[adios] 142/207: Merge tag 'upstream_1.7.0'
Alastair McKinstry
mckinstry at moszumanska.debian.org
Fri Jun 12 06:04:51 UTC 2015
This is an automated email from the git hooks/post-receive script.
mckinstry pushed a commit to branch master
in repository adios.
commit 2dc69dbf346cca00bef54eee05a64b438dadd8a5
Merge: abec36f b5ef974
Author: Alastair McKinstry <mckinstry at debian.org>
Date: Fri Jun 13 23:07:16 2014 +0100
Merge tag 'upstream_1.7.0'
CMakeLists.txt | 123 +-
INSTALL | 12 +-
Makefile.am | 5 +-
Makefile.in | 59 +-
NEWS | 19 +-
aclocal.m4 | 3 +
adios_config | 62 +-
cmake_init | 234 +-
config.h.cmake | 6 +
config.h.in | 18 +
config/ac_cray_pmi.m4 | 4 +-
config/ac_cray_ugni.m4 | 4 +-
config/ac_dataspaces.m4 | 13 +-
config/ac_dimes.m4 | 9 +-
config/ac_fgr.m4 | 67 +
config/ac_glib.m4 | 67 +
config/ac_infiniband.m4 | 8 +-
config/ac_lustre.m4 | 126 +-
config/ac_pami.m4 | 71 +
config/ac_portals.m4 | 4 +-
configure | 2325 ++-
configure.ac | 93 +-
examples/C/Makefile.in | 13 +
examples/C/arrays/Makefile.in | 13 +
examples/C/arrays/arrays_read.c | 2 +-
examples/C/arrays/arrays_write.c | 3 +-
examples/C/attributes/Makefile.in | 13 +
examples/C/attributes/attributes_read.c | 4 +-
examples/C/attributes/attributes_write.c | 3 +-
examples/C/compression_test/Makefile.in | 13 +
examples/C/compression_test/adios_global.c | 1 -
examples/C/compression_test/adios_read_box.c | 2 +-
examples/C/compression_test/genarray3D.c | 18 +-
examples/C/compression_test/read_test.h | 5 +-
examples/C/flexpath_arrays/Makefile.in | 13 +
.../global_range_select/Makefile.in | 13 +
.../flexpath_arrays/global_range_select/arrays.xml | 9 +-
.../global_range_select/arrays_read.c | 79 +-
.../global_range_select/arrays_write.c | 49 +-
.../C/flexpath_arrays/process_select/Makefile.in | 13 +
.../C/flexpath_arrays/process_select/arrays_read.c | 6 +-
.../flexpath_arrays/process_select/arrays_write.c | 3 +-
examples/C/global-array-time/Makefile.in | 13 +
examples/C/global-array-time/adios_globaltime.c | 1 -
.../C/global-array-time/adios_globaltime_no_xml.c | 3 +-
.../C/global-array-time/adios_read_globaltime.c | 3 +-
.../adios_read_globaltime_streaming.c | 10 +-
examples/C/global-array/Makefile.am | 6 +-
examples/C/global-array/Makefile.in | 35 +-
examples/C/global-array/adios_global.c | 1 -
examples/C/global-array/adios_global.xml | 3 +-
examples/C/global-array/adios_global_2files.c | 3 +-
..._no_xml.c => adios_global_aggregate_by_color.c} | 33 +-
examples/C/global-array/adios_global_no_xml.c | 6 +-
examples/C/global-array/adios_read_chunk.c | 14 +-
examples/C/global-array/adios_read_global.c | 3 +-
examples/C/global-array/adios_read_global_no_xml.c | 5 +-
examples/C/global-array/adios_read_gpp.c | 3 +-
examples/C/global-array/adios_read_writeblock.c | 6 +-
examples/C/global-array/no_xml_write_byid.c | 3 +-
examples/C/global-array/read_no_xml_write_byid.c | 5 +-
examples/C/manual/2_adios_write.c | 1 -
examples/C/manual/3_adios_read.c | 2 +-
examples/C/manual/4_adios_nfiles.c | 1 -
examples/C/manual/Makefile.in | 13 +
examples/C/read_all/Makefile.in | 13 +
examples/C/read_all/read_all.c | 79 +-
examples/C/read_all/read_all_v1.c | 11 +-
examples/C/scalars/Makefile.in | 13 +
examples/C/scalars/scalars_read.c | 4 +-
examples/C/scalars/scalars_write.c | 6 +-
examples/C/schema/CMakeLists.txt | 11 +
examples/C/schema/Makefile.am | 18 +-
examples/C/schema/Makefile.in | 80 +-
examples/C/schema/rectilinear2d.c | 4 -
examples/C/schema/rectilinear2d.readme | 2 +
.../{rectilinear2d.c => rectilinear2d_noxml.c} | 92 +-
examples/C/schema/structured2d.c | 4 -
examples/C/schema/structured2d.readme | 3 +-
.../{structured2d.c => structured2d_noxml.c} | 84 +-
examples/C/schema/tri2d.c | 4 -
examples/C/schema/tri2d.readme | 2 +
examples/C/schema/{tri2d.c => tri2d_noxml.c} | 142 +-
examples/C/schema/triangle2d.c | 4 +-
examples/C/schema/uniform2d.c | 4 -
examples/C/schema/uniform2d.readme | 2 +
.../C/schema/{uniform2d.c => uniform2d_noxml.c} | 105 +-
examples/C/stat/Makefile.in | 13 +
examples/C/stat/stat_read.c | 5 +-
examples/C/stat/stat_write.c | 1 -
examples/C/transforms/Makefile.in | 13 +
examples/C/transforms/adios_global.c | 1 -
examples/C/transforms/adios_read_all_3D.c | 15 +-
examples/C/transforms/adios_read_points.c | 8 +-
examples/C/transforms/adios_read_subv.c | 8 +-
examples/C/transforms/adios_read_wb_subpg.c | 11 +-
examples/C/transforms/adios_write_all_3D.c | 2 +-
examples/Fortran/Makefile.in | 13 +
examples/Fortran/arrays/Makefile.in | 13 +
examples/Fortran/global-array-time/Makefile.in | 13 +
examples/Fortran/global-array/Makefile.in | 13 +
.../Fortran/global-array/no_xml_write_byid.F90 | 4 +
examples/Fortran/scalars/Makefile.in | 13 +
examples/Makefile.in | 13 +
examples/coupling/job | 8 +-
examples/coupling/job1 | 2 +
examples/staging/stage_write/genarray_stream.F90 | 7 +-
examples/staging/stage_write/genarray_stream.xml | 22 +-
examples/staging/stage_write/job | 31 +-
examples/staging/stage_write/job.32 | 6 +-
examples/staging/stage_write/make.settings | 2 +-
examples/staging/stage_write/stage_write.c | 22 +-
examples/staging/stage_write/writer_adios | 1 +
runconf | 99 +-
scripts/FindADIOS.cmake | 238 +
src/CMakeLists.txt | 608 +-
src/Makefile.am | 6 +-
src/Makefile.in | 643 +-
src/core/adios.c | 151 +-
src/core/adios_bp_v1.c | 158 +-
src/core/adios_bp_v1.h | 23 +-
src/core/adios_copyspec.c | 3 +-
src/core/adios_copyspec.h | 2 +
src/core/adios_endianness.c | 1 +
src/core/adios_internals.c | 1151 +-
src/core/adios_internals.h | 113 +-
src/core/adios_internals_mxml.c | 259 +-
src/core/adios_read.c | 5 +
src/core/adios_read_hooks.c | 12 +-
src/core/adios_read_hooks.h | 27 +-
src/core/adios_read_v1.c | 14 +-
src/core/adios_selection_util.c | 5 +-
src/core/adios_socket.c | 2 +-
src/core/adios_subvolume.c | 7 +-
src/core/adios_subvolume.h | 4 +-
src/core/adios_timing.h | 2 +
src/core/adios_transport_hooks.c | 34 +-
src/core/adios_transport_hooks.h | 6 +-
src/core/adiosf.c | 23 +-
src/core/adiosf_read.c | 9 +-
src/core/adiosf_read_v1.c | 17 +-
src/core/adiosf_write_mod.f90 | 9 +-
src/core/bp_types.h | 16 +-
src/core/bp_utils.c | 114 +-
src/core/common_adios.c | 12 +-
src/core/common_adios.h | 1 +
src/core/common_read.c | 732 +-
src/core/common_read.h | 5 +
src/core/ds_metadata.h | 8 +
src/core/flexpath.h | 2 +
src/core/mpidummy.c | 66 +-
src/core/qhashtbl.c | 223 +-
src/core/qhashtbl.h | 15 +-
src/core/transforms/adios_patchdata.c | 5 +-
src/core/transforms/adios_transforms_common.c | 5 +-
src/core/transforms/adios_transforms_datablock.c | 3 +-
src/core/transforms/adios_transforms_hooks.c | 49 +-
src/core/transforms/adios_transforms_hooks.h | 7 -
src/core/transforms/adios_transforms_hooks_read.c | 9 +
src/core/transforms/adios_transforms_hooks_read.h | 7 +
src/core/transforms/adios_transforms_hooks_write.c | 1 +
src/core/transforms/adios_transforms_read.c | 14 +-
src/core/transforms/adios_transforms_reqgroup.c | 2 +-
src/core/transforms/adios_transforms_specparse.c | 13 +-
src/core/transforms/adios_transforms_specparse.h | 4 +-
src/core/transforms/adios_transforms_write.c | 36 +-
src/core/transforms/adios_transforms_write.h | 6 +-
.../transforms/plugindetect/detect_plugin_infos.h | 7 +-
.../transforms/plugindetect/plugin_info_types.h | 3 +-
src/core/util.c | 91 +-
src/core/util.h | 3 +
src/public/adios.h | 90 +-
src/public/adios_error.h | 17 +-
src/public/adios_read_v1.h | 8 +-
src/public/adios_read_v1_defs.h | 1 +
src/public/adios_read_v2.h | 44 +-
src/public/adios_read_v2_fwd.h | 43 +
src/public/adios_schema.h | 9 +
src/public/adios_types.h | 8 +
src/public/mpidummy.h | 23 +-
src/read/read_bp.c | 615 +-
src/read/read_bp_staged.c | 127 +-
src/read/read_bp_staged1.c | 14 +-
src/read/read_dataspaces.c | 357 +-
src/read/read_dimes.c | 440 +-
src/read/read_flexpath.c | 433 +-
src/transforms/adios_transform_alacrity_read.c | 2 +
src/transforms/adios_transform_alacrity_write.c | 2 +-
src/transforms/adios_transform_aplod_read.c | 2 +
src/transforms/adios_transform_aplod_write.c | 2 +-
src/transforms/adios_transform_bzip2_read.c | 2 +
src/transforms/adios_transform_bzip2_write.c | 2 +-
src/transforms/adios_transform_identity_read.c | 8 +
src/transforms/adios_transform_identity_write.c | 2 +-
src/transforms/adios_transform_isobar_read.c | 2 +
src/transforms/adios_transform_isobar_write.c | 2 +-
src/transforms/adios_transform_szip_read.c | 2 +
src/transforms/adios_transform_szip_write.c | 2 +-
src/transforms/adios_transform_zlib_read.c | 3 +
src/transforms/adios_transform_zlib_write.c | 5 +-
src/write/adios_dataspaces.c | 360 +-
src/write/adios_dimes.c | 436 +-
src/write/adios_flexpath.c | 165 +-
src/write/adios_mpi.c | 51 +-
src/write/adios_mpi_amr.c | 431 +-
src/write/adios_mpi_bgq.c | 21 +-
src/write/adios_mpi_lustre.c | 75 +-
src/write/adios_nc4.c | 1 +
src/write/adios_nssi.c | 2 +-
src/write/adios_posix.c | 78 +-
src/write/adios_posix1.c | 75 +-
src/write/adios_var_merge.c | 155 +-
tests/C/Makefile.in | 13 +
tests/C/adios_test_c.c | 21 +-
tests/C/flexpath_tests/1D_arr_global/Makefile.am | 2 +-
tests/C/flexpath_tests/1D_arr_global/Makefile.in | 15 +-
tests/C/flexpath_tests/1D_arr_global/reader.c | 5 -
tests/C/flexpath_tests/1D_arr_global/readme.txt | 108 +
tests/C/flexpath_tests/1D_arr_global/writer.c | 2 +-
.../flexpath_tests/1D_arr_global_noxml/Makefile.am | 2 +-
.../flexpath_tests/1D_arr_global_noxml/Makefile.in | 15 +-
.../C/flexpath_tests/1D_arr_global_noxml/reader.c | 5 +-
.../flexpath_tests/1D_arr_global_noxml/readme.txt | 104 +
.../C/flexpath_tests/1D_arr_global_noxml/writer.c | 2 +-
tests/C/flexpath_tests/Makefile.in | 13 +
tests/C/flexpath_tests/common/utils.c | 2 +-
.../flexpath_tests/global_range_select/Makefile.in | 13 +
.../global_range_select/arrays_read.c | 6 +-
tests/C/flexpath_tests/include/test_common.h | 2 +-
tests/C/flexpath_tests/include/utils.h | 1 +
tests/C/flexpath_tests/maya_append/Makefile.in | 13 +
tests/C/flexpath_tests/maya_append/reader.c | 6 +-
tests/C/flexpath_tests/maya_append/writer.c | 2 +-
tests/C/flexpath_tests/maya_noxml/Makefile.in | 13 +
tests/C/flexpath_tests/maya_noxml/reader.c | 4 +-
tests/C/flexpath_tests/maya_noxml/writer.c | 4 +-
tests/C/flexpath_tests/scalar/Makefile.in | 13 +
tests/C/flexpath_tests/scalar/reader.c | 1 -
tests/C/flexpath_tests/scalar/writer.c | 2 +-
tests/Fortran/Makefile.in | 13 +
tests/Makefile.in | 13 +
tests/bp_read/Makefile.am | 2 +
tests/bp_read/Makefile.in | 14 +
tests/bp_read/bp_read_c.c | 16 +-
tests/bp_read/genbp.c | 2 +-
tests/bp_read/testbp_c.xml | 21 +
tests/genarray/CMakeLists.txt | 2 +-
tests/genarray/Makefile.in | 13 +
tests/suite/Makefile.in | 13 +
tests/suite/programs/Makefile.am | 36 +-
tests/suite/programs/Makefile.in | 179 +-
tests/suite/programs/{many_vars.c => big_file.c} | 206 +-
tests/suite/programs/group_free_test.c | 85 +
tests/suite/programs/hashtest.c | 27 +-
tests/suite/programs/many_vars.c | 3 +-
tests/suite/programs/set_path.c | 334 +
tests/suite/programs/set_path_var.c | 353 +
tests/suite/programs/steps_read_file.c | 197 +
tests/suite/programs/steps_read_stream.c | 231 +
tests/suite/programs/steps_write.c | 91 +
tests/suite/programs/transforms_specparse.c | 30 +-
tests/suite/reference/arrays_bpls.txt | 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/no_xml_write_byid_bpls.txt | 2 +-
tests/suite/reference/no_xml_write_byid_f_bpls.txt | 2 +-
tests/suite/reference/scalars_write_bpls.txt | 2 +-
utils/CMakeLists.txt | 1 +
utils/Makefile.am | 4 +-
utils/Makefile.in | 20 +-
utils/adios_lint/Makefile.in | 13 +
utils/adios_lint/adios_lint.c | 4 +-
utils/bp2ascii/Makefile.in | 13 +
utils/bp2ascii/bp2ascii.c | 18 +-
utils/bp2bp/Makefile.in | 13 +
utils/bp2bp/bp2bp.c | 11 +-
utils/bp2h5/Makefile.in | 13 +
utils/bp2ncd/Makefile.in | 13 +
utils/bpdiff/Makefile.in | 13 +
utils/bpdiff/bpdiff.c | 207 +-
utils/bpdump/Makefile.in | 13 +
utils/bpdump/bpdump.c | 31 +-
utils/bpls/Makefile.in | 13 +
utils/bpls/bpls.c | 146 +-
utils/bpls/bpls.h | 2 +-
utils/bpsplit/Makefile.in | 13 +
utils/bpsplit/bpappend.c | 21 +-
utils/bpsplit/bpgettime.c | 5 +-
utils/bpsplit/bpsplit.c | 9 +-
utils/gpp/Makefile.in | 13 +
utils/gpp/ad_config.py | 4 +-
utils/list_methods/CMakeLists.txt | 28 +
utils/list_methods/Makefile.am | 36 +
utils/{bpsplit => list_methods}/Makefile.in | 184 +-
utils/list_methods/list_methods.c | 427 +
utils/skel/CMakeLists.txt | 21 +-
utils/skel/Makefile.am | 26 +-
utils/skel/Makefile.in | 38 +-
utils/skel/bin/skel | 70 +-
utils/skel/etc/Makefile.in | 13 +
utils/skel/etc/templates/Makefile.tmpl | 19 +
utils/skel/etc/templates/create_suite.tmpl | 15 +
utils/skel/etc/templates/replay.tmpl | 5 +
utils/skel/etc/templates/replay_bp.tmpl | 18 +
utils/skel/etc/templates/replay_yaml.tmpl | 10 +
utils/skel/etc/templates/source_write_c.tmpl | 207 +
utils/skel/etc/templates/source_write_fortran.tmpl | 216 +
utils/skel/etc/templates/submit_nautilus.tmpl | 33 +
utils/skel/etc/templates/submit_sith.tmpl | 29 +
utils/skel/etc/templates/xml.tmpl | 29 +
utils/skel/lib/skel_bpy.py | 193 +-
utils/skel/lib/skel_makefile.py | 15 +-
utils/skel/lib/skel_params.py | 50 +-
utils/skel/lib/skel_replay.py | 10 +-
utils/skel/lib/skel_source.py | 17 +-
utils/skel/lib/skel_submit.py | 10 +-
utils/skel/lib/skel_suite.py | 68 +
utils/skel/lib/skel_template.py | 63 +
utils/skel/lib/skel_test_plan.py | 66 +
utils/skel/lib/skel_xml.py | 9 +-
utils/skel/src/Makefile.in | 13 +
utils/skeldump/Makefile.in | 13 +
utils/skeldump/skeldump.c | 23 +-
wrappers/matlab/adiosopenc_staging.c | 427 +
wrappers/matlab/writer.bp | Bin 0 -> 23064 bytes
wrappers/numpy/CMakeLists.txt | 61 -
wrappers/numpy/Makefile | 53 +
wrappers/numpy/Modules/CMakeUtilityFunctions.cmake | 19 -
wrappers/numpy/Modules/FindADIOS.cmake | 136 -
wrappers/numpy/Modules/FindMPI4Py.cmake | 65 -
wrappers/numpy/Modules/FindNumpy.cmake | 57 -
.../Modules/FindPackageHandleStandardArgs.cmake | 260 -
wrappers/numpy/README | 75 +-
wrappers/numpy/adios.cpp | 18457 +++++++++---------
wrappers/numpy/adios.pyx | 502 +-
wrappers/numpy/{adios.cpp => adios_mpi.cpp} | 18951 +++++++++----------
wrappers/numpy/{adios.pyx => adios_mpi.pyx} | 496 +-
wrappers/numpy/conf/CMakeLists.txt | 205 +
wrappers/numpy/conf/MANIFEST.in | 15 +
wrappers/numpy/conf/__init__.py | 0
wrappers/numpy/conf/__init__.pyc | Bin 0 -> 149 bytes
wrappers/numpy/conf/cythonize.bat | 4 +
wrappers/numpy/conf/cythonize.py | 72 +
wrappers/numpy/conf/cythonize.sh | 4 +
wrappers/numpy/conf/epydoc.cfg | 149 +
wrappers/numpy/conf/epydocify.py | 110 +
wrappers/numpy/conf/mpiconfig.py | 363 +
wrappers/numpy/conf/mpiconfig.pyc | Bin 0 -> 11220 bytes
wrappers/numpy/conf/mpidistutils.py | 1534 ++
wrappers/numpy/conf/mpidistutils.pyc | Bin 0 -> 54064 bytes
wrappers/numpy/conf/mpiregexes.py | 75 +
wrappers/numpy/conf/mpiregexes.pyc | Bin 0 -> 2495 bytes
wrappers/numpy/conf/mpiscanner.py | 342 +
wrappers/numpy/conf/mpiscanner.pyc | Bin 0 -> 15203 bytes
wrappers/numpy/example/ncdf2bp.py | 13 +-
wrappers/numpy/mpi.cfg | 184 +
wrappers/numpy/mpiconfig.py | 363 +
wrappers/numpy/mpidistutils.py | 1534 ++
wrappers/numpy/setup.py | 9 +-
wrappers/numpy/{setup.py => setup_mpi.py} | 11 +-
wrappers/numpy/test/adios_noxml_test.py | 29 -
wrappers/numpy/test/adios_read_test.py | 14 -
wrappers/numpy/test/adios_write_test.py | 21 -
wrappers/numpy/test/test_adios_noxml.sh | 15 -
.../{test/test_adios_read.sh => tests/config.xml} | 23 +-
.../test_adios_write.sh => tests/config_mpi.xml} | 18 -
wrappers/numpy/tests/test_adios.py | 51 +
wrappers/numpy/tests/test_adios_mpi.py | 59 +
wrappers/numpy/tests/test_adios_timestep.py | 58 +
370 files changed, 37372 insertions(+), 26267 deletions(-)
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