present,
+ "-i <file>" tells zfp to read the uncompressed input file and compress it
+ to memory. If desired, the compressed stream can be written to an ouptut
+ file using "-z <file>". When -i is absent, on the other hand, -z names
+ the compressed input (not output) file, which is then decompressed. In
+ either case, "-o <file>" can be used to output the reconstructed array
+ resulting from lossy compression and decompression.
+
+ So, to compress a file, use "-i file.in -z file.zfp". To later decompress
+ the file, use "-z file.zfp -o file.out". A single dash "-" can be used in
+ place of a file name to denote standard input or output.
+
+ When reading uncompressed input, the floating-point precision (single or
+ double) must be specified using either -f (float) or -d (double). In
+ addition, the array dimensions must be specified using "-1 nx" (for 1D
+ arrays), "-2 nx ny" (for 2D arrays), or "-3 nx ny nz" (for 3D arrays).
+ For multidimensional arrays, x varies faster than y, which in turn varies
+ faster than z. That is, a 3D input file should correspond to a flattened
+ C array declared as a[nz][ny][nx].
+
+ Note that "-2 nx ny" is not equivalent to "-3 nx ny 1", even though the
+ same number of values are compressed. One invokes the 2D codec, while the
+ other uses the 3D codec, which in this example has to pad the input to an
+ nx * ny * 4 array since arrays are partitioned into blocks of dimensions
+ 4^d. Such padding usually negatively impacts compression.
+
+ Using -h, the array dimensions and type are stored in a header of the
+ compressed stream so that they do not have to be specified on the command
+ line during decompression. The header also stores compression parameters,
+ which are described below.
+
+ zfp accepts several options for specifying how the data is to be compressed.
+ The most general of these, the -c option, takes four constraint parameters
+ that together can be used to achieve various effects. These constraints
+ are:
+
+ minbits: the minimum number of bits used to represent a block
+ maxbits: the maximum number of bits used to represent a block
+ maxprec: the maximum number of bit planes encoded
+ minexp: the smallest bit plane number encoded
+
+ Options -r, -p, and -a provide a simpler interface to setting all of
+ the above parameters (see below). Bit plane e refers to those bits whose
+ place value is 2^e. For instance, in single precision, bit planes -149
+ through 127 are supported (when also counting denormalized numbers); for
+ double precision, bit planes -1074 through 1023 are supported.
+
+ Care must be taken to allow all constraints to be met, as encoding
+ terminates as soon as a single constraint is violated (except minbits,
+ which is satisfied at the end of encoding by padding zeros). The effects
+ of the above four parameters are best explained in terms of the three main
+ compression modes supported by zfp (see Algorithm Overview above for
+ additional details):
+
+ Fixed rate (option -r):
+ In fixed-rate mode, each compressed block of 4^d values in d dimensions
+ is stored using a fixed number of bits specified by the user. This can
+ be achieved using option -c by setting minbits = maxbits, maxprec = 64,
+ and minexp = -1074. The fixed-rate mode is needed to support random
+ access to blocks, where the amortized number of bits used per value is
+ given by rate = maxbits / 4^d. Note that each block stores a leading
+ all-zeros bit and common exponent, and maxbits must be at least 9 for
+ single precision and 12 for double precision.
+
+ Fixed precision (option -p):
+ In fixed-precision mode, the number of bits used to encode a block may
+ vary, but the number of bit planes (i.e. the precision) encoded for the
+ transform coefficients is fixed. This mode is achieved by specifying
+ the precision in maxprec and fully relaxing the size constraints, i.e.
+ minbits = 0, maxbits = 4171, and minexp = -1074. Fixed-precision
+ mode is preferable when relative rather than absolute errors matter.
+
+ Fixed accuracy (option -a):
+ In fixed-accuracy mode, all transform coefficient bit planes up to a
+ minimum bit plane number are encoded. (The actual minimum bit plane
+ is not necessarily minexp, but depends on the dimensionality of the
+ data. The reason for this is that the inverse transform incurs range
+ expansion, and the amount of expansion depends on the number of
+ dimensions.) Thus, minexp should be interpreted as the base-2 logarithm
+ of an absolute error tolerance. In other words, given an uncompressed
+ value f and a reconstructed value g, the absolute difference |f - g|
+ is guaranteed to be at most 2^minexp. (Note that it is not possible to
+ guarantee error tolerances smaller than machine epsilon relative to the
+ largest value within a block.) This error tolerance is not always tight
+ (especially for 3D arrays), but can conservatively be set so that even
+ for worst-case inputs the error tolerance is respected. To achieve
+ fixed accuracy to within 'tolerance', use the -a <tolerance> option,
+ which sets minexp = floor(log2(tolerance)), minbits = 0, maxbits = 4171,
+ and maxprec = 64. As in fixed-precision mode, the number of bits used
+ per block is not fixed but is dictated by the data. Use -a 0 to achieve
+ near-lossless compression. Fixed-accuracy mode gives the highest quality
+ (in terms of absolute error) for a given compression rate, and is
+ preferable when random access is not needed.
+
+ As mentioned above, other combinations of constraints can be used.
+ For example, to ensure that the compressed stream is not larger than
+ the uncompressed one, or that it fits within the amount of memory
+ allocated, one may in conjunction with other constraints set
+ maxbits = 4^d * CHAR_BIT * sizeof(Type), where Type is either float or
+ double. The minbits parameter is useful only in fixed-rate mode--when
+ minbits = maxbits, zero-bits are padded to blocks that compress to fewer
+ than maxbits bits.
+
+ The 'speed' program takes two optional parameters:
+
+ speed [rate] [blocks]
+
+ It measures the throughput of compression and decompression of 3D
+ double-precision data (in megabytes of uncompressed data per second).
+ By default, a rate of 1 bit/value and two million blocks are
+ processed.
+
+ The 'pgm' program illustrates how zfp can be used to compress grayscale
+ images in the pgm format. The usage is:
+
+ pgm <param> <input.pgm >output.pgm
+
+ If param is positive, it is interpreted as the rate in bits per pixel,
+ which ensures that each block of 4x4 pixels is compressed to a fixed
+ number of bits, as in texture compression codecs. If param is negative,
+ then fixed-precision mode is used with precision -param, which tends to
+ give higher quality for the same rate. This use of zfp is not intended
+ to compete with existing texture and image compression formats, but
+ exists merely to demonstrate how to compress 8-bit integer data with zfp.
+
+ Finally, the 'testzfp' program performs regression testing that exercises
+ most of the functionality of libzfp and the array classes. The tests
+ assume the default compiler settings, i.e. with none of the macros in
+ Config defined. By default, small, pregenerated floating-point arrays are
+ used in the test, since they tend to have the same binary representation
+ across platforms, whereas it can be difficult to computationally generate
+ bit-for-bit identical arrays. To test larger arrays, modify the TESTZFP_*
+ macros in Config. When large arrays are used, the (de)compression
+ throughput is also measured and reported in number of uncompressed bytes
+ per second.
+
+
+LIMITATIONS AND MISSING FEATURES
+
+ zfp is released as a beta version with the intent of giving people access
+ to the code and soliciting feedback on how to improve zfp for the first
+ full release. As such, the zfp API is experimental and has not been
+ fixed, and it is entirely possible that future versions will employ a
+ different API or even a different codec.
+
+ Below is a list of known limitations and desirable features that may make
+ it into future versions of zfp.
+
+ - The current version of zfp allows for near lossless compression through
+ suitable parameter choices, but no guarantees are made that bit-for-bit
+ lossless compression is achieved. We envision supporting lossless
+ compression in a future version by compressing the difference between
+ the original data and nearly losslessly compressed data.
+
+ - Special values like infinity and NaN are not supported. Denormalized
+ floating-point numbers are, however, correctly handled. There is an
+ implicit assumption that floating point conforms to IEEE, though
+ extensions to other floating-point formats should be possible with
+ minor effort.
+
+ - No iterators are provided for traversing an array, and currently one
+ has to use integer indexing. Performance could in cases be improved
+ by limiting the traversal to sequential access.
+
+ - It is not possible to access subarrays via pointers, e.g. via
+ double* p = &a[offset]; p[i] = ... A pointer proxy class similar to
+ the reference class would be useful.
+
+ - There currently is no way to make a complete copy of a compressed
+ array, i.e. a = b; does not work for arrays a and b.
+
+ - zfp can potentially provide higher precision than conventional float
+ and double arrays, but the interface currently does not expose this.
+ For example, such added precision could be useful in finite difference
+ computations, where catastrophic cancellation can be an issue when
+ insufficient precision is available.
+
+ - Only single and double precision types are supported. Generalizations
+ to IEEE half and quad precision would be useful. For instance,
+ compressed 64-bit-per-value storage of 128-bit quad-precision numbers
+ could greatly improve the accuracy of double-precision floating-point
+ computations using the same amount of storage.
+
+ - zfp arrays are not thread-safe. We are considering options for
+ supporting multi-threaded access, e.g. for OpenMP parallelization.
+
+ - This version of zfp does not run on the GPU. Some work has been done to
+ port zfp to CUDA, and we expect to release such a version in the future.
+
+
+QUESTIONS, COMMENTS, AND BUG REPORTS
+
+ For bug reports, questions, and suggestions for improvements, please
+ contact Peter Lindstrom at pl at llnl.gov. If you end up using zfp in an
+ application, please consider sharing with the author your success story
+ and/or any issues encountered.
diff --git a/src/zfp/zfp-0.5.0/VERSIONS b/src/zfp/zfp-0.5.0/VERSIONS
new file mode 100644
index 0000000..96d4712
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/VERSIONS
@@ -0,0 +1,161 @@
+zfp 0.5.0, February 29, 2016
+
+ - Modified CODEC to more efficiently encode blocks whose values are all
+ zero or are smaller in magnitude than the absolute error tolerance.
+ This allows representing "empty" blocks using only one bit each. This
+ version is not backwards compatible with prior zfp versions.
+
+ - Changed behavior of zfp_compress and zfp_decompress to not automatically
+ rewind the bit stream. This makes it easier to concatenate multiple
+ compressed bit streams, e.g. when compressing vector fields or multiple
+ scalars together.
+
+ - Added functions for compactly encoding the compression parameters
+ and field meta data, e.g. for producing self-contained compressed
+ streams. Also added functions for reading and writing a header
+ containing these parameters.
+
+ - Changed the zfp example program interface to allow reading and writing
+ compressed streams, optionally with a header. The zfp tool can now be
+ used to compress and decompress files as a stand alone utility.
+
+
+zfp 0.4.1, December 28, 2015
+
+ - Fixed bug that caused segmentation fault when compressing 3D arrays
+ whose dimensions are not multiples of four. Specifically, arrays of
+ dimensions nx * ny * nz, with ny not a multiple of four, were not
+ handled correctly.
+
+ - Modified examples/fields.h to ensure standard compliance. Previously,
+ C99 support was needed to handle the hex float constants, which are
+ not supported in C++98.
+
+ - Added simple.c as a minimal example of how to call the compressor.
+
+ - Changed compilation of diffusion example to output two executables:
+ one with and one without compression.
+
+
+zfp 0.4.0, December 5, 2015
+
+ - Substantial changes to the compression algorithm that improve PSNR
+ by about 6 dB and speed by a factor of 2-3. These changes are not
+ backward compatible with previous versions of zfp.
+
+ - Added support for 31-bit and 63-bit integer data, as well as shorter
+ integer types.
+
+ - Rewrote compression codec entirely in C to make linking and calling
+ easier from other programming languages, and to expose the low-level
+ interface through C instead of C++. This necessitated significant
+ changes to the API as well.
+
+ - Minor changes to the C++ compressed array API, as well as major
+ implementation changes to support the C library. The namespace and
+ public types are now all in lower case.
+
+ - Deprecated support for general fixed-point decorrelating transforms
+ and slimmed down implementation.
+
+ - Added new examples for evaluating the throughput of the (de)compressor
+ and for compressing grayscale images in the pgm format.
+
+ - Added FAQ.
+
+
+zfp 0.3.2, December 3, 2015
+
+ - Fixed bug in Array::get() that caused the wrong cached block to be
+ looked up, thus occasionally copying incorrect values back to parts
+ of the array.
+
+
+zfp 0.3.1, May 6, 2015
+
+ - Fixed rare bug caused by exponent underflow in blocks with no normal
+ and some denormal numbers.
+
+
+zfp 0.3.0, March 3, 2015
+
+ - Modified the default decorrelating transform to one that uses only
+ additions and bit shifts. This new transform, in addition to being
+ faster, also has some theoretical optimality properties and tends to
+ improve rate distortion.
+
+ - Added compile-time support for parameterized transforms, e.g. to
+ support other popular transforms like DCT, HCT, and Walsh-Hadamard.
+
+ - Made forward transform range preserving: (-1, 1) is mapped to (-1, 1).
+ Consequently Q1.62 fixed point can be used throughout.
+
+ - Changed the order in which bits are emitted within each bit plane
+ to be more intelligent. Group tests are now deferred until they
+ are needed, i.e. just before the value bits for the group being
+ tested. This improves the quality of fixed-rate encodings, but
+ has no impact on compressed size.
+
+ - Made several optimizations to improve performance.
+
+ - Added floating-point traits to reduce the number of template
+ parameters. It is now possible to declare a 3D array as
+ Array3<float>, for example.
+
+ - Added functions for setting the array scalar type and dimensions.
+
+ - Consolidated several header files.
+
+ - Added testzfp for regression testing.
+
+
+zfp 0.2.1, December 12, 2014
+
+ - Added Win64 support via Microsoft Visual Studio compiler.
+
+ - Fixed broken support for IBM's xlc compiler.
+
+ - Made several minor changes to suppress compiler warnings.
+
+ - Documented expected output for the diffusion example.
+
+
+zfp 0.2.0, December 2, 2014
+
+ - The compression interface from zfpcompress was relocated to a
+ separate library, called libzfp, and modified to be callable from C.
+ This API now uses a parameter object (zfp_params) to specify array
+ type and dimensions as well as compression parameters.
+
+ - Several utility functions were added to simplify libzfp usage:
+
+ o Functions for setting the rate, precision, and accuracy.
+ Corresponding functions were also added to the Codec class.
+
+ o A function for estimating the buffer size needed for compression.
+
+ - The Array class functionality was expanded:
+
+ o Support for accessing the compressed bit stream stored with an
+ array, e.g. for offline compressed storage and for initializing
+ an already compressed array.
+
+ o Functions for dynamically specifying the cache size.
+
+ o The default cache is now direct-mapped instead of two-way
+ associative.
+
+ - Minor bug fixes:
+
+ o Corrected the value of the lowest possible bit plane to account for
+ both the smallest exponent and the number of bits in the significand.
+
+ o Corrected inconsistent use of rate and precision. The rate refers
+ to the number of compressed bits per floating-point value, while
+ the precision refers to the number of uncompressed bits. The Array
+ API was changed accordingly.
+
+
+zfp 0.1.0, November 12, 2014
+
+ - Initial beta release.
diff --git a/src/zfp/zfp-0.5.0/array/cache.h b/src/zfp/zfp-0.5.0/array/cache.h
new file mode 100644
index 0000000..3359b7d
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/array/cache.h
@@ -0,0 +1,224 @@
+#ifndef CACHE_H
+#define CACHE_H
+
+#include "memory.h"
+
+#ifdef CACHE_PROFILE
+ // maintain stats on hit and miss rates
+ #include <iostream>
+#endif
+
+// direct-mapped or two-way skew-associative write-back cache
+template <class Line>
+class Cache {
+public:
+ // cache line index (zero is reserved for unused lines)
+ typedef uint Index;
+
+ // cache tag containing line meta data
+ class Tag {
+ public:
+ Tag() : x(0) {}
+
+ Tag(Index x, bool d) : x(2 * x + d) {}
+
+ // cache line index
+ Index index() const { return x >> 1; }
+
+ // is line dirty?
+ bool dirty() const { return x & 1; }
+
+ // is line used?
+ bool used() const { return x != 0; }
+
+ // mark line as dirty
+ void mark() { x |= 1u; }
+
+ // mark line as unused
+ void clear() { x = 0; }
+
+ protected:
+ Index x;
+ };
+
+ // sequential iterator for looping over cache lines
+ class const_iterator {
+ public:
+ friend class Cache;
+ class Pair {
+ public:
+ Pair(Line* l, Tag t) : line(l), tag(t) {}
+ Line* line;
+ Tag tag;
+ };
+ const_iterator& operator++()
+ {
+ advance();
+ return *this;
+ }
+ const_iterator operator++(int)
+ {
+ const_iterator iter = *this;
+ advance();
+ return iter;
+ }
+ const Pair& operator*() const { return pair; }
+ const Pair* operator->() const { return &pair; }
+ operator const void*() const { return pair.line ? this : 0; }
+
+ protected:
+ const_iterator(Cache* cache) : c(cache), pair(cache->line, cache->tag[0])
+ {
+ if (!pair.tag.used())
+ advance();
+ }
+ void advance()
+ {
+ if (pair.line) {
+ uint i;
+ for (i = pair.line - c->line + 1; i <= c->mask && !c->tag[i].used(); i++);
+ pair = (i <= c->mask ? Pair(c->line + i, c->tag[i]) : Pair(0, Tag()));
+ }
+ }
+ Cache* c;
+ Pair pair;
+ };
+
+ // allocate cache with at least minsize lines
+ Cache(uint minsize) : tag(0), line(0)
+ {
+ resize(minsize);
+#ifdef CACHE_PROFILE
+ std::cerr << "cache lines=" << mask + 1 << std::endl;
+ hit[0][0] = hit[1][0] = miss[0] = back[0] = 0;
+ hit[0][1] = hit[1][1] = miss[1] = back[1] = 0;
+#endif
+ }
+
+ ~Cache()
+ {
+ deallocate(tag);
+ deallocate(line);
+#ifdef CACHE_PROFILE
+ std::cerr << "cache R1=" << hit[0][0] << " R2=" << hit[1][0] << " RM=" << miss[0] << " RB=" << back[0]
+ << " W1=" << hit[0][1] << " W2=" << hit[1][1] << " WM=" << miss[1] << " WB=" << back[1] << std::endl;
+#endif
+ }
+
+ // cache size in number of lines
+ uint size() const { return mask + 1; }
+
+ // change cache size to at least minsize lines (all contents will be lost)
+ void resize(uint minsize)
+ {
+ for (mask = minsize ? minsize - 1 : 1; mask & (mask + 1); mask |= mask + 1);
+ reallocate(tag, ((size_t)mask + 1) * sizeof(Tag), 0x100);
+ reallocate(line, ((size_t)mask + 1) * sizeof(Line), 0x100);
+ clear();
+ }
+
+ // look up cache line #x and return pointer to it if in the cache;
+ // otherwise return null
+ const Line* lookup(Index x) const
+ {
+ uint i = primary(x);
+ if (tag[i].index() == x)
+ return line + i;
+#ifdef CACHE_TWOWAY
+ uint j = secondary(x);
+ if (tag[j].index() == x)
+ return line + j;
+#endif
+ return 0;
+ }
+
+ // look up cache line #x and set ptr to where x is or should be stored;
+ // if the returned tag does not match x, then the caller must implement
+ // write-back (if the line is in use) and then fetch the requested line
+ Tag access(Line*& ptr, Index x, bool write)
+ {
+ uint i = primary(x);
+ if (tag[i].index() == x) {
+ ptr = line + i;
+ if (write)
+ tag[i].mark();
+#ifdef CACHE_PROFILE
+ hit[0][write]++;
+#endif
+ return tag[i];
+ }
+#ifdef CACHE_TWOWAY
+ uint j = secondary(x);
+ if (tag[j].index() == x) {
+ ptr = line + j;
+ if (write)
+ tag[j].mark();
+#ifdef CACHE_PROFILE
+ shit[write]++;
+#endif
+ return tag[j];
+ }
+ // cache line not found; prefer primary and not dirty slots
+ i = tag[j].used() && (!tag[i].dirty() || tag[j].dirty()) ? i : j;
+#endif
+ ptr = line + i;
+ Tag t = tag[i];
+ tag[i] = Tag(x, write);
+#ifdef CACHE_PROFILE
+ miss[write]++;
+ if (tag[i].dirty())
+ back[write]++;
+#endif
+ return t;
+ }
+
+ // clear cache without writing back
+ void clear()
+ {
+ for (uint i = 0; i <= mask; i++)
+ tag[i].clear();
+ }
+
+ // flush cache line
+ void flush(const Line* l)
+ {
+ uint i = l - line;
+ tag[i].clear();
+ }
+
+ // return iterator to first cache line
+ const_iterator first() { return const_iterator(this); }
+
+protected:
+ uint primary(Index x) const { return x & mask; }
+ uint secondary(Index x) const
+ {
+#ifdef CACHE_FAST_HASH
+ // max entropy hash for 26- to 16-bit mapping (not full avalanche)
+ x -= x << 7;
+ x ^= x >> 16;
+ x -= x << 3;
+#else
+ // Jenkins hash; see http://burtleburtle.net/bob/hash/integer.html
+ x -= x << 6;
+ x ^= x >> 17;
+ x -= x << 9;
+ x ^= x << 4;
+ x -= x << 3;
+ x ^= x << 10;
+ x ^= x >> 15;
+#endif
+ return x & mask;
+ }
+
+ Index mask; // cache line mask
+ Tag* tag; // cache line tags
+ Line* line; // actual decompressed cache lines
+#ifdef CACHE_PROFILE
+ uint64 hit[2][2]; // number of primary/secondary read/write hits
+ uint64 miss[2]; // number of read/write misses
+ uint64 back[2]; // number of write-backs due to read/writes
+#endif
+};
+
+#endif
diff --git a/src/zfp/zfp-0.5.0/array/memory.h b/src/zfp/zfp-0.5.0/array/memory.h
new file mode 100644
index 0000000..551ea90
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/array/memory.h
@@ -0,0 +1,42 @@
+#ifndef MEMORY_H
+#define MEMORY_H
+
+#include <cstdlib>
+#include "types.h"
+
+inline void*
+allocate(size_t size, size_t alignment = 0)
+{
+#if defined(__USE_XOPEN2K) && defined(ALIGNED_ALLOC)
+ void* ptr;
+ if (alignment > 1)
+ posix_memalign(&ptr, alignment, size);
+ else
+ ptr = malloc(size);
+ return ptr;
+#else
+ return new uchar[size];
+#endif
+}
+
+template <typename T>
+inline void
+deallocate(T* ptr)
+{
+#if defined(__USE_XOPEN2K) && defined(ALIGNED_ALLOC)
+ if (ptr)
+ free(ptr);
+#else
+ delete[] ptr;
+#endif
+}
+
+template <typename T>
+inline void
+reallocate(T*& ptr, size_t size, size_t alignment = 0)
+{
+ deallocate(ptr);
+ ptr = static_cast<T*>(allocate(size, alignment));
+}
+
+#endif
diff --git a/src/zfp/zfp-0.5.0/array/zfparray.h b/src/zfp/zfp-0.5.0/array/zfparray.h
new file mode 100644
index 0000000..b27add7
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/array/zfparray.h
@@ -0,0 +1,105 @@
+#ifndef ZFP_ARRAY_H
+#define ZFP_ARRAY_H
+
+#include <algorithm>
+#include <climits>
+#include "zfp.h"
+#include "memory.h"
+
+namespace zfp {
+
+// base class for compressed array of scalars
+class array {
+protected:
+ array(uint dims, zfp_type type) :
+ dims(dims), type(type),
+ nx(0), ny(0), nz(0),
+ bx(0), by(0), bz(0),
+ blocks(0), blkvals(1u << (2 * dims)), blkbits(0), blksize(0),
+ bytes(0), data(0),
+ stream(zfp_stream_open(0)),
+ shape(0)
+ {}
+
+ ~array()
+ {
+ free();
+ zfp_stream_close(stream);
+ }
+
+public:
+ // rate in bits per value
+ double rate() const { return double(blkbits) / blkvals; }
+
+ // set compression rate in bits per value
+ double set_rate(double rate)
+ {
+ rate = zfp_stream_set_rate(stream, rate, type, dims, 1);
+ blkbits = stream->maxbits;
+ blksize = blkbits / CHAR_BIT;
+ alloc();
+ return rate;
+ }
+
+ // empty cache without compressing modified cached blocks
+ virtual void clear_cache() const = 0;
+
+ // flush cache by compressing all modified cached blocks
+ virtual void flush_cache() const = 0;
+
+ // number of bytes of compressed data
+ size_t compressed_size() const { return bytes; }
+
+ // pointer to compressed data for read or write access
+ uchar* compressed_data() const
+ {
+ // first write back any modified cached data
+ flush_cache();
+ return data;
+ }
+
+protected:
+ // allocate memory for compressed data
+ void alloc(bool clear = true)
+ {
+ bytes = blocks * blksize;
+ reallocate(data, bytes, 0x100u);
+ if (clear)
+ std::fill(data, data + bytes, 0);
+ stream_close(stream->stream);
+ zfp_stream_set_bit_stream(stream, stream_open(data, bytes));
+ clear_cache();
+ }
+
+ // free memory associated with compressed data
+ void free()
+ {
+ nx = ny = nz = 0;
+ bx = by = bz = 0;
+ blocks = 0;
+ stream_close(stream->stream);
+ zfp_stream_set_bit_stream(stream, 0);
+ bytes = 0;
+ deallocate(data);
+ data = 0;
+ deallocate(shape);
+ shape = 0;
+ }
+
+ uint dims; // array dimensionality (1, 2, or 3)
+ zfp_type type; // scalar type
+ uint nx, ny, nz; // array dimensions
+ uint bx, by, bz; // array dimensions in number of blocks
+ uint blocks; // number of blocks
+ uint blkvals; // number of values per block
+ size_t blkbits; // number of bits per compressed block
+ size_t blksize; // byte size of single compressed block
+ size_t bytes; // total bytes of compressed data
+ mutable uchar* data; // pointer to compressed data
+ zfp_stream* stream; // compressed stream
+ uchar* shape; // precomputed block dimensions (or null if uniform)
+};
+
+}
+
+#endif
diff --git a/src/zfp/zfp-0.5.0/array/zfparray1.h b/src/zfp/zfp-0.5.0/array/zfparray1.h
new file mode 100644
index 0000000..dffc934
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/array/zfparray1.h
@@ -0,0 +1,243 @@
+#ifndef ZFP_ARRAY1_H
+#define ZFP_ARRAY1_H
+
+#include "zfparray.h"
+#include "zfpcodec.h"
+#include "cache.h"
+
+namespace zfp {
+
+// compressed 1D array of scalars
+template < typename Scalar, class Codec = zfp::codec<Scalar> >
+class array1 : public array {
+public:
+ array1() : array(1, Codec::type) {}
+
+ // constructor of n-sample array using rate bits per value, at least
+ // csize bytes of cache, and optionally initialized from flat array p
+ array1(uint n, double rate, const Scalar* p = 0, size_t csize = 0) :
+ array(1, Codec::type),
+ cache(lines(csize, n))
+ {
+ set_rate(rate);
+ resize(n, p == 0);
+ if (p)
+ set(p);
+ }
+
+ // total number of elements in array
+ size_t size() const { return size_t(nx); }
+
+ // resize the array (all previously stored data will be lost)
+ void resize(uint n, bool clear = true)
+ {
+ if (n == 0)
+ free();
+ else {
+ nx = n;
+ bx = (nx + 3) / 4;
+ blocks = bx;
+ alloc(clear);
+
+ // precompute block dimensions
+ deallocate(shape);
+ if (nx & 3u) {
+ shape = (uchar*)allocate(blocks);
+ uchar* p = shape;
+ for (uint i = 0; i < bx; i++)
+ *p++ = (i == bx - 1 ? -nx & 3u : 0);
+ }
+ else
+ shape = 0;
+ }
+ }
+
+ // cache size in number of bytes
+ size_t cache_size() const { return cache.size() * sizeof(CacheLine); }
+
+ // set minimum cache size in bytes (array dimensions must be known)
+ void set_cache_size(size_t csize)
+ {
+ flush_cache();
+ cache.resize(lines(csize, nx));
+ }
+
+ // empty cache without compressing modified cached blocks
+ void clear_cache() const { cache.clear(); }
+
+ // flush cache by compressing all modified cached blocks
+ void flush_cache() const
+ {
+ for (typename Cache<CacheLine>::const_iterator p = cache.first(); p; p++) {
+ if (p->tag.dirty()) {
+ uint b = p->tag.index() - 1;
+ encode(b, p->line->a);
+ }
+ cache.flush(p->line);
+ }
+ }
+
+ // decompress array and store at p
+ void get(Scalar* p) const
+ {
+ uint b = 0;
+ for (uint i = 0; i < bx; i++, p += 4, b++) {
+ const CacheLine* line = cache.lookup(b + 1);
+ if (line)
+ line->get(p, 1, shape ? shape[b] : 0);
+ else
+ decode(b, p, 1);
+ }
+ }
+
+ // initialize array by copying and compressing data stored at p
+ void set(const Scalar* p)
+ {
+ uint b = 0;
+ for (uint i = 0; i < bx; i++, b++, p += 4)
+ encode(b, p, 1);
+ cache.clear();
+ }
+
+ // reference to a single array value
+ class reference {
+ public:
+ operator Scalar() const { return array->get(i); }
+ reference operator=(const reference& r) { array->set(i, r.operator Scalar()); return *this; }
+ reference operator=(Scalar val) { array->set(i, val); return *this; }
+ reference operator+=(Scalar val) { array->add(i, val); return *this; }
+ reference operator-=(Scalar val) { array->sub(i, val); return *this; }
+ reference operator*=(Scalar val) { array->mul(i, val); return *this; }
+ reference operator/=(Scalar val) { array->div(i, val); return *this; }
+ protected:
+ friend class array1;
+ reference(array1* array, uint i) : array(array), i(i) {}
+ array1* array;
+ uint i;
+ };
+
+ // (i) accessors
+ const Scalar& operator()(uint i) const { return get(i); }
+ reference operator()(uint i) { return reference(this, i); }
+
+ // flat index accessors
+ const Scalar& operator[](uint index) const { return get(index); }
+ reference operator[](uint index) { return reference(this, index); }
+
+protected:
+ // cache line representing one block of decompressed values
+ class CacheLine {
+ public:
+ friend class array1;
+ const Scalar& operator()(uint i) const { return a[index(i)]; }
+ Scalar& operator()(uint i) { return a[index(i)]; }
+ // copy cache line
+ void get(Scalar* p, int sx) const
+ {
+ const Scalar* q = a;
+ for (uint x = 0; x < 4; x++, p += sx, q++)
+ *p = *q;
+ }
+ void get(Scalar* p, int sx, uint shape) const
+ {
+ if (!shape)
+ get(p, sx);
+ else {
+ // determine block dimensions
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ const Scalar* q = a;
+ for (uint x = 0; x < nx; x++, p += sx, q++)
+ *p = *q;
+ }
+ }
+ protected:
+ static uint index(uint i) { return i & 3u; }
+ Scalar a[4];
+ };
+
+ // inspector
+ const Scalar& get(uint i) const
+ {
+ CacheLine* p = line(i, false);
+ return (*p)(i);
+ }
+
+ // mutator
+ void set(uint i, Scalar val)
+ {
+ CacheLine* p = line(i, true);
+ (*p)(i) = val;
+ }
+
+ // in-place updates
+ void add(uint i, Scalar val) { (*line(i, true))(i) += val; }
+ void sub(uint i, Scalar val) { (*line(i, true))(i) -= val; }
+ void mul(uint i, Scalar val) { (*line(i, true))(i) *= val; }
+ void div(uint i, Scalar val) { (*line(i, true))(i) /= val; }
+
+ // return cache line for i; may require write-back and fetch
+ CacheLine* line(uint i, bool write) const
+ {
+ CacheLine* p = 0;
+ uint b = block(i);
+ typename Cache<CacheLine>::Tag t = cache.access(p, b + 1, write);
+ uint c = t.index() - 1;
+ if (c != b) {
+ // write back occupied cache line if it is dirty
+ if (t.dirty())
+ encode(c, p->a);
+ // fetch cache line
+ decode(b, p->a);
+ }
+ return p;
+ }
+
+ // encode block with given index
+ void encode(uint index, const Scalar* block) const
+ {
+ stream_wseek(stream->stream, index * blkbits);
+ Codec::encode_block_1(stream, block, shape ? shape[index] : 0);
+ stream_flush(stream->stream);
+ }
+
+ // encode block with given index from strided array
+ void encode(uint index, const Scalar* p, int sx) const
+ {
+ stream_wseek(stream->stream, index * blkbits);
+ Codec::encode_block_strided_1(stream, p, shape ? shape[index] : 0, sx);
+ stream_flush(stream->stream);
+ }
+
+ // decode block with given index
+ void decode(uint index, Scalar* block) const
+ {
+ stream_rseek(stream->stream, index * blkbits);
+ Codec::decode_block_1(stream, block, shape ? shape[index] : 0);
+ }
+
+ // decode block with given index to strided array
+ void decode(uint index, Scalar* p, int sx) const
+ {
+ stream_rseek(stream->stream, index * blkbits);
+ Codec::decode_block_strided_1(stream, p, shape ? shape[index] : 0, sx);
+ }
+
+ // block index for i
+ static uint block(uint i) { return i / 4; }
+
+ // number of cache lines corresponding to size (or suggested size if zero)
+ static uint lines(size_t size, uint n)
+ {
+ n = uint((size ? size : 8 * sizeof(Scalar)) / sizeof(CacheLine));
+ return std::max(n, 1u);
+ }
+
+ mutable Cache<CacheLine> cache; // cache of decompressed blocks
+};
+
+typedef array1<float> array1f;
+typedef array1<double> array1d;
+
+}
+
+#endif
diff --git a/src/zfp/zfp-0.5.0/array/zfparray2.h b/src/zfp/zfp-0.5.0/array/zfparray2.h
new file mode 100644
index 0000000..f5b32ef
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/array/zfparray2.h
@@ -0,0 +1,273 @@
+#ifndef ZFP_ARRAY2_H
+#define ZFP_ARRAY2_H
+
+#include "zfparray.h"
+#include "zfpcodec.h"
+#include "cache.h"
+
+namespace zfp {
+
+// compressed 2D array of scalars
+template < typename Scalar, class Codec = zfp::codec<Scalar> >
+class array2 : public array {
+public:
+ array2() : array(2, Codec::type) {}
+
+ // constructor of nx * ny array using rate bits per value, at least
+ // csize bytes of cache, and optionally initialized from flat array p
+ array2(uint nx, uint ny, double rate, const Scalar* p = 0, size_t csize = 0) :
+ array(2, Codec::type),
+ cache(lines(csize, nx, ny))
+ {
+ set_rate(rate);
+ resize(nx, ny, p == 0);
+ if (p)
+ set(p);
+ }
+
+ // total number of elements in array
+ size_t size() const { return size_t(nx) * size_t(ny); }
+
+ // array dimensions
+ uint size_x() const { return nx; }
+ uint size_y() const { return ny; }
+
+ // resize the array (all previously stored data will be lost)
+ void resize(uint nx, uint ny, bool clear = true)
+ {
+ if (nx == 0 || ny == 0)
+ free();
+ else {
+ this->nx = nx;
+ this->ny = ny;
+ bx = (nx + 3) / 4;
+ by = (ny + 3) / 4;
+ blocks = bx * by;
+ alloc(clear);
+
+ // precompute block dimensions
+ deallocate(shape);
+ if ((nx | ny) & 3u) {
+ shape = (uchar*)allocate(blocks);
+ uchar* p = shape;
+ for (uint j = 0; j < by; j++)
+ for (uint i = 0; i < bx; i++)
+ *p++ = (i == bx - 1 ? -nx & 3u : 0) + 4 * (j == by - 1 ? -ny & 3u : 0);
+ }
+ else
+ shape = 0;
+ }
+ }
+
+ // cache size in number of bytes
+ size_t cache_size() const { return cache.size() * sizeof(CacheLine); }
+
+ // set minimum cache size in bytes (array dimensions must be known)
+ void set_cache_size(size_t csize)
+ {
+ flush_cache();
+ cache.resize(lines(csize, nx, ny));
+ }
+
+ // empty cache without compressing modified cached blocks
+ void clear_cache() const { cache.clear(); }
+
+ // flush cache by compressing all modified cached blocks
+ void flush_cache() const
+ {
+ for (typename Cache<CacheLine>::const_iterator p = cache.first(); p; p++) {
+ if (p->tag.dirty()) {
+ uint b = p->tag.index() - 1;
+ encode(b, p->line->a);
+ }
+ cache.flush(p->line);
+ }
+ }
+
+ // decompress array and store at p
+ void get(Scalar* p) const
+ {
+ uint b = 0;
+ for (uint j = 0; j < by; j++, p += 4 * (nx - bx))
+ for (uint i = 0; i < bx; i++, p += 4, b++) {
+ const CacheLine* line = cache.lookup(b + 1);
+ if (line)
+ line->get(p, 1, nx, shape ? shape[b] : 0);
+ else
+ decode(b, p, 1, nx);
+ }
+ }
+
+ // initialize array by copying and compressing data stored at p
+ void set(const Scalar* p)
+ {
+ uint b = 0;
+ for (uint j = 0; j < by; j++, p += 4 * (nx - bx))
+ for (uint i = 0; i < bx; i++, p += 4, b++)
+ encode(b, p, 1, nx);
+ cache.clear();
+ }
+
+ // reference to a single array value
+ class reference {
+ public:
+ operator Scalar() const { return array->get(i, j); }
+ reference operator=(const reference& r) { array->set(i, j, r.operator Scalar()); return *this; }
+ reference operator=(Scalar val) { array->set(i, j, val); return *this; }
+ reference operator+=(Scalar val) { array->add(i, j, val); return *this; }
+ reference operator-=(Scalar val) { array->sub(i, j, val); return *this; }
+ reference operator*=(Scalar val) { array->mul(i, j, val); return *this; }
+ reference operator/=(Scalar val) { array->div(i, j, val); return *this; }
+ protected:
+ friend class array2;
+ reference(array2* array, uint i, uint j) : array(array), i(i), j(j) {}
+ array2* array;
+ uint i, j;
+ };
+
+ // (i, j) accessors
+ const Scalar& operator()(uint i, uint j) const { return get(i, j); }
+ reference operator()(uint i, uint j) { return reference(this, i, j); }
+
+ // flat index accessors
+ const Scalar& operator[](uint index) const
+ {
+ uint i, j;
+ ij(i, j, index);
+ return get(i, j);
+ }
+ reference operator[](uint index)
+ {
+ uint i, j;
+ ij(i, j, index);
+ return reference(this, i, j);
+ }
+
+protected:
+ // cache line representing one block of decompressed values
+ class CacheLine {
+ public:
+ friend class array2;
+ const Scalar& operator()(uint i, uint j) const { return a[index(i, j)]; }
+ Scalar& operator()(uint i, uint j) { return a[index(i, j)]; }
+ // copy cache line
+ void get(Scalar* p, int sx, int sy) const
+ {
+ const Scalar* q = a;
+ for (uint y = 0; y < 4; y++, p += sy - 4 * sx)
+ for (uint x = 0; x < 4; x++, p += sx, q++)
+ *p = *q;
+ }
+ void get(Scalar* p, int sx, int sy, uint shape) const
+ {
+ if (!shape)
+ get(p, sx, sy);
+ else {
+ // determine block dimensions
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ uint ny = 4 - (shape & 3u); shape >>= 2;
+ const Scalar* q = a;
+ for (uint y = 0; y < ny; y++, p += sy - nx * sx, q += 4 - nx)
+ for (uint x = 0; x < nx; x++, p += sx, q++)
+ *p = *q;
+ }
+ }
+ protected:
+ static uint index(uint i, uint j) { return (i & 3u) + 4 * (j & 3u); }
+ Scalar a[16];
+ };
+
+ // inspector
+ const Scalar& get(uint i, uint j) const
+ {
+ CacheLine* p = line(i, j, false);
+ return (*p)(i, j);
+ }
+
+ // mutator
+ void set(uint i, uint j, Scalar val)
+ {
+ CacheLine* p = line(i, j, true);
+ (*p)(i, j) = val;
+ }
+
+ // in-place updates
+ void add(uint i, uint j, Scalar val) { (*line(i, j, true))(i, j) += val; }
+ void sub(uint i, uint j, Scalar val) { (*line(i, j, true))(i, j) -= val; }
+ void mul(uint i, uint j, Scalar val) { (*line(i, j, true))(i, j) *= val; }
+ void div(uint i, uint j, Scalar val) { (*line(i, j, true))(i, j) /= val; }
+
+ // return cache line for (i, j); may require write-back and fetch
+ CacheLine* line(uint i, uint j, bool write) const
+ {
+ CacheLine* p = 0;
+ uint b = block(i, j);
+ typename Cache<CacheLine>::Tag t = cache.access(p, b + 1, write);
+ uint c = t.index() - 1;
+ if (c != b) {
+ // write back occupied cache line if it is dirty
+ if (t.dirty())
+ encode(c, p->a);
+ // fetch cache line
+ decode(b, p->a);
+ }
+ return p;
+ }
+
+ // encode block with given index
+ void encode(uint index, const Scalar* block) const
+ {
+ stream_wseek(stream->stream, index * blkbits);
+ Codec::encode_block_2(stream, block, shape ? shape[index] : 0);
+ stream_flush(stream->stream);
+ }
+
+ // encode block with given index from strided array
+ void encode(uint index, const Scalar* p, int sx, int sy) const
+ {
+ stream_wseek(stream->stream, index * blkbits);
+ Codec::encode_block_strided_2(stream, p, shape ? shape[index] : 0, sx, sy);
+ stream_flush(stream->stream);
+ }
+
+ // decode block with given index
+ void decode(uint index, Scalar* block) const
+ {
+ stream_rseek(stream->stream, index * blkbits);
+ Codec::decode_block_2(stream, block, shape ? shape[index] : 0);
+ }
+
+ // decode block with given index to strided array
+ void decode(uint index, Scalar* p, int sx, int sy) const
+ {
+ stream_rseek(stream->stream, index * blkbits);
+ Codec::decode_block_strided_2(stream, p, shape ? shape[index] : 0, sx, sy);
+ }
+
+ // block index for (i, j)
+ uint block(uint i, uint j) const { return (i / 4) + bx * (j / 4); }
+
+ // convert flat index to (i, j)
+ void ij(uint& i, uint& j, uint index) const
+ {
+ i = index % nx;
+ index /= nx;
+ j = index;
+ }
+
+ // number of cache lines corresponding to size (or suggested size if zero)
+ static uint lines(size_t size, uint nx, uint ny)
+ {
+ uint n = uint((size ? size : 8 * nx * sizeof(Scalar)) / sizeof(CacheLine));
+ return std::max(n, 1u);
+ }
+
+ mutable Cache<CacheLine> cache; // cache of decompressed blocks
+};
+
+typedef array2<float> array2f;
+typedef array2<double> array2d;
+
+}
+
+#endif
diff --git a/src/zfp/zfp-0.5.0/array/zfparray3.h b/src/zfp/zfp-0.5.0/array/zfparray3.h
new file mode 100644
index 0000000..cce37d2
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/array/zfparray3.h
@@ -0,0 +1,284 @@
+#ifndef ZFP_ARRAY3_H
+#define ZFP_ARRAY3_H
+
+#include "zfparray.h"
+#include "zfpcodec.h"
+#include "cache.h"
+
+namespace zfp {
+
+// compressed 3D array of scalars
+template < typename Scalar, class Codec = zfp::codec<Scalar> >
+class array3 : public array {
+public:
+ array3() : array(3, Codec::type) {}
+
+ // constructor of nx * ny * nz array using rate bits per value, at least
+ // csize bytes of cache, and optionally initialized from flat array p
+ array3(uint nx, uint ny, uint nz, double rate, const Scalar* p = 0, size_t csize = 0) :
+ array(3, Codec::type),
+ cache(lines(csize, nx, ny, nz))
+ {
+ set_rate(rate);
+ resize(nx, ny, nz, p == 0);
+ if (p)
+ set(p);
+ }
+
+ // total number of elements in array
+ size_t size() const { return size_t(nx) * size_t(ny) * size_t(nz); }
+
+ // array dimensions
+ uint size_x() const { return nx; }
+ uint size_y() const { return ny; }
+ uint size_z() const { return nz; }
+
+ // resize the array (all previously stored data will be lost)
+ void resize(uint nx, uint ny, uint nz, bool clear = true)
+ {
+ if (nx == 0 || ny == 0 || nz == 0)
+ free();
+ else {
+ this->nx = nx;
+ this->ny = ny;
+ this->nz = nz;
+ bx = (nx + 3) / 4;
+ by = (ny + 3) / 4;
+ bz = (nz + 3) / 4;
+ blocks = bx * by * bz;
+ alloc(clear);
+
+ // precompute block dimensions
+ deallocate(shape);
+ if ((nx | ny | nz) & 3u) {
+ shape = (uchar*)allocate(blocks);
+ uchar* p = shape;
+ for (uint k = 0; k < bz; k++)
+ for (uint j = 0; j < by; j++)
+ for (uint i = 0; i < bx; i++)
+ *p++ = (i == bx - 1 ? -nx & 3u : 0) + 4 * ((j == by - 1 ? -ny & 3u : 0) + 4 * (k == bz - 1 ? -nz & 3u : 0));
+ }
+ else
+ shape = 0;
+ }
+ }
+
+ // cache size in number of bytes
+ size_t cache_size() const { return cache.size() * sizeof(CacheLine); }
+
+ // set minimum cache size in bytes (array dimensions must be known)
+ void set_cache_size(size_t csize)
+ {
+ flush_cache();
+ cache.resize(lines(csize, nx, ny, nz));
+ }
+
+ // empty cache without compressing modified cached blocks
+ void clear_cache() const { cache.clear(); }
+
+ // flush cache by compressing all modified cached blocks
+ void flush_cache() const
+ {
+ for (typename Cache<CacheLine>::const_iterator p = cache.first(); p; p++) {
+ if (p->tag.dirty()) {
+ uint b = p->tag.index() - 1;
+ encode(b, p->line->a);
+ }
+ cache.flush(p->line);
+ }
+ }
+
+ // decompress array and store at p
+ void get(Scalar* p) const
+ {
+ uint b = 0;
+ for (uint k = 0; k < bz; k++, p += 4 * nx * (ny - by))
+ for (uint j = 0; j < by; j++, p += 4 * (nx - bx))
+ for (uint i = 0; i < bx; i++, p += 4, b++) {
+ const CacheLine* line = cache.lookup(b + 1);
+ if (line)
+ line->get(p, 1, nx, nx * ny, shape ? shape[b] : 0);
+ else
+ decode(b, p, 1, nx, nx * ny);
+ }
+ }
+
+ // initialize array by copying and compressing data stored at p
+ void set(const Scalar* p)
+ {
+ uint b = 0;
+ for (uint k = 0; k < bz; k++, p += 4 * nx * (ny - by))
+ for (uint j = 0; j < by; j++, p += 4 * (nx - bx))
+ for (uint i = 0; i < bx; i++, p += 4, b++)
+ encode(b, p, 1, nx, nx * ny);
+ cache.clear();
+ }
+
+ // reference to a single array value
+ class reference {
+ public:
+ operator Scalar() const { return array->get(i, j, k); }
+ reference operator=(const reference& r) { array->set(i, j, k, r.operator Scalar()); return *this; }
+ reference operator=(Scalar val) { array->set(i, j, k, val); return *this; }
+ reference operator+=(Scalar val) { array->add(i, j, k, val); return *this; }
+ reference operator-=(Scalar val) { array->sub(i, j, k, val); return *this; }
+ reference operator*=(Scalar val) { array->mul(i, j, k, val); return *this; }
+ reference operator/=(Scalar val) { array->div(i, j, k, val); return *this; }
+ protected:
+ friend class array3;
+ reference(array3* array, uint i, uint j, uint k) : array(array), i(i), j(j), k(k) {}
+ array3* array;
+ uint i, j, k;
+ };
+
+ // (i, j, k) accessors
+ const Scalar& operator()(uint i, uint j, uint k) const { return get(i, j, k); }
+ reference operator()(uint i, uint j, uint k) { return reference(this, i, j, k); }
+
+ // flat index accessors
+ const Scalar& operator[](uint index) const
+ {
+ uint i, j, k;
+ ijk(i, j, k, index);
+ return get(i, j, k);
+ }
+ reference operator[](uint index)
+ {
+ uint i, j, k;
+ ijk(i, j, k, index);
+ return reference(this, i, j, k);
+ }
+
+protected:
+ // cache line representing one block of decompressed values
+ class CacheLine {
+ public:
+ friend class array3;
+ const Scalar& operator()(uint i, uint j, uint k) const { return a[index(i, j, k)]; }
+ Scalar& operator()(uint i, uint j, uint k) { return a[index(i, j, k)]; }
+ // copy cache line
+ void get(Scalar* p, int sx, int sy, int sz) const
+ {
+ const Scalar* q = a;
+ for (uint z = 0; z < 4; z++, p += sz - 4 * sy)
+ for (uint y = 0; y < 4; y++, p += sy - 4 * sx)
+ for (uint x = 0; x < 4; x++, p += sx, q++)
+ *p = *q;
+ }
+ void get(Scalar* p, int sx, int sy, int sz, uint shape) const
+ {
+ if (!shape)
+ get(p, sx, sy, sz);
+ else {
+ // determine block dimensions
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ uint ny = 4 - (shape & 3u); shape >>= 2;
+ uint nz = 4 - (shape & 3u); shape >>= 2;
+ const Scalar* q = a;
+ for (uint z = 0; z < nz; z++, p += sz - ny * sy, q += 16 - 4 * ny)
+ for (uint y = 0; y < ny; y++, p += sy - nx * sx, q += 4 - nx)
+ for (uint x = 0; x < nx; x++, p += sx, q++)
+ *p = *q;
+ }
+ }
+ protected:
+ static uint index(uint i, uint j, uint k) { return (i & 3u) + 4 * ((j & 3u) + 4 * (k & 3u)); }
+ Scalar a[64];
+ };
+
+ // inspector
+ const Scalar& get(uint i, uint j, uint k) const
+ {
+ CacheLine* p = line(i, j, k, false);
+ return (*p)(i, j, k);
+ }
+
+ // mutator
+ void set(uint i, uint j, uint k, Scalar val)
+ {
+ CacheLine* p = line(i, j, k, true);
+ (*p)(i, j, k) = val;
+ }
+
+ // in-place updates
+ void add(uint i, uint j, uint k, Scalar val) { (*line(i, j, k, true))(i, j, k) += val; }
+ void sub(uint i, uint j, uint k, Scalar val) { (*line(i, j, k, true))(i, j, k) -= val; }
+ void mul(uint i, uint j, uint k, Scalar val) { (*line(i, j, k, true))(i, j, k) *= val; }
+ void div(uint i, uint j, uint k, Scalar val) { (*line(i, j, k, true))(i, j, k) /= val; }
+
+ // return cache line for (i, j, k); may require write-back and fetch
+ CacheLine* line(uint i, uint j, uint k, bool write) const
+ {
+ CacheLine* p = 0;
+ uint b = block(i, j, k);
+ typename Cache<CacheLine>::Tag t = cache.access(p, b + 1, write);
+ uint c = t.index() - 1;
+ if (c != b) {
+ // write back occupied cache line if it is dirty
+ if (t.dirty())
+ encode(c, p->a);
+ // fetch cache line
+ decode(b, p->a);
+ }
+ return p;
+ }
+
+ // encode block with given index
+ void encode(uint index, const Scalar* block) const
+ {
+ stream_wseek(stream->stream, index * blkbits);
+ Codec::encode_block_3(stream, block, shape ? shape[index] : 0);
+ stream_flush(stream->stream);
+ }
+
+ // encode block with given index from strided array
+ void encode(uint index, const Scalar* p, int sx, int sy, int sz) const
+ {
+ stream_wseek(stream->stream, index * blkbits);
+ Codec::encode_block_strided_3(stream, p, shape ? shape[index] : 0, sx, sy, sz);
+ stream_flush(stream->stream);
+ }
+
+ // decode block with given index
+ void decode(uint index, Scalar* block) const
+ {
+ stream_rseek(stream->stream, index * blkbits);
+ Codec::decode_block_3(stream, block, shape ? shape[index] : 0);
+ }
+
+ // decode block with given index to strided array
+ void decode(uint index, Scalar* p, int sx, int sy, int sz) const
+ {
+ stream_rseek(stream->stream, index * blkbits);
+ Codec::decode_block_strided_3(stream, p, shape ? shape[index] : 0, sx, sy, sz);
+ }
+
+ // block index for (i, j, k)
+ uint block(uint i, uint j, uint k) const { return (i / 4) + bx * ((j / 4) + by * (k / 4)); }
+
+ // convert flat index to (i, j, k)
+ void ijk(uint& i, uint& j, uint& k, uint index) const
+ {
+ i = index % nx;
+ index /= nx;
+ j = index % ny;
+ index /= ny;
+ k = index;
+ }
+
+ // number of cache lines corresponding to size (or suggested size if zero)
+ static uint lines(size_t size, uint nx, uint ny, uint nz)
+ {
+ uint n = uint((size ? size : 8 * nx * ny * sizeof(Scalar)) / sizeof(CacheLine));
+ return std::max(n, 1u);
+ }
+
+ mutable Cache<CacheLine> cache; // cache of decompressed blocks
+};
+
+typedef array3<float> array3f;
+typedef array3<double> array3d;
+
+}
+
+#endif
diff --git a/src/zfp/zfp-0.5.0/array/zfpcodec.h b/src/zfp/zfp-0.5.0/array/zfpcodec.h
new file mode 100644
index 0000000..2d46744
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/array/zfpcodec.h
@@ -0,0 +1,17 @@
+#ifndef ZFP_CODEC_H
+#define ZFP_CODEC_H
+
+#include "zfp.h"
+
+namespace zfp {
+
+// C++ wrappers around libzfp C functions
+template <typename Scalar>
+struct codec {};
+
+#include "zfpcodecf.h"
+#include "zfpcodecd.h"
+
+}
+
+#endif
diff --git a/src/zfp/zfp-0.5.0/array/zfpcodecd.h b/src/zfp/zfp-0.5.0/array/zfpcodecd.h
new file mode 100644
index 0000000..9e7d893
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/array/zfpcodecd.h
@@ -0,0 +1,149 @@
+// double-precision codec
+template <>
+struct codec<double> {
+ // encode contiguous 1D block
+ static void encode_block_1(zfp_stream* zfp, const double* block, uint shape)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ zfp_encode_partial_block_strided_double_1(zfp, block, nx, 1);
+ }
+ else
+ zfp_encode_block_double_1(zfp, block);
+ }
+
+ // encode 1D block from strided storage
+ static void encode_block_strided_1(zfp_stream* zfp, const double* p, uint shape, int sx)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ zfp_encode_partial_block_strided_double_1(zfp, p, nx, sx);
+ }
+ else
+ zfp_encode_block_strided_double_1(zfp, p, sx);
+ }
+
+ // encode contiguous 2D block
+ static void encode_block_2(zfp_stream* zfp, const double* block, uint shape)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ uint ny = 4 - (shape & 3u); shape >>= 2;
+ zfp_encode_partial_block_strided_double_2(zfp, block, nx, ny, 1, 4);
+ }
+ else
+ zfp_encode_block_double_2(zfp, block);
+ }
+
+ // encode 2D block from strided storage
+ static void encode_block_strided_2(zfp_stream* zfp, const double* p, uint shape, int sx, int sy)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ uint ny = 4 - (shape & 3u); shape >>= 2;
+ zfp_encode_partial_block_strided_double_2(zfp, p, nx, ny, sx, sy);
+ }
+ else
+ zfp_encode_block_strided_double_2(zfp, p, sx, sy);
+ }
+
+ // encode contiguous 3D block
+ static void encode_block_3(zfp_stream* zfp, const double* block, uint shape)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ uint ny = 4 - (shape & 3u); shape >>= 2;
+ uint nz = 4 - (shape & 3u); shape >>= 2;
+ zfp_encode_partial_block_strided_double_3(zfp, block, nx, ny, nz, 1, 4, 16);
+ }
+ else
+ zfp_encode_block_double_3(zfp, block);
+ }
+
+ // encode 3D block from strided storage
+ static void encode_block_strided_3(zfp_stream* zfp, const double* p, uint shape, int sx, int sy, int sz)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ uint ny = 4 - (shape & 3u); shape >>= 2;
+ uint nz = 4 - (shape & 3u); shape >>= 2;
+ zfp_encode_partial_block_strided_double_3(zfp, p, nx, ny, nz, sx, sy, sz);
+ }
+ else
+ zfp_encode_block_strided_double_3(zfp, p, sx, sy, sz);
+ }
+
+ // decode contiguous 1D block
+ static void decode_block_1(zfp_stream* zfp, double* block, uint shape)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ zfp_decode_partial_block_strided_double_1(zfp, block, nx, 1);
+ }
+ else
+ zfp_decode_block_double_1(zfp, block);
+ }
+
+ // decode 1D block to strided storage
+ static void decode_block_strided_1(zfp_stream* zfp, double* p, uint shape, int sx)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ zfp_decode_partial_block_strided_double_1(zfp, p, nx, sx);
+ }
+ else
+ zfp_decode_block_strided_double_1(zfp, p, sx);
+ }
+
+ // decode contiguous 2D block
+ static void decode_block_2(zfp_stream* zfp, double* block, uint shape)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ uint ny = 4 - (shape & 3u); shape >>= 2;
+ zfp_decode_partial_block_strided_double_2(zfp, block, nx, ny, 1, 4);
+ }
+ else
+ zfp_decode_block_double_2(zfp, block);
+ }
+
+ // decode 2D block to strided storage
+ static void decode_block_strided_2(zfp_stream* zfp, double* p, uint shape, int sx, int sy)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ uint ny = 4 - (shape & 3u); shape >>= 2;
+ zfp_decode_partial_block_strided_double_2(zfp, p, nx, ny, sx, sy);
+ }
+ else
+ zfp_decode_block_strided_double_2(zfp, p, sx, sy);
+ }
+
+ // decode contiguous 3D block
+ static void decode_block_3(zfp_stream* zfp, double* block, uint shape)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ uint ny = 4 - (shape & 3u); shape >>= 2;
+ uint nz = 4 - (shape & 3u); shape >>= 2;
+ zfp_decode_partial_block_strided_double_3(zfp, block, nx, ny, nz, 1, 4, 16);
+ }
+ else
+ zfp_decode_block_double_3(zfp, block);
+ }
+
+ // decode 3D block to strided storage
+ static void decode_block_strided_3(zfp_stream* zfp, double* p, uint shape, int sx, int sy, int sz)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ uint ny = 4 - (shape & 3u); shape >>= 2;
+ uint nz = 4 - (shape & 3u); shape >>= 2;
+ zfp_decode_partial_block_strided_double_3(zfp, p, nx, ny, nz, sx, sy, sz);
+ }
+ else
+ zfp_decode_block_strided_double_3(zfp, p, sx, sy, sz);
+ }
+
+ static const zfp_type type = zfp_type_double;
+};
diff --git a/src/zfp/zfp-0.5.0/array/zfpcodecf.h b/src/zfp/zfp-0.5.0/array/zfpcodecf.h
new file mode 100644
index 0000000..1ec74a6
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/array/zfpcodecf.h
@@ -0,0 +1,149 @@
+// single-precision codec
+template <>
+struct codec<float> {
+ // encode contiguous 1D block
+ static void encode_block_1(zfp_stream* zfp, const float* block, uint shape)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ zfp_encode_partial_block_strided_float_1(zfp, block, nx, 1);
+ }
+ else
+ zfp_encode_block_float_1(zfp, block);
+ }
+
+ // encode 1D block from strided storage
+ static void encode_block_strided_1(zfp_stream* zfp, const float* p, uint shape, int sx)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ zfp_encode_partial_block_strided_float_1(zfp, p, nx, sx);
+ }
+ else
+ zfp_encode_block_strided_float_1(zfp, p, sx);
+ }
+
+ // encode contiguous 2D block
+ static void encode_block_2(zfp_stream* zfp, const float* block, uint shape)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ uint ny = 4 - (shape & 3u); shape >>= 2;
+ zfp_encode_partial_block_strided_float_2(zfp, block, nx, ny, 1, 4);
+ }
+ else
+ zfp_encode_block_float_2(zfp, block);
+ }
+
+ // encode 2D block from strided storage
+ static void encode_block_strided_2(zfp_stream* zfp, const float* p, uint shape, int sx, int sy)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ uint ny = 4 - (shape & 3u); shape >>= 2;
+ zfp_encode_partial_block_strided_float_2(zfp, p, nx, ny, sx, sy);
+ }
+ else
+ zfp_encode_block_strided_float_2(zfp, p, sx, sy);
+ }
+
+ // encode contiguous 3D block
+ static void encode_block_3(zfp_stream* zfp, const float* block, uint shape)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ uint ny = 4 - (shape & 3u); shape >>= 2;
+ uint nz = 4 - (shape & 3u); shape >>= 2;
+ zfp_encode_partial_block_strided_float_3(zfp, block, nx, ny, nz, 1, 4, 16);
+ }
+ else
+ zfp_encode_block_float_3(zfp, block);
+ }
+
+ // encode 3D block from strided storage
+ static void encode_block_strided_3(zfp_stream* zfp, const float* p, uint shape, int sx, int sy, int sz)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ uint ny = 4 - (shape & 3u); shape >>= 2;
+ uint nz = 4 - (shape & 3u); shape >>= 2;
+ zfp_encode_partial_block_strided_float_3(zfp, p, nx, ny, nz, sx, sy, sz);
+ }
+ else
+ zfp_encode_block_strided_float_3(zfp, p, sx, sy, sz);
+ }
+
+ // decode contiguous 1D block
+ static void decode_block_1(zfp_stream* zfp, float* block, uint shape)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ zfp_decode_partial_block_strided_float_1(zfp, block, nx, 1);
+ }
+ else
+ zfp_decode_block_float_1(zfp, block);
+ }
+
+ // decode 1D block to strided storage
+ static void decode_block_strided_1(zfp_stream* zfp, float* p, uint shape, int sx)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ zfp_decode_partial_block_strided_float_1(zfp, p, nx, sx);
+ }
+ else
+ zfp_decode_block_strided_float_1(zfp, p, sx);
+ }
+
+ // decode contiguous 2D block
+ static void decode_block_2(zfp_stream* zfp, float* block, uint shape)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ uint ny = 4 - (shape & 3u); shape >>= 2;
+ zfp_decode_partial_block_strided_float_2(zfp, block, nx, ny, 1, 4);
+ }
+ else
+ zfp_decode_block_float_2(zfp, block);
+ }
+
+ // decode 2D block to strided storage
+ static void decode_block_strided_2(zfp_stream* zfp, float* p, uint shape, int sx, int sy)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ uint ny = 4 - (shape & 3u); shape >>= 2;
+ zfp_decode_partial_block_strided_float_2(zfp, p, nx, ny, sx, sy);
+ }
+ else
+ zfp_decode_block_strided_float_2(zfp, p, sx, sy);
+ }
+
+ // decode contiguous 3D block
+ static void decode_block_3(zfp_stream* zfp, float* block, uint shape)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ uint ny = 4 - (shape & 3u); shape >>= 2;
+ uint nz = 4 - (shape & 3u); shape >>= 2;
+ zfp_decode_partial_block_strided_float_3(zfp, block, nx, ny, nz, 1, 4, 16);
+ }
+ else
+ zfp_decode_block_float_3(zfp, block);
+ }
+
+ // decode 3D block to strided storage
+ static void decode_block_strided_3(zfp_stream* zfp, float* p, uint shape, int sx, int sy, int sz)
+ {
+ if (shape) {
+ uint nx = 4 - (shape & 3u); shape >>= 2;
+ uint ny = 4 - (shape & 3u); shape >>= 2;
+ uint nz = 4 - (shape & 3u); shape >>= 2;
+ zfp_decode_partial_block_strided_float_3(zfp, p, nx, ny, nz, sx, sy, sz);
+ }
+ else
+ zfp_decode_block_strided_float_3(zfp, p, sx, sy, sz);
+ }
+
+ static const zfp_type type = zfp_type_float;
+};
diff --git a/src/zfp/zfp-0.5.0/examples/Makefile b/src/zfp/zfp-0.5.0/examples/Makefile
new file mode 100644
index 0000000..4f0ff71
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/examples/Makefile
@@ -0,0 +1,35 @@
+include ../Config
+
+TARGETS = diffusion-raw diffusion-zfp pgm simple speed testzfp zfp
+
+all: $(TARGETS)
+
+diffusion-raw: diffusion.cpp ../lib/libzfp.a
+ $(CXX) $(CXXFLAGS) -DWITHOUT_COMPRESSION -I../array diffusion.cpp -L../lib -lzfp -o diffusion-raw
+
+diffusion-zfp: diffusion.cpp ../lib/libzfp.a
+ $(CXX) $(CXXFLAGS) -I../array diffusion.cpp -L../lib -lzfp -o diffusion-zfp
+
+pgm: pgm.c ../lib/libzfp.a
+ $(CC) $(CFLAGS) pgm.c -L../lib -lzfp -lm -o pgm
+
+simple: simple.c ../lib/libzfp.a
+ $(CC) $(CFLAGS) simple.c -L../lib -lzfp -lm -o simple
+
+speed: speed.c ../lib/libzfp.a
+ $(CC) $(CFLAGS) speed.c -L../lib -lzfp -lm -o speed
+
+testzfp: testzfp.cpp fields.o ../lib/libzfp.a
+ $(CXX) $(CXXFLAGS) -I../array testzfp.cpp fields.o -L../lib -lzfp -o testzfp
+
+fields.o: fields.c
+ $(CC) $(CFLAGS) -c fields.c
+
+zfp: zfp.c ../lib/libzfp.a
+ $(CC) $(CFLAGS) zfp.c -L../lib -lzfp -lm -o zfp
+
+test: testzfp
+ ./testzfp
+
+clean:
+ rm -f $(TARGETS) fields.o
diff --git a/src/zfp/zfp-0.5.0/examples/array2d.h b/src/zfp/zfp-0.5.0/examples/array2d.h
new file mode 100644
index 0000000..7b9f92f
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/examples/array2d.h
@@ -0,0 +1,25 @@
+#ifndef ARRAY2D_H
+#define ARRAY2D_H
+
+#include <climits>
+#include <vector>
+
+typedef unsigned int uint;
+
+// uncompressed 2D double-precision array (for comparison)
+class array2d {
+public:
+ array2d(uint nx, uint ny, uint precision) : nx(nx), ny(ny), data(nx * ny, 0.0) {}
+ size_t size() const { return data.size(); }
+ double rate() const { return CHAR_BIT * sizeof(double); }
+ double& operator()(uint x, uint y) { return data[x + nx * y]; }
+ const double& operator()(uint x, uint y) const { return data[x + nx * y]; }
+ double& operator[](uint i) { return data[i]; }
+ const double& operator[](uint i) const { return data[i]; }
+protected:
+ uint nx;
+ uint ny;
+ std::vector<double> data;
+};
+
+#endif
diff --git a/src/zfp/zfp-0.5.0/examples/diffusion.cpp b/src/zfp/zfp-0.5.0/examples/diffusion.cpp
new file mode 100644
index 0000000..c0c1b4f
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/examples/diffusion.cpp
@@ -0,0 +1,107 @@
+// forward Euler finite difference solution to the heat equation on a 2D grid
+
+#include <algorithm>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <iomanip>
+#include <iostream>
+
+#ifdef WITHOUT_COMPRESSION
+ #include "array2d.h"
+#else
+ #include "zfparray2.h"
+ using namespace zfp;
+#endif
+
+int main(int argc, char* argv[])
+{
+ int nx = 0;
+ int ny = 0;
+ int nt = 0;
+ double rate = 64;
+
+ // parse arguments
+ switch (argc) {
+ case 5:
+ if (sscanf(argv[4], "%d", &nt) != 1)
+ goto usage;
+ // FALLTHROUGH
+ case 4:
+ if (sscanf(argv[2], "%d", &nx) != 1 ||
+ sscanf(argv[3], "%d", &ny) != 1)
+ goto usage;
+ // FALLTHROUGH
+ case 2:
+ if (sscanf(argv[1], "%lf", &rate) != 1)
+ goto usage;
+ // FALLTHROUGH
+ case 1:
+ break;
+ default:
+ usage:
+ std::cerr << "Usage: diffusion [rate] [nx] [ny] [nt]" << std::endl;
+ return EXIT_FAILURE;
+ }
+
+ // grid dimensions
+ if (nx == 0)
+ nx = 100;
+ if (ny == 0)
+ ny = nx;
+
+ // location of point heat source
+ int x0 = (nx - 1) / 2;
+ int y0 = (ny - 1) / 2;
+
+ // constants used in the solution
+ const double k = 0.04;
+ const double dx = 2.0 / (std::max(nx, ny) - 1);
+ const double dy = 2.0 / (std::max(nx, ny) - 1);
+ const double dt = 0.5 * (dx * dx + dy * dy) / (8 * k);
+ const double tfinal = nt ? nt * dt : 1;
+ const double pi = 3.14159265358979323846;
+
+ // initialize u (constructor zero-initializes)
+ array2d u(nx, ny, rate);
+ rate = u.rate();
+ u(x0, y0) = 1;
+
+ // iterate until final time
+ std::cerr.precision(6);
+ double t;
+ for (t = 0; t < tfinal; t += dt) {
+ std::cerr << "t=" << std::fixed << t << std::endl;
+ // compute du/dt
+ array2d du(nx, ny, rate);
+ for (int y = 1; y < ny - 1; y++) {
+ for (int x = 1; x < nx - 1; x++) {
+ double uxx = (u(x - 1, y) - 2 * u(x, y) + u(x + 1, y)) / (dx * dx);
+ double uyy = (u(x, y - 1) - 2 * u(x, y) + u(x, y + 1)) / (dy * dy);
+ du(x, y) = dt * k * (uxx + uyy);
+ }
+ }
+ // take forward Euler step
+ for (uint i = 0; i < u.size(); i++)
+ u[i] += du[i];
+ }
+
+ // compute root mean square error with respect to exact solution
+ double e = 0;
+ double sum = 0;
+ for (int y = 1; y < ny - 1; y++) {
+ double py = dy * (y - y0);
+ for (int x = 1; x < nx - 1; x++) {
+ double px = dx * (x - x0);
+ double f = u(x, y);
+ double g = dx * dy * std::exp(-(px * px + py * py) / (4 * k * t)) / (4 * pi * k * t);
+ e += (f - g) * (f - g);
+ sum += f;
+ }
+ }
+ e = std::sqrt(e / ((nx - 2) * (ny - 2)));
+ std::cerr.unsetf(std::ios::fixed);
+ std::cerr << "rate=" << rate << " sum=" << std::fixed << sum << " error=" << std::setprecision(6) << std::scientific << e << std::endl;
+
+ return 0;
+}
diff --git a/src/zfp/zfp-0.5.0/examples/fields.c b/src/zfp/zfp-0.5.0/examples/fields.c
new file mode 100644
index 0000000..8d4bab4
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/examples/fields.c
@@ -0,0 +1,12201 @@
+/* single- and double-precision fields for regression testing */
+
+const float array_float[3][4096] = {
+#if __STDC_VERSION__ >= 199901L
+/* C99: hex floats for exact reproduction */
+{
+-0x1.1fd6p-9,-0x1.af43p-8,-0x1.66f98p-7,-0x1.f5fep-7,-0x1.42578p-6,-0x1.8986p-6,
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+0x1.4319a4p-2,0x1.1cd016p+0,0x1.5844bap+1,
+}
+#else
+/* C89: decimal floats; may not reproduce exactly */
+{
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+9.70994413e-04,1.66106492e-03,1.10154832e-03,1.87671190e-04,2.62273417e-04,
+3.11580813e-03,1.09863412e-02,2.65595540e-02,-1.09884165e-01,-2.38172367e-01,
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+-1.68253630e-02,1.15354136e-02,1.97334513e-02,1.30863935e-02,2.22953386e-03,
+3.11580813e-03,3.70157994e-02,1.30517736e-01,3.15527499e-01,-3.87451649e-01,
+-8.39795947e-01,-9.69483614e-01,-8.89014781e-01,-6.92139506e-01,-4.53857988e-01,
+-2.30420202e-01,-5.93262427e-02,4.06738780e-02,6.95801601e-02,4.61426340e-02,
+7.86133762e-03,1.09863412e-02,1.30517736e-01,4.60205644e-01,1.11255014e+00,
+-9.36666906e-01,-2.03021216e+00,-2.34373283e+00,-2.14919901e+00,-1.67325187e+00,
+-1.09720469e+00,-5.57042360e-01,-1.43421590e-01,9.83293653e-02,1.68210492e-01,
+1.11550115e-01,1.90048367e-02,2.65595540e-02,3.15527499e-01,1.11255014e+00,
+2.68959737e+00,
+}
+#endif
+};
+
+const double array_double[3][4096] = {
+#if __STDC_VERSION__ >= 199901L
+/* C99: hex floats for exact reproduction */
+{
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+-0x1.2f0bc57cdf8p-5,-0x1.524fb861778p-5,-0x1.757ee424278p-5,-0x1.98994ebd6f8p-5,
+-0x1.bb9efe250f8p-5,-0x1.de8ff852078p-5,-0x1.00b6219d4bcp-4,-0x1.1219f26a1fcp-4,
+-0x1.23737189dfcp-4,-0x1.34c2a1f68bcp-4,-0x1.460786a9c3cp-4,-0x1.5742229cc7cp-4,
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+-0x1.accd53124fcp-4,-0x1.bdca78e15bcp-4,-0x1.cebd6ab673cp-4,-0x1.dfa62b87d7cp-4,
+-0x1.f084be4b67cp-4,-0x1.00ac92fb51ep-3,-0x1.0911b2bf55ep-3,-0x1.1171bfec1fep-3,
+-0x1.19ccbbfbdfep-3,-0x1.2222a86895ep-3,-0x1.2a7386ac11ep-3,-0x1.32bf583ff3ep-3,
+-0x1.3b061e9dabep-3,-0x1.4347db3e79ep-3,-0x1.4b848f9b6dep-3,-0x1.53bc3d2d67ep-3,
+-0x1.5beee56d17ep-3,-0x1.641c89d2fdep-3,-0x1.6c452bd769ep-3,-0x1.7468ccf27bep-3,
+-0x1.7c876e9c23ep-3,-0x1.84a1124c21ep-3,-0x1.8cb5b97a05ep-3,-0x1.94c5659d2fep-3,
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+-0x1.bcc93ff11bep-3,-0x1.c4bb289449ep-3,-0x1.cca8206b1dep-3,-0x1.d49028eb77ep-3,
+-0x1.dc73438b07ep-3,-0x1.e45171bf4dep-3,-0x1.ec2ab4fd99ep-3,-0x1.f3ff0ebb0bep-3,
+-0x1.fbce806c93ep-3,-0x1.01cc85c378fp-2,-0x1.05af58bf5afp-2,-0x1.098fb9e41ffp-2,
+-0x1.0d6da9ebdffp-2,-0x1.114929909afp-2,-0x1.1522398c38fp-2,-0x1.18f8da9889fp-2,
+-0x1.1ccd0d6f45fp-2,-0x1.209ed2ca0cfp-2,-0x1.246e2b6266fp-2,-0x1.283b17f1c3fp-2,
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+-0x1.4a02e2be57fp-2,-0x1.4db7beb642fp-2,-0x1.516a3696d0fp-2,-0x1.551a4b1851fp-2,
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+-0x1.6766f83a73fp-2,-0x1.6b08c79af6fp-2,-0x1.6ea838a3fcfp-2,-0x1.72454c0d15fp-2,
+-0x1.75e0028db9fp-2,-0x1.79785cdd48fp-2,-0x1.7d0e5bb30afp-2,-0x1.80a1ffc62ffp-2,
+-0x1.843349cdcffp-2,-0x1.87c23a80eafp-2,-0x1.8b4ed29668fp-2,-0x1.8ed912c519fp-2,
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+-0x1.a06946206bfp-2,-0x1.a3e585e01efp-2,-0x1.a75f72b614fp-2,-0x1.aad70d585dfp-2,
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+-0x1.4c514e40fdf8p-1,-0x1.4db7dc28a1f8p-1,-0x1.4f1d5c227378p-1,
+-0x1.5081ce85c678p-1,-0x1.51e533a9e2f8p-1,-0x1.53478be604f8p-1,
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+-0x1.ac5a3bd157cp+0,-0x1.18e2678493cp+0,-0x1.1d34a820378p-1,-0x1.25ba37a57ep-3,
+0x1.92c1d0d504p-4,0x1.587ebfaf22p-3,0x1.c8e8c856c4p-4,0x1.37600f2a1p-6,
+0x1.b326d72e1p-6,0x1.4319a39c71p-2,0x1.1cd0169db44p+0,0x1.5844ba81602p+1,
+}
+#else
+/* C89: decimal floats; may not reproduce exactly */
+{
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+-5.5704236405631491e-01,-1.4342158769409252e-01,9.8329368353233804e-02,
+1.6821050408566407e-01,1.1155012376207196e-01,1.9004835900204853e-02,
+2.6559553276683801e-02,3.1552749292700355e-01,1.1125501761455325e+00,
+2.6895974284855129e+00,
+}
+#endif
+};
diff --git a/src/zfp/zfp-0.5.0/examples/fields.h b/src/zfp/zfp-0.5.0/examples/fields.h
new file mode 100644
index 0000000..f558cfb
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/examples/fields.h
@@ -0,0 +1,20 @@
+#ifndef FIELDS_H
+#define FIELDS_H
+
+// single- and double-precision fields for regression testing
+
+extern const float array_float[3][4096];
+extern const double array_double[3][4096];
+
+template <typename Scalar>
+struct Field {
+ static const Scalar (*array)[4096];
+};
+
+template <>
+const float (*Field<float>::array)[4096] = array_float;
+
+template <>
+const double (*Field<double>::array)[4096] = array_double;
+
+#endif
diff --git a/src/zfp/zfp-0.5.0/examples/pgm.c b/src/zfp/zfp-0.5.0/examples/pgm.c
new file mode 100644
index 0000000..92113ad
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/examples/pgm.c
@@ -0,0 +1,112 @@
+/* simple example that shows how zfp can be used to compress pgm images */
+
+#include <limits.h>
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "zfp.h"
+
+int main(int argc, char* argv[])
+{
+ double rate = 0;
+ uint nx, ny;
+ uint x, y;
+ char line[0x100];
+ uchar* image;
+ zfp_field* field;
+ zfp_stream* zfp;
+ bitstream* stream;
+ void* buffer;
+ size_t bytes;
+ size_t size;
+
+ switch (argc) {
+ case 2:
+ if (sscanf(argv[1], "%lf", &rate) != 1)
+ goto usage;
+ break;
+ default:
+ usage:
+ fprintf(stderr, "Usage: pgm <rate|-precision> <input.pgm >output.pgm\n");
+ return EXIT_FAILURE;
+ }
+
+ /* read pgm header */
+ if (!fgets(line, sizeof(line), stdin) || strcmp(line, "P5\n") ||
+ !fgets(line, sizeof(line), stdin) || sscanf(line, "%u%u", &nx, &ny) != 2 ||
+ !fgets(line, sizeof(line), stdin) || strcmp(line, "255\n")) {
+ fprintf(stderr, "error opening image\n");
+ return EXIT_FAILURE;
+ }
+
+ if ((nx & 3u) || (ny & 3u)) {
+ fprintf(stderr, "image dimensions must be multiples of four\n");
+ return EXIT_FAILURE;
+ }
+
+ /* read image data */
+ image = malloc(nx * ny);
+ if (fread(image, sizeof(*image), nx * ny, stdin) != nx * ny) {
+ fprintf(stderr, "error reading image\n");
+ return EXIT_FAILURE;
+ }
+
+ /* create input array */
+ field = zfp_field_2d(image, zfp_type_int32, nx, ny);
+
+ /* initialize compressed stream */
+ zfp = zfp_stream_open(NULL);
+ if (rate < 0)
+ zfp_stream_set_precision(zfp, (uint)floor(0.5 - rate), zfp_type_int32);
+ else
+ zfp_stream_set_rate(zfp, rate, zfp_type_int32, 2, 0);
+ bytes = zfp_stream_maximum_size(zfp, field);
+ buffer = malloc(bytes);
+ stream = stream_open(buffer, bytes);
+ zfp_stream_set_bit_stream(zfp, stream);
+ zfp_field_free(field);
+
+ /* compress */
+ for (y = 0; y < ny; y += 4)
+ for (x = 0; x < nx; x += 4) {
+ uchar ublock[16];
+ int32 iblock[16];
+ uint i, j;
+ for (j = 0; j < 4; j++)
+ for (i = 0; i < 4; i++)
+ ublock[i + 4 * j] = image[x + i + nx * (y + j)];
+ zfp_promote_uint8_to_int32(iblock, ublock, 2);
+ zfp_encode_block_int32_2(zfp, iblock);
+ }
+
+ zfp_stream_flush(zfp);
+ size = zfp_stream_compressed_size(zfp);
+ fprintf(stderr, "%u compressed bytes (%.2f bps)\n", (uint)size, (double)size * CHAR_BIT / (nx * ny));
+
+ /* decompress */
+ zfp_stream_rewind(zfp);
+ for (y = 0; y < ny; y += 4)
+ for (x = 0; x < nx; x += 4) {
+ int32 iblock[16];
+ uchar ublock[16];
+ uint i, j;
+ zfp_decode_block_int32_2(zfp, iblock);
+ zfp_demote_int32_to_uint8(ublock, iblock, 2);
+ for (j = 0; j < 4; j++)
+ for (i = 0; i < 4; i++)
+ image[x + i + nx * (y + j)] = ublock[i + 4 * j];
+ }
+ zfp_stream_close(zfp);
+ stream_close(stream);
+ free(buffer);
+
+ /* output reconstructed image */
+ printf("P5\n");
+ printf("%u %u\n", nx, ny);
+ printf("255\n");
+ fwrite(image, sizeof(*image), nx * ny, stdout);
+ free(image);
+
+ return 0;
+}
diff --git a/src/zfp/zfp-0.5.0/examples/simple.c b/src/zfp/zfp-0.5.0/examples/simple.c
new file mode 100644
index 0000000..4f52f62
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/examples/simple.c
@@ -0,0 +1,99 @@
+/* minimal code example showing how to call the zfp (de)compressor */
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "zfp.h"
+
+/* compress or decompress array */
+static int
+compress(double* array, int nx, int ny, int nz, double tolerance, int decompress)
+{
+ int status = 0; /* return value: 0 = success */
+ zfp_type type; /* array scalar type */
+ zfp_field* field; /* array meta data */
+ zfp_stream* zfp; /* compressed stream */
+ void* buffer; /* storage for compressed stream */
+ size_t bufsize; /* byte size of compressed buffer */
+ bitstream* stream; /* bit stream to write to or read from */
+ size_t zfpsize; /* byte size of compressed stream */
+
+ /* allocate meta data for the 3D array a[nz][ny][nx] */
+ type = zfp_type_double;
+ field = zfp_field_3d(array, type, nx, ny, nz);
+
+ /* allocate meta data for a compressed stream */
+ zfp = zfp_stream_open(NULL);
+
+ /* set compression mode and parameters via one of three functions */
+/* zfp_stream_set_rate(zfp, rate, type, 3, 0); */
+/* zfp_stream_set_precision(zfp, precision, type); */
+ zfp_stream_set_accuracy(zfp, tolerance, type);
+
+ /* allocate buffer for compressed data */
+ bufsize = zfp_stream_maximum_size(zfp, field);
+ buffer = malloc(bufsize);
+
+ /* associate bit stream with allocated buffer */
+ stream = stream_open(buffer, bufsize);
+ zfp_stream_set_bit_stream(zfp, stream);
+ zfp_stream_rewind(zfp);
+
+ /* compress or decompress entire array */
+ if (decompress) {
+ /* read compressed stream and decompress array */
+ zfpsize = fread(buffer, 1, bufsize, stdin);
+ if (!zfp_decompress(zfp, field)) {
+ fprintf(stderr, "decompression failed\n");
+ status = 1;
+ }
+ }
+ else {
+ /* compress array and output compressed stream */
+ zfpsize = zfp_compress(zfp, field);
+ if (!zfpsize) {
+ fprintf(stderr, "compression failed\n");
+ status = 1;
+ }
+ else
+ fwrite(buffer, 1, zfpsize, stdout);
+ }
+
+ /* clean up */
+ zfp_field_free(field);
+ zfp_stream_close(zfp);
+ stream_close(stream);
+ free(buffer);
+ free(array);
+
+ return status;
+}
+
+int main(int argc, char* argv[])
+{
+ /* use -d to decompress rather than compress data */
+ int decompress = (argc == 2 && !strcmp(argv[1], "-d"));
+
+ /* allocate 100x100x100 array of doubles */
+ int nx = 100;
+ int ny = 100;
+ int nz = 100;
+ double* array = malloc(nx * ny * nz * sizeof(double));
+
+ if (!decompress) {
+ /* initialize array to be compressed */
+ int i, j, k;
+ for (k = 0; k < nz; k++)
+ for (j = 0; j < ny; j++)
+ for (i = 0; i < nx; i++) {
+ double x = 2.0 * i / nx;
+ double y = 2.0 * j / ny;
+ double z = 2.0 * k / nz;
+ array[i + nx * (j + ny * k)] = exp(-(x * x + y * y + z * z));
+ }
+ }
+
+ /* compress or decompress array */
+ return compress(array, nx, ny, nz, 1e-3, decompress);
+}
diff --git a/src/zfp/zfp-0.5.0/examples/speed.c b/src/zfp/zfp-0.5.0/examples/speed.c
new file mode 100644
index 0000000..1311da1
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/examples/speed.c
@@ -0,0 +1,136 @@
+/* measure the throughput of encoding and decoding 3D blocks of doubles */
+
+#include <limits.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <time.h>
+#include "zfp.h"
+
+/* example 3D block of (reinterpreted) doubles */
+static const uint64 block[] = {
+0xbf7c3a7bb8495ca9ull,
+0xbf79f9d9058ffdafull,
+0xbf77c7abd0b61999ull,
+0xbf75a42c806bd1daull,
+0xbf738f8f740b8ea8ull,
+0xbf718a050399fef8ull,
+0xbf6f2772ff8c30feull,
+0xbf6b59aa63d22f68ull,
+0xbf67aaf8b80cff9eull,
+0xbf641b9e71983592ull,
+0xbf60abd3f723f2b7ull,
+0xbf5ab7934169cc04ull,
+0xbf54574f6f4897d3ull,
+0xbf4c6e39da7fb99bull,
+0xbf40ae5826a893d1ull,
+0xbf25bce8e19d48e1ull,
+0x3f253bfed65904d7ull,
+0x3f3f18ab46a04cf3ull,
+0x3f4948e7cb74278bull,
+0x3f51427b51aeec2eull,
+0x3f55a0716d8b4b6bull,
+0x3f59be96aeaac56full,
+0x3f5d9d3ba7bfd327ull,
+0x3f609e608469e93eull,
+0x3f624ecbcfa3832cull,
+0x3f63e0202ae84b4dull,
+0x3f6552a61a3f4812ull,
+0x3f66a6ae305af268ull,
+0x3f67dc910e9935bcull,
+0x3f68f4af65036ff7ull,
+0x3f69ef71f24e7182ull,
+0x3f6acd4983da7d43ull,
+0x3f6b8eaef5b348a0ull,
+0x3f6c3423328ffb7aull,
+0x3f6cbe2f33d33034ull,
+0x3f6d2d64018af3acull,
+0x3f6d825ab270c540ull,
+0x3f6dbdb46be996ccull,
+0x3f6de01a6205cca9ull,
+0x3f6dea3dd7813dafull,
+0x3f6ddcd81dc33335ull,
+0x3f6db8aa94de690full,
+0x3f6d7e7eab910d8full,
+0x3f6d2f25df44c187ull,
+0x3f6ccb79bc0e9844ull,
+0x3f6c545bdcaf1795ull,
+0x3f6bcab5ea9237c4ull,
+0x3f6b2f799dcf639bull,
+0x3f6a83a0bd297862ull,
+0x3f69c82d1e0ec5deull,
+0x3f68fe28a4990e53ull,
+0x3f6826a5438d8685ull,
+0x3f6742bcfc5cd5b2ull,
+0x3f665391df231599ull,
+0x3f655a4e0aa7d278ull,
+0x3f645823ac5e0b09ull,
+0x3f634e4d00643085ull,
+0x3f623e0c518426a3ull,
+0x3f6128abf933439aull,
+0x3f600f7e5f92501cull,
+0x3f5de7bbf6db0eb7ull,
+0x3f5bae5aa4792e11ull,
+0x3f5975adf0453ea2ull,
+0x3f57409b1fdc65c4ull,
+};
+
+int main(int argc, char* argv[])
+{
+ size_t n = 0x200000;
+ double rate = 1;
+ zfp_field* field;
+ uint insize;
+ zfp_stream* zfp;
+ bitstream* stream;
+ void* buffer;
+ size_t bytes;
+ clock_t c;
+ double time;
+ uint i;
+
+ switch (argc) {
+ case 3:
+ sscanf(argv[2], "%zu", &n);
+ /* FALLTHROUGH */
+ case 2:
+ sscanf(argv[1], "%lf", &rate);
+ break;
+ }
+
+ /* declare array to compress */
+ field = zfp_field_3d(NULL, zfp_type_double, 4, 4, 4 * n);
+ insize = n * sizeof(block);
+
+ /* allocate storage for compressed bit stream */
+ zfp = zfp_stream_open(NULL);
+ zfp_stream_set_rate(zfp, rate, zfp_field_type(field), zfp_field_dimensionality(field), 0);
+ bytes = zfp_stream_maximum_size(zfp, field);
+ buffer = malloc(bytes);
+ stream = stream_open(buffer, bytes);
+ zfp_stream_set_bit_stream(zfp, stream);
+ zfp_field_free(field);
+
+ /* compress */
+ c = clock();
+ for (i = 0; i < n; i++)
+ zfp_encode_block_double_3(zfp, (const double*)block);
+ zfp_stream_flush(zfp);
+ time = (double)(clock() - c) / CLOCKS_PER_SEC;
+ printf("encode in=%u out=%u %.0f MB/s\n", insize, (uint)stream_size(stream), insize / (1024 * 1024 * time));
+
+ /* decompress */
+ zfp_stream_rewind(zfp);
+ c = clock();
+ for (i = 0; i < n; i++) {
+ double a[64];
+ zfp_decode_block_double_3(zfp, a);
+ }
+ time = (double)(clock() - c) / CLOCKS_PER_SEC;
+ printf("decode in=%u out=%u %.0f MB/s\n", (uint)stream_size(stream), insize, insize / (1024 * 1024 * time));
+
+ zfp_stream_close(zfp);
+ stream_close(stream);
+ free(buffer);
+
+ return 0;
+}
diff --git a/src/zfp/zfp-0.5.0/examples/testzfp.cpp b/src/zfp/zfp-0.5.0/examples/testzfp.cpp
new file mode 100644
index 0000000..7fcc835
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/examples/testzfp.cpp
@@ -0,0 +1,705 @@
+#include <algorithm>
+#include <cmath>
+#include <ctime>
+#include <cstdio>
+#include <cstdlib>
+#include <iomanip>
+#include <iostream>
+#include <limits>
+#include <numeric>
+#include <sstream>
+#include <string>
+#include "zfp.h"
+#include "zfparray1.h"
+#include "zfparray2.h"
+#include "zfparray3.h"
+
+// size of arrays to test
+#ifdef TESTZFP_LARGE_ARRAYS
+ #define TEST_SIZE 16 // 16^6 = 16 M scalars
+ #define WITH_TIMINGS
+#elif defined(TESTZFP_MEDIUM_ARRAYS)
+ #define TEST_SIZE 8 // 8^6 = 256 K scalars
+#else
+ #define TEST_SIZE 4 // 4^6 = 4096 scalars
+ #include "fields.h"
+#endif
+
+typedef unsigned char uchar;
+typedef unsigned long long uint64;
+
+int width = 72; // characters per line
+
+// polynomial x - 3 x^2 + 4 x^4
+template <typename Scalar>
+inline Scalar
+polynomial(volatile Scalar x)
+{
+ // volatile used to ensure bit-for-bit reproducibility across compilers
+ volatile Scalar xx = x * x;
+ volatile Scalar yy = 4 * xx - 3;
+ volatile Scalar p = x + xx * yy;
+ return p;
+}
+
+// initialize array
+template <typename Scalar>
+inline void
+initialize(Scalar* p, int nx, int ny, int nz, Scalar (*f)(Scalar))
+{
+ nx = std::max(nx, 1);
+ ny = std::max(ny, 1);
+ nz = std::max(nz, 1);
+#if TEST_SIZE == 4
+ // use precomputed small arrays for portability
+ uint d = nz == 1 ? ny == 1 ? 0 : 1 : 2;
+ std::copy(&Field<Scalar>::array[d][0], &Field<Scalar>::array[d][0] + nx * ny * nz, p);
+#else
+ for (int k = 0; k < nz; k++) {
+ volatile Scalar z = Scalar(2 * k - nz + 1) / nz;
+ volatile Scalar fz = nz > 1 ? f(z) : Scalar(1);
+ for (int j = 0; j < ny; j++) {
+ volatile Scalar y = Scalar(2 * j - ny + 1) / ny;
+ volatile Scalar fy = ny > 1 ? f(y) : Scalar(1);
+ for (int i = 0; i < nx; i++) {
+ volatile Scalar x = Scalar(2 * i - nx + 1) / nx;
+ volatile Scalar fx = nx > 1 ? f(x) : Scalar(1);
+ *p++ = fx * fy * fz;
+ }
+ }
+ }
+#endif
+}
+
+// compute checksum
+inline uint32
+hash(const void* p, size_t n)
+{
+ uint32 h = 0;
+ for (const uchar* q = static_cast<const uchar*>(p); n; q++, n--) {
+ // Jenkins one-at-a-time hash; see http://www.burtleburtle.net/bob/hash/doobs.html
+ h += *q;
+ h += h << 10;
+ h ^= h >> 6;
+ }
+ h += h << 3;
+ h ^= h >> 11;
+ h += h << 15;
+ return h;
+}
+
+// test fixed-rate mode
+template <typename Scalar>
+inline uint
+test_rate(zfp_stream* stream, const zfp_field* input, double rate, Scalar tolerance)
+{
+ uint failures = 0;
+ uint n = zfp_field_size(input, NULL);
+ uint dims = zfp_field_dimensionality(input);
+ zfp_type type = zfp_field_type(input);
+
+ // allocate memory for compressed data
+ rate = zfp_stream_set_rate(stream, rate, type, dims, 0);
+ size_t bufsize = zfp_stream_maximum_size(stream, input);
+ uchar* buffer = new uchar[bufsize];
+ bitstream* s = stream_open(buffer, bufsize);
+ zfp_stream_set_bit_stream(stream, s);
+
+ // perform compression test
+ std::ostringstream status;
+ status << " compress: ";
+ status << " rate=" << std::fixed << std::setprecision(0) << std::setw(2) << rate;
+#ifdef WITH_TIMINGS
+ clock_t c = clock();
+#endif
+ zfp_stream_rewind(stream);
+ size_t outsize = zfp_compress(stream, input);
+#ifdef WITH_TIMINGS
+ double time = double(clock() - c) / CLOCKS_PER_SEC;
+ double throughput = (n * sizeof(Scalar)) / (0x100000 * time);
+ status << " throughput=" << std::setprecision(1) << std::setw(6) << throughput << " MB/s";
+#endif
+ bool pass = true;
+ // make sure compressed size matches rate
+ size_t bytes = (size_t)floor(rate * zfp_field_size(input, NULL) / CHAR_BIT + 0.5);
+ if (outsize != bytes) {
+ status << " [" << outsize << " != " << bytes << "]";
+ pass = false;
+ }
+ std::cout << std::setw(width) << std::left << status.str() << (pass ? " OK " : "FAIL") << std::endl;
+ if (!pass)
+ failures++;
+
+ // perform decompression test
+ status.str("");
+ status << " decompress:";
+ status << " rate=" << std::fixed << std::setprecision(0) << std::setw(2) << rate;
+ Scalar* g = new Scalar[n];
+ zfp_field* output = zfp_field_alloc();
+ *output = *input;
+ zfp_field_set_pointer(output, g);
+#ifdef WITH_TIMINGS
+ c = clock();
+#endif
+ zfp_stream_rewind(stream);
+ pass = zfp_decompress(stream, output);
+ if (!pass)
+ status << " [decompression failed]";
+ else {
+#ifdef WITH_TIMINGS
+ double time = double(clock() - c) / CLOCKS_PER_SEC;
+ double throughput = (n * sizeof(Scalar)) / (0x100000 * time);
+ status << " throughput=" << std::setprecision(1) << std::setw(6) << throughput << " MB/s";
+#endif
+ // compute max error
+ Scalar* f = static_cast<Scalar*>(zfp_field_pointer(input));
+ Scalar emax = 0;
+ for (uint i = 0; i < n; i++)
+ emax = std::max(emax, std::abs(f[i] - g[i]));
+ status << std::scientific;
+ status.precision(3);
+ // make sure max error is within tolerance
+ if (emax <= tolerance)
+ status << " " << emax << " <= " << tolerance;
+ else {
+ status << " [" << emax << " > " << tolerance << "]";
+ pass = false;
+ }
+ }
+ zfp_field_free(output);
+ delete[] g;
+ stream_close(s);
+ delete[] buffer;
+ std::cout << std::setw(width) << std::left << status.str() << (pass ? " OK " : "FAIL") << std::endl;
+ if (!pass)
+ failures++;
+
+ return failures;
+}
+
+// test fixed-precision mode
+template <typename Scalar>
+inline uint
+test_precision(zfp_stream* stream, const zfp_field* input, uint precision, size_t bytes)
+{
+ uint failures = 0;
+ uint n = zfp_field_size(input, NULL);
+ zfp_type type = zfp_field_type(input);
+
+ // allocate memory for compressed data
+ zfp_stream_set_precision(stream, precision, type);
+ size_t bufsize = zfp_stream_maximum_size(stream, input);
+ uchar* buffer = new uchar[bufsize];
+ bitstream* s = stream_open(buffer, bufsize);
+ zfp_stream_set_bit_stream(stream, s);
+
+ // perform compression test
+ std::ostringstream status;
+ status << " compress: ";
+ status << " precision=" << std::setw(2) << precision;
+ zfp_stream_rewind(stream);
+ size_t outsize = zfp_compress(stream, input);
+ double ratio = double(n * sizeof(Scalar)) / outsize;
+ status << " ratio=" << std::fixed << std::setprecision(3) << std::setw(7) << ratio;
+ bool pass = true;
+ // make sure compressed size agrees
+ if (outsize != bytes) {
+ status << " [" << outsize << " != " << bytes << "]";
+ pass = false;
+ }
+ std::cout << std::setw(width) << std::left << status.str() << (pass ? " OK " : "FAIL") << std::endl;
+ if (!pass)
+ failures++;
+
+ // perform decompression test
+ status.str("");
+ status << " decompress:";
+ status << " precision=" << std::setw(2) << precision;
+ Scalar* g = new Scalar[n];
+ zfp_field* output = zfp_field_alloc();
+ *output = *input;
+ zfp_field_set_pointer(output, g);
+ zfp_stream_rewind(stream);
+ pass = zfp_decompress(stream, output);
+ if (!pass)
+ status << " [decompression failed]";
+ zfp_field_free(output);
+ delete[] g;
+ stream_close(s);
+ delete[] buffer;
+ std::cout << std::setw(width) << std::left << status.str() << (pass ? " OK " : "FAIL") << std::endl;
+ if (!pass)
+ failures++;
+
+ return failures;
+}
+
+// test fixed-accuracy mode
+template <typename Scalar>
+inline uint
+test_accuracy(zfp_stream* stream, const zfp_field* input, Scalar tolerance, size_t bytes)
+{
+ uint failures = 0;
+ uint n = zfp_field_size(input, NULL);
+ zfp_type type = zfp_field_type(input);
+
+ // allocate memory for compressed data
+ tolerance = zfp_stream_set_accuracy(stream, tolerance, type);
+ size_t bufsize = zfp_stream_maximum_size(stream, input);
+ uchar* buffer = new uchar[bufsize];
+ bitstream* s = stream_open(buffer, bufsize);
+ zfp_stream_set_bit_stream(stream, s);
+
+ // perform compression test
+ std::ostringstream status;
+ status << " compress: ";
+ status << " tolerance=" << std::scientific << std::setprecision(3) << tolerance;
+ zfp_stream_rewind(stream);
+ size_t outsize = zfp_compress(stream, input);
+ double ratio = double(n * sizeof(Scalar)) / outsize;
+ status << " ratio=" << std::fixed << std::setprecision(3) << std::setw(7) << ratio;
+ bool pass = true;
+ // make sure compressed size agrees
+ if (outsize != bytes) {
+ status << " [" << outsize << " != " << bytes << "]";
+ pass = false;
+ }
+ std::cout << std::setw(width) << std::left << status.str() << (pass ? " OK " : "FAIL") << std::endl;
+ if (!pass)
+ failures++;
+
+ // perform decompression test
+ status.str("");
+ status << " decompress:";
+ status << " tolerance=" << std::scientific << std::setprecision(3) << tolerance;
+ Scalar* g = new Scalar[n];
+ zfp_field* output = zfp_field_alloc();
+ *output = *input;
+ zfp_field_set_pointer(output, g);
+ zfp_stream_rewind(stream);
+ pass = zfp_decompress(stream, output);
+ if (!pass)
+ status << " [decompression failed]";
+ else {
+ // compute max error
+ Scalar* f = static_cast<Scalar*>(zfp_field_pointer(input));
+ Scalar emax = 0;
+ for (uint i = 0; i < n; i++)
+ emax = std::max(emax, std::abs(f[i] - g[i]));
+ status << std::scientific << std::setprecision(3) << " ";
+ // make sure max error is within tolerance
+ if (emax <= tolerance)
+ status << emax << " <= " << tolerance;
+ else if (tolerance == 0)
+ status << "(" << emax << " > 0)";
+ else {
+ status << "[" << emax << " > " << tolerance << "]";
+ pass = false;
+ }
+ }
+ zfp_field_free(output);
+ delete[] g;
+ stream_close(s);
+ delete[] buffer;
+ std::cout << std::setw(width) << std::left << status.str() << (pass ? " OK " : "FAIL") << std::endl;
+ if (!pass)
+ failures++;
+
+ return failures;
+}
+
+// perform 1D differencing
+template <typename Scalar>
+inline void
+update_array1(zfp::array1<Scalar>& a)
+{
+ for (uint i = 0; i < a.size() - 1; i++)
+ a(i) -= a(i + 1);
+ for (uint i = 0; i < a.size() - 1; i++)
+ a(0) = std::max(a(0), a(i));
+}
+
+// perform 2D differencing
+template <typename Scalar>
+inline void
+update_array2(zfp::array2<Scalar>& a)
+{
+ for (uint j = 0; j < a.size_y(); j++)
+ for (uint i = 0; i < a.size_x() - 1; i++)
+ a(i, j) -= a(i + 1, j);
+ for (uint j = 0; j < a.size_y() - 1; j++)
+ for (uint i = 0; i < a.size_x(); i++)
+ a(i, j) -= a(i, j + 1);
+ for (uint j = 0; j < a.size_y() - 1; j++)
+ for (uint i = 0; i < a.size_x() - 1; i++)
+ a(0, 0) = std::max(a(0, 0), a(i, j));
+}
+
+// perform 3D differencing
+template <typename Scalar>
+inline void
+update_array3(zfp::array3<Scalar>& a)
+{
+ for (uint k = 0; k < a.size_z(); k++)
+ for (uint j = 0; j < a.size_y(); j++)
+ for (uint i = 0; i < a.size_x() - 1; i++)
+ a(i, j, k) -= a(i + 1, j, k);
+ for (uint k = 0; k < a.size_z(); k++)
+ for (uint j = 0; j < a.size_y() - 1; j++)
+ for (uint i = 0; i < a.size_x(); i++)
+ a(i, j, k) -= a(i, j + 1, k);
+ for (uint k = 0; k < a.size_z() - 1; k++)
+ for (uint j = 0; j < a.size_y(); j++)
+ for (uint i = 0; i < a.size_x(); i++)
+ a(i, j, k) -= a(i, j, k + 1);
+ for (uint k = 0; k < a.size_z() - 1; k++)
+ for (uint j = 0; j < a.size_y() - 1; j++)
+ for (uint i = 0; i < a.size_x() - 1; i++)
+ a(0, 0, 0) = std::max(a(0, 0, 0), a(i, j, k));
+}
+
+template <class Array>
+inline void update_array(Array& a);
+
+template <>
+inline void
+update_array(zfp::array1<float>& a) { update_array1(a); }
+
+template <>
+inline void
+update_array(zfp::array1<double>& a) { update_array1(a); }
+
+template <>
+inline void
+update_array(zfp::array2<float>& a) { update_array2(a); }
+
+template <>
+inline void
+update_array(zfp::array2<double>& a) { update_array2(a); }
+
+template <>
+inline void
+update_array(zfp::array3<float>& a) { update_array3(a); }
+
+template <>
+inline void
+update_array(zfp::array3<double>& a) { update_array3(a); }
+
+// test random-accessible array primitive
+template <class Array, typename Scalar>
+inline uint
+test_array(Array& a, const Scalar* f, uint n, double tolerance, double dfmax)
+{
+ uint failures = 0;
+
+ // test construction
+ std::ostringstream status;
+ status << " construct: ";
+ Scalar emax = 0;
+ for (uint i = 0; i < n; i++)
+ emax = std::max(emax, std::abs(f[i] - a[i]));
+ status << std::scientific;
+ status.precision(3);
+ // make sure max error is within tolerance
+ bool pass = true;
+ if (emax <= tolerance)
+ status << " " << emax << " <= " << tolerance;
+ else {
+ status << " [" << emax << " > " << tolerance << "]";
+ pass = false;
+ }
+
+ std::cout << std::setw(width) << std::left << status.str() << (pass ? " OK " : "FAIL") << std::endl;
+ if (!pass)
+ failures++;
+
+ // test array updates
+ status.str("");
+ status << " update: ";
+ update_array(a);
+ Scalar amax = a[0];
+ pass = true;
+ if (std::abs(amax - dfmax) <= 1e-3 * dfmax)
+ status << " " << amax << " ~ " << dfmax;
+ else {
+ status << " [" << amax << " != " << dfmax << "]";
+ pass = false;
+ }
+
+ std::cout << std::setw(width) << std::left << status.str() << (pass ? " OK " : "FAIL") << std::endl;
+ if (!pass)
+ failures++;
+
+ return failures;
+}
+
+// test arrays with m^6 scalars
+template <typename Scalar>
+inline uint
+test(uint m)
+{
+ uint failures = 0;
+ uint n = m * m * m * m * m * m;
+ Scalar* f = new Scalar[n];
+ // test 1D, 2D, and 3D arrays
+ for (uint d = 1; d <= 3; d++) {
+ // determine array size
+ uint nx, ny, nz;
+ zfp_field* field = zfp_field_alloc();
+ zfp_field_set_type(field, zfp::codec<Scalar>::type);
+ zfp_field_set_pointer(field, f);
+ switch (d) {
+ case 1:
+ nx = n;
+ ny = 0;
+ nz = 0;
+ zfp_field_set_size_1d(field, nx);
+ break;
+ case 2:
+ nx = m * m * m;
+ ny = m * m * m;
+ nz = 0;
+ zfp_field_set_size_2d(field, nx, ny);
+ break;
+ case 3:
+ nx = m * m;
+ ny = m * m;
+ nz = m * m;
+ zfp_field_set_size_3d(field, nx, ny, nz);
+ break;
+ }
+ initialize<Scalar>(f, nx, ny, nz, polynomial);
+ uint t = (zfp_field_type(field) == zfp_type_float ? 0 : 1);
+ std::cout << "testing " << d << "D array of " << (t == 0 ? "floats" : "doubles") << std::endl;
+
+ // test data integrity
+ uint32 checksum[2][3] = {
+#if TEST_SIZE == 4
+ { 0xdad6fd69u, 0x000f8df1u, 0x60993f48u },
+ { 0x8d95b1fdu, 0x96a0e601u, 0x66e77c83u },
+#elif TEST_SIZE == 8
+ { 0x269fb420u, 0xfc4fd405u, 0x733b9643u },
+ { 0x3321e28bu, 0xfcb8f0f0u, 0xd0f6d6adu },
+#elif TEST_SIZE == 16
+ { 0x62d6c2b5u, 0x88aa838eu, 0x84f98253u },
+ { 0xf2bd03a4u, 0x10084595u, 0xb8df0e02u },
+#endif
+ };
+ uint32 h = hash(f, n * sizeof(Scalar));
+ if (h != checksum[t][d - 1])
+ std::cout << "warning: array checksum mismatch; tests below may fail" << std::endl;
+
+ // open compressed stream
+ zfp_stream* stream = zfp_stream_open(0);
+
+ // test fixed rate
+ for (uint rate = 2u >> t, i = 0; rate <= 32 * (t + 1); rate *= 4, i++) {
+ // expected max errors
+#if TEST_SIZE == 4
+ Scalar emax[2][3][4] = {
+ {
+ {1.998e+00, 7.767e-03, 0.000e+00},
+ {2.356e-01, 3.939e-04, 7.451e-09},
+ {2.479e-01, 1.525e-03, 7.451e-08},
+ },
+ {
+ {1.998e+00, 9.976e-01, 1.360e-05},
+ {2.944e+00, 2.491e-02, 2.578e-06},
+ {6.103e-01, 3.253e-02, 6.467e-06},
+ }
+ };
+#elif TEST_SIZE == 8
+ Scalar emax[2][3][4] = {
+ {
+ {2.000e+00, 1.425e-03, 0.000e+00},
+ {7.110e-02, 1.264e-05, 2.329e-10},
+ {1.864e-02, 2.814e-05, 1.193e-07},
+ },
+ {
+ {2.000e+00, 1.001e+00, 3.084e-06, 0.000e+00},
+ {2.266e+00, 3.509e-03, 1.784e-08, 0.000e+00},
+ {2.494e-01, 1.473e-03, 7.060e-08, 3.470e-18},
+ }
+ };
+#elif TEST_SIZE == 16
+ Scalar emax[2][3][4] = {
+ {
+ {2.000e+00, 1.304e-03, 0.000e+00},
+ {6.907e-02, 5.961e-07, 2.911e-11},
+ {3.458e-03, 7.153e-07, 2.385e-07},
+ },
+ {
+ {2.000e+00, 1.001e+00, 6.353e-07, 0.000e+00},
+ {2.036e+00, 3.174e-04, 1.646e-10, 5.294e-23},
+ {5.483e-02, 8.559e-05, 4.564e-10, 8.674e-19},
+ }
+ };
+#endif
+ failures += test_rate<Scalar>(stream, field, rate, emax[t][d - 1][i]);
+ }
+
+ if (stream_word_bits != 64)
+ std::cout << "warning: stream word size is smaller than 64; tests below may fail" << std::endl;
+
+ // test fixed precision
+ for (uint prec = 4u << t, i = 0; i < 3; prec *= 2, i++) {
+ // expected compressed sizes
+#if TEST_SIZE == 4
+ size_t bytes[2][3][3] = {
+ {
+ {2176, 3256, 6272},
+ { 576, 1296, 4136},
+ { 128, 720, 4096},
+ },
+ {
+ {3640, 6656, 14576},
+ {1392, 4232, 12312},
+ { 744, 4120, 12304},
+ },
+ };
+#elif TEST_SIZE == 8
+ size_t bytes[2][3][3] = {
+ {
+ {138864, 204456, 349888},
+ { 35216, 63632, 163008},
+ { 8856, 26768, 133360},
+ },
+ {
+ {229048, 374264, 786504},
+ { 69776, 169168, 564192},
+ { 28304, 134904, 588600},
+ },
+ };
+#elif TEST_SIZE == 16
+ size_t bytes[2][3][3] = {
+ {
+ {8886920, 13080944, 21487696},
+ {2240256, 3457592, 7787752},
+ { 570656, 1277128, 4803216},
+ },
+ {
+ {14654848, 23059592, 45965208},
+ { 3850784, 8168520, 25149520},
+ { 1375440, 4901552, 24339800},
+ },
+ };
+#endif
+ failures += test_precision<Scalar>(stream, field, prec, bytes[t][d - 1][i]);
+ }
+
+ // test fixed accuracy
+ for (uint i = 0; i < 3; i++) {
+ Scalar tol[] = { 1e-3, 2 * std::numeric_limits<Scalar>::epsilon(), 0 };
+ // expected compressed sizes
+#if TEST_SIZE == 4
+ size_t bytes[2][3][3] = {
+ {
+ {4752, 10184, 14192},
+ {2920, 8720, 12216},
+ {4264, 10408, 12280},
+ },
+ {
+ {5136, 25416, 30960},
+ {3016, 23664, 28696},
+ {4288, 25280, 28688},
+ },
+ };
+#elif TEST_SIZE == 8
+ size_t bytes[2][3][3] = {
+ {
+ {272208, 552856, 792528},
+ {105440, 329280, 572552},
+ { 90584, 381264, 588528},
+ },
+ {
+ {296672, 1478648, 1834416},
+ {111560, 1250056, 1609720},
+ { 92120, 1327544, 1637168},
+ },
+ };
+#elif TEST_SIZE == 16
+ size_t bytes[2][3][3] = {
+ {
+ {17416688, 32229448, 47431656},
+ { 5327000, 14827440, 28920960},
+ { 2721504, 12688136, 26308832},
+ },
+ {
+ {18982344, 85195360, 107965448},
+ { 5715280, 63417800, 86969224},
+ { 2819224, 66345592, 89157296},
+ },
+ };
+#endif
+ failures += test_accuracy<Scalar>(stream, field, tol[i], bytes[t][d - 1][i]);
+ }
+
+ // test compressed array support
+#if TEST_SIZE == 4
+ Scalar emax[2][3] = {
+ {0.000e+00, 7.451e-09, 7.451e-08},
+ {2.354e-10, 5.731e-09, 2.804e-08},
+ };
+ Scalar dfmax[2][3] = {
+ {4.385e-03, 9.260e-02, 3.760e-01},
+ {4.385e-03, 9.260e-02, 3.760e-01},
+ };
+#elif TEST_SIZE == 8
+ Scalar emax[2][3] = {
+ {0.000e+00, 2.329e-10, 1.193e-07},
+ {1.302e-11, 5.678e-11, 4.148e-10},
+ };
+ Scalar dfmax[2][3] = {
+ {6.866e-05, 1.792e-03, 2.239e-02},
+ {6.866e-05, 1.792e-03, 2.239e-02},
+ };
+#elif TEST_SIZE == 16
+ Scalar emax[2][3] = {
+ {0.000e+00, 2.911e-11, 2.385e-07},
+ {4.464e-13, 3.051e-13, 1.224e-12},
+ };
+ Scalar dfmax[2][3] = {
+ {1.073e-06, 2.906e-05, 4.714e-04},
+ {1.073e-06, 2.880e-05, 4.714e-04},
+ };
+#endif
+ double rate = 24;
+ switch (d) {
+ case 1: {
+ zfp::array1<Scalar> a(nx, rate, f);
+ failures += test_array(a, f, n, emax[t][d - 1], dfmax[t][d - 1]);
+ }
+ break;
+ case 2: {
+ zfp::array2<Scalar> a(nx, ny, rate, f);
+ failures += test_array(a, f, n, emax[t][d - 1], dfmax[t][d - 1]);
+ }
+ break;
+ case 3: {
+ zfp::array3<Scalar> a(nx, ny, nz, rate, f);
+ failures += test_array(a, f, n, emax[t][d - 1], dfmax[t][d - 1]);
+ }
+ break;
+ }
+
+ std::cout << std::endl;
+ zfp_stream_close(stream);
+ zfp_field_free(field);
+ }
+
+ delete[] f;
+ return failures;
+}
+
+int main()
+{
+ uint failures = 0;
+ uint m = TEST_SIZE;
+ failures += test<float>(m);
+ failures += test<double>(m);
+ if (failures)
+ std::cout << failures << " test(s) failed" << std::endl;
+ else
+ std::cout << "all tests passed" << std::endl;
+ return failures ? EXIT_FAILURE : EXIT_SUCCESS;
+}
diff --git a/src/zfp/zfp-0.5.0/examples/zfp.c b/src/zfp/zfp-0.5.0/examples/zfp.c
new file mode 100644
index 0000000..2cdc6f0
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/examples/zfp.c
@@ -0,0 +1,480 @@
+#include <limits.h>
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "zfp.h"
+#include "macros.h"
+
+/*
+File I/O is done using the following combinations of i, o, s, and z:
+- i : read uncompressed
+- z : read compressed
+- i, s: read uncompressed, print stats
+- i, o: read and write uncompressed
+- i, z: read uncompressed, write compressed
+- z, o: read compressed, write uncompressed
+
+The 7 major tasks to be accomplished are:
+- read uncompressed: i
+- read compressed: !i
+- compress: i
+- write compressed: i && z
+- decompress: o || s || (!i && z)
+- write uncompressed: o
+- compute stats: s
+*/
+
+/* compute and print reconstruction error */
+static void
+print_error(const void* fin, const void* fout, zfp_type type, uint n)
+{
+ const float* ff = fin;
+ const double* fd = fin;
+ const float* gf = fout;
+ const double* gd = fout;
+ int single = (type == zfp_type_float);
+ double fmin = single ? ff[0] : fd[0];
+ double fmax = fmin;
+ double erms = 0;
+ double ermsn = 0;
+ double emax = 0;
+ double psnr = 0;
+ uint i;
+
+ for (i = 0; i < n; i++) {
+ double d = fabs(single ? ff[i] - gf[i] : fd[i] - gd[i]);
+ double val = single ? ff[i] : fd[i];
+ emax = MAX(emax, d);
+ erms += d * d;
+ fmin = MIN(fmin, val);
+ fmax = MAX(fmax, val);
+ }
+ erms = sqrt(erms / n);
+ ermsn = erms / (fmax - fmin);
+ psnr = 20 * log10((fmax - fmin) / (2 * erms));
+ fprintf(stderr, " rmse=%.4g nrmse=%.4g maxe=%.4g psnr=%.2f", erms, ermsn, emax, psnr);
+}
+
+static void
+usage()
+{
+ fprintf(stderr, "Usage: zfp <options>\n");
+ fprintf(stderr, "General options:\n");
+ fprintf(stderr, " -h : read/write array and compression parameters from/to compressed header\n");
+ fprintf(stderr, " -q : quiet mode; suppress output\n");
+ fprintf(stderr, " -s : print error statistics\n");
+ fprintf(stderr, "Input and output:\n");
+ fprintf(stderr, " -i <path> : uncompressed binary input file (\"-\" for stdin)\n");
+ fprintf(stderr, " -o <path> : decompressed binary output file (\"-\" for stdout)\n");
+ fprintf(stderr, " -z <path> : compressed input (w/o -i) or output file (\"-\" for stdin/stdout)\n");
+ fprintf(stderr, "Array type and dimensions (needed with -i):\n");
+ fprintf(stderr, " -f : single precision (float type)\n");
+ fprintf(stderr, " -d : double precision (double type)\n");
+ fprintf(stderr, " -1 <nx> : 1D array dimensions\n");
+ fprintf(stderr, " -2 <nx> <ny> : 2D array dimensions\n");
+ fprintf(stderr, " -3 <nx> <ny> <nz> : 3D array dimensions\n");
+ fprintf(stderr, "Compression parameters (needed with -i):\n");
+ fprintf(stderr, " -r <rate> : fixed rate (# compressed bits per floating-point value)\n");
+ fprintf(stderr, " -p <precision> : fixed precision (# uncompressed bits per value)\n");
+ fprintf(stderr, " -a <tolerance> : fixed accuracy (absolute error tolerance)\n");
+ fprintf(stderr, " -c <minbits> <maxbits> <maxprec> <minexp> : advanced usage\n");
+ fprintf(stderr, " minbits : min # bits per 4^d values in d dimensions\n");
+ fprintf(stderr, " maxbits : max # bits per 4^d values in d dimensions (0 for unlimited)\n");
+ fprintf(stderr, " maxprec : max # bits of precision per value (0 for full)\n");
+ fprintf(stderr, " minexp : min bit plane # coded (-1074 for all bit planes)\n");
+ fprintf(stderr, "Examples:\n");
+ fprintf(stderr, " -i file : read uncompressed file and compress to memory\n");
+ fprintf(stderr, " -z file : read compressed file and decompress to memory\n");
+ fprintf(stderr, " -i ifile -z zfile : read uncompressed ifile, write compressed zfile\n");
+ fprintf(stderr, " -z zfile -o ofile : read compressed zfile, write decompressed ofile\n");
+ fprintf(stderr, " -i ifile -o ofile : read ifile, compress, decompress, write ofile\n");
+ fprintf(stderr, " -i file -s : read uncompressed file, compress to memory, print stats\n");
+ fprintf(stderr, " -i - -o - -s : read stdin, compress, decompress, write stdout, print stats\n");
+ fprintf(stderr, " -f -3 100 100 100 -r 16 : 2x fixed-rate compression of 100x100x100 floats\n");
+ fprintf(stderr, " -d -1 1000000 -r 32 : 2x fixed-rate compression of 1M doubles\n");
+ fprintf(stderr, " -d -2 1000 1000 -p 32 : 32-bit precision compression of 1000x1000 doubles\n");
+ fprintf(stderr, " -d -1 1000000 -a 1e-9 : compression of 1M doubles with < 1e-9 max error\n");
+ fprintf(stderr, " -d -1 1000000 -c 64 64 0 -1074 : 4x fixed-rate compression of 1M doubles\n");
+ exit(EXIT_FAILURE);
+}
+
+int main(int argc, char* argv[])
+{
+ /* default settings */
+ zfp_type type = zfp_type_none;
+ size_t typesize = 0;
+ uint dims = 0;
+ uint nx = 0;
+ uint ny = 0;
+ uint nz = 0;
+ double rate = 0;
+ uint precision = 0;
+ double tolerance = 0;
+ uint minbits = ZFP_MIN_BITS;
+ uint maxbits = ZFP_MAX_BITS;
+ uint maxprec = ZFP_MAX_PREC;
+ int minexp = ZFP_MIN_EXP;
+ int header = 0;
+ int quiet = 0;
+ int stats = 0;
+ char* inpath = 0;
+ char* zfppath = 0;
+ char* outpath = 0;
+ char mode = 0;
+
+ /* local variables */
+ int i;
+ zfp_field* field = NULL;
+ zfp_stream* zfp = NULL;
+ bitstream* stream = NULL;
+ void* fi = NULL;
+ void* fo = NULL;
+ void* buffer = NULL;
+ size_t rawsize = 0;
+ size_t zfpsize = 0;
+ size_t bufsize = 0;
+
+ /* parse command-line arguments */
+ for (i = 1; i < argc; i++) {
+ if (argv[i][0] != '-' || argv[i][2])
+ usage();
+ switch (argv[i][1]) {
+ case '1':
+ if (++i == argc || sscanf(argv[i], "%u", &nx) != 1)
+ usage();
+ ny = nz = 1;
+ dims = 1;
+ break;
+ case '2':
+ if (++i == argc || sscanf(argv[i], "%u", &nx) != 1 ||
+ ++i == argc || sscanf(argv[i], "%u", &ny) != 1)
+ usage();
+ nz = 1;
+ dims = 2;
+ break;
+ case '3':
+ if (++i == argc || sscanf(argv[i], "%u", &nx) != 1 ||
+ ++i == argc || sscanf(argv[i], "%u", &ny) != 1 ||
+ ++i == argc || sscanf(argv[i], "%u", &nz) != 1)
+ usage();
+ dims = 3;
+ break;
+ case 'a':
+ if (++i == argc || sscanf(argv[i], "%lf", &tolerance) != 1)
+ usage();
+ mode = 'a';
+ break;
+ case 'c':
+ if (++i == argc || sscanf(argv[i], "%u", &minbits) != 1 ||
+ ++i == argc || sscanf(argv[i], "%u", &maxbits) != 1 ||
+ ++i == argc || sscanf(argv[i], "%u", &maxprec) != 1 ||
+ ++i == argc || sscanf(argv[i], "%d", &minexp) != 1)
+ usage();
+ mode = 'c';
+ break;
+ case 'd':
+ type = zfp_type_double;
+ typesize = sizeof(double);
+ break;
+ case 'f':
+ type = zfp_type_float;
+ typesize = sizeof(float);
+ break;
+ case 'h':
+ header = 1;
+ break;
+ case 'i':
+ if (++i == argc)
+ usage();
+ inpath = argv[i];
+ break;
+ case 'o':
+ if (++i == argc)
+ usage();
+ outpath = argv[i];
+ break;
+ case 'p':
+ if (++i == argc || sscanf(argv[i], "%u", &precision) != 1)
+ usage();
+ mode = 'p';
+ break;
+ case 'q':
+ quiet = 1;
+ break;
+ case 'r':
+ if (++i == argc || sscanf(argv[i], "%lf", &rate) != 1)
+ usage();
+ mode = 'r';
+ break;
+ case 's':
+ stats = 1;
+ break;
+ case 'z':
+ if (++i == argc)
+ usage();
+ zfppath = argv[i];
+ break;
+ default:
+ usage();
+ break;
+ }
+ }
+
+ /* make sure we have an input file */
+ if (!inpath && !zfppath) {
+ fprintf(stderr, "must specify uncompressed or compressed input file via -i or -z\n");
+ return EXIT_FAILURE;
+ }
+
+ /* make sure we know floating-point type */
+ if ((inpath || !header) && !typesize) {
+ fprintf(stderr, "must specify scalar type via -f or -d\n");
+ return EXIT_FAILURE;
+ }
+
+ /* make sure we know array dimensions */
+ if ((inpath || !header) && !dims) {
+ fprintf(stderr, "must specify array dimensions via -1, -2, or -3\n");
+ return EXIT_FAILURE;
+ }
+
+ /* make sure we know (de)compression mode and parameters */
+ if ((inpath || !header) && !mode) {
+ fprintf(stderr, "must specify compression parameters via -a, -c, -p, or -r\n");
+ return EXIT_FAILURE;
+ }
+
+ /* make sure we have input file for stats */
+ if (stats && !inpath) {
+ fprintf(stderr, "must specify input file via -i to compute stats\n");
+ return EXIT_FAILURE;
+ }
+
+ /* make sure meta data comes from header or command line, not both */
+ if (!inpath && zfppath && header && (typesize || dims)) {
+ fprintf(stderr, "cannot specify both field type/size and header\n");
+ return EXIT_FAILURE;
+ }
+
+ zfp = zfp_stream_open(NULL);
+ field = zfp_field_alloc();
+
+ /* read uncompressed or compressed file */
+ if (inpath) {
+ /* read uncompressed input file */
+ FILE* file = !strcmp(inpath, "-") ? stdin : fopen(inpath, "rb");
+ if (!file) {
+ fprintf(stderr, "cannot open input file\n");
+ return EXIT_FAILURE;
+ }
+ rawsize = typesize * nx * ny * nz;
+ fi = malloc(rawsize);
+ if (!fi) {
+ fprintf(stderr, "cannot allocate memory\n");
+ return EXIT_FAILURE;
+ }
+ if (fread(fi, typesize, nx * ny * nz, file) != nx * ny * nz) {
+ fprintf(stderr, "cannot read input file\n");
+ return EXIT_FAILURE;
+ }
+ fclose(file);
+ zfp_field_set_pointer(field, fi);
+ }
+ else {
+ /* read compressed input file in increasingly large chunks */
+ FILE* file = !strcmp(zfppath, "-") ? stdin : fopen(zfppath, "rb");
+ if (!file) {
+ fprintf(stderr, "cannot open compressed file\n");
+ return EXIT_FAILURE;
+ }
+ bufsize = 0x100;
+ do {
+ bufsize *= 2;
+ buffer = realloc(buffer, bufsize);
+ if (!buffer) {
+ fprintf(stderr, "cannot allocate memory\n");
+ return EXIT_FAILURE;
+ }
+ zfpsize += fread((uchar*)buffer + zfpsize, 1, bufsize - zfpsize, file);
+ } while (zfpsize == bufsize);
+ if (ferror(file)) {
+ fprintf(stderr, "cannot read compressed file\n");
+ return EXIT_FAILURE;
+ }
+ fclose(file);
+
+ /* associate bit stream with buffer */
+ stream = stream_open(buffer, bufsize);
+ if (!stream) {
+ fprintf(stderr, "cannot open compressed stream\n");
+ return EXIT_FAILURE;
+ }
+ zfp_stream_set_bit_stream(zfp, stream);
+ }
+
+ /* set field dimensions and (de)compression parameters */
+ if (inpath || !header) {
+ /* initialize uncompressed field */
+ zfp_field_set_type(field, type);
+ switch (dims) {
+ case 1:
+ zfp_field_set_size_1d(field, nx);
+ break;
+ case 2:
+ zfp_field_set_size_2d(field, nx, ny);
+ break;
+ case 3:
+ zfp_field_set_size_3d(field, nx, ny, nz);
+ break;
+ }
+
+ /* set (de)compression mode */
+ switch (mode) {
+ case 'a':
+ zfp_stream_set_accuracy(zfp, tolerance, type);
+ break;
+ case 'p':
+ zfp_stream_set_precision(zfp, precision, type);
+ break;
+ case 'r':
+ zfp_stream_set_rate(zfp, rate, type, dims, 0);
+ break;
+ case 'c':
+ if (!maxbits)
+ maxbits = ZFP_MAX_BITS;
+ if (!maxprec)
+ maxprec = zfp_field_precision(field);
+ if (!zfp_stream_set_params(zfp, minbits, maxbits, maxprec, minexp)) {
+ fprintf(stderr, "invalid compression parameters\n");
+ return EXIT_FAILURE;
+ }
+ break;
+ }
+ }
+
+ /* compress input file if provided */
+ if (inpath) {
+ /* allocate buffer for compressed data */
+ bufsize = zfp_stream_maximum_size(zfp, field);
+ if (!bufsize) {
+ fprintf(stderr, "invalid compression parameters\n");
+ return EXIT_FAILURE;
+ }
+ buffer = malloc(bufsize);
+ if (!buffer) {
+ fprintf(stderr, "cannot allocate memory\n");
+ return EXIT_FAILURE;
+ }
+
+ /* associate compressed bit stream with memory buffer */
+ stream = stream_open(buffer, bufsize);
+ if (!stream) {
+ fprintf(stderr, "cannot open compressed stream\n");
+ return EXIT_FAILURE;
+ }
+ zfp_stream_set_bit_stream(zfp, stream);
+
+ /* optionally write header */
+ if (header && !zfp_write_header(zfp, field, ZFP_HEADER_FULL)) {
+ fprintf(stderr, "cannot write header\n");
+ return EXIT_FAILURE;
+ }
+
+ /* compress data */
+ zfpsize = zfp_compress(zfp, field);
+ if (zfpsize == 0) {
+ fprintf(stderr, "compression failed\n");
+ return EXIT_FAILURE;
+ }
+
+ /* optionally write compressed data */
+ if (zfppath) {
+ FILE* file = !strcmp(zfppath, "-") ? stdout : fopen(zfppath, "wb");
+ if (!file) {
+ fprintf(stderr, "cannot create compressed file\n");
+ return EXIT_FAILURE;
+ }
+ if (fwrite(buffer, 1, zfpsize, file) != zfpsize) {
+ fprintf(stderr, "cannot write compressed file\n");
+ return EXIT_FAILURE;
+ }
+ fclose(file);
+ }
+ }
+
+ /* decompress data if necessary */
+ if ((!inpath && zfppath) || outpath || stats) {
+ /* obtain metadata from header when present */
+ zfp_stream_rewind(zfp);
+ if (header) {
+ if (!zfp_read_header(zfp, field, ZFP_HEADER_FULL)) {
+ fprintf(stderr, "incorrect or missing header\n");
+ return EXIT_FAILURE;
+ }
+ type = field->type;
+ switch (type) {
+ case zfp_type_float:
+ typesize = sizeof(float);
+ break;
+ case zfp_type_double:
+ typesize = sizeof(double);
+ break;
+ default:
+ fprintf(stderr, "unsupported type\n");
+ return EXIT_FAILURE;
+ }
+ nx = MAX(field->nx, 1u);
+ ny = MAX(field->ny, 1u);
+ nz = MAX(field->nz, 1u);
+ }
+
+ /* allocate memory for decompressed data */
+ rawsize = typesize * nx * ny * nz;
+ fo = malloc(rawsize);
+ if (!fo) {
+ fprintf(stderr, "cannot allocate memory\n");
+ return EXIT_FAILURE;
+ }
+ zfp_field_set_pointer(field, fo);
+
+ /* decompress data */
+ if (!zfp_decompress(zfp, field)) {
+ fprintf(stderr, "decompression failed\n");
+ return EXIT_FAILURE;
+ }
+
+ /* optionally write reconstructed data */
+ if (outpath) {
+ FILE* file = !strcmp(outpath, "-") ? stdout : fopen(outpath, "wb");
+ if (!file) {
+ fprintf(stderr, "cannot create output file\n");
+ return EXIT_FAILURE;
+ }
+ if (fwrite(fo, typesize, nx * ny * nz, file) != nx * ny * nz) {
+ fprintf(stderr, "cannot write output file\n");
+ return EXIT_FAILURE;
+ }
+ fclose(file);
+ }
+ }
+
+ /* print compression and error statistics */
+ if (!quiet) {
+ fprintf(stderr, "type=%s nx=%u ny=%u nz=%u", type == zfp_type_float ? "float" : "double", nx, ny, nz);
+ fprintf(stderr, " raw=%lu zfp=%lu ratio=%.3g rate=%.4g", (unsigned long)rawsize, (unsigned long)zfpsize, (double)rawsize / zfpsize, CHAR_BIT * (double)zfpsize / (nx * ny * nz));
+ if (stats)
+ print_error(fi, fo, type, nx * ny * nz);
+ fprintf(stderr, "\n");
+ }
+
+ /* free allocated storage */
+ zfp_field_free(field);
+ zfp_stream_close(zfp);
+ stream_close(stream);
+ free(buffer);
+ free(fi);
+ free(fo);
+
+ return EXIT_SUCCESS;
+}
diff --git a/src/zfp/zfp-0.5.0/inc/bitstream.h b/src/zfp/zfp-0.5.0/inc/bitstream.h
new file mode 100644
index 0000000..37380f6
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/inc/bitstream.h
@@ -0,0 +1,87 @@
+#ifndef BITSTREAM_H
+#define BITSTREAM_H
+
+#include <stddef.h>
+#include "types.h"
+
+/* forward declaration of opaque type */
+typedef struct bitstream bitstream;
+
+extern const size_t stream_word_bits; /* bit stream granularity */
+
+#ifndef _inline
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* allocate and initialize bit stream */
+bitstream* stream_open(void* buffer, size_t bytes);
+
+/* close and deallocate bit stream */
+void stream_close(bitstream* stream);
+
+/* pointer to beginning of stream */
+void* stream_data(const bitstream* stream);
+
+/* current byte size of stream (if flushed) */
+size_t stream_size(const bitstream* stream);
+
+/* byte capacity of stream */
+size_t stream_capacity(const bitstream* stream);
+
+/* number of words per block */
+size_t stream_block(const bitstream* stream);
+
+/* number of blocks between consecutive blocks */
+int stream_delta(const bitstream* stream);
+
+/* read single bit (0 or 1) */
+uint stream_read_bit(bitstream* stream);
+
+/* write single bit */
+uint stream_write_bit(bitstream* stream, uint bit);
+
+/* read 0 <= n <= 64 bits */
+uint64 stream_read_bits(bitstream* stream, uint n);
+
+/* write 0 <= n <= 64 low bits of value and return remaining bits */
+uint64 stream_write_bits(bitstream* stream, uint64 value, uint n);
+
+/* return bit offset to next bit to be read */
+size_t stream_rtell(const bitstream* stream);
+
+/* return bit offset to next bit to be written */
+size_t stream_wtell(const bitstream* stream);
+
+/* rewind stream to beginning */
+void stream_rewind(bitstream* stream);
+
+/* position stream for reading at given bit offset */
+void stream_rseek(bitstream* stream, size_t offset);
+
+/* position stream for writing at given bit offset */
+void stream_wseek(bitstream* stream, size_t offset);
+
+/* skip over the next n bits */
+void stream_skip(bitstream* stream, uint n);
+
+/* append n zero bits to stream */
+void stream_pad(bitstream* stream, uint n);
+
+/* align stream on next word boundary */
+void stream_align(bitstream* stream);
+
+/* flush out any remaining buffered bits */
+void stream_flush(bitstream* stream);
+
+#ifdef BITSTREAM_STRIDED
+/* set block size in number of words and spacing in number of blocks */
+int stream_set_stride(bitstream* stream, uint block, int delta);
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+#endif /* !_inline */
+
+#endif
diff --git a/src/zfp/zfp-0.5.0/inc/macros.h b/src/zfp/zfp-0.5.0/inc/macros.h
new file mode 100644
index 0000000..c7d3184
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/inc/macros.h
@@ -0,0 +1,7 @@
+#ifndef MACROS_H
+#define MACROS_H
+
+#define MIN(x, y) ((x) < (y) ? (x) : (y))
+#define MAX(x, y) ((x) > (y) ? (x) : (y))
+
+#endif
diff --git a/src/zfp/zfp-0.5.0/inc/system.h b/src/zfp/zfp-0.5.0/inc/system.h
new file mode 100644
index 0000000..1cf387e
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/inc/system.h
@@ -0,0 +1,20 @@
+#ifndef SYSTEM_H
+#define SYSTEM_H
+
+#if __STDC_VERSION__ >= 199901L
+ #define _restrict restrict
+#else
+ #define _restrict
+#endif
+
+#ifdef __GNUC__
+ #ifndef CACHE_LINE_SIZE
+ #define CACHE_LINE_SIZE 0x100
+ #endif
+ #define _align(n) __attribute__((aligned(n)))
+ #define _cache_align(x) x _align(CACHE_LINE_SIZE)
+#else
+ #define _cache_align(x) x
+#endif
+
+#endif
diff --git a/src/zfp/zfp-0.5.0/inc/types.h b/src/zfp/zfp-0.5.0/inc/types.h
new file mode 100644
index 0000000..a1361a3
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/inc/types.h
@@ -0,0 +1,30 @@
+#ifndef TYPES_H
+#define TYPES_H
+
+typedef unsigned char uchar;
+typedef unsigned short ushort;
+typedef unsigned int uint;
+
+#if __STDC_VERSION__ >= 199901L
+ #include <stdint.h>
+ typedef int8_t int8;
+ typedef uint8_t uint8;
+ typedef int16_t int16;
+ typedef uint16_t uint16;
+ typedef int32_t int32;
+ typedef uint32_t uint32;
+ typedef int64_t int64;
+ typedef uint64_t uint64;
+#else
+ /* assume common integer types in C89 */
+ typedef signed char int8;
+ typedef unsigned char uint8;
+ typedef signed short int16;
+ typedef unsigned short uint16;
+ typedef signed int int32;
+ typedef unsigned int uint32;
+ typedef signed long long int64; /* not ANSI C89 compliant */
+ typedef unsigned long long uint64; /* not ANSI C89 compliant */
+#endif
+
+#endif
diff --git a/src/zfp/zfp-0.5.0/inc/zfp.h b/src/zfp/zfp-0.5.0/inc/zfp.h
new file mode 100644
index 0000000..ae9f0b2
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/inc/zfp.h
@@ -0,0 +1,549 @@
+/*
+** Copyright (c) 2014-2015, Lawrence Livermore National Security, LLC.
+** Produced at the Lawrence Livermore National Laboratory.
+** Written by Peter Lindstrom.
+** LLNL-CODE-663824.
+** All rights reserved.
+**
+** This file is part of the zfp library.
+** For details, see http://computation.llnl.gov/casc/zfp/.
+**
+** Redistribution and use in source and binary forms, with or without
+** modification, are permitted provided that the following conditions are met:
+**
+** 1. Redistributions of source code must retain the above copyright notice,
+** this list of conditions and the disclaimer below.
+**
+** 2. Redistributions in binary form must reproduce the above copyright notice,
+** this list of conditions and the disclaimer (as noted below) in the
+** documentation and/or other materials provided with the distribution.
+**
+** 3. Neither the name of the LLNS/LLNL nor the names of its contributors may
+** be used to endorse or promote products derived from this software without
+** specific prior written permission.
+**
+** THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+** AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+** IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+** ARE DISCLAIMED. IN NO EVENT SHALL LAWRENCE LIVERMORE NATIONAL SECURITY,
+** LLC, THE U.S. DEPARTMENT OF ENERGY OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+** INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+** (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+** LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+** ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+** (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
+** THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+**
+**
+** Additional BSD Notice
+**
+** 1. This notice is required to be provided under our contract with the U.S.
+** Department of Energy (DOE). This work was produced at Lawrence Livermore
+** National Laboratory under Contract No. DE-AC52-07NA27344 with the DOE.
+
+** 2. Neither the United States Government nor Lawrence Livermore National
+** Security, LLC nor any of their employees, makes any warranty, express or
+** implied, or assumes any liability or responsibility for the accuracy,
+** completeness, or usefulness of any information, apparatus, product, or
+** process disclosed, or represents that its use would not infringe
+** privately-owned rights.
+**
+** 3. Also, reference herein to any specific commercial products, process, or
+** services by trade name, trademark, manufacturer or otherwise does not
+** necessarily constitute or imply its endorsement, recommendation, or
+** favoring by the United States Government or Lawrence Livermore National
+** Security, LLC. The views and opinions of authors expressed herein do not
+** necessarily state or reflect those of the United States Government or
+** Lawrence Livermore National Security, LLC, and shall not be used for
+** advertising or product endorsement purposes.
+*/
+
+#ifndef ZFP_H
+#define ZFP_H
+
+#include "types.h"
+#include "system.h"
+#include "bitstream.h"
+
+/* macros ------------------------------------------------------------------ */
+
+/* library version information */
+#define ZFP_VERSION 0x0050 /* library version number: 0.5.0 */
+#define ZFP_VERSION_MAJOR 0 /* library major version number */
+#define ZFP_VERSION_MINOR 5 /* library minor version number */
+#define ZFP_VERSION_RELEASE 0 /* library release version number */
+
+/* default compression parameters */
+#define ZFP_MIN_BITS 0 /* minimum number of bits per block */
+#define ZFP_MAX_BITS 4171 /* maximum number of bits per block */
+#define ZFP_MAX_PREC 64 /* maximum precision supported */
+#define ZFP_MIN_EXP -1074 /* minimum floating-point base-2 exponent */
+
+/* header masks (enable via bitwise or; reader must use same mask) */
+#define ZFP_HEADER_MAGIC 0x1u /* embed 32-bit magic */
+#define ZFP_HEADER_FIELD 0x2u /* embed 52-bit field type and dimensions */
+#define ZFP_HEADER_PARAMS 0x4u /* embed 12- or 64-bit compression parameters */
+#define ZFP_HEADER_FULL 0x7u /* embed all of the above */
+
+/* number of bits per header entry */
+#define ZFP_MAGIC_BITS 32 /* number of magic word bits */
+#define ZFP_META_BITS 52 /* number of field metadata bits */
+#define ZFP_MODE_SHORT_BITS 12 /* number of mode bits in short format */
+#define ZFP_MODE_LONG_BITS 64 /* number of mode bits in long format */
+#define ZFP_HEADER_BITS 148 /* max number of header bits */
+#define ZFP_MODE_SHORT_MAX ((1u << ZFP_MODE_SHORT_BITS) - 2)
+
+/* types ------------------------------------------------------------------- */
+
+/* compressed stream; use accessors to get/set members */
+typedef struct {
+ uint minbits; /* minimum number of bits to store per block */
+ uint maxbits; /* maximum number of bits to store per block */
+ uint maxprec; /* maximum number of bit planes to store */
+ int minexp; /* minimum floating point bit plane number to store */
+ bitstream* stream; /* compressed bit stream */
+} zfp_stream;
+
+/* scalar type */
+typedef enum {
+ zfp_type_none = 0, /* unspecified type */
+ zfp_type_int32 = 1, /* 32-bit signed integer */
+ zfp_type_int64 = 2, /* 64-bit signed integer */
+ zfp_type_float = 3, /* single precision floating point */
+ zfp_type_double = 4 /* double precision floating point */
+} zfp_type;
+
+/* uncompressed array; use accessors to get/set members */
+typedef struct {
+ zfp_type type; /* scalar type (e.g. int32, double) */
+ uint nx, ny, nz; /* sizes (zero for unused dimensions) */
+ int sx, sy, sz; /* strides (zero for contiguous array a[nz][ny][nx]) */
+ void* data; /* pointer to array data */
+} zfp_field;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* high-level API: compressed stream construction/destruction -------------- */
+
+/* open compressed stream and associate with bit stream */
+zfp_stream* /* allocated compressed stream */
+zfp_stream_open(
+ bitstream* stream /* bit stream to read from and write to (may be NULL) */
+);
+
+/* close and deallocate compressed stream (does not affect bit stream) */
+void
+zfp_stream_close(
+ zfp_stream* stream /* compressed stream */
+);
+
+/* high-level API: compressed stream inspectors ---------------------------- */
+
+/* bit stream associated with compressed stream */
+bitstream* /* bit stream associated with compressed stream */
+zfp_stream_bit_stream(
+ const zfp_stream* stream /* compressed stream */
+);
+
+/* get all compression parameters in a compact representation */
+uint64 /* 12- or 64-bit encoding of parameters */
+zfp_stream_mode(
+ const zfp_stream* zfp /* compressed stream */
+);
+
+/* get all compression parameters (pointers may be NULL) */
+void
+zfp_stream_params(
+ const zfp_stream* stream, /* compressed stream */
+ uint* minbits, /* minimum number of bits per 4^d block */
+ uint* maxbits, /* maximum number of bits per 4^d block */
+ uint* maxprec, /* maximum precision (# bit planes coded) */
+ int* minexp /* minimum base-2 exponent; error <= 2^minexp */
+);
+
+/* byte size of sequentially compressed stream (call after compression) */
+size_t /* actual number of bytes of compressed storage */
+zfp_stream_compressed_size(
+ const zfp_stream* stream /* compressed stream */
+);
+
+/* conservative estimate of compressed size in bytes */
+size_t /* maximum number of bytes of compressed storage */
+zfp_stream_maximum_size(
+ const zfp_stream* stream, /* compressed stream */
+ const zfp_field* field /* array to compress */
+);
+
+/* high-level API: initialization of compressed stream parameters ---------- */
+
+/* associate bit stream with compressed stream */
+void
+zfp_stream_set_bit_stream(
+ zfp_stream* stream, /* compressed stream */
+ bitstream* bs /* bit stream to read from and write to */
+);
+
+/* set size in compressed bits/scalar (fixed-rate mode) */
+double /* actual rate in compressed bits/scalar */
+zfp_stream_set_rate(
+ zfp_stream* stream, /* compressed stream */
+ double rate, /* desired rate in compressed bits/scalar */
+ zfp_type type, /* scalar type to compress */
+ uint dims, /* array dimensionality (1, 2, or 3) */
+ int wra /* nonzero if write random access is needed */
+);
+
+/* set precision in uncompressed bits/scalar (fixed-precision mode) */
+uint /* actual precision */
+zfp_stream_set_precision(
+ zfp_stream* stream, /* compressed stream */
+ uint precision, /* desired precision in uncompressed bits/scalar */
+ zfp_type type /* scalar type to compress */
+);
+
+/* set accuracy as absolute error tolerance (fixed-accuracy mode) */
+double /* actual error tolerance */
+zfp_stream_set_accuracy(
+ zfp_stream* stream, /* compressed stream */
+ double tolerance, /* desired error tolerance */
+ zfp_type type /* scalar type to compress */
+);
+
+/* set all compression parameters from compact representation (expert mode) */
+int /* nonzero upon success */
+zfp_stream_set_mode(
+ zfp_stream* stream, /* compressed stream */
+ uint64 mode /* 12- or 64-bit encoding of parameters */
+);
+
+/* set all compression parameters (expert mode) */
+int /* nonzero upon success */
+zfp_stream_set_params(
+ zfp_stream* stream, /* compressed stream */
+ uint minbits, /* minimum number of bits per 4^d block */
+ uint maxbits, /* maximum number of bits per 4^d block */
+ uint maxprec, /* maximum precision (# bit planes coded) */
+ int minexp /* minimum base-2 exponent; error <= 2^minexp */
+);
+
+/* high-level API: uncompressed array construction/destruction ------------- */
+
+/* allocate field struct */
+zfp_field* /* pointer to default initialized field */
+zfp_field_alloc();
+
+/* allocate metadata for 1D field f[nx] */
+zfp_field* /* allocated field metadata */
+zfp_field_1d(
+ void* pointer, /* pointer to uncompressed scalars (may be NULL) */
+ zfp_type type, /* scalar type */
+ uint nx /* number of scalars */
+);
+
+/* allocate metadata for 2D field f[ny][nx] */
+zfp_field* /* allocated field metadata */
+zfp_field_2d(
+ void* pointer, /* pointer to uncompressed scalars (may be NULL) */
+ zfp_type type, /* scalar type */
+ uint nx, /* number of scalars in x dimension */
+ uint ny /* number of scalars in y dimension */
+);
+
+/* allocate metadata for 3D field f[nz][ny][nx] */
+zfp_field* /* allocated field metadata */
+zfp_field_3d(
+ void* pointer, /* pointer to uncompressed scalars (may be NULL) */
+ zfp_type type, /* scalar type */
+ uint nx, /* number of scalars in x dimension */
+ uint ny, /* number of scalars in y dimension */
+ uint nz /* number of scalars in z dimension */
+);
+
+/* deallocate field metadata */
+void
+zfp_field_free(
+ zfp_field* field /* field metadata */
+);
+
+/* high-level API: uncompressed array inspectors --------------------------- */
+
+/* pointer to first element of field */
+void* /* array pointer */
+zfp_field_pointer(
+ const zfp_field* field /* field metadata */
+);
+
+/* field scalar type */
+zfp_type /* scalar type */
+zfp_field_type(
+ const zfp_field* field /* field metadata */
+);
+
+/* precision of field scalar type */
+uint /* scalar type precision in number of bits */
+zfp_field_precision(
+ const zfp_field* field /* field metadata */
+);
+
+/* field dimensionality (1, 2, or 3) */
+uint /* number of dimensions */
+zfp_field_dimensionality(
+ const zfp_field* field /* field metadata */
+);
+
+/* field size in number of array elements */
+size_t /* total number of scalars */
+zfp_field_size(
+ const zfp_field* field, /* field metadata */
+ uint* size /* number of elements per dimension (may be NULL) */
+);
+
+/* field strides per dimension */
+int /* zero if array is contiguous */
+zfp_field_stride(
+ const zfp_field* field, /* field metadata */
+ int* stride /* stride in elements per dimension (may be NULL) */
+);
+
+/* field scalar type and dimensions */
+uint64 /* compact 52-bit encoding of metadata */
+zfp_field_metadata(
+ const zfp_field* field /* field metadata */
+);
+
+/* high-level API: uncompressed array specification ------------------------ */
+
+/* set pointer to first scalar in field */
+void
+zfp_field_set_pointer(
+ zfp_field* field, /* field metadata */
+ void* pointer /* pointer to first scalar */
+);
+
+/* set field scalar type */
+zfp_type /* actual scalar type */
+zfp_field_set_type(
+ zfp_field* field, /* field metadata */
+ zfp_type type /* desired scalar type */
+);
+
+/* set 1D field size */
+void
+zfp_field_set_size_1d(
+ zfp_field* field, /* field metadata */
+ uint nx /* number of scalars */
+);
+
+/* set 2D field size */
+void
+zfp_field_set_size_2d(
+ zfp_field* field, /* field metadata */
+ uint nx, /* number of scalars in x dimension */
+ uint ny /* number of scalars in y dimension */
+);
+
+/* set 3D field size */
+void
+zfp_field_set_size_3d(
+ zfp_field* field, /* field metadata */
+ uint nx, /* number of scalars in x dimension */
+ uint ny, /* number of scalars in y dimension */
+ uint nz /* number of scalars in z dimension */
+);
+
+/* set 1D field stride in number of scalars */
+void
+zfp_field_set_stride_1d(
+ zfp_field* field, /* field metadata */
+ int sx /* stride in number of scalars: &f[1] - &f[0] */
+);
+
+/* set 2D field strides in number of scalars */
+void
+zfp_field_set_stride_2d(
+ zfp_field* field, /* field metadata */
+ int sx, /* stride in x dimension: &f[0][1] - &f[0][0] */
+ int sy /* stride in y dimension: &f[1][0] - &f[0][0] */
+);
+
+/* set 3D field strides in number of scalars */
+void
+zfp_field_set_stride_3d(
+ zfp_field* field, /* field metadata */
+ int sx, /* stride in x dimension: &f[0][0][1] - &f[0][0][0] */
+ int sy, /* stride in y dimension: &f[0][1][0] - &f[0][0][0] */
+ int sz /* stride in z dimension: &f[1][0][0] - &f[0][0][0] */
+);
+
+/* set field scalar type and dimensions */
+int /* nonzero upon success */
+zfp_field_set_metadata(
+ zfp_field* field, /* field metadata */
+ uint64 meta /* compact 52-bit encoding of metadata */
+);
+
+/* high-level API: compression and decompression --------------------------- */
+
+/* compress entire field (nonzero return value upon success) */
+size_t /* actual number of bytes of compressed storage */
+zfp_compress(
+ zfp_stream* stream, /* compressed stream */
+ const zfp_field* field /* field metadata */
+);
+
+/* decompress entire field (nonzero return value upon success) */
+int /* nonzero upon success */
+zfp_decompress(
+ zfp_stream* stream, /* compressed stream */
+ zfp_field* field /* field metadata */
+);
+
+/* write compression parameters and field metadata (optional) */
+size_t /* number of bits written or zero upon failure */
+zfp_write_header(
+ zfp_stream* stream, /* compressed stream */
+ const zfp_field* field, /* field metadata */
+ uint mask /* information to write */
+);
+
+/* read compression parameters and field metadata when previously written */
+size_t /* number of bits read or zero upon failure */
+zfp_read_header(
+ zfp_stream* stream, /* compressed stream */
+ zfp_field* field, /* field metadata */
+ uint mask /* information to read */
+);
+
+/* low-level API: stream manipulation -------------------------------------- */
+
+/* flush bit stream--must be called after last encode call or between seeks */
+void
+zfp_stream_flush(
+ zfp_stream* stream /* compressed bit stream */
+);
+
+/* align bit stream on next word boundary (decoding analogy to flush) */
+void
+zfp_stream_align(
+ zfp_stream* stream /* compressed bit stream */
+);
+
+/* rewind bit stream to beginning for compression or decompression */
+void
+zfp_stream_rewind(
+ zfp_stream* stream /* compressed bit stream */
+);
+
+/* low-level API: encoder -------------------------------------------------- */
+
+/*
+The functions below all compress either a complete contiguous d-dimensional
+block of 4^d scalars or a complete or partial block assembled from a strided
+array. In the latter case, p points to the first scalar; (nx, ny, nz) specify
+the size of the block, with 1 <= nx, ny, nz <= 4; and (sx, sy, sz) specify the
+strides, i.e. the number of scalars to advance to get to the next scalar along
+each dimension. The functions return the number of bits of compressed storage
+needed for the compressed block.
+*/
+
+/* encode 1D contiguous block of 4 values */
+uint zfp_encode_block_int32_1(zfp_stream* stream, const int32* block);
+uint zfp_encode_block_int64_1(zfp_stream* stream, const int64* block);
+uint zfp_encode_block_float_1(zfp_stream* stream, const float* block);
+uint zfp_encode_block_double_1(zfp_stream* stream, const double* block);
+
+/* encode 1D complete or partial block from strided array */
+uint zfp_encode_block_strided_float_1(zfp_stream* stream, const float* p, int sx);
+uint zfp_encode_block_strided_double_1(zfp_stream* stream, const double* p, int sx);
+uint zfp_encode_partial_block_strided_float_1(zfp_stream* stream, const float* p, uint nx, int sx);
+uint zfp_encode_partial_block_strided_double_1(zfp_stream* stream, const double* p, uint nx, int sx);
+
+/* encode 2D contiguous block of 4x4 values */
+uint zfp_encode_block_int32_2(zfp_stream* stream, const int32* block);
+uint zfp_encode_block_int64_2(zfp_stream* stream, const int64* block);
+uint zfp_encode_block_float_2(zfp_stream* stream, const float* block);
+uint zfp_encode_block_double_2(zfp_stream* stream, const double* block);
+
+/* encode 2D complete or partial block from strided array */
+uint zfp_encode_partial_block_strided_float_2(zfp_stream* stream, const float* p, uint nx, uint ny, int sx, int sy);
+uint zfp_encode_partial_block_strided_double_2(zfp_stream* stream, const double* p, uint nx, uint ny, int sx, int sy);
+uint zfp_encode_block_strided_float_2(zfp_stream* stream, const float* p, int sx, int sy);
+uint zfp_encode_block_strided_double_2(zfp_stream* stream, const double* p, int sx, int sy);
+
+/* encode 3D contiguous block of 4x4x4 values */
+uint zfp_encode_block_int32_3(zfp_stream* stream, const int32* block);
+uint zfp_encode_block_int64_3(zfp_stream* stream, const int64* block);
+uint zfp_encode_block_float_3(zfp_stream* stream, const float* block);
+uint zfp_encode_block_double_3(zfp_stream* stream, const double* block);
+
+/* encode 3D complete or partial block from strided array */
+uint zfp_encode_block_strided_float_3(zfp_stream* stream, const float* p, int sx, int sy, int sz);
+uint zfp_encode_block_strided_double_3(zfp_stream* stream, const double* p, int sx, int sy, int sz);
+uint zfp_encode_partial_block_strided_float_3(zfp_stream* stream, const float* p, uint nx, uint ny, uint nz, int sx, int sy, int sz);
+uint zfp_encode_partial_block_strided_double_3(zfp_stream* stream, const double* p, uint nx, uint ny, uint nz, int sx, int sy, int sz);
+
+/* low-level API: decoder -------------------------------------------------- */
+
+/*
+Each function below decompresses a single block and returns the number of bits
+of compressed storage consumed. See corresponding encoder functions above for
+further details.
+*/
+
+/* decode 1D contiguous block of 4 values */
+uint zfp_decode_block_int32_1(zfp_stream* stream, int32* block);
+uint zfp_decode_block_int64_1(zfp_stream* stream, int64* block);
+uint zfp_decode_block_float_1(zfp_stream* stream, float* block);
+uint zfp_decode_block_double_1(zfp_stream* stream, double* block);
+
+/* decode 1D complete or partial block from strided array */
+uint zfp_decode_block_strided_float_1(zfp_stream* stream, float* p, int sx);
+uint zfp_decode_block_strided_double_1(zfp_stream* stream, double* p, int sx);
+uint zfp_decode_partial_block_strided_float_1(zfp_stream* stream, float* p, uint nx, int sx);
+uint zfp_decode_partial_block_strided_double_1(zfp_stream* stream, double* p, uint nx, int sx);
+
+/* decode 2D contiguous block of 4x4 values */
+uint zfp_decode_block_int32_2(zfp_stream* stream, int32* block);
+uint zfp_decode_block_int64_2(zfp_stream* stream, int64* block);
+uint zfp_decode_block_float_2(zfp_stream* stream, float* block);
+uint zfp_decode_block_double_2(zfp_stream* stream, double* block);
+
+/* decode 2D complete or partial block from strided array */
+uint zfp_decode_block_strided_float_2(zfp_stream* stream, float* p, int sx, int sy);
+uint zfp_decode_block_strided_double_2(zfp_stream* stream, double* p, int sx, int sy);
+uint zfp_decode_partial_block_strided_float_2(zfp_stream* stream, float* p, uint nx, uint ny, int sx, int sy);
+uint zfp_decode_partial_block_strided_double_2(zfp_stream* stream, double* p, uint nx, uint ny, int sx, int sy);
+
+/* decode 3D contiguous block of 4x4x4 values */
+uint zfp_decode_block_int32_3(zfp_stream* stream, int32* block);
+uint zfp_decode_block_int64_3(zfp_stream* stream, int64* block);
+uint zfp_decode_block_float_3(zfp_stream* stream, float* block);
+uint zfp_decode_block_double_3(zfp_stream* stream, double* block);
+
+/* decode 3D complete or partial block from strided array */
+uint zfp_decode_block_strided_float_3(zfp_stream* stream, float* p, int sx, int sy, int sz);
+uint zfp_decode_block_strided_double_3(zfp_stream* stream, double* p, int sx, int sy, int sz);
+uint zfp_decode_partial_block_strided_float_3(zfp_stream* stream, float* p, uint nx, uint ny, uint nz, int sx, int sy, int sz);
+uint zfp_decode_partial_block_strided_double_3(zfp_stream* stream, double* p, uint nx, uint ny, uint nz, int sx, int sy, int sz);
+
+/* low-level API: utility functions ---------------------------------------- */
+
+/* convert dims-dimensional contiguous block to 32-bit integer type */
+void zfp_promote_int8_to_int32(int32* oblock, const int8* iblock, uint dims);
+void zfp_promote_uint8_to_int32(int32* oblock, const uint8* iblock, uint dims);
+void zfp_promote_int16_to_int32(int32* oblock, const int16* iblock, uint dims);
+void zfp_promote_uint16_to_int32(int32* oblock, const uint16* iblock, uint dims);
+
+/* convert dims-dimensional contiguous block from 32-bit integer type */
+void zfp_demote_int32_to_int8(int8* oblock, const int32* iblock, uint dims);
+void zfp_demote_int32_to_uint8(uint8* oblock, const int32* iblock, uint dims);
+void zfp_demote_int32_to_int16(int16* oblock, const int32* iblock, uint dims);
+void zfp_demote_int32_to_uint16(uint16* oblock, const int32* iblock, uint dims);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/src/zfp/zfp-0.5.0/src/Makefile b/src/zfp/zfp-0.5.0/src/Makefile
new file mode 100644
index 0000000..b056161
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/Makefile
@@ -0,0 +1,21 @@
+include ../Config
+
+TARGETS = ../lib/libzfp.a ../lib/libzfp.so
+OBJECTS = bitstream.o decode1f.o decode1d.o encode1f.o encode1d.o decode2f.o decode2d.o encode2f.o encode2d.o decode3f.o decode3d.o encode3f.o encode3d.o zfp.o
+
+../lib/libzfp.a: $(OBJECTS)
+ rm -f $@
+ ar rc $@ $^
+
+../lib/libzfp.so: $(OBJECTS)
+ $(CC) $(CFLAGS) -shared $^ -o $@
+
+.c.o:
+ $(CC) $(CFLAGS) -c $<
+
+static: ../lib/libzfp.a
+
+shared: ../lib/libzfp.so
+
+clean:
+ rm -f $(TARGETS) $(OBJECTS)
diff --git a/src/zfp/zfp-0.5.0/src/bitstream.c b/src/zfp/zfp-0.5.0/src/bitstream.c
new file mode 100644
index 0000000..3a74766
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/bitstream.c
@@ -0,0 +1,4 @@
+#include "bitstream.h"
+#include "inline/bitstream.c"
+
+const size_t stream_word_bits = wsize;
diff --git a/src/zfp/zfp-0.5.0/src/block1.h b/src/zfp/zfp-0.5.0/src/block1.h
new file mode 100644
index 0000000..035d9c9
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/block1.h
@@ -0,0 +1 @@
+#define DIMS 1
diff --git a/src/zfp/zfp-0.5.0/src/block2.h b/src/zfp/zfp-0.5.0/src/block2.h
new file mode 100644
index 0000000..e87ab62
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/block2.h
@@ -0,0 +1 @@
+#define DIMS 2
diff --git a/src/zfp/zfp-0.5.0/src/block3.h b/src/zfp/zfp-0.5.0/src/block3.h
new file mode 100644
index 0000000..a683568
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/block3.h
@@ -0,0 +1 @@
+#define DIMS 3
diff --git a/src/zfp/zfp-0.5.0/src/decode1d.c b/src/zfp/zfp-0.5.0/src/decode1d.c
new file mode 100644
index 0000000..3cb3d1a
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/decode1d.c
@@ -0,0 +1,10 @@
+#include "inline/inline.h"
+#include "zfp.h"
+#include "macros.h"
+#include "block1.h"
+#include "traitsd.h"
+#include "template/template.h"
+#include "template/codec.h"
+#include "template/codec1.c"
+#include "template/decode1.c"
+#include "template/decode.c"
diff --git a/src/zfp/zfp-0.5.0/src/decode1f.c b/src/zfp/zfp-0.5.0/src/decode1f.c
new file mode 100644
index 0000000..0d69982
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/decode1f.c
@@ -0,0 +1,10 @@
+#include "inline/inline.h"
+#include "zfp.h"
+#include "macros.h"
+#include "block1.h"
+#include "traitsf.h"
+#include "template/template.h"
+#include "template/codec.h"
+#include "template/codec1.c"
+#include "template/decode1.c"
+#include "template/decode.c"
diff --git a/src/zfp/zfp-0.5.0/src/decode2d.c b/src/zfp/zfp-0.5.0/src/decode2d.c
new file mode 100644
index 0000000..358d256
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/decode2d.c
@@ -0,0 +1,10 @@
+#include "inline/inline.h"
+#include "zfp.h"
+#include "macros.h"
+#include "block2.h"
+#include "traitsd.h"
+#include "template/template.h"
+#include "template/codec.h"
+#include "template/codec2.c"
+#include "template/decode2.c"
+#include "template/decode.c"
diff --git a/src/zfp/zfp-0.5.0/src/decode2f.c b/src/zfp/zfp-0.5.0/src/decode2f.c
new file mode 100644
index 0000000..1f45b1c
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/decode2f.c
@@ -0,0 +1,10 @@
+#include "inline/inline.h"
+#include "zfp.h"
+#include "macros.h"
+#include "block2.h"
+#include "traitsf.h"
+#include "template/template.h"
+#include "template/codec.h"
+#include "template/codec2.c"
+#include "template/decode2.c"
+#include "template/decode.c"
diff --git a/src/zfp/zfp-0.5.0/src/decode3d.c b/src/zfp/zfp-0.5.0/src/decode3d.c
new file mode 100644
index 0000000..22df744
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/decode3d.c
@@ -0,0 +1,10 @@
+#include "inline/inline.h"
+#include "zfp.h"
+#include "macros.h"
+#include "block3.h"
+#include "traitsd.h"
+#include "template/template.h"
+#include "template/codec.h"
+#include "template/codec3.c"
+#include "template/decode3.c"
+#include "template/decode.c"
diff --git a/src/zfp/zfp-0.5.0/src/decode3f.c b/src/zfp/zfp-0.5.0/src/decode3f.c
new file mode 100644
index 0000000..ca5030c
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/decode3f.c
@@ -0,0 +1,10 @@
+#include "inline/inline.h"
+#include "zfp.h"
+#include "macros.h"
+#include "block3.h"
+#include "traitsf.h"
+#include "template/template.h"
+#include "template/codec.h"
+#include "template/codec3.c"
+#include "template/decode3.c"
+#include "template/decode.c"
diff --git a/src/zfp/zfp-0.5.0/src/encode1d.c b/src/zfp/zfp-0.5.0/src/encode1d.c
new file mode 100644
index 0000000..e4a356c
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/encode1d.c
@@ -0,0 +1,10 @@
+#include "inline/inline.h"
+#include "zfp.h"
+#include "macros.h"
+#include "block1.h"
+#include "traitsd.h"
+#include "template/template.h"
+#include "template/codec.h"
+#include "template/codec1.c"
+#include "template/encode1.c"
+#include "template/encode.c"
diff --git a/src/zfp/zfp-0.5.0/src/encode1f.c b/src/zfp/zfp-0.5.0/src/encode1f.c
new file mode 100644
index 0000000..cd29b49
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/encode1f.c
@@ -0,0 +1,10 @@
+#include "inline/inline.h"
+#include "zfp.h"
+#include "macros.h"
+#include "block1.h"
+#include "traitsf.h"
+#include "template/template.h"
+#include "template/codec.h"
+#include "template/codec1.c"
+#include "template/encode1.c"
+#include "template/encode.c"
diff --git a/src/zfp/zfp-0.5.0/src/encode2d.c b/src/zfp/zfp-0.5.0/src/encode2d.c
new file mode 100644
index 0000000..ccf6a72
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/encode2d.c
@@ -0,0 +1,10 @@
+#include "inline/inline.h"
+#include "zfp.h"
+#include "macros.h"
+#include "block2.h"
+#include "traitsd.h"
+#include "template/template.h"
+#include "template/codec.h"
+#include "template/codec2.c"
+#include "template/encode2.c"
+#include "template/encode.c"
diff --git a/src/zfp/zfp-0.5.0/src/encode2f.c b/src/zfp/zfp-0.5.0/src/encode2f.c
new file mode 100644
index 0000000..3c95e36
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/encode2f.c
@@ -0,0 +1,10 @@
+#include "inline/inline.h"
+#include "zfp.h"
+#include "macros.h"
+#include "block2.h"
+#include "traitsf.h"
+#include "template/template.h"
+#include "template/codec.h"
+#include "template/codec2.c"
+#include "template/encode2.c"
+#include "template/encode.c"
diff --git a/src/zfp/zfp-0.5.0/src/encode3d.c b/src/zfp/zfp-0.5.0/src/encode3d.c
new file mode 100644
index 0000000..a455cb0
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/encode3d.c
@@ -0,0 +1,10 @@
+#include "inline/inline.h"
+#include "zfp.h"
+#include "macros.h"
+#include "block3.h"
+#include "traitsd.h"
+#include "template/template.h"
+#include "template/codec.h"
+#include "template/codec3.c"
+#include "template/encode3.c"
+#include "template/encode.c"
diff --git a/src/zfp/zfp-0.5.0/src/encode3f.c b/src/zfp/zfp-0.5.0/src/encode3f.c
new file mode 100644
index 0000000..c59ce91
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/encode3f.c
@@ -0,0 +1,10 @@
+#include "inline/inline.h"
+#include "zfp.h"
+#include "macros.h"
+#include "block3.h"
+#include "traitsf.h"
+#include "template/template.h"
+#include "template/codec.h"
+#include "template/codec3.c"
+#include "template/encode3.c"
+#include "template/encode.c"
diff --git a/src/zfp/zfp-0.5.0/src/inline/bitstream.c b/src/zfp/zfp-0.5.0/src/inline/bitstream.c
new file mode 100644
index 0000000..5d7846c
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/inline/bitstream.c
@@ -0,0 +1,410 @@
+/*
+High-speed in-memory bit stream I/O that supports reading and writing between
+0 and 64 bits at a time. The implementation, which relies heavily on bit
+shifts, has been carefully written to ensure that all shifts are between
+zero and one less the width of the type being shifted to avoid undefined
+behavior. This occasionally causes somewhat convoluted code.
+
+The following assumptions and restrictions apply:
+
+1. The user must allocate a memory buffer large enough to hold the bit stream,
+ whether for reading, writing, or both. This buffer is associated with the
+ bit stream via stream_open(buffer, bytes), which allocates and returns a
+ pointer to an opaque bit stream struct. Call stream_close(stream) to
+ deallocate this struct.
+
+2. The stream is either in a read or write state (or, initially, in both
+ states). When done writing, call stream_flush(stream) before entering
+ read mode to ensure any buffered bits are output. To enter read mode,
+ call stream_rewind(stream) or stream_rseek(stream, offset) to position
+ the stream at the beginning or at a particular bit offset. Conversely,
+ stream_rewind(stream) or stream_wseek(stream, offset) positions the
+ stream for writing. In read mode, the following functions may be called:
+
+ size_t stream_size(stream);
+ size_t stream_rtell(stream);
+ void stream_rewind(stream);
+ void stream_rseek(stream, offset);
+ void stream_skip(stream, uint n);
+ void stream_align(stream);
+ uint stream_read_bit(stream);
+ uint64 stream_read_bits(stream, n);
+
+ Each of these read calls has a corresponding write call:
+
+ size_t stream_size(stream);
+ size_t stream_wtell(stream);
+ void stream_rewind(stream);
+ void stream_wseek(stream, offset);
+ void stream_pad(stream, n);
+ void stream_flush(stream);
+ uint stream_write_bit(stream, bit);
+ uint64 stream_write_bits(stream, value, n);
+
+3. The stream buffer is an unsigned integer of a user-specified type given
+ by the BIT_STREAM_WORD_TYPE macro. Bits are read and written in units of
+ this integer word type. Supported types are 8, 16, 32, or 64 bits wide.
+ The bit width of the buffer is denoted by 'wsize' and can be accessed via
+ the global variable stream_word_bits. A small wsize allows for fine
+ granularity reads and writes, and may be preferable when working with many
+ small blocks of data that require non-sequential access. The default
+ maximum size of 64 bits ensures maximum speed. Note that even when
+ wsize < 64, it is still possible to read and write up to 64 bits at a time
+ using stream_read_bits() and stream_write_bits().
+
+4. If BIT_STREAM_STRIDED is defined, words read from or written to the stream
+ may be accessed noncontiguously by setting a power-of-two block size (which
+ by default is one word) and a block stride (defaults to zero blocks). The
+ word pointer is always incremented by one word each time a word is accessed.
+ Once advanced past a block boundary, the word pointer is also advanced by
+ the stride to the next block. This feature may be used to store blocks of
+ data interleaved, e.g. for progressive coding or for noncontiguous parallel
+ access to the bit stream Note that the block size is measured in words,
+ while the stride is measured in multiples of the block size. Strided access
+ can have a significant performance penalty.
+
+5. Multiple bits are read and written in order of least to most significant
+ bit. Thus, the statement
+
+ value = stream_write_bits(stream, value, n);
+
+ is essentially equivalent to (but faster than)
+
+ for (i = 0; i < n; i++, value >>= 1)
+ stream_write_bit(value & 1);
+
+ when 0 <= n <= 64. The same holds for read calls, and thus
+
+ value = stream_read_bits(stream, n);
+
+ is essentially equivalent to
+
+ for (i = 0, value = 0; i < n; i++)
+ value += (uint64)stream_read_bit() << i;
+
+ Note that it is possible to write fewer bits than the argument 'value'
+ holds (possibly even zero bits), in which case any unwritten bits are
+ returned.
+
+6. Although the stream_wseek(stream, offset) call allows positioning the
+ stream for writing at any bit offset without any data loss (i.e. all
+ previously written bits preceding the offset remain valid), for efficiency
+ the stream_flush(stream) operation will zero all bits up to the next
+ multiple of wsize bits, thus overwriting bits that were previously stored
+ at that location. Consequently, random write access is effectively
+ supported only at wsize granularity. For sequential access, the largest
+ possible wsize is preferred due to higher speed.
+
+7. It is up to the user to adhere to these rules. For performance reasons,
+ no error checking is done, and in particular buffer overruns are not
+ caught.
+*/
+
+#include <limits.h>
+#include <stdlib.h>
+
+#ifndef _inline
+ #define _inline
+#endif
+
+/* bit stream word/buffer type; granularity of stream I/O operations */
+#ifdef BIT_STREAM_WORD_TYPE
+ /* may be 8-, 16-, 32-, or 64-bit unsigned integer type */
+ typedef BIT_STREAM_WORD_TYPE word;
+#else
+ /* use maximum word size by default for highest speed */
+ typedef uint64 word;
+#endif
+
+/* number of bits in a buffered word */
+#define wsize ((uint)(CHAR_BIT * sizeof(word)))
+
+/* bit stream structure (opaque to caller) */
+struct bitstream {
+ uint bits; /* number of buffered bits (0 <= bits < wsize) */
+ word buffer; /* buffer for incoming/outgoing bits (buffer < 2^bits) */
+ word* ptr; /* pointer to next word to be read/written */
+ word* begin; /* beginning of stream */
+ word* end; /* end of stream (currently unused) */
+#ifdef BIT_STREAM_STRIDED
+ uint mask; /* one less the block size in number of words */
+ int delta; /* number of words between consecutive blocks */
+#endif
+};
+
+/* private functions ------------------------------------------------------- */
+
+/* read a single word from memory */
+static word
+stream_read_word(bitstream* s)
+{
+ word w = *s->ptr++;
+#ifdef BIT_STREAM_STRIDED
+ if (!((s->ptr - s->begin) & s->mask))
+ s->ptr += s->delta;
+#endif
+ return w;
+}
+
+/* write a single word to memory */
+static void
+stream_write_word(bitstream* s, word value)
+{
+ *s->ptr++ = value;
+#ifdef BIT_STREAM_STRIDED
+ if (!((s->ptr - s->begin) & s->mask))
+ s->ptr += s->delta;
+#endif
+}
+
+/* public functions -------------------------------------------------------- */
+
+/* pointer to beginning of stream */
+_inline void*
+stream_data(const bitstream* s)
+{
+ return s->begin;
+}
+
+/* current byte size of stream (if flushed) */
+_inline size_t
+stream_size(const bitstream* s)
+{
+ return sizeof(word) * (s->ptr - s->begin);
+}
+
+/* byte capacity of stream */
+_inline size_t
+stream_capacity(const bitstream* s)
+{
+ return sizeof(word) * (s->end - s->begin);
+}
+
+/* number of blocks between consecutive stream blocks */
+_inline int
+stream_delta(const bitstream* s)
+{
+#ifdef BIT_STREAM_STRIDED
+ return s->delta / (s->mask + 1);
+#else
+ return 0;
+#endif
+}
+
+/* read single bit (0 or 1) */
+_inline uint
+stream_read_bit(bitstream* s)
+{
+ uint bit;
+ if (!s->bits) {
+ s->buffer = stream_read_word(s);
+ s->bits = wsize;
+ }
+ s->bits--;
+ bit = (uint)s->buffer & 1u;
+ s->buffer >>= 1;
+ return bit;
+}
+
+/* write single bit (must be 0 or 1) */
+_inline uint
+stream_write_bit(bitstream* s, uint bit)
+{
+ s->buffer += (word)bit << s->bits;
+ if (++s->bits == wsize) {
+ stream_write_word(s, s->buffer);
+ s->buffer = 0;
+ s->bits = 0;
+ }
+ return bit;
+}
+
+/* read 0 <= n <= 64 bits */
+_inline uint64
+stream_read_bits(bitstream* s, uint n)
+{
+ uint64 value = s->buffer;
+ if (s->bits < n) {
+ /* keep fetching wsize bits until enough bits are buffered */
+ do {
+ /* assert: 0 <= s->bits < n <= 64 */
+ s->buffer = stream_read_word(s);
+ value += (uint64)s->buffer << s->bits;
+ s->bits += wsize;
+ } while (sizeof(s->buffer) < sizeof(value) && s->bits < n);
+ /* assert: 1 <= n <= s->bits < n + wsize */
+ s->bits -= n;
+ if (!s->bits) {
+ /* value holds exactly n bits; no need for masking */
+ s->buffer = 0;
+ }
+ else {
+ /* assert: 1 <= s->bits < wsize */
+ s->buffer >>= wsize - s->bits;
+ /* assert: 1 <= n <= 64 */
+ value &= ((uint64)2 << (n - 1)) - 1;
+ }
+ }
+ else {
+ /* assert: 0 <= n <= s->bits < wsize <= 64 */
+ s->bits -= n;
+ s->buffer >>= n;
+ value &= ((uint64)1 << n) - 1;
+ }
+ return value;
+}
+
+/* write 0 <= n <= 64 low bits of value and return remaining bits */
+_inline uint64
+stream_write_bits(bitstream* s, uint64 value, uint n)
+{
+ /* append bit string to buffer */
+ s->buffer += value << s->bits;
+ s->bits += n;
+ /* is buffer full? */
+ if (s->bits >= wsize) {
+ /* 1 <= n <= 64; decrement n to ensure valid right shifts below */
+ value >>= 1;
+ n--;
+ /* assert: 0 <= n < 64; wsize <= s->bits <= wsize + n */
+ do {
+ /* output wsize bits while buffer is full */
+ s->bits -= wsize;
+ /* assert: 0 <= s->bits <= n */
+ stream_write_word(s, s->buffer);
+ /* assert: 0 <= n - s->bits < 64 */
+ s->buffer = value >> (n - s->bits);
+ } while (sizeof(s->buffer) < sizeof(value) && s->bits >= wsize);
+ }
+ /* assert: 0 <= s->bits < wsize */
+ s->buffer &= ((word)1 << s->bits) - 1;
+ /* assert: 0 <= n < 64 */
+ return value >> n;
+}
+
+/* return bit offset to next bit to be read */
+_inline size_t
+stream_rtell(const bitstream* s)
+{
+ return wsize * (s->ptr - s->begin) - s->bits;
+}
+
+/* return bit offset to next bit to be written */
+_inline size_t
+stream_wtell(const bitstream* s)
+{
+ return wsize * (s->ptr - s->begin) + s->bits;
+}
+
+/* position stream for reading or writing at beginning */
+_inline void
+stream_rewind(bitstream* s)
+{
+ s->ptr = s->begin;
+ s->buffer = 0;
+ s->bits = 0;
+}
+
+/* position stream for reading at given bit offset */
+_inline void
+stream_rseek(bitstream* s, size_t offset)
+{
+ uint n = offset % wsize;
+ s->ptr = s->begin + offset / wsize;
+ if (n) {
+ s->buffer = stream_read_word(s) >> n;
+ s->bits = wsize - n;
+ }
+ else {
+ s->buffer = 0;
+ s->bits = 0;
+ }
+}
+
+/* position stream for writing at given bit offset */
+_inline void
+stream_wseek(bitstream* s, size_t offset)
+{
+ uint n = offset % wsize;
+ s->ptr = s->begin + offset / wsize;
+ if (n) {
+ word buffer = *s->ptr;
+ buffer &= ((word)1 << n) - 1;
+ s->buffer = buffer;
+ s->bits = n;
+ }
+ else {
+ s->buffer = 0;
+ s->bits = 0;
+ }
+}
+
+/* skip over the next n bits (n >= 0) */
+_inline void
+stream_skip(bitstream* s, uint n)
+{
+ stream_rseek(s, stream_rtell(s) + n);
+}
+
+/* append n zero bits to stream (n >= 0) */
+_inline void
+stream_pad(bitstream* s, uint n)
+{
+ for (s->bits += n; s->bits >= wsize; s->bits -= wsize) {
+ stream_write_word(s, s->buffer);
+ s->buffer = 0;
+ }
+}
+
+/* align stream on next word boundary */
+_inline void
+stream_align(bitstream* s)
+{
+ if (s->bits)
+ stream_skip(s, s->bits);
+}
+
+/* write any remaining buffered bits and align stream on next word boundary */
+_inline void
+stream_flush(bitstream* s)
+{
+ if (s->bits)
+ stream_pad(s, wsize - s->bits);
+}
+
+#ifdef BIT_STREAM_STRIDED
+/* set block size in number of words and spacing in number of blocks */
+_inline int
+stream_set_stride(bitstream* s, uint block, int delta)
+{
+ /* ensure block size is a power of two */
+ if (block & (block - 1))
+ return 0;
+ s->mask = block - 1;
+ s->delta = delta * block;
+ return 1;
+}
+#endif
+
+/* allocate and initialize bit stream to user-allocated buffer */
+_inline bitstream*
+stream_open(void* buffer, size_t bytes)
+{
+ bitstream* s = malloc(sizeof(bitstream));
+ if (s) {
+ s->begin = buffer;
+ s->end = s->begin + bytes / sizeof(word);
+#ifdef BIT_STREAM_STRIDED
+ stream_set_stride(s, 0, 0);
+#endif
+ stream_rewind(s);
+ }
+ return s;
+}
+
+/* close and deallocate bit stream */
+_inline void
+stream_close(bitstream* s)
+{
+ free(s);
+}
diff --git a/src/zfp/zfp-0.5.0/src/inline/inline.h b/src/zfp/zfp-0.5.0/src/inline/inline.h
new file mode 100644
index 0000000..50a847f
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/inline/inline.h
@@ -0,0 +1,12 @@
+#ifndef INLINE_H
+#define INLINE_H
+
+#ifndef _inline
+ #if __STDC_VERSION__ >= 199901L
+ #define _inline static inline
+ #else
+ #define _inline static
+ #endif
+#endif
+
+#endif
diff --git a/src/zfp/zfp-0.5.0/src/template/codec.h b/src/zfp/zfp-0.5.0/src/template/codec.h
new file mode 100644
index 0000000..e7149a9
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/template/codec.h
@@ -0,0 +1,3 @@
+#define PERM _t1(perm, DIMS) /* coefficient order */
+#define BLOCK_SIZE (1 << (2 * DIMS)) /* values per block */
+#define EBIAS ((1 << (EBITS - 1)) - 1) /* exponent bias */
diff --git a/src/zfp/zfp-0.5.0/src/template/codec1.c b/src/zfp/zfp-0.5.0/src/template/codec1.c
new file mode 100644
index 0000000..f391832
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/template/codec1.c
@@ -0,0 +1,11 @@
+/* order coefficients by polynomial degree/frequency */
+_cache_align(static const uchar perm_1[4]) = {
+ 0, 1, 2, 3
+};
+
+/* maximum number of bit planes to encode */
+static uint
+_t2(precision, Scalar, 1)(int maxexp, uint maxprec, int minexp)
+{
+ return MIN(maxprec, MAX(0, maxexp - minexp + 4));
+}
diff --git a/src/zfp/zfp-0.5.0/src/template/codec2.c b/src/zfp/zfp-0.5.0/src/template/codec2.c
new file mode 100644
index 0000000..1215642
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/template/codec2.c
@@ -0,0 +1,39 @@
+#define index(i, j) ((i) + 4 * (j))
+
+/* order coefficients (i, j) by i + j, then i^2 + j^2 */
+_cache_align(static const uchar perm_2[16]) = {
+ index(0, 0), /* 0 : 0 */
+
+ index(1, 0), /* 1 : 1 */
+ index(0, 1), /* 2 : 1 */
+
+ index(1, 1), /* 3 : 2 */
+
+ index(2, 0), /* 4 : 2 */
+ index(0, 2), /* 5 : 2 */
+
+ index(2, 1), /* 6 : 3 */
+ index(1, 2), /* 7 : 3 */
+
+ index(3, 0), /* 8 : 3 */
+ index(0, 3), /* 9 : 3 */
+
+ index(2, 2), /* 10 : 4 */
+
+ index(3, 1), /* 11 : 4 */
+ index(1, 3), /* 12 : 4 */
+
+ index(3, 2), /* 13 : 5 */
+ index(2, 3), /* 14 : 5 */
+
+ index(3, 3), /* 15 : 6 */
+};
+
+#undef index
+
+/* maximum number of bit planes to encode */
+static uint
+_t2(precision, Scalar, 2)(int maxexp, uint maxprec, int minexp)
+{
+ return MIN(maxprec, MAX(0, maxexp - minexp + 6));
+}
diff --git a/src/zfp/zfp-0.5.0/src/template/codec3.c b/src/zfp/zfp-0.5.0/src/template/codec3.c
new file mode 100644
index 0000000..72d9d9c
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/template/codec3.c
@@ -0,0 +1,97 @@
+#define index(i, j, k) ((i) + 4 * ((j) + 4 * (k)))
+
+/* order coefficients (i, j, k) by i + j + k, then i^2 + j^2 + k^2 */
+_cache_align(static const uchar perm_3[64]) = {
+ index(0, 0, 0), /* 0 : 0 */
+
+ index(1, 0, 0), /* 1 : 1 */
+ index(0, 1, 0), /* 2 : 1 */
+ index(0, 0, 1), /* 3 : 1 */
+
+ index(0, 1, 1), /* 4 : 2 */
+ index(1, 0, 1), /* 5 : 2 */
+ index(1, 1, 0), /* 6 : 2 */
+
+ index(2, 0, 0), /* 7 : 2 */
+ index(0, 2, 0), /* 8 : 2 */
+ index(0, 0, 2), /* 9 : 2 */
+
+ index(1, 1, 1), /* 10 : 3 */
+
+ index(2, 1, 0), /* 11 : 3 */
+ index(2, 0, 1), /* 12 : 3 */
+ index(0, 2, 1), /* 13 : 3 */
+ index(1, 2, 0), /* 14 : 3 */
+ index(1, 0, 2), /* 15 : 3 */
+ index(0, 1, 2), /* 16 : 3 */
+
+ index(3, 0, 0), /* 17 : 3 */
+ index(0, 3, 0), /* 18 : 3 */
+ index(0, 0, 3), /* 19 : 3 */
+
+ index(2, 1, 1), /* 20 : 4 */
+ index(1, 2, 1), /* 21 : 4 */
+ index(1, 1, 2), /* 22 : 4 */
+
+ index(0, 2, 2), /* 23 : 4 */
+ index(2, 0, 2), /* 24 : 4 */
+ index(2, 2, 0), /* 25 : 4 */
+
+ index(3, 1, 0), /* 26 : 4 */
+ index(3, 0, 1), /* 27 : 4 */
+ index(0, 3, 1), /* 28 : 4 */
+ index(1, 3, 0), /* 29 : 4 */
+ index(1, 0, 3), /* 30 : 4 */
+ index(0, 1, 3), /* 31 : 4 */
+
+ index(1, 2, 2), /* 32 : 5 */
+ index(2, 1, 2), /* 33 : 5 */
+ index(2, 2, 1), /* 34 : 5 */
+
+ index(3, 1, 1), /* 35 : 5 */
+ index(1, 3, 1), /* 36 : 5 */
+ index(1, 1, 3), /* 37 : 5 */
+
+ index(3, 2, 0), /* 38 : 5 */
+ index(3, 0, 2), /* 39 : 5 */
+ index(0, 3, 2), /* 40 : 5 */
+ index(2, 3, 0), /* 41 : 5 */
+ index(2, 0, 3), /* 42 : 5 */
+ index(0, 2, 3), /* 43 : 5 */
+
+ index(2, 2, 2), /* 44 : 6 */
+
+ index(3, 2, 1), /* 45 : 6 */
+ index(3, 1, 2), /* 46 : 6 */
+ index(1, 3, 2), /* 47 : 6 */
+ index(2, 3, 1), /* 48 : 6 */
+ index(2, 1, 3), /* 49 : 6 */
+ index(1, 2, 3), /* 50 : 6 */
+
+ index(0, 3, 3), /* 51 : 6 */
+ index(3, 0, 3), /* 52 : 6 */
+ index(3, 3, 0), /* 53 : 6 */
+
+ index(3, 2, 2), /* 54 : 7 */
+ index(2, 3, 2), /* 55 : 7 */
+ index(2, 2, 3), /* 56 : 7 */
+
+ index(1, 3, 3), /* 57 : 7 */
+ index(3, 1, 3), /* 58 : 7 */
+ index(3, 3, 1), /* 59 : 7 */
+
+ index(2, 3, 3), /* 60 : 8 */
+ index(3, 2, 3), /* 61 : 8 */
+ index(3, 3, 2), /* 62 : 8 */
+
+ index(3, 3, 3), /* 63 : 9 */
+};
+
+#undef index
+
+/* maximum number of bit planes to encode */
+static uint
+_t2(precision, Scalar, 3)(int maxexp, uint maxprec, int minexp)
+{
+ return MIN(maxprec, MAX(0, maxexp - minexp + 8));
+}
diff --git a/src/zfp/zfp-0.5.0/src/template/compress.c b/src/zfp/zfp-0.5.0/src/template/compress.c
new file mode 100644
index 0000000..af89ef0
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/template/compress.c
@@ -0,0 +1,104 @@
+/* compress 1d contiguous array */
+static void
+_t2(compress, Scalar, 1)(zfp_stream* stream, const zfp_field* field)
+{
+ const Scalar* data = field->data;
+ uint nx = field->nx;
+ uint mx = nx & ~3u;
+ uint x;
+
+ for (x = 0; x < mx; x += 4, data += 4)
+ _t2(zfp_encode_block, Scalar, 1)(stream, data);
+ if (x < nx)
+ _t2(zfp_encode_partial_block_strided, Scalar, 1)(stream, data, nx - x, 1);
+}
+
+/* compress 1d strided array */
+static void
+_t2(compress_strided, Scalar, 1)(zfp_stream* stream, const zfp_field* field)
+{
+ const Scalar* data = field->data;
+ uint nx = field->nx;
+ uint mx = nx & ~3u;
+ int sx = field->sx ? field->sx : 1;
+ uint x;
+
+ for (x = 0; x < mx; x += 4, data += 4 * sx)
+ _t2(zfp_encode_block_strided, Scalar, 1)(stream, data, sx);
+ if (x < nx)
+ _t2(zfp_encode_partial_block_strided, Scalar, 1)(stream, data, nx - x, sx);
+}
+
+/* compress 2d strided array */
+static void
+_t2(compress_strided, Scalar, 2)(zfp_stream* stream, const zfp_field* field)
+{
+ const Scalar* data = field->data;
+ uint nx = field->nx;
+ uint ny = field->ny;
+ uint mx = nx & ~3u;
+ uint my = ny & ~3u;
+ int sx = field->sx ? field->sx : 1;
+ int sy = field->sy ? field->sy : nx;
+ uint x, y;
+
+ for (y = 0; y < my; y += 4, data += 4 * sy - mx * sx) {
+ for (x = 0; x < mx; x += 4, data += 4 * sx)
+ _t2(zfp_encode_block_strided, Scalar, 2)(stream, data, sx, sy);
+ if (x < nx)
+ _t2(zfp_encode_partial_block_strided, Scalar, 2)(stream, data, nx - x, 4, sx, sy);
+ }
+ if (y < ny) {
+ for (x = 0; x < mx; x += 4, data += 4 * sx)
+ _t2(zfp_encode_partial_block_strided, Scalar, 2)(stream, data, 4, ny - y, sx, sy);
+ if (x < nx)
+ _t2(zfp_encode_partial_block_strided, Scalar, 2)(stream, data, nx - x, ny - y, sx, sy);
+ }
+}
+
+/* compress 3d strided array */
+static void
+_t2(compress_strided, Scalar, 3)(zfp_stream* stream, const zfp_field* field)
+{
+ const Scalar* data = field->data;
+ uint nx = field->nx;
+ uint ny = field->ny;
+ uint nz = field->nz;
+ uint mx = nx & ~3u;
+ uint my = ny & ~3u;
+ uint mz = nz & ~3u;
+ int sx = field->sx ? field->sx : 1;
+ int sy = field->sy ? field->sy : nx;
+ int sz = field->sz ? field->sz : nx * ny;
+ uint x, y, z;
+
+ for (z = 0; z < mz; z += 4, data += 4 * sz - my * sy) {
+ for (y = 0; y < my; y += 4, data += 4 * sy - mx * sx) {
+ for (x = 0; x < mx; x += 4, data += 4 * sx)
+ _t2(zfp_encode_block_strided, Scalar, 3)(stream, data, sx, sy, sz);
+ if (x < nx)
+ _t2(zfp_encode_partial_block_strided, Scalar, 3)(stream, data, nx - x, 4, 4, sx, sy, sz);
+ }
+ if (y < ny) {
+ for (x = 0; x < mx; x += 4, data += 4 * sx)
+ _t2(zfp_encode_partial_block_strided, Scalar, 3)(stream, data, 4, ny - y, 4, sx, sy, sz);
+ if (x < nx)
+ _t2(zfp_encode_partial_block_strided, Scalar, 3)(stream, data, nx - x, ny - y, 4, sx, sy, sz);
+ data -= mx * sx;
+ }
+ }
+ if (z < nz) {
+ for (y = 0; y < my; y += 4, data += 4 * sy - mx * sx) {
+ for (x = 0; x < mx; x += 4, data += 4 * sx)
+ _t2(zfp_encode_partial_block_strided, Scalar, 3)(stream, data, 4, 4, nz - z, sx, sy, sz);
+ if (x < nx)
+ _t2(zfp_encode_partial_block_strided, Scalar, 3)(stream, data, nx - x, 4, nz - z, sx, sy, sz);
+ }
+ if (y < ny) {
+ for (x = 0; x < mx; x += 4, data += 4 * sx)
+ _t2(zfp_encode_partial_block_strided, Scalar, 3)(stream, data, 4, ny - y, nz - z, sx, sy, sz);
+ if (x < nx)
+ _t2(zfp_encode_partial_block_strided, Scalar, 3)(stream, data, nx - x, ny - y, nz - z, sx, sy, sz);
+ }
+ }
+}
diff --git a/src/zfp/zfp-0.5.0/src/template/decode.c b/src/zfp/zfp-0.5.0/src/template/decode.c
new file mode 100644
index 0000000..f7b6a14
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/template/decode.c
@@ -0,0 +1,165 @@
+#include <limits.h>
+#include <math.h>
+#include "../inline/inline.h"
+#include "../inline/bitstream.c"
+
+/* private functions ------------------------------------------------------- */
+
+/* map integer x relative to exponent e to floating-point number */
+static Scalar
+_t1(dequantize, Scalar)(Int x, int e)
+{
+ return LDEXP(x, e - (CHAR_BIT * (int)sizeof(Scalar) - 2));
+}
+
+/* inverse block-floating-point transform from signed integers */
+static void
+_t1(inv_cast, Scalar)(const Int* iblock, Scalar* fblock, uint n, int emax)
+{
+ /* compute power-of-two scale factor s */
+ Scalar s = _t1(dequantize, Scalar)(1, emax);
+ /* compute p-bit float x = s*y where |y| <= 2^(p-2) - 1 */
+ do
+ *fblock++ = (Scalar)(s * *iblock++);
+ while (--n);
+}
+
+/* inverse lifting transform of 4-vector */
+static void
+_t1(inv_lift, Int)(Int* p, uint s)
+{
+ Int x, y, z, w;
+ x = *p; p += s;
+ y = *p; p += s;
+ z = *p; p += s;
+ w = *p; p += s;
+
+ /*
+ ** non-orthogonal transform
+ ** ( 4 6 -4 -1) (x)
+ ** 1/4 * ( 4 2 4 5) (y)
+ ** ( 4 -2 4 -5) (z)
+ ** ( 4 -6 -4 1) (w)
+ */
+ y += w >> 1; w -= y >> 1;
+ y += w; w <<= 1; w -= y;
+ z += x; x <<= 1; x -= z;
+ y += z; z <<= 1; z -= y;
+ w += x; x <<= 1; x -= w;
+
+ p -= s; *p = w;
+ p -= s; *p = z;
+ p -= s; *p = y;
+ p -= s; *p = x;
+}
+
+/* map two's complement signed integer to negabinary unsigned integer */
+static Int
+_t1(uint2int, UInt)(UInt x)
+{
+ return (Int)((x ^ NBMASK) - NBMASK);
+}
+
+/* reorder unsigned coefficients and convert to signed integer */
+static void
+_t1(inv_order, Int)(const UInt* ublock, Int* iblock, const uchar* perm, uint n)
+{
+ do
+ iblock[*perm++] = _t1(uint2int, UInt)(*ublock++);
+ while (--n);
+}
+
+/* decompress sequence of size unsigned integers */
+static uint
+_t1(decode_ints, UInt)(bitstream* _restrict stream, uint maxbits, uint maxprec, UInt* _restrict data, uint size)
+{
+ /* make a copy of bit stream to avoid aliasing */
+ bitstream s = *stream;
+ uint intprec = CHAR_BIT * (uint)sizeof(UInt);
+ uint kmin = intprec > maxprec ? intprec - maxprec : 0;
+ uint bits = maxbits;
+ uint i, k, m, n;
+ uint64 x;
+
+ /* initialize data array to all zeros */
+ for (i = 0; i < size; i++)
+ data[i] = 0;
+
+ /* decode one bit plane at a time from MSB to LSB */
+ for (k = intprec, n = 0; bits && k-- > kmin;) {
+ /* decode first n bits of bit plane #k */
+ m = MIN(n, bits);
+ bits -= m;
+ x = stream_read_bits(&s, m);
+ /* unary run-length decode remainder of bit plane */
+ for (; n < size && bits && (bits--, stream_read_bit(&s)); x += (uint64)1 << n++)
+ for (; n < size - 1 && bits && (bits--, !stream_read_bit(&s)); n++)
+ ;
+ /* deposit bit plane from x */
+ for (i = 0; x; i++, x >>= 1)
+ data[i] += (UInt)(x & 1u) << k;
+ }
+
+ *stream = s;
+ return maxbits - bits;
+}
+
+/* decode block of integers */
+uint
+_t2(decode_block, Int, DIMS)(bitstream* stream, int minbits, int maxbits, int maxprec, Int* iblock)
+{
+ int bits;
+ _cache_align(UInt ublock[BLOCK_SIZE]);
+ /* decode integer coefficients */
+ bits = _t1(decode_ints, UInt)(stream, maxbits, maxprec, ublock, BLOCK_SIZE);
+ /* read at least minbits bits */
+ if (bits < minbits) {
+ stream_skip(stream, minbits - bits);
+ bits = minbits;
+ }
+ /* reorder unsigned coefficients and convert to signed integer */
+ _t1(inv_order, Int)(ublock, iblock, PERM, BLOCK_SIZE);
+ /* perform decorrelating transform */
+ _t2(inv_xform, Int, DIMS)(iblock);
+ return bits;
+}
+
+/* public functions -------------------------------------------------------- */
+
+/* decode contiguous floating-point block */
+uint
+_t2(zfp_decode_block, Int, DIMS)(zfp_stream* zfp, Int* iblock)
+{
+ return _t2(decode_block, Int, DIMS)(zfp->stream, zfp->minbits, zfp->maxbits, zfp->maxprec, iblock);
+}
+
+/* decode contiguous floating-point block */
+uint
+_t2(zfp_decode_block, Scalar, DIMS)(zfp_stream* zfp, Scalar* fblock)
+{
+ /* test if block has nonzero values */
+ if (stream_read_bit(zfp->stream)) {
+ _cache_align(Int iblock[BLOCK_SIZE]);
+ /* decode common exponent */
+ uint ebits = EBITS + 1;
+ int emax = stream_read_bits(zfp->stream, ebits - 1) - EBIAS;
+ int maxprec = _t2(precision, Scalar, DIMS)(emax, zfp->maxprec, zfp->minexp);
+ /* decode integer block */
+ uint bits = _t2(decode_block, Int, DIMS)(zfp->stream, zfp->minbits - ebits, zfp->maxbits - ebits, maxprec, iblock);
+ /* perform inverse block-floating-point transform */
+ _t1(inv_cast, Scalar)(iblock, fblock, BLOCK_SIZE, emax);
+ return ebits + bits;
+ }
+ else {
+ /* set all values to zero */
+ uint i;
+ for (i = 0; i < BLOCK_SIZE; i++)
+ *fblock++ = 0;
+ if (zfp->minbits > 1) {
+ stream_skip(zfp->stream, zfp->minbits - 1);
+ return zfp->minbits;
+ }
+ else
+ return 1;
+ }
+}
diff --git a/src/zfp/zfp-0.5.0/src/template/decode1.c b/src/zfp/zfp-0.5.0/src/template/decode1.c
new file mode 100644
index 0000000..c6c6cb0
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/template/decode1.c
@@ -0,0 +1,55 @@
+static void _t1(inv_lift, Int)(Int* p, uint s);
+
+/* private functions ------------------------------------------------------- */
+
+/* scatter 4-value block to strided array */
+static void
+_t2(scatter, Scalar, 1)(const Scalar* q, Scalar* p, int sx)
+{
+ uint x;
+ for (x = 0; x < 4; x++, p += sx)
+ *p = *q++;
+}
+
+/* scatter nx-value block to strided array */
+static void
+_t2(scatter_partial, Scalar, 1)(const Scalar* q, Scalar* p, uint nx, int sx)
+{
+ uint x;
+ for (x = 0; x < nx; x++, p += sx)
+ *p = *q++;
+}
+
+/* inverse decorrelating 1D transform */
+static void
+_t2(inv_xform, Int, 1)(Int* p)
+{
+ /* transform along x */
+ _t1(inv_lift, Int)(p, 1);
+}
+
+/* public functions -------------------------------------------------------- */
+
+/* decode 4-value floating-point block and store at p using stride sx */
+uint
+_t2(zfp_decode_block_strided, Scalar, 1)(zfp_stream* stream, Scalar* p, int sx)
+{
+ /* decode contiguous block */
+ _cache_align(Scalar fblock[4]);
+ uint bits = _t2(zfp_decode_block, Scalar, 1)(stream, fblock);
+ /* scatter block to strided array */
+ _t2(scatter, Scalar, 1)(fblock, p, sx);
+ return bits;
+}
+
+/* decode nx-value floating-point block and store at p using stride sx */
+uint
+_t2(zfp_decode_partial_block_strided, Scalar, 1)(zfp_stream* stream, Scalar* p, uint nx, int sx)
+{
+ /* decode contiguous block */
+ _cache_align(Scalar fblock[4]);
+ uint bits = _t2(zfp_decode_block, Scalar, 1)(stream, fblock);
+ /* scatter block to strided array */
+ _t2(scatter_partial, Scalar, 1)(fblock, p, nx, sx);
+ return bits;
+}
diff --git a/src/zfp/zfp-0.5.0/src/template/decode2.c b/src/zfp/zfp-0.5.0/src/template/decode2.c
new file mode 100644
index 0000000..34626dd
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/template/decode2.c
@@ -0,0 +1,62 @@
+static void _t1(inv_lift, Int)(Int* p, uint s);
+
+/* private functions ------------------------------------------------------- */
+
+/* scatter 4*4 block to strided array */
+static void
+_t2(scatter, Scalar, 2)(const Scalar* q, Scalar* p, int sx, int sy)
+{
+ uint x, y;
+ for (y = 0; y < 4; y++, p += sy - 4 * sx)
+ for (x = 0; x < 4; x++, p += sx)
+ *p = *q++;
+}
+
+/* scatter nx*ny block to strided array */
+static void
+_t2(scatter_partial, Scalar, 2)(const Scalar* q, Scalar* p, uint nx, uint ny, int sx, int sy)
+{
+ uint x, y;
+ for (y = 0; y < ny; y++, p += sy - nx * sx, q += 4 - nx)
+ for (x = 0; x < nx; x++, p += sx, q++)
+ *p = *q;
+}
+
+/* inverse decorrelating 2D transform */
+static void
+_t2(inv_xform, Int, 2)(Int* p)
+{
+ uint x, y;
+ /* transform along y */
+ for (x = 0; x < 4; x++)
+ _t1(inv_lift, Int)(p + 1 * x, 4);
+ /* transform along x */
+ for (y = 0; y < 4; y++)
+ _t1(inv_lift, Int)(p + 4 * y, 1);
+}
+
+/* public functions -------------------------------------------------------- */
+
+/* decode 4*4 floating-point block and store at p using strides (sx, sy) */
+uint
+_t2(zfp_decode_block_strided, Scalar, 2)(zfp_stream* stream, Scalar* p, int sx, int sy)
+{
+ /* decode contiguous block */
+ _cache_align(Scalar fblock[16]);
+ uint bits = _t2(zfp_decode_block, Scalar, 2)(stream, fblock);
+ /* scatter block to strided array */
+ _t2(scatter, Scalar, 2)(fblock, p, sx, sy);
+ return bits;
+}
+
+/* decode nx*ny floating-point block and store at p using strides (sx, sy) */
+uint
+_t2(zfp_decode_partial_block_strided, Scalar, 2)(zfp_stream* stream, Scalar* p, uint nx, uint ny, int sx, int sy)
+{
+ /* decode contiguous block */
+ _cache_align(Scalar fblock[16]);
+ uint bits = _t2(zfp_decode_block, Scalar, 2)(stream, fblock);
+ /* scatter block to strided array */
+ _t2(scatter_partial, Scalar, 2)(fblock, p, nx, ny, sx, sy);
+ return bits;
+}
diff --git a/src/zfp/zfp-0.5.0/src/template/decode3.c b/src/zfp/zfp-0.5.0/src/template/decode3.c
new file mode 100644
index 0000000..b69fb2d
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/template/decode3.c
@@ -0,0 +1,70 @@
+static void _t1(inv_lift, Int)(Int* p, uint s);
+
+/* private functions ------------------------------------------------------- */
+
+/* scatter 4*4*4 block to strided array */
+static void
+_t2(scatter, Scalar, 3)(const Scalar* q, Scalar* p, int sx, int sy, int sz)
+{
+ uint x, y, z;
+ for (z = 0; z < 4; z++, p += sz - 4 * sy)
+ for (y = 0; y < 4; y++, p += sy - 4 * sx)
+ for (x = 0; x < 4; x++, p += sx)
+ *p = *q++;
+}
+
+/* scatter nx*ny*nz block to strided array */
+static void
+_t2(scatter_partial, Scalar, 3)(const Scalar* q, Scalar* p, uint nx, uint ny, uint nz, int sx, int sy, int sz)
+{
+ uint x, y, z;
+ for (z = 0; z < nz; z++, p += sz - ny * sy, q += 4 * (4 - ny))
+ for (y = 0; y < ny; y++, p += sy - nx * sx, q += 4 - nx)
+ for (x = 0; x < nx; x++, p += sx, q++)
+ *p = *q;
+}
+
+/* inverse decorrelating 3D transform */
+static void
+_t2(inv_xform, Int, 3)(Int* p)
+{
+ uint x, y, z;
+ /* transform along z */
+ for (y = 0; y < 4; y++)
+ for (x = 0; x < 4; x++)
+ _t1(inv_lift, Int)(p + 1 * x + 4 * y, 16);
+ /* transform along y */
+ for (x = 0; x < 4; x++)
+ for (z = 0; z < 4; z++)
+ _t1(inv_lift, Int)(p + 16 * z + 1 * x, 4);
+ /* transform along x */
+ for (z = 0; z < 4; z++)
+ for (y = 0; y < 4; y++)
+ _t1(inv_lift, Int)(p + 4 * y + 16 * z, 1);
+}
+
+/* public functions -------------------------------------------------------- */
+
+/* decode 4*4*4 floating-point block and store at p using strides (sx, sy, sz) */
+uint
+_t2(zfp_decode_block_strided, Scalar, 3)(zfp_stream* stream, Scalar* p, int sx, int sy, int sz)
+{
+ /* decode contiguous block */
+ _cache_align(Scalar fblock[64]);
+ uint bits = _t2(zfp_decode_block, Scalar, 3)(stream, fblock);
+ /* scatter block to strided array */
+ _t2(scatter, Scalar, 3)(fblock, p, sx, sy, sz);
+ return bits;
+}
+
+/* decode nx*ny*nz floating-point block and store at p using strides (sx, sy, sz) */
+uint
+_t2(zfp_decode_partial_block_strided, Scalar, 3)(zfp_stream* stream, Scalar* p, uint nx, uint ny, uint nz, int sx, int sy, int sz)
+{
+ /* decode contiguous block */
+ _cache_align(Scalar fblock[64]);
+ uint bits = _t2(zfp_decode_block, Scalar, 3)(stream, fblock);
+ /* scatter block to strided array */
+ _t2(scatter_partial, Scalar, 3)(fblock, p, nx, ny, nz, sx, sy, sz);
+ return bits;
+}
diff --git a/src/zfp/zfp-0.5.0/src/template/decompress.c b/src/zfp/zfp-0.5.0/src/template/decompress.c
new file mode 100644
index 0000000..b3702d3
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/template/decompress.c
@@ -0,0 +1,104 @@
+/* decompress 1d contiguous array */
+static void
+_t2(decompress, Scalar, 1)(zfp_stream* stream, zfp_field* field)
+{
+ Scalar* data = field->data;
+ uint nx = field->nx;
+ uint mx = nx & ~3u;
+ uint x;
+
+ for (x = 0; x < mx; x += 4, data += 4)
+ _t2(zfp_decode_block, Scalar, 1)(stream, data);
+ if (x < nx)
+ _t2(zfp_decode_partial_block_strided, Scalar, 1)(stream, data, nx - x, 1);
+}
+
+/* decompress 1d strided array */
+static void
+_t2(decompress_strided, Scalar, 1)(zfp_stream* stream, zfp_field* field)
+{
+ Scalar* data = field->data;
+ uint nx = field->nx;
+ uint mx = nx & ~3u;
+ int sx = field->sx;
+ uint x;
+
+ for (x = 0; x < mx; x += 4, data += 4 * sx)
+ _t2(zfp_decode_block_strided, Scalar, 1)(stream, data, sx);
+ if (x < nx)
+ _t2(zfp_decode_partial_block_strided, Scalar, 1)(stream, data, nx - x, sx);
+}
+
+/* decompress 2d strided array */
+static void
+_t2(decompress_strided, Scalar, 2)(zfp_stream* stream, zfp_field* field)
+{
+ Scalar* data = field->data;
+ uint nx = field->nx;
+ uint ny = field->ny;
+ uint mx = nx & ~3u;
+ uint my = ny & ~3u;
+ int sx = field->sx ? field->sx : 1;
+ int sy = field->sy ? field->sy : nx;
+ uint x, y;
+
+ for (y = 0; y < my; y += 4, data += 4 * sy - mx * sx) {
+ for (x = 0; x < mx; x += 4, data += 4 * sx)
+ _t2(zfp_decode_block_strided, Scalar, 2)(stream, data, sx, sy);
+ if (x < nx)
+ _t2(zfp_decode_partial_block_strided, Scalar, 2)(stream, data, nx - x, 4, sx, sy);
+ }
+ if (y < ny) {
+ for (x = 0; x < mx; x += 4, data += 4 * sx)
+ _t2(zfp_decode_partial_block_strided, Scalar, 2)(stream, data, 4, ny - y, sx, sy);
+ if (x < nx)
+ _t2(zfp_decode_partial_block_strided, Scalar, 2)(stream, data, nx - x, ny - y, sx, sy);
+ }
+}
+
+/* decompress 3d strided array */
+static void
+_t2(decompress_strided, Scalar, 3)(zfp_stream* stream, zfp_field* field)
+{
+ Scalar* data = field->data;
+ uint nx = field->nx;
+ uint ny = field->ny;
+ uint nz = field->nz;
+ uint mx = nx & ~3u;
+ uint my = ny & ~3u;
+ uint mz = nz & ~3u;
+ int sx = field->sx ? field->sx : 1;
+ int sy = field->sy ? field->sy : nx;
+ int sz = field->sz ? field->sz : nx * ny;
+ uint x, y, z;
+
+ for (z = 0; z < mz; z += 4, data += 4 * sz - my * sy) {
+ for (y = 0; y < my; y += 4, data += 4 * sy - mx * sx) {
+ for (x = 0; x < mx; x += 4, data += 4 * sx)
+ _t2(zfp_decode_block_strided, Scalar, 3)(stream, data, sx, sy, sz);
+ if (x < nx)
+ _t2(zfp_decode_partial_block_strided, Scalar, 3)(stream, data, nx - x, 4, 4, sx, sy, sz);
+ }
+ if (y < ny) {
+ for (x = 0; x < mx; x += 4, data += 4 * sx)
+ _t2(zfp_decode_partial_block_strided, Scalar, 3)(stream, data, 4, ny - y, 4, sx, sy, sz);
+ if (x < nx)
+ _t2(zfp_decode_partial_block_strided, Scalar, 3)(stream, data, nx - x, ny - y, 4, sx, sy, sz);
+ data -= mx * sx;
+ }
+ }
+ if (z < nz) {
+ for (y = 0; y < my; y += 4, data += 4 * sy - mx * sx) {
+ for (x = 0; x < mx; x += 4, data += 4 * sx)
+ _t2(zfp_decode_partial_block_strided, Scalar, 3)(stream, data, 4, 4, nz - z, sx, sy, sz);
+ if (x < nx)
+ _t2(zfp_decode_partial_block_strided, Scalar, 3)(stream, data, nx - x, 4, nz - z, sx, sy, sz);
+ }
+ if (y < ny) {
+ for (x = 0; x < mx; x += 4, data += 4 * sx)
+ _t2(zfp_decode_partial_block_strided, Scalar, 3)(stream, data, 4, ny - y, nz - z, sx, sy, sz);
+ if (x < nx)
+ _t2(zfp_decode_partial_block_strided, Scalar, 3)(stream, data, nx - x, ny - y, nz - z, sx, sy, sz);
+ }
+ }
+}
diff --git a/src/zfp/zfp-0.5.0/src/template/encode.c b/src/zfp/zfp-0.5.0/src/template/encode.c
new file mode 100644
index 0000000..0221254
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/template/encode.c
@@ -0,0 +1,216 @@
+#include <limits.h>
+#include <math.h>
+#include <stdio.h>
+#include "../inline/inline.h"
+#include "../inline/bitstream.c"
+
+/* private functions ------------------------------------------------------- */
+
+/* return normalized floating-point exponent for x >= 0 */
+static int
+_t1(exponent, Scalar)(Scalar x)
+{
+ if (x > 0) {
+ int e;
+ FREXP(x, &e);
+ /* clamp exponent in case x is denormal */
+ return MAX(e, 1 - EBIAS);
+ }
+ return -EBIAS;
+}
+
+/* compute maximum exponent in block of n values */
+static int
+_t1(exponent_block, Scalar)(const Scalar* p, uint n)
+{
+ Scalar max = 0;
+ do {
+ Scalar f = FABS(*p++);
+ if (max < f)
+ max = f;
+ } while (--n);
+ return _t1(exponent, Scalar)(max);
+}
+
+/* map floating-point number x to integer relative to exponent e */
+static Scalar
+_t1(quantize, Scalar)(Scalar x, int e)
+{
+ return LDEXP(x, (CHAR_BIT * (int)sizeof(Scalar) - 2) - e);
+}
+
+/* forward block-floating-point transform to signed integers */
+static void
+_t1(fwd_cast, Scalar)(Int* iblock, const Scalar* fblock, uint n, int emax)
+{
+ /* compute power-of-two scale factor s */
+ Scalar s = _t1(quantize, Scalar)(1, emax);
+ /* compute p-bit int y = s*x where x is floating and |y| <= 2^(p-2) - 1 */
+ do
+ *iblock++ = (Int)(s * *fblock++);
+ while (--n);
+}
+
+/* pad partial block of width n <= 4 and stride s */
+static void
+_t1(pad_block, Scalar)(Scalar* p, uint n, uint s)
+{
+ switch (n) {
+ case 0:
+ p[0 * s] = 0;
+ /* FALLTHROUGH */
+ case 1:
+ p[1 * s] = p[0 * s];
+ /* FALLTHROUGH */
+ case 2:
+ p[2 * s] = p[1 * s];
+ /* FALLTHROUGH */
+ case 3:
+ p[3 * s] = p[0 * s];
+ /* FALLTHROUGH */
+ default:
+ break;
+ }
+}
+
+/* forward lifting transform of 4-vector */
+static void
+_t1(fwd_lift, Int)(Int* p, uint s)
+{
+ Int x, y, z, w;
+ x = *p; p += s;
+ y = *p; p += s;
+ z = *p; p += s;
+ w = *p; p += s;
+
+ /*
+ ** non-orthogonal transform
+ ** ( 4 4 4 4) (x)
+ ** 1/16 * ( 5 1 -1 -5) (y)
+ ** (-4 4 4 -4) (z)
+ ** (-2 6 -6 2) (w)
+ */
+ x += w; x >>= 1; w -= x;
+ z += y; z >>= 1; y -= z;
+ x += z; x >>= 1; z -= x;
+ w += y; w >>= 1; y -= w;
+ w += y >> 1; y -= w >> 1;
+
+ p -= s; *p = w;
+ p -= s; *p = z;
+ p -= s; *p = y;
+ p -= s; *p = x;
+}
+
+/* map two's complement signed integer to negabinary unsigned integer */
+static UInt
+_t1(int2uint, Int)(Int x)
+{
+ return ((UInt)x + NBMASK) ^ NBMASK;
+}
+
+/* reorder signed coefficients and convert to unsigned integer */
+static void
+_t1(fwd_order, Int)(UInt* ublock, const Int* iblock, const uchar* perm, uint n)
+{
+ do
+ *ublock++ = _t1(int2uint, Int)(iblock[*perm++]);
+ while (--n);
+}
+
+/* compress sequence of size unsigned integers */
+static uint
+_t1(encode_ints, UInt)(bitstream* _restrict stream, uint maxbits, uint maxprec, const UInt* _restrict data, uint size)
+{
+ /* make a copy of bit stream to avoid aliasing */
+ bitstream s = *stream;
+ uint intprec = CHAR_BIT * (uint)sizeof(UInt);
+ uint kmin = intprec > maxprec ? intprec - maxprec : 0;
+ uint bits = maxbits;
+ uint i, k, m, n;
+ uint64 x;
+
+ /* encode one bit plane at a time from MSB to LSB */
+ for (k = intprec, n = 0; bits && k-- > kmin;) {
+ /* step 1: extract bit plane #k to x */
+ x = 0;
+ for (i = 0; i < size; i++)
+ x += (uint64)((data[i] >> k) & 1u) << i;
+ /* step 2: encode first n bits of bit plane */
+ m = MIN(n, bits);
+ bits -= m;
+ x = stream_write_bits(&s, x, m);
+ /* step 3: unary run-length encode remainder of bit plane */
+ for (; n < size && bits && (bits--, stream_write_bit(&s, !!x)); x >>= 1, n++)
+ for (; n < size - 1 && bits && (bits--, !stream_write_bit(&s, x & 1u)); x >>= 1, n++)
+ ;
+ }
+
+ *stream = s;
+ return maxbits - bits;
+}
+
+/* encode block of integers */
+static uint
+_t2(encode_block, Int, DIMS)(bitstream* stream, int minbits, int maxbits, int maxprec, Int* iblock)
+{
+ int bits;
+ _cache_align(UInt ublock[BLOCK_SIZE]);
+ /* perform decorrelating transform */
+ _t2(fwd_xform, Int, DIMS)(iblock);
+ /* reorder signed coefficients and convert to unsigned integer */
+ _t1(fwd_order, Int)(ublock, iblock, PERM, BLOCK_SIZE);
+ /* encode integer coefficients */
+ bits = _t1(encode_ints, UInt)(stream, maxbits, maxprec, ublock, BLOCK_SIZE);
+ /* write at least minbits bits by padding with zeros */
+ if (bits < minbits) {
+ stream_pad(stream, minbits - bits);
+ bits = minbits;
+ }
+ return bits;
+}
+
+/* public functions -------------------------------------------------------- */
+
+/* encode contiguous integer block */
+uint
+_t2(zfp_encode_block, Int, DIMS)(zfp_stream* zfp, const Int* iblock)
+{
+ _cache_align(Int block[BLOCK_SIZE]);
+ uint i;
+ /* copy block */
+ for (i = 0; i < BLOCK_SIZE; i++)
+ block[i] = iblock[i];
+ return _t2(encode_block, Int, DIMS)(zfp->stream, zfp->minbits, zfp->maxbits, zfp->maxprec, block);
+}
+
+/* encode contiguous floating-point block */
+uint
+_t2(zfp_encode_block, Scalar, DIMS)(zfp_stream* zfp, const Scalar* fblock)
+{
+ /* compute maximum exponent */
+ int emax = _t1(exponent_block, Scalar)(fblock, BLOCK_SIZE);
+ int maxprec = _t2(precision, Scalar, DIMS)(emax, zfp->maxprec, zfp->minexp);
+ uint e = maxprec ? emax + EBIAS : 0;
+ /* encode block only if biased exponent is nonzero */
+ if (e) {
+ _cache_align(Int iblock[BLOCK_SIZE]);
+ /* encode common exponent; LSB indicates that exponent is nonzero */
+ int ebits = EBITS + 1;
+ stream_write_bits(zfp->stream, 2 * e + 1, ebits);
+ /* perform forward block-floating-point transform */
+ _t1(fwd_cast, Scalar)(iblock, fblock, BLOCK_SIZE, emax);
+ /* encode integer block */
+ return ebits + _t2(encode_block, Int, DIMS)(zfp->stream, zfp->minbits - ebits, zfp->maxbits - ebits, maxprec, iblock);
+ }
+ else {
+ /* write single zero-bit to indicate that all values are zero */
+ stream_write_bit(zfp->stream, 0);
+ if (zfp->minbits > 1) {
+ stream_pad(zfp->stream, zfp->minbits - 1);
+ return zfp->minbits;
+ }
+ else
+ return 1;
+ }
+}
diff --git a/src/zfp/zfp-0.5.0/src/template/encode1.c b/src/zfp/zfp-0.5.0/src/template/encode1.c
new file mode 100644
index 0000000..0d5d979
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/template/encode1.c
@@ -0,0 +1,55 @@
+static void _t1(pad_block, Scalar)(Scalar* p, uint n, uint s);
+static void _t1(fwd_lift, Int)(Int* p, uint s);
+
+/* private functions ------------------------------------------------------- */
+
+/* gather 4-value block from strided array */
+static void
+_t2(gather, Scalar, 1)(Scalar* q, const Scalar* p, int sx)
+{
+ uint x;
+ for (x = 0; x < 4; x++, p += sx)
+ *q++ = *p;
+}
+
+/* gather nx-value block from strided array */
+static void
+_t2(gather_partial, Scalar, 1)(Scalar* q, const Scalar* p, uint nx, int sx)
+{
+ uint x;
+ for (x = 0; x < nx; x++, p += sx)
+ q[x] = *p;
+ _t1(pad_block, Scalar)(q, nx, 1);
+}
+
+/* forward decorrelating 1D transform */
+static void
+_t2(fwd_xform, Int, 1)(Int* p)
+{
+ /* transform along x */
+ _t1(fwd_lift, Int)(p, 1);
+}
+
+/* public functions -------------------------------------------------------- */
+
+/* encode 4-value floating-point block stored at p using stride sx */
+uint
+_t2(zfp_encode_block_strided, Scalar, 1)(zfp_stream* stream, const Scalar* p, int sx)
+{
+ /* gather block from strided array */
+ _cache_align(Scalar fblock[4]);
+ _t2(gather, Scalar, 1)(fblock, p, sx);
+ /* encode floating-point block */
+ return _t2(zfp_encode_block, Scalar, 1)(stream, fblock);
+}
+
+/* encode nx-value floating-point block stored at p using stride sx */
+uint
+_t2(zfp_encode_partial_block_strided, Scalar, 1)(zfp_stream* stream, const Scalar* p, uint nx, int sx)
+{
+ /* gather block from strided array */
+ _cache_align(Scalar fblock[4]);
+ _t2(gather_partial, Scalar, 1)(fblock, p, nx, sx);
+ /* encode floating-point block */
+ return _t2(zfp_encode_block, Scalar, 1)(stream, fblock);
+}
diff --git a/src/zfp/zfp-0.5.0/src/template/encode2.c b/src/zfp/zfp-0.5.0/src/template/encode2.c
new file mode 100644
index 0000000..36661e3
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/template/encode2.c
@@ -0,0 +1,65 @@
+static void _t1(pad_block, Scalar)(Scalar* p, uint n, uint s);
+static void _t1(fwd_lift, Int)(Int* p, uint s);
+
+/* private functions ------------------------------------------------------- */
+
+/* gather 4*4 block from strided array */
+static void
+_t2(gather, Scalar, 2)(Scalar* q, const Scalar* p, int sx, int sy)
+{
+ uint x, y;
+ for (y = 0; y < 4; y++, p += sy - 4 * sx)
+ for (x = 0; x < 4; x++, p += sx)
+ *q++ = *p;
+}
+
+/* gather nx*ny block from strided array */
+static void
+_t2(gather_partial, Scalar, 2)(Scalar* q, const Scalar* p, uint nx, uint ny, int sx, int sy)
+{
+ uint x, y;
+ for (y = 0; y < ny; y++, p += sy - nx * sx) {
+ for (x = 0; x < nx; x++, p += sx)
+ q[4 * y + x] = *p;
+ _t1(pad_block, Scalar)(q + 4 * y, nx, 1);
+ }
+ for (x = 0; x < 4; x++)
+ _t1(pad_block, Scalar)(q + x, ny, 4);
+}
+
+/* forward decorrelating 2D transform */
+static void
+_t2(fwd_xform, Int, 2)(Int* p)
+{
+ uint x, y;
+ /* transform along x */
+ for (y = 0; y < 4; y++)
+ _t1(fwd_lift, Int)(p + 4 * y, 1);
+ /* transform along y */
+ for (x = 0; x < 4; x++)
+ _t1(fwd_lift, Int)(p + 1 * x, 4);
+}
+
+/* public functions -------------------------------------------------------- */
+
+/* encode 4*4 floating-point block stored at p using strides (sx, sy) */
+uint
+_t2(zfp_encode_block_strided, Scalar, 2)(zfp_stream* stream, const Scalar* p, int sx, int sy)
+{
+ /* gather block from strided array */
+ _cache_align(Scalar fblock[16]);
+ _t2(gather, Scalar, 2)(fblock, p, sx, sy);
+ /* encode floating-point block */
+ return _t2(zfp_encode_block, Scalar, 2)(stream, fblock);
+}
+
+/* encode nx*ny floating-point block stored at p using strides (sx, sy) */
+uint
+_t2(zfp_encode_partial_block_strided, Scalar, 2)(zfp_stream* stream, const Scalar* p, uint nx, uint ny, int sx, int sy)
+{
+ /* gather block from strided array */
+ _cache_align(Scalar fblock[16]);
+ _t2(gather_partial, Scalar, 2)(fblock, p, nx, ny, sx, sy);
+ /* encode floating-point block */
+ return _t2(zfp_encode_block, Scalar, 2)(stream, fblock);
+}
diff --git a/src/zfp/zfp-0.5.0/src/template/encode3.c b/src/zfp/zfp-0.5.0/src/template/encode3.c
new file mode 100644
index 0000000..25f0d7f
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/template/encode3.c
@@ -0,0 +1,77 @@
+static void _t1(pad_block, Scalar)(Scalar* p, uint n, uint s);
+static void _t1(fwd_lift, Int)(Int* p, uint s);
+
+/* private functions ------------------------------------------------------- */
+
+/* gather 4*4*4 block from strided array */
+static void
+_t2(gather, Scalar, 3)(Scalar* q, const Scalar* p, int sx, int sy, int sz)
+{
+ uint x, y, z;
+ for (z = 0; z < 4; z++, p += sz - 4 * sy)
+ for (y = 0; y < 4; y++, p += sy - 4 * sx)
+ for (x = 0; x < 4; x++, p += sx)
+ *q++ = *p;
+}
+
+/* gather nx*ny*nz block from strided array */
+static void
+_t2(gather_partial, Scalar, 3)(Scalar* q, const Scalar* p, uint nx, uint ny, uint nz, int sx, int sy, int sz)
+{
+ uint x, y, z;
+ for (z = 0; z < nz; z++, p += sz - ny * sy) {
+ for (y = 0; y < ny; y++, p += sy - nx * sx) {
+ for (x = 0; x < nx; x++, p += sx)
+ q[16 * z + 4 * y + x] = *p;
+ _t1(pad_block, Scalar)(q + 16 * z + 4 * y, nx, 1);
+ }
+ for (x = 0; x < 4; x++)
+ _t1(pad_block, Scalar)(q + 16 * z + x, ny, 4);
+ }
+ for (y = 0; y < 4; y++)
+ for (x = 0; x < 4; x++)
+ _t1(pad_block, Scalar)(q + 4 * y + x, nz, 16);
+}
+
+/* forward decorrelating 3D transform */
+static void
+_t2(fwd_xform, Int, 3)(Int* p)
+{
+ uint x, y, z;
+ /* transform along x */
+ for (z = 0; z < 4; z++)
+ for (y = 0; y < 4; y++)
+ _t1(fwd_lift, Int)(p + 4 * y + 16 * z, 1);
+ /* transform along y */
+ for (x = 0; x < 4; x++)
+ for (z = 0; z < 4; z++)
+ _t1(fwd_lift, Int)(p + 16 * z + 1 * x, 4);
+ /* transform along z */
+ for (y = 0; y < 4; y++)
+ for (x = 0; x < 4; x++)
+ _t1(fwd_lift, Int)(p + 1 * x + 4 * y, 16);
+}
+
+/* public functions -------------------------------------------------------- */
+
+/* encode 4*4*4 floating-point block stored at p using strides (sx, sy, sz) */
+uint
+_t2(zfp_encode_block_strided, Scalar, 3)(zfp_stream* stream, const Scalar* p, int sx, int sy, int sz)
+{
+ /* gather block from strided array */
+ _cache_align(Scalar fblock[64]);
+ _t2(gather, Scalar, 3)(fblock, p, sx, sy, sz);
+ /* encode floating-point block */
+ return _t2(zfp_encode_block, Scalar, 3)(stream, fblock);
+}
+
+/* encode nx*ny*nz floating-point block stored at p using strides (sx, sy, sz) */
+uint
+_t2(zfp_encode_partial_block_strided, Scalar, 3)(zfp_stream* stream, const Scalar* p, uint nx, uint ny, uint nz, int sx, int sy, int sz)
+{
+ /* gather block from strided array */
+ _cache_align(Scalar fblock[64]);
+ _t2(gather_partial, Scalar, 3)(fblock, p, nx, ny, nz, sx, sy, sz);
+ /* encode floating-point block */
+ return _t2(zfp_encode_block, Scalar, 3)(stream, fblock);
+}
diff --git a/src/zfp/zfp-0.5.0/src/template/template.h b/src/zfp/zfp-0.5.0/src/template/template.h
new file mode 100644
index 0000000..fd5becf
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/template/template.h
@@ -0,0 +1,12 @@
+#ifndef TEMPLATE_H
+#define TEMPLATE_H
+
+/* concatenation */
+#define _cat2(x, y) x ## _ ## y
+#define _cat3(x, y, z) x ## _ ## y ## _ ## z
+
+/* 1- and 2-argument function templates */
+#define _t1(function, arg) _cat2(function, arg)
+#define _t2(function, type, dims) _cat3(function, type, dims)
+
+#endif
diff --git a/src/zfp/zfp-0.5.0/src/traitsd.h b/src/zfp/zfp-0.5.0/src/traitsd.h
new file mode 100644
index 0000000..a9767ef
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/traitsd.h
@@ -0,0 +1,11 @@
+/* double-precision floating-point traits */
+
+#define Scalar double /* floating-point type */
+#define Int int64 /* corresponding signed integer type */
+#define UInt uint64 /* corresponding unsigned integer type */
+#define EBITS 11 /* number of exponent bits */
+#define NBMASK 0xaaaaaaaaaaaaaaaaull /* negabinary mask */
+
+#define FABS(x) fabs(x)
+#define FREXP(x, e) frexp(x, e)
+#define LDEXP(x, e) ldexp(x, e)
diff --git a/src/zfp/zfp-0.5.0/src/traitsf.h b/src/zfp/zfp-0.5.0/src/traitsf.h
new file mode 100644
index 0000000..ba262ac
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/traitsf.h
@@ -0,0 +1,17 @@
+/* single-precision floating-point traits */
+
+#define Scalar float /* floating-point type */
+#define Int int32 /* corresponding signed integer type */
+#define UInt uint32 /* corresponding unsigned integer type */
+#define EBITS 8 /* number of exponent bits */
+#define NBMASK 0xaaaaaaaau /* negabinary mask */
+
+#if __STDC_VERSION__ >= 199901L
+ #define FABS(x) fabsf(x)
+ #define FREXP(x, e) frexpf(x, e)
+ #define LDEXP(x, e) ldexpf(x, e)
+#else
+ #define FABS(x) (float)fabs(x)
+ #define FREXP(x, e) (void)frexp(x, e)
+ #define LDEXP(x, e) (float)ldexp(x, e)
+#endif
diff --git a/src/zfp/zfp-0.5.0/src/zfp.c b/src/zfp/zfp-0.5.0/src/zfp.c
new file mode 100644
index 0000000..79fc9e8
--- /dev/null
+++ b/src/zfp/zfp-0.5.0/src/zfp.c
@@ -0,0 +1,719 @@
+#include <limits.h>
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include "zfp.h"
+#include "macros.h"
+#include "template/template.h"
+
+#define Scalar float
+#include "template/compress.c"
+#include "template/decompress.c"
+#undef Scalar
+
+#define Scalar double
+#include "template/compress.c"
+#include "template/decompress.c"
+#undef Scalar
+
+/* private functions ------------------------------------------------------- */
+
+static uint
+type_precision(zfp_type type)
+{
+ switch (type) {
+ case zfp_type_int32:
+ return CHAR_BIT * (uint)sizeof(int32);
+ case zfp_type_int64:
+ return CHAR_BIT * (uint)sizeof(int64);
+ case zfp_type_float:
+ return CHAR_BIT * (uint)sizeof(float);
+ case zfp_type_double:
+ return CHAR_BIT * (uint)sizeof(double);
+ default:
+ return 0;
+ }
+}
+
+/* public functions: fields ------------------------------------------------ */
+
+zfp_field*
+zfp_field_alloc()
+{
+ zfp_field* field = malloc(sizeof(zfp_field));
+ if (field) {
+ field->type = zfp_type_none;
+ field->nx = field->ny = field->nz = 0;
+ field->sx = field->sy = field->sz = 0;
+ field->data = 0;
+ }
+ return field;
+}
+
+zfp_field*
+zfp_field_1d(void* data, zfp_type type, uint nx)
+{
+ zfp_field* field = zfp_field_alloc();
+ if (field) {
+ field->type = type;
+ field->nx = nx;
+ field->data = data;
+ }
+ return field;
+}
+
+zfp_field*
+zfp_field_2d(void* data, zfp_type type, uint nx, uint ny)
+{
+ zfp_field* field = zfp_field_alloc();
+ if (field) {
+ field->type = type;
+ field->nx = nx;
+ field->ny = ny;
+ field->data = data;
+ }
+ return field;
+}
+
+zfp_field*
+zfp_field_3d(void* data, zfp_type type, uint nx, uint ny, uint nz)
+{
+ zfp_field* field = zfp_field_alloc();
+ if (field) {
+ field->type = type;
+ field->nx = nx;
+ field->ny = ny;
+ field->nz = nz;
+ field->data = data;
+ }
+ return field;
+}
+
+void
+zfp_field_free(zfp_field* field)
+{
+ free(field);
+}
+
+void*
+zfp_field_pointer(const zfp_field* field)
+{
+ return field->data;
+}
+
+zfp_type
+zfp_field_type(const zfp_field* field)
+{
+ return field->type;
+}
+
+uint
+zfp_field_precision(const zfp_field* field)
+{
+ return type_precision(field->type);
+}
+
+uint
+zfp_field_dimensionality(const zfp_field* field)
+{
+ return field->nx ? field->ny ? field->nz ? 3 : 2 : 1 : 0;
+}
+
+size_t
+zfp_field_size(const zfp_field* field, uint* size)
+{
+ if (size)
+ switch (zfp_field_dimensionality(field)) {
+ case 3:
+ size[2] = field->sz;
+ /* FALLTHROUGH */
+ case 2:
+ size[1] = field->sy;
+ /* FALLTHROUGH */
+ case 1:
+ size[0] = field->sx;
+ break;
+ }
+ return (size_t)MAX(field->nx, 1u) * (size_t)MAX(field->ny, 1u) * (size_t)MAX(field->nz, 1u);
+}
+
+int
+zfp_field_stride(const zfp_field* field, int* stride)
+{
+ if (stride)
+ switch (zfp_field_dimensionality(field)) {
+ case 3:
+ stride[2] = field->sz ? field->sz : field->nx * field->ny;
+ /* FALLTHROUGH */
+ case 2:
+ stride[1] = field->sy ? field->sy : field->nx;
+ /* FALLTHROUGH */
+ case 1:
+ stride[0] = field->sx ? field->sx : 1;
+ break;
+ }
+ return field->sx || field->sy || field->sz;
+}
+
+uint64
+zfp_field_metadata(const zfp_field* field)
+{
+ uint64 meta = 0;
+ /* 48 bits for dimensions */
+ switch (zfp_field_dimensionality(field)) {
+ case 1:
+ meta <<= 48; meta += field->nx - 1;
+ break;
+ case 2:
+ meta <<= 24; meta += field->ny - 1;
+ meta <<= 24; meta += field->nx - 1;
+ break;
+ case 3:
+ meta <<= 16; meta += field->nz - 1;
+ meta <<= 16; meta += field->ny - 1;
+ meta <<= 16; meta += field->nx - 1;
+ break;
+ }
+ /* 2 bits for dimensionality (1D, 2D, 3D, 4D) */
+ meta <<= 2; meta += zfp_field_dimensionality(field) - 1;
+ /* 2 bits for scalar type */
+ meta <<= 2; meta += field->type - 1;
+ return meta;
+}
+
+void
+zfp_field_set_pointer(zfp_field* field, void* data)
+{
+ field->data = data;
+}
+
+zfp_type
+zfp_field_set_type(zfp_field* field, zfp_type type)
+{
+ switch (type) {
+ case zfp_type_int32:
+ case zfp_type_int64:
+ case zfp_type_float:
+ case zfp_type_double:
+ field->type = type;
+ return type;
+ default:
+ return zfp_type_none;
+ }
+}
+
+void
+zfp_field_set_size_1d(zfp_field* field, uint n)
+{
+ field->nx = n;
+ field->ny = 0;
+ field->nz = 0;
+}
+
+void
+zfp_field_set_size_2d(zfp_field* field, uint nx, uint ny)
+{
+ field->nx = nx;
+ field->ny = ny;
+ field->nz = 0;
+}
+
+void
+zfp_field_set_size_3d(zfp_field* field, uint nx, uint ny, uint nz)
+{
+ field->nx = nx;
+ field->ny = ny;
+ field->nz = nz;
+}
+
+void
+zfp_field_set_stride_1d(zfp_field* field, int sx)
+{
+ field->sx = sx;
+ field->sy = 0;
+ field->sz = 0;
+}
+
+void
+zfp_field_set_stride_2d(zfp_field* field, int sx, int sy)
+{
+ field->sx = sx;
+ field->sy = sy;
+ field->sz = 0;
+}
+
+void
+zfp_field_set_stride_3d(zfp_field* field, int sx, int sy, int sz)
+{
+ field->sx = sx;
+ field->sy = sy;
+ field->sz = sz;
+}
+
+int
+zfp_field_set_metadata(zfp_field* field, uint64 meta)
+{
+ uint dims;
+ field->type = (zfp_type)((meta & 0x3u) + 1); meta >>= 2;
+ dims = (meta & 0x3u) + 1; meta >>= 2;
+ switch (dims) {
+ case 1:
+ field->nx = (meta & 0xffffffffffffull) + 1; meta >>= 48;
+ break;
+ case 2:
+ field->nx = (meta & 0xffffffull) + 1; meta >>= 24;
+ field->ny = (meta & 0xffffffull) + 1; meta >>= 24;
+ break;
+ case 3:
+ field->nx = (meta & 0xffffull) + 1; meta >>= 16;
+ field->ny = (meta & 0xffffull) + 1; meta >>= 16;
+ field->nz = (meta & 0xffffull) + 1; meta >>= 16;
+ break;
+ }
+ field->sx = field->sy = field->sz = 0;
+ return 1;
+}
+
+/* public functions: zfp compressed stream --------------------------------- */
+
+zfp_stream*
+zfp_stream_open(bitstream* stream)
+{
+ zfp_stream* zfp = malloc(sizeof(zfp_stream));
+ if (zfp) {
+ zfp->stream = stream;
+ zfp->minbits = ZFP_MIN_BITS;
+ zfp->maxbits = ZFP_MAX_BITS;
+ zfp->maxprec = ZFP_MAX_PREC;
+ zfp->minexp = ZFP_MIN_EXP;
+ }
+ return zfp;
+}
+
+void
+zfp_stream_close(zfp_stream* zfp)
+{
+ free(zfp);
+}
+
+bitstream*
+zfp_stream_bit_stream(const zfp_stream* zfp)
+{
+ return zfp->stream;
+}
+
+uint64
+zfp_stream_mode(const zfp_stream* zfp)
+{
+ uint64 mode = 0;
+ uint minbits;
+ uint maxbits;
+ uint maxprec;
+ uint minexp;
+
+ /* fixed rate? */
+ if (zfp->minbits == zfp->maxbits &&
+ 1 <= zfp->maxbits && zfp->maxbits <= 2048 &&
+ zfp->maxprec >= ZFP_MAX_PREC &&
+ zfp->minexp <= ZFP_MIN_EXP)
+ return zfp->maxbits - 1;
+
+ /* fixed precision? */
+ if (zfp->minbits <= ZFP_MIN_BITS &&
+ zfp->maxbits >= ZFP_MAX_BITS &&
+ 1 <= zfp->maxprec && zfp->maxprec <= 128 &&
+ zfp->minexp <= ZFP_MIN_EXP)
+ return zfp->maxprec + 2047;
+
+ /* fixed accuracy? */
+ if (zfp->minbits <= ZFP_MIN_BITS &&
+ zfp->maxbits >= ZFP_MAX_BITS &&
+ zfp->maxprec >= ZFP_MAX_PREC &&
+ -1074 <= zfp->minexp && zfp->minexp <= 843)
+ return zfp->minexp + 3251;
+
+ /* encode each parameter separately */
+ minbits = MAX(1, MIN(zfp->minbits, 0x8000u)) - 1;
+ maxbits = MAX(1, MIN(zfp->maxbits, 0x8000u)) - 1;
+ maxprec = MAX(1, MIN(zfp->maxprec, 0x0080u)) - 1;
+ minexp = MAX(0, MIN(zfp->minexp + 16495, 0x7fff));
+ mode <<= 15; mode += minexp;
+ mode <<= 7; mode += maxprec;
+ mode <<= 15; mode += maxbits;
+ mode <<= 15; mode += minbits;
+ mode <<= 12; mode += 0xfffu;
+
+ return mode;
+}
+
+void
+zfp_stream_params(const zfp_stream* zfp, uint* minbits, uint* maxbits, uint* maxprec, int* minexp)
+{
+ if (minbits)
+ *minbits = zfp->minbits;
+ if (maxbits)
+ *maxbits = zfp->maxbits;
+ if (maxprec)
+ *maxprec = zfp->maxprec;
+ if (minexp)
+ *minexp = zfp->minexp;
+}
+
+size_t
+zfp_stream_compressed_size(const zfp_stream* zfp)
+{
+ return stream_size(zfp->stream);
+}
+
+size_t
+zfp_stream_maximum_size(const zfp_stream* zfp, const zfp_field* field)
+{
+ uint dims = zfp_field_dimensionality(field);
+ uint mx = (MAX(field->nx, 1u) + 3) / 4;
+ uint my = (MAX(field->ny, 1u) + 3) / 4;
+ uint mz = (MAX(field->nz, 1u) + 3) / 4;
+ size_t blocks = (size_t)mx * (size_t)my * (size_t)mz;
+ uint values = 1u << (2 * dims);
+ uint maxbits = 1;
+
+ if (!dims)
+ return 0;
+ switch (field->type) {
+ case zfp_type_none:
+ return 0;
+ case zfp_type_float:
+ maxbits += 8;
+ break;
+ case zfp_type_double:
+ maxbits += 11;
+ break;
+ default:
+ break;
+ }
+ maxbits += values - 1 + values * MIN(zfp->maxprec, type_precision(field->type));
+ maxbits = MIN(maxbits, zfp->maxbits);
+ maxbits = MAX(maxbits, zfp->minbits);
+ return ((ZFP_HEADER_BITS + blocks * maxbits + stream_word_bits - 1) & ~(stream_word_bits - 1)) / CHAR_BIT;
+}
+
+void
+zfp_stream_set_bit_stream(zfp_stream* zfp, bitstream* stream)
+{
+ zfp->stream = stream;
+}
+
+double
+zfp_stream_set_rate(zfp_stream* zfp, double rate, zfp_type type, uint dims, int wra)
+{
+ uint n = 1u << (2 * dims);
+ uint bits = (uint)floor(n * rate + 0.5);
+ switch (type) {
+ case zfp_type_float:
+ bits = MAX(bits, 1 + 8u);
+ break;
+ case zfp_type_double:
+ bits = MAX(bits, 1 + 11u);
+ break;
+ default:
+ break;
+ }
+ if (wra) {
+ /* for write random access, round up to next multiple of stream word size */
+ bits += stream_word_bits - 1;
+ bits &= ~(stream_word_bits - 1);
+ }
+ zfp->minbits = bits;
+ zfp->maxbits = bits;
+ zfp->maxprec = type_precision(type);
+ zfp->minexp = ZFP_MIN_EXP;
+ return (double)bits / n;
+}
+
+uint
+zfp_stream_set_precision(zfp_stream* zfp, uint precision, zfp_type type)
+{
+ uint maxprec = type_precision(type);
+ zfp->minbits = ZFP_MIN_BITS;
+ zfp->maxbits = ZFP_MAX_BITS;
+ zfp->maxprec = precision ? MIN(maxprec, precision) : maxprec;
+ zfp->minexp = ZFP_MIN_EXP;
+ return zfp->maxprec;
+}
+
+double
+zfp_stream_set_accuracy(zfp_stream* zfp, double tolerance, zfp_type type)
+{
+ int emin = ZFP_MIN_EXP;
+ if (tolerance > 0) {
+ /* tolerance = x * 2^emin, with 0.5 <= x < 1 */
+ frexp(tolerance, &emin);
+ emin--;
+ /* assert: 2^emin <= tolerance < 2^(emin+1) */
+ }
+ zfp->minbits = ZFP_MIN_BITS;
+ zfp->maxbits = ZFP_MAX_BITS;
+ zfp->maxprec = type_precision(type);
+ zfp->minexp = emin;
+ return tolerance > 0 ? ldexp(1.0, emin) : 0;
+}
+
+int
+zfp_stream_set_mode(zfp_stream* zfp, uint64 mode)
+{
+ if (mode <= ZFP_MODE_SHORT_MAX) {
+ /* 12-bit encoding of one of three modes */
+ if (mode < 2048) {
+ /* fixed rate */
+ zfp->minbits = zfp->maxbits = (uint)mode + 1;
+ zfp->maxprec = ZFP_MAX_PREC;
+ zfp->minexp = ZFP_MIN_EXP;
+ }
+ else if (mode < 2176) {
+ /* fixed precision */
+ zfp->minbits = ZFP_MIN_BITS;
+ zfp->maxbits = ZFP_MAX_BITS;
+ zfp->maxprec = (uint)mode - 2047;
+ zfp->minexp = ZFP_MIN_EXP;
+ }
+ else {
+ /* fixed accuracy */
+ zfp->minbits = ZFP_MIN_BITS;
+ zfp->maxbits = ZFP_MAX_BITS;
+ zfp->maxprec = ZFP_MAX_PREC;
+ zfp->minexp = (uint)mode - 3251;
+ }
+ }
+ else {
+ /* 64-bit encoding */
+ mode >>= 12; zfp->minbits = ((uint)mode & 0x7fffu) + 1;
+ mode >>= 15; zfp->maxbits = ((uint)mode & 0x7fffu) + 1;
+ mode >>= 15; zfp->maxprec = ((uint)mode & 0x007fu) + 1;
+ mode >>= 7; zfp->minexp = ((uint)mode & 0x7fffu) - 16495;
+ }
+
+ return 1;
+}
+
+int
+zfp_stream_set_params(zfp_stream* zfp, uint minbits, uint maxbits, uint maxprec, int minexp)
+{
+ if (minbits > maxbits || !(0 < maxprec && maxprec <= 64))
+ return 0;
+ zfp->minbits = minbits;
+ zfp->maxbits = maxbits;
+ zfp->maxprec = maxprec;
+ zfp->minexp = minexp;
+ return 1;
+}
+
+void
+zfp_stream_flush(zfp_stream* zfp)
+{
+ stream_flush(zfp->stream);
+}
+
+void
+zfp_stream_align(zfp_stream* zfp)
+{
+ stream_align(zfp->stream);
+}
+
+void
+zfp_stream_rewind(zfp_stream* zfp)
+{
+ stream_rewind(zfp->stream);
+}
+
+/* public functions: utility functions --------------------------------------*/
+
+void
+zfp_promote_int8_to_int32(int32* oblock, const int8* iblock, uint dims)
+{
+ uint count = 1u << (2 * dims);
+ while (count--)
+ *oblock++ = (int32)*iblock++ << 23;
+}
+
+void
+zfp_promote_uint8_to_int32(int32* oblock, const uint8* iblock, uint dims)
+{
+ uint count = 1u << (2 * dims);
+ while (count--)
+ *oblock++ = ((int32)*iblock++ - 0x80) << 23;
+}
+
+void
+zfp_promote_int16_to_int32(int32* oblock, const int16* iblock, uint dims)
+{
+ uint count = 1u << (2 * dims);
+ while (count--)
+ *oblock++ = (int32)*iblock++ << 15;
+}
+
+void
+zfp_promote_uint16_to_int32(int32* oblock, const uint16* iblock, uint dims)
+{
+ uint count = 1u << (2 * dims);
+ while (count--)
+ *oblock++ = ((int32)*iblock++ - 0x8000) << 15;
+}
+
+void
+zfp_demote_int32_to_int8(int8* oblock, const int32* iblock, uint dims)
+{
+ uint count = 1u << (2 * dims);
+ while (count--) {
+ int32 i = *iblock++ >> 23;
+ *oblock++ = MAX(-0x80, MIN(i, 0x7f));
+ }
+}
+
+void
+zfp_demote_int32_to_uint8(uint8* oblock, const int32* iblock, uint dims)
+{
+ uint count = 1u << (2 * dims);
+ while (count--) {
+ int32 i = (*iblock++ >> 23) + 0x80;
+ *oblock++ = MAX(0x00, MIN(i, 0xff));
+ }
+}
+
+void
+zfp_demote_int32_to_int16(int16* oblock, const int32* iblock, uint dims)
+{
+ uint count = 1u << (2 * dims);
+ while (count--) {
+ int32 i = *iblock++ >> 15;
+ *oblock++ = MAX(-0x8000, MIN(i, 0x7fff));
+ }
+}
+
+void
+zfp_demote_int32_to_uint16(uint16* oblock, const int32* iblock, uint dims)
+{
+ uint count = 1u << (2 * dims);
+ while (count--) {
+ int32 i = (*iblock++ >> 15) + 0x8000;
+ *oblock++ = MAX(0x0000, MIN(i, 0xffff));
+ }
+}
+
+/* public functions: compression and decompression --------------------------*/
+
+size_t
+zfp_compress(zfp_stream* zfp, const zfp_field* field)
+{
+ void (*compress[2][3][2])(zfp_stream*, const zfp_field*) = {
+ {{ compress_float_1, compress_double_1 },
+ { compress_strided_float_2, compress_strided_double_2 },
+ { compress_strided_float_3, compress_strided_double_3 }},
+ {{ compress_strided_float_1, compress_strided_double_1 },
+ { compress_strided_float_2, compress_strided_double_2 },
+ { compress_strided_float_3, compress_strided_double_3 }},
+ };
+ uint dims = zfp_field_dimensionality(field);
+ uint type = field->type;
+ uint strided = zfp_field_stride(field, NULL);
+
+ switch (type) {
+ case zfp_type_float:
+ case zfp_type_double:
+ break;
+ default:
+ return 0;
+ }
+
+ compress[strided][dims - 1][type - zfp_type_float](zfp, field);
+ stream_flush(zfp->stream);
+
+ return stream_size(zfp->stream);
+}
+
+int
+zfp_decompress(zfp_stream* zfp, zfp_field* field)
+{
+ void (*decompress[2][3][2])(zfp_stream*, zfp_field*) = {
+ {{ decompress_float_1, decompress_double_1 },
+ { decompress_strided_float_2, decompress_strided_double_2 },
+ { decompress_strided_float_3, decompress_strided_double_3 }},
+ {{ decompress_strided_float_1, decompress_strided_double_1 },
+ { decompress_strided_float_2, decompress_strided_double_2 },
+ { decompress_strided_float_3, decompress_strided_double_3 }},
+ };
+ uint dims = zfp_field_dimensionality(field);
+ uint type = field->type;
+ uint strided = zfp_field_stride(field, NULL);
+
+ switch (type) {
+ case zfp_type_float:
+ case zfp_type_double:
+ break;
+ default:
+ return 0;
+ }
+
+ decompress[strided][dims - 1][type - zfp_type_float](zfp, field);
+ stream_align(zfp->stream);
+
+ return 1;
+}
+
+size_t
+zfp_write_header(zfp_stream* zfp, const zfp_field* field, uint mask)
+{
+ size_t bits = 0;
+ /* 32-bit magic */
+ if (mask & ZFP_HEADER_MAGIC) {
+ stream_write_bits(zfp->stream, 'z', 8);
+ stream_write_bits(zfp->stream, 'f', 8);
+ stream_write_bits(zfp->stream, 'p', 8);
+ stream_write_bits(zfp->stream, ZFP_VERSION >> 4, 8);
+ bits += ZFP_MAGIC_BITS;
+ }
+ /* 52-bit field metadata */
+ if (mask & ZFP_HEADER_FIELD) {
+ uint64 meta = zfp_field_metadata(field);
+ stream_write_bits(zfp->stream, meta, ZFP_META_BITS);
+ bits += ZFP_META_BITS;
+ }
+ /* 12- or 64-bit compression parameters */
+ if (mask & ZFP_HEADER_PARAMS) {
+ uint64 mode = zfp_stream_mode(zfp);
+ uint size = mode > ZFP_MODE_SHORT_MAX ? ZFP_MODE_LONG_BITS : ZFP_MODE_SHORT_BITS;
+ stream_write_bits(zfp->stream, mode, size);
+ bits += size;
+ }
+ return bits;
+}
+
+size_t
+zfp_read_header(zfp_stream* zfp, zfp_field* field, uint mask)
+{
+ size_t bits = 0;
+ if (mask & ZFP_HEADER_MAGIC) {
+ if (stream_read_bits(zfp->stream, 8) != 'z' ||
+ stream_read_bits(zfp->stream, 8) != 'f' ||
+ stream_read_bits(zfp->stream, 8) != 'p' ||
+ stream_read_bits(zfp->stream, 8) != (ZFP_VERSION >> 4))
+ return 0;
+ bits += ZFP_MAGIC_BITS;
+ }
+ if (mask & ZFP_HEADER_FIELD) {
+ uint64 meta = stream_read_bits(zfp->stream, ZFP_META_BITS);
+ if (!zfp_field_set_metadata(field, meta))
+ return 0;
+ bits += ZFP_META_BITS;
+ }
+ if (mask & ZFP_HEADER_PARAMS) {
+ uint64 mode = stream_read_bits(zfp->stream, ZFP_MODE_SHORT_BITS);
+ bits += ZFP_MODE_SHORT_BITS;
+ if (mode > ZFP_MODE_SHORT_MAX) {
+ uint size = ZFP_MODE_LONG_BITS - ZFP_MODE_SHORT_BITS;
+ mode += stream_read_bits(zfp->stream, size) << ZFP_MODE_SHORT_BITS;
+ bits += size;
+ }
+ if (!zfp_stream_set_mode(zfp, mode))
+ return 0;
+ }
+ return bits;
+}
diff --git a/tests/C/Makefile.in b/tests/C/Makefile.in
index 8a580e6..6eaa73f 100644
--- a/tests/C/Makefile.in
+++ b/tests/C/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -449,6 +449,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/C/fgr_tests/Makefile.in b/tests/C/fgr_tests/Makefile.in
index e8d7f49..8795cf4 100644
--- a/tests/C/fgr_tests/Makefile.in
+++ b/tests/C/fgr_tests/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -407,6 +407,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/C/flexpath_tests/1D_arr_global/Makefile.in b/tests/C/flexpath_tests/1D_arr_global/Makefile.in
index f4cac27..2a55814 100644
--- a/tests/C/flexpath_tests/1D_arr_global/Makefile.in
+++ b/tests/C/flexpath_tests/1D_arr_global/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -415,6 +415,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/C/flexpath_tests/1D_arr_global/reader.c b/tests/C/flexpath_tests/1D_arr_global/reader.c
index 0dcfe25..e67cb0a 100644
--- a/tests/C/flexpath_tests/1D_arr_global/reader.c
+++ b/tests/C/flexpath_tests/1D_arr_global/reader.c
@@ -152,17 +152,15 @@ int main (int argc, char **argv){
p_test_failed("%s: rank %d\n", test_result.name, rank);
-#ifdef FLEXPATH_METHOD
- adios_release_step(adios_handler);
+ adios_release_step(adios_handle);
// 0 - next available step, block for max 30 seconds until the next step
// is available
- adios_advance_step(adios_handler, 0, 30);
+ 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());
}
-#endif
just_clean:
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 f1fba39..8f11e6a 100644
--- a/tests/C/flexpath_tests/1D_arr_global_noxml/Makefile.in
+++ b/tests/C/flexpath_tests/1D_arr_global_noxml/Makefile.in
@@ -110,7 +110,7 @@ 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_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 \
@@ -422,6 +422,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
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 e87224b..fab08c6 100644
--- a/tests/C/flexpath_tests/1D_arr_global_noxml/writer.c
+++ b/tests/C/flexpath_tests/1D_arr_global_noxml/writer.c
@@ -66,9 +66,9 @@ int main(int argc, char ** argv){
int64_t adios_grp;
// now declare a group
- adios_declare_group(&adios_grp, "temperature", "iter", adios_flag_yes);
+ adios_declare_group(&adios_grp, "temperature", "iter", adios_stat_default);
- 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);
diff --git a/tests/C/flexpath_tests/Makefile.in b/tests/C/flexpath_tests/Makefile.in
index af7cf17..dddcd69 100644
--- a/tests/C/flexpath_tests/Makefile.in
+++ b/tests/C/flexpath_tests/Makefile.in
@@ -107,7 +107,7 @@ 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_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 \
@@ -413,6 +413,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/C/flexpath_tests/global_range_select/Makefile.in b/tests/C/flexpath_tests/global_range_select/Makefile.in
index c05d198..bcde1a9 100644
--- a/tests/C/flexpath_tests/global_range_select/Makefile.in
+++ b/tests/C/flexpath_tests/global_range_select/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -414,6 +414,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/C/flexpath_tests/maya_append/Makefile.in b/tests/C/flexpath_tests/maya_append/Makefile.in
index e0b5051..12544b8 100644
--- a/tests/C/flexpath_tests/maya_append/Makefile.in
+++ b/tests/C/flexpath_tests/maya_append/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -415,6 +415,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/C/flexpath_tests/maya_append/writer.c b/tests/C/flexpath_tests/maya_append/writer.c
index a5aaa2d..f562c33 100644
--- a/tests/C/flexpath_tests/maya_append/writer.c
+++ b/tests/C/flexpath_tests/maya_append/writer.c
@@ -66,7 +66,7 @@ int main(int argc, char ** argv){
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_flag_no);
+ adios_declare_group(&adios_grp, GRP_NAME, "", adios_stat_default);
uint64_t adios_groupsize = 0;
diff --git a/tests/C/flexpath_tests/maya_noxml/Makefile.in b/tests/C/flexpath_tests/maya_noxml/Makefile.in
index e07a53d..3ae1812 100644
--- a/tests/C/flexpath_tests/maya_noxml/Makefile.in
+++ b/tests/C/flexpath_tests/maya_noxml/Makefile.in
@@ -110,7 +110,7 @@ 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_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 \
@@ -421,6 +421,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/C/flexpath_tests/maya_noxml/writer.c b/tests/C/flexpath_tests/maya_noxml/writer.c
index d2c07b4..8e1b990 100644
--- a/tests/C/flexpath_tests/maya_noxml/writer.c
+++ b/tests/C/flexpath_tests/maya_noxml/writer.c
@@ -67,7 +67,7 @@ int main(int argc, char ** argv){
int64_t adios_grp = 0;
// now declare a group
- adios_declare_group(&adios_grp, "carpet_checkpoint", "", adios_flag_no);
+ adios_declare_group(&adios_grp, "carpet_checkpoint", "", adios_stat_default);
uint64_t adios_groupsize = 0;
diff --git a/tests/C/flexpath_tests/scalar/Makefile.in b/tests/C/flexpath_tests/scalar/Makefile.in
index 6675732..fe81a63 100644
--- a/tests/C/flexpath_tests/scalar/Makefile.in
+++ b/tests/C/flexpath_tests/scalar/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -415,6 +415,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/C/flexpath_tests/scalar/writer.c b/tests/C/flexpath_tests/scalar/writer.c
index 9c29390..17d2e61 100644
--- a/tests/C/flexpath_tests/scalar/writer.c
+++ b/tests/C/flexpath_tests/scalar/writer.c
@@ -44,7 +44,7 @@ int main(int argc, char ** argv){
MPI_Comm_rank (comm, &rank);
MPI_Comm_size (comm, &size);
- SET_ERROR_IF_ZERO(adios_init(adios_opts.xml_adios_init_filename, comm), err_count);
+ SET_ERROR_IF_NOT_ZERO(adios_init(adios_opts.xml_adios_init_filename, comm), err_count);
RET_IF_ERROR(err_count, rank);
uint64_t adios_groupsize, adios_totalsize;
diff --git a/tests/C/query/Makefile.in b/tests/C/query/Makefile.in
index a5d1d2a..feef088 100644
--- a/tests/C/query/Makefile.in
+++ b/tests/C/query/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -415,6 +415,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/C/query/alacrity/Makefile.in b/tests/C/query/alacrity/Makefile.in
index f95074f..f099486 100644
--- a/tests/C/query/alacrity/Makefile.in
+++ b/tests/C/query/alacrity/Makefile.in
@@ -113,7 +113,7 @@ 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_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 \
@@ -459,6 +459,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/C/query/common/Makefile.in b/tests/C/query/common/Makefile.in
index 15c8e2c..8dcd42a 100644
--- a/tests/C/query/common/Makefile.in
+++ b/tests/C/query/common/Makefile.in
@@ -111,7 +111,7 @@ 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_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 \
@@ -439,6 +439,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/C/query/fastbit/Makefile.in b/tests/C/query/fastbit/Makefile.in
index 6c29c80..ac21b1e 100644
--- a/tests/C/query/fastbit/Makefile.in
+++ b/tests/C/query/fastbit/Makefile.in
@@ -112,7 +112,7 @@ 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_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 \
@@ -414,6 +414,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/Fortran/Makefile.in b/tests/Fortran/Makefile.in
index 94e243f..e4d50c8 100644
--- a/tests/Fortran/Makefile.in
+++ b/tests/Fortran/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -404,6 +404,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/Makefile.in b/tests/Makefile.in
index 0fbd754..4fcdd2d 100644
--- a/tests/Makefile.in
+++ b/tests/Makefile.in
@@ -110,7 +110,7 @@ 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_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 \
@@ -416,6 +416,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/bp_read/Makefile.in b/tests/bp_read/Makefile.in
index 7dcf363..7b4cfef 100644
--- a/tests/bp_read/Makefile.in
+++ b/tests/bp_read/Makefile.in
@@ -113,7 +113,7 @@ 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_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 \
@@ -455,6 +455,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/genarray/Makefile.in b/tests/genarray/Makefile.in
index 90902cd..5a37f21 100644
--- a/tests/genarray/Makefile.in
+++ b/tests/genarray/Makefile.in
@@ -110,7 +110,7 @@ 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_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 \
@@ -428,6 +428,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/suite/Makefile.in b/tests/suite/Makefile.in
index 3d55113..241a952 100644
--- a/tests/suite/Makefile.in
+++ b/tests/suite/Makefile.in
@@ -107,7 +107,7 @@ 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_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 \
@@ -413,6 +413,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/suite/programs/Makefile.in b/tests/suite/programs/Makefile.in
index db0518d..4297e96 100644
--- a/tests/suite/programs/Makefile.in
+++ b/tests/suite/programs/Makefile.in
@@ -111,7 +111,7 @@ 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_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 \
@@ -903,6 +903,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/suite/programs/big_file.c b/tests/suite/programs/big_file.c
index 874347b..88cde53 100644
--- a/tests/suite/programs/big_file.c
+++ b/tests/suite/programs/big_file.c
@@ -125,7 +125,7 @@ int main (int argc, char ** argv)
printE ("%s\n", adios_errmsg());
}
- adios_declare_group (&m_adios_group, "bigdata", "iter", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "bigdata", "iter", adios_stat_default);
adios_select_method (m_adios_group, "MPI", "", "");
diff --git a/tests/suite/programs/blocks.c b/tests/suite/programs/blocks.c
index 0920033..5000130 100644
--- a/tests/suite/programs/blocks.c
+++ b/tests/suite/programs/blocks.c
@@ -95,7 +95,7 @@ int write_blocks ()
int64_t m_adios_group;
int64_t m_adios_file;
- adios_declare_group (&m_adios_group, "restart", "", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "restart", "", adios_stat_default);
adios_select_method (m_adios_group, "MPI", "", "");
adios_define_var (m_adios_group, "NX"
diff --git a/tests/suite/programs/connect_to_space_subset.c b/tests/suite/programs/connect_to_space_subset.c
index 85699d8..36a2205 100644
--- a/tests/suite/programs/connect_to_space_subset.c
+++ b/tests/suite/programs/connect_to_space_subset.c
@@ -121,7 +121,7 @@ int main (int argc, char ** argv)
if (iconnect)
{
- adios_declare_group (&m_adios_group, "connect", "iter", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "connect", "iter", adios_stat_default);
adios_select_method (m_adios_group, "DATASPACES", "verbose=4", "");
adios_define_var (m_adios_group, "ldim1", "", adios_integer, 0, 0, 0);
adios_define_var (m_adios_group, "gdim1", "", adios_integer, 0, 0, 0);
diff --git a/tests/suite/programs/examples/Makefile.in b/tests/suite/programs/examples/Makefile.in
index 6741230..7d9f693 100644
--- a/tests/suite/programs/examples/Makefile.in
+++ b/tests/suite/programs/examples/Makefile.in
@@ -107,7 +107,7 @@ 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_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 \
@@ -413,6 +413,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/suite/programs/examples/attributes/Makefile.in b/tests/suite/programs/examples/attributes/Makefile.in
index 436c430..b775687 100644
--- a/tests/suite/programs/examples/attributes/Makefile.in
+++ b/tests/suite/programs/examples/attributes/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -416,6 +416,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/suite/programs/examples/global_array/Makefile.in b/tests/suite/programs/examples/global_array/Makefile.in
index bf6b386..72729db 100644
--- a/tests/suite/programs/examples/global_array/Makefile.in
+++ b/tests/suite/programs/examples/global_array/Makefile.in
@@ -115,7 +115,7 @@ 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_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 \
@@ -544,6 +544,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/suite/programs/examples/global_array/global_array_F.xml b/tests/suite/programs/examples/global_array/global_array_F.xml
index cb368c6..9922d88 100644
--- a/tests/suite/programs/examples/global_array/global_array_F.xml
+++ b/tests/suite/programs/examples/global_array/global_array_F.xml
@@ -1,6 +1,6 @@
<?xml version="1.0"?>
<adios-config host-language="Fortran">
- <adios-group name="temperature">
+ <adios-group name="temperature" stats="On">
<var name="NX" type="integer"/>
<var name="size" type="integer"/>
<var name="rank" type="integer"/>
diff --git a/tests/suite/programs/examples/global_array/global_array_aggregate_by_color_C.c b/tests/suite/programs/examples/global_array/global_array_aggregate_by_color_C.c
index 29f504e..1d9ce01 100644
--- a/tests/suite/programs/examples/global_array/global_array_aggregate_by_color_C.c
+++ b/tests/suite/programs/examples/global_array/global_array_aggregate_by_color_C.c
@@ -55,7 +55,7 @@ int main (int argc, char ** argv)
int64_t m_adios_group;
int64_t m_adios_file;
- adios_declare_group (&m_adios_group, "restart", "iter", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "restart", "iter", adios_stat_default);
// split into 2 groups
color = (rank % 2 == 0 ? 0 : 1);
diff --git a/tests/suite/programs/examples/global_array/global_array_write_byid_noxml_C.c b/tests/suite/programs/examples/global_array/global_array_write_byid_noxml_C.c
index 5c17e29..044829b 100644
--- a/tests/suite/programs/examples/global_array/global_array_write_byid_noxml_C.c
+++ b/tests/suite/programs/examples/global_array/global_array_write_byid_noxml_C.c
@@ -62,7 +62,7 @@ int main (int argc, char ** argv)
int64_t m_adios_file;
int64_t var_ids[nblocks];
- adios_declare_group (&m_adios_group, "restart", "iter", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "restart", "iter", adios_stat_default);
adios_select_method (m_adios_group, "MPI", "", "");
for (i = 0; i < nblocks; i++)
diff --git a/tests/suite/programs/examples/global_array/global_array_write_byid_noxml_F.F90 b/tests/suite/programs/examples/global_array/global_array_write_byid_noxml_F.F90
index 9e51cf4..5f57248 100644
--- a/tests/suite/programs/examples/global_array/global_array_write_byid_noxml_F.F90
+++ b/tests/suite/programs/examples/global_array/global_array_write_byid_noxml_F.F90
@@ -43,7 +43,7 @@ program no_xml_write_byid
call adios_init_noxml (comm, adios_err)
call adios_set_max_buffer_size (10)
- call adios_declare_group (m_adios_group, "restart", "iter", 1, adios_err)
+ call adios_declare_group (m_adios_group, "restart", "iter", ADIOS_STAT_DEFAULT, adios_err)
call adios_select_method (m_adios_group, "MPI", "", "", adios_err)
G = 2 * NX * size
diff --git a/tests/suite/programs/examples/global_array/global_array_write_noxml_C.c b/tests/suite/programs/examples/global_array/global_array_write_noxml_C.c
index 88c86f4..a7bafe2 100644
--- a/tests/suite/programs/examples/global_array/global_array_write_noxml_C.c
+++ b/tests/suite/programs/examples/global_array/global_array_write_noxml_C.c
@@ -55,7 +55,7 @@ int main (int argc, char ** argv)
int64_t m_adios_group;
int64_t m_adios_file;
- adios_declare_group (&m_adios_group, "restart", "iter", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "restart", "iter", adios_stat_default);
adios_select_method (m_adios_group, "MPI", "", "");
diff --git a/tests/suite/programs/examples/global_array/global_array_write_noxml_F.F90 b/tests/suite/programs/examples/global_array/global_array_write_noxml_F.F90
index 8ec3c01..74d65f2 100644
--- a/tests/suite/programs/examples/global_array/global_array_write_noxml_F.F90
+++ b/tests/suite/programs/examples/global_array/global_array_write_noxml_F.F90
@@ -37,7 +37,7 @@ program adios_global
call adios_init_noxml (comm, adios_err)
call adios_set_max_buffer_size (10)
- call adios_declare_group (m_adios_group, "restart", "iter", 1, adios_err)
+ call adios_declare_group (m_adios_group, "restart", "iter", ADIOS_STAT_DEFAULT, adios_err)
call adios_select_method (m_adios_group, "MPI", "", "", adios_err)
! This example doesn't use varid during writing.
diff --git a/tests/suite/programs/examples/global_array_time/Makefile.am b/tests/suite/programs/examples/global_array_time/Makefile.am
index 73b0fde..cafa035 100644
--- a/tests/suite/programs/examples/global_array_time/Makefile.am
+++ b/tests/suite/programs/examples/global_array_time/Makefile.am
@@ -28,7 +28,7 @@ global_array_time_read_as_stream_C_LDADD += $(ADIOSREADLIB_LDADD)
CLEANFILES = *.bp *.ch *.fh
CC=$(MPICC)
-EXTRA_DIST = global_array_time_C.xml global_array_time_F.xml
+EXTRA_DIST = global_array_time_C.xml global_array_time_F.xml global_array_time_aggr_C.xml
if BUILD_FORTRAN
check_PROGRAMS += global_array_time_write_F
diff --git a/tests/suite/programs/examples/global_array_time/Makefile.in b/tests/suite/programs/examples/global_array_time/Makefile.in
index ec95d33..eeec105 100644
--- a/tests/suite/programs/examples/global_array_time/Makefile.in
+++ b/tests/suite/programs/examples/global_array_time/Makefile.in
@@ -111,7 +111,7 @@ 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_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 \
@@ -466,6 +466,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
@@ -544,7 +547,7 @@ global_array_time_read_as_stream_C_LDADD = \
$(top_builddir)/src/libadiosread.a $(ADIOSREADLIB_LDADD)
global_array_time_read_as_stream_C_LDFLAGS = $(ADIOSREADLIB_LDFLAGS)
CLEANFILES = *.bp *.ch *.fh
-EXTRA_DIST = global_array_time_C.xml global_array_time_F.xml
+EXTRA_DIST = global_array_time_C.xml global_array_time_F.xml global_array_time_aggr_C.xml
@BUILD_FORTRAN_TRUE at global_array_time_write_F_SOURCES = global_array_time_write_F.F90
@BUILD_FORTRAN_TRUE at global_array_time_write_F_LDADD = \
@BUILD_FORTRAN_TRUE@ $(top_builddir)/src/libadiosf.a \
diff --git a/examples/C/global-array-time/adios_globaltime.xml b/tests/suite/programs/examples/global_array_time/global_array_time_aggr_C.xml
similarity index 90%
copy from examples/C/global-array-time/adios_globaltime.xml
copy to tests/suite/programs/examples/global_array_time/global_array_time_aggr_C.xml
index a0d308d..ff4e6a8 100644
--- a/examples/C/global-array-time/adios_globaltime.xml
+++ b/tests/suite/programs/examples/global_array_time/global_array_time_aggr_C.xml
@@ -20,8 +20,9 @@
</adios-group>
<method group="restart" method="MPI"/>
+ <time-aggregation group="restart" buffer-size=3000/>
- <buffer max-size-MB="1"/>
+ <buffer max-size-MB="5"/>
</adios-config>
diff --git a/tests/suite/programs/examples/global_array_time/global_array_time_write_C.c b/tests/suite/programs/examples/global_array_time/global_array_time_write_C.c
index 4485352..fb4e037 100644
--- a/tests/suite/programs/examples/global_array_time/global_array_time_write_C.c
+++ b/tests/suite/programs/examples/global_array_time/global_array_time_write_C.c
@@ -11,48 +11,48 @@
#include "adios.h"
int main (int argc, char ** argv)
{
- char filename [256];
- int rank, size, i, it;
- int NX = 10;
+ char filename [256];
+ int rank, size, i, it;
+ int NX = 10;
// NY = 1 for testing purpose
- int NY = 1;
- double t[NX];
- double p[NY];
-
- /* ADIOS variables declarations for matching gwrite_temperature.ch */
- uint64_t adios_groupsize, adios_totalsize;
- int64_t adios_handle;
- MPI_Comm comm=MPI_COMM_WORLD;
+ int NY = 1;
+ double t[NX];
+ double p[NY];
+
+ /* 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_C.xml", comm);
- strcpy (filename, "global_array_time_C.bp");
- for (it =1; it <= 13; it++) {
-
- for (i = 0; i < NX; i++)
- t[i] = it*100.0 + rank*NX + i;
-
- for (i = 0; i < NY; i++)
- p[i] = it*1000.0 + rank*NY + i;
-
- if (it==1)
- adios_open (&adios_handle, "restart", filename, "w", comm);
- else
- adios_open (&adios_handle, "restart", filename, "a", 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;
+ MPI_Init (&argc, &argv);
+ MPI_Comm_rank (MPI_COMM_WORLD, &rank);
+ MPI_Comm_size (comm, &size);
+
+ adios_init ("global_array_time_C.xml", comm);
+ strcpy (filename, "global_array_time_C.bp");
+ for (it =1; it <= 13; it++) {
+
+ for (i = 0; i < NX; i++)
+ t[i] = it*100.0 + rank*NX + i;
+
+ for (i = 0; i < NY; i++)
+ p[i] = it*1000.0 + rank*NY + i;
+
+ if (it==1)
+ adios_open (&adios_handle, "restart", filename, "w", comm);
+ else
+ adios_open (&adios_handle, "restart", filename, "a", 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/Makefile.in b/tests/suite/programs/examples/local_array/Makefile.in
index 3b734b3..71a4362 100644
--- a/tests/suite/programs/examples/local_array/Makefile.in
+++ b/tests/suite/programs/examples/local_array/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -416,6 +416,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/suite/programs/examples/scalars/Makefile.in b/tests/suite/programs/examples/scalars/Makefile.in
index f52834f..d11ba96 100644
--- a/tests/suite/programs/examples/scalars/Makefile.in
+++ b/tests/suite/programs/examples/scalars/Makefile.in
@@ -110,7 +110,7 @@ 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_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 \
@@ -458,6 +458,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/suite/programs/examples/scalars/scalars_read_C.c b/tests/suite/programs/examples/scalars/scalars_read_C.c
index dca789d..3ae4764 100644
--- a/tests/suite/programs/examples/scalars/scalars_read_C.c
+++ b/tests/suite/programs/examples/scalars/scalars_read_C.c
@@ -60,6 +60,7 @@ int main (int argc, char ** argv)
MPI_Init (&argc, &argv);
MPI_Comm_rank (comm, &rank);
+ FILE* outf = fopen ("c_read.txt", "w");
strcpy (filename, "scalars_C.bp");
adios_read_init_method (method, comm, "verbose=3");
@@ -83,28 +84,29 @@ int main (int argc, char ** argv)
adios_perform_reads (f,1);
if (rank == 0) {
- printf("byte v1 = %d\n", v1);
- printf("short v2 = %d\n", v2);
- printf("integer v3 = %d\n", v3);
- printf("long v4 = %lld\n", v4);
+ 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);
- printf("uns.byte v5 = %u\n", v5);
- printf("uns.short v6 = %u\n", v6);
- printf("uns.int v7 = %u\n", v7);
- printf("uns.long v8 = %llu\n", v8);
+ 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);
- printf("float v9 = %g\n", v9);
- printf("double v10 = %g\n", v10);
+ fprintf (outf, "float v9 = %g\n", v9);
+ fprintf (outf, "double v10 = %g\n", v10);
- printf("string v11 = %s\n", v11);
+ fprintf (outf, "string v11 = %s\n", v11);
- printf("complex v12 = (%g, i%g)\n", v12.r, v12.i);
- printf("dbl-complex v13 = (%g, i%g)\n", v13.r, v13.i);
+ fprintf (outf, "complex v12 = (%g, i%g)\n", v12.r, v12.i);
+ fprintf (outf, "dbl-complex v13 = (%g, i%g)\n", v13.r, v13.i);
}
adios_read_close (f);
MPI_Barrier (comm);
adios_read_finalize_method (ADIOS_READ_METHOD_BP);
+ fclose (outf);
MPI_Finalize ();
return 0;
diff --git a/tests/suite/programs/examples/scalars/scalars_read_F.F90 b/tests/suite/programs/examples/scalars/scalars_read_F.F90
index 3c4bb83..46e094e 100644
--- a/tests/suite/programs/examples/scalars/scalars_read_F.F90
+++ b/tests/suite/programs/examples/scalars/scalars_read_F.F90
@@ -46,6 +46,8 @@ program scalars_read
call MPI_Comm_rank (comm, rank, ierr)
call MPI_Comm_size (comm, size, ierr);
+ OPEN(1,FILE="f_read.txt",FORM="FORMATTED",STATUS="REPLACE",ACTION="WRITE")
+
call adios_read_init_method (method, comm, "verbose=3", ierr);
call adios_read_open (f, filename, method, comm, ADIOS_LOCKMODE_NONE, 1.0, ierr);
@@ -74,23 +76,23 @@ program scalars_read
! the above variables contain the value only at this point
if (rank == 0) then
- write (*, '("int*1 v1 = ",i3)') v1
- write (*, '("int*2 v2 = ",i3)') v2
- write (*, '("int*4 v3 = ",i3)') v3
- write (*, '("int*8 v4 = ",i3)') v4
+ write (1, '("int*1 v1 = ",i3)') v1
+ write (1, '("int*2 v2 = ",i3)') v2
+ write (1, '("int*4 v3 = ",i3)') v3
+ write (1, '("int*8 v4 = ",i3)') v4
- write (*, '("int*1 v5 = ",i3)') v5
- write (*, '("int*2 v6 = ",i3)') v6
- write (*, '("int*4 v7 = ",i3)') v7
- write (*, '("int*8 v8 = ",i3)') v8
+ write (1, '("int*1 v5 = ",i3)') v5
+ write (1, '("int*2 v6 = ",i3)') v6
+ write (1, '("int*4 v7 = ",i3)') v7
+ write (1, '("int*8 v8 = ",i3)') v8
- write (*, '("real*4 v9 = ",f6.2)') v9
- write (*, '("real*8 v10 = ",f6.2)') v10
+ write (1, '("real*4 v9 = ",f6.2)') v9
+ write (1, '("real*8 v10 = ",f6.2)') v10
- write (*, '("string v11 = ",a)') trim(v11)
+ write (1, '("string v11 = ",a)') trim(v11)
- write (*, '("complex*8 v12 = (",f6.2,", ", f6.2,")")') v12
- write (*, '("complex*16 v13 = (",f6.2,", ", f6.2,")")') v13
+ write (1, '("complex*8 v12 = (",f6.2,", ", f6.2,")")') v12
+ write (1, '("complex*16 v13 = (",f6.2,", ", f6.2,")")') v13
endif
call adios_read_close (f, ierr)
@@ -98,5 +100,7 @@ program scalars_read
call adios_read_finalize_method (method, ierr);
call MPI_Finalize (ierr);
+ CLOSE(UNIT=1)
+
end program
diff --git a/tests/suite/programs/many_vars.c b/tests/suite/programs/many_vars.c
index 21eec35..f8b49c4 100644
--- a/tests/suite/programs/many_vars.c
+++ b/tests/suite/programs/many_vars.c
@@ -173,7 +173,7 @@ int main (int argc, char ** argv)
printE ("%s\n", adios_errmsg());
}
- adios_declare_group (&m_adios_group, "multiblock", "iter", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "multiblock", "iter", adios_stat_default);
adios_select_method (m_adios_group, "MPI", "", "");
diff --git a/tests/suite/programs/reuse_dim.c b/tests/suite/programs/reuse_dim.c
index 05ff720..f3b2648 100755
--- a/tests/suite/programs/reuse_dim.c
+++ b/tests/suite/programs/reuse_dim.c
@@ -101,7 +101,7 @@ int declare_group ()
adios_set_max_buffer_size (10);
- adios_declare_group (&m_adios_group, "restart", "iter", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "restart", "iter", adios_stat_default);
adios_select_method (m_adios_group, "MPI", "verbose=2", "");
adios_define_var (m_adios_group, "NX"
diff --git a/tests/suite/programs/selections.c b/tests/suite/programs/selections.c
index 9f3adda..db8ec35 100644
--- a/tests/suite/programs/selections.c
+++ b/tests/suite/programs/selections.c
@@ -182,7 +182,7 @@ int main (int argc, char ** argv)
if (do_write) {
- adios_declare_group (&m_adios_group, "selections", "iter", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "selections", "iter", adios_stat_default);
adios_select_method (m_adios_group, write_method, "verbose=2", "");
define_vars();
diff --git a/tests/suite/programs/steps_write.c b/tests/suite/programs/steps_write.c
index 938e5aa..2077561 100644
--- a/tests/suite/programs/steps_write.c
+++ b/tests/suite/programs/steps_write.c
@@ -44,7 +44,7 @@ int main (int argc, char ** argv)
int64_t m_adios_group;
int64_t m_adios_file;
- adios_declare_group (&m_adios_group, "steps", "", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "steps", "", adios_stat_default);
adios_select_method (m_adios_group, "MPI", "", "");
diff --git a/tests/suite/reference/attributes_bpls.txt b/tests/suite/reference/attributes_bpls.txt
index d35afc6..8e36b8d 100644
--- a/tests/suite/reference/attributes_bpls.txt
+++ b/tests/suite/reference/attributes_bpls.txt
@@ -12,7 +12,7 @@ File info:
integer rank scalar = 0
double mean scalar = 4.5
string date scalar = "Nov, 2009"
- double temperature {5, 10} = 0 / 49 / 24.5 / 14.4309
+ double temperature {5, 10} = 0 / 49 / null / null
integer temperature/number of levels attr = 1
string temperature/description attr = "Global array written from 'size' processes"
double temperature/mean value attr = 4.5
diff --git a/tests/suite/reference/global_array_no_xml_bpls.txt b/tests/suite/reference/global_array_no_xml_bpls.txt
index 688c7c4..6229a0f 100644
--- a/tests/suite/reference/global_array_no_xml_bpls.txt
+++ b/tests/suite/reference/global_array_no_xml_bpls.txt
@@ -10,7 +10,7 @@ File info:
integer NX scalar = 100
integer Global_bounds scalar = 2100
integer Offsets scalar = 0
- double temperature {2100} = 0 / 2099 / 1049.5 / 606.218
+ double temperature {2100} = 0 / 2099 / null / null
( 0) 0 1 2 3 4 5 6 7 8 9
( 10) 10 11 12 13 14 15 16 17 18 19
( 20) 20 21 22 23 24 25 26 27 28 29
diff --git a/tests/suite/reference/global_array_no_xml_f_bpls.txt b/tests/suite/reference/global_array_no_xml_f_bpls.txt
index 28e14cb..fd84ffa 100644
--- a/tests/suite/reference/global_array_no_xml_f_bpls.txt
+++ b/tests/suite/reference/global_array_no_xml_f_bpls.txt
@@ -10,7 +10,7 @@ File info:
integer NX scalar = 10
integer G scalar = 140
integer O scalar = 0
- double temperature {140} = 0 / 139 / 69.5 / 40.4135
+ double temperature {140} = 0 / 139 / null / null
( 0) 0 1 2 3 4 5 6 7 8 9
( 10) 10 11 12 13 14 15 16 17 18 19
( 20) 20 21 22 23 24 25 26 27 28 29
diff --git a/tests/suite/reference/global_array_time_bpls.txt b/tests/suite/reference/global_array_time_bpls.txt
index 5409d2c..0274eb7 100644
--- a/tests/suite/reference/global_array_time_bpls.txt
+++ b/tests/suite/reference/global_array_time_bpls.txt
@@ -2,6 +2,6 @@
integer NY 13*scalar = 1 / 1 / 1 / 0
integer size 13*scalar = 9 / 9 / 9 / 0
integer rank 13*scalar = 0 / 8 / 4 / 2.58199
- double temperature 13*{9, 10} = 100 / 1389 / 744.5 / 375.067
- double pressure 13*{9, 1} = 1000 / 13008 / 7004 / 3741.66
+ double temperature 13*{9, 10} = 100 / 1389 / null / null
+ double pressure 13*{9, 1} = 1000 / 13008 / null / null
string temperature/description attr = "Global array written from 'size' processes over several timesteps"
diff --git a/tests/suite/reference/local_array_C_bpls.txt b/tests/suite/reference/local_array_C_bpls.txt
index 8057cf9..eb8ac1c 100644
--- a/tests/suite/reference/local_array_C_bpls.txt
+++ b/tests/suite/reference/local_array_C_bpls.txt
@@ -9,5 +9,5 @@ File info:
integer NX scalar = 10
integer NY scalar = 100
- double var_double_2Darray {10, 100} = 0 / 49.99 / 24.995 / 14.4338
- integer var_int_1Darray {10} = 0 / 49 / 24.5 / 14.4309
+ double var_double_2Darray {10, 100} = 0 / 49.99 / null / null
+ integer var_int_1Darray {10} = 0 / 49 / null / null
diff --git a/tests/suite/reference/no_xml_write_byid_bpls.txt b/tests/suite/reference/no_xml_write_byid_bpls.txt
index ebd3f35..b21d8dc 100644
--- a/tests/suite/reference/no_xml_write_byid_bpls.txt
+++ b/tests/suite/reference/no_xml_write_byid_bpls.txt
@@ -7,7 +7,7 @@ File info:
bp version: 3
statistics: Min / Max / Avg / Std_dev
- double temperature {2100} = 0 / 2099 / 1049.5 / 606.218
+ double temperature {2100} = 0 / 2099 / null / null
( 0) 0 1 2 3 4 5 6 7 8 9
( 10) 10 11 12 13 14 15 16 17 18 19
( 20) 20 21 22 23 24 25 26 27 28 29
diff --git a/tests/suite/reference/no_xml_write_byid_f_bpls.txt b/tests/suite/reference/no_xml_write_byid_f_bpls.txt
index 1185625..da7098a 100644
--- a/tests/suite/reference/no_xml_write_byid_f_bpls.txt
+++ b/tests/suite/reference/no_xml_write_byid_f_bpls.txt
@@ -7,7 +7,7 @@ File info:
bp version: 3
statistics: Min / Max / Avg / Std_dev
- double temperature {140} = 0 / 139 / 69.5 / 40.4135
+ double temperature {140} = 0 / 139 / null / null
( 0) 0 1 2 3 4 5 6 7 8 9
( 10) 10 11 12 13 14 15 16 17 18 19
( 20) 20 21 22 23 24 25 26 27 28 29
diff --git a/tests/suite/test.sh b/tests/suite/test.sh
index 95ff3fe..575d20a 100755
--- a/tests/suite/test.sh
+++ b/tests/suite/test.sh
@@ -75,9 +75,15 @@ do
done
shift $(($OPTIND - 1))
-# get source path
-SRCDIR=`dirname $0`
+# get source path
+pushd `dirname $0` >/dev/null
+#SRCDIR=`dirname $0`
+SRCDIR=$PWD
TRUNKDISTANCE=../..
+pushd $TRUNKDISTANCE >/dev/null
+BUILDTRUNKDIR=$PWD
+popd >/dev/null
+popd >/dev/null
if [ "${SRCDIR:0:1}" != "/" ]; then
echo "WARNING: Jobs on some systems do not have access to any directory but to "
@@ -88,7 +94,7 @@ if [ "${SRCDIR:0:1}" != "/" ]; then
fi
# check if Fortran codes were built
-if [ -f $SRCDIR/$TRUNKDISTANCE/src/libadiosf.a ]; then
+if [ -f $BUILDTRUNKDIR/src/libadiosf.a ]; then
HAVE_FORTRAN=yes
else
echo "WARNING: Fortran binaries are not built, so test will not use them"
@@ -97,7 +103,8 @@ fi
# Print info before running tests
echo "Settings:"
-echo " Test source directory: $SRCDIR"
+echo " Test script directory: $SRCDIR"
+echo " Test source trunk dir: $BUILDTRUNKDIR"
echo " Run command: $MPIRUN"
echo " Run command np option: $NP_MPIRUN"
echo " Max. processes to use: $MAXPROCS"
@@ -140,7 +147,7 @@ for TESTSCRIPT in $TESTS; do
pushd work.$TEST >/dev/null
if [ "${SRCDIR:0:1}" == "/" ]; then
TESTSRCDIR=$SRCDIR
- TRUNKDIR=$SRCDIR/$TRUNKDISTANCE
+ TRUNKDIR=$BUILDTRUNKDIR
else
# we are one level deeper now
TESTSRCDIR=../$SRCDIR
diff --git a/tests/suite/tests/01_scalars.sh b/tests/suite/tests/01_scalars.sh
index bd67b7c..044ba13 100755
--- a/tests/suite/tests/01_scalars.sh
+++ b/tests/suite/tests/01_scalars.sh
@@ -46,7 +46,7 @@ if [ $? != 0 ]; then
fi
echo "Run C scalars_read"
-$MPIRUN $NP_MPIRUN $PROCS $EXEOPT ./scalars_read_C > c_read.txt
+$MPIRUN $NP_MPIRUN $PROCS $EXEOPT ./scalars_read_C # produces c_read.txt
EX=$?
if [ $? != 0 ]; then
echo "ERROR: C version of scalars_read failed with exit code $EX"
@@ -90,7 +90,7 @@ if [ $? != 0 ]; then
fi
echo "Run Fortran scalars_read"
-$MPIRUN $NP_MPIRUN $PROCS $EXEOPT ./scalars_read_F > f_read.txt
+$MPIRUN $NP_MPIRUN $PROCS $EXEOPT ./scalars_read_F # produces f_read.txt
EX=$?
if [ $? != 0 ]; then
echo "ERROR: Fortran version of scalars_read failed with exit code $EX"
diff --git a/tests/suite/tests/05_global_array_time.sh b/tests/suite/tests/05_global_array_time.sh
index 0227c92..5f1b585 100755
--- a/tests/suite/tests/05_global_array_time.sh
+++ b/tests/suite/tests/05_global_array_time.sh
@@ -23,6 +23,7 @@ cp $SRCDIR/programs/examples/global_array_time/global_array_time_write_C .
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 .
# Insert transform=X if requested by user
add_transform_to_xmls
@@ -41,6 +42,7 @@ diff -q c_bpls.txt $SRCDIR/reference/global_array_time_bpls.txt
if [ $? != 0 ]; then
echo "ERROR: global_array_time_write_C produced a file different from the reference."
echo "Compare \"bpls -la $PWD/global_array_time_C.bp | grep -v -e endianness -e 'file size'\" to reference $SRCDIR/reference/global_array_time_bpls.txt"
+ exit 1
fi
###################################################
@@ -81,12 +83,59 @@ if [ $? != 0 ]; then
exit 1
fi
+###################################################
+# run the time-aggregation test
+
+echo "Run C global_array_time_write_C with time-aggregation turned on in subdir time_aggr/ with various buffer sizes:"
+mkdir -p time_aggr
+pushd time_aggr >/dev/null
+$TRUNKDIR/utils/bpls/bpls -la ../global_array_time_C.bp -D -d temperature -n 10 > c_bpls_non_aggr.txt
+
+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
+ $MPIRUN $NP_MPIRUN $PROCS $EXEOPT ../global_array_time_write_C
+ EX=$?
+ if [ ! -f global_array_time_C.bp ]; then
+ echo "ERROR: global_array_time_write_C failed. No BP file is created. Exit code=$EX"
+ exit 1
+ fi
+
+ mv global_array_time_C.xml global_array_time_C_$BUFSIZE.xml
+ mv global_array_time_C.bp global_array_time_C_$BUFSIZE.bp
+
+ echo " Check output with bpls"
+ $TRUNKDIR/utils/bpls/bpls -la global_array_time_C_$BUFSIZE.bp | grep -v -e endianness -e 'file size' > c_bpls_$BUFSIZE.txt
+ diff -q c_bpls_$BUFSIZE.txt $SRCDIR/reference/global_array_time_bpls.txt
+ if [ $? != 0 ]; then
+ echo "ERROR: global_array_time_write_C with time aggregation with buffer size $BUFSIZE produced a file different from the reference."
+ echo "Compare \"bpls -la $PWD/global_array_time_C_$BUFSIZE.bp | grep -v -e endianness -e 'file size'\" to reference $SRCDIR/reference/global_array_time_bpls.txt"
+ exit 1
+ fi
+
+ echo " Check output with bpls even more. Dump data and compare to non-time-aggregated version"
+ $TRUNKDIR/utils/bpls/bpls -la global_array_time_C_$BUFSIZE.bp -D -d temperature -n 10 > c_bpls_aggr_$BUFSIZE.txt
+ diff -q c_bpls_non_aggr.txt c_bpls_aggr_$BUFSIZE.txt
+ if [ $? != 0 ]; then
+ echo "ERROR: global_array_time_write_C with time aggregation with buffer size $BUFSIZE produced a file different from the file without time aggregation."
+ echo "Compare \"bpls -la $PWD/global_array_time_C.bp -D -d temperature -n 10\" "
+ echo "to \"bpls -la $PWD/../global_array_time_C_$BUFSIZE.bp -D -d temperature -n 10\" "
+ exit 1
+ fi
+done
+
+
+popd >/dev/null
+
+
+###################################################
+# run the Fortran tests too if available
if [ $HAVE_FORTRAN != yes ]; then
exit 0
fi
-###################################################
-# run the Fortran tests too if available
+
cp $SRCDIR/programs/examples/global_array_time/global_array_time_write_F .
cp $SRCDIR/programs/examples/global_array_time/global_array_time_F.xml .
diff --git a/tests/suite/tests/19_query.sh b/tests/suite/tests/19_query.sh
index 13c885e..6d87fb2 100755
--- a/tests/suite/tests/19_query.sh
+++ b/tests/suite/tests/19_query.sh
@@ -238,9 +238,11 @@ function query_datasets() {
echo "====== COMPUTING EXPECTED OUTPUT OF QUERY $QUERY_NAME ON DATASET $DSID IN $FILEMODE MODE ======"
echo
set -o xtrace
- $MPIRUN_SERIAL "$QUERY_SEQSCAN_EXE_LOCAL" "$NOINDEX_DS" "$QUERY_XML_LOCAL" "$FILEMODE" > "$EXPECTED_POINTS_FILE" ||
+ $MPIRUN_SERIAL "$QUERY_SEQSCAN_EXE_LOCAL" "$NOINDEX_DS" "$QUERY_XML_LOCAL" "$FILEMODE" > "$EXPECTED_POINTS_FILE".raw ||
die "ERROR: $QUERY_SEQSCAN_EXE_LOCAL failed with exit code $?"
set +o xtrace
+ # filter out job manager's output line at the end of stdout
+ grep -v "^Application" "$EXPECTED_POINTS_FILE".raw > "$EXPECTED_POINTS_FILE"
# NOTE: the sequential scan program produces a point list that is guaranteed to be sorted in C array order, so no need to sort it here
done
@@ -270,9 +272,12 @@ function query_datasets() {
echo "====== RUNNING QUERY $QUERY_NAME USING QUERY ENGINE $QUERY_ENGINE ON DATASET $DSID IN $FILEMODE MODE ======"
echo
set -o xtrace
- $MPIRUN_SERIAL "$QUERY_EXE_LOCAL" "$INDEXED_DS" "$QUERY_XML_LOCAL" "$QUERY_ENGINE" "$FILEMODE" > "$OUTPUT_POINTS_FILE" ||
+ $MPIRUN_SERIAL "$QUERY_EXE_LOCAL" "$INDEXED_DS" "$QUERY_XML_LOCAL" "$QUERY_ENGINE" "$FILEMODE" > "$OUTPUT_POINTS_FILE".raw ||
die "ERROR: $QUERY_EXE_LOCAL failed with exit code $?"
set +o xtrace
+ # filter out job manager's output line at the end of stdout
+ grep -v "^Application" "$OUTPUT_POINTS_FILE".raw > "$OUTPUT_POINTS_FILE"
+
# Sort the output points in C array order, since the query engine makes no guarantee as to the ordering of the results
# Sort file in place (-o FILE) with numerical sort order (-n) on each of the first 9 fields (-k1,1 ...)
diff --git a/tests/test_src/CMakeLists.txt b/tests/test_src/CMakeLists.txt
index 370cab1..6cfe1d6 100644
--- a/tests/test_src/CMakeLists.txt
+++ b/tests/test_src/CMakeLists.txt
@@ -12,7 +12,7 @@ link_directories(${PROJECT_BINARY_DIR}/tests/test_src)
set(C_PROGS_READONLY hashtest copy_subvolume text_to_pairstruct test_strutil points_1DtoND trim_spaces)
if(BUILD_WRITE)
- set(C_PROGS_WRITE transforms_specparse group_free_test query_minmax read_points_2d read_points_3d)
+ set(C_PROGS_WRITE transforms_specparse group_free_test query_minmax read_points_2d read_points_3d array_attribute)
endif(BUILD_WRITE)
if(BUILD_FORTRAN)
diff --git a/tests/test_src/Makefile.am b/tests/test_src/Makefile.am
index 1478a71..036f227 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 read_points_3d
+ test_C += transforms_specparse group_free_test query_minmax read_points_2d array_attribute array_attribute
endif
if BUILD_FORTRAN
@@ -103,11 +103,11 @@ 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) $(ADIOSLIB_EXTRA_LDFLAGS)
+array_attribute_CPPFLAGS = -I$(top_srcdir)/src $(ADIOSLIB_SEQ_CPPFLAGS) -I$(top_builddir)/src/public
+array_attribute.o: array_attribute.c
#
# FORTRAN Tests
diff --git a/tests/test_src/Makefile.in b/tests/test_src/Makefile.in
index b8fec8e..e396bdb 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 read_points_3d
+ at BUILD_WRITE_TRUE@am__append_1 = transforms_specparse group_free_test query_minmax read_points_2d array_attribute array_attribute
check_PROGRAMS = $(am__EXEEXT_2) $(am__EXEEXT_3)
TESTS = $(am__EXEEXT_2) $(am__EXEEXT_3)
subdir = tests/test_src
@@ -122,7 +122,7 @@ 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_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
$(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
@@ -141,20 +141,30 @@ CONFIG_CLEAN_VPATH_FILES =
@BUILD_WRITE_TRUE@ group_free_test$(EXEEXT) \
@BUILD_WRITE_TRUE@ query_minmax$(EXEEXT) \
@BUILD_WRITE_TRUE@ read_points_2d$(EXEEXT) \
- at BUILD_WRITE_TRUE@ read_points_3d$(EXEEXT)
+ at BUILD_WRITE_TRUE@ array_attribute$(EXEEXT) \
+ at BUILD_WRITE_TRUE@ array_attribute$(EXEEXT)
am__EXEEXT_2 = hashtest$(EXEEXT) copy_subvolume$(EXEEXT) \
text_to_pairstruct$(EXEEXT) test_strutil$(EXEEXT) \
points_1DtoND$(EXEEXT) trim_spaces$(EXEEXT) $(am__EXEEXT_1)
@BUILD_FORTRAN_TRUE at am__EXEEXT_3 = selection_api$(EXEEXT)
-am_copy_subvolume_OBJECTS = copy_subvolume-copy_subvolume.$(OBJEXT)
-copy_subvolume_OBJECTS = $(am_copy_subvolume_OBJECTS)
+am_array_attribute_OBJECTS = \
+ array_attribute-array_attribute.$(OBJEXT)
+array_attribute_OBJECTS = $(am_array_attribute_OBJECTS)
am__DEPENDENCIES_1 =
-copy_subvolume_DEPENDENCIES = \
- $(top_builddir)/src/libadiosread_nompi.a $(am__DEPENDENCIES_1)
+array_attribute_DEPENDENCIES = $(top_builddir)/src/libadios_nompi.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 =
+array_attribute_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \
+ $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \
+ $(AM_CFLAGS) $(CFLAGS) $(array_attribute_LDFLAGS) $(LDFLAGS) \
+ -o $@
+am_copy_subvolume_OBJECTS = copy_subvolume-copy_subvolume.$(OBJEXT)
+copy_subvolume_OBJECTS = $(am_copy_subvolume_OBJECTS)
+copy_subvolume_DEPENDENCIES = \
+ $(top_builddir)/src/libadiosread_nompi.a $(am__DEPENDENCIES_1)
copy_subvolume_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \
$(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \
$(AM_CFLAGS) $(CFLAGS) $(copy_subvolume_LDFLAGS) $(LDFLAGS) -o \
@@ -197,14 +207,6 @@ 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 = \
@@ -294,16 +296,16 @@ 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 = $(copy_subvolume_SOURCES) $(group_free_test_SOURCES) \
- $(hashtest_SOURCES) $(points_1DtoND_SOURCES) \
- $(query_minmax_SOURCES) $(read_points_2d_SOURCES) \
- $(read_points_3d_SOURCES) $(selection_api_SOURCES) \
+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)
-DIST_SOURCES = $(copy_subvolume_SOURCES) $(group_free_test_SOURCES) \
- $(hashtest_SOURCES) $(points_1DtoND_SOURCES) \
- $(query_minmax_SOURCES) $(read_points_2d_SOURCES) \
- $(read_points_3d_SOURCES) $(selection_api_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)
am__can_run_installinfo = \
@@ -749,6 +751,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
@@ -870,10 +875,10 @@ 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) $(ADIOSLIB_EXTRA_LDFLAGS)
+array_attribute_CPPFLAGS = -I$(top_srcdir)/src $(ADIOSLIB_SEQ_CPPFLAGS) -I$(top_builddir)/src/public
selection_api_SOURCES = selection_api.F90
selection_api_LDADD = $(top_builddir)/src/libadiosreadf_nompi.a $(ADIOSREADLIB_SEQ_LDADD)
selection_api_LDFLAGS = $(AM_LDFLAGS) $(ADIOSREADLIB_SEQ_LDFLAGS)
@@ -927,6 +932,10 @@ clean-checkPROGRAMS:
echo " rm -f" $$list; \
rm -f $$list
+array_attribute$(EXEEXT): $(array_attribute_OBJECTS) $(array_attribute_DEPENDENCIES) $(EXTRA_array_attribute_DEPENDENCIES)
+ @rm -f array_attribute$(EXEEXT)
+ $(AM_V_CCLD)$(array_attribute_LINK) $(array_attribute_OBJECTS) $(array_attribute_LDADD) $(LIBS)
+
copy_subvolume$(EXEEXT): $(copy_subvolume_OBJECTS) $(copy_subvolume_DEPENDENCIES) $(EXTRA_copy_subvolume_DEPENDENCIES)
@rm -f copy_subvolume$(EXEEXT)
$(AM_V_CCLD)$(copy_subvolume_LINK) $(copy_subvolume_OBJECTS) $(copy_subvolume_LDADD) $(LIBS)
@@ -951,10 +960,6 @@ read_points_2d$(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) $(LIBS)
@@ -981,13 +986,13 @@ mostlyclean-compile:
distclean-compile:
-rm -f *.tab.c
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/array_attribute-array_attribute.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/copy_subvolume-copy_subvolume.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/group_free_test-group_free_test.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/hashtest-hashtest.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(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@
@@ -1023,6 +1028,20 @@ distclean-compile:
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(AM_V_CC at am__nodep@)$(LTCOMPILE) -c -o $@ $<
+array_attribute-array_attribute.o: array_attribute.c
+ at am__fastdepCC_TRUE@ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(array_attribute_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) -MT array_attribute-array_attribute.o -MD -MP -MF $(DEPDIR)/array_attribute-array_attribute.Tpo -c -o array_attribute-array_attribute.o `test -f 'array_attribute.c' || echo '$(srcdir)/'`array_attribute.c
+ at am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/array_attribute-array_attribute.Tpo $(DEPDIR)/array_attribute-array_attribute.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ $(AM_V_CC)source='array_attribute.c' object='array_attribute-array_attribute.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(AM_V_CC at am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(array_attribute_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) -c -o array_attribute-array_attribute.o `test -f 'array_attribute.c' || echo '$(srcdir)/'`array_attribute.c
+
+array_attribute-array_attribute.obj: array_attribute.c
+ at am__fastdepCC_TRUE@ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(array_attribute_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) -MT array_attribute-array_attribute.obj -MD -MP -MF $(DEPDIR)/array_attribute-array_attribute.Tpo -c -o array_attribute-array_attribute.obj `if test -f 'array_attribute.c'; then $(CYGPATH_W) 'array_attribute.c'; else $(CYGPATH_W) '$(srcdir)/array_attribute.c'; fi`
+ at am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/array_attribute-array_attribute.Tpo $(DEPDIR)/array_attribute-array_attribute.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ $(AM_V_CC)source='array_attribute.c' object='array_attribute-array_attribute.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(AM_V_CC at am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(array_attribute_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) -c -o array_attribute-array_attribute.obj `if test -f 'array_attribute.c'; then $(CYGPATH_W) 'array_attribute.c'; else $(CYGPATH_W) '$(srcdir)/array_attribute.c'; fi`
+
copy_subvolume-copy_subvolume.o: copy_subvolume.c
@am__fastdepCC_TRUE@ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(copy_subvolume_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) -MT copy_subvolume-copy_subvolume.o -MD -MP -MF $(DEPDIR)/copy_subvolume-copy_subvolume.Tpo -c -o copy_subvolume-copy_subvolume.o `test -f 'copy_subvolume.c' || echo '$(srcdir)/'`copy_subvolume.c
@am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/copy_subvolume-copy_subvolume.Tpo $(DEPDIR)/copy_subvolume-copy_subvolume.Po
@@ -1107,20 +1126,6 @@ read_points_2d-read_points_2d.obj: read_points_2d.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(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 $(DEPDIR)/test_strutil-test_strutil.Po
@@ -1446,9 +1451,9 @@ read_points_2d.log: read_points_2d$(EXEEXT)
--log-file $$b.log --trs-file $$b.trs \
$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
"$$tst" $(AM_TESTS_FD_REDIRECT)
-read_points_3d.log: read_points_3d$(EXEEXT)
- @p='read_points_3d$(EXEEXT)'; \
- b='read_points_3d'; \
+array_attribute.log: array_attribute$(EXEEXT)
+ @p='array_attribute$(EXEEXT)'; \
+ b='array_attribute'; \
$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
--log-file $$b.log --trs-file $$b.trs \
$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
@@ -1642,7 +1647,7 @@ 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.
# Otherwise a system limit (for SysV at least) may be exceeded.
diff --git a/tests/test_src/array_attribute.c b/tests/test_src/array_attribute.c
new file mode 100644
index 0000000..7df7f26
--- /dev/null
+++ b/tests/test_src/array_attribute.c
@@ -0,0 +1,327 @@
+/*
+ * 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 Example: write/read string array and other array attributes
+ *
+ * How to run: ./array_attributes
+ * Output: adios_global_no_xml.bp
+ * ADIOS config file: None
+ *
+*/
+
+/* This example will write/read string array attributes. */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <inttypes.h>
+#include <string.h>
+#include "public/adios.h"
+#include "public/adios_types.h"
+#include "public/adios_read.h"
+
+#ifdef DMALLOC
+#include "dmalloc.h"
+#endif
+
+char filename [] = "array_attribute.bp";
+const int someints[5] = {5,4,3,2,1};
+const double somedoubles[5] = {5.55555, 4.4444, 3.333, 2.22, 1.1};
+char single_string[] = "A single string attribute";
+char *three_strings[] = {"X","Yy","ZzZ"};
+char *patchnames[] = {"arms", "deflector-bottom", "deflector-edge", "deflector-top",
+ "nozzle-inner", "nozzle-outer", "outer", "inlet", "outer-top",
+ "procBoundary0to1", "procBoundary0to2", "procBoundary0to5",
+ "procBoundary0to6", "procBoundary0to7", "procBoundary0to8",
+ "procBoundary0to13", "procBoundary0to14", "procBoundary0to185",
+ "procBoundary0to68", "procBoundary0to71", "procBoundary0to72"};
+char* patchtypes[] = {"wall", "wall", "wall", "wall", "wall", "wall",
+ "patch", "patch", "patch", "processor", "processor", "processor",
+ "processor", "processor", "processor", "processor", "processor",
+ "processor", "processor", "processor", "processor"};
+char* U[] = {"fixedValue", "fixedValue", "fixedValue", "fixedValue",
+ "fixedValue", "fixedValue", "pressureInletOutletVelocity",
+ "flowRateInletVelocity", "pressureInletOutletVelocity",
+ "processor", "processor", "processor", "processor", "processor",
+ "processor", "processor", "processor", "processor", "processor",
+ "processor", "processor"};
+char U_class[] = "volVectorField";
+char* alphawater[] = {"zeroGradient", "zeroGradient", "zeroGradient",
+ "zeroGradient", "zeroGradient", "zeroGradient", "inletOutlet",
+ "fixedValue", "inletOutlet", "processor", "processor", "processor",
+ "processor", "processor", "processor", "processor", "processor",
+ "processor", "processor", "processor", "processor"};
+char alphawater_class[] = "volScalarField";
+char* alphaPhi[] = {"calculated", "calculated", "calculated", "calculated",
+ "calculated", "calculated", "calculated", "calculated", "calculated",
+ "processor", "processor", "processor", "processor", "processor",
+ "processor", "processor", "processor", "processor", "processor",
+ "processor", "processor"};
+char alphaPhi_class[] = "surfaceScalarField";
+char* k[] = {"fixedValue", "fixedValue", "fixedValue", "fixedValue",
+ "fixedValue", "fixedValue", "inletOutlet", "fixedValue", "inletOutlet",
+ "processor", "processor", "processor", "processor", "processor",
+ "processor", "processor", "processor", "processor", "processor",
+ "processor", "processor"};
+char k_class[] = "volScalarField";
+char* nut[] = {"zeroGradient", "zeroGradient", "zeroGradient", "zeroGradient",
+ "zeroGradient", "zeroGradient", "zeroGradient", "zeroGradient",
+ "zeroGradient", "processor", "processor", "processor", "processor",
+ "processor", "processor", "processor", "processor", "processor",
+ "processor", "processor", "processor"};
+char nut_class[] = "volScalarField";
+char* p[] = {"calculated", "calculated", "calculated", "calculated",
+ "calculated", "calculated", "calculated", "calculated", "calculated",
+ "processor", "processor", "processor", "processor", "processor",
+ "processor", "processor", "processor", "processor", "processor",
+ "processor", "processor"};
+char p_class[] = "volScalarField";
+char* p_rgh[] = {"fixedFluxPressure", "fixedFluxPressure", "fixedFluxPressure",
+ "fixedFluxPressure", "fixedFluxPressure", "fixedFluxPressure",
+ "totalPressure", "fixedFluxPressure", "totalPressure", "processor",
+ "processor", "processor", "processor", "processor", "processor",
+ "processor", "processor", "processor", "processor", "processor", "processor"};
+char p_rgh_class[] = "volScalarField";
+char* phi[] = {"calculated", "calculated", "calculated", "calculated",
+ "calculated", "calculated", "calculated", "calculated", "calculated",
+ "processor", "processor", "processor", "processor", "processor",
+ "processor", "processor", "processor", "processor", "processor",
+ "processor", "processor"};
+char phi_class[] = "surfaceScalarField";
+
+MPI_Comm comm;
+int rank, size;
+
+int write_attrs();
+int read_attrs();
+
+int main (int argc, char ** argv)
+{
+
+ int ret;
+ comm = MPI_COMM_WORLD;
+ MPI_Init (&argc, &argv);
+ MPI_Comm_rank (comm, &rank);
+ MPI_Comm_size (comm, &size);
+ adios_init_noxml (comm);
+ adios_read_init_method(ADIOS_READ_METHOD_BP, comm, "");
+ adios_set_max_buffer_size (10);
+
+ ret = write_attrs();
+ if (!ret)
+ ret = read_attrs();
+
+ MPI_Barrier (comm);
+ adios_finalize (rank);
+ adios_read_finalize_method(ADIOS_READ_METHOD_BP);
+
+ MPI_Finalize ();
+ return ret;
+}
+
+int write_attrs()
+{
+ int64_t m_adios_group;
+ int64_t m_adios_file;
+ uint64_t adios_groupsize, adios_totalsize;
+ double var = 3.14159;
+
+ adios_declare_group (&m_adios_group, "attrs", "", adios_stat_default);
+ adios_select_method (m_adios_group, "POSIX", "", "");
+
+ adios_define_var (m_adios_group, "v","", adios_double, "", "", "");
+
+ // add some attributes
+ adios_define_attribute_byvalue (m_adios_group,
+ "single_string","", adios_string, 1, single_string);
+ adios_define_attribute_byvalue (m_adios_group,
+ "three_strings","", adios_string_array, 3, three_strings);
+ adios_define_attribute_byvalue (m_adios_group,
+ "single_int", "", adios_integer, 1, &someints);
+ adios_define_attribute_byvalue (m_adios_group,
+ "single_double","", adios_double, 1, &somedoubles);
+ adios_define_attribute_byvalue (m_adios_group,
+ "five_ints", "", adios_integer, 5, &someints);
+ adios_define_attribute_byvalue (m_adios_group,
+ "five_double", "", adios_double, 5, &somedoubles);
+
+ adios_define_attribute_byvalue (m_adios_group, "region0/patch-names","", adios_string_array, 21, patchnames);
+ adios_define_attribute_byvalue (m_adios_group, "region0/patch-types","", adios_string_array, 21, patchtypes);
+ adios_define_attribute_byvalue (m_adios_group, "region0/field/U/patch-types","", adios_string_array, 21, U);
+ adios_define_attribute_byvalue (m_adios_group, "region0/field/U/class","", adios_string, 1, U_class);
+ adios_define_attribute_byvalue (m_adios_group, "region0/field/alpha.water/patch-types","", adios_string_array, 21, alphawater);
+ adios_define_attribute_byvalue (m_adios_group, "region0/field/alpha.water/class","", adios_string, 1, alphawater_class);
+ adios_define_attribute_byvalue (m_adios_group, "region0/field/alphaPhi/patch-types","", adios_string_array, 21, alphaPhi);
+ adios_define_attribute_byvalue (m_adios_group, "region0/field/alphaPhi/class","", adios_string, 1, alphaPhi_class);
+ adios_define_attribute_byvalue (m_adios_group, "region0/field/k/patch-types","", adios_string_array, 21, k);
+ adios_define_attribute_byvalue (m_adios_group, "region0/field/k/class","", adios_string, 1, k_class);
+ adios_define_attribute_byvalue (m_adios_group, "region0/field/nut/patch-types","", adios_string_array, 21, nut);
+ adios_define_attribute_byvalue (m_adios_group, "region0/field/nut/class","", adios_string, 1, nut_class);
+ adios_define_attribute_byvalue (m_adios_group, "region0/field/p/patch-types","", adios_string_array, 21, p);
+ adios_define_attribute_byvalue (m_adios_group, "region0/field/p/class","", adios_string, 1, p_class);
+ adios_define_attribute_byvalue (m_adios_group, "region0/field/p_rgh/patch-types","", adios_string_array, 21, p_rgh);
+ adios_define_attribute_byvalue (m_adios_group, "region0/field/p_rgh/class","", adios_string, 1, p_rgh_class);
+ adios_define_attribute_byvalue (m_adios_group, "region0/field/phi/patch-types","", adios_string_array, 21, phi);
+ adios_define_attribute_byvalue (m_adios_group, "region0/field/phi/class","", adios_string, 1, phi_class);
+
+
+ adios_open (&m_adios_file, "attrs", filename, "w", comm);
+ adios_groupsize = adios_type_size(adios_double, NULL);
+ adios_group_size (m_adios_file, adios_groupsize, &adios_totalsize);
+ adios_write (m_adios_file, "v", &var);
+ adios_close (m_adios_file);
+ MPI_Barrier (comm);
+ return 0;
+}
+
+void print_attr (enum ADIOS_DATATYPES attr_type, int attr_size, const void * data)
+{
+ int type_size = adios_type_size (attr_type, data);
+ int nelems = attr_size / type_size;
+ int k;
+ const char *p = (const char*)data;
+ for (k=0; k<nelems; k++)
+ {
+ if (k>0) printf(", ");
+ switch (attr_type)
+ {
+ case adios_integer:
+ printf ("%d", *(const int *)p);
+ break;
+ case adios_double:
+ printf ("%e", *(const double *)p);
+ break;
+ case adios_string:
+ printf ("\"%s\"", (const char *)p);
+ break;
+ case adios_string_array:
+ printf ("\"%s\"", *(const char **)p);
+ break;
+ default:
+ printf ("??????\n");
+ }
+ p=p+type_size;
+ }
+ printf("\n");
+}
+
+int check_attr (ADIOS_FILE *f, const char *aname, const void* orig)
+{
+ enum ADIOS_DATATYPES attr_type;
+ int attr_size, i;
+ void * data = NULL;
+ int ret = adios_get_attr(f, aname, &attr_type, &attr_size, &data);
+ if (ret != err_no_error)
+ {
+ printf ("Error getting attribute %s: %s\n", aname, adios_errmsg());
+ return adios_errno;
+ }
+ int type_size = adios_type_size (attr_type, data);
+ int nelems = attr_size / type_size;
+ for (i = 0; i < nelems; ++i) {
+ int different;
+ if (attr_type == adios_string_array) {
+ different = strcmp( *((char**)data+i), *((const char**)orig+i) );
+ } else {
+ different = (memcmp((char*)data+i*type_size, (const char*)orig+i*type_size, type_size));
+ }
+ if (different)
+ {
+ printf ("Attribute %s element %d does not match "
+ "the original written value on %d bytes:\n\t",
+ aname, i, type_size);
+ print_attr(attr_type, attr_size, data);
+ printf (" != \n\t");
+ print_attr(attr_type, attr_size, orig);
+ switch (attr_type)
+ {
+ case adios_integer:
+ printf ("%d != %d\n", *(int *)data, *(const int *)orig);
+ break;
+ case adios_double:
+ printf ("%g != %g\n", *(double *)data, *(const double *)orig);
+ break;
+ case adios_string:
+ printf ("\"%s\" != \"%s\"\n", (char *)data, (const char *)orig);
+ break;
+ case adios_string_array:
+ printf ("\"%s\" != \"%s\"\n", *(char **)data, *(const char **)orig);
+ break;
+ default:
+ printf ("??????\n");
+ }
+ return -999;
+ }
+ }
+
+ free (data);
+ return err_no_error;
+}
+
+int read_attrs()
+{
+ int ret = 0;
+ ADIOS_FILE * f = adios_read_open (filename, ADIOS_READ_METHOD_BP,
+ comm, ADIOS_LOCKMODE_NONE, 0.0);
+ if (f == NULL)
+ {
+ printf ("%s\n", adios_errmsg());
+ ret = adios_errno;
+ goto finish;
+ }
+
+ if (!rank)
+ {
+ printf("Found %d attributes\n", f->nattrs);
+ /*
+ // Print all attributes
+ int j;
+ enum ADIOS_DATATYPES attr_type;
+ int attr_size;
+ void * data = NULL;
+ for (j=0; j < f->nattrs; j++)
+ {
+ adios_get_attr_byid (f, j, &attr_type, &attr_size, &data);
+ printf ("attr: %s %s = ", adios_type_to_string(attr_type), f->attr_namelist[j]);
+ print_attr (f, attr_type, attr_size, data);
+ free (data);
+ data = 0;
+ }
+ */
+ ret = check_attr(f, "single_string", single_string);
+ if (ret != err_no_error)
+ goto finish;
+ ret = check_attr(f, "single_int", someints);
+ if (ret != err_no_error)
+ goto finish;
+ ret = check_attr(f, "single_double", somedoubles);
+ if (ret != err_no_error)
+ goto finish;
+ ret = check_attr(f, "five_ints", someints);
+ if (ret != err_no_error)
+ goto finish;
+ ret = check_attr(f, "five_double", somedoubles);
+ if (ret != err_no_error)
+ goto finish;
+ ret = check_attr(f, "three_strings", three_strings);
+ if (ret != err_no_error)
+ goto finish;
+ ret = check_attr(f, "region0/patch-names", patchnames);
+ if (ret != err_no_error)
+ goto finish;
+ ret = check_attr(f, "region0/field/p_rgh/patch-types", p_rgh);
+ if (ret != err_no_error)
+ goto finish;
+
+ }
+
+finish:
+ MPI_Barrier (comm);
+ adios_read_close (f);
+ return 0;
+}
+
+
diff --git a/tests/test_src/group_free_test.c b/tests/test_src/group_free_test.c
index cb417ff..87b471f 100644
--- a/tests/test_src/group_free_test.c
+++ b/tests/test_src/group_free_test.c
@@ -55,7 +55,7 @@ int main (int argc, char ** argv)
for (j = 0; j < NGROUPS; j++)
{
sprintf (groupname, "group%1.1d", j);
- adios_declare_group (&groupid[j], groupname, "", adios_flag_yes);
+ adios_declare_group (&groupid[j], groupname, "", adios_stat_default);
adios_select_method (groupid[j], "MPI", "", "");
for (i = 0; i < NBLOCKS; i++)
diff --git a/tests/test_src/query_minmax.c b/tests/test_src/query_minmax.c
index cd73749..21ce790 100644
--- a/tests/test_src/query_minmax.c
+++ b/tests/test_src/query_minmax.c
@@ -144,7 +144,7 @@ int main (int argc, char ** argv)
printE ("%s\n", adios_errmsg());
}
- adios_declare_group (&m_adios_group, "query_minmax", "", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "query_minmax", "", adios_stat_default);
adios_select_method (m_adios_group, "POSIX", "", "");
diff --git a/tests/test_src/read_points_2d.c b/tests/test_src/read_points_2d.c
index e1a19e0..5a02fa3 100644
--- a/tests/test_src/read_points_2d.c
+++ b/tests/test_src/read_points_2d.c
@@ -171,7 +171,7 @@ int main (int argc, char ** argv)
printE ("%s\n", adios_errmsg());
}
- adios_declare_group (&m_adios_group, "read_points", "", adios_flag_yes);
+ adios_declare_group (&m_adios_group, "read_points", "", adios_stat_default);
adios_select_method (m_adios_group, "POSIX", "", "");
diff --git a/tests/test_src/read_points_3d.c b/tests/test_src/read_points_3d.c
deleted file mode 100644
index c1c16eb..0000000
--- a/tests/test_src/read_points_3d.c
+++ /dev/null
@@ -1,774 +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.
- */
-
-/* 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_flag_yes);
- 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 0363ab4..7a90f7b 100644
--- a/utils/Makefile.in
+++ b/utils/Makefile.in
@@ -112,7 +112,7 @@ 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_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 \
@@ -420,6 +420,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/utils/adios_lint/Makefile.in b/utils/adios_lint/Makefile.in
index aebccba..d920b0f 100644
--- a/utils/adios_lint/Makefile.in
+++ b/utils/adios_lint/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -409,6 +409,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/utils/adios_list_methods/Makefile.in b/utils/adios_list_methods/Makefile.in
index fd5309d..72ce646 100644
--- a/utils/adios_list_methods/Makefile.in
+++ b/utils/adios_list_methods/Makefile.in
@@ -117,7 +117,7 @@ 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_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 \
@@ -460,6 +460,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/utils/adios_list_methods/adios_list_methods.c b/utils/adios_list_methods/adios_list_methods.c
index f936ddd..0112ce1 100644
--- a/utils/adios_list_methods/adios_list_methods.c
+++ b/utils/adios_list_methods/adios_list_methods.c
@@ -29,416 +29,79 @@
#include <regex.h> // regular expression matching
#include <fnmatch.h> // shell pattern matching
-#include "core/adios_internals.h" // write hooks and adios_transport_struct
-#include "core/adios_read_hooks.h" // read hooks and adios_read_hooks_struct
-#include "core/transforms/adios_transforms_hooks.h"
-#include "core/transforms/adios_transforms_hooks_read.h"
-#include "core/transforms/adios_transforms_read.h"
-#include "query/adios_query_hooks.h"
-
-
-int print_data(void *data, int item, enum ADIOS_DATATYPES adiosvartype);
-
-
#ifdef WRITE
-static struct adios_transport_struct * adios_transports = 0;
+#include "public/adios.h"
#endif
-static struct adios_read_hooks_struct * adios_read_hooks = 0;
-static struct adios_query_hooks_struct * adios_query_hooks = 0;
+#include "public/adios_read.h"
+#include "public/adios_transform_methods.h"
+#include "public/adios_query.h"
+
int main (int argc, char ** argv) {
- int rank, size, i;
+ int rank = 0, i;
+#ifndef _NOMPI // added only to enable compiling with Score-P and other libs substituting MPI
MPI_Comm comm = MPI_COMM_WORLD;
-
MPI_Init(&argc,&argv);
MPI_Comm_rank(comm,&rank);
- MPI_Comm_size(comm,&size);
+#endif
#ifdef WRITE
- adios_init_transports (&adios_transports);
+ adios_init_noxml(MPI_COMM_WORLD);
+#endif
+
+#ifndef _NOMPI
+ adios_read_init_method(ADIOS_READ_METHOD_BP, MPI_COMM_WORLD, "");
+#else
+ adios_read_init_method(ADIOS_READ_METHOD_BP, 1, "");
#endif
- adios_read_hooks_init (&adios_read_hooks);
- adios_transform_read_init();
- adios_query_hooks_init(&adios_query_hooks);
if(rank==0) {
#ifdef WRITE
- // print all write methods
- printf ("Available write methods (in XML <method> element or in adios_select_method()):\n");
- for (i = 0; i < ADIOS_METHOD_COUNT; i++) {
- if (adios_transports[i].method_name) {
- printf(" \"%s\"\n", adios_transports[i].method_name);
- }
- }
+ printf ("Available write methods (in XML <method> element or in adios_select_method()):\n");
+ ADIOS_AVAILABLE_WRITE_METHODS * wm = adios_available_write_methods();
+ if (wm) {
+ for (i = 0; i < wm->nmethods; i++) {
+ printf(" \"%s\"\n", wm->name[i]);
+ }
+ adios_available_write_methods_free(wm);
+ }
#endif
printf ("Available read methods (constants after #include \"adios_read.h\"):\n");
- for (i = 0; i < ADIOS_READ_METHOD_COUNT; i++) {
- if (adios_read_hooks[i].method_name) {
- printf(" %s (=%d)\n", adios_read_hooks[i].method_name, i);
- }
+ ADIOS_AVAILABLE_READ_METHODS * rm = adios_available_read_methods();
+ if (rm) {
+ for (i = 0; i < rm->nmethods; i++) {
+ printf(" %s (=%d)\n", rm->name[i], rm->methodID[i]);
+ }
+ adios_available_read_methods_free(rm);
}
printf ("Available data transformation methods (in XML transform tags in <var> elements):\n");
- for (i = (int)adios_transform_none; i < num_adios_transform_types; i++) {
- if (adios_transform_is_implemented((enum ADIOS_TRANSFORM_TYPE)i)) {
- printf(" \"%s\"\t: %s\n",
- adios_transform_plugin_primary_xml_alias((enum ADIOS_TRANSFORM_TYPE)i),
- adios_transform_plugin_desc((enum ADIOS_TRANSFORM_TYPE)i));
+ ADIOS_AVAILABLE_TRANSFORM_METHODS * t = adios_available_transform_methods();
+ if (t) {
+ for (i=0; i<t->ntransforms; i++)
+ {
+ printf(" \"%s\"\t: %s\n", t->name[i], t->description[i]);
}
+ adios_available_transform_methods_free(t);
}
+
printf ("Available query methods (in adios_query_set_method()):\n");
- for (i = 0; i < ADIOS_QUERY_METHOD_COUNT; i++) {
- const enum ADIOS_QUERY_METHOD method = (enum ADIOS_QUERY_METHOD)i;
- if (adios_query_hooks[method].method_name) {
- printf(" %s (=%d)\n", adios_query_hooks[method].method_name, i);
- }
+ ADIOS_AVAILABLE_QUERY_METHODS * qm = adios_available_query_methods();
+ if (qm) {
+ for (i = 0; i < qm->nmethods; i++) {
+ printf(" %s (=%d)\n", qm->name[i], qm->methodID[i]);
+ }
+ adios_available_query_methods_free(qm);
}
}
+#ifndef _NOMPI // added only to enable compiling with Score-P and other libs substituting MPI
MPI_Barrier(comm);
MPI_Finalize();
+#endif
return(0);
}
-
-//check whether or not s+c goes over the global bound of v
-//input:
-//loc (tell you whether the overflow occurs, var definition or read/write)
-//v (var info)
-//s (offsets array)
-//c (chunk block / local bounds array)
-
-void checkOverflow(int loc, ADIOS_VARINFO* v, uint64_t* s, uint64_t* c) {
- int j;
- for(j=0; j<v->ndim; j++){
- if(s[j]+c[j]>v->dims[j]){
- if(loc==0)
- printf("in define: ");
- else //loc == 1
- printf("in read/write: ");
- printf("bound overflow happened. use debug mode\n");
- }
- }
-}
-
-//tell you what the size per element is based on the type
-//input:
-//adiosvartype (variable type structure)
-//elemsize (pointer to the element size that you should set)
-//output:
-//tells you whether or not the adiosvartype is known.
-
-int getTypeInfo( enum ADIOS_DATATYPES adiosvartype, int* elemsize){
-
- switch(adiosvartype) {
- case adios_unsigned_byte:
- *elemsize = 1;
- break;
- case adios_byte:
- *elemsize = 1;
- break;
- case adios_string:
- *elemsize = 1;
- break;
-
- case adios_unsigned_short:
- *elemsize = 2;
- break;
- case adios_short:
- *elemsize = 2;
- break;
-
- case adios_unsigned_integer:
- *elemsize = 4;
- break;
- case adios_integer:
- *elemsize = 4;
- break;
-
- case adios_unsigned_long:
- *elemsize = 8;
- break;
- case adios_long:
- *elemsize = 8;
- break;
-
- case adios_real:
- *elemsize = 4;
- break;
-
- case adios_double:
- *elemsize = 8;
- break;
-
- case adios_complex:
- *elemsize = 8;
- break;
-
- case adios_double_complex:
- *elemsize = 16;
- break;
-
- case adios_long_double: // do not know how to print
- //*elemsize = 16;
- default:
- return 1;
- }
- return 0;
-}
-
-
-//advance s by "by" number of elements.
-//NOTE: you have to first make sure "by" doesn't go over "s" yourself. The function doesn't check this. If not, it could lead to error.
-//input:
-//v (variable info pointer)
-//s (offset array pointer to start from)
-//by (by how much elements do you want to advance?)
-//rank (rank of your process)
-
-void rS(ADIOS_VARINFO* v, uint64_t* s, uint64_t by, int rank){
-
- int q;
- uint64_t bulk = 1;
-
- for(q=1; q<v->ndim; q++)
- bulk *= v->dims[q];
-
- for(q=0; q<v->ndim; q++){
-
- //if(bulk == 0)
- //break;
-
- if(by == 0)
- break;
-
- uint64_t inc = by/bulk;
-
- if(inc >= 1){
-
- if(s[q]+inc<v->dims[q]){
- s[q] += inc;
- }else{
- //s[q-1]++;
-
- uint64_t r = 1;
- while(1){
- if(s[q-r]+1 < v->dims[q-r]){
- s[q-r]++;
- break;
- }else{
- s[q-r] = 0;
- r++;
- }
- }
-
- uint64_t uinc = v->dims[q]-s[q];
- uint64_t new_inc = inc - uinc;
- s[q] = new_inc;
- }
- by -= inc*bulk;
-
- }
-
-
- if(q+1<v->ndim)
- bulk /= v->dims[q+1];
- }
-
-}
-
-
-//set chunk array block "c" based on the advised chunk_size
-//NOTE: c has to be all 1's; otherwise, there would be error.
-//input:
-//chunk_size (advised chunk_size)
-//v (variable info pointer)
-//c (chunk array block you want to set)
-
-void calcC(uint64_t chunk_size, ADIOS_VARINFO* v, uint64_t* c){
- int i;
- uint64_t tot = 1;
- uint64_t t;
- for(i=v->ndim-1; i>=0; i--){
-
- if(v->dims[i]*tot<=chunk_size){
- c[i] = v->dims[i];
- tot *= v->dims[i];
- }else{
- t = chunk_size/tot;
- c[i] = t;
- break;
- }
- }
-
-}
-
-
-//Calculate rough best estimate for chunk_size
-//Input:
-//total_size (total number of elements in the array)
-//mne (maximum number of elements per for the chunk_size)
-//np (number of cores you have)
-//Output:
-//chunk_size (in terms of the number of elements)
-
-uint64_t calcChunkSize(uint64_t total_size, uint64_t mne, int np){
-
- uint64_t chunk_size = 0;
- if((total_size/np) <= mne)
- chunk_size = total_size/np;
- else
- chunk_size = mne;
-
- if(chunk_size<1)
- chunk_size = 1;
-
- return chunk_size;
-
-}
-
-//based on the the theoretical c you want to use, this function gives the real c, "uc" that you can use for the local bounds,
-//without going out of the global bounds, starting from offset s
-//NOTE: uc has to be all 1's
-//Input:
-//v (variable info pointer)
-//s (offset pointer)
-//c (chunk array block you want to use)
-//uc (real chunk array calculated that you can use as local bounds)
-//chunk_size (basically the product of dimensions of c)
-//Output:
-//remain_chunk (the number of elements still left to process after you process uc block of elements)
-
-uint64_t checkBound(ADIOS_VARINFO* v, uint64_t* s, uint64_t* c, uint64_t* uc, uint64_t chunk_size){
- int i;
- uint64_t remain_chunk = chunk_size;
- int used_chunk = 1;
- for(i=v->ndim-1;i>=0;i--){
- if(s[i]+c[i]-1>=v->dims[i]){
- uc[i] = v->dims[i]-s[i];
- break;
- }
- uc[i] = c[i];
- }
-
- int j;
-
- for(j=0; j<v->ndim; j++)
- used_chunk *= uc[j];
- remain_chunk -= used_chunk;
-
- return remain_chunk;
-
-}
-
-
-//copy elements from "from" to "to"
-
-void arrCopy(uint64_t* from, uint64_t* to){
- int i;
- for(i=0; i<10; i++)
- to[i] = from[i];
-}
-
-
-void getbasename (char *path, char **dirname, char **basename)
-{
- char *work, *ptr;
-
- work = strdup(path);
- if (work[strlen(work)-1] == '/' && strlen(work)>1)
- work[strlen(work)-1] = '\0';
-
- ptr = rindex(work, '/');
- if (ptr && ptr != work) {
- // found a / and but not the beginning / of a full path
- ptr[0] = 0;
- *dirname = strdup(work);
- ptr[0] = '/';
- *basename = strdup(ptr+1);
- } else if (ptr == work) {
- // found / as the first character
- *dirname = strdup("");
- *basename = strdup(ptr+1);
- } else {
- *dirname = NULL; //strdup(".");
- *basename = strdup(work);
- }
- free(work);
-}
-
-
-int print_data(void *data, int item, enum ADIOS_DATATYPES adiosvartype)
-{
- if (data == NULL) {
- printf ( "null ");
- return 0;
- }
- // print next data item into vstr
- switch(adiosvartype) {
- case adios_unsigned_byte:
- printf ("%hhu", ((unsigned char *) data)[item]);
- break;
- case adios_byte:
- printf ("%hhd", ((signed char *) data)[item]);
- break;
- case adios_string:
- printf ("\"%s\"", ((char *) data)+item);
- break;
- case adios_string_array:
- // we expect one elemet of the array here
- printf("\"%s\"", *((char **)data+item));
- break;
-
- case adios_unsigned_short:
- printf ("%hu", ((unsigned short *) data)[item]);
- break;
- case adios_short:
- printf ("%hd", ((signed short *) data)[item]);
- break;
-
- case adios_unsigned_integer:
- printf ("%u", ((unsigned int *) data)[item]);
- break;
- case adios_integer:
- printf ("%d", ((signed int *) data)[item]);
- break;
-
- case adios_unsigned_long:
- printf ("%" PRIu64, ((uint64_t *) data)[item]);
- break;
- case adios_long:
- printf ("%" PRId64, ((int64_t *) data)[item]);
- break;
-
- case adios_real:
- printf ("%g", ((float *) data)[item]);
- break;
-
- case adios_double:
- printf ("%g", ((double *) data)[item]);
- break;
-
-
- case adios_long_double:
- //printf ("%g ", ((double *) data)[item]);
- printf ("????????");
- break;
-
-
- case adios_complex:
- printf ("(%g,i%g)", ((float *) data)[2*item], ((float *) data)[2*item+1]);
- break;
-
- case adios_double_complex:
- printf ("(%g,i%g)", ((double *) data)[2*item], ((double *) data)[2*item+1]);
- break;
-
- case adios_unknown:
- break;
- } // end switch
- return 0;
-}
-
diff --git a/utils/bp2ascii/Makefile.in b/utils/bp2ascii/Makefile.in
index 825bb69..1e1b32a 100644
--- a/utils/bp2ascii/Makefile.in
+++ b/utils/bp2ascii/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -407,6 +407,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/utils/bp2bp/Makefile.in b/utils/bp2bp/Makefile.in
index 4ec0035..7fb309e 100644
--- a/utils/bp2bp/Makefile.in
+++ b/utils/bp2bp/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -410,6 +410,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/utils/bp2h5/Makefile.in b/utils/bp2h5/Makefile.in
index eecbdab..5a44569 100644
--- a/utils/bp2h5/Makefile.in
+++ b/utils/bp2h5/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -412,6 +412,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/utils/bp2h5/bp2h5.c b/utils/bp2h5/bp2h5.c
index 9c500c7..fa746bd 100644
--- a/utils/bp2h5/bp2h5.c
+++ b/utils/bp2h5/bp2h5.c
@@ -43,9 +43,11 @@
#include "dmalloc.h"
#endif
-typedef int bool;
-#define false 0
-#define true 1
+#ifndef bool
+ typedef int bool;
+# define false 0
+# define true 1
+#endif
bool noindex = false; // do no print array indices with data
bool printByteAsChar = false; // print 8 bit integer arrays as string
diff --git a/utils/bp2ncd/Makefile.in b/utils/bp2ncd/Makefile.in
index 76454d9..809e5fb 100644
--- a/utils/bp2ncd/Makefile.in
+++ b/utils/bp2ncd/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -410,6 +410,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/utils/bpdiff/Makefile.in b/utils/bpdiff/Makefile.in
index 74ff5ad..4669821 100644
--- a/utils/bpdiff/Makefile.in
+++ b/utils/bpdiff/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -409,6 +409,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/utils/bpdump/Makefile.in b/utils/bpdump/Makefile.in
index ca6fe5a..06e83ff 100644
--- a/utils/bpdump/Makefile.in
+++ b/utils/bpdump/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -408,6 +408,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/utils/bpls/Makefile.in b/utils/bpls/Makefile.in
index 7b9649f..161fa49 100644
--- a/utils/bpls/Makefile.in
+++ b/utils/bpls/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -408,6 +408,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/utils/bpmeta/Makefile.in b/utils/bpmeta/Makefile.in
index 80d25ea..5736f44 100644
--- a/utils/bpmeta/Makefile.in
+++ b/utils/bpmeta/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -408,6 +408,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/utils/bprecover/Makefile.in b/utils/bprecover/Makefile.in
index 824da28..946020b 100644
--- a/utils/bprecover/Makefile.in
+++ b/utils/bprecover/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -409,6 +409,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/utils/bpsplit/Makefile.in b/utils/bpsplit/Makefile.in
index ac5a691..551cb7b 100644
--- a/utils/bpsplit/Makefile.in
+++ b/utils/bpsplit/Makefile.in
@@ -109,7 +109,7 @@ 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_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 \
@@ -424,6 +424,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/utils/fastbit/Makefile.in b/utils/fastbit/Makefile.in
index eb2c3be..1a32496 100644
--- a/utils/fastbit/Makefile.in
+++ b/utils/fastbit/Makefile.in
@@ -109,7 +109,7 @@ 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_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
$(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
@@ -410,6 +410,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/utils/gpp/CMakeLists.txt b/utils/gpp/CMakeLists.txt
index 374ca51..61fbf57 100644
--- a/utils/gpp/CMakeLists.txt
+++ b/utils/gpp/CMakeLists.txt
@@ -1,5 +1,6 @@
CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/gpp.py.in ${CMAKE_CURRENT_BINARY_DIR}/gpp.py @ONLY)
-install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/gpp.py ad_config.py type_mapper.py DESTINATION ${bindir})
+install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/gpp.py DESTINATION ${bindir})
+install(FILES ad_config.py type_mapper.py DESTINATION ${libdir}/python)
file(COPY ad_config.py type_mapper.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
diff --git a/utils/gpp/Makefile.am b/utils/gpp/Makefile.am
index 041e5ca..02ad29d 100644
--- a/utils/gpp/Makefile.am
+++ b/utils/gpp/Makefile.am
@@ -1,5 +1,10 @@
-dist_bin_SCRIPTS = gpp.py ad_config.py type_mapper.py
+dist_bin_SCRIPTS = gpp.py
+pythonlibdir=@libdir@/python
+dist_pythonlib_DATA = ad_config.py type_mapper.py
all-local:
test "$(srcdir)" = "$(builddir)" || cp $(srcdir)/ad_config.py $(srcdir)/type_mapper.py $(builddir); chmod a+x *.py
+
+
+
diff --git a/utils/gpp/Makefile.in b/utils/gpp/Makefile.in
index 9433dea..05e5992 100644
--- a/utils/gpp/Makefile.in
+++ b/utils/gpp/Makefile.in
@@ -14,6 +14,7 @@
@SET_MAKE@
+
VPATH = @srcdir@
am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
am__make_running_with_option = \
@@ -80,7 +81,7 @@ build_triplet = @build@
host_triplet = @host@
subdir = utils/gpp
DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
- $(srcdir)/gpp.py.in $(dist_bin_SCRIPTS)
+ $(srcdir)/gpp.py.in $(dist_bin_SCRIPTS) $(dist_pythonlib_DATA)
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/ac_alacrity.m4 \
$(top_srcdir)/config/ac_aplod.m4 \
@@ -109,7 +110,7 @@ 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_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 \
@@ -151,7 +152,7 @@ am__uninstall_files_from_dir = { \
|| { echo " ( cd '$$dir' && rm -f" $$files ")"; \
$(am__cd) "$$dir" && rm -f $$files; }; \
}
-am__installdirs = "$(DESTDIR)$(bindir)"
+am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(pythonlibdir)"
SCRIPTS = $(dist_bin_SCRIPTS)
AM_V_P = $(am__v_P_ at AM_V@)
am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
@@ -172,6 +173,7 @@ am__can_run_installinfo = \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
+DATA = $(dist_pythonlib_DATA)
am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
@@ -384,6 +386,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
@@ -445,7 +450,9 @@ target_alias = @target_alias@
top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
-dist_bin_SCRIPTS = gpp.py ad_config.py type_mapper.py
+dist_bin_SCRIPTS = gpp.py
+pythonlibdir = @libdir@/python
+dist_pythonlib_DATA = ad_config.py type_mapper.py
all: all-am
.SUFFIXES:
@@ -522,6 +529,27 @@ mostlyclean-libtool:
clean-libtool:
-rm -rf .libs _libs
+install-dist_pythonlibDATA: $(dist_pythonlib_DATA)
+ @$(NORMAL_INSTALL)
+ @list='$(dist_pythonlib_DATA)'; test -n "$(pythonlibdir)" || list=; \
+ if test -n "$$list"; then \
+ echo " $(MKDIR_P) '$(DESTDIR)$(pythonlibdir)'"; \
+ $(MKDIR_P) "$(DESTDIR)$(pythonlibdir)" || exit 1; \
+ fi; \
+ for p in $$list; do \
+ if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+ echo "$$d$$p"; \
+ done | $(am__base_list) | \
+ while read files; do \
+ echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(pythonlibdir)'"; \
+ $(INSTALL_DATA) $$files "$(DESTDIR)$(pythonlibdir)" || exit $$?; \
+ done
+
+uninstall-dist_pythonlibDATA:
+ @$(NORMAL_UNINSTALL)
+ @list='$(dist_pythonlib_DATA)'; test -n "$(pythonlibdir)" || list=; \
+ files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+ dir='$(DESTDIR)$(pythonlibdir)'; $(am__uninstall_files_from_dir)
tags TAGS:
ctags CTAGS:
@@ -561,9 +589,9 @@ distdir: $(DISTFILES)
done
check-am: all-am
check: check-am
-all-am: Makefile $(SCRIPTS) all-local
+all-am: Makefile $(SCRIPTS) $(DATA) all-local
installdirs:
- for dir in "$(DESTDIR)$(bindir)"; do \
+ for dir in "$(DESTDIR)$(bindir)" "$(DESTDIR)$(pythonlibdir)"; do \
test -z "$$dir" || $(MKDIR_P) "$$dir"; \
done
install: install-am
@@ -616,7 +644,7 @@ info: info-am
info-am:
-install-data-am:
+install-data-am: install-dist_pythonlibDATA
install-dvi: install-dvi-am
@@ -660,7 +688,7 @@ ps: ps-am
ps-am:
-uninstall-am: uninstall-dist_binSCRIPTS
+uninstall-am: uninstall-dist_binSCRIPTS uninstall-dist_pythonlibDATA
.MAKE: install-am install-strip
@@ -668,14 +696,16 @@ uninstall-am: uninstall-dist_binSCRIPTS
clean-libtool cscopelist-am ctags-am distclean \
distclean-generic distclean-libtool distdir dvi dvi-am html \
html-am info info-am install install-am install-data \
- install-data-am install-dist_binSCRIPTS install-dvi \
- install-dvi-am install-exec install-exec-am install-html \
- install-html-am install-info install-info-am install-man \
- install-pdf install-pdf-am install-ps install-ps-am \
- install-strip installcheck installcheck-am installdirs \
- maintainer-clean maintainer-clean-generic mostlyclean \
- mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
- tags-am uninstall uninstall-am uninstall-dist_binSCRIPTS
+ install-data-am install-dist_binSCRIPTS \
+ install-dist_pythonlibDATA install-dvi install-dvi-am \
+ install-exec install-exec-am install-html install-html-am \
+ install-info install-info-am install-man install-pdf \
+ install-pdf-am install-ps install-ps-am install-strip \
+ installcheck installcheck-am installdirs maintainer-clean \
+ maintainer-clean-generic mostlyclean mostlyclean-generic \
+ mostlyclean-libtool pdf pdf-am ps ps-am tags-am uninstall \
+ uninstall-am uninstall-dist_binSCRIPTS \
+ uninstall-dist_pythonlibDATA
all-local:
diff --git a/utils/gpp/gpp.py b/utils/gpp/gpp.py
index 7c0c4c0..01c9c9c 100755
--- a/utils/gpp/gpp.py
+++ b/utils/gpp/gpp.py
@@ -1,8 +1,15 @@
-#!/sw/sith/python/2.7.3/rhel6_gnu4.4.6/bin/python
+#!/usr/bin/python
import sys
import os
+# Make sure that the gpp modules are available...
+# ...for the installed gpp
+sys.path.insert (0, os.path.dirname(sys.argv[0]) + '/../lib/python')
+
+# ...for the gpp in the utils dir of the adios source
+#sys.path.insert (0, os.path.dirname(sys.argv[0]))
+
import ad_config
import type_mapper
diff --git a/utils/gpp/gpp.py.in b/utils/gpp/gpp.py.in
index 7a61d4e..cbb0d88 100755
--- a/utils/gpp/gpp.py.in
+++ b/utils/gpp/gpp.py.in
@@ -3,6 +3,13 @@
import sys
import os
+# Make sure that the gpp modules are available...
+# ...for the installed gpp
+sys.path.insert (0, os.path.dirname(sys.argv[0]) + '/../lib/python')
+
+# ...for the gpp in the utils dir of the adios source
+#sys.path.insert (0, os.path.dirname(sys.argv[0]))
+
import ad_config
import type_mapper
diff --git a/utils/skel/CMakeLists.txt b/utils/skel/CMakeLists.txt
index ee9eaf4..aafb54b 100644
--- a/utils/skel/CMakeLists.txt
+++ b/utils/skel/CMakeLists.txt
@@ -3,7 +3,7 @@ add_subdirectory(src)
CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/lib/skel_have_adios_timing.py.in ${CMAKE_CURRENT_BINARY_DIR}/lib/skel_have_adios_timing.py)
-install(PROGRAMS bin/skel bin/set_method.sh bin/skel_extract.py bin/skel_cat.py DESTINATION ${bindir})
+install(PROGRAMS bin/skel bin/skel_set_method.sh bin/skel_extract.py bin/skel_cat.py DESTINATION ${bindir})
install(FILES lib/adios.py
lib/argparse.py
@@ -16,6 +16,9 @@ install(FILES lib/adios.py
lib/skel_settings.py
lib/skel_source.py
lib/skel_submit.py
+ lib/skel_suite.py
+ lib/skel_template.py
+ lib/skel_test_plan.py
lib/skel_xml.py
lib/skelconf.py
${CMAKE_CURRENT_BINARY_DIR}/lib/skel_have_adios_timing.py
@@ -24,16 +27,20 @@ install(FILES lib/adios.py
install(FILES etc/templates/Makefile.default.tpl
- etc/templates/submit_sith.tpl
- etc/templates/submit_jaguar.tpl
- etc/templates/Makefile.tmpl
- etc/templates/source_write_c.tmpl
- etc/templates/source_write_fortran.tmpl
- etc/templates/submit_sith.tmpl
- etc/templates/xml.tmpl
- etc/templates/replay_bp.tmpl
- etc/templates/replay_yaml.tmpl
- DESTINATION ${prefix}/etc/skel/templates)
+ etc/templates/submit_sith.tpl
+ etc/templates/submit_jaguar.tpl
+ etc/templates/submit_nautilus.tpl
+ etc/templates/submit_nautilus.tmpl
+ etc/templates/Makefile.tmpl
+ etc/templates/create_suite.tmpl
+ etc/templates/source_write_c.tmpl
+ etc/templates/source_write_fortran.tmpl
+ etc/templates/submit_sith.tmpl
+ etc/templates/xml.tmpl
+ etc/templates/replay.tmpl
+ etc/templates/replay_bp.tmpl
+ etc/templates/replay_yaml.tmpl
+ DESTINATION ${prefix}/etc/skel/templates)
@@ -44,5 +51,5 @@ install(FILES etc/templates/Makefile.default.tpl
# etc/templates/submit_sith.tpl
# DESTINATION ${PROJECT_BINARY_DIR}/utils/skel)
-#install(FILES bin/skel bin/set_method.sh bin/skel_extract.py DESTINATION ${CMAKE_INSTALL_PREFIX}/bin)
+#install(FILES bin/skel bin/skel_set_method.sh bin/skel_extract.py DESTINATION ${CMAKE_INSTALL_PREFIX}/bin)
#install(FILES lib/adios.py lib/argparse.py lib/skel_cat.py lib/skel_install.py lib/skel_makefile.py lib/skel_params.py lib/skel_settings.py lib/skel_source.py lib/skel_submit.py lib/skel_xml.py lib/skelconf.py lib/typeMapper.py DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/python)
diff --git a/utils/skel/Makefile.am b/utils/skel/Makefile.am
index bf6fe53..2c92a51 100644
--- a/utils/skel/Makefile.am
+++ b/utils/skel/Makefile.am
@@ -5,7 +5,7 @@ if HAVE_MPI
endif
-dist_bin_SCRIPTS = bin/skel bin/set_method.sh bin/skel_extract.py bin/skel_cat.py
+dist_bin_SCRIPTS = bin/skel bin/skel_set_method.sh bin/skel_extract.py bin/skel_cat.py
pythonlibdir=@libdir@/python
diff --git a/utils/skel/Makefile.in b/utils/skel/Makefile.in
index 1b79af7..aacf829 100644
--- a/utils/skel/Makefile.in
+++ b/utils/skel/Makefile.in
@@ -112,7 +112,7 @@ 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_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 \
@@ -449,6 +449,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
@@ -511,7 +514,7 @@ top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
SUBDIRS = etc $(am__append_1)
-dist_bin_SCRIPTS = bin/skel bin/set_method.sh bin/skel_extract.py bin/skel_cat.py
+dist_bin_SCRIPTS = bin/skel bin/skel_set_method.sh bin/skel_extract.py bin/skel_cat.py
pythonlibdir = @libdir@/python
dist_pythonlib_DATA = \
lib/adios.py \
diff --git a/utils/skel/bin/set_method.sh b/utils/skel/bin/skel_set_method.sh
similarity index 100%
rename from utils/skel/bin/set_method.sh
rename to utils/skel/bin/skel_set_method.sh
diff --git a/utils/skel/etc/Makefile.in b/utils/skel/etc/Makefile.in
index 3902026..036e92f 100644
--- a/utils/skel/etc/Makefile.in
+++ b/utils/skel/etc/Makefile.in
@@ -108,7 +108,7 @@ 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_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 \
@@ -383,6 +383,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/utils/skel/etc/templates/Makefile.default.tpl b/utils/skel/etc/templates/Makefile.default.tpl
index f5ade84..b69bc9d 100644
--- a/utils/skel/etc/templates/Makefile.default.tpl
+++ b/utils/skel/etc/templates/Makefile.default.tpl
@@ -39,7 +39,7 @@ deploy:
cp $(APP)_skel.xml $(DEST_DIR)/$(APP)_skel.xml.in
cp $(CTESTS) submit* $(DEST_DIR)
cp $(FTESTS) submit* $(DEST_DIR)
- cp $(prefix)/bin/set_method.sh $(DEST_DIR)
+ cp $(prefix)/bin/skel_set_method.sh $(DEST_DIR)
cp $(prefix)/bin/skel_cat.py $(DEST_DIR)
clean:
diff --git a/utils/skel/etc/templates/submit_jaguar.tpl b/utils/skel/etc/templates/submit_jaguar.tpl
index 637c4b4..701e622 100644
--- a/utils/skel/etc/templates/submit_jaguar.tpl
+++ b/utils/skel/etc/templates/submit_jaguar.tpl
@@ -20,7 +20,7 @@ for i in {1..$$ITERATIONS$$}
do
echo $$METHOD$$
$$PRE_RM$$
-set_method.sh $$METHOD$$ $$APP$$_skel.xml.in $$APP$$_skel.xml $$METHOD_PARAMS$$
+skel_set_method.sh $$METHOD$$ $$APP$$_skel.xml.in $$APP$$_skel.xml $$METHOD_PARAMS$$
aprun -n $$CORES_USED$$ ./$$EXEC$$
$$POST_RM$$
done
diff --git a/utils/skel/etc/templates/submit_nautilus.tmpl b/utils/skel/etc/templates/submit_nautilus.tmpl
index 03dec75..183f91b 100644
--- a/utils/skel/etc/templates/submit_nautilus.tmpl
+++ b/utils/skel/etc/templates/submit_nautilus.tmpl
@@ -21,7 +21,7 @@ for i in {1..$$ITERATIONS$$}
do
echo $$METHOD$$
$$PRE_RM$$
-./set_method.sh $$METHOD$$ $$APP$$_skel.xml.in $$APP$$_skel.xml
+./skel_set_method.sh $$METHOD$$ $$APP$$_skel.xml.in $$APP$$_skel.xml
mpiexec ./$$EXEC$$
mv $$APP$$_skel_time.xml $$APP$$_skel_time_${PBS_JOBID}_${i}.xml
$$POST_RM$$
diff --git a/utils/skel/etc/templates/submit_nautilus.tpl b/utils/skel/etc/templates/submit_nautilus.tpl
index 03dec75..183f91b 100644
--- a/utils/skel/etc/templates/submit_nautilus.tpl
+++ b/utils/skel/etc/templates/submit_nautilus.tpl
@@ -21,7 +21,7 @@ for i in {1..$$ITERATIONS$$}
do
echo $$METHOD$$
$$PRE_RM$$
-./set_method.sh $$METHOD$$ $$APP$$_skel.xml.in $$APP$$_skel.xml
+./skel_set_method.sh $$METHOD$$ $$APP$$_skel.xml.in $$APP$$_skel.xml
mpiexec ./$$EXEC$$
mv $$APP$$_skel_time.xml $$APP$$_skel_time_${PBS_JOBID}_${i}.xml
$$POST_RM$$
diff --git a/utils/skel/etc/templates/submit_sith.tmpl b/utils/skel/etc/templates/submit_sith.tmpl
index 65e2005..9928313 100644
--- a/utils/skel/etc/templates/submit_sith.tmpl
+++ b/utils/skel/etc/templates/submit_sith.tmpl
@@ -19,7 +19,7 @@ do
echo $bpy.get_method()
##dpre_rm
rm -rf out*
-./set_method.sh $bpy.get_method() ${project}_skel.xml.in ${project}_skel.xml
+./skel_set_method.sh $bpy.get_method() ${project}_skel.xml.in ${project}_skel.xml
mpirun -n $bpy.get_num_procs() $executable
mv skel_time.xml ${project}_skel_time_\${PBS_JOBID}_\${i}.xml
##dpost_rm
diff --git a/utils/skel/etc/templates/submit_sith.tpl b/utils/skel/etc/templates/submit_sith.tpl
index c9537b0..212285b 100644
--- a/utils/skel/etc/templates/submit_sith.tpl
+++ b/utils/skel/etc/templates/submit_sith.tpl
@@ -17,7 +17,7 @@ for i in {1..$$ITERATIONS$$}
do
echo $$METHOD$$
$$PRE_RM$$
-./set_method.sh $$METHOD$$ $$APP$$_skel.xml.in $$APP$$_skel.xml
+./skel_set_method.sh $$METHOD$$ $$APP$$_skel.xml.in $$APP$$_skel.xml
mpirun -n $$CORES_USED$$ ./$$EXEC$$
mv skel_time.xml $$APP$$_skel_time_${PBS_JOBID}_${i}.xml
$$POST_RM$$
diff --git a/utils/skel/src/Makefile.in b/utils/skel/src/Makefile.in
index f4f725d..8d4cddc 100644
--- a/utils/skel/src/Makefile.in
+++ b/utils/skel/src/Makefile.in
@@ -111,7 +111,7 @@ 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_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 \
@@ -443,6 +443,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/utils/skeldump/Makefile.in b/utils/skeldump/Makefile.in
index 2fbeec8..5439dbc 100644
--- a/utils/skeldump/Makefile.in
+++ b/utils/skeldump/Makefile.in
@@ -109,7 +109,7 @@ 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_szip.m4 $(top_srcdir)/config/ac_zfp.m4 \
$(top_srcdir)/config/ac_zlib.m4 \
$(top_srcdir)/config/acx_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
@@ -408,6 +408,9 @@ VERSION = @VERSION@
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MICRO = @VERSION_MICRO@
VERSION_MINOR = @VERSION_MINOR@
+ZFP_CPPFLAGS = @ZFP_CPPFLAGS@
+ZFP_LDFLAGS = @ZFP_LDFLAGS@
+ZFP_LIBS = @ZFP_LIBS@
ZLIB_CPPFLAGS = @ZLIB_CPPFLAGS@
ZLIB_LDFLAGS = @ZLIB_LDFLAGS@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/utils/skeldump/skeldump.c b/utils/skeldump/skeldump.c
index 97f6f9a..cf0a265 100644
--- a/utils/skeldump/skeldump.c
+++ b/utils/skeldump/skeldump.c
@@ -562,7 +562,7 @@ int doList_group (ADIOS_FILE *fp)
matches = matchesAMask(names[n]);
- if (matches) {
+ if (matches && strncmp("/__adios__", names[n], 10)) { // Ignore timing vars
nVarsMatched++;
fprintf (outf, " {\n");
diff --git a/wrappers/java/CMakeLists.txt b/wrappers/java/CMakeLists.txt
index ad29b78..8cfd5eb 100644
--- a/wrappers/java/CMakeLists.txt
+++ b/wrappers/java/CMakeLists.txt
@@ -15,14 +15,14 @@ include_directories (${JNI_INCLUDE_DIRS})
option (ADIOS_USE_MPI "Use parallel ADIOS" ON)
find_package (ADIOS REQUIRED)
-add_definitions (${ADIOS_COMPILE_FLAGS})
+add_definitions (${ADIOS_COMPILE_FLAGS})
add_definitions (-DADIOS_USE_READ_API_1)
include_directories (${ADIOS_INCLUDE_PATH})
if (ADIOS_USE_MPI)
find_package (MPI REQUIRED)
include_directories (${MPI_CXX_INCLUDE_PATH})
- add_definitions (-DADIOS_USE_MPI)
+ add_definitions (-DADIOS_USE_MPI)
else ()
find_package (MPI REQUIRED)
endif()
@@ -30,6 +30,7 @@ endif()
set (SRC
gov_ornl_ccs_AdiosDatatype.cxx
gov_ornl_ccs_AdiosFlag.cxx
+ gov_ornl_ccs_AdiosStatisticsFlag.cxx
gov_ornl_ccs_AdiosBufferAllocWhen.cxx
gov_ornl_ccs_Adios.cxx
gov_ornl_ccs_AdiosFile.cxx
@@ -93,4 +94,3 @@ install (FILES ${CMAKE_CURRENT_BINARY_DIR}/AdiosJava.jar DESTINATION lib)
ENABLE_TESTING()
add_test (test1 ${CMAKE_CURRENT_SOURCE_DIR}/test/test1.sh ${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/test AdiosTest)
add_test (test2 ${CMAKE_CURRENT_SOURCE_DIR}/test/test2.sh ${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/test AdiosNoxmlTest)
-
diff --git a/wrappers/java/gov/ornl/ccs/Adios.java b/wrappers/java/gov/ornl/ccs/Adios.java
index e9fc96c..fb8d934 100644
--- a/wrappers/java/gov/ornl/ccs/Adios.java
+++ b/wrappers/java/gov/ornl/ccs/Adios.java
@@ -66,7 +66,7 @@ public class Adios
{
return adios_init(xml_fname, comm);
}
-
+
/* Call adios_open. Return a group handler */
public static long Open(String group_name, String file_name, String mode, long comm)
{
@@ -232,16 +232,16 @@ public class Adios
{
return adios_init_noxml(comm);
}
-
+
/* Call adios_allocate_buffer */
public static int AllocateBuffer(AdiosBufferAllocWhen when, long size)
{
return adios_allocate_buffer(when.getCode(), size);
}
-
+
/* Call adios_declare_group */
- public static long DeclareGroup(String name, String time_index, AdiosFlag stats)
+ public static long DeclareGroup(String name, String time_index, AdiosStatisticsFlag stats)
{
return adios_declare_group(name, time_index, stats.getCode());
}
diff --git a/wrappers/java/gov_ornl_ccs_Adios.cxx b/wrappers/java/gov_ornl_ccs_Adios.cxx
index a448125..c7f6736 100644
--- a/wrappers/java/gov_ornl_ccs_Adios.cxx
+++ b/wrappers/java/gov_ornl_ccs_Adios.cxx
@@ -62,8 +62,8 @@
* Method: adios_init
* Signature: (Ljava/lang/String;)I
*/
-JNIEXPORT jint JNICALL
-Java_gov_ornl_ccs_Adios_adios_1init
+JNIEXPORT jint JNICALL
+Java_gov_ornl_ccs_Adios_adios_1init
(JNIEnv *env, jclass cls, jstring xml_fname, jlong comm)
{
//std::cout << __FUNCTION__ << "..." << std::endl;
@@ -74,7 +74,7 @@ Java_gov_ornl_ccs_Adios_adios_1init
result = adios_init(str_xml_fname, (MPI_Comm) comm);
//std::cout << "result = " << result << std::endl;
-
+
STR_FREE(xml_fname);
return result;
@@ -141,7 +141,7 @@ JNIEXPORT jlong JNICALL Java_gov_ornl_ccs_Adios_adios_1group_1size
* Signature: (JLjava/lang/String;D)I
*/
FUNC_WRITE_ONE (
- Java_gov_ornl_ccs_Adios_adios_1write__JLjava_lang_String_2B,
+ Java_gov_ornl_ccs_Adios_adios_1write__JLjava_lang_String_2B,
jbyte)
FUNC_WRITE_ONE (
@@ -231,9 +231,9 @@ JNIEXPORT jint JNICALL Java_gov_ornl_ccs_Adios_adios_1mpi_1init
{
int argc = env->GetArrayLength(args);
char **argv;
- int result;
-
- for (int i = 0; i < argc; i++)
+ int result;
+
+ for (int i = 0; i < argc; i++)
{
jstring jstr = (jstring) env->GetObjectArrayElement(args, i);
const char *chr = env->GetStringUTFChars(jstr, 0);
@@ -247,10 +247,10 @@ JNIEXPORT jint JNICALL Java_gov_ornl_ccs_Adios_adios_1mpi_1init
result = MPI_Init(&argc, &argv);
- for (int i = 0; i < argc; i++)
+ for (int i = 0; i < argc; i++)
{
//free(argv[i]);
- delete[] argv[i];
+ delete[] argv[i];
}
return result;
@@ -266,7 +266,7 @@ JNIEXPORT jint JNICALL Java_gov_ornl_ccs_Adios_adios_1mpi_1comm_1rank
{
int rank;
MPI_Comm_rank((MPI_Comm) comm, &rank);
-
+
return rank;
}
@@ -280,7 +280,7 @@ JNIEXPORT jint JNICALL Java_gov_ornl_ccs_Adios_adios_1mpi_1comm_1size
{
int size;
MPI_Comm_size((MPI_Comm) comm, &size);
-
+
return size;
}
@@ -354,7 +354,7 @@ JNIEXPORT jlong JNICALL Java_gov_ornl_ccs_Adios_adios_1open_1and_1set_1group_1si
* Method: adios_init_noxml
* Signature: ()I
*/
-JNIEXPORT jint JNICALL
+JNIEXPORT jint JNICALL
Java_gov_ornl_ccs_Adios_adios_1init_1noxml
(JNIEnv *env, jclass cls, jlong comm)
{
@@ -386,7 +386,7 @@ JNIEXPORT jlong JNICALL Java_gov_ornl_ccs_Adios_adios_1declare_1group
STR_ALLOC(name);
STR_ALLOC(time_index);
- result = adios_declare_group(&id_p, str_name, str_time_index, (ADIOS_FLAG) stats);
+ result = adios_declare_group(&id_p, str_name, str_time_index, (ADIOS_STATISTICS_FLAG) stats);
STR_FREE(name);
STR_FREE(time_index);
@@ -411,7 +411,7 @@ JNIEXPORT jint JNICALL Java_gov_ornl_ccs_Adios_adios_1define_1var
STR_ALLOC(local_offsets);
result = adios_define_var((int64_t) group_id, str_name, str_path, (ADIOS_DATATYPES) type, str_dimensions, str_global_dimensions, str_local_offsets);
-
+
STR_FREE(name);
STR_FREE(path);
STR_FREE(dimensions);
@@ -430,12 +430,12 @@ JNIEXPORT jint JNICALL Java_gov_ornl_ccs_Adios_adios_1define_1attribute
(JNIEnv * env, jclass cls, jlong group_id, jstring name, jstring path, jint type, jstring value, jstring var)
{
int result;
-
+
STR_ALLOC(name);
STR_ALLOC(path);
STR_ALLOC(value);
STR_ALLOC(var);
-
+
result = adios_define_attribute((int64_t) group_id, str_name, str_path, (ADIOS_DATATYPES) type, str_value, str_var);
STR_FREE(name);
@@ -455,17 +455,17 @@ JNIEXPORT jint JNICALL Java_gov_ornl_ccs_Adios_adios_1select_1method
(JNIEnv * env, jclass cls, jlong group_id, jstring method, jstring parameters, jstring base_path)
{
int result;
-
+
STR_ALLOC(method);
STR_ALLOC(parameters);
STR_ALLOC(base_path);
-
+
result = adios_select_method((int64_t) group_id, str_method, str_parameters, str_base_path);
STR_FREE(method);
STR_FREE(parameters);
STR_FREE(base_path);
-
+
return result;
}
@@ -574,5 +574,3 @@ FUNC_READ_ARRAY(
Java_gov_ornl_ccs_Adios_adios_1read__JLjava_lang_String_2_3D,
jdouble,
Double);
-
-
diff --git a/wrappers/java/test/AdiosNoxmlTest.java b/wrappers/java/test/AdiosNoxmlTest.java
index d151121..8998a1e 100644
--- a/wrappers/java/test/AdiosNoxmlTest.java
+++ b/wrappers/java/test/AdiosNoxmlTest.java
@@ -8,7 +8,7 @@ public class AdiosNoxmlTest
public static void main(String[] args)
{
System.out.println(">>> AdiosJava Noxml Test Drive");
-
+
System.out.println(">>> ADIOS NOXML API ... ");
Adios.MPI_Init(new String[0]);
long comm = Adios.MPI_COMM_WORLD();
@@ -20,7 +20,7 @@ public class AdiosNoxmlTest
Adios.Init_Noxml(comm);
Adios.AllocateBuffer(AdiosBufferAllocWhen.NOW, 10);
- long group_id = Adios.DeclareGroup("restart", "iter", AdiosFlag.YES);
+ long group_id = Adios.DeclareGroup("restart", "iter", AdiosStatisticsFlag.MINMAX);
Adios.SelectMethod(group_id, "MPI", "", "");
Adios.DefineVar(group_id, "NX", "", AdiosDatatype.INTEGER, "", "", "");
Adios.DefineVar(group_id, "G", "", AdiosDatatype.INTEGER, "", "", "");
@@ -30,7 +30,7 @@ public class AdiosNoxmlTest
System.out.println(">>> ADIOS Write API ... ");
long adios_handle = Adios.Open ("restart", "adios_noxml.bp", "w", comm);
- int NX = 10;
+ int NX = 10;
int G = NX * size;
int O = NX * rank;
@@ -40,16 +40,16 @@ public class AdiosNoxmlTest
}
long groupsize = 4 + 4 + 4 + 8 * (1) * (NX);
-
+
long adios_totalsize = Adios.SetGroupSize(adios_handle, groupsize);
-
+
Adios.Write (adios_handle, "NX", NX);
Adios.Write (adios_handle, "G", G);
Adios.Write (adios_handle, "O", O);
Adios.Write (adios_handle, "temperature", t);
Adios.Close (adios_handle);
-
- Adios.Finalize (rank);
+
+ Adios.Finalize (rank);
Adios.MPI_Finalize();
System.out.println(">>> Done.");
diff --git a/wrappers/numpy/adios.cpp b/wrappers/numpy/adios.cpp
index 24a46d7..dc001f0 100644
--- a/wrappers/numpy/adios.cpp
+++ b/wrappers/numpy/adios.cpp
@@ -795,7 +795,7 @@ 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":381
+/* "adios.pyx":465
* cdef MPI_Comm read_init_comm
*
* cpdef init(str config, MPI_Comm comm = MPI_COMM_WORLD): # <<<<<<<<<<<<<<
@@ -807,7 +807,7 @@ struct __pyx_opt_args_5adios_init {
MPI_Comm comm;
};
-/* "adios.pyx":386
+/* "adios.pyx":470
* return adios_init(s2b(config), init_comm)
*
* cpdef int64_t open(str group_name, # <<<<<<<<<<<<<<
@@ -819,7 +819,7 @@ struct __pyx_opt_args_5adios_open {
MPI_Comm comm;
};
-/* "adios.pyx":401
+/* "adios.pyx":485
* return total_size
*
* cpdef int write (int64_t fd_p, str name, val, dtype=None): # <<<<<<<<<<<<<<
@@ -831,7 +831,7 @@ struct __pyx_opt_args_5adios_write {
PyObject *dtype;
};
-/* "adios.pyx":441
+/* "adios.pyx":525
* return adios_close(fd_p)
*
* cpdef int finalize(int mype = 0): # <<<<<<<<<<<<<<
@@ -843,7 +843,7 @@ struct __pyx_opt_args_5adios_finalize {
int mype;
};
-/* "adios.pyx":448
+/* "adios.pyx":532
* ## ====================
*
* cpdef int init_noxml(MPI_Comm comm = MPI_COMM_WORLD): # <<<<<<<<<<<<<<
@@ -855,12 +855,12 @@ struct __pyx_opt_args_5adios_init_noxml {
MPI_Comm comm;
};
-/* "adios.pyx":458
+/* "adios.pyx":542
* buffer_size)
*
* cpdef int64_t declare_group(str name, # <<<<<<<<<<<<<<
* str time_index = "",
- * int stats = 1):
+ * int stats = adios_stat_default):
*/
struct __pyx_opt_args_5adios_declare_group {
int __pyx_n;
@@ -868,10 +868,10 @@ struct __pyx_opt_args_5adios_declare_group {
int stats;
};
-/* "adios.pyx":468
+/* "adios.pyx":552
* return id
*
- * cpdef int define_var(int64_t group_id, # <<<<<<<<<<<<<<
+ * cpdef int64_t define_var(int64_t group_id, # <<<<<<<<<<<<<<
* str name,
* str path,
*/
@@ -882,7 +882,7 @@ struct __pyx_opt_args_5adios_define_var {
PyObject *local_offsets;
};
-/* "adios.pyx":540
+/* "adios.pyx":719
* <void *> val_.data)
*
* cpdef int select_method (int64_t group, # <<<<<<<<<<<<<<
@@ -895,7 +895,7 @@ struct __pyx_opt_args_5adios_select_method {
PyObject *base_path;
};
-/* "adios.pyx":554
+/* "adios.pyx":746
* ## ====================
*
* cpdef np.dtype adios2npdtype(ADIOS_DATATYPES t, int strlen = 1): # <<<<<<<<<<<<<<
@@ -907,7 +907,7 @@ struct __pyx_opt_args_5adios_adios2npdtype {
int strlen;
};
-/* "adios.pyx":683
+/* "adios.pyx":875
*
* """ Call adios_read_init_method """
* cpdef int read_init(str method_name = "BP", # <<<<<<<<<<<<<<
@@ -921,7 +921,7 @@ struct __pyx_opt_args_5adios_read_init {
PyObject *parameters;
};
-/* "adios.pyx":693
+/* "adios.pyx":885
*
* """ Call adios_read_finalize_method """
* cpdef int read_finalize(str method_name = "BP"): # <<<<<<<<<<<<<<
@@ -933,7 +933,7 @@ struct __pyx_opt_args_5adios_read_finalize {
PyObject *method_name;
};
-/* "adios.pyx":870
+/* "adios.pyx":1062
* adios_release_step(self.fp)
*
* cpdef advance(self, int last = 0, float timeout_sec = 0.0): # <<<<<<<<<<<<<<
@@ -946,7 +946,7 @@ struct __pyx_opt_args_5adios_4file_advance {
float timeout_sec;
};
-/* "adios.pyx":1168
+/* "adios.pyx":1360
* self.nsteps = self.vp.nsteps
*
* cpdef read_points(self, tuple points = (), from_steps = None, nsteps = None): # <<<<<<<<<<<<<<
@@ -960,7 +960,7 @@ struct __pyx_opt_args_5adios_3var_read_points {
PyObject *nsteps;
};
-/* "adios.pyx":1224
+/* "adios.pyx":1416
* return var
*
* cpdef read_writeblock(self, int rank, from_steps = None, nsteps = None): # <<<<<<<<<<<<<<
@@ -973,7 +973,7 @@ struct __pyx_opt_args_5adios_3var_read_writeblock {
PyObject *nsteps;
};
-/* "adios.pyx":1265
+/* "adios.pyx":1457
* return var
*
* cpdef read(self, tuple offset = (), tuple count = (), tuple scalar = (), # <<<<<<<<<<<<<<
@@ -991,7 +991,7 @@ struct __pyx_opt_args_5adios_3var_read {
PyObject *step_scalar;
};
-/* "adios.pyx":698
+/* "adios.pyx":890
*
* ## dict for handling '/' prefix
* cdef class softdict(dict): # <<<<<<<<<<<<<<
@@ -1003,7 +1003,7 @@ struct __pyx_obj_5adios_softdict {
};
-/* "adios.pyx":722
+/* "adios.pyx":914
*
* ## Python class for ADIOS_FILE structure
* cdef class file(dict): # <<<<<<<<<<<<<<
@@ -1030,7 +1030,7 @@ struct __pyx_obj_5adios_file {
};
-/* "adios.pyx":994
+/* "adios.pyx":1186
* return list(s-set(['']))
*
* cdef class blockinfo(object): # <<<<<<<<<<<<<<
@@ -1046,7 +1046,7 @@ struct __pyx_obj_5adios_blockinfo {
};
-/* "adios.pyx":1029
+/* "adios.pyx":1221
* self.count)
*
* cdef class var(dict): # <<<<<<<<<<<<<<
@@ -1069,7 +1069,7 @@ struct __pyx_obj_5adios_var {
};
-/* "adios.pyx":1494
+/* "adios.pyx":1686
* return self.attrs.keys()
*
* cdef class attr(object): # <<<<<<<<<<<<<<
@@ -1085,7 +1085,7 @@ struct __pyx_obj_5adios_attr {
};
-/* "adios.pyx":1580
+/* "adios.pyx":1772
* (self.name, self.dtype, self.value)
*
* cdef class group(dict): # <<<<<<<<<<<<<<
@@ -1101,7 +1101,7 @@ struct __pyx_obj_5adios_group {
};
-/* "adios.pyx":1692
+/* "adios.pyx":1884
*
* ## Helper dict
* cdef class smartdict(dict): # <<<<<<<<<<<<<<
@@ -1114,7 +1114,7 @@ struct __pyx_obj_5adios_smartdict {
};
-/* "adios.pyx":1704
+/* "adios.pyx":1896
* self.factory(key, value)
*
* cdef class writer(object): # <<<<<<<<<<<<<<
@@ -1133,10 +1133,11 @@ struct __pyx_obj_5adios_writer {
MPI_Comm comm;
PyObject *vars;
PyObject *attrs;
+ uint64_t timeaggregation_buffersize;
};
-/* "adios.pyx":1922
+/* "adios.pyx":2150
* self.close()
*
* cdef class attrinfo(object): # <<<<<<<<<<<<<<
@@ -1152,7 +1153,7 @@ struct __pyx_obj_5adios_attrinfo {
};
-/* "adios.pyx":1975
+/* "adios.pyx":2203
* self.dtype)
*
* cdef class varinfo(object): # <<<<<<<<<<<<<<
@@ -1166,11 +1167,12 @@ struct __pyx_obj_5adios_varinfo {
PyObject *gdim;
PyObject *offset;
PyObject *value;
+ PyObject *transform;
};
-/* "adios.pyx":722
+/* "adios.pyx":914
*
* ## Python class for ADIOS_FILE structure
* cdef class file(dict): # <<<<<<<<<<<<<<
@@ -1187,7 +1189,7 @@ struct __pyx_vtabstruct_5adios_file {
static struct __pyx_vtabstruct_5adios_file *__pyx_vtabptr_5adios_file;
-/* "adios.pyx":1029
+/* "adios.pyx":1221
* self.count)
*
* cdef class var(dict): # <<<<<<<<<<<<<<
@@ -1594,6 +1596,24 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
#define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
#endif
+/* PyObjectSetAttrStr.proto */
+#if CYTHON_COMPILING_IN_CPYTHON
+#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);
+ if (likely(tp->tp_setattro))
+ return tp->tp_setattro(obj, attr_name, value);
+#if PY_MAJOR_VERSION < 3
+ if (likely(tp->tp_setattr))
+ return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value);
+#endif
+ return PyObject_SetAttr(obj, attr_name, value);
+}
+#else
+#define __Pyx_PyObject_DelAttrStr(o,n) PyObject_DelAttr(o,n)
+#define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v)
+#endif
+
/* PyObjectCallMethod0.proto */
static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name);
@@ -1613,24 +1633,6 @@ static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* dict, int is_dict,
static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* dict_or_iter, Py_ssize_t orig_length, Py_ssize_t* ppos,
PyObject** pkey, PyObject** pvalue, PyObject** pitem, int is_dict);
-/* PyObjectSetAttrStr.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
-#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);
- if (likely(tp->tp_setattro))
- return tp->tp_setattro(obj, attr_name, value);
-#if PY_MAJOR_VERSION < 3
- if (likely(tp->tp_setattr))
- return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value);
-#endif
- return PyObject_SetAttr(obj, attr_name, value);
-}
-#else
-#define __Pyx_PyObject_DelAttrStr(o,n) PyObject_DelAttr(o,n)
-#define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v)
-#endif
-
/* py_dict_values.proto */
static CYTHON_INLINE PyObject* __Pyx_PyDict_Values(PyObject* d);
@@ -1930,10 +1932,28 @@ static int __pyx_f_5adios_finalize(int __pyx_skip_dispatch, struct __pyx_opt_arg
static int __pyx_f_5adios_init_noxml(int __pyx_skip_dispatch, struct __pyx_opt_args_5adios_init_noxml *__pyx_optional_args); /*proto*/
static int __pyx_f_5adios_allocate_buffer(int, uint64_t, int __pyx_skip_dispatch); /*proto*/
static int64_t __pyx_f_5adios_declare_group(PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5adios_declare_group *__pyx_optional_args); /*proto*/
-static int __pyx_f_5adios_define_var(int64_t, PyObject *, PyObject *, int, int __pyx_skip_dispatch, struct __pyx_opt_args_5adios_define_var *__pyx_optional_args); /*proto*/
+static int64_t __pyx_f_5adios_define_var(int64_t, PyObject *, PyObject *, int, int __pyx_skip_dispatch, struct __pyx_opt_args_5adios_define_var *__pyx_optional_args); /*proto*/
+static int __pyx_f_5adios_define_schema_version(int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_5adios_define_var_mesh(int64_t, PyObject *, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_5adios_define_var_centering(int64_t, PyObject *, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_5adios_define_var_timesteps(PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_5adios_define_var_timescale(PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_5adios_define_var_timeseriesformat(PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_5adios_define_var_hyperslab(PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_5adios_define_mesh_timevarying(PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_5adios_define_mesh_timesteps(PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_5adios_define_mesh_timescale(PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_5adios_define_mesh_timeseriesformat(PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_5adios_define_mesh_uniform(PyObject *, PyObject *, PyObject *, PyObject *, PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_5adios_define_mesh_rectilinear(PyObject *, PyObject *, PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_5adios_define_mesh_structured(PyObject *, PyObject *, PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_5adios_define_mesh_unstructured(PyObject *, PyObject *, PyObject *, PyObject *, PyObject *, PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
static int __pyx_f_5adios_define_attribute(int64_t, PyObject *, PyObject *, int, PyObject *, PyObject *, int __pyx_skip_dispatch); /*proto*/
static int __pyx_f_5adios_define_attribute_byvalue(int64_t, PyObject *, PyObject *, PyObject *, int __pyx_skip_dispatch); /*proto*/
static int __pyx_f_5adios_select_method(int64_t, PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5adios_select_method *__pyx_optional_args); /*proto*/
+static int __pyx_f_5adios_set_transform(int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static void __pyx_f_5adios_set_max_buffer_size(int64_t, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_5adios_set_time_aggregation(int64_t, uint64_t, int64_t, int __pyx_skip_dispatch); /*proto*/
static PyArray_Descr *__pyx_f_5adios_adios2npdtype(ADIOS_DATATYPES, int __pyx_skip_dispatch, struct __pyx_opt_args_5adios_adios2npdtype *__pyx_optional_args); /*proto*/
static PyObject *__pyx_f_5adios_printfile(ADIOS_FILE *); /*proto*/
static PyObject *__pyx_f_5adios_printvar(ADIOS_VARINFO *); /*proto*/
@@ -2005,6 +2025,7 @@ static const char __pyx_k_byte[] = "byte";
static const char __pyx_k_char[] = "char";
static const char __pyx_k_comm[] = "comm";
static const char __pyx_k_copy[] = "copy";
+static const char __pyx_k_data[] = "data";
static const char __pyx_k_dims[] = "dims";
static const char __pyx_k_fd_p[] = "fd_p";
static const char __pyx_k_file[] = "file";
@@ -2081,8 +2102,10 @@ static const char __pyx_k_module[] = "__module__";
static const char __pyx_k_morder[] = "morder";
static const char __pyx_k_mshape[] = "mshape";
static const char __pyx_k_nattrs[] = "nattrs";
+static const char __pyx_k_nspace[] = "nspace";
static const char __pyx_k_nsteps[] = "nsteps";
static const char __pyx_k_offset[] = "offset";
+static const char __pyx_k_origin[] = "origin";
static const char __pyx_k_points[] = "points";
static const char __pyx_k_rstrip[] = "rstrip";
static const char __pyx_k_scalar[] = "scalar";
@@ -2093,6 +2116,7 @@ static const char __pyx_k_uint16[] = "uint16";
static const char __pyx_k_uint32[] = "uint32";
static const char __pyx_k_uint64[] = "uint64";
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_Reading[] = "Reading ... ";
@@ -2106,13 +2130,17 @@ static const char __pyx_k_float16[] = "float16";
static const char __pyx_k_float32[] = "float32";
static const char __pyx_k_float64[] = "float64";
static const char __pyx_k_getitem[] = "__getitem__";
+static const char __pyx_k_groupid[] = "groupid";
static const char __pyx_k_integer[] = "integer";
static const char __pyx_k_is_open[] = "is_open";
+static const char __pyx_k_maximum[] = "maximum";
+static const char __pyx_k_npoints[] = "npoints";
static const char __pyx_k_prepare[] = "__prepare__";
static const char __pyx_k_readvar[] = "_readvar";
static const char __pyx_k_replace[] = "replace";
static const char __pyx_k_reshape[] = "reshape";
static const char __pyx_k_setitem[] = "__setitem__";
+static const char __pyx_k_spacing[] = "spacing";
static const char __pyx_k_unknown[] = "unknown";
static const char __pyx_k_varname[] = "varname";
static const char __pyx_k_version[] = "version";
@@ -2129,6 +2157,7 @@ static const char __pyx_k_group_id[] = "group_id";
static const char __pyx_k_is_noxml[] = "is_noxml";
static const char __pyx_k_itemsize[] = "itemsize";
static const char __pyx_k_iterkeys[] = "iterkeys";
+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_";
@@ -2136,11 +2165,14 @@ static const char __pyx_k_tostring[] = "tostring";
static const char __pyx_k_AdiosFile[] = "=== AdiosFile ===";
static const char __pyx_k_TypeError[] = "TypeError";
static const char __pyx_k_base_path[] = "base_path";
+static const char __pyx_k_cell_type[] = "cell_type";
+static const char __pyx_k_centering[] = "centering";
static const char __pyx_k_complex64[] = "complex64";
static const char __pyx_k_complex_2[] = "complex";
static const char __pyx_k_data_size[] = "data_size";
static const char __pyx_k_enumerate[] = "enumerate";
static const char __pyx_k_file_size[] = "file_size";
+static const char __pyx_k_hyperslab[] = "hyperslab";
static const char __pyx_k_is_static[] = "is_static";
static const char __pyx_k_is_stream[] = "is_stream";
static const char __pyx_k_iteritems[] = "iteritems";
@@ -2149,10 +2181,14 @@ static const char __pyx_k_lock_mode[] = "lock_mode";
static const char __pyx_k_metaclass[] = "__metaclass__";
static const char __pyx_k_printself[] = "printself";
static const char __pyx_k_readvar_2[] = "readvar";
+static const char __pyx_k_timescale[] = "timescale";
+static const char __pyx_k_timesteps[] = "timesteps";
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_ValueError[] = "ValueError";
+static const char __pyx_k_buffersize[] = "buffersize";
static const char __pyx_k_complex128[] = "complex128";
static const char __pyx_k_contiguous[] = "contiguous";
static const char __pyx_k_dimensions[] = "dimensions";
@@ -2166,14 +2202,18 @@ static const char __pyx_k_selections[] = "selections";
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_READ_METHOD[] = "READ_METHOD";
static const char __pyx_k_buffer_size[] = "buffer_size";
static const char __pyx_k_concatenate[] = "concatenate";
+static const char __pyx_k_coordinates[] = "coordinates";
static const char __pyx_k_long_double[] = "long_double";
static const char __pyx_k_method_name[] = "method_name";
static const char __pyx_k_read_points[] = "read_points";
static const char __pyx_k_step_scalar[] = "step_scalar";
+static const char __pyx_k_syncgroupid[] = "syncgroupid";
static const char __pyx_k_timeout_sec[] = "timeout_sec";
+static const char __pyx_k_timevarying[] = "timevarying";
static const char __pyx_k_BP_AGGREGATE[] = "BP_AGGREGATE";
static const char __pyx_k_RuntimeError[] = "RuntimeError";
static const char __pyx_k_current_step[] = "current_step";
@@ -2192,6 +2232,7 @@ static const char __pyx_k_unsigned_long[] = "unsigned_long";
static const char __pyx_k_FancySelection[] = "FancySelection";
static const char __pyx_k_double_complex[] = "double_complex";
static const char __pyx_k_exception_type[] = "exception_type";
+static const char __pyx_k_schema_version[] = "schema_version";
static const char __pyx_k_unsigned_short[] = "unsigned_short";
static const char __pyx_k_Not_a_valid_var[] = "Not a valid var";
static const char __pyx_k_Not_an_open_var[] = "Not an open var";
@@ -2203,24 +2244,26 @@ 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_var_read_line_1265[] = "var.read (line 1265)";
+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_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";
+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_1804[] = "writer.define_var (line 1804)";
+static const char __pyx_k_writer_define_var_line_2020[] = "writer.define_var (line 2020)";
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_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_1782[] = "writer.declare_group (line 1782)";
+static const char __pyx_k_writer_declare_group_line_1983[] = "writer.declare_group (line 1983)";
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, value=%r)";
-static const char __pyx_k_Define_a_variable_associated_wi[] = "\n Define a variable associated with the file.\n\n Args:\n varname (str): variable name.\n ldim (tuple, optional): local dimension (default: tuple())\n gdim (tuple, optional): global dimension (default: tuple())\n offset (tuple, optional): offset (default: tuple())\n\n Example:\n\n Write 'temperature' variable of size of 2x3 array.\n\n >>> fw.defi [...]
+static const char __pyx_k_AdiosVarinfo_name_r_ldim_r_gdim[] = "AdiosVarinfo (name=%r, ldim=%r, gdim=%r, offset=%r, transform=%r, value=%r)";
+static const char __pyx_k_Define_a_variable_associated_wi[] = "\n Define a variable associated with the file.\n\n Args:\n varname (str): variable name\n ldim (tuple, optional): local dimension (default: tuple())\n gdim (tuple, optional): global dimension (default: tuple())\n offset (tuple, optional): offset (default: tuple())\n transform (str): transform name\n\n Example:\n\n Write 'temperature' variable o [...]
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)";
@@ -2337,8 +2380,11 @@ static PyObject *__pyx_n_s_base_path;
static PyObject *__pyx_n_s_bool;
static PyObject *__pyx_n_s_bpls;
static PyObject *__pyx_n_s_buffer_size;
+static PyObject *__pyx_n_s_buffersize;
static PyObject *__pyx_n_s_byte;
static PyObject *__pyx_kp_s_bytes;
+static PyObject *__pyx_n_s_cell_type;
+static PyObject *__pyx_n_s_centering;
static PyObject *__pyx_n_s_char;
static PyObject *__pyx_n_s_close;
static PyObject *__pyx_n_s_comm;
@@ -2349,9 +2395,11 @@ static PyObject *__pyx_n_s_complex_2;
static PyObject *__pyx_n_s_concatenate;
static PyObject *__pyx_n_s_config;
static PyObject *__pyx_n_s_contiguous;
+static PyObject *__pyx_n_s_coordinates;
static PyObject *__pyx_n_s_copy;
static PyObject *__pyx_n_s_count;
static PyObject *__pyx_n_s_current_step;
+static PyObject *__pyx_n_s_data;
static PyObject *__pyx_n_s_data_size;
static PyObject *__pyx_n_s_declare_group;
static PyObject *__pyx_n_s_define;
@@ -2391,7 +2439,9 @@ static PyObject *__pyx_n_s_gname;
static PyObject *__pyx_n_s_group;
static PyObject *__pyx_n_s_group_id;
static PyObject *__pyx_n_s_group_name;
+static PyObject *__pyx_n_s_groupid;
static PyObject *__pyx_n_s_hl;
+static PyObject *__pyx_n_s_hyperslab;
static PyObject *__pyx_n_s_import;
static PyObject *__pyx_n_s_index;
static PyObject *__pyx_n_s_init;
@@ -2419,6 +2469,8 @@ static PyObject *__pyx_n_s_lock_mode;
static PyObject *__pyx_n_s_long;
static PyObject *__pyx_n_s_long_double;
static PyObject *__pyx_n_s_main;
+static PyObject *__pyx_n_s_maximum;
+static PyObject *__pyx_n_s_meshname;
static PyObject *__pyx_n_s_metaclass;
static PyObject *__pyx_n_s_method;
static PyObject *__pyx_n_s_method_name;
@@ -2435,11 +2487,14 @@ static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou;
static PyObject *__pyx_n_s_ndim;
static PyObject *__pyx_n_s_normalize_key;
static PyObject *__pyx_n_s_np;
+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_n_s_nvars;
static PyObject *__pyx_n_s_offset;
static PyObject *__pyx_n_s_order;
+static PyObject *__pyx_n_s_origin;
static PyObject *__pyx_n_s_os;
static PyObject *__pyx_n_s_parameters;
static PyObject *__pyx_n_s_path;
@@ -2465,13 +2520,16 @@ static PyObject *__pyx_n_s_replace;
static PyObject *__pyx_n_s_reshape;
static PyObject *__pyx_n_s_rstrip;
static PyObject *__pyx_n_s_scalar;
+static PyObject *__pyx_n_s_schema_version;
static PyObject *__pyx_n_s_sel;
static PyObject *__pyx_n_s_select;
static PyObject *__pyx_n_s_selections;
+static PyObject *__pyx_n_s_set_time_aggregation;
static PyObject *__pyx_n_s_setitem;
static PyObject *__pyx_n_s_shape;
static PyObject *__pyx_n_s_short;
static PyObject *__pyx_n_s_size;
+static PyObject *__pyx_n_s_spacing;
static PyObject *__pyx_n_s_split;
static PyObject *__pyx_n_s_start;
static PyObject *__pyx_n_s_startswith;
@@ -2482,13 +2540,20 @@ static PyObject *__pyx_n_s_string_2;
static PyObject *__pyx_n_s_string_array;
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_test;
static PyObject *__pyx_n_s_time_index;
static PyObject *__pyx_n_s_time_steps;
static PyObject *__pyx_n_s_timeout_sec;
+static PyObject *__pyx_n_s_timescale;
+static PyObject *__pyx_n_s_timeseries;
+static PyObject *__pyx_n_s_timesteps;
+static PyObject *__pyx_n_s_timevarying;
static PyObject *__pyx_n_s_tostring;
static PyObject *__pyx_n_s_traceback;
+static PyObject *__pyx_n_s_transform;
+static PyObject *__pyx_n_s_transform_type_str;
static PyObject *__pyx_n_s_type;
static PyObject *__pyx_n_s_uint16;
static PyObject *__pyx_n_s_uint32;
@@ -2505,8 +2570,9 @@ static PyObject *__pyx_n_s_val;
static PyObject *__pyx_n_s_value;
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_1265;
+static PyObject *__pyx_kp_u_var_read_line_1457;
static PyObject *__pyx_n_s_varid;
static PyObject *__pyx_n_s_varname;
static PyObject *__pyx_n_s_vars;
@@ -2515,8 +2581,8 @@ 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_1782;
-static PyObject *__pyx_kp_u_writer_define_var_line_1804;
+static PyObject *__pyx_kp_u_writer_declare_group_line_1983;
+static PyObject *__pyx_kp_u_writer_define_var_line_2020;
static PyObject *__pyx_n_s_xrange;
static PyObject *__pyx_n_s_zeros;
static PyObject *__pyx_n_s_zip;
@@ -2540,14 +2606,32 @@ static PyObject *__pyx_pf_5adios_32init_noxml(CYTHON_UNUSED PyObject *__pyx_self
static PyObject *__pyx_pf_5adios_34allocate_buffer(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_when, uint64_t __pyx_v_buffer_size); /* proto */
static PyObject *__pyx_pf_5adios_36declare_group(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_name, PyObject *__pyx_v_time_index, int __pyx_v_stats); /* proto */
static PyObject *__pyx_pf_5adios_38define_var(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group_id, PyObject *__pyx_v_name, PyObject *__pyx_v_path, int __pyx_v_atype, PyObject *__pyx_v_dimensions, PyObject *__pyx_v_global_dimensions, PyObject *__pyx_v_local_offsets); /* proto */
-static PyObject *__pyx_pf_5adios_40define_attribute(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group, PyObject *__pyx_v_name, PyObject *__pyx_v_path, int __pyx_v_atype, PyObject *__pyx_v_value, PyObject *__pyx_v_var); /* proto */
-static PyObject *__pyx_pf_5adios_42define_attribute_byvalue(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group, PyObject *__pyx_v_name, PyObject *__pyx_v_path, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5adios_44select_method(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group, PyObject *__pyx_v_method, PyObject *__pyx_v_parameters, PyObject *__pyx_v_base_path); /* proto */
-static PyObject *__pyx_pf_5adios_46adios2npdtype(CYTHON_UNUSED PyObject *__pyx_self, ADIOS_DATATYPES __pyx_v_t, int __pyx_v_strlen); /* proto */
-static PyObject *__pyx_pf_5adios_48np2adiostype(CYTHON_UNUSED PyObject *__pyx_self, PyArray_Descr *__pyx_v_nptype); /* proto */
-static PyObject *__pyx_pf_5adios_50adiostype2string(CYTHON_UNUSED PyObject *__pyx_self, ADIOS_DATATYPES __pyx_v_type); /* proto */
-static PyObject *__pyx_pf_5adios_52read_init(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method_name, MPI_Comm __pyx_v_comm, PyObject *__pyx_v_parameters); /* proto */
-static PyObject *__pyx_pf_5adios_54read_finalize(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method_name); /* proto */
+static PyObject *__pyx_pf_5adios_40define_schema_version(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group_id, PyObject *__pyx_v_schema_version); /* proto */
+static PyObject *__pyx_pf_5adios_42define_var_mesh(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group_id, PyObject *__pyx_v_varname, PyObject *__pyx_v_meshname); /* proto */
+static PyObject *__pyx_pf_5adios_44define_var_centering(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group_id, PyObject *__pyx_v_varname, PyObject *__pyx_v_centering); /* proto */
+static PyObject *__pyx_pf_5adios_46define_var_timesteps(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_timesteps, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_5adios_48define_var_timescale(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_timescale, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_5adios_50define_var_timeseriesformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_timeseries, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_5adios_52define_var_hyperslab(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_hyperslab, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_5adios_54define_mesh_timevarying(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_timevarying, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_5adios_56define_mesh_timesteps(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_timesteps, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_5adios_58define_mesh_timescale(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_timescale, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_5adios_60define_mesh_timeseriesformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_timeseries, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_5adios_62define_mesh_uniform(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_dimensions, PyObject *__pyx_v_origin, PyObject *__pyx_v_spacing, PyObject *__pyx_v_maximum, PyObject *__pyx_v_nspace, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_5adios_64define_mesh_rectilinear(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_dimensions, PyObject *__pyx_v_coordinates, PyObject *__pyx_v_nspace, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_5adios_66define_mesh_structured(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_dimensions, PyObject *__pyx_v_points, PyObject *__pyx_v_nspace, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_5adios_68define_mesh_unstructured(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_points, PyObject *__pyx_v_data, PyObject *__pyx_v_count, PyObject *__pyx_v_cell_type, PyObject *__pyx_v_npoints, PyObject *__pyx_v_nspace, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_5adios_70define_attribute(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group, PyObject *__pyx_v_name, PyObject *__pyx_v_path, int __pyx_v_atype, PyObject *__pyx_v_value, PyObject *__pyx_v_var); /* proto */
+static PyObject *__pyx_pf_5adios_72define_attribute_byvalue(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group, PyObject *__pyx_v_name, PyObject *__pyx_v_path, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_5adios_74select_method(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group, PyObject *__pyx_v_method, PyObject *__pyx_v_parameters, PyObject *__pyx_v_base_path); /* proto */
+static PyObject *__pyx_pf_5adios_76set_transform(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_var_id, PyObject *__pyx_v_transform_type_str); /* proto */
+static PyObject *__pyx_pf_5adios_78set_max_buffer_size(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_max_buffer_size_MB); /* proto */
+static PyObject *__pyx_pf_5adios_80set_time_aggregation(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_groupid, uint64_t __pyx_v_buffersize, int64_t __pyx_v_syncgroupid); /* proto */
+static PyObject *__pyx_pf_5adios_82adios2npdtype(CYTHON_UNUSED PyObject *__pyx_self, ADIOS_DATATYPES __pyx_v_t, int __pyx_v_strlen); /* proto */
+static PyObject *__pyx_pf_5adios_84np2adiostype(CYTHON_UNUSED PyObject *__pyx_self, PyArray_Descr *__pyx_v_nptype); /* proto */
+static PyObject *__pyx_pf_5adios_86adiostype2string(CYTHON_UNUSED PyObject *__pyx_self, ADIOS_DATATYPES __pyx_v_type); /* proto */
+static PyObject *__pyx_pf_5adios_88read_init(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method_name, MPI_Comm __pyx_v_comm, PyObject *__pyx_v_parameters); /* proto */
+static PyObject *__pyx_pf_5adios_90read_finalize(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method_name); /* proto */
static PyObject *__pyx_pf_5adios_8softdict___getitem__(struct __pyx_obj_5adios_softdict *__pyx_v_self, PyObject *__pyx_v_varname); /* proto */
static PyObject *__pyx_pf_5adios_4file_4name___get__(struct __pyx_obj_5adios_file *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_5adios_4file_5nvars___get__(struct __pyx_obj_5adios_file *__pyx_v_self); /* proto */
@@ -2645,17 +2729,19 @@ static PyObject *__pyx_pf_5adios_6writer_8is_noxml___get__(struct __pyx_obj_5adi
static PyObject *__pyx_pf_5adios_6writer_4mode___get__(struct __pyx_obj_5adios_writer *__pyx_v_self); /* proto */
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 PyObject *__pyx_pf_5adios_6writer_4define_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); /* proto */
-static PyObject *__pyx_pf_5adios_6writer_6define_attr(struct __pyx_obj_5adios_writer *__pyx_v_self, PyObject *__pyx_v_attrname); /* proto */
-static PyObject *__pyx_pf_5adios_6writer_8define_dynamic_attr(struct __pyx_obj_5adios_writer *__pyx_v_self, PyObject *__pyx_v_attrname, PyObject *__pyx_v_varname, PyObject *__pyx_v_dtype); /* proto */
-static int __pyx_pf_5adios_6writer_10__setitem__(struct __pyx_obj_5adios_writer *__pyx_v_self, PyObject *__pyx_v_name, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5adios_6writer_12__getitem__(struct __pyx_obj_5adios_writer *__pyx_v_self, PyObject *__pyx_v_name); /* proto */
-static PyObject *__pyx_pf_5adios_6writer_14close(struct __pyx_obj_5adios_writer *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5adios_6writer_16__repr__(struct __pyx_obj_5adios_writer *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5adios_6writer_18__enter__(struct __pyx_obj_5adios_writer *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5adios_6writer_20__exit__(struct __pyx_obj_5adios_writer *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_exception_type, CYTHON_UNUSED PyObject *__pyx_v_exception_value, CYTHON_UNUSED PyObject *__pyx_v_traceback); /* 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 */
+static PyObject *__pyx_pf_5adios_6writer_10define_dynamic_attr(struct __pyx_obj_5adios_writer *__pyx_v_self, PyObject *__pyx_v_attrname, PyObject *__pyx_v_varname, PyObject *__pyx_v_dtype); /* proto */
+static int __pyx_pf_5adios_6writer_12__setitem__(struct __pyx_obj_5adios_writer *__pyx_v_self, PyObject *__pyx_v_name, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_5adios_6writer_14__getitem__(struct __pyx_obj_5adios_writer *__pyx_v_self, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_5adios_6writer_16close(struct __pyx_obj_5adios_writer *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5adios_6writer_18__repr__(struct __pyx_obj_5adios_writer *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5adios_6writer_20__enter__(struct __pyx_obj_5adios_writer *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5adios_6writer_22__exit__(struct __pyx_obj_5adios_writer *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_exception_type, CYTHON_UNUSED PyObject *__pyx_v_exception_value, CYTHON_UNUSED PyObject *__pyx_v_traceback); /* proto */
static PyObject *__pyx_pf_5adios_8attrinfo_4name___get__(struct __pyx_obj_5adios_attrinfo *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_5adios_8attrinfo_9is_static___get__(struct __pyx_obj_5adios_attrinfo *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_5adios_8attrinfo_5dtype___get__(struct __pyx_obj_5adios_attrinfo *__pyx_v_self); /* proto */
@@ -2664,7 +2750,9 @@ static int __pyx_pf_5adios_8attrinfo_5value_2__set__(struct __pyx_obj_5adios_att
static int __pyx_pf_5adios_8attrinfo___init__(struct __pyx_obj_5adios_attrinfo *__pyx_v_self, PyObject *__pyx_v_name, PyObject *__pyx_v_value, PyObject *__pyx_v_dtype, int __pyx_v_is_static); /* proto */
static PyObject *__pyx_pf_5adios_8attrinfo_2define(struct __pyx_obj_5adios_attrinfo *__pyx_v_self, int64_t __pyx_v_gid); /* proto */
static PyObject *__pyx_pf_5adios_8attrinfo_4__repr__(struct __pyx_obj_5adios_attrinfo *__pyx_v_self); /* proto */
-static int __pyx_pf_5adios_7varinfo___init__(struct __pyx_obj_5adios_varinfo *__pyx_v_self, PyObject *__pyx_v_name, PyObject *__pyx_v_ldim, PyObject *__pyx_v_gdim, PyObject *__pyx_v_offset, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5adios_7varinfo_9transform___get__(struct __pyx_obj_5adios_varinfo *__pyx_v_self); /* proto */
+static int __pyx_pf_5adios_7varinfo_9transform_2__set__(struct __pyx_obj_5adios_varinfo *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_5adios_7varinfo___init__(struct __pyx_obj_5adios_varinfo *__pyx_v_self, PyObject *__pyx_v_name, PyObject *__pyx_v_ldim, PyObject *__pyx_v_gdim, PyObject *__pyx_v_offset, PyObject *__pyx_v_value, PyObject *__pyx_v_transform); /* proto */
static PyObject *__pyx_pf_5adios_7varinfo_2define(struct __pyx_obj_5adios_varinfo *__pyx_v_self, int64_t __pyx_v_gid); /* proto */
static PyObject *__pyx_pf_5adios_7varinfo_4bytes(struct __pyx_obj_5adios_varinfo *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_5adios_7varinfo_6write(struct __pyx_obj_5adios_varinfo *__pyx_v_self, int64_t __pyx_v_fd); /* proto */
@@ -2681,8 +2769,8 @@ static int __pyx_pf_5adios_7varinfo_6offset_4__del__(struct __pyx_obj_5adios_var
static PyObject *__pyx_pf_5adios_7varinfo_5value___get__(struct __pyx_obj_5adios_varinfo *__pyx_v_self); /* proto */
static int __pyx_pf_5adios_7varinfo_5value_2__set__(struct __pyx_obj_5adios_varinfo *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
static int __pyx_pf_5adios_7varinfo_5value_4__del__(struct __pyx_obj_5adios_varinfo *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5adios_56readvar(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fname, PyObject *__pyx_v_varname); /* proto */
-static PyObject *__pyx_pf_5adios_58bpls(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fname); /* proto */
+static PyObject *__pyx_pf_5adios_92readvar(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fname, PyObject *__pyx_v_varname); /* proto */
+static PyObject *__pyx_pf_5adios_94bpls(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fname); /* proto */
static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
static PyObject *__pyx_tp_new_5adios_softdict(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
@@ -2717,13 +2805,14 @@ static PyObject *__pyx_int_neg_1;
static MPI_Comm __pyx_k__7;
static MPI_Comm __pyx_k__8;
static MPI_Comm __pyx_k__9;
-static MPI_Comm __pyx_k__11;
-static MPI_Comm __pyx_k__15;
-static ADIOS_LOCKMODE __pyx_k__16;
-static MPI_Comm __pyx_k__53;
-static PyObject *__pyx_k__54;
+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 PyObject *__pyx_k__57;
static PyObject *__pyx_k__59;
static PyObject *__pyx_k__60;
static PyObject *__pyx_k__61;
@@ -2732,46 +2821,45 @@ static PyObject *__pyx_slice__4;
static PyObject *__pyx_slice__5;
static PyObject *__pyx_tuple__2;
static PyObject *__pyx_tuple__6;
-static PyObject *__pyx_slice__14;
-static PyObject *__pyx_slice__21;
-static PyObject *__pyx_slice__23;
-static PyObject *__pyx_slice__26;
-static PyObject *__pyx_slice__31;
-static PyObject *__pyx_slice__35;
+static PyObject *__pyx_slice__15;
+static PyObject *__pyx_slice__22;
+static PyObject *__pyx_slice__24;
+static PyObject *__pyx_slice__27;
+static PyObject *__pyx_slice__32;
static PyObject *__pyx_slice__36;
static PyObject *__pyx_slice__37;
static PyObject *__pyx_slice__38;
static PyObject *__pyx_slice__39;
static PyObject *__pyx_slice__40;
static PyObject *__pyx_slice__41;
-static PyObject *__pyx_slice__46;
-static PyObject *__pyx_slice__48;
-static PyObject *__pyx_slice__51;
-static PyObject *__pyx_tuple__12;
+static PyObject *__pyx_slice__42;
+static PyObject *__pyx_slice__47;
+static PyObject *__pyx_slice__49;
+static PyObject *__pyx_slice__52;
static PyObject *__pyx_tuple__13;
-static PyObject *__pyx_tuple__17;
+static PyObject *__pyx_tuple__14;
static PyObject *__pyx_tuple__18;
static PyObject *__pyx_tuple__19;
static PyObject *__pyx_tuple__20;
-static PyObject *__pyx_tuple__22;
-static PyObject *__pyx_tuple__24;
+static PyObject *__pyx_tuple__21;
+static PyObject *__pyx_tuple__23;
static PyObject *__pyx_tuple__25;
-static PyObject *__pyx_tuple__27;
+static PyObject *__pyx_tuple__26;
static PyObject *__pyx_tuple__28;
static PyObject *__pyx_tuple__29;
static PyObject *__pyx_tuple__30;
-static PyObject *__pyx_tuple__32;
+static PyObject *__pyx_tuple__31;
static PyObject *__pyx_tuple__33;
static PyObject *__pyx_tuple__34;
-static PyObject *__pyx_tuple__42;
+static PyObject *__pyx_tuple__35;
static PyObject *__pyx_tuple__43;
static PyObject *__pyx_tuple__44;
static PyObject *__pyx_tuple__45;
-static PyObject *__pyx_tuple__47;
-static PyObject *__pyx_tuple__49;
+static PyObject *__pyx_tuple__46;
+static PyObject *__pyx_tuple__48;
static PyObject *__pyx_tuple__50;
-static PyObject *__pyx_tuple__52;
-static PyObject *__pyx_tuple__57;
+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;
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return __pyx_r;
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__pyx_r = adios_close(__pyx_v_fd_p);
goto __pyx_L0;
- /* "adios.pyx":438
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- __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 441, __pyx_L1_error)
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+ /* "adios.pyx":535
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goto __pyx_L0;
- /* "adios.pyx":448
+ /* "adios.pyx":532
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return __pyx_r;
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goto __pyx_L4_argument_unpacking_done;
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- __Pyx_RaiseArgtupleInvalid("allocate_buffer", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 453, __pyx_L3_error)
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return __pyx_r;
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PyObject *__pyx_v_time_index = ((PyObject*)__pyx_kp_s__10);
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-static char __pyx_doc_5adios_36declare_group[] = "declare_group(str name, str time_index='', int stats=1) -> int64_t";
+static char __pyx_doc_5adios_36declare_group[] = "declare_group(str name, str time_index='', int stats=adios_stat_default) -> int64_t";
static PyObject *__pyx_pw_5adios_37declare_group(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_name = 0;
PyObject *__pyx_v_time_index = 0;
@@ -6351,7 +6439,7 @@ static PyObject *__pyx_pw_5adios_37declare_group(PyObject *__pyx_self, PyObject
}
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@@ -6365,21 +6453,21 @@ static PyObject *__pyx_pw_5adios_37declare_group(PyObject *__pyx_self, PyObject
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__pyx_v_time_index = ((PyObject*)values[1]);
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- __Pyx_RaiseArgtupleInvalid("declare_group", 0, 1, 3, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 458, __pyx_L3_error)
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/* function exit code */
@@ -6403,7 +6491,7 @@ static PyObject *__pyx_pf_5adios_36declare_group(CYTHON_UNUSED PyObject *__pyx_s
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__pyx_t_2.stats = __pyx_v_stats;
__pyx_t_1 = __pyx_f_5adios_declare_group(__pyx_v_name, 0, &__pyx_t_2);
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return __pyx_r;
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-/* "adios.pyx":468
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*
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* str name,
* str path,
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PyObject *__pyx_v_local_offsets = ((PyObject*)__pyx_kp_s__10);
- int __pyx_r;
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__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
char *__pyx_t_2;
@@ -6458,62 +6546,62 @@ static int __pyx_f_5adios_define_var(int64_t __pyx_v_group_id, PyObject *__pyx_v
}
}
- /* "adios.pyx":476
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* s2b(path),
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- /* "adios.pyx":477
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+ * cpdef int64_t define_var(int64_t group_id, # <<<<<<<<<<<<<<
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@@ -6552,7 +6640,7 @@ static int __pyx_f_5adios_define_var(int64_t __pyx_v_group_id, PyObject *__pyx_v
/* Python wrapper */
static PyObject *__pyx_pw_5adios_39define_var(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
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+static char __pyx_doc_5adios_38define_var[] = "define_var(int64_t group_id, str name, str path, int atype, str dimensions='', str global_dimensions='', str local_offsets='') -> int64_t";
static PyObject *__pyx_pw_5adios_39define_var(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
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else {
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__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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@@ -7238,7 +9978,7 @@ static int __pyx_f_5adios_define_attribute_byvalue(int64_t __pyx_v_group, PyObje
goto __pyx_L8;
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@@ -7248,53 +9988,53 @@ static int __pyx_f_5adios_define_attribute_byvalue(int64_t __pyx_v_group, PyObje
/*else*/ {
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__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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goto __pyx_L5;
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}
}
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__Pyx_GIVEREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1);
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PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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__Pyx_GIVEREF(__pyx_n_s_nsteps);
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__Pyx_GIVEREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1);
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__Pyx_GIVEREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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return __pyx_r;
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+/* "adios.pyx":803
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goto __pyx_L3;
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if (__pyx_t_1) {
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goto __pyx_L3;
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goto __pyx_L3;
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if (__pyx_t_1) {
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goto __pyx_L3;
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if (__pyx_t_1) {
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goto __pyx_L3;
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if (__pyx_t_1) {
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}
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+static PyObject *__pyx_pw_5adios_89read_init(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_method_name = 0;
MPI_Comm __pyx_v_comm;
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} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
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}
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} else {
- __pyx_v_comm = __pyx_k__11;
+ __pyx_v_comm = __pyx_k__12;
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goto __pyx_L4_argument_unpacking_done;
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- __Pyx_RaiseArgtupleInvalid("read_init", 0, 0, 3, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 683, __pyx_L3_error)
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- __pyx_r = __pyx_pf_5adios_52read_init(__pyx_self, __pyx_v_method_name, __pyx_v_comm, __pyx_v_parameters);
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+ __pyx_r = __pyx_pf_5adios_88read_init(__pyx_self, __pyx_v_method_name, __pyx_v_comm, __pyx_v_parameters);
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goto __pyx_L0;
@@ -10516,7 +13601,7 @@ static PyObject *__pyx_pw_5adios_53read_init(PyObject *__pyx_self, PyObject *__p
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+static PyObject *__pyx_pf_5adios_88read_init(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method_name, MPI_Comm __pyx_v_comm, PyObject *__pyx_v_parameters) {
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- __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 683, __pyx_L1_error)
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__Pyx_GOTREF(__pyx_t_1);
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return __pyx_r;
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*
* def __enter__(self): # <<<<<<<<<<<<<<
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*/
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__Pyx_RefNannySetupContext("__enter__", 0);
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*
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "adios.pyx":1130
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*/
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+ /* "adios.pyx":1327
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__Pyx_DECREF(__pyx_v_self->name);
__pyx_v_self->name = __pyx_v_name;
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__pyx_v_self->varid = __pyx_t_3;
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__pyx_v_self->ndim = __pyx_t_3;
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__pyx_v_self->dims = ((PyObject*)__pyx_t_5);
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__pyx_v_self->nsteps = __pyx_t_3;
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goto __pyx_L5;
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*/
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+ /* "adios.pyx":1408
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@@ -18759,18 +21844,18 @@ static PyObject *__pyx_f_5adios_3var_read_points(struct __pyx_obj_5adios_var *__
*/
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- /* "adios.pyx":1218
+ /* "adios.pyx":1410
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- /* "adios.pyx":1219
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*/
adios_perform_reads(__pyx_v_self->file->fp, 1);
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*/
adios_selection_delete(__pyx_v_sel);
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goto __pyx_L0;
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*
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*/
__pyx_v_sel = adios_selection_writeblock(__pyx_v_rank);
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+ /* "adios.pyx":1452
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*
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*/
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*/
adios_selection_delete(__pyx_v_sel);
- /* "adios.pyx":1263
+ /* "adios.pyx":1455
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__pyx_t_4 = 0;
goto __pyx_L0;
- /* "adios.pyx":1375
+ /* "adios.pyx":1567
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*/
}
- /* "adios.pyx":1378
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goto __pyx_L0;
}
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values[2] = ((PyObject*)__pyx_empty_tuple);
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return __pyx_r;
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return __pyx_r;
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return __pyx_r;
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- /* "adios.pyx":1762
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PyObject *__pyx_v_offset = 0;
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- PyObject* values[5] = {0,0,0,0,0};
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values[3] = __pyx_k__61;
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if (value) { values[4] = value; kw_args--; }
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__pyx_t_6 = 0;
goto __pyx_L0;
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- * str(offset_).replace(' ', '').strip('(,)'))
+ /* "adios.pyx":2262
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return __pyx_r;
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}
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return __pyx_r;
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+ * return ("AdiosVarinfo (name=%r, ldim=%r, gdim=%r, offset=%r, transform=%r, value=%r)") % \
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+ * return ("AdiosVarinfo (name=%r, ldim=%r, gdim=%r, offset=%r, transform=%r, value=%r)") % \
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__Pyx_GIVEREF(__pyx_v_self->offset);
PyTuple_SET_ITEM(__pyx_t_1, 3, __pyx_v_self->offset);
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+ * return ("AdiosVarinfo (name=%r, ldim=%r, gdim=%r, offset=%r, transform=%r, value=%r)") % \
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return __pyx_r;
}
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return __pyx_r;
}
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return __pyx_r;
}
-/* "adios.pyx":1979
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* cdef public gdim
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* cdef public value
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*/
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return __pyx_r;
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return __pyx_r;
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-static PyObject *__pyx_pw_5adios_57readvar(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
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PyObject *__pyx_v_fname = 0;
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case 1:
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- if (unlikely(__pyx_t_8 == -1)) __PYX_ERR(0, 2077, __pyx_L1_error)
+ if (unlikely(__pyx_t_8 == -1)) __PYX_ERR(0, 2319, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_7);
__Pyx_XDECREF_SET(__pyx_v_k, __pyx_t_7);
__pyx_t_7 = 0;
- if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_v_k))) __PYX_ERR(0, 2077, __pyx_L1_error)
+ if (unlikely(__Pyx_ListComp_Append(__pyx_t_1, (PyObject*)__pyx_v_k))) __PYX_ERR(0, 2319, __pyx_L1_error)
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyList_AsTuple(((PyObject*)__pyx_t_1)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2077, __pyx_L1_error)
+ __pyx_t_2 = PyList_AsTuple(((PyObject*)__pyx_t_1)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2319, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_attrs, __pyx_t_2) < 0) __PYX_ERR(0, 2074, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_attrs, __pyx_t_2) < 0) __PYX_ERR(0, 2316, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "adios.pyx":2078
+ /* "adios.pyx":2320
* 'vars': tuple([ k for k in f.vars.iterkeys() ]),
* 'attrs': tuple([ k for k in f.attrs.iterkeys() ]),
* 'time_steps': (f.current_step, f.last_step), # <<<<<<<<<<<<<<
* 'file_size': f.file_size}
*/
- __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_f->current_step); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2078, __pyx_L1_error)
+ __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_f->current_step); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2320, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_f->last_step); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2078, __pyx_L1_error)
+ __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_f->last_step); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2320, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 2078, __pyx_L1_error)
+ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 2320, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_7);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2);
@@ -32373,23 +36265,23 @@ static PyObject *__pyx_pf_5adios_58bpls(CYTHON_UNUSED PyObject *__pyx_self, PyOb
PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_1);
__pyx_t_2 = 0;
__pyx_t_1 = 0;
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_time_steps, __pyx_t_7) < 0) __PYX_ERR(0, 2074, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_time_steps, __pyx_t_7) < 0) __PYX_ERR(0, 2316, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- /* "adios.pyx":2079
+ /* "adios.pyx":2321
* 'attrs': tuple([ k for k in f.attrs.iterkeys() ]),
* 'time_steps': (f.current_step, f.last_step),
* 'file_size': f.file_size} # <<<<<<<<<<<<<<
*/
- __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_f->file_size); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 2079, __pyx_L1_error)
+ __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_f->file_size); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 2321, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_7);
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_file_size, __pyx_t_7) < 0) __PYX_ERR(0, 2074, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_file_size, __pyx_t_7) < 0) __PYX_ERR(0, 2316, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_r = __pyx_t_3;
__pyx_t_3 = 0;
goto __pyx_L0;
- /* "adios.pyx":2064
+ /* "adios.pyx":2306
* return v.read(from_steps=0, nsteps=v.nsteps)
*
* def bpls(fname): # <<<<<<<<<<<<<<
@@ -35932,7 +39824,7 @@ static PyObject *__pyx_sq_item_5adios_writer(PyObject *o, Py_ssize_t i) {
static int __pyx_mp_ass_subscript_5adios_writer(PyObject *o, PyObject *i, PyObject *v) {
if (v) {
- return __pyx_pw_5adios_6writer_11__setitem__(o, i, v);
+ return __pyx_pw_5adios_6writer_13__setitem__(o, i, v);
}
else {
PyErr_Format(PyExc_NotImplementedError,
@@ -35965,14 +39857,19 @@ static PyObject *__pyx_getprop_5adios_6writer_attrs(PyObject *o, CYTHON_UNUSED v
return __pyx_pw_5adios_6writer_5attrs_1__get__(o);
}
+static PyObject *__pyx_getprop_5adios_6writer_timeaggregation_buffersize(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5adios_6writer_26timeaggregation_buffersize_1__get__(o);
+}
+
static PyMethodDef __pyx_methods_5adios_writer[] = {
{"declare_group", (PyCFunction)__pyx_pw_5adios_6writer_3declare_group, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_6writer_2declare_group},
- {"define_var", (PyCFunction)__pyx_pw_5adios_6writer_5define_var, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_6writer_4define_var},
- {"define_attr", (PyCFunction)__pyx_pw_5adios_6writer_7define_attr, METH_O, __pyx_doc_5adios_6writer_6define_attr},
- {"define_dynamic_attr", (PyCFunction)__pyx_pw_5adios_6writer_9define_dynamic_attr, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_6writer_8define_dynamic_attr},
- {"close", (PyCFunction)__pyx_pw_5adios_6writer_15close, METH_NOARGS, __pyx_doc_5adios_6writer_14close},
- {"__enter__", (PyCFunction)__pyx_pw_5adios_6writer_19__enter__, METH_NOARGS, __pyx_doc_5adios_6writer_18__enter__},
- {"__exit__", (PyCFunction)__pyx_pw_5adios_6writer_21__exit__, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_6writer_20__exit__},
+ {"set_time_aggregation", (PyCFunction)__pyx_pw_5adios_6writer_5set_time_aggregation, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_6writer_4set_time_aggregation},
+ {"define_var", (PyCFunction)__pyx_pw_5adios_6writer_7define_var, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_6writer_6define_var},
+ {"define_attr", (PyCFunction)__pyx_pw_5adios_6writer_9define_attr, METH_O, __pyx_doc_5adios_6writer_8define_attr},
+ {"define_dynamic_attr", (PyCFunction)__pyx_pw_5adios_6writer_11define_dynamic_attr, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_6writer_10define_dynamic_attr},
+ {"close", (PyCFunction)__pyx_pw_5adios_6writer_17close, METH_NOARGS, __pyx_doc_5adios_6writer_16close},
+ {"__enter__", (PyCFunction)__pyx_pw_5adios_6writer_21__enter__, METH_NOARGS, __pyx_doc_5adios_6writer_20__enter__},
+ {"__exit__", (PyCFunction)__pyx_pw_5adios_6writer_23__exit__, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_6writer_22__exit__},
{0, 0, 0, 0}
};
@@ -35983,6 +39880,7 @@ static struct PyGetSetDef __pyx_getsets_5adios_writer[] = {
{(char *)"mode", __pyx_getprop_5adios_6writer_mode, 0, (char *)" Writing mode: overwrite or append. ", 0},
{(char *)"vars", __pyx_getprop_5adios_6writer_vars, 0, (char *)" Dictionary of variables to write. ", 0},
{(char *)"attrs", __pyx_getprop_5adios_6writer_attrs, 0, (char *)" Dictionary of attributes to write. ", 0},
+ {(char *)"timeaggregation_buffersize", __pyx_getprop_5adios_6writer_timeaggregation_buffersize, 0, (char *)" Get time-aggregation buffersize. ", 0},
{0, 0, 0, 0, 0}
};
@@ -36001,7 +39899,7 @@ static PySequenceMethods __pyx_tp_as_sequence_writer = {
static PyMappingMethods __pyx_tp_as_mapping_writer = {
0, /*mp_length*/
- __pyx_pw_5adios_6writer_13__getitem__, /*mp_subscript*/
+ __pyx_pw_5adios_6writer_15__getitem__, /*mp_subscript*/
__pyx_mp_ass_subscript_5adios_writer, /*mp_ass_subscript*/
};
@@ -36020,7 +39918,7 @@ static PyTypeObject __pyx_type_5adios_writer = {
#if PY_MAJOR_VERSION >= 3
0, /*tp_as_async*/
#endif
- __pyx_pw_5adios_6writer_17__repr__, /*tp_repr*/
+ __pyx_pw_5adios_6writer_19__repr__, /*tp_repr*/
0, /*tp_as_number*/
&__pyx_tp_as_sequence_writer, /*tp_as_sequence*/
&__pyx_tp_as_mapping_writer, /*tp_as_mapping*/
@@ -36229,6 +40127,7 @@ static PyObject *__pyx_tp_new_5adios_varinfo(PyTypeObject *t, CYTHON_UNUSED PyOb
p->gdim = Py_None; Py_INCREF(Py_None);
p->offset = Py_None; Py_INCREF(Py_None);
p->value = Py_None; Py_INCREF(Py_None);
+ p->transform = ((PyObject*)Py_None); Py_INCREF(Py_None);
return o;
}
@@ -36245,6 +40144,7 @@ static void __pyx_tp_dealloc_5adios_varinfo(PyObject *o) {
Py_CLEAR(p->gdim);
Py_CLEAR(p->offset);
Py_CLEAR(p->value);
+ Py_CLEAR(p->transform);
(*Py_TYPE(o)->tp_free)(o);
}
@@ -36284,6 +40184,20 @@ static int __pyx_tp_clear_5adios_varinfo(PyObject *o) {
return 0;
}
+static PyObject *__pyx_getprop_5adios_7varinfo_transform(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5adios_7varinfo_9transform_1__get__(o);
+}
+
+static int __pyx_setprop_5adios_7varinfo_transform(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+ if (v) {
+ return __pyx_pw_5adios_7varinfo_9transform_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
+
static PyObject *__pyx_getprop_5adios_7varinfo_ldim(PyObject *o, CYTHON_UNUSED void *x) {
return __pyx_pw_5adios_7varinfo_4ldim_1__get__(o);
}
@@ -36344,6 +40258,7 @@ static PyMethodDef __pyx_methods_5adios_varinfo[] = {
};
static struct PyGetSetDef __pyx_getsets_5adios_varinfo[] = {
+ {(char *)"transform", __pyx_getprop_5adios_7varinfo_transform, __pyx_setprop_5adios_7varinfo_transform, (char *)" Transform method ", 0},
{(char *)"ldim", __pyx_getprop_5adios_7varinfo_ldim, __pyx_setprop_5adios_7varinfo_ldim, (char *)"ldim: object", 0},
{(char *)"gdim", __pyx_getprop_5adios_7varinfo_gdim, __pyx_setprop_5adios_7varinfo_gdim, (char *)"gdim: object", 0},
{(char *)"offset", __pyx_getprop_5adios_7varinfo_offset, __pyx_setprop_5adios_7varinfo_offset, (char *)"offset: object", 0},
@@ -36377,7 +40292,7 @@ static PyTypeObject __pyx_type_5adios_varinfo = {
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*/
- "varinfo(str name, ldim=<\077\077?>, gdim=<\077\077?>, offset=<\077\077?>, value=None)", /*tp_doc*/
+ "varinfo(str name, ldim=<\077\077?>, gdim=<\077\077?>, offset=<\077\077?>, value=None, transform=None)", /*tp_doc*/
__pyx_tp_traverse_5adios_varinfo, /*tp_traverse*/
__pyx_tp_clear_5adios_varinfo, /*tp_clear*/
0, /*tp_richcompare*/
@@ -36429,14 +40344,32 @@ static PyMethodDef __pyx_methods[] = {
{"allocate_buffer", (PyCFunction)__pyx_pw_5adios_35allocate_buffer, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_34allocate_buffer},
{"declare_group", (PyCFunction)__pyx_pw_5adios_37declare_group, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_36declare_group},
{"define_var", (PyCFunction)__pyx_pw_5adios_39define_var, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_38define_var},
- {"define_attribute", (PyCFunction)__pyx_pw_5adios_41define_attribute, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_40define_attribute},
- {"define_attribute_byvalue", (PyCFunction)__pyx_pw_5adios_43define_attribute_byvalue, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_42define_attribute_byvalue},
- {"select_method", (PyCFunction)__pyx_pw_5adios_45select_method, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_44select_method},
- {"adios2npdtype", (PyCFunction)__pyx_pw_5adios_47adios2npdtype, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_46adios2npdtype},
- {"np2adiostype", (PyCFunction)__pyx_pw_5adios_49np2adiostype, METH_O, __pyx_doc_5adios_48np2adiostype},
- {"adiostype2string", (PyCFunction)__pyx_pw_5adios_51adiostype2string, METH_O, __pyx_doc_5adios_50adiostype2string},
- {"read_init", (PyCFunction)__pyx_pw_5adios_53read_init, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_52read_init},
- {"read_finalize", (PyCFunction)__pyx_pw_5adios_55read_finalize, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_54read_finalize},
+ {"define_schema_version", (PyCFunction)__pyx_pw_5adios_41define_schema_version, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_40define_schema_version},
+ {"define_var_mesh", (PyCFunction)__pyx_pw_5adios_43define_var_mesh, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_42define_var_mesh},
+ {"define_var_centering", (PyCFunction)__pyx_pw_5adios_45define_var_centering, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_44define_var_centering},
+ {"define_var_timesteps", (PyCFunction)__pyx_pw_5adios_47define_var_timesteps, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_46define_var_timesteps},
+ {"define_var_timescale", (PyCFunction)__pyx_pw_5adios_49define_var_timescale, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_48define_var_timescale},
+ {"define_var_timeseriesformat", (PyCFunction)__pyx_pw_5adios_51define_var_timeseriesformat, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_50define_var_timeseriesformat},
+ {"define_var_hyperslab", (PyCFunction)__pyx_pw_5adios_53define_var_hyperslab, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_52define_var_hyperslab},
+ {"define_mesh_timevarying", (PyCFunction)__pyx_pw_5adios_55define_mesh_timevarying, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_54define_mesh_timevarying},
+ {"define_mesh_timesteps", (PyCFunction)__pyx_pw_5adios_57define_mesh_timesteps, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_56define_mesh_timesteps},
+ {"define_mesh_timescale", (PyCFunction)__pyx_pw_5adios_59define_mesh_timescale, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_58define_mesh_timescale},
+ {"define_mesh_timeseriesformat", (PyCFunction)__pyx_pw_5adios_61define_mesh_timeseriesformat, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_60define_mesh_timeseriesformat},
+ {"define_mesh_uniform", (PyCFunction)__pyx_pw_5adios_63define_mesh_uniform, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_62define_mesh_uniform},
+ {"define_mesh_rectilinear", (PyCFunction)__pyx_pw_5adios_65define_mesh_rectilinear, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_64define_mesh_rectilinear},
+ {"define_mesh_structured", (PyCFunction)__pyx_pw_5adios_67define_mesh_structured, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_66define_mesh_structured},
+ {"define_mesh_unstructured", (PyCFunction)__pyx_pw_5adios_69define_mesh_unstructured, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_68define_mesh_unstructured},
+ {"define_attribute", (PyCFunction)__pyx_pw_5adios_71define_attribute, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_70define_attribute},
+ {"define_attribute_byvalue", (PyCFunction)__pyx_pw_5adios_73define_attribute_byvalue, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_72define_attribute_byvalue},
+ {"select_method", (PyCFunction)__pyx_pw_5adios_75select_method, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_74select_method},
+ {"set_transform", (PyCFunction)__pyx_pw_5adios_77set_transform, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_76set_transform},
+ {"set_max_buffer_size", (PyCFunction)__pyx_pw_5adios_79set_max_buffer_size, METH_O, __pyx_doc_5adios_78set_max_buffer_size},
+ {"set_time_aggregation", (PyCFunction)__pyx_pw_5adios_81set_time_aggregation, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_80set_time_aggregation},
+ {"adios2npdtype", (PyCFunction)__pyx_pw_5adios_83adios2npdtype, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_82adios2npdtype},
+ {"np2adiostype", (PyCFunction)__pyx_pw_5adios_85np2adiostype, METH_O, __pyx_doc_5adios_84np2adiostype},
+ {"adiostype2string", (PyCFunction)__pyx_pw_5adios_87adiostype2string, METH_O, __pyx_doc_5adios_86adiostype2string},
+ {"read_init", (PyCFunction)__pyx_pw_5adios_89read_init, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_88read_init},
+ {"read_finalize", (PyCFunction)__pyx_pw_5adios_91read_finalize, METH_VARARGS|METH_KEYWORDS, __pyx_doc_5adios_90read_finalize},
{0, 0, 0, 0}
};
@@ -36556,8 +40489,11 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__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},
+ {&__pyx_n_s_buffersize, __pyx_k_buffersize, sizeof(__pyx_k_buffersize), 0, 0, 1, 1},
{&__pyx_n_s_byte, __pyx_k_byte, sizeof(__pyx_k_byte), 0, 0, 1, 1},
{&__pyx_kp_s_bytes, __pyx_k_bytes, sizeof(__pyx_k_bytes), 0, 0, 1, 0},
+ {&__pyx_n_s_cell_type, __pyx_k_cell_type, sizeof(__pyx_k_cell_type), 0, 0, 1, 1},
+ {&__pyx_n_s_centering, __pyx_k_centering, sizeof(__pyx_k_centering), 0, 0, 1, 1},
{&__pyx_n_s_char, __pyx_k_char, sizeof(__pyx_k_char), 0, 0, 1, 1},
{&__pyx_n_s_close, __pyx_k_close, sizeof(__pyx_k_close), 0, 0, 1, 1},
{&__pyx_n_s_comm, __pyx_k_comm, sizeof(__pyx_k_comm), 0, 0, 1, 1},
@@ -36568,9 +40504,11 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_concatenate, __pyx_k_concatenate, sizeof(__pyx_k_concatenate), 0, 0, 1, 1},
{&__pyx_n_s_config, __pyx_k_config, sizeof(__pyx_k_config), 0, 0, 1, 1},
{&__pyx_n_s_contiguous, __pyx_k_contiguous, sizeof(__pyx_k_contiguous), 0, 0, 1, 1},
+ {&__pyx_n_s_coordinates, __pyx_k_coordinates, sizeof(__pyx_k_coordinates), 0, 0, 1, 1},
{&__pyx_n_s_copy, __pyx_k_copy, sizeof(__pyx_k_copy), 0, 0, 1, 1},
{&__pyx_n_s_count, __pyx_k_count, sizeof(__pyx_k_count), 0, 0, 1, 1},
{&__pyx_n_s_current_step, __pyx_k_current_step, sizeof(__pyx_k_current_step), 0, 0, 1, 1},
+ {&__pyx_n_s_data, __pyx_k_data, sizeof(__pyx_k_data), 0, 0, 1, 1},
{&__pyx_n_s_data_size, __pyx_k_data_size, sizeof(__pyx_k_data_size), 0, 0, 1, 1},
{&__pyx_n_s_declare_group, __pyx_k_declare_group, sizeof(__pyx_k_declare_group), 0, 0, 1, 1},
{&__pyx_n_s_define, __pyx_k_define, sizeof(__pyx_k_define), 0, 0, 1, 1},
@@ -36610,7 +40548,9 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_group, __pyx_k_group, sizeof(__pyx_k_group), 0, 0, 1, 1},
{&__pyx_n_s_group_id, __pyx_k_group_id, sizeof(__pyx_k_group_id), 0, 0, 1, 1},
{&__pyx_n_s_group_name, __pyx_k_group_name, sizeof(__pyx_k_group_name), 0, 0, 1, 1},
+ {&__pyx_n_s_groupid, __pyx_k_groupid, sizeof(__pyx_k_groupid), 0, 0, 1, 1},
{&__pyx_n_s_hl, __pyx_k_hl, sizeof(__pyx_k_hl), 0, 0, 1, 1},
+ {&__pyx_n_s_hyperslab, __pyx_k_hyperslab, sizeof(__pyx_k_hyperslab), 0, 0, 1, 1},
{&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1},
{&__pyx_n_s_index, __pyx_k_index, sizeof(__pyx_k_index), 0, 0, 1, 1},
{&__pyx_n_s_init, __pyx_k_init, sizeof(__pyx_k_init), 0, 0, 1, 1},
@@ -36638,6 +40578,8 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_long, __pyx_k_long, sizeof(__pyx_k_long), 0, 0, 1, 1},
{&__pyx_n_s_long_double, __pyx_k_long_double, sizeof(__pyx_k_long_double), 0, 0, 1, 1},
{&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1},
+ {&__pyx_n_s_maximum, __pyx_k_maximum, sizeof(__pyx_k_maximum), 0, 0, 1, 1},
+ {&__pyx_n_s_meshname, __pyx_k_meshname, sizeof(__pyx_k_meshname), 0, 0, 1, 1},
{&__pyx_n_s_metaclass, __pyx_k_metaclass, sizeof(__pyx_k_metaclass), 0, 0, 1, 1},
{&__pyx_n_s_method, __pyx_k_method, sizeof(__pyx_k_method), 0, 0, 1, 1},
{&__pyx_n_s_method_name, __pyx_k_method_name, sizeof(__pyx_k_method_name), 0, 0, 1, 1},
@@ -36654,11 +40596,14 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_ndim, __pyx_k_ndim, sizeof(__pyx_k_ndim), 0, 0, 1, 1},
{&__pyx_n_s_normalize_key, __pyx_k_normalize_key, sizeof(__pyx_k_normalize_key), 0, 0, 1, 1},
{&__pyx_n_s_np, __pyx_k_np, sizeof(__pyx_k_np), 0, 0, 1, 1},
+ {&__pyx_n_s_npoints, __pyx_k_npoints, sizeof(__pyx_k_npoints), 0, 0, 1, 1},
+ {&__pyx_n_s_nspace, __pyx_k_nspace, sizeof(__pyx_k_nspace), 0, 0, 1, 1},
{&__pyx_n_s_nsteps, __pyx_k_nsteps, sizeof(__pyx_k_nsteps), 0, 0, 1, 1},
{&__pyx_n_s_numpy, __pyx_k_numpy, sizeof(__pyx_k_numpy), 0, 0, 1, 1},
{&__pyx_n_s_nvars, __pyx_k_nvars, sizeof(__pyx_k_nvars), 0, 0, 1, 1},
{&__pyx_n_s_offset, __pyx_k_offset, sizeof(__pyx_k_offset), 0, 0, 1, 1},
{&__pyx_n_s_order, __pyx_k_order, sizeof(__pyx_k_order), 0, 0, 1, 1},
+ {&__pyx_n_s_origin, __pyx_k_origin, sizeof(__pyx_k_origin), 0, 0, 1, 1},
{&__pyx_n_s_os, __pyx_k_os, sizeof(__pyx_k_os), 0, 0, 1, 1},
{&__pyx_n_s_parameters, __pyx_k_parameters, sizeof(__pyx_k_parameters), 0, 0, 1, 1},
{&__pyx_n_s_path, __pyx_k_path, sizeof(__pyx_k_path), 0, 0, 1, 1},
@@ -36684,13 +40629,16 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_reshape, __pyx_k_reshape, sizeof(__pyx_k_reshape), 0, 0, 1, 1},
{&__pyx_n_s_rstrip, __pyx_k_rstrip, sizeof(__pyx_k_rstrip), 0, 0, 1, 1},
{&__pyx_n_s_scalar, __pyx_k_scalar, sizeof(__pyx_k_scalar), 0, 0, 1, 1},
+ {&__pyx_n_s_schema_version, __pyx_k_schema_version, sizeof(__pyx_k_schema_version), 0, 0, 1, 1},
{&__pyx_n_s_sel, __pyx_k_sel, sizeof(__pyx_k_sel), 0, 0, 1, 1},
{&__pyx_n_s_select, __pyx_k_select, sizeof(__pyx_k_select), 0, 0, 1, 1},
{&__pyx_n_s_selections, __pyx_k_selections, sizeof(__pyx_k_selections), 0, 0, 1, 1},
+ {&__pyx_n_s_set_time_aggregation, __pyx_k_set_time_aggregation, sizeof(__pyx_k_set_time_aggregation), 0, 0, 1, 1},
{&__pyx_n_s_setitem, __pyx_k_setitem, sizeof(__pyx_k_setitem), 0, 0, 1, 1},
{&__pyx_n_s_shape, __pyx_k_shape, sizeof(__pyx_k_shape), 0, 0, 1, 1},
{&__pyx_n_s_short, __pyx_k_short, sizeof(__pyx_k_short), 0, 0, 1, 1},
{&__pyx_n_s_size, __pyx_k_size, sizeof(__pyx_k_size), 0, 0, 1, 1},
+ {&__pyx_n_s_spacing, __pyx_k_spacing, sizeof(__pyx_k_spacing), 0, 0, 1, 1},
{&__pyx_n_s_split, __pyx_k_split, sizeof(__pyx_k_split), 0, 0, 1, 1},
{&__pyx_n_s_start, __pyx_k_start, sizeof(__pyx_k_start), 0, 0, 1, 1},
{&__pyx_n_s_startswith, __pyx_k_startswith, sizeof(__pyx_k_startswith), 0, 0, 1, 1},
@@ -36701,13 +40649,20 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_string_array, __pyx_k_string_array, sizeof(__pyx_k_string_array), 0, 0, 1, 1},
{&__pyx_n_s_strip, __pyx_k_strip, sizeof(__pyx_k_strip), 0, 0, 1, 1},
{&__pyx_n_s_strlen, __pyx_k_strlen, sizeof(__pyx_k_strlen), 0, 0, 1, 1},
+ {&__pyx_n_s_syncgroupid, __pyx_k_syncgroupid, sizeof(__pyx_k_syncgroupid), 0, 0, 1, 1},
{&__pyx_n_s_t, __pyx_k_t, sizeof(__pyx_k_t), 0, 0, 1, 1},
{&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1},
{&__pyx_n_s_time_index, __pyx_k_time_index, sizeof(__pyx_k_time_index), 0, 0, 1, 1},
{&__pyx_n_s_time_steps, __pyx_k_time_steps, sizeof(__pyx_k_time_steps), 0, 0, 1, 1},
{&__pyx_n_s_timeout_sec, __pyx_k_timeout_sec, sizeof(__pyx_k_timeout_sec), 0, 0, 1, 1},
+ {&__pyx_n_s_timescale, __pyx_k_timescale, sizeof(__pyx_k_timescale), 0, 0, 1, 1},
+ {&__pyx_n_s_timeseries, __pyx_k_timeseries, sizeof(__pyx_k_timeseries), 0, 0, 1, 1},
+ {&__pyx_n_s_timesteps, __pyx_k_timesteps, sizeof(__pyx_k_timesteps), 0, 0, 1, 1},
+ {&__pyx_n_s_timevarying, __pyx_k_timevarying, sizeof(__pyx_k_timevarying), 0, 0, 1, 1},
{&__pyx_n_s_tostring, __pyx_k_tostring, sizeof(__pyx_k_tostring), 0, 0, 1, 1},
{&__pyx_n_s_traceback, __pyx_k_traceback, sizeof(__pyx_k_traceback), 0, 0, 1, 1},
+ {&__pyx_n_s_transform, __pyx_k_transform, sizeof(__pyx_k_transform), 0, 0, 1, 1},
+ {&__pyx_n_s_transform_type_str, __pyx_k_transform_type_str, sizeof(__pyx_k_transform_type_str), 0, 0, 1, 1},
{&__pyx_n_s_type, __pyx_k_type, sizeof(__pyx_k_type), 0, 0, 1, 1},
{&__pyx_n_s_uint16, __pyx_k_uint16, sizeof(__pyx_k_uint16), 0, 0, 1, 1},
{&__pyx_n_s_uint32, __pyx_k_uint32, sizeof(__pyx_k_uint32), 0, 0, 1, 1},
@@ -36724,8 +40679,9 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_value, __pyx_k_value, sizeof(__pyx_k_value), 0, 0, 1, 1},
{&__pyx_n_s_values, __pyx_k_values, sizeof(__pyx_k_values), 0, 0, 1, 1},
{&__pyx_n_s_var, __pyx_k_var, sizeof(__pyx_k_var), 0, 0, 1, 1},
+ {&__pyx_n_s_var_id, __pyx_k_var_id, sizeof(__pyx_k_var_id), 0, 0, 1, 1},
{&__pyx_n_s_var_namelist, __pyx_k_var_namelist, sizeof(__pyx_k_var_namelist), 0, 0, 1, 1},
- {&__pyx_kp_u_var_read_line_1265, __pyx_k_var_read_line_1265, sizeof(__pyx_k_var_read_line_1265), 0, 1, 0, 0},
+ {&__pyx_kp_u_var_read_line_1457, __pyx_k_var_read_line_1457, sizeof(__pyx_k_var_read_line_1457), 0, 1, 0, 0},
{&__pyx_n_s_varid, __pyx_k_varid, sizeof(__pyx_k_varid), 0, 0, 1, 1},
{&__pyx_n_s_varname, __pyx_k_varname, sizeof(__pyx_k_varname), 0, 0, 1, 1},
{&__pyx_n_s_vars, __pyx_k_vars, sizeof(__pyx_k_vars), 0, 0, 1, 1},
@@ -36734,8 +40690,8 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_w, __pyx_k_w, sizeof(__pyx_k_w), 0, 0, 1, 1},
{&__pyx_n_s_when, __pyx_k_when, sizeof(__pyx_k_when), 0, 0, 1, 1},
{&__pyx_n_s_write, __pyx_k_write, sizeof(__pyx_k_write), 0, 0, 1, 1},
- {&__pyx_kp_u_writer_declare_group_line_1782, __pyx_k_writer_declare_group_line_1782, sizeof(__pyx_k_writer_declare_group_line_1782), 0, 1, 0, 0},
- {&__pyx_kp_u_writer_define_var_line_1804, __pyx_k_writer_define_var_line_1804, sizeof(__pyx_k_writer_define_var_line_1804), 0, 1, 0, 0},
+ {&__pyx_kp_u_writer_declare_group_line_1983, __pyx_k_writer_declare_group_line_1983, sizeof(__pyx_k_writer_declare_group_line_1983), 0, 1, 0, 0},
+ {&__pyx_kp_u_writer_define_var_line_2020, __pyx_k_writer_define_var_line_2020, sizeof(__pyx_k_writer_define_var_line_2020), 0, 1, 0, 0},
{&__pyx_n_s_xrange, __pyx_k_xrange, sizeof(__pyx_k_xrange), 0, 0, 1, 1},
{&__pyx_n_s_zeros, __pyx_k_zeros, sizeof(__pyx_k_zeros), 0, 0, 1, 1},
{&__pyx_n_s_zip, __pyx_k_zip, sizeof(__pyx_k_zip), 0, 0, 1, 1},
@@ -36748,15 +40704,15 @@ static int __Pyx_InitCachedBuiltins(void) {
#else
__pyx_builtin_xrange = __Pyx_GetBuiltinName(__pyx_n_s_xrange); if (!__pyx_builtin_xrange) __PYX_ERR(0, 71, __pyx_L1_error)
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- __pyx_builtin_Ellipsis = __Pyx_GetBuiltinName(__pyx_n_s_Ellipsis); if (!__pyx_builtin_Ellipsis) __PYX_ERR(0, 358, __pyx_L1_error)
- __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) __PYX_ERR(0, 594, __pyx_L1_error)
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@@ -36790,506 +40746,495 @@ static int __Pyx_InitCachedConstants(void) {
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__Pyx_GIVEREF(__pyx_slice__3);
- /* "adios.pyx":359
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__Pyx_GOTREF(__pyx_slice__4);
__Pyx_GIVEREF(__pyx_slice__4);
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PyTuple_SET_ITEM(__pyx_tuple__6, 0, __pyx_slice__5);
__Pyx_GIVEREF(__pyx_tuple__6);
- /* "adios.pyx":708
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- __Pyx_GOTREF(__pyx_slice__14);
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+ /* "adios.pyx":1054
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- __Pyx_GOTREF(__pyx_tuple__18);
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- __Pyx_GOTREF(__pyx_tuple__19);
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- /* "adios.pyx":912
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- __Pyx_GOTREF(__pyx_tuple__20);
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- /* "adios.pyx":913
+ /* "adios.pyx":1105
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@@ -37523,11 +41468,11 @@ PyMODINIT_FUNC PyInit_adios(void)
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@@ -38328,9 +42291,9 @@ PyMODINIT_FUNC PyInit_adios(void)
*/
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diff --git a/wrappers/numpy/adios.pyx b/wrappers/numpy/adios.pyx
index 7bde3cf..fe7226d 100644
--- a/wrappers/numpy/adios.pyx
+++ b/wrappers/numpy/adios.pyx
@@ -107,6 +107,13 @@ cdef extern from "adios_types.h":
ctypedef enum ADIOS_FLAG:
pass
+ ctypedef enum ADIOS_STATISTICS_FLAG:
+ adios_stat_no
+ adios_stat_minmax
+ adios_stat_full
+ adios_stat_default
+ adios_stat_no_do_not_use_this
+
cdef extern from "adios.h":
ctypedef int MPI_Comm
int MPI_COMM_WORLD
@@ -147,9 +154,9 @@ cdef extern from "adios.h":
cdef int adios_declare_group (int64_t * id,
char * name,
char * time_index,
- ADIOS_FLAG stats)
+ ADIOS_STATISTICS_FLAG stats)
- cdef int adios_define_var (int64_t group_id,
+ cdef int64_t adios_define_var (int64_t group_id,
char * name,
char * path,
ADIOS_DATATYPES type,
@@ -157,6 +164,74 @@ cdef extern from "adios.h":
char * global_dimensions,
char * local_offsets)
+ ### Ab hier:
+ cdef int adios_define_schema_version (int64_t group_id, char * schema_version)
+
+ cdef int adios_define_var_mesh (int64_t group_id , const char * varname ,
+ const char * meshname)
+
+ cdef int adios_define_var_centering (int64_t group_id , const char * varname ,
+ const char * centering)
+
+ cdef int adios_define_var_timesteps (const char * timesteps , int64_t group_id ,
+ const char * name)
+
+ 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)
+
+ cdef int adios_define_mesh_uniform (char * dimensions,
+ char * origin,
+ char * spacing,
+ char * maximum,
+ char * nspace,
+ 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,
+ char * cell_type,
+ char * npoints,
+ char * nspace,
+ int64_t group_id,
+ const char * name
+ )
+
+ ### Bis hier
+
cdef int adios_define_attribute (int64_t group,
char * name,
char * path,
@@ -176,6 +251,15 @@ cdef extern from "adios.h":
char * parameters,
char * base_path)
+ cdef int adios_set_transform (int64_t var_id, const char *transform_type_str)
+
+ cdef void adios_set_max_buffer_size (uint64_t max_buffer_size_MB)
+
+ cdef int adios_set_time_aggregation(int64_t groupid,
+ uint64_t buffersize,
+ int64_t syncgroupid)
+
+
cdef extern from "adios_selection.h":
ctypedef enum ADIOS_SELECTION_TYPE:
ADIOS_SELECTION_BOUNDINGBOX
@@ -457,15 +541,15 @@ cpdef int allocate_buffer(int when,
cpdef int64_t declare_group(str name,
str time_index = "",
- int stats = 1):
+ int stats = adios_stat_default):
cdef int64_t id = 0
adios_declare_group (&id,
s2b(name),
s2b(time_index),
- <ADIOS_FLAG> stats)
+ <ADIOS_STATISTICS_FLAG> stats)
return id
-cpdef int define_var(int64_t group_id,
+cpdef int64_t define_var(int64_t group_id,
str name,
str path,
int atype,
@@ -480,6 +564,101 @@ cpdef int define_var(int64_t group_id,
s2b(global_dimensions),
s2b(local_offsets))
+cpdef int define_schema_version (int64_t group_id, str schema_version):
+ return adios_define_schema_version (group_id, s2b(schema_version))
+
+cpdef int define_var_mesh (int64_t group_id, str varname, str meshname):
+ return adios_define_var_mesh (group_id, s2b(varname), s2b(meshname))
+
+cpdef int define_var_centering (int64_t group_id, str varname, str centering):
+ return adios_define_var_centering (group_id, s2b(varname), s2b(centering))
+
+cpdef int define_var_timesteps (str timesteps, int64_t group_id, str name):
+ return adios_define_var_timesteps (s2b(timesteps), group_id, s2b(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,
+ str maximum,
+ str nspace,
+ int64_t group_id,
+ str name
+ ):
+ return adios_define_mesh_uniform (s2b(dimensions),
+ s2b(origin),
+ s2b(spacing),
+ s2b(maximum),
+ s2b(nspace),
+ 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,
+ int64_t group_id,
+ str name
+ ):
+ return adios_define_mesh_structured (s2b(dimensions),
+ s2b(points),
+ s2b(nspace),
+ group_id,
+ s2b(name)
+ )
+
+cpdef int define_mesh_unstructured (str points,
+ str data,
+ str count,
+ str cell_type,
+ str npoints,
+ str nspace,
+ int64_t group_id,
+ str name
+ ):
+ return adios_define_mesh_unstructured (s2b(points),
+ s2b(data),
+ s2b(count),
+ s2b(cell_type),
+ s2b(npoints),
+ s2b(nspace),
+ group_id,
+ s2b(name)
+ )
+
cpdef int define_attribute (int64_t group,
str name,
str path,
@@ -546,6 +725,19 @@ cpdef int select_method (int64_t group,
s2b(parameters),
s2b(base_path))
+cpdef int set_transform (int64_t var_id, str transform_type_str):
+ return adios_set_transform (var_id, s2b(transform_type_str))
+
+cpdef void set_max_buffer_size (int64_t max_buffer_size_MB):
+ adios_set_max_buffer_size (max_buffer_size_MB)
+
+cpdef int set_time_aggregation (int64_t groupid,
+ uint64_t buffersize,
+ int64_t syncgroupid):
+ return adios_set_time_aggregation (groupid,
+ buffersize,
+ syncgroupid)
+
## ====================
## ADIOS Read API (V2)
@@ -843,7 +1035,7 @@ cdef class file(dict):
self.close()
def __enter__(self):
- """ Enter for with statemetn """
+ """ Enter for with statement """
return self
def __exit__(self, exception_type, exception_value, traceback):
@@ -1729,6 +1921,8 @@ cdef class writer(object):
cpdef dict vars
cpdef dict attrs
+ cpdef uint64_t timeaggregation_buffersize
+
property fname:
""" The filename to write. """
def __get__(self):
@@ -1759,10 +1953,16 @@ cdef class writer(object):
def __get__(self):
return self.attrs
+ property timeaggregation_buffersize:
+ """ Get time-aggregation buffersize. """
+ def __get__(self):
+ return self.timeaggregation_buffersize
+
def __init__(self, str fname,
bint is_noxml = True,
str mode = "w",
MPI_Comm comm = MPI_COMM_WORLD):
+ self.gid = 0
self.fname = fname
self.method = ""
self.method_params = ""
@@ -1771,6 +1971,7 @@ cdef class writer(object):
self.comm = comm
self.vars = dict()
self.attrs = dict()
+ self.timeaggregation_buffersize = 0
init_noxml(comm)
##def __var_factory__(self, name, value):
@@ -1779,7 +1980,7 @@ cdef class writer(object):
##def __attr_factory__(self, name, value):
## print "attr_factory:", name, value
- def declare_group(self, str gname,
+ def declare_group(self, str gname = None,
str method = "POSIX1",
str method_params = ""):
"""
@@ -1795,24 +1996,41 @@ cdef class writer(object):
>>> fw.declare_group('group', method='MPI_, method_params='verbose=3')
"""
- self.gid = declare_group(gname, "", 1)
- self.gname = gname
+ if gname is not None:
+ self.gname = gname
+
+ if self.gname is None:
+ self.gname = "group"
+
+ self.gid = declare_group(self.gname, "", adios_stat_default)
self.method = method
self.method_params = method_params
select_method(self.gid, self.method, self.method_params, "")
+ self.set_time_aggregation()
+
+ def set_time_aggregation(self, buffer_size = None):
+ """
+ Set time-aggregation buffersize.
+ """
+ if buffer_size is not None:
+ self.timeaggregation_buffersize = buffer_size
+ if self.gid > 0:
+ set_time_aggregation (self.gid, self.timeaggregation_buffersize, 0);
def define_var(self, str varname,
ldim = tuple(),
gdim = tuple(),
- offset = tuple()):
+ offset = tuple(),
+ transform = None):
"""
Define a variable associated with the file.
Args:
- varname (str): variable name.
+ varname (str): variable name
ldim (tuple, optional): local dimension (default: tuple())
gdim (tuple, optional): global dimension (default: tuple())
offset (tuple, optional): offset (default: tuple())
+ transform (str): transform name
Example:
@@ -1821,7 +2039,7 @@ cdef class writer(object):
>>> fw.define_var ('temperature', (2,3))
"""
- self.vars[varname] = varinfo(varname, ldim, gdim, offset)
+ self.vars[varname] = varinfo(varname, ldim, gdim, offset, transform=transform)
def define_attr(self, str attrname):
"""
@@ -1837,13 +2055,22 @@ cdef class writer(object):
str varname,
dtype):
self.attrs[attrname] = attrinfo(attrname, varname, dtype, is_static=False)
+
def __setitem__(self, name, val):
if self.vars.has_key(name):
- self.vars[name] = val
+ if not isinstance(val, varinfo):
+ self.vars[name].value = val
+ else:
+ self.vars[name] = val
elif self.attrs.has_key(name):
- self.attrs[name] = val
+ if not isinstance(val, attrinfo):
+ self.attrs[name] = attrinfo(name, val, np.array(val).dtype)
+ else:
+ self.attrs[name].value = val
else:
- self.vars[name] = val
+ n = np.array(val)
+ self.vars[name] = varinfo(name, n.shape)
+ self.vars[name].value = val
def __getitem__(self, name):
if self.vars.has_key(name):
@@ -1857,8 +2084,8 @@ cdef class writer(object):
"""
Write variables and attributes to a file and close the writer.
"""
- if self.gname is None:
- self.declare_group("group")
+ if self.gid == 0:
+ self.declare_group()
fd = open(self.gname, self.fname, self.mode)
@@ -1871,7 +2098,8 @@ cdef class writer(object):
extra_vars[key] = varinfo(key, n.shape)
extra_vars[key].value = val
else:
- if self.is_noxml: val.define(self.gid)
+ if self.is_noxml:
+ val.define(self.gid)
for key, val in extra_vars.iteritems():
if self.is_noxml: val.define(self.gid)
@@ -1912,7 +2140,7 @@ cdef class writer(object):
self.mode)
def __enter__(self):
- """ Enter for with statemetn """
+ """ Enter for with statement """
return self
def __exit__(self, exception_type, exception_value, traceback):
@@ -1978,17 +2206,27 @@ cdef class varinfo(object):
cdef public gdim
cdef public offset
cdef public value
+ cdef str transform
+
+ property transform:
+ """ Transform method """
+ def __get__(self):
+ return self.fname
+ def __set__(self, value):
+ self.transform = value
def __init__(self, str name,
ldim = tuple(),
gdim = tuple(),
offset = tuple(),
- value = None):
+ value = None,
+ transform = None):
self.name = name
self.ldim = ldim
self.gdim = gdim
self.offset = offset
self.value = value
+ self.transform = transform
def define(self, int64_t gid):
if self.value is None:
@@ -2012,11 +2250,15 @@ cdef class varinfo(object):
atype = np2adiostype(val_.dtype)
## No space allowed
- define_var(gid, self.name, "", atype,
+ cdef int64_t varid = 0;
+ varid = define_var(gid, self.name, "", atype,
str(ldim_).replace(' ', '').strip('(,)'),
str(gdim_).replace(' ', '').strip('(,)'),
str(offset_).replace(' ', '').strip('(,)'))
+ if (self.transform is not None):
+ set_transform(varid, self.transform)
+
def bytes(self):
val_ = self.value
if not isinstance(self.value, (np.ndarray)):
@@ -2032,8 +2274,8 @@ cdef class varinfo(object):
write(fd, self.name, val_)
def __repr__(self):
- return ("AdiosVarinfo (name=%r, ldim=%r, gdim=%r, offset=%r, value=%r)") % \
- (self.name, self.ldim, self.gdim, self.offset, self.value)
+ return ("AdiosVarinfo (name=%r, ldim=%r, gdim=%r, offset=%r, transform=%r, value=%r)") % \
+ (self.name, self.ldim, self.gdim, self.offset, self.transform, self.value)
## Aliases
File = file
diff --git a/wrappers/numpy/adios_mpi.cpp b/wrappers/numpy/adios_mpi.cpp
index e03d7b6..ca2bd99 100644
--- a/wrappers/numpy/adios_mpi.cpp
+++ b/wrappers/numpy/adios_mpi.cpp
@@ -817,7 +817,7 @@ 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":380
+/* "adios_mpi.pyx":464
* cdef MPI.Comm read_init_comm
*
* cpdef init(str config, MPI.Comm comm = MPI.COMM_WORLD): # <<<<<<<<<<<<<<
@@ -829,7 +829,7 @@ struct __pyx_opt_args_9adios_mpi_init {
struct PyMPICommObject *comm;
};
-/* "adios_mpi.pyx":385
+/* "adios_mpi.pyx":469
* return adios_init(s2b(config), init_comm.ob_mpi)
*
* cpdef int64_t open(str group_name, # <<<<<<<<<<<<<<
@@ -841,7 +841,7 @@ struct __pyx_opt_args_9adios_mpi_open {
struct PyMPICommObject *comm;
};
-/* "adios_mpi.pyx":400
+/* "adios_mpi.pyx":484
* return total_size
*
* cpdef int write (int64_t fd_p, str name, val, dtype=None): # <<<<<<<<<<<<<<
@@ -853,7 +853,7 @@ struct __pyx_opt_args_9adios_mpi_write {
PyObject *dtype;
};
-/* "adios_mpi.pyx":440
+/* "adios_mpi.pyx":524
* return adios_close(fd_p)
*
* cpdef int finalize(int mype = 0): # <<<<<<<<<<<<<<
@@ -865,7 +865,7 @@ struct __pyx_opt_args_9adios_mpi_finalize {
int mype;
};
-/* "adios_mpi.pyx":447
+/* "adios_mpi.pyx":531
* ## ====================
*
* cpdef int init_noxml(MPI.Comm comm = MPI.COMM_WORLD): # <<<<<<<<<<<<<<
@@ -877,12 +877,12 @@ struct __pyx_opt_args_9adios_mpi_init_noxml {
struct PyMPICommObject *comm;
};
-/* "adios_mpi.pyx":457
+/* "adios_mpi.pyx":541
* buffer_size)
*
* cpdef int64_t declare_group(str name, # <<<<<<<<<<<<<<
* str time_index = "",
- * int stats = 1):
+ * int stats = adios_stat_default):
*/
struct __pyx_opt_args_9adios_mpi_declare_group {
int __pyx_n;
@@ -890,10 +890,10 @@ struct __pyx_opt_args_9adios_mpi_declare_group {
int stats;
};
-/* "adios_mpi.pyx":467
+/* "adios_mpi.pyx":551
* return id
*
- * cpdef int define_var(int64_t group_id, # <<<<<<<<<<<<<<
+ * cpdef int64_t define_var(int64_t group_id, # <<<<<<<<<<<<<<
* str name,
* str path,
*/
@@ -904,7 +904,7 @@ struct __pyx_opt_args_9adios_mpi_define_var {
PyObject *local_offsets;
};
-/* "adios_mpi.pyx":539
+/* "adios_mpi.pyx":718
* <void *> val_.data)
*
* cpdef int select_method (int64_t group, # <<<<<<<<<<<<<<
@@ -917,7 +917,7 @@ struct __pyx_opt_args_9adios_mpi_select_method {
PyObject *base_path;
};
-/* "adios_mpi.pyx":553
+/* "adios_mpi.pyx":745
* ## ====================
*
* cpdef np.dtype adios2npdtype(ADIOS_DATATYPES t, int strlen = 1): # <<<<<<<<<<<<<<
@@ -929,7 +929,7 @@ struct __pyx_opt_args_9adios_mpi_adios2npdtype {
int strlen;
};
-/* "adios_mpi.pyx":682
+/* "adios_mpi.pyx":874
*
* """ Call adios_read_init_method """
* cpdef int read_init(str method_name = "BP", # <<<<<<<<<<<<<<
@@ -943,7 +943,7 @@ struct __pyx_opt_args_9adios_mpi_read_init {
PyObject *parameters;
};
-/* "adios_mpi.pyx":692
+/* "adios_mpi.pyx":884
*
* """ Call adios_read_finalize_method """
* cpdef int read_finalize(str method_name = "BP"): # <<<<<<<<<<<<<<
@@ -955,7 +955,7 @@ struct __pyx_opt_args_9adios_mpi_read_finalize {
PyObject *method_name;
};
-/* "adios_mpi.pyx":869
+/* "adios_mpi.pyx":1061
* adios_release_step(self.fp)
*
* cpdef advance(self, int last = 0, float timeout_sec = 0.0): # <<<<<<<<<<<<<<
@@ -968,7 +968,7 @@ struct __pyx_opt_args_9adios_mpi_4file_advance {
float timeout_sec;
};
-/* "adios_mpi.pyx":1167
+/* "adios_mpi.pyx":1359
* self.nsteps = self.vp.nsteps
*
* cpdef read_points(self, tuple points = (), from_steps = None, nsteps = None): # <<<<<<<<<<<<<<
@@ -982,7 +982,7 @@ struct __pyx_opt_args_9adios_mpi_3var_read_points {
PyObject *nsteps;
};
-/* "adios_mpi.pyx":1223
+/* "adios_mpi.pyx":1415
* return var
*
* cpdef read_writeblock(self, int rank, from_steps = None, nsteps = None): # <<<<<<<<<<<<<<
@@ -995,7 +995,7 @@ struct __pyx_opt_args_9adios_mpi_3var_read_writeblock {
PyObject *nsteps;
};
-/* "adios_mpi.pyx":1264
+/* "adios_mpi.pyx":1456
* return var
*
* cpdef read(self, tuple offset = (), tuple count = (), tuple scalar = (), # <<<<<<<<<<<<<<
@@ -1307,7 +1307,7 @@ typedef struct PyMPIFileObject PyMPIFileObject;
__PYX_EXTERN_C DL_EXPORT(PyTypeObject) PyMPIFile_Type;
-/* "adios_mpi.pyx":697
+/* "adios_mpi.pyx":889
*
* ## dict for handling '/' prefix
* cdef class softdict(dict): # <<<<<<<<<<<<<<
@@ -1319,7 +1319,7 @@ struct __pyx_obj_9adios_mpi_softdict {
};
-/* "adios_mpi.pyx":721
+/* "adios_mpi.pyx":913
*
* ## Python class for ADIOS_FILE structure
* cdef class file(dict): # <<<<<<<<<<<<<<
@@ -1346,7 +1346,7 @@ struct __pyx_obj_9adios_mpi_file {
};
-/* "adios_mpi.pyx":993
+/* "adios_mpi.pyx":1185
* return list(s-set(['']))
*
* cdef class blockinfo(object): # <<<<<<<<<<<<<<
@@ -1362,7 +1362,7 @@ struct __pyx_obj_9adios_mpi_blockinfo {
};
-/* "adios_mpi.pyx":1028
+/* "adios_mpi.pyx":1220
* self.count)
*
* cdef class var(dict): # <<<<<<<<<<<<<<
@@ -1385,7 +1385,7 @@ struct __pyx_obj_9adios_mpi_var {
};
-/* "adios_mpi.pyx":1493
+/* "adios_mpi.pyx":1685
* return self.attrs.keys()
*
* cdef class attr(object): # <<<<<<<<<<<<<<
@@ -1401,7 +1401,7 @@ struct __pyx_obj_9adios_mpi_attr {
};
-/* "adios_mpi.pyx":1579
+/* "adios_mpi.pyx":1771
* (self.name, self.dtype, self.value)
*
* cdef class group(dict): # <<<<<<<<<<<<<<
@@ -1417,7 +1417,7 @@ struct __pyx_obj_9adios_mpi_group {
};
-/* "adios_mpi.pyx":1691
+/* "adios_mpi.pyx":1883
*
* ## Helper dict
* cdef class smartdict(dict): # <<<<<<<<<<<<<<
@@ -1430,7 +1430,7 @@ struct __pyx_obj_9adios_mpi_smartdict {
};
-/* "adios_mpi.pyx":1703
+/* "adios_mpi.pyx":1895
* self.factory(key, value)
*
* cdef class writer(object): # <<<<<<<<<<<<<<
@@ -1449,10 +1449,11 @@ struct __pyx_obj_9adios_mpi_writer {
struct PyMPICommObject *comm;
PyObject *vars;
PyObject *attrs;
+ uint64_t timeaggregation_buffersize;
};
-/* "adios_mpi.pyx":1921
+/* "adios_mpi.pyx":2149
* self.close()
*
* cdef class attrinfo(object): # <<<<<<<<<<<<<<
@@ -1468,7 +1469,7 @@ struct __pyx_obj_9adios_mpi_attrinfo {
};
-/* "adios_mpi.pyx":1974
+/* "adios_mpi.pyx":2202
* self.dtype)
*
* cdef class varinfo(object): # <<<<<<<<<<<<<<
@@ -1482,11 +1483,12 @@ struct __pyx_obj_9adios_mpi_varinfo {
PyObject *gdim;
PyObject *offset;
PyObject *value;
+ PyObject *transform;
};
-/* "adios_mpi.pyx":721
+/* "adios_mpi.pyx":913
*
* ## Python class for ADIOS_FILE structure
* cdef class file(dict): # <<<<<<<<<<<<<<
@@ -1503,7 +1505,7 @@ struct __pyx_vtabstruct_9adios_mpi_file {
static struct __pyx_vtabstruct_9adios_mpi_file *__pyx_vtabptr_9adios_mpi_file;
-/* "adios_mpi.pyx":1028
+/* "adios_mpi.pyx":1220
* self.count)
*
* cdef class var(dict): # <<<<<<<<<<<<<<
@@ -1910,6 +1912,24 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
#define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
#endif
+/* PyObjectSetAttrStr.proto */
+#if CYTHON_COMPILING_IN_CPYTHON
+#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);
+ if (likely(tp->tp_setattro))
+ return tp->tp_setattro(obj, attr_name, value);
+#if PY_MAJOR_VERSION < 3
+ if (likely(tp->tp_setattr))
+ return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value);
+#endif
+ return PyObject_SetAttr(obj, attr_name, value);
+}
+#else
+#define __Pyx_PyObject_DelAttrStr(o,n) PyObject_DelAttr(o,n)
+#define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v)
+#endif
+
/* PyObjectCallMethod0.proto */
static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name);
@@ -1929,24 +1949,6 @@ static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* dict, int is_dict,
static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* dict_or_iter, Py_ssize_t orig_length, Py_ssize_t* ppos,
PyObject** pkey, PyObject** pvalue, PyObject** pitem, int is_dict);
-/* PyObjectSetAttrStr.proto */
-#if CYTHON_COMPILING_IN_CPYTHON
-#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);
- if (likely(tp->tp_setattro))
- return tp->tp_setattro(obj, attr_name, value);
-#if PY_MAJOR_VERSION < 3
- if (likely(tp->tp_setattr))
- return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value);
-#endif
- return PyObject_SetAttr(obj, attr_name, value);
-}
-#else
-#define __Pyx_PyObject_DelAttrStr(o,n) PyObject_DelAttr(o,n)
-#define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v)
-#endif
-
/* py_dict_values.proto */
static CYTHON_INLINE PyObject* __Pyx_PyDict_Values(PyObject* d);
@@ -2266,10 +2268,28 @@ static int __pyx_f_9adios_mpi_finalize(int __pyx_skip_dispatch, struct __pyx_opt
static int __pyx_f_9adios_mpi_init_noxml(int __pyx_skip_dispatch, struct __pyx_opt_args_9adios_mpi_init_noxml *__pyx_optional_args); /*proto*/
static int __pyx_f_9adios_mpi_allocate_buffer(int, uint64_t, int __pyx_skip_dispatch); /*proto*/
static int64_t __pyx_f_9adios_mpi_declare_group(PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_9adios_mpi_declare_group *__pyx_optional_args); /*proto*/
-static int __pyx_f_9adios_mpi_define_var(int64_t, PyObject *, PyObject *, int, int __pyx_skip_dispatch, struct __pyx_opt_args_9adios_mpi_define_var *__pyx_optional_args); /*proto*/
+static int64_t __pyx_f_9adios_mpi_define_var(int64_t, PyObject *, PyObject *, int, int __pyx_skip_dispatch, struct __pyx_opt_args_9adios_mpi_define_var *__pyx_optional_args); /*proto*/
+static int __pyx_f_9adios_mpi_define_schema_version(int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_9adios_mpi_define_var_mesh(int64_t, PyObject *, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_9adios_mpi_define_var_centering(int64_t, PyObject *, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_9adios_mpi_define_var_timesteps(PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_9adios_mpi_define_var_timescale(PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_9adios_mpi_define_var_timeseriesformat(PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_9adios_mpi_define_var_hyperslab(PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_9adios_mpi_define_mesh_timevarying(PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_9adios_mpi_define_mesh_timesteps(PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_9adios_mpi_define_mesh_timescale(PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_9adios_mpi_define_mesh_timeseriesformat(PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_9adios_mpi_define_mesh_uniform(PyObject *, PyObject *, PyObject *, PyObject *, PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_9adios_mpi_define_mesh_rectilinear(PyObject *, PyObject *, PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_9adios_mpi_define_mesh_structured(PyObject *, PyObject *, PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_9adios_mpi_define_mesh_unstructured(PyObject *, PyObject *, PyObject *, PyObject *, PyObject *, PyObject *, int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
static int __pyx_f_9adios_mpi_define_attribute(int64_t, PyObject *, PyObject *, int, PyObject *, PyObject *, int __pyx_skip_dispatch); /*proto*/
static int __pyx_f_9adios_mpi_define_attribute_byvalue(int64_t, PyObject *, PyObject *, PyObject *, int __pyx_skip_dispatch); /*proto*/
static int __pyx_f_9adios_mpi_select_method(int64_t, PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_9adios_mpi_select_method *__pyx_optional_args); /*proto*/
+static int __pyx_f_9adios_mpi_set_transform(int64_t, PyObject *, int __pyx_skip_dispatch); /*proto*/
+static void __pyx_f_9adios_mpi_set_max_buffer_size(int64_t, int __pyx_skip_dispatch); /*proto*/
+static int __pyx_f_9adios_mpi_set_time_aggregation(int64_t, uint64_t, int64_t, int __pyx_skip_dispatch); /*proto*/
static PyArray_Descr *__pyx_f_9adios_mpi_adios2npdtype(ADIOS_DATATYPES, int __pyx_skip_dispatch, struct __pyx_opt_args_9adios_mpi_adios2npdtype *__pyx_optional_args); /*proto*/
static PyObject *__pyx_f_9adios_mpi_printfile(ADIOS_FILE *); /*proto*/
static PyObject *__pyx_f_9adios_mpi_printvar(ADIOS_VARINFO *); /*proto*/
@@ -2343,6 +2363,7 @@ static const char __pyx_k_byte[] = "byte";
static const char __pyx_k_char[] = "char";
static const char __pyx_k_comm[] = "comm";
static const char __pyx_k_copy[] = "copy";
+static const char __pyx_k_data[] = "data";
static const char __pyx_k_dims[] = "dims";
static const char __pyx_k_fd_p[] = "fd_p";
static const char __pyx_k_file[] = "file";
@@ -2419,8 +2440,10 @@ static const char __pyx_k_module[] = "__module__";
static const char __pyx_k_morder[] = "morder";
static const char __pyx_k_mshape[] = "mshape";
static const char __pyx_k_nattrs[] = "nattrs";
+static const char __pyx_k_nspace[] = "nspace";
static const char __pyx_k_nsteps[] = "nsteps";
static const char __pyx_k_offset[] = "offset";
+static const char __pyx_k_origin[] = "origin";
static const char __pyx_k_points[] = "points";
static const char __pyx_k_rstrip[] = "rstrip";
static const char __pyx_k_scalar[] = "scalar";
@@ -2431,6 +2454,7 @@ static const char __pyx_k_uint16[] = "uint16";
static const char __pyx_k_uint32[] = "uint32";
static const char __pyx_k_uint64[] = "uint64";
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_Reading[] = "Reading ... ";
@@ -2444,13 +2468,17 @@ static const char __pyx_k_float16[] = "float16";
static const char __pyx_k_float32[] = "float32";
static const char __pyx_k_float64[] = "float64";
static const char __pyx_k_getitem[] = "__getitem__";
+static const char __pyx_k_groupid[] = "groupid";
static const char __pyx_k_integer[] = "integer";
static const char __pyx_k_is_open[] = "is_open";
+static const char __pyx_k_maximum[] = "maximum";
+static const char __pyx_k_npoints[] = "npoints";
static const char __pyx_k_prepare[] = "__prepare__";
static const char __pyx_k_readvar[] = "_readvar";
static const char __pyx_k_replace[] = "replace";
static const char __pyx_k_reshape[] = "reshape";
static const char __pyx_k_setitem[] = "__setitem__";
+static const char __pyx_k_spacing[] = "spacing";
static const char __pyx_k_unknown[] = "unknown";
static const char __pyx_k_varname[] = "varname";
static const char __pyx_k_version[] = "version";
@@ -2467,6 +2495,7 @@ static const char __pyx_k_group_id[] = "group_id";
static const char __pyx_k_is_noxml[] = "is_noxml";
static const char __pyx_k_itemsize[] = "itemsize";
static const char __pyx_k_iterkeys[] = "iterkeys";
+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_";
@@ -2476,11 +2505,14 @@ static const char __pyx_k_COMM_SELF[] = "COMM_SELF";
static const char __pyx_k_TypeError[] = "TypeError";
static const char __pyx_k_adios_mpi[] = "adios_mpi";
static const char __pyx_k_base_path[] = "base_path";
+static const char __pyx_k_cell_type[] = "cell_type";
+static const char __pyx_k_centering[] = "centering";
static const char __pyx_k_complex64[] = "complex64";
static const char __pyx_k_complex_2[] = "complex";
static const char __pyx_k_data_size[] = "data_size";
static const char __pyx_k_enumerate[] = "enumerate";
static const char __pyx_k_file_size[] = "file_size";
+static const char __pyx_k_hyperslab[] = "hyperslab";
static const char __pyx_k_is_static[] = "is_static";
static const char __pyx_k_is_stream[] = "is_stream";
static const char __pyx_k_iteritems[] = "iteritems";
@@ -2489,11 +2521,15 @@ static const char __pyx_k_lock_mode[] = "lock_mode";
static const char __pyx_k_metaclass[] = "__metaclass__";
static const char __pyx_k_printself[] = "printself";
static const char __pyx_k_readvar_2[] = "readvar";
+static const char __pyx_k_timescale[] = "timescale";
+static const char __pyx_k_timesteps[] = "timesteps";
static const char __pyx_k_traceback[] = "traceback";
+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_ValueError[] = "ValueError";
+static const char __pyx_k_buffersize[] = "buffersize";
static const char __pyx_k_complex128[] = "complex128";
static const char __pyx_k_contiguous[] = "contiguous";
static const char __pyx_k_dimensions[] = "dimensions";
@@ -2508,14 +2544,18 @@ static const char __pyx_k_selections[] = "selections";
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_READ_METHOD[] = "READ_METHOD";
static const char __pyx_k_buffer_size[] = "buffer_size";
static const char __pyx_k_concatenate[] = "concatenate";
+static const char __pyx_k_coordinates[] = "coordinates";
static const char __pyx_k_long_double[] = "long_double";
static const char __pyx_k_method_name[] = "method_name";
static const char __pyx_k_read_points[] = "read_points";
static const char __pyx_k_step_scalar[] = "step_scalar";
+static const char __pyx_k_syncgroupid[] = "syncgroupid";
static const char __pyx_k_timeout_sec[] = "timeout_sec";
+static const char __pyx_k_timevarying[] = "timevarying";
static const char __pyx_k_BP_AGGREGATE[] = "BP_AGGREGATE";
static const char __pyx_k_RuntimeError[] = "RuntimeError";
static const char __pyx_k_current_step[] = "current_step";
@@ -2534,6 +2574,7 @@ static const char __pyx_k_unsigned_long[] = "unsigned_long";
static const char __pyx_k_FancySelection[] = "FancySelection";
static const char __pyx_k_double_complex[] = "double_complex";
static const char __pyx_k_exception_type[] = "exception_type";
+static const char __pyx_k_schema_version[] = "schema_version";
static const char __pyx_k_unsigned_short[] = "unsigned_short";
static const char __pyx_k_Not_a_valid_var[] = "Not a valid var";
static const char __pyx_k_Not_an_open_var[] = "Not an open var";
@@ -2545,24 +2586,26 @@ 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_var_read_line_1264[] = "var.read (line 1264)";
+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_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";
+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_1803[] = "writer.define_var (line 1803)";
+static const char __pyx_k_writer_define_var_line_2019[] = "writer.define_var (line 2019)";
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_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_1781[] = "writer.declare_group (line 1781)";
+static const char __pyx_k_writer_declare_group_line_1982[] = "writer.declare_group (line 1982)";
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, value=%r)";
-static const char __pyx_k_Define_a_variable_associated_wi[] = "\n Define a variable associated with the file.\n\n Args:\n varname (str): variable name.\n ldim (tuple, optional): local dimension (default: tuple())\n gdim (tuple, optional): global dimension (default: tuple())\n offset (tuple, optional): offset (default: tuple())\n\n Example:\n\n Write 'temperature' variable of size of 2x3 array.\n\n >>> fw.defi [...]
+static const char __pyx_k_AdiosVarinfo_name_r_ldim_r_gdim[] = "AdiosVarinfo (name=%r, ldim=%r, gdim=%r, offset=%r, transform=%r, value=%r)";
+static const char __pyx_k_Define_a_variable_associated_wi[] = "\n Define a variable associated with the file.\n\n Args:\n varname (str): variable name\n ldim (tuple, optional): local dimension (default: tuple())\n gdim (tuple, optional): global dimension (default: tuple())\n offset (tuple, optional): offset (default: tuple())\n transform (str): transform name\n\n Example:\n\n Write 'temperature' variable o [...]
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)";
@@ -2684,8 +2727,11 @@ static PyObject *__pyx_n_s_base_path;
static PyObject *__pyx_n_s_bool;
static PyObject *__pyx_n_s_bpls;
static PyObject *__pyx_n_s_buffer_size;
+static PyObject *__pyx_n_s_buffersize;
static PyObject *__pyx_n_s_byte;
static PyObject *__pyx_kp_s_bytes;
+static PyObject *__pyx_n_s_cell_type;
+static PyObject *__pyx_n_s_centering;
static PyObject *__pyx_n_s_char;
static PyObject *__pyx_n_s_close;
static PyObject *__pyx_n_s_comm;
@@ -2696,9 +2742,11 @@ static PyObject *__pyx_n_s_complex_2;
static PyObject *__pyx_n_s_concatenate;
static PyObject *__pyx_n_s_config;
static PyObject *__pyx_n_s_contiguous;
+static PyObject *__pyx_n_s_coordinates;
static PyObject *__pyx_n_s_copy;
static PyObject *__pyx_n_s_count;
static PyObject *__pyx_n_s_current_step;
+static PyObject *__pyx_n_s_data;
static PyObject *__pyx_n_s_data_size;
static PyObject *__pyx_n_s_declare_group;
static PyObject *__pyx_n_s_define;
@@ -2738,7 +2786,9 @@ static PyObject *__pyx_n_s_gname;
static PyObject *__pyx_n_s_group;
static PyObject *__pyx_n_s_group_id;
static PyObject *__pyx_n_s_group_name;
+static PyObject *__pyx_n_s_groupid;
static PyObject *__pyx_n_s_hl;
+static PyObject *__pyx_n_s_hyperslab;
static PyObject *__pyx_n_s_import;
static PyObject *__pyx_n_s_index;
static PyObject *__pyx_n_s_init;
@@ -2766,6 +2816,8 @@ static PyObject *__pyx_n_s_lock_mode;
static PyObject *__pyx_n_s_long;
static PyObject *__pyx_n_s_long_double;
static PyObject *__pyx_n_s_main;
+static PyObject *__pyx_n_s_maximum;
+static PyObject *__pyx_n_s_meshname;
static PyObject *__pyx_n_s_metaclass;
static PyObject *__pyx_n_s_method;
static PyObject *__pyx_n_s_method_name;
@@ -2783,11 +2835,14 @@ static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou;
static PyObject *__pyx_n_s_ndim;
static PyObject *__pyx_n_s_normalize_key;
static PyObject *__pyx_n_s_np;
+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_n_s_nvars;
static PyObject *__pyx_n_s_offset;
static PyObject *__pyx_n_s_order;
+static PyObject *__pyx_n_s_origin;
static PyObject *__pyx_n_s_os;
static PyObject *__pyx_n_s_parameters;
static PyObject *__pyx_n_s_path;
@@ -2813,13 +2868,16 @@ static PyObject *__pyx_n_s_replace;
static PyObject *__pyx_n_s_reshape;
static PyObject *__pyx_n_s_rstrip;
static PyObject *__pyx_n_s_scalar;
+static PyObject *__pyx_n_s_schema_version;
static PyObject *__pyx_n_s_sel;
static PyObject *__pyx_n_s_select;
static PyObject *__pyx_n_s_selections;
+static PyObject *__pyx_n_s_set_time_aggregation;
static PyObject *__pyx_n_s_setitem;
static PyObject *__pyx_n_s_shape;
static PyObject *__pyx_n_s_short;
static PyObject *__pyx_n_s_size;
+static PyObject *__pyx_n_s_spacing;
static PyObject *__pyx_n_s_split;
static PyObject *__pyx_n_s_start;
static PyObject *__pyx_n_s_startswith;
@@ -2830,13 +2888,20 @@ static PyObject *__pyx_n_s_string_2;
static PyObject *__pyx_n_s_string_array;
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_test;
static PyObject *__pyx_n_s_time_index;
static PyObject *__pyx_n_s_time_steps;
static PyObject *__pyx_n_s_timeout_sec;
+static PyObject *__pyx_n_s_timescale;
+static PyObject *__pyx_n_s_timeseries;
+static PyObject *__pyx_n_s_timesteps;
+static PyObject *__pyx_n_s_timevarying;
static PyObject *__pyx_n_s_tostring;
static PyObject *__pyx_n_s_traceback;
+static PyObject *__pyx_n_s_transform;
+static PyObject *__pyx_n_s_transform_type_str;
static PyObject *__pyx_n_s_type;
static PyObject *__pyx_n_s_uint16;
static PyObject *__pyx_n_s_uint32;
@@ -2853,8 +2918,9 @@ static PyObject *__pyx_n_s_val;
static PyObject *__pyx_n_s_value;
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_1264;
+static PyObject *__pyx_kp_u_var_read_line_1456;
static PyObject *__pyx_n_s_varid;
static PyObject *__pyx_n_s_varname;
static PyObject *__pyx_n_s_vars;
@@ -2863,8 +2929,8 @@ 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_1781;
-static PyObject *__pyx_kp_u_writer_define_var_line_1803;
+static PyObject *__pyx_kp_u_writer_declare_group_line_1982;
+static PyObject *__pyx_kp_u_writer_define_var_line_2019;
static PyObject *__pyx_n_s_xrange;
static PyObject *__pyx_n_s_zeros;
static PyObject *__pyx_n_s_zip;
@@ -2888,14 +2954,32 @@ static PyObject *__pyx_pf_9adios_mpi_32init_noxml(CYTHON_UNUSED PyObject *__pyx_
static PyObject *__pyx_pf_9adios_mpi_34allocate_buffer(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_when, uint64_t __pyx_v_buffer_size); /* proto */
static PyObject *__pyx_pf_9adios_mpi_36declare_group(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_name, PyObject *__pyx_v_time_index, int __pyx_v_stats); /* proto */
static PyObject *__pyx_pf_9adios_mpi_38define_var(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group_id, PyObject *__pyx_v_name, PyObject *__pyx_v_path, int __pyx_v_atype, PyObject *__pyx_v_dimensions, PyObject *__pyx_v_global_dimensions, PyObject *__pyx_v_local_offsets); /* proto */
-static PyObject *__pyx_pf_9adios_mpi_40define_attribute(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group, PyObject *__pyx_v_name, PyObject *__pyx_v_path, int __pyx_v_atype, PyObject *__pyx_v_value, PyObject *__pyx_v_var); /* proto */
-static PyObject *__pyx_pf_9adios_mpi_42define_attribute_byvalue(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group, PyObject *__pyx_v_name, PyObject *__pyx_v_path, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9adios_mpi_44select_method(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group, PyObject *__pyx_v_method, PyObject *__pyx_v_parameters, PyObject *__pyx_v_base_path); /* proto */
-static PyObject *__pyx_pf_9adios_mpi_46adios2npdtype(CYTHON_UNUSED PyObject *__pyx_self, ADIOS_DATATYPES __pyx_v_t, int __pyx_v_strlen); /* proto */
-static PyObject *__pyx_pf_9adios_mpi_48np2adiostype(CYTHON_UNUSED PyObject *__pyx_self, PyArray_Descr *__pyx_v_nptype); /* proto */
-static PyObject *__pyx_pf_9adios_mpi_50adiostype2string(CYTHON_UNUSED PyObject *__pyx_self, ADIOS_DATATYPES __pyx_v_type); /* proto */
-static PyObject *__pyx_pf_9adios_mpi_52read_init(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method_name, struct PyMPICommObject *__pyx_v_comm, PyObject *__pyx_v_parameters); /* proto */
-static PyObject *__pyx_pf_9adios_mpi_54read_finalize(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method_name); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_40define_schema_version(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group_id, PyObject *__pyx_v_schema_version); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_42define_var_mesh(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group_id, PyObject *__pyx_v_varname, PyObject *__pyx_v_meshname); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_44define_var_centering(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group_id, PyObject *__pyx_v_varname, PyObject *__pyx_v_centering); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_46define_var_timesteps(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_timesteps, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_48define_var_timescale(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_timescale, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_50define_var_timeseriesformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_timeseries, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_52define_var_hyperslab(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_hyperslab, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_54define_mesh_timevarying(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_timevarying, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_56define_mesh_timesteps(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_timesteps, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_58define_mesh_timescale(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_timescale, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_60define_mesh_timeseriesformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_timeseries, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_62define_mesh_uniform(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_dimensions, PyObject *__pyx_v_origin, PyObject *__pyx_v_spacing, PyObject *__pyx_v_maximum, PyObject *__pyx_v_nspace, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_64define_mesh_rectilinear(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_dimensions, PyObject *__pyx_v_coordinates, PyObject *__pyx_v_nspace, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_66define_mesh_structured(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_dimensions, PyObject *__pyx_v_points, PyObject *__pyx_v_nspace, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_68define_mesh_unstructured(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_points, PyObject *__pyx_v_data, PyObject *__pyx_v_count, PyObject *__pyx_v_cell_type, PyObject *__pyx_v_npoints, PyObject *__pyx_v_nspace, int64_t __pyx_v_group_id, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_70define_attribute(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group, PyObject *__pyx_v_name, PyObject *__pyx_v_path, int __pyx_v_atype, PyObject *__pyx_v_value, PyObject *__pyx_v_var); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_72define_attribute_byvalue(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group, PyObject *__pyx_v_name, PyObject *__pyx_v_path, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_74select_method(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_group, PyObject *__pyx_v_method, PyObject *__pyx_v_parameters, PyObject *__pyx_v_base_path); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_76set_transform(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_var_id, PyObject *__pyx_v_transform_type_str); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_78set_max_buffer_size(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_max_buffer_size_MB); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_80set_time_aggregation(CYTHON_UNUSED PyObject *__pyx_self, int64_t __pyx_v_groupid, uint64_t __pyx_v_buffersize, int64_t __pyx_v_syncgroupid); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_82adios2npdtype(CYTHON_UNUSED PyObject *__pyx_self, ADIOS_DATATYPES __pyx_v_t, int __pyx_v_strlen); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_84np2adiostype(CYTHON_UNUSED PyObject *__pyx_self, PyArray_Descr *__pyx_v_nptype); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_86adiostype2string(CYTHON_UNUSED PyObject *__pyx_self, ADIOS_DATATYPES __pyx_v_type); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_88read_init(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method_name, struct PyMPICommObject *__pyx_v_comm, PyObject *__pyx_v_parameters); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_90read_finalize(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method_name); /* proto */
static PyObject *__pyx_pf_9adios_mpi_8softdict___getitem__(struct __pyx_obj_9adios_mpi_softdict *__pyx_v_self, PyObject *__pyx_v_varname); /* proto */
static PyObject *__pyx_pf_9adios_mpi_4file_4name___get__(struct __pyx_obj_9adios_mpi_file *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_9adios_mpi_4file_5nvars___get__(struct __pyx_obj_9adios_mpi_file *__pyx_v_self); /* proto */
@@ -2993,17 +3077,19 @@ static PyObject *__pyx_pf_9adios_mpi_6writer_8is_noxml___get__(struct __pyx_obj_
static PyObject *__pyx_pf_9adios_mpi_6writer_4mode___get__(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_9adios_mpi_6writer_4vars___get__(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self); /* proto */
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 */
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, struct PyMPICommObject *__pyx_v_comm); /* 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); /* proto */
-static PyObject *__pyx_pf_9adios_mpi_6writer_4define_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); /* proto */
-static PyObject *__pyx_pf_9adios_mpi_6writer_6define_attr(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self, PyObject *__pyx_v_attrname); /* proto */
-static PyObject *__pyx_pf_9adios_mpi_6writer_8define_dynamic_attr(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self, PyObject *__pyx_v_attrname, PyObject *__pyx_v_varname, PyObject *__pyx_v_dtype); /* proto */
-static int __pyx_pf_9adios_mpi_6writer_10__setitem__(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self, PyObject *__pyx_v_name, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9adios_mpi_6writer_12__getitem__(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self, PyObject *__pyx_v_name); /* proto */
-static PyObject *__pyx_pf_9adios_mpi_6writer_14close(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9adios_mpi_6writer_16__repr__(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9adios_mpi_6writer_18__enter__(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9adios_mpi_6writer_20__exit__(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_exception_type, CYTHON_UNUSED PyObject *__pyx_v_exception_value, CYTHON_UNUSED PyObject *__pyx_v_traceback); /* 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 */
+static PyObject *__pyx_pf_9adios_mpi_6writer_10define_dynamic_attr(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self, PyObject *__pyx_v_attrname, PyObject *__pyx_v_varname, PyObject *__pyx_v_dtype); /* proto */
+static int __pyx_pf_9adios_mpi_6writer_12__setitem__(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self, PyObject *__pyx_v_name, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_6writer_14__getitem__(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_6writer_16close(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_6writer_18__repr__(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_6writer_20__enter__(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_6writer_22__exit__(struct __pyx_obj_9adios_mpi_writer *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_exception_type, CYTHON_UNUSED PyObject *__pyx_v_exception_value, CYTHON_UNUSED PyObject *__pyx_v_traceback); /* proto */
static PyObject *__pyx_pf_9adios_mpi_8attrinfo_4name___get__(struct __pyx_obj_9adios_mpi_attrinfo *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_9adios_mpi_8attrinfo_9is_static___get__(struct __pyx_obj_9adios_mpi_attrinfo *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_9adios_mpi_8attrinfo_5dtype___get__(struct __pyx_obj_9adios_mpi_attrinfo *__pyx_v_self); /* proto */
@@ -3012,7 +3098,9 @@ static int __pyx_pf_9adios_mpi_8attrinfo_5value_2__set__(struct __pyx_obj_9adios
static int __pyx_pf_9adios_mpi_8attrinfo___init__(struct __pyx_obj_9adios_mpi_attrinfo *__pyx_v_self, PyObject *__pyx_v_name, PyObject *__pyx_v_value, PyObject *__pyx_v_dtype, int __pyx_v_is_static); /* proto */
static PyObject *__pyx_pf_9adios_mpi_8attrinfo_2define(struct __pyx_obj_9adios_mpi_attrinfo *__pyx_v_self, int64_t __pyx_v_gid); /* proto */
static PyObject *__pyx_pf_9adios_mpi_8attrinfo_4__repr__(struct __pyx_obj_9adios_mpi_attrinfo *__pyx_v_self); /* proto */
-static int __pyx_pf_9adios_mpi_7varinfo___init__(struct __pyx_obj_9adios_mpi_varinfo *__pyx_v_self, PyObject *__pyx_v_name, PyObject *__pyx_v_ldim, PyObject *__pyx_v_gdim, PyObject *__pyx_v_offset, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_7varinfo_9transform___get__(struct __pyx_obj_9adios_mpi_varinfo *__pyx_v_self); /* proto */
+static int __pyx_pf_9adios_mpi_7varinfo_9transform_2__set__(struct __pyx_obj_9adios_mpi_varinfo *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_9adios_mpi_7varinfo___init__(struct __pyx_obj_9adios_mpi_varinfo *__pyx_v_self, PyObject *__pyx_v_name, PyObject *__pyx_v_ldim, PyObject *__pyx_v_gdim, PyObject *__pyx_v_offset, PyObject *__pyx_v_value, PyObject *__pyx_v_transform); /* proto */
static PyObject *__pyx_pf_9adios_mpi_7varinfo_2define(struct __pyx_obj_9adios_mpi_varinfo *__pyx_v_self, int64_t __pyx_v_gid); /* proto */
static PyObject *__pyx_pf_9adios_mpi_7varinfo_4bytes(struct __pyx_obj_9adios_mpi_varinfo *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_9adios_mpi_7varinfo_6write(struct __pyx_obj_9adios_mpi_varinfo *__pyx_v_self, int64_t __pyx_v_fd); /* proto */
@@ -3029,8 +3117,8 @@ static int __pyx_pf_9adios_mpi_7varinfo_6offset_4__del__(struct __pyx_obj_9adios
static PyObject *__pyx_pf_9adios_mpi_7varinfo_5value___get__(struct __pyx_obj_9adios_mpi_varinfo *__pyx_v_self); /* proto */
static int __pyx_pf_9adios_mpi_7varinfo_5value_2__set__(struct __pyx_obj_9adios_mpi_varinfo *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
static int __pyx_pf_9adios_mpi_7varinfo_5value_4__del__(struct __pyx_obj_9adios_mpi_varinfo *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9adios_mpi_56readvar(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fname, PyObject *__pyx_v_varname); /* proto */
-static PyObject *__pyx_pf_9adios_mpi_58bpls(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fname); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_92readvar(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fname, PyObject *__pyx_v_varname); /* proto */
+static PyObject *__pyx_pf_9adios_mpi_94bpls(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fname); /* proto */
static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
static PyObject *__pyx_tp_new_9adios_mpi_softdict(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
@@ -3065,13 +3153,14 @@ static PyObject *__pyx_int_neg_1;
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/* function exit code */
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return __pyx_r;
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goto __pyx_L5_argtuple_error;
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@@ -6598,7 +6686,7 @@ static PyObject *__pyx_pf_9adios_mpi_34allocate_buffer(CYTHON_UNUSED PyObject *_
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return __pyx_r;
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+ adios_declare_group((&__pyx_v_id), __pyx_t_2, __pyx_t_4, ((ADIOS_STATISTICS_FLAG)__pyx_v_stats));
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* s2b(time_index),
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+ * <ADIOS_STATISTICS_FLAG> stats)
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*/
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goto __pyx_L0;
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static PyObject *__pyx_pw_9adios_mpi_37declare_group(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
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PyObject *__pyx_v_time_index = 0;
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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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return __pyx_r;
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*
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PyObject *__pyx_v_global_dimensions = ((PyObject*)__pyx_kp_s__10);
PyObject *__pyx_v_local_offsets = ((PyObject*)__pyx_kp_s__10);
- int __pyx_r;
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PyObject *__pyx_t_1 = NULL;
char *__pyx_t_2;
@@ -6863,62 +6951,62 @@ static int __pyx_f_9adios_mpi_define_var(int64_t __pyx_v_group_id, PyObject *__p
}
}
- /* "adios_mpi.pyx":475
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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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* s2b(dimensions),
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__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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*/
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__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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}
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goto __pyx_L5;
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+ /* "adios_mpi.pyx":711
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*/
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}
__pyx_L5:;
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@@ -7823,9 +10563,9 @@ static int __pyx_f_9adios_mpi_define_attribute_byvalue(int64_t __pyx_v_group, Py
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+static PyObject *__pyx_pw_9adios_mpi_73define_attribute_byvalue(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
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int64_t __pyx_v_group;
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else {
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/* function exit code */
goto __pyx_L0;
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return __pyx_r;
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* <void *> val_.data)
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@@ -7936,7 +10676,7 @@ static PyObject *__pyx_pf_9adios_mpi_42define_attribute_byvalue(CYTHON_UNUSED Py
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*/
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+static PyObject *__pyx_pw_9adios_mpi_75select_method(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_f_9adios_mpi_select_method(int64_t __pyx_v_group, PyObject *__pyx_v_method, CYTHON_UNUSED int __pyx_skip_dispatch, struct __pyx_opt_args_9adios_mpi_select_method *__pyx_optional_args) {
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}
}
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* str base_path = ""):
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* s2b(parameters),
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* s2b(method),
* s2b(parameters),
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*
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* str parameters = "",
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/* Python wrapper */
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-static PyObject *__pyx_pw_9adios_mpi_45select_method(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
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else {
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goto __pyx_L3;
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goto __pyx_L3;
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- /* "adios_mpi.pyx":617
+ /* "adios_mpi.pyx":809
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goto __pyx_L3;
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goto __pyx_L3;
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goto __pyx_L3;
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return __pyx_r;
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__Pyx_RefNannySetupContext("__init__", 0);
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*/
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__pyx_v_self->vars = ((struct __pyx_obj_9adios_mpi_softdict *)__pyx_t_1);
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__pyx_t_1 = 0;
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goto __pyx_L3;
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__pyx_t_7 = __pyx_v_self->fp->nattrs;
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__pyx_v_self->current_step = __pyx_t_7;
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__pyx_v_self->last_step = __pyx_t_7;
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__pyx_v_self->endianness = __pyx_t_7;
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__pyx_v_self->file_size = __pyx_t_8;
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*/
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*/
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*/
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+ /* "adios_mpi.pyx":1409
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*/
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*/
}
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goto __pyx_L0;
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return __pyx_r;
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-static PyObject *__pyx_pw_9adios_mpi_6writer_5define_var(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pw_9adios_mpi_6writer_7define_var(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9adios_mpi_6writer_6define_var[] = "writer.define_var(self, str varname, ldim=<\077\077?>, gdim=<\077\077?>, offset=<\077\077?>, transform=None)\n\n Define a variable associated with the file.\n\n Args:\n varname (str): variable name\n ldim (tuple, optional): local dimension (default: tuple())\n gdim (tuple, optional): global dimension (default: tuple())\n offset (tuple, optional): offset (default: tuple())\n [...]
+static PyObject *__pyx_pw_9adios_mpi_6writer_7define_var(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_varname = 0;
PyObject *__pyx_v_ldim = 0;
PyObject *__pyx_v_gdim = 0;
PyObject *__pyx_v_offset = 0;
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- values[2] = __pyx_k__55;
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+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_varname,&__pyx_n_s_ldim,&__pyx_n_s_gdim,&__pyx_n_s_offset,&__pyx_n_s_transform,0};
+ PyObject* values[5] = {0,0,0,0,0};
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+ /* "adios_mpi.pyx":2023
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Py_ssize_t kw_args;
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switch (pos_args) {
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PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_offset);
if (value) { values[3] = value; kw_args--; }
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+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_varname), (&PyString_Type), 1, "varname", 1))) __PYX_ERR(0, 2019, __pyx_L1_error)
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+
+ /* "adios_mpi.pyx":2019
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- /* "adios_mpi.pyx":1803
- * select_method(self.gid, self.method, self.method_params, "")
+ /* "adios_mpi.pyx":2019
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*
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__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
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@@ -28672,8 +32115,8 @@ static PyObject *__pyx_pf_9adios_mpi_6writer_4define_var(struct __pyx_obj_9adios
return __pyx_r;
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-/* "adios_mpi.pyx":1825
- * self.vars[varname] = varinfo(varname, ldim, gdim, offset)
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*
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@@ -28681,14 +32124,14 @@ static PyObject *__pyx_pf_9adios_mpi_6writer_4define_var(struct __pyx_obj_9adios
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+static PyObject *__pyx_pw_9adios_mpi_6writer_9define_attr(PyObject *__pyx_v_self, PyObject *__pyx_v_attrname); /*proto*/
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- /* "adios_mpi.pyx":1825
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return __pyx_r;
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if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_varname)) != 0)) kw_args--;
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goto __pyx_L4_argument_unpacking_done;
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- __Pyx_RaiseArgtupleInvalid("define_dynamic_attr", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 1835, __pyx_L3_error)
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if (__pyx_t_2) {
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+ /* "adios_mpi.pyx":2232
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*/
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+ * return ("AdiosVarinfo (name=%r, ldim=%r, gdim=%r, offset=%r, transform=%r, value=%r)") % \ # <<<<<<<<<<<<<<
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+ * return ("AdiosVarinfo (name=%r, ldim=%r, gdim=%r, offset=%r, transform=%r, value=%r)") % \
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return __pyx_r;
}
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return __pyx_r;
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return __pyx_r;
}
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* cdef public ldim
* cdef public gdim
* cdef public offset # <<<<<<<<<<<<<<
* cdef public value
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+ * cdef str transform
*/
/* Python wrapper */
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return __pyx_r;
}
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* cdef public gdim
* cdef public offset
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/* Python wrapper */
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return __pyx_r;
}
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PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "iterkeys");
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PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "iterkeys");
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* 'vars': tuple([ k for k in f.vars.iterkeys() ]),
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PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
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- /* "adios_mpi.pyx":2063
+ /* "adios_mpi.pyx":2305
* return v.read(from_steps=0, nsteps=v.nsteps)
*
* def bpls(fname): # <<<<<<<<<<<<<<
@@ -36379,7 +40271,7 @@ static PyObject *__pyx_sq_item_9adios_mpi_writer(PyObject *o, Py_ssize_t i) {
static int __pyx_mp_ass_subscript_9adios_mpi_writer(PyObject *o, PyObject *i, PyObject *v) {
if (v) {
- return __pyx_pw_9adios_mpi_6writer_11__setitem__(o, i, v);
+ return __pyx_pw_9adios_mpi_6writer_13__setitem__(o, i, v);
}
else {
PyErr_Format(PyExc_NotImplementedError,
@@ -36412,14 +40304,19 @@ static PyObject *__pyx_getprop_9adios_mpi_6writer_attrs(PyObject *o, CYTHON_UNUS
return __pyx_pw_9adios_mpi_6writer_5attrs_1__get__(o);
}
+static PyObject *__pyx_getprop_9adios_mpi_6writer_timeaggregation_buffersize(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_9adios_mpi_6writer_26timeaggregation_buffersize_1__get__(o);
+}
+
static PyMethodDef __pyx_methods_9adios_mpi_writer[] = {
{"declare_group", (PyCFunction)__pyx_pw_9adios_mpi_6writer_3declare_group, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_6writer_2declare_group},
- {"define_var", (PyCFunction)__pyx_pw_9adios_mpi_6writer_5define_var, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_6writer_4define_var},
- {"define_attr", (PyCFunction)__pyx_pw_9adios_mpi_6writer_7define_attr, METH_O, __pyx_doc_9adios_mpi_6writer_6define_attr},
- {"define_dynamic_attr", (PyCFunction)__pyx_pw_9adios_mpi_6writer_9define_dynamic_attr, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_6writer_8define_dynamic_attr},
- {"close", (PyCFunction)__pyx_pw_9adios_mpi_6writer_15close, METH_NOARGS, __pyx_doc_9adios_mpi_6writer_14close},
- {"__enter__", (PyCFunction)__pyx_pw_9adios_mpi_6writer_19__enter__, METH_NOARGS, __pyx_doc_9adios_mpi_6writer_18__enter__},
- {"__exit__", (PyCFunction)__pyx_pw_9adios_mpi_6writer_21__exit__, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_6writer_20__exit__},
+ {"set_time_aggregation", (PyCFunction)__pyx_pw_9adios_mpi_6writer_5set_time_aggregation, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_6writer_4set_time_aggregation},
+ {"define_var", (PyCFunction)__pyx_pw_9adios_mpi_6writer_7define_var, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_6writer_6define_var},
+ {"define_attr", (PyCFunction)__pyx_pw_9adios_mpi_6writer_9define_attr, METH_O, __pyx_doc_9adios_mpi_6writer_8define_attr},
+ {"define_dynamic_attr", (PyCFunction)__pyx_pw_9adios_mpi_6writer_11define_dynamic_attr, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_6writer_10define_dynamic_attr},
+ {"close", (PyCFunction)__pyx_pw_9adios_mpi_6writer_17close, METH_NOARGS, __pyx_doc_9adios_mpi_6writer_16close},
+ {"__enter__", (PyCFunction)__pyx_pw_9adios_mpi_6writer_21__enter__, METH_NOARGS, __pyx_doc_9adios_mpi_6writer_20__enter__},
+ {"__exit__", (PyCFunction)__pyx_pw_9adios_mpi_6writer_23__exit__, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_6writer_22__exit__},
{0, 0, 0, 0}
};
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{(char *)"mode", __pyx_getprop_9adios_mpi_6writer_mode, 0, (char *)" Writing mode: overwrite or append. ", 0},
{(char *)"vars", __pyx_getprop_9adios_mpi_6writer_vars, 0, (char *)" Dictionary of variables to write. ", 0},
{(char *)"attrs", __pyx_getprop_9adios_mpi_6writer_attrs, 0, (char *)" Dictionary of attributes to write. ", 0},
+ {(char *)"timeaggregation_buffersize", __pyx_getprop_9adios_mpi_6writer_timeaggregation_buffersize, 0, (char *)" Get time-aggregation buffersize. ", 0},
{0, 0, 0, 0, 0}
};
@@ -36448,7 +40346,7 @@ static PySequenceMethods __pyx_tp_as_sequence_writer = {
static PyMappingMethods __pyx_tp_as_mapping_writer = {
0, /*mp_length*/
- __pyx_pw_9adios_mpi_6writer_13__getitem__, /*mp_subscript*/
+ __pyx_pw_9adios_mpi_6writer_15__getitem__, /*mp_subscript*/
__pyx_mp_ass_subscript_9adios_mpi_writer, /*mp_ass_subscript*/
};
@@ -36467,7 +40365,7 @@ static PyTypeObject __pyx_type_9adios_mpi_writer = {
#if PY_MAJOR_VERSION >= 3
0, /*tp_as_async*/
#endif
- __pyx_pw_9adios_mpi_6writer_17__repr__, /*tp_repr*/
+ __pyx_pw_9adios_mpi_6writer_19__repr__, /*tp_repr*/
0, /*tp_as_number*/
&__pyx_tp_as_sequence_writer, /*tp_as_sequence*/
&__pyx_tp_as_mapping_writer, /*tp_as_mapping*/
@@ -36676,6 +40574,7 @@ static PyObject *__pyx_tp_new_9adios_mpi_varinfo(PyTypeObject *t, CYTHON_UNUSED
p->gdim = Py_None; Py_INCREF(Py_None);
p->offset = Py_None; Py_INCREF(Py_None);
p->value = Py_None; Py_INCREF(Py_None);
+ p->transform = ((PyObject*)Py_None); Py_INCREF(Py_None);
return o;
}
@@ -36692,6 +40591,7 @@ static void __pyx_tp_dealloc_9adios_mpi_varinfo(PyObject *o) {
Py_CLEAR(p->gdim);
Py_CLEAR(p->offset);
Py_CLEAR(p->value);
+ Py_CLEAR(p->transform);
(*Py_TYPE(o)->tp_free)(o);
}
@@ -36731,6 +40631,20 @@ static int __pyx_tp_clear_9adios_mpi_varinfo(PyObject *o) {
return 0;
}
+static PyObject *__pyx_getprop_9adios_mpi_7varinfo_transform(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_9adios_mpi_7varinfo_9transform_1__get__(o);
+}
+
+static int __pyx_setprop_9adios_mpi_7varinfo_transform(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+ if (v) {
+ return __pyx_pw_9adios_mpi_7varinfo_9transform_3__set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
+
static PyObject *__pyx_getprop_9adios_mpi_7varinfo_ldim(PyObject *o, CYTHON_UNUSED void *x) {
return __pyx_pw_9adios_mpi_7varinfo_4ldim_1__get__(o);
}
@@ -36791,6 +40705,7 @@ static PyMethodDef __pyx_methods_9adios_mpi_varinfo[] = {
};
static struct PyGetSetDef __pyx_getsets_9adios_mpi_varinfo[] = {
+ {(char *)"transform", __pyx_getprop_9adios_mpi_7varinfo_transform, __pyx_setprop_9adios_mpi_7varinfo_transform, (char *)" Transform method ", 0},
{(char *)"ldim", __pyx_getprop_9adios_mpi_7varinfo_ldim, __pyx_setprop_9adios_mpi_7varinfo_ldim, (char *)"ldim: object", 0},
{(char *)"gdim", __pyx_getprop_9adios_mpi_7varinfo_gdim, __pyx_setprop_9adios_mpi_7varinfo_gdim, (char *)"gdim: object", 0},
{(char *)"offset", __pyx_getprop_9adios_mpi_7varinfo_offset, __pyx_setprop_9adios_mpi_7varinfo_offset, (char *)"offset: object", 0},
@@ -36824,7 +40739,7 @@ static PyTypeObject __pyx_type_9adios_mpi_varinfo = {
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*/
- "varinfo(str name, ldim=<\077\077?>, gdim=<\077\077?>, offset=<\077\077?>, value=None)", /*tp_doc*/
+ "varinfo(str name, ldim=<\077\077?>, gdim=<\077\077?>, offset=<\077\077?>, value=None, transform=None)", /*tp_doc*/
__pyx_tp_traverse_9adios_mpi_varinfo, /*tp_traverse*/
__pyx_tp_clear_9adios_mpi_varinfo, /*tp_clear*/
0, /*tp_richcompare*/
@@ -36876,14 +40791,32 @@ static PyMethodDef __pyx_methods[] = {
{"allocate_buffer", (PyCFunction)__pyx_pw_9adios_mpi_35allocate_buffer, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_34allocate_buffer},
{"declare_group", (PyCFunction)__pyx_pw_9adios_mpi_37declare_group, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_36declare_group},
{"define_var", (PyCFunction)__pyx_pw_9adios_mpi_39define_var, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_38define_var},
- {"define_attribute", (PyCFunction)__pyx_pw_9adios_mpi_41define_attribute, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_40define_attribute},
- {"define_attribute_byvalue", (PyCFunction)__pyx_pw_9adios_mpi_43define_attribute_byvalue, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_42define_attribute_byvalue},
- {"select_method", (PyCFunction)__pyx_pw_9adios_mpi_45select_method, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_44select_method},
- {"adios2npdtype", (PyCFunction)__pyx_pw_9adios_mpi_47adios2npdtype, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_46adios2npdtype},
- {"np2adiostype", (PyCFunction)__pyx_pw_9adios_mpi_49np2adiostype, METH_O, __pyx_doc_9adios_mpi_48np2adiostype},
- {"adiostype2string", (PyCFunction)__pyx_pw_9adios_mpi_51adiostype2string, METH_O, __pyx_doc_9adios_mpi_50adiostype2string},
- {"read_init", (PyCFunction)__pyx_pw_9adios_mpi_53read_init, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_52read_init},
- {"read_finalize", (PyCFunction)__pyx_pw_9adios_mpi_55read_finalize, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_54read_finalize},
+ {"define_schema_version", (PyCFunction)__pyx_pw_9adios_mpi_41define_schema_version, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_40define_schema_version},
+ {"define_var_mesh", (PyCFunction)__pyx_pw_9adios_mpi_43define_var_mesh, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_42define_var_mesh},
+ {"define_var_centering", (PyCFunction)__pyx_pw_9adios_mpi_45define_var_centering, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_44define_var_centering},
+ {"define_var_timesteps", (PyCFunction)__pyx_pw_9adios_mpi_47define_var_timesteps, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_46define_var_timesteps},
+ {"define_var_timescale", (PyCFunction)__pyx_pw_9adios_mpi_49define_var_timescale, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_48define_var_timescale},
+ {"define_var_timeseriesformat", (PyCFunction)__pyx_pw_9adios_mpi_51define_var_timeseriesformat, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_50define_var_timeseriesformat},
+ {"define_var_hyperslab", (PyCFunction)__pyx_pw_9adios_mpi_53define_var_hyperslab, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_52define_var_hyperslab},
+ {"define_mesh_timevarying", (PyCFunction)__pyx_pw_9adios_mpi_55define_mesh_timevarying, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_54define_mesh_timevarying},
+ {"define_mesh_timesteps", (PyCFunction)__pyx_pw_9adios_mpi_57define_mesh_timesteps, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_56define_mesh_timesteps},
+ {"define_mesh_timescale", (PyCFunction)__pyx_pw_9adios_mpi_59define_mesh_timescale, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_58define_mesh_timescale},
+ {"define_mesh_timeseriesformat", (PyCFunction)__pyx_pw_9adios_mpi_61define_mesh_timeseriesformat, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_60define_mesh_timeseriesformat},
+ {"define_mesh_uniform", (PyCFunction)__pyx_pw_9adios_mpi_63define_mesh_uniform, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_62define_mesh_uniform},
+ {"define_mesh_rectilinear", (PyCFunction)__pyx_pw_9adios_mpi_65define_mesh_rectilinear, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_64define_mesh_rectilinear},
+ {"define_mesh_structured", (PyCFunction)__pyx_pw_9adios_mpi_67define_mesh_structured, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_66define_mesh_structured},
+ {"define_mesh_unstructured", (PyCFunction)__pyx_pw_9adios_mpi_69define_mesh_unstructured, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_68define_mesh_unstructured},
+ {"define_attribute", (PyCFunction)__pyx_pw_9adios_mpi_71define_attribute, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_70define_attribute},
+ {"define_attribute_byvalue", (PyCFunction)__pyx_pw_9adios_mpi_73define_attribute_byvalue, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_72define_attribute_byvalue},
+ {"select_method", (PyCFunction)__pyx_pw_9adios_mpi_75select_method, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_74select_method},
+ {"set_transform", (PyCFunction)__pyx_pw_9adios_mpi_77set_transform, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_76set_transform},
+ {"set_max_buffer_size", (PyCFunction)__pyx_pw_9adios_mpi_79set_max_buffer_size, METH_O, __pyx_doc_9adios_mpi_78set_max_buffer_size},
+ {"set_time_aggregation", (PyCFunction)__pyx_pw_9adios_mpi_81set_time_aggregation, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_80set_time_aggregation},
+ {"adios2npdtype", (PyCFunction)__pyx_pw_9adios_mpi_83adios2npdtype, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_82adios2npdtype},
+ {"np2adiostype", (PyCFunction)__pyx_pw_9adios_mpi_85np2adiostype, METH_O, __pyx_doc_9adios_mpi_84np2adiostype},
+ {"adiostype2string", (PyCFunction)__pyx_pw_9adios_mpi_87adiostype2string, METH_O, __pyx_doc_9adios_mpi_86adiostype2string},
+ {"read_init", (PyCFunction)__pyx_pw_9adios_mpi_89read_init, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_88read_init},
+ {"read_finalize", (PyCFunction)__pyx_pw_9adios_mpi_91read_finalize, METH_VARARGS|METH_KEYWORDS, __pyx_doc_9adios_mpi_90read_finalize},
{0, 0, 0, 0}
};
@@ -37008,8 +40941,11 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__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},
+ {&__pyx_n_s_buffersize, __pyx_k_buffersize, sizeof(__pyx_k_buffersize), 0, 0, 1, 1},
{&__pyx_n_s_byte, __pyx_k_byte, sizeof(__pyx_k_byte), 0, 0, 1, 1},
{&__pyx_kp_s_bytes, __pyx_k_bytes, sizeof(__pyx_k_bytes), 0, 0, 1, 0},
+ {&__pyx_n_s_cell_type, __pyx_k_cell_type, sizeof(__pyx_k_cell_type), 0, 0, 1, 1},
+ {&__pyx_n_s_centering, __pyx_k_centering, sizeof(__pyx_k_centering), 0, 0, 1, 1},
{&__pyx_n_s_char, __pyx_k_char, sizeof(__pyx_k_char), 0, 0, 1, 1},
{&__pyx_n_s_close, __pyx_k_close, sizeof(__pyx_k_close), 0, 0, 1, 1},
{&__pyx_n_s_comm, __pyx_k_comm, sizeof(__pyx_k_comm), 0, 0, 1, 1},
@@ -37020,9 +40956,11 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_concatenate, __pyx_k_concatenate, sizeof(__pyx_k_concatenate), 0, 0, 1, 1},
{&__pyx_n_s_config, __pyx_k_config, sizeof(__pyx_k_config), 0, 0, 1, 1},
{&__pyx_n_s_contiguous, __pyx_k_contiguous, sizeof(__pyx_k_contiguous), 0, 0, 1, 1},
+ {&__pyx_n_s_coordinates, __pyx_k_coordinates, sizeof(__pyx_k_coordinates), 0, 0, 1, 1},
{&__pyx_n_s_copy, __pyx_k_copy, sizeof(__pyx_k_copy), 0, 0, 1, 1},
{&__pyx_n_s_count, __pyx_k_count, sizeof(__pyx_k_count), 0, 0, 1, 1},
{&__pyx_n_s_current_step, __pyx_k_current_step, sizeof(__pyx_k_current_step), 0, 0, 1, 1},
+ {&__pyx_n_s_data, __pyx_k_data, sizeof(__pyx_k_data), 0, 0, 1, 1},
{&__pyx_n_s_data_size, __pyx_k_data_size, sizeof(__pyx_k_data_size), 0, 0, 1, 1},
{&__pyx_n_s_declare_group, __pyx_k_declare_group, sizeof(__pyx_k_declare_group), 0, 0, 1, 1},
{&__pyx_n_s_define, __pyx_k_define, sizeof(__pyx_k_define), 0, 0, 1, 1},
@@ -37062,7 +41000,9 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_group, __pyx_k_group, sizeof(__pyx_k_group), 0, 0, 1, 1},
{&__pyx_n_s_group_id, __pyx_k_group_id, sizeof(__pyx_k_group_id), 0, 0, 1, 1},
{&__pyx_n_s_group_name, __pyx_k_group_name, sizeof(__pyx_k_group_name), 0, 0, 1, 1},
+ {&__pyx_n_s_groupid, __pyx_k_groupid, sizeof(__pyx_k_groupid), 0, 0, 1, 1},
{&__pyx_n_s_hl, __pyx_k_hl, sizeof(__pyx_k_hl), 0, 0, 1, 1},
+ {&__pyx_n_s_hyperslab, __pyx_k_hyperslab, sizeof(__pyx_k_hyperslab), 0, 0, 1, 1},
{&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1},
{&__pyx_n_s_index, __pyx_k_index, sizeof(__pyx_k_index), 0, 0, 1, 1},
{&__pyx_n_s_init, __pyx_k_init, sizeof(__pyx_k_init), 0, 0, 1, 1},
@@ -37090,6 +41030,8 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_long, __pyx_k_long, sizeof(__pyx_k_long), 0, 0, 1, 1},
{&__pyx_n_s_long_double, __pyx_k_long_double, sizeof(__pyx_k_long_double), 0, 0, 1, 1},
{&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1},
+ {&__pyx_n_s_maximum, __pyx_k_maximum, sizeof(__pyx_k_maximum), 0, 0, 1, 1},
+ {&__pyx_n_s_meshname, __pyx_k_meshname, sizeof(__pyx_k_meshname), 0, 0, 1, 1},
{&__pyx_n_s_metaclass, __pyx_k_metaclass, sizeof(__pyx_k_metaclass), 0, 0, 1, 1},
{&__pyx_n_s_method, __pyx_k_method, sizeof(__pyx_k_method), 0, 0, 1, 1},
{&__pyx_n_s_method_name, __pyx_k_method_name, sizeof(__pyx_k_method_name), 0, 0, 1, 1},
@@ -37107,11 +41049,14 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_ndim, __pyx_k_ndim, sizeof(__pyx_k_ndim), 0, 0, 1, 1},
{&__pyx_n_s_normalize_key, __pyx_k_normalize_key, sizeof(__pyx_k_normalize_key), 0, 0, 1, 1},
{&__pyx_n_s_np, __pyx_k_np, sizeof(__pyx_k_np), 0, 0, 1, 1},
+ {&__pyx_n_s_npoints, __pyx_k_npoints, sizeof(__pyx_k_npoints), 0, 0, 1, 1},
+ {&__pyx_n_s_nspace, __pyx_k_nspace, sizeof(__pyx_k_nspace), 0, 0, 1, 1},
{&__pyx_n_s_nsteps, __pyx_k_nsteps, sizeof(__pyx_k_nsteps), 0, 0, 1, 1},
{&__pyx_n_s_numpy, __pyx_k_numpy, sizeof(__pyx_k_numpy), 0, 0, 1, 1},
{&__pyx_n_s_nvars, __pyx_k_nvars, sizeof(__pyx_k_nvars), 0, 0, 1, 1},
{&__pyx_n_s_offset, __pyx_k_offset, sizeof(__pyx_k_offset), 0, 0, 1, 1},
{&__pyx_n_s_order, __pyx_k_order, sizeof(__pyx_k_order), 0, 0, 1, 1},
+ {&__pyx_n_s_origin, __pyx_k_origin, sizeof(__pyx_k_origin), 0, 0, 1, 1},
{&__pyx_n_s_os, __pyx_k_os, sizeof(__pyx_k_os), 0, 0, 1, 1},
{&__pyx_n_s_parameters, __pyx_k_parameters, sizeof(__pyx_k_parameters), 0, 0, 1, 1},
{&__pyx_n_s_path, __pyx_k_path, sizeof(__pyx_k_path), 0, 0, 1, 1},
@@ -37137,13 +41082,16 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_reshape, __pyx_k_reshape, sizeof(__pyx_k_reshape), 0, 0, 1, 1},
{&__pyx_n_s_rstrip, __pyx_k_rstrip, sizeof(__pyx_k_rstrip), 0, 0, 1, 1},
{&__pyx_n_s_scalar, __pyx_k_scalar, sizeof(__pyx_k_scalar), 0, 0, 1, 1},
+ {&__pyx_n_s_schema_version, __pyx_k_schema_version, sizeof(__pyx_k_schema_version), 0, 0, 1, 1},
{&__pyx_n_s_sel, __pyx_k_sel, sizeof(__pyx_k_sel), 0, 0, 1, 1},
{&__pyx_n_s_select, __pyx_k_select, sizeof(__pyx_k_select), 0, 0, 1, 1},
{&__pyx_n_s_selections, __pyx_k_selections, sizeof(__pyx_k_selections), 0, 0, 1, 1},
+ {&__pyx_n_s_set_time_aggregation, __pyx_k_set_time_aggregation, sizeof(__pyx_k_set_time_aggregation), 0, 0, 1, 1},
{&__pyx_n_s_setitem, __pyx_k_setitem, sizeof(__pyx_k_setitem), 0, 0, 1, 1},
{&__pyx_n_s_shape, __pyx_k_shape, sizeof(__pyx_k_shape), 0, 0, 1, 1},
{&__pyx_n_s_short, __pyx_k_short, sizeof(__pyx_k_short), 0, 0, 1, 1},
{&__pyx_n_s_size, __pyx_k_size, sizeof(__pyx_k_size), 0, 0, 1, 1},
+ {&__pyx_n_s_spacing, __pyx_k_spacing, sizeof(__pyx_k_spacing), 0, 0, 1, 1},
{&__pyx_n_s_split, __pyx_k_split, sizeof(__pyx_k_split), 0, 0, 1, 1},
{&__pyx_n_s_start, __pyx_k_start, sizeof(__pyx_k_start), 0, 0, 1, 1},
{&__pyx_n_s_startswith, __pyx_k_startswith, sizeof(__pyx_k_startswith), 0, 0, 1, 1},
@@ -37154,13 +41102,20 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_string_array, __pyx_k_string_array, sizeof(__pyx_k_string_array), 0, 0, 1, 1},
{&__pyx_n_s_strip, __pyx_k_strip, sizeof(__pyx_k_strip), 0, 0, 1, 1},
{&__pyx_n_s_strlen, __pyx_k_strlen, sizeof(__pyx_k_strlen), 0, 0, 1, 1},
+ {&__pyx_n_s_syncgroupid, __pyx_k_syncgroupid, sizeof(__pyx_k_syncgroupid), 0, 0, 1, 1},
{&__pyx_n_s_t, __pyx_k_t, sizeof(__pyx_k_t), 0, 0, 1, 1},
{&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1},
{&__pyx_n_s_time_index, __pyx_k_time_index, sizeof(__pyx_k_time_index), 0, 0, 1, 1},
{&__pyx_n_s_time_steps, __pyx_k_time_steps, sizeof(__pyx_k_time_steps), 0, 0, 1, 1},
{&__pyx_n_s_timeout_sec, __pyx_k_timeout_sec, sizeof(__pyx_k_timeout_sec), 0, 0, 1, 1},
+ {&__pyx_n_s_timescale, __pyx_k_timescale, sizeof(__pyx_k_timescale), 0, 0, 1, 1},
+ {&__pyx_n_s_timeseries, __pyx_k_timeseries, sizeof(__pyx_k_timeseries), 0, 0, 1, 1},
+ {&__pyx_n_s_timesteps, __pyx_k_timesteps, sizeof(__pyx_k_timesteps), 0, 0, 1, 1},
+ {&__pyx_n_s_timevarying, __pyx_k_timevarying, sizeof(__pyx_k_timevarying), 0, 0, 1, 1},
{&__pyx_n_s_tostring, __pyx_k_tostring, sizeof(__pyx_k_tostring), 0, 0, 1, 1},
{&__pyx_n_s_traceback, __pyx_k_traceback, sizeof(__pyx_k_traceback), 0, 0, 1, 1},
+ {&__pyx_n_s_transform, __pyx_k_transform, sizeof(__pyx_k_transform), 0, 0, 1, 1},
+ {&__pyx_n_s_transform_type_str, __pyx_k_transform_type_str, sizeof(__pyx_k_transform_type_str), 0, 0, 1, 1},
{&__pyx_n_s_type, __pyx_k_type, sizeof(__pyx_k_type), 0, 0, 1, 1},
{&__pyx_n_s_uint16, __pyx_k_uint16, sizeof(__pyx_k_uint16), 0, 0, 1, 1},
{&__pyx_n_s_uint32, __pyx_k_uint32, sizeof(__pyx_k_uint32), 0, 0, 1, 1},
@@ -37177,8 +41132,9 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_value, __pyx_k_value, sizeof(__pyx_k_value), 0, 0, 1, 1},
{&__pyx_n_s_values, __pyx_k_values, sizeof(__pyx_k_values), 0, 0, 1, 1},
{&__pyx_n_s_var, __pyx_k_var, sizeof(__pyx_k_var), 0, 0, 1, 1},
+ {&__pyx_n_s_var_id, __pyx_k_var_id, sizeof(__pyx_k_var_id), 0, 0, 1, 1},
{&__pyx_n_s_var_namelist, __pyx_k_var_namelist, sizeof(__pyx_k_var_namelist), 0, 0, 1, 1},
- {&__pyx_kp_u_var_read_line_1264, __pyx_k_var_read_line_1264, sizeof(__pyx_k_var_read_line_1264), 0, 1, 0, 0},
+ {&__pyx_kp_u_var_read_line_1456, __pyx_k_var_read_line_1456, sizeof(__pyx_k_var_read_line_1456), 0, 1, 0, 0},
{&__pyx_n_s_varid, __pyx_k_varid, sizeof(__pyx_k_varid), 0, 0, 1, 1},
{&__pyx_n_s_varname, __pyx_k_varname, sizeof(__pyx_k_varname), 0, 0, 1, 1},
{&__pyx_n_s_vars, __pyx_k_vars, sizeof(__pyx_k_vars), 0, 0, 1, 1},
@@ -37187,8 +41143,8 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_w, __pyx_k_w, sizeof(__pyx_k_w), 0, 0, 1, 1},
{&__pyx_n_s_when, __pyx_k_when, sizeof(__pyx_k_when), 0, 0, 1, 1},
{&__pyx_n_s_write, __pyx_k_write, sizeof(__pyx_k_write), 0, 0, 1, 1},
- {&__pyx_kp_u_writer_declare_group_line_1781, __pyx_k_writer_declare_group_line_1781, sizeof(__pyx_k_writer_declare_group_line_1781), 0, 1, 0, 0},
- {&__pyx_kp_u_writer_define_var_line_1803, __pyx_k_writer_define_var_line_1803, sizeof(__pyx_k_writer_define_var_line_1803), 0, 1, 0, 0},
+ {&__pyx_kp_u_writer_declare_group_line_1982, __pyx_k_writer_declare_group_line_1982, sizeof(__pyx_k_writer_declare_group_line_1982), 0, 1, 0, 0},
+ {&__pyx_kp_u_writer_define_var_line_2019, __pyx_k_writer_define_var_line_2019, sizeof(__pyx_k_writer_define_var_line_2019), 0, 1, 0, 0},
{&__pyx_n_s_xrange, __pyx_k_xrange, sizeof(__pyx_k_xrange), 0, 0, 1, 1},
{&__pyx_n_s_zeros, __pyx_k_zeros, sizeof(__pyx_k_zeros), 0, 0, 1, 1},
{&__pyx_n_s_zip, __pyx_k_zip, sizeof(__pyx_k_zip), 0, 0, 1, 1},
@@ -37201,15 +41157,15 @@ static int __Pyx_InitCachedBuiltins(void) {
#else
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@@ -37968,9 +41913,9 @@ PyMODINIT_FUNC PyInit_adios_mpi(void)
/*--- Function export code ---*/
/*--- Type init code ---*/
__pyx_type_9adios_mpi_softdict.tp_base = (&PyDict_Type);
- if (PyType_Ready(&__pyx_type_9adios_mpi_softdict) < 0) __PYX_ERR(0, 697, __pyx_L1_error)
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__pyx_type_9adios_mpi_softdict.tp_print = 0;
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__pyx_vtable_9adios_mpi_file.close = (PyObject *(*)(struct __pyx_obj_9adios_mpi_file *, int __pyx_skip_dispatch))__pyx_f_9adios_mpi_4file_close;
@@ -37978,11 +41923,11 @@ PyMODINIT_FUNC PyInit_adios_mpi(void)
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{
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@@ -37992,7 +41937,7 @@ PyMODINIT_FUNC PyInit_adios_mpi(void)
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@@ -38000,12 +41945,12 @@ PyMODINIT_FUNC PyInit_adios_mpi(void)
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@@ -38047,24 +41992,24 @@ PyMODINIT_FUNC PyInit_adios_mpi(void)
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+ * value = None,
+ * transform = None):
*/
- __pyx_t_1 = __Pyx_PyObject_Call(((PyObject *)(&PyTuple_Type)), __pyx_empty_tuple, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1984, __pyx_L1_error)
+ __pyx_t_1 = __Pyx_PyObject_Call(((PyObject *)(&PyTuple_Type)), __pyx_empty_tuple, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2220, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_1);
__pyx_k__61 = __pyx_t_1;
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- /* "adios_mpi.pyx":2038
+ /* "adios_mpi.pyx":2280
*
* ## Aliases
* File = file # <<<<<<<<<<<<<<
* Var = var
* Attr = attr
*/
- if (PyDict_SetItem(__pyx_d, __pyx_n_s_File, ((PyObject *)__pyx_ptype_9adios_mpi_file)) < 0) __PYX_ERR(0, 2038, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s_File, ((PyObject *)__pyx_ptype_9adios_mpi_file)) < 0) __PYX_ERR(0, 2280, __pyx_L1_error)
- /* "adios_mpi.pyx":2039
+ /* "adios_mpi.pyx":2281
* ## Aliases
* File = file
* Var = var # <<<<<<<<<<<<<<
* Attr = attr
* Writer = writer
*/
- if (PyDict_SetItem(__pyx_d, __pyx_n_s_Var, ((PyObject *)__pyx_ptype_9adios_mpi_var)) < 0) __PYX_ERR(0, 2039, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s_Var, ((PyObject *)__pyx_ptype_9adios_mpi_var)) < 0) __PYX_ERR(0, 2281, __pyx_L1_error)
- /* "adios_mpi.pyx":2040
+ /* "adios_mpi.pyx":2282
* File = file
* Var = var
* Attr = attr # <<<<<<<<<<<<<<
* Writer = writer
* Attrinfo = attrinfo
*/
- if (PyDict_SetItem(__pyx_d, __pyx_n_s_Attr, ((PyObject *)__pyx_ptype_9adios_mpi_attr)) < 0) __PYX_ERR(0, 2040, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s_Attr, ((PyObject *)__pyx_ptype_9adios_mpi_attr)) < 0) __PYX_ERR(0, 2282, __pyx_L1_error)
- /* "adios_mpi.pyx":2041
+ /* "adios_mpi.pyx":2283
* Var = var
* Attr = attr
* Writer = writer # <<<<<<<<<<<<<<
* Attrinfo = attrinfo
* Varinfo = varinfo
*/
- if (PyDict_SetItem(__pyx_d, __pyx_n_s_Writer, ((PyObject *)__pyx_ptype_9adios_mpi_writer)) < 0) __PYX_ERR(0, 2041, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s_Writer, ((PyObject *)__pyx_ptype_9adios_mpi_writer)) < 0) __PYX_ERR(0, 2283, __pyx_L1_error)
- /* "adios_mpi.pyx":2042
+ /* "adios_mpi.pyx":2284
* Attr = attr
* Writer = writer
* Attrinfo = attrinfo # <<<<<<<<<<<<<<
* Varinfo = varinfo
*
*/
- if (PyDict_SetItem(__pyx_d, __pyx_n_s_Attrinfo, ((PyObject *)__pyx_ptype_9adios_mpi_attrinfo)) < 0) __PYX_ERR(0, 2042, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s_Attrinfo, ((PyObject *)__pyx_ptype_9adios_mpi_attrinfo)) < 0) __PYX_ERR(0, 2284, __pyx_L1_error)
- /* "adios_mpi.pyx":2043
+ /* "adios_mpi.pyx":2285
* Writer = writer
* Attrinfo = attrinfo
* Varinfo = varinfo # <<<<<<<<<<<<<<
*
* ## ====================
*/
- if (PyDict_SetItem(__pyx_d, __pyx_n_s_Varinfo, ((PyObject *)__pyx_ptype_9adios_mpi_varinfo)) < 0) __PYX_ERR(0, 2043, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s_Varinfo, ((PyObject *)__pyx_ptype_9adios_mpi_varinfo)) < 0) __PYX_ERR(0, 2285, __pyx_L1_error)
- /* "adios_mpi.pyx":2049
+ /* "adios_mpi.pyx":2291
* ## ====================
*
* def readvar(fname, varname): # <<<<<<<<<<<<<<
* """ Retrieve a variable value from an Adios file.
*
*/
- __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_9adios_mpi_57readvar, NULL, __pyx_n_s_adios_mpi); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2049, __pyx_L1_error)
+ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_9adios_mpi_93readvar, NULL, __pyx_n_s_adios_mpi); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2291, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_d, __pyx_n_s_readvar_2, __pyx_t_1) < 0) __PYX_ERR(0, 2049, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s_readvar_2, __pyx_t_1) < 0) __PYX_ERR(0, 2291, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "adios_mpi.pyx":2063
+ /* "adios_mpi.pyx":2305
* 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_1 = PyCFunction_NewEx(&__pyx_mdef_9adios_mpi_59bpls, NULL, __pyx_n_s_adios_mpi); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2063, __pyx_L1_error)
+ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_9adios_mpi_95bpls, NULL, __pyx_n_s_adios_mpi); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2305, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_d, __pyx_n_s_bpls, __pyx_t_1) < 0) __PYX_ERR(0, 2063, __pyx_L1_error)
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s_bpls, __pyx_t_1) < 0) __PYX_ERR(0, 2305, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
/* "adios_mpi.pyx":1
@@ -38916,9 +42879,9 @@ PyMODINIT_FUNC PyInit_adios_mpi(void)
*/
__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_t_1, __pyx_kp_u_var_read_line_1264, __pyx_kp_u_Perform_read_Read_data_from_an) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
- if (PyDict_SetItem(__pyx_t_1, __pyx_kp_u_writer_declare_group_line_1781, __pyx_kp_u_Define_a_group_associated_with) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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diff --git a/wrappers/numpy/adios_mpi.pyx b/wrappers/numpy/adios_mpi.pyx
index 79d8ecd..b8fb588 100644
--- a/wrappers/numpy/adios_mpi.pyx
+++ b/wrappers/numpy/adios_mpi.pyx
@@ -107,6 +107,13 @@ cdef extern from "adios_types.h":
ctypedef enum ADIOS_FLAG:
pass
+ ctypedef enum ADIOS_STATISTICS_FLAG:
+ adios_stat_no
+ adios_stat_minmax
+ adios_stat_full
+ adios_stat_default
+ adios_stat_no_do_not_use_this
+
cdef extern from "adios.h":
ctypedef struct MPI_Comm:
pass
@@ -146,9 +153,9 @@ cdef extern from "adios.h":
cdef int adios_declare_group (int64_t * id,
char * name,
char * time_index,
- ADIOS_FLAG stats)
+ ADIOS_STATISTICS_FLAG stats)
- cdef int adios_define_var (int64_t group_id,
+ cdef int64_t adios_define_var (int64_t group_id,
char * name,
char * path,
ADIOS_DATATYPES type,
@@ -156,6 +163,74 @@ cdef extern from "adios.h":
char * global_dimensions,
char * local_offsets)
+ ### Ab hier:
+ cdef int adios_define_schema_version (int64_t group_id, char * schema_version)
+
+ cdef int adios_define_var_mesh (int64_t group_id , const char * varname ,
+ const char * meshname)
+
+ cdef int adios_define_var_centering (int64_t group_id , const char * varname ,
+ const char * centering)
+
+ cdef int adios_define_var_timesteps (const char * timesteps , int64_t group_id ,
+ const char * name)
+
+ 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)
+
+ cdef int adios_define_mesh_uniform (char * dimensions,
+ char * origin,
+ char * spacing,
+ char * maximum,
+ char * nspace,
+ 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,
+ char * cell_type,
+ char * npoints,
+ char * nspace,
+ int64_t group_id,
+ const char * name
+ )
+
+ ### Bis hier
+
cdef int adios_define_attribute (int64_t group,
char * name,
char * path,
@@ -175,6 +250,15 @@ cdef extern from "adios.h":
char * parameters,
char * base_path)
+ cdef int adios_set_transform (int64_t var_id, const char *transform_type_str)
+
+ cdef void adios_set_max_buffer_size (uint64_t max_buffer_size_MB)
+
+ cdef int adios_set_time_aggregation(int64_t groupid,
+ uint64_t buffersize,
+ int64_t syncgroupid)
+
+
cdef extern from "adios_selection.h":
ctypedef enum ADIOS_SELECTION_TYPE:
ADIOS_SELECTION_BOUNDINGBOX
@@ -456,15 +540,15 @@ cpdef int allocate_buffer(int when,
cpdef int64_t declare_group(str name,
str time_index = "",
- int stats = 1):
+ int stats = adios_stat_default):
cdef int64_t id = 0
adios_declare_group (&id,
s2b(name),
s2b(time_index),
- <ADIOS_FLAG> stats)
+ <ADIOS_STATISTICS_FLAG> stats)
return id
-cpdef int define_var(int64_t group_id,
+cpdef int64_t define_var(int64_t group_id,
str name,
str path,
int atype,
@@ -479,6 +563,101 @@ cpdef int define_var(int64_t group_id,
s2b(global_dimensions),
s2b(local_offsets))
+cpdef int define_schema_version (int64_t group_id, str schema_version):
+ return adios_define_schema_version (group_id, s2b(schema_version))
+
+cpdef int define_var_mesh (int64_t group_id, str varname, str meshname):
+ return adios_define_var_mesh (group_id, s2b(varname), s2b(meshname))
+
+cpdef int define_var_centering (int64_t group_id, str varname, str centering):
+ return adios_define_var_centering (group_id, s2b(varname), s2b(centering))
+
+cpdef int define_var_timesteps (str timesteps, int64_t group_id, str name):
+ return adios_define_var_timesteps (s2b(timesteps), group_id, s2b(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,
+ str maximum,
+ str nspace,
+ int64_t group_id,
+ str name
+ ):
+ return adios_define_mesh_uniform (s2b(dimensions),
+ s2b(origin),
+ s2b(spacing),
+ s2b(maximum),
+ s2b(nspace),
+ 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,
+ int64_t group_id,
+ str name
+ ):
+ return adios_define_mesh_structured (s2b(dimensions),
+ s2b(points),
+ s2b(nspace),
+ group_id,
+ s2b(name)
+ )
+
+cpdef int define_mesh_unstructured (str points,
+ str data,
+ str count,
+ str cell_type,
+ str npoints,
+ str nspace,
+ int64_t group_id,
+ str name
+ ):
+ return adios_define_mesh_unstructured (s2b(points),
+ s2b(data),
+ s2b(count),
+ s2b(cell_type),
+ s2b(npoints),
+ s2b(nspace),
+ group_id,
+ s2b(name)
+ )
+
cpdef int define_attribute (int64_t group,
str name,
str path,
@@ -545,6 +724,19 @@ cpdef int select_method (int64_t group,
s2b(parameters),
s2b(base_path))
+cpdef int set_transform (int64_t var_id, str transform_type_str):
+ return adios_set_transform (var_id, s2b(transform_type_str))
+
+cpdef void set_max_buffer_size (int64_t max_buffer_size_MB):
+ adios_set_max_buffer_size (max_buffer_size_MB)
+
+cpdef int set_time_aggregation (int64_t groupid,
+ uint64_t buffersize,
+ int64_t syncgroupid):
+ return adios_set_time_aggregation (groupid,
+ buffersize,
+ syncgroupid)
+
## ====================
## ADIOS Read API (V2)
@@ -842,7 +1034,7 @@ cdef class file(dict):
self.close()
def __enter__(self):
- """ Enter for with statemetn """
+ """ Enter for with statement """
return self
def __exit__(self, exception_type, exception_value, traceback):
@@ -1728,6 +1920,8 @@ cdef class writer(object):
cpdef dict vars
cpdef dict attrs
+ cpdef uint64_t timeaggregation_buffersize
+
property fname:
""" The filename to write. """
def __get__(self):
@@ -1758,10 +1952,16 @@ cdef class writer(object):
def __get__(self):
return self.attrs
+ property timeaggregation_buffersize:
+ """ Get time-aggregation buffersize. """
+ def __get__(self):
+ return self.timeaggregation_buffersize
+
def __init__(self, str fname,
bint is_noxml = True,
str mode = "w",
MPI.Comm comm = MPI.COMM_WORLD):
+ self.gid = 0
self.fname = fname
self.method = ""
self.method_params = ""
@@ -1770,6 +1970,7 @@ cdef class writer(object):
self.comm = comm
self.vars = dict()
self.attrs = dict()
+ self.timeaggregation_buffersize = 0
init_noxml(comm)
##def __var_factory__(self, name, value):
@@ -1778,7 +1979,7 @@ cdef class writer(object):
##def __attr_factory__(self, name, value):
## print "attr_factory:", name, value
- def declare_group(self, str gname,
+ def declare_group(self, str gname = None,
str method = "POSIX1",
str method_params = ""):
"""
@@ -1794,24 +1995,41 @@ cdef class writer(object):
>>> fw.declare_group('group', method='MPI', method_params='verbose=3')
"""
- self.gid = declare_group(gname, "", 1)
- self.gname = gname
+ if gname is not None:
+ self.gname = gname
+
+ if self.gname is None:
+ self.gname = "group"
+
+ self.gid = declare_group(self.gname, "", adios_stat_default)
self.method = method
self.method_params = method_params
select_method(self.gid, self.method, self.method_params, "")
+ self.set_time_aggregation()
+
+ def set_time_aggregation(self, buffer_size = None):
+ """
+ Set time-aggregation buffersize.
+ """
+ if buffer_size is not None:
+ self.timeaggregation_buffersize = buffer_size
+ if self.gid > 0:
+ set_time_aggregation (self.gid, self.timeaggregation_buffersize, 0);
def define_var(self, str varname,
ldim = tuple(),
gdim = tuple(),
- offset = tuple()):
+ offset = tuple(),
+ transform = None):
"""
Define a variable associated with the file.
Args:
- varname (str): variable name.
+ varname (str): variable name
ldim (tuple, optional): local dimension (default: tuple())
gdim (tuple, optional): global dimension (default: tuple())
offset (tuple, optional): offset (default: tuple())
+ transform (str): transform name
Example:
@@ -1820,7 +2038,7 @@ cdef class writer(object):
>>> fw.define_var ('temperature', (2,3))
"""
- self.vars[varname] = varinfo(varname, ldim, gdim, offset)
+ self.vars[varname] = varinfo(varname, ldim, gdim, offset, transform=transform)
def define_attr(self, str attrname):
"""
@@ -1836,13 +2054,22 @@ cdef class writer(object):
str varname,
dtype):
self.attrs[attrname] = attrinfo(attrname, varname, dtype, is_static=False)
+
def __setitem__(self, name, val):
if self.vars.has_key(name):
- self.vars[name] = val
+ if not isinstance(val, varinfo):
+ self.vars[name].value = val
+ else:
+ self.vars[name] = val
elif self.attrs.has_key(name):
- self.attrs[name] = val
+ if not isinstance(val, attrinfo):
+ self.attrs[name] = attrinfo(name, val, np.array(val).dtype)
+ else:
+ self.attrs[name].value = val
else:
- self.vars[name] = val
+ n = np.array(val)
+ self.vars[name] = varinfo(name, n.shape)
+ self.vars[name].value = val
def __getitem__(self, name):
if self.vars.has_key(name):
@@ -1856,8 +2083,8 @@ cdef class writer(object):
"""
Write variables and attributes to a file and close the writer.
"""
- if self.gname is None:
- self.declare_group("group")
+ if self.gid == 0:
+ self.declare_group()
fd = open(self.gname, self.fname, self.mode)
@@ -1870,7 +2097,8 @@ cdef class writer(object):
extra_vars[key] = varinfo(key, n.shape)
extra_vars[key].value = val
else:
- if self.is_noxml: val.define(self.gid)
+ if self.is_noxml:
+ val.define(self.gid)
for key, val in extra_vars.iteritems():
if self.is_noxml: val.define(self.gid)
@@ -1911,7 +2139,7 @@ cdef class writer(object):
self.mode)
def __enter__(self):
- """ Enter for with statemetn """
+ """ Enter for with statement """
return self
def __exit__(self, exception_type, exception_value, traceback):
@@ -1977,17 +2205,27 @@ cdef class varinfo(object):
cdef public gdim
cdef public offset
cdef public value
+ cdef str transform
+
+ property transform:
+ """ Transform method """
+ def __get__(self):
+ return self.fname
+ def __set__(self, value):
+ self.transform = value
def __init__(self, str name,
ldim = tuple(),
gdim = tuple(),
offset = tuple(),
- value = None):
+ value = None,
+ transform = None):
self.name = name
self.ldim = ldim
self.gdim = gdim
self.offset = offset
self.value = value
+ self.transform = transform
def define(self, int64_t gid):
if self.value is None:
@@ -2011,11 +2249,15 @@ cdef class varinfo(object):
atype = np2adiostype(val_.dtype)
## No space allowed
- define_var(gid, self.name, "", atype,
+ cdef int64_t varid = 0;
+ varid = define_var(gid, self.name, "", atype,
str(ldim_).replace(' ', '').strip('(,)'),
str(gdim_).replace(' ', '').strip('(,)'),
str(offset_).replace(' ', '').strip('(,)'))
+ if (self.transform is not None):
+ set_transform(varid, self.transform)
+
def bytes(self):
val_ = self.value
if not isinstance(self.value, (np.ndarray)):
@@ -2031,8 +2273,8 @@ cdef class varinfo(object):
write(fd, self.name, val_)
def __repr__(self):
- return ("AdiosVarinfo (name=%r, ldim=%r, gdim=%r, offset=%r, value=%r)") % \
- (self.name, self.ldim, self.gdim, self.offset, self.value)
+ return ("AdiosVarinfo (name=%r, ldim=%r, gdim=%r, offset=%r, transform=%r, value=%r)") % \
+ (self.name, self.ldim, self.gdim, self.offset, self.transform, self.value)
## Aliases
File = file
diff --git a/wrappers/numpy/build-and-install.sh b/wrappers/numpy/build-and-install.sh
new file mode 100755
index 0000000..8de14d3
--- /dev/null
+++ b/wrappers/numpy/build-and-install.sh
@@ -0,0 +1,14 @@
+#!/bin/bash -v
+rm -rf ./build
+sed -f adios_mpi2serial.sed adios_mpi.pyx > adios.pyx
+cython -X embedsignature=True --cplus adios.pyx
+cython -X embedsignature=True --cplus adios_mpi.pyx
+[ $? -ne 0 ] && exit $?
+CC=clang CXX=clang++ python setup.py install --user
+python setup_mpi.py install --user
+
+#cd doc
+#touch source/index.rst
+#make html
+#cd ..
+
diff --git a/wrappers/numpy/doc/source/build.rst b/wrappers/numpy/doc/source/build.rst
index 2043346..8b4d31b 100644
--- a/wrappers/numpy/doc/source/build.rst
+++ b/wrappers/numpy/doc/source/build.rst
@@ -12,24 +12,24 @@ 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 +41,8 @@ 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 +50,6 @@ then use the following command:
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
diff --git a/wrappers/numpy/src/__init__.py b/wrappers/numpy/src/__init__.py
index d72a1b3..415bfcc 100644
--- a/wrappers/numpy/src/__init__.py
+++ b/wrappers/numpy/src/__init__.py
@@ -1,2 +1,2 @@
from .adios import *
-__version__ = '1.9.1b19'
+__version__ = '1.11.0b1'
diff --git a/wrappers/numpy/src_mpi/__init__.py b/wrappers/numpy/src_mpi/__init__.py
index da69a47..bb65a2d 100644
--- a/wrappers/numpy/src_mpi/__init__.py
+++ b/wrappers/numpy/src_mpi/__init__.py
@@ -1,2 +1,2 @@
from .adios_mpi import *
-__version__ = '1.9.1b19'
+__version__ = '1.11.0b1'
diff --git a/wrappers/numpy/test/test_adios_writer_unittest.py b/wrappers/numpy/test/test_adios_writer_unittest.py
index 4ccfe54..5bc17a2 100644
--- a/wrappers/numpy/test/test_adios_writer_unittest.py
+++ b/wrappers/numpy/test/test_adios_writer_unittest.py
@@ -153,5 +153,48 @@ class AdiosTestCase(ut.TestCase):
self.assertEqual(f.nvars, 3)
self.assertEqual(f._nvars[...], NVARS)
+ def test_writer_transform(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)
+ fw.declare_group("group", method="POSIX1")
+
+ fw['NX'] = NX
+ fw['val1'] = val1
+ fw['val2'] = val2
+ fw['val1'].transform = 'identity'
+ 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())
+
+ def test_writer_timeaggregation(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)
+ fw.declare_group("group", method="POSIX1")
+ fw.set_time_aggregation(3200)
+
+ fw['NX'] = NX
+ fw['val1'] = val1
+ fw['val2'] = val2
+ fw.close()
+ ad.finalize()
+
+ 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_attribute.py b/wrappers/numpy/tests/test_adios_attribute.py
index 1c87c45..3f0e9e7 100644
--- a/wrappers/numpy/tests/test_adios_attribute.py
+++ b/wrappers/numpy/tests/test_adios_attribute.py
@@ -16,7 +16,8 @@ init = "verbose=3;"
## Init
ad.init_noxml()
-ad.allocate_buffer (ad.BUFFER_ALLOC_WHEN.NOW, 10);
+ad.set_max_buffer_size (10)
+
g = ad.declare_group("temperature", "", 1)
ad.define_var(g, "NX", "", ad.DATATYPE.integer, "", "", "")
ad.define_var(g, "size", "", ad.DATATYPE.integer, "", "", "")
diff --git a/wrappers/numpy/tests/test_adios_mpi_writer.py b/wrappers/numpy/tests/test_adios_mpi_writer.py
index 5efeb97..8f44e0c 100644
--- a/wrappers/numpy/tests/test_adios_mpi_writer.py
+++ b/wrappers/numpy/tests/test_adios_mpi_writer.py
@@ -5,11 +5,13 @@ Example:
$ mpiexec -n 4 python ./test_adios_mpi_writer.py
"""
+""" Import ADIOS Python/Numpy wrapper """
import adios_mpi as ad
import numpy as np
+""" Require MPI4Py installed """
from mpi4py import MPI
-## Init
+""" Init """
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
size = comm.Get_size()
@@ -18,17 +20,21 @@ size = comm.Get_size()
print("\n>>> Prepare ... (rank = %d)\n" % rank)
fname = 'adios_test_mpi_writer.bp'
NX = 10
-t = np.array(list(range(NX*size)), dtype=np.float64) + rank*NX
+t = np.arange(NX*size, dtype=np.float64) + rank*NX
gdim = (size, NX)
+ldim = (1, NX)
offset = (rank, 0)
+""" Writing """
print("\n>>> Writing ... (rank = %d)\n" % rank)
ad.init_noxml()
-ad.allocate_buffer (ad.BUFFER_ALLOC_WHEN.NOW, 10);
+ad.set_max_buffer_size (100);
fw = ad.writer(fname, comm=comm)
fw.declare_group('group', method='MPI')
-fw.define_var('temperature', ldim=(1,NX), gdim=gdim, offset=offset)
+#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')
fw['NX'] = NX
fw['size'] = size
@@ -36,7 +42,7 @@ fw['temperature'] = t
fw.attrs['/temperature/description'] = "Global array written from 'size' processes"
fw.close()
-## Reading
+""" Reading """
if rank == 0:
print("\n>>> Reading ...\n")
@@ -48,3 +54,5 @@ if rank == 0:
print(key, '=', val.value)
print("\n>>> Done.\n")
+
+ad.finalize()
diff --git a/wrappers/numpy/tests/test_adios_writer.py b/wrappers/numpy/tests/test_adios_writer.py
index 646352a..35be3d9 100644
--- a/wrappers/numpy/tests/test_adios_writer.py
+++ b/wrappers/numpy/tests/test_adios_writer.py
@@ -2,9 +2,10 @@
"""
Example:
-$ python ./test_adios_write.py
+$ python ./test_adios_writer.py
"""
+""" Import ADIOS Python/Numpy wrapper """
import adios as ad
import numpy as np
@@ -12,12 +13,12 @@ print("\n>>> Prepare ...\n")
fname = 'adios_test_writer.bp'
NX = 10
size = 2
-t = np.array(list(range(NX*size)), dtype=np.float64)
-tt = t.reshape((size, NX))
+tt = np.arange(NX*size, dtype=np.float64).reshape((size, NX))
+""" Writing """
print("\n>>> Writing ...\n")
ad.init_noxml()
-ad.allocate_buffer (ad.BUFFER_ALLOC_WHEN.NOW, 10);
+ad.set_max_buffer_size (10)
fw = ad.writer(fname)
fw.declare_group('group', method='POSIX1')
@@ -25,10 +26,11 @@ fw.declare_group('group', method='POSIX1')
fw['NX'] = NX
fw['size'] = size
fw['temperature'] = tt
+fw['temperature'].transform = "zfp:accuracy=0.001"
fw.attrs['/temperature/description'] = "Global array written from 'size' processes"
fw.close()
-## Reading
+""" Reading """
print("\n>>> Reading ...\n")
f = ad.file(fname)
@@ -38,5 +40,6 @@ for key, val in f.vars.items():
for key, val in f.attrs.items():
print(key, '=', val.value)
-## Testing
+""" Finalizing """
print("\n>>> Done.\n")
+ad.finalize()
--
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