diff options
| author | David Young <dyoung@hdfgroup.org> | 2022-03-10 16:17:13 (GMT) |
|---|---|---|
| committer | David Young <dyoung@hdfgroup.org> | 2022-03-10 16:17:13 (GMT) |
| commit | 069f75648a62af448df60626e1c797631ac220bd (patch) | |
| tree | bb03c9fbd6f8f83dcf7338ee0afcb1ddb0136dfa | |
| parent | e8bcb24e3fafc3dabc2a039c0e2be40b8e3bb1bb (diff) | |
| parent | d5ddf61803f30e87bdfa629339fabf6fe1eb4a3c (diff) | |
| download | hdf5-069f75648a62af448df60626e1c797631ac220bd.zip hdf5-069f75648a62af448df60626e1c797631ac220bd.tar.gz hdf5-069f75648a62af448df60626e1c797631ac220bd.tar.bz2 | |
Merge remote-tracking branch 'thg/develop' into feature/h5detect
178 files changed, 13267 insertions, 6220 deletions
diff --git a/.github/FUNDING.yml b/.github/FUNDING.yml new file mode 100644 index 0000000..7c4daaf --- /dev/null +++ b/.github/FUNDING.yml @@ -0,0 +1,3 @@ +# These are supported funding model platforms + +custom: "https://hdfgroup.org/about-us/donate-to-the-hdf-group/" diff --git a/CMakeFilters.cmake b/CMakeFilters.cmake index 51ac61c..725390b 100644 --- a/CMakeFilters.cmake +++ b/CMakeFilters.cmake @@ -19,7 +19,7 @@ include (FetchContent) set (HDF5_ALLOW_EXTERNAL_SUPPORT "NO" CACHE STRING "Allow External Library Building (NO GIT TGZ)") set_property (CACHE HDF5_ALLOW_EXTERNAL_SUPPORT PROPERTY STRINGS NO GIT TGZ) if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ") - option (ZLIB_USE_EXTERNAL "Use External Library Building for ZLIB" 1) + option (ZLIB_USE_EXTERNAL "Use External Library Building for HDF5_ZLIB" 1) option (SZIP_USE_EXTERNAL "Use External Library Building for SZIP" 1) if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT") set (ZLIB_URL ${ZLIB_GIT_URL} CACHE STRING "Path to zlib git repository") @@ -82,7 +82,7 @@ if (HDF5_ENABLE_Z_LIB_SUPPORT) set (H5_HAVE_ZLIB_H 1) set (H5_HAVE_LIBZ 1) if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") - message (VERBOSE "Filter ZLIB is built") + message (VERBOSE "Filter HDF5_ZLIB is built") endif () else () message (FATAL_ERROR " ZLib is Required for ZLib support in HDF5") @@ -100,7 +100,7 @@ if (HDF5_ENABLE_Z_LIB_SUPPORT) set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${ZLIB_STATIC_LIBRARY}) INCLUDE_DIRECTORIES (${ZLIB_INCLUDE_DIRS}) if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") - message (VERBOSE "Filter ZLIB is ON") + message (VERBOSE "Filter HDF5_ZLIB is ON") endif () endif () @@ -149,9 +149,9 @@ if (HDF5_ENABLE_SZIP_SUPPORT) if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") message (VERBOSE "... with library AEC") endif () - set (SZ_PACKAGE_NAME ${LIBAEC_PACKAGE_NAME}) + set (SZIP_PACKAGE_NAME ${LIBAEC_PACKAGE_NAME}) else () - set (SZ_PACKAGE_NAME ${SZIP_PACKAGE_NAME}) + set (SZIP_PACKAGE_NAME ${SZIP_PACKAGE_NAME}) endif () else () message (FATAL_ERROR "SZIP is Required for SZIP support in HDF5") diff --git a/CMakeInstallation.cmake b/CMakeInstallation.cmake index 609cd7e..b5efebf 100644 --- a/CMakeInstallation.cmake +++ b/CMakeInstallation.cmake @@ -395,13 +395,19 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED AND NOT HDF5_NO_PACKAGES) set (CPACK_PACKAGING_INSTALL_PREFIX "/${CPACK_PACKAGE_INSTALL_DIRECTORY}") set (CPACK_COMPONENTS_ALL_IN_ONE_PACKAGE ON) + list (APPEND CPACK_GENERATOR "DEB") set (CPACK_DEBIAN_PACKAGE_SECTION "Libraries") set (CPACK_DEBIAN_PACKAGE_MAINTAINER "${HDF5_PACKAGE_BUGREPORT}") -# list (APPEND CPACK_GENERATOR "RPM") + list (APPEND CPACK_GENERATOR "RPM") set (CPACK_RPM_PACKAGE_RELEASE "1") + set (CPACK_RPM_PACKAGE_RELEASE_DIST ON) set (CPACK_RPM_COMPONENT_INSTALL ON) set (CPACK_RPM_PACKAGE_RELOCATABLE ON) + set (CPACK_RPM_FILE_NAME "RPM-DEFAULT") + set (CPACK_RPM_PACKAGE_NAME "${CPACK_PACKAGE_NAME}") + set (CPACK_RPM_PACKAGE_VERSION "${CPACK_PACKAGE_VERSION}") + set (CPACK_RPM_PACKAGE_VENDOR "${CPACK_PACKAGE_VENDOR}") set (CPACK_RPM_PACKAGE_LICENSE "BSD-style") set (CPACK_RPM_PACKAGE_GROUP "Development/Libraries") set (CPACK_RPM_PACKAGE_URL "${HDF5_PACKAGE_URL}") @@ -442,11 +448,11 @@ The HDF5 data model, file format, API, library, and tools are open and distribut if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ") if (ZLIB_FOUND AND ZLIB_USE_EXTERNAL) if (WIN32) - set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};ZLIB;ALL;/") + set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};HDF5_ZLIB;ALL;/") else () - set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};ZLIB;libraries;/") - set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};ZLIB;headers;/") - set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};ZLIB;configinstall;/") + set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};HDF5_ZLIB;libraries;/") + set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};HDF5_ZLIB;headers;/") + set (CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${ZLIB_INCLUDE_DIR_GEN};HDF5_ZLIB;configinstall;/") endif () endif () if (SZIP_FOUND AND SZIP_USE_EXTERNAL) diff --git a/CMakeLists.txt b/CMakeLists.txt index 59595b6..cad378b 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -708,10 +708,14 @@ if (HDF5_ENABLE_PARALLEL) # Used by Parallel Compression feature set (PARALLEL_FILTERED_WRITES ON) - CHECK_SYMBOL_EXISTS (MPI_Mprobe "mpi.h" H5_HAVE_MPI_Mprobe) - CHECK_SYMBOL_EXISTS (MPI_Imrecv "mpi.h" H5_HAVE_MPI_Imrecv) - if (NOT H5_HAVE_MPI_Mprobe OR NOT H5_HAVE_MPI_Imrecv) - message (WARNING "The MPI_Mprobe and/or MPI_Imrecv functions could not be located. + CHECK_SYMBOL_EXISTS (MPI_Ibarrier "mpi.h" H5_HAVE_MPI_Ibarrier) + CHECK_SYMBOL_EXISTS (MPI_Issend "mpi.h" H5_HAVE_MPI_Issend) + CHECK_SYMBOL_EXISTS (MPI_Iprobe "mpi.h" H5_HAVE_MPI_Iprobe) + CHECK_SYMBOL_EXISTS (MPI_Irecv "mpi.h" H5_HAVE_MPI_Irecv) + if (H5_HAVE_MPI_Ibarrier AND H5_HAVE_MPI_Issend AND H5_HAVE_MPI_Iprobe AND H5_HAVE_MPI_Irecv) + set (H5_HAVE_PARALLEL_FILTERED_WRITES 1) + else () + message (WARNING "The MPI_Ibarrier/MPI_Issend/MPI_Iprobe/MPI_Irecv functions could not be located. Parallel writes of filtered data will be disabled.") set (PARALLEL_FILTERED_WRITES OFF) endif () @@ -895,10 +899,10 @@ add_subdirectory (src) if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ") if (ZLIB_FOUND AND ZLIB_USE_EXTERNAL) if (NOT ONLY_SHARED_LIBS) - add_dependencies (${HDF5_LIB_TARGET} ZLIB) + add_dependencies (${HDF5_LIB_TARGET} HDF5_ZLIB) endif () if (BUILD_SHARED_LIBS) - add_dependencies (${HDF5_LIBSH_TARGET} ZLIB) + add_dependencies (${HDF5_LIBSH_TARGET} HDF5_ZLIB) endif () endif () if (SZIP_FOUND AND SZIP_USE_EXTERNAL) @@ -40,6 +40,7 @@ ./.github/workflows/main.yml _DO_NOT_DISTRIBUTE_ ./.github/workflows/pr-check.yml _DO_NOT_DISTRIBUTE_ ./.github/workflows/codespell.yml _DO_NOT_DISTRIBUTE_ +./.github/FUNDING.yml _DO_NOT_DISTRIBUTE_ ./m4/aclocal_fc.m4 ./m4/aclocal_fc.f90 @@ -332,6 +333,8 @@ ./examples/h5_ref2reg_deprec.c ./examples/h5_shared_mesg.c ./examples/ph5example.c +./examples/ph5_filtered_writes.c +./examples/ph5_filtered_writes_no_sel.c ./examples/h5_vds.c ./examples/h5_vds-exc.c ./examples/h5_vds-exclim.c @@ -617,6 +620,7 @@ ./release_docs/HISTORY-1_8.txt ./release_docs/HISTORY-1_10.txt ./release_docs/HISTORY-1_12.txt +./release_docs/HISTORY-1_13.txt ./release_docs/INSTALL ./release_docs/INSTALL_CMake.txt ./release_docs/INSTALL_Cygwin.txt @@ -3771,8 +3775,8 @@ ./tools/test/perform/CMakeTests.cmake ./utils/CMakeLists.txt -./utils/test/CMakeLists.txt ./utils/mirror_vfd/CMakeLists.txt +./utils/test/CMakeLists.txt # CMake-specific User Scripts ./config/cmake/CTestScript.cmake @@ -3888,3 +3892,7 @@ ./utils/Makefile.in ./utils/mirror_vfd/Makefile.in ./utils/test/Makefile.in +./utils/tools/Makefile.in +./utils/tools/h5dwalk/Makefile.in +./utils/tools/test/Makefile.in +./utils/tools/test/h5dwalk/Makefile.in @@ -1,4 +1,4 @@ -HDF5 version 1.13.1-1 currently under development +HDF5 version 1.13.2-1 currently under development  diff --git a/c++/src/H5AbstractDs.cpp b/c++/src/H5AbstractDs.cpp index eeb0155..70d8531 100644 --- a/c++/src/H5AbstractDs.cpp +++ b/c++/src/H5AbstractDs.cpp @@ -302,7 +302,7 @@ AbstractDs::getStrType() const //-------------------------------------------------------------------------- // Function: AbstractDs::getVarLenType -///\brief Returns the floating-point datatype of this abstract dataset, +///\brief Returns the variable length datatype of this abstract dataset, /// which can be a dataset or an attribute. ///\return VarLenType instance ///\exception H5::DataTypeIException diff --git a/c++/src/H5Location.h b/c++/src/H5Location.h index e990ec8..0aec4d2 100644 --- a/c++/src/H5Location.h +++ b/c++/src/H5Location.h @@ -334,7 +334,7 @@ class H5_DLLCPP H5Location : public IdComponent { #endif // DOXYGEN_SHOULD_SKIP_THIS // Noop destructor. - virtual ~H5Location(); + virtual ~H5Location() override; }; // end of H5Location } // namespace H5 diff --git a/c++/src/cpp_doc_config b/c++/src/cpp_doc_config index 3eb7645..1e26187 100644 --- a/c++/src/cpp_doc_config +++ b/c++/src/cpp_doc_config @@ -38,7 +38,7 @@ PROJECT_NAME = # could be handy for archiving the generated documentation or if some version # control system is used. -PROJECT_NUMBER = "1.13.1-1, currently under development" +PROJECT_NUMBER = "1.13.2-1, currently under development" # Using the PROJECT_BRIEF tag one can provide an optional one line description # for a project that appears at the top of each page and should give viewer a diff --git a/c++/test/titerate.cpp b/c++/test/titerate.cpp index bc4d892..57761ea 100644 --- a/c++/test/titerate.cpp +++ b/c++/test/titerate.cpp @@ -351,7 +351,7 @@ test_iter_group(FileAccPropList &fapl) * Purpose Open an attribute and verify that it has a the correct name *------------------------------------------------------------------------- */ -const H5std_string FILE_NAME("titerate.h5"); +const H5std_string FILE_NAME("test_member_access.h5"); const H5std_string GRP_NAME("/Group_A"); const H5std_string FDATASET_NAME("file dset"); const H5std_string GDATASET_NAME("group dset"); @@ -396,6 +396,9 @@ test_HDFFV_9920() int attr_data[2] = {100, 200}; hsize_t dims[1] = {DIM1}; + /* Output message about test being performed */ + SUBTEST("Member access"); + try { // Create a new file and a group in it H5File file(FILE_NAME, H5F_ACC_TRUNC); @@ -425,6 +428,7 @@ test_HDFFV_9920() printelems(file, FDATASET_NAME, FATTR_NAME); printelems(gr1, GDATASET_NAME, GATTR_NAME); + PASSED(); } // end of try block // Catch all failures for handling in the same way @@ -473,4 +477,5 @@ extern "C" void cleanup_iterate() { HDremove(FILE_ITERATE.c_str()); + HDremove(FILE_NAME.c_str()); } // cleanup_iterate diff --git a/config/cmake/CTestCustom.cmake b/config/cmake/CTestCustom.cmake index f958804..9517e4b 100644 --- a/config/cmake/CTestCustom.cmake +++ b/config/cmake/CTestCustom.cmake @@ -19,6 +19,8 @@ set (CTEST_CUSTOM_MAXIMUM_FAILED_TEST_OUTPUT_SIZE 50000) set (CTEST_CUSTOM_WARNING_EXCEPTION ${CTEST_CUSTOM_WARNING_EXCEPTION} "note.*expected.*void.*but argument is of type.*volatile" + "plugin-build.*:[ \t]*warning" + "CMake Warning*stamp" "src.ZLIB.*:[ \t]*warning" "warning LNK4197:.*ZLIB-prefix" "src.SZIP.*:[ \t]*warning" diff --git a/config/cmake/H5pubconf.h.in b/config/cmake/H5pubconf.h.in index 1f7f4b1..4956c97 100644 --- a/config/cmake/H5pubconf.h.in +++ b/config/cmake/H5pubconf.h.in @@ -265,6 +265,9 @@ /* Define if we have parallel support */ #cmakedefine H5_HAVE_PARALLEL @H5_HAVE_PARALLEL@ +/* Define if we have support for writing to filtered datasets in parallel */ +#cmakedefine H5_HAVE_PARALLEL_FILTERED_WRITES @H5_HAVE_PARALLEL_FILTERED_WRITES@ + /* Define if both pread and pwrite exist. */ #cmakedefine H5_HAVE_PREADWRITE @H5_HAVE_PREADWRITE@ diff --git a/config/cmake/HDF5PluginMacros.cmake b/config/cmake/HDF5PluginMacros.cmake index 4e05399..dbed15c 100644 --- a/config/cmake/HDF5PluginMacros.cmake +++ b/config/cmake/HDF5PluginMacros.cmake @@ -57,8 +57,8 @@ macro (EXTERNAL_PLUGIN_LIBRARY compress_type) add_dependencies (h5ex_d_mafisc ${HDF5_LIBSH_TARGET}) target_include_directories (h5ex_d_mafisc PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR}") endif () - if (ENABLE_SZF) - add_dependencies (h5szf ${HDF5_LIBSH_TARGET}) + if (ENABLE_SZ) + add_dependencies (h5sz ${HDF5_LIBSH_TARGET}) add_dependencies (h5ex_d_sz ${HDF5_LIBSH_TARGET}) target_include_directories (h5ex_d_sz PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR}") endif () diff --git a/config/cmake/HDF5_Examples.cmake.in b/config/cmake/HDF5_Examples.cmake.in index db638fd..9ff9b6f 100644 --- a/config/cmake/HDF5_Examples.cmake.in +++ b/config/cmake/HDF5_Examples.cmake.in @@ -83,12 +83,12 @@ set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DSITE:STRING=${CTEST_SITE} -DBUILDN ############################################################################################################### if(WIN32) set(SITE_OS_NAME "Windows") - set(ENV{HDF5_DIR} "${INSTALLDIR}/share/cmake") + set(ENV{HDF5_ROOT} "${INSTALLDIR}") set(CTEST_BINARY_NAME ${CTEST_SOURCE_NAME}\\build) set(CTEST_SOURCE_DIRECTORY "${CTEST_DASHBOARD_ROOT}\\${CTEST_SOURCE_NAME}") set(CTEST_BINARY_DIRECTORY "${CTEST_DASHBOARD_ROOT}\\${CTEST_BINARY_NAME}") else() - set(ENV{HDF5_DIR} "${INSTALLDIR}/share/cmake") + set(ENV{HDF5_ROOT} "${INSTALLDIR}") set(ENV{LD_LIBRARY_PATH} "${INSTALLDIR}/lib") set(CTEST_BINARY_NAME ${CTEST_SOURCE_NAME}/build) set(CTEST_SOURCE_DIRECTORY "${CTEST_DASHBOARD_ROOT}/${CTEST_SOURCE_NAME}") diff --git a/config/cmake/cacheinit.cmake b/config/cmake/cacheinit.cmake index e423deb..221c0c9 100644 --- a/config/cmake/cacheinit.cmake +++ b/config/cmake/cacheinit.cmake @@ -47,12 +47,12 @@ set (HDF5_MINGW_STATIC_GCC_LIBS ON CACHE BOOL "Statically link libgcc/libstdc++" set (HDF5_ALLOW_EXTERNAL_SUPPORT "NO" CACHE STRING "Allow External Library Building (NO GIT TGZ)" FORCE) set_property (CACHE HDF5_ALLOW_EXTERNAL_SUPPORT PROPERTY STRINGS NO GIT TGZ) -set (ZLIB_TGZ_NAME "ZLib.tar.gz" CACHE STRING "Use ZLib from compressed file" FORCE) +set (ZLIB_TGZ_NAME "ZLib.tar.gz" CACHE STRING "Use HDF5_ZLib from compressed file" FORCE) set (SZIP_TGZ_NAME "SZip.tar.gz" CACHE STRING "Use SZip from compressed file" FORCE) set (SZAEC_TGZ_NAME "LIBAEC.tar.gz" CACHE STRING "Use SZip AEC from compressed file" FORCE) set (USE_LIBAEC ON CACHE BOOL "Use libaec szip replacement" FORCE) -set (ZLIB_PACKAGE_NAME "zlib" CACHE STRING "Name of ZLIB package" FORCE) +set (ZLIB_PACKAGE_NAME "zlib" CACHE STRING "Name of HDF5_ZLIB package" FORCE) set (LIBAEC_PACKAGE_NAME "libaec" CACHE STRING "Name of AEC SZIP package" FORCE) set (SZIP_PACKAGE_NAME "szip" CACHE STRING "Name of SZIP package" FORCE) @@ -85,12 +85,12 @@ set (BLOSC_TGZ_NAME "c-blosc.tar.gz" CACHE STRING "Use BLOSC from compressed fil set (BLOSC_PACKAGE_NAME "blosc" CACHE STRING "Name of BLOSC package" FORCE) -set (ZLIB_GIT_URL "https://git@bitbucket.hdfgroup.org/scm/test/zlib.git" CACHE STRING "Use ZLIB from HDF repo" FORCE) -set (ZLIB_GIT_BRANCH "master" CACHE STRING "" FORCE) +set (BLOSC_ZLIB_GIT_URL "https://git@bitbucket.hdfgroup.org/scm/test/zlib.git" CACHE STRING "Use BLOSC_ZLIB from HDF repo" FORCE) +set (BLOSC_ZLIB_GIT_BRANCH "master" CACHE STRING "" FORCE) -set (ZLIB_TGZ_NAME "ZLib.tar.gz" CACHE STRING "Use ZLib from compressed file" FORCE) +set (BLOSC_ZLIB_TGZ_NAME "ZLib.tar.gz" CACHE STRING "Use BLOSC_ZLib from compressed file" FORCE) -set (ZLIB_PACKAGE_NAME "zlib" CACHE STRING "Name of ZLIB package" FORCE) +set (BLOSC_ZLIB_PACKAGE_NAME "zlib" CACHE STRING "Name of BLOSC_ZLIB package" FORCE) ####### # bzip2 @@ -159,15 +159,15 @@ set (LZF_PACKAGE_NAME "lzf" CACHE STRING "Name of LZF package" FORCE) #set (MAFISC_PACKAGE_NAME "mafisc" CACHE STRING "Name of MAFISC package" FORCE) ###### -# szf +# sz ###### -set (SZF_GIT_URL "https://github.com/disheng222/SZ" CACHE STRING "Use SZ from github repository" FORCE) -set (SZF_GIT_BRANCH "master" CACHE STRING "" FORCE) +set (SZ_GIT_URL "https://github.com/disheng222/SZ" CACHE STRING "Use SZ filter from github repository" FORCE) +set (SZ_GIT_BRANCH "master" CACHE STRING "" FORCE) -set (SZF_TGZ_NAME "szf.tar.gz" CACHE STRING "Use SZ from compressed file" FORCE) +set (SZ_TGZ_NAME "szf.tar.gz" CACHE STRING "Use SZ filter from compressed file" FORCE) -set (SZF_PACKAGE_NAME "szf" CACHE STRING "Name of SZ package" FORCE) +set (SZ_PACKAGE_NAME "SZ" CACHE STRING "Name of SZ filter package" FORCE) ###### # zfp diff --git a/config/cmake/hdf5-config.cmake.in b/config/cmake/hdf5-config.cmake.in index 589fa5f..35cee4f 100644 --- a/config/cmake/hdf5-config.cmake.in +++ b/config/cmake/hdf5-config.cmake.in @@ -116,7 +116,7 @@ if (NOT TARGET "@HDF5_PACKAGE@") include (@PACKAGE_SHARE_INSTALL_DIR@/@ZLIB_PACKAGE_NAME@@HDF_PACKAGE_EXT@-targets.cmake) endif () if (${HDF5_PACKAGE_NAME}_ENABLE_SZIP_SUPPORT AND ${HDF5_PACKAGE_NAME}_PACKAGE_EXTLIBS) - include (@PACKAGE_SHARE_INSTALL_DIR@/@SZ_PACKAGE_NAME@@HDF_PACKAGE_EXT@-targets.cmake) + include (@PACKAGE_SHARE_INSTALL_DIR@/@SZIP_PACKAGE_NAME@@HDF_PACKAGE_EXT@-targets.cmake) endif () include (@PACKAGE_SHARE_INSTALL_DIR@/@HDF5_PACKAGE@@HDF_PACKAGE_EXT@-targets.cmake) endif () diff --git a/config/cmake/libh5cc.in b/config/cmake/libh5cc.in index ecdd13e..f5d8d4c 100644 --- a/config/cmake/libh5cc.in +++ b/config/cmake/libh5cc.in @@ -27,6 +27,27 @@ prg=$dir/$(basename -- "$prg") || exit printf '%s\n' "$prg" printf 'dir is %s\n' "$dir" + +# Show the configuration summary of the library recorded in the +# libhdf5.settings file reside in the lib directory. +showconfigure() +{ + cat $dir/lib/libhdf5.settings + status=$? +} + export PKG_CONFIG_PATH=$dir/lib/pkgconfig -@_PKG_CONFIG_COMPILER@ $@ `pkg-config --define-variable=prefix=$dir --cflags --libs @_PKG_CONFIG_LIBNAME@` +for arg in $@ ; do + case "$arg" in + -showconfig) + showconfigure + exit $status + ;; + *) + @_PKG_CONFIG_COMPILER@ $@ `pkg-config --define-variable=prefix=$dir --cflags --libs @_PKG_CONFIG_LIBNAME@` + status=$? + exit $status + ;; + esac +done diff --git a/config/cmake/scripts/HDF5config.cmake b/config/cmake/scripts/HDF5config.cmake index 2f5af77..9a3ead2 100644 --- a/config/cmake/scripts/HDF5config.cmake +++ b/config/cmake/scripts/HDF5config.cmake @@ -37,7 +37,7 @@ cmake_minimum_required (VERSION 3.12) # CTEST_SOURCE_NAME - source folder ############################################################################## -set (CTEST_SOURCE_VERSION "1.13.1") +set (CTEST_SOURCE_VERSION "1.13.2") set (CTEST_SOURCE_VERSEXT "-1") ############################################################################## @@ -68,7 +68,7 @@ endif () # build generator must be defined if (NOT DEFINED BUILD_GENERATOR) - message (FATAL_ERROR "BUILD_GENERATOR must be defined - Unix, VS2019, VS201964, VS2017, or VS201764, VS2015, VS201564") + message (FATAL_ERROR "BUILD_GENERATOR must be defined - Unix, VS2019, VS201964, VS2017, VS201764, VS2015, VS201564") endif () ################################################################### diff --git a/config/cmake_ext_mod/ConfigureChecks.cmake b/config/cmake_ext_mod/ConfigureChecks.cmake index b322948..6242b12 100644 --- a/config/cmake_ext_mod/ConfigureChecks.cmake +++ b/config/cmake_ext_mod/ConfigureChecks.cmake @@ -224,61 +224,61 @@ set (HDF_EXTRA_C_FLAGS) set (HDF_EXTRA_FLAGS) if (MINGW OR NOT WINDOWS) if (CMAKE_SYSTEM_NAME MATCHES "Linux") - # Linux Specific flags - # This was originally defined as _POSIX_SOURCE which was updated to - # _POSIX_C_SOURCE=199506L to expose a greater amount of POSIX - # functionality so clock_gettime and CLOCK_MONOTONIC are defined - # correctly. This was later updated to 200112L so that - # posix_memalign() is visible for the direct VFD code on Linux - # systems. - # POSIX feature information can be found in the gcc manual at: - # http://www.gnu.org/s/libc/manual/html_node/Feature-Test-Macros.html - set (HDF_EXTRA_C_FLAGS -D_POSIX_C_SOURCE=200809L) - - # Need to add this so that O_DIRECT is visible for the direct - # VFD on Linux systems. - set (HDF_EXTRA_C_FLAGS ${HDF_EXTRA_C_FLAGS} -D_GNU_SOURCE) - - option (HDF_ENABLE_LARGE_FILE "Enable support for large (64-bit) files on Linux." ON) - if (HDF_ENABLE_LARGE_FILE AND NOT DEFINED TEST_LFS_WORKS_RUN) - set (msg "Performing TEST_LFS_WORKS") - try_run (TEST_LFS_WORKS_RUN TEST_LFS_WORKS_COMPILE - ${CMAKE_BINARY_DIR} - ${HDF_RESOURCES_EXT_DIR}/HDFTests.c - COMPILE_DEFINITIONS "-DTEST_LFS_WORKS" - ) - - # The LARGEFILE definitions were from the transition period - # and are probably no longer needed. The FILE_OFFSET_BITS - # check should be generalized for all POSIX systems as it - # is in the Autotools. - if (TEST_LFS_WORKS_COMPILE) - if (TEST_LFS_WORKS_RUN MATCHES 0) - set (TEST_LFS_WORKS 1 CACHE INTERNAL ${msg}) - set (LARGEFILE 1) - set (HDF_EXTRA_FLAGS ${HDF_EXTRA_FLAGS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE) - if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") - message (VERBOSE "${msg}... yes") - endif () - else () - set (TEST_LFS_WORKS "" CACHE INTERNAL ${msg}) - if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") - message (VERBOSE "${msg}... no") - endif () - file (APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log - "Test TEST_LFS_WORKS Run failed with the following exit code:\n ${TEST_LFS_WORKS_RUN}\n" - ) - endif () - else () - set (TEST_LFS_WORKS "" CACHE INTERNAL ${msg}) - if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") - message (VERBOSE "${msg}... no") - endif () - file (APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log - "Test TEST_LFS_WORKS Compile failed\n" - ) - endif () - endif () + # Linux Specific flags + # This was originally defined as _POSIX_SOURCE which was updated to + # _POSIX_C_SOURCE=199506L to expose a greater amount of POSIX + # functionality so clock_gettime and CLOCK_MONOTONIC are defined + # correctly. This was later updated to 200112L so that + # posix_memalign() is visible for the direct VFD code on Linux + # systems. + # POSIX feature information can be found in the gcc manual at: + # http://www.gnu.org/s/libc/manual/html_node/Feature-Test-Macros.html + set (HDF_EXTRA_C_FLAGS -D_POSIX_C_SOURCE=200809L) + + # Need to add this so that O_DIRECT is visible for the direct + # VFD on Linux systems. + set (HDF_EXTRA_C_FLAGS ${HDF_EXTRA_C_FLAGS} -D_GNU_SOURCE) + + option (HDF_ENABLE_LARGE_FILE "Enable support for large (64-bit) files on Linux." ON) + if (HDF_ENABLE_LARGE_FILE AND NOT DEFINED TEST_LFS_WORKS_RUN) + set (msg "Performing TEST_LFS_WORKS") + try_run (TEST_LFS_WORKS_RUN TEST_LFS_WORKS_COMPILE + ${CMAKE_BINARY_DIR} + ${HDF_RESOURCES_EXT_DIR}/HDFTests.c + COMPILE_DEFINITIONS "-DTEST_LFS_WORKS" + ) + + # The LARGEFILE definitions were from the transition period + # and are probably no longer needed. The FILE_OFFSET_BITS + # check should be generalized for all POSIX systems as it + # is in the Autotools. + if (TEST_LFS_WORKS_COMPILE) + if (TEST_LFS_WORKS_RUN MATCHES 0) + set (TEST_LFS_WORKS 1 CACHE INTERNAL ${msg}) + set (LARGEFILE 1) + set (HDF_EXTRA_FLAGS ${HDF_EXTRA_FLAGS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE) + if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") + message (VERBOSE "${msg}... yes") + endif () + else () + set (TEST_LFS_WORKS "" CACHE INTERNAL ${msg}) + if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") + message (VERBOSE "${msg}... no") + endif () + file (APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log + "Test TEST_LFS_WORKS Run failed with the following exit code:\n ${TEST_LFS_WORKS_RUN}\n" + ) + endif () + else () + set (TEST_LFS_WORKS "" CACHE INTERNAL ${msg}) + if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15.0") + message (VERBOSE "${msg}... no") + endif () + file (APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log + "Test TEST_LFS_WORKS Compile failed\n" + ) + endif () + endif () set (CMAKE_REQUIRED_DEFINITIONS ${CMAKE_REQUIRED_DEFINITIONS} ${HDF_EXTRA_FLAGS}) endif () endif () diff --git a/config/cmake_ext_mod/HDFLibMacros.cmake b/config/cmake_ext_mod/HDFLibMacros.cmake index 2af3229..40d06e7 100644 --- a/config/cmake_ext_mod/HDFLibMacros.cmake +++ b/config/cmake_ext_mod/HDFLibMacros.cmake @@ -139,11 +139,11 @@ macro (EXTERNAL_SZIP_LIBRARY compress_type encoding) # add_subdirectory(${szip_SOURCE_DIR} ${szip_BINARY_DIR}) # endif() # -##include (${BINARY_DIR}/${SZ_PACKAGE_NAME}${HDF_PACKAGE_EXT}-targets.cmake) +##include (${BINARY_DIR}/${SZIP_PACKAGE_NAME}${HDF_PACKAGE_EXT}-targets.cmake) # Create imported target szip-static if (USE_LIBAEC) add_library(${HDF_PACKAGE_NAMESPACE}sz-static STATIC IMPORTED) - HDF_IMPORT_SET_LIB_OPTIONS (${HDF_PACKAGE_NAMESPACE}sz-static "sz" STATIC "") + HDF_IMPORT_SET_LIB_OPTIONS (${HDF_PACKAGE_NAMESPACE}sz-static "szaec" STATIC "") add_dependencies (${HDF_PACKAGE_NAMESPACE}sz-static SZIP) add_library(${HDF_PACKAGE_NAMESPACE}aec-static STATIC IMPORTED) HDF_IMPORT_SET_LIB_OPTIONS (${HDF_PACKAGE_NAMESPACE}aec-static "aec" STATIC "") @@ -188,7 +188,7 @@ endmacro () #------------------------------------------------------------------------------- macro (EXTERNAL_ZLIB_LIBRARY compress_type) if (${compress_type} MATCHES "GIT") - EXTERNALPROJECT_ADD (ZLIB + EXTERNALPROJECT_ADD (HDF5_ZLIB GIT_REPOSITORY ${ZLIB_URL} GIT_TAG ${ZLIB_BRANCH} INSTALL_COMMAND "" @@ -207,7 +207,7 @@ macro (EXTERNAL_ZLIB_LIBRARY compress_type) -DPACKAGE_NAMESPACE=${HDF_PACKAGE_NAMESPACE} ) elseif (${compress_type} MATCHES "TGZ") - EXTERNALPROJECT_ADD (ZLIB + EXTERNALPROJECT_ADD (HDF5_ZLIB URL ${ZLIB_URL} URL_MD5 "" INSTALL_COMMAND "" @@ -226,19 +226,15 @@ macro (EXTERNAL_ZLIB_LIBRARY compress_type) -DPACKAGE_NAMESPACE=${HDF_PACKAGE_NAMESPACE} ) endif () - externalproject_get_property (ZLIB BINARY_DIR SOURCE_DIR) + externalproject_get_property (HDF5_ZLIB BINARY_DIR SOURCE_DIR) - if (WIN32) - set (ZLIB_LIB_NAME "zlib") - else () - set (ZLIB_LIB_NAME "z") - endif () + set (ZLIB_LIB_NAME "z") ##include (${BINARY_DIR}/${ZLIB_PACKAGE_NAME}${HDF_PACKAGE_EXT}-targets.cmake) # Create imported target zlib-static add_library(${HDF_PACKAGE_NAMESPACE}zlib-static STATIC IMPORTED) # add_library(${HDF_PACKAGE_NAMESPACE}zlib-static ALIAS zlib-static) HDF_IMPORT_SET_LIB_OPTIONS (${HDF_PACKAGE_NAMESPACE}zlib-static ${ZLIB_LIB_NAME} STATIC "") - add_dependencies (${HDF_PACKAGE_NAMESPACE}zlib-static ZLIB) + add_dependencies (${HDF_PACKAGE_NAMESPACE}zlib-static HDF5_ZLIB) set (ZLIB_STATIC_LIBRARY "${HDF_PACKAGE_NAMESPACE}zlib-static") set (ZLIB_LIBRARIES ${ZLIB_STATIC_LIBRARY}) @@ -256,6 +252,6 @@ macro (PACKAGE_ZLIB_LIBRARY compress_type) ) set (EXTERNAL_HEADER_LIST ${EXTERNAL_HEADER_LIST} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/zconf.h) if (${compress_type} MATCHES "GIT" OR ${compress_type} MATCHES "TGZ") - add_dependencies (ZLIB-GenHeader-Copy ZLIB) + add_dependencies (ZLIB-GenHeader-Copy HDF5_ZLIB) endif () endmacro () diff --git a/config/cmake_ext_mod/HDFMacros.cmake b/config/cmake_ext_mod/HDFMacros.cmake index 09492e7..0f9b367 100644 --- a/config/cmake_ext_mod/HDFMacros.cmake +++ b/config/cmake_ext_mod/HDFMacros.cmake @@ -356,7 +356,7 @@ macro (HDF_DIR_PATHS package_prefix) endif () endif () if (NOT ${package_prefix}_INSTALL_CMAKE_DIR) - set (${package_prefix}_INSTALL_CMAKE_DIR share/cmake) + set (${package_prefix}_INSTALL_CMAKE_DIR cmake) endif () # Always use full RPATH, i.e. don't skip the full RPATH for the build tree diff --git a/configure.ac b/configure.ac index 4cf329c..e426632 100644 --- a/configure.ac +++ b/configure.ac @@ -23,7 +23,7 @@ AC_PREREQ([2.69]) ## NOTE: Do not forget to change the version number here when we do a ## release!!! ## -AC_INIT([HDF5], [1.13.1-1], [help@hdfgroup.org]) +AC_INIT([HDF5], [1.13.2-1], [help@hdfgroup.org]) AC_CONFIG_SRCDIR([src/H5.c]) AC_CONFIG_HEADERS([src/H5config.h]) @@ -2710,9 +2710,11 @@ AC_ARG_ENABLE([memory-alloc-sanity-check], [Enable this option to turn on internal memory allocation sanity checking. This could cause more memory use and somewhat slower allocation. - This option is orthogonal to the - --enable-using-memchecker option. - [default=yes if debug build, otherwise no] + This option may also cause issues with HDF5 + filter plugins, so should not be enabled if + filters are to be used. This option is orthogonal + to the --enable-using-memchecker option. + [default=no] ])], [MEMORYALLOCSANITYCHECK=$enableval]) @@ -2722,11 +2724,10 @@ AC_SUBST([MEMORYALLOCSANITYCHECK]) ## Set default if test "X-$MEMORYALLOCSANITYCHECK" = X- ; then - if test "X-$BUILD_MODE" = "X-debug" ; then - MEMORYALLOCSANITYCHECK=yes - else - MEMORYALLOCSANITYCHECK=no - fi +# Should consider enabling this option by default for +# 'developer' builds if that build mode is added in +# the future + MEMORYALLOCSANITYCHECK=no fi case "X-$MEMORYALLOCSANITYCHECK" in @@ -2987,11 +2988,11 @@ if test -n "$PARALLEL"; then fi ## ---------------------------------------------------------------------- - ## Check for the MPI-3 functions necessary for the Parallel Compression + ## Check for the MPI functions necessary for the Parallel Compression ## feature. If these are not present, issue a warning that Parallel ## Compression will be disabled. ## - AC_MSG_CHECKING([for MPI_Mprobe and MPI_Imrecv functions]) + AC_MSG_CHECKING([for MPI_Ibarrier/MPI_Issend/MPI_Iprobe/MPI_Irecv functions]) AC_LINK_IFELSE( [AC_LANG_PROGRAM( @@ -2999,16 +3000,19 @@ if test -n "$PARALLEL"; then #include <mpi.h> ]], [[ - MPI_Message message; + int flag; MPI_Init(0, (void *) 0); - MPI_Mprobe(0, 0, 0, &message, (void *) 0); - MPI_Imrecv((void *) 0, 0, 0, (void *) 0, (void *) 0); + MPI_Ibarrier(0, (void *) 0); + MPI_Issend((void *) 0, 0, 0, 0, 0, 0, (void *) 0); + MPI_Iprobe(0, 0, 0, &flag, (void *) 0); + MPI_Irecv((void *) 0, 0, 0, 0, 0, 0, (void *) 0); ]] )], [AC_MSG_RESULT([yes]) - PARALLEL_FILTERED_WRITES=yes], + PARALLEL_FILTERED_WRITES=yes + AC_DEFINE([HAVE_PARALLEL_FILTERED_WRITES], [1], [Define if we have support for writing to filtered datasets in parallel])], [AC_MSG_RESULT([no]) - AC_MSG_WARN([A simple MPI program using the MPI_Mprobe and MPI_Imrecv functions could not be compiled and linked. + AC_MSG_WARN([A simple MPI program using the MPI_Ibarrier, MPI_Issend, MPI_Iprobe and MPI_Irecv functions could not be compiled and linked. Parallel writes of filtered data will be disabled.]) PARALLEL_FILTERED_WRITES=no] ) diff --git a/doxygen/aliases b/doxygen/aliases index f83a875..11fa691 100644 --- a/doxygen/aliases +++ b/doxygen/aliases @@ -299,7 +299,7 @@ ALIASES += ref_rfc20130630="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/Design- ALIASES += ref_rfc20130316="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/HDF5DynamicallyLoadedFilters.pdf\">HDF5 Dynamically Loaded Filters</a>" ALIASES += ref_rfc20121114="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/DECTRIS%20Integration%20RFC%202012-11-29.pdf\">Direct Chunk Write</a>" ALIASES += ref_rfc20121024="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/FileSpaceManagement.pdf\">HDF5 File Space Management</a>" -ALIASES += ref_rfc20120828="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/H5HPC_MultiDset_RW_IO_RFC_v4_20130320.docx.pdf\">New HDF5 API Routines for HPC Applications</a>" +ALIASES += ref_rfc20120828="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/H5HPC_MultiDset_RW_IO_RFC_v6_20220124.pdf\">New HDF5 API Routines for HPC Applications - Read/Write Multiple Datasets in an HDF5 file</a>" ALIASES += ref_rfc20120523="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/paged_aggregation.pdf\">HDF5 File Space Management: Paged Aggregation</a>" ALIASES += ref_rfc20120501="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/HDF5FileImageOperations.pdf\">HDF5 File Image Operations</a>" ALIASES += ref_rfc20120305="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC%20PHDF5%20Consistency%20Semantics%20MC%20120328.docx.pdf\">Enabling a Strict Consistency Semantics Model in Parallel HDF5</a>" diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt index 9ab870f..3f329c1 100644 --- a/examples/CMakeLists.txt +++ b/examples/CMakeLists.txt @@ -42,6 +42,14 @@ set (examples h5_vds-percival-unlim-maxmin ) +if (H5_HAVE_PARALLEL) + set (parallel_examples + ph5example + ph5_filtered_writes + ph5_filtered_writes_no_sel + ) +endif () + foreach (example ${examples}) add_executable (${example} ${HDF5_EXAMPLES_SOURCE_DIR}/${example}.c) target_include_directories (${example} PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") @@ -63,23 +71,25 @@ foreach (example ${examples}) endforeach () if (H5_HAVE_PARALLEL) - add_executable (ph5example ${HDF5_EXAMPLES_SOURCE_DIR}/ph5example.c) - target_include_directories (ph5example PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") - if (NOT BUILD_SHARED_LIBS) - TARGET_C_PROPERTIES (ph5example STATIC) - target_link_libraries (ph5example PRIVATE ${HDF5_LIB_TARGET} ${MPI_C_LIBRARIES}) - else () - TARGET_C_PROPERTIES (ph5example SHARED) - target_link_libraries (ph5example PRIVATE ${HDF5_LIBSH_TARGET} ${MPI_C_LIBRARIES}) - endif () - set_target_properties (ph5example PROPERTIES FOLDER examples) + foreach (parallel_example ${parallel_examples}) + add_executable (${parallel_example} ${HDF5_EXAMPLES_SOURCE_DIR}/${parallel_example}.c) + target_include_directories (${parallel_example} PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + if (NOT BUILD_SHARED_LIBS) + TARGET_C_PROPERTIES (${parallel_example} STATIC) + target_link_libraries (${parallel_example} PRIVATE ${HDF5_LIB_TARGET} ${MPI_C_LIBRARIES}) + else () + TARGET_C_PROPERTIES (${parallel_example} SHARED) + target_link_libraries (${parallel_example} PRIVATE ${HDF5_LIBSH_TARGET} ${MPI_C_LIBRARIES}) + endif () + set_target_properties (${parallel_example} PROPERTIES FOLDER examples) - #----------------------------------------------------------------------------- - # Add Target to clang-format - #----------------------------------------------------------------------------- - if (HDF5_ENABLE_FORMATTERS) - clang_format (HDF5_EXAMPLES_ph5example_FORMAT ph5example) - endif () + #----------------------------------------------------------------------------- + # Add Target to clang-format + #----------------------------------------------------------------------------- + if (HDF5_ENABLE_FORMATTERS) + clang_format (HDF5_EXAMPLES_${parallel_example}_FORMAT ${parallel_example}) + endif () + endforeach () endif () if (BUILD_TESTING AND HDF5_TEST_EXAMPLES) diff --git a/examples/CMakeTests.cmake b/examples/CMakeTests.cmake index 70142c8..3e24ba0 100644 --- a/examples/CMakeTests.cmake +++ b/examples/CMakeTests.cmake @@ -101,22 +101,26 @@ if (H5_HAVE_PARALLEL AND HDF5_TEST_PARALLEL AND NOT WIN32) # Ensure that 24 is a multiple of the number of processes. # The number 24 corresponds to SPACE1_DIM1 and SPACE1_DIM2 defined in ph5example.c math(EXPR NUMPROCS "24 / ((24 + ${MPIEXEC_MAX_NUMPROCS} - 1) / ${MPIEXEC_MAX_NUMPROCS})") - if (HDF5_ENABLE_USING_MEMCHECKER) - add_test (NAME MPI_TEST_EXAMPLES-ph5example COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:ph5example> ${MPIEXEC_POSTFLAGS}) - else () - add_test (NAME MPI_TEST_EXAMPLES-ph5example COMMAND "${CMAKE_COMMAND}" - -D "TEST_PROGRAM=${MPIEXEC_EXECUTABLE};${MPIEXEC_NUMPROC_FLAG};${NUMPROCS};${MPIEXEC_PREFLAGS};$<TARGET_FILE:ph5example>;${MPIEXEC_POSTFLAGS}" - -D "TEST_ARGS:STRING=" - -D "TEST_EXPECT=0" - -D "TEST_OUTPUT=ph5example.out" - -D "TEST_REFERENCE:STRING=PHDF5 tests finished with no errors" - -D "TEST_FILTER:STRING=PHDF5 tests finished with no errors" - -D "TEST_FOLDER=${PROJECT_BINARY_DIR}" - -P "${HDF_RESOURCES_EXT_DIR}/grepTest.cmake" - ) - endif () - if (last_test) - set_tests_properties (MPI_TEST_EXAMPLES-ph5example PROPERTIES DEPENDS ${last_test}) - endif () - set (last_test "MPI_TEST_EXAMPLES-ph5example") + + foreach (parallel_example ${parallel_examples}) + if (HDF5_ENABLE_USING_MEMCHECKER) + add_test (NAME MPI_TEST_EXAMPLES-${parallel_example} COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:${parallel_example}> ${MPIEXEC_POSTFLAGS}) + else () + add_test (NAME MPI_TEST_EXAMPLES-${parallel_example} COMMAND "${CMAKE_COMMAND}" + -D "TEST_PROGRAM=${MPIEXEC_EXECUTABLE};${MPIEXEC_NUMPROC_FLAG};${NUMPROCS};${MPIEXEC_PREFLAGS};$<TARGET_FILE:${parallel_example}>;${MPIEXEC_POSTFLAGS}" + -D "TEST_ARGS:STRING=" + -D "TEST_EXPECT=0" + -D "TEST_SKIP_COMPARE=TRUE" + -D "TEST_OUTPUT=${parallel_example}.out" + -D "TEST_REFERENCE:STRING=PHDF5 example finished with no errors" + #-D "TEST_FILTER:STRING=PHDF5 tests finished with no errors" + -D "TEST_FOLDER=${PROJECT_BINARY_DIR}" + -P "${HDF_RESOURCES_EXT_DIR}/grepTest.cmake" + ) + endif () + if (last_test) + set_tests_properties (MPI_TEST_EXAMPLES-${parallel_example} PROPERTIES DEPENDS ${last_test}) + endif () + set (last_test "MPI_TEST_EXAMPLES-${parallel_example}") + endforeach () endif () diff --git a/examples/Makefile.am b/examples/Makefile.am index 7b5aa63..161f789 100644 --- a/examples/Makefile.am +++ b/examples/Makefile.am @@ -20,7 +20,7 @@ include $(top_srcdir)/config/commence.am if BUILD_PARALLEL_CONDITIONAL - EXAMPLE_PROG_PARA = ph5example + EXAMPLE_PROG_PARA = ph5example ph5_filtered_writes ph5_filtered_writes_no_sel endif INSTALL_SCRIPT_FILES = run-c-ex.sh @@ -50,7 +50,7 @@ INSTALL_FILES = h5_write.c h5_read.c h5_extend_write.c h5_chunk_read.c h5_compou h5_group.c h5_select.c h5_attribute.c h5_mount.c h5_drivers.c \ h5_reference_deprec.c h5_ref_extern.c h5_ref_compat.c h5_ref2reg_deprec.c \ h5_extlink.c h5_elink_unix2win.c h5_shared_mesg.c h5_debug_trace.c \ - ph5example.c \ + ph5example.c ph5_filtered_writes.c ph5_filtered_writes_no_sel.c \ h5_vds.c h5_vds-exc.c h5_vds-exclim.c h5_vds-eiger.c h5_vds-simpleIO.c \ h5_vds-percival.c h5_vds-percival-unlim.c h5_vds-percival-unlim-maxmin.c @@ -119,6 +119,8 @@ h5_reference_deprec: $(srcdir)/h5_reference_deprec.c h5_ref2reg_deprec: $(srcdir)/h5_ref2reg_deprec.c h5_drivers: $(srcdir)/h5_drivers.c ph5example: $(srcdir)/ph5example.c +ph5_filtered_writes: $(srcdir)/ph5_filtered_writes.c +ph5_filtered_writes_no_sel: $(srcdir)/ph5_filtered_writes_no_sel.c h5_dtransform: $(srcdir)/h5_dtransform.c h5_extlink: $(srcdir)/h5_extlink.c $(EXTLINK_DIRS) h5_elink_unix2win: $(srcdir)/h5_elink_unix2win.c $(EXTLINK_DIRS) diff --git a/examples/ph5_filtered_writes.c b/examples/ph5_filtered_writes.c new file mode 100644 index 0000000..0f399dd --- /dev/null +++ b/examples/ph5_filtered_writes.c @@ -0,0 +1,490 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://www.hdfgroup.org/licenses. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/* + * Example of using the parallel HDF5 library to write to datasets + * with filters applied to them. + * + * If the HDF5_NOCLEANUP environment variable is set, the file that + * this example creates will not be removed as the example finishes. + * + * The need of requirement of parallel file prefix is that in general + * the current working directory in which compiling is done, is not suitable + * for parallel I/O and there is no standard pathname for parallel file + * systems. In some cases, the parallel file name may even need some + * parallel file type prefix such as: "pfs:/GF/...". Therefore, this + * example parses the HDF5_PARAPREFIX environment variable for a prefix, + * if one is needed. + */ + +#include <stdlib.h> + +#include "hdf5.h" + +#if defined(H5_HAVE_PARALLEL) && defined(H5_HAVE_PARALLEL_FILTERED_WRITES) + +#define EXAMPLE_FILE "ph5_filtered_writes.h5" +#define EXAMPLE_DSET1_NAME "DSET1" +#define EXAMPLE_DSET2_NAME "DSET2" + +#define EXAMPLE_DSET_DIMS 2 +#define EXAMPLE_DSET_CHUNK_DIM_SIZE 10 + +/* Dataset datatype */ +#define HDF5_DATATYPE H5T_NATIVE_INT +typedef int C_DATATYPE; + +#ifndef PATH_MAX +#define PATH_MAX 512 +#endif + +/* Global variables */ +int mpi_rank, mpi_size; + +/* + * Routine to set an HDF5 filter on the given DCPL + */ +static void +set_filter(hid_t dcpl_id) +{ + htri_t filter_avail; + + /* + * Check if 'deflate' filter is available + */ + filter_avail = H5Zfilter_avail(H5Z_FILTER_DEFLATE); + if (filter_avail < 0) + return; + else if (filter_avail) { + /* + * Set 'deflate' filter with reasonable + * compression level on DCPL + */ + H5Pset_deflate(dcpl_id, 6); + } + else { + /* + * Set Fletcher32 checksum filter on DCPL + * since it is always available in HDF5 + */ + H5Pset_fletcher32(dcpl_id); + } +} + +/* + * Routine to fill a data buffer with data. Assumes + * dimension rank is 2 and data is stored contiguous. + */ +void +fill_databuf(hsize_t start[], hsize_t count[], hsize_t stride[], C_DATATYPE *data) +{ + C_DATATYPE *dataptr = data; + hsize_t i, j; + + /* Use MPI rank value for data */ + for (i = 0; i < count[0]; i++) { + for (j = 0; j < count[1]; j++) { + *dataptr++ = mpi_rank; + } + } +} + +/* Cleanup created file */ +static void +cleanup(char *filename) +{ + hbool_t do_cleanup = getenv(HDF5_NOCLEANUP) ? 0 : 1; + + if (do_cleanup) + MPI_File_delete(filename, MPI_INFO_NULL); +} + +/* + * Routine to write to a dataset in a fashion + * where no chunks in the dataset are written + * to by more than 1 MPI rank. This will + * generally give the best performance as the + * MPI ranks will need the least amount of + * inter-process communication. + */ +static void +write_dataset_no_overlap(hid_t file_id, hid_t dxpl_id) +{ + C_DATATYPE data[EXAMPLE_DSET_CHUNK_DIM_SIZE][4 * EXAMPLE_DSET_CHUNK_DIM_SIZE]; + hsize_t dataset_dims[EXAMPLE_DSET_DIMS]; + hsize_t chunk_dims[EXAMPLE_DSET_DIMS]; + hsize_t start[EXAMPLE_DSET_DIMS]; + hsize_t stride[EXAMPLE_DSET_DIMS]; + hsize_t count[EXAMPLE_DSET_DIMS]; + size_t i, j; + hid_t dset_id = H5I_INVALID_HID; + hid_t dcpl_id = H5I_INVALID_HID; + hid_t file_dataspace = H5I_INVALID_HID; + + /* + * ------------------------------------ + * Setup Dataset Creation Property List + * ------------------------------------ + */ + + dcpl_id = H5Pcreate(H5P_DATASET_CREATE); + + /* + * REQUIRED: Dataset chunking must be enabled to + * apply a data filter to the dataset. + * Chunks in the dataset are of size + * EXAMPLE_DSET_CHUNK_DIM_SIZE x EXAMPLE_DSET_CHUNK_DIM_SIZE. + */ + chunk_dims[0] = EXAMPLE_DSET_CHUNK_DIM_SIZE; + chunk_dims[1] = EXAMPLE_DSET_CHUNK_DIM_SIZE; + H5Pset_chunk(dcpl_id, EXAMPLE_DSET_DIMS, chunk_dims); + + /* Set filter to be applied to created datasets */ + set_filter(dcpl_id); + + /* + * ------------------------------------ + * Define the dimensions of the dataset + * and create it + * ------------------------------------ + */ + + /* + * Create a dataset composed of 4 chunks + * per MPI rank. The first dataset dimension + * scales according to the number of MPI ranks. + * The second dataset dimension stays fixed + * according to the chunk size. + */ + dataset_dims[0] = EXAMPLE_DSET_CHUNK_DIM_SIZE * mpi_size; + dataset_dims[1] = 4 * EXAMPLE_DSET_CHUNK_DIM_SIZE; + + file_dataspace = H5Screate_simple(EXAMPLE_DSET_DIMS, dataset_dims, NULL); + + /* Create the dataset */ + dset_id = H5Dcreate2(file_id, EXAMPLE_DSET1_NAME, HDF5_DATATYPE, file_dataspace, H5P_DEFAULT, dcpl_id, + H5P_DEFAULT); + + /* + * ------------------------------------ + * Setup selection in the dataset for + * each MPI rank + * ------------------------------------ + */ + + /* + * Each MPI rank's selection covers a + * single chunk in the first dataset + * dimension. Each MPI rank's selection + * covers 4 chunks in the second dataset + * dimension. This leads to each MPI rank + * writing to 4 chunks of the dataset. + */ + start[0] = mpi_rank * EXAMPLE_DSET_CHUNK_DIM_SIZE; + start[1] = 0; + stride[0] = 1; + stride[1] = 1; + count[0] = EXAMPLE_DSET_CHUNK_DIM_SIZE; + count[1] = 4 * EXAMPLE_DSET_CHUNK_DIM_SIZE; + + H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL); + + /* + * -------------------------------------- + * Fill data buffer with MPI rank's rank + * value to make it easy to see which + * part of the dataset each rank wrote to + * -------------------------------------- + */ + + fill_databuf(start, count, stride, &data[0][0]); + + /* + * --------------------------------- + * Write to the dataset collectively + * --------------------------------- + */ + + H5Dwrite(dset_id, HDF5_DATATYPE, H5S_BLOCK, file_dataspace, dxpl_id, data); + + /* + * -------------- + * Close HDF5 IDs + * -------------- + */ + + H5Sclose(file_dataspace); + H5Pclose(dcpl_id); + H5Dclose(dset_id); +} + +/* + * Routine to write to a dataset in a fashion + * where every chunk in the dataset is written + * to by every MPI rank. This will generally + * give the worst performance as the MPI ranks + * will need the most amount of inter-process + * communication. + */ +static void +write_dataset_overlap(hid_t file_id, hid_t dxpl_id) +{ + C_DATATYPE *data = NULL; + hsize_t dataset_dims[EXAMPLE_DSET_DIMS]; + hsize_t chunk_dims[EXAMPLE_DSET_DIMS]; + hsize_t start[EXAMPLE_DSET_DIMS]; + hsize_t stride[EXAMPLE_DSET_DIMS]; + hsize_t count[EXAMPLE_DSET_DIMS]; + size_t i, j; + hid_t dset_id = H5I_INVALID_HID; + hid_t dcpl_id = H5I_INVALID_HID; + hid_t file_dataspace = H5I_INVALID_HID; + + /* + * ------------------------------------ + * Setup Dataset Creation Property List + * ------------------------------------ + */ + + dcpl_id = H5Pcreate(H5P_DATASET_CREATE); + + /* + * REQUIRED: Dataset chunking must be enabled to + * apply a data filter to the dataset. + * Chunks in the dataset are of size + * mpi_size x EXAMPLE_DSET_CHUNK_DIM_SIZE. + */ + chunk_dims[0] = mpi_size; + chunk_dims[1] = EXAMPLE_DSET_CHUNK_DIM_SIZE; + H5Pset_chunk(dcpl_id, EXAMPLE_DSET_DIMS, chunk_dims); + + /* Set filter to be applied to created datasets */ + set_filter(dcpl_id); + + /* + * ------------------------------------ + * Define the dimensions of the dataset + * and create it + * ------------------------------------ + */ + + /* + * Create a dataset composed of N chunks, + * where N is the number of MPI ranks. The + * first dataset dimension scales according + * to the number of MPI ranks. The second + * dataset dimension stays fixed according + * to the chunk size. + */ + dataset_dims[0] = mpi_size * chunk_dims[0]; + dataset_dims[1] = EXAMPLE_DSET_CHUNK_DIM_SIZE; + + file_dataspace = H5Screate_simple(EXAMPLE_DSET_DIMS, dataset_dims, NULL); + + /* Create the dataset */ + dset_id = H5Dcreate2(file_id, EXAMPLE_DSET2_NAME, HDF5_DATATYPE, file_dataspace, H5P_DEFAULT, dcpl_id, + H5P_DEFAULT); + + /* + * ------------------------------------ + * Setup selection in the dataset for + * each MPI rank + * ------------------------------------ + */ + + /* + * Each MPI rank's selection covers + * part of every chunk in the first + * dimension. Each MPI rank's selection + * covers all of every chunk in the + * second dimension. This leads to + * each MPI rank writing an equal + * amount of data to every chunk + * in the dataset. + */ + start[0] = mpi_rank; + start[1] = 0; + stride[0] = chunk_dims[0]; + stride[1] = 1; + count[0] = mpi_size; + count[1] = EXAMPLE_DSET_CHUNK_DIM_SIZE; + + H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL); + + /* + * -------------------------------------- + * Fill data buffer with MPI rank's rank + * value to make it easy to see which + * part of the dataset each rank wrote to + * -------------------------------------- + */ + + data = malloc(mpi_size * EXAMPLE_DSET_CHUNK_DIM_SIZE * sizeof(C_DATATYPE)); + + fill_databuf(start, count, stride, data); + + /* + * --------------------------------- + * Write to the dataset collectively + * --------------------------------- + */ + + H5Dwrite(dset_id, HDF5_DATATYPE, H5S_BLOCK, file_dataspace, dxpl_id, data); + + free(data); + + /* + * -------------- + * Close HDF5 IDs + * -------------- + */ + + H5Sclose(file_dataspace); + H5Pclose(dcpl_id); + H5Dclose(dset_id); +} + +int +main(int argc, char **argv) +{ + MPI_Comm comm = MPI_COMM_WORLD; + MPI_Info info = MPI_INFO_NULL; + hid_t file_id = H5I_INVALID_HID; + hid_t fapl_id = H5I_INVALID_HID; + hid_t dxpl_id = H5I_INVALID_HID; + char * par_prefix = NULL; + char filename[PATH_MAX]; + + MPI_Init(&argc, &argv); + MPI_Comm_size(comm, &mpi_size); + MPI_Comm_rank(comm, &mpi_rank); + + /* + * ---------------------------------- + * Start parallel access to HDF5 file + * ---------------------------------- + */ + + /* Setup File Access Property List with parallel I/O access */ + fapl_id = H5Pcreate(H5P_FILE_ACCESS); + H5Pset_fapl_mpio(fapl_id, comm, info); + + /* + * OPTIONAL: Set collective metadata reads on FAPL to allow + * parallel writes to filtered datasets to perform + * better at scale. While not strictly necessary, + * this is generally recommended. + */ + H5Pset_all_coll_metadata_ops(fapl_id, true); + + /* + * OPTIONAL: Set the latest file format version for HDF5 in + * order to gain access to different dataset chunk + * index types and better data encoding methods. + * While not strictly necessary, this is generally + * recommended. + */ + H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST); + + /* Parse any parallel prefix and create filename */ + par_prefix = getenv("HDF5_PARAPREFIX"); + + snprintf(filename, PATH_MAX, "%s%s%s", par_prefix ? par_prefix : "", par_prefix ? "/" : "", EXAMPLE_FILE); + + /* Create HDF5 file */ + file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id); + + /* + * -------------------------------------- + * Setup Dataset Transfer Property List + * with collective I/O + * -------------------------------------- + */ + + dxpl_id = H5Pcreate(H5P_DATASET_XFER); + + /* + * REQUIRED: Setup collective I/O for the dataset + * write operations. Parallel writes to + * filtered datasets MUST be collective, + * even if some ranks have no data to + * contribute to the write operation. + * + * Refer to the 'ph5_filtered_writes_no_sel' + * example to see how to setup a dataset + * write when one or more MPI ranks have + * no data to contribute to the write + * operation. + */ + H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE); + + /* + * -------------------------------- + * Create and write to each dataset + * -------------------------------- + */ + + /* + * Write to a dataset in a fashion where no + * chunks in the dataset are written to by + * more than 1 MPI rank. This will generally + * give the best performance as the MPI ranks + * will need the least amount of inter-process + * communication. + */ + write_dataset_no_overlap(file_id, dxpl_id); + + /* + * Write to a dataset in a fashion where + * every chunk in the dataset is written + * to by every MPI rank. This will generally + * give the worst performance as the MPI ranks + * will need the most amount of inter-process + * communication. + */ + write_dataset_overlap(file_id, dxpl_id); + + /* + * ------------------ + * Close all HDF5 IDs + * ------------------ + */ + + H5Pclose(dxpl_id); + H5Pclose(fapl_id); + H5Fclose(file_id); + + printf("PHDF5 example finished with no errors\n"); + + /* + * ------------------------------------ + * Cleanup created HDF5 file and finish + * ------------------------------------ + */ + + cleanup(filename); + + MPI_Finalize(); + + return 0; +} + +#else + +int +main(void) +{ + printf("HDF5 not configured with parallel support or parallel filtered writes are disabled!\n"); + return 0; +} + +#endif diff --git a/examples/ph5_filtered_writes_no_sel.c b/examples/ph5_filtered_writes_no_sel.c new file mode 100644 index 0000000..2e29838 --- /dev/null +++ b/examples/ph5_filtered_writes_no_sel.c @@ -0,0 +1,370 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://www.hdfgroup.org/licenses. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/* + * Example of using the parallel HDF5 library to collectively write to + * datasets with filters applied to them when one or MPI ranks do not + * have data to contribute to the dataset. + * + * If the HDF5_NOCLEANUP environment variable is set, the file that + * this example creates will not be removed as the example finishes. + * + * The need of requirement of parallel file prefix is that in general + * the current working directory in which compiling is done, is not suitable + * for parallel I/O and there is no standard pathname for parallel file + * systems. In some cases, the parallel file name may even need some + * parallel file type prefix such as: "pfs:/GF/...". Therefore, this + * example parses the HDF5_PARAPREFIX environment variable for a prefix, + * if one is needed. + */ + +#include <stdlib.h> + +#include "hdf5.h" + +#if defined(H5_HAVE_PARALLEL) && defined(H5_HAVE_PARALLEL_FILTERED_WRITES) + +#define EXAMPLE_FILE "ph5_filtered_writes_no_sel.h5" +#define EXAMPLE_DSET_NAME "DSET" + +#define EXAMPLE_DSET_DIMS 2 +#define EXAMPLE_DSET_CHUNK_DIM_SIZE 10 + +/* Dataset datatype */ +#define HDF5_DATATYPE H5T_NATIVE_INT +typedef int C_DATATYPE; + +#ifndef PATH_MAX +#define PATH_MAX 512 +#endif + +/* Global variables */ +int mpi_rank, mpi_size; + +/* + * Routine to set an HDF5 filter on the given DCPL + */ +static void +set_filter(hid_t dcpl_id) +{ + htri_t filter_avail; + + /* + * Check if 'deflate' filter is available + */ + filter_avail = H5Zfilter_avail(H5Z_FILTER_DEFLATE); + if (filter_avail < 0) + return; + else if (filter_avail) { + /* + * Set 'deflate' filter with reasonable + * compression level on DCPL + */ + H5Pset_deflate(dcpl_id, 6); + } + else { + /* + * Set Fletcher32 checksum filter on DCPL + * since it is always available in HDF5 + */ + H5Pset_fletcher32(dcpl_id); + } +} + +/* + * Routine to fill a data buffer with data. Assumes + * dimension rank is 2 and data is stored contiguous. + */ +void +fill_databuf(hsize_t start[], hsize_t count[], hsize_t stride[], C_DATATYPE *data) +{ + C_DATATYPE *dataptr = data; + hsize_t i, j; + + /* Use MPI rank value for data */ + for (i = 0; i < count[0]; i++) { + for (j = 0; j < count[1]; j++) { + *dataptr++ = mpi_rank; + } + } +} + +/* Cleanup created file */ +static void +cleanup(char *filename) +{ + hbool_t do_cleanup = getenv(HDF5_NOCLEANUP) ? 0 : 1; + + if (do_cleanup) + MPI_File_delete(filename, MPI_INFO_NULL); +} + +/* + * Routine to write to a dataset in a fashion + * where no chunks in the dataset are written + * to by more than 1 MPI rank. This will + * generally give the best performance as the + * MPI ranks will need the least amount of + * inter-process communication. + */ +static void +write_dataset_some_no_sel(hid_t file_id, hid_t dxpl_id) +{ + C_DATATYPE data[EXAMPLE_DSET_CHUNK_DIM_SIZE][4 * EXAMPLE_DSET_CHUNK_DIM_SIZE]; + hsize_t dataset_dims[EXAMPLE_DSET_DIMS]; + hsize_t chunk_dims[EXAMPLE_DSET_DIMS]; + hsize_t start[EXAMPLE_DSET_DIMS]; + hsize_t stride[EXAMPLE_DSET_DIMS]; + hsize_t count[EXAMPLE_DSET_DIMS]; + hbool_t no_selection; + size_t i, j; + hid_t dset_id = H5I_INVALID_HID; + hid_t dcpl_id = H5I_INVALID_HID; + hid_t file_dataspace = H5I_INVALID_HID; + + /* + * ------------------------------------ + * Setup Dataset Creation Property List + * ------------------------------------ + */ + + dcpl_id = H5Pcreate(H5P_DATASET_CREATE); + + /* + * REQUIRED: Dataset chunking must be enabled to + * apply a data filter to the dataset. + * Chunks in the dataset are of size + * EXAMPLE_DSET_CHUNK_DIM_SIZE x EXAMPLE_DSET_CHUNK_DIM_SIZE. + */ + chunk_dims[0] = EXAMPLE_DSET_CHUNK_DIM_SIZE; + chunk_dims[1] = EXAMPLE_DSET_CHUNK_DIM_SIZE; + H5Pset_chunk(dcpl_id, EXAMPLE_DSET_DIMS, chunk_dims); + + /* Set filter to be applied to created datasets */ + set_filter(dcpl_id); + + /* + * ------------------------------------ + * Define the dimensions of the dataset + * and create it + * ------------------------------------ + */ + + /* + * Create a dataset composed of 4 chunks + * per MPI rank. The first dataset dimension + * scales according to the number of MPI ranks. + * The second dataset dimension stays fixed + * according to the chunk size. + */ + dataset_dims[0] = EXAMPLE_DSET_CHUNK_DIM_SIZE * mpi_size; + dataset_dims[1] = 4 * EXAMPLE_DSET_CHUNK_DIM_SIZE; + + file_dataspace = H5Screate_simple(EXAMPLE_DSET_DIMS, dataset_dims, NULL); + + /* Create the dataset */ + dset_id = H5Dcreate2(file_id, EXAMPLE_DSET_NAME, HDF5_DATATYPE, file_dataspace, H5P_DEFAULT, dcpl_id, + H5P_DEFAULT); + + /* + * ------------------------------------ + * Setup selection in the dataset for + * each MPI rank + * ------------------------------------ + */ + + /* + * Odd rank value MPI ranks do not + * contribute any data to the dataset. + */ + no_selection = (mpi_rank % 2) == 1; + + if (no_selection) { + /* + * MPI ranks not contributing data to + * the dataset should call H5Sselect_none + * on the file dataspace that will be + * passed to H5Dwrite. + */ + H5Sselect_none(file_dataspace); + } + else { + /* + * Even MPI ranks contribute data to + * the dataset. Each MPI rank's selection + * covers a single chunk in the first dataset + * dimension. Each MPI rank's selection + * covers 4 chunks in the second dataset + * dimension. This leads to each contributing + * MPI rank writing to 4 chunks of the dataset. + */ + start[0] = mpi_rank * EXAMPLE_DSET_CHUNK_DIM_SIZE; + start[1] = 0; + stride[0] = 1; + stride[1] = 1; + count[0] = EXAMPLE_DSET_CHUNK_DIM_SIZE; + count[1] = 4 * EXAMPLE_DSET_CHUNK_DIM_SIZE; + + H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL); + + /* + * -------------------------------------- + * Fill data buffer with MPI rank's rank + * value to make it easy to see which + * part of the dataset each rank wrote to + * -------------------------------------- + */ + + fill_databuf(start, count, stride, &data[0][0]); + } + + /* + * --------------------------------- + * Write to the dataset collectively + * --------------------------------- + */ + + H5Dwrite(dset_id, HDF5_DATATYPE, no_selection ? H5S_ALL : H5S_BLOCK, file_dataspace, dxpl_id, data); + + /* + * -------------- + * Close HDF5 IDs + * -------------- + */ + + H5Sclose(file_dataspace); + H5Pclose(dcpl_id); + H5Dclose(dset_id); +} + +int +main(int argc, char **argv) +{ + MPI_Comm comm = MPI_COMM_WORLD; + MPI_Info info = MPI_INFO_NULL; + hid_t file_id = H5I_INVALID_HID; + hid_t fapl_id = H5I_INVALID_HID; + hid_t dxpl_id = H5I_INVALID_HID; + char * par_prefix = NULL; + char filename[PATH_MAX]; + + MPI_Init(&argc, &argv); + MPI_Comm_size(comm, &mpi_size); + MPI_Comm_rank(comm, &mpi_rank); + + /* + * ---------------------------------- + * Start parallel access to HDF5 file + * ---------------------------------- + */ + + /* Setup File Access Property List with parallel I/O access */ + fapl_id = H5Pcreate(H5P_FILE_ACCESS); + H5Pset_fapl_mpio(fapl_id, comm, info); + + /* + * OPTIONAL: Set collective metadata reads on FAPL to allow + * parallel writes to filtered datasets to perform + * better at scale. While not strictly necessary, + * this is generally recommended. + */ + H5Pset_all_coll_metadata_ops(fapl_id, true); + + /* + * OPTIONAL: Set the latest file format version for HDF5 in + * order to gain access to different dataset chunk + * index types and better data encoding methods. + * While not strictly necessary, this is generally + * recommended. + */ + H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST); + + /* Parse any parallel prefix and create filename */ + par_prefix = getenv("HDF5_PARAPREFIX"); + + snprintf(filename, PATH_MAX, "%s%s%s", par_prefix ? par_prefix : "", par_prefix ? "/" : "", EXAMPLE_FILE); + + /* Create HDF5 file */ + file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id); + + /* + * -------------------------------------- + * Setup Dataset Transfer Property List + * with collective I/O + * -------------------------------------- + */ + + dxpl_id = H5Pcreate(H5P_DATASET_XFER); + + /* + * REQUIRED: Setup collective I/O for the dataset + * write operations. Parallel writes to + * filtered datasets MUST be collective, + * even if some ranks have no data to + * contribute to the write operation. + */ + H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE); + + /* + * -------------------------------- + * Create and write to the dataset + * -------------------------------- + */ + + /* + * Write to a dataset in a fashion where no + * chunks in the dataset are written to by + * more than 1 MPI rank and some MPI ranks + * have nothing to contribute to the dataset. + * In this case, the MPI ranks that have no + * data to contribute must still participate + * in the collective H5Dwrite call, but should + * call H5Sselect_none on the file dataspace + * passed to the H5Dwrite call. + */ + write_dataset_some_no_sel(file_id, dxpl_id); + + /* + * ------------------ + * Close all HDF5 IDs + * ------------------ + */ + + H5Pclose(dxpl_id); + H5Pclose(fapl_id); + H5Fclose(file_id); + + printf("PHDF5 example finished with no errors\n"); + + /* + * ------------------------------------ + * Cleanup created HDF5 file and finish + * ------------------------------------ + */ + + cleanup(filename); + + MPI_Finalize(); + + return 0; +} + +#else + +int +main(void) +{ + printf("HDF5 not configured with parallel support or parallel filtered writes are disabled!\n"); + return 0; +} + +#endif diff --git a/examples/ph5example.c b/examples/ph5example.c index 23af477..36fbfd5 100644 --- a/examples/ph5example.c +++ b/examples/ph5example.c @@ -1073,11 +1073,11 @@ main(int argc, char **argv) finish: if (mpi_rank == 0) { /* only process 0 reports */ if (nerrors) - printf("***PHDF5 tests detected %d errors***\n", nerrors); + printf("***PHDF5 example detected %d errors***\n", nerrors); else { - printf("===================================\n"); - printf("PHDF5 tests finished with no errors\n"); - printf("===================================\n"); + printf("=====================================\n"); + printf("PHDF5 example finished with no errors\n"); + printf("=====================================\n"); } } if (docleanup) diff --git a/fortran/src/H5Df.c b/fortran/src/H5Df.c index 5c46cb3..a780683 100644 --- a/fortran/src/H5Df.c +++ b/fortran/src/H5Df.c @@ -495,10 +495,10 @@ h5dget_storage_size_c(hid_t_f *dset_id, hsize_t_f *size) c_dset_id = (hid_t)*dset_id; c_size = H5Dget_storage_size(c_dset_id); - if (c_size == 0) - return ret_value; - *size = (hsize_t_f)c_size; - ret_value = 0; + if (c_size != 0) { + ret_value = 0; + } + *size = (hsize_t_f)c_size; return ret_value; } diff --git a/fortran/src/H5Dff.F90 b/fortran/src/H5Dff.F90 index 655cf1c..6b77a8c 100644 --- a/fortran/src/H5Dff.F90 +++ b/fortran/src/H5Dff.F90 @@ -1625,8 +1625,7 @@ CONTAINS ! Inputs: ! fill_value - fill value ! space_id - memory space selection identifier -! buf - data buffer iin memory ro apply selection to -! - of k-th dimension of the buf array +! buf - memory buffer containing the selection to be filled ! Outputs: ! hdferr: - error code ! Success: 0 @@ -1676,8 +1675,7 @@ CONTAINS ! Inputs: ! fill_value - fill value ! space_id - memory space selection identifier -! buf - data buffer iin memory ro apply selection to -! - of k-th dimension of the buf array +! buf - memory buffer containing the selection to be filled ! Outputs: ! hdferr: - error code ! Success: 0 @@ -1724,8 +1722,7 @@ CONTAINS ! Inputs: ! fill_value - fill value ! space_id - memory space selection identifier - ! buf - data buffer iin memory ro apply selection to - ! - of k-th dimension of the buf array + ! buf - memory buffer containing the selection to be filled ! Outputs: ! hdferr: - error code ! Success: 0 @@ -1799,8 +1796,7 @@ CONTAINS ! Inputs: ! fill_value - fill value ! space_id - memory space selection identifier -! buf - data buffer iin memory ro apply selection to -! - of k-th dimension of the buf array +! buf - memory buffer containing the selection to be filled ! Outputs: ! hdferr: - error code ! Success: 0 diff --git a/hl/c++/test/ptableTest.cpp b/hl/c++/test/ptableTest.cpp index 9db56e0..33199f1 100644 --- a/hl/c++/test/ptableTest.cpp +++ b/hl/c++/test/ptableTest.cpp @@ -622,7 +622,7 @@ TestHDFFV_9758() s1[i].a = static_cast<int>(i); s1[i].b = 1.0F * static_cast<float>(i * i); s1[i].c = 1.0 / static_cast<double>(i + 1); - HDsprintf(s1[i].d, "string%" PRIuHSIZE "", i); + HDsnprintf(s1[i].d, STRING_LENGTH, "string%" PRIuHSIZE "", i); s1[i].e = static_cast<int>(100 + i); } diff --git a/hl/test/test_file_image.c b/hl/test/test_file_image.c index 6bb36e4..4448e41 100644 --- a/hl/test/test_file_image.c +++ b/hl/test/test_file_image.c @@ -109,12 +109,13 @@ test_file_image(size_t open_images, size_t nflags, const unsigned *flags) input_flags[i] = flags[(nflags + i) % nflags]; /* allocate name buffer for image i */ - filename[i] = (char *)HDmalloc(sizeof(char) * 32); + size_t filenamelength = sizeof(char) * 32; + filename[i] = (char *)HDmalloc(filenamelength); if (!filename[i]) FAIL_PUTS_ERROR("HDmalloc() failed"); /* create file name */ - HDsprintf(filename[i], "image_file%d.h5", (int)i); + HDsnprintf(filename[i], filenamelength, "image_file%d.h5", (int)i); /* create file */ if ((file_id[i] = H5Fcreate(filename[i], H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) diff --git a/hl/test/test_packet_vlen.c b/hl/test/test_packet_vlen.c index e704944..aa88a6c 100644 --- a/hl/test/test_packet_vlen.c +++ b/hl/test/test_packet_vlen.c @@ -109,7 +109,7 @@ test_VLof_atomic(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -246,7 +246,7 @@ test_VLof_comptype(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -418,7 +418,7 @@ test_compound_VL_VLtype(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -582,7 +582,7 @@ test_VLof_VLtype(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -1144,7 +1144,7 @@ testfl_VLof_atomic(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -1281,7 +1281,7 @@ testfl_VLof_comptype(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -1453,7 +1453,7 @@ testfl_compound_VL_VLtype(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -1617,7 +1617,7 @@ testfl_VLof_VLtype(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ diff --git a/hl/tools/h5watch/extend_dset.c b/hl/tools/h5watch/extend_dset.c index 624eebc..7756506 100644 --- a/hl/tools/h5watch/extend_dset.c +++ b/hl/tools/h5watch/extend_dset.c @@ -392,7 +392,7 @@ error: *********************************************************************** */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { char *dname = NULL; char *fname = NULL; diff --git a/hl/tools/h5watch/h5watch.c b/hl/tools/h5watch/h5watch.c index 94ca4f1..5a6fe6f 100644 --- a/hl/tools/h5watch/h5watch.c +++ b/hl/tools/h5watch/h5watch.c @@ -51,7 +51,7 @@ static herr_t process_cmpd_fields(hid_t fid, char *dsetname); static herr_t check_dataset(hid_t fid, char *dsetname); static void leave(int ret); static void usage(const char *prog); -static void parse_command_line(int argc, const char *argv[]); +static void parse_command_line(int argc, const char *const *argv); /* * Command-line options: The user can only specify long-named parameters. @@ -665,7 +665,7 @@ usage(const char *prog) *------------------------------------------------------------------------- */ static void -parse_command_line(int argc, const char *argv[]) +parse_command_line(int argc, const char *const *argv) { int opt; /* Command line option */ int tmp; @@ -790,7 +790,7 @@ catch_signal(int H5_ATTR_UNUSED signo) *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { char drivername[50]; /* VFD name */ char *fname = NULL; /* File name */ @@ -819,7 +819,7 @@ main(int argc, const char *argv[]) } /* parse command line options */ - parse_command_line(argc, argv); + parse_command_line(argc, (const char *const *)argv); if (argc <= H5_optind) { error_msg("missing dataset name\n"); diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java index 49a539b..3180ede 100644 --- a/java/src/hdf/hdf5lib/H5.java +++ b/java/src/hdf/hdf5lib/H5.java @@ -216,7 +216,7 @@ import hdf.hdf5lib.structs.H5O_token_t; * exception handlers to print out the HDF-5 error stack. * <hr> * - * @version HDF5 1.13.1 <BR> + * @version HDF5 1.13.2 <BR> * <b>See also: <a href ="./hdf.hdf5lib.HDFArray.html"> hdf.hdf5lib.HDFArray</a> </b><BR> * <a href ="./hdf.hdf5lib.HDF5Constants.html"> hdf.hdf5lib.HDF5Constants</a><BR> * <a href ="./hdf.hdf5lib.HDF5CDataTypes.html"> hdf.hdf5lib.HDF5CDataTypes</a><BR> @@ -239,7 +239,7 @@ public class H5 implements java.io.Serializable { * * Make sure to update the versions number when a different library is used. */ - public final static int LIB_VERSION[] = { 1, 13, 1 }; + public final static int LIB_VERSION[] = { 1, 13, 2 }; /** * add system property to load library by path diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c index 02e99af..5a01dc9 100644 --- a/java/src/jni/h5util.c +++ b/java/src/jni/h5util.c @@ -182,7 +182,7 @@ size_t h5str_convert(JNIEnv *env, char **in_str, hid_t container, hid_t tid, void *out_buf, size_t out_buf_offset) { unsigned char *ucptr = NULL; - static char fmt_llong[8], fmt_ullong[8]; + char fmt_llong[8], fmt_ullong[8]; H5T_class_t tclass = H5T_NO_CLASS; const char delimiter[] = " ," H5_COMPOUND_BEGIN_INDICATOR H5_COMPOUND_END_INDICATOR H5_ARRAY_BEGIN_INDICATOR H5_ARRAY_END_INDICATOR H5_VLEN_BEGIN_INDICATOR H5_VLEN_END_INDICATOR; @@ -211,10 +211,10 @@ h5str_convert(JNIEnv *env, char **in_str, hid_t container, hid_t tid, void *out_ /* Build default formats for long long types */ if (!fmt_llong[0]) { - if (HDsprintf(fmt_llong, "%%%sd", H5_PRINTF_LL_WIDTH) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: HDsprintf failure"); - if (HDsprintf(fmt_ullong, "%%%su", H5_PRINTF_LL_WIDTH) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: HDsprintf failure"); + if (HDsnprintf(fmt_llong, sizeof(fmt_llong), "%%%sd", H5_PRINTF_LL_WIDTH) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: HDsnprintf failure"); + if (HDsnprintf(fmt_ullong, sizeof(fmt_ullong), "%%%su", H5_PRINTF_LL_WIDTH) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: HDsnprintf failure"); } /* end if */ switch (tclass) { @@ -759,7 +759,7 @@ size_t h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *in_buf, int expand_data) { unsigned char *ucptr = (unsigned char *)in_buf; - static char fmt_llong[8], fmt_ullong[8]; + char fmt_llong[8], fmt_ullong[8]; H5T_class_t tclass = H5T_NO_CLASS; size_t typeSize = 0; H5T_sign_t nsign = H5T_SGN_ERROR; @@ -794,11 +794,12 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i HDmemcpy(&tmp_float, cptr, sizeof(float)); - if (NULL == (this_str = (char *)HDmalloc(25))) + size_t this_len = 25; + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%g", tmp_float) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%g", tmp_float) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); break; } @@ -808,11 +809,12 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i HDmemcpy(&tmp_double, cptr, sizeof(double)); - if (NULL == (this_str = (char *)HDmalloc(25))) + size_t this_len = 25; + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%g", tmp_double) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, "%g", this_len, tmp_double) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); break; } @@ -822,11 +824,12 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i HDmemcpy(&tmp_ldouble, cptr, sizeof(long double)); - if (NULL == (this_str = (char *)HDmalloc(27))) + size_t this_len = 27; + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%Lg", tmp_ldouble) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%Lg", tmp_ldouble) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); break; } @@ -888,25 +891,26 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i unsigned char tmp_uchar = 0; char tmp_char = 0; + size_t this_len = 7; if (H5T_SGN_NONE == nsign) { HDmemcpy(&tmp_uchar, cptr, sizeof(unsigned char)); - if (NULL == (this_str = (char *)HDmalloc(7))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%hhu", tmp_uchar) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%hhu", tmp_uchar) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } else { HDmemcpy(&tmp_char, cptr, sizeof(char)); - if (NULL == (this_str = (char *)HDmalloc(7))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%hhd", tmp_char) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%hhd", tmp_char) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } break; @@ -916,25 +920,26 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i unsigned short tmp_ushort = 0; short tmp_short = 0; + size_t this_len = 9; if (H5T_SGN_NONE == nsign) { HDmemcpy(&tmp_ushort, cptr, sizeof(unsigned short)); - if (NULL == (this_str = (char *)HDmalloc(9))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%hu", tmp_ushort) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%hu", tmp_ushort) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } else { HDmemcpy(&tmp_short, cptr, sizeof(short)); - if (NULL == (this_str = (char *)HDmalloc(9))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%hd", tmp_short) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%hd", tmp_short) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } break; @@ -944,25 +949,26 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i unsigned int tmp_uint = 0; int tmp_int = 0; + size_t this_len = 14; if (H5T_SGN_NONE == nsign) { HDmemcpy(&tmp_uint, cptr, sizeof(unsigned int)); - if (NULL == (this_str = (char *)HDmalloc(14))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%u", tmp_uint) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%u", tmp_uint) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } else { HDmemcpy(&tmp_int, cptr, sizeof(int)); - if (NULL == (this_str = (char *)HDmalloc(14))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%d", tmp_int) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%d", tmp_int) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } break; @@ -972,25 +978,26 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i unsigned long tmp_ulong = 0; long tmp_long = 0; + size_t this_len = 23; if (H5T_SGN_NONE == nsign) { HDmemcpy(&tmp_ulong, cptr, sizeof(unsigned long)); - if (NULL == (this_str = (char *)HDmalloc(23))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%lu", tmp_ulong) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%lu", tmp_ulong) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } else { HDmemcpy(&tmp_long, cptr, sizeof(long)); - if (NULL == (this_str = (char *)HDmalloc(23))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%ld", tmp_long) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%ld", tmp_long) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } break; @@ -1001,25 +1008,26 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i unsigned long long tmp_ullong = 0; long long tmp_llong = 0; + size_t this_len = 25; if (H5T_SGN_NONE == nsign) { HDmemcpy(&tmp_ullong, cptr, sizeof(unsigned long long)); - if (NULL == (this_str = (char *)HDmalloc(25))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, fmt_ullong, tmp_ullong) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, fmt_ullong, tmp_ullong) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } else { HDmemcpy(&tmp_llong, cptr, sizeof(long long)); - if (NULL == (this_str = (char *)HDmalloc(25))) + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, fmt_llong, tmp_llong) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, fmt_llong, tmp_llong) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } break; @@ -1079,17 +1087,18 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i else { size_t i; - if (NULL == (this_str = (char *)HDmalloc(4 * (typeSize + 1)))) + size_t this_len = 4 * (typeSize + 1); + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (1 == typeSize) { - if (HDsprintf(this_str, "%#02x", ucptr[0]) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%#02x", ucptr[0]) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } else { for (i = 0; i < typeSize; i++) - if (HDsprintf(this_str, "%s%02x", i ? ":" : "", ucptr[i]) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%s%02x", i ? ":" : "", ucptr[i]) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } } @@ -1134,11 +1143,12 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i else H5_LIBRARY_ERROR(ENVONLY); - if (NULL == (this_str = (char *)HDmalloc(14))) + size_t this_len = 14; + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR( ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%u-", (unsigned)oi.type) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%u-", (unsigned)oi.type) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); if (!h5str_append(out_str, this_str)) H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); HDfree(this_str); @@ -1150,11 +1160,13 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i H5Otoken_to_str(tid, &oi.token, &token_str); - if (NULL == (this_str = (char *)HDmalloc(64 + strlen(token_str) + 1))) + size_t this_len = 64 + strlen(token_str) + 1; + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR( ENVONLY, "h5str_sprintf: failed to allocate string buffer"); - if (HDsprintf(this_str, "%lu:%s", oi.fileno, token_str) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%lu:%s", oi.fileno, token_str) < + 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); H5free_memory(token_str); } @@ -1307,17 +1319,18 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i /* All other types get printed as hexadecimal */ - if (NULL == (this_str = (char *)HDmalloc(4 * (typeSize + 1)))) + size_t this_len = 4 * (typeSize + 1); + if (NULL == (this_str = (char *)HDmalloc(this_len))) H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer"); if (1 == typeSize) { - if (HDsprintf(this_str, "%#02x", ucptr[0]) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%#02x", ucptr[0]) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } else { for (i = 0; i < typeSize; i++) - if (HDsprintf(this_str, "%s%02x", i ? ":" : "", ucptr[i]) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsprintf failure"); + if (HDsnprintf(this_str, this_len, "%s%02x", i ? ":" : "", ucptr[i]) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure"); } break; @@ -1519,8 +1532,9 @@ h5str_dump_region_blocks(JNIEnv *env, h5str_t *str, hid_t region_space, hid_t re for (j = 0; j < ndims; j++) { tmp_str[0] = '\0'; - if (HDsprintf(tmp_str, "%s%lu", j ? "," : "(", (unsigned long)ptdata[i * 2 * ndims + j]) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks: HDsprintf failure"); + if (HDsnprintf(tmp_str, sizeof(tmp_str), "%s%lu", j ? "," : "(", + (unsigned long)ptdata[i * 2 * ndims + j]) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks: HDsnprintf failure"); if (!h5str_append(str, tmp_str)) H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); @@ -1529,9 +1543,9 @@ h5str_dump_region_blocks(JNIEnv *env, h5str_t *str, hid_t region_space, hid_t re for (j = 0; j < ndims; j++) { tmp_str[0] = '\0'; - if (HDsprintf(tmp_str, "%s%lu", j ? "," : ")-(", - (unsigned long)ptdata[i * 2 * ndims + j + ndims]) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks: HDsprintf failure"); + if (HDsnprintf(tmp_str, sizeof(tmp_str), "%s%lu", j ? "," : ")-(", + (unsigned long)ptdata[i * 2 * ndims + j + ndims]) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_blocks: HDsnprintf failure"); if (!h5str_append(str, tmp_str)) H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); @@ -1696,8 +1710,9 @@ h5str_dump_region_points(JNIEnv *env, h5str_t *str, hid_t region_space, hid_t re for (j = 0; j < ndims; j++) { tmp_str[0] = '\0'; - if (HDsprintf(tmp_str, "%s%lu", j ? "," : "(", (unsigned long)(ptdata[i * ndims + j])) < 0) - H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_points: HDsprintf failure"); + if (HDsnprintf(tmp_str, sizeof(tmp_str), "%s%lu", j ? "," : "(", + (unsigned long)(ptdata[i * ndims + j])) < 0) + H5_JNI_FATAL_ERROR(ENVONLY, "h5str_dump_region_points: HDsnprintf failure"); if (!h5str_append(str, tmp_str)) H5_ASSERTION_ERROR(ENVONLY, "Unable to append string."); diff --git a/java/test/TestH5.java b/java/test/TestH5.java index 1f81f09..168f28a 100644 --- a/java/test/TestH5.java +++ b/java/test/TestH5.java @@ -287,7 +287,7 @@ public class TestH5 { */ @Test public void testH5get_libversion() { - int libversion[] = { 1, 13, 1 }; + int libversion[] = { 1, 13, 2 }; try { H5.H5get_libversion(libversion); @@ -326,7 +326,7 @@ public class TestH5 { */ @Test public void testH5check_version() { - int majnum = 1, minnum = 13, relnum = 1; + int majnum = 1, minnum = 13, relnum = 2; try { H5.H5check_version(majnum, minnum, relnum); diff --git a/java/test/TestH5OcopyOld.java b/java/test/TestH5OcopyOld.java index b360cd0..e547051 100644 --- a/java/test/TestH5OcopyOld.java +++ b/java/test/TestH5OcopyOld.java @@ -32,7 +32,7 @@ import org.junit.rules.TestName; public class TestH5OcopyOld { @Rule public TestName testname = new TestName(); - private static final String FILENAME = "testRefsattribute.h5"; + private static final String FILENAME = "testRefsattributeO.h5"; private static final int DIM_X = 4; private static final int DIM_Y = 6; long H5fid = HDF5Constants.H5I_INVALID_HID; @@ -140,7 +140,6 @@ public class TestH5OcopyOld { byte[] dset_data = new byte[16]; long attribute_id = HDF5Constants.H5I_INVALID_HID; - try { rbuf0 = H5.H5Rcreate(H5fid, "/G1", HDF5Constants.H5R_OBJECT, -1); rbuf1 = H5.H5Rcreate(H5fid, "DS2", HDF5Constants.H5R_OBJECT, -1); diff --git a/release_docs/HISTORY-1_13.txt b/release_docs/HISTORY-1_13.txt new file mode 100644 index 0000000..91320a1 --- /dev/null +++ b/release_docs/HISTORY-1_13.txt @@ -0,0 +1,2149 @@ +HDF5 History +============ + +This file contains development history of the HDF5 1.13 releases from +the develop branch + +01. Release Information for hdf5-1.13.0 +02. Release Information for hdf5-1.13.1 + +[Search on the string '%%%%' for section breaks of each release.] + +%%%%1.13.0%%%% + +HDF5 version 1.13.0 released on 2021-12-01 +================================================================================ + + +INTRODUCTION +============ + +This document describes the differences between this release and the previous +HDF5 release. It contains information on the platforms tested and known +problems in this release. For more details check the HISTORY*.txt files in the +HDF5 source. + +Note that documentation in the links below will be updated at the time of each +final release. + +Links to HDF5 documentation can be found on The HDF5 web page: + + https://portal.hdfgroup.org/display/HDF5/HDF5 + +The official HDF5 releases can be obtained from: + + https://www.hdfgroup.org/downloads/hdf5/ + +Changes from Release to Release and New Features in the HDF5-1.13.x release series +can be found at: + + https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- New platforms, languages and compilers tested +- Bug Fixes since HDF5-1.12.0 +- Platforms Tested +- Known Problems +- CMake vs. Autotools installations + + +New Features +============ + + Configuration: + ------------- + - Added new configure option to support building parallel tools. + See Tools below (autotools - CMake): + --enable-parallel-tools HDF5_BUILD_PARALLEL_TOOLS + + (RAW - 2021/10/25) + + - Added new configure options to enable dimension scales APIs (H5DS*) to + use new object references with the native VOL connector (aka native HDF5 + library). New references are always used for non-native terminal VOL + connectors (e.g., DAOS). + + Autotools --enable-dimension-scales-with-new-ref + CMake HDF5_DIMENSION_SCALES_NEW_REF=ON + + (EIP - 2021/10/25, HDFFV-11180) + + - Refactored the utils folder. + + Added subfolder test and moved the 'swmr_check_compat_vfd.c file' + from test into utils/test. Deleted the duplicate swmr_check_compat_vfd.c + file in hl/tools/h5watch folder. Also fixed vfd check options. + + (ADB - 2021/10/18) + + - Changed autotools and CMake configurations to derive both + compilation warnings-as-errors and warnings-only-warn configurations + from the same files, 'config/*/*error*'. Removed redundant files + 'config/*/*noerror*'. + + (DCY - 2021/09/29) + + - Added new option to control the build of High-Level tools + that default ON/enabled. + + Add configure options (autotools - CMake): + --enable-hltools HDF5_BUILD_HL_TOOLS + + Disabling this option prevents building the gif tool which + contains the following CVEs: + HDFFV-10592 CVE-2018-17433 + HDFFV-10593 CVE-2018-17436 + HDFFV-11048 CVE-2020-10809 + + (ADB - 2021/09/16, HDFFV-11266) + + - Adds C++ Autotools configuration file for Intel + + * Checks for icpc as the compiler + * Sets std=c++11 + * Copies most non-warning flags from intel-flags + + (DER - 2021/06/02) + + - Adds C++ Autotools configuration file for PGI + + * Checks for pgc++ as the compiler name (was: pgCC) + * Sets -std=c++11 + * Other options basically match new C options (below) + + (DER - 2021/06/02) + + - Updates PGI C options + + * -Minform set to warn (was: inform) to suppress spurious messages + * Sets -gopt -O2 as debug options + * Sets -O4 as 'high optimization' option + * Sets -O0 as 'no optimization' option + * Removes specific settings for PGI 9 and 10 + + (DER - 2021/06/02) + + - A C++11-compliant compiler is now required to build the C++ wrappers + + CMAKE_CXX_STANDARD is now set to 11 when building with CMake and + -std=c++11 is added when building with clang/gcc via the Autotools. + + (DER - 2021/05/27) + + - CMake will now run the shell script tests in test/ by default + + The test directory includes several shell script tests that previously + were not run by CMake. These are now run by default. TEST_SHELL_SCRIPTS + has been set to ON and SH_PROGRAM has been set to bash (some test + scripts use bash-isms). Platforms without bash (e.g., Windows) will + ignore the script tests. + + (DER - 2021/05/23) + + - Removed unused HDF5_ENABLE_HSIZET option from CMake + + This has been unused for some time and has no effect. + + (DER - 2021/05/23) + + - CMake no longer builds the C++ library by default + + HDF5_BUILD_CPP_LIB now defaults to OFF, which is in line with the + Autotools build defaults. + + (DER - 2021/04/20) + + - Removal of pre-VS2015 work-arounds + + HDF5 now requires Visual Studio 2015 or greater, so old work-around + code and definitions have been removed, including: + + * <inttypes.h> + * snprintf and vsnprintf + * llround, llroundf, lround, lroundf, round, roundf + * strtoll and strtoull + * va_copy + * struct timespec + + (DER - 2021/03/22) + + - Add CMake variable HDF5_LIB_INFIX + + This infix is added to all library names after 'hdf5'. + e.g. the infix '_openmpi' results in the library name 'libhdf5_openmpi.so' + This name is used in packages on debian based systems. + (see https://packages.debian.org/jessie/amd64/libhdf5-openmpi-8/filelist) + + (barcode - 2021/03/22) + + - On macOS, Universal Binaries can now be built, allowing native execution on + both Intel and Apple Silicon (ARM) based Macs. + + To do so, set CMAKE_OSX_ARCHITECTURES="x86_64;arm64" + + (SAM - 2021/02/07, github-311) + + - Added a configure-time option to control certain compiler warnings + diagnostics + + A new configure-time option was added that allows some compiler warnings + diagnostics to have the default operation. This is mainly intended for + library developers and currently only works for gcc 10 and above. The + diagnostics flags apply to C, C++ and Fortran compilers and will appear + in "H5 C Flags", H5 C++ Flags" and H5 Fortran Flags, respectively. They + will NOT be exported to h5cc, etc. + + The default is OFF, which will disable the warnings URL and color attributes + for the warnings output. ON will not add the flags and allow default behavior. + + Autotools: --enable-diags + + CMake: HDF5_ENABLE_BUILD_DIAGS + + (ADB - 2021/02/05, HDFFV-11213) + + - CMake option to build the HDF filter plugins project as an external project + + The HDF filter plugins project is a collection of registered compression + filters that can be dynamically loaded when needed to access data stored + in a hdf5 file. This CMake-only option allows the plugins to be built and + distributed with the hdf5 library and tools. Like the options for szip and + zlib, either a tgz file or a git repository can be specified for the source. + + The option was refactored to use the CMake FetchContent process. This allows + more control over the filter targets, but required external project command + options to be moved to a CMake include file, HDF5PluginCache.cmake. Also + enabled the filter examples to be used as tests for operation of the + filter plugins. + + (ADB - 2020/12/10, OESS-98) + + - FreeBSD Autotools configuration now defaults to 'cc' and 'c++' compilers + + On FreeBSD, the autotools defaulted to 'gcc' as the C compiler and did + not process C++ options. Since FreeBSD 10, the default compiler has + been clang (via 'cc'). + + The default compilers have been set to 'cc' for C and 'c++' for C++, + which will pick up clang and clang++ respectively on FreeBSD 10+. + Additionally, clang options are now set correctly for both C and C++ + and g++ options will now be set if that compiler is being used (an + omission from the former functionality). + + (DER - 2020/11/28, HDFFV-11193) + + - Fixed POSIX problems when building w/ gcc on Solaris + + When building on Solaris using gcc, the POSIX symbols were not + being set correctly, which could lead to issues like clock_gettime() + not being found. + + The standard is now set to gnu99 when building with gcc on Solaris, + which allows POSIX things to be #defined and linked correctly. This + differs slightly from the gcc norm, where we set the standard to c99 + and manually set POSIX #define symbols. + + (DER - 2020/11/25, HDFFV-11191) + + - Added a configure-time option to consider certain compiler warnings + as errors + + A new configure-time option was added that converts some compiler warnings + to errors. This is mainly intended for library developers and currently + only works for gcc and clang. The warnings that are considered errors + will appear in the generated libhdf5.settings file. These warnings apply + to C and C++ code and will appear in "H5 C Flags" and H5 C++ Flags", + respectively. They will NOT be exported to h5cc, etc. + + The default is OFF. Building with this option may fail when compiling + on operating systems and with compiler versions not commonly used by + the library developers. Compilation may also fail when headers not + under the control of the library developers (e.g., mpi.h, hdfs.h) raise + warnings. + + Autotools: --enable-warnings-as-errors + + CMake: HDF5_ENABLE_WARNINGS_AS_ERRORS + + (DER - 2020/11/23, HDFFV-11189) + + - Autotools and CMake target added to produce doxygen generated documentation + + The default is OFF or disabled. + Autoconf option is '--enable-doxygen' + autotools make target is 'doxygen' and will build all doxygen targets + CMake configure option is 'HDF5_BUILD_DOC'. + CMake target is 'doxygen' for all available doxygen targets + CMake target is 'hdf5lib_doc' for the src subdirectory + + (ADB - 2020/11/03) + + - CMake option to use MSVC naming conventions with MinGW + + HDF5_MSVC_NAMING_CONVENTION option enable to use MSVC naming conventions + when using a MinGW toolchain + + (xan - 2020/10/30) + + - CMake option to statically link gcc libs with MinGW + + HDF5_MINGW_STATIC_GCC_LIBS allows to statically link libg/libstdc++ + with the MinGW toolchain + + (xan - 2020/10/30) + + - CMake option to build the HDF filter plugins project as an external project + + The HDF filter plugins project is a collection of registered compression + filters that can be dynamically loaded when needed to access data stored + in a hdf5 file. This CMake-only option allows the plugins to be built and + distributed with the hdf5 library and tools. Like the options for szip and + zlib, either a tgz file or a git repository can be specified for the source. + + The necessary options are (see the INSTALL_CMake.txt file): + HDF5_ENABLE_PLUGIN_SUPPORT + PLUGIN_TGZ_NAME or PLUGIN_GIT_URL + There are more options necessary for various filters and the plugin project + documents should be referenced. + + (ADB - 2020/09/27, OESS-98) + + - Added CMake option to format source files + + HDF5_ENABLE_FORMATTERS option will enable creation of targets using the + pattern - HDF5_*_SRC_FORMAT - where * corresponds to the source folder + or tool folder. All sources can be formatted by executing the format target; + make format + + (ADB - 2020/08/24) + + - Add file locking configure and CMake options + + HDF5 1.10.0 introduced a file locking scheme, primarily to help + enforce SWMR setup. Formerly, the only user-level control of the scheme + was via the HDF5_USE_FILE_LOCKING environment variable. + + This change introduces configure-time options that control whether + or not file locking will be used and whether or not the library + ignores errors when locking has been disabled on the file system + (useful on some HPC Lustre installations). + + In both the Autotools and CMake, the settings have the effect of changing + the default property list settings (see the H5Pset/get_file_locking() + entry, below). + + The yes/no/best-effort file locking configure setting has also been + added to the libhdf5.settings file. + + Autotools: + + An --enable-file-locking=(yes|no|best-effort) option has been added. + + yes: Use file locking. + no: Do not use file locking. + best-effort: Use file locking and ignore "disabled" errors. + + CMake: + + Two self-explanatory options have been added: + + HDF5_USE_FILE_LOCKING + HDF5_IGNORE_DISABLED_FILE_LOCKS + + Setting both of these to ON is the equivalent to the Autotools' + best-effort setting. + + NOTE: + The precedence order of the various file locking control mechanisms is: + + 1) HDF5_USE_FILE_LOCKING environment variable (highest) + + 2) H5Pset_file_locking() + + 3) configure/CMake options (which set the property list defaults) + + 4) library defaults (currently best-effort) + + (DER - 2020/07/30, HDFFV-11092) + + - CMake option to link the generated Fortran MOD files into the include + directory. + + The Fortran generation of MOD files by a Fortran compile can produce + different binary files between SHARED and STATIC compiles with different + compilers and/or different platforms. Note that it has been found that + different versions of Fortran compilers will produce incompatible MOD + files. Currently, CMake will locate these MOD files in subfolders of + the include directory and add that path to the Fortran library target + in the CMake config file, which can be used by the CMake find library + process. For other build systems using the binary from a CMake install, + a new CMake configuration can be used to copy the pre-chosen version + of the Fortran MOD files into the install include directory. + + The default will depend on the configuration of + BUILD_STATIC_LIBS and BUILD_SHARED_LIBS: + YES YES Default to SHARED + YES NO Default to STATIC + NO YES Default to SHARED + NO NO Default to SHARED + The defaults can be overridden by setting the config option + HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC + + (ADB - 2020/07/09, HDFFV-11116) + + - CMake option to use AEC (open source SZip) library instead of SZip + + The open source AEC library is a replacement library for SZip. In + order to use it for hdf5 the libaec CMake source was changed to add + "-fPIC" and exclude test files. Autotools does not build the + compression libraries within hdf5 builds. New option USE_LIBAEC is + required to compensate for the different files produced by AEC build. + + (ADB - 2020/04/22, OESS-65) + + - CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER + + Some handcrafted tests in HDFTests.c has been removed and the CMake + CHECK_STRUCT_HAS_MEMBER module has been used. + + (ADB - 2020/03/24, TRILAB-24) + + - Both build systems use same set of warnings flags + + GNU C, C++ and gfortran warnings flags were moved to files in a config + sub-folder named gnu-warnings. Flags that only are available for a specific + version of the compiler are in files named with that version. + Clang C warnings flags were moved to files in a config sub-folder + named clang-warnings. + Intel C, Fortran warnings flags were moved to files in a config sub-folder + named intel-warnings. + + There are flags in named "error-xxx" files with warnings that may + be promoted to errors. Some source files may still need fixes. + + There are also pairs of files named "developer-xxx" and "no-developer-xxx" + that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the + configure option:--enable-developer-warnings. + + In addition, CMake no longer applies these warnings for examples. + + (ADB - 2020/03/24, TRILAB-192) + + - Added test script for file size compare + + If CMake minimum version is at least 3.14, the fileCompareTest.cmake + script will compare file sizes. + + (ADB - 2020/02/24, HDFFV-11036) + + - Update CMake minimum version to 3.12 + + Updated CMake minimum version to 3.12 and added version checks + for Windows features. + + (ADB - 2020/02/05, TRILABS-142) + + - Fixed CMake include properties for Fortran libraries + + Corrected the library properties for Fortran to use the + correct path for the Fortran module files. + + (ADB - 2020/02/04, HDFFV-11012) + + - Added common warnings files for gnu and intel + + Added warnings files to use one common set of flags + during configure for both autotools and CMake build + systems. The initial implementation only affects a + general set of flags for gnu and intel compilers. + + (ADB - 2020/01/17) + + - Added new options to CMake for control of testing + + Added CMake options (default ON); + HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL + combined with: + HDF5_TEST_TOOLS + HDF5_TEST_EXAMPLES + HDF5_TEST_SWMR + HDF5_TEST_FORTRAN + HDF5_TEST_CPP + HDF5_TEST_JAVA + + (ADB - 2020/01/15, HDFFV-11001) + + - Added Clang sanitizers to CMake for analyzer support if compiler is clang. + + Added CMake code and files to execute the Clang sanitizers if + HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option + is set to one of the following: + Address + Memory + MemoryWithOrigins + Undefined + Thread + Leak + 'Address;Undefined' + + (ADB - 2019/12/12, TRILAB-135) + + - Update CMake for VS2019 support + + CMake added support for VS2019 in version 3.15. Changes to the CMake + generator setting required changes to scripts. Also updated version + references in CMake files as necessary. + + (ADB - 2019/11/18, HDFFV-10962) + + - Update CMake options to match new autotools options + + Add configure options (autotools - CMake): + enable-asserts HDF5_ENABLE_ASSERTS + enable-symbols HDF5_ENABLE_SYMBOLS + enable-profiling HDF5_ENABLE_PROFILING + enable-optimization HDF5_ENABLE_OPTIMIZATION + In addition NDEBUG is no longer forced defined and relies on the CMake + process. + + (ADB - 2019/10/07, HDFFV-100901, HDFFV-10637, TRILAB-97) + + + Library: + -------- + - Adds new file driver-level memory copy operation for + "ctl" callback and updates compact dataset I/O routines + to utilize it + + When accessing an HDF5 file with a file driver that uses + memory allocated in special ways (e.g., without standard + library's `malloc`), a crash could be observed when HDF5 + tries to perform `memcpy` operations on such a memory + region. + + These changes add a new H5FD_FEAT_MEMMANAGE VFD feature + flag, which, if specified as supported by a VFD, will + inform HDF5 that the VFD either uses special memory + management routines or wishes to perform memory management + in a specific way. Therefore, this flag instructs HDF5 to + ask the file driver to perform memory management for + certain operations. + + These changes also introduce a new "ctl" callback + operation identified by the H5FD_CTL__MEM_COPY op code. + This operation simply asks a VFD to perform a memory copy. + The arguments to this operation are passed to the "ctl" + callback's "input" parameter as a pointer to a struct + defined as: + + struct H5FD_ctl_memcpy_args_t { + void * dstbuf; /**< Destination buffer */ + hsize_t dst_off; /**< Offset within destination buffer */ + const void *srcbuf; /**< Source buffer */ + hsize_t src_off; /**< Offset within source buffer */ + size_t len; /**< Length of data to copy from source buffer */ + } H5FD_ctl_memcpy_args_t; + + Further, HDF5's compact dataset I/O routines were + identified as a problematic area that could cause a crash + for VFDs that make use of special memory management. Those + I/O routines were therefore updated to make use of this new + "ctl" callback operation in order to ask the underlying + file driver to correctly handle memory copies. + + (JTH - 2021/09/28) + + - Adds new "ctl" callback to VFD H5FD_class_t structure + with the following prototype: + + herr_t (*ctl)(H5FD_t *file, uint64_t op_code, + uint64_t flags, const void *input, + void **output); + + This newly-added "ctl" callback allows Virtual File + Drivers to intercept and handle arbitrary operations + identified by an operation code. Its parameters are + as follows: + + `file` [in] - A pointer to the file to be operated on + `op_code` [in] - The operation code identifying the + operation to be performed + `flags` [in] - Flags governing the behavior of the + operation performed (see H5FDpublic.h + for a list of valid flags) + `input` [in] - A pointer to arguments passed to the + VFD performing the operation + `output` [out] - A pointer for the receiving VFD to + use for output from the operation + + (JRM - 2021/08/16) + + - Change how the release part of version, in major.minor.release is checked + for compatibility + + The HDF5 library uses a function, H5check_version, to check that + the version defined in the header files, which is used to compile an + application is compatible with the version codified in the library, which + the application loads at runtime. This previously required an exact match + or the library would print a warning, dump the build settings and then + abort or continue. An environment variable controlled the logic. + + Now the function first checks that the library release version, in + major.minor.release, is not older than the version in the headers. + Secondly, if the release version is different, it checks if either + the library version or the header version is in the exception list, in + which case the release part of version, in major.minor.release, must + be exact. An environment variable still controls the logic. + + (ADB - 2021/07/27) + + - gcc warning suppression macros were moved out of H5public.h + + The HDF5 library uses a set of macros to suppress warnings on gcc. + These warnings were originally located in H5public.h so that the + multi VFD (which only uses public headers) could also make use of them + but internal macros should not be publicly exposed like this. + + These macros have now been moved to H5private.h. Pending future multi + VFD refactoring, the macros have been duplicated in H5FDmulti.c to + suppress the format string warnings there. + + (DER - 2021/06/03) + + - H5Gcreate1() now rejects size_hint parameters larger than UINT32_MAX + + The size_hint value is ultimately stored in a uint32_t struct field, + so specifying a value larger than this on a 64-bit machine can cause + undefined behavior including crashing the system. + + The documentation for this API call was also incorrect, stating that + passing a negative value would cause the library to use a default + value. Instead, passing a "negative" value actually passes a very large + value, which is probably not what the user intends and can cause + crashes on 64-bit systems. + + The Doxygen documentation has been updated and passing values larger + than UINT32_MAX for size_hint will now produce a normal HDF5 error. + + (DER - 2021/04/29, HDFFV-11241) + + + - H5Pset_fapl_log() no longer crashes when passed an invalid fapl ID + + When passed an invalid fapl ID, H5Pset_fapl_log() would usually + segfault when attempting to free an uninitialized pointer in the error + handling code. This behavior is more common in release builds or + when the memory sanitization checks were not selected as a build + option. + + The pointer is now correctly initialized and the API call now + produces a normal HDF5 error when fed an invalid fapl ID. + + (DER - 2021/04/28, HDFFV-11240) + + - Fixes a segfault when H5Pset_mdc_log_options() is called multiple times + + The call incorrectly attempts to free an internal copy of the previous + log location string, which causes a segfault. This only happens + when the call is invoked multiple times on the same property list. + On the first call to a given fapl, the log location is set to NULL so + the segfault does not occur. + + The string is now handled properly and the segfault no longer occurs. + + (DER - 2021/04/27, HDFFV-11239) + + - HSYS_GOTO_ERROR now emits the results of GetLastError() on Windows + + HSYS_GOTO_ERROR is an internal macro that is used to produce error + messages when system calls fail. These strings include errno and the + the associated strerror() value, which are not particularly useful + when a Win32 API call fails. + + On Windows, this macro has been updated to include the result of + GetLastError(). When a system call fails on Windows, usually only + one of errno and GetLastError() will be useful, however we emit both + for the user to parse. The Windows error message is not emitted as + it would be awkward to free the FormatMessage() buffer given the + existing HDF5 error framework. Users will have to look up the error + codes in MSDN. + + The format string on Windows has been changed from: + + "%s, errno = %d, error message = '%s'" + + to: + + "%s, errno = %d, error message = '%s', Win32 GetLastError() = %"PRIu32"" + + for those inclined to parse it for error values. + + (DER - 2021/03/21) + + - File locking now works on Windows + + Since version 1.10.0, the HDF5 library has used a file locking scheme + to help enforce one reader at a time accessing an HDF5 file, which can + be helpful when setting up readers and writers to use the single- + writer/multiple-readers (SWMR) access pattern. + + In the past, this was only functional on POSIX systems where flock() or + fcntl() were present. Windows used a no-op stub that always succeeded. + + HDF5 now uses LockFileEx() and UnlockFileEx() to lock the file using the + same scheme as POSIX systems. We lock the entire file when we set up the + locks (by passing DWORDMAX as both size parameters to LockFileEx()). + + (DER - 2021/03/19, HDFFV-10191) + + - H5Epush_ret() now requires a trailing semicolon + + H5Epush_ret() is a function-like macro that has been changed to + contain a `do {} while(0)` loop. Consequently, a trailing semicolon + is now required to end the `while` statement. Previously, a trailing + semi would work, but was not mandatory. This change was made to allow + clang-format to correctly format the source code. + + (SAM - 2021/03/03) + + - Improved performance of H5Sget_select_elem_pointlist + + Modified library to cache the point after the last block of points + retrieved by H5Sget_select_elem_pointlist, so a subsequent call to the + same function to retrieve the next block of points from the list can + proceed immediately without needing to iterate over the point list. + + (NAF - 2021/01/19) + + - Replaced H5E_ATOM with H5E_ID in H5Epubgen.h + + The term "atom" is archaic and not in line with current HDF5 library + terminology, which uses "ID" instead. "Atom" has mostly been purged + from the library internals and this change removes H5E_ATOM from + the H5Epubgen.h (exposed via H5Epublic.h) and replaces it with + H5E_ID. + + (DER - 2020/11/24, HDFFV-11190) + + - Add a new public function H5Ssel_iter_reset + + This function resets a dataspace selection iterator back to an + initial state so that it may be used for iteration once more. + This can be useful when needing to iterate over a selection + multiple times without having to repeatedly create/destroy + a selection iterator for that dataspace selection. + + (JTH - 2020/09/18) + + - Remove HDFS VFD stubs + + The original implementation of the HDFS VFD included non-functional + versions of the following public API calls when the HDFS VFD is + not built as a part of the HDF5 library: + + * H5FD_hdfs_init() + * H5Pget_fapl_hdfs() + * H5Pset_fapl_hdfs() + + They will remain present in HDF5 1.10 and HDF5 1.12 releases + for binary compatibility purposes but have been removed as of 1.14.0. + + Note that this has nothing to do with the real HDFS VFD API calls + that are fully functional when the HDFS VFD is configured and built. + + We simply changed: + + #ifdef LIBHDFS + <real API call> + #else + <useless stub> + #endif + + to: + + #ifdef LIBHDFS + <real API call> + #endif + + Which is how the other optional VFDs are handled. + + (DER - 2020/08/27) + + - Add Mirror VFD + + Use TCP/IP sockets to perform write-only (W/O) file I/O on a remote + machine. Must be used in conjunction with the Splitter VFD. + + (JOS - 2020/03/13, TBD) + + - Add Splitter VFD + + Maintain separate R/W and W/O channels for "concurrent" file writes + to two files using a single HDF5 file handle. + + (JOS - 2020/03/13, TBD) + + - Refactored public exposure of haddr_t type in favor of "object tokens" + + To better accommodate HDF5 VOL connectors where "object addresses in a file" + may not make much sense, the following changes were made to the library: + + * Introduced new H5O_token_t "object token" type, which represents a + unique and permanent identifier for referencing an HDF5 object within + a container; these "object tokens" are meant to replace object addresses. + Along with the new type, a new H5Oopen_by_token API call was introduced + to open an object by a token, similar to how object addresses were + previously used with H5Oopen_by_addr. + + * Introduced new H5Lget_info2, H5Lget_info_by_idx2, H5Literate2, H5Literate_by_name2, + H5Lvisit2 and H5Lvisit_by_name2 API calls, along with their associated H5L_info2_t + struct and H5L_iterate2_t callback function, which work with the newly-introduced + object tokens, instead of object addresses. The original functions have been + renamed to version 1 functions and are deprecated in favor of the new version 2 + functions. The H5L_info_t and H5L_iterate_t types have been renamed to version 1 + types and are now deprecated in favor of their version 2 counterparts. For each of + the functions and types, compatibility macros take place of the original symbols. + + * Introduced new H5Oget_info3, H5Oget_info_by_name3, H5Oget_info_by_idx3, + H5Ovisit3 and H5Ovisit_by_name3 API calls, along with their associated H5O_info2_t + struct and H5O_iterate2_t callback function, which work with the newly-introduced + object tokens, instead of object addresses. The version 2 functions are now + deprecated in favor of the version 3 functions. The H5O_info_t and H5O_iterate_t + types have been renamed to version 1 types and are now deprecated in favor of their + version 2 counterparts. For each, compatibility macros take place of the original + symbols. + + * Introduced new H5Oget_native_info, H5Oget_native_info_by_name and + H5Oget_native_info_by_idx API calls, along with their associated H5O_native_info_t + struct, which are used to retrieve the native HDF5 file format-specific information + about an object. This information (such as object header info and B-tree/heap info) + has been removed from the new H5O_info2_t struct so that the more generic + H5Oget_info(_by_name/_by_idx)3 routines will not try to retrieve it for non-native + VOL connectors. + + * Added new H5Otoken_cmp, H5Otoken_to_str and H5Otoken_from_str routines to compare + two object tokens, convert an object token into a nicely-readable string format and + to convert an object token string back into a real object token, respectively. + + (DER, QAK, JTH - 2020/01/16) + + - Add new public function H5Sselect_adjust. + + This function shifts a dataspace selection by a specified logical offset + within the dataspace extent. This can be useful for VOL developers to + implement chunked datasets. + + (NAF - 2019/11/18) + + - Add new public function H5Sselect_project_intersection. + + This function computes the intersection between two dataspace selections + and projects that intersection into a third selection. This can be useful + for VOL developers to implement chunked or virtual datasets. + + (NAF - 2019/11/13, ID-148) + + - Add new public function H5VLget_file_type. + + This function returns a datatype equivalent to the supplied datatype but + with the location set to be in the file. This datatype can then be used + with H5Tconvert to convert data between file and in-memory representation. + This function is intended for use only by VOL connector developers. + + (NAF - 2019/11/08, ID-127) + + + Parallel Library: + ----------------- + - + + + Fortran Library: + ---------------- + - H5Fget_name_f fixed to handle correctly trailing whitespaces and + newly allocated buffers. + + (MSB - 2021/08/30, github-826,972) + + - Add wrappers for H5Pset/get_file_locking() API calls + + h5pget_file_locking_f() + h5pset_file_locking_f() + + See the configure option discussion for HDFFV-11092 (above) for more + information on the file locking feature and how it's controlled. + + (DER - 2020/07/30, HDFFV-11092) + + C++ Library: + ------------ + - Add wrappers for H5Pset/get_file_locking() API calls + + FileAccPropList::setFileLocking() + FileAccPropList::getFileLocking() + + See the configure option discussion for HDFFV-11092 (above) for more + information on the file locking feature and how it's controlled. + + (DER - 2020/07/30, HDFFV-11092) + + + Java Library: + ------------- + - Replaced HDF5AtomException with HDF5IdException + + Since H5E_ATOM changed to H5E_ID in the C library, the Java exception + that wraps the error category was also renamed. Its functionality + remains unchanged aside from the name. + + (See also the HDFFV-11190 note in the C library section) + + (DER - 2020/11/24, HDFFV-11190) + + - Added new H5S functions. + + H5Sselect_copy, H5Sselect_shape_same, H5Sselect_adjust, + H5Sselect_intersect_block, H5Sselect_project_intersection, + H5Scombine_hyperslab, H5Smodify_select, H5Scombine_select + wrapper functions added. + + (ADB - 2020/10/27, HDFFV-10868) + + - Add wrappers for H5Pset/get_file_locking() API calls + + H5Pset_file_locking() + H5Pget_use_file_locking() + H5Pget_ignore_disabled_file_locking() + + Unlike the C++ and Fortran wrappers, there are separate getters for the + two file locking settings, each of which returns a boolean value. + + See the configure option discussion for HDFFV-11092 (above) for more + information on the file locking feature and how it's controlled. + + (DER - 2020/07/30, HDFFV-11092) + + - Added ability to test java library with VOLs. + + Created a new CMake script that combines the java and vol test scripts. + + (ADB - 2020/02/03, HDFFV-10996) + + - Tests fail for non-English locales. + + In the JUnit tests with a non-English locale, only the part before + the decimal comma is replaced by XXXX and this leads to a comparison + error. Changed the regex for the Time substitution. + + (ADB - 2020/01/09, HDFFV-10995) + + + Tools: + ------ + - Added a new (unix ONLY) parallel meta tool 'h5dwalk', which utilizes the + mpifileutils (https://hpc.github.io/mpifileutils) open source utility + library to enable parallel execution of other HDF5 tools. + This approach can greatly enhance the serial hdf5 tool performance over large + collections of files by utilizing MPI parallelism to distribute an application + load over many independent MPI ranks and files. + + An introduction to the mpifileutils library and initial 'User Guide' for + the new 'h5dwalk" tool can be found at: + https://github.com/HDFGroup/hdf5doc/tree/master/RFCs/HDF5/tools/parallel_tools + + (RAW - 2021/10/25) + + - Refactored the perform tools and removed depends on test library. + + Moved the perf and h5perf tools from tools/test/perform to + tools/src/h5perf so that they can be installed. This required + that the test library dependency be removed by copying the + needed functions from h5test.c. + The standalone scripts and other perform tools remain in the + tools/test/perform folder. + + (ADB - 2021/08/10) + + - Removed partial long exceptions + + Some of the tools accepted shortened versions of the long options + (ex: --datas instead of --dataset). These were implemented inconsistently, + are difficult to maintian, and occasionally block useful long option + names. These partial long options have been removed from all the tools. + + (DER - 2021/08/03) + + - h5repack added help text for user-defined filters. + + Added help text line that states the valid values of the filter flag + for user-defined filters; + filter_flag: 1 is OPTIONAL or 0 is MANDATORY + + (ADB - 2021/01/14, HDFFV-11099) + + - Added h5delete tool + + Deleting HDF5 storage when using the VOL can be tricky when the VOL + does not create files. The h5delete tool is a simple wrapper around + the H5Fdelete() API call that uses the VOL specified in the + HDF5_VOL_CONNECTOR environment variable to delete a "file". If + the call to H5Fdelete() fails, the tool will attempt to use + the POSIX remove(3) call to remove the file. + + Note that the HDF5 library does currently have support for + H5Fdelete() in the native VOL connector. + + (DER - 2020/12/16) + + - h5repack added options to control how external links are handled. + + Currently h5repack preserves external links and cannot copy and merge + data from the external files. Two options, merge and prune, were added to + control how to merge data from an external link into the resulting file. + --merge Follow external soft link recursively and merge data. + --prune Do not follow external soft links and remove link. + --merge --prune Follow external link, merge data and remove dangling link. + + (ADB - 2020/08/05, HDFFV-9984) + + - h5repack was fixed to repack the reference attributes properly. + The code line that checks if the update of reference inside a compound + datatype is misplaced outside the code block loop that carries out the + check. In consequence, the next attribute that is not the reference + type was repacked again as the reference type and caused the failure of + repacking. The fix is to move the corresponding code line to the correct + code block. + + (KY -2020/02/07, HDFFV-11014) + + - h5diff was updated to use the new reference APIs. + + h5diff uses the new reference APIs to compare references. + Attribute references can also be compared. + + (ADB - 2019/12/19, HDFFV-10980) + + - h5dump and h5ls were updated to use the new reference APIs. + + The tools library now use the new reference APIs to inspect a + file. Also the DDL spec was updated to reflect the format + changes produced with the new APIs. The export API and support + functions in the JNI were updated to match. + + (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877) + + + High-Level APIs: + ---------------- + - added set/get for unsigned long long attributes + + The attribute writing high-level API has been expanded to include + public set/get functions for ULL attributes, analogously to the + existing set/get for other types. + + (AF - 2021/09/08) + + C Packet Table API: + ------------------- + - + + Internal header file: + --------------------- + - + + Documentation: + -------------- + - + + +New platforms, languages and compilers tested +============================================= + - Linux 5.13.14-200.fc34 #1 SMP x86_64 GNU/Linux Fedora34 + - Linux 5.11.0-34-generic #36-Ubuntu SMP x86_64 GNU/Linux Ubuntu 20.04 + - Linux 5.3.18-22-default #1 SMP x86_64 GNU/Linux SUSE15sp2 + - Linux-4.14.0-115.21.2 #1 SMP ppc64le GNU/Linux + - Linux-4.12.14-150.75-default #1 SMP x86_64 GNU/Linux + - macOS Apple M1 11.6 Darwin 20.6.0 arm64 + - macOS Big Sur 11.3.1 Darwin 20.4.0 x86_64 + - clang versions 11.0.1, 12.0.5 + - Visual Studio 2019 w/ clang 12.0.0 with MSVC-like command-line + + +Bug Fixes since HDF5-1.12.0 release +=================================== + Library + ------- + - Fixed an H5Pget_filter_by_id1/2() assert w/ out of range filter IDs + + Both H5Pget_filter_by_id1 and 2 did not range check the filter ID, which + could trip as assert in debug versions of the library. The library now + returns a normal HDF5 error when the filter ID is out of range. + + (DER - 2021/11/23, HDFFV-11286) + + - Fixed an issue with collective metadata reads being permanently disabled + after a dataset chunk lookup operation. This would usually cause a + mismatched MPI_Bcast and MPI_ERR_TRUNCATE issue in the library for + simple cases of H5Dcreate() -> H5Dwrite() -> H5Dcreate(). + + (JTH - 2021/11/08, HDFFV-11090) + + - Fixed cross platform incompatibility of references within variable length + types + + Reference types within variable length types previously could not be + read on a platform with different endianness from where they were + written. Fixed so cross platform portability is restored. + + (NAF - 2021/09/30) + + - Detection of simple data transform function "x" + + In the case of the simple data transform function "x" the (parallel) + library recognizes this is the same as not applying this data transform + function. This improves the I/O performance. In the case of the parallel + library, it also avoids breaking to independent I/O, which makes it + possible to apply a filter when writing or reading data to or from + the HDF5 file. + + (JWSB - 2021/09/13) + + - Fixed an invalid read and memory leak when parsing corrupt file space + info messages + + When the corrupt file from CVE-2020-10810 was parsed by the library, + the code that imports the version 0 file space info object header + message to the version 1 struct could read past the buffer read from + the disk, causing an invalid memory read. Not catching this error would + cause downstream errors that eventually resulted in a previously + allocated buffer to be unfreed when the library shut down. In builds + where the free lists are in use, this could result in an infinite loop + and SIGABRT when the library shuts down. + + We now track the buffer size and raise an error on attempts to read + past the end of it. + + (DER - 2021/08/12, HDFFV-11053) + + + - Fixed CVE-2018-14460 + + The tool h5repack produced a segfault when the rank in dataspace + message was corrupted, causing invalid read while decoding the + dimension sizes. + + The problem was fixed by ensuring that decoding the dimension sizes + and max values will not go beyond the end of the buffer. + + (BMR - 2021/05/12, HDFFV-11223) + + - Fixed CVE-2018-11206 + + The tool h5dump produced a segfault when the size of a fill value + message was corrupted and caused a buffer overflow. + + The problem was fixed by verifying the fill value's size + against the buffer size before attempting to access the buffer. + + (BMR - 2021/03/15, HDFFV-10480) + + - Fixed CVE-2018-14033 (same issue as CVE-2020-10811) + + The tool h5dump produced a segfault when the storage size message + was corrupted and caused a buffer overflow. + + The problem was fixed by verifying the storage size against the + buffer size before attempting to access the buffer. + + (BMR - 2021/03/15, HDFFV-11159/HDFFV-11049) + + - Remove underscores on header file guards + + Header file guards used a variety of underscores at the beginning of the define. + + Removed all leading (some trailing) underscores from header file guards. + + (ADB - 2021/03/03, #361) + + - Fixed a segmentation fault + + A segmentation fault occurred with a Mathworks corrupted file. + + A detection of accessing a null pointer was added to prevent the problem. + + (BMR - 2021/02/19, HDFFV-11150) + + - Fixed issue with MPI communicator and info object not being + copied into new FAPL retrieved from H5F_get_access_plist + + Added logic to copy the MPI communicator and info object into + the output FAPL. MPI communicator is retrieved from the VFD, while + the MPI info object is retrieved from the file's original FAPL. + + (JTH - 2021/02/15, HDFFV-11109) + + - Fixed problems with vlens and refs inside compound using + H5VLget_file_type() + + Modified library to properly ref count H5VL_object_t structs and only + consider file vlen and reference types to be equal if their files are + the same. + + (NAF - 2021/01/22) + + - Fixed CVE-2018-17432 + + The tool h5repack produced a segfault on a corrupted file which had + invalid rank for scalar or NULL datatype. + + The problem was fixed by modifying the dataspace encode and decode + functions to detect and report invalid rank. h5repack now fails + with an error message for the corrupted file. + + (BMR - 2020/10/26, HDFFV-10590) + + - Creation of dataset with optional filter + + When the combination of type, space, etc doesn't work for filter + and the filter is optional, it was supposed to be skipped but it was + not skipped and the creation failed. + + Allowed the creation of the dataset in such a situation. + + (BMR - 2020/08/13, HDFFV-10933) + + - Explicitly declared dlopen to use RTLD_LOCAL + + dlopen documentation states that if neither RTLD_GLOBAL nor + RTLD_LOCAL are specified, then the default behavior is unspecified. + The default on linux is usually RTLD_LOCAL while macos will default + to RTLD_GLOBAL. + + (ADB - 2020/08/12, HDFFV-11127) + + - H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which + causes asserts/errors when passed to other dataspace API calls. + + H5S_NO_CLASS is an internal class value that should not have been + exposed via a public API call. + + In debug builds of the library, this can cause assert() function to + trip. In non-debug builds, it will produce normal library errors. + + The new library behavior is for H5Sset_extent_none() to convert + the dataspace into one of type H5S_NULL, which is better handled + by the library and easier for developers to reason about. + + (DER - 2020/07/27, HDFFV-11027) + + - Fixed issues CVE-2018-13870 and CVE-2018-13869 + + When a buffer overflow occurred because a name length was corrupted + and became very large, h5dump crashed on memory access violation. + + A check for reading pass the end of the buffer was added to multiple + locations to prevent the crashes and h5dump now simply fails with an + error message when this error condition occurs. + + (BMR - 2020/07/22, HDFFV-11120 and HDFFV-11121) + + - Fixed the segmentation fault when reading attributes with multiple threads + + It was reported that the reading of attributes with variable length string + datatype will crash with segmentation fault particularly when the number of + threads is high (>16 threads). The problem was due to the file pointer that + was set in the variable length string datatype for the attribute. That file + pointer was already closed when the attribute was accessed. + + The problem was fixed by setting the file pointer to the current opened file pointer + when the attribute was accessed. Similar patch up was done before when reading + dataset with variable length string datatype. + + (VC - 2020/07/13, HDFFV-11080) + + - Fixed CVE-2020-10810 + + The tool h5clear produced a segfault during an error recovery in + the superblock decoding. An internal pointer was reset to prevent + further accessing when it is not assigned with a value. + + (BMR - 2020/06/29, HDFFV-11053) + + - Fixed CVE-2018-17435 + + The tool h52gif produced a segfault when the size of an attribute + message was corrupted and caused a buffer overflow. + + The problem was fixed by verifying the attribute message's size + against the buffer size before accessing the buffer. h52gif was + also fixed to display the failure instead of silently exiting + after the segfault was eliminated. + + (BMR - 2020/06/19, HDFFV-10591) + + + Java Library + ------------ + - JNI utility function does not handle new references. + + The JNI utility function for converting reference data to string did + not use the new APIs. In addition to fixing that function, added new + java tests for using the new APIs. + + (ADB - 2021/02/16, HDFFV-11212) + + - The H5FArray.java class, in which virtually the entire execution time + is spent using the HDFNativeData method that converts from an array + of bytes to an array of the destination Java type. + + 1. Convert the entire byte array into a 1-d array of the desired type, + rather than performing 1 conversion per row; + 2. Use the Java Arrays method copyOfRange to grab the section of the + array from (1) that is desired to be inserted into the destination array. + + (PGT,ADB - 2020/12/13, HDFFV-10865) + + - Added ability to test java library with VOLs. + + Created a new CMake script that combines the java and vol test scripts. + + (ADB - 2020/02/03, HDFFV-10996) + + - Tests fail for non-English locales. + + In the JUnit tests with a non-English locale, only the part before + the decimal comma is replaced by XXXX and this leads to a comparison + error. Changed the regex for the Time substitution. + + (ADB - 2020/01/09, HDFFV-10995) + + + Configuration + ------------- + - Corrected path searched by CMake find_package command + + The install path for cmake find_package files had been changed to use + "share/cmake" + for all platforms. However the trailing "hdf5" directory was not removed. + This "hdf5" additional directory has been removed. + + (ADB - 2021/09/27) + + - Corrected pkg-config compile script + + It was discovered that the position of the "$@" argument for the command + in the compile script may fail on some platforms and configurations. The + position of the "$@"command argument was moved before the pkg-config sub command. + + (ADB - 2021/08/30) + + - Fixed CMake C++ compiler flags + + A recent refactoring of the C++ configure files accidentally removed the + file that executed the enable_language command for C++ needed by the + HDFCXXCompilerFlags.cmake file. Also updated the intel warnings files, + including adding support for windows platforms. + + (ADB - 2021/08/10) + + - Better support for libaec (open-source Szip library) in CMake + + Implemented better support for libaec 1.0.5 (or later) library. This version + of libaec contains improvements for better integration with HDF5. Furthermore, + the variable USE_LIBAEC_STATIC has been introduced to allow to make use of + static version of libaec library. Use libaec_DIR or libaec_ROOT to set + the location in which libaec can be found. + + Be aware, the Szip library of libaec 1.0.4 depends on another library within + libaec library. This dependency is not specified in the current CMake + configuration which means that one can not use the static Szip library of + libaec 1.0.4 when building HDF5. This has been resolved in libaec 1.0.5. + + (JWSB - 2021/06/22) + + - Refactor CMake configure for Fortran + + The Fortran configure tests for KINDs reused a single output file that was + read to form the Integer and Real Kinds defines. However, if config was run + more then once, the CMake completed variable prevented the tests from executing + again and the last value saved in the file was used to create the define. + Creating separate files for each KIND solved the issue. + + In addition the test for H5_PAC_C_MAX_REAL_PRECISION was not pulling in + defines for proper operation and did not define H5_PAC_C_MAX_REAL_PRECISION + correctly for a zero value. This was fixed by supplying the required defines. + In addition it was moved from the Fortran specific HDF5UseFortran.camke file + to the C centric ConfigureChecks.cmake file. + + (ADB - 2021/06/03) + + - Move emscripten flag to compile flags + + The emscripten flag, -O0, was removed from target_link_libraries command + to the correct target_compile_options command. + + (ADB - 2021/04/26 HDFFV-11083) + + - Remove arbitrary warning flag groups from CMake builds + + The arbitrary groups were created to reduce the quantity of warnings being + reported that overwhelmed testing report systems. Considerable work has + been accomplished to reduce the warning count and these arbitrary groups + are no longer needed. + Also the default for all warnings, HDF5_ENABLE_ALL_WARNINGS, is now ON. + + Visual Studio warnings C4100, C4706, and C4127 have been moved to + developer warnings, HDF5_ENABLE_DEV_WARNINGS, and are disabled for normal builds. + + (ADB - 2021/03/22, HDFFV-11228) + + - Reclassify CMake messages, to allow new modes and --log-level option + + CMake message commands have a mode argument. By default, STATUS mode + was chosen for any non-error message. CMake version 3.15 added additional + modes, NOTICE, VERBOSE, DEBUG and TRACE. All message commands with a mode + of STATUS were reviewed and most were reclassified as VERBOSE. The new + mode was protected by a check for a CMake version of at least 3.15. If CMake + version 3.17 or above is used, the user can use the command line option + of "--log-level" to further restrict which message commands are displayed. + + (ADB - 2021/01/11, HDFFV-11144) + + - Fixes Autotools determination of the stat struct having an st_blocks field + + A missing parenthesis in an autoconf macro prevented building the test + code used to determine if the stat struct contains the st_blocks field. + Now that the test functions correctly, the H5_HAVE_STAT_ST_BLOCKS #define + found in H5pubconf.h will be defined correctly on both the Autotools and + CMake. This #define is only used in the tests and does not affect the + HDF5 C library. + + (DER - 2021/01/07, HDFFV-11201) + + - Add missing ENV variable line to hdfoptions.cmake file + + Using the build options to use system SZIP/ZLIB libraries need to also + specify the library root directory. Setting the {library}_ROOT ENV + variable was added to the hdfoptions.cmake file. + + (ADB - 2020/10/19 HDFFV-11108) + + + Tools + ----- + - Changed how h5dump and h5ls identify long double. + + Long double support is not consistent across platforms. Tools will always + identify long double as 128-bit [little/big]-endian float nn-bit precision. + New test file created for datasets with attributes for float, double and + long double. In addition any unknown integer or float datatype will now + also show the number of bits for precision. + These files are also used in the java tests. + + (ADB - 2021/03/24, HDFFV-11229,HDFFV-11113) + + - Fixed tools argument parsing. + + Tools parsing used the length of the option from the long array to match + the option from the command line. This incorrectly matched a shorter long + name option that happened to be a subset of another long option. + Changed to match whole names. + + (ADB - 2021/01/19, HDFFV-11106) + + - The tools library was updated by standardizing the error stack process. + + General sequence is: + h5tools_setprogname(PROGRAMNAME); + h5tools_setstatus(EXIT_SUCCESS); + h5tools_init(); + ... process the command-line (check for error-stack enable) ... + h5tools_error_report(); + ... (do work) ... + h5diff_exit(ret); + + (ADB - 2020/07/20, HDFFV-11066) + + - h5diff fixed a command line parsing error. + + h5diff would ignore the argument to -d (delta) if it is smaller than DBL_EPSILON. + The macro H5_DBL_ABS_EQUAL was removed and a direct value comparison was used. + + (ADB - 2020/07/20, HDFFV-10897) + + - h5diff added a command line option to ignore attributes. + + h5diff would ignore all objects with a supplied path if the exclude-path argument is used. + Adding the exclude-attribute argument will only exclude attributes, with the supplied path, + from comparison. + + (ADB - 2020/07/20, HDFFV-5935) + + - h5diff added another level to the verbose argument to print filenames. + + Added verbose level 3 that is level 2 plus the filenames. The levels are: + 0 : Identical to '-v' or '--verbose' + 1 : All level 0 information plus one-line attribute status summary + 2 : All level 1 information plus extended attribute status report + 3 : All level 2 information plus file names + + (ADB - 2020/07/20, HDFFV-1005) + + - h5repack was fixed to repack the reference attributes properly. + + The code line that checks if the update of reference inside a compound + datatype is misplaced outside the code block loop that carries out the + check. In consequence, the next attribute that is not the reference + type was repacked again as the reference type and caused the failure of + repacking. The fix is to move the corresponding code line to the correct + code block. + + (KY -2020/02/10, HDFFV-11014) + + - h5diff was updated to use the new reference APIs. + + h5diff uses the new reference APIs to compare references. + Attribute references can also be compared. + + (ADB - 2019/12/19, HDFFV-10980) + + - h5dump and h5ls were updated to use the new reference APIs. + + The tools library now use the new reference APIs to inspect a + file. Also the DDL spec was updated to reflect the format + changes produced with the new APIs. The export API and support + functions in the JNI were updated to match. + + (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877) + + + Performance + ------------- + - + + + Fortran API + ----------- + - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f. + + (MSB - 2020/02/18, HDFFV-11029) + + + High-Level Library + ------------------ + - Fixed HL_test_packet, test for packet table vlen of vlen. + + Incorrect length assignment. + + (ADB - 2021/10/14) + + + Fortran High-Level APIs + ----------------------- + - + + + Documentation + ------------- + - + + + F90 APIs + -------- + - + + + C++ APIs + -------- + - Added DataSet::operator= + + Some compilers complain if the copy constructor is given explicitly + but the assignment operator is implicitly set to default. + + (2021/05/19) + + + Testing + ------- + - Stopped java/test/junit.sh.in installing libs for testing under ${prefix} + + Lib files needed are now copied to a subdirectory in the java/test + directory, and on Macs the loader path for libhdf5.xxxs.so is changed + in the temporary copy of libhdf5_java.dylib. + + (LRK, 2020/07/02, HDFFV-11063) + + +Platforms Tested +=================== + + Linux 5.13.14-200.fc34 GNU gcc (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1) + #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1) + Fedora34 clang version 12.0.1 (Fedora 12.0.1-1.fc34) + (cmake and autotools) + + Linux 5.11.0-34-generic GNU gcc (GCC) 9.3.0-17ubuntu1 + #36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.3.0-17ubuntu1 + Ubuntu 20.04 Ubuntu clang version 10.0.0-4 + (cmake and autotools) + + Linux 5.8.0-63-generic GNU gcc (GCC) 10.3.0-1ubuntu1 + #71-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 10.3.0-1ubuntu1 + Ubuntu20.10 Ubuntu clang version 11.0.0-2 + (cmake and autotools) + + Linux 5.3.18-22-default GNU gcc (SUSE Linux) 7.5.0 + #1 SMP x86_64 GNU/Linux GNU Fortran (SUSE Linux) 7.5.0 + SUSE15sp2 clang version 7.0.1 (tags/RELEASE_701/final 349238) + (cmake and autotools) + + Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release + #1 SMP ppc64le GNU/Linux clang 8.0.1, 11.0.1 + (lassen) GCC 7.3.1 + XL 16.1.1.2 + (cmake) + + Linux-4.12.14-150.75-default cray-mpich/7.7.10 + #1 SMP x86_64 GNU/Linux GCC 7.3.0, 8.2.0 + (cori) Intel (R) Version 19.0.3.199 + (cmake) + + Linux-4.12.14-197.86-default cray-mpich/7.7.6 + # 1SMP x86_64 GNU/Linux GCC 7.3.0, 9.3.0, 10.2.0 + (mutrino) Intel (R) Version 17.0.4, 18.0.5, 19.1.3 + (cmake) + + Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + #1 SMP ppc64be GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + + Linux 3.10.0-1160.24.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + Centos7 Version 4.8.5 20150623 (Red Hat 4.8.5-4) + (jelly/kituo/moohan) Version 4.9.3, Version 5.3.0, Version 6.3.0, + Version 7.2.0, Version 8.3.0, Version 9.1.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + GNU C (gcc) and C++ (g++) 4.8.5 compilers + with NAG Fortran Compiler Release 6.1(Tozai) + Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers + with NAG Fortran Compiler Release 6.1(Tozai) + MPICH 3.1.4 compiled with GCC 4.9.3 + MPICH 3.3 compiled with GCC 7.2.0 + OpenMPI 2.1.6 compiled with icc 18.0.1 + OpenMPI 3.1.3 and 4.0.0 compiled with GCC 7.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86_64; + Version 19.10-0 + + Linux-3.10.0-1127.0.0.1chaos openmpi-4.0.0 + #1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1 + (quartz) GCC 7.3.0, 8.1.0 + Intel 16.0.4, 18.0.2, 19.0.4 + + macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11) + Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0 + (macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609 + + macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9) + Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0 + (bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228 + + macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4) + 64-bit gfortran GNU Fortran (GCC) 6.3.0 + (bear) Intel icc/icpc/ifort version 19.0.4.233 20190416 + + macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2) + 64-bit gfortran GNU Fortran (GCC) 7.4.0 + (kite) Intel icc/icpc/ifort version 17.0.2 + + Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1011test) Intel icc/icpc/ifort version 16.0.2 + + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + Centos6 Version 4.4.7 20120313 + (platypus) Version 4.9.3, 5.3.0, 6.2.0 + MPICH 3.1.4 compiled with GCC 4.9.3 + PGI C, Fortran, C++ for 64-bit target on + x86_64; + Version 19.10-0 + + Windows 10 x64 Visual Studio 2015 w/ Intel C/C++/Fortran 18 (cmake) + Visual Studio 2017 w/ Intel C/C++/Fortran 19 (cmake) + Visual Studio 2019 w/ clang 12.0.0 + with MSVC-like command-line (C/C++ only - cmake) + Visual Studio 2019 w/ Intel Fortran 19 (cmake) + Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake) + + +Known Problems +============== + Setting a variable-length dataset fill value will leak the memory allocated + for the p field of the hvl_t struct. A fix is in progress for this. + HDFFV-10840 + + CMake files do not behave correctly with paths containing spaces. + Do not use spaces in paths because the required escaping for handling spaces + results in very complex and fragile build files. + ADB - 2019/05/07 + + At present, metadata cache images may not be generated by parallel + applications. Parallel applications can read files with metadata cache + images, but since this is a collective operation, a deadlock is possible + if one or more processes do not participate. + + CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA + issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler. + + The subsetting option in ph5diff currently will fail and should be avoided. + The subsetting option works correctly in serial h5diff. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + +CMake vs. Autotools installations +================================= +While both build systems produce similar results, there are differences. +Each system produces the same set of folders on linux (only CMake works +on standard Windows); bin, include, lib and share. Autotools places the +COPYING and RELEASE.txt file in the root folder, CMake places them in +the share folder. + +The bin folder contains the tools and the build scripts. Additionally, CMake +creates dynamic versions of the tools with the suffix "-shared". Autotools +installs one set of tools depending on the "--enable-shared" configuration +option. + build scripts + ------------- + Autotools: h5c++, h5cc, h5fc + CMake: h5c++, h5cc, h5hlc++, h5hlcc + +The include folder holds the header files and the fortran mod files. CMake +places the fortran mod files into separate shared and static subfolders, +while Autotools places one set of mod files into the include folder. Because +CMake produces a tools library, the header files for tools will appear in +the include folder. + +The lib folder contains the library files, and CMake adds the pkgconfig +subfolder with the hdf5*.pc files used by the bin/build scripts created by +the CMake build. CMake separates the C interface code from the fortran code by +creating C-stub libraries for each Fortran library. In addition, only CMake +installs the tools library. The names of the szip libraries are different +between the build systems. + +The share folder will have the most differences because CMake builds include +a number of CMake specific files for support of CMake's find_package and support +for the HDF5 Examples CMake project. + +The issues with the gif tool are: + HDFFV-10592 CVE-2018-17433 + HDFFV-10593 CVE-2018-17436 + HDFFV-11048 CVE-2020-10809 +These CVE issues have not yet been addressed and can be avoided by not building +the gif tool. Disable building the High-Level tools with these options: + autotools: --disable-hltools + cmake: HDF5_BUILD_HL_TOOLS=OFF + + +%%%%1.13.1%%%% + +HDF5 version 1.13.1 released on 2022-03-02 +================================================================================ + + +INTRODUCTION +============ + +This document describes the differences between this release and the previous +HDF5 release. It contains information on the platforms tested and known +problems in this release. For more details check the HISTORY*.txt files in the +HDF5 source. + +Note that documentation in the links below will be updated at the time of each +final release. + +Links to HDF5 documentation can be found on The HDF5 web page: + + https://portal.hdfgroup.org/display/HDF5/HDF5 + +The official HDF5 releases can be obtained from: + + https://www.hdfgroup.org/downloads/hdf5/ + +Changes from Release to Release and New Features in the HDF5-1.13.x release series +can be found at: + + https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS +======== + +- New Features +- Support for new platforms and languages +- Bug Fixes since HDF5-1.13.0 +- Platforms Tested +- Known Problems +- CMake vs. Autotools installations + + +New Features +============ + + Configuration: + ------------- + - CPack will now generate RPM/DEB packages. + + Enabled the RPM and DEB CPack generators on linux. In addition to + generating STGZ and TGZ packages, CPack will try to package the + library for RPM and DEB packages. This is the initial attempt and + may change as issues are resolved. + + (ADB - 2022/01/27) + + - Added new option to the h5cc scripts produced by CMake. + + Add -showconfig option to h5cc scripts to cat the + libhdf5.settings file to the standard output. + + (ADB - 2022/01/25) + + - CMake will now run the PowerShell script tests in test/ by default + on Windows. + + The test directory includes several shell script tests that previously + were not run by CMake on Windows. These are now run by default. + If TEST_SHELL_SCRIPTS is ON and PWSH is found, the PowerShell scripts + will execute. Similar to the bash scripts on unix platforms. + + (ADB - 2021/11/23) + + + Library: + -------- + - Add a new public function, H5ESget_requests() + + This function allows the user to retrieve request pointers from an event + set. It is intended for use primarily by VOL plugin developers. + + (NAF - 2022/01/11) + + + Parallel Library: + ----------------- + - Several improvements to parallel compression feature, including: + + * Improved support for collective I/O (for both writes and reads) + + * Significant reduction of memory usage for the feature as a whole + + * Reduction of copying of application data buffers passed to H5Dwrite + + * Addition of support for incremental file space allocation for filtered + datasets created in parallel. Incremental file space allocation is the + default for these types of datasets (early file space allocation is + also still supported), while early file space allocation is still the + default (and only supported at allocation time) for unfiltered datasets + created in parallel. Incremental file space allocation should help with + parallel HDF5 applications that wish to use fill values on filtered + datasets, but would typically avoid doing so since dataset creation in + parallel would often take an excessive amount of time. Since these + datasets previously used early file space allocation, HDF5 would + allocate space for and write fill values to every chunk in the dataset + at creation time, leading to noticeable overhead. Instead, with + incremental file space allocation, allocation of file space for chunks + and writing of fill values to those chunks will be delayed until each + individual chunk is initially written to. + + * Addition of support for HDF5's "don't filter partial edge chunks" flag + (https://portal.hdfgroup.org/display/HDF5/H5P_SET_CHUNK_OPTS) + + * Addition of proper support for HDF5 fill values with the feature + + * Addition of 'H5_HAVE_PARALLEL_FILTERED_WRITES' macro to H5pubconf.h + so HDF5 applications can determine at compile-time whether the feature + is available + + * Addition of simple examples (ph5_filtered_writes.c and + ph5_filtered_writes_no_sel.c) under examples directory to demonstrate + usage of the feature + + * Improved coverage of regression testing for the feature + + (JTH - 2022/2/23) + + +Support for new platforms, languages and compilers +================================================== + - None + + +Bug Fixes since HDF5-1.13.0 release +=================================== + Library + ------- + - Fixed a metadata cache bug when resizing a pinned/protected cache entry + + When resizing a pinned/protected cache entry, the metadata + cache code previously would wait until after resizing the + entry to attempt to log the newly-dirtied entry. This + caused H5C_resize_entry to mark the entry as dirty and made + H5AC_resize_entry think that it didn't need to add the + newly-dirtied entry to the dirty entries skiplist. + + Thus, a subsequent H5AC__log_moved_entry would think it + needed to allocate a new entry for insertion into the dirty + entry skip list, since the entry didGn't exist on that list. + This caused an assertion failure, as the code to allocate a + new entry assumes that the entry is not dirty. + + (JRM - 2022/02/28) + + - Issue #1436 identified a problem with the H5_VERS_RELEASE check in the + H5check_version function. + + Investigating the original fix, #812, we discovered some inconsistencies + with a new block added to check H5_VERS_RELEASE for incompatibilities. + This new block was not using the new warning text dealing with the + H5_VERS_RELEASE check and would cause the warning to be duplicated. + + By removing the H5_VERS_RELEASE argument in the first check for + H5_VERS_MAJOR and H5_VERS_MINOR, the second check would only check + the H5_VERS_RELEASE for incompatible release versions. This adheres + to the statement that except for the develop branch, all release versions + in a major.minor maintenance branch should be compatible. The prerequisite + is that an application will not use any APIs not present in all release versions. + + (ADB - 2022/02/24, #1438) + + - Unified handling of collective metadata reads to correctly fix old bugs + + Due to MPI-related issues occurring in HDF5 from mismanagement of the + status of collective metadata reads, they were forced to be disabled + during chunked dataset raw data I/O in the HDF5 1.10.5 release. This + wouldn't generally have affected application performance because HDF5 + already disables collective metadata reads during chunk lookup, since + it is generally unlikely that the same chunks will be read by all MPI + ranks in the I/O operation. However, this was only a partial solution + that wasn't granular enough. + + This change now unifies the handling of the file-global flag and the + API context-level flag for collective metadata reads in order to + simplify querying of the true status of collective metadata reads. Thus, + collective metadata reads are once again enabled for chunked dataset + raw data I/O, but manually controlled at places where some processing + occurs on MPI rank 0 only and would cause issues when collective + metadata reads are enabled. + + (JTH - 2021/11/16, HDFFV-10501/HDFFV-10562) + + - Fixed several potential MPI deadlocks in library failure conditions + + In the parallel library, there were several places where MPI rank 0 + could end up skipping past collective MPI operations when some failure + occurs in rank 0-specific processing. This would lead to deadlocks + where rank 0 completes an operation while other ranks wait in the + collective operation. These places have been rewritten to have rank 0 + push an error and try to cleanup after the failure, then continue to + participate in the collective operation to the best of its ability. + + (JTH - 2021/11/09) + + +Platforms Tested +=================== + + Linux 5.13.14-200.fc34 GNU gcc (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1) + #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1) + Fedora34 clang version 12.0.1 (Fedora 12.0.1-1.fc34) + (cmake and autotools) + + Linux 5.11.0-34-generic GNU gcc (GCC) 9.3.0-17ubuntu1 + #36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.3.0-17ubuntu1 + Ubuntu 20.04 Ubuntu clang version 10.0.0-4 + (cmake and autotools) + + Linux 5.8.0-63-generic GNU gcc (GCC) 10.3.0-1ubuntu1 + #71-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 10.3.0-1ubuntu1 + Ubuntu20.10 Ubuntu clang version 11.0.0-2 + (cmake and autotools) + + Linux 5.3.18-22-default GNU gcc (SUSE Linux) 7.5.0 + #1 SMP x86_64 GNU/Linux GNU Fortran (SUSE Linux) 7.5.0 + SUSE15sp2 clang version 7.0.1 (tags/RELEASE_701/final 349238) + (cmake and autotools) + + Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release + #1 SMP ppc64le GNU/Linux clang 8.0.1, 11.0.1 + (lassen) GCC 7.3.1 + XL 16.1.1.2 + (cmake) + + Linux-3.10.0-1160.49.1 openmpi-intel/4.1 + #1 SMP x86_64 GNU/Linux Intel(R) Version 18.0.5, 19.1.2 + (chama) (cmake) + + Linux-4.12.14-150.75-default cray-mpich/7.7.10 + #1 SMP x86_64 GNU/Linux GCC 7.3.0, 8.2.0 + (cori) Intel (R) Version 19.0.3.199 + (cmake) + + Linux-4.12.14-197.86-default cray-mpich/7.7.6 + # 1SMP x86_64 GNU/Linux GCC 7.3.0, 9.3.0, 10.2.0 + (mutrino) Intel (R) Version 17.0.4, 18.0.5, 19.1.3 + (cmake) + + Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + #1 SMP ppc64be GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) + + Linux 3.10.0-1160.24.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + Centos7 Version 4.8.5 20150623 (Red Hat 4.8.5-4) + (jelly/kituo/moohan) Version 4.9.3, Version 5.3.0, Version 6.3.0, + Version 7.2.0, Version 8.3.0, Version 9.1.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + GNU C (gcc) and C++ (g++) 4.8.5 compilers + with NAG Fortran Compiler Release 6.1(Tozai) + Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers + with NAG Fortran Compiler Release 6.1(Tozai) + MPICH 3.1.4 compiled with GCC 4.9.3 + MPICH 3.3 compiled with GCC 7.2.0 + OpenMPI 2.1.6 compiled with icc 18.0.1 + OpenMPI 3.1.3 and 4.0.0 compiled with GCC 7.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86_64; + Version 19.10-0 + + Linux-3.10.0-1127.0.0.1chaos openmpi-4.0.0 + #1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1 + (quartz) GCC 7.3.0, 8.1.0 + Intel 16.0.4, 18.0.2, 19.0.4 + + macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11) + Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0 + (macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609 + + macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9) + Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0 + (bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228 + + macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4) + 64-bit gfortran GNU Fortran (GCC) 6.3.0 + (bear) Intel icc/icpc/ifort version 19.0.4.233 20190416 + + macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2) + 64-bit gfortran GNU Fortran (GCC) 7.4.0 + (kite) Intel icc/icpc/ifort version 17.0.2 + + Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1011test) Intel icc/icpc/ifort version 16.0.2 + + + Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + Centos6 Version 4.4.7 20120313 + (platypus) Version 4.9.3, 5.3.0, 6.2.0 + MPICH 3.1.4 compiled with GCC 4.9.3 + PGI C, Fortran, C++ for 64-bit target on + x86_64; + Version 19.10-0 + + Windows 10 x64 Visual Studio 2015 w/ Intel C/C++/Fortran 18 (cmake) + Visual Studio 2017 w/ Intel C/C++/Fortran 19 (cmake) + Visual Studio 2019 w/ clang 12.0.0 + with MSVC-like command-line (C/C++ only - cmake) + Visual Studio 2019 w/ Intel Fortran 19 (cmake) + Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake) + + +Known Problems +============== + Setting a variable-length dataset fill value will leak the memory allocated + for the p field of the hvl_t struct. A fix is in progress for this. + HDFFV-10840 + + CMake files do not behave correctly with paths containing spaces. + Do not use spaces in paths because the required escaping for handling spaces + results in very complex and fragile build files. + ADB - 2019/05/07 + + At present, metadata cache images may not be generated by parallel + applications. Parallel applications can read files with metadata cache + images, but since this is a collective operation, a deadlock is possible + if one or more processes do not participate. + + CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA + issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler. + + The subsetting option in ph5diff currently will fail and should be avoided. + The subsetting option works correctly in serial h5diff. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + +CMake vs. Autotools installations +================================= +While both build systems produce similar results, there are differences. +Each system produces the same set of folders on linux (only CMake works +on standard Windows); bin, include, lib and share. Autotools places the +COPYING and RELEASE.txt file in the root folder, CMake places them in +the share folder. + +The bin folder contains the tools and the build scripts. Additionally, CMake +creates dynamic versions of the tools with the suffix "-shared". Autotools +installs one set of tools depending on the "--enable-shared" configuration +option. + build scripts + ------------- + Autotools: h5c++, h5cc, h5fc + CMake: h5c++, h5cc, h5hlc++, h5hlcc + +The include folder holds the header files and the fortran mod files. CMake +places the fortran mod files into separate shared and static subfolders, +while Autotools places one set of mod files into the include folder. Because +CMake produces a tools library, the header files for tools will appear in +the include folder. + +The lib folder contains the library files, and CMake adds the pkgconfig +subfolder with the hdf5*.pc files used by the bin/build scripts created by +the CMake build. CMake separates the C interface code from the fortran code by +creating C-stub libraries for each Fortran library. In addition, only CMake +installs the tools library. The names of the szip libraries are different +between the build systems. + +The share folder will have the most differences because CMake builds include +a number of CMake specific files for support of CMake's find_package and support +for the HDF5 Examples CMake project. + +The issues with the gif tool are: + HDFFV-10592 CVE-2018-17433 + HDFFV-10593 CVE-2018-17436 + HDFFV-11048 CVE-2020-10809 +These CVE issues have not yet been addressed and can be avoided by not building +the gif tool. Disable building the High-Level tools with these options: + autotools: --disable-hltools + cmake: HDF5_BUILD_HL_TOOLS=OFF diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index bba27c9..5e488be 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -1,4 +1,4 @@ -HDF5 version 1.13.1-1 currently under development +HDF5 version 1.13.2-1 currently under development ================================================================================ @@ -36,7 +36,7 @@ CONTENTS - New Features - Support for new platforms and languages -- Bug Fixes since HDF5-1.12.0 +- Bug Fixes since HDF5-1.13.1 - Platforms Tested - Known Problems - CMake vs. Autotools installations @@ -47,822 +47,29 @@ New Features Configuration: ------------- - - CMake will now run the PowerShell script tests in test/ by default - on Windows. + - HDF5 memory allocation sanity checking is now off by default for + Autotools debug builds - The test directory includes several shell script tests that previously - were not run by CMake on Windows. These are now run by default. - If TEST_SHELL_SCRIPTS is ON and PWSH is found, the PowerShell scripts - will execute. Similar to the bash scripts on unix platforms. + HDF5 can be configured to perform sanity checking on internal memory + allocations by adding heap canaries to these allocations. However, + enabling this option can cause issues with external filter plugins + when working with (reallocating/freeing/allocating and passing back) + buffers. - (ADB - 2021/11/23) + Previously, this option was off by default for all CMake build types, + but only off by default for non-debug Autotools builds. Since debug + is the default build mode for HDF5 when built from source with + Autotools, this can result in surprising segfaults that don't occur + when an application is built against a release version of HDF5. + Therefore, this option is now off by default for all build types + across both CMake and Autotools. - - Added new configure option to support building parallel tools. - See Tools below (autotools - CMake): - --enable-parallel-tools HDF5_BUILD_PARALLEL_TOOLS - - (RAW - 2021/10/25) - - - Added new configure options to enable dimension scales APIs (H5DS*) to - use new object references with the native VOL connector (aka native HDF5 - library). New references are always used for non-native terminal VOL - connectors (e.g., DAOS). - - Autotools --enable-dimension-scales-with-new-ref - CMake HDF5_DIMENSION_SCALES_NEW_REF=ON - - (EIP - 2021/10/25, HDFFV-11180) - - - Refactored the utils folder. - - Added subfolder test and moved the 'swmr_check_compat_vfd.c file' - from test into utils/test. Deleted the duplicate swmr_check_compat_vfd.c - file in hl/tools/h5watch folder. Also fixed vfd check options. - - (ADB - 2021/10/18) - - - Changed autotools and CMake configurations to derive both - compilation warnings-as-errors and warnings-only-warn configurations - from the same files, 'config/*/*error*'. Removed redundant files - 'config/*/*noerror*'. - - (DCY - 2021/09/29) - - - Added new option to control the build of High-Level tools - that default ON/enabled. - - Add configure options (autotools - CMake): - --enable-hltools HDF5_BUILD_HL_TOOLS - - Disabling this option prevents building the gif tool which - contains the following CVEs: - HDFFV-10592 CVE-2018-17433 - HDFFV-10593 CVE-2018-17436 - HDFFV-11048 CVE-2020-10809 - - (ADB - 2021/09/16, HDFFV-11266) - - - Adds C++ Autotools configuration file for Intel - - * Checks for icpc as the compiler - * Sets std=c++11 - * Copies most non-warning flags from intel-flags - - (DER - 2021/06/02) - - - Adds C++ Autotools configuration file for PGI - - * Checks for pgc++ as the compiler name (was: pgCC) - * Sets -std=c++11 - * Other options basically match new C options (below) - - (DER - 2021/06/02) - - - Updates PGI C options - - * -Minform set to warn (was: inform) to suppress spurious messages - * Sets -gopt -O2 as debug options - * Sets -O4 as 'high optimization' option - * Sets -O0 as 'no optimization' option - * Removes specific settings for PGI 9 and 10 - - (DER - 2021/06/02) - - - A C++11-compliant compiler is now required to build the C++ wrappers - - CMAKE_CXX_STANDARD is now set to 11 when building with CMake and - -std=c++11 is added when building with clang/gcc via the Autotools. - - (DER - 2021/05/27) - - - CMake will now run the shell script tests in test/ by default - - The test directory includes several shell script tests that previously - were not run by CMake. These are now run by default. TEST_SHELL_SCRIPTS - has been set to ON and SH_PROGRAM has been set to bash (some test - scripts use bash-isms). Platforms without bash (e.g., Windows) will - ignore the script tests. - - (DER - 2021/05/23) - - - Removed unused HDF5_ENABLE_HSIZET option from CMake - - This has been unused for some time and has no effect. - - (DER - 2021/05/23) - - - CMake no longer builds the C++ library by default - - HDF5_BUILD_CPP_LIB now defaults to OFF, which is in line with the - Autotools build defaults. - - (DER - 2021/04/20) - - - Removal of pre-VS2015 work-arounds - - HDF5 now requires Visual Studio 2015 or greater, so old work-around - code and definitions have been removed, including: - - * <inttypes.h> - * snprintf and vsnprintf - * llround, llroundf, lround, lroundf, round, roundf - * strtoll and strtoull - * va_copy - * struct timespec - - (DER - 2021/03/22) - - - Add CMake variable HDF5_LIB_INFIX - - This infix is added to all library names after 'hdf5'. - e.g. the infix '_openmpi' results in the library name 'libhdf5_openmpi.so' - This name is used in packages on debian based systems. - (see https://packages.debian.org/jessie/amd64/libhdf5-openmpi-8/filelist) - - (barcode - 2021/03/22) - - - On macOS, Universal Binaries can now be built, allowing native execution on - both Intel and Apple Silicon (ARM) based Macs. - - To do so, set CMAKE_OSX_ARCHITECTURES="x86_64;arm64" - - (SAM - 2021/02/07, github-311) - - - Added a configure-time option to control certain compiler warnings - diagnostics - - A new configure-time option was added that allows some compiler warnings - diagnostics to have the default operation. This is mainly intended for - library developers and currently only works for gcc 10 and above. The - diagnostics flags apply to C, C++ and Fortran compilers and will appear - in "H5 C Flags", H5 C++ Flags" and H5 Fortran Flags, respectively. They - will NOT be exported to h5cc, etc. - - The default is OFF, which will disable the warnings URL and color attributes - for the warnings output. ON will not add the flags and allow default behavior. - - Autotools: --enable-diags - - CMake: HDF5_ENABLE_BUILD_DIAGS - - (ADB - 2021/02/05, HDFFV-11213) - - - CMake option to build the HDF filter plugins project as an external project - - The HDF filter plugins project is a collection of registered compression - filters that can be dynamically loaded when needed to access data stored - in a hdf5 file. This CMake-only option allows the plugins to be built and - distributed with the hdf5 library and tools. Like the options for szip and - zlib, either a tgz file or a git repository can be specified for the source. - - The option was refactored to use the CMake FetchContent process. This allows - more control over the filter targets, but required external project command - options to be moved to a CMake include file, HDF5PluginCache.cmake. Also - enabled the filter examples to be used as tests for operation of the - filter plugins. - - (ADB - 2020/12/10, OESS-98) - - - FreeBSD Autotools configuration now defaults to 'cc' and 'c++' compilers - - On FreeBSD, the autotools defaulted to 'gcc' as the C compiler and did - not process C++ options. Since FreeBSD 10, the default compiler has - been clang (via 'cc'). - - The default compilers have been set to 'cc' for C and 'c++' for C++, - which will pick up clang and clang++ respectively on FreeBSD 10+. - Additionally, clang options are now set correctly for both C and C++ - and g++ options will now be set if that compiler is being used (an - omission from the former functionality). - - (DER - 2020/11/28, HDFFV-11193) - - - Fixed POSIX problems when building w/ gcc on Solaris - - When building on Solaris using gcc, the POSIX symbols were not - being set correctly, which could lead to issues like clock_gettime() - not being found. - - The standard is now set to gnu99 when building with gcc on Solaris, - which allows POSIX things to be #defined and linked correctly. This - differs slightly from the gcc norm, where we set the standard to c99 - and manually set POSIX #define symbols. - - (DER - 2020/11/25, HDFFV-11191) - - - Added a configure-time option to consider certain compiler warnings - as errors - - A new configure-time option was added that converts some compiler warnings - to errors. This is mainly intended for library developers and currently - only works for gcc and clang. The warnings that are considered errors - will appear in the generated libhdf5.settings file. These warnings apply - to C and C++ code and will appear in "H5 C Flags" and H5 C++ Flags", - respectively. They will NOT be exported to h5cc, etc. - - The default is OFF. Building with this option may fail when compiling - on operating systems and with compiler versions not commonly used by - the library developers. Compilation may also fail when headers not - under the control of the library developers (e.g., mpi.h, hdfs.h) raise - warnings. - - Autotools: --enable-warnings-as-errors - - CMake: HDF5_ENABLE_WARNINGS_AS_ERRORS - - (DER - 2020/11/23, HDFFV-11189) - - - Autotools and CMake target added to produce doxygen generated documentation - - The default is OFF or disabled. - Autoconf option is '--enable-doxygen' - autotools make target is 'doxygen' and will build all doxygen targets - CMake configure option is 'HDF5_BUILD_DOC'. - CMake target is 'doxygen' for all available doxygen targets - CMake target is 'hdf5lib_doc' for the src subdirectory - - (ADB - 2020/11/03) - - - CMake option to use MSVC naming conventions with MinGW - - HDF5_MSVC_NAMING_CONVENTION option enable to use MSVC naming conventions - when using a MinGW toolchain - - (xan - 2020/10/30) - - - CMake option to statically link gcc libs with MinGW - - HDF5_MINGW_STATIC_GCC_LIBS allows to statically link libg/libstdc++ - with the MinGW toolchain - - (xan - 2020/10/30) - - - CMake option to build the HDF filter plugins project as an external project - - The HDF filter plugins project is a collection of registered compression - filters that can be dynamically loaded when needed to access data stored - in a hdf5 file. This CMake-only option allows the plugins to be built and - distributed with the hdf5 library and tools. Like the options for szip and - zlib, either a tgz file or a git repository can be specified for the source. - - The necessary options are (see the INSTALL_CMake.txt file): - HDF5_ENABLE_PLUGIN_SUPPORT - PLUGIN_TGZ_NAME or PLUGIN_GIT_URL - There are more options necessary for various filters and the plugin project - documents should be referenced. - - (ADB - 2020/09/27, OESS-98) - - - Added CMake option to format source files - - HDF5_ENABLE_FORMATTERS option will enable creation of targets using the - pattern - HDF5_*_SRC_FORMAT - where * corresponds to the source folder - or tool folder. All sources can be formatted by executing the format target; - make format - - (ADB - 2020/08/24) - - - Add file locking configure and CMake options - - HDF5 1.10.0 introduced a file locking scheme, primarily to help - enforce SWMR setup. Formerly, the only user-level control of the scheme - was via the HDF5_USE_FILE_LOCKING environment variable. - - This change introduces configure-time options that control whether - or not file locking will be used and whether or not the library - ignores errors when locking has been disabled on the file system - (useful on some HPC Lustre installations). - - In both the Autotools and CMake, the settings have the effect of changing - the default property list settings (see the H5Pset/get_file_locking() - entry, below). - - The yes/no/best-effort file locking configure setting has also been - added to the libhdf5.settings file. - - Autotools: - - An --enable-file-locking=(yes|no|best-effort) option has been added. - - yes: Use file locking. - no: Do not use file locking. - best-effort: Use file locking and ignore "disabled" errors. - - CMake: - - Two self-explanatory options have been added: - - HDF5_USE_FILE_LOCKING - HDF5_IGNORE_DISABLED_FILE_LOCKS - - Setting both of these to ON is the equivalent to the Autotools' - best-effort setting. - - NOTE: - The precedence order of the various file locking control mechanisms is: - - 1) HDF5_USE_FILE_LOCKING environment variable (highest) - - 2) H5Pset_file_locking() - - 3) configure/CMake options (which set the property list defaults) - - 4) library defaults (currently best-effort) - - (DER - 2020/07/30, HDFFV-11092) - - - CMake option to link the generated Fortran MOD files into the include - directory. - - The Fortran generation of MOD files by a Fortran compile can produce - different binary files between SHARED and STATIC compiles with different - compilers and/or different platforms. Note that it has been found that - different versions of Fortran compilers will produce incompatible MOD - files. Currently, CMake will locate these MOD files in subfolders of - the include directory and add that path to the Fortran library target - in the CMake config file, which can be used by the CMake find library - process. For other build systems using the binary from a CMake install, - a new CMake configuration can be used to copy the pre-chosen version - of the Fortran MOD files into the install include directory. - - The default will depend on the configuration of - BUILD_STATIC_LIBS and BUILD_SHARED_LIBS: - YES YES Default to SHARED - YES NO Default to STATIC - NO YES Default to SHARED - NO NO Default to SHARED - The defaults can be overridden by setting the config option - HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC - - (ADB - 2020/07/09, HDFFV-11116) - - - CMake option to use AEC (open source SZip) library instead of SZip - - The open source AEC library is a replacement library for SZip. In - order to use it for hdf5 the libaec CMake source was changed to add - "-fPIC" and exclude test files. Autotools does not build the - compression libraries within hdf5 builds. New option USE_LIBAEC is - required to compensate for the different files produced by AEC build. - - (ADB - 2020/04/22, OESS-65) - - - CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER - - Some handcrafted tests in HDFTests.c has been removed and the CMake - CHECK_STRUCT_HAS_MEMBER module has been used. - - (ADB - 2020/03/24, TRILAB-24) - - - Both build systems use same set of warnings flags - - GNU C, C++ and gfortran warnings flags were moved to files in a config - sub-folder named gnu-warnings. Flags that only are available for a specific - version of the compiler are in files named with that version. - Clang C warnings flags were moved to files in a config sub-folder - named clang-warnings. - Intel C, Fortran warnings flags were moved to files in a config sub-folder - named intel-warnings. - - There are flags in named "error-xxx" files with warnings that may - be promoted to errors. Some source files may still need fixes. - - There are also pairs of files named "developer-xxx" and "no-developer-xxx" - that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the - configure option:--enable-developer-warnings. - - In addition, CMake no longer applies these warnings for examples. - - (ADB - 2020/03/24, TRILAB-192) - - - Added test script for file size compare - - If CMake minimum version is at least 3.14, the fileCompareTest.cmake - script will compare file sizes. - - (ADB - 2020/02/24, HDFFV-11036) - - - Update CMake minimum version to 3.12 - - Updated CMake minimum version to 3.12 and added version checks - for Windows features. - - (ADB - 2020/02/05, TRILABS-142) - - - Fixed CMake include properties for Fortran libraries - - Corrected the library properties for Fortran to use the - correct path for the Fortran module files. - - (ADB - 2020/02/04, HDFFV-11012) - - - Added common warnings files for gnu and intel - - Added warnings files to use one common set of flags - during configure for both autotools and CMake build - systems. The initial implementation only affects a - general set of flags for gnu and intel compilers. - - (ADB - 2020/01/17) - - - Added new options to CMake for control of testing - - Added CMake options (default ON); - HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL - combined with: - HDF5_TEST_TOOLS - HDF5_TEST_EXAMPLES - HDF5_TEST_SWMR - HDF5_TEST_FORTRAN - HDF5_TEST_CPP - HDF5_TEST_JAVA - - (ADB - 2020/01/15, HDFFV-11001) - - - Added Clang sanitizers to CMake for analyzer support if compiler is clang. - - Added CMake code and files to execute the Clang sanitizers if - HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option - is set to one of the following: - Address - Memory - MemoryWithOrigins - Undefined - Thread - Leak - 'Address;Undefined' - - (ADB - 2019/12/12, TRILAB-135) - - - Update CMake for VS2019 support - - CMake added support for VS2019 in version 3.15. Changes to the CMake - generator setting required changes to scripts. Also updated version - references in CMake files as necessary. - - (ADB - 2019/11/18, HDFFV-10962) - - - Update CMake options to match new autotools options - - Add configure options (autotools - CMake): - enable-asserts HDF5_ENABLE_ASSERTS - enable-symbols HDF5_ENABLE_SYMBOLS - enable-profiling HDF5_ENABLE_PROFILING - enable-optimization HDF5_ENABLE_OPTIMIZATION - In addition NDEBUG is no longer forced defined and relies on the CMake - process. - - (ADB - 2019/10/07, HDFFV-100901, HDFFV-10637, TRILAB-97) + (JTH - 2022/03/01) Library: -------- - - Add a new public function, H5ESget_requests() - - This function allows the user to retrieve request pointers from an event - set. It is intended for use primarily by VOL plug in developers. - - (NAF - 2022/01/11) - - - Adds new file driver-level memory copy operation for - "ctl" callback and updates compact dataset I/O routines - to utilize it - - When accessing an HDF5 file with a file driver that uses - memory allocated in special ways (e.g., without standard - library's `malloc`), a crash could be observed when HDF5 - tries to perform `memcpy` operations on such a memory - region. - - These changes add a new H5FD_FEAT_MEMMANAGE VFD feature - flag, which, if specified as supported by a VFD, will - inform HDF5 that the VFD either uses special memory - management routines or wishes to perform memory management - in a specific way. Therefore, this flag instructs HDF5 to - ask the file driver to perform memory management for - certain operations. - - These changes also introduce a new "ctl" callback - operation identified by the H5FD_CTL__MEM_COPY op code. - This operation simply asks a VFD to perform a memory copy. - The arguments to this operation are passed to the "ctl" - callback's "input" parameter as a pointer to a struct - defined as: - - struct H5FD_ctl_memcpy_args_t { - void * dstbuf; /**< Destination buffer */ - hsize_t dst_off; /**< Offset within destination buffer */ - const void *srcbuf; /**< Source buffer */ - hsize_t src_off; /**< Offset within source buffer */ - size_t len; /**< Length of data to copy from source buffer */ - } H5FD_ctl_memcpy_args_t; - - Further, HDF5's compact dataset I/O routines were - identified as a problematic area that could cause a crash - for VFDs that make use of special memory management. Those - I/O routines were therefore updated to make use of this new - "ctl" callback operation in order to ask the underlying - file driver to correctly handle memory copies. - - (JTH - 2021/09/28) - - - Adds new "ctl" callback to VFD H5FD_class_t structure - with the following prototype: - - herr_t (*ctl)(H5FD_t *file, uint64_t op_code, - uint64_t flags, const void *input, - void **output); - - This newly-added "ctl" callback allows Virtual File - Drivers to intercept and handle arbitrary operations - identified by an operation code. Its parameters are - as follows: - - `file` [in] - A pointer to the file to be operated on - `op_code` [in] - The operation code identifying the - operation to be performed - `flags` [in] - Flags governing the behavior of the - operation performed (see H5FDpublic.h - for a list of valid flags) - `input` [in] - A pointer to arguments passed to the - VFD performing the operation - `output` [out] - A pointer for the receiving VFD to - use for output from the operation - - (JRM - 2021/08/16) - - - Change how the release part of version, in major.minor.release is checked - for compatibility - - The HDF5 library uses a function, H5check_version, to check that - the version defined in the header files, which is used to compile an - application is compatible with the version codified in the library, which - the application loads at runtime. This previously required an exact match - or the library would print a warning, dump the build settings and then - abort or continue. An environment variable controlled the logic. - - Now the function first checks that the library release version, in - major.minor.release, is not older than the version in the headers. - Secondly, if the release version is different, it checks if either - the library version or the header version is in the exception list, in - which case the release part of version, in major.minor.release, must - be exact. An environment variable still controls the logic. - - (ADB - 2021/07/27) - - - gcc warning suppression macros were moved out of H5public.h - - The HDF5 library uses a set of macros to suppress warnings on gcc. - These warnings were originally located in H5public.h so that the - multi VFD (which only uses public headers) could also make use of them - but internal macros should not be publicly exposed like this. - - These macros have now been moved to H5private.h. Pending future multi - VFD refactoring, the macros have been duplicated in H5FDmulti.c to - suppress the format string warnings there. - - (DER - 2021/06/03) - - - H5Gcreate1() now rejects size_hint parameters larger than UINT32_MAX - - The size_hint value is ultimately stored in a uint32_t struct field, - so specifying a value larger than this on a 64-bit machine can cause - undefined behavior including crashing the system. - - The documentation for this API call was also incorrect, stating that - passing a negative value would cause the library to use a default - value. Instead, passing a "negative" value actually passes a very large - value, which is probably not what the user intends and can cause - crashes on 64-bit systems. - - The Doxygen documentation has been updated and passing values larger - than UINT32_MAX for size_hint will now produce a normal HDF5 error. - - (DER - 2021/04/29, HDFFV-11241) - - - - H5Pset_fapl_log() no longer crashes when passed an invalid fapl ID - - When passed an invalid fapl ID, H5Pset_fapl_log() would usually - segfault when attempting to free an uninitialized pointer in the error - handling code. This behavior is more common in release builds or - when the memory sanitization checks were not selected as a build - option. - - The pointer is now correctly initialized and the API call now - produces a normal HDF5 error when fed an invalid fapl ID. - - (DER - 2021/04/28, HDFFV-11240) - - - Fixes a segfault when H5Pset_mdc_log_options() is called multiple times - - The call incorrectly attempts to free an internal copy of the previous - log location string, which causes a segfault. This only happens - when the call is invoked multiple times on the same property list. - On the first call to a given fapl, the log location is set to NULL so - the segfault does not occur. - - The string is now handled properly and the segfault no longer occurs. - - (DER - 2021/04/27, HDFFV-11239) - - - HSYS_GOTO_ERROR now emits the results of GetLastError() on Windows - - HSYS_GOTO_ERROR is an internal macro that is used to produce error - messages when system calls fail. These strings include errno and the - the associated strerror() value, which are not particularly useful - when a Win32 API call fails. - - On Windows, this macro has been updated to include the result of - GetLastError(). When a system call fails on Windows, usually only - one of errno and GetLastError() will be useful, however we emit both - for the user to parse. The Windows error message is not emitted as - it would be awkward to free the FormatMessage() buffer given the - existing HDF5 error framework. Users will have to look up the error - codes in MSDN. - - The format string on Windows has been changed from: - - "%s, errno = %d, error message = '%s'" - - to: - - "%s, errno = %d, error message = '%s', Win32 GetLastError() = %"PRIu32"" - - for those inclined to parse it for error values. - - (DER - 2021/03/21) - - - File locking now works on Windows - - Since version 1.10.0, the HDF5 library has used a file locking scheme - to help enforce one reader at a time accessing an HDF5 file, which can - be helpful when setting up readers and writers to use the single- - writer/multiple-readers (SWMR) access pattern. - - In the past, this was only functional on POSIX systems where flock() or - fcntl() were present. Windows used a no-op stub that always succeeded. - - HDF5 now uses LockFileEx() and UnlockFileEx() to lock the file using the - same scheme as POSIX systems. We lock the entire file when we set up the - locks (by passing DWORDMAX as both size parameters to LockFileEx()). - - (DER - 2021/03/19, HDFFV-10191) - - - H5Epush_ret() now requires a trailing semicolon - - H5Epush_ret() is a function-like macro that has been changed to - contain a `do {} while(0)` loop. Consequently, a trailing semicolon - is now required to end the `while` statement. Previously, a trailing - semi would work, but was not mandatory. This change was made to allow - clang-format to correctly format the source code. - - (SAM - 2021/03/03) - - - Improved performance of H5Sget_select_elem_pointlist - - Modified library to cache the point after the last block of points - retrieved by H5Sget_select_elem_pointlist, so a subsequent call to the - same function to retrieve the next block of points from the list can - proceed immediately without needing to iterate over the point list. - - (NAF - 2021/01/19) - - - Replaced H5E_ATOM with H5E_ID in H5Epubgen.h - - The term "atom" is archaic and not in line with current HDF5 library - terminology, which uses "ID" instead. "Atom" has mostly been purged - from the library internals and this change removes H5E_ATOM from - the H5Epubgen.h (exposed via H5Epublic.h) and replaces it with - H5E_ID. - - (DER - 2020/11/24, HDFFV-11190) - - - Add a new public function H5Ssel_iter_reset - - This function resets a dataspace selection iterator back to an - initial state so that it may be used for iteration once more. - This can be useful when needing to iterate over a selection - multiple times without having to repeatedly create/destroy - a selection iterator for that dataspace selection. - - (JTH - 2020/09/18) - - - Remove HDFS VFD stubs - - The original implementation of the HDFS VFD included non-functional - versions of the following public API calls when the HDFS VFD is - not built as a part of the HDF5 library: - - * H5FD_hdfs_init() - * H5Pget_fapl_hdfs() - * H5Pset_fapl_hdfs() - - They will remain present in HDF5 1.10 and HDF5 1.12 releases - for binary compatibility purposes but have been removed as of 1.14.0. - - Note that this has nothing to do with the real HDFS VFD API calls - that are fully functional when the HDFS VFD is configured and built. - - We simply changed: - - #ifdef LIBHDFS - <real API call> - #else - <useless stub> - #endif - - to: - - #ifdef LIBHDFS - <real API call> - #endif - - Which is how the other optional VFDs are handled. - - (DER - 2020/08/27) - - - Add Mirror VFD - - Use TCP/IP sockets to perform write-only (W/O) file I/O on a remote - machine. Must be used in conjunction with the Splitter VFD. - - (JOS - 2020/03/13, TBD) - - - Add Splitter VFD - - Maintain separate R/W and W/O channels for "concurrent" file writes - to two files using a single HDF5 file handle. - - (JOS - 2020/03/13, TBD) - - - Refactored public exposure of haddr_t type in favor of "object tokens" - - To better accommodate HDF5 VOL connectors where "object addresses in a file" - may not make much sense, the following changes were made to the library: - - * Introduced new H5O_token_t "object token" type, which represents a - unique and permanent identifier for referencing an HDF5 object within - a container; these "object tokens" are meant to replace object addresses. - Along with the new type, a new H5Oopen_by_token API call was introduced - to open an object by a token, similar to how object addresses were - previously used with H5Oopen_by_addr. - - * Introduced new H5Lget_info2, H5Lget_info_by_idx2, H5Literate2, H5Literate_by_name2, - H5Lvisit2 and H5Lvisit_by_name2 API calls, along with their associated H5L_info2_t - struct and H5L_iterate2_t callback function, which work with the newly-introduced - object tokens, instead of object addresses. The original functions have been - renamed to version 1 functions and are deprecated in favor of the new version 2 - functions. The H5L_info_t and H5L_iterate_t types have been renamed to version 1 - types and are now deprecated in favor of their version 2 counterparts. For each of - the functions and types, compatibility macros take place of the original symbols. - - * Introduced new H5Oget_info3, H5Oget_info_by_name3, H5Oget_info_by_idx3, - H5Ovisit3 and H5Ovisit_by_name3 API calls, along with their associated H5O_info2_t - struct and H5O_iterate2_t callback function, which work with the newly-introduced - object tokens, instead of object addresses. The version 2 functions are now - deprecated in favor of the version 3 functions. The H5O_info_t and H5O_iterate_t - types have been renamed to version 1 types and are now deprecated in favor of their - version 2 counterparts. For each, compatibility macros take place of the original - symbols. - - * Introduced new H5Oget_native_info, H5Oget_native_info_by_name and - H5Oget_native_info_by_idx API calls, along with their associated H5O_native_info_t - struct, which are used to retrieve the native HDF5 file format-specific information - about an object. This information (such as object header info and B-tree/heap info) - has been removed from the new H5O_info2_t struct so that the more generic - H5Oget_info(_by_name/_by_idx)3 routines will not try to retrieve it for non-native - VOL connectors. - - * Added new H5Otoken_cmp, H5Otoken_to_str and H5Otoken_from_str routines to compare - two object tokens, convert an object token into a nicely-readable string format and - to convert an object token string back into a real object token, respectively. - - (DER, QAK, JTH - 2020/01/16) - - - Add new public function H5Sselect_adjust. - - This function shifts a dataspace selection by a specified logical offset - within the dataspace extent. This can be useful for VOL developers to - implement chunked datasets. - - (NAF - 2019/11/18) - - - Add new public function H5Sselect_project_intersection. - - This function computes the intersection between two dataspace selections - and projects that intersection into a third selection. This can be useful - for VOL developers to implement chunked or virtual datasets. - - (NAF - 2019/11/13, ID-148) - - - Add new public function H5VLget_file_type. - - This function returns a datatype equivalent to the supplied datatype but - with the location set to be in the file. This datatype can then be used - with H5Tconvert to convert data between file and in-memory representation. - This function is intended for use only by VOL connector developers. - - (NAF - 2019/11/08, ID-127) + - Parallel Library: @@ -872,663 +79,69 @@ New Features Fortran Library: ---------------- - - H5Fget_name_f fixed to handle correctly trailing whitespaces and - newly allocated buffers. - - (MSB - 2021/08/30, github-826,972) - - - Add wrappers for H5Pset/get_file_locking() API calls - - h5pget_file_locking_f() - h5pset_file_locking_f() - - See the configure option discussion for HDFFV-11092 (above) for more - information on the file locking feature and how it's controlled. + - - (DER - 2020/07/30, HDFFV-11092) C++ Library: ------------ - - Add wrappers for H5Pset/get_file_locking() API calls - - FileAccPropList::setFileLocking() - FileAccPropList::getFileLocking() - - See the configure option discussion for HDFFV-11092 (above) for more - information on the file locking feature and how it's controlled. - - (DER - 2020/07/30, HDFFV-11092) + - Java Library: ------------- - - Replaced HDF5AtomException with HDF5IdException - - Since H5E_ATOM changed to H5E_ID in the C library, the Java exception - that wraps the error category was also renamed. Its functionality - remains unchanged aside from the name. - - (See also the HDFFV-11190 note in the C library section) - - (DER - 2020/11/24, HDFFV-11190) - - - Added new H5S functions. - - H5Sselect_copy, H5Sselect_shape_same, H5Sselect_adjust, - H5Sselect_intersect_block, H5Sselect_project_intersection, - H5Scombine_hyperslab, H5Smodify_select, H5Scombine_select - wrapper functions added. - - (ADB - 2020/10/27, HDFFV-10868) - - - Add wrappers for H5Pset/get_file_locking() API calls - - H5Pset_file_locking() - H5Pget_use_file_locking() - H5Pget_ignore_disabled_file_locking() - - Unlike the C++ and Fortran wrappers, there are separate getters for the - two file locking settings, each of which returns a boolean value. - - See the configure option discussion for HDFFV-11092 (above) for more - information on the file locking feature and how it's controlled. - - (DER - 2020/07/30, HDFFV-11092) - - - Added ability to test java library with VOLs. - - Created a new CMake script that combines the java and vol test scripts. - - (ADB - 2020/02/03, HDFFV-10996) - - - Tests fail for non-English locales. - - In the JUnit tests with a non-English locale, only the part before - the decimal comma is replaced by XXXX and this leads to a comparison - error. Changed the regex for the Time substitution. - - (ADB - 2020/01/09, HDFFV-10995) + - Tools: ------ - - Added a new (unix ONLY) parallel meta tool 'h5dwalk', which utilizes the - mpifileutils (https://hpc.github.io/mpifileutils) open source utility - library to enable parallel execution of other HDF5 tools. - This approach can greatly enhance the serial hdf5 tool performance over large - collections of files by utilizing MPI parallelism to distribute an application - load over many independent MPI ranks and files. - - An introduction to the mpifileutils library and initial 'User Guide' for - the new 'h5dwalk" tool can be found at: - https://github.com/HDFGroup/hdf5doc/tree/master/RFCs/HDF5/tools/parallel_tools - - (RAW - 2021/10/25) - - - Refactored the perform tools and removed depends on test library. - - Moved the perf and h5perf tools from tools/test/perform to - tools/src/h5perf so that they can be installed. This required - that the test library dependency be removed by copying the - needed functions from h5test.c. - The standalone scripts and other perform tools remain in the - tools/test/perform folder. - - (ADB - 2021/08/10) - - - Removed partial long exceptions - - Some of the tools accepted shortened versions of the long options - (ex: --datas instead of --dataset). These were implemented inconsistently, - are difficult to maintian, and occasionally block useful long option - names. These partial long options have been removed from all the tools. - - (DER - 2021/08/03) - - - h5repack added help text for user-defined filters. - - Added help text line that states the valid values of the filter flag - for user-defined filters; - filter_flag: 1 is OPTIONAL or 0 is MANDATORY - - (ADB - 2021/01/14, HDFFV-11099) - - - Added h5delete tool - - Deleting HDF5 storage when using the VOL can be tricky when the VOL - does not create files. The h5delete tool is a simple wrapper around - the H5Fdelete() API call that uses the VOL specified in the - HDF5_VOL_CONNECTOR environment variable to delete a "file". If - the call to H5Fdelete() fails, the tool will attempt to use - the POSIX remove(3) call to remove the file. - - Note that the HDF5 library does currently have support for - H5Fdelete() in the native VOL connector. - - (DER - 2020/12/16) - - - h5repack added options to control how external links are handled. - - Currently h5repack preserves external links and cannot copy and merge - data from the external files. Two options, merge and prune, were added to - control how to merge data from an external link into the resulting file. - --merge Follow external soft link recursively and merge data. - --prune Do not follow external soft links and remove link. - --merge --prune Follow external link, merge data and remove dangling link. - - (ADB - 2020/08/05, HDFFV-9984) - - - h5repack was fixed to repack the reference attributes properly. - The code line that checks if the update of reference inside a compound - datatype is misplaced outside the code block loop that carries out the - check. In consequence, the next attribute that is not the reference - type was repacked again as the reference type and caused the failure of - repacking. The fix is to move the corresponding code line to the correct - code block. - - (KY -2020/02/07, HDFFV-11014) - - - h5diff was updated to use the new reference APIs. - - h5diff uses the new reference APIs to compare references. - Attribute references can also be compared. - - (ADB - 2019/12/19, HDFFV-10980) - - - h5dump and h5ls were updated to use the new reference APIs. - - The tools library now use the new reference APIs to inspect a - file. Also the DDL spec was updated to reflect the format - changes produced with the new APIs. The export API and support - functions in the JNI were updated to match. - - (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877) + - High-Level APIs: ---------------- - - added set/get for unsigned long long attributes - - The attribute writing high-level API has been expanded to include - public set/get functions for ULL attributes, analogously to the - existing set/get for other types. + - - (AF - 2021/09/08) C Packet Table API: ------------------- - + Internal header file: --------------------- - + Documentation: -------------- - + Support for new platforms, languages and compilers ================================================== - -Bug Fixes since HDF5-1.12.0 release + +Bug Fixes since HDF5-1.13.1 release =================================== Library ------- - - Fixed an H5Pget_filter_by_id1/2() assert w/ out of range filter IDs - - Both H5Pget_filter_by_id1 and 2 did not range check the filter ID, which - could trip as assert in debug versions of the library. The library now - returns a normal HDF5 error when the filter ID is out of range. - - (DER - 2021/11/23, HDFFV-11286) - - - Fixed several potential MPI deadlocks in library failure conditions - - In the parallel library, there were several places where MPI rank 0 - could end up skipping past collective MPI operations when some failure - occurs in rank 0-specific processing. This would lead to deadlocks - where rank 0 completes an operation while other ranks wait in the - collective operation. These places have been rewritten to have rank 0 - push an error and try to cleanup after the failure, then continue to - participate in the collective operation to the best of its ability. - - (JTH - 2021/11/09) - - - Fixed an issue with collective metadata reads being permanently disabled - after a dataset chunk lookup operation. This would usually cause a - mismatched MPI_Bcast and MPI_ERR_TRUNCATE issue in the library for - simple cases of H5Dcreate() -> H5Dwrite() -> H5Dcreate(). - - (JTH - 2021/11/08, HDFFV-11090) - - - Fixed cross platform incompatibility of references within variable length - types - - Reference types within variable length types previously could not be - read on a platform with different endianness from where they were - written. Fixed so cross platform portability is restored. - - (NAF - 2021/09/30) - - - Detection of simple data transform function "x" - - In the case of the simple data transform function "x" the (parallel) - library recognizes this is the same as not applying this data transform - function. This improves the I/O performance. In the case of the parallel - library, it also avoids breaking to independent I/O, which makes it - possible to apply a filter when writing or reading data to or from - the HDF5 file. - - (JWSB - 2021/09/13) - - - Fixed an invalid read and memory leak when parsing corrupt file space - info messages - - When the corrupt file from CVE-2020-10810 was parsed by the library, - the code that imports the version 0 file space info object header - message to the version 1 struct could read past the buffer read from - the disk, causing an invalid memory read. Not catching this error would - cause downstream errors that eventually resulted in a previously - allocated buffer to be unfreed when the library shut down. In builds - where the free lists are in use, this could result in an infinite loop - and SIGABRT when the library shuts down. - - We now track the buffer size and raise an error on attempts to read - past the end of it. - - (DER - 2021/08/12, HDFFV-11053) - - - - Fixed CVE-2018-14460 - - The tool h5repack produced a segfault when the rank in dataspace - message was corrupted, causing invalid read while decoding the - dimension sizes. - - The problem was fixed by ensuring that decoding the dimension sizes - and max values will not go beyond the end of the buffer. - - (BMR - 2021/05/12, HDFFV-11223) - - - Fixed CVE-2018-11206 - - The tool h5dump produced a segfault when the size of a fill value - message was corrupted and caused a buffer overflow. - - The problem was fixed by verifying the fill value's size - against the buffer size before attempting to access the buffer. - - (BMR - 2021/03/15, HDFFV-10480) - - - Fixed CVE-2018-14033 (same issue as CVE-2020-10811) - - The tool h5dump produced a segfault when the storage size message - was corrupted and caused a buffer overflow. - - The problem was fixed by verifying the storage size against the - buffer size before attempting to access the buffer. - - (BMR - 2021/03/15, HDFFV-11159/HDFFV-11049) - - - Remove underscores on header file guards - - Header file guards used a variety of underscores at the beginning of the define. - - Removed all leading (some trailing) underscores from header file guards. - - (ADB - 2021/03/03, #361) - - - Fixed a segmentation fault - - A segmentation fault occurred with a Mathworks corrupted file. - - A detection of accessing a null pointer was added to prevent the problem. - - (BMR - 2021/02/19, HDFFV-11150) - - - Fixed issue with MPI communicator and info object not being - copied into new FAPL retrieved from H5F_get_access_plist - - Added logic to copy the MPI communicator and info object into - the output FAPL. MPI communicator is retrieved from the VFD, while - the MPI info object is retrieved from the file's original FAPL. - - (JTH - 2021/02/15, HDFFV-11109) - - - Fixed problems with vlens and refs inside compound using - H5VLget_file_type() - - Modified library to properly ref count H5VL_object_t structs and only - consider file vlen and reference types to be equal if their files are - the same. - - (NAF - 2021/01/22) - - - Fixed CVE-2018-17432 - - The tool h5repack produced a segfault on a corrupted file which had - invalid rank for scalar or NULL datatype. - - The problem was fixed by modifying the dataspace encode and decode - functions to detect and report invalid rank. h5repack now fails - with an error message for the corrupted file. - - (BMR - 2020/10/26, HDFFV-10590) - - - Creation of dataset with optional filter - - When the combination of type, space, etc doesn't work for filter - and the filter is optional, it was supposed to be skipped but it was - not skipped and the creation failed. - - Allowed the creation of the dataset in such a situation. - - (BMR - 2020/08/13, HDFFV-10933) - - - Explicitly declared dlopen to use RTLD_LOCAL - - dlopen documentation states that if neither RTLD_GLOBAL nor - RTLD_LOCAL are specified, then the default behavior is unspecified. - The default on linux is usually RTLD_LOCAL while macos will default - to RTLD_GLOBAL. - - (ADB - 2020/08/12, HDFFV-11127) - - - H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which - causes asserts/errors when passed to other dataspace API calls. - - H5S_NO_CLASS is an internal class value that should not have been - exposed via a public API call. - - In debug builds of the library, this can cause assert() function to - trip. In non-debug builds, it will produce normal library errors. - - The new library behavior is for H5Sset_extent_none() to convert - the dataspace into one of type H5S_NULL, which is better handled - by the library and easier for developers to reason about. - - (DER - 2020/07/27, HDFFV-11027) - - - Fixed issues CVE-2018-13870 and CVE-2018-13869 - - When a buffer overflow occurred because a name length was corrupted - and became very large, h5dump crashed on memory access violation. - - A check for reading pass the end of the buffer was added to multiple - locations to prevent the crashes and h5dump now simply fails with an - error message when this error condition occurs. - - (BMR - 2020/07/22, HDFFV-11120 and HDFFV-11121) - - - Fixed the segmentation fault when reading attributes with multiple threads - - It was reported that the reading of attributes with variable length string - datatype will crash with segmentation fault particularly when the number of - threads is high (>16 threads). The problem was due to the file pointer that - was set in the variable length string datatype for the attribute. That file - pointer was already closed when the attribute was accessed. - - The problem was fixed by setting the file pointer to the current opened file pointer - when the attribute was accessed. Similar patch up was done before when reading - dataset with variable length string datatype. - - (VC - 2020/07/13, HDFFV-11080) - - - Fixed CVE-2020-10810 - - The tool h5clear produced a segfault during an error recovery in - the superblock decoding. An internal pointer was reset to prevent - further accessing when it is not assigned with a value. - - (BMR - 2020/06/29, HDFFV-11053) - - - Fixed CVE-2018-17435 - - The tool h52gif produced a segfault when the size of an attribute - message was corrupted and caused a buffer overflow. - - The problem was fixed by verifying the attribute message's size - against the buffer size before accessing the buffer. h52gif was - also fixed to display the failure instead of silently exiting - after the segfault was eliminated. - - (BMR - 2020/06/19, HDFFV-10591) + - Java Library ------------ - - JNI utility function does not handle new references. - - The JNI utility function for converting reference data to string did - not use the new APIs. In addition to fixing that function, added new - java tests for using the new APIs. - - (ADB - 2021/02/16, HDFFV-11212) - - - The H5FArray.java class, in which virtually the entire execution time - is spent using the HDFNativeData method that converts from an array - of bytes to an array of the destination Java type. - - 1. Convert the entire byte array into a 1-d array of the desired type, - rather than performing 1 conversion per row; - 2. Use the Java Arrays method copyOfRange to grab the section of the - array from (1) that is desired to be inserted into the destination array. - - (PGT,ADB - 2020/12/13, HDFFV-10865) - - - Added ability to test java library with VOLs. - - Created a new CMake script that combines the java and vol test scripts. - - (ADB - 2020/02/03, HDFFV-10996) - - - Tests fail for non-English locales. - - In the JUnit tests with a non-English locale, only the part before - the decimal comma is replaced by XXXX and this leads to a comparison - error. Changed the regex for the Time substitution. - - (ADB - 2020/01/09, HDFFV-10995) + - Configuration ------------- - - Corrected path searched by CMake find_package command - - The install path for cmake find_package files had been changed to use - "share/cmake" - for all platforms. However the trailing "hdf5" directory was not removed. - This "hdf5" additional directory has been removed. - - (ADB - 2021/09/27) - - - Corrected pkg-config compile script - - It was discovered that the position of the "$@" argument for the command - in the compile script may fail on some platforms and configurations. The - position of the "$@"command argument was moved before the pkg-config sub command. - - (ADB - 2021/08/30) - - - Fixed CMake C++ compiler flags - - A recent refactoring of the C++ configure files accidentally removed the - file that executed the enable_language command for C++ needed by the - HDFCXXCompilerFlags.cmake file. Also updated the intel warnings files, - including adding support for windows platforms. - - (ADB - 2021/08/10) - - - Better support for libaec (open-source Szip library) in CMake - - Implemented better support for libaec 1.0.5 (or later) library. This version - of libaec contains improvements for better integration with HDF5. Furthermore, - the variable USE_LIBAEC_STATIC has been introduced to allow to make use of - static version of libaec library. Use libaec_DIR or libaec_ROOT to set - the location in which libaec can be found. - - Be aware, the Szip library of libaec 1.0.4 depends on another library within - libaec library. This dependency is not specified in the current CMake - configuration which means that one can not use the static Szip library of - libaec 1.0.4 when building HDF5. This has been resolved in libaec 1.0.5. - - (JWSB - 2021/06/22) - - - Refactor CMake configure for Fortran - - The Fortran configure tests for KINDs reused a single output file that was - read to form the Integer and Real Kinds defines. However, if config was run - more then once, the CMake completed variable prevented the tests from executing - again and the last value saved in the file was used to create the define. - Creating separate files for each KIND solved the issue. - - In addition the test for H5_PAC_C_MAX_REAL_PRECISION was not pulling in - defines for proper operation and did not define H5_PAC_C_MAX_REAL_PRECISION - correctly for a zero value. This was fixed by supplying the required defines. - In addition it was moved from the Fortran specific HDF5UseFortran.camke file - to the C centric ConfigureChecks.cmake file. - - (ADB - 2021/06/03) - - - Move emscripten flag to compile flags - - The emscripten flag, -O0, was removed from target_link_libraries command - to the correct target_compile_options command. - - (ADB - 2021/04/26 HDFFV-11083) - - - Remove arbitrary warning flag groups from CMake builds - - The arbitrary groups were created to reduce the quantity of warnings being - reported that overwhelmed testing report systems. Considerable work has - been accomplished to reduce the warning count and these arbitrary groups - are no longer needed. - Also the default for all warnings, HDF5_ENABLE_ALL_WARNINGS, is now ON. - - Visual Studio warnings C4100, C4706, and C4127 have been moved to - developer warnings, HDF5_ENABLE_DEV_WARNINGS, and are disabled for normal builds. - - (ADB - 2021/03/22, HDFFV-11228) - - - Reclassify CMake messages, to allow new modes and --log-level option - - CMake message commands have a mode argument. By default, STATUS mode - was chosen for any non-error message. CMake version 3.15 added additional - modes, NOTICE, VERBOSE, DEBUG and TRACE. All message commands with a mode - of STATUS were reviewed and most were reclassified as VERBOSE. The new - mode was protected by a check for a CMake version of at least 3.15. If CMake - version 3.17 or above is used, the user can use the command line option - of "--log-level" to further restrict which message commands are displayed. - - (ADB - 2021/01/11, HDFFV-11144) - - - Fixes Autotools determination of the stat struct having an st_blocks field - - A missing parenthesis in an autoconf macro prevented building the test - code used to determine if the stat struct contains the st_blocks field. - Now that the test functions correctly, the H5_HAVE_STAT_ST_BLOCKS #define - found in H5pubconf.h will be defined correctly on both the Autotools and - CMake. This #define is only used in the tests and does not affect the - HDF5 C library. - - (DER - 2021/01/07, HDFFV-11201) - - - Add missing ENV variable line to hdfoptions.cmake file - - Using the build options to use system SZIP/ZLIB libraries need to also - specify the library root directory. Setting the {library}_ROOT ENV - variable was added to the hdfoptions.cmake file. - - (ADB - 2020/10/19 HDFFV-11108) + - Tools ----- - - Changed how h5dump and h5ls identify long double. - - Long double support is not consistent across platforms. Tools will always - identify long double as 128-bit [little/big]-endian float nn-bit precision. - New test file created for datasets with attributes for float, double and - long double. In addition any unknown integer or float datatype will now - also show the number of bits for precision. - These files are also used in the java tests. - - (ADB - 2021/03/24, HDFFV-11229,HDFFV-11113) - - - Fixed tools argument parsing. - - Tools parsing used the length of the option from the long array to match - the option from the command line. This incorrectly matched a shorter long - name option that happened to be a subset of another long option. - Changed to match whole names. - - (ADB - 2021/01/19, HDFFV-11106) - - - The tools library was updated by standardizing the error stack process. - - General sequence is: - h5tools_setprogname(PROGRAMNAME); - h5tools_setstatus(EXIT_SUCCESS); - h5tools_init(); - ... process the command-line (check for error-stack enable) ... - h5tools_error_report(); - ... (do work) ... - h5diff_exit(ret); - - (ADB - 2020/07/20, HDFFV-11066) - - - h5diff fixed a command line parsing error. - - h5diff would ignore the argument to -d (delta) if it is smaller than DBL_EPSILON. - The macro H5_DBL_ABS_EQUAL was removed and a direct value comparison was used. - - (ADB - 2020/07/20, HDFFV-10897) - - - h5diff added a command line option to ignore attributes. - - h5diff would ignore all objects with a supplied path if the exclude-path argument is used. - Adding the exclude-attribute argument will only exclude attributes, with the supplied path, - from comparison. - - (ADB - 2020/07/20, HDFFV-5935) - - - h5diff added another level to the verbose argument to print filenames. - - Added verbose level 3 that is level 2 plus the filenames. The levels are: - 0 : Identical to '-v' or '--verbose' - 1 : All level 0 information plus one-line attribute status summary - 2 : All level 1 information plus extended attribute status report - 3 : All level 2 information plus file names - - (ADB - 2020/07/20, HDFFV-1005) - - - h5repack was fixed to repack the reference attributes properly. - - The code line that checks if the update of reference inside a compound - datatype is misplaced outside the code block loop that carries out the - check. In consequence, the next attribute that is not the reference - type was repacked again as the reference type and caused the failure of - repacking. The fix is to move the corresponding code line to the correct - code block. - - (KY -2020/02/10, HDFFV-11014) - - - h5diff was updated to use the new reference APIs. - - h5diff uses the new reference APIs to compare references. - Attribute references can also be compared. - - (ADB - 2019/12/19, HDFFV-10980) - - - h5dump and h5ls were updated to use the new reference APIs. - - The tools library now use the new reference APIs to inspect a - file. Also the DDL spec was updated to reflect the format - changes produced with the new APIs. The export API and support - functions in the JNI were updated to match. - - (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877) + - Performance @@ -1538,18 +151,12 @@ Bug Fixes since HDF5-1.12.0 release Fortran API ----------- - - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f. - - (MSB - 2020/02/18, HDFFV-11029) + - High-Level Library ------------------ - - Fixed HL_test_packet, test for packet table vlen of vlen. - - Incorrect length assignment. - - (ADB - 2021/10/14) + - Fortran High-Level APIs @@ -1569,23 +176,7 @@ Bug Fixes since HDF5-1.12.0 release C++ APIs -------- - - Added DataSet::operator= - - Some compilers complain if the copy constructor is given explicitly - but the assignment operator is implicitly set to default. - - (2021/05/19) - - - Testing - ------- - - Stopped java/test/junit.sh.in installing libs for testing under ${prefix} - - Lib files needed are now copied to a subdirectory in the java/test - directory, and on Macs the loader path for libhdf5.xxxs.so is changed - in the temporary copy of libhdf5_java.dylib. - - (LRK, 2020/07/02, HDFFV-11063) + - Platforms Tested diff --git a/release_docs/USING_CMake_Examples.txt b/release_docs/USING_CMake_Examples.txt index a12a952..920705b 100644 --- a/release_docs/USING_CMake_Examples.txt +++ b/release_docs/USING_CMake_Examples.txt @@ -20,15 +20,14 @@ Notes: This short instruction is written for users who want to quickly I. Preconditions ======================================================================== - 1. We suggest you obtain the latest CMake for windows from the Kitware + 1. We suggest you obtain the latest CMake for your platform from the Kitware web site. The HDF5 1.13.x product requires a minimum CMake version of 3.12. If you are using VS2019, the minimum version is 3.15. 2. You have installed the HDF5 library built with CMake, by executing the HDF Install Utility (the *.msi file in the binary package for - Windows or the *.sh on Linux). If you are using a Windows platform, - you can obtain a pre-built Windows binary from The HDF Group's website - at www.hdfgroup.org. + Windows or the *.sh on Linux). You can obtain pre-built binaries + from The HDF Group's website at www.hdfgroup.org. diff --git a/release_docs/USING_HDF5_CMake.txt b/release_docs/USING_HDF5_CMake.txt index 792c719..abe1906 100644 --- a/release_docs/USING_HDF5_CMake.txt +++ b/release_docs/USING_HDF5_CMake.txt @@ -29,27 +29,30 @@ Notes: This short instruction is written for users who want to quickly of using a ctest script for building and testing. See INSTALL_CMake.txt for more information. + 4. See https://cmake.org/cmake/help/latest/command/find_package.html + for more information on the CMake "Config Mode Search Procedure". ======================================================================== I. Preconditions ======================================================================== - 1. We suggest you obtain the latest CMake for windows from the Kitware + 1. We suggest you obtain the latest CMake for your platform from the Kitware web site. The HDF5 1.13.x product requires a minimum CMake version - of 3.12. + of 3.12. If you are using VS2019, the minimum version is 3.15. 2. You have installed the HDF5 library built with CMake, by executing the HDF Install Utility (the *.msi file in the binary package for - Windows). You can obtain pre-built binaries from The HDF Group's website at - www.hdfgroup.org. + Windows or the *.sh on Linux). You can obtain pre-built binaries + from The HDF Group's website at www.hdfgroup.org. - 3. Set the environment variable HDF5_DIR to the installed location of - the config files for HDF5. + 3. Set the HDF5_ROOT CMake variable, -DHDF5_ROOT=<install_path> + or environment variable, set(ENV{HDF5_ROOT} "<install_path>") + to the installed location of HDF5. On Windows: - HDF5_DIR=C:/Program Files/HDF_Group/HDF5/1.13.x/cmake + HDF5_ROOT=C:/Program Files/HDF_Group/HDF5/1.13.x/ On unix: - HDF5_DIR=<install root folder>/HDF_Group/HDF5/1.13.x/cmake + HDF5_ROOT=<install root folder>/HDF_Group/HDF5/1.13.x/ If you are using shared libraries, you may need to add to the path environment variable. Set the path environment variable to the @@ -70,9 +70,9 @@ static int H5__mpi_delete_cb(MPI_Comm comm, int keyval, void *attr_val, int *fla /* Library Private Variables */ /*****************************/ -/* Library incompatible release versions */ -const unsigned VERS_RELEASE_EXCEPTIONS[] = {0}; -const unsigned VERS_RELEASE_EXCEPTIONS_SIZE = 0; +/* Library incompatible release versions, develop releases are incompatible by design */ +const unsigned VERS_RELEASE_EXCEPTIONS[] = {0, 1, 2}; +const unsigned VERS_RELEASE_EXCEPTIONS_SIZE = 3; /* statically initialize block for pthread_once call used in initializing */ /* the first global mutex */ @@ -954,6 +954,7 @@ H5check_version(unsigned majnum, unsigned minnum, unsigned relnum) static int checked = 0; /* If we've already checked the version info */ static unsigned int disable_version_check = 0; /* Set if the version check should be disabled */ static const char * version_mismatch_warning = VERSION_MISMATCH_WARNING; + static const char * release_mismatch_warning = RELEASE_MISMATCH_WARNING; herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_API_NOINIT_NOERR_NOFS @@ -974,10 +975,7 @@ H5check_version(unsigned majnum, unsigned minnum, unsigned relnum) } /* H5_VERS_MAJOR and H5_VERS_MINOR must match */ - /* Cast relnum to int to avoid warning for unsigned < 0 comparison - * in first release versions */ - if (H5_VERS_MAJOR != majnum || H5_VERS_MINOR != minnum || H5_VERS_RELEASE > (int)relnum) { - + if (H5_VERS_MAJOR != majnum || H5_VERS_MINOR != minnum) { switch (disable_version_check) { case 0: HDfprintf(stderr, "%s%s", version_mismatch_warning, @@ -1012,9 +1010,10 @@ H5check_version(unsigned majnum, unsigned minnum, unsigned relnum) break; } /* end switch */ - } /* end if (H5_VERS_MAJOR != majnum || H5_VERS_MINOR != minnum || H5_VERS_RELEASE > relnum) */ + } /* end if (H5_VERS_MAJOR != majnum || H5_VERS_MINOR != minnum) */ /* H5_VERS_RELEASE should be compatible, we will only add checks for exceptions */ + /* Library develop release versions are incompatible by design */ if (H5_VERS_RELEASE != relnum) { for (unsigned i = 0; i < VERS_RELEASE_EXCEPTIONS_SIZE; i++) { /* Check for incompatible headers or incompatible library */ @@ -1022,7 +1021,7 @@ H5check_version(unsigned majnum, unsigned minnum, unsigned relnum) switch (disable_version_check) { case 0: HDfprintf( - stderr, "%s%s", version_mismatch_warning, + stderr, "%s%s", release_mismatch_warning, "You can, at your own risk, disable this warning by setting the environment\n" "variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.\n" "Setting it to 2 or higher will suppress the warning messages totally.\n"); @@ -1041,7 +1040,7 @@ H5check_version(unsigned majnum, unsigned minnum, unsigned relnum) "%s'HDF5_DISABLE_VERSION_CHECK' " "environment variable is set to %d, application will\n" "continue at your own risk.\n", - version_mismatch_warning, disable_version_check); + release_mismatch_warning, disable_version_check); /* Mention the versions we are referring to */ HDfprintf(stderr, "Headers are %u.%u.%u, library is %u.%u.%u\n", majnum, minnum, relnum, (unsigned)H5_VERS_MAJOR, (unsigned)H5_VERS_MINOR, @@ -1440,21 +1440,82 @@ H5AC_resize_entry(void *thing, size_t new_size) cache_ptr = entry_ptr->cache_ptr; HDassert(cache_ptr); - /* Resize the entry */ - if (H5C_resize_entry(thing, new_size) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTRESIZE, FAIL, "can't resize entry") - #ifdef H5_HAVE_PARALLEL - { + /* Log the generation of dirty bytes of metadata iff: + * + * 1) The entry is clean on entry, and this resize will dirty it + * (i.e. the current and new sizes are different), and + * + * 2) This is a parallel computation -- which it is if the aux_ptr + * is non-null. + * + * A few points to note about this section of the code: + * + * 1) This call must occur before the call to H5C_resize_entry() since + * H5AC__log_dirtied_entry() expects the target entry to be clean + * on entry. + * + * 2) This code has some basic issues in terms of the number of bytes + * added to the dirty bytes count. + * + * First, it adds the initial entry size to aux_ptr->dirty_bytes, + * not the final size. Note that this code used to use the final + * size, but code to support this has been removed from + * H5AC__log_dirtied_entry() for reasons unknown since I wrote this + * code. + * + * As long as all ranks do the same thing here, this probably doesn't + * matter much, although it will delay initiation of sync points. + * + * A more interesting point is that this code will not increment + * aux_ptr->dirty_bytes if a dirty entry is resized. At first glance + * this seems major, as particularly with the older file formats, + * resizes can be quite large. However, this is probably not an + * issue either, since such resizes will be accompanied by large + * amounts of dirty metadata creation in other areas -- which will + * cause aux_ptr->dirty_bytes to be incremented. + * + * The bottom line is that this code is probably OK, but the above + * points should be kept in mind. + * + * One final observation: This comment is occasioned by a bug caused + * by moving the call to H5AC__log_dirtied_entry() after the call to + * H5C_resize_entry(), and then only calling H5AC__log_dirtied_entry() + * if entry_ptr->is_dirty was false. + * + * Since H5C_resize_entry() marks the target entry dirty unless there + * is not change in size, this had the effect of not calling + * H5AC__log_dirtied_entry() when it should be, and corrupting + * the cleaned and dirtied lists used by rank 0 in the parallel + * version of the metadata cache. + * + * The point here is that you should be very careful when working with + * this code, and not modify it unless you fully understand it. + * + * JRM -- 2/28/22 + */ + + if ((!entry_ptr->is_dirty) && (entry_ptr->size != new_size)) { + + /* the entry is clean, and will be marked dirty in the resize + * operation. + */ H5AC_aux_t *aux_ptr; aux_ptr = (H5AC_aux_t *)H5C_get_aux_ptr(cache_ptr); - if ((!entry_ptr->is_dirty) && (NULL != aux_ptr)) + + if (NULL != aux_ptr) { + if (H5AC__log_dirtied_entry(entry_ptr) < 0) HGOTO_ERROR(H5E_CACHE, H5E_CANTMARKDIRTY, FAIL, "can't log dirtied entry") + } } #endif /* H5_HAVE_PARALLEL */ + /* Resize the entry */ + if (H5C_resize_entry(thing, new_size) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTRESIZE, FAIL, "can't resize entry") + done: /* If currently logging, generate a message */ if (cache_ptr != NULL && cache_ptr->log_info != NULL) @@ -138,16 +138,6 @@ static herr_t H5C__generate_image(H5F_t *f, H5C_t *cache_ptr, H5C_cache_entry_t static herr_t H5C__verify_len_eoa(H5F_t *f, const H5C_class_t *type, haddr_t addr, size_t *len, hbool_t actual); -#if H5C_DO_SLIST_SANITY_CHECKS -static hbool_t H5C__entry_in_skip_list(H5C_t *cache_ptr, H5C_cache_entry_t *target_ptr); -#endif /* H5C_DO_SLIST_SANITY_CHECKS */ - -#if H5C_DO_EXTREME_SANITY_CHECKS -static herr_t H5C__validate_lru_list(H5C_t *cache_ptr); -static herr_t H5C__validate_pinned_entry_list(H5C_t *cache_ptr); -static herr_t H5C__validate_protected_entry_list(H5C_t *cache_ptr); -#endif /* H5C_DO_EXTREME_SANITY_CHECKS */ - #ifndef NDEBUG static void H5C__assert_flush_dep_nocycle(const H5C_cache_entry_t *entry, const H5C_cache_entry_t *base_entry); @@ -996,7 +986,7 @@ H5C_expunge_entry(H5F_t *f, const H5C_class_t *type, haddr_t addr, unsigned flag HDassert(H5F_addr_defined(addr)); #if H5C_DO_EXTREME_SANITY_CHECKS - if (H5C__validate_lru_list(cache_ptr) < 0) + if (H5C_validate_lru_list(cache_ptr) < 0) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "LRU extreme sanity check failed on entry") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -1031,7 +1021,7 @@ H5C_expunge_entry(H5F_t *f, const H5C_class_t *type, haddr_t addr, unsigned flag done: #if H5C_DO_EXTREME_SANITY_CHECKS - if (H5C__validate_lru_list(cache_ptr) < 0) + if (H5C_validate_lru_list(cache_ptr) < 0) HDONE_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "LRU extreme sanity check failed on exit") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -1138,8 +1128,8 @@ H5C_flush_cache(H5F_t *f, unsigned flags) #endif /* H5C_DO_SANITY_CHECKS */ #if H5C_DO_EXTREME_SANITY_CHECKS - if ((H5C__validate_protected_entry_list(cache_ptr) < 0) || - (H5C__validate_pinned_entry_list(cache_ptr) < 0) || (H5C__validate_lru_list(cache_ptr) < 0)) + if ((H5C_validate_protected_entry_list(cache_ptr) < 0) || + (H5C_validate_pinned_entry_list(cache_ptr) < 0) || (H5C_validate_lru_list(cache_ptr) < 0)) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "an extreme sanity check failed on entry") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -1314,8 +1304,8 @@ H5C_insert_entry(H5F_t *f, const H5C_class_t *type, haddr_t addr, void *thing, u #if H5C_DO_EXTREME_SANITY_CHECKS /* no need to verify that entry is not already in the index as */ /* we already make that check below. */ - if ((H5C__validate_protected_entry_list(cache_ptr) < 0) || - (H5C__validate_pinned_entry_list(cache_ptr) < 0) || (H5C__validate_lru_list(cache_ptr) < 0)) + if ((H5C_validate_protected_entry_list(cache_ptr) < 0) || + (H5C_validate_pinned_entry_list(cache_ptr) < 0) || (H5C_validate_lru_list(cache_ptr) < 0)) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "an extreme sanity check failed on entry") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -1424,6 +1414,7 @@ H5C_insert_entry(H5F_t *f, const H5C_class_t *type, haddr_t addr, void *thing, u entry_ptr->serialization_count = 0; #endif /* NDEBUG */ + /* initialize tag list fields */ entry_ptr->tl_next = NULL; entry_ptr->tl_prev = NULL; entry_ptr->tag_info = NULL; @@ -1503,8 +1494,8 @@ H5C_insert_entry(H5F_t *f, const H5C_class_t *type, haddr_t addr, void *thing, u H5C__UPDATE_RP_FOR_INSERTION(cache_ptr, entry_ptr, FAIL) #if H5C_DO_EXTREME_SANITY_CHECKS - if ((H5C__validate_protected_entry_list(cache_ptr) < 0) || - (H5C__validate_pinned_entry_list(cache_ptr) < 0) || (H5C__validate_lru_list(cache_ptr) < 0)) + if ((H5C_validate_protected_entry_list(cache_ptr) < 0) || + (H5C_validate_pinned_entry_list(cache_ptr) < 0) || (H5C_validate_lru_list(cache_ptr) < 0)) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "an extreme sanity check failed just before done") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -1518,23 +1509,32 @@ H5C_insert_entry(H5F_t *f, const H5C_class_t *type, haddr_t addr, void *thing, u #ifdef H5_HAVE_PARALLEL if (H5F_HAS_FEATURE(f, H5FD_FEAT_HAS_MPI)) - coll_access = H5CX_get_coll_metadata_read(); + coll_access = H5F_get_coll_metadata_reads(f); entry_ptr->coll_access = coll_access; if (coll_access) { H5C__INSERT_IN_COLL_LIST(cache_ptr, entry_ptr, FAIL) /* Make sure the size of the collective entries in the cache remain in check */ - if (cache_ptr->max_cache_size * 80 < cache_ptr->coll_list_size * 100) - if (H5C_clear_coll_entries(cache_ptr, TRUE) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "can't clear collective metadata entries") - } /* end if */ + if (H5P_USER_TRUE == H5F_COLL_MD_READ(f)) { + if (cache_ptr->max_cache_size * 80 < cache_ptr->coll_list_size * 100) { + if (H5C_clear_coll_entries(cache_ptr, TRUE) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "can't clear collective metadata entries") + } /* end if */ + } /* end if */ + else { + if (cache_ptr->max_cache_size * 40 < cache_ptr->coll_list_size * 100) { + if (H5C_clear_coll_entries(cache_ptr, TRUE) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "can't clear collective metadata entries") + } /* end if */ + } /* end else */ + } /* end if */ #endif done: #if H5C_DO_EXTREME_SANITY_CHECKS - if ((H5C__validate_protected_entry_list(cache_ptr) < 0) || - (H5C__validate_pinned_entry_list(cache_ptr) < 0) || (H5C__validate_lru_list(cache_ptr) < 0)) + if ((H5C_validate_protected_entry_list(cache_ptr) < 0) || + (H5C_validate_pinned_entry_list(cache_ptr) < 0) || (H5C_validate_lru_list(cache_ptr) < 0)) HDONE_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "an extreme sanity check failed on exit") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -1858,8 +1858,8 @@ H5C_move_entry(H5C_t *cache_ptr, const H5C_class_t *type, haddr_t old_addr, hadd HDassert(H5F_addr_ne(old_addr, new_addr)); #if H5C_DO_EXTREME_SANITY_CHECKS - if ((H5C__validate_protected_entry_list(cache_ptr) < 0) || - (H5C__validate_pinned_entry_list(cache_ptr) < 0) || (H5C__validate_lru_list(cache_ptr) < 0)) + if ((H5C_validate_protected_entry_list(cache_ptr) < 0) || + (H5C_validate_pinned_entry_list(cache_ptr) < 0) || (H5C_validate_lru_list(cache_ptr) < 0)) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "an extreme sanity check failed on entry") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -1964,8 +1964,8 @@ H5C_move_entry(H5C_t *cache_ptr, const H5C_class_t *type, haddr_t old_addr, hadd done: #if H5C_DO_EXTREME_SANITY_CHECKS - if ((H5C__validate_protected_entry_list(cache_ptr) < 0) || - (H5C__validate_pinned_entry_list(cache_ptr) < 0) || (H5C__validate_lru_list(cache_ptr) < 0)) + if ((H5C_validate_protected_entry_list(cache_ptr) < 0) || + (H5C_validate_pinned_entry_list(cache_ptr) < 0) || (H5C_validate_lru_list(cache_ptr) < 0)) HDONE_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "an extreme sanity check failed on exit") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -2011,8 +2011,7 @@ H5C_resize_entry(void *thing, size_t new_size) HGOTO_ERROR(H5E_CACHE, H5E_BADTYPE, FAIL, "Entry isn't pinned or protected??") #if H5C_DO_EXTREME_SANITY_CHECKS - if ((H5C__validate_protected_entry_list(cache_ptr) < 0) || - (H5C__validate_pinned_entry_list(cache_ptr) < 0)) + if ((H5C_validate_protected_entry_list(cache_ptr) < 0) || (H5C_validate_pinned_entry_list(cache_ptr) < 0)) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "an extreme sanity check failed on entry") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -2108,8 +2107,7 @@ H5C_resize_entry(void *thing, size_t new_size) done: #if H5C_DO_EXTREME_SANITY_CHECKS - if ((H5C__validate_protected_entry_list(cache_ptr) < 0) || - (H5C__validate_pinned_entry_list(cache_ptr) < 0)) + if ((H5C_validate_protected_entry_list(cache_ptr) < 0) || (H5C_validate_pinned_entry_list(cache_ptr) < 0)) HDONE_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "an extreme sanity check failed on exit") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -2149,8 +2147,8 @@ H5C_pin_protected_entry(void *thing) HDassert(cache_ptr->magic == H5C__H5C_T_MAGIC); #if H5C_DO_EXTREME_SANITY_CHECKS - if ((H5C__validate_protected_entry_list(cache_ptr) < 0) || - (H5C__validate_pinned_entry_list(cache_ptr) < 0) || (H5C__validate_lru_list(cache_ptr) < 0)) + if ((H5C_validate_protected_entry_list(cache_ptr) < 0) || + (H5C_validate_pinned_entry_list(cache_ptr) < 0) || (H5C_validate_lru_list(cache_ptr) < 0)) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "an extreme sanity check failed on entry") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -2164,8 +2162,8 @@ H5C_pin_protected_entry(void *thing) done: #if H5C_DO_EXTREME_SANITY_CHECKS - if ((H5C__validate_protected_entry_list(cache_ptr) < 0) || - (H5C__validate_pinned_entry_list(cache_ptr) < 0) || (H5C__validate_lru_list(cache_ptr) < 0)) + if ((H5C_validate_protected_entry_list(cache_ptr) < 0) || + (H5C_validate_pinned_entry_list(cache_ptr) < 0) || (H5C_validate_lru_list(cache_ptr) < 0)) HDONE_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "an extreme sanity check failed on exit") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -2228,8 +2226,8 @@ H5C_protect(H5F_t *f, const H5C_class_t *type, haddr_t addr, void *udata, unsign HDassert(H5F_addr_defined(addr)); #if H5C_DO_EXTREME_SANITY_CHECKS - if ((H5C__validate_protected_entry_list(cache_ptr) < 0) || - (H5C__validate_pinned_entry_list(cache_ptr) < 0) || (H5C__validate_lru_list(cache_ptr) < 0)) + if ((H5C_validate_protected_entry_list(cache_ptr) < 0) || + (H5C_validate_pinned_entry_list(cache_ptr) < 0) || (H5C_validate_lru_list(cache_ptr) < 0)) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, NULL, "an extreme sanity check failed on entry") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -2248,7 +2246,7 @@ H5C_protect(H5F_t *f, const H5C_class_t *type, haddr_t addr, void *udata, unsign #ifdef H5_HAVE_PARALLEL if (H5F_HAS_FEATURE(f, H5FD_FEAT_HAS_MPI)) - coll_access = H5CX_get_coll_metadata_read(); + coll_access = H5F_get_coll_metadata_reads(f); #endif /* H5_HAVE_PARALLEL */ /* first check to see if the target is in cache */ @@ -2600,16 +2598,24 @@ H5C_protect(H5F_t *f, const H5C_class_t *type, haddr_t addr, void *udata, unsign #ifdef H5_HAVE_PARALLEL /* Make sure the size of the collective entries in the cache remain in check */ - if (coll_access) - if (cache_ptr->max_cache_size * 80 < cache_ptr->coll_list_size * 100) - if (H5C_clear_coll_entries(cache_ptr, TRUE) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, NULL, "can't clear collective metadata entries") -#endif /* H5_HAVE_PARALLEL */ + if (coll_access) { + if (H5P_USER_TRUE == H5F_COLL_MD_READ(f)) { + if (cache_ptr->max_cache_size * 80 < cache_ptr->coll_list_size * 100) + if (H5C_clear_coll_entries(cache_ptr, TRUE) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, NULL, "can't clear collective metadata entries") + } /* end if */ + else { + if (cache_ptr->max_cache_size * 40 < cache_ptr->coll_list_size * 100) + if (H5C_clear_coll_entries(cache_ptr, TRUE) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, NULL, "can't clear collective metadata entries") + } /* end else */ + } /* end if */ +#endif /* H5_HAVE_PARALLEL */ done: #if H5C_DO_EXTREME_SANITY_CHECKS - if ((H5C__validate_protected_entry_list(cache_ptr) < 0) || - (H5C__validate_pinned_entry_list(cache_ptr) < 0) || (H5C__validate_lru_list(cache_ptr) < 0)) + if ((H5C_validate_protected_entry_list(cache_ptr) < 0) || + (H5C_validate_pinned_entry_list(cache_ptr) < 0) || (H5C_validate_lru_list(cache_ptr) < 0)) HDONE_ERROR(H5E_CACHE, H5E_SYSTEM, NULL, "an extreme sanity check failed on exit") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -3082,8 +3088,8 @@ H5C_unpin_entry(void *_entry_ptr) HDassert(cache_ptr->magic == H5C__H5C_T_MAGIC); #if H5C_DO_EXTREME_SANITY_CHECKS - if ((H5C__validate_protected_entry_list(cache_ptr) < 0) || - (H5C__validate_pinned_entry_list(cache_ptr) < 0) || (H5C__validate_lru_list(cache_ptr) < 0)) + if ((H5C_validate_protected_entry_list(cache_ptr) < 0) || + (H5C_validate_pinned_entry_list(cache_ptr) < 0) || (H5C_validate_lru_list(cache_ptr) < 0)) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "an extreme sanity check failed on entry") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -3093,8 +3099,8 @@ H5C_unpin_entry(void *_entry_ptr) done: #if H5C_DO_EXTREME_SANITY_CHECKS - if ((H5C__validate_protected_entry_list(cache_ptr) < 0) || - (H5C__validate_pinned_entry_list(cache_ptr) < 0) || (H5C__validate_lru_list(cache_ptr) < 0)) + if ((H5C_validate_protected_entry_list(cache_ptr) < 0) || + (H5C_validate_pinned_entry_list(cache_ptr) < 0) || (H5C_validate_lru_list(cache_ptr) < 0)) HDONE_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "an extreme sanity check failed on exit") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -3261,8 +3267,8 @@ H5C_unprotect(H5F_t *f, haddr_t addr, void *thing, unsigned flags) was_clean = !(entry_ptr->is_dirty); #if H5C_DO_EXTREME_SANITY_CHECKS - if ((H5C__validate_protected_entry_list(cache_ptr) < 0) || - (H5C__validate_pinned_entry_list(cache_ptr) < 0) || (H5C__validate_lru_list(cache_ptr) < 0)) + if ((H5C_validate_protected_entry_list(cache_ptr) < 0) || + (H5C_validate_pinned_entry_list(cache_ptr) < 0) || (H5C_validate_lru_list(cache_ptr) < 0)) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "an extreme sanity check failed on entry") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -3528,8 +3534,8 @@ H5C_unprotect(H5F_t *f, haddr_t addr, void *thing, unsigned flags) done: #if H5C_DO_EXTREME_SANITY_CHECKS - if ((H5C__validate_protected_entry_list(cache_ptr) < 0) || - (H5C__validate_pinned_entry_list(cache_ptr) < 0) || (H5C__validate_lru_list(cache_ptr) < 0)) + if ((H5C_validate_protected_entry_list(cache_ptr) < 0) || + (H5C_validate_pinned_entry_list(cache_ptr) < 0) || (H5C_validate_lru_list(cache_ptr) < 0)) HDONE_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "an extreme sanity check failed on exit") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -6063,8 +6069,8 @@ H5C__flush_ring(H5F_t *f, H5C_ring_t ring, unsigned flags) HDassert(ring < H5C_RING_NTYPES); #if H5C_DO_EXTREME_SANITY_CHECKS - if ((H5C__validate_protected_entry_list(cache_ptr) < 0) || - (H5C__validate_pinned_entry_list(cache_ptr) < 0) || (H5C__validate_lru_list(cache_ptr) < 0)) + if ((H5C_validate_protected_entry_list(cache_ptr) < 0) || + (H5C_validate_pinned_entry_list(cache_ptr) < 0) || (H5C_validate_lru_list(cache_ptr) < 0)) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "an extreme sanity check failed on entry") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -7411,6 +7417,7 @@ H5C__load_entry(H5F_t *f, entry->serialization_count = 0; #endif /* NDEBUG */ + /* initialize tag list fields */ entry->tl_next = NULL; entry->tl_prev = NULL; entry->tag_info = NULL; @@ -7739,7 +7746,7 @@ done: /*------------------------------------------------------------------------- * - * Function: H5C__validate_lru_list + * Function: H5C_validate_lru_list * * Purpose: Debugging function that scans the LRU list for errors. * @@ -7754,15 +7761,15 @@ done: *------------------------------------------------------------------------- */ #if H5C_DO_EXTREME_SANITY_CHECKS -static herr_t -H5C__validate_lru_list(H5C_t *cache_ptr) +herr_t +H5C_validate_lru_list(H5C_t *cache_ptr) { int32_t len = 0; size_t size = 0; H5C_cache_entry_t *entry_ptr = NULL; herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_STATIC + FUNC_ENTER_NOAPI(FAIL) HDassert(cache_ptr); HDassert(cache_ptr->magic == H5C__H5C_T_MAGIC); @@ -7771,51 +7778,48 @@ H5C__validate_lru_list(H5C_t *cache_ptr) (cache_ptr->LRU_head_ptr != cache_ptr->LRU_tail_ptr)) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 1 failed") - if (cache_ptr->LRU_list_len < 0) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 2 failed") - if ((cache_ptr->LRU_list_len == 1) && ((cache_ptr->LRU_head_ptr != cache_ptr->LRU_tail_ptr) || (cache_ptr->LRU_head_ptr == NULL) || (cache_ptr->LRU_head_ptr->size != cache_ptr->LRU_list_size))) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 3 failed") + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 2 failed") if ((cache_ptr->LRU_list_len >= 1) && ((cache_ptr->LRU_head_ptr == NULL) || (cache_ptr->LRU_head_ptr->prev != NULL) || (cache_ptr->LRU_tail_ptr == NULL) || (cache_ptr->LRU_tail_ptr->next != NULL))) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 4 failed") + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 3 failed") entry_ptr = cache_ptr->LRU_head_ptr; while (entry_ptr != NULL) { if ((entry_ptr != cache_ptr->LRU_head_ptr) && ((entry_ptr->prev == NULL) || (entry_ptr->prev->next != entry_ptr))) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 5 failed") + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 4 failed") if ((entry_ptr != cache_ptr->LRU_tail_ptr) && ((entry_ptr->next == NULL) || (entry_ptr->next->prev != entry_ptr))) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 6 failed") + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 5 failed") if ((entry_ptr->is_pinned) || (entry_ptr->pinned_from_client) || (entry_ptr->pinned_from_cache)) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 7 failed") + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 6 failed") len++; size += entry_ptr->size; entry_ptr = entry_ptr->next; } - if ((cache_ptr->LRU_list_len != len) || (cache_ptr->LRU_list_size != size)) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 8 failed") + if ((cache_ptr->LRU_list_len != (uint32_t)len) || (cache_ptr->LRU_list_size != size)) + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 7 failed") done: if (ret_value != SUCCEED) HDassert(0); FUNC_LEAVE_NOAPI(ret_value) -} /* H5C__validate_lru_list() */ +} /* H5C_validate_lru_list() */ #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ /*------------------------------------------------------------------------- * - * Function: H5C__validate_pinned_entry_list + * Function: H5C_validate_pinned_entry_list * * Purpose: Debugging function that scans the pinned entry list for * errors. @@ -7831,15 +7835,15 @@ done: *------------------------------------------------------------------------- */ #if H5C_DO_EXTREME_SANITY_CHECKS -static herr_t -H5C__validate_pinned_entry_list(H5C_t *cache_ptr) +herr_t +H5C_validate_pinned_entry_list(H5C_t *cache_ptr) { int32_t len = 0; size_t size = 0; H5C_cache_entry_t *entry_ptr = NULL; herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_STATIC + FUNC_ENTER_NOAPI(FAIL) HDassert(cache_ptr); HDassert(cache_ptr->magic == H5C__H5C_T_MAGIC); @@ -7848,54 +7852,51 @@ H5C__validate_pinned_entry_list(H5C_t *cache_ptr) (cache_ptr->pel_head_ptr != cache_ptr->pel_tail_ptr)) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 1 failed") - if (cache_ptr->pel_len < 0) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 2 failed") - if ((cache_ptr->pel_len == 1) && ((cache_ptr->pel_head_ptr != cache_ptr->pel_tail_ptr) || (cache_ptr->pel_head_ptr == NULL) || (cache_ptr->pel_head_ptr->size != cache_ptr->pel_size))) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 3 failed") + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 2 failed") if ((cache_ptr->pel_len >= 1) && ((cache_ptr->pel_head_ptr == NULL) || (cache_ptr->pel_head_ptr->prev != NULL) || (cache_ptr->pel_tail_ptr == NULL) || (cache_ptr->pel_tail_ptr->next != NULL))) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 4 failed") + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 3 failed") entry_ptr = cache_ptr->pel_head_ptr; while (entry_ptr != NULL) { if ((entry_ptr != cache_ptr->pel_head_ptr) && ((entry_ptr->prev == NULL) || (entry_ptr->prev->next != entry_ptr))) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 5 failed") + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 4 failed") if ((entry_ptr != cache_ptr->pel_tail_ptr) && ((entry_ptr->next == NULL) || (entry_ptr->next->prev != entry_ptr))) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 6 failed") + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 5 failed") if (!entry_ptr->is_pinned) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 7 failed") + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 6 failed") if (!(entry_ptr->pinned_from_client || entry_ptr->pinned_from_cache)) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 8 failed") + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 7 failed") len++; size += entry_ptr->size; entry_ptr = entry_ptr->next; } - if ((cache_ptr->pel_len != len) || (cache_ptr->pel_size != size)) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 9 failed") + if ((cache_ptr->pel_len != (uint32_t)len) || (cache_ptr->pel_size != size)) + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 8 failed") done: if (ret_value != SUCCEED) HDassert(0); FUNC_LEAVE_NOAPI(ret_value) -} /* H5C__validate_pinned_entry_list() */ +} /* H5C_validate_pinned_entry_list() */ #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ /*------------------------------------------------------------------------- * - * Function: H5C__validate_protected_entry_list + * Function: H5C_validate_protected_entry_list * * Purpose: Debugging function that scans the protected entry list for * errors. @@ -7911,15 +7912,15 @@ done: *------------------------------------------------------------------------- */ #if H5C_DO_EXTREME_SANITY_CHECKS -static herr_t -H5C__validate_protected_entry_list(H5C_t *cache_ptr) +herr_t +H5C_validate_protected_entry_list(H5C_t *cache_ptr) { int32_t len = 0; size_t size = 0; H5C_cache_entry_t *entry_ptr = NULL; herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_STATIC + FUNC_ENTER_NOAPI(FAIL) HDassert(cache_ptr); HDassert(cache_ptr->magic == H5C__H5C_T_MAGIC); @@ -7928,54 +7929,51 @@ H5C__validate_protected_entry_list(H5C_t *cache_ptr) (cache_ptr->pl_head_ptr != cache_ptr->pl_tail_ptr)) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 1 failed") - if (cache_ptr->pl_len < 0) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 2 failed") - if ((cache_ptr->pl_len == 1) && ((cache_ptr->pl_head_ptr != cache_ptr->pl_tail_ptr) || (cache_ptr->pl_head_ptr == NULL) || (cache_ptr->pl_head_ptr->size != cache_ptr->pl_size))) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 3 failed") + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 2 failed") if ((cache_ptr->pl_len >= 1) && ((cache_ptr->pl_head_ptr == NULL) || (cache_ptr->pl_head_ptr->prev != NULL) || (cache_ptr->pl_tail_ptr == NULL) || (cache_ptr->pl_tail_ptr->next != NULL))) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 4 failed") + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 3 failed") entry_ptr = cache_ptr->pl_head_ptr; while (entry_ptr != NULL) { if ((entry_ptr != cache_ptr->pl_head_ptr) && ((entry_ptr->prev == NULL) || (entry_ptr->prev->next != entry_ptr))) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 5 failed") + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 4 failed") if ((entry_ptr != cache_ptr->pl_tail_ptr) && ((entry_ptr->next == NULL) || (entry_ptr->next->prev != entry_ptr))) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 6 failed") + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 5 failed") if (!entry_ptr->is_protected) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 7 failed") + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 6 failed") if (entry_ptr->is_read_only && (entry_ptr->ro_ref_count <= 0)) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 8 failed") + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 7 failed") len++; size += entry_ptr->size; entry_ptr = entry_ptr->next; } - if ((cache_ptr->pl_len != len) || (cache_ptr->pl_size != size)) - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 9 failed") + if ((cache_ptr->pl_len != (uint32_t)len) || (cache_ptr->pl_size != size)) + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Check 8 failed") done: if (ret_value != SUCCEED) HDassert(0); FUNC_LEAVE_NOAPI(ret_value) -} /* H5C__validate_protected_entry_list() */ +} /* H5C_validate_protected_entry_list() */ #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ /*------------------------------------------------------------------------- * - * Function: H5C__entry_in_skip_list + * Function: H5C_entry_in_skip_list * * Purpose: Debugging function that scans skip list to see if it * is in present. We need this, as it is possible for @@ -7989,8 +7987,8 @@ done: *------------------------------------------------------------------------- */ #if H5C_DO_SLIST_SANITY_CHECKS -static hbool_t -H5C__entry_in_skip_list(H5C_t *cache_ptr, H5C_cache_entry_t *target_ptr) +hbool_t +H5C_entry_in_skip_list(H5C_t *cache_ptr, H5C_cache_entry_t *target_ptr) { H5SL_node_t *node_ptr; hbool_t in_slist; @@ -8018,7 +8016,7 @@ H5C__entry_in_skip_list(H5C_t *cache_ptr, H5C_cache_entry_t *target_ptr) } return (in_slist); -} /* H5C__entry_in_skip_list() */ +} /* H5C_entry_in_skip_list() */ #endif /* H5C_DO_SLIST_SANITY_CHECKS */ /*------------------------------------------------------------------------- @@ -8508,8 +8506,8 @@ H5C__serialize_cache(H5F_t *f) #endif /* H5C_DO_SANITY_CHECKS */ #if H5C_DO_EXTREME_SANITY_CHECKS - if ((H5C__validate_protected_entry_list(cache_ptr) < 0) || - (H5C__validate_pinned_entry_list(cache_ptr) < 0) || (H5C__validate_lru_list(cache_ptr) < 0)) + if ((H5C_validate_protected_entry_list(cache_ptr) < 0) || + (H5C_validate_pinned_entry_list(cache_ptr) < 0) || (H5C_validate_lru_list(cache_ptr) < 0)) HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "an extreme sanity check failed on entry") #endif /* H5C_DO_EXTREME_SANITY_CHECKS */ @@ -1423,7 +1423,7 @@ done: * Purpose: Sanity checks and sets up collective operations. * * Note: Should be called for all API routines that modify file - * file metadata but don't pass in an access property list. + * metadata but don't pass in an access property list. * * Return: Non-negative on success / Negative on failure * diff --git a/src/H5Cepoch.c b/src/H5Cepoch.c index 3434fed..8655881 100644 --- a/src/H5Cepoch.c +++ b/src/H5Cepoch.c @@ -78,22 +78,21 @@ static herr_t H5C__epoch_marker_fsf_size(const void H5_ATTR_UNUSED *thing, /* Local Variables */ /*******************/ -const H5AC_class_t H5AC_EPOCH_MARKER[1] = {{ - /* id = */ H5AC_EPOCH_MARKER_ID, - /* name = */ "epoch marker", - /* mem_type = */ H5FD_MEM_DEFAULT, /* value doesn't matter */ - /* flags = */ H5AC__CLASS_NO_FLAGS_SET, - /* get_initial_load_size = */ H5C__epoch_marker_get_initial_load_size, - /* get_final_load_size = */ H5C__epoch_marker_get_final_load_size, - /* verify_chksum = */ H5C__epoch_marker_verify_chksum, - /* deserialize = */ H5C__epoch_marker_deserialize, - /* image_len = */ H5C__epoch_marker_image_len, - /* pre_serialize = */ H5C__epoch_marker_pre_serialize, - /* serialize = */ H5C__epoch_marker_serialize, - /* notify = */ H5C__epoch_marker_notify, - /* free_icr = */ H5C__epoch_marker_free_icr, - /* fsf_size = */ H5C__epoch_marker_fsf_size, -}}; +const H5AC_class_t H5AC_EPOCH_MARKER[1] = { + {/* id = */ H5AC_EPOCH_MARKER_ID, + /* name = */ "epoch marker", + /* mem_type = */ H5FD_MEM_DEFAULT, /* value doesn't matter */ + /* flags = */ H5AC__CLASS_NO_FLAGS_SET, + /* get_initial_load_size = */ H5C__epoch_marker_get_initial_load_size, + /* get_final_load_size = */ H5C__epoch_marker_get_final_load_size, + /* verify_chksum = */ H5C__epoch_marker_verify_chksum, + /* deserialize = */ H5C__epoch_marker_deserialize, + /* image_len = */ H5C__epoch_marker_image_len, + /* pre_serialize = */ H5C__epoch_marker_pre_serialize, + /* serialize = */ H5C__epoch_marker_serialize, + /* notify = */ H5C__epoch_marker_notify, + /* free_icr = */ H5C__epoch_marker_free_icr, + /* fsf_size = */ H5C__epoch_marker_fsf_size}}; /*************************************************************************** * Class functions for H5C__EPOCH_MAKER_TYPE: diff --git a/src/H5Cpkg.h b/src/H5Cpkg.h index 30b86b9..61c3afc 100644 --- a/src/H5Cpkg.h +++ b/src/H5Cpkg.h @@ -1011,7 +1011,7 @@ if ( ( (cache_ptr) == NULL ) || \ ( H5C__HASH_FCN((entry_ptr)->addr) >= H5C__HASH_TABLE_LEN ) || \ ( (cache_ptr)->index_size != \ ((cache_ptr)->clean_index_size + \ - (cache_ptr)->dirty_index_size) ) || \ + (cache_ptr)->dirty_index_size) ) || \ ( (cache_ptr)->index_size < ((cache_ptr)->clean_index_size) ) || \ ( (cache_ptr)->index_size < ((cache_ptr)->dirty_index_size) ) || \ ( (entry_ptr)->ring <= H5C_RING_UNDEFINED ) || \ @@ -1034,7 +1034,7 @@ if ( ( (cache_ptr) == NULL ) || \ ( (cache_ptr)->magic != H5C__H5C_T_MAGIC ) || \ ( (cache_ptr)->index_size != \ ((cache_ptr)->clean_index_size + \ - (cache_ptr)->dirty_index_size) ) || \ + (cache_ptr)->dirty_index_size) ) || \ ( (cache_ptr)->index_size < ((cache_ptr)->clean_index_size) ) || \ ( (cache_ptr)->index_size < ((cache_ptr)->dirty_index_size) ) || \ ( (cache_ptr)->index_ring_len[(entry_ptr)->ring] == 0 ) || \ @@ -1071,7 +1071,7 @@ if ( ( (cache_ptr) == NULL ) || \ ( (entry_ptr)->ht_prev != NULL ) ) || \ ( (cache_ptr)->index_size != \ ((cache_ptr)->clean_index_size + \ - (cache_ptr)->dirty_index_size) ) || \ + (cache_ptr)->dirty_index_size) ) || \ ( (cache_ptr)->index_size < ((cache_ptr)->clean_index_size) ) || \ ( (cache_ptr)->index_size < ((cache_ptr)->dirty_index_size) ) || \ ( (entry_ptr)->ring <= H5C_RING_UNDEFINED ) || \ @@ -1102,7 +1102,7 @@ if ( ( (cache_ptr) == NULL ) || \ ( (entry_ptr)->ht_prev != NULL ) || \ ( (cache_ptr)->index_size != \ ((cache_ptr)->clean_index_size + \ - (cache_ptr)->dirty_index_size) ) || \ + (cache_ptr)->dirty_index_size) ) || \ ( (cache_ptr)->index_size < ((cache_ptr)->clean_index_size) ) || \ ( (cache_ptr)->index_size < ((cache_ptr)->dirty_index_size) ) || \ ( (cache_ptr)->index_ring_len[(entry_ptr)->ring] > \ @@ -1161,7 +1161,7 @@ if ( ( (cache_ptr) == NULL ) || \ } #define H5C__PRE_HT_ENTRY_SIZE_CHANGE_SC(cache_ptr, old_size, new_size, \ - entry_ptr, was_clean) \ + entry_ptr, was_clean) \ if ( ( (cache_ptr) == NULL ) || \ ( (cache_ptr)->index_len <= 0 ) || \ ( (cache_ptr)->index_size <= 0 ) || \ @@ -1175,9 +1175,9 @@ if ( ( (cache_ptr) == NULL ) || \ ( (cache_ptr)->index_size < ((cache_ptr)->clean_index_size) ) || \ ( (cache_ptr)->index_size < ((cache_ptr)->dirty_index_size) ) || \ ( ( !( was_clean ) || \ - ( (cache_ptr)->clean_index_size < (old_size) ) ) && \ - ( ( (was_clean) ) || \ - ( (cache_ptr)->dirty_index_size < (old_size) ) ) ) || \ + ( (cache_ptr)->clean_index_size < (old_size) ) ) && \ + ( ( (was_clean) ) || \ + ( (cache_ptr)->dirty_index_size < (old_size) ) ) ) || \ ( (entry_ptr) == NULL ) || \ ( (entry_ptr)->ring <= H5C_RING_UNDEFINED ) || \ ( (entry_ptr)->ring >= H5C_RING_NTYPES ) || \ @@ -1196,20 +1196,20 @@ if ( ( (cache_ptr) == NULL ) || \ } #define H5C__POST_HT_ENTRY_SIZE_CHANGE_SC(cache_ptr, old_size, new_size, \ - entry_ptr) \ + entry_ptr) \ if ( ( (cache_ptr) == NULL ) || \ ( (cache_ptr)->index_len <= 0 ) || \ ( (cache_ptr)->index_size <= 0 ) || \ ( (new_size) > (cache_ptr)->index_size ) || \ ( (cache_ptr)->index_size != \ - ((cache_ptr)->clean_index_size + \ + ((cache_ptr)->clean_index_size + \ (cache_ptr)->dirty_index_size) ) || \ ( (cache_ptr)->index_size < ((cache_ptr)->clean_index_size) ) || \ ( (cache_ptr)->index_size < ((cache_ptr)->dirty_index_size) ) || \ ( ( !((entry_ptr)->is_dirty ) || \ - ( (cache_ptr)->dirty_index_size < (new_size) ) ) && \ - ( ( ((entry_ptr)->is_dirty) ) || \ - ( (cache_ptr)->clean_index_size < (new_size) ) ) ) || \ + ( (cache_ptr)->dirty_index_size < (new_size) ) ) && \ + ( ( ((entry_ptr)->is_dirty) ) || \ + ( (cache_ptr)->clean_index_size < (new_size) ) ) ) || \ ( ( (cache_ptr)->index_len == 1 ) && \ ( (cache_ptr)->index_size != (new_size) ) ) || \ ( (cache_ptr)->index_ring_len[(entry_ptr)->ring] > \ @@ -1465,10 +1465,10 @@ if ( ( (cache_ptr)->index_size != \ H5C__PRE_HT_UPDATE_FOR_ENTRY_CLEAN_SC(cache_ptr, entry_ptr); \ (cache_ptr)->dirty_index_size -= (entry_ptr)->size; \ ((cache_ptr)->dirty_index_ring_size[entry_ptr->ring]) \ - -= (entry_ptr)->size; \ + -= (entry_ptr)->size; \ (cache_ptr)->clean_index_size += (entry_ptr)->size; \ ((cache_ptr)->clean_index_ring_size[entry_ptr->ring]) \ - += (entry_ptr)->size; \ + += (entry_ptr)->size; \ H5C__POST_HT_UPDATE_FOR_ENTRY_CLEAN_SC(cache_ptr, entry_ptr); \ } @@ -1477,18 +1477,18 @@ if ( ( (cache_ptr)->index_size != \ H5C__PRE_HT_UPDATE_FOR_ENTRY_DIRTY_SC(cache_ptr, entry_ptr); \ (cache_ptr)->clean_index_size -= (entry_ptr)->size; \ ((cache_ptr)->clean_index_ring_size[entry_ptr->ring]) \ - -= (entry_ptr)->size; \ + -= (entry_ptr)->size; \ (cache_ptr)->dirty_index_size += (entry_ptr)->size; \ ((cache_ptr)->dirty_index_ring_size[entry_ptr->ring]) \ - += (entry_ptr)->size; \ + += (entry_ptr)->size; \ H5C__POST_HT_UPDATE_FOR_ENTRY_DIRTY_SC(cache_ptr, entry_ptr); \ } #define H5C__UPDATE_INDEX_FOR_SIZE_CHANGE(cache_ptr, old_size, new_size, \ - entry_ptr, was_clean) \ + entry_ptr, was_clean) \ { \ H5C__PRE_HT_ENTRY_SIZE_CHANGE_SC(cache_ptr, old_size, new_size, \ - entry_ptr, was_clean) \ + entry_ptr, was_clean) \ (cache_ptr)->index_size -= (old_size); \ (cache_ptr)->index_size += (new_size); \ ((cache_ptr)->index_ring_size[entry_ptr->ring]) -= (old_size); \ @@ -1497,14 +1497,14 @@ if ( ( (cache_ptr)->index_size != \ (cache_ptr)->clean_index_size -= (old_size); \ ((cache_ptr)->clean_index_ring_size[entry_ptr->ring])-= (old_size); \ } else { \ - (cache_ptr)->dirty_index_size -= (old_size); \ + (cache_ptr)->dirty_index_size -= (old_size); \ ((cache_ptr)->dirty_index_ring_size[entry_ptr->ring])-= (old_size); \ } \ if((entry_ptr)->is_dirty) { \ (cache_ptr)->dirty_index_size += (new_size); \ ((cache_ptr)->dirty_index_ring_size[entry_ptr->ring])+= (new_size); \ } else { \ - (cache_ptr)->clean_index_size += (new_size); \ + (cache_ptr)->clean_index_size += (new_size); \ ((cache_ptr)->clean_index_ring_size[entry_ptr->ring])+= (new_size); \ } \ H5C__DLL_UPDATE_FOR_SIZE_CHANGE((cache_ptr)->il_len, \ @@ -1791,7 +1791,7 @@ if ( ( (cache_ptr)->index_size != \ } else { /* slist disabled */ \ \ HDassert( (cache_ptr)->slist_len == 0 ); \ - HDassert( (cache_ptr)->slist_size == 0 ); \ + HDassert( (cache_ptr)->slist_size == 0 ); \ } \ } /* H5C__REMOVE_ENTRY_FROM_SLIST */ @@ -2033,16 +2033,16 @@ if ( ( (cache_ptr)->index_size != \ /* modified LRU specific code */ \ \ /* remove the entry from the LRU list, and re-insert it at the head.\ - */ \ + */ \ \ H5C__DLL_REMOVE((entry_ptr), (cache_ptr)->LRU_head_ptr, \ (cache_ptr)->LRU_tail_ptr, \ - (cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_len, \ (cache_ptr)->LRU_list_size, (fail_val)) \ \ H5C__DLL_PREPEND((entry_ptr), (cache_ptr)->LRU_head_ptr, \ (cache_ptr)->LRU_tail_ptr, \ - (cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_len, \ (cache_ptr)->LRU_list_size, (fail_val)) \ \ /* Use the dirty flag to infer whether the entry is on the clean or \ @@ -2096,16 +2096,16 @@ if ( ( (cache_ptr)->index_size != \ /* modified LRU specific code */ \ \ /* remove the entry from the LRU list, and re-insert it at the head \ - */ \ + */ \ \ H5C__DLL_REMOVE((entry_ptr), (cache_ptr)->LRU_head_ptr, \ (cache_ptr)->LRU_tail_ptr, \ - (cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_len, \ (cache_ptr)->LRU_list_size, (fail_val)) \ \ H5C__DLL_PREPEND((entry_ptr), (cache_ptr)->LRU_head_ptr, \ (cache_ptr)->LRU_tail_ptr, \ - (cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_len, \ (cache_ptr)->LRU_list_size, (fail_val)) \ \ /* End modified LRU specific code. */ \ @@ -2288,28 +2288,28 @@ if ( ( (cache_ptr)->index_size != \ /* modified LRU specific code */ \ \ /* remove the entry from the LRU list, and re-insert it at the \ - * head. \ - */ \ + * head. \ + */ \ \ H5C__DLL_REMOVE((entry_ptr), (cache_ptr)->LRU_head_ptr, \ (cache_ptr)->LRU_tail_ptr, \ - (cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_len, \ (cache_ptr)->LRU_list_size, (fail_val)) \ \ H5C__DLL_PREPEND((entry_ptr), (cache_ptr)->LRU_head_ptr, \ (cache_ptr)->LRU_tail_ptr, \ - (cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_len, \ (cache_ptr)->LRU_list_size, (fail_val)) \ \ /* since the entry is being flushed or cleared, one would think \ - * that it must be dirty -- but that need not be the case. Use the \ - * dirty flag to infer whether the entry is on the clean or dirty \ - * LRU list, and remove it. Then insert it at the head of the \ - * clean LRU list. \ + * that it must be dirty -- but that need not be the case. Use the \ + * dirty flag to infer whether the entry is on the clean or dirty \ + * LRU list, and remove it. Then insert it at the head of the \ + * clean LRU list. \ * \ * The function presumes that a dirty entry will be either cleared \ - * or flushed shortly, so it is OK if we put a dirty entry on the \ - * clean LRU list. \ + * or flushed shortly, so it is OK if we put a dirty entry on the \ + * clean LRU list. \ */ \ \ if ( (entry_ptr)->is_dirty ) { \ @@ -2350,17 +2350,17 @@ if ( ( (cache_ptr)->index_size != \ /* modified LRU specific code */ \ \ /* remove the entry from the LRU list, and re-insert it at the \ - * head. \ - */ \ + * head. \ + */ \ \ H5C__DLL_REMOVE((entry_ptr), (cache_ptr)->LRU_head_ptr, \ (cache_ptr)->LRU_tail_ptr, \ - (cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_len, \ (cache_ptr)->LRU_list_size, (fail_val)) \ \ H5C__DLL_PREPEND((entry_ptr), (cache_ptr)->LRU_head_ptr, \ (cache_ptr)->LRU_tail_ptr, \ - (cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_len, \ (cache_ptr)->LRU_list_size, (fail_val)) \ \ /* End modified LRU specific code. */ \ @@ -2424,7 +2424,7 @@ if ( ( (cache_ptr)->index_size != \ \ H5C__DLL_APPEND((entry_ptr), (cache_ptr)->LRU_head_ptr, \ (cache_ptr)->LRU_tail_ptr, \ - (cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_len, \ (cache_ptr)->LRU_list_size, (fail_val)) \ \ /* insert the entry at the tail of the clean or dirty LRU list as \ @@ -2465,7 +2465,7 @@ if ( ( (cache_ptr)->index_size != \ (cache_ptr)->pel_tail_ptr, \ (cache_ptr)->pel_len, \ (cache_ptr)->pel_size, (fail_val)) \ - \ + \ } else { \ \ /* modified LRU specific code */ \ @@ -2474,7 +2474,7 @@ if ( ( (cache_ptr)->index_size != \ \ H5C__DLL_APPEND((entry_ptr), (cache_ptr)->LRU_head_ptr, \ (cache_ptr)->LRU_tail_ptr, \ - (cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_len, \ (cache_ptr)->LRU_list_size, (fail_val)) \ \ /* End modified LRU specific code. */ \ @@ -2558,7 +2558,7 @@ if ( ( (cache_ptr)->index_size != \ \ H5C__DLL_PREPEND((entry_ptr), (cache_ptr)->LRU_head_ptr, \ (cache_ptr)->LRU_tail_ptr, \ - (cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_len, \ (cache_ptr)->LRU_list_size, (fail_val)) \ \ /* insert the entry at the head of the clean or dirty LRU list as \ @@ -2599,7 +2599,7 @@ if ( ( (cache_ptr)->index_size != \ (cache_ptr)->pel_tail_ptr, \ (cache_ptr)->pel_len, \ (cache_ptr)->pel_size, (fail_val)) \ - \ + \ } else { \ \ /* modified LRU specific code */ \ @@ -2608,7 +2608,7 @@ if ( ( (cache_ptr)->index_size != \ \ H5C__DLL_PREPEND((entry_ptr), (cache_ptr)->LRU_head_ptr, \ (cache_ptr)->LRU_tail_ptr, \ - (cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_len, \ (cache_ptr)->LRU_list_size, (fail_val)) \ \ /* End modified LRU specific code. */ \ @@ -2677,12 +2677,12 @@ if ( ( (cache_ptr)->index_size != \ HDassert( !((entry_ptr)->is_read_only) ); \ HDassert( ((entry_ptr)->ro_ref_count) == 0 ); \ HDassert( (entry_ptr)->size > 0 ); \ - \ + \ if ( (entry_ptr)->is_pinned ) { \ \ H5C__DLL_REMOVE((entry_ptr), (cache_ptr)->pel_head_ptr, \ - (cache_ptr)->pel_tail_ptr, \ - (cache_ptr)->pel_len, \ + (cache_ptr)->pel_tail_ptr, \ + (cache_ptr)->pel_len, \ (cache_ptr)->pel_size, (fail_val)) \ \ } else { \ @@ -2693,7 +2693,7 @@ if ( ( (cache_ptr)->index_size != \ \ H5C__DLL_REMOVE((entry_ptr), (cache_ptr)->LRU_head_ptr, \ (cache_ptr)->LRU_tail_ptr, \ - (cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_len, \ (cache_ptr)->LRU_list_size, (fail_val)) \ \ /* Similarly, remove the entry from the clean or dirty LRU list \ @@ -2739,12 +2739,12 @@ if ( ( (cache_ptr)->index_size != \ HDassert( !((entry_ptr)->is_read_only) ); \ HDassert( ((entry_ptr)->ro_ref_count) == 0 ); \ HDassert( (entry_ptr)->size > 0 ); \ - \ + \ if ( (entry_ptr)->is_pinned ) { \ \ H5C__DLL_REMOVE((entry_ptr), (cache_ptr)->pel_head_ptr, \ - (cache_ptr)->pel_tail_ptr, \ - (cache_ptr)->pel_len, \ + (cache_ptr)->pel_tail_ptr, \ + (cache_ptr)->pel_len, \ (cache_ptr)->pel_size, (fail_val)) \ \ } else { \ @@ -2755,7 +2755,7 @@ if ( ( (cache_ptr)->index_size != \ \ H5C__DLL_REMOVE((entry_ptr), (cache_ptr)->LRU_head_ptr, \ (cache_ptr)->LRU_tail_ptr, \ - (cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_len, \ (cache_ptr)->LRU_list_size, (fail_val)) \ \ /* End modified LRU specific code. */ \ @@ -2804,21 +2804,21 @@ if ( ( (cache_ptr)->index_size != \ HDassert( ((entry_ptr)->ro_ref_count) == 0 ); \ HDassert( (entry_ptr)->size > 0 ); \ \ - if ( ! ( (entry_ptr)->is_pinned ) && ! ( (entry_ptr->is_protected ) ) ) { \ - \ + if ( ! ( (entry_ptr)->is_pinned ) && ! ( (entry_ptr->is_protected ) ) ) {\ + \ /* modified LRU specific code */ \ \ /* remove the entry from the LRU list, and re-insert it at the head. \ - */ \ + */ \ \ H5C__DLL_REMOVE((entry_ptr), (cache_ptr)->LRU_head_ptr, \ (cache_ptr)->LRU_tail_ptr, \ - (cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_len, \ (cache_ptr)->LRU_list_size, (fail_val)) \ \ H5C__DLL_PREPEND((entry_ptr), (cache_ptr)->LRU_head_ptr, \ (cache_ptr)->LRU_tail_ptr, \ - (cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_len, \ (cache_ptr)->LRU_list_size, (fail_val)) \ \ /* remove the entry from either the clean or dirty LUR list as \ @@ -2827,7 +2827,7 @@ if ( ( (cache_ptr)->index_size != \ if ( was_dirty ) { \ \ H5C__AUX_DLL_REMOVE((entry_ptr), \ - (cache_ptr)->dLRU_head_ptr, \ + (cache_ptr)->dLRU_head_ptr, \ (cache_ptr)->dLRU_tail_ptr, \ (cache_ptr)->dLRU_list_len, \ (cache_ptr)->dLRU_list_size, \ @@ -2836,34 +2836,34 @@ if ( ( (cache_ptr)->index_size != \ } else { \ \ H5C__AUX_DLL_REMOVE((entry_ptr), \ - (cache_ptr)->cLRU_head_ptr, \ + (cache_ptr)->cLRU_head_ptr, \ (cache_ptr)->cLRU_tail_ptr, \ (cache_ptr)->cLRU_list_len, \ (cache_ptr)->cLRU_list_size, \ - (fail_val)) \ + (fail_val)) \ } \ \ /* insert the entry at the head of either the clean or dirty \ - * LRU list as appropriate. \ + * LRU list as appropriate. \ */ \ \ if ( (entry_ptr)->is_dirty ) { \ \ H5C__AUX_DLL_PREPEND((entry_ptr), \ - (cache_ptr)->dLRU_head_ptr, \ + (cache_ptr)->dLRU_head_ptr, \ (cache_ptr)->dLRU_tail_ptr, \ (cache_ptr)->dLRU_list_len, \ (cache_ptr)->dLRU_list_size, \ - (fail_val)) \ + (fail_val)) \ \ } else { \ \ H5C__AUX_DLL_PREPEND((entry_ptr), \ - (cache_ptr)->cLRU_head_ptr, \ + (cache_ptr)->cLRU_head_ptr, \ (cache_ptr)->cLRU_tail_ptr, \ (cache_ptr)->cLRU_list_len, \ (cache_ptr)->cLRU_list_size, \ - (fail_val)) \ + (fail_val)) \ } \ \ /* End modified LRU specific code. */ \ @@ -2872,7 +2872,7 @@ if ( ( (cache_ptr)->index_size != \ #else /* H5C_MAINTAIN_CLEAN_AND_DIRTY_LRU_LISTS */ -#define H5C__UPDATE_RP_FOR_MOVE(cache_ptr, entry_ptr, was_dirty, fail_val) \ +#define H5C__UPDATE_RP_FOR_MOVE(cache_ptr, entry_ptr, was_dirty, fail_val) \ { \ HDassert( (cache_ptr) ); \ HDassert( (cache_ptr)->magic == H5C__H5C_T_MAGIC ); \ @@ -2881,21 +2881,21 @@ if ( ( (cache_ptr)->index_size != \ HDassert( ((entry_ptr)->ro_ref_count) == 0 ); \ HDassert( (entry_ptr)->size > 0 ); \ \ - if ( ! ( (entry_ptr)->is_pinned ) && ! ( (entry_ptr->is_protected ) ) ) { \ - \ + if ( ! ( (entry_ptr)->is_pinned ) && ! ( (entry_ptr->is_protected ) ) ) {\ + \ /* modified LRU specific code */ \ \ /* remove the entry from the LRU list, and re-insert it at the head. \ - */ \ + */ \ \ H5C__DLL_REMOVE((entry_ptr), (cache_ptr)->LRU_head_ptr, \ (cache_ptr)->LRU_tail_ptr, \ - (cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_len, \ (cache_ptr)->LRU_list_size, (fail_val)) \ \ H5C__DLL_PREPEND((entry_ptr), (cache_ptr)->LRU_head_ptr, \ (cache_ptr)->LRU_tail_ptr, \ - (cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_len, \ (cache_ptr)->LRU_list_size, (fail_val)) \ \ /* End modified LRU specific code. */ \ @@ -2952,49 +2952,49 @@ if ( ( (cache_ptr)->index_size != \ \ if ( (entry_ptr)->coll_access ) { \ \ - H5C__DLL_UPDATE_FOR_SIZE_CHANGE((cache_ptr)->coll_list_len, \ - (cache_ptr)->coll_list_size, \ - (entry_ptr)->size, \ - (new_size)); \ - \ + H5C__DLL_UPDATE_FOR_SIZE_CHANGE((cache_ptr)->coll_list_len, \ + (cache_ptr)->coll_list_size, \ + (entry_ptr)->size, \ + (new_size)); \ + \ } \ \ if ( (entry_ptr)->is_pinned ) { \ \ - H5C__DLL_UPDATE_FOR_SIZE_CHANGE((cache_ptr)->pel_len, \ - (cache_ptr)->pel_size, \ - (entry_ptr)->size, \ - (new_size)); \ - \ + H5C__DLL_UPDATE_FOR_SIZE_CHANGE((cache_ptr)->pel_len, \ + (cache_ptr)->pel_size, \ + (entry_ptr)->size, \ + (new_size)); \ + \ } else { \ \ /* modified LRU specific code */ \ \ - /* Update the size of the LRU list */ \ + /* Update the size of the LRU list */ \ \ - H5C__DLL_UPDATE_FOR_SIZE_CHANGE((cache_ptr)->LRU_list_len, \ - (cache_ptr)->LRU_list_size, \ - (entry_ptr)->size, \ - (new_size)); \ + H5C__DLL_UPDATE_FOR_SIZE_CHANGE((cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_size, \ + (entry_ptr)->size, \ + (new_size)); \ \ /* Similarly, update the size of the clean or dirty LRU list as \ - * appropriate. At present, the entry must be clean, but that \ - * could change. \ + * appropriate. At present, the entry must be clean, but that \ + * could change. \ */ \ \ if ( (entry_ptr)->is_dirty ) { \ \ - H5C__DLL_UPDATE_FOR_SIZE_CHANGE((cache_ptr)->dLRU_list_len, \ - (cache_ptr)->dLRU_list_size, \ - (entry_ptr)->size, \ - (new_size)); \ + H5C__DLL_UPDATE_FOR_SIZE_CHANGE((cache_ptr)->dLRU_list_len, \ + (cache_ptr)->dLRU_list_size, \ + (entry_ptr)->size, \ + (new_size)); \ \ } else { \ \ - H5C__DLL_UPDATE_FOR_SIZE_CHANGE((cache_ptr)->cLRU_list_len, \ - (cache_ptr)->cLRU_list_size, \ - (entry_ptr)->size, \ - (new_size)); \ + H5C__DLL_UPDATE_FOR_SIZE_CHANGE((cache_ptr)->cLRU_list_len, \ + (cache_ptr)->cLRU_list_size, \ + (entry_ptr)->size, \ + (new_size)); \ } \ \ /* End modified LRU specific code. */ \ @@ -3017,21 +3017,21 @@ if ( ( (cache_ptr)->index_size != \ \ if ( (entry_ptr)->is_pinned ) { \ \ - H5C__DLL_UPDATE_FOR_SIZE_CHANGE((cache_ptr)->pel_len, \ - (cache_ptr)->pel_size, \ - (entry_ptr)->size, \ - (new_size)); \ + H5C__DLL_UPDATE_FOR_SIZE_CHANGE((cache_ptr)->pel_len, \ + (cache_ptr)->pel_size, \ + (entry_ptr)->size, \ + (new_size)); \ \ } else { \ \ /* modified LRU specific code */ \ \ - /* Update the size of the LRU list */ \ + /* Update the size of the LRU list */ \ \ - H5C__DLL_UPDATE_FOR_SIZE_CHANGE((cache_ptr)->LRU_list_len, \ - (cache_ptr)->LRU_list_size, \ - (entry_ptr)->size, \ - (new_size)); \ + H5C__DLL_UPDATE_FOR_SIZE_CHANGE((cache_ptr)->LRU_list_len, \ + (cache_ptr)->LRU_list_size, \ + (entry_ptr)->size, \ + (new_size)); \ \ /* End modified LRU specific code. */ \ } \ @@ -3318,7 +3318,7 @@ if ( ( (hd_ptr) == NULL ) || \ ( (Size) < (entry_ptr)->size ) || \ ( ( (Size) == (entry_ptr)->size ) && ( ! ( (len) == 1 ) ) ) || \ ( ( (entry_ptr)->coll_prev == NULL ) && ( (hd_ptr) != (entry_ptr) ) ) || \ - ( ( (entry_ptr)->coll_next == NULL ) && ( (tail_ptr) != (entry_ptr) ) ) || \ + ( ( (entry_ptr)->coll_next == NULL ) && ( (tail_ptr) != (entry_ptr) ) ) ||\ ( ( (len) == 1 ) && \ ( ! ( ( (hd_ptr) == (entry_ptr) ) && ( (tail_ptr) == (entry_ptr) ) && \ ( (entry_ptr)->coll_next == NULL ) && \ @@ -3350,10 +3350,10 @@ if ( ( ( ( (head_ptr) == NULL ) || ( (tail_ptr) == NULL ) ) && \ ) \ ) { \ HDassert(0 && "COLL DLL sanity check failed"); \ - HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, (fv), "COLL DLL sanity check failed") \ + HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, (fv), "COLL DLL sanity check failed")\ } -#define H5C__COLL_DLL_PRE_INSERT_SC(entry_ptr, hd_ptr, tail_ptr, len, Size, fv) \ +#define H5C__COLL_DLL_PRE_INSERT_SC(entry_ptr, hd_ptr, tail_ptr, len, Size, fv)\ if ( ( (entry_ptr) == NULL ) || \ ( (entry_ptr)->coll_next != NULL ) || \ ( (entry_ptr)->coll_prev != NULL ) || \ @@ -5074,7 +5074,7 @@ H5_DLL herr_t H5C__generate_cache_image(H5F_t *f, H5C_t *cache_ptr); H5_DLL herr_t H5C__load_cache_image(H5F_t *f); H5_DLL herr_t H5C__mark_flush_dep_serialized(H5C_cache_entry_t * entry_ptr); H5_DLL herr_t H5C__mark_flush_dep_unserialized(H5C_cache_entry_t * entry_ptr); -H5_DLL herr_t H5C__make_space_in_cache(H5F_t * f, size_t space_needed, +H5_DLL herr_t H5C__make_space_in_cache(H5F_t * f, size_t space_needed, hbool_t write_permitted); H5_DLL herr_t H5C__flush_marked_entries(H5F_t * f); H5_DLL herr_t H5C__serialize_cache(H5F_t *f); diff --git a/src/H5Cprivate.h b/src/H5Cprivate.h index 8a1043e..9514443 100644 --- a/src/H5Cprivate.h +++ b/src/H5Cprivate.h @@ -2292,6 +2292,16 @@ H5_DLL herr_t H5C_cache_image_status(H5F_t *f, hbool_t *load_ci_ptr, hbool_t * H5_DLL hbool_t H5C_cache_image_pending(const H5C_t *cache_ptr); H5_DLL herr_t H5C_get_mdc_image_info(const H5C_t *cache_ptr, haddr_t *image_addr, hsize_t *image_len); +#if H5C_DO_SLIST_SANITY_CHECKS +H5_DLL hbool_t H5C_entry_in_skip_list(H5C_t *cache_ptr, H5C_cache_entry_t *target_ptr); +#endif + +#if H5C_DO_EXTREME_SANITY_CHECKS +H5_DLL herr_t H5C_validate_lru_list(H5C_t *cache_ptr); +H5_DLL herr_t H5C_validate_pinned_entry_list(H5C_t *cache_ptr); +H5_DLL herr_t H5C_validate_protected_entry_list(H5C_t *cache_ptr); +#endif /* H5C_DO_EXTREME_SANITY_CHECKS */ + /* Logging functions */ H5_DLL herr_t H5C_start_logging(H5C_t *cache); H5_DLL herr_t H5C_stop_logging(H5C_t *cache); diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index 5d7c1b2..e4d8706 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -239,10 +239,14 @@ typedef struct H5D_chunk_file_iter_ud_t { #ifdef H5_HAVE_PARALLEL /* information to construct a collective I/O operation for filling chunks */ -typedef struct H5D_chunk_coll_info_t { - size_t num_io; /* Number of write operations */ - haddr_t *addr; /* array of the file addresses of the write operation */ -} H5D_chunk_coll_info_t; +typedef struct H5D_chunk_coll_fill_info_t { + size_t num_chunks; /* Number of chunks in the write operation */ + struct chunk_coll_fill_info { + haddr_t addr; /* File address of the chunk */ + size_t chunk_size; /* Size of the chunk in the file */ + hbool_t unfiltered_partial_chunk; + } * chunk_info; +} H5D_chunk_coll_fill_info_t; #endif /* H5_HAVE_PARALLEL */ typedef struct H5D_chunk_iter_ud_t { @@ -287,9 +291,6 @@ static int H5D__chunk_format_convert_cb(const H5D_chunk_rec_t *chunk_rec, void * /* Helper routines */ static herr_t H5D__chunk_set_info_real(H5O_layout_chunk_t *layout, unsigned ndims, const hsize_t *curr_dims, const hsize_t *max_dims); -static void * H5D__chunk_mem_alloc(size_t size, const H5O_pline_t *pline); -static void * H5D__chunk_mem_xfree(void *chk, const void *pline); -static void * H5D__chunk_mem_realloc(void *chk, size_t size, const H5O_pline_t *pline); static herr_t H5D__chunk_cinfo_cache_reset(H5D_chunk_cached_t *last); static herr_t H5D__chunk_cinfo_cache_update(H5D_chunk_cached_t *last, const H5D_chunk_ud_t *udata); static hbool_t H5D__chunk_cinfo_cache_found(const H5D_chunk_cached_t *last, H5D_chunk_ud_t *udata); @@ -306,8 +307,6 @@ static herr_t H5D__chunk_mem_cb(void *elem, const H5T_t *type, unsigned ndims, static unsigned H5D__chunk_hash_val(const H5D_shared_t *shared, const hsize_t *scaled); static herr_t H5D__chunk_flush_entry(const H5D_t *dset, H5D_rdcc_ent_t *ent, hbool_t reset); static herr_t H5D__chunk_cache_evict(const H5D_t *dset, H5D_rdcc_ent_t *ent, hbool_t flush); -static hbool_t H5D__chunk_is_partial_edge_chunk(unsigned dset_ndims, const uint32_t *chunk_dims, - const hsize_t *chunk_scaled, const hsize_t *dset_dims); static void * H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t relax, hbool_t prev_unfilt_chunk); static herr_t H5D__chunk_unlock(const H5D_io_info_t *io_info, const H5D_chunk_ud_t *udata, hbool_t dirty, @@ -315,9 +314,9 @@ static herr_t H5D__chunk_unlock(const H5D_io_info_t *io_info, const H5D_chunk_ static herr_t H5D__chunk_cache_prune(const H5D_t *dset, size_t size); static herr_t H5D__chunk_prune_fill(H5D_chunk_it_ud1_t *udata, hbool_t new_unfilt_chunk); #ifdef H5_HAVE_PARALLEL -static herr_t H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_info_t *chunk_info, - size_t chunk_size, const void *fill_buf); -static int H5D__chunk_cmp_addr(const void *addr1, const void *addr2); +static herr_t H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_fill_info_t *chunk_fill_info, + const void *fill_buf, const void *partial_chunk_fill_buf); +static int H5D__chunk_cmp_coll_fill_info(const void *_entry1, const void *_entry2); #endif /* H5_HAVE_PARALLEL */ /* Debugging helper routine callback */ @@ -1362,7 +1361,7 @@ done: * *------------------------------------------------------------------------- */ -static void * +void * H5D__chunk_mem_alloc(size_t size, const H5O_pline_t *pline) { void *ret_value = NULL; /* Return value */ @@ -1393,7 +1392,7 @@ H5D__chunk_mem_alloc(size_t size, const H5O_pline_t *pline) * *------------------------------------------------------------------------- */ -static void * +void * H5D__chunk_mem_xfree(void *chk, const void *_pline) { const H5O_pline_t *pline = (const H5O_pline_t *)_pline; @@ -1417,7 +1416,7 @@ H5D__chunk_mem_xfree(void *chk, const void *_pline) * calls H5D__chunk_mem_xfree and discards the return value. *------------------------------------------------------------------------- */ -static void +void H5D__chunk_mem_free(void *chk, const void *_pline) { (void)H5D__chunk_mem_xfree(chk, _pline); @@ -1437,7 +1436,7 @@ H5D__chunk_mem_free(void *chk, const void *_pline) * *------------------------------------------------------------------------- */ -static void * +void * H5D__chunk_mem_realloc(void *chk, size_t size, const H5O_pline_t *pline) { void *ret_value = NULL; /* Return value */ @@ -3178,7 +3177,9 @@ H5D__chunk_lookup(const H5D_t *dset, const hsize_t *scaled, H5D_chunk_ud_t *udat unsigned idx = 0; /* Index of chunk in cache, if present */ hbool_t found = FALSE; /* In cache? */ #ifdef H5_HAVE_PARALLEL - hbool_t reenable_coll_md_reads = FALSE; + H5P_coll_md_read_flag_t md_reads_file_flag; + hbool_t md_reads_context_flag; + hbool_t restore_md_reads_state = FALSE; #endif herr_t ret_value = SUCCEED; /* Return value */ @@ -3252,11 +3253,10 @@ H5D__chunk_lookup(const H5D_t *dset, const hsize_t *scaled, H5D_chunk_ud_t *udat * processes. */ if (H5F_HAS_FEATURE(idx_info.f, H5FD_FEAT_HAS_MPI)) { - hbool_t do_coll_md_reads = H5CX_get_coll_metadata_read(); - if (do_coll_md_reads) { - H5CX_set_coll_metadata_read(FALSE); - reenable_coll_md_reads = TRUE; - } + md_reads_file_flag = H5P_FORCE_FALSE; + md_reads_context_flag = FALSE; + H5F_set_coll_metadata_reads(idx_info.f, &md_reads_file_flag, &md_reads_context_flag); + restore_md_reads_state = TRUE; } #endif /* H5_HAVE_PARALLEL */ @@ -3302,8 +3302,8 @@ H5D__chunk_lookup(const H5D_t *dset, const hsize_t *scaled, H5D_chunk_ud_t *udat done: #ifdef H5_HAVE_PARALLEL /* Re-enable collective metadata reads if we disabled them */ - if (reenable_coll_md_reads) - H5CX_set_coll_metadata_read(TRUE); + if (restore_md_reads_state) + H5F_set_coll_metadata_reads(dset->oloc.file, &md_reads_file_flag, &md_reads_context_flag); #endif /* H5_HAVE_PARALLEL */ FUNC_LEAVE_NOAPI(ret_value) @@ -4319,8 +4319,8 @@ H5D__chunk_allocate(const H5D_io_info_t *io_info, hbool_t full_overwrite, const hbool_t blocks_written = FALSE; /* Flag to indicate that chunk was actually written */ hbool_t using_mpi = FALSE; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */ - H5D_chunk_coll_info_t chunk_info; /* chunk address information for doing I/O */ -#endif /* H5_HAVE_PARALLEL */ + H5D_chunk_coll_fill_info_t chunk_fill_info; /* chunk address information for doing I/O */ +#endif /* H5_HAVE_PARALLEL */ hbool_t carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */ unsigned space_ndims; /* Dataset's space rank */ const hsize_t * space_dim; /* Dataset's dataspace dimensions */ @@ -4367,8 +4367,8 @@ H5D__chunk_allocate(const H5D_io_info_t *io_info, hbool_t full_overwrite, const using_mpi = TRUE; /* init chunk info stuff for collective I/O */ - chunk_info.num_io = 0; - chunk_info.addr = NULL; + chunk_fill_info.num_chunks = 0; + chunk_fill_info.chunk_info = NULL; } /* end if */ #endif /* H5_HAVE_PARALLEL */ @@ -4640,19 +4640,26 @@ H5D__chunk_allocate(const H5D_io_info_t *io_info, hbool_t full_overwrite, const if (using_mpi) { /* collect all chunk addresses to be written to write collectively at the end */ - /* allocate/resize address array if no more space left */ - /* Note that if we add support for parallel filters we must - * also store an array of chunk sizes and pass it to the - * apporpriate collective write function */ - if (0 == chunk_info.num_io % 1024) - if (NULL == (chunk_info.addr = (haddr_t *)H5MM_realloc( - chunk_info.addr, (chunk_info.num_io + 1024) * sizeof(haddr_t)))) + + /* allocate/resize chunk info array if no more space left */ + if (0 == chunk_fill_info.num_chunks % 1024) { + void *tmp_realloc; + + if (NULL == (tmp_realloc = H5MM_realloc(chunk_fill_info.chunk_info, + (chunk_fill_info.num_chunks + 1024) * + sizeof(struct chunk_coll_fill_info)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, - "memory allocation failed for chunk addresses") + "memory allocation failed for chunk fill info") - /* Store the chunk's address for later */ - chunk_info.addr[chunk_info.num_io] = udata.chunk_block.offset; - chunk_info.num_io++; + chunk_fill_info.chunk_info = tmp_realloc; + } + + /* Store info about the chunk for later */ + chunk_fill_info.chunk_info[chunk_fill_info.num_chunks].addr = udata.chunk_block.offset; + chunk_fill_info.chunk_info[chunk_fill_info.num_chunks].chunk_size = chunk_size; + chunk_fill_info.chunk_info[chunk_fill_info.num_chunks].unfiltered_partial_chunk = + (*fill_buf == unfilt_fill_buf); + chunk_fill_info.num_chunks++; /* Indicate that blocks will be written */ blocks_written = TRUE; @@ -4725,7 +4732,7 @@ H5D__chunk_allocate(const H5D_io_info_t *io_info, hbool_t full_overwrite, const #ifdef H5_HAVE_PARALLEL /* do final collective I/O */ if (using_mpi && blocks_written) - if (H5D__chunk_collective_fill(dset, &chunk_info, chunk_size, fb_info.fill_buf) < 0) + if (H5D__chunk_collective_fill(dset, &chunk_fill_info, fb_info.fill_buf, unfilt_fill_buf) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file") #endif /* H5_HAVE_PARALLEL */ @@ -4741,8 +4748,8 @@ done: unfilt_fill_buf = H5D__chunk_mem_xfree(unfilt_fill_buf, &def_pline); #ifdef H5_HAVE_PARALLEL - if (using_mpi && chunk_info.addr) - H5MM_free(chunk_info.addr); + if (using_mpi && chunk_fill_info.chunk_info) + H5MM_free(chunk_fill_info.chunk_info); #endif FUNC_LEAVE_NOAPI(ret_value) @@ -4936,27 +4943,35 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_info_t *chunk_info, size_t chunk_size, - const void *fill_buf) +H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_fill_info_t *chunk_fill_info, + const void *fill_buf, const void *partial_chunk_fill_buf) { - MPI_Comm mpi_comm = MPI_COMM_NULL; /* MPI communicator for file */ - int mpi_rank = (-1); /* This process's rank */ - int mpi_size = (-1); /* MPI Comm size */ - int mpi_code; /* MPI return code */ - size_t num_blocks; /* Number of blocks between processes. */ - size_t leftover_blocks; /* Number of leftover blocks to handle */ - int blocks, leftover, block_len; /* converted to int for MPI */ + MPI_Comm mpi_comm = MPI_COMM_NULL; /* MPI communicator for file */ + int mpi_rank = (-1); /* This process's rank */ + int mpi_size = (-1); /* MPI Comm size */ + int mpi_code; /* MPI return code */ + size_t num_blocks; /* Number of blocks between processes. */ + size_t leftover_blocks; /* Number of leftover blocks to handle */ + int blocks, leftover; /* converted to int for MPI */ MPI_Aint * chunk_disp_array = NULL; + MPI_Aint * block_disps = NULL; int * block_lens = NULL; MPI_Datatype mem_type = MPI_BYTE, file_type = MPI_BYTE; H5FD_mpio_xfer_t prev_xfer_mode; /* Previous data xfer mode */ hbool_t have_xfer_mode = FALSE; /* Whether the previous xffer mode has been retrieved */ - hbool_t need_addr_sort = FALSE; - int i; /* Local index variable */ + hbool_t need_sort = FALSE; + size_t i; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC + /* + * If a separate fill buffer is provided for partial chunks, ensure + * that the "don't filter partial edge chunks" flag is set. + */ + if (partial_chunk_fill_buf) + HDassert(dset->shared->layout.u.chunk.flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS); + /* Get the MPI communicator */ if (MPI_COMM_NULL == (mpi_comm = H5F_mpi_get_comm(dset->oloc.file))) HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator") @@ -4972,39 +4987,89 @@ H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_info_t *chunk_info, /* Distribute evenly the number of blocks between processes. */ if (mpi_size == 0) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "Resulted in division by zero") - num_blocks = (size_t)(chunk_info->num_io / (size_t)mpi_size); /* value should be the same on all procs */ + num_blocks = + (size_t)(chunk_fill_info->num_chunks / (size_t)mpi_size); /* value should be the same on all procs */ /* After evenly distributing the blocks between processes, are there any * leftover blocks for each individual process (round-robin)? */ - leftover_blocks = (size_t)(chunk_info->num_io % (size_t)mpi_size); + leftover_blocks = (size_t)(chunk_fill_info->num_chunks % (size_t)mpi_size); /* Cast values to types needed by MPI */ H5_CHECKED_ASSIGN(blocks, int, num_blocks, size_t); H5_CHECKED_ASSIGN(leftover, int, leftover_blocks, size_t); - H5_CHECKED_ASSIGN(block_len, int, chunk_size, size_t); /* Check if we have any chunks to write on this rank */ if (num_blocks > 0 || (leftover && leftover > mpi_rank)) { + MPI_Aint partial_fill_buf_disp = 0; + hbool_t all_same_block_len = TRUE; + /* Allocate buffers */ - /* (MSC - should not need block_lens if MPI_type_create_hindexed_block is working) */ - if (NULL == (block_lens = (int *)H5MM_malloc((size_t)(blocks + 1) * sizeof(int)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk lengths buffer") if (NULL == (chunk_disp_array = (MPI_Aint *)H5MM_malloc((size_t)(blocks + 1) * sizeof(MPI_Aint)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk file displacement buffer") - for (i = 0; i < blocks; i++) { - /* store the chunk address as an MPI_Aint */ - chunk_disp_array[i] = (MPI_Aint)(chunk_info->addr[i + (mpi_rank * blocks)]); + if (partial_chunk_fill_buf) { + MPI_Aint fill_buf_addr; + MPI_Aint partial_fill_buf_addr; - /* MSC - should not need this if MPI_type_create_hindexed_block is working */ - block_lens[i] = block_len; + /* Calculate the displacement between the fill buffer and partial chunk fill buffer */ + if (MPI_SUCCESS != (mpi_code = MPI_Get_address(fill_buf, &fill_buf_addr))) + HMPI_GOTO_ERROR(FAIL, "MPI_Get_address failed", mpi_code) + if (MPI_SUCCESS != (mpi_code = MPI_Get_address(partial_chunk_fill_buf, &partial_fill_buf_addr))) + HMPI_GOTO_ERROR(FAIL, "MPI_Get_address failed", mpi_code) + +#if MPI_VERSION >= 3 && MPI_SUBVERSION >= 1 + partial_fill_buf_disp = MPI_Aint_diff(partial_fill_buf_addr, fill_buf_addr); +#else + partial_fill_buf_disp = partial_fill_buf_addr - fill_buf_addr; +#endif - /* Make sure that the addresses in the datatype are - * monotonically non-decreasing + /* + * Allocate all-zero block displacements array. If a block's displacement + * is left as zero, that block will be written to from the regular fill + * buffer. If a block represents an unfiltered partial edge chunk, its + * displacement will be set so that the block is written to from the + * unfiltered fill buffer. */ - if (i && (chunk_disp_array[i] < chunk_disp_array[i - 1])) - need_addr_sort = TRUE; + if (NULL == (block_disps = (MPI_Aint *)H5MM_calloc((size_t)(blocks + 1) * sizeof(MPI_Aint)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate block displacements buffer") + } + + /* + * Perform initial scan of chunk info list to: + * - make sure that chunk addresses are monotonically non-decreasing + * - check if all blocks have the same length + */ + for (i = 1; i < chunk_fill_info->num_chunks; i++) { + if (chunk_fill_info->chunk_info[i].addr < chunk_fill_info->chunk_info[i - 1].addr) + need_sort = TRUE; + + if (chunk_fill_info->chunk_info[i].chunk_size != chunk_fill_info->chunk_info[i - 1].chunk_size) + all_same_block_len = FALSE; + } + + if (need_sort) + HDqsort(chunk_fill_info->chunk_info, chunk_fill_info->num_chunks, + sizeof(struct chunk_coll_fill_info), H5D__chunk_cmp_coll_fill_info); + + /* Allocate buffer for block lengths if necessary */ + if (!all_same_block_len) + if (NULL == (block_lens = (int *)H5MM_malloc((size_t)(blocks + 1) * sizeof(int)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk lengths buffer") + + for (i = 0; i < (size_t)blocks; i++) { + size_t idx = i + (size_t)(mpi_rank * blocks); + + /* store the chunk address as an MPI_Aint */ + chunk_disp_array[i] = (MPI_Aint)(chunk_fill_info->chunk_info[idx].addr); + + if (!all_same_block_len) + H5_CHECKED_ASSIGN(block_lens[i], int, chunk_fill_info->chunk_info[idx].chunk_size, size_t); + + if (chunk_fill_info->chunk_info[idx].unfiltered_partial_chunk) { + HDassert(partial_chunk_fill_buf); + block_disps[i] = partial_fill_buf_disp; + } } /* end for */ /* Calculate if there are any leftover blocks after evenly @@ -5012,32 +5077,71 @@ H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_info_t *chunk_info, * to processes 0 -> leftover. */ if (leftover && leftover > mpi_rank) { - chunk_disp_array[blocks] = (MPI_Aint)chunk_info->addr[(blocks * mpi_size) + mpi_rank]; - if (blocks && (chunk_disp_array[blocks] < chunk_disp_array[blocks - 1])) - need_addr_sort = TRUE; - block_lens[blocks] = block_len; + chunk_disp_array[blocks] = + (MPI_Aint)chunk_fill_info->chunk_info[(blocks * mpi_size) + mpi_rank].addr; + + if (!all_same_block_len) + H5_CHECKED_ASSIGN(block_lens[blocks], int, + chunk_fill_info->chunk_info[(blocks * mpi_size) + mpi_rank].chunk_size, + size_t); + + if (chunk_fill_info->chunk_info[(blocks * mpi_size) + mpi_rank].unfiltered_partial_chunk) { + HDassert(partial_chunk_fill_buf); + block_disps[blocks] = partial_fill_buf_disp; + } + blocks++; } - /* Ensure that the blocks are sorted in monotonically non-decreasing - * order of offset in the file. - */ - if (need_addr_sort) - HDqsort(chunk_disp_array, (size_t)blocks, sizeof(MPI_Aint), H5D__chunk_cmp_addr); + /* Create file and memory types for the write operation */ + if (all_same_block_len) { + int block_len; + + H5_CHECKED_ASSIGN(block_len, int, chunk_fill_info->chunk_info[0].chunk_size, size_t); + + mpi_code = + MPI_Type_create_hindexed_block(blocks, block_len, chunk_disp_array, MPI_BYTE, &file_type); + if (mpi_code != MPI_SUCCESS) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed_block failed", mpi_code) + + if (partial_chunk_fill_buf) { + /* + * If filters are disabled for partial edge chunks, those chunks could + * potentially have the same block length as the other chunks, but still + * need to be written to using the unfiltered fill buffer. Use an hindexed + * block type rather than an hvector. + */ + mpi_code = + MPI_Type_create_hindexed_block(blocks, block_len, block_disps, MPI_BYTE, &mem_type); + if (mpi_code != MPI_SUCCESS) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed_block failed", mpi_code) + } + else { + mpi_code = MPI_Type_create_hvector(blocks, block_len, 0, MPI_BYTE, &mem_type); + if (mpi_code != MPI_SUCCESS) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hvector failed", mpi_code) + } + } + else { + /* + * Currently, different block lengths implies that there are partial + * edge chunks and the "don't filter partial edge chunks" flag is set. + */ + HDassert(partial_chunk_fill_buf); + HDassert(block_lens); + HDassert(block_disps); + + mpi_code = MPI_Type_create_hindexed(blocks, block_lens, chunk_disp_array, MPI_BYTE, &file_type); + if (mpi_code != MPI_SUCCESS) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code) + + mpi_code = MPI_Type_create_hindexed(blocks, block_lens, block_disps, MPI_BYTE, &mem_type); + if (mpi_code != MPI_SUCCESS) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code) + } - /* MSC - should use this if MPI_type_create_hindexed block is working: - * mpi_code = MPI_Type_create_hindexed_block(blocks, block_len, chunk_disp_array, MPI_BYTE, - * &file_type); - */ - mpi_code = MPI_Type_create_hindexed(blocks, block_lens, chunk_disp_array, MPI_BYTE, &file_type); - if (mpi_code != MPI_SUCCESS) - HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code) if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(&file_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) - - mpi_code = MPI_Type_create_hvector(blocks, block_len, 0, MPI_BYTE, &mem_type); - if (mpi_code != MPI_SUCCESS) - HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hvector failed", mpi_code) if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(&mem_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) } /* end if */ @@ -5080,39 +5184,25 @@ done: if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&mem_type))) HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) H5MM_xfree(chunk_disp_array); + H5MM_xfree(block_disps); H5MM_xfree(block_lens); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_collective_fill() */ static int -H5D__chunk_cmp_addr(const void *addr1, const void *addr2) +H5D__chunk_cmp_coll_fill_info(const void *_entry1, const void *_entry2) { - MPI_Aint _addr1 = (MPI_Aint)0, _addr2 = (MPI_Aint)0; - int ret_value = 0; + const struct chunk_coll_fill_info *entry1; + const struct chunk_coll_fill_info *entry2; FUNC_ENTER_STATIC_NOERR - _addr1 = *((const MPI_Aint *)addr1); - _addr2 = *((const MPI_Aint *)addr2); + entry1 = (const struct chunk_coll_fill_info *)_entry1; + entry2 = (const struct chunk_coll_fill_info *)_entry2; -#if MPI_VERSION >= 3 && MPI_SUBVERSION >= 1 - { - MPI_Aint diff = MPI_Aint_diff(_addr1, _addr2); - - if (diff < (MPI_Aint)0) - ret_value = -1; - else if (diff > (MPI_Aint)0) - ret_value = 1; - else - ret_value = 0; - } -#else - ret_value = (_addr1 > _addr2) - (_addr1 < _addr2); -#endif - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D__chunk_cmp_addr() */ + FUNC_LEAVE_NOAPI(H5F_addr_cmp(entry1->addr, entry2->addr)) +} /* end H5D__chunk_cmp_coll_fill_info() */ #endif /* H5_HAVE_PARALLEL */ /*------------------------------------------------------------------------- @@ -6826,7 +6916,7 @@ done: * *------------------------------------------------------------------------- */ -static hbool_t +hbool_t H5D__chunk_is_partial_edge_chunk(unsigned dset_ndims, const uint32_t *chunk_dims, const hsize_t scaled[], const hsize_t *dset_dims) { @@ -7121,6 +7211,89 @@ done: } /* end H5D__chunk_format_convert() */ /*------------------------------------------------------------------------- + * Function: H5D__chunk_index_empty_cb + * + * Purpose: Callback function that simply stops iteration and sets the + * `empty` parameter to FALSE if called. If this callback is + * entered, it means that the chunk index contains at least + * one chunk, so is not empty. + * + * Return: H5_ITER_STOP + * + *------------------------------------------------------------------------- + */ +static int +H5D__chunk_index_empty_cb(const H5D_chunk_rec_t H5_ATTR_UNUSED *chunk_rec, void *_udata) +{ + hbool_t *empty = (hbool_t *)_udata; + int ret_value = H5_ITER_STOP; + + FUNC_ENTER_STATIC_NOERR + + *empty = FALSE; + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__chunk_index_empty_cb() */ + +/*------------------------------------------------------------------------- + * Function: H5D__chunk_index_empty + * + * Purpose: Determines whether a chunk index is empty (has no chunks + * inserted into it yet). + * + * Note: This routine is meant to be a little more performant than + * just counting the number of chunks in the index. In the + * future, this is probably a callback that the chunk index + * ops structure should provide. + * + * Return: Non-negative on Success/Negative on failure + * + *------------------------------------------------------------------------- + */ +herr_t +H5D__chunk_index_empty(const H5D_t *dset, hbool_t *empty) +{ + H5D_chk_idx_info_t idx_info; /* Chunked index info */ + H5D_rdcc_ent_t * ent; /* Cache entry */ + const H5D_rdcc_t * rdcc = NULL; /* Raw data chunk cache */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr) + + HDassert(dset); + HDassert(dset->shared); + HDassert(empty); + + rdcc = &(dset->shared->cache.chunk); /* raw data chunk cache */ + HDassert(rdcc); + + /* Search for cached chunks that haven't been written out */ + for (ent = rdcc->head; ent; ent = ent->next) + /* Flush the chunk out to disk, to make certain the size is correct later */ + if (H5D__chunk_flush_entry(dset, ent, FALSE) < 0) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer") + + /* Compose chunked index info struct */ + idx_info.f = dset->oloc.file; + idx_info.pline = &dset->shared->dcpl_cache.pline; + idx_info.layout = &dset->shared->layout.u.chunk; + idx_info.storage = &dset->shared->layout.storage.u.chunk; + + *empty = TRUE; + + if (H5F_addr_defined(idx_info.storage->idx_addr)) { + /* Iterate over the allocated chunks */ + if ((dset->shared->layout.storage.u.chunk.ops->iterate)(&idx_info, H5D__chunk_index_empty_cb, empty) < + 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, + "unable to retrieve allocated chunk information from index") + } + +done: + FUNC_LEAVE_NOAPI_TAG(ret_value) +} /* end H5D__chunk_index_empty() */ + +/*------------------------------------------------------------------------- * Function: H5D__get_num_chunks_cb * * Purpose: Callback function that increments the number of written diff --git a/src/H5Dint.c b/src/H5Dint.c index c9ea6bd..cc17265 100644 --- a/src/H5Dint.c +++ b/src/H5Dint.c @@ -378,40 +378,18 @@ H5D__get_space_status(const H5D_t *dset, H5D_space_status_t *allocation) /* Check for chunked layout */ if (dset->shared->layout.type == H5D_CHUNKED) { - hsize_t space_allocated; /* The number of bytes allocated for chunks */ - hssize_t snelmts; /* Temporary holder for number of elements in dataspace */ - hsize_t nelmts; /* Number of elements in dataspace */ - size_t dt_size; /* Size of datatype */ - hsize_t full_size; /* The number of bytes in the dataset when fully populated */ - - /* For chunked layout set the space status by the storage size */ - /* Get the dataset's dataspace */ - HDassert(dset->shared->space); - - /* Get the total number of elements in dataset's dataspace */ - if ((snelmts = H5S_GET_EXTENT_NPOINTS(dset->shared->space)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve number of elements in dataspace") - nelmts = (hsize_t)snelmts; - - /* Get the size of the dataset's datatype */ - if (0 == (dt_size = H5T_GET_SIZE(dset->shared->type))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve size of datatype") - - /* Compute the maximum size of the dataset in bytes */ - full_size = nelmts * dt_size; - - /* Check for overflow during multiplication */ - if (nelmts != (full_size / dt_size)) - HGOTO_ERROR(H5E_DATASET, H5E_OVERFLOW, FAIL, "size of dataset's storage overflowed") - - /* Difficult to error check, since the error value is 0 and 0 is a valid value... :-/ */ - if (H5D__get_storage_size(dset, &space_allocated) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get size of dataset's storage") - - /* Decide on how much of the space is allocated */ - if (space_allocated == 0) + hsize_t n_chunks_total = dset->shared->layout.u.chunk.nchunks; + hsize_t n_chunks_alloc = 0; + + if (H5D__get_num_chunks(dset, dset->shared->space, &n_chunks_alloc) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, + "unable to retrieve number of allocated chunks in dataset") + + HDassert(n_chunks_alloc <= n_chunks_total); + + if (n_chunks_alloc == 0) *allocation = H5D_SPACE_STATUS_NOT_ALLOCATED; - else if (space_allocated == full_size) + else if (n_chunks_alloc == n_chunks_total) *allocation = H5D_SPACE_STATUS_ALLOCATED; else *allocation = H5D_SPACE_STATUS_PART_ALLOCATED; @@ -1301,10 +1279,19 @@ H5D__create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, hid_t HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest indexing") } /* end if */ - /* Check if this dataset is going into a parallel file and set space allocation time */ + /* Check if the file driver would like to force early space allocation */ if (H5F_HAS_FEATURE(file, H5FD_FEAT_ALLOCATE_EARLY)) new_dset->shared->dcpl_cache.fill.alloc_time = H5D_ALLOC_TIME_EARLY; + /* + * Check if this dataset is going into a parallel file and set space allocation time. + * If the dataset has filters applied to it, writes to the dataset must be collective, + * so we don't need to force early space allocation. Otherwise, we force early space + * allocation to facilitate independent raw data operations. + */ + if (H5F_HAS_FEATURE(file, H5FD_FEAT_HAS_MPI) && (new_dset->shared->dcpl_cache.pline.nused == 0)) + new_dset->shared->dcpl_cache.fill.alloc_time = H5D_ALLOC_TIME_EARLY; + /* Set the dataset's I/O operations */ if (H5D__layout_set_io_ops(new_dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize I/O operations") diff --git a/src/H5Dio.c b/src/H5Dio.c index 1ea3f07..e226a0a 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -300,6 +300,7 @@ H5D__write(H5D_t *dataset, hid_t mem_type_id, H5S_t *mem_space, H5S_t *file_spac H5D_io_info_t io_info; /* Dataset I/O info */ H5D_type_info_t type_info; /* Datatype info for operation */ hbool_t type_info_init = FALSE; /* Whether the datatype info has been initialized */ + hbool_t should_alloc_space = FALSE; /* Whether or not to initialize dataset's storage */ H5S_t * projected_mem_space = NULL; /* If not NULL, ptr to dataspace containing a */ /* projection of the supplied mem_space to a new */ /* dataspace with rank equal to that of */ @@ -432,8 +433,20 @@ H5D__write(H5D_t *dataset, hid_t mem_type_id, H5S_t *mem_space, H5S_t *file_spac HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up I/O operation") /* Allocate dataspace and initialize it if it hasn't been. */ - if (nelmts > 0 && dataset->shared->dcpl_cache.efl.nused == 0 && - !(*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage)) { + should_alloc_space = dataset->shared->dcpl_cache.efl.nused == 0 && + !(*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage); + + /* + * If not using an MPI-based VFD, we only need to allocate + * and initialize storage if there's a selection in the + * dataset's dataspace. Otherwise, we always need to participate + * in the storage allocation since this may use collective + * operations and we will hang if we don't participate. + */ + if (!H5F_HAS_FEATURE(dataset->oloc.file, H5FD_FEAT_HAS_MPI)) + should_alloc_space = should_alloc_space && (nelmts > 0); + + if (should_alloc_space) { hssize_t file_nelmts; /* Number of elements in file dataset's dataspace */ hbool_t full_overwrite; /* Whether we are over-writing all the elements */ @@ -808,98 +821,35 @@ H5D__ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset, const H5S_t *file_ io_info->io_ops.single_write = H5D__mpio_select_write; } /* end if */ else { - int comm_size = 0; - - /* Retrieve size of MPI communicator used for file */ - if ((comm_size = H5F_shared_mpi_get_size(io_info->f_sh)) < 0) - HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "can't get MPI communicator size") - /* Check if there are any filters in the pipeline. If there are, * we cannot break to independent I/O if this is a write operation * with multiple ranks involved; otherwise, there will be metadata * inconsistencies in the file. */ - if (comm_size > 1 && io_info->op_type == H5D_IO_OP_WRITE && - io_info->dset->shared->dcpl_cache.pline.nused > 0) { - H5D_mpio_no_collective_cause_t cause; - uint32_t local_no_collective_cause; - uint32_t global_no_collective_cause; - hbool_t local_error_message_previously_written = FALSE; - hbool_t global_error_message_previously_written = FALSE; - size_t idx; - size_t cause_strings_len; - char local_no_collective_cause_string[512] = ""; - char global_no_collective_cause_string[512] = ""; - const char * cause_strings[] = { - "independent I/O was requested", - "datatype conversions were required", - "data transforms needed to be applied", - "optimized MPI types flag wasn't set", - "one of the dataspaces was neither simple nor scalar", - "dataset was not contiguous or chunked", - "parallel writes to filtered datasets are disabled", - "an error occurred while checking if collective I/O was possible"}; - - cause_strings_len = sizeof(cause_strings) / sizeof(cause_strings[0]); - - if (H5CX_get_mpio_local_no_coll_cause(&local_no_collective_cause) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, - "unable to get local no collective cause value") - if (H5CX_get_mpio_global_no_coll_cause(&global_no_collective_cause) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, - "unable to get global no collective cause value") - - /* Append each of the "reason for breaking collective I/O" error messages to the - * local and global no collective cause strings */ - for (cause = 1, idx = 0; - (cause < H5D_MPIO_NO_COLLECTIVE_MAX_CAUSE) && (idx < cause_strings_len); - cause <<= 1, idx++) { - if (cause & local_no_collective_cause) { - size_t local_buffer_space = sizeof(local_no_collective_cause_string) - - HDstrlen(local_no_collective_cause_string) - 1; - - /* Check if there were any previous error messages included. If so, prepend a - * semicolon to separate the messages. - */ - if (local_buffer_space && local_error_message_previously_written) { - HDstrncat(local_no_collective_cause_string, "; ", local_buffer_space); - local_buffer_space -= MIN(local_buffer_space, 2); - } - - if (local_buffer_space) - HDstrncat(local_no_collective_cause_string, cause_strings[idx], - local_buffer_space); - - local_error_message_previously_written = TRUE; - } /* end if */ - - if (cause & global_no_collective_cause) { - size_t global_buffer_space = sizeof(global_no_collective_cause_string) - - HDstrlen(global_no_collective_cause_string) - 1; - - /* Check if there were any previous error messages included. If so, prepend a - * semicolon to separate the messages. - */ - if (global_buffer_space && global_error_message_previously_written) { - HDstrncat(global_no_collective_cause_string, "; ", global_buffer_space); - global_buffer_space -= MIN(global_buffer_space, 2); - } - - if (global_buffer_space) - HDstrncat(global_no_collective_cause_string, cause_strings[idx], - global_buffer_space); - - global_error_message_previously_written = TRUE; - } /* end if */ - } /* end for */ - - HGOTO_ERROR(H5E_IO, H5E_NO_INDEPENDENT, FAIL, - "Can't perform independent write with filters in pipeline.\n" - " The following caused a break from collective I/O:\n" - " Local causes: %s\n" - " Global causes: %s", - local_no_collective_cause_string, global_no_collective_cause_string); - } /* end if */ + if (io_info->op_type == H5D_IO_OP_WRITE && io_info->dset->shared->dcpl_cache.pline.nused > 0) { + int comm_size = 0; + + /* Retrieve size of MPI communicator used for file */ + if ((comm_size = H5F_shared_mpi_get_size(io_info->f_sh)) < 0) + HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "can't get MPI communicator size") + + if (comm_size > 1) { + char local_no_coll_cause_string[512]; + char global_no_coll_cause_string[512]; + + if (H5D__mpio_get_no_coll_cause_strings(local_no_coll_cause_string, 512, + global_no_coll_cause_string, 512) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, + "can't get reasons for breaking collective I/O") + + HGOTO_ERROR(H5E_IO, H5E_NO_INDEPENDENT, FAIL, + "Can't perform independent write with filters in pipeline.\n" + " The following caused a break from collective I/O:\n" + " Local causes: %s\n" + " Global causes: %s", + local_no_coll_cause_string, global_no_coll_cause_string); + } + } /* If we won't be doing collective I/O, but the user asked for * collective I/O, change the request to use independent I/O diff --git a/src/H5Dlayout.c b/src/H5Dlayout.c index 6c4fc12..6fdec05 100644 --- a/src/H5Dlayout.c +++ b/src/H5Dlayout.c @@ -213,7 +213,7 @@ H5D__layout_meta_size(const H5F_t *f, const H5O_layout_t *layout, hbool_t includ ret_value++; /* Dimension sizes */ - ret_value += layout->u.chunk.ndims * layout->u.chunk.enc_bytes_per_dim; + ret_value += layout->u.chunk.ndims * (size_t)layout->u.chunk.enc_bytes_per_dim; /* Type of chunk index */ ret_value++; diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c index cf8a6ef..527fc7b 100644 --- a/src/H5Dmpio.c +++ b/src/H5Dmpio.c @@ -36,6 +36,7 @@ #include "H5Eprivate.h" /* Error handling */ #include "H5Fprivate.h" /* File access */ #include "H5FDprivate.h" /* File drivers */ +#include "H5FLprivate.h" /* Free Lists */ #include "H5Iprivate.h" /* IDs */ #include "H5MMprivate.h" /* Memory management */ #include "H5Oprivate.h" /* Object headers */ @@ -43,6 +44,15 @@ #include "H5Sprivate.h" /* Dataspaces */ #include "H5VMprivate.h" /* Vector */ +/* uthash is an external, header-only hash table implementation. + * + * We include the file directly in src/ and #define a few functions + * to use our internal memory calls. + */ +#define uthash_malloc(sz) H5MM_malloc(sz) +#define uthash_free(ptr, sz) H5MM_free(ptr) /* Ignoring sz is intentional */ +#include "uthash.h" + #ifdef H5_HAVE_PARALLEL /****************/ @@ -81,9 +91,54 @@ /* Macros to represent the regularity of the selection for multiple chunk IO case. */ #define H5D_CHUNK_SELECT_REG 1 +/* + * Threshold value for redistributing shared filtered chunks + * on all MPI ranks, or just MPI rank 0 + */ +#define H5D_CHUNK_REDISTRIBUTE_THRES ((size_t)((25 * H5_MB) / sizeof(H5D_chunk_redistribute_info_t))) + +/* + * Initial allocation size for the arrays that hold + * buffers for chunk modification data that is sent + * to other ranks and the MPI_Request objects for + * those send operations + */ +#define H5D_CHUNK_NUM_SEND_MSGS_INIT 64 + +/* + * Define a tag value for the MPI messages sent/received for + * chunk modification data + */ +#define H5D_CHUNK_MOD_DATA_TAG 64 + +/* + * Macro to initialize a H5D_chk_idx_info_t + * structure, given a pointer to a H5D_io_info_t + * structure + */ +#define H5D_MPIO_INIT_CHUNK_IDX_INFO(index_info, io_info_ptr) \ + do { \ + index_info.f = (io_info_ptr)->dset->oloc.file; \ + index_info.pline = &((io_info_ptr)->dset->shared->dcpl_cache.pline); \ + index_info.layout = &((io_info_ptr)->dset->shared->layout.u.chunk); \ + index_info.storage = &((io_info_ptr)->dset->shared->layout.storage.u.chunk); \ + } while (0) + +/* + * Macro to initialize a H5D_chunk_ud_t structure + * given a pointer to a H5D_chk_idx_info_t structure + */ +#define H5D_MPIO_INIT_CHUNK_UD_INFO(chunk_ud, index_info_ptr) \ + do { \ + HDmemset(&chunk_ud, 0, sizeof(H5D_chunk_ud_t)); \ + chunk_ud.common.layout = (index_info_ptr)->layout; \ + chunk_ud.common.storage = (index_info_ptr)->storage; \ + } while (0) + /******************/ /* Local Typedefs */ /******************/ + /* Combine chunk address and chunk info into a struct for better performance. */ typedef struct H5D_chunk_addr_info_t { haddr_t chunk_addr; @@ -100,115 +155,137 @@ typedef enum H5D_mpio_no_rank0_bcast_cause_t { } H5D_mpio_no_rank0_bcast_cause_t; /* + * Information necessary for re-allocating file space for a chunk + * during a parallel write of a chunked dataset with filters + * applied. + */ +typedef struct H5D_chunk_alloc_info_t { + H5F_block_t chunk_current; + H5F_block_t chunk_new; + hsize_t chunk_idx; +} H5D_chunk_alloc_info_t; + +/* + * Information for a chunk pertaining to the dataset's chunk + * index entry for the chunk + */ +typedef struct H5D_chunk_index_info_t { + hsize_t chunk_idx; + unsigned filter_mask; + hbool_t need_insert; +} H5D_chunk_index_info_t; + +/* * Information about a single chunk when performing collective filtered I/O. All * of the fields of one of these structs are initialized at the start of collective - * filtered I/O in the function H5D__construct_filtered_io_info_list(). + * filtered I/O in the function H5D__mpio_collective_filtered_chunk_io_setup(). This + * struct's fields are as follows: * - * This struct's fields are as follows: + * index_info - A structure containing the information needed when collectively + * re-inserting the chunk into the dataset's chunk index. The structure + * is distributed to all ranks during the re-insertion operation. Its fields + * are as follows: * - * index - The "Index" of the chunk in the dataset. The index of a chunk is used during - * the collective re-insertion of chunks into the chunk index after the collective - * I/O has been performed. + * chunk_idx - The index of the chunk in the dataset's chunk index. * - * scaled - The scaled coordinates of the chunk in the dataset's file dataspace. The - * coordinates are used in both the collective re-allocation of space in the file - * and the collective re-insertion of chunks into the chunk index after the collective - * I/O has been performed. + * filter_mask - A bit-mask that indicates which filters are to be applied to the + * chunk. Each filter in a chunk's filter pipeline has a bit position + * that can be masked to disable that particular filter for the chunk. + * This filter mask is saved alongside the chunk in the file. * - * full_overwrite - A flag which determines whether or not a chunk needs to be read from the - * file when being updated. If a chunk is being fully overwritten (the entire - * extent is selected in its file dataspace), then it is not necessary to - * read the chunk from the file. However, if the chunk is not being fully - * overwritten, it has to be read from the file in order to update the chunk - * without trashing the parts of the chunk that are not selected. + * need_insert - A flag which determines whether or not a chunk needs to be re-inserted into + * the chunk index after the write operation. * - * num_writers - The total number of processors writing to this chunk. This field is used - * when the new owner of a chunk is receiving messages, which contain selections in - * the chunk and data to update the chunk with, from other processors which have this - * chunk selected in the I/O operation. The new owner must know how many processors it - * should expect messages from so that it can post an equal number of receive calls. + * chunk_info - A pointer to the chunk's H5D_chunk_info_t structure, which contains useful + * information like the dataspaces containing the selection in the chunk. * - * io_size - The total size of I/O to this chunk. This field is an accumulation of the size of - * I/O to the chunk from each processor which has the chunk selected and is used to - * determine the value for the previous full_overwrite flag. + * chunk_current - The address in the file and size of this chunk before the filtering + * operation. When reading a chunk from the file, this field is used to + * read the correct amount of bytes. It is also used when redistributing + * shared chunks among MPI ranks and as a parameter to the chunk file + * space reallocation function. * - * buf - A pointer which serves the dual purpose of holding either the chunk data which is to be - * written to the file or the chunk data which has been read from the file. + * chunk_new - The address in the file and size of this chunk after the filtering + * operation. This field is relevant when collectively re-allocating space + * in the file for all of the chunks written to in the I/O operation, as + * their sizes may have changed after their data has been filtered. * - * chunk_states - In the case of dataset writes only, this struct is used to track a chunk's size and - * address in the file before and after the filtering operation has occurred. + * need_read - A flag which determines whether or not a chunk needs to be read from the + * file. During writes, if a chunk is being fully overwritten (the entire extent + * is selected in its file dataspace), then it is not necessary to read the chunk + * from the file. However, if the chunk is not being fully overwritten, it has to + * be read from the file in order to update the chunk without trashing the parts + * of the chunk that are not selected. During reads, this field should generally + * be true, but may be false if the chunk isn't allocated, for example. * - * Its fields are as follows: + * skip_filter_pline - A flag which determines whether to skip calls to the filter pipeline + * for this chunk. This flag is mostly useful for correct handling of + * partial edge chunks when the "don't filter partial edge chunks" flag + * is set on the dataset's DCPL. * - * chunk_current - The address in the file and size of this chunk before the filtering - * operation. When reading a chunk from the file, this field is used to - * read the correct amount of bytes. It is also used when redistributing - * shared chunks among processors and as a parameter to the chunk file - * space reallocation function. + * io_size - The total size of I/O to this chunk. This field is an accumulation of the size of + * I/O to the chunk from each MPI rank which has the chunk selected and is used to + * determine the value for the previous `full_overwrite` flag. * - * new_chunk - The address in the file and size of this chunk after the filtering - * operation. This field is relevant when collectively re-allocating space - * in the file for all of the chunks written to in the I/O operation, as - * their sizes may have changed after their data has been filtered. + * chunk_buf_size - The size in bytes of the data buffer allocated for the chunk * - * owners - In the case of dataset writes only, this struct is used to manage which single processor - * will ultimately write data out to the chunk. It allows the other processors to act according - * to the decision and send their selection in the chunk, as well as the data they wish - * to update the chunk with, to the processor which is writing to the chunk. + * orig_owner - The MPI rank which originally had this chunk selected at the beginning of + * the collective filtered I/O operation. This field is currently used when + * redistributing shared chunks among MPI ranks. * - * Its fields are as follows: + * new_owner - The MPI rank which has been selected to perform the modifications to this chunk. * - * original_owner - The processor which originally had this chunk selected at the beginning of - * the collective filtered I/O operation. This field is currently used when - * redistributing shared chunks among processors. + * num_writers - The total number of MPI ranks writing to this chunk. This field is used when + * the new owner of a chunk is receiving messages from other MPI ranks that + * contain their selections in the chunk and the data to update the chunk with. + * The new owner must know how many MPI ranks it should expect messages from so + * that it can post an equal number of receive calls. * - * new_owner - The processor which has been selected to perform the write to this chunk. + * buf - A pointer which serves the dual purpose of holding either the chunk data which is to be + * written to the file or the chunk data which has been read from the file. * - * async_info - In the case of dataset writes only, this struct is used by the owning processor of the - * chunk in order to manage the MPI send and receive calls made between it and all of - * the other processors which have this chunk selected in the I/O operation. + * hh - A handle for hash tables provided by the uthash.h header * - * Its fields are as follows: - * - * receive_requests_array - An array containing one MPI_Request for each of the - * asynchronous MPI receive calls the owning processor of this - * chunk makes to another processor in order to receive that - * processor's chunk modification data and selection in the chunk. - * - * receive_buffer_array - An array of buffers into which the owning processor of this chunk - * will store chunk modification data and the selection in the chunk - * received from another processor. - * - * num_receive_requests - The number of entries in the receive_request_array and - * receive_buffer_array fields. */ typedef struct H5D_filtered_collective_io_info_t { - hsize_t index; - hsize_t scaled[H5O_LAYOUT_NDIMS]; - hbool_t full_overwrite; - size_t num_writers; - size_t io_size; - void * buf; - - struct { - H5F_block_t chunk_current; - H5F_block_t new_chunk; - } chunk_states; - - struct { - int original_owner; - int new_owner; - } owners; - - struct { - MPI_Request * receive_requests_array; - unsigned char **receive_buffer_array; - int num_receive_requests; - } async_info; + H5D_chunk_index_info_t index_info; + + H5D_chunk_info_t *chunk_info; + H5F_block_t chunk_current; + H5F_block_t chunk_new; + hbool_t need_read; + hbool_t skip_filter_pline; + size_t io_size; + size_t chunk_buf_size; + int orig_owner; + int new_owner; + int num_writers; + void * buf; + + UT_hash_handle hh; } H5D_filtered_collective_io_info_t; -/* Function pointer typedef for sort function */ -typedef int (*H5D_mpio_sort_func_cb_t)(const void *, const void *); +/* + * Information necessary for redistributing shared chunks during + * a parallel write of a chunked dataset with filters applied. + */ +typedef struct H5D_chunk_redistribute_info_t { + H5F_block_t chunk_block; + hsize_t chunk_idx; + int orig_owner; + int new_owner; + int num_writers; +} H5D_chunk_redistribute_info_t; + +/* + * Information used when re-inserting a chunk into a dataset's + * chunk index during a parallel write of a chunked dataset with + * filters applied. + */ +typedef struct H5D_chunk_insert_info_t { + H5F_block_t chunk_block; + H5D_chunk_index_info_t index_info; +} H5D_chunk_insert_info_t; /********************/ /* Local Prototypes */ @@ -216,53 +293,98 @@ typedef int (*H5D_mpio_sort_func_cb_t)(const void *, const void *); static herr_t H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5D_chunk_map_t *fm); static herr_t H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - H5D_chunk_map_t *fm); + H5D_chunk_map_t *fm, int mpi_rank, int mpi_size); static herr_t H5D__multi_chunk_filtered_collective_io(H5D_io_info_t * io_info, - const H5D_type_info_t *type_info, H5D_chunk_map_t *fm); + const H5D_type_info_t *type_info, H5D_chunk_map_t *fm, + int mpi_rank, int mpi_size); static herr_t H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - H5D_chunk_map_t *fm, int sum_chunk); + H5D_chunk_map_t *fm, int sum_chunk, int mpi_rank, int mpi_size); static herr_t H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - H5D_chunk_map_t *fm); + H5D_chunk_map_t *fm, int mpi_rank, int mpi_size); static herr_t H5D__inter_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, const H5S_t *file_space, const H5S_t *mem_space); static herr_t H5D__final_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, MPI_Datatype mpi_file_type, MPI_Datatype mpi_buf_type); static herr_t H5D__sort_chunk(H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, - H5D_chunk_addr_info_t chunk_addr_info_array[], int many_chunk_opt); + H5D_chunk_addr_info_t chunk_addr_info_array[], int many_chunk_opt, int mpi_rank, + int mpi_size); static herr_t H5D__obtain_mpio_mode(H5D_io_info_t *io_info, H5D_chunk_map_t *fm, uint8_t assign_io_mode[], - haddr_t chunk_addr[]); + haddr_t chunk_addr[], int mpi_rank, int mpi_size); static herr_t H5D__mpio_get_sum_chunk(const H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, int *sum_chunkf); -static herr_t H5D__construct_filtered_io_info_list(const H5D_io_info_t * io_info, - const H5D_type_info_t * type_info, - const H5D_chunk_map_t * fm, - H5D_filtered_collective_io_info_t **chunk_list, - size_t * num_entries); -#if MPI_VERSION >= 3 -static herr_t H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t * io_info, - const H5D_type_info_t * type_info, - const H5D_chunk_map_t * fm, - H5D_filtered_collective_io_info_t *local_chunk_array, - size_t *local_chunk_array_num_entries); -#endif -static herr_t H5D__mpio_array_gatherv(void *local_array, size_t local_array_num_entries, - size_t array_entry_size, void **gathered_array, - size_t *gathered_array_num_entries, hbool_t allgather, int root, - MPI_Comm comm, int (*sort_func)(const void *, const void *)); -static herr_t H5D__mpio_filtered_collective_write_type(H5D_filtered_collective_io_info_t *chunk_list, - size_t num_entries, MPI_Datatype *new_mem_type, - hbool_t *mem_type_derived, MPI_Datatype *new_file_type, - hbool_t *file_type_derived); -static herr_t H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk_entry, - const H5D_io_info_t * io_info, - const H5D_type_info_t * type_info, - const H5D_chunk_map_t * fm); +static herr_t H5D__mpio_collective_filtered_chunk_io_setup(const H5D_io_info_t * io_info, + const H5D_type_info_t * type_info, + const H5D_chunk_map_t * fm, + H5D_filtered_collective_io_info_t **chunk_list, + size_t *num_entries, int mpi_rank); +static herr_t H5D__mpio_redistribute_shared_chunks(H5D_filtered_collective_io_info_t *chunk_list, + size_t chunk_list_num_entries, + const H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, + int mpi_rank, int mpi_size, + size_t **rank_chunks_assigned_map); +static herr_t H5D__mpio_redistribute_shared_chunks_int(H5D_filtered_collective_io_info_t *chunk_list, + size_t * num_chunks_assigned_map, + hbool_t all_ranks_involved, + const H5D_io_info_t * io_info, + const H5D_chunk_map_t *fm, int mpi_rank, int mpi_size); +static herr_t H5D__mpio_share_chunk_modification_data(H5D_filtered_collective_io_info_t *chunk_list, + size_t *chunk_list_num_entries, H5D_io_info_t *io_info, + const H5D_type_info_t *type_info, int mpi_rank, + int mpi_size, + H5D_filtered_collective_io_info_t **chunk_hash_table, + unsigned char *** chunk_msg_bufs, + int * chunk_msg_bufs_len); +static herr_t H5D__mpio_collective_filtered_chunk_common_io(H5D_filtered_collective_io_info_t *chunk_list, + size_t chunk_list_num_entries, + const H5D_io_info_t * io_info, + const H5D_type_info_t *type_info, int mpi_size); +static herr_t H5D__mpio_collective_filtered_chunk_read(H5D_filtered_collective_io_info_t *chunk_list, + size_t chunk_list_num_entries, + const H5D_io_info_t * io_info, + const H5D_type_info_t *type_info, int mpi_rank, + int mpi_size); +static herr_t H5D__mpio_collective_filtered_chunk_update(H5D_filtered_collective_io_info_t *chunk_list, + size_t chunk_list_num_entries, + H5D_filtered_collective_io_info_t *chunk_hash_table, + unsigned char ** chunk_msg_bufs, + int chunk_msg_bufs_len, const H5D_io_info_t *io_info, + const H5D_type_info_t *type_info, int mpi_rank, + int mpi_size); +static herr_t H5D__mpio_collective_filtered_chunk_reallocate(H5D_filtered_collective_io_info_t *chunk_list, + size_t chunk_list_num_entries, + size_t * num_chunks_assigned_map, + H5D_io_info_t * io_info, + H5D_chk_idx_info_t *idx_info, int mpi_rank, + int mpi_size); +static herr_t H5D__mpio_collective_filtered_chunk_reinsert(H5D_filtered_collective_io_info_t *chunk_list, + size_t chunk_list_num_entries, + size_t * num_chunks_assigned_map, + H5D_io_info_t * io_info, + H5D_chk_idx_info_t *idx_info, int mpi_rank, + int mpi_size); +static herr_t H5D__mpio_get_chunk_redistribute_info_types(MPI_Datatype *contig_type, + hbool_t * contig_type_derived, + MPI_Datatype *resized_type, + hbool_t * resized_type_derived); +static herr_t H5D__mpio_get_chunk_alloc_info_types(MPI_Datatype *contig_type, hbool_t *contig_type_derived, + MPI_Datatype *resized_type, hbool_t *resized_type_derived); +static herr_t H5D__mpio_get_chunk_insert_info_types(MPI_Datatype *contig_type, hbool_t *contig_type_derived, + MPI_Datatype *resized_type, + hbool_t * resized_type_derived); +static herr_t H5D__mpio_collective_filtered_io_type(H5D_filtered_collective_io_info_t *chunk_list, + size_t num_entries, H5D_io_op_type_t op_type, + MPI_Datatype *new_mem_type, hbool_t *mem_type_derived, + MPI_Datatype *new_file_type, hbool_t *file_type_derived); static int H5D__cmp_chunk_addr(const void *chunk_addr_info1, const void *chunk_addr_info2); static int H5D__cmp_filtered_collective_io_info_entry(const void *filtered_collective_io_info_entry1, const void *filtered_collective_io_info_entry2); -#if MPI_VERSION >= 3 -static int H5D__cmp_filtered_collective_io_info_entry_owner(const void *filtered_collective_io_info_entry1, - const void *filtered_collective_io_info_entry2); +static int H5D__cmp_chunk_redistribute_info(const void *entry1, const void *entry2); +static int H5D__cmp_chunk_redistribute_info_orig_owner(const void *entry1, const void *entry2); + +#ifdef H5Dmpio_DEBUG +static herr_t H5D__mpio_debug_init(void); +static herr_t H5D__mpio_dump_collective_filtered_chunk_list(H5D_filtered_collective_io_info_t *chunk_list, + size_t chunk_list_num_entries, int mpi_rank); #endif /*********************/ @@ -273,6 +395,188 @@ static int H5D__cmp_filtered_collective_io_info_entry_owner(const void *filtered /* Local Variables */ /*******************/ +/* Declare extern free list to manage the H5S_sel_iter_t struct */ +H5FL_EXTERN(H5S_sel_iter_t); + +#ifdef H5Dmpio_DEBUG + +/* Flags to control debug actions in this file. + * (Meant to be indexed by characters) + * + * These flags can be set with either (or both) the environment variable + * "H5D_mpio_Debug" set to a string containing one or more characters + * (flags) or by setting them as a string value for the + * "H5D_mpio_debug_key" MPI Info key. + * + * Supported characters in 'H5D_mpio_Debug' string: + * 't' trace function entry and exit + * 'f' log to file rather than debugging stream + * 'm' show (rough) memory usage statistics + * 'c' show critical timing information + * + * To only show output from a particular MPI rank, specify its rank + * number as a character, e.g.: + * + * '0' only show output from rank 0 + * + * To only show output from a particular range (up to 8 ranks supported + * between 0-9) of MPI ranks, specify the start and end ranks separated + * by a hyphen, e.g.: + * + * '0-7' only show output from ranks 0 through 7 + * + */ +static int H5D_mpio_debug_flags_s[256]; +static int H5D_mpio_debug_rank_s[8] = {-1, -1, -1, -1, -1, -1, -1, -1}; +static hbool_t H5D_mpio_debug_inited = FALSE; +static const char *const trace_in_pre = "-> "; +static const char *const trace_out_pre = "<- "; +static int debug_indent = 0; +static FILE * debug_stream = NULL; + +/* Determine if this rank should output debugging info */ +#define H5D_MPIO_DEBUG_THIS_RANK(rank) \ + (H5D_mpio_debug_rank_s[0] < 0 || rank == H5D_mpio_debug_rank_s[0] || rank == H5D_mpio_debug_rank_s[1] || \ + rank == H5D_mpio_debug_rank_s[2] || rank == H5D_mpio_debug_rank_s[3] || \ + rank == H5D_mpio_debug_rank_s[4] || rank == H5D_mpio_debug_rank_s[5] || \ + rank == H5D_mpio_debug_rank_s[6] || rank == H5D_mpio_debug_rank_s[7]) + +/* Print some debugging string */ +#define H5D_MPIO_DEBUG(rank, string) \ + do { \ + if (debug_stream && H5D_MPIO_DEBUG_THIS_RANK(rank)) { \ + HDfprintf(debug_stream, "%*s(Rank %d) " string "\n", debug_indent, "", rank); \ + fflush(debug_stream); \ + } \ + } while (0) + +/* Print some debugging string with printf-style arguments */ +#define H5D_MPIO_DEBUG_VA(rank, string, ...) \ + do { \ + if (debug_stream && H5D_MPIO_DEBUG_THIS_RANK(rank)) { \ + HDfprintf(debug_stream, "%*s(Rank %d) " string "\n", debug_indent, "", rank, __VA_ARGS__); \ + fflush(debug_stream); \ + } \ + } while (0) + +#define H5D_MPIO_TRACE_ENTER(rank) \ + do { \ + hbool_t trace_flag = H5D_mpio_debug_flags_s[(int)'t']; \ + \ + if (trace_flag) { \ + H5D_MPIO_DEBUG_VA(rank, "%s%s", trace_in_pre, __func__); \ + debug_indent += (int)strlen(trace_in_pre); \ + } \ + } while (0) + +#define H5D_MPIO_TRACE_EXIT(rank) \ + do { \ + hbool_t trace_flag = H5D_mpio_debug_flags_s[(int)'t']; \ + \ + if (trace_flag) { \ + debug_indent -= (int)strlen(trace_out_pre); \ + H5D_MPIO_DEBUG_VA(rank, "%s%s", trace_out_pre, __func__); \ + } \ + } while (0) + +#define H5D_MPIO_TIME_START(rank, op_name) \ + { \ + hbool_t time_flag = H5D_mpio_debug_flags_s[(int)'c']; \ + double start_time = 0.0, end_time = 0.0; \ + const char *const op = op_name; \ + \ + if (time_flag) { \ + start_time = MPI_Wtime(); \ + } + +#define H5D_MPIO_TIME_STOP(rank) \ + if (time_flag) { \ + end_time = MPI_Wtime(); \ + H5D_MPIO_DEBUG_VA(rank, "'%s' took %f seconds", op, (end_time - start_time)); \ + } \ + } + +/*--------------------------------------------------------------------------- + * Function: H5D__mpio_parse_debug_str + * + * Purpose: Parse a string for H5Dmpio-related debugging flags + * + * Returns: N/A + * + *--------------------------------------------------------------------------- + */ +static void +H5D__mpio_parse_debug_str(const char *s) +{ + FUNC_ENTER_STATIC_NOERR + + HDassert(s); + + while (*s) { + int c = (int)(*s); + + if (c >= (int)'0' && c <= (int)'9') { + hbool_t range = FALSE; + + if (*(s + 1) && *(s + 2)) + range = (int)*(s + 1) == '-' && (int)*(s + 2) >= (int)'0' && (int)*(s + 2) <= (int)'9'; + + if (range) { + int start_rank = c - (int)'0'; + int end_rank = (int)*(s + 2) - '0'; + int num_ranks = end_rank - start_rank + 1; + int i; + + if (num_ranks > 8) { + end_rank = start_rank + 7; + num_ranks = 8; + } + + for (i = 0; i < num_ranks; i++) + H5D_mpio_debug_rank_s[i] = start_rank++; + + s += 3; + } + else + H5D_mpio_debug_rank_s[0] = c - (int)'0'; + } + else + H5D_mpio_debug_flags_s[c]++; + + s++; + } + + FUNC_LEAVE_NOAPI_VOID +} + +static herr_t +H5D__mpio_debug_init(void) +{ + const char *debug_str; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_STATIC_NOERR + + HDassert(!H5D_mpio_debug_inited); + + /* Clear the debug flag buffer */ + HDmemset(H5D_mpio_debug_flags_s, 0, sizeof(H5D_mpio_debug_flags_s)); + + /* Retrieve and parse the H5Dmpio debug string */ + debug_str = HDgetenv("H5D_mpio_Debug"); + if (debug_str) + H5D__mpio_parse_debug_str(debug_str); + + if (H5DEBUG(D)) + debug_stream = H5DEBUG(D); + + H5D_mpio_debug_inited = TRUE; + + FUNC_LEAVE_NOAPI(ret_value) +} + +#endif + /*------------------------------------------------------------------------- * Function: H5D__mpio_opt_possible * @@ -347,14 +651,9 @@ H5D__mpio_opt_possible(const H5D_io_info_t *io_info, const H5S_t *file_space, co * use collective IO will defer until each chunk IO is reached. */ -#if MPI_VERSION < 3 - /* - * Don't allow parallel writes to filtered datasets if the MPI version - * is less than 3. The functions needed (MPI_Mprobe and MPI_Imrecv) will - * not be available. - */ - if (io_info->op_type == H5D_IO_OP_WRITE && io_info->dset->shared->layout.type == H5D_CHUNKED && - io_info->dset->shared->dcpl_cache.pline.nused > 0) +#ifndef H5_HAVE_PARALLEL_FILTERED_WRITES + /* Don't allow writes to filtered datasets if the functionality is disabled */ + if (io_info->op_type == H5D_IO_OP_WRITE && io_info->dset->shared->dcpl_cache.pline.nused > 0) local_cause[0] |= H5D_MPIO_PARALLEL_FILTERED_WRITES_DISABLED; #endif @@ -437,6 +736,150 @@ done: } /* H5D__mpio_opt_possible() */ /*------------------------------------------------------------------------- + * Function: H5D__mpio_get_no_coll_cause_strings + * + * Purpose: When collective I/O is broken internally, it can be useful + * for users to see a representative string for the reason(s) + * why it was broken. This routine inspects the current + * "cause" flags from the API context and prints strings into + * the caller's buffers for the local and global reasons that + * collective I/O was broken. + * + * Return: Non-negative on success/Negative on failure + * + *------------------------------------------------------------------------- + */ +herr_t +H5D__mpio_get_no_coll_cause_strings(char *local_cause, size_t local_cause_len, char *global_cause, + size_t global_cause_len) +{ + uint32_t local_no_coll_cause; + uint32_t global_no_coll_cause; + size_t local_cause_bytes_written = 0; + size_t global_cause_bytes_written = 0; + int nbits; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_PACKAGE + + HDassert((local_cause && local_cause_len > 0) || (global_cause && global_cause_len > 0)); + + /* + * Use compile-time assertion so this routine is updated + * when any new "no collective cause" values are added + */ + HDcompile_assert(H5D_MPIO_NO_COLLECTIVE_MAX_CAUSE == (H5D_mpio_no_collective_cause_t)256); + + /* Initialize output buffers */ + if (local_cause) + *local_cause = '\0'; + if (global_cause) + *global_cause = '\0'; + + /* Retrieve the local and global cause flags from the API context */ + if (H5CX_get_mpio_local_no_coll_cause(&local_no_coll_cause) < 0) + HGOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, "unable to get local no collective cause value") + if (H5CX_get_mpio_global_no_coll_cause(&global_no_coll_cause) < 0) + HGOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, "unable to get global no collective cause value") + + /* + * Append each of the "reason for breaking collective I/O" + * error messages to the local and global cause string buffers + */ + nbits = 8 * sizeof(local_no_coll_cause); + for (int bit_pos = 0; bit_pos < nbits; bit_pos++) { + H5D_mpio_no_collective_cause_t cur_cause; + const char * cause_str; + size_t buf_space_left; + + cur_cause = (H5D_mpio_no_collective_cause_t)(1 << bit_pos); + if (cur_cause == H5D_MPIO_NO_COLLECTIVE_MAX_CAUSE) + break; + + switch (cur_cause) { + case H5D_MPIO_SET_INDEPENDENT: + cause_str = "independent I/O was requested"; + break; + case H5D_MPIO_DATATYPE_CONVERSION: + cause_str = "datatype conversions were required"; + break; + case H5D_MPIO_DATA_TRANSFORMS: + cause_str = "data transforms needed to be applied"; + break; + case H5D_MPIO_MPI_OPT_TYPES_ENV_VAR_DISABLED: + cause_str = "optimized MPI types flag wasn't set"; + break; + case H5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES: + cause_str = "one of the dataspaces was neither simple nor scalar"; + break; + case H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET: + cause_str = "dataset was not contiguous or chunked"; + break; + case H5D_MPIO_PARALLEL_FILTERED_WRITES_DISABLED: + cause_str = "parallel writes to filtered datasets are disabled"; + break; + case H5D_MPIO_ERROR_WHILE_CHECKING_COLLECTIVE_POSSIBLE: + cause_str = "an error occurred while checking if collective I/O was possible"; + break; + case H5D_MPIO_COLLECTIVE: + case H5D_MPIO_NO_COLLECTIVE_MAX_CAUSE: + default: + HDassert(0 && "invalid no collective cause reason"); + break; + } + + /* + * Determine if the local reasons for breaking collective I/O + * included the current cause + */ + if (local_cause && (cur_cause & local_no_coll_cause)) { + buf_space_left = local_cause_len - local_cause_bytes_written; + + /* + * Check if there were any previous error messages included. If + * so, prepend a semicolon to separate the messages. + */ + if (buf_space_left && local_cause_bytes_written) { + HDstrncat(local_cause, "; ", buf_space_left); + local_cause_bytes_written += MIN(buf_space_left, 2); + buf_space_left -= MIN(buf_space_left, 2); + } + + if (buf_space_left) { + HDstrncat(local_cause, cause_str, buf_space_left); + local_cause_bytes_written += MIN(buf_space_left, HDstrlen(cause_str)); + } + } + + /* + * Determine if the global reasons for breaking collective I/O + * included the current cause + */ + if (global_cause && (cur_cause & global_no_coll_cause)) { + buf_space_left = global_cause_len - global_cause_bytes_written; + + /* + * Check if there were any previous error messages included. If + * so, prepend a semicolon to separate the messages. + */ + if (buf_space_left && global_cause_bytes_written) { + HDstrncat(global_cause, "; ", buf_space_left); + global_cause_bytes_written += MIN(buf_space_left, 2); + buf_space_left -= MIN(buf_space_left, 2); + } + + if (buf_space_left) { + HDstrncat(global_cause, cause_str, buf_space_left); + global_cause_bytes_written += MIN(buf_space_left, HDstrlen(cause_str)); + } + } + } + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__mpio_get_no_coll_cause_strings() */ + +/*------------------------------------------------------------------------- * Function: H5D__mpio_select_read * * Purpose: MPI-IO function to read directly from app buffer to file. @@ -500,145 +943,6 @@ done: } /* end H5D__mpio_select_write() */ /*------------------------------------------------------------------------- - * Function: H5D__mpio_array_gatherv - * - * Purpose: Given an array, specified in local_array, by each processor - * calling this function, collects each array into a single - * array which is then either gathered to the processor - * specified by root, when allgather is false, or is - * distributed back to all processors when allgather is true. - * - * The number of entries in the array contributed by an - * individual processor and the size of each entry should be - * specified in local_array_num_entries and array_entry_size, - * respectively. - * - * The MPI communicator to use should be specified for comm. - * - * If the sort_func argument is supplied, the array is sorted - * before the function returns. - * - * Note: if allgather is specified as true, root is ignored. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Jordan Henderson - * Sunday, April 9th, 2017 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D__mpio_array_gatherv(void *local_array, size_t local_array_num_entries, size_t array_entry_size, - void **_gathered_array, size_t *_gathered_array_num_entries, hbool_t allgather, - int root, MPI_Comm comm, H5D_mpio_sort_func_cb_t sort_func) -{ - size_t gathered_array_num_entries = 0; /* The size of the newly-constructed array */ - void * gathered_array = NULL; /* The newly-constructed array returned to the caller */ - int *receive_counts_array = NULL; /* Array containing number of entries each processor is contributing */ - int *displacements_array = - NULL; /* Array of displacements where each processor places its data in the final array */ - int mpi_code, mpi_rank, mpi_size; - int sendcount; - herr_t ret_value = SUCCEED; - - FUNC_ENTER_STATIC - - HDassert(_gathered_array); - HDassert(_gathered_array_num_entries); - - MPI_Comm_size(comm, &mpi_size); - MPI_Comm_rank(comm, &mpi_rank); - - /* Determine the size of the end result array by collecting the number - * of entries contributed by each processor into a single total. - */ - if (MPI_SUCCESS != (mpi_code = MPI_Allreduce(&local_array_num_entries, &gathered_array_num_entries, 1, - MPI_INT, MPI_SUM, comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code) - - /* If 0 entries resulted from the collective operation, no processor is contributing anything and there is - * nothing to do */ - if (gathered_array_num_entries > 0) { - /* - * If gathering to all processors, all processors need to allocate space for the resulting array, as - * well as the receive counts and displacements arrays for the collective MPI_Allgatherv call. - * Otherwise, only the root processor needs to allocate the space for an MPI_Gatherv call. - */ - if (allgather || (mpi_rank == root)) { - if (NULL == (gathered_array = H5MM_malloc(gathered_array_num_entries * array_entry_size))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate gathered array") - - if (NULL == (receive_counts_array = (int *)H5MM_malloc((size_t)mpi_size * sizeof(int)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate receive counts array") - - if (NULL == (displacements_array = (int *)H5MM_malloc((size_t)mpi_size * sizeof(int)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate receive displacements array") - } /* end if */ - - /* - * If gathering to all processors, inform each processor of how many entries each other processor is - * contributing to the resulting array by collecting the counts into each processor's "receive counts" - * array. Otherwise, inform only the root processor of how many entries each other processor is - * contributing. - */ - if (allgather) { - if (MPI_SUCCESS != (mpi_code = MPI_Allgather(&local_array_num_entries, 1, MPI_INT, - receive_counts_array, 1, MPI_INT, comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Allgather failed", mpi_code) - } /* end if */ - else { - if (MPI_SUCCESS != (mpi_code = MPI_Gather(&local_array_num_entries, 1, MPI_INT, - receive_counts_array, 1, MPI_INT, root, comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Gather failed", mpi_code) - } /* end else */ - - if (allgather || (mpi_rank == root)) { - size_t i; - - /* Multiply each receive count by the size of the array entry, since the data is sent as bytes. */ - for (i = 0; i < (size_t)mpi_size; i++) - H5_CHECKED_ASSIGN(receive_counts_array[i], int, - (size_t)receive_counts_array[i] * array_entry_size, size_t); - - /* Set receive buffer offsets for the collective MPI_Allgatherv/MPI_Gatherv call. */ - displacements_array[0] = 0; - for (i = 1; i < (size_t)mpi_size; i++) - displacements_array[i] = displacements_array[i - 1] + receive_counts_array[i - 1]; - } /* end if */ - - /* As the data is sent as bytes, calculate the true sendcount for the data. */ - H5_CHECKED_ASSIGN(sendcount, int, local_array_num_entries *array_entry_size, size_t); - - if (allgather) { - if (MPI_SUCCESS != - (mpi_code = MPI_Allgatherv(local_array, sendcount, MPI_BYTE, gathered_array, - receive_counts_array, displacements_array, MPI_BYTE, comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Allgatherv failed", mpi_code) - } /* end if */ - else { - if (MPI_SUCCESS != - (mpi_code = MPI_Gatherv(local_array, sendcount, MPI_BYTE, gathered_array, - receive_counts_array, displacements_array, MPI_BYTE, root, comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Gatherv failed", mpi_code) - } /* end else */ - - if (sort_func && (allgather || (mpi_rank == root))) - HDqsort(gathered_array, gathered_array_num_entries, array_entry_size, sort_func); - } /* end if */ - - *_gathered_array = gathered_array; - *_gathered_array_num_entries = gathered_array_num_entries; - -done: - if (receive_counts_array) - H5MM_free(receive_counts_array); - if (displacements_array) - H5MM_free(displacements_array); - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D__mpio_array_gatherv() */ - -/*------------------------------------------------------------------------- * Function: H5D__mpio_get_sum_chunk * * Purpose: Routine for obtaining total number of chunks to cover @@ -793,11 +1097,17 @@ static herr_t H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5D_chunk_map_t *fm) { H5FD_mpio_chunk_opt_t chunk_opt_mode; - int io_option = H5D_MULTI_CHUNK_IO_MORE_OPT; - int sum_chunk = -1; +#ifdef H5Dmpio_DEBUG + hbool_t log_file_flag = FALSE; + FILE * debug_log_file = NULL; +#endif #ifdef H5_HAVE_INSTRUMENTED_LIBRARY htri_t temp_not_link_io = FALSE; #endif + int io_option = H5D_MULTI_CHUNK_IO_MORE_OPT; + int sum_chunk = -1; + int mpi_rank; + int mpi_size; herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC @@ -808,9 +1118,35 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf HDassert(type_info); HDassert(fm); - /* Disable collective metadata reads for chunked dataset I/O operations - * in order to prevent potential hangs */ - H5CX_set_coll_metadata_read(FALSE); + /* Obtain the current rank of the process and the number of ranks */ + if ((mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file)) < 0) + HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain MPI rank") + if ((mpi_size = H5F_mpi_get_size(io_info->dset->oloc.file)) < 0) + HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain MPI size") + +#ifdef H5Dmpio_DEBUG + /* Initialize file-level debugging if not initialized */ + if (!H5D_mpio_debug_inited && H5D__mpio_debug_init() < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize H5Dmpio debugging") + + /* Open file for debugging if necessary */ + log_file_flag = H5D_mpio_debug_flags_s[(int)'f']; + if (log_file_flag) { + char debug_log_filename[1024]; + time_t time_now; + + HDsnprintf(debug_log_filename, 1024, "H5Dmpio_debug.rank%d", mpi_rank); + + if (NULL == (debug_log_file = HDfopen(debug_log_filename, "a"))) + HGOTO_ERROR(H5E_IO, H5E_OPENERROR, FAIL, "couldn't open debugging log file") + + /* Print a short header for this I/O operation */ + time_now = time(NULL); + HDfprintf(debug_log_file, "##### %s", asctime(localtime(&time_now))); + + debug_stream = debug_log_file; + } +#endif /* Check the optional property list for the collective chunk IO optimization option */ if (H5CX_get_mpio_chunk_opt_mode(&chunk_opt_mode) < 0) @@ -824,13 +1160,10 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf /* via default path. branch by num threshold */ else { unsigned one_link_chunk_io_threshold; /* Threshold to use single collective I/O for all chunks */ - int mpi_size; /* Number of processes in MPI job */ if (H5D__mpio_get_sum_chunk(io_info, fm, &sum_chunk) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSWAP, FAIL, "unable to obtain the total chunk number of all processes"); - if ((mpi_size = H5F_mpi_get_size(io_info->dset->oloc.file)) < 0) - HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi size") /* Get the chunk optimization option threshold */ if (H5CX_get_mpio_chunk_opt_num(&one_link_chunk_io_threshold) < 0) @@ -876,22 +1209,12 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf case H5D_ONE_LINK_CHUNK_IO_MORE_OPT: /* Check if there are any filters in the pipeline */ if (io_info->dset->shared->dcpl_cache.pline.nused > 0) { - /* For now, Multi-chunk IO must be forced for parallel filtered read, - * so that data can be unfiltered as it is received. There is significant - * complexity in unfiltering the data when it is read all at once into a - * single buffer. - */ - if (io_info->op_type == H5D_IO_OP_READ) { - if (H5D__multi_chunk_filtered_collective_io(io_info, type_info, fm) < 0) - HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, - "couldn't finish optimized multiple filtered chunk MPI-IO") - } /* end if */ - else if (H5D__link_chunk_filtered_collective_io(io_info, type_info, fm) < 0) + if (H5D__link_chunk_filtered_collective_io(io_info, type_info, fm, mpi_rank, mpi_size) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish filtered linked chunk MPI-IO") } /* end if */ else /* Perform unfiltered link chunk collective IO */ - if (H5D__link_chunk_collective_io(io_info, type_info, fm, sum_chunk) < 0) + if (H5D__link_chunk_collective_io(io_info, type_info, fm, sum_chunk, mpi_rank, mpi_size) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish linked chunk MPI-IO") break; @@ -899,18 +1222,28 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf default: /* multiple chunk IO via threshold */ /* Check if there are any filters in the pipeline */ if (io_info->dset->shared->dcpl_cache.pline.nused > 0) { - if (H5D__multi_chunk_filtered_collective_io(io_info, type_info, fm) < 0) + if (H5D__multi_chunk_filtered_collective_io(io_info, type_info, fm, mpi_rank, mpi_size) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish optimized multiple filtered chunk MPI-IO") } /* end if */ else /* Perform unfiltered multi chunk collective IO */ - if (H5D__multi_chunk_collective_io(io_info, type_info, fm) < 0) + if (H5D__multi_chunk_collective_io(io_info, type_info, fm, mpi_rank, mpi_size) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish optimized multiple chunk MPI-IO") break; } /* end switch */ done: +#ifdef H5Dmpio_DEBUG + /* Close debugging log file */ + if (debug_log_file) { + HDfprintf(debug_log_file, "##############\n\n"); + if (EOF == HDfclose(debug_log_file)) + HDONE_ERROR(H5E_IO, H5E_CLOSEERROR, FAIL, "couldn't close debugging log file") + debug_stream = H5DEBUG(D); + } +#endif + FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_collective_io */ @@ -993,7 +1326,7 @@ done: */ static herr_t H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5D_chunk_map_t *fm, - int sum_chunk) + int sum_chunk, int mpi_rank, int mpi_size) { H5D_chunk_addr_info_t *chunk_addr_info_array = NULL; MPI_Datatype chunk_final_mtype; /* Final memory MPI datatype for all chunks with selection */ @@ -1074,9 +1407,8 @@ H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *typ /* Set up the base storage address for this chunk */ io_info->store = &ctg_store; -#ifdef H5D_DEBUG - if (H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "before inter_collective_io for total chunk = 1 \n"); +#ifdef H5Dmpio_DEBUG + H5D_MPIO_DEBUG(mpi_rank, "before inter_collective_io for total chunk = 1"); #endif /* Perform I/O */ @@ -1092,9 +1424,8 @@ H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *typ num_chunk = H5SL_count(fm->sel_chunks); H5_CHECK_OVERFLOW(num_chunk, size_t, int); -#ifdef H5D_DEBUG - if (H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "total_chunks = %zu, num_chunk = %zu\n", total_chunks, num_chunk); +#ifdef H5Dmpio_DEBUG + H5D_MPIO_DEBUG_VA(mpi_rank, "total_chunks = %zu, num_chunk = %zu", total_chunks, num_chunk); #endif /* Set up MPI datatype for chunks selected */ @@ -1125,18 +1456,17 @@ H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *typ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk file is derived datatype flags buffer") -#ifdef H5D_DEBUG - if (H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "before sorting the chunk address \n"); +#ifdef H5Dmpio_DEBUG + H5D_MPIO_DEBUG(mpi_rank, "before sorting chunk addresses"); #endif + /* Sort the chunk address */ - if (H5D__sort_chunk(io_info, fm, chunk_addr_info_array, sum_chunk) < 0) + if (H5D__sort_chunk(io_info, fm, chunk_addr_info_array, sum_chunk, mpi_rank, mpi_size) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSWAP, FAIL, "unable to sort chunk address") ctg_store.contig.dset_addr = chunk_addr_info_array[0].chunk_addr; -#ifdef H5D_DEBUG - if (H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "after sorting the chunk address \n"); +#ifdef H5Dmpio_DEBUG + H5D_MPIO_DEBUG(mpi_rank, "after sorting chunk addresses"); #endif /* Obtain MPI derived datatype from all individual chunks */ @@ -1241,9 +1571,9 @@ H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *typ /* No chunks selected for this process */ mpi_buf_count = (hsize_t)0; } /* end else */ -#ifdef H5D_DEBUG - if (H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "before coming to final collective IO\n"); + +#ifdef H5Dmpio_DEBUG + H5D_MPIO_DEBUG(mpi_rank, "before coming to final collective I/O"); #endif /* Set up the base storage address for this chunk */ @@ -1256,11 +1586,11 @@ H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *typ } /* end else */ done: -#ifdef H5D_DEBUG - if (H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "before freeing memory inside H5D_link_collective_io ret_value = %d\n", - ret_value); +#ifdef H5Dmpio_DEBUG + H5D_MPIO_DEBUG_VA(mpi_rank, "before freeing memory inside H5D_link_collective_io ret_value = %d", + ret_value); #endif + /* Release resources */ if (chunk_addr_info_array) H5MM_xfree(chunk_addr_info_array); @@ -1293,68 +1623,89 @@ done: /*------------------------------------------------------------------------- * Function: H5D__link_chunk_filtered_collective_io * - * Purpose: Routine for one collective IO with one MPI derived datatype - * to link with all filtered chunks - * - * 1. Construct a list of selected chunks in the collective IO - * operation - * A. If any chunk is being written to by more than 1 - * process, the process writing to the chunk which - * currently has the least amount of chunks assigned - * to it becomes the new owner (in the case of ties, - * the lowest MPI rank becomes the new owner) - * 2. If the operation is a write operation - * A. Loop through each chunk in the operation - * I. If this is not a full overwrite of the chunk - * a) Read the chunk from file and pass the chunk - * through the filter pipeline in reverse order - * (Unfilter the chunk) + * Purpose: Performs collective I/O on filtered chunks by creating a + * single MPI derived datatype to link with all filtered + * chunks. The general algorithm is as follows: + * + * 1. Construct a list of selected chunks in the collective + * I/O operation + * 2. If the operation is a read operation + * A. Ensure that the list of chunks is sorted in + * monotonically non-decreasing order of chunk offset + * in the file + * B. Participate in a collective read of chunks from + * the file + * C. Loop through each selected chunk, unfiltering it and + * scattering the data to the application's read buffer + * 3. If the operation is a write operation + * A. Redistribute any chunks being written by more than 1 + * MPI rank, such that the chunk is only owned by 1 MPI + * rank. The rank writing to the chunk which currently + * has the least amount of chunks assigned to it becomes + * the new owner (in the case of ties, the lowest MPI + * rank becomes the new owner) + * B. Participate in a collective read of chunks from the + * file + * C. Loop through each chunk selected in the operation + * and for each chunk: + * I. If we actually read the chunk from the file (if + * a chunk is being fully overwritten, we skip + * reading it), pass the chunk through the filter + * pipeline in reverse order (unfilter the chunk) * II. Update the chunk data with the modifications from - * the owning process + * the owning MPI rank * III. Receive any modification data from other - * processes and update the chunk data with these + * ranks and update the chunk data with those * modifications * IV. Filter the chunk - * B. Contribute the modified chunks to an array gathered - * by all processes which contains the new sizes of - * every chunk modified in the collective IO operation - * C. All processes collectively re-allocate each chunk - * from the gathered array with their new sizes after - * the filter operation - * D. If this process has any chunks selected in the IO - * operation, create an MPI derived type for memory and - * file to write out the process' selected chunks to the - * file - * E. Perform the collective write - * F. All processes collectively re-insert each modified + * D. Contribute the modified chunks to an array gathered + * by all ranks which contains information for + * re-allocating space in the file for every chunk + * modified. Then, each rank collectively re-allocates + * each chunk from the gathered array with their new + * sizes after the filter operation + * E. Proceed with the collective write operation for all + * the modified chunks + * F. Contribute the modified chunks to an array gathered + * by all ranks which contains information for + * re-inserting every chunk modified into the chunk + * index. Then, each rank collectively re-inserts each * chunk from the gathered array into the chunk index * + * TODO: Note that steps D. and F. here are both collective + * operations that partially share data from the + * H5D_filtered_collective_io_info_t structure. To + * try to conserve on memory a bit, the distributed + * arrays these operations create are discarded after + * each operation is performed. If memory consumption + * here proves to not be an issue, the necessary data + * for both operations could be combined into a single + * structure so that only one collective MPI operation + * is needed to carry out both operations, rather than + * two. * * Return: Non-negative on success/Negative on failure * - * Programmer: Jordan Henderson - * Friday, Nov. 4th, 2016 - * *------------------------------------------------------------------------- */ static herr_t H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - H5D_chunk_map_t *fm) + H5D_chunk_map_t *fm, int mpi_rank, int mpi_size) { - H5D_filtered_collective_io_info_t *chunk_list = NULL; /* The list of chunks being read/written */ - H5D_filtered_collective_io_info_t *collective_chunk_list = - NULL; /* The list of chunks used during collective operations */ - H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */ - MPI_Datatype mem_type = MPI_BYTE; - MPI_Datatype file_type = MPI_BYTE; - hbool_t mem_type_is_derived = FALSE; - hbool_t file_type_is_derived = FALSE; - size_t chunk_list_num_entries; - size_t collective_chunk_list_num_entries; - size_t * num_chunks_selected_array = NULL; /* Array of number of chunks selected on each process */ - size_t i; /* Local index variable */ - int mpi_rank, mpi_size, mpi_code; - herr_t ret_value = SUCCEED; + H5D_filtered_collective_io_info_t *chunk_list = NULL; /* The list of chunks being read/written */ + H5D_filtered_collective_io_info_t *chunk_hash_table = NULL; + unsigned char ** chunk_msg_bufs = NULL; + H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */ + MPI_Datatype mem_type = MPI_BYTE; + MPI_Datatype file_type = MPI_BYTE; + hbool_t mem_type_is_derived = FALSE; + hbool_t file_type_is_derived = FALSE; + size_t * rank_chunks_assigned_map = NULL; + size_t chunk_list_num_entries; + size_t i; + int chunk_msg_bufs_len = 0; + int mpi_code; + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC @@ -1362,11 +1713,12 @@ H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_in HDassert(type_info); HDassert(fm); - /* Obtain the current rank of the process and the number of processes */ - if ((mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file)) < 0) - HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi rank") - if ((mpi_size = H5F_mpi_get_size(io_info->dset->oloc.file)) < 0) - HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi size") +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TRACE_ENTER(mpi_rank); + H5D_MPIO_DEBUG_VA(mpi_rank, "Performing Linked-chunk I/O (%s) with MPI Comm size of %d", + io_info->op_type == H5D_IO_OP_WRITE ? "write" : "read", mpi_size); + H5D_MPIO_TIME_START(mpi_rank, "Linked-chunk I/O"); +#endif /* Set the actual-chunk-opt-mode property. */ H5CX_set_mpio_actual_chunk_opt(H5D_MPIO_LINK_CHUNK); @@ -1377,123 +1729,127 @@ H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_in H5CX_set_mpio_actual_io_mode(H5D_MPIO_CHUNK_COLLECTIVE); /* Build a list of selected chunks in the collective io operation */ - if (H5D__construct_filtered_io_info_list(io_info, type_info, fm, &chunk_list, &chunk_list_num_entries) < - 0) + if (H5D__mpio_collective_filtered_chunk_io_setup(io_info, type_info, fm, &chunk_list, + &chunk_list_num_entries, mpi_rank) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "couldn't construct filtered I/O info list") - if (io_info->op_type == H5D_IO_OP_WRITE) { /* Filtered collective write */ + if (io_info->op_type == H5D_IO_OP_READ) { /* Filtered collective read */ + if (H5D__mpio_collective_filtered_chunk_read(chunk_list, chunk_list_num_entries, io_info, type_info, + mpi_rank, mpi_size) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't read filtered chunks") + } + else { /* Filtered collective write */ H5D_chk_idx_info_t index_info; - H5D_chunk_ud_t udata; hsize_t mpi_buf_count; - /* Construct chunked index info */ - index_info.f = io_info->dset->oloc.file; - index_info.pline = &(io_info->dset->shared->dcpl_cache.pline); - index_info.layout = &(io_info->dset->shared->layout.u.chunk); - index_info.storage = &(io_info->dset->shared->layout.storage.u.chunk); - - /* Set up chunk information for insertion to chunk index */ - udata.common.layout = index_info.layout; - udata.common.storage = index_info.storage; - udata.filter_mask = 0; - - /* Iterate through all the chunks in the collective write operation, - * updating each chunk with the data modifications from other processes, - * then re-filtering the chunk. - */ - for (i = 0; i < chunk_list_num_entries; i++) - if (mpi_rank == chunk_list[i].owners.new_owner) - if (H5D__filtered_collective_chunk_entry_io(&chunk_list[i], io_info, type_info, fm) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "couldn't process chunk entry") - - /* Gather the new chunk sizes to all processes for a collective reallocation - * of the chunks in the file. + H5D_MPIO_INIT_CHUNK_IDX_INFO(index_info, io_info); + + if (mpi_size > 1) { + /* Redistribute shared chunks being written to */ + if (H5D__mpio_redistribute_shared_chunks(chunk_list, chunk_list_num_entries, io_info, fm, + mpi_rank, mpi_size, &rank_chunks_assigned_map) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to redistribute shared chunks") + + /* Send any chunk modification messages for chunks this rank no longer owns */ + if (H5D__mpio_share_chunk_modification_data(chunk_list, &chunk_list_num_entries, io_info, + type_info, mpi_rank, mpi_size, &chunk_hash_table, + &chunk_msg_bufs, &chunk_msg_bufs_len) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, + "unable to send chunk modification data between MPI ranks") + + /* Make sure the local chunk list was updated correctly */ + HDassert(chunk_list_num_entries == rank_chunks_assigned_map[mpi_rank]); + } + + /* Proceed to update all the chunks this rank owns with its own + * modification data and data from other ranks, before re-filtering + * the chunks. As chunk reads are done collectively here, all ranks + * must participate. */ - if (H5D__mpio_array_gatherv(chunk_list, chunk_list_num_entries, - sizeof(H5D_filtered_collective_io_info_t), - (void **)&collective_chunk_list, &collective_chunk_list_num_entries, true, - 0, io_info->comm, NULL) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL, "couldn't gather new chunk sizes") - - /* Collectively re-allocate the modified chunks (from each process) in the file */ - for (i = 0; i < collective_chunk_list_num_entries; i++) { - hbool_t insert; - - if (H5D__chunk_file_alloc(&index_info, &collective_chunk_list[i].chunk_states.chunk_current, - &collective_chunk_list[i].chunk_states.new_chunk, &insert, - collective_chunk_list[i].scaled) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate chunk") - } /* end for */ - - if (NULL == (num_chunks_selected_array = (size_t *)H5MM_malloc((size_t)mpi_size * sizeof(size_t)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate num chunks selected array") - - if (MPI_SUCCESS != - (mpi_code = MPI_Allgather(&chunk_list_num_entries, 1, MPI_UNSIGNED_LONG_LONG, - num_chunks_selected_array, 1, MPI_UNSIGNED_LONG_LONG, io_info->comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Allgather failed", mpi_code) - - /* If this process has any chunks selected, create a MPI type for collectively - * writing out the chunks to file. Otherwise, the process contributes to the + if (H5D__mpio_collective_filtered_chunk_update(chunk_list, chunk_list_num_entries, chunk_hash_table, + chunk_msg_bufs, chunk_msg_bufs_len, io_info, type_info, + mpi_rank, mpi_size) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "couldn't update modified chunks") + + /* Free up resources used by chunk hash table now that we're done updating chunks */ + HASH_CLEAR(hh, chunk_hash_table); + + /* All ranks now collectively re-allocate file space for all chunks */ + if (H5D__mpio_collective_filtered_chunk_reallocate(chunk_list, chunk_list_num_entries, + rank_chunks_assigned_map, io_info, &index_info, + mpi_rank, mpi_size) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, + "couldn't collectively re-allocate file space for chunks") + + /* If this rank has any chunks selected, create a MPI type for collectively + * writing out the chunks to file. Otherwise, the rank contributes to the * collective write with a none type. */ - if (chunk_list_num_entries) { - size_t offset; - - /* During the collective re-allocation of chunks in the file, the record for each - * chunk is only updated in the collective array, not in the local copy of chunks on each - * process. However, each process needs the updated chunk records so that they can create - * a MPI type for the collective write that will write to the chunk's possible new locations - * in the file instead of the old ones. This ugly hack seems to be the best solution to - * copy the information back to the local array and avoid having to modify the collective - * write type function in an ugly way so that it will accept the collective array instead - * of the local array. This works correctly because the array gather function guarantees - * that the chunk data in the collective array is ordered in blocks by rank. - */ - for (i = 0, offset = 0; i < (size_t)mpi_rank; i++) - offset += num_chunks_selected_array[i]; - - H5MM_memcpy(chunk_list, &collective_chunk_list[offset], - num_chunks_selected_array[mpi_rank] * sizeof(H5D_filtered_collective_io_info_t)); + if (H5D__mpio_collective_filtered_io_type(chunk_list, chunk_list_num_entries, io_info->op_type, + &mem_type, &mem_type_is_derived, &file_type, + &file_type_is_derived) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, + "couldn't create MPI type for writing filtered chunks") - /* Create single MPI type encompassing each selection in the dataspace */ - if (H5D__mpio_filtered_collective_write_type(chunk_list, chunk_list_num_entries, &mem_type, - &mem_type_is_derived, &file_type, - &file_type_is_derived) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "couldn't create MPI link chunk I/O type") + mpi_buf_count = (file_type_is_derived || mem_type_is_derived) ? 1 : 0; - /* Override the write buffer to point to the address of the first - * chunk data buffer + /* Setup contig storage info for I/O operation */ + if (chunk_list_num_entries) { + /* + * Override the write buffer to point to the first + * chunk's data buffer */ io_info->u.wbuf = chunk_list[0].buf; - } /* end if */ - - /* We have a single, complicated MPI datatype for both memory & file */ - mpi_buf_count = (mem_type_is_derived && file_type_is_derived) ? (hsize_t)1 : (hsize_t)0; - /* Set up the base storage address for this operation */ - ctg_store.contig.dset_addr = 0; /* Write address must be set to address 0 */ - io_info->store = &ctg_store; + /* + * Setup the base storage address for this operation + * to be the first chunk's file address + */ + ctg_store.contig.dset_addr = chunk_list[0].chunk_new.offset; + } + else + ctg_store.contig.dset_addr = 0; /* Perform I/O */ + io_info->store = &ctg_store; if (H5D__final_collective_io(io_info, type_info, mpi_buf_count, file_type, mem_type) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish MPI-IO") + /* Free up resources in anticipation of following collective operation */ + for (i = 0; i < chunk_list_num_entries; i++) { + if (chunk_list[i].buf) { + H5MM_free(chunk_list[i].buf); + chunk_list[i].buf = NULL; + } + } + /* Participate in the collective re-insertion of all chunks modified - * in this iteration into the chunk index + * into the chunk index */ - for (i = 0; i < collective_chunk_list_num_entries; i++) { - udata.chunk_block = collective_chunk_list[i].chunk_states.new_chunk; - udata.common.scaled = collective_chunk_list[i].scaled; - udata.chunk_idx = collective_chunk_list[i].index; - - if ((index_info.storage->ops->insert)(&index_info, &udata, io_info->dset) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk address into index") - } /* end for */ - } /* end if */ + if (H5D__mpio_collective_filtered_chunk_reinsert(chunk_list, chunk_list_num_entries, + rank_chunks_assigned_map, io_info, &index_info, + mpi_rank, mpi_size) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, + "couldn't collectively re-insert modified chunks into chunk index") + } done: - /* Free resources used by a process which had some selection */ + /* Free the MPI buf and file types, if they were derived */ + if (mem_type_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&mem_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + if (file_type_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&file_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + + if (chunk_msg_bufs) { + for (i = 0; i < (size_t)chunk_msg_bufs_len; i++) + H5MM_free(chunk_msg_bufs[i]); + + H5MM_free(chunk_msg_bufs); + } + + HASH_CLEAR(hh, chunk_hash_table); + + /* Free resources used by a rank which had some selection */ if (chunk_list) { for (i = 0; i < chunk_list_num_entries; i++) if (chunk_list[i].buf) @@ -1502,16 +1858,13 @@ done: H5MM_free(chunk_list); } /* end if */ - if (num_chunks_selected_array) - H5MM_free(num_chunks_selected_array); - if (collective_chunk_list) - H5MM_free(collective_chunk_list); + if (rank_chunks_assigned_map) + H5MM_free(rank_chunks_assigned_map); - /* Free the MPI buf and file types, if they were derived */ - if (mem_type_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&mem_type))) - HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) - if (file_type_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&file_type))) - HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TIME_STOP(mpi_rank); + H5D_MPIO_TRACE_EXIT(mpi_rank); +#endif FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__link_chunk_filtered_collective_io() */ @@ -1534,7 +1887,8 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5D_chunk_map_t *fm) +H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5D_chunk_map_t *fm, + int mpi_rank, int mpi_size) { H5D_io_info_t ctg_io_info; /* Contiguous I/O info object */ H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */ @@ -1547,11 +1901,8 @@ H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *ty H5FD_mpio_collective_opt_t last_coll_opt_mode = H5FD_MPIO_COLLECTIVE_IO; /* Last parallel transfer with independent IO or collective IO with this mode */ - size_t total_chunk; /* Total # of chunks in dataset */ -#ifdef H5Dmpio_DEBUG - int mpi_rank; -#endif - size_t u; /* Local index variable */ + size_t total_chunk; /* Total # of chunks in dataset */ + size_t u; /* Local index variable */ H5D_mpio_actual_io_mode_t actual_io_mode = H5D_MPIO_NO_COLLECTIVE; /* Local variable for tracking the I/O mode used. */ herr_t ret_value = SUCCEED; @@ -1561,10 +1912,6 @@ H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *ty /* Set the actual chunk opt mode property */ H5CX_set_mpio_actual_chunk_opt(H5D_MPIO_MULTI_CHUNK); -#ifdef H5Dmpio_DEBUG - mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file); -#endif - /* Retrieve total # of chunks in dataset */ H5_CHECKED_ASSIGN(total_chunk, size_t, fm->layout->u.chunk.nchunks, hsize_t); HDassert(total_chunk != 0); @@ -1572,13 +1919,13 @@ H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *ty /* Allocate memories */ chunk_io_option = (uint8_t *)H5MM_calloc(total_chunk); chunk_addr = (haddr_t *)H5MM_calloc(total_chunk * sizeof(haddr_t)); -#ifdef H5D_DEBUG - if (H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "total_chunk %zu\n", total_chunk); + +#ifdef H5Dmpio_DEBUG + H5D_MPIO_DEBUG_VA(mpi_rank, "total_chunk %zu", total_chunk); #endif /* Obtain IO option for each chunk */ - if (H5D__obtain_mpio_mode(io_info, fm, chunk_io_option, chunk_addr) < 0) + if (H5D__obtain_mpio_mode(io_info, fm, chunk_io_option, chunk_addr, mpi_rank, mpi_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTRECV, FAIL, "unable to obtain MPIO mode") /* Set up contiguous I/O info object */ @@ -1606,9 +1953,8 @@ H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *ty H5S_t * fspace; /* Dataspace describing chunk & selection in it */ H5S_t * mspace; /* Dataspace describing selection in memory corresponding to this chunk */ -#ifdef H5D_DEBUG - if (H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "mpi_rank = %d, chunk index = %zu\n", mpi_rank, u); +#ifdef H5Dmpio_DEBUG + H5D_MPIO_DEBUG_VA(mpi_rank, "mpi_rank = %d, chunk index = %zu", mpi_rank, u); #endif /* Get the chunk info for this chunk, if there are elements selected */ chunk_info = fm->select_chunk[u]; @@ -1626,10 +1972,9 @@ H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *ty * needs to contribute MPI NONE TYPE. */ if (chunk_io_option[u] == H5D_CHUNK_IO_MODE_COL) { -#ifdef H5D_DEBUG - if (H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "inside collective chunk IO mpi_rank = %d, chunk index = %zu\n", - mpi_rank, u); +#ifdef H5Dmpio_DEBUG + H5D_MPIO_DEBUG_VA(mpi_rank, "inside collective chunk IO mpi_rank = %d, chunk index = %zu", + mpi_rank, u); #endif /* Set the file & memory dataspaces */ @@ -1665,10 +2010,9 @@ H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *ty HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish shared collective MPI-IO") } /* end if */ else { /* possible independent IO for this chunk */ -#ifdef H5D_DEBUG - if (H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "inside independent IO mpi_rank = %d, chunk index = %zu\n", mpi_rank, - u); +#ifdef H5Dmpio_DEBUG + H5D_MPIO_DEBUG_VA(mpi_rank, "inside independent IO mpi_rank = %d, chunk index = %zu", mpi_rank, + u); #endif HDassert(chunk_io_option[u] == 0); @@ -1698,9 +2042,8 @@ H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *ty /* Perform the I/O */ if (H5D__inter_collective_io(&ctg_io_info, type_info, fspace, mspace) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish shared collective MPI-IO") -#ifdef H5D_DEBUG - if (H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "after inter collective IO\n"); +#ifdef H5Dmpio_DEBUG + H5D_MPIO_DEBUG(mpi_rank, "after inter collective IO"); #endif } /* end else */ } /* end for */ @@ -1720,80 +2063,101 @@ done: /*------------------------------------------------------------------------- * Function: H5D__multi_chunk_filtered_collective_io * - * Purpose: To do filtered collective IO iteratively to save on memory. - * While link_chunk_filtered_collective_io will construct and - * work on a list of all of the chunks selected in the IO - * operation at once, this function works iteratively on a set - * of chunks at a time; at most one chunk per rank per - * iteration. - * - * 1. Construct a list of selected chunks in the collective IO - * operation - * A. If any chunk is being written to by more than 1 - * process, the process writing to the chunk which - * currently has the least amount of chunks assigned - * to it becomes the new owner (in the case of ties, - * the lowest MPI rank becomes the new owner) - * 2. If the operation is a read operation - * A. Loop through each chunk in the operation - * I. Read the chunk from the file - * II. Unfilter the chunk - * III. Scatter the read chunk data to the user's buffer - * 3. If the operation is a write operation - * A. Loop through each chunk in the operation - * I. If this is not a full overwrite of the chunk - * a) Read the chunk from file and pass the chunk - * through the filter pipeline in reverse order - * (Unfilter the chunk) - * II. Update the chunk data with the modifications from - * the owning process - * III. Receive any modification data from other - * processes and update the chunk data with these - * modifications - * IV. Filter the chunk - * V. Contribute the chunk to an array gathered by - * all processes which contains every chunk - * modified in this iteration (up to one chunk - * per process, some processes may not have a - * selection/may have less chunks to work on than - * other processes) - * VI. All processes collectively re-allocate each - * chunk from the gathered array with their new - * sizes after the filter operation - * VII. Proceed with the collective write operation - * for the chunks modified on this iteration - * VIII. All processes collectively re-insert each - * chunk from the gathered array into the chunk - * index + * Purpose: Performs collective I/O on filtered chunks iteratively to + * save on memory and potentially get better performance + * depending on the average number of chunks per rank. While + * linked-chunk I/O will construct and work on a list of all + * of the chunks selected in the I/O operation at once, this + * function works iteratively on a set of chunks at a time; at + * most one chunk per rank per iteration. The general + * algorithm is as follows: + * + * 1. Construct a list of selected chunks in the collective + * I/O operation + * 2. If the operation is a read operation, loop an amount of + * times equal to the maximum number of chunks selected on + * any particular rank and on each iteration: + * A. Participate in a collective read of chunks from + * the file (ranks that run out of chunks still need + * to participate) + * B. Unfilter the chunk that was read (if any) + * C. Scatter the read chunk's data to the application's + * read buffer + * 3. If the operation is a write operation, redistribute any + * chunks being written to by more than 1 MPI rank, such + * that the chunk is only owned by 1 MPI rank. The rank + * writing to the chunk which currently has the least + * amount of chunks assigned to it becomes the new owner + * (in the case of ties, the lowest MPI rank becomes the + * new owner). Then, loop an amount of times equal to the + * maximum number of chunks selected on any particular + * rank and on each iteration: + * A. Participate in a collective read of chunks from + * the file (ranks that run out of chunks still need + * to participate) + * I. If we actually read a chunk from the file (if + * a chunk is being fully overwritten, we skip + * reading it), pass the chunk through the filter + * pipeline in reverse order (unfilter the chunk) + * B. Update the chunk data with the modifications from + * the owning rank + * C. Receive any modification data from other ranks and + * update the chunk data with those modifications + * D. Filter the chunk + * E. Contribute the chunk to an array gathered by + * all ranks which contains information for + * re-allocating space in the file for every chunk + * modified in this iteration (up to one chunk per + * rank; some ranks may not have a selection/may have + * less chunks to work on than other ranks). Then, + * each rank collectively re-allocates each chunk + * from the gathered array with their new sizes + * after the filter operation + * F. Proceed with the collective write operation + * for the chunks modified on this iteration + * G. Contribute the chunk to an array gathered by + * all ranks which contains information for + * re-inserting every chunk modified on this + * iteration into the chunk index. Then, each rank + * collectively re-inserts each chunk from the + * gathered array into the chunk index + * + * TODO: Note that steps E. and G. here are both collective + * operations that partially share data from the + * H5D_filtered_collective_io_info_t structure. To + * try to conserve on memory a bit, the distributed + * arrays these operations create are discarded after + * each operation is performed. If memory consumption + * here proves to not be an issue, the necessary data + * for both operations could be combined into a single + * structure so that only one collective MPI operation + * is needed to carry out both operations, rather than + * two. * * Return: Non-negative on success/Negative on failure * - * Programmer: Jordan Henderson - * Friday, Dec. 2nd, 2016 - * *------------------------------------------------------------------------- */ static herr_t H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - H5D_chunk_map_t *fm) + H5D_chunk_map_t *fm, int mpi_rank, int mpi_size) { - H5D_filtered_collective_io_info_t *chunk_list = NULL; /* The list of chunks being read/written */ - H5D_filtered_collective_io_info_t *collective_chunk_list = - NULL; /* The list of chunks used during collective operations */ - H5D_storage_t store; /* union of EFL and chunk pointer in file space */ - H5D_io_info_t ctg_io_info; /* Contiguous I/O info object */ - H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */ - MPI_Datatype *file_type_array = NULL; - MPI_Datatype *mem_type_array = NULL; - hbool_t * file_type_is_derived_array = NULL; - hbool_t * mem_type_is_derived_array = NULL; - hbool_t * has_chunk_selected_array = - NULL; /* Array of whether or not each process is contributing a chunk to each iteration */ - size_t chunk_list_num_entries; - size_t collective_chunk_list_num_entries; - size_t i, j; /* Local index variable */ - int mpi_rank, mpi_size, mpi_code; - herr_t ret_value = SUCCEED; + H5D_filtered_collective_io_info_t *chunk_list = NULL; /* The list of chunks being read/written */ + H5D_filtered_collective_io_info_t *chunk_hash_table = NULL; + unsigned char ** chunk_msg_bufs = NULL; + H5D_io_info_t ctg_io_info; /* Contiguous I/O info object */ + H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */ + MPI_Datatype mem_type = MPI_BYTE; + MPI_Datatype file_type = MPI_BYTE; + hbool_t mem_type_is_derived = FALSE; + hbool_t file_type_is_derived = FALSE; + hbool_t have_chunk_to_process; + size_t chunk_list_num_entries; + size_t i; + size_t max_num_chunks; + int chunk_msg_bufs_len = 0; + int mpi_code; + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC @@ -1801,11 +2165,12 @@ H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_i HDassert(type_info); HDassert(fm); - /* Obtain the current rank of the process and the number of processes */ - if ((mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file)) < 0) - HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi rank") - if ((mpi_size = H5F_mpi_get_size(io_info->dset->oloc.file)) < 0) - HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi size") +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TRACE_ENTER(mpi_rank); + H5D_MPIO_DEBUG_VA(mpi_rank, "Performing Multi-chunk I/O (%s) with MPI Comm size of %d", + io_info->op_type == H5D_IO_OP_WRITE ? "write" : "read", mpi_size); + H5D_MPIO_TIME_START(mpi_rank, "Multi-chunk I/O"); +#endif /* Set the actual chunk opt mode property */ H5CX_set_mpio_actual_chunk_opt(H5D_MPIO_MULTI_CHUNK); @@ -1816,10 +2181,19 @@ H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_i H5CX_set_mpio_actual_io_mode(H5D_MPIO_CHUNK_COLLECTIVE); /* Build a list of selected chunks in the collective IO operation */ - if (H5D__construct_filtered_io_info_list(io_info, type_info, fm, &chunk_list, &chunk_list_num_entries) < - 0) + if (H5D__mpio_collective_filtered_chunk_io_setup(io_info, type_info, fm, &chunk_list, + &chunk_list_num_entries, mpi_rank) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "couldn't construct filtered I/O info list") + /* Retrieve the maximum number of chunks selected for any rank */ + if (MPI_SUCCESS != (mpi_code = MPI_Allreduce(&chunk_list_num_entries, &max_num_chunks, 1, + MPI_UNSIGNED_LONG_LONG, MPI_MAX, io_info->comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code) + + /* If no one has anything selected at all, end the operation */ + if (0 == max_num_chunks) + HGOTO_DONE(SUCCEED); + /* Set up contiguous I/O info object */ H5MM_memcpy(&ctg_io_info, io_info, sizeof(ctg_io_info)); ctg_io_info.store = &ctg_store; @@ -1827,190 +2201,147 @@ H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_i /* Initialize temporary contiguous storage info */ ctg_store.contig.dset_size = (hsize_t)io_info->dset->shared->layout.u.chunk.size; - ctg_store.contig.dset_addr = 0; - - /* Set dataset storage for I/O info */ - io_info->store = &store; if (io_info->op_type == H5D_IO_OP_READ) { /* Filtered collective read */ - for (i = 0; i < chunk_list_num_entries; i++) - if (H5D__filtered_collective_chunk_entry_io(&chunk_list[i], io_info, type_info, fm) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't process chunk entry") - } /* end if */ + for (i = 0; i < max_num_chunks; i++) { + /* Check if this rank has a chunk to work on for this iteration */ + have_chunk_to_process = (i < chunk_list_num_entries); + + if (H5D__mpio_collective_filtered_chunk_read(have_chunk_to_process ? &chunk_list[i] : NULL, + have_chunk_to_process ? 1 : 0, io_info, type_info, + mpi_rank, mpi_size) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't read filtered chunks") + + if (have_chunk_to_process && chunk_list[i].buf) { + H5MM_free(chunk_list[i].buf); + chunk_list[i].buf = NULL; + } + } + } else { /* Filtered collective write */ H5D_chk_idx_info_t index_info; - H5D_chunk_ud_t udata; - size_t max_num_chunks; hsize_t mpi_buf_count; /* Construct chunked index info */ - index_info.f = io_info->dset->oloc.file; - index_info.pline = &(io_info->dset->shared->dcpl_cache.pline); - index_info.layout = &(io_info->dset->shared->layout.u.chunk); - index_info.storage = &(io_info->dset->shared->layout.storage.u.chunk); - - /* Set up chunk information for insertion to chunk index */ - udata.common.layout = index_info.layout; - udata.common.storage = index_info.storage; - udata.filter_mask = 0; - - /* Retrieve the maximum number of chunks being written among all processes */ - if (MPI_SUCCESS != (mpi_code = MPI_Allreduce(&chunk_list_num_entries, &max_num_chunks, 1, - MPI_UNSIGNED_LONG_LONG, MPI_MAX, io_info->comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code) - - /* If no one is writing anything at all, end the operation */ - if (!(max_num_chunks > 0)) - HGOTO_DONE(SUCCEED); - - /* Allocate arrays for storing MPI file and mem types and whether or not the - * types were derived. - */ - if (NULL == (file_type_array = (MPI_Datatype *)H5MM_malloc(max_num_chunks * sizeof(MPI_Datatype)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate file type array") - - if (NULL == (file_type_is_derived_array = (hbool_t *)H5MM_calloc(max_num_chunks * sizeof(hbool_t)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate file type is derived array") - - if (NULL == (mem_type_array = (MPI_Datatype *)H5MM_malloc(max_num_chunks * sizeof(MPI_Datatype)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate mem type array") - - if (NULL == (mem_type_is_derived_array = (hbool_t *)H5MM_calloc(max_num_chunks * sizeof(hbool_t)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate mem type is derived array") - - /* Iterate over the max number of chunks among all processes, as this process could - * have no chunks left to work on, but it still needs to participate in the collective - * re-allocation and re-insertion of chunks modified by other processes. + H5D_MPIO_INIT_CHUNK_IDX_INFO(index_info, io_info); + + if (mpi_size > 1) { + /* Redistribute shared chunks being written to */ + if (H5D__mpio_redistribute_shared_chunks(chunk_list, chunk_list_num_entries, io_info, fm, + mpi_rank, mpi_size, NULL) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to redistribute shared chunks") + + /* Send any chunk modification messages for chunks this rank no longer owns */ + if (H5D__mpio_share_chunk_modification_data(chunk_list, &chunk_list_num_entries, io_info, + type_info, mpi_rank, mpi_size, &chunk_hash_table, + &chunk_msg_bufs, &chunk_msg_bufs_len) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, + "unable to send chunk modification data between MPI ranks") + } + + /* Iterate over the max number of chunks among all ranks, as this rank could + * have no chunks left to work on, but it still needs to participate in the + * collective re-allocation and re-insertion of chunks modified by other ranks. */ for (i = 0; i < max_num_chunks; i++) { - /* Check if this process has a chunk to work on for this iteration */ - hbool_t have_chunk_to_process = - (i < chunk_list_num_entries) && (mpi_rank == chunk_list[i].owners.new_owner); - - if (have_chunk_to_process) - if (H5D__filtered_collective_chunk_entry_io(&chunk_list[i], io_info, type_info, fm) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "couldn't process chunk entry") + /* Check if this rank has a chunk to work on for this iteration */ + have_chunk_to_process = (i < chunk_list_num_entries) && (mpi_rank == chunk_list[i].new_owner); - /* Gather the new chunk sizes to all processes for a collective re-allocation - * of the chunks in the file + /* Proceed to update the chunk this rank owns (if any left) with its + * own modification data and data from other ranks, before re-filtering + * the chunks. As chunk reads are done collectively here, all ranks + * must participate. */ - if (H5D__mpio_array_gatherv(&chunk_list[i], have_chunk_to_process ? 1 : 0, - sizeof(H5D_filtered_collective_io_info_t), - (void **)&collective_chunk_list, &collective_chunk_list_num_entries, - true, 0, io_info->comm, NULL) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL, "couldn't gather new chunk sizes") - - /* Participate in the collective re-allocation of all chunks modified - * in this iteration. + if (H5D__mpio_collective_filtered_chunk_update(have_chunk_to_process ? &chunk_list[i] : NULL, + have_chunk_to_process ? 1 : 0, chunk_hash_table, + chunk_msg_bufs, chunk_msg_bufs_len, io_info, + type_info, mpi_rank, mpi_size) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "couldn't update modified chunks") + + /* All ranks now collectively re-allocate file space for all chunks */ + if (H5D__mpio_collective_filtered_chunk_reallocate(have_chunk_to_process ? &chunk_list[i] : NULL, + have_chunk_to_process ? 1 : 0, NULL, io_info, + &index_info, mpi_rank, mpi_size) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, + "couldn't collectively re-allocate file space for chunks") + + /* + * If this rank has a chunk to work on, create a MPI type + * for writing out the chunk. Otherwise, the rank will + * use MPI_BYTE for the file and memory type and specify + * a count of 0. */ - for (j = 0; j < collective_chunk_list_num_entries; j++) { - hbool_t insert = FALSE; - - if (H5D__chunk_file_alloc(&index_info, &collective_chunk_list[j].chunk_states.chunk_current, - &collective_chunk_list[j].chunk_states.new_chunk, &insert, - chunk_list[j].scaled) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate chunk") - } /* end for */ - - if (NULL == - (has_chunk_selected_array = (hbool_t *)H5MM_malloc((size_t)mpi_size * sizeof(hbool_t)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate num chunks selected array") + if (H5D__mpio_collective_filtered_io_type( + have_chunk_to_process ? &chunk_list[i] : NULL, have_chunk_to_process ? 1 : 0, + io_info->op_type, &mem_type, &mem_type_is_derived, &file_type, &file_type_is_derived) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, + "couldn't create MPI type for writing filtered chunks") - if (MPI_SUCCESS != - (mpi_code = MPI_Allgather(&have_chunk_to_process, 1, MPI_C_BOOL, has_chunk_selected_array, 1, - MPI_C_BOOL, io_info->comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Allgather failed", mpi_code) + mpi_buf_count = (file_type_is_derived || mem_type_is_derived) ? 1 : 0; - /* If this process has a chunk to work on, create a MPI type for the - * memory and file for writing out the chunk - */ + /* Override the write buffer to point to the chunk data buffer */ if (have_chunk_to_process) { - size_t offset; - int mpi_type_count; - - for (j = 0, offset = 0; j < (size_t)mpi_rank; j++) - offset += has_chunk_selected_array[j]; - - /* Collect the new chunk info back to the local copy, since only the record in the - * collective array gets updated by the chunk re-allocation */ - H5MM_memcpy(&chunk_list[i].chunk_states.new_chunk, - &collective_chunk_list[offset].chunk_states.new_chunk, - sizeof(chunk_list[i].chunk_states.new_chunk)); - - H5_CHECKED_ASSIGN(mpi_type_count, int, chunk_list[i].chunk_states.new_chunk.length, hsize_t); - - /* Create MPI memory type for writing to chunk */ - if (MPI_SUCCESS != - (mpi_code = MPI_Type_contiguous(mpi_type_count, MPI_BYTE, &mem_type_array[i]))) - HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) - if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(&mem_type_array[i]))) - HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) - mem_type_is_derived_array[i] = TRUE; - - /* Create MPI file type for writing to chunk */ - if (MPI_SUCCESS != - (mpi_code = MPI_Type_contiguous(mpi_type_count, MPI_BYTE, &file_type_array[i]))) - HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) - if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(&file_type_array[i]))) - HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) - file_type_is_derived_array[i] = TRUE; - - mpi_buf_count = 1; - - /* Set up the base storage address for this operation */ - ctg_store.contig.dset_addr = chunk_list[i].chunk_states.new_chunk.offset; - - /* Override the write buffer to point to the address of the - * chunk data buffer + /* + * Override the write buffer to point to the + * chunk's data buffer */ ctg_io_info.u.wbuf = chunk_list[i].buf; - } /* end if */ - else { - mem_type_array[i] = file_type_array[i] = MPI_BYTE; - mpi_buf_count = 0; - } /* end else */ + + /* + * Setup the base storage address for this + * operation to be the chunk's file address + */ + ctg_store.contig.dset_addr = chunk_list[i].chunk_new.offset; + } + else + ctg_store.contig.dset_addr = 0; /* Perform the I/O */ - if (H5D__final_collective_io(&ctg_io_info, type_info, mpi_buf_count, file_type_array[i], - mem_type_array[i]) < 0) + if (H5D__final_collective_io(&ctg_io_info, type_info, mpi_buf_count, file_type, mem_type) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish MPI-IO") + /* Free up resources in anticipation of following collective operation */ + if (have_chunk_to_process && chunk_list[i].buf) { + H5MM_free(chunk_list[i].buf); + chunk_list[i].buf = NULL; + } + /* Participate in the collective re-insertion of all chunks modified * in this iteration into the chunk index */ - for (j = 0; j < collective_chunk_list_num_entries; j++) { - udata.chunk_block = collective_chunk_list[j].chunk_states.new_chunk; - udata.common.scaled = collective_chunk_list[j].scaled; - udata.chunk_idx = collective_chunk_list[j].index; - - if ((index_info.storage->ops->insert)(&index_info, &udata, io_info->dset) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, - "unable to insert chunk address into index") - } /* end for */ + if (H5D__mpio_collective_filtered_chunk_reinsert(have_chunk_to_process ? &chunk_list[i] : NULL, + have_chunk_to_process ? 1 : 0, NULL, io_info, + &index_info, mpi_rank, mpi_size) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, + "couldn't collectively re-insert modified chunks into chunk index") + + /* Free the MPI types, if they were derived */ + if (mem_type_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&mem_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + mem_type_is_derived = FALSE; + if (file_type_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&file_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + file_type_is_derived = FALSE; + } /* end for */ + } - if (collective_chunk_list) { - H5MM_free(collective_chunk_list); - collective_chunk_list = NULL; - } /* end if */ - if (has_chunk_selected_array) { - H5MM_free(has_chunk_selected_array); - has_chunk_selected_array = NULL; - } /* end if */ - } /* end for */ +done: + /* Free the MPI buf and file types, if they were derived */ + if (mem_type_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&mem_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + if (file_type_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&file_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) - /* Free the MPI file and memory types, if they were derived */ - for (i = 0; i < max_num_chunks; i++) { - if (file_type_is_derived_array[i]) - if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&file_type_array[i]))) - HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + if (chunk_msg_bufs) { + for (i = 0; i < (size_t)chunk_msg_bufs_len; i++) + H5MM_free(chunk_msg_bufs[i]); - if (mem_type_is_derived_array[i]) - if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&mem_type_array[i]))) - HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) - } /* end for */ - } /* end else */ + H5MM_free(chunk_msg_bufs); + } -done: + HASH_CLEAR(hh, chunk_hash_table); + + /* Free resources used by a rank which had some selection */ if (chunk_list) { for (i = 0; i < chunk_list_num_entries; i++) if (chunk_list[i].buf) @@ -2019,16 +2350,10 @@ done: H5MM_free(chunk_list); } /* end if */ - if (collective_chunk_list) - H5MM_free(collective_chunk_list); - if (file_type_array) - H5MM_free(file_type_array); - if (mem_type_array) - H5MM_free(mem_type_array); - if (file_type_is_derived_array) - H5MM_free(file_type_is_derived_array); - if (mem_type_is_derived_array) - H5MM_free(mem_type_is_derived_array); +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TIME_STOP(mpi_rank); + H5D_MPIO_TRACE_EXIT(mpi_rank); +#endif FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__multi_chunk_filtered_collective_io() */ @@ -2054,11 +2379,22 @@ H5D__inter_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf hbool_t mbt_is_derived = FALSE; hbool_t mft_is_derived = FALSE; MPI_Datatype mpi_file_type, mpi_buf_type; - int mpi_code; /* MPI return code */ - herr_t ret_value = SUCCEED; /* return value */ + int mpi_code; /* MPI return code */ +#ifdef H5Dmpio_DEBUG + int mpi_rank; +#endif + herr_t ret_value = SUCCEED; /* return value */ FUNC_ENTER_STATIC +#ifdef H5Dmpio_DEBUG + mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file); + H5D_MPIO_TRACE_ENTER(mpi_rank); + H5D_MPIO_TIME_START(mpi_rank, "Inter collective I/O"); + if (mpi_rank < 0) + HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain MPI rank") +#endif + if ((file_space != NULL) && (mem_space != NULL)) { int mpi_file_count; /* Number of file "objects" to transfer */ hsize_t *permute_map = NULL; /* array that holds the mapping from the old, @@ -2117,9 +2453,8 @@ H5D__inter_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf mft_is_derived = FALSE; } /* end else */ -#ifdef H5D_DEBUG - if (H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "before final collective IO \n"); +#ifdef H5Dmpio_DEBUG + H5D_MPIO_DEBUG(mpi_rank, "before final collective I/O"); #endif /* Perform final collective I/O operation */ @@ -2133,9 +2468,10 @@ done: if (mft_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&mpi_file_type))) HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) -#ifdef H5D_DEBUG - if (H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "before leaving inter_collective_io ret_value = %d\n", ret_value); +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TIME_STOP(mpi_rank); + H5D_MPIO_DEBUG_VA(mpi_rank, "before leaving inter_collective_io ret_value = %d", ret_value); + H5D_MPIO_TRACE_EXIT(mpi_rank); #endif FUNC_LEAVE_NOAPI(ret_value) @@ -2157,10 +2493,21 @@ static herr_t H5D__final_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t mpi_buf_count, MPI_Datatype mpi_file_type, MPI_Datatype mpi_buf_type) { +#ifdef H5Dmpio_DEBUG + int mpi_rank; +#endif herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC +#ifdef H5Dmpio_DEBUG + mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file); + H5D_MPIO_TRACE_ENTER(mpi_rank); + H5D_MPIO_TIME_START(mpi_rank, "Final collective I/O"); + if (mpi_rank < 0) + HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain MPI rank") +#endif + /* Pass buf type, file type to the file driver. */ if (H5CX_set_mpi_coll_datatypes(mpi_buf_type, mpi_file_type) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set MPI-I/O collective I/O datatypes") @@ -2175,10 +2522,12 @@ H5D__final_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf } /* end else */ done: -#ifdef H5D_DEBUG - if (H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "ret_value before leaving final_collective_io=%d\n", ret_value); +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TIME_STOP(mpi_rank); + H5D_MPIO_DEBUG_VA(mpi_rank, "ret_value before leaving final_collective_io=%d", ret_value); + H5D_MPIO_TRACE_EXIT(mpi_rank); #endif + FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__final_collective_io */ @@ -2220,62 +2569,149 @@ H5D__cmp_chunk_addr(const void *chunk_addr_info1, const void *chunk_addr_info2) * * Return: -1, 0, 1 * - * Programmer: Jordan Henderson - * Wednesday, Nov. 30th, 2016 - * *------------------------------------------------------------------------- */ static int H5D__cmp_filtered_collective_io_info_entry(const void *filtered_collective_io_info_entry1, const void *filtered_collective_io_info_entry2) { - haddr_t addr1 = HADDR_UNDEF, addr2 = HADDR_UNDEF; + const H5D_filtered_collective_io_info_t *entry1; + const H5D_filtered_collective_io_info_t *entry2; + haddr_t addr1 = HADDR_UNDEF; + haddr_t addr2 = HADDR_UNDEF; + int ret_value; FUNC_ENTER_STATIC_NOERR - addr1 = ((const H5D_filtered_collective_io_info_t *)filtered_collective_io_info_entry1) - ->chunk_states.new_chunk.offset; - addr2 = ((const H5D_filtered_collective_io_info_t *)filtered_collective_io_info_entry2) - ->chunk_states.new_chunk.offset; + entry1 = (const H5D_filtered_collective_io_info_t *)filtered_collective_io_info_entry1; + entry2 = (const H5D_filtered_collective_io_info_t *)filtered_collective_io_info_entry2; - FUNC_LEAVE_NOAPI(H5F_addr_cmp(addr1, addr2)) -} /* end H5D__cmp_filtered_collective_io_info_entry() */ + addr1 = entry1->chunk_new.offset; + addr2 = entry2->chunk_new.offset; -#if MPI_VERSION >= 3 + /* + * If both chunk addresses are defined, H5F_addr_cmp is safe to use. + * Otherwise, if both addresses aren't defined, compared chunk + * entries based on their chunk index. Finally, if only one chunk + * address is defined, return the appropriate value based on which + * is defined. + */ + if (H5F_addr_defined(addr1) && H5F_addr_defined(addr2)) { + ret_value = H5F_addr_cmp(addr1, addr2); + } + else if (!H5F_addr_defined(addr1) && !H5F_addr_defined(addr2)) { + hsize_t chunk_idx1 = entry1->index_info.chunk_idx; + hsize_t chunk_idx2 = entry2->index_info.chunk_idx; + + ret_value = (chunk_idx1 > chunk_idx2) - (chunk_idx1 < chunk_idx2); + } + else + ret_value = H5F_addr_defined(addr1) ? 1 : -1; + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__cmp_filtered_collective_io_info_entry() */ /*------------------------------------------------------------------------- - * Function: H5D__cmp_filtered_collective_io_info_entry_owner + * Function: H5D__cmp_chunk_redistribute_info * - * Purpose: Routine to compare filtered collective chunk io info - * entries's original owner fields + * Purpose: Routine to compare two H5D_chunk_redistribute_info_t + * structures * - * Description: Callback for qsort() to compare filtered collective chunk - * io info entries's original owner fields + * Description: Callback for qsort() to compare two + * H5D_chunk_redistribute_info_t structures * - * Return: The difference between the two - * H5D_filtered_collective_io_info_t's original owner fields + * Return: -1, 0, 1 * - * Programmer: Jordan Henderson - * Monday, Apr. 10th, 2017 + *------------------------------------------------------------------------- + */ +static int +H5D__cmp_chunk_redistribute_info(const void *_entry1, const void *_entry2) +{ + const H5D_chunk_redistribute_info_t *entry1; + const H5D_chunk_redistribute_info_t *entry2; + hsize_t chunk_index1; + hsize_t chunk_index2; + int ret_value; + + FUNC_ENTER_STATIC_NOERR + + entry1 = (const H5D_chunk_redistribute_info_t *)_entry1; + entry2 = (const H5D_chunk_redistribute_info_t *)_entry2; + + chunk_index1 = entry1->chunk_idx; + chunk_index2 = entry2->chunk_idx; + + if (chunk_index1 == chunk_index2) { + int orig_owner1 = entry1->orig_owner; + int orig_owner2 = entry2->orig_owner; + + ret_value = (orig_owner1 > orig_owner2) - (orig_owner1 < orig_owner2); + } + else + ret_value = (chunk_index1 > chunk_index2) - (chunk_index1 < chunk_index2); + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__cmp_chunk_redistribute_info() */ + +/*------------------------------------------------------------------------- + * Function: H5D__cmp_chunk_redistribute_info_orig_owner + * + * Purpose: Routine to compare the original owning MPI rank for two + * H5D_chunk_redistribute_info_t structures + * + * Description: Callback for qsort() to compare the original owning MPI + * rank for two H5D_chunk_redistribute_info_t + * structures + * + * Return: -1, 0, 1 * *------------------------------------------------------------------------- */ static int -H5D__cmp_filtered_collective_io_info_entry_owner(const void *filtered_collective_io_info_entry1, - const void *filtered_collective_io_info_entry2) +H5D__cmp_chunk_redistribute_info_orig_owner(const void *_entry1, const void *_entry2) { - int owner1 = -1, owner2 = -1; + const H5D_chunk_redistribute_info_t *entry1; + const H5D_chunk_redistribute_info_t *entry2; + int owner1 = -1; + int owner2 = -1; + int ret_value; FUNC_ENTER_STATIC_NOERR - owner1 = ((const H5D_filtered_collective_io_info_t *)filtered_collective_io_info_entry1) - ->owners.original_owner; - owner2 = ((const H5D_filtered_collective_io_info_t *)filtered_collective_io_info_entry2) - ->owners.original_owner; + entry1 = (const H5D_chunk_redistribute_info_t *)_entry1; + entry2 = (const H5D_chunk_redistribute_info_t *)_entry2; - FUNC_LEAVE_NOAPI(owner1 - owner2) -} /* end H5D__cmp_filtered_collective_io_info_entry_owner() */ -#endif + owner1 = entry1->orig_owner; + owner2 = entry2->orig_owner; + + if (owner1 == owner2) { + haddr_t addr1 = entry1->chunk_block.offset; + haddr_t addr2 = entry2->chunk_block.offset; + + /* + * If both chunk addresses are defined, H5F_addr_cmp is safe to use. + * Otherwise, if both addresses aren't defined, compared chunk + * entries based on their chunk index. Finally, if only one chunk + * address is defined, return the appropriate value based on which + * is defined. + */ + if (H5F_addr_defined(addr1) && H5F_addr_defined(addr2)) { + ret_value = H5F_addr_cmp(addr1, addr2); + } + else if (!H5F_addr_defined(addr1) && !H5F_addr_defined(addr2)) { + hsize_t chunk_idx1 = entry1->chunk_idx; + hsize_t chunk_idx2 = entry2->chunk_idx; + + ret_value = (chunk_idx1 > chunk_idx2) - (chunk_idx1 < chunk_idx2); + } + else + ret_value = H5F_addr_defined(addr1) ? 1 : -1; + } + else + ret_value = (owner1 > owner2) - (owner1 < owner2); + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__cmp_chunk_redistribute_info_orig_owner() */ /*------------------------------------------------------------------------- * Function: H5D__sort_chunk @@ -2304,26 +2740,24 @@ H5D__cmp_filtered_collective_io_info_entry_owner(const void *filtered_collective */ static herr_t H5D__sort_chunk(H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, - H5D_chunk_addr_info_t chunk_addr_info_array[], int sum_chunk) + H5D_chunk_addr_info_t chunk_addr_info_array[], int sum_chunk, int mpi_rank, int mpi_size) { - H5SL_node_t * chunk_node; /* Current node in chunk skip list */ - H5D_chunk_info_t *chunk_info; /* Current chunking info. of this node. */ - haddr_t chunk_addr; /* Current chunking address of this node */ - haddr_t *total_chunk_addr_array = NULL; /* The array of chunk address for the total number of chunk */ - hbool_t do_sort = FALSE; /* Whether the addresses need to be sorted */ - int bsearch_coll_chunk_threshold; - int many_chunk_opt = H5D_OBTAIN_ONE_CHUNK_ADDR_IND; - int mpi_size; /* Number of MPI processes */ - int mpi_code; /* MPI return code */ - int i; /* Local index variable */ - herr_t ret_value = SUCCEED; /* Return value */ + H5SL_node_t * chunk_node; /* Current node in chunk skip list */ + H5D_chunk_info_t *chunk_info; /* Current chunking info. of this node. */ + haddr_t chunk_addr; /* Current chunking address of this node */ + haddr_t *total_chunk_addr_array = NULL; /* The array of chunk address for the total number of chunk */ + H5P_coll_md_read_flag_t md_reads_file_flag; + hbool_t md_reads_context_flag; + hbool_t restore_md_reads_state = FALSE; + hbool_t do_sort = FALSE; /* Whether the addresses need to be sorted */ + int bsearch_coll_chunk_threshold; + int many_chunk_opt = H5D_OBTAIN_ONE_CHUNK_ADDR_IND; + int mpi_code; /* MPI return code */ + int i; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC - /* Retrieve # of MPI processes */ - if ((mpi_size = H5F_mpi_get_size(io_info->dset->oloc.file)) < 0) - HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi size") - /* Calculate the actual threshold to obtain all chunk addresses collectively * The bigger this number is, the more possible the use of obtaining chunk * address collectively. @@ -2337,30 +2771,47 @@ H5D__sort_chunk(H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, ((sum_chunk / mpi_size) >= H5D_ALL_CHUNK_ADDR_THRES_COL_NUM)) many_chunk_opt = H5D_OBTAIN_ALL_CHUNK_ADDR_COL; -#ifdef H5D_DEBUG - if (H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "many_chunk_opt= %d\n", many_chunk_opt); +#ifdef H5Dmpio_DEBUG + H5D_MPIO_DEBUG_VA(mpi_rank, "many_chunk_opt = %d", many_chunk_opt); #endif /* If we need to optimize the way to obtain the chunk address */ if (many_chunk_opt != H5D_OBTAIN_ONE_CHUNK_ADDR_IND) { - int mpi_rank; - -#ifdef H5D_DEBUG - if (H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "Coming inside H5D_OBTAIN_ALL_CHUNK_ADDR_COL\n"); +#ifdef H5Dmpio_DEBUG + H5D_MPIO_DEBUG(mpi_rank, "Coming inside H5D_OBTAIN_ALL_CHUNK_ADDR_COL"); #endif /* Allocate array for chunk addresses */ if (NULL == (total_chunk_addr_array = (haddr_t *)H5MM_malloc(sizeof(haddr_t) * (size_t)fm->layout->u.chunk.nchunks))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate memory chunk address array") - /* Retrieve all the chunk addresses with process 0 */ - if ((mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file)) < 0) - HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi rank") - if (mpi_rank == 0) { - if (H5D__chunk_addrmap(io_info, total_chunk_addr_array) < 0) { + herr_t result; + + /* + * If enabled, disable collective metadata reads here. + * Since the chunk address mapping is done on rank 0 + * only here, it will cause problems if collective + * metadata reads are enabled. + */ + if (H5F_get_coll_metadata_reads(io_info->dset->oloc.file)) { + md_reads_file_flag = H5P_FORCE_FALSE; + md_reads_context_flag = FALSE; + H5F_set_coll_metadata_reads(io_info->dset->oloc.file, &md_reads_file_flag, + &md_reads_context_flag); + restore_md_reads_state = TRUE; + } + + result = H5D__chunk_addrmap(io_info, total_chunk_addr_array); + + /* Ensure that we restore the old collective metadata reads state */ + if (restore_md_reads_state) { + H5F_set_coll_metadata_reads(io_info->dset->oloc.file, &md_reads_file_flag, + &md_reads_context_flag); + restore_md_reads_state = FALSE; + } + + if (result < 0) { size_t u; /* Clear total chunk address array */ @@ -2413,10 +2864,10 @@ H5D__sort_chunk(H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, chunk_node = H5SL_next(chunk_node); } /* end while */ -#ifdef H5D_DEBUG - if (H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "before Qsort\n"); +#ifdef H5Dmpio_DEBUG + H5D_MPIO_DEBUG(mpi_rank, "before Qsort"); #endif + if (do_sort) { size_t num_chunks = H5SL_count(fm->sel_chunks); @@ -2424,6 +2875,10 @@ H5D__sort_chunk(H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, } /* end if */ done: + /* Re-enable collective metadata reads if we disabled them */ + if (restore_md_reads_state) + H5F_set_coll_metadata_reads(io_info->dset->oloc.file, &md_reads_file_flag, &md_reads_context_flag); + if (total_chunk_addr_array) H5MM_xfree(total_chunk_addr_array); @@ -2469,22 +2924,24 @@ done: */ static herr_t H5D__obtain_mpio_mode(H5D_io_info_t *io_info, H5D_chunk_map_t *fm, uint8_t assign_io_mode[], - haddr_t chunk_addr[]) + haddr_t chunk_addr[], int mpi_rank, int mpi_size) { - size_t total_chunks; - unsigned percent_nproc_per_chunk, threshold_nproc_per_chunk; - uint8_t * io_mode_info = NULL; - uint8_t * recv_io_mode_info = NULL; - uint8_t * mergebuf = NULL; - uint8_t * tempbuf; - H5SL_node_t * chunk_node; - H5D_chunk_info_t *chunk_info; - int mpi_size, mpi_rank; - MPI_Comm comm; - int root; - size_t ic; - int mpi_code; - herr_t ret_value = SUCCEED; + size_t total_chunks; + unsigned percent_nproc_per_chunk, threshold_nproc_per_chunk; + uint8_t * io_mode_info = NULL; + uint8_t * recv_io_mode_info = NULL; + uint8_t * mergebuf = NULL; + uint8_t * tempbuf; + H5SL_node_t * chunk_node; + H5D_chunk_info_t * chunk_info; + H5P_coll_md_read_flag_t md_reads_file_flag; + hbool_t md_reads_context_flag; + hbool_t restore_md_reads_state = FALSE; + MPI_Comm comm; + int root; + size_t ic; + int mpi_code; + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC @@ -2492,12 +2949,6 @@ H5D__obtain_mpio_mode(H5D_io_info_t *io_info, H5D_chunk_map_t *fm, uint8_t assig root = 0; comm = io_info->comm; - /* Obtain the number of process and the current rank of the process */ - if ((mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file)) < 0) - HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi rank") - if ((mpi_size = H5F_mpi_get_size(io_info->dset->oloc.file)) < 0) - HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi size") - /* Setup parameters */ H5_CHECKED_ASSIGN(total_chunks, size_t, fm->layout->u.chunk.nchunks, hsize_t); if (H5CX_get_mpio_chunk_opt_ratio(&percent_nproc_per_chunk) < 0) @@ -2544,6 +2995,20 @@ H5D__obtain_mpio_mode(H5D_io_info_t *io_info, H5D_chunk_map_t *fm, uint8_t assig size_t nproc; unsigned *nproc_per_chunk; + /* + * If enabled, disable collective metadata reads here. + * Since the chunk address mapping is done on rank 0 + * only here, it will cause problems if collective + * metadata reads are enabled. + */ + if (H5F_get_coll_metadata_reads(io_info->dset->oloc.file)) { + md_reads_file_flag = H5P_FORCE_FALSE; + md_reads_context_flag = FALSE; + H5F_set_coll_metadata_reads(io_info->dset->oloc.file, &md_reads_file_flag, + &md_reads_context_flag); + restore_md_reads_state = TRUE; + } + /* pre-computing: calculate number of processes and regularity of the selection occupied in each chunk */ if (NULL == (nproc_per_chunk = (unsigned *)H5MM_calloc(total_chunks * sizeof(unsigned)))) @@ -2610,6 +3075,10 @@ H5D__obtain_mpio_mode(H5D_io_info_t *io_info, H5D_chunk_map_t *fm, uint8_t assig #endif done: + /* Re-enable collective metadata reads if we disabled them */ + if (restore_md_reads_state) + H5F_set_coll_metadata_reads(io_info->dset->oloc.file, &md_reads_file_flag, &md_reads_context_flag); + if (io_mode_info) H5MM_free(io_mode_info); if (mergebuf) @@ -2623,34 +3092,32 @@ done: } /* end H5D__obtain_mpio_mode() */ /*------------------------------------------------------------------------- - * Function: H5D__construct_filtered_io_info_list + * Function: H5D__mpio_collective_filtered_chunk_io_setup * * Purpose: Constructs a list of entries which contain the necessary * information for inter-process communication when performing * collective io on filtered chunks. This list is used by - * each process when performing I/O on locally selected chunks - * and also in operations that must be collectively done - * on every chunk, such as chunk re-allocation, insertion of - * chunks into the chunk index, etc. + * each MPI rank when performing I/O on locally selected + * chunks and also in operations that must be collectively + * done on every chunk, such as chunk re-allocation, insertion + * of chunks into the chunk index, etc. * * Return: Non-negative on success/Negative on failure * - * Programmer: Jordan Henderson - * Tuesday, January 10th, 2017 - * *------------------------------------------------------------------------- */ static herr_t -H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - const H5D_chunk_map_t * fm, - H5D_filtered_collective_io_info_t **chunk_list, size_t *num_entries) +H5D__mpio_collective_filtered_chunk_io_setup(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, + const H5D_chunk_map_t * fm, + H5D_filtered_collective_io_info_t **chunk_list, + size_t *num_entries, int mpi_rank) { - H5D_filtered_collective_io_info_t *local_info_array = - NULL; /* The list of initially selected chunks for this process */ - size_t num_chunks_selected; - size_t i; - int mpi_rank; - herr_t ret_value = SUCCEED; + H5D_filtered_collective_io_info_t *local_info_array = NULL; + H5D_chunk_ud_t udata; + hbool_t filter_partial_edge_chunks; + size_t num_chunks_selected; + size_t i; + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC @@ -2660,19 +3127,23 @@ H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info, const H5D_typ HDassert(chunk_list); HDassert(num_entries); - if ((mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file)) < 0) - HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi rank") +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TRACE_ENTER(mpi_rank); + H5D_MPIO_TIME_START(mpi_rank, "Filtered Collective I/O Setup"); +#endif - /* Each process builds a local list of the chunks they have selected */ + /* Each rank builds a local list of the chunks they have selected */ if ((num_chunks_selected = H5SL_count(fm->sel_chunks))) { H5D_chunk_info_t *chunk_info; - H5D_chunk_ud_t udata; H5SL_node_t * chunk_node; hsize_t select_npoints; - hssize_t chunk_npoints; + hbool_t need_sort = FALSE; - if (NULL == (local_info_array = (H5D_filtered_collective_io_info_t *)H5MM_malloc( - num_chunks_selected * sizeof(H5D_filtered_collective_io_info_t)))) + /* Determine whether partial edge chunks should be filtered */ + filter_partial_edge_chunks = !(io_info->dset->shared->layout.u.chunk.flags & + H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS); + + if (NULL == (local_info_array = H5MM_malloc(num_chunks_selected * sizeof(*local_info_array)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate local io info array buffer") chunk_node = H5SL_first(fm->sel_chunks); @@ -2683,275 +3154,787 @@ H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info, const H5D_typ if (H5D__chunk_lookup(io_info->dset, chunk_info->scaled, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") - local_info_array[i].index = chunk_info->index; - local_info_array[i].chunk_states.chunk_current = local_info_array[i].chunk_states.new_chunk = - udata.chunk_block; - local_info_array[i].num_writers = 0; - local_info_array[i].owners.original_owner = local_info_array[i].owners.new_owner = mpi_rank; - local_info_array[i].buf = NULL; - - local_info_array[i].async_info.num_receive_requests = 0; - local_info_array[i].async_info.receive_buffer_array = NULL; - local_info_array[i].async_info.receive_requests_array = NULL; - - H5MM_memcpy(local_info_array[i].scaled, chunk_info->scaled, sizeof(chunk_info->scaled)); - - select_npoints = H5S_GET_SELECT_NPOINTS(chunk_info->mspace); - local_info_array[i].io_size = (size_t)select_npoints * type_info->src_type_size; - - /* Currently the full overwrite status of a chunk is only obtained on a per-process - * basis. This means that if the total selection in the chunk, as determined by the combination - * of selections of all of the processes interested in the chunk, covers the entire chunk, - * the performance optimization of not reading the chunk from the file is still valid, but - * is not applied in the current implementation. Something like an appropriately placed - * MPI_Allreduce or a running total of the number of chunk points selected during chunk - * redistribution should suffice for implementing this case - JTH. + /* Initialize rank-local chunk info */ + local_info_array[i].chunk_info = chunk_info; + local_info_array[i].chunk_buf_size = 0; + local_info_array[i].num_writers = 0; + local_info_array[i].orig_owner = mpi_rank; + local_info_array[i].new_owner = mpi_rank; + local_info_array[i].buf = NULL; + + select_npoints = H5S_GET_SELECT_NPOINTS(chunk_info->fspace); + local_info_array[i].io_size = (size_t)select_npoints * type_info->dst_type_size; + + /* + * Determine whether this chunk will need to be read from the file. If this is + * a read operation, the chunk will be read. If this is a write operation, we + * generally need to read a filtered chunk from the file before modifying it, + * unless the chunk is being fully overwritten. + * + * TODO: Currently the full overwrite status of a chunk is only obtained on a + * per-rank basis. This means that if the total selection in the chunk, as + * determined by the combination of selections of all of the ranks interested in + * the chunk, covers the entire chunk, the performance optimization of not reading + * the chunk from the file is still valid, but is not applied in the current + * implementation. + * + * To implement this case, a few approaches were considered: + * + * - Keep a running total (distributed to each rank) of the number of chunk + * elements selected during chunk redistribution and compare that to the total + * number of elements in the chunk once redistribution is finished + * + * - Process all incoming chunk messages before doing I/O (these are currently + * processed AFTER doing I/O), combine the owning rank's selection in a chunk + * with the selections received from other ranks and check to see whether that + * combined selection covers the entire chunk + * + * The first approach will be dangerous if the application performs an overlapping + * write to a chunk, as the number of selected elements can equal or exceed the + * number of elements in the chunk without the whole chunk selection being covered. + * While it might be considered erroneous for an application to do an overlapping + * write, we don't explicitly disallow it. + * + * The second approach contains a bit of complexity in that part of the chunk + * messages will be needed before doing I/O and part will be needed after doing I/O. + * Since modification data from chunk messages can't be applied until after any I/O + * is performed (otherwise, we'll overwrite any applied modification data), chunk + * messages are currently entirely processed after I/O. However, in order to determine + * if a chunk is being fully overwritten, we need the dataspace portion of the chunk + * messages before doing I/O. The naive way to do this is to process chunk messages + * twice, using just the relevant information from the message before and after I/O. + * The better way would be to avoid processing chunk messages twice by extracting (and + * keeping around) the dataspace portion of the message before I/O and processing the + * rest of the chunk message after I/O. Note that the dataspace portion of each chunk + * message is used to correctly apply chunk modification data from the message, so + * must be kept around both before and after I/O in this case. + */ + if (io_info->op_type == H5D_IO_OP_READ) + local_info_array[i].need_read = TRUE; + else { + local_info_array[i].need_read = + local_info_array[i].io_size < (size_t)io_info->dset->shared->layout.u.chunk.size; + } + + local_info_array[i].skip_filter_pline = FALSE; + if (!filter_partial_edge_chunks) { + /* + * If this is a partial edge chunk and the "don't filter partial edge + * chunks" flag is set, make sure not to apply filters to the chunk. + */ + if (H5D__chunk_is_partial_edge_chunk(io_info->dset->shared->ndims, + io_info->dset->shared->layout.u.chunk.dim, + chunk_info->scaled, io_info->dset->shared->curr_dims)) + local_info_array[i].skip_filter_pline = TRUE; + } + + /* Initialize the chunk's shared info */ + local_info_array[i].chunk_current = udata.chunk_block; + local_info_array[i].chunk_new = udata.chunk_block; + + /* + * Check if the list is not in ascending order of offset in the file + * or has unallocated chunks. In either case, the list should get + * sorted. + */ + if (i) { + haddr_t curr_chunk_offset = local_info_array[i].chunk_current.offset; + haddr_t prev_chunk_offset = local_info_array[i - 1].chunk_current.offset; + + if (!H5F_addr_defined(prev_chunk_offset) || !H5F_addr_defined(curr_chunk_offset) || + (curr_chunk_offset < prev_chunk_offset)) + need_sort = TRUE; + } + + /* + * Extensible arrays may calculate a chunk's index a little differently + * than normal when the dataset's unlimited dimension is not the + * slowest-changing dimension, so set the index here based on what the + * extensible array code calculated instead of what was calculated + * in the chunk file mapping. */ - if ((chunk_npoints = H5S_GET_EXTENT_NPOINTS(chunk_info->fspace)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid") - local_info_array[i].full_overwrite = - (local_info_array[i].io_size >= (hsize_t)chunk_npoints * type_info->dst_type_size) ? TRUE - : FALSE; + if (io_info->dset->shared->layout.u.chunk.idx_type == H5D_CHUNK_IDX_EARRAY) + local_info_array[i].index_info.chunk_idx = udata.chunk_idx; + else + local_info_array[i].index_info.chunk_idx = chunk_info->index; + + local_info_array[i].index_info.filter_mask = udata.filter_mask; + local_info_array[i].index_info.need_insert = FALSE; chunk_node = H5SL_next(chunk_node); - } /* end for */ - } /* end if */ + } - /* Redistribute shared chunks to new owners as necessary */ - if (io_info->op_type == H5D_IO_OP_WRITE) -#if MPI_VERSION >= 3 - if (H5D__chunk_redistribute_shared_chunks(io_info, type_info, fm, local_info_array, - &num_chunks_selected) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to redistribute shared chunks") -#else - HGOTO_ERROR( - H5E_DATASET, H5E_WRITEERROR, FAIL, - "unable to redistribute shared chunks - MPI version < 3 (MPI_Mprobe and MPI_Imrecv missing)") + /* Ensure the chunk list is sorted in ascending order of offset in the file */ + if (need_sort) + HDqsort(local_info_array, num_chunks_selected, sizeof(H5D_filtered_collective_io_info_t), + H5D__cmp_filtered_collective_io_info_entry); + +#ifdef H5Dmpio_DEBUG + H5D__mpio_dump_collective_filtered_chunk_list(local_info_array, num_chunks_selected, mpi_rank); #endif + } + else if (H5F_get_coll_metadata_reads(io_info->dset->oloc.file)) { + hsize_t scaled[H5O_LAYOUT_NDIMS] = {0}; + + /* + * If this rank has no selection in the dataset and collective + * metadata reads are enabled, do a fake lookup of a chunk to + * ensure that this rank has the chunk index opened. Otherwise, + * only the ranks that had a selection will have opened the + * chunk index and they will have done so independently. Therefore, + * when ranks with no selection participate in later collective + * metadata reads, they will try to open the chunk index collectively + * and issues will occur since other ranks won't participate. + * + * In the future, we should consider having a chunk index "open" + * callback that can be used to ensure collectivity between ranks + * in a more natural way, but this hack should suffice for now. + */ + if (H5D__chunk_lookup(io_info->dset, scaled, &udata) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") + } *chunk_list = local_info_array; *num_entries = num_chunks_selected; done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D__construct_filtered_io_info_list() */ +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TIME_STOP(mpi_rank); + H5D_MPIO_TRACE_EXIT(mpi_rank); +#endif -#if MPI_VERSION >= 3 + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__mpio_collective_filtered_chunk_io_setup() */ /*------------------------------------------------------------------------- - * Function: H5D__chunk_redistribute_shared_chunks - * - * Purpose: When performing a collective write on a Dataset with - * filters applied, this function is used to redistribute any - * chunks which are selected by more than one process, so as - * to preserve file integrity after the write by ensuring - * that any shared chunks are only modified by one process. - * - * The current implementation follows this 3-phase process: - * - * - Collect everyone's list of chunks into one large list, - * sort the list in increasing order of chunk offset in the - * file and hand the list off to rank 0 - * - * - Rank 0 scans the list looking for matching runs of chunk - * offset in the file (corresponding to a shared chunk which - * has been selected by more than one rank in the I/O - * operation) and for each shared chunk, it redistributes - * the chunk to the process writing to the chunk which - * currently has the least amount of chunks assigned to it - * by modifying the "new_owner" field in each of the list - * entries corresponding to that chunk - * - * - After the chunks have been redistributed, rank 0 re-sorts - * the list in order of previous owner so that each rank - * will get back exactly the array that they contributed to - * the redistribution operation, with the "new_owner" field - * of each chunk they are modifying having possibly been - * modified. Rank 0 then scatters each segment of the list - * back to its corresponding rank + * Function: H5D__mpio_redistribute_shared_chunks + * + * Purpose: When performing a parallel write on a chunked Dataset with + * filters applied, we must ensure that any particular chunk + * is only written to by a single MPI rank in order to avoid + * potential data races on the chunk. This function is used to + * redistribute (by assigning ownership to a single rank) any + * chunks which are selected by more than one MPI rank. + * + * An initial Allgather is performed to determine how many + * chunks each rank has selected in the write operation and + * then that number is compared against a threshold value to + * determine whether chunk redistribution should be done on + * MPI rank 0 only, or on all MPI ranks. * * Return: Non-negative on success/Negative on failure * - * Programmer: Jordan Henderson - * Monday, May 1, 2017 + *------------------------------------------------------------------------- + */ +static herr_t +H5D__mpio_redistribute_shared_chunks(H5D_filtered_collective_io_info_t *chunk_list, + size_t chunk_list_num_entries, const H5D_io_info_t *io_info, + const H5D_chunk_map_t *fm, int mpi_rank, int mpi_size, + size_t **rank_chunks_assigned_map) +{ + hbool_t redistribute_on_all_ranks; + size_t *num_chunks_map = NULL; + size_t coll_chunk_list_size = 0; + size_t i; + int mpi_code; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_STATIC + + HDassert(chunk_list || 0 == chunk_list_num_entries); + HDassert(io_info); + HDassert(fm); + HDassert(mpi_size > 1); /* No chunk sharing is possible for MPI Comm size of 1 */ + +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TRACE_ENTER(mpi_rank); + H5D_MPIO_TIME_START(mpi_rank, "Redistribute shared chunks"); +#endif + + /* + * Allocate an array for each rank to keep track of the number of + * chunks assigned to any other rank in order to cut down on future + * MPI communication. + */ + if (NULL == (num_chunks_map = H5MM_malloc((size_t)mpi_size * sizeof(*num_chunks_map)))) + HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "couldn't allocate assigned chunks array") + + /* Perform initial Allgather to determine the collective chunk list size */ + if (MPI_SUCCESS != (mpi_code = MPI_Allgather(&chunk_list_num_entries, 1, H5_SIZE_T_AS_MPI_TYPE, + num_chunks_map, 1, H5_SIZE_T_AS_MPI_TYPE, io_info->comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Allgather failed", mpi_code) + + for (i = 0; i < (size_t)mpi_size; i++) + coll_chunk_list_size += num_chunks_map[i]; + + /* + * Determine whether we should perform chunk redistribution on all + * ranks or just rank 0. For a relatively small number of chunks, + * we redistribute on all ranks to cut down on MPI communication + * overhead. For a larger number of chunks, we redistribute on + * rank 0 only to cut down on memory usage. + */ + redistribute_on_all_ranks = coll_chunk_list_size < H5D_CHUNK_REDISTRIBUTE_THRES; + + if (H5D__mpio_redistribute_shared_chunks_int(chunk_list, num_chunks_map, redistribute_on_all_ranks, + io_info, fm, mpi_rank, mpi_size) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTREDISTRIBUTE, FAIL, "can't redistribute shared chunks") + + /* + * If the caller provided a pointer for the mapping from + * rank value -> number of chunks assigned, return that + * mapping here. + */ + if (rank_chunks_assigned_map) { + /* + * If we performed chunk redistribution on rank 0 only, distribute + * the rank value -> number of chunks assigned mapping back to all + * ranks. + */ + if (!redistribute_on_all_ranks) { + if (MPI_SUCCESS != + (mpi_code = MPI_Bcast(num_chunks_map, mpi_size, H5_SIZE_T_AS_MPI_TYPE, 0, io_info->comm))) + HMPI_GOTO_ERROR(FAIL, "couldn't broadcast chunk mapping to other ranks", mpi_code) + } + + *rank_chunks_assigned_map = num_chunks_map; + } + +done: + if (!rank_chunks_assigned_map || (ret_value < 0)) { + num_chunks_map = H5MM_xfree(num_chunks_map); + } + +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TIME_STOP(mpi_rank); + H5D_MPIO_TRACE_EXIT(mpi_rank); +#endif + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__mpio_redistribute_shared_chunks() */ + +/*------------------------------------------------------------------------- + * Function: H5D__mpio_redistribute_shared_chunks_int + * + * Purpose: Routine to perform redistribution of shared chunks during + * parallel writes to datasets with filters applied. + * + * If `all_ranks_involved` is TRUE, chunk redistribution + * occurs on all MPI ranks. This is usually done when there + * is a relatively small number of chunks involved in order to + * cut down on MPI communication overhead while increasing + * total memory usage a bit. + * + * If `all_ranks_involved` is FALSE, only rank 0 will perform + * chunk redistribution. This is usually done when there is + * a relatively large number of chunks involved in order to + * cut down on total memory usage at the cost of increased + * overhead from MPI communication. + * + * This implementation is as follows: + * + * - All MPI ranks send their list of selected chunks to the + * ranks involved in chunk redistribution. Then, the + * involved ranks sort this new list in order of chunk + * index. + * + * - The involved ranks scan the list looking for matching + * runs of chunk index values (corresponding to a shared + * chunk which has been selected by more than one rank in + * the I/O operation) and for each shared chunk, + * redistribute the chunk to the MPI rank writing to the + * chunk which currently has the least amount of chunks + * assigned to it. This is done by modifying the "new_owner" + * field in each of the list entries corresponding to that + * chunk. The involved ranks then re-sort the list in order + * of original chunk owner so that each rank's section of + * contributed chunks is contiguous in the collective chunk + * list. + * + * - If chunk redistribution occurred on all ranks, each rank + * scans through the collective chunk list to find their + * contributed section of chunks and uses that to update + * their local chunk list with the newly-updated "new_owner" + * and "num_writers" fields. If chunk redistribution + * occurred only on rank 0, an MPI_Scatterv operation will + * be used to scatter the segments of the collective chunk + * list from rank 0 back to the corresponding ranks. + * + * Return: Non-negative on success/Negative on failure * *------------------------------------------------------------------------- */ static herr_t -H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - const H5D_chunk_map_t * fm, - H5D_filtered_collective_io_info_t *local_chunk_array, - size_t * local_chunk_array_num_entries) +H5D__mpio_redistribute_shared_chunks_int(H5D_filtered_collective_io_info_t *chunk_list, + size_t *num_chunks_assigned_map, hbool_t all_ranks_involved, + const H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, + int mpi_rank, int mpi_size) { - H5D_filtered_collective_io_info_t *shared_chunks_info_array = - NULL; /* The list of all chunks selected in the operation by all processes */ - H5S_sel_iter_t *mem_iter = NULL; /* Memory iterator for H5D__gather_mem */ - unsigned char **mod_data = - NULL; /* Array of chunk modification data buffers sent by a process to new chunk owners */ - MPI_Request *send_requests = NULL; /* Array of MPI_Isend chunk modification data send requests */ - MPI_Status * send_statuses = NULL; /* Array of MPI_Isend chunk modification send statuses */ - hbool_t mem_iter_init = FALSE; - size_t shared_chunks_info_array_num_entries = 0; - size_t num_send_requests = 0; - size_t * num_assigned_chunks_array = NULL; - size_t i, last_assigned_idx; - int * send_counts = NULL; - int * send_displacements = NULL; - int scatter_recvcount_int; - int mpi_rank, mpi_size, mpi_code; + MPI_Datatype struct_type; + MPI_Datatype packed_type; + hbool_t struct_type_derived = FALSE; + hbool_t packed_type_derived = FALSE; + size_t i; + size_t coll_chunk_list_num_entries = 0; + void * coll_chunk_list = NULL; + int * counts_disps_array = NULL; + int * counts_ptr = NULL; + int * displacements_ptr = NULL; + int num_chunks_int; + int mpi_code; herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC + HDassert(num_chunks_assigned_map); + HDassert(chunk_list || 0 == num_chunks_assigned_map[mpi_rank]); HDassert(io_info); - HDassert(type_info); HDassert(fm); - HDassert(local_chunk_array_num_entries); + HDassert(mpi_size > 1); - if ((mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file)) < 0) - HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi rank") - if ((mpi_size = H5F_mpi_get_size(io_info->dset->oloc.file)) < 0) - HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi size") +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TRACE_ENTER(mpi_rank); + H5D_MPIO_TIME_START(mpi_rank, "Redistribute shared chunks (internal)"); +#endif - /* Set to latest format for encoding dataspace */ - H5CX_set_libver_bounds(NULL); + /* + * Make sure it's safe to cast this rank's number + * of chunks to be sent into an int for MPI + */ + H5_CHECKED_ASSIGN(num_chunks_int, int, num_chunks_assigned_map[mpi_rank], size_t); + + /* + * Phase 1 - Participate in collective gathering of every rank's + * list of chunks to the ranks which are performing the redistribution + * operation. + */ - if (*local_chunk_array_num_entries) - if (NULL == (send_requests = - (MPI_Request *)H5MM_malloc(*local_chunk_array_num_entries * sizeof(MPI_Request)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate send requests buffer") + if (all_ranks_involved || (mpi_rank == 0)) { + /* + * Allocate array to store the receive counts of each rank, as well as + * the displacements into the final array where each rank will place + * their data. The first half of the array contains the receive counts + * (in rank order), while the latter half contains the displacements + * (also in rank order). + */ + if (NULL == (counts_disps_array = H5MM_malloc(2 * (size_t)mpi_size * sizeof(*counts_disps_array)))) { + /* Push an error, but still participate in collective gather operation */ + HDONE_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, + "couldn't allocate receive counts and displacements array") + } + else { + /* Set the receive counts from the assigned chunks map */ + counts_ptr = counts_disps_array; - if (NULL == (mem_iter = (H5S_sel_iter_t *)H5MM_malloc(sizeof(H5S_sel_iter_t)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate memory iterator") + for (i = 0; i < (size_t)mpi_size; i++) + H5_CHECKED_ASSIGN(counts_ptr[i], int, num_chunks_assigned_map[i], size_t); + + /* Set the displacements into the receive buffer for the gather operation */ + displacements_ptr = &counts_disps_array[mpi_size]; + + *displacements_ptr = 0; + for (i = 1; i < (size_t)mpi_size; i++) + displacements_ptr[i] = displacements_ptr[i - 1] + counts_ptr[i - 1]; + } + } + + /* + * Construct MPI derived types for extracting information + * necessary for MPI communication + */ + if (H5D__mpio_get_chunk_redistribute_info_types(&packed_type, &packed_type_derived, &struct_type, + &struct_type_derived) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, + "can't create derived datatypes for chunk redistribution info") + + /* Perform gather operation */ + if (H5_mpio_gatherv_alloc(chunk_list, num_chunks_int, struct_type, counts_ptr, displacements_ptr, + packed_type, all_ranks_involved, 0, io_info->comm, mpi_rank, mpi_size, + &coll_chunk_list, &coll_chunk_list_num_entries) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL, + "can't gather chunk redistribution info to involved ranks") + + /* + * If all ranks are redistributing shared chunks, we no + * longer need the receive counts and displacements array + */ + if (all_ranks_involved) { + counts_disps_array = H5MM_xfree(counts_disps_array); + } - /* Gather every rank's list of chunks to rank 0 to allow it to perform the redistribution operation. After - * this call, the gathered list will initially be sorted in increasing order of chunk offset in the file. + /* + * Phase 2 - Involved ranks now redistribute any shared chunks to new + * owners as necessary. */ - if (H5D__mpio_array_gatherv(local_chunk_array, *local_chunk_array_num_entries, - sizeof(H5D_filtered_collective_io_info_t), (void **)&shared_chunks_info_array, - &shared_chunks_info_array_num_entries, false, 0, io_info->comm, - H5D__cmp_filtered_collective_io_info_entry) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL, "couldn't gather array") - /* Rank 0 redistributes any shared chunks to new owners as necessary */ - if (mpi_rank == 0) { - if (NULL == (send_counts = (int *)H5MM_calloc((size_t)mpi_size * sizeof(int)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate send counts buffer") + if (all_ranks_involved || (mpi_rank == 0)) { + H5D_chunk_redistribute_info_t *chunk_entry; + hsize_t curr_chunk_idx; + size_t set_begin_index; + int num_writers; + int new_chunk_owner; - if (NULL == (send_displacements = (int *)H5MM_malloc((size_t)mpi_size * sizeof(int)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate send displacements buffer") + /* Clear the mapping from rank value -> number of assigned chunks */ + HDmemset(num_chunks_assigned_map, 0, (size_t)mpi_size * sizeof(*num_chunks_assigned_map)); - if (NULL == (num_assigned_chunks_array = (size_t *)H5MM_calloc((size_t)mpi_size * sizeof(size_t)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, - "unable to allocate number of assigned chunks array") + /* Sort collective chunk list according to chunk index */ + HDqsort(coll_chunk_list, coll_chunk_list_num_entries, sizeof(H5D_chunk_redistribute_info_t), + H5D__cmp_chunk_redistribute_info); - for (i = 0; i < shared_chunks_info_array_num_entries;) { - H5D_filtered_collective_io_info_t *chunk_entry; - haddr_t last_seen_addr = shared_chunks_info_array[i].chunk_states.chunk_current.offset; - size_t set_begin_index = i; - size_t num_writers = 0; - int new_chunk_owner = shared_chunks_info_array[i].owners.original_owner; + /* + * Process all chunks in the collective chunk list. + * Note that the loop counter is incremented by both + * the outer loop (while processing each entry in + * the collective chunk list) and the inner loop + * (while processing duplicate entries for shared + * chunks). + */ + chunk_entry = &((H5D_chunk_redistribute_info_t *)coll_chunk_list)[0]; + for (i = 0; i < coll_chunk_list_num_entries;) { + /* Set chunk's initial new owner to its original owner */ + new_chunk_owner = chunk_entry->orig_owner; + + /* + * Set the current chunk index so we know when we've processed + * all duplicate entries for a particular shared chunk + */ + curr_chunk_idx = chunk_entry->chunk_idx; - /* Process each set of duplicate entries caused by another process writing to the same chunk */ - do { - chunk_entry = &shared_chunks_info_array[i]; + /* Reset the initial number of writers to this chunk */ + num_writers = 0; - send_counts[chunk_entry->owners.original_owner] += (int)sizeof(*chunk_entry); + /* Set index for the beginning of this section of duplicate chunk entries */ + set_begin_index = i; - /* The new owner of the chunk is determined by the process + /* + * Process each chunk entry in the set for the current + * (possibly shared) chunk and increment the loop counter + * while doing so. + */ + do { + /* + * The new owner of the chunk is determined by the rank * writing to the chunk which currently has the least amount * of chunks assigned to it */ - if (num_assigned_chunks_array[chunk_entry->owners.original_owner] < - num_assigned_chunks_array[new_chunk_owner]) - new_chunk_owner = chunk_entry->owners.original_owner; + if (num_chunks_assigned_map[chunk_entry->orig_owner] < + num_chunks_assigned_map[new_chunk_owner]) + new_chunk_owner = chunk_entry->orig_owner; + /* Update the number of writers to this particular chunk */ num_writers++; - } while (++i < shared_chunks_info_array_num_entries && - shared_chunks_info_array[i].chunk_states.chunk_current.offset == last_seen_addr); - /* Set all of the chunk entries' "new_owner" fields */ + chunk_entry++; + } while (++i < coll_chunk_list_num_entries && chunk_entry->chunk_idx == curr_chunk_idx); + + /* We should never have more writers to a chunk than the number of MPI ranks */ + HDassert(num_writers <= mpi_size); + + /* Set all processed chunk entries' "new_owner" and "num_writers" fields */ for (; set_begin_index < i; set_begin_index++) { - shared_chunks_info_array[set_begin_index].owners.new_owner = new_chunk_owner; - shared_chunks_info_array[set_begin_index].num_writers = num_writers; - } /* end for */ + H5D_chunk_redistribute_info_t *entry; - num_assigned_chunks_array[new_chunk_owner]++; - } /* end for */ + entry = &((H5D_chunk_redistribute_info_t *)coll_chunk_list)[set_begin_index]; + + entry->new_owner = new_chunk_owner; + entry->num_writers = num_writers; + } + + /* Update the number of chunks assigned to the MPI rank that now owns this chunk */ + num_chunks_assigned_map[new_chunk_owner]++; + } - /* Sort the new list in order of previous owner so that each original owner of a chunk - * entry gets that entry back, with the possibly newly-modified "new_owner" field + /* + * Re-sort the collective chunk list in order of original chunk owner + * so that each rank's section of contributed chunks is contiguous in + * the collective chunk list. + * + * NOTE: this re-sort is frail in that it needs to sort the collective + * chunk list so that each rank's section of contributed chunks + * is in the exact order it was contributed in, or things will + * be scrambled when each rank's local chunk list is updated. + * Therefore, the sorting algorithm here is tied to the one + * used during the I/O setup operation. Specifically, chunks + * are first sorted by ascending order of offset in the file and + * then by chunk index. In the future, a better redistribution + * algorithm may be devised that doesn't rely on frail sorting, + * but the current implementation is a quick and naive approach. */ - if (shared_chunks_info_array_num_entries > 1) - HDqsort(shared_chunks_info_array, shared_chunks_info_array_num_entries, - sizeof(H5D_filtered_collective_io_info_t), - H5D__cmp_filtered_collective_io_info_entry_owner); - - send_displacements[0] = 0; - for (i = 1; i < (size_t)mpi_size; i++) - send_displacements[i] = send_displacements[i - 1] + send_counts[i - 1]; - } /* end if */ + HDqsort(coll_chunk_list, coll_chunk_list_num_entries, sizeof(H5D_chunk_redistribute_info_t), + H5D__cmp_chunk_redistribute_info_orig_owner); + } - /* Scatter the segments of the list back to each process */ - H5_CHECKED_ASSIGN(scatter_recvcount_int, int, - *local_chunk_array_num_entries * sizeof(H5D_filtered_collective_io_info_t), size_t); - if (MPI_SUCCESS != - (mpi_code = MPI_Scatterv(shared_chunks_info_array, send_counts, send_displacements, MPI_BYTE, - local_chunk_array, scatter_recvcount_int, MPI_BYTE, 0, io_info->comm))) - HMPI_GOTO_ERROR(FAIL, "unable to scatter shared chunks info buffer", mpi_code) + if (all_ranks_involved) { + /* + * If redistribution occurred on all ranks, search for the section + * in the collective chunk list corresponding to this rank's locally + * selected chunks and update the local list after redistribution. + */ + for (i = 0; i < coll_chunk_list_num_entries; i++) + if (mpi_rank == ((H5D_chunk_redistribute_info_t *)coll_chunk_list)[i].orig_owner) + break; - if (shared_chunks_info_array) { - H5MM_free(shared_chunks_info_array); - shared_chunks_info_array = NULL; - } /* end if */ + for (size_t j = 0; j < (size_t)num_chunks_int; j++) { + H5D_chunk_redistribute_info_t *coll_entry; + + coll_entry = &((H5D_chunk_redistribute_info_t *)coll_chunk_list)[i++]; + + chunk_list[j].new_owner = coll_entry->new_owner; + chunk_list[j].num_writers = coll_entry->num_writers; + } + } + else { + /* + * If redistribution occurred only on rank 0, scatter the segments + * of the collective chunk list back to each rank so that their + * local chunk lists get updated + */ + if (MPI_SUCCESS != + (mpi_code = MPI_Scatterv(coll_chunk_list, counts_ptr, displacements_ptr, packed_type, chunk_list, + num_chunks_int, struct_type, 0, io_info->comm))) + HMPI_GOTO_ERROR(FAIL, "unable to scatter shared chunks info buffer", mpi_code) + } + +#ifdef H5Dmpio_DEBUG + H5D__mpio_dump_collective_filtered_chunk_list(chunk_list, num_chunks_assigned_map[mpi_rank], mpi_rank); +#endif + +done: + H5MM_free(coll_chunk_list); + + if (struct_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&struct_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + } + if (packed_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&packed_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + } + + H5MM_free(counts_disps_array); + +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TIME_STOP(mpi_rank); + H5D_MPIO_TRACE_EXIT(mpi_rank); +#endif + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__mpio_redistribute_shared_chunks_int() */ + +/*------------------------------------------------------------------------- + * Function: H5D__mpio_share_chunk_modification_data + * + * Purpose: When performing a parallel write on a chunked dataset with + * filters applied, we must first ensure that any particular + * chunk is only written to by a single MPI rank in order to + * avoid potential data races on the chunk. Once dataset + * chunks have been redistributed in a suitable manner, each + * MPI rank must send its chunk data to other ranks for each + * chunk it no longer owns. + * + * The current implementation here follows the Nonblocking + * Consensus algorithm described in: + * http://unixer.de/publications/img/hoefler-dsde-protocols.pdf + * + * First, each MPI rank scans through its list of selected + * chunks and does the following for each chunk: + * + * * If a chunk in the MPI rank's chunk list is still owned + * by that rank, the rank checks how many messages are + * incoming for that chunk and adds that to its running + * total. Then, the rank updates its local chunk list so + * that any previous chunk entries for chunks that are no + * longer owned by the rank get overwritten by chunk + * entries for chunks the rank still owns. Since the data + * for the chunks no longer owned will have already been + * sent, those chunks can effectively be discarded. + * * If a chunk in the MPI rank's chunk list is no longer + * owned by that rank, the rank sends the data it wishes to + * update the chunk with to the MPI rank that now has + * ownership of that chunk. To do this, it encodes the + * chunk's index, its selection in the chunk and its + * modification data into a buffer and then posts a + * non-blocking MPI_Issend to the owning rank. + * + * Once this step is complete, all MPI ranks allocate arrays + * to hold chunk message receive buffers and MPI request + * objects for each non-blocking receive they will post for + * incoming chunk modification messages. Then, all MPI ranks + * enter a loop that alternates between non-blocking + * MPI_Iprobe calls to probe for incoming messages and + * MPI_Testall calls to see if all send requests have + * completed. As chunk modification messages arrive, + * non-blocking MPI_Irecv calls will be posted for each + * message. + * + * Once all send requests have completed, an MPI_Ibarrier is + * posted and the loop then alternates between MPI_Iprobe + * calls and MPI_Test calls to check if all ranks have reached + * the non-blocking barrier. Once all ranks have reached the + * barrier, processing can move on to updating the selected + * chunks that are owned in the operation. + * + * Any chunk messages that were received from other ranks + * will be returned through the `chunk_msg_bufs` array and + * `chunk_msg_bufs_len` will be set appropriately. + * + * NOTE: The use of non-blocking sends and receives of chunk + * data here may contribute to large amounts of memory + * usage/MPI request overhead if the number of shared + * chunks is high. If this becomes a problem, it may be + * useful to split the message receiving loop away so + * that chunk modification messages can be received and + * processed immediately (MPI_Recv) using a single chunk + * message buffer. However, it's possible this may + * degrade performance since the chunk message sends + * are synchronous (MPI_Issend) in the Nonblocking + * Consensus algorithm. + * + * Return: Non-negative on success/Negative on failure + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__mpio_share_chunk_modification_data(H5D_filtered_collective_io_info_t *chunk_list, + size_t *chunk_list_num_entries, H5D_io_info_t *io_info, + const H5D_type_info_t *type_info, int mpi_rank, int mpi_size, + H5D_filtered_collective_io_info_t **chunk_hash_table, + unsigned char ***chunk_msg_bufs, int *chunk_msg_bufs_len) +{ +#if MPI_VERSION >= 3 + H5D_filtered_collective_io_info_t *chunk_table = NULL; + H5S_sel_iter_t * mem_iter = NULL; + unsigned char ** msg_send_bufs = NULL; + unsigned char ** msg_recv_bufs = NULL; + MPI_Request * send_requests = NULL; + MPI_Request * recv_requests = NULL; + MPI_Request ibarrier = MPI_REQUEST_NULL; + hbool_t mem_iter_init = FALSE; + hbool_t ibarrier_posted = FALSE; + size_t send_bufs_nalloc = 0; + size_t num_send_requests = 0; + size_t num_recv_requests = 0; + size_t num_msgs_incoming = 0; + size_t last_assigned_idx; + size_t i; + int mpi_code; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_STATIC + + HDassert(chunk_list_num_entries); + HDassert(chunk_list || 0 == *chunk_list_num_entries); + HDassert(io_info); + HDassert(type_info); + HDassert(mpi_size > 1); + HDassert(chunk_msg_bufs); + HDassert(chunk_msg_bufs_len); + +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TRACE_ENTER(mpi_rank); + H5D_MPIO_TIME_START(mpi_rank, "Share chunk modification data"); +#endif + + /* Set to latest format for encoding dataspace */ + H5CX_set_libver_bounds(NULL); + + if (*chunk_list_num_entries) { + /* Allocate a selection iterator for iterating over chunk dataspaces */ + if (NULL == (mem_iter = H5FL_MALLOC(H5S_sel_iter_t))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate dataspace selection iterator") - /* Now that the chunks have been redistributed, each process must send its modification data - * to the new owners of any of the chunks it previously possessed. Accordingly, each process - * must also issue asynchronous receives for any messages it may receive for each of the - * chunks it is assigned, in order to avoid potential deadlocking issues. + /* + * Allocate send buffer and MPI_Request arrays for non-blocking + * sends of outgoing chunk messages + */ + send_bufs_nalloc = H5D_CHUNK_NUM_SEND_MSGS_INIT; + if (NULL == (msg_send_bufs = H5MM_malloc(send_bufs_nalloc * sizeof(*msg_send_bufs)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, + "couldn't allocate chunk modification message buffer array") + + if (NULL == (send_requests = H5MM_malloc(send_bufs_nalloc * sizeof(*send_requests)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate send requests array") + } + + /* + * For each chunk this rank owns, add to the total number of + * incoming MPI messages, then update the local chunk list to + * overwrite any previous chunks no longer owned by this rank. + * Since the data for those chunks will have already been sent, + * this rank should no longer be interested in them and they + * can effectively be discarded. This bookkeeping also makes + * the code for the collective file space re-allocation and + * chunk re-insertion operations a bit simpler. + * + * For each chunk this rank doesn't own, use non-blocking + * synchronous sends to send the data this rank is writing to + * the rank that does own the chunk. */ - if (*local_chunk_array_num_entries) - if (NULL == (mod_data = (unsigned char **)H5MM_malloc(*local_chunk_array_num_entries * - sizeof(unsigned char *)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate modification data buffer array") - - /* Perform all the sends on the chunks that this rank doesn't own */ - /* (Sends and recvs must be two separate loops, to avoid deadlock) */ - for (i = 0, last_assigned_idx = 0; i < *local_chunk_array_num_entries; i++) { - H5D_filtered_collective_io_info_t *chunk_entry = &local_chunk_array[i]; - - if (mpi_rank != chunk_entry->owners.new_owner) { - H5D_chunk_info_t *chunk_info = NULL; + for (i = 0, last_assigned_idx = 0; i < *chunk_list_num_entries; i++) { + H5D_filtered_collective_io_info_t *chunk_entry = &chunk_list[i]; + + if (mpi_rank == chunk_entry->new_owner) { + num_msgs_incoming += (size_t)(chunk_entry->num_writers - 1); + + /* + * Overwrite chunk entries this rank doesn't own with entries that it + * does own, since it has sent the necessary data and is no longer + * interested in the chunks it doesn't own. + */ + chunk_list[last_assigned_idx] = chunk_list[i]; + + /* + * Since, at large scale, a chunk's index value may be larger than + * the maximum value that can be stored in an int, we cannot rely + * on using a chunk's index value as the tag for the MPI messages + * sent/received for a chunk. Therefore, add this chunk to a hash + * table with the chunk's index as a key so that we can quickly find + * the chunk when processing chunk messages that were received. The + * message itself will contain the chunk's index so we can update + * the correct chunk with the received data. + */ + HASH_ADD(hh, chunk_table, index_info.chunk_idx, sizeof(hsize_t), &chunk_list[last_assigned_idx]); + + last_assigned_idx++; + } + else { + H5D_chunk_info_t *chunk_info = chunk_entry->chunk_info; unsigned char * mod_data_p = NULL; hsize_t iter_nelmts; - size_t mod_data_size; + size_t mod_data_size = 0; + size_t space_size = 0; - /* Look up the chunk and get its file and memory dataspaces */ - if (NULL == (chunk_info = (H5D_chunk_info_t *)H5SL_search(fm->sel_chunks, &chunk_entry->index))) - HGOTO_ERROR(H5E_DATASPACE, H5E_NOTFOUND, FAIL, "can't locate chunk in skip list") + /* Add the size of the chunk index to the encoded size */ + mod_data_size += sizeof(hsize_t); - /* Determine size of serialized chunk file dataspace, plus the size of - * the data being written - */ - if (H5S_encode(chunk_info->fspace, &mod_data_p, &mod_data_size) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "unable to get encoded dataspace size") + /* Determine size of serialized chunk file dataspace */ + if (H5S_encode(chunk_info->fspace, &mod_data_p, &space_size) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get encoded dataspace size") + mod_data_size += space_size; + /* Determine size of data being written */ iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace); - H5_CHECK_OVERFLOW(iter_nelmts, hsize_t, size_t); + mod_data_size += (size_t)iter_nelmts * type_info->src_type_size; - if (NULL == (mod_data[num_send_requests] = (unsigned char *)H5MM_malloc(mod_data_size))) + if (NULL == (msg_send_bufs[num_send_requests] = H5MM_malloc(mod_data_size))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, - "couldn't allocate chunk modification send buffer") + "couldn't allocate chunk modification message buffer") + + mod_data_p = msg_send_bufs[num_send_requests]; + + /* Store the chunk's index into the buffer */ + HDmemcpy(mod_data_p, &chunk_entry->index_info.chunk_idx, sizeof(hsize_t)); + mod_data_p += sizeof(hsize_t); /* Serialize the chunk's file dataspace into the buffer */ - mod_data_p = mod_data[num_send_requests]; if (H5S_encode(chunk_info->fspace, &mod_data_p, &mod_data_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "unable to encode dataspace") /* Initialize iterator for memory selection */ - if (H5S_select_iter_init(mem_iter, chunk_info->mspace, type_info->src_type_size, 0) < 0) + if (H5S_select_iter_init(mem_iter, chunk_info->mspace, type_info->src_type_size, + H5S_SEL_ITER_SHARE_WITH_DATASPACE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information") mem_iter_init = TRUE; @@ -2960,466 +3943,2057 @@ H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t *io_info, const H5D_ty if (0 == H5D__gather_mem(io_info->u.wbuf, mem_iter, (size_t)iter_nelmts, mod_data_p)) HGOTO_ERROR(H5E_IO, H5E_CANTGATHER, FAIL, "couldn't gather from write buffer") - /* Send modification data to new owner */ + /* + * Ensure that the size of the chunk data being sent can be + * safely cast to an int for MPI. Note that this should + * generally be OK for now (unless a rank is sending a + * whole 32-bit-sized chunk of data + its encoded selection), + * but if we allow larger than 32-bit-sized chunks in the + * future, this may become a problem and derived datatypes + * will need to be used. + */ H5_CHECK_OVERFLOW(mod_data_size, size_t, int) - H5_CHECK_OVERFLOW(chunk_entry->index, hsize_t, int) + + /* Send modification data to new owner */ if (MPI_SUCCESS != - (mpi_code = MPI_Isend(mod_data[num_send_requests], (int)mod_data_size, MPI_BYTE, - chunk_entry->owners.new_owner, (int)chunk_entry->index, io_info->comm, - &send_requests[num_send_requests]))) - HMPI_GOTO_ERROR(FAIL, "MPI_Isend failed", mpi_code) + (mpi_code = MPI_Issend(msg_send_bufs[num_send_requests], (int)mod_data_size, MPI_BYTE, + chunk_entry->new_owner, H5D_CHUNK_MOD_DATA_TAG, io_info->comm, + &send_requests[num_send_requests]))) + HMPI_GOTO_ERROR(FAIL, "MPI_Issend failed", mpi_code) + + num_send_requests++; + + /* Resize send buffer and send request arrays if necessary */ + if (num_send_requests == send_bufs_nalloc) { + void *tmp_alloc; + + send_bufs_nalloc = (size_t)((double)send_bufs_nalloc * 1.5); + + if (NULL == + (tmp_alloc = H5MM_realloc(msg_send_bufs, send_bufs_nalloc * sizeof(*msg_send_bufs)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, + "couldn't resize chunk modification message buffer array") + msg_send_bufs = tmp_alloc; - if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0) + if (NULL == + (tmp_alloc = H5MM_realloc(send_requests, send_bufs_nalloc * sizeof(*send_requests)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't resize send requests array") + send_requests = tmp_alloc; + } + + if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release memory selection iterator") mem_iter_init = FALSE; + } + } - num_send_requests++; - } /* end if */ - } /* end for */ + /* Check if the number of send or receive requests will overflow an int (MPI requirement) */ + if (num_send_requests > INT_MAX || num_msgs_incoming > INT_MAX) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, + "too many shared chunks in parallel filtered write operation") - /* Perform all the recvs on the chunks this rank owns */ - for (i = 0, last_assigned_idx = 0; i < *local_chunk_array_num_entries; i++) { - H5D_filtered_collective_io_info_t *chunk_entry = &local_chunk_array[i]; + H5_CHECK_OVERFLOW(num_send_requests, size_t, int) + H5_CHECK_OVERFLOW(num_msgs_incoming, size_t, int) - if (mpi_rank == chunk_entry->owners.new_owner) { - /* Allocate all necessary buffers for an asynchronous receive operation */ - if (chunk_entry->num_writers > 1) { - MPI_Message message; - MPI_Status status; - size_t j; + /* + * Allocate receive buffer and MPI_Request arrays for non-blocking + * receives of incoming chunk messages + */ + if (num_msgs_incoming) { + if (NULL == (msg_recv_bufs = H5MM_malloc(num_msgs_incoming * sizeof(*msg_recv_bufs)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, + "couldn't allocate chunk modification message buffer array") - chunk_entry->async_info.num_receive_requests = (int)chunk_entry->num_writers - 1; - if (NULL == (chunk_entry->async_info.receive_requests_array = (MPI_Request *)H5MM_malloc( - (size_t)chunk_entry->async_info.num_receive_requests * sizeof(MPI_Request)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate async requests array") + if (NULL == (recv_requests = H5MM_malloc(num_msgs_incoming * sizeof(*recv_requests)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate receive requests array") + } - if (NULL == - (chunk_entry->async_info.receive_buffer_array = (unsigned char **)H5MM_malloc( - (size_t)chunk_entry->async_info.num_receive_requests * sizeof(unsigned char *)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate async receive buffers") + /* Process any incoming messages until everyone is done */ + do { + MPI_Status status; + int msg_flag; - for (j = 0; j < chunk_entry->num_writers - 1; j++) { - int count = 0; + /* Probe for an incoming message from any rank */ + if (MPI_SUCCESS != (mpi_code = MPI_Iprobe(MPI_ANY_SOURCE, H5D_CHUNK_MOD_DATA_TAG, io_info->comm, + &msg_flag, &status))) + HMPI_GOTO_ERROR(FAIL, "MPI_Iprobe failed", mpi_code) - /* Probe for a particular message from any process, removing that message - * from the receive queue in the process and allocating that much memory - * for the asynchronous receive - */ - if (MPI_SUCCESS != (mpi_code = MPI_Mprobe(MPI_ANY_SOURCE, (int)chunk_entry->index, - io_info->comm, &message, &status))) - HMPI_GOTO_ERROR(FAIL, "MPI_Mprobe failed", mpi_code) - - if (MPI_SUCCESS != (mpi_code = MPI_Get_count(&status, MPI_BYTE, &count))) - HMPI_GOTO_ERROR(FAIL, "MPI_Get_count failed", mpi_code) - - HDassert(count >= 0); - if (NULL == (chunk_entry->async_info.receive_buffer_array[j] = - (unsigned char *)H5MM_malloc((size_t)count * sizeof(char *)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, - "unable to allocate modification data receive buffer") - - if (MPI_SUCCESS != (mpi_code = MPI_Imrecv( - chunk_entry->async_info.receive_buffer_array[j], count, MPI_BYTE, - &message, &chunk_entry->async_info.receive_requests_array[j]))) - HMPI_GOTO_ERROR(FAIL, "MPI_Imrecv failed", mpi_code) - } /* end for */ - } /* end if */ - - local_chunk_array[last_assigned_idx++] = local_chunk_array[i]; - } /* end else */ - } /* end for */ + /* + * If a message was found, allocate a buffer for the message and + * post a non-blocking receive to receive it + */ + if (msg_flag) { +#if MPI_VERSION >= 3 + MPI_Count msg_size = 0; - *local_chunk_array_num_entries = last_assigned_idx; + if (MPI_SUCCESS != (mpi_code = MPI_Get_elements_x(&status, MPI_BYTE, &msg_size))) + HMPI_GOTO_ERROR(FAIL, "MPI_Get_elements_x failed", mpi_code) - /* Wait for all async send requests to complete before returning */ - if (num_send_requests) { - if (NULL == (send_statuses = (MPI_Status *)H5MM_malloc(num_send_requests * sizeof(MPI_Status)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate send statuses buffer") + H5_CHECK_OVERFLOW(msg_size, MPI_Count, int) +#else + int msg_size = 0; - H5_CHECK_OVERFLOW(num_send_requests, size_t, int); - if (MPI_SUCCESS != (mpi_code = MPI_Waitall((int)num_send_requests, send_requests, send_statuses))) - HMPI_GOTO_ERROR(FAIL, "MPI_Waitall failed", mpi_code) - } /* end if */ + if (MPI_SUCCESS != (mpi_code = MPI_Get_elements(&status, MPI_BYTE, &msg_size))) + HMPI_GOTO_ERROR(FAIL, "MPI_Get_elements failed", mpi_code) +#endif -done: - /* Now that all async send requests have completed, free up the send - * buffers used in the async operations + if (msg_size <= 0) + HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "invalid chunk modification message size") + + HDassert((num_recv_requests + 1) <= num_msgs_incoming); + if (NULL == + (msg_recv_bufs[num_recv_requests] = H5MM_malloc((size_t)msg_size * sizeof(unsigned char)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, + "couldn't allocate chunk modification message receive buffer") + + if (MPI_SUCCESS != (mpi_code = MPI_Irecv(msg_recv_bufs[num_recv_requests], (int)msg_size, + MPI_BYTE, status.MPI_SOURCE, H5D_CHUNK_MOD_DATA_TAG, + io_info->comm, &recv_requests[num_recv_requests]))) + HMPI_GOTO_ERROR(FAIL, "MPI_Irecv failed", mpi_code) + + num_recv_requests++; + } + + if (ibarrier_posted) { + int ibarrier_completed; + + if (MPI_SUCCESS != (mpi_code = MPI_Test(&ibarrier, &ibarrier_completed, MPI_STATUS_IGNORE))) + HMPI_GOTO_ERROR(FAIL, "MPI_Test failed", mpi_code) + + if (ibarrier_completed) + break; + } + else { + int all_sends_completed; + + /* Determine if all send requests have completed */ + if (MPI_SUCCESS != (mpi_code = MPI_Testall((int)num_send_requests, send_requests, + &all_sends_completed, MPI_STATUSES_IGNORE))) + HMPI_GOTO_ERROR(FAIL, "MPI_Testall failed", mpi_code) + + if (all_sends_completed) { + /* Post non-blocking barrier */ + if (MPI_SUCCESS != (mpi_code = MPI_Ibarrier(io_info->comm, &ibarrier))) + HMPI_GOTO_ERROR(FAIL, "MPI_Ibarrier failed", mpi_code) + ibarrier_posted = TRUE; + + /* + * Now that all send requests have completed, free up the + * send buffers used in the non-blocking operations + */ + if (msg_send_bufs) { + for (i = 0; i < num_send_requests; i++) { + if (msg_send_bufs[i]) + H5MM_free(msg_send_bufs[i]); + } + + msg_send_bufs = H5MM_xfree(msg_send_bufs); + } + } + } + } while (1); + + /* + * Ensure all receive requests have completed before moving on. + * For linked-chunk I/O, more overlap with computation could + * theoretically be achieved by returning the receive requests + * array and postponing this wait until during chunk updating + * when the data is really needed. However, multi-chunk I/O + * only updates a chunk at a time and the messages may not come + * in the order that chunks are processed. So, the safest way to + * support both I/O modes is to simply make sure all messages + * are available. */ - for (i = 0; i < num_send_requests; i++) { - if (mod_data[i]) - H5MM_free(mod_data[i]); - } /* end for */ + if (MPI_SUCCESS != (mpi_code = MPI_Waitall((int)num_recv_requests, recv_requests, MPI_STATUSES_IGNORE))) + HMPI_GOTO_ERROR(FAIL, "MPI_Waitall failed", mpi_code) + + /* Set the new number of locally-selected chunks */ + *chunk_list_num_entries = last_assigned_idx; + + /* Return chunk message buffers if any were received */ + *chunk_hash_table = chunk_table; + *chunk_msg_bufs = msg_recv_bufs; + *chunk_msg_bufs_len = (int)num_recv_requests; + +done: + if (ret_value < 0) { + /* If this rank failed, make sure to participate in collective barrier */ + if (!ibarrier_posted) { + if (MPI_SUCCESS != (mpi_code = MPI_Ibarrier(io_info->comm, &ibarrier))) + HMPI_GOTO_ERROR(FAIL, "MPI_Ibarrier failed", mpi_code) + } + + if (num_send_requests) { + for (i = 0; i < num_send_requests; i++) { + MPI_Cancel(&send_requests[i]); + } + } + + if (recv_requests) { + for (i = 0; i < num_recv_requests; i++) { + MPI_Cancel(&recv_requests[i]); + } + } + + if (msg_recv_bufs) { + for (i = 0; i < num_recv_requests; i++) { + H5MM_free(msg_recv_bufs[i]); + } + + H5MM_free(msg_recv_bufs); + } + HASH_CLEAR(hh, chunk_table); + } + + if (recv_requests) + H5MM_free(recv_requests); if (send_requests) H5MM_free(send_requests); - if (send_statuses) - H5MM_free(send_statuses); - if (send_counts) - H5MM_free(send_counts); - if (send_displacements) - H5MM_free(send_displacements); - if (mod_data) - H5MM_free(mod_data); - if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator") - if (mem_iter) - H5MM_free(mem_iter); - if (num_assigned_chunks_array) - H5MM_free(num_assigned_chunks_array); - if (shared_chunks_info_array) - H5MM_free(shared_chunks_info_array); + + if (msg_send_bufs) { + for (i = 0; i < num_send_requests; i++) { + if (msg_send_bufs[i]) + H5MM_free(msg_send_bufs[i]); + } + + H5MM_free(msg_send_bufs); + } + + if (mem_iter) { + if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release dataspace selection iterator") + mem_iter = H5FL_FREE(H5S_sel_iter_t, mem_iter); + } + +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TIME_STOP(mpi_rank); + H5D_MPIO_TRACE_EXIT(mpi_rank); +#endif FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D__chunk_redistribute_shared_chunks() */ +#else + FUNC_ENTER_STATIC + HERROR( + H5E_DATASET, H5E_WRITEERROR, + "unable to send chunk modification data between MPI ranks - MPI version < 3 (MPI_Ibarrier missing)") + FUNC_LEAVE_NOAPI(FAIL) #endif +} /* end H5D__mpio_share_chunk_modification_data() */ /*------------------------------------------------------------------------- - * Function: H5D__mpio_filtered_collective_write_type + * Function: H5D__mpio_collective_filtered_chunk_common_io * - * Purpose: Constructs a MPI derived datatype for both the memory and - * the file for a collective write of filtered chunks. The - * datatype contains the offsets in the file and the locations - * of the filtered chunk data buffers. + * Purpose: This routine performs the common part of collective I/O + * when reading or writing filtered chunks collectively. * * Return: Non-negative on success/Negative on failure * - * Programmer: Jordan Henderson - * Tuesday, November 22, 2016 - * *------------------------------------------------------------------------- */ static herr_t -H5D__mpio_filtered_collective_write_type(H5D_filtered_collective_io_info_t *chunk_list, size_t num_entries, - MPI_Datatype *new_mem_type, hbool_t *mem_type_derived, - MPI_Datatype *new_file_type, hbool_t *file_type_derived) +H5D__mpio_collective_filtered_chunk_common_io(H5D_filtered_collective_io_info_t *chunk_list, + size_t chunk_list_num_entries, const H5D_io_info_t *io_info, + const H5D_type_info_t *type_info, int mpi_size) { - MPI_Aint *write_buf_array = NULL; /* Relative displacements of filtered chunk data buffers */ - MPI_Aint *file_offset_array = NULL; /* Chunk offsets in the file */ - int * length_array = NULL; /* Filtered Chunk lengths */ - herr_t ret_value = SUCCEED; + H5D_io_info_t coll_io_info; + H5D_storage_t ctg_store; + MPI_Datatype file_type = MPI_DATATYPE_NULL; + MPI_Datatype mem_type = MPI_DATATYPE_NULL; + hbool_t mem_type_is_derived = FALSE; + hbool_t file_type_is_derived = FALSE; + hsize_t mpi_buf_count; + haddr_t base_read_offset = HADDR_UNDEF; + size_t num_chunks; + size_t i; + char fake_buf; /* Used as a fake buffer for ranks with no chunks, thus a NULL buf pointer */ + int mpi_code; + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC - HDassert(chunk_list); - HDassert(new_mem_type); - HDassert(mem_type_derived); - HDassert(new_file_type); - HDassert(file_type_derived); + HDassert(chunk_list || 0 == chunk_list_num_entries); + HDassert(io_info); + HDassert(type_info); - if (num_entries > 0) { - size_t i; - int mpi_code; - void * base_buf; - - H5_CHECK_OVERFLOW(num_entries, size_t, int); - - /* Allocate arrays */ - if (NULL == (length_array = (int *)H5MM_malloc((size_t)num_entries * sizeof(int)))) - HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, - "memory allocation failed for filtered collective write length array") - if (NULL == (write_buf_array = (MPI_Aint *)H5MM_malloc((size_t)num_entries * sizeof(MPI_Aint)))) - HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, - "memory allocation failed for filtered collective write buf length array") - if (NULL == (file_offset_array = (MPI_Aint *)H5MM_malloc((size_t)num_entries * sizeof(MPI_Aint)))) - HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, - "memory allocation failed for collective write offset array") - - /* Ensure the list is sorted in ascending order of offset in the file */ - HDqsort(chunk_list, num_entries, sizeof(H5D_filtered_collective_io_info_t), - H5D__cmp_filtered_collective_io_info_entry); + /* Initialize temporary I/O info */ + coll_io_info = *io_info; - base_buf = chunk_list[0].buf; - for (i = 0; i < num_entries; i++) { - /* Set up the offset in the file, the length of the chunk data, and the relative - * displacement of the chunk data write buffer - */ - file_offset_array[i] = (MPI_Aint)chunk_list[i].chunk_states.new_chunk.offset; - length_array[i] = (int)chunk_list[i].chunk_states.new_chunk.length; - write_buf_array[i] = (MPI_Aint)chunk_list[i].buf - (MPI_Aint)base_buf; - } /* end for */ + /* + * Construct MPI derived datatype for collective I/O on chunks + */ + if (H5D__mpio_collective_filtered_io_type(chunk_list, chunk_list_num_entries, io_info->op_type, &mem_type, + &mem_type_is_derived, &file_type, &file_type_is_derived) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "couldn't create MPI I/O type for chunk I/O") - /* Create memory MPI type */ - if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)num_entries, length_array, - write_buf_array, MPI_BYTE, new_mem_type))) - HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code) - *mem_type_derived = TRUE; - if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_mem_type))) - HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) - - /* Create file MPI type */ - if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)num_entries, length_array, - file_offset_array, MPI_BYTE, new_file_type))) - HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code) - *file_type_derived = TRUE; - if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_file_type))) - HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) - } /* end if */ + /* + * For reads, determine how many chunks are actually being read. + * Note that if this is a read during a write operation + * (read chunk -> unfilter -> modify -> write back), some + * chunks may not need to be read if they're being fully + * overwritten during a write operation. + */ + if (io_info->op_type == H5D_IO_OP_READ) { + for (i = 0, num_chunks = 0; i < chunk_list_num_entries; i++) { + HDassert(chunk_list[i].buf); + + if (chunk_list[i].need_read) { + if (!H5F_addr_defined(base_read_offset)) + base_read_offset = chunk_list[i].chunk_current.offset; + + num_chunks++; + } + } + } + else + num_chunks = chunk_list_num_entries; + + /* + * If this rank doesn't have a selection, it can + * skip I/O if independent I/O was requested at + * the low level, or if the MPI communicator size + * is 1. + * + * Otherwise, this rank has to participate in + * collective I/O, but probably has a NULL buf + * pointer, so override to a fake buffer since our + * write/read function expects one. + */ + if (num_chunks == 0) { + H5FD_mpio_collective_opt_t coll_opt_mode; + + /* Get the collective_opt property to check whether the application wants to do IO individually. */ + if (H5CX_get_mpio_coll_opt(&coll_opt_mode) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get MPI-I/O collective_opt property") + + if ((mpi_size == 1) || (H5FD_MPIO_INDIVIDUAL_IO == coll_opt_mode)) { + HGOTO_DONE(SUCCEED) + } + else { + if (io_info->op_type == H5D_IO_OP_WRITE) + coll_io_info.u.wbuf = &fake_buf; + else + coll_io_info.u.rbuf = &fake_buf; + } + } + + /* + * Setup for I/O operation + */ + + mpi_buf_count = (num_chunks) ? 1 : 0; + + if (num_chunks) { + /* + * Setup the base storage address for this operation + * to be the first chunk's file address + */ + if (io_info->op_type == H5D_IO_OP_WRITE) + ctg_store.contig.dset_addr = chunk_list[0].chunk_new.offset; + else + ctg_store.contig.dset_addr = base_read_offset; + } + else + ctg_store.contig.dset_addr = 0; + + ctg_store.contig.dset_size = (hsize_t)io_info->dset->shared->layout.u.chunk.size; + coll_io_info.store = &ctg_store; + + /* Perform I/O */ + if (H5D__final_collective_io(&coll_io_info, type_info, mpi_buf_count, file_type, mem_type) < 0) + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "couldn't finish MPI I/O") done: - if (write_buf_array) - H5MM_free(write_buf_array); - if (file_offset_array) - H5MM_free(file_offset_array); - if (length_array) - H5MM_free(length_array); + /* Free the MPI buf and file types, if they were derived */ + if (mem_type_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&mem_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + if (file_type_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&file_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D__mpio_filtered_collective_write_type() */ +} /* end H5D__mpio_collective_filtered_chunk_common_io() */ /*------------------------------------------------------------------------- - * Function: H5D__filtered_collective_chunk_entry_io + * Function: H5D__mpio_collective_filtered_chunk_read * - * Purpose: Given an entry for a filtered chunk, performs the necessary - * steps for updating the chunk data during a collective - * write, or for reading the chunk from file during a - * collective read. + * Purpose: This routine coordinates a collective read across all ranks + * of the chunks they have selected. Each rank will then go + * and * * Return: Non-negative on success/Negative on failure * - * Programmer: Jordan Henderson - * Wednesday, January 18, 2017 - * *------------------------------------------------------------------------- */ static herr_t -H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk_entry, - const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - const H5D_chunk_map_t *fm) +H5D__mpio_collective_filtered_chunk_read(H5D_filtered_collective_io_info_t *chunk_list, + size_t chunk_list_num_entries, const H5D_io_info_t *io_info, + const H5D_type_info_t *type_info, int mpi_rank, int mpi_size) { - H5D_chunk_info_t *chunk_info = NULL; - H5S_sel_iter_t * mem_iter = NULL; /* Memory iterator for H5D__scatter_mem/H5D__gather_mem */ - H5S_sel_iter_t * file_iter = NULL; - H5Z_EDC_t err_detect; /* Error detection info */ - H5Z_cb_t filter_cb; /* I/O filter callback function */ - unsigned filter_mask = 0; - hsize_t iter_nelmts; /* Number of points to iterate over for the chunk IO operation */ - hssize_t extent_npoints; - hsize_t true_chunk_size; - hbool_t mem_iter_init = FALSE; - hbool_t file_iter_init = FALSE; - size_t buf_size; - size_t i; - H5S_t * dataspace = NULL; /* Other process' dataspace for the chunk */ - void * tmp_gath_buf = NULL; /* Temporary gather buffer to gather into from application buffer - before scattering out to the chunk data buffer (when writing data), - or vice versa (when reading data) */ - int mpi_code; - herr_t ret_value = SUCCEED; + H5D_fill_buf_info_t fb_info; + H5D_chunk_info_t * chunk_info = NULL; + H5D_io_info_t coll_io_info; + H5Z_EDC_t err_detect; /* Error detection info */ + H5Z_cb_t filter_cb; /* I/O filter callback function */ + hsize_t file_chunk_size = 0; + hsize_t iter_nelmts; /* Number of points to iterate over for the chunk IO operation */ + hbool_t should_fill = FALSE; + hbool_t fb_info_init = FALSE; + hbool_t index_empty = FALSE; + size_t i; + H5S_t * fill_space = NULL; + void * base_read_buf = NULL; + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC - HDassert(chunk_entry); + HDassert(chunk_list || 0 == chunk_list_num_entries); HDassert(io_info); HDassert(type_info); - HDassert(fm); - /* Retrieve filter settings from API context */ - if (H5CX_get_err_detect(&err_detect) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get error detection info") - if (H5CX_get_filter_cb(&filter_cb) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get I/O filter callback function") +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TRACE_ENTER(mpi_rank); + H5D_MPIO_TIME_START(mpi_rank, "Filtered collective chunk read"); +#else + (void)mpi_rank; +#endif + + /* Initialize temporary I/O info */ + coll_io_info = *io_info; + coll_io_info.u.rbuf = NULL; - /* Look up the chunk and get its file and memory dataspaces */ - if (NULL == (chunk_info = (H5D_chunk_info_t *)H5SL_search(fm->sel_chunks, &chunk_entry->index))) - HGOTO_ERROR(H5E_DATASPACE, H5E_NOTFOUND, FAIL, "can't locate chunk in skip list") + if (chunk_list_num_entries) { + /* Retrieve filter settings from API context */ + if (H5CX_get_err_detect(&err_detect) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get error detection info") + if (H5CX_get_filter_cb(&filter_cb) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get I/O filter callback function") - if ((extent_npoints = H5S_GET_EXTENT_NPOINTS(chunk_info->fspace)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid") - true_chunk_size = (hsize_t)extent_npoints * type_info->src_type_size; + /* Set size of full chunks in dataset */ + file_chunk_size = io_info->dset->shared->layout.u.chunk.size; - /* If the size of the filtered chunk is larger than the number of points in the - * chunk file space extent times the datatype size, allocate enough space to hold the - * whole filtered chunk. Otherwise, allocate a buffer equal to the size of the - * chunk so that the unfiltering operation doesn't have to grow the buffer. + /* Determine if fill values should be "read" for unallocated chunks */ + should_fill = (io_info->dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_ALLOC) || + ((io_info->dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_IFSET) && + io_info->dset->shared->dcpl_cache.fill.fill_defined); + } + + /* + * Allocate memory buffers for all chunks being read. Chunk data buffers are of + * the largest size between the chunk's current filtered size and the chunk's true + * size, as calculated by the number of elements in the chunk's file space extent + * multiplied by the datatype size. This tries to ensure that: + * + * * If we're reading the chunk and the filter normally reduces the chunk size, + * the unfiltering operation won't need to grow the buffer. + * * If we're reading the chunk and the filter normally grows the chunk size, + * we make sure to read into a buffer of size equal to the filtered chunk's + * size; reading into a (smaller) buffer of size equal to the unfiltered + * chunk size would of course be bad. */ - buf_size = MAX(chunk_entry->chunk_states.chunk_current.length, true_chunk_size); + for (i = 0; i < chunk_list_num_entries; i++) { + HDassert(chunk_list[i].need_read); + + chunk_list[i].chunk_buf_size = MAX(chunk_list[i].chunk_current.length, file_chunk_size); + + if (NULL == (chunk_list[i].buf = H5MM_malloc(chunk_list[i].chunk_buf_size))) { + /* Push an error, but participate in collective read */ + HDONE_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk data buffer") + break; + } + + /* + * Check if chunk is currently allocated. If not, don't try to + * read it from the file. Instead, just fill the chunk buffer + * with the fill value if necessary. + */ + if (H5F_addr_defined(chunk_list[i].chunk_current.offset)) { + /* Set first read buffer */ + if (!base_read_buf) + base_read_buf = chunk_list[i].buf; + + /* Set chunk's new length for eventual filter pipeline calls */ + if (chunk_list[i].skip_filter_pline) + chunk_list[i].chunk_new.length = file_chunk_size; + else + chunk_list[i].chunk_new.length = chunk_list[i].chunk_current.length; + } + else { + chunk_list[i].need_read = FALSE; + + /* Set chunk's new length for eventual filter pipeline calls */ + chunk_list[i].chunk_new.length = file_chunk_size; + + if (should_fill) { + /* Initialize fill value buffer if not already initialized */ + if (!fb_info_init) { + hsize_t chunk_dims[H5S_MAX_RANK]; + + HDassert(io_info->dset->shared->ndims == io_info->dset->shared->layout.u.chunk.ndims - 1); + for (size_t j = 0; j < io_info->dset->shared->layout.u.chunk.ndims - 1; j++) + chunk_dims[j] = (hsize_t)io_info->dset->shared->layout.u.chunk.dim[j]; + + /* Get a dataspace for filling chunk memory buffers */ + if (NULL == (fill_space = H5S_create_simple( + io_info->dset->shared->layout.u.chunk.ndims - 1, chunk_dims, NULL))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create chunk fill dataspace") + + /* Initialize fill value buffer */ + if (H5D__fill_init(&fb_info, NULL, (H5MM_allocate_t)H5D__chunk_mem_alloc, + (void *)&io_info->dset->shared->dcpl_cache.pline, + (H5MM_free_t)H5D__chunk_mem_free, + (void *)&io_info->dset->shared->dcpl_cache.pline, + &io_info->dset->shared->dcpl_cache.fill, io_info->dset->shared->type, + io_info->dset->shared->type_id, 0, file_chunk_size) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill value buffer") + + fb_info_init = TRUE; + } - if (NULL == (chunk_entry->buf = H5MM_malloc(buf_size))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk data buffer") + /* Write fill value to memory buffer */ + HDassert(fb_info.fill_buf); + if (H5D__fill(fb_info.fill_buf, io_info->dset->shared->type, chunk_list[i].buf, + type_info->mem_type, fill_space) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "couldn't fill chunk buffer with fill value") + } + } + } - /* If this is not a full chunk overwrite or this is a read operation, the chunk must be - * read from the file and unfiltered. + /* + * If dataset is incrementally allocated and hasn't been written to + * yet, the chunk index should be empty. In this case, a collective + * read of chunks is essentially a no-op, so avoid it here. */ - if (!chunk_entry->full_overwrite || io_info->op_type == H5D_IO_OP_READ) { - H5FD_mpio_xfer_t xfer_mode; /* Parallel transfer for this request */ + index_empty = FALSE; + if (io_info->dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_INCR) + if (H5D__chunk_index_empty(io_info->dset, &index_empty) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "couldn't determine if chunk index is empty") - chunk_entry->chunk_states.new_chunk.length = chunk_entry->chunk_states.chunk_current.length; + if (!index_empty) { + /* + * Override the read buffer to point to the address of + * the first chunk data buffer being read into + */ + if (base_read_buf) + coll_io_info.u.rbuf = base_read_buf; - /* Currently, these chunk reads are done independently and will likely - * cause issues with collective metadata reads enabled. In the future, - * this should be refactored to use collective chunk reads - JTH */ + /* Perform collective chunk read */ + if (H5D__mpio_collective_filtered_chunk_common_io(chunk_list, chunk_list_num_entries, &coll_io_info, + type_info, mpi_size) < 0) + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "couldn't finish collective filtered chunk read") + } - /* Get the original state of parallel I/O transfer mode */ - if (H5CX_get_io_xfer_mode(&xfer_mode) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get MPI-I/O transfer mode") + /* + * Iterate through all the read chunks, unfiltering them and scattering their + * data out to the application's read buffer. + */ + for (i = 0; i < chunk_list_num_entries; i++) { + chunk_info = chunk_list[i].chunk_info; + + /* Unfilter the chunk, unless we didn't read it from the file */ + if (chunk_list[i].need_read && !chunk_list[i].skip_filter_pline) { + if (H5Z_pipeline(&io_info->dset->shared->dcpl_cache.pline, H5Z_FLAG_REVERSE, + &(chunk_list[i].index_info.filter_mask), err_detect, filter_cb, + (size_t *)&chunk_list[i].chunk_new.length, &chunk_list[i].chunk_buf_size, + &chunk_list[i].buf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTFILTER, FAIL, "couldn't unfilter chunk for modifying") + } + + /* Scatter the chunk data to the read buffer */ + iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->fspace); + + if (H5D_select_io_mem(io_info->u.rbuf, chunk_info->mspace, chunk_list[i].buf, chunk_info->fspace, + type_info->src_type_size, (size_t)iter_nelmts) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't copy chunk data to read buffer") + } - /* Change the xfer_mode to independent for handling the I/O */ - if (H5CX_set_io_xfer_mode(H5FD_MPIO_INDEPENDENT) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set MPI-I/O transfer mode") +done: + /* Free all resources used by entries in the chunk list */ + for (i = 0; i < chunk_list_num_entries; i++) { + if (chunk_list[i].buf) { + H5MM_free(chunk_list[i].buf); + chunk_list[i].buf = NULL; + } + } - if (H5F_shared_block_read(io_info->f_sh, H5FD_MEM_DRAW, - chunk_entry->chunk_states.chunk_current.offset, - chunk_entry->chunk_states.new_chunk.length, chunk_entry->buf) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "unable to read raw data chunk") + /* Release the fill buffer info, if it's been initialized */ + if (fb_info_init && H5D__fill_term(&fb_info) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info") + if (fill_space && (H5S_close(fill_space) < 0)) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "can't close fill space") - /* Return to the original I/O transfer mode setting */ - if (H5CX_set_io_xfer_mode(xfer_mode) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set MPI-I/O transfer mode") +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TIME_STOP(mpi_rank); + H5D_MPIO_TRACE_EXIT(mpi_rank); +#endif - if (H5Z_pipeline(&io_info->dset->shared->dcpl_cache.pline, H5Z_FLAG_REVERSE, &filter_mask, err_detect, - filter_cb, (size_t *)&chunk_entry->chunk_states.new_chunk.length, &buf_size, - &chunk_entry->buf) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTFILTER, FAIL, "couldn't unfilter chunk for modifying") - } /* end if */ - else { - chunk_entry->chunk_states.new_chunk.length = true_chunk_size; - } /* end else */ + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__mpio_collective_filtered_chunk_read() */ - /* Initialize iterator for memory selection */ - if (NULL == (mem_iter = (H5S_sel_iter_t *)H5MM_malloc(sizeof(H5S_sel_iter_t)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate memory iterator") +/*------------------------------------------------------------------------- + * Function: H5D__mpio_collective_filtered_chunk_update + * + * Purpose: When performing a parallel write on a chunked dataset with + * filters applied, all ranks must update their owned chunks + * with their own modification data and data from other ranks. + * This routine is responsible for coordinating that process. + * + * Return: Non-negative on success/Negative on failure + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__mpio_collective_filtered_chunk_update(H5D_filtered_collective_io_info_t *chunk_list, + size_t chunk_list_num_entries, + H5D_filtered_collective_io_info_t *chunk_hash_table, + unsigned char **chunk_msg_bufs, int chunk_msg_bufs_len, + const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, + int mpi_rank, int mpi_size) +{ + H5D_fill_buf_info_t fb_info; + H5D_chunk_info_t * chunk_info = NULL; + H5S_sel_iter_t * sel_iter = NULL; /* Dataspace selection iterator for H5D__scatter_mem */ + H5D_io_info_t coll_io_info; + H5Z_EDC_t err_detect; /* Error detection info */ + H5Z_cb_t filter_cb; /* I/O filter callback function */ + hsize_t file_chunk_size = 0; + hsize_t iter_nelmts; /* Number of points to iterate over for the chunk IO operation */ + hbool_t should_fill = FALSE; + hbool_t fb_info_init = FALSE; + hbool_t sel_iter_init = FALSE; + hbool_t index_empty = FALSE; + size_t i; + H5S_t * dataspace = NULL; + H5S_t * fill_space = NULL; + void * base_read_buf = NULL; + herr_t ret_value = SUCCEED; - if (H5S_select_iter_init(mem_iter, chunk_info->mspace, type_info->src_type_size, 0) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information") - mem_iter_init = TRUE; + FUNC_ENTER_STATIC - /* If this is a read operation, scatter the read chunk data to the user's buffer. - * - * If this is a write operation, update the chunk data buffer with the modifications - * from the current process, then apply any modifications from other processes. Finally, - * filter the newly-updated chunk. - */ - switch (io_info->op_type) { - case H5D_IO_OP_READ: - if (NULL == (file_iter = (H5S_sel_iter_t *)H5MM_malloc(sizeof(H5S_sel_iter_t)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate file iterator") + HDassert(chunk_list || 0 == chunk_list_num_entries); + HDassert((chunk_msg_bufs && chunk_hash_table) || 0 == chunk_msg_bufs_len); + HDassert(io_info); + HDassert(type_info); - if (H5S_select_iter_init(file_iter, chunk_info->fspace, type_info->src_type_size, 0) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, - "unable to initialize memory selection information") - file_iter_init = TRUE; +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TRACE_ENTER(mpi_rank); + H5D_MPIO_TIME_START(mpi_rank, "Filtered collective chunk update"); +#endif - iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->fspace); + if (chunk_list_num_entries) { + /* Retrieve filter settings from API context */ + if (H5CX_get_err_detect(&err_detect) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get error detection info") + if (H5CX_get_filter_cb(&filter_cb) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get I/O filter callback function") - if (NULL == (tmp_gath_buf = H5MM_malloc(iter_nelmts * type_info->src_type_size))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate temporary gather buffer") + /* Set size of full chunks in dataset */ + file_chunk_size = io_info->dset->shared->layout.u.chunk.size; - if (!H5D__gather_mem(chunk_entry->buf, file_iter, (size_t)iter_nelmts, tmp_gath_buf)) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "couldn't gather from chunk buffer") + /* Determine if fill values should be written to chunks */ + should_fill = (io_info->dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_ALLOC) || + ((io_info->dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_IFSET) && + io_info->dset->shared->dcpl_cache.fill.fill_defined); + } - iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace); + /* + * Allocate memory buffers for all owned chunks. Chunk data buffers are of the + * largest size between the chunk's current filtered size and the chunk's true + * size, as calculated by the number of elements in the chunk's file space extent + * multiplied by the datatype size. This tries to ensure that: + * + * * If we're fully overwriting the chunk and the filter normally reduces the + * chunk size, we simply have the exact buffer size required to hold the + * unfiltered chunk data. + * * If we're fully overwriting the chunk and the filter normally grows the + * chunk size (e.g., fletcher32 filter), the final filtering operation + * (hopefully) won't need to grow the buffer. + * * If we're reading the chunk and the filter normally reduces the chunk size, + * the unfiltering operation won't need to grow the buffer. + * * If we're reading the chunk and the filter normally grows the chunk size, + * we make sure to read into a buffer of size equal to the filtered chunk's + * size; reading into a (smaller) buffer of size equal to the unfiltered + * chunk size would of course be bad. + */ + for (i = 0; i < chunk_list_num_entries; i++) { + HDassert(mpi_rank == chunk_list[i].new_owner); + + chunk_list[i].chunk_buf_size = MAX(chunk_list[i].chunk_current.length, file_chunk_size); - if (H5D__scatter_mem(tmp_gath_buf, mem_iter, (size_t)iter_nelmts, io_info->u.rbuf) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't scatter to read buffer") + /* + * If this chunk hasn't been allocated yet and we aren't writing + * out fill values to it, make sure to 0-fill its memory buffer + * so we don't use uninitialized memory. + */ + if (!H5F_addr_defined(chunk_list[i].chunk_current.offset) && !should_fill) + chunk_list[i].buf = H5MM_calloc(chunk_list[i].chunk_buf_size); + else + chunk_list[i].buf = H5MM_malloc(chunk_list[i].chunk_buf_size); + if (NULL == chunk_list[i].buf) { + /* Push an error, but participate in collective read */ + HDONE_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk data buffer") break; + } + + /* Set chunk's new length for eventual filter pipeline calls */ + if (chunk_list[i].need_read) { + /* + * Check if chunk is currently allocated. If not, don't try to + * read it from the file. Instead, just fill the chunk buffer + * with the fill value if fill values are to be written. + */ + if (H5F_addr_defined(chunk_list[i].chunk_current.offset)) { + /* Set first read buffer */ + if (!base_read_buf) + base_read_buf = chunk_list[i].buf; + + /* Set chunk's new length for eventual filter pipeline calls */ + if (chunk_list[i].skip_filter_pline) + chunk_list[i].chunk_new.length = file_chunk_size; + else + chunk_list[i].chunk_new.length = chunk_list[i].chunk_current.length; + } + else { + chunk_list[i].need_read = FALSE; + + /* Set chunk's new length for eventual filter pipeline calls */ + chunk_list[i].chunk_new.length = file_chunk_size; + + if (should_fill) { + /* Initialize fill value buffer if not already initialized */ + if (!fb_info_init) { + hsize_t chunk_dims[H5S_MAX_RANK]; + + HDassert(io_info->dset->shared->ndims == + io_info->dset->shared->layout.u.chunk.ndims - 1); + for (size_t j = 0; j < io_info->dset->shared->layout.u.chunk.ndims - 1; j++) + chunk_dims[j] = (hsize_t)io_info->dset->shared->layout.u.chunk.dim[j]; + + /* Get a dataspace for filling chunk memory buffers */ + if (NULL == (fill_space = H5S_create_simple( + io_info->dset->shared->layout.u.chunk.ndims - 1, chunk_dims, NULL))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to create chunk fill dataspace") + + /* Initialize fill value buffer */ + if (H5D__fill_init(&fb_info, NULL, (H5MM_allocate_t)H5D__chunk_mem_alloc, + (void *)&io_info->dset->shared->dcpl_cache.pline, + (H5MM_free_t)H5D__chunk_mem_free, + (void *)&io_info->dset->shared->dcpl_cache.pline, + &io_info->dset->shared->dcpl_cache.fill, + io_info->dset->shared->type, io_info->dset->shared->type_id, 0, + file_chunk_size) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill value buffer") + + fb_info_init = TRUE; + } + + /* Write fill value to memory buffer */ + HDassert(fb_info.fill_buf); + if (H5D__fill(fb_info.fill_buf, io_info->dset->shared->type, chunk_list[i].buf, + type_info->mem_type, fill_space) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "couldn't fill chunk buffer with fill value") + } + } + } + else + chunk_list[i].chunk_new.length = file_chunk_size; + } - case H5D_IO_OP_WRITE: - iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace); + /* + * If dataset is incrementally allocated and hasn't been written to + * yet, the chunk index should be empty. In this case, a collective + * read of chunks is essentially a no-op, so avoid it here. + */ + index_empty = FALSE; + if (io_info->dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_INCR) + if (H5D__chunk_index_empty(io_info->dset, &index_empty) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "couldn't determine if chunk index is empty") - if (NULL == (tmp_gath_buf = H5MM_malloc(iter_nelmts * type_info->src_type_size))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate temporary gather buffer") + if (!index_empty) { + /* + * Setup for I/O operation + */ - /* Gather modification data from the application write buffer into a temporary buffer */ - if (0 == H5D__gather_mem(io_info->u.wbuf, mem_iter, (size_t)iter_nelmts, tmp_gath_buf)) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "couldn't gather from write buffer") + /* Initialize temporary I/O info */ + coll_io_info = *io_info; + coll_io_info.op_type = H5D_IO_OP_READ; - if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator") - mem_iter_init = FALSE; + /* Override the read buffer to point to the address of the first + * chunk data buffer being read into + */ + if (base_read_buf) + coll_io_info.u.rbuf = base_read_buf; - /* Initialize iterator for file selection */ - if (H5S_select_iter_init(mem_iter, chunk_info->fspace, type_info->dst_type_size, 0) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, - "unable to initialize file selection information") - mem_iter_init = TRUE; + /* Read all chunks that need to be read from the file */ + if (H5D__mpio_collective_filtered_chunk_common_io(chunk_list, chunk_list_num_entries, &coll_io_info, + type_info, mpi_size) < 0) + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "couldn't finish collective filtered chunk read") + } - iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->fspace); + /* + * Now that all owned chunks have been read, update the chunks + * with modification data from the owning rank and other ranks. + */ - /* Scatter the owner's modification data into the chunk data buffer according to - * the file space. - */ - if (H5D__scatter_mem(tmp_gath_buf, mem_iter, (size_t)iter_nelmts, chunk_entry->buf) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't scatter to chunk data buffer") + /* Process all chunks with data from the owning rank first */ + for (i = 0; i < chunk_list_num_entries; i++) { + HDassert(mpi_rank == chunk_list[i].new_owner); - if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator") - mem_iter_init = FALSE; + chunk_info = chunk_list[i].chunk_info; - if (MPI_SUCCESS != - (mpi_code = MPI_Waitall(chunk_entry->async_info.num_receive_requests, - chunk_entry->async_info.receive_requests_array, MPI_STATUSES_IGNORE))) - HMPI_GOTO_ERROR(FAIL, "MPI_Waitall failed", mpi_code) + /* + * If this chunk wasn't being fully overwritten, we read it from + * the file, so we need to unfilter it + */ + if (chunk_list[i].need_read && !chunk_list[i].skip_filter_pline) { + if (H5Z_pipeline(&io_info->dset->shared->dcpl_cache.pline, H5Z_FLAG_REVERSE, + &(chunk_list[i].index_info.filter_mask), err_detect, filter_cb, + (size_t *)&chunk_list[i].chunk_new.length, &chunk_list[i].chunk_buf_size, + &chunk_list[i].buf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTFILTER, FAIL, "couldn't unfilter chunk for modifying") + } + + iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace); + + if (H5D_select_io_mem(chunk_list[i].buf, chunk_info->fspace, io_info->u.wbuf, chunk_info->mspace, + type_info->dst_type_size, (size_t)iter_nelmts) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "couldn't copy chunk data to write buffer") + } - /* For each asynchronous receive call previously posted, receive the chunk modification - * buffer from another rank and update the chunk data - */ - for (i = 0; i < (size_t)chunk_entry->async_info.num_receive_requests; i++) { - const unsigned char *mod_data_p; + /* Allocate iterator for memory selection */ + if (NULL == (sel_iter = H5FL_MALLOC(H5S_sel_iter_t))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate memory iterator") - /* Decode the process' chunk file dataspace */ - mod_data_p = chunk_entry->async_info.receive_buffer_array[i]; - if (NULL == (dataspace = H5S_decode(&mod_data_p))) + /* Now process all received chunk message buffers */ + for (i = 0; i < (size_t)chunk_msg_bufs_len; i++) { + H5D_filtered_collective_io_info_t *chunk_entry = NULL; + const unsigned char * msg_ptr = chunk_msg_bufs[i]; + hsize_t chunk_idx; + + if (msg_ptr) { + /* Retrieve the chunk's index value */ + HDmemcpy(&chunk_idx, msg_ptr, sizeof(hsize_t)); + msg_ptr += sizeof(hsize_t); + + /* Find the chunk entry according to its chunk index */ + HASH_FIND(hh, chunk_hash_table, &chunk_idx, sizeof(hsize_t), chunk_entry); + HDassert(chunk_entry); + HDassert(mpi_rank == chunk_entry->new_owner); + + /* + * Only process the chunk if its data buffer is allocated. + * In the case of multi-chunk I/O, we're only working on + * a chunk at a time, so we need to skip over messages + * that aren't for the chunk we're currently working on. + */ + if (!chunk_entry->buf) + continue; + else { + /* Decode the chunk file dataspace from the message */ + if (NULL == (dataspace = H5S_decode(&msg_ptr))) HGOTO_ERROR(H5E_DATASET, H5E_CANTDECODE, FAIL, "unable to decode dataspace") - if (H5S_select_iter_init(mem_iter, dataspace, type_info->dst_type_size, 0) < 0) + if (H5S_select_iter_init(sel_iter, dataspace, type_info->dst_type_size, + H5S_SEL_ITER_SHARE_WITH_DATASPACE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information") - mem_iter_init = TRUE; + sel_iter_init = TRUE; iter_nelmts = H5S_GET_SELECT_NPOINTS(dataspace); /* Update the chunk data with the received modification data */ - if (H5D__scatter_mem(mod_data_p, mem_iter, (size_t)iter_nelmts, chunk_entry->buf) < 0) + if (H5D__scatter_mem(msg_ptr, sel_iter, (size_t)iter_nelmts, chunk_entry->buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "couldn't scatter to write buffer") - if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0) + if (H5S_SELECT_ITER_RELEASE(sel_iter) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator") - mem_iter_init = FALSE; + sel_iter_init = FALSE; + if (dataspace) { if (H5S_close(dataspace) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTFREE, FAIL, "can't close dataspace") dataspace = NULL; } - H5MM_free(chunk_entry->async_info.receive_buffer_array[i]); - } /* end for */ - /* Filter the chunk */ - if (H5Z_pipeline(&io_info->dset->shared->dcpl_cache.pline, 0, &filter_mask, err_detect, filter_cb, - (size_t *)&chunk_entry->chunk_states.new_chunk.length, &buf_size, - &chunk_entry->buf) < 0) + H5MM_free(chunk_msg_bufs[i]); + chunk_msg_bufs[i] = NULL; + } + } + } + + /* Finally, filter all the chunks */ + for (i = 0; i < chunk_list_num_entries; i++) { + if (!chunk_list[i].skip_filter_pline) { + if (H5Z_pipeline(&io_info->dset->shared->dcpl_cache.pline, 0, + &(chunk_list[i].index_info.filter_mask), err_detect, filter_cb, + (size_t *)&chunk_list[i].chunk_new.length, &chunk_list[i].chunk_buf_size, + &chunk_list[i].buf) < 0) HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "output pipeline failed") + } #if H5_SIZEOF_SIZE_T > 4 - /* Check for the chunk expanding too much to encode in a 32-bit value */ - if (chunk_entry->chunk_states.new_chunk.length > ((size_t)0xffffffff)) - HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "chunk too large for 32-bit length") + /* Check for the chunk expanding too much to encode in a 32-bit value */ + if (chunk_list[i].chunk_new.length > ((size_t)0xffffffff)) + HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "chunk too large for 32-bit length") #endif - break; + } - default: - HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "invalid I/O operation") - } /* end switch */ +done: + if (sel_iter) { + if (sel_iter_init && H5S_SELECT_ITER_RELEASE(sel_iter) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator") + sel_iter = H5FL_FREE(H5S_sel_iter_t, sel_iter); + } + if (dataspace && (H5S_close(dataspace) < 0)) + HDONE_ERROR(H5E_DATASPACE, H5E_CANTFREE, FAIL, "can't close dataspace") + if (fill_space && (H5S_close(fill_space) < 0)) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "can't close fill space") + + /* Release the fill buffer info, if it's been initialized */ + if (fb_info_init && H5D__fill_term(&fb_info) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info") + + /* On failure, try to free all resources used by entries in the chunk list */ + if (ret_value < 0) { + for (i = 0; i < chunk_list_num_entries; i++) { + if (chunk_list[i].buf) { + H5MM_free(chunk_list[i].buf); + chunk_list[i].buf = NULL; + } + } + } + +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TIME_STOP(mpi_rank); + H5D_MPIO_TRACE_EXIT(mpi_rank); +#endif + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__mpio_collective_filtered_chunk_update() */ + +/*------------------------------------------------------------------------- + * Function: H5D__mpio_collective_filtered_chunk_reallocate + * + * Purpose: When performing a parallel write on a chunked dataset with + * filters applied, all ranks must eventually get together and + * perform a collective reallocation of space in the file for + * all chunks that were modified on all ranks. This routine is + * responsible for coordinating that process. + * + * Return: Non-negative on success/Negative on failure + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__mpio_collective_filtered_chunk_reallocate(H5D_filtered_collective_io_info_t *chunk_list, + size_t chunk_list_num_entries, size_t *num_chunks_assigned_map, + H5D_io_info_t *io_info, H5D_chk_idx_info_t *idx_info, + int mpi_rank, int mpi_size) +{ + H5D_chunk_alloc_info_t *collective_list = NULL; + MPI_Datatype send_type; + MPI_Datatype recv_type; + hbool_t send_type_derived = FALSE; + hbool_t recv_type_derived = FALSE; + hbool_t need_sort = FALSE; + size_t collective_num_entries = 0; + size_t num_local_chunks_processed = 0; + size_t i; + void * gathered_array = NULL; + int * counts_disps_array = NULL; + int * counts_ptr = NULL; + int * displacements_ptr = NULL; + int mpi_code; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_STATIC + + HDassert(chunk_list || 0 == chunk_list_num_entries); + HDassert(io_info); + HDassert(idx_info); + HDassert(idx_info->storage->idx_type != H5D_CHUNK_IDX_NONE); + +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TRACE_ENTER(mpi_rank); + H5D_MPIO_TIME_START(mpi_rank, "Reallocation of chunk file space"); +#endif + + /* + * Make sure it's safe to cast this rank's number + * of chunks to be sent into an int for MPI + */ + H5_CHECK_OVERFLOW(chunk_list_num_entries, size_t, int); + + /* Create derived datatypes for the chunk file space info needed */ + if (H5D__mpio_get_chunk_alloc_info_types(&recv_type, &recv_type_derived, &send_type, &send_type_derived) < + 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, + "can't create derived datatypes for chunk file space info") + + /* + * Gather the new chunk sizes to all ranks for a collective reallocation + * of the chunks in the file. + */ + if (num_chunks_assigned_map) { + /* + * If a mapping between rank value -> number of assigned chunks has + * been provided (usually during linked-chunk I/O), we can use this + * to optimize MPI overhead a bit since MPI ranks won't need to + * first inform each other about how many chunks they're contributing. + */ + if (NULL == (counts_disps_array = H5MM_malloc(2 * (size_t)mpi_size * sizeof(*counts_disps_array)))) { + /* Push an error, but still participate in collective gather operation */ + HDONE_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, + "couldn't allocate receive counts and displacements array") + } + else { + /* Set the receive counts from the assigned chunks map */ + counts_ptr = counts_disps_array; + + for (i = 0; i < (size_t)mpi_size; i++) + H5_CHECKED_ASSIGN(counts_ptr[i], int, num_chunks_assigned_map[i], size_t); + + /* Set the displacements into the receive buffer for the gather operation */ + displacements_ptr = &counts_disps_array[mpi_size]; + + *displacements_ptr = 0; + for (i = 1; i < (size_t)mpi_size; i++) + displacements_ptr[i] = displacements_ptr[i - 1] + counts_ptr[i - 1]; + } + + /* Perform gather operation */ + if (H5_mpio_gatherv_alloc(chunk_list, (int)chunk_list_num_entries, send_type, counts_ptr, + displacements_ptr, recv_type, TRUE, 0, io_info->comm, mpi_rank, mpi_size, + &gathered_array, &collective_num_entries) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL, "can't gather chunk file space info to/from ranks") + } + else { + /* + * If no mapping between rank value -> number of assigned chunks has + * been provided (usually during multi-chunk I/O), all MPI ranks will + * need to first inform other ranks about how many chunks they're + * contributing before performing the actual gather operation. Use + * the 'simple' MPI_Allgatherv wrapper for this. + */ + if (H5_mpio_gatherv_alloc_simple(chunk_list, (int)chunk_list_num_entries, send_type, recv_type, TRUE, + 0, io_info->comm, mpi_rank, mpi_size, &gathered_array, + &collective_num_entries) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL, "can't gather chunk file space info to/from ranks") + } + + /* Collectively re-allocate the modified chunks (from each rank) in the file */ + collective_list = (H5D_chunk_alloc_info_t *)gathered_array; + for (i = 0, num_local_chunks_processed = 0; i < collective_num_entries; i++) { + H5D_chunk_alloc_info_t *coll_entry = &collective_list[i]; + hbool_t need_insert; + hbool_t update_local_chunk; + + if (H5D__chunk_file_alloc(idx_info, &coll_entry->chunk_current, &coll_entry->chunk_new, &need_insert, + NULL) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate chunk") + + /* + * If we just re-allocated a chunk that is local to this + * rank, make sure to update the chunk entry in the local + * chunk list + */ + update_local_chunk = + (num_local_chunks_processed < chunk_list_num_entries) && + (coll_entry->chunk_idx == chunk_list[num_local_chunks_processed].index_info.chunk_idx); + + if (update_local_chunk) { + H5D_filtered_collective_io_info_t *local_chunk; + + local_chunk = &chunk_list[num_local_chunks_processed]; + + /* Sanity check that this chunk is actually local */ + HDassert(mpi_rank == local_chunk->orig_owner); + HDassert(mpi_rank == local_chunk->new_owner); + + local_chunk->chunk_new = coll_entry->chunk_new; + local_chunk->index_info.need_insert = need_insert; + + /* + * Since chunk reallocation can move chunks around, check if + * the local chunk list is still in ascending offset of order + * in the file + */ + if (num_local_chunks_processed) { + haddr_t curr_chunk_offset = local_chunk->chunk_new.offset; + haddr_t prev_chunk_offset = chunk_list[num_local_chunks_processed - 1].chunk_new.offset; + + HDassert(H5F_addr_defined(prev_chunk_offset) && H5F_addr_defined(curr_chunk_offset)); + if (curr_chunk_offset < prev_chunk_offset) + need_sort = TRUE; + } + + num_local_chunks_processed++; + } + } + + HDassert(chunk_list_num_entries == num_local_chunks_processed); + + /* + * Ensure this rank's local chunk list is sorted in + * ascending order of offset in the file + */ + if (need_sort) + HDqsort(chunk_list, chunk_list_num_entries, sizeof(H5D_filtered_collective_io_info_t), + H5D__cmp_filtered_collective_io_info_entry); + +done: + H5MM_free(gathered_array); + H5MM_free(counts_disps_array); + + if (send_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&send_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + } + if (recv_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&recv_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + } + +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TIME_STOP(mpi_rank); + H5D_MPIO_TRACE_EXIT(mpi_rank); +#endif + + FUNC_LEAVE_NOAPI(ret_value) +} /* H5D__mpio_collective_filtered_chunk_reallocate() */ + +/*------------------------------------------------------------------------- + * Function: H5D__mpio_collective_filtered_chunk_reinsert + * + * Purpose: When performing a parallel write on a chunked dataset with + * filters applied, all ranks must eventually get together and + * perform a collective reinsertion into the dataset's chunk + * index of chunks that were modified. This routine is + * responsible for coordinating that process. + * + * Return: Non-negative on success/Negative on failure + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__mpio_collective_filtered_chunk_reinsert(H5D_filtered_collective_io_info_t *chunk_list, + size_t chunk_list_num_entries, size_t *num_chunks_assigned_map, + H5D_io_info_t *io_info, H5D_chk_idx_info_t *idx_info, + int mpi_rank, int mpi_size) +{ + H5D_chunk_ud_t chunk_ud; + MPI_Datatype send_type; + MPI_Datatype recv_type; + hbool_t send_type_derived = FALSE; + hbool_t recv_type_derived = FALSE; + hsize_t scaled_coords[H5O_LAYOUT_NDIMS]; + size_t collective_num_entries = 0; + size_t i; + void * gathered_array = NULL; + int * counts_disps_array = NULL; + int * counts_ptr = NULL; + int * displacements_ptr = NULL; + int mpi_code; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_STATIC + + HDassert(chunk_list || 0 == chunk_list_num_entries); + HDassert(io_info); + HDassert(idx_info); + +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TRACE_ENTER(mpi_rank); + H5D_MPIO_TIME_START(mpi_rank, "Reinsertion of modified chunks into chunk index"); +#endif + + /* Only re-insert chunks if index has an insert method */ + if (!idx_info->storage->ops->insert) + HGOTO_DONE(SUCCEED); + + /* + * Make sure it's safe to cast this rank's number + * of chunks to be sent into an int for MPI + */ + H5_CHECK_OVERFLOW(chunk_list_num_entries, size_t, int); + + /* Create derived datatypes for the chunk re-insertion info needed */ + if (H5D__mpio_get_chunk_insert_info_types(&recv_type, &recv_type_derived, &send_type, + &send_type_derived) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, + "can't create derived datatypes for chunk re-insertion info") + + /* + * Gather information to all ranks for a collective re-insertion + * of the modified chunks into the chunk index + */ + if (num_chunks_assigned_map) { + /* + * If a mapping between rank value -> number of assigned chunks has + * been provided (usually during linked-chunk I/O), we can use this + * to optimize MPI overhead a bit since MPI ranks won't need to + * first inform each other about how many chunks they're contributing. + */ + if (NULL == (counts_disps_array = H5MM_malloc(2 * (size_t)mpi_size * sizeof(*counts_disps_array)))) { + /* Push an error, but still participate in collective gather operation */ + HDONE_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, + "couldn't allocate receive counts and displacements array") + } + else { + /* Set the receive counts from the assigned chunks map */ + counts_ptr = counts_disps_array; + + for (i = 0; i < (size_t)mpi_size; i++) + H5_CHECKED_ASSIGN(counts_ptr[i], int, num_chunks_assigned_map[i], size_t); + + /* Set the displacements into the receive buffer for the gather operation */ + displacements_ptr = &counts_disps_array[mpi_size]; + + *displacements_ptr = 0; + for (i = 1; i < (size_t)mpi_size; i++) + displacements_ptr[i] = displacements_ptr[i - 1] + counts_ptr[i - 1]; + } + + /* Perform gather operation */ + if (H5_mpio_gatherv_alloc(chunk_list, (int)chunk_list_num_entries, send_type, counts_ptr, + displacements_ptr, recv_type, TRUE, 0, io_info->comm, mpi_rank, mpi_size, + &gathered_array, &collective_num_entries) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL, + "can't gather chunk index re-insertion info to/from ranks") + } + else { + /* + * If no mapping between rank value -> number of assigned chunks has + * been provided (usually during multi-chunk I/O), all MPI ranks will + * need to first inform other ranks about how many chunks they're + * contributing before performing the actual gather operation. Use + * the 'simple' MPI_Allgatherv wrapper for this. + */ + if (H5_mpio_gatherv_alloc_simple(chunk_list, (int)chunk_list_num_entries, send_type, recv_type, TRUE, + 0, io_info->comm, mpi_rank, mpi_size, &gathered_array, + &collective_num_entries) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL, + "can't gather chunk index re-insertion info to/from ranks") + } + + /* Initialize static chunk udata fields from chunk index info */ + H5D_MPIO_INIT_CHUNK_UD_INFO(chunk_ud, idx_info); + + for (i = 0; i < collective_num_entries; i++) { + H5D_chunk_insert_info_t *coll_entry = &((H5D_chunk_insert_info_t *)gathered_array)[i]; + + /* + * We only need to reinsert this chunk if we had to actually + * allocate or reallocate space in the file for it + */ + if (!coll_entry->index_info.need_insert) + continue; + + chunk_ud.chunk_block = coll_entry->chunk_block; + chunk_ud.chunk_idx = coll_entry->index_info.chunk_idx; + chunk_ud.filter_mask = coll_entry->index_info.filter_mask; + chunk_ud.common.scaled = scaled_coords; + + /* Calculate scaled coordinates for the chunk */ + if (idx_info->layout->idx_type == H5D_CHUNK_IDX_EARRAY && idx_info->layout->u.earray.unlim_dim > 0) { + /* + * Extensible arrays where the unlimited dimension is not + * the slowest-changing dimension "swizzle" the coordinates + * to move the unlimited dimension value to offset 0. Therefore, + * we use the "swizzled" down chunks to calculate the "swizzled" + * scaled coordinates and then we undo the "swizzle" operation. + * + * TODO: In the future, this is something that should be handled + * by the particular chunk index rather than manually + * here. Likely, the chunk index ops should get a new + * callback that accepts a chunk index and provides the + * caller with the scaled coordinates for that chunk. + */ + H5VM_array_calc_pre(chunk_ud.chunk_idx, io_info->dset->shared->ndims, + idx_info->layout->u.earray.swizzled_down_chunks, scaled_coords); + + H5VM_unswizzle_coords(hsize_t, scaled_coords, idx_info->layout->u.earray.unlim_dim); + } + else { + H5VM_array_calc_pre(chunk_ud.chunk_idx, io_info->dset->shared->ndims, + io_info->dset->shared->layout.u.chunk.down_chunks, scaled_coords); + } + + scaled_coords[io_info->dset->shared->ndims] = 0; + +#ifndef NDEBUG + /* + * If a matching local chunk entry is found, the + * `chunk_info` structure (which contains the chunk's + * pre-computed scaled coordinates) will be valid + * for this rank. Compare those coordinates against + * the calculated coordinates above to make sure + * they match. + */ + for (size_t dbg_idx = 0; dbg_idx < chunk_list_num_entries; dbg_idx++) { + if (coll_entry->index_info.chunk_idx == chunk_list[dbg_idx].index_info.chunk_idx) { + hbool_t coords_match = !HDmemcmp(scaled_coords, chunk_list[dbg_idx].chunk_info->scaled, + io_info->dset->shared->ndims * sizeof(hsize_t)); + + HDassert(coords_match && "Calculated scaled coordinates for chunk didn't match " + "chunk's actual scaled coordinates!"); + break; + } + } +#endif + + if ((idx_info->storage->ops->insert)(idx_info, &chunk_ud, io_info->dset) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk address into index") + } + +done: + H5MM_free(gathered_array); + H5MM_free(counts_disps_array); + + if (send_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&send_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + } + if (recv_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&recv_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + } + +#ifdef H5Dmpio_DEBUG + H5D_MPIO_TIME_STOP(mpi_rank); + H5D_MPIO_TRACE_EXIT(mpi_rank); +#endif + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__mpio_collective_filtered_chunk_reinsert() */ + +/*------------------------------------------------------------------------- + * Function: H5D__mpio_get_chunk_redistribute_info_types + * + * Purpose: Constructs MPI derived datatypes for communicating the + * info from a H5D_filtered_collective_io_info_t structure + * that is necessary for redistributing shared chunks during a + * collective write of filtered chunks. + * + * The datatype returned through `contig_type` has an extent + * equal to the size of an H5D_chunk_redistribute_info_t + * structure and is suitable for communicating that structure + * type. + * + * The datatype returned through `resized_type` has an extent + * equal to the size of an H5D_filtered_collective_io_info_t + * structure. This makes it suitable for sending an array of + * those structures, while extracting out just the info + * necessary for the chunk redistribution operation during + * communication. + * + * Return: Non-negative on success/Negative on failure + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__mpio_get_chunk_redistribute_info_types(MPI_Datatype *contig_type, hbool_t *contig_type_derived, + MPI_Datatype *resized_type, hbool_t *resized_type_derived) +{ + MPI_Datatype struct_type = MPI_DATATYPE_NULL; + hbool_t struct_type_derived = FALSE; + MPI_Datatype chunk_block_type = MPI_DATATYPE_NULL; + hbool_t chunk_block_type_derived = FALSE; + MPI_Datatype types[5]; + MPI_Aint displacements[5]; + int block_lengths[5]; + int field_count; + int mpi_code; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_STATIC + + HDassert(contig_type); + HDassert(contig_type_derived); + HDassert(resized_type); + HDassert(resized_type_derived); + + *contig_type_derived = FALSE; + *resized_type_derived = FALSE; + + /* Create struct type for the inner H5F_block_t structure */ + if (H5F_mpi_get_file_block_type(FALSE, &chunk_block_type, &chunk_block_type_derived) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't create derived type for chunk file description") + + field_count = 5; + HDassert(field_count == (sizeof(types) / sizeof(MPI_Datatype))); + + /* + * Create structure type to pack chunk H5F_block_t structure + * next to chunk_idx, orig_owner, new_owner and num_writers + * fields + */ + block_lengths[0] = 1; + block_lengths[1] = 1; + block_lengths[2] = 1; + block_lengths[3] = 1; + block_lengths[4] = 1; + displacements[0] = offsetof(H5D_chunk_redistribute_info_t, chunk_block); + displacements[1] = offsetof(H5D_chunk_redistribute_info_t, chunk_idx); + displacements[2] = offsetof(H5D_chunk_redistribute_info_t, orig_owner); + displacements[3] = offsetof(H5D_chunk_redistribute_info_t, new_owner); + displacements[4] = offsetof(H5D_chunk_redistribute_info_t, num_writers); + types[0] = chunk_block_type; + types[1] = HSIZE_AS_MPI_TYPE; + types[2] = MPI_INT; + types[3] = MPI_INT; + types[4] = MPI_INT; + if (MPI_SUCCESS != + (mpi_code = MPI_Type_create_struct(field_count, block_lengths, displacements, types, contig_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code) + *contig_type_derived = TRUE; + + if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(contig_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) + + /* Create struct type to extract the chunk_current, chunk_idx, orig_owner, + * new_owner and num_writers fields from a H5D_filtered_collective_io_info_t + * structure + */ + block_lengths[0] = 1; + block_lengths[1] = 1; + block_lengths[2] = 1; + block_lengths[3] = 1; + block_lengths[4] = 1; + displacements[0] = offsetof(H5D_filtered_collective_io_info_t, chunk_current); + displacements[1] = offsetof(H5D_filtered_collective_io_info_t, index_info.chunk_idx); + displacements[2] = offsetof(H5D_filtered_collective_io_info_t, orig_owner); + displacements[3] = offsetof(H5D_filtered_collective_io_info_t, new_owner); + displacements[4] = offsetof(H5D_filtered_collective_io_info_t, num_writers); + types[0] = chunk_block_type; + types[1] = HSIZE_AS_MPI_TYPE; + types[2] = MPI_INT; + types[3] = MPI_INT; + types[4] = MPI_INT; + if (MPI_SUCCESS != + (mpi_code = MPI_Type_create_struct(field_count, block_lengths, displacements, types, &struct_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code) + struct_type_derived = TRUE; + + if (MPI_SUCCESS != (mpi_code = MPI_Type_create_resized( + struct_type, 0, sizeof(H5D_filtered_collective_io_info_t), resized_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_resized failed", mpi_code) + *resized_type_derived = TRUE; + + if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(resized_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) + +done: + if (struct_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&struct_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + } + if (chunk_block_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&chunk_block_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + } + + if (ret_value < 0) { + if (*resized_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(resized_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + *resized_type_derived = FALSE; + } + if (*contig_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(contig_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + *contig_type_derived = FALSE; + } + } + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__mpio_get_chunk_redistribute_info_types() */ + +/*------------------------------------------------------------------------- + * Function: H5D__mpio_get_chunk_alloc_info_types + * + * Purpose: Constructs MPI derived datatypes for communicating the info + * from a H5D_filtered_collective_io_info_t structure that is + * necessary for re-allocating file space during a collective + * write of filtered chunks. + * + * The datatype returned through `contig_type` has an extent + * equal to the size of an H5D_chunk_alloc_info_t structure + * and is suitable for communicating that structure type. + * + * The datatype returned through `resized_type` has an extent + * equal to the size of an H5D_filtered_collective_io_info_t + * structure. This makes it suitable for sending an array of + * those structures, while extracting out just the info + * necessary for the chunk file space reallocation operation + * during communication. + * + * Return: Non-negative on success/Negative on failure + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__mpio_get_chunk_alloc_info_types(MPI_Datatype *contig_type, hbool_t *contig_type_derived, + MPI_Datatype *resized_type, hbool_t *resized_type_derived) +{ + MPI_Datatype struct_type = MPI_DATATYPE_NULL; + hbool_t struct_type_derived = FALSE; + MPI_Datatype chunk_block_type = MPI_DATATYPE_NULL; + hbool_t chunk_block_type_derived = FALSE; + MPI_Datatype types[3]; + MPI_Aint displacements[3]; + int block_lengths[3]; + int field_count; + int mpi_code; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_STATIC + + HDassert(contig_type); + HDassert(contig_type_derived); + HDassert(resized_type); + HDassert(resized_type_derived); + + *contig_type_derived = FALSE; + *resized_type_derived = FALSE; + + /* Create struct type for the inner H5F_block_t structure */ + if (H5F_mpi_get_file_block_type(FALSE, &chunk_block_type, &chunk_block_type_derived) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't create derived type for chunk file description") + + field_count = 3; + HDassert(field_count == (sizeof(types) / sizeof(MPI_Datatype))); + + /* + * Create structure type to pack both chunk H5F_block_t structures + * next to chunk_idx field + */ + block_lengths[0] = 1; + block_lengths[1] = 1; + block_lengths[2] = 1; + displacements[0] = offsetof(H5D_chunk_alloc_info_t, chunk_current); + displacements[1] = offsetof(H5D_chunk_alloc_info_t, chunk_new); + displacements[2] = offsetof(H5D_chunk_alloc_info_t, chunk_idx); + types[0] = chunk_block_type; + types[1] = chunk_block_type; + types[2] = HSIZE_AS_MPI_TYPE; + if (MPI_SUCCESS != + (mpi_code = MPI_Type_create_struct(field_count, block_lengths, displacements, types, contig_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code) + *contig_type_derived = TRUE; + + if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(contig_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) + + /* + * Create struct type to extract the chunk_current, chunk_new and chunk_idx + * fields from a H5D_filtered_collective_io_info_t structure + */ + block_lengths[0] = 1; + block_lengths[1] = 1; + block_lengths[2] = 1; + displacements[0] = offsetof(H5D_filtered_collective_io_info_t, chunk_current); + displacements[1] = offsetof(H5D_filtered_collective_io_info_t, chunk_new); + displacements[2] = offsetof(H5D_filtered_collective_io_info_t, index_info.chunk_idx); + types[0] = chunk_block_type; + types[1] = chunk_block_type; + types[2] = HSIZE_AS_MPI_TYPE; + if (MPI_SUCCESS != + (mpi_code = MPI_Type_create_struct(field_count, block_lengths, displacements, types, &struct_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code) + struct_type_derived = TRUE; + + if (MPI_SUCCESS != (mpi_code = MPI_Type_create_resized( + struct_type, 0, sizeof(H5D_filtered_collective_io_info_t), resized_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_resized failed", mpi_code) + *resized_type_derived = TRUE; + + if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(resized_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) + +done: + if (struct_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&struct_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + } + if (chunk_block_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&chunk_block_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + } + + if (ret_value < 0) { + if (*resized_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(resized_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + *resized_type_derived = FALSE; + } + if (*contig_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(contig_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + *contig_type_derived = FALSE; + } + } + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__mpio_get_chunk_alloc_info_types() */ + +/*------------------------------------------------------------------------- + * Function: H5D__mpio_get_chunk_insert_info_types + * + * Purpose: Constructs MPI derived datatypes for communicating the + * information necessary when reinserting chunks into a + * dataset's chunk index. This includes the chunk's new offset + * and size (H5F_block_t) and the inner `index_info` structure + * of a H5D_filtered_collective_io_info_t structure. + * + * The datatype returned through `contig_type` has an extent + * equal to the size of an H5D_chunk_insert_info_t structure + * and is suitable for communicating that structure type. + * + * The datatype returned through `resized_type` has an extent + * equal to the size of the encompassing + * H5D_filtered_collective_io_info_t structure. This makes it + * suitable for sending an array of + * H5D_filtered_collective_io_info_t structures, while + * extracting out just the information needed during + * communication. + * + * Return: Non-negative on success/Negative on failure + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__mpio_get_chunk_insert_info_types(MPI_Datatype *contig_type, hbool_t *contig_type_derived, + MPI_Datatype *resized_type, hbool_t *resized_type_derived) +{ + MPI_Datatype struct_type = MPI_DATATYPE_NULL; + hbool_t struct_type_derived = FALSE; + MPI_Datatype chunk_block_type = MPI_DATATYPE_NULL; + hbool_t chunk_block_type_derived = FALSE; + MPI_Aint contig_type_extent; + MPI_Datatype types[4]; + MPI_Aint displacements[4]; + int block_lengths[4]; + int field_count; + int mpi_code; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_STATIC + + HDassert(contig_type); + HDassert(contig_type_derived); + HDassert(resized_type); + HDassert(resized_type_derived); + + *contig_type_derived = FALSE; + *resized_type_derived = FALSE; + + /* Create struct type for an H5F_block_t structure */ + if (H5F_mpi_get_file_block_type(FALSE, &chunk_block_type, &chunk_block_type_derived) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't create derived type for chunk file description") + + field_count = 4; + HDassert(field_count == (sizeof(types) / sizeof(MPI_Datatype))); + + /* + * Create struct type to pack information into memory as follows: + * + * Chunk's new Offset/Size (H5F_block_t) -> + * Chunk Index Info (H5D_chunk_index_info_t) + */ + block_lengths[0] = 1; + block_lengths[1] = 1; + block_lengths[2] = 1; + block_lengths[3] = 1; + displacements[0] = offsetof(H5D_chunk_insert_info_t, chunk_block); + displacements[1] = offsetof(H5D_chunk_insert_info_t, index_info.chunk_idx); + displacements[2] = offsetof(H5D_chunk_insert_info_t, index_info.filter_mask); + displacements[3] = offsetof(H5D_chunk_insert_info_t, index_info.need_insert); + types[0] = chunk_block_type; + types[1] = HSIZE_AS_MPI_TYPE; + types[2] = MPI_UNSIGNED; + types[3] = MPI_C_BOOL; + if (MPI_SUCCESS != + (mpi_code = MPI_Type_create_struct(field_count, block_lengths, displacements, types, &struct_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code) + struct_type_derived = TRUE; + + contig_type_extent = (MPI_Aint)(sizeof(H5F_block_t) + sizeof(H5D_chunk_index_info_t)); + + if (MPI_SUCCESS != (mpi_code = MPI_Type_create_resized(struct_type, 0, contig_type_extent, contig_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_resized failed", mpi_code) + *contig_type_derived = TRUE; + + if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(contig_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) + + struct_type_derived = FALSE; + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&struct_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + + /* + * Create struct type to correctly extract all needed + * information from a H5D_filtered_collective_io_info_t + * structure. + */ + displacements[0] = offsetof(H5D_filtered_collective_io_info_t, chunk_new); + displacements[1] = offsetof(H5D_filtered_collective_io_info_t, index_info.chunk_idx); + displacements[2] = offsetof(H5D_filtered_collective_io_info_t, index_info.filter_mask); + displacements[3] = offsetof(H5D_filtered_collective_io_info_t, index_info.need_insert); + if (MPI_SUCCESS != + (mpi_code = MPI_Type_create_struct(field_count, block_lengths, displacements, types, &struct_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code) + struct_type_derived = TRUE; + + if (MPI_SUCCESS != (mpi_code = MPI_Type_create_resized( + struct_type, 0, sizeof(H5D_filtered_collective_io_info_t), resized_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_resized failed", mpi_code) + *resized_type_derived = TRUE; + + if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(resized_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) + +done: + if (struct_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&struct_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + } + if (chunk_block_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&chunk_block_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + } + + if (ret_value < 0) { + if (*resized_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(resized_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + *resized_type_derived = FALSE; + } + if (*contig_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(contig_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + *contig_type_derived = FALSE; + } + } + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__mpio_get_chunk_insert_info_types() */ + +/*------------------------------------------------------------------------- + * Function: H5D__mpio_collective_filtered_io_type + * + * Purpose: Constructs a MPI derived datatype for both the memory and + * the file for a collective I/O operation on filtered chunks. + * The datatype contains the chunk offsets and lengths in the + * file and the locations of the chunk data buffers to read + * into/write from. + * + * Return: Non-negative on success/Negative on failure + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__mpio_collective_filtered_io_type(H5D_filtered_collective_io_info_t *chunk_list, size_t num_entries, + H5D_io_op_type_t op_type, MPI_Datatype *new_mem_type, + hbool_t *mem_type_derived, MPI_Datatype *new_file_type, + hbool_t *file_type_derived) +{ + MPI_Aint *io_buf_array = NULL; /* Relative displacements of filtered chunk data buffers */ + MPI_Aint *file_offset_array = NULL; /* Chunk offsets in the file */ + int * length_array = NULL; /* Filtered Chunk lengths */ + int mpi_code; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_STATIC + + HDassert(chunk_list || 0 == num_entries); + HDassert(new_mem_type); + HDassert(mem_type_derived); + HDassert(new_file_type); + HDassert(file_type_derived); + + *mem_type_derived = FALSE; + *file_type_derived = FALSE; + *new_mem_type = MPI_BYTE; + *new_file_type = MPI_BYTE; + + if (num_entries > 0) { + H5F_block_t *chunk_block; + size_t last_valid_idx = 0; + size_t i; + int chunk_count; + + /* + * Determine number of chunks for I/O operation and + * setup for derived datatype creation if I/O operation + * includes multiple chunks + */ + if (num_entries == 1) { + /* Set last valid index to 0 for contiguous datatype creation */ + last_valid_idx = 0; + + if (op_type == H5D_IO_OP_WRITE) + chunk_count = 1; + else + chunk_count = chunk_list[0].need_read ? 1 : 0; + } + else { + MPI_Aint chunk_buf; + MPI_Aint base_buf; + haddr_t base_offset = HADDR_UNDEF; + + H5_CHECK_OVERFLOW(num_entries, size_t, int); + + /* Allocate arrays */ + if (NULL == (length_array = H5MM_malloc((size_t)num_entries * sizeof(int)))) + HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, + "memory allocation failed for filtered collective I/O length array") + if (NULL == (io_buf_array = H5MM_malloc((size_t)num_entries * sizeof(MPI_Aint)))) + HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, + "memory allocation failed for filtered collective I/O buf length array") + if (NULL == (file_offset_array = H5MM_malloc((size_t)num_entries * sizeof(MPI_Aint)))) + HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, + "memory allocation failed for filtered collective I/O offset array") + + /* + * If doing a write, we can set the base chunk offset + * and base chunk data buffer right away. + * + * If doing a read, some chunks may be skipped over + * for reading if they aren't yet allocated in the + * file. Therefore, we have to find the first chunk + * actually being read in order to set the base chunk + * offset and base chunk data buffer. + */ + if (op_type == H5D_IO_OP_WRITE) { +#if MPI_VERSION >= 3 + if (MPI_SUCCESS != (mpi_code = MPI_Get_address(chunk_list[0].buf, &base_buf))) + HMPI_GOTO_ERROR(FAIL, "MPI_Get_address failed", mpi_code) +#else + base_buf = (MPI_Aint)chunk_list[0].buf; +#endif + + base_offset = chunk_list[0].chunk_new.offset; + } + + for (i = 0, chunk_count = 0; i < num_entries; i++) { + if (op_type == H5D_IO_OP_READ) { + /* + * If this chunk isn't being read, don't add it + * to the MPI type we're building up for I/O + */ + if (!chunk_list[i].need_read) + continue; + + /* + * If this chunk is being read, go ahead and + * set the base chunk offset and base chunk + * data buffer if we haven't already + */ + if (!H5F_addr_defined(base_offset)) { +#if MPI_VERSION >= 3 + if (MPI_SUCCESS != (mpi_code = MPI_Get_address(chunk_list[i].buf, &base_buf))) + HMPI_GOTO_ERROR(FAIL, "MPI_Get_address failed", mpi_code) +#else + base_buf = (MPI_Aint)chunk_list[i].buf; +#endif + + base_offset = chunk_list[i].chunk_current.offset; + } + } + + /* Set convenience pointer for current chunk block */ + chunk_block = + (op_type == H5D_IO_OP_READ) ? &chunk_list[i].chunk_current : &chunk_list[i].chunk_new; + + /* + * Set the current chunk entry's offset in the file, relative to + * the first chunk entry + */ + HDassert(H5F_addr_defined(chunk_block->offset)); + file_offset_array[chunk_count] = (MPI_Aint)(chunk_block->offset - base_offset); + + /* + * Ensure the chunk list is sorted in ascending ordering of + * offset in the file + */ + if (chunk_count) + HDassert(file_offset_array[chunk_count] > file_offset_array[chunk_count - 1]); + + /* Set the current chunk entry's size for the I/O operation */ + H5_CHECK_OVERFLOW(chunk_block->length, hsize_t, int); + length_array[chunk_count] = (int)chunk_block->length; + + /* + * Set the displacement of the chunk entry's chunk data buffer, + * relative to the first entry's data buffer + */ +#if MPI_VERSION >= 3 && MPI_SUBVERSION >= 1 + if (MPI_SUCCESS != (mpi_code = MPI_Get_address(chunk_list[i].buf, &chunk_buf))) + HMPI_GOTO_ERROR(FAIL, "MPI_Get_address failed", mpi_code) + + io_buf_array[chunk_count] = MPI_Aint_diff(chunk_buf, base_buf); +#else + chunk_buf = (MPI_Aint)chunk_list[i].buf; + io_buf_array[chunk_count] = chunk_buf - base_buf; +#endif + + /* + * Set last valid index in case only a single chunk will + * be involved in the I/O operation + */ + last_valid_idx = i; + + chunk_count++; + } /* end for */ + } + + /* + * Create derived datatypes for the chunk list if this + * rank has any chunks to work on + */ + if (chunk_count > 0) { + if (chunk_count == 1) { + int chunk_len; + + /* Single chunk - use a contiguous type for both memory and file */ + + /* Ensure that we can cast chunk size to an int for MPI */ + chunk_block = (op_type == H5D_IO_OP_READ) ? &chunk_list[last_valid_idx].chunk_current + : &chunk_list[last_valid_idx].chunk_new; + H5_CHECKED_ASSIGN(chunk_len, int, chunk_block->length, hsize_t); + + if (MPI_SUCCESS != (mpi_code = MPI_Type_contiguous(chunk_len, MPI_BYTE, new_file_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) + *new_mem_type = *new_file_type; + + /* + * Since we use the same datatype for both memory and file, only + * mark the file type as derived so the caller doesn't try to + * free the same type twice + */ + *mem_type_derived = FALSE; + *file_type_derived = TRUE; + + if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_file_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) + } + else { + HDassert(file_offset_array); + HDassert(length_array); + HDassert(io_buf_array); + + /* Multiple chunks - use an hindexed type for both memory and file */ + + /* Create memory MPI type */ + if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed( + chunk_count, length_array, io_buf_array, MPI_BYTE, new_mem_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code) + *mem_type_derived = TRUE; + + if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_mem_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) + + /* Create file MPI type */ + if (MPI_SUCCESS != + (mpi_code = MPI_Type_create_hindexed(chunk_count, length_array, file_offset_array, + MPI_BYTE, new_file_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code) + *file_type_derived = TRUE; + + if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_file_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) + } + } + } /* end if */ done: - if (chunk_entry->async_info.receive_buffer_array) - H5MM_free(chunk_entry->async_info.receive_buffer_array); - if (chunk_entry->async_info.receive_requests_array) - H5MM_free(chunk_entry->async_info.receive_requests_array); - if (tmp_gath_buf) - H5MM_free(tmp_gath_buf); - if (file_iter_init && H5S_SELECT_ITER_RELEASE(file_iter) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator") - if (file_iter) - H5MM_free(file_iter); - if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator") - if (mem_iter) - H5MM_free(mem_iter); - if (dataspace) - if (H5S_close(dataspace) < 0) - HDONE_ERROR(H5E_DATASPACE, H5E_CANTFREE, FAIL, "can't close dataspace") + if (file_offset_array) + H5MM_free(file_offset_array); + if (io_buf_array) + H5MM_free(io_buf_array); + if (length_array) + H5MM_free(length_array); + + if (ret_value < 0) { + if (*file_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(new_file_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + *file_type_derived = FALSE; + } + if (*mem_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(new_mem_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + *mem_type_derived = FALSE; + } + } FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D__filtered_collective_chunk_entry_io() */ +} /* end H5D__mpio_collective_filtered_io_type() */ + +#ifdef H5Dmpio_DEBUG + +static herr_t +H5D__mpio_dump_collective_filtered_chunk_list(H5D_filtered_collective_io_info_t *chunk_list, + size_t chunk_list_num_entries, int mpi_rank) +{ + H5D_filtered_collective_io_info_t *chunk_entry; + size_t i; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_STATIC_NOERR + + H5D_MPIO_DEBUG(mpi_rank, "CHUNK LIST: ["); + for (i = 0; i < chunk_list_num_entries; i++) { + unsigned chunk_rank; + + chunk_entry = &chunk_list[i]; + + HDassert(chunk_entry->chunk_info); + chunk_rank = (unsigned)H5S_GET_EXTENT_NDIMS(chunk_entry->chunk_info->fspace); + + H5D_MPIO_DEBUG(mpi_rank, " {"); + H5D_MPIO_DEBUG_VA(mpi_rank, " - Entry %zu -", i); + + H5D_MPIO_DEBUG(mpi_rank, " - Chunk Fspace Info -"); + H5D_MPIO_DEBUG_VA(mpi_rank, + " Chunk Current Info: { Offset: %" PRIuHADDR ", Length: %" PRIuHADDR " }", + chunk_entry->chunk_current.offset, chunk_entry->chunk_current.length); + H5D_MPIO_DEBUG_VA(mpi_rank, " Chunk New Info: { Offset: %" PRIuHADDR ", Length: %" PRIuHADDR " }", + chunk_entry->chunk_new.offset, chunk_entry->chunk_new.length); + + H5D_MPIO_DEBUG(mpi_rank, " - Chunk Insert Info -"); + H5D_MPIO_DEBUG_VA(mpi_rank, + " Chunk Scaled Coords (4-d): { %" PRIuHSIZE ", %" PRIuHSIZE ", %" PRIuHSIZE + ", %" PRIuHSIZE " }", + chunk_rank < 1 ? 0 : chunk_entry->chunk_info->scaled[0], + chunk_rank < 2 ? 0 : chunk_entry->chunk_info->scaled[1], + chunk_rank < 3 ? 0 : chunk_entry->chunk_info->scaled[2], + chunk_rank < 4 ? 0 : chunk_entry->chunk_info->scaled[3]); + H5D_MPIO_DEBUG_VA(mpi_rank, " Chunk Index: %" PRIuHSIZE, chunk_entry->index_info.chunk_idx); + H5D_MPIO_DEBUG_VA(mpi_rank, " Filter Mask: %u", chunk_entry->index_info.filter_mask); + H5D_MPIO_DEBUG_VA(mpi_rank, " Need Insert: %s", + chunk_entry->index_info.need_insert ? "YES" : "NO"); + + H5D_MPIO_DEBUG(mpi_rank, " - Other Info -"); + H5D_MPIO_DEBUG_VA(mpi_rank, " Chunk Info Ptr: %p", (void *)chunk_entry->chunk_info); + H5D_MPIO_DEBUG_VA(mpi_rank, " Need Read: %s", chunk_entry->need_read ? "YES" : "NO"); + H5D_MPIO_DEBUG_VA(mpi_rank, " Chunk I/O Size: %zu", chunk_entry->io_size); + H5D_MPIO_DEBUG_VA(mpi_rank, " Chunk Buffer Size: %zu", chunk_entry->chunk_buf_size); + H5D_MPIO_DEBUG_VA(mpi_rank, " Original Owner: %d", chunk_entry->orig_owner); + H5D_MPIO_DEBUG_VA(mpi_rank, " New Owner: %d", chunk_entry->new_owner); + H5D_MPIO_DEBUG_VA(mpi_rank, " # of Writers: %d", chunk_entry->num_writers); + H5D_MPIO_DEBUG_VA(mpi_rank, " Chunk Data Buffer Ptr: %p", (void *)chunk_entry->buf); + + H5D_MPIO_DEBUG(mpi_rank, " }"); + } + H5D_MPIO_DEBUG(mpi_rank, "]"); + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__mpio_dump_collective_filtered_chunk_list() */ + +#endif + #endif /* H5_HAVE_PARALLEL */ diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h index 49c95a5..a424929 100644 --- a/src/H5Dpkg.h +++ b/src/H5Dpkg.h @@ -559,6 +559,7 @@ H5_DLL herr_t H5D__alloc_storage(const H5D_io_info_t *io_info, H5D_time_alloc_t hbool_t full_overwrite, hsize_t old_dim[]); H5_DLL herr_t H5D__get_storage_size(const H5D_t *dset, hsize_t *storage_size); H5_DLL herr_t H5D__get_chunk_storage_size(H5D_t *dset, const hsize_t *offset, hsize_t *storage_size); +H5_DLL herr_t H5D__chunk_index_empty(const H5D_t *dset, hbool_t *empty); H5_DLL herr_t H5D__get_num_chunks(const H5D_t *dset, const H5S_t *space, hsize_t *nchunks); H5_DLL herr_t H5D__get_chunk_info(const H5D_t *dset, const H5S_t *space, hsize_t chk_idx, hsize_t *coord, unsigned *filter_mask, haddr_t *offset, hsize_t *size); @@ -591,6 +592,10 @@ H5_DLL herr_t H5D__select_read(const H5D_io_info_t *io_info, const H5D_type_info H5_DLL herr_t H5D__select_write(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, H5S_t *file_space, H5S_t *mem_space); +/* Functions that perform direct copying between memory buffers */ +H5_DLL herr_t H5D_select_io_mem(void *dst_buf, const H5S_t *dst_space, const void *src_buf, + const H5S_t *src_space, size_t elmt_size, size_t nelmts); + /* Functions that perform scatter-gather serial I/O operations */ H5_DLL herr_t H5D__scatter_mem(const void *_tscat_buf, H5S_sel_iter_t *iter, size_t nelmts, void *_buf); H5_DLL size_t H5D__gather_mem(const void *_buf, H5S_sel_iter_t *iter, size_t nelmts, @@ -635,7 +640,13 @@ H5_DLL herr_t H5D__chunk_allocate(const H5D_io_info_t *io_info, hbool_t full_ov const hsize_t old_dim[]); H5_DLL herr_t H5D__chunk_file_alloc(const H5D_chk_idx_info_t *idx_info, const H5F_block_t *old_chunk, H5F_block_t *new_chunk, hbool_t *need_insert, const hsize_t *scaled); +H5_DLL void * H5D__chunk_mem_alloc(size_t size, const H5O_pline_t *pline); +H5_DLL void H5D__chunk_mem_free(void *chk, const void *_pline); +H5_DLL void * H5D__chunk_mem_xfree(void *chk, const void *pline); +H5_DLL void * H5D__chunk_mem_realloc(void *chk, size_t size, const H5O_pline_t *pline); H5_DLL herr_t H5D__chunk_update_old_edge_chunks(H5D_t *dset, hsize_t old_dim[]); +H5_DLL hbool_t H5D__chunk_is_partial_edge_chunk(unsigned dset_ndims, const uint32_t *chunk_dims, + const hsize_t *chunk_scaled, const hsize_t *dset_dims); H5_DLL herr_t H5D__chunk_prune_by_extent(H5D_t *dset, const hsize_t *old_dim); H5_DLL herr_t H5D__chunk_set_sizes(H5D_t *dset); #ifdef H5_HAVE_PARALLEL @@ -694,11 +705,11 @@ H5_DLL herr_t H5D__fill_term(H5D_fill_buf_info_t *fb_info); #ifdef H5_HAVE_PARALLEL -#ifdef H5S_DEBUG +#ifdef H5D_DEBUG #ifndef H5Dmpio_DEBUG #define H5Dmpio_DEBUG #endif /*H5Dmpio_DEBUG*/ -#endif /*H5S_DEBUG*/ +#endif /*H5D_DEBUG*/ /* MPI-IO function to read, it will select either regular or irregular read */ H5_DLL herr_t H5D__mpio_select_read(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, H5S_t *file_space, H5S_t *mem_space); @@ -727,6 +738,8 @@ H5_DLL herr_t H5D__chunk_collective_write(H5D_io_info_t *io_info, const H5D_type * memory and the file */ H5_DLL htri_t H5D__mpio_opt_possible(const H5D_io_info_t *io_info, const H5S_t *file_space, const H5S_t *mem_space, const H5D_type_info_t *type_info); +H5_DLL herr_t H5D__mpio_get_no_coll_cause_strings(char *local_cause, size_t local_cause_len, + char *global_cause, size_t global_cause_len); #endif /* H5_HAVE_PARALLEL */ diff --git a/src/H5Dselect.c b/src/H5Dselect.c index e64d657..f464ca5 100644 --- a/src/H5Dselect.c +++ b/src/H5Dselect.c @@ -105,6 +105,9 @@ H5D__select_io(const H5D_io_info_t *io_info, size_t elmt_size, size_t nelmts, H5 HDassert(io_info->store); HDassert(io_info->u.rbuf); + if (elmt_size == 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, FAIL, "invalid elmt_size of 0") + /* Check for only one element in selection */ if (nelmts == 1) { hsize_t single_mem_off; /* Offset in memory */ @@ -226,8 +229,6 @@ H5D__select_io(const H5D_io_info_t *io_info, size_t elmt_size, size_t nelmts, H5 /* Decrement number of elements left to process */ HDassert(((size_t)tmp_file_len % elmt_size) == 0); - if (elmt_size == 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, FAIL, "Resulted in division by zero") nelmts -= ((size_t)tmp_file_len / elmt_size); } /* end while */ } /* end else */ @@ -257,6 +258,188 @@ done: } /* end H5D__select_io() */ /*------------------------------------------------------------------------- + * Function: H5D_select_io_mem + * + * Purpose: Perform memory copies directly between two memory buffers + * according to the selections in the `dst_space` and + * `src_space` dataspaces. + * + * Note: This routine is [basically] the same as H5D__select_io, + * with the only difference being that the readvv/writevv + * calls are exchanged for H5VM_memcpyvv calls. Changes should + * be made to both routines. + * + * Return: Non-negative on success/Negative on failure + * + *------------------------------------------------------------------------- + */ +herr_t +H5D_select_io_mem(void *dst_buf, const H5S_t *dst_space, const void *src_buf, const H5S_t *src_space, + size_t elmt_size, size_t nelmts) +{ + H5S_sel_iter_t *dst_sel_iter = NULL; /* Destination dataspace iteration info */ + H5S_sel_iter_t *src_sel_iter = NULL; /* Source dataspace iteration info */ + hbool_t dst_sel_iter_init = FALSE; /* Destination dataspace selection iterator initialized? */ + hbool_t src_sel_iter_init = FALSE; /* Source dataspace selection iterator initialized? */ + hsize_t * dst_off = NULL; /* Pointer to sequence offsets in destination buffer */ + hsize_t * src_off = NULL; /* Pointer to sequence offsets in source buffer */ + size_t * dst_len = NULL; /* Pointer to sequence lengths in destination buffer */ + size_t * src_len = NULL; /* Pointer to sequence lengths in source buffer */ + size_t curr_dst_seq; /* Current destination buffer sequence to operate on */ + size_t curr_src_seq; /* Current source buffer sequence to operate on */ + size_t dst_nseq; /* Number of sequences generated for destination buffer */ + size_t src_nseq; /* Number of sequences generated for source buffer */ + size_t dxpl_vec_size; /* Vector length from API context's DXPL */ + size_t vec_size; /* Vector length */ + ssize_t bytes_copied; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_NOAPI(FAIL) + + HDassert(dst_buf); + HDassert(dst_space); + HDassert(src_buf); + HDassert(src_space); + + if (elmt_size == 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, FAIL, "invalid elmt_size of 0") + + /* Check for only one element in selection */ + if (nelmts == 1) { + hsize_t single_dst_off; /* Offset in dst_space */ + hsize_t single_src_off; /* Offset in src_space */ + size_t single_dst_len; /* Length in dst_space */ + size_t single_src_len; /* Length in src_space */ + + /* Get offset of first element in selections */ + if (H5S_SELECT_OFFSET(dst_space, &single_dst_off) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve destination selection offset") + if (H5S_SELECT_OFFSET(src_space, &single_src_off) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve source selection offset") + + /* Set up necessary information for I/O operation */ + dst_nseq = src_nseq = 1; + curr_dst_seq = curr_src_seq = 0; + single_dst_off *= elmt_size; + single_src_off *= elmt_size; + single_dst_len = single_src_len = elmt_size; + + /* Perform vectorized memcpy from src_buf to dst_buf */ + if ((bytes_copied = + H5VM_memcpyvv(dst_buf, dst_nseq, &curr_dst_seq, &single_dst_len, &single_dst_off, src_buf, + src_nseq, &curr_src_seq, &single_src_len, &single_src_off)) < 0) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed") + + HDassert(((size_t)bytes_copied % elmt_size) == 0); + } + else { + unsigned sel_iter_flags = H5S_SEL_ITER_GET_SEQ_LIST_SORTED | H5S_SEL_ITER_SHARE_WITH_DATASPACE; + size_t dst_nelem; /* Number of elements used in destination buffer sequences */ + size_t src_nelem; /* Number of elements used in source buffer sequences */ + + /* Get info from API context */ + if (H5CX_get_vec_size(&dxpl_vec_size) < 0) + HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "can't retrieve I/O vector size") + + /* Allocate the vector I/O arrays */ + if (dxpl_vec_size > H5D_IO_VECTOR_SIZE) + vec_size = dxpl_vec_size; + else + vec_size = H5D_IO_VECTOR_SIZE; + + if (NULL == (dst_len = H5FL_SEQ_MALLOC(size_t, vec_size))) + HGOTO_ERROR(H5E_IO, H5E_CANTALLOC, FAIL, "can't allocate I/O length vector array") + if (NULL == (dst_off = H5FL_SEQ_MALLOC(hsize_t, vec_size))) + HGOTO_ERROR(H5E_IO, H5E_CANTALLOC, FAIL, "can't allocate I/O offset vector array") + if (NULL == (src_len = H5FL_SEQ_MALLOC(size_t, vec_size))) + HGOTO_ERROR(H5E_IO, H5E_CANTALLOC, FAIL, "can't allocate I/O length vector array") + if (NULL == (src_off = H5FL_SEQ_MALLOC(hsize_t, vec_size))) + HGOTO_ERROR(H5E_IO, H5E_CANTALLOC, FAIL, "can't allocate I/O offset vector array") + + /* Allocate the dataspace selection iterators */ + if (NULL == (dst_sel_iter = H5FL_MALLOC(H5S_sel_iter_t))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate destination selection iterator") + if (NULL == (src_sel_iter = H5FL_MALLOC(H5S_sel_iter_t))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate source selection iterator") + + /* Initialize destination selection iterator */ + if (H5S_select_iter_init(dst_sel_iter, dst_space, elmt_size, sel_iter_flags) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator") + dst_sel_iter_init = TRUE; /* Destination selection iteration info has been initialized */ + + /* Initialize source selection iterator */ + if (H5S_select_iter_init(src_sel_iter, src_space, elmt_size, H5S_SEL_ITER_SHARE_WITH_DATASPACE) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator") + src_sel_iter_init = TRUE; /* Source selection iteration info has been initialized */ + + /* Initialize sequence counts */ + curr_dst_seq = curr_src_seq = 0; + dst_nseq = src_nseq = 0; + + /* Loop, until all bytes are processed */ + while (nelmts > 0) { + /* Check if more destination buffer sequences are needed */ + if (curr_dst_seq >= dst_nseq) { + /* Get sequences for destination selection */ + if (H5S_SELECT_ITER_GET_SEQ_LIST(dst_sel_iter, vec_size, nelmts, &dst_nseq, &dst_nelem, + dst_off, dst_len) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "sequence length generation failed") + + /* Start at the beginning of the sequences again */ + curr_dst_seq = 0; + } + + /* Check if more source buffer sequences are needed */ + if (curr_src_seq >= src_nseq) { + /* Get sequences for source selection */ + if (H5S_SELECT_ITER_GET_SEQ_LIST(src_sel_iter, vec_size, nelmts, &src_nseq, &src_nelem, + src_off, src_len) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "sequence length generation failed") + + /* Start at the beginning of the sequences again */ + curr_src_seq = 0; + } /* end if */ + + /* Perform vectorized memcpy from src_buf to dst_buf */ + if ((bytes_copied = H5VM_memcpyvv(dst_buf, dst_nseq, &curr_dst_seq, dst_len, dst_off, src_buf, + src_nseq, &curr_src_seq, src_len, src_off)) < 0) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed") + + /* Decrement number of elements left to process */ + HDassert(((size_t)bytes_copied % elmt_size) == 0); + nelmts -= ((size_t)bytes_copied / elmt_size); + } + } + +done: + /* Release selection iterators */ + if (src_sel_iter) { + if (src_sel_iter_init && H5S_SELECT_ITER_RELEASE(src_sel_iter) < 0) + HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator") + + src_sel_iter = H5FL_FREE(H5S_sel_iter_t, src_sel_iter); + } + if (dst_sel_iter) { + if (dst_sel_iter_init && H5S_SELECT_ITER_RELEASE(dst_sel_iter) < 0) + HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator") + + dst_sel_iter = H5FL_FREE(H5S_sel_iter_t, dst_sel_iter); + } + + /* Release vector arrays, if allocated */ + if (src_off) + src_off = H5FL_SEQ_FREE(hsize_t, src_off); + if (src_len) + src_len = H5FL_SEQ_FREE(size_t, src_len); + if (dst_off) + dst_off = H5FL_SEQ_FREE(hsize_t, dst_off); + if (dst_len) + dst_len = H5FL_SEQ_FREE(size_t, dst_len); + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_select_io_mem() */ + +/*------------------------------------------------------------------------- * Function: H5D__select_read * * Purpose: Reads directly from file into application memory. @@ -269,7 +269,7 @@ H5ESget_requests(hid_t es_id, H5_iter_order_t order, hid_t *connector_ids, void herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_API(FAIL) - H5TRACE5("e", "iIo*i**xx", es_id, order, connector_ids, requests, count); + H5TRACE6("e", "iIo*i**xzx", es_id, order, connector_ids, requests, array_len, count); /* Check arguments */ if (NULL == (es = H5I_object_verify(es_id, H5I_EVENTSET))) @@ -928,9 +928,10 @@ H5FD_cmp(const H5FD_t *f1, const H5FD_t *f2) { int ret_value = -1; /* Return value */ - FUNC_ENTER_NOAPI_NOERR /* return value is arbitrary */ + FUNC_ENTER_NOAPI_NOERR; /* return value is arbitrary */ - if ((!f1 || !f1->cls) && (!f2 || !f2->cls)) HGOTO_DONE(0) + if ((!f1 || !f1->cls) && (!f2 || !f2->cls)) + HGOTO_DONE(0) if (!f1 || !f1->cls) HGOTO_DONE(-1) if (!f2 || !f2->cls) diff --git a/src/H5FDmirror_priv.h b/src/H5FDmirror_priv.h index 6a7b13e..f647c21 100644 --- a/src/H5FDmirror_priv.h +++ b/src/H5FDmirror_priv.h @@ -28,10 +28,10 @@ extern "C" { * = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = */ -/* The maximum allowed size for a receiving buffer when accepting bytes to +/* Define the maximum allowed size for a receiving buffer when accepting bytes to * write. Writes larger than this size are performed by multiple accept-write * steps by the Writer. */ -#define H5FD_MIRROR_DATA_BUFFER_MAX H5_GB /* 1 Gigabyte */ +#define H5FD_MIRROR_DATA_BUFFER_MAX (1024 * 1024 * 1024) /* 1 Gigabyte */ #define H5FD_MIRROR_XMIT_CURR_VERSION 1 #define H5FD_MIRROR_XMIT_MAGIC 0x87F8005B diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c index 1feff43..4aa8a96 100644 --- a/src/H5FDmpio.c +++ b/src/H5FDmpio.c @@ -188,6 +188,41 @@ H5FD__mpio_parse_debug_str(const char *s) FUNC_LEAVE_NOAPI_VOID } /* end H5FD__mpio_parse_debug_str() */ + +/*--------------------------------------------------------------------------- + * Function: H5FD__mem_t_to_str + * + * Purpose: Returns a string representing the enum value in an H5FD_mem_t + * enum + * + * Returns: H5FD_mem_t enum value string + * + *--------------------------------------------------------------------------- + */ +static const char * +H5FD__mem_t_to_str(H5FD_mem_t mem_type) +{ + switch (mem_type) { + case H5FD_MEM_NOLIST: + return "H5FD_MEM_NOLIST"; + case H5FD_MEM_DEFAULT: + return "H5FD_MEM_DEFAULT"; + case H5FD_MEM_SUPER: + return "H5FD_MEM_SUPER"; + case H5FD_MEM_BTREE: + return "H5FD_MEM_BTREE"; + case H5FD_MEM_DRAW: + return "H5FD_MEM_DRAW"; + case H5FD_MEM_GHEAP: + return "H5FD_MEM_GHEAP"; + case H5FD_MEM_LHEAP: + return "H5FD_MEM_LHEAP"; + case H5FD_MEM_OHDR: + return "H5FD_MEM_OHDR"; + default: + return "(Unknown)"; + } +} #endif /* H5FDmpio_DEBUG */ /*------------------------------------------------------------------------- @@ -994,7 +1029,6 @@ H5FD__mpio_query(const H5FD_t H5_ATTR_UNUSED *_file, unsigned long *flags /* out *flags |= H5FD_FEAT_AGGREGATE_METADATA; /* OK to aggregate metadata allocations */ *flags |= H5FD_FEAT_AGGREGATE_SMALLDATA; /* OK to aggregate "small" raw data allocations */ *flags |= H5FD_FEAT_HAS_MPI; /* This driver uses MPI */ - *flags |= H5FD_FEAT_ALLOCATE_EARLY; /* Allocate space early instead of late */ *flags |= H5FD_FEAT_DEFAULT_VFD_COMPATIBLE; /* VFD creates a file which can be opened with the default VFD */ } /* end if */ @@ -1172,6 +1206,7 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU int n; #endif hbool_t use_view_this_time = FALSE; + hbool_t derived_type = FALSE; hbool_t rank0_bcast = FALSE; /* If read-with-rank0-and-bcast flag was used */ #ifdef H5FDmpio_DEBUG hbool_t H5FD_mpio_debug_t_flag = (H5FD_mpio_debug_flags_s[(int)'t'] && H5FD_MPIO_TRACE_THIS_RANK(file)); @@ -1199,8 +1234,6 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU if (H5FD_mpi_haddr_to_MPIOff(addr, &mpi_off /*out*/) < 0) HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "can't convert from haddr to MPI off") size_i = (int)size; - if ((hsize_t)size_i != size) - HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "can't convert from size to size_i") /* Only look for MPI views for raw data transfers */ if (type == H5FD_MEM_DRAW) { @@ -1304,6 +1337,21 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code) } /* end if */ else { + if (size != (hsize_t)size_i) { + /* If HERE, then we need to work around the integer size limit + * of 2GB. The input size_t size variable cannot fit into an integer, + * but we can get around that limitation by creating a different datatype + * and then setting the integer size (or element count) to 1 when using + * the derived_type. + */ + + if (H5_mpio_create_large_type(size, 0, MPI_BYTE, &buf_type) < 0) + HGOTO_ERROR(H5E_INTERNAL, H5E_CANTGET, FAIL, "can't create MPI-I/O datatype") + + derived_type = TRUE; + size_i = 1; + } + #ifdef H5FDmpio_DEBUG if (H5FD_mpio_debug_r_flag) HDfprintf(stderr, "%s: (%d) doing MPI independent IO\n", __func__, file->mpi_rank); @@ -1366,8 +1414,8 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU #ifdef H5FDmpio_DEBUG if (H5FD_mpio_debug_r_flag) - HDfprintf(stderr, "%s: (%d) mpi_off = %ld bytes_read = %lld\n", __func__, file->mpi_rank, - (long)mpi_off, bytes_read); + HDfprintf(stderr, "%s: (%d) mpi_off = %ld bytes_read = %lld type = %s\n", __func__, file->mpi_rank, + (long)mpi_off, bytes_read, H5FD__mem_t_to_str(type)); #endif /* @@ -1377,6 +1425,9 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU HDmemset((char *)buf + bytes_read, 0, (size_t)n); done: + if (derived_type) + MPI_Type_free(&buf_type); + #ifdef H5FDmpio_DEBUG if (H5FD_mpio_debug_t_flag) HDfprintf(stderr, "%s: (%d) Leaving\n", __func__, file->mpi_rank); @@ -1489,20 +1540,6 @@ H5FD__mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, h */ mpi_off = 0; } /* end if */ - else if (size != (hsize_t)size_i) { - /* If HERE, then we need to work around the integer size limit - * of 2GB. The input size_t size variable cannot fit into an integer, - * but we can get around that limitation by creating a different datatype - * and then setting the integer size (or element count) to 1 when using - * the derived_type. - */ - - if (H5_mpio_create_large_type(size, 0, MPI_BYTE, &buf_type) < 0) - HGOTO_ERROR(H5E_INTERNAL, H5E_CANTGET, FAIL, "can't create MPI-I/O datatype") - - derived_type = TRUE; - size_i = 1; - } /* Write the data. */ if (use_view_this_time) { @@ -1548,6 +1585,21 @@ H5FD__mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, h HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code) } /* end if */ else { + if (size != (hsize_t)size_i) { + /* If HERE, then we need to work around the integer size limit + * of 2GB. The input size_t size variable cannot fit into an integer, + * but we can get around that limitation by creating a different datatype + * and then setting the integer size (or element count) to 1 when using + * the derived_type. + */ + + if (H5_mpio_create_large_type(size, 0, MPI_BYTE, &buf_type) < 0) + HGOTO_ERROR(H5E_INTERNAL, H5E_CANTGET, FAIL, "can't create MPI-I/O datatype") + + derived_type = TRUE; + size_i = 1; + } + #ifdef H5FDmpio_DEBUG if (H5FD_mpio_debug_w_flag) HDfprintf(stderr, "%s: (%d) doing MPI independent IO\n", __func__, file->mpi_rank); @@ -1583,8 +1635,8 @@ H5FD__mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, h #ifdef H5FDmpio_DEBUG if (H5FD_mpio_debug_w_flag) - HDfprintf(stderr, "%s: (%d) mpi_off = %ld bytes_written = %lld\n", __func__, file->mpi_rank, - (long)mpi_off, bytes_written); + HDfprintf(stderr, "%s: (%d) mpi_off = %ld bytes_written = %lld type = %s\n", __func__, + file->mpi_rank, (long)mpi_off, bytes_written, H5FD__mem_t_to_str(type)); #endif /* Each process will keep track of its perceived EOF value locally, and diff --git a/src/H5Fmpi.c b/src/H5Fmpi.c index 53d2d78..02d8d52 100644 --- a/src/H5Fmpi.c +++ b/src/H5Fmpi.c @@ -31,11 +31,12 @@ /***********/ /* Headers */ /***********/ -#include "H5private.h" /* Generic Functions */ -#include "H5Eprivate.h" /* Error handling */ -#include "H5Fpkg.h" /* File access */ -#include "H5FDprivate.h" /* File drivers */ -#include "H5Iprivate.h" /* IDs */ +#include "H5private.h" /* Generic Functions */ +#include "H5CXprivate.h" /* API Contexts */ +#include "H5Eprivate.h" /* Error handling */ +#include "H5Fpkg.h" /* File access */ +#include "H5FDprivate.h" /* File drivers */ +#include "H5Iprivate.h" /* IDs */ #include "H5VLnative_private.h" /* Native VOL connector */ @@ -402,4 +403,189 @@ H5F_mpi_retrieve_comm(hid_t loc_id, hid_t acspl_id, MPI_Comm *mpi_comm) done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5F_mpi_retrieve_comm */ + +/*------------------------------------------------------------------------- + * Function: H5F_get_coll_metadata_reads + * + * Purpose: Determines whether collective metadata reads should be + * performed. This routine is meant to be the single source of + * truth for the collective metadata reads status, as it + * coordinates between the file-global flag and the flag set + * for the current operation in the current API context. + * + * Return: TRUE/FALSE (can't fail) + * + *------------------------------------------------------------------------- + */ +hbool_t +H5F_get_coll_metadata_reads(const H5F_t *file) +{ + H5P_coll_md_read_flag_t file_flag = H5P_USER_FALSE; + hbool_t ret_value = FALSE; + + FUNC_ENTER_NOAPI_NOERR + + HDassert(file && file->shared); + + /* Retrieve the file-global flag */ + file_flag = H5F_COLL_MD_READ(file); + + /* If file flag is set to H5P_FORCE_FALSE, exit early + * with FALSE, since collective metadata reads have + * been explicitly disabled somewhere in the library. + */ + if (H5P_FORCE_FALSE == file_flag) + ret_value = FALSE; + else { + /* If file flag is set to H5P_USER_TRUE, ignore + * any settings in the API context. A file-global + * setting of H5P_USER_TRUE for collective metadata + * reads should ignore any settings on an Access + * Property List for an individual operation. + */ + if (H5P_USER_TRUE == file_flag) + ret_value = TRUE; + else { + /* Get the collective metadata reads flag from + * the current API context. + */ + ret_value = H5CX_get_coll_metadata_read(); + } + } + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5F_get_coll_metadata_reads() */ + +/*------------------------------------------------------------------------- + * Function: H5F_set_coll_metadata_reads + * + * Purpose: Used to temporarily modify the collective metadata reads + * status. This is useful for cases where either: + * + * * Collective metadata reads are enabled, but need to be + * disabled for an operation about to occur that may trigger + * an independent metadata read (such as only rank 0 doing + * something) + * + * * Metadata reads are currently independent, but it is + * guaranteed that the application has maintained + * collectivity at the interface level (e.g., an operation + * that modifies metadata is being performed). In this case, + * it should be safe to enable collective metadata reads, + * barring any internal library issues that may occur + * + * After completion, the `file_flag` parameter will be set to + * the previous value of the file-global collective metadata + * reads flag. The `context_flag` parameter will be set to the + * previous value of the API context's collective metadata + * reads flag. Another call to this routine should be made to + * restore these values (see below warning). + * + * !! WARNING !! + * It is dangerous to modify the collective metadata reads + * status, as this can cause crashes, hangs and corruption in + * the HDF5 file when improperly done. Therefore, the + * `file_flag` and `context_flag` parameters are both + * mandatory, and it is assumed that the caller will guarantee + * these settings are restored with another call to this + * routine once the bracketed operation is complete. + * !! WARNING !! + * + * Return: Nothing + * + *------------------------------------------------------------------------- + */ +void +H5F_set_coll_metadata_reads(H5F_t *file, H5P_coll_md_read_flag_t *file_flag, hbool_t *context_flag) +{ + H5P_coll_md_read_flag_t prev_file_flag = H5P_USER_FALSE; + hbool_t prev_context_flag = FALSE; + + FUNC_ENTER_NOAPI_NOERR + + HDassert(file && file->shared); + HDassert(file_flag); + HDassert(context_flag); + + /* Save old state */ + prev_file_flag = H5F_COLL_MD_READ(file); + prev_context_flag = H5CX_get_coll_metadata_read(); + + /* Set new desired state */ + if (prev_file_flag != *file_flag) { + file->shared->coll_md_read = *file_flag; + *file_flag = prev_file_flag; + } + if (prev_context_flag != *context_flag) { + H5CX_set_coll_metadata_read(*context_flag); + *context_flag = prev_context_flag; + } + + FUNC_LEAVE_NOAPI_VOID +} /* end H5F_set_coll_metadata_reads() */ + +/*------------------------------------------------------------------------- + * Function: H5F_mpi_get_file_block_type + * + * Purpose: Creates an MPI derived datatype for communicating an + * H5F_block_t structure. If `commit` is specified as TRUE, + * the resulting datatype will be committed and ready for + * use in communication. Otherwise, the type is only suitable + * for building other derived types. + * + * If TRUE is returned through `new_type_derived`, this lets + * the caller know that the datatype has been derived and + * should be freed with MPI_Type_free once it is no longer + * needed. + * + * Return: Non-negative on success/Negative on failure + * + *------------------------------------------------------------------------- + */ +herr_t +H5F_mpi_get_file_block_type(hbool_t commit, MPI_Datatype *new_type, hbool_t *new_type_derived) +{ + MPI_Datatype types[2]; + MPI_Aint displacements[2]; + int block_lengths[2]; + int field_count; + int mpi_code; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_NOAPI(FAIL) + + HDassert(new_type); + HDassert(new_type_derived); + + *new_type_derived = FALSE; + + field_count = 2; + HDassert(field_count == sizeof(types) / sizeof(MPI_Datatype)); + + block_lengths[0] = 1; + block_lengths[1] = 1; + displacements[0] = offsetof(H5F_block_t, offset); + displacements[1] = offsetof(H5F_block_t, length); + types[0] = HADDR_AS_MPI_TYPE; + types[1] = HSIZE_AS_MPI_TYPE; + if (MPI_SUCCESS != + (mpi_code = MPI_Type_create_struct(field_count, block_lengths, displacements, types, new_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code) + *new_type_derived = TRUE; + + if (commit && MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) + +done: + if (ret_value < 0) { + if (*new_type_derived) { + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(new_type))) + HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) + *new_type_derived = FALSE; + } + } + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5F_mpi_get_file_block_type() */ + #endif /* H5_HAVE_PARALLEL */ diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h index a5ccbab..67e153e 100644 --- a/src/H5Fprivate.h +++ b/src/H5Fprivate.h @@ -962,6 +962,9 @@ H5_DLL MPI_Comm H5F_mpi_get_comm(const H5F_t *f); H5_DLL int H5F_shared_mpi_get_size(const H5F_shared_t *f_sh); H5_DLL int H5F_mpi_get_size(const H5F_t *f); H5_DLL herr_t H5F_mpi_retrieve_comm(hid_t loc_id, hid_t acspl_id, MPI_Comm *mpi_comm); +H5_DLL herr_t H5F_mpi_get_file_block_type(hbool_t commit, MPI_Datatype *new_type, hbool_t *new_type_derived); +H5_DLL hbool_t H5F_get_coll_metadata_reads(const H5F_t *f); +H5_DLL void H5F_set_coll_metadata_reads(H5F_t *f, H5P_coll_md_read_flag_t *file_flag, hbool_t *context_flag); #endif /* H5_HAVE_PARALLEL */ /* External file cache routines */ diff --git a/src/H5Ocache.c b/src/H5Ocache.c index ba47da3..c7586cc 100644 --- a/src/H5Ocache.c +++ b/src/H5Ocache.c @@ -346,7 +346,7 @@ H5O__cache_deserialize(const void *image, size_t len, void *_udata, hbool_t *dir done: /* Release the [possibly partially initialized] object header on errors */ if (!ret_value && oh) - if (H5O__free(oh) < 0) + if (H5O__free(oh, FALSE) < 0) HDONE_ERROR(H5E_OHDR, H5E_CANTRELEASE, NULL, "unable to destroy object header data") FUNC_LEAVE_NOAPI(ret_value) @@ -639,7 +639,7 @@ H5O__cache_free_icr(void *_thing) HDassert(oh->cache_info.type == H5AC_OHDR); /* Destroy object header */ - if (H5O__free(oh) < 0) + if (H5O__free(oh, FALSE) < 0) HGOTO_ERROR(H5E_OHDR, H5E_CANTRELEASE, FAIL, "can't destroy object header") done: @@ -1242,7 +1242,7 @@ H5O__prefix_deserialize(const uint8_t *_image, H5O_cache_ud_t *udata) /* Save the object header for later use in 'deserialize' callback */ udata->oh = oh; - if (H5O__free(saved_oh) < 0) + if (H5O__free(saved_oh, FALSE) < 0) HGOTO_ERROR(H5E_OHDR, H5E_CANTRELEASE, FAIL, "can't destroy object header") udata->free_oh = FALSE; } @@ -1255,7 +1255,7 @@ H5O__prefix_deserialize(const uint8_t *_image, H5O_cache_ud_t *udata) done: /* Release the [possibly partially initialized] object header on errors */ if (ret_value < 0 && oh) - if (H5O__free(oh) < 0) + if (H5O__free(oh, FALSE) < 0) HDONE_ERROR(H5E_OHDR, H5E_CANTRELEASE, FAIL, "unable to destroy object header data") FUNC_LEAVE_NOAPI(ret_value) diff --git a/src/H5Ocopy.c b/src/H5Ocopy.c index 05dfc72..0b0bb55 100644 --- a/src/H5Ocopy.c +++ b/src/H5Ocopy.c @@ -33,7 +33,6 @@ #include "H5Aprivate.h" /* Attributes */ #include "H5CXprivate.h" /* API Contexts */ #include "H5Eprivate.h" /* Error handling */ -#include "H5ESprivate.h" /* Event Sets */ #include "H5FLprivate.h" /* Free lists */ #include "H5Iprivate.h" /* IDs */ #include "H5HGprivate.h" /* Global Heaps */ @@ -772,7 +771,7 @@ done: /* Free destination object header on failure */ if (ret_value < 0) { if (oh_dst && !inserted) { - if (H5O__free(oh_dst) < 0) + if (H5O__free(oh_dst, TRUE) < 0) HDONE_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "unable to destroy object header data") if (H5O_loc_reset(oloc_dst) < 0) HDONE_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "unable to destroy object header data") diff --git a/src/H5Ocopy_ref.c b/src/H5Ocopy_ref.c index f1f8aaf..1cda3ea 100644 --- a/src/H5Ocopy_ref.c +++ b/src/H5Ocopy_ref.c @@ -288,21 +288,22 @@ H5O__copy_expand_ref_object2(H5O_loc_t *src_oloc, hid_t tid_src, const H5T_t *dt size_t nbytes_src, H5O_loc_t *dst_oloc, H5G_loc_t *dst_root_loc, void *buf_dst, size_t ref_count, H5O_copy_t *cpy_info) { - H5T_t * dt_mem = NULL; /* Memory datatype */ - H5T_t * dt_dst = NULL; /* Destination datatype */ - hid_t tid_mem = H5I_INVALID_HID; /* Datatype ID for memory datatype */ - hid_t tid_dst = H5I_INVALID_HID; /* Datatype ID for memory datatype */ - H5T_path_t *tpath_src_mem = NULL, *tpath_mem_dst = NULL; /* Datatype conversion paths */ - size_t i; /* Local index variable */ - hbool_t reg_tid_src = (tid_src == H5I_INVALID_HID); - hid_t dst_loc_id = H5I_INVALID_HID; - void * conv_buf = NULL; /* Buffer for converting data */ - size_t conv_buf_size = 0; /* Buffer size */ - void * reclaim_buf = NULL; /* Buffer for reclaiming data */ - H5S_t * buf_space = NULL; /* Dataspace describing buffer */ - hsize_t buf_dim[1] = {ref_count}; /* Dimension for buffer */ - size_t token_size = H5F_SIZEOF_ADDR(src_oloc->file); - herr_t ret_value = SUCCEED; + H5T_t * dt_mem = NULL; /* Memory datatype */ + H5T_t * dt_dst = NULL; /* Destination datatype */ + hid_t tid_mem = H5I_INVALID_HID; /* Datatype ID for memory datatype */ + hid_t tid_dst = H5I_INVALID_HID; /* Datatype ID for memory datatype */ + H5T_path_t * tpath_src_mem = NULL, *tpath_mem_dst = NULL; /* Datatype conversion paths */ + size_t i; /* Local index variable */ + hbool_t reg_tid_src = (tid_src == H5I_INVALID_HID); + hid_t dst_loc_id = H5I_INVALID_HID; + void * conv_buf = NULL; /* Buffer for converting data */ + size_t conv_buf_size = 0; /* Buffer size */ + void * reclaim_buf = NULL; /* Buffer for reclaiming data */ + H5S_t * buf_space = NULL; /* Dataspace describing buffer */ + hsize_t buf_dim[1] = {ref_count}; /* Dimension for buffer */ + size_t token_size = H5F_SIZEOF_ADDR(src_oloc->file); + const unsigned char zeros[H5R_REF_BUF_SIZE] = {0}; + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC @@ -353,29 +354,34 @@ H5O__copy_expand_ref_object2(H5O_loc_t *src_oloc, hid_t tid_src, const H5T_t *dt /* Making equivalent references in the destination file */ for (i = 0; i < ref_count; i++) { - H5R_ref_t * ref_ptr = (H5R_ref_t *)conv_buf; - H5R_ref_priv_t *ref = (H5R_ref_priv_t *)&ref_ptr[i]; - H5O_token_t tmp_token = {0}; - - /* Get src object address */ - if (H5R__get_obj_token(ref, &tmp_token, &token_size) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTGET, FAIL, "unable to get object token") - if (H5VL_native_token_to_addr(src_oloc->file, H5I_FILE, tmp_token, &src_oloc->addr) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTUNSERIALIZE, FAIL, "can't deserialize object token into address") - - /* Attempt to copy object from source to destination file */ - if (H5O__copy_obj_by_ref(src_oloc, dst_oloc, dst_root_loc, cpy_info) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object") - - /* Set dst object address */ - if (H5VL_native_addr_to_token(dst_oloc->file, H5I_FILE, dst_oloc->addr, &tmp_token) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTSERIALIZE, FAIL, "can't serialize address into object token") - if (H5R__set_obj_token(ref, (const H5O_token_t *)&tmp_token, token_size) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTSET, FAIL, "unable to set object token") - /* Do not set app_ref since references are released once the copy is done */ - if (H5R__set_loc_id(ref, dst_loc_id, TRUE, FALSE) < 0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTSET, FAIL, "unable to set destination loc id") - } /* end for */ + H5R_ref_t * ref_ptr = (H5R_ref_t *)conv_buf; + H5R_ref_priv_t *ref = (H5R_ref_priv_t *)&ref_ptr[i]; + + /* Check for null reference - only expand reference if it is not null */ + if (HDmemcmp(ref, zeros, H5R_REF_BUF_SIZE)) { + H5O_token_t tmp_token = {0}; + + /* Get src object address */ + if (H5R__get_obj_token(ref, &tmp_token, &token_size) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTGET, FAIL, "unable to get object token") + if (H5VL_native_token_to_addr(src_oloc->file, H5I_FILE, tmp_token, &src_oloc->addr) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTUNSERIALIZE, FAIL, + "can't deserialize object token into address") + + /* Attempt to copy object from source to destination file */ + if (H5O__copy_obj_by_ref(src_oloc, dst_oloc, dst_root_loc, cpy_info) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object") + + /* Set dst object address */ + if (H5VL_native_addr_to_token(dst_oloc->file, H5I_FILE, dst_oloc->addr, &tmp_token) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTSERIALIZE, FAIL, "can't serialize address into object token") + if (H5R__set_obj_token(ref, (const H5O_token_t *)&tmp_token, token_size) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTSET, FAIL, "unable to set object token") + /* Do not set app_ref since references are released once the copy is done */ + if (H5R__set_loc_id(ref, dst_loc_id, TRUE, FALSE) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTSET, FAIL, "unable to set destination loc id") + } /* end if */ + } /* end for */ /* Copy into another buffer, to reclaim memory later */ if (NULL == (reclaim_buf = H5FL_BLK_MALLOC(type_conv, conv_buf_size))) diff --git a/src/H5Odtype.c b/src/H5Odtype.c index fa49924..9af79f4 100644 --- a/src/H5Odtype.c +++ b/src/H5Odtype.c @@ -1731,7 +1731,7 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_NO_CLASS: case H5T_NCLASSES: default: - HDsprintf(buf, "H5T_CLASS_%d", (int)(dt->shared->type)); + HDsnprintf(buf, sizeof(buf), "H5T_CLASS_%d", (int)(dt->shared->type)); s = buf; break; } /* end switch */ @@ -1746,7 +1746,7 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt HDfprintf(stream, "%*s%-*s %u\n", indent, "", fwidth, "Number of members:", dt->shared->u.compnd.nmembs); for (i = 0; i < dt->shared->u.compnd.nmembs; i++) { - HDsprintf(buf, "Member %u:", i); + HDsnprintf(buf, sizeof(buf), "Member %u:", i); HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth, buf, dt->shared->u.compnd.memb[i].name); HDfprintf(stream, "%*s%-*s %lu\n", indent + 3, "", MAX(0, fwidth - 3), "Byte offset:", (unsigned long)(dt->shared->u.compnd.memb[i].offset)); @@ -1759,7 +1759,7 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt HDfprintf(stream, "%*s%-*s %u\n", indent, "", fwidth, "Number of members:", dt->shared->u.enumer.nmembs); for (i = 0; i < dt->shared->u.enumer.nmembs; i++) { - HDsprintf(buf, "Member %u:", i); + HDsnprintf(buf, sizeof(buf), "Member %u:", i); HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth, buf, dt->shared->u.enumer.name[i]); HDfprintf(stream, "%*s%-*s 0x", indent, "", fwidth, "Raw bytes of value:"); for (k = 0; k < dt->shared->parent->shared->size; k++) @@ -1799,13 +1799,14 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_CSET_RESERVED_13: case H5T_CSET_RESERVED_14: case H5T_CSET_RESERVED_15: - HDsprintf(buf, "H5T_CSET_RESERVED_%d", (int)(dt->shared->u.atomic.u.s.cset)); + HDsnprintf(buf, sizeof(buf), "H5T_CSET_RESERVED_%d", (int)(dt->shared->u.atomic.u.s.cset)); s = buf; break; case H5T_CSET_ERROR: default: - HDsprintf(buf, "Unknown character set: %d", (int)(dt->shared->u.atomic.u.s.cset)); + HDsnprintf(buf, sizeof(buf), "Unknown character set: %d", + (int)(dt->shared->u.atomic.u.s.cset)); s = buf; break; } /* end switch */ @@ -1837,13 +1838,14 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_STR_RESERVED_13: case H5T_STR_RESERVED_14: case H5T_STR_RESERVED_15: - HDsprintf(buf, "H5T_STR_RESERVED_%d", (int)(dt->shared->u.atomic.u.s.pad)); + HDsnprintf(buf, sizeof(buf), "H5T_STR_RESERVED_%d", (int)(dt->shared->u.atomic.u.s.pad)); s = buf; break; case H5T_STR_ERROR: default: - HDsprintf(buf, "Unknown string padding: %d", (int)(dt->shared->u.atomic.u.s.pad)); + HDsnprintf(buf, sizeof(buf), "Unknown string padding: %d", + (int)(dt->shared->u.atomic.u.s.pad)); s = buf; break; } /* end switch */ @@ -1862,7 +1864,7 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_VLEN_BADTYPE: case H5T_VLEN_MAXTYPE: default: - HDsprintf(buf, "H5T_VLEN_%d", dt->shared->u.vlen.type); + HDsnprintf(buf, sizeof(buf), "H5T_VLEN_%d", dt->shared->u.vlen.type); s = buf; break; } /* end switch */ @@ -1880,7 +1882,7 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_LOC_BADLOC: case H5T_LOC_MAXLOC: default: - HDsprintf(buf, "H5T_LOC_%d", (int)dt->shared->u.vlen.loc); + HDsnprintf(buf, sizeof(buf), "H5T_LOC_%d", (int)dt->shared->u.vlen.loc); s = buf; break; } /* end switch */ @@ -1911,13 +1913,13 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_CSET_RESERVED_13: case H5T_CSET_RESERVED_14: case H5T_CSET_RESERVED_15: - HDsprintf(buf, "H5T_CSET_RESERVED_%d", (int)(dt->shared->u.vlen.cset)); + HDsnprintf(buf, sizeof(buf), "H5T_CSET_RESERVED_%d", (int)(dt->shared->u.vlen.cset)); s = buf; break; case H5T_CSET_ERROR: default: - HDsprintf(buf, "Unknown character set: %d", (int)(dt->shared->u.vlen.cset)); + HDsnprintf(buf, sizeof(buf), "Unknown character set: %d", (int)(dt->shared->u.vlen.cset)); s = buf; break; } /* end switch */ @@ -1949,13 +1951,13 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_STR_RESERVED_13: case H5T_STR_RESERVED_14: case H5T_STR_RESERVED_15: - HDsprintf(buf, "H5T_STR_RESERVED_%d", (int)(dt->shared->u.vlen.pad)); + HDsnprintf(buf, sizeof(buf), "H5T_STR_RESERVED_%d", (int)(dt->shared->u.vlen.pad)); s = buf; break; case H5T_STR_ERROR: default: - HDsprintf(buf, "Unknown string padding: %d", (int)(dt->shared->u.vlen.pad)); + HDsnprintf(buf, sizeof(buf), "Unknown string padding: %d", (int)(dt->shared->u.vlen.pad)); s = buf; break; } /* end switch */ @@ -1995,7 +1997,7 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_ORDER_ERROR: default: - HDsprintf(buf, "H5T_ORDER_%d", dt->shared->u.atomic.order); + HDsnprintf(buf, sizeof(buf), "H5T_ORDER_%d", dt->shared->u.atomic.order); s = buf; break; } /* end switch */ @@ -2069,9 +2071,9 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_NPAD: default: if (dt->shared->u.atomic.u.f.pad < 0) - HDsprintf(buf, "H5T_PAD_%d", -(dt->shared->u.atomic.u.f.pad)); + HDsnprintf(buf, sizeof(buf), "H5T_PAD_%d", -(dt->shared->u.atomic.u.f.pad)); else - HDsprintf(buf, "bit-%d", dt->shared->u.atomic.u.f.pad); + HDsnprintf(buf, sizeof(buf), "bit-%d", dt->shared->u.atomic.u.f.pad); s = buf; break; } /* end switch */ @@ -2092,7 +2094,7 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_NORM_ERROR: default: - HDsprintf(buf, "H5T_NORM_%d", (int)(dt->shared->u.atomic.u.f.norm)); + HDsnprintf(buf, sizeof(buf), "H5T_NORM_%d", (int)(dt->shared->u.atomic.u.f.norm)); s = buf; } /* end switch */ HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth, "Normalization:", s); @@ -2129,7 +2131,7 @@ H5O__dtype_debug(H5F_t *f, const void *mesg, FILE *stream, int indent, int fwidt case H5T_SGN_ERROR: case H5T_NSGN: default: - HDsprintf(buf, "H5T_SGN_%d", (int)(dt->shared->u.atomic.u.i.sign)); + HDsnprintf(buf, sizeof(buf), "H5T_SGN_%d", (int)(dt->shared->u.atomic.u.i.sign)); s = buf; break; } /* end switch */ diff --git a/src/H5Oint.c b/src/H5Oint.c index ee79b0c..2348790 100644 --- a/src/H5Oint.c +++ b/src/H5Oint.c @@ -289,7 +289,7 @@ H5O_create(H5F_t *f, size_t size_hint, size_t initial_rc, hid_t ocpl_id, H5O_loc HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, FAIL, "Can't apply object header to file") done: - if ((FAIL == ret_value) && (NULL != oh) && (H5O__free(oh) < 0)) + if ((FAIL == ret_value) && (NULL != oh) && (H5O__free(oh, TRUE) < 0)) HDONE_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "can't delete object header") FUNC_LEAVE_NOAPI(ret_value) @@ -353,7 +353,7 @@ H5O_create_ohdr(H5F_t *f, hid_t ocpl_id) ret_value = oh; done: - if ((NULL == ret_value) && (NULL != oh) && (H5O__free(oh) < 0)) + if ((NULL == ret_value) && (NULL != oh) && (H5O__free(oh, TRUE) < 0)) HDONE_ERROR(H5E_OHDR, H5E_CANTFREE, NULL, "can't delete object header") FUNC_LEAVE_NOAPI(ret_value) @@ -3014,7 +3014,7 @@ H5O_get_proxy(const H5O_t *oh) *------------------------------------------------------------------------- */ herr_t -H5O__free(H5O_t *oh) +H5O__free(H5O_t *oh, hbool_t force) { unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ @@ -3038,10 +3038,12 @@ H5O__free(H5O_t *oh) for (u = 0; u < oh->nmesgs; u++) { #ifndef NDEBUG /* Verify that message is clean, unless it could have been marked - * dirty by decoding */ + * dirty by decoding, or if this is a forced free (in case of + * failure during creation of the object some messages may be dirty) + */ if (oh->ndecode_dirtied && oh->mesg[u].dirty) oh->ndecode_dirtied--; - else + else if (!force) HDassert(oh->mesg[u].dirty == 0); #endif /* NDEBUG */ diff --git a/src/H5Opkg.h b/src/H5Opkg.h index ebfe636..1fe918d 100644 --- a/src/H5Opkg.h +++ b/src/H5Opkg.h @@ -551,7 +551,7 @@ H5_DLL herr_t H5O__visit(H5G_loc_t *loc, const char *obj_name, H5_index_t idx_ty H5O_iterate2_t op, void *op_data, unsigned fields); H5_DLL herr_t H5O__inc_rc(H5O_t *oh); H5_DLL herr_t H5O__dec_rc(H5O_t *oh); -H5_DLL herr_t H5O__free(H5O_t *oh); +H5_DLL herr_t H5O__free(H5O_t *oh, hbool_t force); /* Object header message routines */ H5_DLL herr_t H5O__msg_alloc(H5F_t *f, H5O_t *oh, const H5O_msg_class_t *type, unsigned *mesg_flags, diff --git a/src/H5PLpath.c b/src/H5PLpath.c index 87ff831..b86fd6e 100644 --- a/src/H5PLpath.c +++ b/src/H5PLpath.c @@ -709,7 +709,7 @@ H5PL__path_table_iterate_process_path(const char *plugin_path, H5PL_iterate_type /* Specify a file mask. *.* = We want everything! - * skip the path if the directory can't be opened */ - HDsprintf(service, "%s\\*.dll", plugin_path); + HDsnprintf(service, sizeof(service), "%s\\*.dll", plugin_path); if ((hFind = FindFirstFileA(service, &fdFile)) == INVALID_HANDLE_VALUE) HGOTO_DONE(H5_ITER_CONT) @@ -934,7 +934,7 @@ H5PL__find_plugin_in_path(const H5PL_search_params_t *search_params, hbool_t *fo *found = FALSE; /* Specify a file mask. *.* = We want everything! */ - HDsprintf(service, "%s\\*.dll", dir); + HDsnprintf(service, sizeof(service), "%s\\*.dll", dir); if ((hFind = FindFirstFileA(service, &fdFile)) == INVALID_HANDLE_VALUE) HGOTO_ERROR(H5E_PLUGIN, H5E_OPENERROR, FAIL, "can't open directory") diff --git a/src/H5Pfapl.c b/src/H5Pfapl.c index 47c17db..2c3caa8 100644 --- a/src/H5Pfapl.c +++ b/src/H5Pfapl.c @@ -5284,15 +5284,14 @@ H5P__decode_coll_md_read_flag_t(const void **_pp, void *_value) * Function: H5Pset_all_coll_metadata_ops * * Purpose: Tell the library whether the metadata read operations will - * be done collectively (1) or not (0). Default is independent. - * With collective mode, the library will optimize access to - * metadata operations on the file. + * be done collectively (1) or not (0). Default is independent. + * With collective mode, the library will optimize access to + * metadata operations on the file. * * Note: This routine accepts file access property lists, link - * access property lists, attribute access property lists, - * dataset access property lists, group access property lists, - * named datatype access property lists, - * and dataset transfer property lists. + * access property lists, attribute access property lists, + * dataset access property lists, group access property lists + * and named datatype access property lists. * * Return: Non-negative on success/Negative on failure * @@ -5312,7 +5311,7 @@ H5Pset_all_coll_metadata_ops(hid_t plist_id, hbool_t is_collective) H5TRACE2("e", "ib", plist_id, is_collective); /* Compare the property list's class against the other class */ - /* (Dataset, group, attribute, and named datype access property lists + /* (Dataset, group, attribute, and named datatype access property lists * are sub-classes of link access property lists -QAK) */ if (TRUE != H5P_isa_class(plist_id, H5P_LINK_ACCESS) && TRUE != H5P_isa_class(plist_id, H5P_FILE_ACCESS)) @@ -5342,10 +5341,9 @@ done: * Purpose: Gets information about collective metadata read mode. * * Note: This routine accepts file access property lists, link - * access property lists, attribute access property lists, - * dataset access property lists, group access property lists, - * named datatype access property lists, - * and dataset transfer property lists. + * access property lists, attribute access property lists, + * dataset access property lists, group access property lists, + * and named datatype access property lists. * * Return: Non-negative on success/Negative on failure * @@ -5363,7 +5361,7 @@ H5Pget_all_coll_metadata_ops(hid_t plist_id, hbool_t *is_collective /*out*/) H5TRACE2("e", "ix", plist_id, is_collective); /* Compare the property list's class against the other class */ - /* (Dataset, group, attribute, and named datype access property lists + /* (Dataset, group, attribute, and named datatype access property lists * are sub-classes of link access property lists -QAK) */ if (TRUE != H5P_isa_class(plist_id, H5P_LINK_ACCESS) && TRUE != H5P_isa_class(plist_id, H5P_FILE_ACCESS)) diff --git a/src/H5Tcommit.c b/src/H5Tcommit.c index e99494a..a3a1aa0 100644 --- a/src/H5Tcommit.c +++ b/src/H5Tcommit.c @@ -1127,7 +1127,7 @@ H5T_open(const H5G_loc_t *loc) done: if (ret_value == NULL) { if (dt) { - if (shared_fo == NULL) { /* Need to free shared of */ + if (shared_fo == NULL) { /* Need to free shared file object */ if (dt->shared->owned_vol_obj && H5VL_free_object(dt->shared->owned_vol_obj) < 0) HDONE_ERROR(H5E_DATATYPE, H5E_CANTCLOSEOBJ, NULL, "unable to close owned VOL object") dt->shared = H5FL_FREE(H5T_shared_t, dt->shared); diff --git a/src/H5Tnative.c b/src/H5Tnative.c index 44c6d45..d56ac99 100644 --- a/src/H5Tnative.c +++ b/src/H5Tnative.c @@ -43,7 +43,7 @@ static herr_t H5T__cmp_offset(size_t *comp_size, size_t *offset, size_t elem_siz * * Purpose: High-level API to return the native type of a datatype. * The native type is chosen by matching the size and class of - * querried datatype from the following native premitive + * queried datatype from the following native primitive * datatypes: * H5T_NATIVE_CHAR H5T_NATIVE_UCHAR * H5T_NATIVE_SHORT H5T_NATIVE_USHORT @@ -56,7 +56,7 @@ static herr_t H5T__cmp_offset(size_t *comp_size, size_t *offset, size_t elem_siz * H5T_NATIVE_LDOUBLE * * Compound, array, enum, and VL types all choose among these - * types for their members. Time, Bifield, Opaque, Reference + * types for their members. Time, Bitfield, Opaque, Reference * types are only copy out. * * Return: Success: Returns the native data type if successful. @@ -696,7 +696,7 @@ H5_GCC_DIAG_OFF("duplicated-branches") /*------------------------------------------------------------------------- * Function: H5T__get_native_float * - * Purpose: Returns the native floatt type of a datatype. + * Purpose: Returns the native float type of a datatype. * * Return: Success: Returns the native data type if successful. * diff --git a/src/H5VLcallback.c b/src/H5VLcallback.c index 4cf4d53..0c5c73d 100644 --- a/src/H5VLcallback.c +++ b/src/H5VLcallback.c @@ -30,7 +30,7 @@ #include "H5private.h" /* Generic Functions */ #include "H5Eprivate.h" /* Error handling */ #include "H5ESprivate.h" /* Event Sets */ -#include "H5Fprivate.h" /* File access */ +#include "H5Fprivate.h" /* File access */ #include "H5Iprivate.h" /* IDs */ #include "H5MMprivate.h" /* Memory management */ #include "H5Pprivate.h" /* Property lists */ diff --git a/src/H5VLnative.h b/src/H5VLnative.h index fe8ede2..5e43c4e 100644 --- a/src/H5VLnative.h +++ b/src/H5VLnative.h @@ -74,7 +74,7 @@ typedef union H5VL_native_attr_optional_args_t { #define H5VL_NATIVE_DATASET_CHUNK_WRITE 7 /* H5Dchunk_write */ #define H5VL_NATIVE_DATASET_GET_VLEN_BUF_SIZE 8 /* H5Dvlen_get_buf_size */ #define H5VL_NATIVE_DATASET_GET_OFFSET 9 /* H5Dget_offset */ -#define H5VL_NATIVE_DATASET_CHUNK_ITER 10 /* H5Dget_offset */ +#define H5VL_NATIVE_DATASET_CHUNK_ITER 10 /* H5Dchunk_iter */ /* NOTE: If values over 1023 are added, the H5VL_RESERVED_NATIVE_OPTIONAL macro * must be updated. */ @@ -208,8 +208,8 @@ typedef union H5VL_native_dataset_optional_args_t { #ifdef H5_HAVE_PARALLEL #define H5VL_NATIVE_FILE_GET_MPI_ATOMICITY 26 /* H5Fget_mpi_atomicity */ #define H5VL_NATIVE_FILE_SET_MPI_ATOMICITY 27 /* H5Fset_mpi_atomicity */ -#endif /* H5_HAVE_PARALLEL */ -#define H5VL_NATIVE_FILE_POST_OPEN 28 /* Adjust file after open, with wrapping context */ +#endif +#define H5VL_NATIVE_FILE_POST_OPEN 28 /* Adjust file after open, with wrapping context */ /* NOTE: If values over 1023 are added, the H5VL_RESERVED_NATIVE_OPTIONAL macro * must be updated. */ @@ -594,14 +594,9 @@ H5Z__flush_file_cb(void *obj_ptr, hid_t H5_ATTR_UNUSED obj_id, void H5_ATTR_PARA /* Do a global flush if the file is opened for write */ if (H5F_ACC_RDWR & H5F_INTENT(f)) { -/* When parallel HDF5 is defined, check for collective metadata reads on this - * file and set the flag for metadata I/O in the API context. -QAK, 2018/02/14 - */ #ifdef H5_HAVE_PARALLEL /* Check if MPIO driver is used */ if (H5F_HAS_FEATURE(f, H5FD_FEAT_HAS_MPI)) { - H5P_coll_md_read_flag_t coll_md_read; /* Do all metadata reads collectively */ - /* Sanity check for collectively calling H5Zunregister, if requested */ /* (Sanity check assumes that a barrier on one file's comm * is sufficient (i.e. that there aren't different comms for @@ -621,13 +616,8 @@ H5Z__flush_file_cb(void *obj_ptr, hid_t H5_ATTR_UNUSED obj_id, void H5_ATTR_PARA /* Set the "sanity checked" flag */ object->sanity_checked = TRUE; } /* end if */ - - /* Check whether to use the collective metadata read DXPL */ - coll_md_read = H5F_COLL_MD_READ(f); - if (H5P_USER_TRUE == coll_md_read) - H5CX_set_coll_metadata_read(TRUE); - } /* end if */ -#endif /* H5_HAVE_PARALLEL */ + } /* end if */ +#endif /* H5_HAVE_PARALLEL */ /* Call the flush routine for mounted file hierarchies */ if (H5F_flush_mounts((H5F_t *)obj_ptr) < 0) diff --git a/src/H5Znbit.c b/src/H5Znbit.c index 21363bc..905d417 100644 --- a/src/H5Znbit.c +++ b/src/H5Znbit.c @@ -975,7 +975,7 @@ H5Z__filter_nbit(unsigned flags, size_t cd_nelmts, const unsigned cd_values[], s /* input; decompress */ if (flags & H5Z_FLAG_REVERSE) { - size_out = d_nelmts * cd_values[4]; /* cd_values[4] stores datatype size */ + size_out = d_nelmts * (size_t)cd_values[4]; /* cd_values[4] stores datatype size */ /* allocate memory space for decompressed buffer */ if (NULL == (outbuf = (unsigned char *)H5MM_malloc(size_out))) @@ -1170,7 +1170,8 @@ H5Z__nbit_decompress_one_array(unsigned char *data, size_t data_offset, unsigned n = total_size / p.size; for (i = 0; i < n; i++) - H5Z__nbit_decompress_one_atomic(data, data_offset + i * p.size, buffer, j, buf_len, &p); + H5Z__nbit_decompress_one_atomic(data, data_offset + i * (size_t)p.size, buffer, j, buf_len, + &p); break; case H5Z_NBIT_ARRAY: @@ -1178,8 +1179,8 @@ H5Z__nbit_decompress_one_array(unsigned char *data, size_t data_offset, unsigned n = total_size / base_size; /* number of base_type elements inside the array datatype */ begin_index = *parms_index; for (i = 0; i < n; i++) { - if (H5Z__nbit_decompress_one_array(data, data_offset + i * base_size, buffer, j, buf_len, - parms, parms_index) < 0) + if (H5Z__nbit_decompress_one_array(data, data_offset + i * (size_t)base_size, buffer, j, + buf_len, parms, parms_index) < 0) HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "can't decompress array") *parms_index = begin_index; } @@ -1190,8 +1191,8 @@ H5Z__nbit_decompress_one_array(unsigned char *data, size_t data_offset, unsigned n = total_size / base_size; /* number of base_type elements inside the array datatype */ begin_index = *parms_index; for (i = 0; i < n; i++) { - if (H5Z__nbit_decompress_one_compound(data, data_offset + i * base_size, buffer, j, buf_len, - parms, parms_index) < 0) + if (H5Z__nbit_decompress_one_compound(data, data_offset + i * (size_t)base_size, buffer, j, + buf_len, parms, parms_index) < 0) HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "can't decompress compound") *parms_index = begin_index; } @@ -1291,7 +1292,7 @@ H5Z__nbit_decompress(unsigned char *data, unsigned d_nelmts, unsigned char *buff FUNC_ENTER_STATIC /* may not have to initialize to zeros */ - HDmemset(data, 0, d_nelmts * parms[4]); + HDmemset(data, 0, d_nelmts * (size_t)parms[4]); /* initialization before the loop */ j = 0; @@ -1309,7 +1310,7 @@ H5Z__nbit_decompress(unsigned char *data, unsigned d_nelmts, unsigned char *buff HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "invalid datatype precision/offset") for (i = 0; i < d_nelmts; i++) - H5Z__nbit_decompress_one_atomic(data, i * p.size, buffer, &j, &buf_len, &p); + H5Z__nbit_decompress_one_atomic(data, i * (size_t)p.size, buffer, &j, &buf_len, &p); break; case H5Z_NBIT_ARRAY: @@ -1468,7 +1469,7 @@ H5Z__nbit_compress_one_array(unsigned char *data, size_t data_offset, unsigned c p.offset = parms[(*parms_index)++]; n = total_size / p.size; for (i = 0; i < n; i++) - H5Z__nbit_compress_one_atomic(data, data_offset + i * p.size, buffer, j, buf_len, &p); + H5Z__nbit_compress_one_atomic(data, data_offset + i * (size_t)p.size, buffer, j, buf_len, &p); break; case H5Z_NBIT_ARRAY: @@ -1476,8 +1477,8 @@ H5Z__nbit_compress_one_array(unsigned char *data, size_t data_offset, unsigned c n = total_size / base_size; /* number of base_type elements inside the array datatype */ begin_index = *parms_index; for (i = 0; i < n; i++) { - H5Z__nbit_compress_one_array(data, data_offset + i * base_size, buffer, j, buf_len, parms, - parms_index); + H5Z__nbit_compress_one_array(data, data_offset + i * (size_t)base_size, buffer, j, buf_len, + parms, parms_index); *parms_index = begin_index; } break; @@ -1487,8 +1488,8 @@ H5Z__nbit_compress_one_array(unsigned char *data, size_t data_offset, unsigned c n = total_size / base_size; /* number of base_type elements inside the array datatype */ begin_index = *parms_index; for (i = 0; i < n; i++) { - H5Z__nbit_compress_one_compound(data, data_offset + i * base_size, buffer, j, buf_len, parms, - parms_index); + H5Z__nbit_compress_one_compound(data, data_offset + i * (size_t)base_size, buffer, j, buf_len, + parms, parms_index); *parms_index = begin_index; } break; @@ -1574,7 +1575,7 @@ H5Z__nbit_compress(unsigned char *data, unsigned d_nelmts, unsigned char *buffer p.offset = parms[7]; for (i = 0; i < d_nelmts; i++) - H5Z__nbit_compress_one_atomic(data, i * p.size, buffer, &new_size, &buf_len, &p); + H5Z__nbit_compress_one_atomic(data, i * (size_t)p.size, buffer, &new_size, &buf_len, &p); break; case H5Z_NBIT_ARRAY: diff --git a/src/H5Zscaleoffset.c b/src/H5Zscaleoffset.c index 5bdc51c..46c1a10 100644 --- a/src/H5Zscaleoffset.c +++ b/src/H5Zscaleoffset.c @@ -1240,7 +1240,7 @@ H5Z__filter_scaleoffset(unsigned flags, size_t cd_nelmts, const unsigned cd_valu p.minbits = minbits; /* calculate size of output buffer after decompression */ - size_out = d_nelmts * p.size; + size_out = d_nelmts * (size_t)p.size; /* allocate memory space for decompressed buffer */ if (NULL == (outbuf = (unsigned char *)H5MM_malloc(size_out))) @@ -1403,7 +1403,7 @@ H5Z__scaleoffset_convert(void *buf, unsigned d_nelmts, unsigned dtype_size) unsigned char *buffer, temp; buffer = (unsigned char *)buf; - for (i = 0; i < d_nelmts * dtype_size; i += dtype_size) + for (i = 0; i < d_nelmts * (size_t)dtype_size; i += dtype_size) for (j = 0; j < dtype_size / 2; j++) { /* swap pair of bytes */ temp = buffer[i + j]; @@ -1681,7 +1681,7 @@ H5Z__scaleoffset_decompress(unsigned char *data, unsigned d_nelmts, unsigned cha unsigned buf_len; /* must initialize to zeros */ - for (i = 0; i < d_nelmts * p.size; i++) + for (i = 0; i < d_nelmts * (size_t)p.size; i++) data[i] = 0; /* initialization before the loop */ diff --git a/src/H5mpi.c b/src/H5mpi.c index aea0104..15fb785 100644 --- a/src/H5mpi.c +++ b/src/H5mpi.c @@ -549,4 +549,237 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5_mpio_create_large_type() */ +/*------------------------------------------------------------------------- + * Function: H5_mpio_gatherv_alloc + * + * Purpose: A wrapper around MPI_(All)gatherv that performs allocation + * of the receive buffer on the caller's behalf. This + * routine's parameters are as follows: + * + * `send_buf` - The buffer that data will be sent from for + * the calling MPI rank. Analogous to + * MPI_(All)gatherv's `sendbuf` parameter. + * + * `send_count` - The number of `send_type` elements in the + * send buffer. Analogous to MPI_(All)gatherv's + * `sendcount` parameter. + * + * `send_type` - The MPI Datatype of the elements in the send + * buffer. Analogous to MPI_(All)gatherv's + * `sendtype` parameter. + * + * `recv_counts` - An array containing the number of elements + * to be received from each MPI rank. + * Analogous to MPI_(All)gatherv's `recvcount` + * parameter. + * + * `displacements` - An array containing the displacements + * in the receive buffer where data from + * each MPI rank should be placed. Analogous + * to MPI_(All)gatherv's `displs` parameter. + * + * `recv_type` - The MPI Datatype of the elements in the + * receive buffer. Analogous to + * MPI_(All)gatherv's `recvtype` parameter. + * + * `allgather` - Specifies whether the gather operation to be + * performed should be MPI_Allgatherv (TRUE) or + * MPI_Gatherv (FALSE). + * + * `root` - For MPI_Gatherv operations, specifies the rank + * that will receive the data sent by other ranks. + * Analogous to MPI_Gatherv's `root` parameter. For + * MPI_Allgatherv operations, this parameter is + * ignored. + * + * `comm` - Specifies the MPI Communicator for the operation. + * Analogous to MPI_(All)gatherv's `comm` parameter. + * + * `mpi_rank` - Specifies the calling rank's rank value, as + * obtained by calling MPI_Comm_rank on the + * MPI Communicator `comm`. + * + * `mpi_size` - Specifies the MPI Communicator size, as + * obtained by calling MPI_Comm_size on the + * MPI Communicator `comm`. + * + * `out_buf` - Resulting buffer that is allocated and + * returned to the caller after data has been + * gathered into it. Returned only to the rank + * specified by `root` for MPI_Gatherv + * operations, or to all ranks for + * MPI_Allgatherv operations. + * + * `out_buf_num_entries` - The number of elements in the + * resulting buffer, in terms of + * the MPI Datatype provided for + * `recv_type`. + * + * Notes: This routine is collective across `comm`. + * + * Return: Non-negative on success/Negative on failure + * + *------------------------------------------------------------------------- + */ +herr_t +H5_mpio_gatherv_alloc(void *send_buf, int send_count, MPI_Datatype send_type, const int recv_counts[], + const int displacements[], MPI_Datatype recv_type, hbool_t allgather, int root, + MPI_Comm comm, int mpi_rank, int mpi_size, void **out_buf, size_t *out_buf_num_entries) +{ + size_t recv_buf_num_entries = 0; + void * recv_buf = NULL; +#if MPI_VERSION >= 3 + MPI_Count type_lb; + MPI_Count type_extent; +#else + MPI_Aint type_lb; + MPI_Aint type_extent; +#endif + int mpi_code; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_NOAPI(FAIL) + + HDassert(send_buf || send_count == 0); + if (allgather || (mpi_rank == root)) + HDassert(out_buf && out_buf_num_entries); + + /* Retrieve the extent of the MPI Datatype being used */ +#if MPI_VERSION >= 3 + if (MPI_SUCCESS != (mpi_code = MPI_Type_get_extent_x(recv_type, &type_lb, &type_extent))) +#else + if (MPI_SUCCESS != (mpi_code = MPI_Type_get_extent(recv_type, &type_lb, &type_extent))) +#endif + HMPI_GOTO_ERROR(FAIL, "MPI_Type_get_extent(_x) failed", mpi_code) + + if (type_extent < 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "MPI recv_type had a negative extent") + + /* + * Calculate the total size of the buffer being + * returned and allocate it + */ + if (allgather || (mpi_rank == root)) { + size_t i; + size_t buf_size; + + for (i = 0, recv_buf_num_entries = 0; i < (size_t)mpi_size; i++) + recv_buf_num_entries += (size_t)recv_counts[i]; + buf_size = recv_buf_num_entries * (size_t)type_extent; + + /* If our buffer size is 0, there's nothing to do */ + if (buf_size == 0) + HGOTO_DONE(SUCCEED) + + if (NULL == (recv_buf = H5MM_malloc(buf_size))) + /* Push an error, but still participate in collective gather operation */ + HDONE_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "couldn't allocate receive buffer") + } + + /* Perform gather operation */ + if (allgather) { + if (MPI_SUCCESS != (mpi_code = MPI_Allgatherv(send_buf, send_count, send_type, recv_buf, recv_counts, + displacements, recv_type, comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Allgatherv failed", mpi_code) + } + else { + if (MPI_SUCCESS != (mpi_code = MPI_Gatherv(send_buf, send_count, send_type, recv_buf, recv_counts, + displacements, recv_type, root, comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Gatherv failed", mpi_code) + } + + if (allgather || (mpi_rank == root)) { + *out_buf = recv_buf; + *out_buf_num_entries = recv_buf_num_entries; + } + +done: + if (ret_value < 0) { + if (recv_buf) + H5MM_free(recv_buf); + } + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5_mpio_gatherv_alloc() */ + +/*------------------------------------------------------------------------- + * Function: H5_mpio_gatherv_alloc_simple + * + * Purpose: A slightly simplified interface to H5_mpio_gatherv_alloc + * which calculates the receive counts and receive buffer + * displacements for the caller. + * + * Notes: This routine is collective across `comm`. + * + * Return: Non-negative on success/Negative on failure + * + *------------------------------------------------------------------------- + */ +herr_t +H5_mpio_gatherv_alloc_simple(void *send_buf, int send_count, MPI_Datatype send_type, MPI_Datatype recv_type, + hbool_t allgather, int root, MPI_Comm comm, int mpi_rank, int mpi_size, + void **out_buf, size_t *out_buf_num_entries) +{ + int * recv_counts_disps_array = NULL; + int mpi_code; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_NOAPI(FAIL) + + HDassert(send_buf || send_count == 0); + if (allgather || (mpi_rank == root)) + HDassert(out_buf && out_buf_num_entries); + + /* + * Allocate array to store the receive counts of each rank, as well as + * the displacements into the final array where each rank will place + * their data. The first half of the array contains the receive counts + * (in rank order), while the latter half contains the displacements + * (also in rank order). + */ + if (allgather || (mpi_rank == root)) { + if (NULL == + (recv_counts_disps_array = H5MM_malloc(2 * (size_t)mpi_size * sizeof(*recv_counts_disps_array)))) + /* Push an error, but still participate in collective gather operation */ + HDONE_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, + "couldn't allocate receive counts and displacements array") + } + + /* Collect each rank's send count to interested ranks */ + if (allgather) { + if (MPI_SUCCESS != + (mpi_code = MPI_Allgather(&send_count, 1, MPI_INT, recv_counts_disps_array, 1, MPI_INT, comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Allgather failed", mpi_code) + } + else { + if (MPI_SUCCESS != + (mpi_code = MPI_Gather(&send_count, 1, MPI_INT, recv_counts_disps_array, 1, MPI_INT, root, comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Gather failed", mpi_code) + } + + /* Set the displacements into the receive buffer for the gather operation */ + if (allgather || (mpi_rank == root)) { + size_t i; + int * displacements_ptr; + + displacements_ptr = &recv_counts_disps_array[mpi_size]; + + *displacements_ptr = 0; + for (i = 1; i < (size_t)mpi_size; i++) + displacements_ptr[i] = displacements_ptr[i - 1] + recv_counts_disps_array[i - 1]; + } + + /* Perform gather operation */ + if (H5_mpio_gatherv_alloc(send_buf, send_count, send_type, recv_counts_disps_array, + &recv_counts_disps_array[mpi_size], recv_type, allgather, root, comm, mpi_rank, + mpi_size, out_buf, out_buf_num_entries) < 0) + HGOTO_ERROR(H5E_LIB, H5E_CANTGATHER, FAIL, "can't gather data") + +done: + if (recv_counts_disps_array) + H5MM_free(recv_counts_disps_array); + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5_mpio_gatherv_alloc_simple() */ + #endif /* H5_HAVE_PARALLEL */ diff --git a/src/H5private.h b/src/H5private.h index fa52e7f..d67163f 100644 --- a/src/H5private.h +++ b/src/H5private.h @@ -387,6 +387,25 @@ #define HSSIZET_MAX ((hssize_t)LLONG_MAX) #define HSSIZET_MIN (~(HSSIZET_MAX)) +#ifdef H5_HAVE_PARALLEL + +/* Define a type for safely sending size_t values with MPI */ +#if SIZE_MAX == UCHAR_MAX +#define H5_SIZE_T_AS_MPI_TYPE MPI_UNSIGNED_CHAR +#elif SIZE_MAX == USHRT_MAX +#define H5_SIZE_T_AS_MPI_TYPE MPI_UNSIGNED_SHORT +#elif SIZE_MAX == UINT_MAX +#define H5_SIZE_T_AS_MPI_TYPE MPI_UNSIGNED +#elif SIZE_MAX == ULONG_MAX +#define H5_SIZE_T_AS_MPI_TYPE MPI_UNSIGNED_LONG +#elif SIZE_MAX == ULLONG_MAX +#define H5_SIZE_T_AS_MPI_TYPE MPI_UNSIGNED_LONG_LONG +#else +#error "no suitable MPI type for size_t" +#endif + +#endif /* H5_HAVE_PARALLEL */ + /* * Types and max sizes for POSIX I/O. * OS X (Darwin) is odd since the max I/O size does not match the types. @@ -508,6 +527,9 @@ #define H5_GCC_CLANG_DIAG_ON(x) #endif +/* Function pointer typedef for qsort */ +typedef int (*H5_sort_func_cb_t)(const void *, const void *); + /* Typedefs and functions for timing certain parts of the library. */ /* A set of elapsed/user/system times emitted as a time point by the @@ -2602,7 +2624,8 @@ struct h5_long_options { */ }; -H5_DLL int H5_get_option(int argc, const char **argv, const char *opt, const struct h5_long_options *l_opt); +H5_DLL int H5_get_option(int argc, const char *const *argv, const char *opt, + const struct h5_long_options *l_opt); #ifdef H5_HAVE_PARALLEL /* Generic MPI functions */ @@ -2616,6 +2639,14 @@ H5_DLL herr_t H5_mpi_comm_cmp(MPI_Comm comm1, MPI_Comm comm2, int *result); H5_DLL herr_t H5_mpi_info_cmp(MPI_Info info1, MPI_Info info2, int *result); H5_DLL herr_t H5_mpio_create_large_type(hsize_t num_elements, MPI_Aint stride_bytes, MPI_Datatype old_type, MPI_Datatype *new_type); +H5_DLL herr_t H5_mpio_gatherv_alloc(void *send_buf, int send_count, MPI_Datatype send_type, + const int recv_counts[], const int displacements[], + MPI_Datatype recv_type, hbool_t allgather, int root, MPI_Comm comm, + int mpi_rank, int mpi_size, void **out_buf, size_t *out_buf_num_entries); +H5_DLL herr_t H5_mpio_gatherv_alloc_simple(void *send_buf, int send_count, MPI_Datatype send_type, + MPI_Datatype recv_type, hbool_t allgather, int root, MPI_Comm comm, + int mpi_rank, int mpi_size, void **out_buf, + size_t *out_buf_num_entries); #endif /* H5_HAVE_PARALLEL */ /* Functions for debugging */ diff --git a/src/H5public.h b/src/H5public.h index 6a3911c..3f9848a 100644 --- a/src/H5public.h +++ b/src/H5public.h @@ -83,7 +83,7 @@ /** * For tweaks, bug-fixes, or development */ -#define H5_VERS_RELEASE 1 +#define H5_VERS_RELEASE 2 /** * For pre-releases like \c snap0. Empty string for official releases. */ @@ -91,7 +91,7 @@ /** * Full version string */ -#define H5_VERS_INFO "HDF5 library version: 1.13.1-1" +#define H5_VERS_INFO "HDF5 library version: 1.13.2-1" #define H5check() H5check_version(H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE) @@ -289,6 +289,11 @@ typedef long long ssize_t; * \internal Defined as a (minimum) 64-bit integer type. */ typedef uint64_t hsize_t; + +#ifdef H5_HAVE_PARALLEL +#define HSIZE_AS_MPI_TYPE MPI_UINT64_T +#endif + /** * The size of file objects. Used when negative values are needed to indicate errors. * @@ -323,7 +328,7 @@ typedef uint64_t haddr_t; #define HADDR_MAX (HADDR_UNDEF - 1) #ifdef H5_HAVE_PARALLEL -#define HADDR_AS_MPI_TYPE MPI_LONG_LONG_INT +#define HADDR_AS_MPI_TYPE MPI_UINT64_T #endif //! <!-- [H5_iter_order_t_snip] --> diff --git a/src/H5system.c b/src/H5system.c index 9a966b0..ee9077e 100644 --- a/src/H5system.c +++ b/src/H5system.c @@ -956,7 +956,7 @@ const char *H5_optarg; /* Flag argument (or value) */ *------------------------------------------------------------------------- */ int -H5_get_option(int argc, const char **argv, const char *opts, const struct h5_long_options *l_opts) +H5_get_option(int argc, const char *const *argv, const char *opts, const struct h5_long_options *l_opts) { static int sp = 1; /* character index in current token */ int optchar = '?'; /* option character passed back to user */ diff --git a/src/H5timer.c b/src/H5timer.c index b2cc5f0..b5dba97 100644 --- a/src/H5timer.c +++ b/src/H5timer.c @@ -193,17 +193,26 @@ H5_now_usec(void) struct timespec ts; HDclock_gettime(CLOCK_MONOTONIC, &ts); - now = (uint64_t)(ts.tv_sec * (1000 * 1000)) + (uint64_t)(ts.tv_nsec / 1000); + + /* Cast all values in this expression to uint64_t to ensure that all intermediate + * calculations are done in 64 bit, to prevent overflow */ + now = ((uint64_t)ts.tv_sec * ((uint64_t)1000 * (uint64_t)1000)) + + ((uint64_t)ts.tv_nsec / (uint64_t)1000); } #elif defined(H5_HAVE_GETTIMEOFDAY) { struct timeval now_tv; HDgettimeofday(&now_tv, NULL); - now = (uint64_t)(now_tv.tv_sec * (1000 * 1000)) + (uint64_t)now_tv.tv_usec; + + /* Cast all values in this expression to uint64_t to ensure that all intermediate + * calculations are done in 64 bit, to prevent overflow */ + now = ((uint64_t)now_tv.tv_sec * ((uint64_t)1000 * (uint64_t)1000)) + (uint64_t)now_tv.tv_usec; } #else /* H5_HAVE_GETTIMEOFDAY */ - now = (uint64_t)(HDtime(NULL) * (1000 * 1000)); + /* Cast all values in this expression to uint64_t to ensure that all intermediate calculations + * are done in 64 bit, to prevent overflow */ + now = ((uint64_t)HDtime(NULL) * ((uint64_t)1000 * (uint64_t)1000)); #endif /* H5_HAVE_GETTIMEOFDAY */ return (now); diff --git a/src/H5trace.c b/src/H5trace.c index 5d15fee..8790a88 100644 --- a/src/H5trace.c +++ b/src/H5trace.c @@ -4023,7 +4023,7 @@ H5_trace(const double *returning, const char *func, const char *type, ...) H5_timer_get_times(function_timer, &function_times); H5_timer_get_times(running_timer, &running_times); - HDsprintf(tmp, "%.6f", (function_times.elapsed - running_times.elapsed)); + HDsnprintf(tmp, sizeof(tmp), "%.6f", (function_times.elapsed - running_times.elapsed)); H5RS_asprintf_cat(rs, " %*s ", (int)HDstrlen(tmp), ""); } for (i = 0; i < current_depth; i++) diff --git a/test/CMakeTests.cmake b/test/CMakeTests.cmake index b2ed8e8..4e828f8 100644 --- a/test/CMakeTests.cmake +++ b/test/CMakeTests.cmake @@ -649,10 +649,11 @@ set_tests_properties (H5TEST-tcheck_version-minor PROPERTIES WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}/H5TEST WILL_FAIL "true" ) -# release + 1 should pass +# release + 1 should pass on non-develop branches add_test (NAME H5TEST-tcheck_version-release COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR} $<TARGET_FILE:tcheck_version> "-tr") set_tests_properties (H5TEST-tcheck_version-release PROPERTIES WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}/H5TEST + WILL_FAIL "true" ) ############################################################################## diff --git a/test/cache_api.c b/test/cache_api.c index 2d642a6..6e897ec 100644 --- a/test/cache_api.c +++ b/test/cache_api.c @@ -1082,7 +1082,7 @@ mdc_api_call_smoke_check(int express_test, unsigned paged, hid_t fcpl_id) /* create the dataset */ if (pass) { - HDsprintf(dset_name, "/dset%03d", i); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", i); dataset_ids[i] = H5Dcreate2(file_id, dset_name, H5T_STD_I32BE, dataspace_id, H5P_DEFAULT, properties, H5P_DEFAULT); diff --git a/test/cache_common.c b/test/cache_common.c index 207daa1..9becfa8 100644 --- a/test/cache_common.c +++ b/test/cache_common.c @@ -2317,8 +2317,8 @@ verify_clean(void) void verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_entry_status expected[]) { - static char msg[256]; - int i; + char msg[256]; + int i; i = 0; while ((pass) && (i < num_entries)) { @@ -2330,14 +2330,15 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if ((!expected[i].in_cache) && ((expected[i].is_protected) || (expected[i].is_pinned))) { pass = FALSE; - HDsprintf(msg, "%d: Contradictory data in expected[%d].\n", tag, i); + HDsnprintf(msg, sizeof(msg), "%d: Contradictory data in expected[%d].\n", tag, i); failure_mssg = msg; } if ((!expected[i].in_cache) && (expected[i].is_dirty) && (!entry_ptr->expunged)) { pass = FALSE; - HDsprintf(msg, "%d: expected[%d] specs non-expunged, dirty, non-resident.\n", tag, i); + HDsnprintf(msg, sizeof(msg), "%d: expected[%d] specs non-expunged, dirty, non-resident.\n", tag, + i); failure_mssg = msg; } @@ -2348,9 +2349,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (in_cache != expected[i].in_cache) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) in cache actual/expected = %d/%d.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, (int)in_cache, - (int)expected[i].in_cache); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) in cache actual/expected = %d/%d.\n", tag, + (int)expected[i].entry_type, (int)expected[i].entry_index, (int)in_cache, + (int)expected[i].in_cache); failure_mssg = msg; } } @@ -2360,9 +2361,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->size != expected[i].size) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) size actual/expected = %ld/%ld.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, (long)(entry_ptr->size), - (long)expected[i].size); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) size actual/expected = %ld/%ld.\n", tag, + (int)expected[i].entry_type, (int)expected[i].entry_index, (long)(entry_ptr->size), + (long)expected[i].size); failure_mssg = msg; } } @@ -2372,9 +2373,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->header.size != expected[i].size) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) header size actual/expected = %ld/%ld.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, - (long)(entry_ptr->header.size), (long)expected[i].size); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) header size actual/expected = %ld/%ld.\n", + tag, (int)expected[i].entry_type, (int)expected[i].entry_index, + (long)(entry_ptr->header.size), (long)expected[i].size); failure_mssg = msg; } } @@ -2384,9 +2385,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->at_main_addr != expected[i].at_main_addr) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) at main addr actual/expected = %d/%d.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, - (int)(entry_ptr->at_main_addr), (int)expected[i].at_main_addr); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) at main addr actual/expected = %d/%d.\n", tag, + (int)expected[i].entry_type, (int)expected[i].entry_index, + (int)(entry_ptr->at_main_addr), (int)expected[i].at_main_addr); failure_mssg = msg; } } @@ -2396,9 +2397,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->is_dirty != expected[i].is_dirty) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) is_dirty actual/expected = %d/%d.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, - (int)(entry_ptr->is_dirty), (int)expected[i].is_dirty); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) is_dirty actual/expected = %d/%d.\n", tag, + (int)expected[i].entry_type, (int)expected[i].entry_index, + (int)(entry_ptr->is_dirty), (int)expected[i].is_dirty); failure_mssg = msg; } } @@ -2408,9 +2409,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->header.is_dirty != expected[i].is_dirty) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) header is_dirty actual/expected = %d/%d.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, - (int)(entry_ptr->header.is_dirty), (int)expected[i].is_dirty); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) header is_dirty actual/expected = %d/%d.\n", + tag, (int)expected[i].entry_type, (int)expected[i].entry_index, + (int)(entry_ptr->header.is_dirty), (int)expected[i].is_dirty); failure_mssg = msg; } } @@ -2420,9 +2421,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->is_protected != expected[i].is_protected) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) is_protected actual/expected = %d/%d.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, - (int)(entry_ptr->is_protected), (int)expected[i].is_protected); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) is_protected actual/expected = %d/%d.\n", tag, + (int)expected[i].entry_type, (int)expected[i].entry_index, + (int)(entry_ptr->is_protected), (int)expected[i].is_protected); failure_mssg = msg; } } @@ -2432,9 +2433,10 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->header.is_protected != expected[i].is_protected) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) header is_protected actual/expected = %d/%d.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, - (int)(entry_ptr->header.is_protected), (int)expected[i].is_protected); + HDsnprintf(msg, sizeof(msg), + "%d entry (%d, %d) header is_protected actual/expected = %d/%d.\n", tag, + (int)expected[i].entry_type, (int)expected[i].entry_index, + (int)(entry_ptr->header.is_protected), (int)expected[i].is_protected); failure_mssg = msg; } } @@ -2444,9 +2446,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->is_pinned != expected[i].is_pinned) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) is_pinned actual/expected = %d/%d.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, - (int)(entry_ptr->is_pinned), (int)expected[i].is_pinned); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) is_pinned actual/expected = %d/%d.\n", tag, + (int)expected[i].entry_type, (int)expected[i].entry_index, + (int)(entry_ptr->is_pinned), (int)expected[i].is_pinned); failure_mssg = msg; } } @@ -2456,9 +2458,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->is_corked != expected[i].is_corked) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) is_corked actual/expected = %d/%d.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, - (int)(entry_ptr->is_corked), (int)expected[i].is_corked); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) is_corked actual/expected = %d/%d.\n", tag, + (int)expected[i].entry_type, (int)expected[i].entry_index, + (int)(entry_ptr->is_corked), (int)expected[i].is_corked); failure_mssg = msg; } } @@ -2468,9 +2470,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (entry_ptr->header.is_pinned != expected[i].is_pinned) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) header is_pinned actual/expected = %d/%d.\n", tag, - (int)expected[i].entry_type, (int)expected[i].entry_index, - (int)(entry_ptr->header.is_pinned), (int)expected[i].is_pinned); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) header is_pinned actual/expected = %d/%d.\n", + tag, (int)expected[i].entry_type, (int)expected[i].entry_index, + (int)(entry_ptr->header.is_pinned), (int)expected[i].is_pinned); failure_mssg = msg; } } @@ -2482,11 +2484,12 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ (entry_ptr->destroyed != expected[i].destroyed)) { pass = FALSE; - HDsprintf(msg, "%d entry (%d,%d) deserialized = %d(%d), serialized = %d(%d), dest = %d(%d)\n", - tag, (int)expected[i].entry_type, (int)expected[i].entry_index, - (int)(entry_ptr->deserialized), (int)(expected[i].deserialized), - (int)(entry_ptr->serialized), (int)(expected[i].serialized), - (int)(entry_ptr->destroyed), (int)(expected[i].destroyed)); + HDsnprintf(msg, sizeof(msg), + "%d entry (%d,%d) deserialized = %d(%d), serialized = %d(%d), dest = %d(%d)\n", + tag, (int)expected[i].entry_type, (int)expected[i].entry_index, + (int)(entry_ptr->deserialized), (int)(expected[i].deserialized), + (int)(entry_ptr->serialized), (int)(expected[i].serialized), + (int)(entry_ptr->destroyed), (int)(expected[i].destroyed)); failure_mssg = msg; } } @@ -2497,18 +2500,19 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (pass) { if (entry_ptr->flush_dep_npar != expected[i].flush_dep_npar) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) flush_dep_npar actual/expected = %u/%u.\n", tag, - expected[i].entry_type, expected[i].entry_index, entry_ptr->flush_dep_npar, - expected[i].flush_dep_npar); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) flush_dep_npar actual/expected = %u/%u.\n", + tag, expected[i].entry_type, expected[i].entry_index, entry_ptr->flush_dep_npar, + expected[i].flush_dep_npar); failure_mssg = msg; } /* end if */ } /* end if */ if ((pass) && (in_cache)) { if (entry_ptr->header.flush_dep_nparents != expected[i].flush_dep_npar) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) header flush_dep_nparents actual/expected = %u/%u.\n", tag, - expected[i].entry_type, expected[i].entry_index, - entry_ptr->header.flush_dep_nparents, expected[i].flush_dep_npar); + HDsnprintf(msg, sizeof(msg), + "%d entry (%d, %d) header flush_dep_nparents actual/expected = %u/%u.\n", tag, + expected[i].entry_type, expected[i].entry_index, + entry_ptr->header.flush_dep_nparents, expected[i].flush_dep_npar); failure_mssg = msg; } /* end if */ } /* end if */ @@ -2519,9 +2523,10 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ for (u = 0; u < entry_ptr->flush_dep_npar; u++) { if (entry_ptr->flush_dep_par_type[u] != expected[i].flush_dep_par_type[u]) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) flush_dep_par_type[%u] actual/expected = %d/%d.\n", tag, - expected[i].entry_type, expected[i].entry_index, u, - entry_ptr->flush_dep_par_type[u], expected[i].flush_dep_par_type[u]); + HDsnprintf(msg, sizeof(msg), + "%d entry (%d, %d) flush_dep_par_type[%u] actual/expected = %d/%d.\n", tag, + expected[i].entry_type, expected[i].entry_index, u, + entry_ptr->flush_dep_par_type[u], expected[i].flush_dep_par_type[u]); failure_mssg = msg; } /* end if */ } /* end for */ @@ -2530,9 +2535,10 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ for (u = 0; u < entry_ptr->flush_dep_npar; u++) { if (entry_ptr->flush_dep_par_idx[u] != expected[i].flush_dep_par_idx[u]) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) flush_dep_par_idx[%u] actual/expected = %d/%d.\n", tag, - expected[i].entry_type, expected[i].entry_index, u, - entry_ptr->flush_dep_par_idx[u], expected[i].flush_dep_par_idx[u]); + HDsnprintf(msg, sizeof(msg), + "%d entry (%d, %d) flush_dep_par_idx[%u] actual/expected = %d/%d.\n", tag, + expected[i].entry_type, expected[i].entry_index, u, + entry_ptr->flush_dep_par_idx[u], expected[i].flush_dep_par_idx[u]); failure_mssg = msg; } /* end if */ } /* end for */ @@ -2542,37 +2548,39 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (pass) { if (entry_ptr->flush_dep_nchd != expected[i].flush_dep_nchd) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) flush_dep_nchd actual/expected = %u/%u.\n", tag, - expected[i].entry_type, expected[i].entry_index, entry_ptr->flush_dep_nchd, - expected[i].flush_dep_nchd); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) flush_dep_nchd actual/expected = %u/%u.\n", + tag, expected[i].entry_type, expected[i].entry_index, entry_ptr->flush_dep_nchd, + expected[i].flush_dep_nchd); failure_mssg = msg; } /* end if */ } /* end if */ if ((pass) && (in_cache)) { if (entry_ptr->header.flush_dep_nchildren != expected[i].flush_dep_nchd) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) header flush_dep_nchildren actual/expected = %u/%u.\n", tag, - expected[i].entry_type, expected[i].entry_index, - entry_ptr->header.flush_dep_nchildren, expected[i].flush_dep_nchd); + HDsnprintf(msg, sizeof(msg), + "%d entry (%d, %d) header flush_dep_nchildren actual/expected = %u/%u.\n", tag, + expected[i].entry_type, expected[i].entry_index, + entry_ptr->header.flush_dep_nchildren, expected[i].flush_dep_nchd); failure_mssg = msg; } /* end if */ } /* end if */ if (pass) { if (entry_ptr->flush_dep_ndirty_chd != expected[i].flush_dep_ndirty_chd) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) flush_dep_ndirty_chd actual/expected = %u/%u.\n", tag, - expected[i].entry_type, expected[i].entry_index, entry_ptr->flush_dep_ndirty_chd, - expected[i].flush_dep_ndirty_chd); + HDsnprintf(msg, sizeof(msg), + "%d entry (%d, %d) flush_dep_ndirty_chd actual/expected = %u/%u.\n", tag, + expected[i].entry_type, expected[i].entry_index, entry_ptr->flush_dep_ndirty_chd, + expected[i].flush_dep_ndirty_chd); failure_mssg = msg; } /* end if */ } /* end if */ if ((pass) && (in_cache)) { if (entry_ptr->header.flush_dep_ndirty_children != expected[i].flush_dep_ndirty_chd) { pass = FALSE; - HDsprintf(msg, - "%d entry (%d, %d) header flush_dep_ndirty_children actual/expected = %u/%u.\n", - tag, expected[i].entry_type, expected[i].entry_index, - entry_ptr->header.flush_dep_ndirty_children, expected[i].flush_dep_ndirty_chd); + HDsnprintf(msg, sizeof(msg), + "%d entry (%d, %d) header flush_dep_ndirty_children actual/expected = %u/%u.\n", + tag, expected[i].entry_type, expected[i].entry_index, + entry_ptr->header.flush_dep_ndirty_children, expected[i].flush_dep_ndirty_chd); failure_mssg = msg; } /* end if */ } /* end if */ @@ -2581,9 +2589,9 @@ verify_entry_status(H5C_t *cache_ptr, int tag, int num_entries, struct expected_ if (pass) { if (expected[i].flush_order >= 0 && entry_ptr->flush_order != (unsigned)expected[i].flush_order) { pass = FALSE; - HDsprintf(msg, "%d entry (%d, %d) flush_order actual/expected = %u/%d.\n", tag, - expected[i].entry_type, expected[i].entry_index, entry_ptr->flush_order, - expected[i].flush_order); + HDsnprintf(msg, sizeof(msg), "%d entry (%d, %d) flush_order actual/expected = %u/%d.\n", tag, + expected[i].entry_type, expected[i].entry_index, entry_ptr->flush_order, + expected[i].flush_order); failure_mssg = msg; } /* end if */ } /* end if */ diff --git a/test/cache_image.c b/test/cache_image.c index d3961a8..419eb58 100644 --- a/test/cache_image.c +++ b/test/cache_image.c @@ -164,7 +164,7 @@ create_datasets(hid_t file_id, int min_dset, int max_dset) /* create the dataset */ if (pass) { - HDsprintf(dset_name, "/dset%03d", i); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", i); dataset_ids[i] = H5Dcreate2(file_id, dset_name, H5T_STD_I32BE, dataspace_id, H5P_DEFAULT, properties, H5P_DEFAULT); @@ -443,7 +443,7 @@ delete_datasets(hid_t file_id, int min_dset, int max_dset) i = min_dset; while ((pass) && (i <= max_dset)) { - HDsprintf(dset_name, "/dset%03d", i); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", i); if (H5Ldelete(file_id, dset_name, H5P_DEFAULT) < 0) { @@ -1019,7 +1019,7 @@ verify_datasets(hid_t file_id, int min_dset, int max_dset) /* open the dataset */ if (pass) { - HDsprintf(dset_name, "/dset%03d", i); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", i); dataset_ids[i] = H5Dopen2(file_id, dset_name, H5P_DEFAULT); if (dataset_ids[i] < 0) { @@ -4624,7 +4624,7 @@ cache_image_smoke_check_5(hbool_t single_file_vfd) /* 2) Create a process specific group. */ if (pass) { - HDsprintf(process_group_name, "/process_%d", min_group); + HDsnprintf(process_group_name, sizeof(process_group_name), "/process_%d", min_group); proc_gid = H5Gcreate2(file_id, process_group_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); @@ -4728,7 +4728,7 @@ cache_image_smoke_check_5(hbool_t single_file_vfd) if (pass) { max_group++; - HDsprintf(process_group_name, "/process_%d", max_group); + HDsnprintf(process_group_name, sizeof(process_group_name), "/process_%d", max_group); proc_gid = H5Gcreate2(file_id, process_group_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); @@ -4802,7 +4802,7 @@ cache_image_smoke_check_5(hbool_t single_file_vfd) /* 11) Validate all the zoos. */ i = min_group; while (pass && i <= max_group) { - HDsprintf(process_group_name, "/process_%d", i); + HDsnprintf(process_group_name, sizeof(process_group_name), "/process_%d", i); validate_zoo(file_id, process_group_name, i++); } @@ -4854,7 +4854,7 @@ cache_image_smoke_check_5(hbool_t single_file_vfd) i = min_group; while ((pass) && (i <= max_group)) { - HDsprintf(process_group_name, "/process_%d", i); + HDsnprintf(process_group_name, sizeof(process_group_name), "/process_%d", i); validate_zoo(file_id, process_group_name, i++); } @@ -4914,7 +4914,7 @@ cache_image_smoke_check_5(hbool_t single_file_vfd) */ i = min_group; while ((pass) && (i <= max_group)) { - HDsprintf(process_group_name, "/process_%d", i); + HDsnprintf(process_group_name, sizeof(process_group_name), "/process_%d", i); validate_zoo(file_id, process_group_name, i++); } diff --git a/test/cmpd_dset.c b/test/cmpd_dset.c index 04a931c..024b6c0 100644 --- a/test/cmpd_dset.c +++ b/test/cmpd_dset.c @@ -1766,7 +1766,7 @@ test_pack_ooo(void) /* Insert the compound members in the random order previously generated */ for (i = 0; i < PACK_NMEMBS; i++) { - HDsprintf(name, "%05d", i); + HDsnprintf(name, sizeof(name), "%05d", i); if (i == sub_cmpd_order) { if (H5Tinsert(cmpd, name, (size_t)(4 * order[i]), sub_cmpd) < 0) PACK_OOO_ERROR @@ -1799,7 +1799,7 @@ test_pack_ooo(void) /* Insert the compound members in the random order previously generated */ for (i = 0; i < PACK_NMEMBS; i++) { - HDsprintf(name, "%05d", i); + HDsnprintf(name, sizeof(name), "%05d", i); if (i == sub_cmpd_order) { if (H5Tinsert(cmpd, name, (size_t)(4 * order[i]), sub_cmpd) < 0) PACK_OOO_ERROR @@ -1834,7 +1834,7 @@ test_pack_ooo(void) /* Insert the compound members in reverse order, with compound last */ for (i = 0; i < PACK_NMEMBS; i++) { - HDsprintf(name, "%05d", i); + HDsnprintf(name, sizeof(name), "%05d", i); if (i == PACK_NMEMBS - 1) { if (H5Tinsert(cmpd, name, (size_t)(4 * (PACK_NMEMBS - i - 1)), sub_cmpd) < 0) PACK_OOO_ERROR @@ -1867,7 +1867,7 @@ test_pack_ooo(void) /* Insert the compound members in reverse order, with compound last */ for (i = 0; i < PACK_NMEMBS; i++) { - HDsprintf(name, "%05d", i); + HDsnprintf(name, sizeof(name), "%05d", i); if (i == PACK_NMEMBS - 1) { if (H5Tinsert(cmpd, name, (size_t)(4 * (PACK_NMEMBS - i - 1)), sub_cmpd) < 0) PACK_OOO_ERROR @@ -1902,7 +1902,7 @@ test_pack_ooo(void) /* Insert the compound members in forward order, with compound first */ for (i = 0; i < PACK_NMEMBS; i++) { - HDsprintf(name, "%05d", i); + HDsnprintf(name, sizeof(name), "%05d", i); if (i == 0) { if (H5Tinsert(cmpd, name, (size_t)(4 * i), sub_cmpd) < 0) PACK_OOO_ERROR @@ -1935,7 +1935,7 @@ test_pack_ooo(void) /* Insert the compound members in forward order */ for (i = 0; i < PACK_NMEMBS; i++) { - HDsprintf(name, "%05d", i); + HDsnprintf(name, sizeof(name), "%05d", i); if (i == 0) { if (H5Tinsert(cmpd, name, (size_t)(4 * i), sub_cmpd) < 0) PACK_OOO_ERROR diff --git a/test/del_many_dense_attrs.c b/test/del_many_dense_attrs.c index cf7f607..78aba3b 100644 --- a/test/del_many_dense_attrs.c +++ b/test/del_many_dense_attrs.c @@ -119,7 +119,7 @@ main(void) /* Create attributes in the group */ for (i = ATTR_COUNT; i >= 0; i--) { /* Set up the attribute name */ - HDsprintf(aname, "%s%d", basename, i); + HDsnprintf(aname, sizeof(aname), "%s%d", basename, i); /* Create the attribute */ if ((aid = H5Acreate2(gid, aname, tid, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) @@ -165,7 +165,7 @@ main(void) /* Delete the attributes */ for (i = 0; i <= ATTR_COUNT; i++) { /* Set up the attribute name */ - HDsprintf(aname, "%s%d", basename, i); + HDsnprintf(aname, sizeof(aname), "%s%d", basename, i); /* Delete the attribute */ if (H5Adelete(gid, aname) < 0) diff --git a/test/dtransform.c b/test/dtransform.c index 9f7e659..1f6d48b 100644 --- a/test/dtransform.c +++ b/test/dtransform.c @@ -122,9 +122,8 @@ const int transformData[ROWS][COLS] = {{36, 31, 25, 19, 13, 7, 1, 5, 11, 16, 22, { \ TYPE array[ROWS][COLS]; \ const char *f_to_c = "(5/9.0)*(x-32)"; \ - /* utrans is a transform for unsigned types: no negative numbers involved and results are < 255 to \ - * fit into uchar */ \ - const char *utrans = "((x+100)/4)*3"; \ + /* utrans is a transform for char types: numbers are restricted from -128 to 127, fits into char */ \ + const char *utrans = "(x/4+25)*3"; \ \ hid_t dataspace, dxpl_id_f_to_c, dxpl_id_utrans, dset, dset_nn, dt_nn; \ H5T_order_t order; \ @@ -211,9 +210,8 @@ const int transformData[ROWS][COLS] = {{36, 31, 25, 19, 13, 7, 1, 5, 11, 16, 22, { \ TYPE array[ROWS][COLS]; \ const char *f_to_c = "(5/9.0)*(x-32)"; \ - /* utrans is a transform for unsigned types: no negative numbers involved and results are < 255 to \ - * fit into uchar */ \ - const char *utrans = "((x+100)/4)*3"; \ + /* utrans is a transform for char types: numbers are restricted from -128 to 127, fits into char */ \ + const char *utrans = "(x/4+25)*3"; \ \ hid_t dataspace, dxpl_id_f_to_c, dxpl_id_utrans, cparms, memspace, dset_chunk, filespace; \ hsize_t dim[2] = {ROWS, COLS}; \ @@ -314,7 +312,7 @@ main(void) const char *simple = "(4/2) * ( (2 + 4)/(5 - 2.5))"; /* this equals 4.8 */ const char *polynomial = "(2+x)* ((x-8)/2)"; /* inverses the utrans transform in init_test to get back original array */ - const char *utrans_inv = "(x/3)*4 - 100"; + const char *utrans_inv = "(x/3 - 25)*4"; if ((file_id = H5Fcreate("dtransform.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR; @@ -436,9 +434,8 @@ static int init_test(hid_t file_id) { const char *f_to_c = "(5/9.0)*(x-32)"; - /* utrans is a transform for unsigned types: no negative numbers involved and results are < 255 to fit - * into uchar */ - const char *utrans = "((x+100)/4)*3"; + /* utrans is a transform for char types: numbers are restricted from -128 to 127, fits into char */ + const char *utrans = "(x/4+25)*3"; hid_t dataspace = -1; hid_t dxpl_id_f_to_c = -1; diff --git a/test/dtypes.c b/test/dtypes.c index a6b2beb..d2064b7 100644 --- a/test/dtypes.c +++ b/test/dtypes.c @@ -4969,7 +4969,7 @@ test_conv_str_2(void) } /* end for */ /* Do the conversions */ - HDsprintf(s, "Testing random string conversion speed"); + HDsnprintf(s, sizeof(s), "Testing random string conversion speed"); HDprintf("%-70s", s); HDfflush(stdout); if (H5Tconvert(c_type, f_type, nelmts, buf, NULL, H5P_DEFAULT) < 0) @@ -5184,14 +5184,14 @@ test_conv_enum_1(void) buf[u] = HDrand() % 26; /* Conversions */ - HDsprintf(s, "Testing random enum conversion O(N)"); + HDsnprintf(s, sizeof(s), "Testing random enum conversion O(N)"); HDprintf("%-70s", s); HDfflush(stdout); if (H5Tconvert(t1, t2, nelmts, buf, NULL, H5P_DEFAULT) < 0) goto error; PASSED(); - HDsprintf(s, "Testing random enum conversion O(N log N)"); + HDsnprintf(s, sizeof(s), "Testing random enum conversion O(N log N)"); HDprintf("%-70s", s); HDfflush(stdout); if (H5Tconvert(t2, t1, nelmts, buf, NULL, H5P_DEFAULT) < 0) diff --git a/test/earray.c b/test/earray.c index 4763d51..7c8dd1f 100644 --- a/test/earray.c +++ b/test/earray.c @@ -2543,15 +2543,16 @@ main(void) /* Test first element in data block */ nelmts = (hsize_t)((hsize_t)1 + cparam.idx_blk_elmts + tparam.sblk_info[sblk].start_idx + (tparam.sblk_info[sblk].dblk_nelmts * dblk)); - HDsprintf(test_str, "setting first element of array's data block #%llu", - (unsigned long long)ndblks); + HDsnprintf(test_str, sizeof(test_str), + "setting first element of array's data block #%llu", + (unsigned long long)ndblks); nerrors += test_set_elmts(fapl, &cparam, &tparam, nelmts, test_str); /* Test all elements in data block */ nelmts = (hsize_t)(cparam.idx_blk_elmts + tparam.sblk_info[sblk].start_idx + (tparam.sblk_info[sblk].dblk_nelmts * (dblk + 1))); - HDsprintf(test_str, "setting all elements of array's data block #%llu", - (unsigned long long)ndblks); + HDsnprintf(test_str, sizeof(test_str), "setting all elements of array's data block #%llu", + (unsigned long long)ndblks); nerrors += test_set_elmts(fapl, &cparam, &tparam, nelmts, test_str); /* Increment data block being tested */ diff --git a/test/enc_dec_plist.c b/test/enc_dec_plist.c index 60b229a..0a73273 100644 --- a/test/enc_dec_plist.c +++ b/test/enc_dec_plist.c @@ -199,8 +199,8 @@ main(void) /* Display testing info */ low_string = h5_get_version_string(low); high_string = h5_get_version_string(high); - HDsprintf(msg, "Testing ENCODE/DECODE with file version bounds: (%s, %s):", low_string, - high_string); + HDsnprintf(msg, sizeof(msg), + "Testing ENCODE/DECODE with file version bounds: (%s, %s):", low_string, high_string); HDputs(msg); if (VERBOSE_MED) diff --git a/test/event_set.c b/test/event_set.c index 22df510..c2a17b1 100644 --- a/test/event_set.c +++ b/test/event_set.c @@ -344,25 +344,49 @@ test_es_get_requests(void) TEST_ERROR /* Get only connector IDs */ - count = 3; + count = 3; + connector_ids[0] = H5I_INVALID_HID; + connector_ids[1] = H5I_INVALID_HID; if (H5ESget_requests(es_id, H5_ITER_NATIVE, connector_ids, NULL, 2, &count) < 0) TEST_ERROR if (count != 0) TEST_ERROR + if (connector_ids[0] != H5I_INVALID_HID) + TEST_ERROR + if (connector_ids[1] != H5I_INVALID_HID) + TEST_ERROR /* Get only requests */ - count = 3; + count = 3; + requests[0] = NULL; + requests[1] = NULL; if (H5ESget_requests(es_id, H5_ITER_NATIVE, NULL, requests, 2, &count) < 0) TEST_ERROR if (count != 0) TEST_ERROR + if (requests[0] != NULL) + TEST_ERROR + if (requests[1] != NULL) + TEST_ERROR /* Get both */ - count = 3; + count = 3; + connector_ids[0] = H5I_INVALID_HID; + connector_ids[1] = H5I_INVALID_HID; + requests[0] = NULL; + requests[1] = NULL; if (H5ESget_requests(es_id, H5_ITER_NATIVE, connector_ids, requests, 2, &count) < 0) TEST_ERROR if (count != 0) TEST_ERROR + if (connector_ids[0] != H5I_INVALID_HID) + TEST_ERROR + if (connector_ids[1] != H5I_INVALID_HID) + TEST_ERROR + if (requests[0] != NULL) + TEST_ERROR + if (requests[1] != NULL) + TEST_ERROR /* Insert event into event set */ if (H5ESinsert_request(es_id, connector_ids_g[0], &req_targets[0]) < 0) diff --git a/test/external.c b/test/external.c index 281593c..11185b3 100644 --- a/test/external.c +++ b/test/external.c @@ -890,8 +890,8 @@ test_write_file_set(hid_t fapl) for (i = 0; i < N_EXT_FILES; i++) { char name1[64], name2[64]; - HDsprintf(name1, "extern_%dr.raw", i + 1); - HDsprintf(name2, "extern_%dw.raw", i + 1); + HDsnprintf(name1, sizeof(name1), "extern_%dr.raw", i + 1); + HDsnprintf(name2, sizeof(name2), "extern_%dw.raw", i + 1); if (!files_have_same_contents(name1, name2)) FAIL_PUTS_ERROR(" Output differs from expected value.") } /* end for */ diff --git a/test/external_common.c b/test/external_common.c index c37fd16..3f04260 100644 --- a/test/external_common.c +++ b/test/external_common.c @@ -59,9 +59,9 @@ reset_raw_data_files(hbool_t is_env) /* Open file */ if (is_env) - HDsprintf(filename, "extern_env_%lur.raw", (unsigned long)i + 1); + HDsnprintf(filename, sizeof(filename), "extern_env_%lur.raw", (unsigned long)i + 1); else - HDsprintf(filename, "extern_%lur.raw", (unsigned long)i + 1); + HDsnprintf(filename, sizeof(filename), "extern_%lur.raw", (unsigned long)i + 1); if ((fd = HDopen(filename, O_RDWR | O_CREAT | O_TRUNC, H5_POSIX_CREATE_MODE_RW)) < 0) goto error; @@ -96,9 +96,9 @@ reset_raw_data_files(hbool_t is_env) /* Open file */ if (is_env) - HDsprintf(filename, "extern_env_%luw.raw", (unsigned long)i + 1); + HDsnprintf(filename, sizeof(filename), "extern_env_%luw.raw", (unsigned long)i + 1); else - HDsprintf(filename, "extern_%luw.raw", (unsigned long)i + 1); + HDsnprintf(filename, sizeof(filename), "extern_%luw.raw", (unsigned long)i + 1); if ((fd = HDopen(filename, O_RDWR | O_CREAT | O_TRUNC, H5_POSIX_CREATE_MODE_RW)) < 0) goto error; diff --git a/test/fheap.c b/test/fheap.c index 5ded20f..b897063 100644 --- a/test/fheap.c +++ b/test/fheap.c @@ -466,40 +466,24 @@ error: return (1); } /* add_obj() */ -/*------------------------------------------------------------------------- - * Function: get_del_string - * - * Purpose: Return string describing the kind of deletion to perform - * - * Return: Success: 0 - * - * Failure: 1 - * - * Programmer: Quincey Koziol - * Monday, June 6, 2006 - * - *------------------------------------------------------------------------- - */ -static char * +/* Return a string describing the kind of deletion to perform. */ +static const char * get_del_string(const fheap_test_param_t *tparam) { - char *str; - /* Remove half of total objects from heap */ if (tparam->del_dir == FHEAP_DEL_FORWARD) if (tparam->drain_half == FHEAP_DEL_DRAIN_ALL) - str = H5MM_strdup("(all - forward)"); + return "(all - forward)"; else - str = H5MM_strdup("(half, refill, all - forward)"); + return "(half, refill, all - forward)"; else if (tparam->del_dir == FHEAP_DEL_REVERSE) if (tparam->drain_half == FHEAP_DEL_DRAIN_ALL) - str = H5MM_strdup("(all - reverse)"); + return "(all - reverse)"; else - str = H5MM_strdup("(half, refill, all - reverse)"); + return "(half, refill, all - reverse)"; else - str = H5MM_strdup("(all - deleting heap)"); + return "(all - deleting heap)"; - return (str); } /* get_del_string() */ /*------------------------------------------------------------------------- @@ -547,28 +531,20 @@ get_fill_size(const fheap_test_param_t *tparam) * *------------------------------------------------------------------------- */ -/* Disable warning for "format not a string literal" here -QAK */ -/* - * This pragma only needs to surround the snprintf() calls with - * test_desc in the code below, but early (4.4.7, at least) gcc only - * allows diagnostic pragmas to be toggled outside of functions. - */ -H5_GCC_CLANG_DIAG_OFF("format-nonliteral") static int begin_test(fheap_test_param_t *tparam, const char *base_desc, fheap_heap_ids_t *keep_ids, size_t *fill_size) { - char *del_str = NULL; /* Deletion order description */ - char *test_desc = NULL; /* Test description */ + char * test_desc; /* Test description */ + const char *del_str = get_del_string(tparam); /* * Test filling & removing all (small) objects from root direct block of absolute heap */ - del_str = get_del_string(tparam); - HDassert(del_str); - test_desc = (char *)H5MM_malloc(HDstrlen(del_str) + HDstrlen(base_desc)); - HDsprintf(test_desc, base_desc, del_str); + size_t test_desc_len = strlen(base_desc) + sizeof(" ") + strlen(del_str); + test_desc = H5MM_malloc(test_desc_len); + (void)HDsnprintf(test_desc, test_desc_len, "%s %s", base_desc, del_str); + TESTING(test_desc); - H5MM_xfree(del_str); H5MM_xfree(test_desc); /* Initialize the heap ID structure */ @@ -581,7 +557,6 @@ begin_test(fheap_test_param_t *tparam, const char *base_desc, fheap_heap_ids_t * /* Success */ return (0); } /* end begin_test() */ -H5_GCC_CLANG_DIAG_ON("format-nonliteral") /*------------------------------------------------------------------------- * Function: reopen_file @@ -7769,7 +7744,7 @@ test_man_remove_root_direct(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_ size_t fill_size; /* Size of objects for "bulk" filled blocks */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "removing all objects from root direct block of absolute heap %s"; + const char *base_desc = "removing all objects from root direct block of absolute heap"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -7842,7 +7817,7 @@ test_man_remove_two_direct(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t size_t fill_size; /* Size of objects for "bulk" filled blocks */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "removing all objects from two direct blocks of absolute heap %s"; + const char *base_desc = "removing all objects from two direct blocks of absolute heap"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -7930,7 +7905,7 @@ test_man_remove_first_row(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t size_t fill_size; /* Size of objects for "bulk" filled blocks */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "removing all objects from first row of direct blocks of absolute heap %s"; + const char *base_desc = "removing all objects from first row of direct blocks of absolute heap"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -8000,7 +7975,7 @@ test_man_remove_first_two_rows(hid_t fapl, H5HF_create_t *cparam, fheap_test_par size_t fill_size; /* Size of objects for "bulk" filled blocks */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "removing all objects from first two rows of direct blocks of absolute heap %s"; + const char *base_desc = "removing all objects from first two rows of direct blocks of absolute heap"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -8072,7 +8047,7 @@ test_man_remove_first_four_rows(hid_t fapl, H5HF_create_t *cparam, fheap_test_pa size_t fill_size; /* Size of objects for "bulk" filled blocks */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "removing all objects from first four rows of direct blocks of absolute heap %s"; + const char *base_desc = "removing all objects from first four rows of direct blocks of absolute heap"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -8148,7 +8123,7 @@ test_man_remove_all_root_direct(hid_t fapl, H5HF_create_t *cparam, fheap_test_pa size_t fill_size; /* Size of objects for "bulk" filled blocks */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "removing all objects from all direct blocks of root group in absolute heap %s"; + const char *base_desc = "removing all objects from all direct blocks of root group in absolute heap"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -8218,7 +8193,7 @@ test_man_remove_2nd_indirect(hid_t fapl, H5HF_create_t *cparam, fheap_test_param size_t fill_size; /* Size of objects for "bulk" filled blocks */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "removing all objects from 2nd level indirect blocks of absolute heap %s"; + const char *base_desc = "removing all objects from 2nd level indirect blocks of absolute heap"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -8292,7 +8267,7 @@ test_man_remove_3rd_indirect(hid_t fapl, H5HF_create_t *cparam, fheap_test_param size_t fill_size; /* Size of objects for "bulk" filled blocks */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "removing all objects from 3rd level indirect blocks of absolute heap %s"; + const char *base_desc = "removing all objects from 3rd level indirect blocks of absolute heap"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -8373,8 +8348,7 @@ test_man_skip_start_block(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t size_t obj_size; /* Size of object */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = - "inserting object that is too large for starting block, then remove all objects %s"; + const char *base_desc = "inserting object that is too large for starting block, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -8453,7 +8427,7 @@ test_man_skip_start_block_add_back(hid_t fapl, H5HF_create_t *cparam, fheap_test fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ const char *base_desc = - "skipping starting block, then adding object back to first block, then remove all objects %s"; + "skipping starting block, then adding object back to first block, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -8553,7 +8527,7 @@ test_man_skip_start_block_add_skipped(hid_t fapl, H5HF_create_t *cparam, fheap_t fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ const char *base_desc = - "skipping starting block, then adding objects to backfill and extend, then remove all objects %s"; + "skipping starting block, then adding objects to backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -8662,7 +8636,7 @@ test_man_skip_2nd_block(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *t fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ const char *base_desc = "insert object to initial block, then add object too large for starting direct " - "blocks, then remove all objects %s"; + "blocks, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -8761,7 +8735,7 @@ test_man_skip_2nd_block_add_skipped(hid_t fapl, H5HF_create_t *cparam, fheap_tes unsigned v; /* Local index variables */ /* Test description */ const char *base_desc = "insert object to initial block, then add object too large for starting direct " - "blocks, then backfill and extend, then remove all objects %s"; + "blocks, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -8907,7 +8881,7 @@ test_man_fill_one_partial_skip_2nd_block_add_skipped(hid_t fapl, H5HF_create_t * unsigned u; /* Local index variable */ /* Test description */ const char *base_desc = - "skipping blocks with indirect root, then backfill and extend, then remove all objects %s"; + "skipping blocks with indirect root, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -9072,7 +9046,7 @@ test_man_fill_row_skip_add_skipped(hid_t fapl, H5HF_create_t *cparam, fheap_test fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ const char *base_desc = - "filling first row, then skipping rows, then backfill and extend, then remove all objects %s"; + "filling first row, then skipping rows, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -9202,7 +9176,7 @@ test_man_skip_direct_skip_indirect_two_rows_add_skipped(hid_t fapl, H5HF_create_ unsigned v; /* Local index variables */ /* Test description */ const char *base_desc = "skipping direct blocks to last row and skipping two rows of root indirect " - "block, then backfill and extend, then remove all objects %s"; + "block, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -9328,7 +9302,7 @@ test_man_fill_direct_skip_indirect_start_block_add_skipped(hid_t fapl, H5HF_crea fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ const char *base_desc = "filling direct blocks and skipping blocks in non-root indirect block, then " - "backfill and extend, then remove all objects %s"; + "backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -9457,7 +9431,7 @@ test_man_fill_direct_skip_2nd_indirect_start_block_add_skipped(hid_t fapl, H5HF_ unsigned u; /* Local index variable */ /* Test description */ const char *base_desc = "filling direct blocks and skipping row of non-root indirect blocks, then " - "backfill and extend, then remove all objects %s"; + "backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -9589,7 +9563,7 @@ test_man_fill_2nd_direct_less_one_wrap_start_block_add_skipped(hid_t fapl, H5HF_ /* Test description */ const char *base_desc = "filling direct blocks, filling 2nd level indirect blocks, except last one, and insert object too " - "large for 2nd level indirect blocks, then backfill and extend, then remove all objects %s"; + "large for 2nd level indirect blocks, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -9735,7 +9709,7 @@ test_man_fill_direct_skip_2nd_indirect_skip_2nd_block_add_skipped(hid_t fapl, H5 unsigned u; /* Local index variable */ /* Test description */ const char *base_desc = "filling direct blocks and skipping row of non-root indirect blocks, then skip " - "row of direct blocks, then backfill and extend, then remove all objects %s"; + "row of direct blocks, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -9898,7 +9872,7 @@ test_man_fill_direct_skip_indirect_two_rows_add_skipped(hid_t fapl, H5HF_create_ unsigned u, v; /* Local index variables */ /* Test description */ const char *base_desc = "filling direct blocks and skipping two rows of root indirect block, then " - "backfill and extend, then remove all objects %s"; + "backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -10055,7 +10029,7 @@ test_man_fill_direct_skip_indirect_two_rows_skip_indirect_row_add_skipped(hid_t /* Test description */ const char *base_desc = "filling direct blocks and skipping two rows of root indirect block, skip one row of root indirect " - "block, then backfill and extend, then remove all objects %s"; + "block, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -10235,7 +10209,7 @@ test_man_fill_2nd_direct_skip_start_block_add_skipped(hid_t fapl, H5HF_create_t /* Test description */ const char *base_desc = "filling direct blocks, filling 2nd level indirect blocks, and skip first rows of direct blocks of " - "3rd level indirect block, then backfill and extend, then remove all objects %s"; + "3rd level indirect block, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -10367,7 +10341,7 @@ test_man_fill_2nd_direct_skip_2nd_indirect_start_block_add_skipped(hid_t fapl, H const char *base_desc = "filling direct blocks, filling 2nd level indirect blocks, filling 3rd level indirect block's direct " "blocks, and skip first rows of direct blocks of 3rd level indirect block's 2nd level indirect " - "block, then backfill and extend, then remove all objects %s"; + "block, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -10511,7 +10485,7 @@ test_man_fill_2nd_direct_fill_direct_skip_3rd_indirect_start_block_add_skipped(h /* Test description */ const char *base_desc = "filling direct blocks, filling 2nd level indirect blocks, filling 3rd level " "indirect block's direct blocks, and skip first row of indirect blocks of 3rd " - "level indirect block, then backfill and extend, then remove all objects %s"; + "level indirect block, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -10664,7 +10638,7 @@ test_man_fill_2nd_direct_fill_direct_skip2_3rd_indirect_start_block_add_skipped( /* Test description */ const char *base_desc = "filling direct blocks, filling 2nd level indirect blocks, filling 3rd level " "indirect block's direct blocks, and skip first two rows of indirect blocks of " - "3rd level indirect block, then backfill and extend, then remove all objects %s"; + "3rd level indirect block, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -10822,7 +10796,7 @@ test_man_fill_3rd_direct_less_one_fill_direct_wrap_start_block_add_skipped(hid_t const char *base_desc = "filling direct blocks, filling 2nd level indirect blocks, filling first row of 3rd level indirect " "blocks, except last one, fill all direct blocks in last 3rd level indirect block, and insert object " - "too large for it's 2nd level indirect blocks, then backfill and extend, then remove all objects %s"; + "too large for it's 2nd level indirect blocks, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -10986,7 +10960,7 @@ test_man_fill_1st_row_3rd_direct_fill_2nd_direct_less_one_wrap_start_block_add_s "filling direct blocks, filling 2nd level indirect blocks, filling first row of 3rd level indirect " "blocks, fill all direct blocks in next 3rd level indirect block, fill all 1st row of 2nd level " "indirect blocks, except last one, and insert object too large for 2nd level indirect block, then " - "backfill and extend, then remove all objects %s"; + "backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -11154,7 +11128,7 @@ test_man_fill_3rd_direct_fill_direct_skip_start_block_add_skipped(hid_t fapl, H5 const char *base_desc = "filling direct blocks, filling 2nd level indirect blocks, filling 3rd level indirect blocks, fill " "4th level indirect block's direct blocks, and skip first row of 2nd indirect blocks of 4th level " - "indirect block, then backfill and extend, then remove all objects %s"; + "indirect block, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -11318,7 +11292,7 @@ test_man_fill_3rd_direct_fill_2nd_direct_fill_direct_skip_3rd_indirect_start_blo "filling direct blocks, filling 2nd level indirect blocks, filling 3rd level indirect blocks, fill " "4th level indirect block's direct, 2nd level indirect blocks and 3rd level direct block, and skip " "first row of 2nd indirect blocks of 4th level indirect block's 3rd level indirect block, then " - "backfill and extend, then remove all objects %s"; + "backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -11502,7 +11476,7 @@ test_man_fill_3rd_direct_fill_2nd_direct_fill_direct_skip_3rd_indirect_two_rows_ "first row of 4th level indirect blocks, fill 2nd row 4th level indirect block's direct, 2nd level " "indirect blocks, first row of 3rd level indirect blocks, 3rd level direct block in 2nd row, and " "skip first row of 2nd indirect blocks of 4th level indirect block's 3rd level indirect block, then " - "backfill and extend, then remove all objects %s"; + "backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -11721,7 +11695,7 @@ test_man_fill_3rd_direct_fill_2nd_direct_fill_direct_skip_3rd_indirect_wrap_star "filling direct blocks, filling 2nd level indirect blocks, filling 3rd level indirect blocks, fill " "first row of 3rd level indirect blocks in 4th level indirect block except last 3rd level block, " "fill direct blocks in 3rd level block, and skip row of 2nd indirect blocks of 4th level indirect " - "block's 3rd level indirect block, then backfill and extend, then remove all objects %s"; + "block's 3rd level indirect block, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -11922,7 +11896,7 @@ test_man_fill_4th_direct_less_one_fill_2nd_direct_fill_direct_skip_3rd_indirect_ "first row of 4th level indirect blocks, except last one, fill first row of 3rd level indirect " "blocks in last 4th level indirect block except last 3rd level block, fill direct blocks in 3rd " "level block, and skip row of 2nd indirect blocks of 4th level indirect block's 3rd level indirect " - "block, then backfill and extend, then remove all objects %s"; + "block, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -12143,7 +12117,7 @@ test_man_frag_simple(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tpar fheap_heap_state_t state; /* State of fractal heap */ unsigned u; /* Local index variables */ /* Test description */ - const char *base_desc = "fragmenting small blocks, then backfill and extend, then remove all objects %s"; + const char *base_desc = "fragmenting small blocks, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -12275,7 +12249,7 @@ test_man_frag_direct(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tpar fheap_heap_state_t state; /* State of fractal heap */ unsigned u, v; /* Local index variables */ /* Test description */ - const char *base_desc = "fragmenting direct blocks, then backfill and extend, then remove all objects %s"; + const char *base_desc = "fragmenting direct blocks, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -12449,7 +12423,7 @@ test_man_frag_2nd_direct(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t * unsigned u, v; /* Local index variables */ /* Test description */ const char *base_desc = "fill root direct blocks, then fragment 2nd level indirect block's direct " - "blocks, then backfill and extend, then remove all objects %s"; + "blocks, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -12561,7 +12535,7 @@ test_man_frag_3rd_direct(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t * /* Test description */ const char *base_desc = "fill root direct blocks and 2nd level indirect blocks, then fragment 3rd level indirect block's " - "direct blocks, then backfill and extend, then remove all objects %s"; + "direct blocks, then backfill and extend, then remove all objects"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, &fill_size) < 0) @@ -12675,7 +12649,7 @@ test_huge_insert_one(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tpar unsigned char obj_type; /* Type of storage for object */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "insert one huge object, then remove %s"; + const char *base_desc = "insert one huge object, then remove"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -12826,7 +12800,7 @@ test_huge_insert_two(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tpar unsigned char obj_type; /* Type of storage for object */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "insert two huge objects, then remove %s"; + const char *base_desc = "insert two huge objects, then remove"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -13057,7 +13031,7 @@ test_huge_insert_three(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tp unsigned char obj_type; /* Type of storage for object */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "insert three huge objects, then remove %s"; + const char *base_desc = "insert three huge objects, then remove"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -13364,7 +13338,7 @@ test_huge_insert_mix(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tpar unsigned char obj_type; /* Type of storage for object */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "insert mix of normal & huge objects, then remove %s"; + const char *base_desc = "insert mix of normal & huge objects, then remove"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -13788,7 +13762,7 @@ test_filtered_huge(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tparam hbool_t huge_ids_direct; /* Are 'huge' objects directly accessed? */ hbool_t pline_init = FALSE; /* Whether the I/O pipeline has been initialized */ /* Test description */ - const char *base_desc = "insert 'huge' object into heap with I/O filters, then remove %s"; + const char *base_desc = "insert 'huge' object into heap with I/O filters, then remove"; /* Copy heap creation properties */ HDmemcpy(&tmp_cparam, cparam, sizeof(H5HF_create_t)); @@ -13996,7 +13970,7 @@ test_tiny_insert_one(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tpar unsigned char obj_type; /* Type of storage for object */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "insert one tiny object, then remove %s"; + const char *base_desc = "insert one tiny object, then remove"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -14147,7 +14121,7 @@ test_tiny_insert_two(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tpar unsigned char obj_type; /* Type of storage for object */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "insert two tiny objects, then remove %s"; + const char *base_desc = "insert two tiny objects, then remove"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -14383,7 +14357,7 @@ test_tiny_insert_mix(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_t *tpar unsigned char obj_type; /* Type of storage for object */ fheap_heap_state_t state; /* State of fractal heap */ /* Test description */ - const char *base_desc = "insert mix of normal, huge & tiny objects, then remove %s"; + const char *base_desc = "insert mix of normal, huge & tiny objects, then remove"; /* Perform common test initialization operations */ if (begin_test(tparam, base_desc, &keep_ids, NULL) < 0) @@ -14984,7 +14958,7 @@ test_filtered_man_root_direct(hid_t fapl, H5HF_create_t *cparam, fheap_test_para fheap_heap_state_t state; /* State of fractal heap */ unsigned deflate_level; /* Deflation level */ /* Test description */ - const char *base_desc = "insert one 'managed' object into heap with I/O filters, then remove %s"; + const char *base_desc = "insert one 'managed' object into heap with I/O filters, then remove"; /* Copy heap creation properties */ HDmemcpy(&tmp_cparam, cparam, sizeof(H5HF_create_t)); @@ -15158,7 +15132,7 @@ test_filtered_man_root_indirect(hid_t fapl, H5HF_create_t *cparam, fheap_test_pa fheap_heap_state_t state; /* State of fractal heap */ unsigned deflate_level; /* Deflation level */ /* Test description */ - const char *base_desc = "insert two 'managed' objects into heap with I/O filters, then remove %s"; + const char *base_desc = "insert two 'managed' objects into heap with I/O filters, then remove"; /* Copy heap creation properties */ HDmemcpy(&tmp_cparam, cparam, sizeof(H5HF_create_t)); diff --git a/test/flushrefresh.c b/test/flushrefresh.c index 2757bbf..0c10238 100644 --- a/test/flushrefresh.c +++ b/test/flushrefresh.c @@ -93,7 +93,7 @@ FILE *errorfile; /* ===================== */ /* Main */ -int main(int argc, const char *argv[]); +int main(int argc, char *argv[]); /* Flush Test Framework */ herr_t test_flush(void); @@ -137,7 +137,7 @@ herr_t end_verification(void); *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { /* Variables */ const char *envval = NULL; diff --git a/test/genall5.c b/test/genall5.c index f3b0e6a..ca96eeb 100644 --- a/test/genall5.c +++ b/test/genall5.c @@ -306,7 +306,7 @@ ns_grp_c(hid_t fid, const char *group_name, unsigned nlinks) while ((pass) && (u < nlinks)) { char linkname[16]; - HDsprintf(linkname, "%u", u); + HDsnprintf(linkname, sizeof(linkname), "%u", u); if (0 == (u % 3)) { ret = H5Lcreate_soft(group_name, gid, linkname, H5P_DEFAULT, H5P_DEFAULT); @@ -474,7 +474,7 @@ vrfy_ns_grp_c(hid_t fid, const char *group_name, unsigned nlinks) char linkname[16]; htri_t link_exists; - HDsprintf(linkname, "%u", u); + HDsnprintf(linkname, sizeof(linkname), "%u", u); link_exists = H5Lexists(gid, linkname, H5P_DEFAULT); if (link_exists < 0) { @@ -715,7 +715,7 @@ ns_grp_d(hid_t fid, const char *group_name, unsigned nlinks) while ((pass) && (u < nlinks)) { char linkname[16]; - HDsprintf(linkname, "%u", u); + HDsnprintf(linkname, sizeof(linkname), "%u", u); if (0 == (u % 3)) { ret = H5Lcreate_soft(group_name, gid, linkname, H5P_DEFAULT, H5P_DEFAULT); @@ -883,7 +883,7 @@ vrfy_ns_grp_d(hid_t fid, const char *group_name, unsigned nlinks) char linkname[16]; htri_t link_exists; - HDsprintf(linkname, "%u", u); + HDsnprintf(linkname, sizeof(linkname), "%u", u); link_exists = H5Lexists(gid, linkname, H5P_DEFAULT); if (link_exists < 0) { @@ -1321,7 +1321,7 @@ os_grp_n(hid_t fid, const char *group_name, int proc_num, unsigned nlinks) while ((pass) && (u < nlinks)) { char linkname[32]; - HDsprintf(linkname, "ln%d_%u", proc_num, u); + HDsnprintf(linkname, sizeof(linkname), "ln%d_%u", proc_num, u); if (0 == (u % 2)) { ret = H5Lcreate_soft(group_name, gid, linkname, H5P_DEFAULT, H5P_DEFAULT); @@ -1479,7 +1479,7 @@ vrfy_os_grp_n(hid_t fid, const char *group_name, int proc_num, unsigned nlinks) char linkname[32]; htri_t link_exists; - HDsprintf(linkname, "ln%d_%u", proc_num, u); + HDsnprintf(linkname, sizeof(linkname), "ln%d_%u", proc_num, u); link_exists = H5Lexists(gid, linkname, H5P_DEFAULT); if (link_exists < 0) { @@ -3056,26 +3056,26 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) /* Add & verify an empty "new style" group */ if (pass) { - HDsprintf(full_path, "%s/A", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/A", base_path); HDassert(HDstrlen(full_path) < 1024); ns_grp_0(fid, full_path); } if (pass) { - HDsprintf(full_path, "%s/A", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/A", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ns_grp_0(fid, full_path); } /* Add & verify a compact "new style" group (3 link messages) */ if (pass) { - HDsprintf(full_path, "%s/B", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/B", base_path); HDassert(HDstrlen(full_path) < 1024); ns_grp_c(fid, full_path, 3); } if (pass) { - HDsprintf(full_path, "%s/B", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/B", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ns_grp_c(fid, full_path, 3); } @@ -3084,26 +3084,26 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * fractal heap) */ if (pass) { - HDsprintf(full_path, "%s/C", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/C", base_path); HDassert(HDstrlen(full_path) < 1024); ns_grp_d(fid, full_path, 300); } if (pass) { - HDsprintf(full_path, "%s/C", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/C", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ns_grp_d(fid, full_path, 300); } /* Add & verify an empty "old style" group to file */ if (pass) { - HDsprintf(full_path, "%s/D", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/D", base_path); HDassert(HDstrlen(full_path) < 1024); os_grp_0(fid, full_path); } if (pass) { - HDsprintf(full_path, "%s/D", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/D", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_os_grp_0(fid, full_path); } @@ -3112,13 +3112,13 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * local heap) to file */ if (pass) { - HDsprintf(full_path, "%s/E", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/E", base_path); HDassert(HDstrlen(full_path) < 1024); os_grp_n(fid, full_path, proc_num, 300); } if (pass) { - HDsprintf(full_path, "%s/E", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/E", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_os_grp_n(fid, full_path, proc_num, 300); } @@ -3127,13 +3127,13 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * to file */ if (pass) { - HDsprintf(full_path, "%s/F", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/F", base_path); HDassert(HDstrlen(full_path) < 1024); ds_ctg_i(fid, full_path, FALSE); } if (pass) { - HDsprintf(full_path, "%s/F", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/F", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_ctg_i(fid, full_path, FALSE); } @@ -3142,13 +3142,13 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * to file */ if (pass) { - HDsprintf(full_path, "%s/G", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/G", base_path); HDassert(HDstrlen(full_path) < 1024); ds_ctg_i(fid, full_path, TRUE); } if (pass) { - HDsprintf(full_path, "%s/G", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/G", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_ctg_i(fid, full_path, TRUE); } @@ -3157,13 +3157,13 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * to file */ if (pass) { - HDsprintf(full_path, "%s/H", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/H", base_path); HDassert(HDstrlen(full_path) < 1024); ds_chk_i(fid, full_path, FALSE); } if (pass) { - HDsprintf(full_path, "%s/H", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/H", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_chk_i(fid, full_path, FALSE); } @@ -3172,13 +3172,13 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * to file */ if (pass) { - HDsprintf(full_path, "%s/I", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/I", base_path); HDassert(HDstrlen(full_path) < 1024); ds_chk_i(fid, full_path, TRUE); } if (pass) { - HDsprintf(full_path, "%s/I", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/I", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_chk_i(fid, full_path, TRUE); } @@ -3187,13 +3187,13 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * to file */ if (pass) { - HDsprintf(full_path, "%s/J", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/J", base_path); HDassert(HDstrlen(full_path) < 1024); ds_cpt_i(fid, full_path, FALSE); } if (pass) { - HDsprintf(full_path, "%s/J", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/J", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_cpt_i(fid, full_path, FALSE); } @@ -3202,13 +3202,13 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * to file */ if (pass) { - HDsprintf(full_path, "%s/K", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/K", base_path); HDassert(HDstrlen(full_path) < 1024); ds_cpt_i(fid, full_path, TRUE); } if (pass) { - HDsprintf(full_path, "%s/K", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/K", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_cpt_i(fid, full_path, TRUE); } @@ -3217,13 +3217,13 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * (but no data) to file */ if (pass) { - HDsprintf(full_path, "%s/L", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/L", base_path); HDassert(HDstrlen(full_path) < 1024); ds_ctg_v(fid, full_path, FALSE); } if (pass) { - HDsprintf(full_path, "%s/L", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/L", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_ctg_v(fid, full_path, FALSE); } @@ -3232,13 +3232,13 @@ create_zoo(hid_t fid, const char *base_path, int proc_num) * (and data) to file */ if (pass) { - HDsprintf(full_path, "%s/M", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/M", base_path); HDassert(HDstrlen(full_path) < 1024); ds_ctg_v(fid, full_path, TRUE); } if (pass) { - HDsprintf(full_path, "%s/M", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/M", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_ctg_v(fid, full_path, TRUE); } @@ -3281,14 +3281,14 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) /* validate an empty "new style" group */ if (pass) { - HDsprintf(full_path, "%s/A", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/A", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ns_grp_0(fid, full_path); } /* validate a compact "new style" group (3 link messages) */ if (pass) { - HDsprintf(full_path, "%s/B", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/B", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ns_grp_c(fid, full_path, 3); } @@ -3297,14 +3297,14 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * fractal heap) */ if (pass) { - HDsprintf(full_path, "%s/C", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/C", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ns_grp_d(fid, full_path, 300); } /* validate an empty "old style" group in file */ if (pass) { - HDsprintf(full_path, "%s/D", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/D", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_os_grp_0(fid, full_path); } @@ -3313,7 +3313,7 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * local heap) */ if (pass) { - HDsprintf(full_path, "%s/E", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/E", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_os_grp_n(fid, full_path, proc_num, 300); } @@ -3322,7 +3322,7 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * in file. */ if (pass) { - HDsprintf(full_path, "%s/F", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/F", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_ctg_i(fid, full_path, FALSE); } @@ -3331,7 +3331,7 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * in file. */ if (pass) { - HDsprintf(full_path, "%s/G", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/G", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_ctg_i(fid, full_path, TRUE); } @@ -3340,7 +3340,7 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * in file */ if (pass) { - HDsprintf(full_path, "%s/H", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/H", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_chk_i(fid, full_path, FALSE); } @@ -3349,7 +3349,7 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * in file */ if (pass) { - HDsprintf(full_path, "%s/I", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/I", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_chk_i(fid, full_path, TRUE); } @@ -3358,7 +3358,7 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * in file */ if (pass) { - HDsprintf(full_path, "%s/J", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/J", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_cpt_i(fid, full_path, FALSE); } @@ -3367,7 +3367,7 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * in file */ if (pass) { - HDsprintf(full_path, "%s/K", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/K", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_cpt_i(fid, full_path, TRUE); } @@ -3376,7 +3376,7 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * (but no data) to file */ if (pass) { - HDsprintf(full_path, "%s/L", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/L", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_ctg_v(fid, full_path, FALSE); } @@ -3385,7 +3385,7 @@ validate_zoo(hid_t fid, const char *base_path, int proc_num) * (and data) to file */ if (pass) { - HDsprintf(full_path, "%s/M", base_path); + HDsnprintf(full_path, sizeof(full_path), "%s/M", base_path); HDassert(HDstrlen(full_path) < 1024); vrfy_ds_ctg_v(fid, full_path, TRUE); } diff --git a/test/page_buffer.c b/test/page_buffer.c index c078ce8..64e88fb 100644 --- a/test/page_buffer.c +++ b/test/page_buffer.c @@ -120,28 +120,28 @@ create_file(char *filename, hid_t fcpl, hid_t fapl) for (i = 0; i < NUM_DSETS; i++) { - HDsprintf(dset_name, "D1dset%d", i); + HDsnprintf(dset_name, sizeof(dset_name), "D1dset%d", i); if ((dset_id = H5Dcreate2(grp_id, dset_name, H5T_NATIVE_INT, filespace, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR; if (H5Dclose(dset_id) < 0) FAIL_STACK_ERROR; - HDsprintf(dset_name, "D2dset%d", i); + HDsnprintf(dset_name, sizeof(dset_name), "D2dset%d", i); if ((dset_id = H5Dcreate2(grp_id, dset_name, H5T_NATIVE_INT, filespace, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR; if (H5Dclose(dset_id) < 0) FAIL_STACK_ERROR; - HDsprintf(dset_name, "D3dset%d", i); + HDsnprintf(dset_name, sizeof(dset_name), "D3dset%d", i); if ((dset_id = H5Dcreate2(grp_id, dset_name, H5T_NATIVE_INT, filespace, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR; if (H5Dclose(dset_id) < 0) FAIL_STACK_ERROR; - HDsprintf(dset_name, "dset%d", i); + HDsnprintf(dset_name, sizeof(dset_name), "dset%d", i); if ((dset_id = H5Dcreate2(grp_id, dset_name, H5T_NATIVE_INT, filespace, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR; @@ -166,13 +166,13 @@ create_file(char *filename, hid_t fcpl, hid_t fapl) } } - HDsprintf(dset_name, "D1dset%d", i); + HDsnprintf(dset_name, sizeof(dset_name), "D1dset%d", i); if (H5Ldelete(grp_id, dset_name, H5P_DEFAULT) < 0) FAIL_STACK_ERROR; - HDsprintf(dset_name, "D2dset%d", i); + HDsnprintf(dset_name, sizeof(dset_name), "D2dset%d", i); if (H5Ldelete(grp_id, dset_name, H5P_DEFAULT) < 0) FAIL_STACK_ERROR; - HDsprintf(dset_name, "D3dset%d", i); + HDsnprintf(dset_name, sizeof(dset_name), "D3dset%d", i); if (H5Ldelete(grp_id, dset_name, H5P_DEFAULT) < 0) FAIL_STACK_ERROR; } @@ -259,7 +259,7 @@ open_file(char *filename, hid_t fapl, hsize_t page_size, size_t page_buffer_size for (i = 0; i < NUM_DSETS; i++) { - HDsprintf(dset_name, "dset%d", i); + HDsnprintf(dset_name, sizeof(dset_name), "dset%d", i); if ((dset_id = H5Dopen2(grp_id, dset_name, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR; diff --git a/test/reserved.c b/test/reserved.c index f864329..08e747e 100644 --- a/test/reserved.c +++ b/test/reserved.c @@ -71,7 +71,7 @@ rsrv_heap(void) } H5E_END_TRY - HDsprintf(dset_name, "Dset %d", i); + HDsnprintf(dset_name, sizeof(dset_name), "Dset %d", i); H5E_BEGIN_TRY { @@ -115,7 +115,7 @@ rsrv_heap(void) if (H5open() < 0) TEST_ERROR; - HDsprintf(dset_name, "Dset %d", i - 2); + HDsnprintf(dset_name, sizeof(dset_name), "Dset %d", i - 2); file_id = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT); if (file_id < 0) @@ -218,7 +218,7 @@ rsrv_ohdr(void) } /* end for */ for (i = 0; i < 2000; i++) { - HDsprintf(attrname, "attr %d", i); + HDsnprintf(attrname, sizeof(attrname), "attr %d", i); H5E_BEGIN_TRY { aid = H5Screate_simple(2, dims, NULL); diff --git a/test/swmr_addrem_writer.c b/test/swmr_addrem_writer.c index d39a698..c705d6b 100644 --- a/test/swmr_addrem_writer.c +++ b/test/swmr_addrem_writer.c @@ -283,7 +283,7 @@ usage(void) } int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t fid; /* File ID for file opened */ long nops = 0; /* # of times to grow or shrink the dataset */ diff --git a/test/swmr_common.c b/test/swmr_common.c index 2201427..b359bc6 100644 --- a/test/swmr_common.c +++ b/test/swmr_common.c @@ -202,13 +202,12 @@ generate_symbols(void) unsigned u, v; /* Local index variables */ for (u = 0; u < NLEVELS; u++) { - symbol_info[u] = (symbol_info_t *)HDmalloc(symbol_count[u] * sizeof(symbol_info_t)); + symbol_info[u] = HDmalloc(symbol_count[u] * sizeof(symbol_info_t)); for (v = 0; v < symbol_count[u]; v++) { char name_buf[64]; generate_name(name_buf, u, v); - symbol_info[u][v].name = (char *)HDmalloc(HDstrlen(name_buf) + 1); - HDstrcpy(symbol_info[u][v].name, name_buf); + symbol_info[u][v].name = HDstrdup(name_buf); symbol_info[u][v].dsid = -1; symbol_info[u][v].nrecords = 0; } /* end for */ diff --git a/test/swmr_generator.c b/test/swmr_generator.c index e1423b6..93cfa0f 100644 --- a/test/swmr_generator.c +++ b/test/swmr_generator.c @@ -258,7 +258,7 @@ usage(void) } /* end usage() */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { int comp_level = -1; /* Compression level (-1 is no compression) */ hbool_t verbose = TRUE; /* Whether to emit some informational messages */ diff --git a/test/swmr_reader.c b/test/swmr_reader.c index 836e1cc..e849f67 100644 --- a/test/swmr_reader.c +++ b/test/swmr_reader.c @@ -387,7 +387,7 @@ usage(void) } int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { long nseconds = 0; /* # of seconds to test */ int poll_time = 1; /* # of seconds between polling */ diff --git a/test/swmr_remove_reader.c b/test/swmr_remove_reader.c index 910bc74..94cb7f8 100644 --- a/test/swmr_remove_reader.c +++ b/test/swmr_remove_reader.c @@ -371,7 +371,7 @@ usage(void) } int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { long nseconds = 0; /* # of seconds to test */ int poll_time = 1; /* # of seconds between polling */ diff --git a/test/swmr_remove_writer.c b/test/swmr_remove_writer.c index e52f4e2..3604935 100644 --- a/test/swmr_remove_writer.c +++ b/test/swmr_remove_writer.c @@ -217,7 +217,7 @@ usage(void) } int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t fid; /* File ID for file opened */ long nshrinks = 0; /* # of times to shrink the dataset */ diff --git a/test/swmr_sparse_reader.c b/test/swmr_sparse_reader.c index 00eb2e0..8f1c781 100644 --- a/test/swmr_sparse_reader.c +++ b/test/swmr_sparse_reader.c @@ -117,7 +117,7 @@ check_dataset(hid_t fid, unsigned verbose, const symbol_info_t *symbol, symbol_t (uintmax_t)start[0], (uintmax_t)start[1]); /* Read record from dataset */ - record->rec_id = (uint64_t)ULLONG_MAX; + record->rec_id = UINT64_MAX; if (H5Dread(dsid, symbol_tid, rec_sid, file_sid, H5P_DEFAULT, record) < 0) return -1; @@ -342,7 +342,7 @@ usage(void) } /* end usage() */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { long nrecords = 0; /* # of records to read */ int poll_time = 1; /* # of seconds to sleep when waiting for writer */ diff --git a/test/swmr_sparse_writer.c b/test/swmr_sparse_writer.c index a4fc93e..96eff6c 100644 --- a/test/swmr_sparse_writer.c +++ b/test/swmr_sparse_writer.c @@ -318,7 +318,7 @@ usage(void) } int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t fid; /* File ID for file opened */ long nrecords = 0; /* # of records to append */ diff --git a/test/swmr_start_write.c b/test/swmr_start_write.c index 3ddd57a..d046b40 100644 --- a/test/swmr_start_write.c +++ b/test/swmr_start_write.c @@ -352,7 +352,7 @@ usage(void) *H5Fstart_swmr_write(), add_records(), H5Fclose(). */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t fid; /* File ID for file opened */ long nrecords = 0; /* # of records to append */ diff --git a/test/swmr_writer.c b/test/swmr_writer.c index de8b054..c4178f0 100644 --- a/test/swmr_writer.c +++ b/test/swmr_writer.c @@ -275,7 +275,7 @@ usage(void) } int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t fid; /* File ID for file opened */ long nrecords = 0; /* # of records to append */ diff --git a/test/tattr.c b/test/tattr.c index d66fcc3..2859f4c 100644 --- a/test/tattr.c +++ b/test/tattr.c @@ -2094,7 +2094,7 @@ test_attr_dense_verify(hid_t loc_id, unsigned max_attr) /* Re-open all the attributes by name and verify the data */ for (u = 0; u < max_attr; u++) { /* Open attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Aopen(loc_id, attrname, H5P_DEFAULT); CHECK(attr, FAIL, "H5Aopen"); @@ -2119,7 +2119,7 @@ test_attr_dense_verify(hid_t loc_id, unsigned max_attr) CHECK(attr, FAIL, "H5Aopen_by_idx"); /* Verify Name */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); name_len = H5Aget_name(attr, (size_t)ATTR_NAME_LEN, check_name); VERIFY(name_len, HDstrlen(attrname), "H5Aget_name"); if (HDstrcmp(check_name, attrname) != 0) @@ -2219,7 +2219,7 @@ test_attr_dense_create(hid_t fcpl, hid_t fapl) /* Add attributes, until just before converting to dense storage */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -2238,7 +2238,7 @@ test_attr_dense_create(hid_t fcpl, hid_t fapl) /* Add one more attribute, to push into "dense" storage */ /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -2361,7 +2361,7 @@ test_attr_dense_open(hid_t fcpl, hid_t fapl) /* Add attributes, until just before converting to dense storage */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -2384,7 +2384,7 @@ test_attr_dense_open(hid_t fcpl, hid_t fapl) /* Add one more attribute, to push into "dense" storage */ /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -2523,7 +2523,7 @@ test_attr_dense_delete(hid_t fcpl, hid_t fapl) /* Add attributes, until well into dense storage */ for (u = 0; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -2568,7 +2568,7 @@ test_attr_dense_delete(hid_t fcpl, hid_t fapl) /* Delete attributes until the attributes revert to compact storage again */ for (u--; u >= min_dense; u--) { /* Delete attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -2582,7 +2582,7 @@ test_attr_dense_delete(hid_t fcpl, hid_t fapl) VERIFY(is_dense, TRUE, "H5O__is_attr_dense_test"); /* Delete one more attribute, which should cause reversion to compact storage */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -2595,7 +2595,7 @@ test_attr_dense_delete(hid_t fcpl, hid_t fapl) CHECK(ret, FAIL, "test_attr_dense_verify"); /* Delete another attribute, to verify deletion in compact storage */ - HDsprintf(attrname, "attr %02u", (u - 1)); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", (u - 1)); ret = H5Adelete(dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -2724,7 +2724,7 @@ test_attr_dense_rename(hid_t fcpl, hid_t fapl) /* Add attributes, until well into dense storage */ for (u = 0; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, H5I_INVALID_HID, "H5Acreate2"); @@ -2790,7 +2790,7 @@ test_attr_dense_rename(hid_t fcpl, hid_t fapl) unsigned value; /* Attribute value */ /* Open attribute */ - HDsprintf(attrname, "new attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "new attr %02u", u); attr = H5Aopen(dataset, attrname, H5P_DEFAULT); CHECK(attr, H5I_INVALID_HID, "H5Aopen"); @@ -2914,7 +2914,7 @@ test_attr_dense_unlink(hid_t fcpl, hid_t fapl) /* Add attributes, until well into dense storage */ for (u = 0; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -3057,7 +3057,7 @@ test_attr_dense_limits(hid_t fcpl, hid_t fapl) /* Create attribute */ u = 0; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -3077,7 +3077,7 @@ test_attr_dense_limits(hid_t fcpl, hid_t fapl) /* Create attribute */ u = 1; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -3107,7 +3107,7 @@ test_attr_dense_limits(hid_t fcpl, hid_t fapl) /* Delete attribute */ u = 0; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -3216,7 +3216,7 @@ test_attr_dense_dup_ids(hid_t fcpl, hid_t fapl) /* Add attributes, until just before converting to dense storage */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -3239,7 +3239,7 @@ test_attr_dense_dup_ids(hid_t fcpl, hid_t fapl) CHECK(sid2, FAIL, "H5Screate_simple"); /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_INT, sid2, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -3522,7 +3522,7 @@ test_attr_dense_dup_ids(hid_t fcpl, hid_t fapl) /* Delete a few attributes until the storage switches to compact */ for (u = min_dense - 1; u <= max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); add_attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(add_attr, FAIL, "H5Acreate2"); @@ -3590,7 +3590,7 @@ test_attr_dense_dup_ids(hid_t fcpl, hid_t fapl) /* Add attributes, until just before converting to dense storage */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(gid1, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -3756,7 +3756,7 @@ test_attr_big(hid_t fcpl, hid_t fapl) /* Create attribute */ u = 0; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -3774,7 +3774,7 @@ test_attr_big(hid_t fcpl, hid_t fapl) /* Create attribute */ u = 1; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -3792,7 +3792,7 @@ test_attr_big(hid_t fcpl, hid_t fapl) /* Create attribute */ u = 2; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, big_sid, H5P_DEFAULT, H5P_DEFAULT); if (low == H5F_LIBVER_LATEST) { CHECK(attr, FAIL, "H5Acreate2"); @@ -3815,7 +3815,7 @@ test_attr_big(hid_t fcpl, hid_t fapl) /* Create attribute */ u = 3; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(dataset, attrname, H5T_NATIVE_UINT, big_sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -3837,7 +3837,7 @@ test_attr_big(hid_t fcpl, hid_t fapl) /* Delete attribute */ u = 1; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -3851,7 +3851,7 @@ test_attr_big(hid_t fcpl, hid_t fapl) /* Delete attribute */ u = 3; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -3865,7 +3865,7 @@ test_attr_big(hid_t fcpl, hid_t fapl) /* Delete attribute */ u = 2; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -3879,7 +3879,7 @@ test_attr_big(hid_t fcpl, hid_t fapl) /* Delete attribute */ u = 0; - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -4278,7 +4278,7 @@ test_attr_many(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create many attributes */ for (u = 0; u < nattr; u++) { - HDsprintf(attrname, "a-%06u", u); + HDsnprintf(attrname, sizeof(attrname), "a-%06u", u); exists = H5Aexists(gid, attrname); VERIFY(exists, FALSE, "H5Aexists"); @@ -4330,7 +4330,7 @@ test_attr_many(hbool_t new_format, hid_t fcpl, hid_t fapl) for (u = 0; u < nattr; u++) { unsigned value; /* Attribute value */ - HDsprintf(attrname, "a-%06u", u); + HDsnprintf(attrname, sizeof(attrname), "a-%06u", u); exists = H5Aexists(gid, attrname); VERIFY(exists, TRUE, "H5Aexists"); @@ -4578,7 +4578,7 @@ test_attr_corder_create_compact(hid_t fcpl, hid_t fapl) /* Create several attributes, but keep storage in compact form */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -4667,7 +4667,7 @@ test_attr_corder_create_compact(hid_t fcpl, hid_t fapl) H5A_info_t ainfo; /* Attribute information */ /* Retrieve information for attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Aget_info_by_name(my_dataset, ".", attrname, &ainfo, H5P_DEFAULT); CHECK(ret, FAIL, "H5Aget_info_by_name"); @@ -4782,7 +4782,7 @@ test_attr_corder_create_dense(hid_t fcpl, hid_t fapl) /* Create several attributes, but keep storage in compact form */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -4805,7 +4805,7 @@ test_attr_corder_create_dense(hid_t fcpl, hid_t fapl) } /* end for */ /* Create another attribute, to push into dense storage */ - HDsprintf(attrname, "attr %02u", max_compact); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", max_compact); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -4898,7 +4898,7 @@ test_attr_corder_create_dense(hid_t fcpl, hid_t fapl) H5A_info_t ainfo; /* Attribute information */ /* Retrieve information for attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Aget_info_by_name(my_dataset, ".", attrname, &ainfo, H5P_DEFAULT); CHECK(ret, FAIL, "H5Aget_info_by_name"); @@ -5171,7 +5171,7 @@ test_attr_corder_transition(hid_t fcpl, hid_t fapl) /* Create several attributes, but keep storage in compact form */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -5194,7 +5194,7 @@ test_attr_corder_transition(hid_t fcpl, hid_t fapl) } /* end for */ /* Create another attribute, to push into dense storage */ - HDsprintf(attrname, "attr %02u", max_compact); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", max_compact); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -5222,7 +5222,7 @@ test_attr_corder_transition(hid_t fcpl, hid_t fapl) /* Delete several attributes from object, until attribute storage resumes compact form */ for (u = max_compact; u >= min_dense; u--) { - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(my_dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -5242,7 +5242,7 @@ test_attr_corder_transition(hid_t fcpl, hid_t fapl) } /* end for */ /* Delete another attribute, to push attribute storage into compact form */ - HDsprintf(attrname, "attr %02u", (min_dense - 1)); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", (min_dense - 1)); ret = H5Adelete(my_dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -5258,7 +5258,7 @@ test_attr_corder_transition(hid_t fcpl, hid_t fapl) /* Re-add attributes to get back into dense form */ for (u = (min_dense - 1); u < (max_compact + 1); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -5345,7 +5345,7 @@ test_attr_corder_transition(hid_t fcpl, hid_t fapl) /* Delete several attributes from object, until attribute storage resumes compact form */ for (u = max_compact; u >= min_dense; u--) { - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(my_dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -5365,7 +5365,7 @@ test_attr_corder_transition(hid_t fcpl, hid_t fapl) } /* end for */ /* Delete another attribute, to push attribute storage into compact form */ - HDsprintf(attrname, "attr %02u", (min_dense - 1)); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", (min_dense - 1)); ret = H5Adelete(my_dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); @@ -5381,7 +5381,7 @@ test_attr_corder_transition(hid_t fcpl, hid_t fapl) /* Re-add attributes to get back into dense form */ for (u = (min_dense - 1); u < (max_compact + 1); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -5410,11 +5410,11 @@ test_attr_corder_transition(hid_t fcpl, hid_t fapl) /* Delete all attributes */ for (u = max_compact; u > 0; u--) { - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); ret = H5Adelete(my_dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); } /* end for */ - HDsprintf(attrname, "attr %02u", 0); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", 0); ret = H5Adelete(my_dataset, attrname); CHECK(ret, FAIL, "H5Adelete"); } /* end for */ @@ -5554,7 +5554,7 @@ test_attr_corder_delete(hid_t fcpl, hid_t fapl) /* Create attributes, until attribute storage is in dense form */ for (u = 0; u < max_compact * 2; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -5897,7 +5897,7 @@ test_attr_info_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create attributes, up to limit of compact form */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -5937,7 +5937,7 @@ test_attr_info_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create more attributes, to push into dense form */ for (; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -6381,7 +6381,7 @@ test_attr_delete_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create attributes, up to limit of compact form */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -6456,9 +6456,9 @@ test_attr_delete_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) ret = (herr_t)H5Aget_name_by_idx(my_dataset, ".", idx_type, order, (hsize_t)0, tmpname, (size_t)NAME_BUF_SIZE, H5P_DEFAULT); if (order == H5_ITER_INC) - HDsprintf(attrname, "attr %02u", (u + 1)); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", (u + 1)); else - HDsprintf(attrname, "attr %02u", (max_compact - (u + 2))); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", (max_compact - (u + 2))); ret = HDstrcmp(attrname, tmpname); VERIFY(ret, 0, "H5Aget_name_by_idx"); } /* end for */ @@ -6494,7 +6494,7 @@ test_attr_delete_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create more attributes, to push into dense form */ for (u = 0; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -6584,9 +6584,10 @@ test_attr_delete_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) ret = (herr_t)H5Aget_name_by_idx(my_dataset, ".", idx_type, order, (hsize_t)0, tmpname, (size_t)NAME_BUF_SIZE, H5P_DEFAULT); if (order == H5_ITER_INC) - HDsprintf(attrname, "attr %02u", (u + 1)); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", (u + 1)); else - HDsprintf(attrname, "attr %02u", ((max_compact * 2) - (u + 2))); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", + ((max_compact * 2) - (u + 2))); ret = HDstrcmp(attrname, tmpname); VERIFY(ret, 0, "H5Aget_name_by_idx"); } /* end for */ @@ -6628,7 +6629,7 @@ test_attr_delete_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create attributes, to push into dense form */ for (u = 0; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -6697,9 +6698,10 @@ test_attr_delete_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) ret = (herr_t)H5Aget_name_by_idx(my_dataset, ".", idx_type, order, (hsize_t)u, tmpname, (size_t)NAME_BUF_SIZE, H5P_DEFAULT); if (order == H5_ITER_INC) - HDsprintf(attrname, "attr %02u", ((u * 2) + 1)); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", ((u * 2) + 1)); else - HDsprintf(attrname, "attr %02u", ((max_compact * 2) - ((u * 2) + 2))); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", + ((max_compact * 2) - ((u * 2) + 2))); ret = HDstrcmp(attrname, tmpname); VERIFY(ret, 0, "H5Aget_name_by_idx"); } /* end for */ @@ -6749,9 +6751,10 @@ test_attr_delete_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) ret = (herr_t)H5Aget_name_by_idx(my_dataset, ".", idx_type, order, (hsize_t)0, tmpname, (size_t)NAME_BUF_SIZE, H5P_DEFAULT); if (order == H5_ITER_INC) - HDsprintf(attrname, "attr %02u", ((u * 2) + 3)); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", ((u * 2) + 3)); else - HDsprintf(attrname, "attr %02u", ((max_compact * 2) - ((u * 2) + 4))); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", + ((max_compact * 2) - ((u * 2) + 4))); ret = HDstrcmp(attrname, tmpname); VERIFY(ret, 0, "H5Aget_name_by_idx"); } /* end for */ @@ -6832,7 +6835,7 @@ attr_iterate2_cb(hid_t loc_id, const char *attr_name, const H5A_info_t *info, vo } /* end if */ /* Verify name of link */ - HDsprintf(attrname, "attr %02u", (unsigned)my_info.corder); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", (unsigned)my_info.corder); if (HDstrcmp(attr_name, attrname) != 0) return (H5_ITER_ERROR); @@ -7342,7 +7345,7 @@ test_attr_iterate2(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create attributes, up to limit of compact form */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -7414,7 +7417,7 @@ test_attr_iterate2(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create more attributes, to push into dense form */ for (u = max_compact; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -7706,7 +7709,7 @@ test_attr_open_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create attributes, up to limit of compact form */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -7765,7 +7768,7 @@ test_attr_open_by_idx(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create more attributes, to push into dense form */ for (u = max_compact; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -7870,7 +7873,7 @@ attr_open_check(hid_t fid, const char *dsetname, hid_t obj_id, unsigned max_attr /* Open each attribute on object by index and check that it's the correct one */ for (u = 0; u < max_attrs; u++) { /* Open the attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr_id = H5Aopen(obj_id, attrname, H5P_DEFAULT); CHECK(attr_id, FAIL, "H5Aopen"); @@ -8039,7 +8042,7 @@ test_attr_open_by_name(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create attributes, up to limit of compact form */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -8105,7 +8108,7 @@ test_attr_open_by_name(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create more attributes, to push into dense form */ for (u = max_compact; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate2(my_dataset, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate2"); @@ -8288,7 +8291,7 @@ test_attr_create_by_name(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create attributes, up to limit of compact form */ for (u = 0; u < max_compact; u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate_by_name(fid, dsetname, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate_by_name"); @@ -8345,7 +8348,7 @@ test_attr_create_by_name(hbool_t new_format, hid_t fcpl, hid_t fapl) /* Create more attributes, to push into dense form */ for (u = max_compact; u < (max_compact * 2); u++) { /* Create attribute */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); attr = H5Acreate_by_name(fid, dsetname, attrname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); CHECK(attr, FAIL, "H5Acreate_by_name"); @@ -8570,7 +8573,7 @@ test_attr_shared_write(hid_t fcpl, hid_t fapl) /* Add attributes to each dataset, until after converting to dense storage */ for (u = 0; u < max_compact * 2; u++) { /* Create attribute name */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); /* Alternate between creating "small" & "big" attributes */ if (u % 2) { @@ -8907,7 +8910,7 @@ test_attr_shared_rename(hid_t fcpl, hid_t fapl) /* Add attributes to each dataset, until after converting to dense storage */ for (u = 0; u < max_compact * 2; u++) { /* Create attribute name */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); /* Alternate between creating "small" & "big" attributes */ if (u % 2) { @@ -9354,7 +9357,7 @@ test_attr_shared_delete(hid_t fcpl, hid_t fapl) /* Add attributes to each dataset, until after converting to dense storage */ for (u = 0; u < max_compact * 2; u++) { /* Create attribute name */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); /* Alternate between creating "small" & "big" attributes */ if (u % 2) { @@ -9462,7 +9465,7 @@ test_attr_shared_delete(hid_t fcpl, hid_t fapl) /* Delete attributes from second dataset */ for (u = 0; u < max_compact * 2; u++) { /* Create attribute name */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); /* Delete second dataset's attribute */ ret = H5Adelete_by_name(fid, DSET2_NAME, attrname, H5P_DEFAULT); @@ -9726,7 +9729,7 @@ test_attr_shared_unlink(hid_t fcpl, hid_t fapl) /* Add attributes to each dataset, until after converting to dense storage */ for (u = 0; u < max_compact * 2; u++) { /* Create attribute name */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); /* Alternate between creating "small" & "big" attributes */ if (u % 2) { @@ -9850,7 +9853,7 @@ test_attr_shared_unlink(hid_t fcpl, hid_t fapl) /* Check ref count on attributes of first dataset */ for (u = 0; u < max_compact * 2; u++) { /* Create attribute name */ - HDsprintf(attrname, "attr %02u", u); + HDsnprintf(attrname, sizeof(attrname), "attr %02u", u); /* Open attribute on first dataset */ attr = H5Aopen(dataset, attrname, H5P_DEFAULT); diff --git a/test/tmisc.c b/test/tmisc.c index a28e12e..f8bf602 100644 --- a/test/tmisc.c +++ b/test/tmisc.c @@ -1083,7 +1083,7 @@ test_misc6(void) /* Loop through adding attributes to each dataset */ for (u = 0; u < MISC6_NUMATTR; u++) { /* Create name for attribute */ - HDsprintf(attr_name, "Attr#%u", u); + HDsnprintf(attr_name, sizeof(attr_name), "Attr#%u", u); /* Open the file */ loc_id = H5Fopen(MISC6_FILE, H5F_ACC_RDWR, H5P_DEFAULT); @@ -3034,7 +3034,7 @@ test_misc18(void) /* Loop creating attributes on each dataset, flushing them to the file each time */ for (u = 0; u < 10; u++) { /* Set up attribute name */ - HDsprintf(attr_name, "Attr %u", u); + HDsnprintf(attr_name, sizeof(attr_name), "Attr %u", u); /* Create & close attribute on first dataset */ aid = H5Acreate2(did1, attr_name, H5T_STD_U32LE, sid, H5P_DEFAULT, H5P_DEFAULT); @@ -5504,7 +5504,7 @@ test_misc30(void) CHECK(ret, FAIL, "test_misc30_get_info"); } - HDsprintf(gname, "/g0/group%d", i); + HDsnprintf(gname, sizeof(gname), "/g0/group%d", i); gid = H5Gcreate2(fid, gname, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); CHECK(gid, FAIL, "H5Gcreate2"); diff --git a/test/trefstr.c b/test/trefstr.c index d0575ab..89e62db 100644 --- a/test/trefstr.c +++ b/test/trefstr.c @@ -309,7 +309,7 @@ test_refstr_asprintf_cat(void) /* Get pointer to raw string in ref-counted string */ s = H5RS_get_str(rs); CHECK_PTR(s, "H5RS_get_str"); - HDsprintf(buf, "%d-%s", (int)10, "foo"); + HDsnprintf(buf, sizeof(buf), "%d-%s", (int)10, "foo"); cmp = HDstrcmp(s, buf); VERIFY(cmp, 0, "HDstrcmp"); @@ -320,7 +320,7 @@ test_refstr_asprintf_cat(void) /* Get pointer to raw string in ref-counted string */ s = H5RS_get_str(rs); CHECK_PTR(s, "H5RS_get_str"); - HDsprintf(buf, "%d-%s-%f", (int)10, "foo", (double)20.0); + HDsnprintf(buf, sizeof(buf), "%d-%s-%f", (int)10, "foo", (double)20.0); cmp = HDstrcmp(s, buf); VERIFY(cmp, 0, "HDstrcmp"); @@ -360,7 +360,7 @@ test_refstr_acat(void) /* Get pointer to raw string in ref-counted string */ s = H5RS_get_str(rs); CHECK_PTR(s, "H5RS_get_str"); - HDsprintf(buf, "%s", "foo"); + HDsnprintf(buf, sizeof(buf), "%s", "foo"); cmp = HDstrcmp(s, buf); VERIFY(cmp, 0, "HDstrcmp"); @@ -371,7 +371,7 @@ test_refstr_acat(void) /* Get pointer to raw string in ref-counted string */ s = H5RS_get_str(rs); CHECK_PTR(s, "H5RS_get_str"); - HDsprintf(buf, "%s", "foobar"); + HDsnprintf(buf, sizeof(buf), "%s", "foobar"); cmp = HDstrcmp(s, buf); VERIFY(cmp, 0, "HDstrcmp"); @@ -386,7 +386,7 @@ test_refstr_acat(void) /* Get pointer to raw string in ref-counted string */ s = H5RS_get_str(rs); CHECK_PTR(s, "H5RS_get_str"); - HDsprintf(buf, "%s", "foobar"); + HDsnprintf(buf, sizeof(buf), "%s", "foobar"); large_str2 = HDmalloc(1024 + 6); CHECK_PTR(large_str2, "HDmalloc"); HDstrcpy(large_str2, "foobar"); diff --git a/test/tselect.c b/test/tselect.c index d9b625b..0d4176b 100644 --- a/test/tselect.c +++ b/test/tselect.c @@ -10862,13 +10862,15 @@ test_shape_same_dr__full_space_vs_slice(int test_num, int small_rank, int large_ HDassert(edge_size > 0); HDassert(edge_size <= 1000); - HDsprintf(test_desc_0, "\tn-cube slice through m-cube (n <= m) test %d.\n", test_num); + HDsnprintf(test_desc_0, sizeof(test_desc_0), "\tn-cube slice through m-cube (n <= m) test %d.\n", + test_num); MESSAGE(7, (test_desc_0)); /* This statement must be updated if SS_DR_MAX_RANK is changed */ - HDsprintf(test_desc_1, "\t\tranks: %d/%d offset: %d dim_selected: %d/%d/%d/%d/%d.\n", small_rank, - large_rank, offset, (int)dim_selected[0], (int)dim_selected[1], (int)dim_selected[2], - (int)dim_selected[3], (int)dim_selected[4]); + HDsnprintf(test_desc_1, sizeof(test_desc_1), + "\t\tranks: %d/%d offset: %d dim_selected: %d/%d/%d/%d/%d.\n", small_rank, large_rank, offset, + (int)dim_selected[0], (int)dim_selected[1], (int)dim_selected[2], (int)dim_selected[3], + (int)dim_selected[4]); MESSAGE(7, (test_desc_1)); /* copy the edge size into the dims array */ @@ -11120,15 +11122,16 @@ test_shape_same_dr__checkerboard(int test_num, int small_rank, int large_rank, i HDassert(dims_selected >= 0); HDassert(dims_selected <= large_rank); - HDsprintf(test_desc_0, "\tcheckerboard n-cube slice through m-cube (n <= m) test %d.\n", test_num); + HDsnprintf(test_desc_0, sizeof(test_desc_0), + "\tcheckerboard n-cube slice through m-cube (n <= m) test %d.\n", test_num); MESSAGE(7, (test_desc_0)); /* This statement must be updated if SS_DR_MAX_RANK is changed */ - HDsprintf(test_desc_1, - "\tranks: %d/%d edge/chkr size: %d/%d offset: %d dim_selected: %d/%d/%d/%d/%d:%d.\n", - small_rank, large_rank, (int)edge_size, (int)checker_size, offset, (int)dim_selected[0], - (int)dim_selected[1], (int)dim_selected[2], (int)dim_selected[3], (int)dim_selected[4], - dims_selected); + HDsnprintf(test_desc_1, sizeof(test_desc_1), + "\tranks: %d/%d edge/chkr size: %d/%d offset: %d dim_selected: %d/%d/%d/%d/%d:%d.\n", + small_rank, large_rank, (int)edge_size, (int)checker_size, offset, (int)dim_selected[0], + (int)dim_selected[1], (int)dim_selected[2], (int)dim_selected[3], (int)dim_selected[4], + dims_selected); MESSAGE(7, (test_desc_1)); /* copy the edge size into the dims array */ @@ -11664,15 +11667,16 @@ test_shape_same_dr__irregular(int test_num, int small_rank, int large_rank, int HDassert(dims_selected >= 0); HDassert(dims_selected <= large_rank); - HDsprintf(test_desc_0, "\tirregular sub set of n-cube slice through m-cube (n <= m) test %d.\n", - test_num); + HDsnprintf(test_desc_0, sizeof(test_desc_0), + "\tirregular sub set of n-cube slice through m-cube (n <= m) test %d.\n", test_num); MESSAGE(7, (test_desc_0)); /* This statement must be updated if SS_DR_MAX_RANK is changed */ - HDsprintf(test_desc_1, "\tranks: %d/%d edge: %d s/p offset: %d/%d dim_selected: %d/%d/%d/%d/%d:%d.\n", - small_rank, large_rank, edge_size, slice_offset, pattern_offset, (int)dim_selected[0], - (int)dim_selected[1], (int)dim_selected[2], (int)dim_selected[3], (int)dim_selected[4], - dims_selected); + HDsnprintf(test_desc_1, sizeof(test_desc_1), + "\tranks: %d/%d edge: %d s/p offset: %d/%d dim_selected: %d/%d/%d/%d/%d:%d.\n", small_rank, + large_rank, edge_size, slice_offset, pattern_offset, (int)dim_selected[0], + (int)dim_selected[1], (int)dim_selected[2], (int)dim_selected[3], (int)dim_selected[4], + dims_selected); MESSAGE(7, (test_desc_1)); /* copy the edge size into the dims array */ diff --git a/test/tvlstr.c b/test/tvlstr.c index 68f6124..5168d39 100644 --- a/test/tvlstr.c +++ b/test/tvlstr.c @@ -817,33 +817,33 @@ test_vl_rewrite(void) /* Create in file 1 */ for (i = 0; i < REWRITE_NDATASETS; i++) { - HDsprintf(name, "/set_%d", i); + HDsnprintf(name, sizeof(name), "/set_%d", i); write_scalar_dset(file1, type, space, name, name); } /* Effectively copy data from file 1 to 2 */ for (i = 0; i < REWRITE_NDATASETS; i++) { - HDsprintf(name, "/set_%d", i); + HDsnprintf(name, sizeof(name), "/set_%d", i); read_scalar_dset(file1, type, space, name, name); write_scalar_dset(file2, type, space, name, name); } /* Read back from file 2 */ for (i = 0; i < REWRITE_NDATASETS; i++) { - HDsprintf(name, "/set_%d", i); + HDsnprintf(name, sizeof(name), "/set_%d", i); read_scalar_dset(file2, type, space, name, name); } /* end for */ /* Remove from file 2. */ for (i = 0; i < REWRITE_NDATASETS; i++) { - HDsprintf(name, "/set_%d", i); + HDsnprintf(name, sizeof(name), "/set_%d", i); ret = H5Ldelete(file2, name, H5P_DEFAULT); CHECK(ret, FAIL, "H5Ldelete"); } /* end for */ /* Effectively copy from file 1 to file 2 */ for (i = 0; i < REWRITE_NDATASETS; i++) { - HDsprintf(name, "/set_%d", i); + HDsnprintf(name, sizeof(name), "/set_%d", i); read_scalar_dset(file1, type, space, name, name); write_scalar_dset(file2, type, space, name, name); } /* end for */ diff --git a/test/vds_env.c b/test/vds_env.c index 17c3876..e01f2e0 100644 --- a/test/vds_env.c +++ b/test/vds_env.c @@ -346,8 +346,9 @@ main(void) /* Display testing info */ low_string = h5_get_version_string(low); high_string = h5_get_version_string(high); - HDsprintf(msg, "Testing virtual dataset with file version bounds: (%s, %s):", low_string, - high_string); + HDsnprintf(msg, sizeof(msg), + "Testing virtual dataset with file version bounds: (%s, %s):", low_string, + high_string); HDputs(msg); for (bit_config = 0; bit_config < TEST_IO_NTESTS; bit_config++) { diff --git a/testpar/t_2Gio.c b/testpar/t_2Gio.c index 2be4ae4..911be2c 100644 --- a/testpar/t_2Gio.c +++ b/testpar/t_2Gio.c @@ -3047,7 +3047,7 @@ compress_readAll(void) nerrors++; } -#if MPI_VERSION >= 3 +#ifdef H5_HAVE_PARALLEL_FILTERED_WRITES ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, xfer_plist, data_read); VRFY((ret >= 0), "H5Dwrite succeeded"); #endif @@ -3853,12 +3853,6 @@ actual_io_mode_tests(void) * TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL: * Test for Externl-File storage as the cause of breaking collective I/O. * - * TEST_FILTERS: - * Test for using filter (checksum) as the cause of breaking collective I/O. - * Note: TEST_FILTERS mode will not work until H5Dcreate and H5write is supported for mpio and filter - * feature. Use test_no_collective_cause_mode_filter() function instead. - * - * * Programmer: Jonathan Kim * Date: Aug, 2012 */ @@ -3898,9 +3892,6 @@ test_no_collective_cause_mode(int selection_mode) hid_t file_space = -1; hsize_t chunk_dims[MAX_RANK]; herr_t ret; -#ifdef LATER /* fletcher32 */ - H5Z_filter_t filter_info; -#endif /* LATER */ /* set to global value as default */ int l_facc_type = facc_type; char message[256]; @@ -3932,21 +3923,6 @@ test_no_collective_cause_mode(int selection_mode) is_chunked = 0; } -#ifdef LATER /* fletcher32 */ - if (selection_mode & TEST_FILTERS) { - ret = H5Zfilter_avail(H5Z_FILTER_FLETCHER32); - VRFY((ret >= 0), "Fletcher32 filter is available.\n"); - - ret = H5Zget_filter_info(H5Z_FILTER_FLETCHER32, &filter_info); - VRFY(((filter_info & H5Z_FILTER_CONFIG_ENCODE_ENABLED) || - (filter_info & H5Z_FILTER_CONFIG_DECODE_ENABLED)), - "Fletcher32 filter encoding and decoding available.\n"); - - ret = H5Pset_fletcher32(dcpl); - VRFY((ret >= 0), "set filter (flecher32) succeeded"); - } -#endif /* LATER */ - if (selection_mode & TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES) { sid = H5Screate(H5S_NULL); VRFY((sid >= 0), "H5Screate_simple succeeded"); @@ -4022,14 +3998,6 @@ test_no_collective_cause_mode(int selection_mode) no_collective_cause_global_expected |= H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET; } -#ifdef LATER /* fletcher32 */ - if (selection_mode & TEST_FILTERS) { - test_name = "Broken Collective I/O - Filter is required"; - no_collective_cause_local_expected |= H5D_MPIO_FILTERS; - no_collective_cause_global_expected |= H5D_MPIO_FILTERS; - } -#endif /* LATER */ - if (selection_mode & TEST_COLLECTIVE) { test_name = "Broken Collective I/O - Not Broken"; no_collective_cause_local_expected = H5D_MPIO_COLLECTIVE; @@ -4166,240 +4134,6 @@ test_no_collective_cause_mode(int selection_mode) return; } -#if 0 -/* - * Function: test_no_collective_cause_mode_filter - * - * Purpose: - * Test specific for using filter as a caus of broken collective I/O and - * checks that the H5Pget_mpio_no_collective_cause properties in the DXPL - * have the correct values. - * - * NOTE: - * This is a temporary function. - * test_no_collective_cause_mode(TEST_FILTERS) will replace this when - * H5Dcreate and H5write support for mpio and filter feature. - * - * Input: - * TEST_FILTERS_READ: - * Test for using filter (checksum) as the cause of breaking collective I/O. - * - * Programmer: Jonathan Kim - * Date: Aug, 2012 - */ -static void -test_no_collective_cause_mode_filter(int selection_mode) -{ - uint32_t no_collective_cause_local_read = 0; - uint32_t no_collective_cause_local_expected = 0; - uint32_t no_collective_cause_global_read = 0; - uint32_t no_collective_cause_global_expected = 0; - - const char * filename; - const char * test_name; - hbool_t is_chunked=1; - int mpi_size = -1; - int mpi_rank = -1; - int length; - int * buffer; - int i; - MPI_Comm mpi_comm = MPI_COMM_NULL; - MPI_Info mpi_info = MPI_INFO_NULL; - hid_t fid = -1; - hid_t sid = -1; - hid_t dataset = -1; - hid_t data_type = H5T_NATIVE_INT; - hid_t fapl_write = -1; - hid_t fapl_read = -1; - hid_t dcpl = -1; - hid_t dxpl = -1; - hsize_t dims[MAX_RANK]; - hid_t mem_space = -1; - hid_t file_space = -1; - hsize_t chunk_dims[MAX_RANK]; - herr_t ret; -#ifdef LATER /* fletcher32 */ - H5Z_filter_t filter_info; -#endif /* LATER */ - char message[256]; - - /* Set up MPI parameters */ - MPI_Comm_size(test_comm, &mpi_size); - MPI_Comm_rank(test_comm, &mpi_rank); - - MPI_Barrier(test_comm); - - HDassert(mpi_size >= 1); - - mpi_comm = test_comm; - mpi_info = MPI_INFO_NULL; - - /* Create the dataset creation plist */ - dcpl = H5Pcreate(H5P_DATASET_CREATE); - VRFY((dcpl >= 0), "dataset creation plist created successfully"); - - if (selection_mode == TEST_FILTERS_READ ) { -#ifdef LATER /* fletcher32 */ - ret = H5Zfilter_avail(H5Z_FILTER_FLETCHER32); - VRFY ((ret >=0 ), "Fletcher32 filter is available.\n"); - - ret = H5Zget_filter_info (H5Z_FILTER_FLETCHER32, (unsigned int *) &filter_info); - VRFY ( ( (filter_info & H5Z_FILTER_CONFIG_ENCODE_ENABLED) || (filter_info & H5Z_FILTER_CONFIG_DECODE_ENABLED) ) , "Fletcher32 filter encoding and decoding available.\n"); - - ret = H5Pset_fletcher32(dcpl); - VRFY((ret >= 0),"set filter (flecher32) succeeded"); -#endif /* LATER */ - } - else { - VRFY(0, "Unexpected mode, only test for TEST_FILTERS_READ."); - } - - /* Create the basic Space */ - dims[0] = dim0; - dims[1] = dim1; - sid = H5Screate_simple (MAX_RANK, dims, NULL); - VRFY((sid >= 0), "H5Screate_simple succeeded"); - - - filename = (const char *)GetTestParameters(); - HDassert(filename != NULL); - - /* Setup the file access template */ - fapl_write = create_faccess_plist(mpi_comm, mpi_info, FACC_DEFAULT); - VRFY((fapl_write >= 0), "create_faccess_plist() succeeded"); - - fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_write); - VRFY((fid >= 0), "H5Fcreate succeeded"); - - /* If we are not testing contiguous datasets */ - if(is_chunked) { - /* Set up chunk information. */ - chunk_dims[0] = dims[0]/mpi_size; - chunk_dims[1] = dims[1]; - ret = H5Pset_chunk(dcpl, 2, chunk_dims); - VRFY((ret >= 0),"chunk creation property list succeeded"); - } - - - /* Create the dataset */ - dataset = H5Dcreate2(fid, DSET_NOCOLCAUSE, data_type, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT); - VRFY((dataset >= 0), "H5Dcreate2() dataset succeeded"); - -#ifdef LATER /* fletcher32 */ - /* Set expected cause */ - test_name = "Broken Collective I/O - Filter is required"; - no_collective_cause_local_expected = H5D_MPIO_FILTERS; - no_collective_cause_global_expected = H5D_MPIO_FILTERS; -#endif /* LATER */ - - /* Get the file dataspace */ - file_space = H5Dget_space(dataset); - VRFY((file_space >= 0), "H5Dget_space succeeded"); - - /* Create the memory dataspace */ - mem_space = H5Screate_simple (MAX_RANK, dims, NULL); - VRFY((mem_space >= 0), "mem_space created"); - - /* Get the number of elements in the selection */ - length = dim0 * dim1; - - /* Allocate and initialize the buffer */ - buffer = (int *)HDmalloc(sizeof(int) * length); - VRFY((buffer != NULL), "HDmalloc of buffer succeeded"); - for(i = 0; i < length; i++) - buffer[i] = i; - - /* Set up the dxpl for the write */ - dxpl = H5Pcreate(H5P_DATASET_XFER); - VRFY((dxpl >= 0), "H5Pcreate(H5P_DATASET_XFER) succeeded"); - - if (selection_mode == TEST_FILTERS_READ) { - /* To test read in collective I/O mode , write in independent mode - * because write fails with mpio + filter */ - ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_INDEPENDENT); - VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); - } - else { - /* To test write in collective I/O mode. */ - ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE); - VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); - } - - - /* Write */ - ret = H5Dwrite(dataset, data_type, mem_space, file_space, dxpl, buffer); - - if(ret < 0) H5Eprint2(H5E_DEFAULT, stdout); - VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded"); - - - /* Make a copy of the dxpl to test the read operation */ - dxpl = H5Pcopy(dxpl); - VRFY((dxpl >= 0), "H5Pcopy succeeded"); - - if (dataset) - H5Dclose(dataset); - if (fapl_write) - H5Pclose(fapl_write); - if (fid) - H5Fclose(fid); - - - /*--------------------- - * Test Read access - *---------------------*/ - - /* Setup the file access template */ - fapl_read = create_faccess_plist(mpi_comm, mpi_info, facc_type); - VRFY((fapl_read >= 0), "create_faccess_plist() succeeded"); - - fid = H5Fopen (filename, H5F_ACC_RDONLY, fapl_read); - dataset = H5Dopen2 (fid, DSET_NOCOLCAUSE, H5P_DEFAULT); - - /* Set collective I/O properties in the dxpl. */ - ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE); - VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); - - /* Read */ - ret = H5Dread(dataset, data_type, mem_space, file_space, dxpl, buffer); - - if(ret < 0) H5Eprint2(H5E_DEFAULT, stdout); - VRFY((ret >= 0), "H5Dread() dataset multichunk read succeeded"); - - /* Get the cause of broken collective I/O */ - ret = H5Pget_mpio_no_collective_cause (dxpl, &no_collective_cause_local_read, &no_collective_cause_global_read); - VRFY((ret >= 0), "retrieving no collective cause succeeded" ); - - /* Test values */ - HDmemset (message, 0, sizeof (message)); - HDsprintf(message, "Local cause of Broken Collective I/O has the correct value for %s.\n",test_name); - VRFY((no_collective_cause_local_read == (uint32_t)no_collective_cause_local_expected), message); - HDmemset (message, 0, sizeof (message)); - HDsprintf(message, "Global cause of Broken Collective I/O has the correct value for %s.\n",test_name); - VRFY((no_collective_cause_global_read == (uint32_t)no_collective_cause_global_expected), message); - - /* Release some resources */ - if (sid) - H5Sclose(sid); - if (fapl_read) - H5Pclose(fapl_read); - if (dcpl) - H5Pclose(dcpl); - if (dxpl) - H5Pclose(dxpl); - if (dataset) - H5Dclose(dataset); - if (mem_space) - H5Sclose(mem_space); - if (file_space) - H5Sclose(file_space); - if (fid) - H5Fclose(fid); - HDfree(buffer); - return; -} -#endif - /* Function: no_collective_cause_tests * * Purpose: Tests cases for broken collective IO. @@ -4420,13 +4154,6 @@ no_collective_cause_tests(void) test_no_collective_cause_mode(TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES); test_no_collective_cause_mode(TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT); test_no_collective_cause_mode(TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL); -#ifdef LATER /* fletcher32 */ - /* TODO: use this instead of below TEST_FILTERS_READ when H5Dcreate and - * H5Dwrite is ready for mpio + filter feature. - */ - /* test_no_collective_cause_mode (TEST_FILTERS); */ - test_no_collective_cause_mode_filter(TEST_FILTERS_READ); -#endif /* LATER */ /* * Test combined causes diff --git a/testpar/t_bigio.c b/testpar/t_bigio.c index 4df624b..0a971c5 100644 --- a/testpar/t_bigio.c +++ b/testpar/t_bigio.c @@ -1107,13 +1107,15 @@ single_rank_independent_io(void) HDprintf("\nSingle Rank Independent I/O\n"); if (MAIN_PROCESS) { - hsize_t dims[] = {LARGE_DIM}; - hid_t file_id = -1; - hid_t fapl_id = -1; - hid_t dset_id = -1; - hid_t fspace_id = -1; - hid_t mspace_id = -1; - void * data = NULL; + hsize_t dims[] = {LARGE_DIM}; + hid_t file_id = -1; + hid_t fapl_id = -1; + hid_t dset_id = -1; + hid_t fspace_id = -1; + hid_t mspace_id = -1; + herr_t ret; + int * data = NULL; + uint64_t i; fapl_id = H5Pcreate(H5P_FILE_ACCESS); VRFY_G((fapl_id >= 0), "H5P_FILE_ACCESS"); @@ -1135,6 +1137,10 @@ single_rank_independent_io(void) data = malloc(LARGE_DIM * sizeof(int)); + /* Initialize data */ + for (i = 0; i < LARGE_DIM; i++) + data[i] = (int)(i % (uint64_t)DXFER_BIGCOUNT); + if (mpi_rank_g == 0) H5Sselect_all(fspace_id); else @@ -1143,7 +1149,24 @@ single_rank_independent_io(void) dims[0] = LARGE_DIM; mspace_id = H5Screate_simple(1, dims, NULL); VRFY_G((mspace_id >= 0), "H5Screate_simple mspace_id succeeded"); + + /* Write data */ H5Dwrite(dset_id, H5T_NATIVE_INT, mspace_id, fspace_id, H5P_DEFAULT, data); + VRFY_G((ret >= 0), "H5Dwrite succeeded"); + + /* Wipe buffer */ + HDmemset(data, 0, LARGE_DIM * sizeof(int)); + + /* Read data back */ + H5Dread(dset_id, H5T_NATIVE_INT, mspace_id, fspace_id, H5P_DEFAULT, data); + VRFY_G((ret >= 0), "H5Dread succeeded"); + + /* Verify data */ + for (i = 0; i < LARGE_DIM; i++) + if (data[i] != (int)(i % (uint64_t)DXFER_BIGCOUNT)) { + HDfprintf(stderr, "verify failed\n"); + exit(1); + } free(data); H5Sclose(mspace_id); diff --git a/testpar/t_cache.c b/testpar/t_cache.c index 8c96756..70ada01 100644 --- a/testpar/t_cache.c +++ b/testpar/t_cache.c @@ -6488,7 +6488,7 @@ trace_file_check(int metadata_write_strategy) } /* end if */ if (nerrors == 0) { - HDsprintf(trace_file_name, "t_cache_trace.txt.%d", (int)file_mpi_rank); + HDsnprintf(trace_file_name, sizeof(trace_file_name), "t_cache_trace.txt.%d", (int)file_mpi_rank); if ((trace_file_ptr = HDfopen(trace_file_name, "r")) == NULL) { @@ -6623,13 +6623,15 @@ trace_file_check(int metadata_write_strategy) static hbool_t smoke_check_6(int metadata_write_strategy) { - hbool_t success = TRUE; - int i; - int max_nerrors; - hid_t fid = -1; - H5F_t * file_ptr = NULL; - H5C_t * cache_ptr = NULL; - struct mssg_t mssg; + H5P_coll_md_read_flag_t md_reads_file_flag; + hbool_t md_reads_context_flag; + hbool_t success = TRUE; + int i; + int max_nerrors; + hid_t fid = -1; + H5F_t * file_ptr = NULL; + H5C_t * cache_ptr = NULL; + struct mssg_t mssg; switch (metadata_write_strategy) { @@ -6685,7 +6687,9 @@ smoke_check_6(int metadata_write_strategy) virt_num_data_entries = NUM_DATA_ENTRIES; /* insert the first half collectively */ - H5CX_set_coll_metadata_read(TRUE); + md_reads_file_flag = H5P_USER_TRUE; + md_reads_context_flag = TRUE; + H5F_set_coll_metadata_reads(file_ptr, &md_reads_file_flag, &md_reads_context_flag); for (i = 0; i < virt_num_data_entries / 2; i++) { struct datum *entry_ptr; entry_ptr = &(data[i]); @@ -6704,9 +6708,13 @@ smoke_check_6(int metadata_write_strategy) H5_CHECK_OVERFLOW(cache_ptr->max_cache_size, size_t, double); HDassert((double)cache_ptr->max_cache_size * 0.8 > cache_ptr->coll_list_size); } + /* Restore collective metadata reads state */ + H5F_set_coll_metadata_reads(file_ptr, &md_reads_file_flag, &md_reads_context_flag); /* insert the other half independently */ - H5CX_set_coll_metadata_read(FALSE); + md_reads_file_flag = H5P_USER_FALSE; + md_reads_context_flag = FALSE; + H5F_set_coll_metadata_reads(file_ptr, &md_reads_file_flag, &md_reads_context_flag); for (i = virt_num_data_entries / 2; i < virt_num_data_entries; i++) { struct datum *entry_ptr; entry_ptr = &(data[i]); @@ -6724,6 +6732,8 @@ smoke_check_6(int metadata_write_strategy) /* Make sure coll entries do not cross the 80% threshold */ HDassert((double)cache_ptr->max_cache_size * 0.8 > cache_ptr->coll_list_size); } + /* Restore collective metadata reads state */ + H5F_set_coll_metadata_reads(file_ptr, &md_reads_file_flag, &md_reads_context_flag); /* flush the file */ if (H5Fflush(fid, H5F_SCOPE_GLOBAL) < 0) { @@ -6734,7 +6744,9 @@ smoke_check_6(int metadata_write_strategy) } /* Protect the first half of the entries collectively */ - H5CX_set_coll_metadata_read(TRUE); + md_reads_file_flag = H5P_USER_TRUE; + md_reads_context_flag = TRUE; + H5F_set_coll_metadata_reads(file_ptr, &md_reads_file_flag, &md_reads_context_flag); for (i = 0; i < (virt_num_data_entries / 2); i++) { struct datum *entry_ptr; entry_ptr = &(data[i]); @@ -6752,9 +6764,13 @@ smoke_check_6(int metadata_write_strategy) /* Make sure coll entries do not cross the 80% threshold */ HDassert((double)cache_ptr->max_cache_size * 0.8 > cache_ptr->coll_list_size); } + /* Restore collective metadata reads state */ + H5F_set_coll_metadata_reads(file_ptr, &md_reads_file_flag, &md_reads_context_flag); /* protect the other half independently */ - H5CX_set_coll_metadata_read(FALSE); + md_reads_file_flag = H5P_USER_FALSE; + md_reads_context_flag = FALSE; + H5F_set_coll_metadata_reads(file_ptr, &md_reads_file_flag, &md_reads_context_flag); for (i = virt_num_data_entries / 2; i < virt_num_data_entries; i++) { struct datum *entry_ptr; entry_ptr = &(data[i]); @@ -6772,6 +6788,8 @@ smoke_check_6(int metadata_write_strategy) /* Make sure coll entries do not cross the 80% threshold */ HDassert((double)cache_ptr->max_cache_size * 0.8 > cache_ptr->coll_list_size); } + /* Restore collective metadata reads state */ + H5F_set_coll_metadata_reads(file_ptr, &md_reads_file_flag, &md_reads_context_flag); for (i = 0; i < (virt_num_data_entries); i++) { unlock_entry(file_ptr, i, H5AC__NO_FLAGS_SET); diff --git a/testpar/t_cache_image.c b/testpar/t_cache_image.c index feb4325..4229a77 100644 --- a/testpar/t_cache_image.c +++ b/testpar/t_cache_image.c @@ -477,7 +477,7 @@ create_data_sets(hid_t file_id, int min_dset, int max_dset) /* create the dataset */ if (pass) { - HDsprintf(dset_name, "/dset%03d", i); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", i); dataset_ids[i] = H5Dcreate2(file_id, dset_name, H5T_STD_I32BE, dataspace_id, H5P_DEFAULT, properties, H5P_DEFAULT); @@ -766,7 +766,7 @@ delete_data_sets(hid_t file_id, int min_dset, int max_dset) while ( ( pass ) && ( i <= max_dset ) ) { - HDsprintf(dset_name, "/dset%03d", i); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", i); if ( H5Ldelete(file_id, dset_name, H5P_DEFAULT) < 0) { @@ -1334,7 +1334,7 @@ par_create_dataset(int dset_num, hid_t file_id, int mpi_rank, int mpi_size) show_progress = (show_progress && (mpi_rank == 0)); verbose = (verbose && (mpi_rank == 0)); - HDsprintf(dset_name, "/dset%03d", dset_num); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", dset_num); if (show_progress) { HDfprintf(stdout, "%s: dset name = \"%s\".\n", fcn_name, dset_name); @@ -1707,7 +1707,7 @@ par_delete_dataset(int dset_num, hid_t file_id, int mpi_rank) show_progress = (show_progress && (mpi_rank == 0)); - HDsprintf(dset_name, "/dset%03d", dset_num); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", dset_num); if (show_progress) { HDfprintf(stdout, "%s: dset name = \"%s\".\n", fcn_name, dset_name); @@ -1840,7 +1840,7 @@ par_verify_dataset(int dset_num, hid_t file_id, int mpi_rank) show_progress = (show_progress && (mpi_rank == 0)); verbose = (verbose && (mpi_rank == 0)); - HDsprintf(dset_name, "/dset%03d", dset_num); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", dset_num); if (show_progress) { HDfprintf(stdout, "%s: dset name = \"%s\".\n", fcn_name, dset_name); @@ -2208,7 +2208,7 @@ serial_verify_dataset(int dset_num, hid_t file_id, int mpi_size) hid_t dset_id = -1; hid_t filespace_id = -1; - HDsprintf(dset_name, "/dset%03d", dset_num); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", dset_num); if (show_progress) { HDfprintf(stdout, "%s: dset name = \"%s\".\n", fcn_name, dset_name); @@ -2460,7 +2460,7 @@ verify_data_sets(hid_t file_id, int min_dset, int max_dset) /* open the dataset */ if (pass) { - HDsprintf(dset_name, "/dset%03d", i); + HDsnprintf(dset_name, sizeof(dset_name), "/dset%03d", i); dataset_ids[i] = H5Dopen2(file_id, dset_name, H5P_DEFAULT); if (dataset_ids[i] < 0) { diff --git a/testpar/t_coll_md_read.c b/testpar/t_coll_md_read.c index 66f3151..cabdea0 100644 --- a/testpar/t_coll_md_read.c +++ b/testpar/t_coll_md_read.c @@ -34,10 +34,9 @@ #define MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS 2 -#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DATASET_NAME "linked_chunk_io_sort_chunk_issue" -#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_Y_DIM_SCALE 20000 -#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE 1 -#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS 1 +#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_COLL_THRESH_NUM 10000 +#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DATASET_NAME "linked_chunk_io_sort_chunk_issue" +#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS 1 /* * A test for issue HDFFV-10501. A parallel hang was reported which occurred @@ -339,21 +338,34 @@ test_multi_chunk_io_addrmap_issue(void) * collective metadata reads being made only by process 0 in H5D__sort_chunk(). * * NOTE: Due to the way that the threshold value which pertains to this test - * is currently calculated within HDF5, there are several conditions that this - * test must maintain. Refer to the function H5D__sort_chunk in H5Dmpio.c for - * a better idea of why. + * is currently calculated within HDF5, the following two conditions must be + * true to trigger the issue: * - * Condition 1: We need to make sure that the test always selects every single - * chunk in the dataset. It is fine if the selection is split up among multiple - * ranks, but their combined selection must cover the whole dataset. + * Condition 1: A certain threshold ratio must be met in order to have HDF5 + * obtain all chunk addresses collectively inside H5D__sort_chunk(). This is + * given by the following: * - * Condition 2: The number of chunks in the dataset divided by the number of MPI - * ranks must exceed or equal 10000. In other words, each MPI rank must be - * responsible for 10000 or more unique chunks. + * (sum_chunk * 100) / (dataset_nchunks * mpi_size) >= 30% * - * Condition 3: This test will currently only be reliably reproducible for 2 or 3 - * MPI ranks. The threshold value calculated reduces to a constant 100 / mpi_size, - * and is compared against a default value of 30%. + * where: + * * `sum_chunk` is the combined sum of the number of chunks selected in + * the dataset by all ranks (chunks selected by more than one rank count + * individually toward the sum for each rank selecting that chunk) + * * `dataset_nchunks` is the number of chunks in the dataset (selected + * or not) + * * `mpi_size` is the size of the MPI Communicator + * + * Condition 2: `sum_chunk` divided by `mpi_size` must exceed or equal a certain + * threshold (as of this writing, 10000). + * + * To satisfy both these conditions, we #define a macro, + * LINK_CHUNK_IO_SORT_CHUNK_ISSUE_COLL_THRESH_NUM, which corresponds to the + * value of the H5D_ALL_CHUNK_ADDR_THRES_COL_NUM macro in H5Dmpio.c (the + * 10000 threshold from condition 2). We then create a dataset of that many + * chunks and have each MPI rank write to and read from a piece of every single + * chunk in the dataset. This ensures chunk utilization is the max possible + * and exceeds our 30% target ratio, while always exactly matching the numeric + * chunk threshold value of condition 2. * * Failure in this test may either cause a hang, or, due to how the MPI calls * pertaining to this issue might mistakenly match up, may cause an MPI error @@ -375,10 +387,9 @@ void test_link_chunk_io_sort_chunk_issue(void) { const char *filename; - hsize_t * dataset_dims = NULL; - hsize_t max_dataset_dims[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS]; - hsize_t sel_dims[1]; - hsize_t chunk_dims[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS] = {LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS}; + hsize_t dataset_dims[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS]; + hsize_t sel_dims[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS]; + hsize_t chunk_dims[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS]; hsize_t start[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS]; hsize_t stride[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS]; hsize_t count[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS]; @@ -412,14 +423,13 @@ test_link_chunk_io_sort_chunk_issue(void) file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id); VRFY((file_id >= 0), "H5Fcreate succeeded"); - dataset_dims = HDmalloc(LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS * sizeof(*dataset_dims)); - VRFY((dataset_dims != NULL), "malloc succeeded"); - - dataset_dims[0] = (hsize_t)LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE * (hsize_t)mpi_size * - (hsize_t)LINK_CHUNK_IO_SORT_CHUNK_ISSUE_Y_DIM_SCALE; - max_dataset_dims[0] = H5S_UNLIMITED; + /* + * Create a one-dimensional dataset of exactly LINK_CHUNK_IO_SORT_CHUNK_ISSUE_COLL_THRESH_NUM + * chunks, where every rank writes to a piece of every single chunk to keep utilization high. + */ + dataset_dims[0] = (hsize_t)mpi_size * (hsize_t)LINK_CHUNK_IO_SORT_CHUNK_ISSUE_COLL_THRESH_NUM; - fspace_id = H5Screate_simple(LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS, dataset_dims, max_dataset_dims); + fspace_id = H5Screate_simple(LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS, dataset_dims, NULL); VRFY((fspace_id >= 0), "H5Screate_simple succeeded"); /* @@ -428,6 +438,9 @@ test_link_chunk_io_sort_chunk_issue(void) dcpl_id = H5Pcreate(H5P_DATASET_CREATE); VRFY((dcpl_id >= 0), "H5Pcreate succeeded"); + /* Chunk size is equal to MPI size since each rank writes to a piece of every chunk */ + chunk_dims[0] = (hsize_t)mpi_size; + VRFY((H5Pset_chunk(dcpl_id, LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS, chunk_dims) >= 0), "H5Pset_chunk succeeded"); @@ -437,23 +450,21 @@ test_link_chunk_io_sort_chunk_issue(void) /* * Setup hyperslab selection to split the dataset among the ranks. - * - * The ranks will write rows across the dataset. */ - stride[0] = LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE; - count[0] = (dataset_dims[0] / LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE) / (hsize_t)mpi_size; - start[0] = count[0] * (hsize_t)mpi_rank; - block[0] = LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE; + start[0] = (hsize_t)mpi_rank; + stride[0] = (hsize_t)mpi_size; + count[0] = LINK_CHUNK_IO_SORT_CHUNK_ISSUE_COLL_THRESH_NUM; + block[0] = 1; VRFY((H5Sselect_hyperslab(fspace_id, H5S_SELECT_SET, start, stride, count, block) >= 0), "H5Sselect_hyperslab succeeded"); - sel_dims[0] = count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE); + sel_dims[0] = count[0]; mspace_id = H5Screate_simple(1, sel_dims, NULL); VRFY((mspace_id >= 0), "H5Screate_simple succeeded"); - data = HDcalloc(1, count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE) * sizeof(int)); + data = HDcalloc(1, count[0] * sizeof(int)); VRFY((data != NULL), "calloc succeeded"); dxpl_id = H5Pcreate(H5P_DATASET_XFER); @@ -476,33 +487,25 @@ test_link_chunk_io_sort_chunk_issue(void) VRFY((H5Pset_dxpl_mpio_chunk_opt(dxpl_id, H5FD_MPIO_CHUNK_ONE_IO) >= 0), "H5Pset_dxpl_mpio_chunk_opt succeeded"); - read_buf = HDmalloc(count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE) * sizeof(int)); + read_buf = HDmalloc(count[0] * sizeof(int)); VRFY((read_buf != NULL), "malloc succeeded"); VRFY((H5Sselect_hyperslab(fspace_id, H5S_SELECT_SET, start, stride, count, block) >= 0), "H5Sselect_hyperslab succeeded"); - sel_dims[0] = count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE); + sel_dims[0] = count[0]; VRFY((H5Sclose(mspace_id) >= 0), "H5Sclose succeeded"); mspace_id = H5Screate_simple(1, sel_dims, NULL); VRFY((mspace_id >= 0), "H5Screate_simple succeeded"); - read_buf = HDrealloc(read_buf, count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE) * sizeof(int)); - VRFY((read_buf != NULL), "realloc succeeded"); - /* * Finally have each rank read their section of data back from the dataset. */ VRFY((H5Dread(dset_id, H5T_NATIVE_INT, mspace_id, fspace_id, dxpl_id, read_buf) >= 0), "H5Dread succeeded"); - if (dataset_dims) { - HDfree(dataset_dims); - dataset_dims = NULL; - } - if (data) { HDfree(data); data = NULL; diff --git a/testpar/t_dset.c b/testpar/t_dset.c index 9f922e3..8616bef 100644 --- a/testpar/t_dset.c +++ b/testpar/t_dset.c @@ -2605,7 +2605,7 @@ compress_readAll(void) nerrors++; } -#if MPI_VERSION >= 3 +#ifdef H5_HAVE_PARALLEL_FILTERED_WRITES ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, xfer_plist, data_read); VRFY((ret >= 0), "H5Dwrite succeeded"); #endif @@ -3418,12 +3418,6 @@ actual_io_mode_tests(void) * TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL: * Test for Externl-File storage as the cause of breaking collective I/O. * - * TEST_FILTERS: - * Test for using filter (checksum) as the cause of breaking collective I/O. - * Note: TEST_FILTERS mode will not work until H5Dcreate and H5write is supported for mpio and filter - * feature. Use test_no_collective_cause_mode_filter() function instead. - * - * * Programmer: Jonathan Kim * Date: Aug, 2012 */ @@ -3465,9 +3459,6 @@ test_no_collective_cause_mode(int selection_mode) hid_t file_space = -1; hsize_t chunk_dims[RANK]; herr_t ret; -#ifdef LATER /* fletcher32 */ - H5Z_filter_t filter_info; -#endif /* LATER */ /* set to global value as default */ int l_facc_type = facc_type; char message[256]; @@ -3499,21 +3490,6 @@ test_no_collective_cause_mode(int selection_mode) is_chunked = 0; } -#ifdef LATER /* fletcher32 */ - if (selection_mode & TEST_FILTERS) { - ret = H5Zfilter_avail(H5Z_FILTER_FLETCHER32); - VRFY((ret >= 0), "Fletcher32 filter is available.\n"); - - ret = H5Zget_filter_info(H5Z_FILTER_FLETCHER32, &filter_info); - VRFY(((filter_info & H5Z_FILTER_CONFIG_ENCODE_ENABLED) || - (filter_info & H5Z_FILTER_CONFIG_DECODE_ENABLED)), - "Fletcher32 filter encoding and decoding available.\n"); - - ret = H5Pset_fletcher32(dcpl); - VRFY((ret >= 0), "set filter (flecher32) succeeded"); - } -#endif /* LATER */ - if (selection_mode & TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES) { sid = H5Screate(H5S_NULL); VRFY((sid >= 0), "H5Screate_simple succeeded"); @@ -3589,14 +3565,6 @@ test_no_collective_cause_mode(int selection_mode) no_collective_cause_global_expected |= H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET; } -#ifdef LATER /* fletcher32 */ - if (selection_mode & TEST_FILTERS) { - test_name = "Broken Collective I/O - Filter is required"; - no_collective_cause_local_expected |= H5D_MPIO_FILTERS; - no_collective_cause_global_expected |= H5D_MPIO_FILTERS; - } -#endif /* LATER */ - if (selection_mode & TEST_COLLECTIVE) { test_name = "Broken Collective I/O - Not Broken"; no_collective_cause_local_expected = H5D_MPIO_COLLECTIVE; @@ -3699,10 +3667,12 @@ test_no_collective_cause_mode(int selection_mode) /* Test values */ HDmemset(message, 0, sizeof(message)); - HDsprintf(message, "Local cause of Broken Collective I/O has the correct value for %s.\n", test_name); + HDsnprintf(message, sizeof(message), + "Local cause of Broken Collective I/O has the correct value for %s.\n", test_name); VRFY((no_collective_cause_local_write == no_collective_cause_local_expected), message); HDmemset(message, 0, sizeof(message)); - HDsprintf(message, "Global cause of Broken Collective I/O has the correct value for %s.\n", test_name); + HDsnprintf(message, sizeof(message), + "Global cause of Broken Collective I/O has the correct value for %s.\n", test_name); VRFY((no_collective_cause_global_write == no_collective_cause_global_expected), message); /* Release some resources */ @@ -3733,240 +3703,6 @@ test_no_collective_cause_mode(int selection_mode) return; } -/* - * Function: test_no_collective_cause_mode_filter - * - * Purpose: - * Test specific for using filter as a caus of broken collective I/O and - * checks that the H5Pget_mpio_no_collective_cause properties in the DXPL - * have the correct values. - * - * NOTE: - * This is a temporary function. - * test_no_collective_cause_mode(TEST_FILTERS) will replace this when - * H5Dcreate and H5write support for mpio and filter feature. - * - * Input: - * TEST_FILTERS_READ: - * Test for using filter (checksum) as the cause of breaking collective I/O. - * - * Programmer: Jonathan Kim - * Date: Aug, 2012 - */ -#ifdef LATER -static void -test_no_collective_cause_mode_filter(int selection_mode) -{ - uint32_t no_collective_cause_local_read = 0; - uint32_t no_collective_cause_local_expected = 0; - uint32_t no_collective_cause_global_read = 0; - uint32_t no_collective_cause_global_expected = 0; - - const char *filename; - const char *test_name = "I/O"; - hbool_t is_chunked = 1; - int mpi_size = -1; - int mpi_rank = -1; - int length; - int * buffer; - int i; - MPI_Comm mpi_comm = MPI_COMM_NULL; - MPI_Info mpi_info = MPI_INFO_NULL; - hid_t fid = -1; - hid_t sid = -1; - hid_t dataset = -1; - hid_t data_type = H5T_NATIVE_INT; - hid_t fapl_write = -1; - hid_t fapl_read = -1; - hid_t dcpl = -1; - hid_t dxpl = -1; - hsize_t dims[RANK]; - hid_t mem_space = -1; - hid_t file_space = -1; - hsize_t chunk_dims[RANK]; - herr_t ret; -#ifdef LATER /* fletcher32 */ - H5Z_filter_t filter_info; -#endif /* LATER */ - char message[256]; - - /* Set up MPI parameters */ - MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); - MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); - - MPI_Barrier(MPI_COMM_WORLD); - - HDassert(mpi_size >= 1); - - mpi_comm = MPI_COMM_WORLD; - mpi_info = MPI_INFO_NULL; - - /* Create the dataset creation plist */ - dcpl = H5Pcreate(H5P_DATASET_CREATE); - VRFY((dcpl >= 0), "dataset creation plist created successfully"); - - if (selection_mode == TEST_FILTERS_READ) { -#ifdef LATER /* fletcher32 */ - ret = H5Zfilter_avail(H5Z_FILTER_FLETCHER32); - VRFY((ret >= 0), "Fletcher32 filter is available.\n"); - - ret = H5Zget_filter_info(H5Z_FILTER_FLETCHER32, (unsigned int *)&filter_info); - VRFY(((filter_info & H5Z_FILTER_CONFIG_ENCODE_ENABLED) || - (filter_info & H5Z_FILTER_CONFIG_DECODE_ENABLED)), - "Fletcher32 filter encoding and decoding available.\n"); - - ret = H5Pset_fletcher32(dcpl); - VRFY((ret >= 0), "set filter (flecher32) succeeded"); -#endif /* LATER */ - } - else { - VRFY(0, "Unexpected mode, only test for TEST_FILTERS_READ."); - } - - /* Create the basic Space */ - dims[0] = (hsize_t)dim0; - dims[1] = (hsize_t)dim1; - sid = H5Screate_simple(RANK, dims, NULL); - VRFY((sid >= 0), "H5Screate_simple succeeded"); - - filename = (const char *)GetTestParameters(); - HDassert(filename != NULL); - - /* Setup the file access template */ - fapl_write = create_faccess_plist(mpi_comm, mpi_info, FACC_DEFAULT); - VRFY((fapl_write >= 0), "create_faccess_plist() succeeded"); - - fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_write); - VRFY((fid >= 0), "H5Fcreate succeeded"); - - /* If we are not testing contiguous datasets */ - if (is_chunked) { - /* Set up chunk information. */ - chunk_dims[0] = dims[0] / (hsize_t)mpi_size; - chunk_dims[1] = dims[1]; - ret = H5Pset_chunk(dcpl, 2, chunk_dims); - VRFY((ret >= 0), "chunk creation property list succeeded"); - } - - /* Create the dataset */ - dataset = H5Dcreate2(fid, DSET_NOCOLCAUSE, data_type, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT); - VRFY((dataset >= 0), "H5Dcreate2() dataset succeeded"); - -#ifdef LATER /* fletcher32 */ - /* Set expected cause */ - test_name = "Broken Collective I/O - Filter is required"; - no_collective_cause_local_expected = H5D_MPIO_FILTERS; - no_collective_cause_global_expected = H5D_MPIO_FILTERS; -#endif /* LATER */ - - /* Get the file dataspace */ - file_space = H5Dget_space(dataset); - VRFY((file_space >= 0), "H5Dget_space succeeded"); - - /* Create the memory dataspace */ - mem_space = H5Screate_simple(RANK, dims, NULL); - VRFY((mem_space >= 0), "mem_space created"); - - /* Get the number of elements in the selection */ - length = dim0 * dim1; - - /* Allocate and initialize the buffer */ - buffer = (int *)HDmalloc(sizeof(int) * length); - VRFY((buffer != NULL), "HDmalloc of buffer succeeded"); - for (i = 0; i < length; i++) - buffer[i] = i; - - /* Set up the dxpl for the write */ - dxpl = H5Pcreate(H5P_DATASET_XFER); - VRFY((dxpl >= 0), "H5Pcreate(H5P_DATASET_XFER) succeeded"); - - if (selection_mode == TEST_FILTERS_READ) { - /* To test read in collective I/O mode , write in independent mode - * because write fails with mpio + filter */ - ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_INDEPENDENT); - VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); - } - else { - /* To test write in collective I/O mode. */ - ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE); - VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); - } - - /* Write */ - ret = H5Dwrite(dataset, data_type, mem_space, file_space, dxpl, buffer); - - if (ret < 0) - H5Eprint2(H5E_DEFAULT, stdout); - VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded"); - - /* Make a copy of the dxpl to test the read operation */ - dxpl = H5Pcopy(dxpl); - VRFY((dxpl >= 0), "H5Pcopy succeeded"); - - if (dataset) - H5Dclose(dataset); - if (fapl_write) - H5Pclose(fapl_write); - if (fid) - H5Fclose(fid); - - /*--------------------- - * Test Read access - *---------------------*/ - - /* Setup the file access template */ - fapl_read = create_faccess_plist(mpi_comm, mpi_info, facc_type); - VRFY((fapl_read >= 0), "create_faccess_plist() succeeded"); - - fid = H5Fopen(filename, H5F_ACC_RDONLY, fapl_read); - dataset = H5Dopen2(fid, DSET_NOCOLCAUSE, H5P_DEFAULT); - - /* Set collective I/O properties in the dxpl. */ - ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE); - VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); - - /* Read */ - ret = H5Dread(dataset, data_type, mem_space, file_space, dxpl, buffer); - - if (ret < 0) - H5Eprint2(H5E_DEFAULT, stdout); - VRFY((ret >= 0), "H5Dread() dataset multichunk read succeeded"); - - /* Get the cause of broken collective I/O */ - ret = H5Pget_mpio_no_collective_cause(dxpl, &no_collective_cause_local_read, - &no_collective_cause_global_read); - VRFY((ret >= 0), "retrieving no collective cause succeeded"); - - /* Test values */ - HDmemset(message, 0, sizeof(message)); - HDsprintf(message, "Local cause of Broken Collective I/O has the correct value for %s.\n", test_name); - VRFY((no_collective_cause_local_read == (uint32_t)no_collective_cause_local_expected), message); - HDmemset(message, 0, sizeof(message)); - HDsprintf(message, "Global cause of Broken Collective I/O has the correct value for %s.\n", test_name); - VRFY((no_collective_cause_global_read == (uint32_t)no_collective_cause_global_expected), message); - - /* Release some resources */ - if (sid) - H5Sclose(sid); - if (fapl_read) - H5Pclose(fapl_read); - if (dcpl) - H5Pclose(dcpl); - if (dxpl) - H5Pclose(dxpl); - if (dataset) - H5Dclose(dataset); - if (mem_space) - H5Sclose(mem_space); - if (file_space) - H5Sclose(file_space); - if (fid) - H5Fclose(fid); - HDfree(buffer); - return; -} -#endif - /* Function: no_collective_cause_tests * * Purpose: Tests cases for broken collective IO. @@ -3987,13 +3723,6 @@ no_collective_cause_tests(void) test_no_collective_cause_mode(TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES); test_no_collective_cause_mode(TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT); test_no_collective_cause_mode(TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL); -#ifdef LATER /* fletcher32 */ - /* TODO: use this instead of below TEST_FILTERS_READ when H5Dcreate and - * H5Dwrite is ready for mpio + filter feature. - */ - /* test_no_collective_cause_mode (TEST_FILTERS); */ - test_no_collective_cause_mode_filter(TEST_FILTERS_READ); -#endif /* LATER */ /* * Test combined causes diff --git a/testpar/t_file.c b/testpar/t_file.c index 6c6ac69..229fd6c 100644 --- a/testpar/t_file.c +++ b/testpar/t_file.c @@ -514,25 +514,25 @@ create_file(const char *filename, hid_t fcpl, hid_t fapl, int metadata_write_str VRFY((mem_dataspace >= 0), ""); for (k = 0; k < NUM_DSETS; k++) { - HDsprintf(dset_name, "D1dset%d", k); + HDsnprintf(dset_name, sizeof(dset_name), "D1dset%d", k); dset_id = H5Dcreate2(grp_id, dset_name, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dset_id >= 0), ""); ret = H5Dclose(dset_id); VRFY((ret == 0), ""); - HDsprintf(dset_name, "D2dset%d", k); + HDsnprintf(dset_name, sizeof(dset_name), "D2dset%d", k); dset_id = H5Dcreate2(grp_id, dset_name, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dset_id >= 0), ""); ret = H5Dclose(dset_id); VRFY((ret == 0), ""); - HDsprintf(dset_name, "D3dset%d", k); + HDsnprintf(dset_name, sizeof(dset_name), "D3dset%d", k); dset_id = H5Dcreate2(grp_id, dset_name, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dset_id >= 0), ""); ret = H5Dclose(dset_id); VRFY((ret == 0), ""); - HDsprintf(dset_name, "dset%d", k); + HDsnprintf(dset_name, sizeof(dset_name), "dset%d", k); dset_id = H5Dcreate2(grp_id, dset_name, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dset_id >= 0), ""); @@ -555,13 +555,13 @@ create_file(const char *filename, hid_t fcpl, hid_t fapl, int metadata_write_str for (i = 0; i < num_elements; i++) VRFY((data_array[i] == mpi_rank + 1), "Dataset Verify failed"); - HDsprintf(dset_name, "D1dset%d", k); + HDsnprintf(dset_name, sizeof(dset_name), "D1dset%d", k); ret = H5Ldelete(grp_id, dset_name, H5P_DEFAULT); VRFY((ret == 0), ""); - HDsprintf(dset_name, "D2dset%d", k); + HDsnprintf(dset_name, sizeof(dset_name), "D2dset%d", k); ret = H5Ldelete(grp_id, dset_name, H5P_DEFAULT); VRFY((ret == 0), ""); - HDsprintf(dset_name, "D3dset%d", k); + HDsnprintf(dset_name, sizeof(dset_name), "D3dset%d", k); ret = H5Ldelete(grp_id, dset_name, H5P_DEFAULT); VRFY((ret == 0), ""); } @@ -667,7 +667,7 @@ open_file(const char *filename, hid_t fapl, int metadata_write_strategy, hsize_t VRFY((mem_dataspace >= 0), ""); for (k = 0; k < NUM_DSETS; k++) { - HDsprintf(dset_name, "dset%d", k); + HDsnprintf(dset_name, sizeof(dset_name), "dset%d", k); dset_id = H5Dopen2(grp_id, dset_name, H5P_DEFAULT); VRFY((dset_id >= 0), ""); diff --git a/testpar/t_filters_parallel.c b/testpar/t_filters_parallel.c index 78af0fb..8a55519 100644 --- a/testpar/t_filters_parallel.c +++ b/testpar/t_filters_parallel.c @@ -26,73 +26,139 @@ const char *FILENAME[] = {"t_filters_parallel", NULL}; char filenames[1][256]; +static MPI_Comm comm = MPI_COMM_WORLD; +static MPI_Info info = MPI_INFO_NULL; +static int mpi_rank; +static int mpi_size; + int nerrors = 0; -size_t cur_filter_idx = 0; -#define GZIP_INDEX 0 -#define FLETCHER32_INDEX 1 +/* Arrays of filter ID values and filter names (should match each other) */ +H5Z_filter_t filterIDs[] = { + H5Z_FILTER_DEFLATE, H5Z_FILTER_SHUFFLE, H5Z_FILTER_FLETCHER32, + H5Z_FILTER_SZIP, H5Z_FILTER_NBIT, H5Z_FILTER_SCALEOFFSET, +}; + +const char *filterNames[] = {"Deflate", "Shuffle", "Fletcher32", "SZIP", "Nbit", "ScaleOffset"}; -#define ARRAY_SIZE(a) sizeof(a) / sizeof(a[0]) +/* Function pointer typedef for test functions */ +typedef void (*test_func)(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, + hid_t dxpl_id); + +/* Typedef for filter arguments for user-defined filters */ +typedef struct filter_options_t { + unsigned int flags; + size_t cd_nelmts; + const unsigned int cd_values[]; +} filter_options_t; /* - * Used to check if a filter is available before running a test. + * Enum for verify_space_alloc_status which specifies + * how many chunks have been written to in a dataset */ -#define CHECK_CUR_FILTER_AVAIL() \ - { \ - htri_t filter_is_avail; \ - \ - if (cur_filter_idx == GZIP_INDEX) { \ - if ((filter_is_avail = H5Zfilter_avail(H5Z_FILTER_DEFLATE)) != TRUE) { \ - if (MAINPROCESS) { \ - HDputs(" - SKIPPED - Deflate filter not available"); \ - } \ - return; \ - } \ - } \ - } +typedef enum num_chunks_written_t { + DATASET_JUST_CREATED, + NO_CHUNKS_WRITTEN, + SOME_CHUNKS_WRITTEN, + ALL_CHUNKS_WRITTEN +} num_chunks_written_t; -static herr_t set_dcpl_filter(hid_t dcpl); +static herr_t set_dcpl_filter(hid_t dcpl_id, H5Z_filter_t filter_id, filter_options_t *filter_options); +static herr_t verify_space_alloc_status(hid_t dset_id, hid_t dcpl_id, num_chunks_written_t chunks_written); -#if MPI_VERSION >= 3 +#ifdef H5_HAVE_PARALLEL_FILTERED_WRITES /* Tests for writing data in parallel */ -static void test_write_one_chunk_filtered_dataset(void); -static void test_write_filtered_dataset_no_overlap(void); -static void test_write_filtered_dataset_overlap(void); -static void test_write_filtered_dataset_single_no_selection(void); -static void test_write_filtered_dataset_all_no_selection(void); -static void test_write_filtered_dataset_point_selection(void); -static void test_write_filtered_dataset_interleaved_write(void); -static void test_write_transformed_filtered_dataset_no_overlap(void); -static void test_write_3d_filtered_dataset_no_overlap_separate_pages(void); -static void test_write_3d_filtered_dataset_no_overlap_same_pages(void); -static void test_write_3d_filtered_dataset_overlap(void); -static void test_write_cmpd_filtered_dataset_no_conversion_unshared(void); -static void test_write_cmpd_filtered_dataset_no_conversion_shared(void); -static void test_write_cmpd_filtered_dataset_type_conversion_unshared(void); -static void test_write_cmpd_filtered_dataset_type_conversion_shared(void); +static void test_write_one_chunk_filtered_dataset(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); +static void test_write_filtered_dataset_no_overlap(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); +static void test_write_filtered_dataset_no_overlap_partial(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); +static void test_write_filtered_dataset_overlap(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); +static void test_write_filtered_dataset_single_unlim_dim_no_overlap(const char * parent_group, + H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_write_filtered_dataset_single_unlim_dim_overlap(const char * parent_group, + H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_write_filtered_dataset_multi_unlim_dim_no_overlap(const char * parent_group, + H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_write_filtered_dataset_multi_unlim_dim_overlap(const char * parent_group, + H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_write_filtered_dataset_single_no_selection(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); +static void test_write_filtered_dataset_all_no_selection(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); +static void test_write_filtered_dataset_point_selection(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); +static void test_write_filtered_dataset_interleaved_write(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); +static void test_write_transformed_filtered_dataset_no_overlap(const char * parent_group, + H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_write_3d_filtered_dataset_no_overlap_separate_pages(const char * parent_group, + H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_write_3d_filtered_dataset_no_overlap_same_pages(const char * parent_group, + H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_write_3d_filtered_dataset_overlap(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); +static void test_write_cmpd_filtered_dataset_no_conversion_unshared(const char * parent_group, + H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_write_cmpd_filtered_dataset_no_conversion_shared(const char * parent_group, + H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_write_cmpd_filtered_dataset_type_conversion_unshared(const char * parent_group, + H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_write_cmpd_filtered_dataset_type_conversion_shared(const char * parent_group, + H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); #endif /* Tests for reading data in parallel */ -static void test_read_one_chunk_filtered_dataset(void); -static void test_read_filtered_dataset_no_overlap(void); -static void test_read_filtered_dataset_overlap(void); -static void test_read_filtered_dataset_single_no_selection(void); -static void test_read_filtered_dataset_all_no_selection(void); -static void test_read_filtered_dataset_point_selection(void); -static void test_read_filtered_dataset_interleaved_read(void); -static void test_read_transformed_filtered_dataset_no_overlap(void); -static void test_read_3d_filtered_dataset_no_overlap_separate_pages(void); -static void test_read_3d_filtered_dataset_no_overlap_same_pages(void); -static void test_read_3d_filtered_dataset_overlap(void); -static void test_read_cmpd_filtered_dataset_no_conversion_unshared(void); -static void test_read_cmpd_filtered_dataset_no_conversion_shared(void); -static void test_read_cmpd_filtered_dataset_type_conversion_unshared(void); -static void test_read_cmpd_filtered_dataset_type_conversion_shared(void); - -#if MPI_VERSION >= 3 -/* Other miscellaneous tests */ -static void test_shrinking_growing_chunks(void); -#endif +static void test_read_one_chunk_filtered_dataset(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); +static void test_read_filtered_dataset_no_overlap(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); +static void test_read_filtered_dataset_overlap(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); +static void test_read_filtered_dataset_single_no_selection(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); +static void test_read_filtered_dataset_all_no_selection(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); +static void test_read_filtered_dataset_point_selection(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); +static void test_read_filtered_dataset_interleaved_read(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); +static void test_read_transformed_filtered_dataset_no_overlap(const char * parent_group, + H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_read_3d_filtered_dataset_no_overlap_separate_pages(const char * parent_group, + H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_read_3d_filtered_dataset_no_overlap_same_pages(const char * parent_group, + H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_read_3d_filtered_dataset_overlap(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); +static void test_read_cmpd_filtered_dataset_no_conversion_unshared(const char * parent_group, + H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_read_cmpd_filtered_dataset_no_conversion_shared(const char * parent_group, + H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_read_cmpd_filtered_dataset_type_conversion_unshared(const char * parent_group, + H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_read_cmpd_filtered_dataset_type_conversion_shared(const char * parent_group, + H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); /* * Tests for attempting to round-trip the data going from @@ -103,21 +169,40 @@ static void test_shrinking_growing_chunks(void); * * written in parallel -> read serially */ -static void test_write_serial_read_parallel(void); -#if MPI_VERSION >= 3 -static void test_write_parallel_read_serial(void); -#endif +static void test_write_serial_read_parallel(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); -static MPI_Comm comm = MPI_COMM_WORLD; -static MPI_Info info = MPI_INFO_NULL; -static int mpi_rank; -static int mpi_size; +#ifdef H5_HAVE_PARALLEL_FILTERED_WRITES +static void test_write_parallel_read_serial(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); -static void (*tests[])(void) = { -#if MPI_VERSION >= 3 +/* Other miscellaneous tests */ +static void test_shrinking_growing_chunks(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_edge_chunks_no_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_edge_chunks_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_edge_chunks_partial_write(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_fill_values(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, + hid_t dxpl_id); +static void test_fill_value_undefined(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +static void test_fill_time_never(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id); +#endif + +static test_func tests[] = { +#ifdef H5_HAVE_PARALLEL_FILTERED_WRITES test_write_one_chunk_filtered_dataset, test_write_filtered_dataset_no_overlap, + test_write_filtered_dataset_no_overlap_partial, test_write_filtered_dataset_overlap, + test_write_filtered_dataset_single_unlim_dim_no_overlap, + test_write_filtered_dataset_single_unlim_dim_overlap, + test_write_filtered_dataset_multi_unlim_dim_no_overlap, + test_write_filtered_dataset_multi_unlim_dim_overlap, test_write_filtered_dataset_single_no_selection, test_write_filtered_dataset_all_no_selection, test_write_filtered_dataset_point_selection, @@ -147,33 +232,168 @@ static void (*tests[])(void) = { test_read_cmpd_filtered_dataset_type_conversion_unshared, test_read_cmpd_filtered_dataset_type_conversion_shared, test_write_serial_read_parallel, -#if MPI_VERSION >= 3 +#ifdef H5_HAVE_PARALLEL_FILTERED_WRITES test_write_parallel_read_serial, test_shrinking_growing_chunks, + test_edge_chunks_no_overlap, + test_edge_chunks_overlap, + test_edge_chunks_partial_write, + test_fill_values, + test_fill_value_undefined, + test_fill_time_never, #endif }; /* * Function to call the appropriate HDF5 filter-setting function - * depending on the currently set index. Used to re-run the tests + * depending on the given filter ID. Used to re-run the tests * with different filters to check that the data still comes back * correctly under a variety of circumstances, such as the * Fletcher32 checksum filter increasing the size of the chunk. */ static herr_t -set_dcpl_filter(hid_t dcpl) +set_dcpl_filter(hid_t dcpl_id, H5Z_filter_t filter_id, filter_options_t *filter_options) +{ + switch (filter_id) { + case H5Z_FILTER_DEFLATE: + return H5Pset_deflate(dcpl_id, DEFAULT_DEFLATE_LEVEL); + case H5Z_FILTER_SHUFFLE: + return H5Pset_shuffle(dcpl_id); + case H5Z_FILTER_FLETCHER32: + return H5Pset_fletcher32(dcpl_id); + case H5Z_FILTER_SZIP: { + unsigned pixels_per_block = H5_SZIP_MAX_PIXELS_PER_BLOCK; + hsize_t chunk_dims[H5S_MAX_RANK] = {0}; + size_t i, chunk_nelemts; + + VRFY(H5Pget_chunk(dcpl_id, H5S_MAX_RANK, chunk_dims) >= 0, "H5Pget_chunk succeeded"); + + for (i = 0, chunk_nelemts = 1; i < H5S_MAX_RANK; i++) + if (chunk_dims[i] > 0) + chunk_nelemts *= chunk_dims[i]; + + if (chunk_nelemts < H5_SZIP_MAX_PIXELS_PER_BLOCK) { + /* + * Can't set SZIP for chunk of 1 data element. + * Pixels-per-block value must be both even + * and non-zero. + */ + if (chunk_nelemts == 1) + return SUCCEED; + + if ((chunk_nelemts % 2) == 0) + pixels_per_block = (unsigned)chunk_nelemts; + else + pixels_per_block = (unsigned)(chunk_nelemts - 1); + } + else + pixels_per_block = H5_SZIP_MAX_PIXELS_PER_BLOCK; + + return H5Pset_szip(dcpl_id, 0, pixels_per_block); + } + case H5Z_FILTER_NBIT: + return H5Pset_nbit(dcpl_id); + case H5Z_FILTER_SCALEOFFSET: + return H5Pset_scaleoffset(dcpl_id, H5Z_SO_INT, 0); + default: { + if (!filter_options) + return FAIL; + + return H5Pset_filter(dcpl_id, filter_id, filter_options->flags, filter_options->cd_nelmts, + filter_options->cd_values); + } + } +} + +/* + * Function to verify the status of dataset storage space allocation + * based on the dataset's allocation time setting and how many chunks + * in the dataset have been written to. + */ +static herr_t +verify_space_alloc_status(hid_t dset_id, hid_t dcpl_id, num_chunks_written_t chunks_written) { - switch (cur_filter_idx) { - case GZIP_INDEX: - return H5Pset_deflate(dcpl, DEFAULT_DEFLATE_LEVEL); - case FLETCHER32_INDEX: - return H5Pset_fletcher32(dcpl); - default: - return H5Pset_deflate(dcpl, DEFAULT_DEFLATE_LEVEL); + int nfilters; + herr_t ret_value = SUCCEED; + + VRFY(((nfilters = H5Pget_nfilters(dcpl_id)) >= 0), "H5Pget_nfilters succeeded"); + + /* + * Only verify space allocation status when there are filters + * in the dataset's filter pipeline. When filters aren't in the + * pipeline, the space allocation time and status can vary based + * on whether the file was created in parallel or serial mode. + */ + if (nfilters > 0) { + H5D_space_status_t space_status; + H5D_alloc_time_t alloc_time; + + VRFY((H5Pget_alloc_time(dcpl_id, &alloc_time) >= 0), "H5Pget_alloc_time succeeded"); + VRFY((H5Dget_space_status(dset_id, &space_status) >= 0), "H5Dget_space_status succeeded"); + + switch (alloc_time) { + case H5D_ALLOC_TIME_EARLY: + /* + * Early space allocation should always result in the + * full dataset storage space being allocated. + */ + VRFY(space_status == H5D_SPACE_STATUS_ALLOCATED, "verified space allocation status"); + break; + case H5D_ALLOC_TIME_LATE: + /* + * Late space allocation should always result in the + * full dataset storage space being allocated when + * the dataset gets written to. However, if the dataset + * is extended the dataset's space allocation status + * can become partly allocated until the dataset is + * written to again. + */ + if (chunks_written == SOME_CHUNKS_WRITTEN || chunks_written == ALL_CHUNKS_WRITTEN) + VRFY((space_status == H5D_SPACE_STATUS_ALLOCATED) || + (space_status == H5D_SPACE_STATUS_PART_ALLOCATED), + "verified space allocation status"); + else if (chunks_written == NO_CHUNKS_WRITTEN) + /* + * A special case where we wrote to a dataset that + * uses late space allocation, but the write was + * either a no-op (no selection in the dataset + * from any rank) or something caused the write to + * fail late in the process of performing the actual + * write. In either case, space should still have + * been allocated. + */ + VRFY(space_status == H5D_SPACE_STATUS_ALLOCATED, "verified space allocation status"); + else + VRFY(space_status == H5D_SPACE_STATUS_NOT_ALLOCATED, "verified space allocation status"); + break; + case H5D_ALLOC_TIME_DEFAULT: + case H5D_ALLOC_TIME_INCR: + /* + * Incremental space allocation should result in + * the dataset's storage space being incrementally + * allocated as chunks are written to. Once all chunks + * have been written to, the space allocation should be + * seen as fully allocated. + */ + if (chunks_written == SOME_CHUNKS_WRITTEN) + VRFY((space_status == H5D_SPACE_STATUS_PART_ALLOCATED), + "verified space allocation status"); + else if (chunks_written == ALL_CHUNKS_WRITTEN) + VRFY((space_status == H5D_SPACE_STATUS_ALLOCATED), "verified space allocation status"); + else + VRFY(space_status == H5D_SPACE_STATUS_NOT_ALLOCATED, "verified space allocation status"); + break; + default: + if (MAINPROCESS) + MESG("unknown space allocation time"); + MPI_Abort(MPI_COMM_WORLD, 1); + } } + + return ret_value; } -#if MPI_VERSION >= 3 +#ifdef H5_HAVE_PARALLEL_FILTERED_WRITES /* * Tests parallel write of filtered data in the special * case where a dataset is composed of a single chunk. @@ -182,7 +402,8 @@ set_dcpl_filter(hid_t dcpl) * 02/01/2017 */ static void -test_write_one_chunk_filtered_dataset(void) +test_write_one_chunk_filtered_dataset(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; @@ -195,26 +416,18 @@ test_write_one_chunk_filtered_dataset(void) hsize_t count[WRITE_ONE_CHUNK_FILTERED_DATASET_DIMS]; hsize_t block[WRITE_ONE_CHUNK_FILTERED_DATASET_DIMS]; size_t i, data_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to one-chunk filtered dataset"); - CHECK_CUR_FILTER_AVAIL(); - - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_ONE_CHUNK_FILTERED_DATASET_NROWS; @@ -231,19 +444,21 @@ test_write_one_chunk_filtered_dataset(void) VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_ONE_CHUNK_FILTERED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, WRITE_ONE_CHUNK_FILTERED_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, + dset_id = H5Dcreate2(group_id, WRITE_ONE_CHUNK_FILTERED_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes @@ -293,15 +508,12 @@ test_write_one_chunk_filtered_dataset(void) ((C_DATATYPE)i / (WRITE_ONE_CHUNK_FILTERED_DATASET_CH_NROWS / mpi_size * WRITE_ONE_CHUNK_FILTERED_DATASET_CH_NCOLS)); - /* Create property list for collective dataset write */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - - VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, data) >= 0), + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + if (data) HDfree(data); @@ -311,10 +523,10 @@ test_write_one_chunk_filtered_dataset(void) read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - dset_id = H5Dopen2(file_id, "/" WRITE_ONE_CHUNK_FILTERED_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, WRITE_ONE_CHUNK_FILTERED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); @@ -324,10 +536,11 @@ test_write_one_chunk_filtered_dataset(void) if (read_buf) HDfree(read_buf); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -343,7 +556,8 @@ test_write_one_chunk_filtered_dataset(void) * 02/01/2017 */ static void -test_write_filtered_dataset_no_overlap(void) +test_write_filtered_dataset_no_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; @@ -356,27 +570,18 @@ test_write_filtered_dataset_no_overlap(void) hsize_t count[WRITE_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t block[WRITE_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS]; size_t i, data_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to unshared filtered chunks"); - CHECK_CUR_FILTER_AVAIL(); - - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_NROWS; @@ -393,20 +598,22 @@ test_write_filtered_dataset_no_overlap(void) VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, WRITE_UNSHARED_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, + dset_id = H5Dcreate2(group_id, WRITE_UNSHARED_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes @@ -454,15 +661,168 @@ test_write_filtered_dataset_no_overlap(void) correct_buf[i] = (C_DATATYPE)((i % (dataset_dims[0] / (hsize_t)mpi_size * dataset_dims[1])) + (i / (dataset_dims[0] / (hsize_t)mpi_size * dataset_dims[1]))); - /* Create property list for collective dataset write */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), + "Dataset write succeeded"); - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); - VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, data) >= 0), + if (data) + HDfree(data); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + /* Verify the correct data was written */ + read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); + VRFY((NULL != read_buf), "HDcalloc succeeded"); + + dset_id = H5Dopen2(group_id, WRITE_UNSHARED_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset open succeeded"); + + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); + + if (correct_buf) + HDfree(correct_buf); + if (read_buf) + HDfree(read_buf); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); + VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); + + return; +} + +/* + * Tests parallel write of filtered data in the case where only + * one process is writing to a particular chunk in the operation + * and that process only writes to part of a chunk. + */ +static void +test_write_filtered_dataset_no_overlap_partial(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) +{ + C_DATATYPE *data = NULL; + C_DATATYPE *read_buf = NULL; + C_DATATYPE *correct_buf = NULL; + hsize_t dataset_dims[WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_DIMS]; + hsize_t chunk_dims[WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_DIMS]; + hsize_t sel_dims[WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_DIMS]; + hsize_t start[WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_DIMS]; + hsize_t stride[WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_DIMS]; + hsize_t count[WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_DIMS]; + hsize_t block[WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_DIMS]; + size_t i, data_size, correct_buf_size; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID; + + if (MAINPROCESS) + HDputs("Testing partial write to unshared filtered chunks"); + + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); + VRFY((file_id >= 0), "Test file open succeeded"); + + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + + /* Create the dataspace for the dataset */ + dataset_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_NROWS; + dataset_dims[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_NCOLS; + chunk_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NROWS; + chunk_dims[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NCOLS; + sel_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NROWS; + sel_dims[1] = (hsize_t)(WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_NCOLS / + WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NCOLS); + + filespace = H5Screate_simple(WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_DIMS, dataset_dims, NULL); + VRFY((filespace >= 0), "File dataspace creation succeeded"); + + /* Create chunked dataset */ + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); + + VRFY((H5Pset_chunk(plist_id, WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_DIMS, chunk_dims) >= 0), + "Chunk size set"); + + /* Add test filter to the pipeline */ + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); + + dset_id = H5Dcreate2(group_id, WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_NAME, HDF5_DATATYPE_NAME, + filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset creation succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + + /* Each process defines the dataset selection in memory and writes + * it to the hyperslab in the file + */ + count[0] = 1; + count[1] = (hsize_t)(WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_NCOLS / + WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NCOLS); + stride[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NROWS; + stride[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NCOLS; + block[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NROWS; + block[1] = (hsize_t)1; + start[0] = ((hsize_t)mpi_rank * (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NROWS * count[0]); + start[1] = 0; + + if (VERBOSE_MED) { + HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE + ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE + ", %" PRIuHSIZE " ]\n", + mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); + HDfflush(stdout); + } + + /* Select hyperslab in the file */ + filespace = H5Dget_space(dset_id); + VRFY((filespace >= 0), "File dataspace retrieval succeeded"); + + VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), + "Hyperslab selection succeeded"); + + /* Fill data buffer */ + data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); + correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); + + data = (C_DATATYPE *)HDcalloc(1, data_size); + VRFY((NULL != data), "HDcalloc succeeded"); + + correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); + VRFY((NULL != correct_buf), "HDcalloc succeeded"); + + for (i = 0; i < data_size / sizeof(*data); i++) + data[i] = (C_DATATYPE)GEN_DATA(i); + + for (i = 0; i < (size_t)mpi_size; i++) { + size_t rank_n_elems = (size_t)(mpi_size * (WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NROWS * + WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NCOLS)); + size_t data_idx = i; + + for (size_t j = 0; j < rank_n_elems; j++) { + if ((j % WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NCOLS) == 0) { + correct_buf[(i * rank_n_elems) + j] = (C_DATATYPE)data_idx; + data_idx++; + } + } + } + + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + if (data) HDfree(data); @@ -472,10 +832,10 @@ test_write_filtered_dataset_no_overlap(void) read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - dset_id = H5Dopen2(file_id, "/" WRITE_UNSHARED_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); @@ -485,10 +845,10 @@ test_write_filtered_dataset_no_overlap(void) if (read_buf) HDfree(read_buf); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); - VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -505,7 +865,8 @@ test_write_filtered_dataset_no_overlap(void) * 02/01/2017 */ static void -test_write_filtered_dataset_overlap(void) +test_write_filtered_dataset_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; @@ -518,27 +879,18 @@ test_write_filtered_dataset_overlap(void) hsize_t count[WRITE_SHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t block[WRITE_SHARED_FILTERED_CHUNKS_DATASET_DIMS]; size_t i, data_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to shared filtered chunks"); - CHECK_CUR_FILTER_AVAIL(); - - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_NROWS; @@ -555,20 +907,22 @@ test_write_filtered_dataset_overlap(void) VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_SHARED_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, WRITE_SHARED_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, + dset_id = H5Dcreate2(group_id, WRITE_SHARED_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes @@ -616,15 +970,12 @@ test_write_filtered_dataset_overlap(void) (dataset_dims[1] * (i / ((hsize_t)mpi_size * dataset_dims[1]))) + (i % dataset_dims[1]) + (((i % ((hsize_t)mpi_size * dataset_dims[1])) / dataset_dims[1]) % dataset_dims[1])); - /* Create property list for collective dataset write */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - - VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, data) >= 0), + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + if (data) HDfree(data); @@ -634,10 +985,10 @@ test_write_filtered_dataset_overlap(void) read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - dset_id = H5Dopen2(file_id, "/" WRITE_SHARED_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, WRITE_SHARED_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); @@ -647,10 +998,650 @@ test_write_filtered_dataset_overlap(void) if (read_buf) HDfree(read_buf); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); + VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); + + return; +} + +/* + * Tests parallel write of filtered data in the case where + * a dataset has a single unlimited dimension and each + * MPI rank writes to its own separate chunk. On each + * iteration, the dataset is extended in its extensible + * dimension by "MPI size" chunks per rank and the new + * chunks are written to, read back and verified. + */ +static void +test_write_filtered_dataset_single_unlim_dim_no_overlap(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) +{ + C_DATATYPE *data = NULL; + C_DATATYPE *read_buf = NULL; + hsize_t dataset_dims[WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS]; + hsize_t max_dims[WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS]; + hsize_t chunk_dims[WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS]; + hsize_t sel_dims[WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS]; + hsize_t start[WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS]; + hsize_t stride[WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS]; + hsize_t count[WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS]; + hsize_t block[WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS]; + size_t i, data_size; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID; + + if (MAINPROCESS) + HDputs("Testing write to unshared filtered chunks w/ single unlimited dimension"); + + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); + VRFY((file_id >= 0), "Test file open succeeded"); + + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + + /* Create the dataspace for the dataset */ + dataset_dims[0] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_NROWS; + dataset_dims[1] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_NCOLS; + max_dims[0] = dataset_dims[0]; + max_dims[1] = H5S_UNLIMITED; + chunk_dims[0] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_CH_NROWS; + chunk_dims[1] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_CH_NCOLS; + sel_dims[0] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_CH_NROWS; + sel_dims[1] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_NCOLS; + + filespace = H5Screate_simple(WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS, dataset_dims, max_dims); + VRFY((filespace >= 0), "File dataspace creation succeeded"); + + /* Create chunked dataset */ + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); + + VRFY((H5Pset_chunk(plist_id, WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS, chunk_dims) >= 0), + "Chunk size set"); + + /* Add test filter to the pipeline */ + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); + + dset_id = H5Dcreate2(group_id, WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, + H5P_DEFAULT, plist_id, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset creation succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + + /* Fill data buffer */ + data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); + + data = (C_DATATYPE *)HDcalloc(1, data_size); + VRFY((NULL != data), "HDcalloc succeeded"); + + read_buf = (C_DATATYPE *)HDcalloc(1, data_size); + VRFY((NULL != read_buf), "HDcalloc succeeded"); + + for (i = 0; i < data_size / sizeof(*data); i++) + data[i] = (C_DATATYPE)GEN_DATA(i); + + for (i = 0; i < (size_t)WRITE_UNSHARED_ONE_UNLIM_DIM_NLOOPS; i++) { + /* Select hyperslab in the file */ + filespace = H5Dget_space(dset_id); + VRFY((filespace >= 0), "File dataspace retrieval succeeded"); + + /* Each process defines the dataset selection in memory and writes + * it to the hyperslab in the file + */ + count[0] = 1; + count[1] = + (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_NCOLS / (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_CH_NCOLS; + stride[0] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_CH_NROWS; + stride[1] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_CH_NCOLS; + block[0] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_CH_NROWS; + block[1] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_CH_NCOLS; + start[0] = ((hsize_t)mpi_rank * block[0] * count[0]); + start[1] = i * count[1] * block[1]; + + if (VERBOSE_MED) { + HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE + ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE + ", %" PRIuHSIZE " ]\n", + mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], + block[1]); + HDfflush(stdout); + } + + VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), + "Hyperslab selection succeeded"); + + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), + "Dataset write succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + dset_id = H5Dopen2(group_id, WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_NAME, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset open succeeded"); + + HDmemset(read_buf, 255, data_size); + + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + /* Verify the correct data was written */ + VRFY((0 == HDmemcmp(read_buf, data, data_size)), "Data verification succeeded"); + + if (i < (size_t)WRITE_UNSHARED_ONE_UNLIM_DIM_NLOOPS - 1) { + /* Extend the dataset by count[1] chunks in the extensible dimension */ + dataset_dims[1] += count[1] * block[1]; + VRFY(H5Dset_extent(dset_id, dataset_dims) >= 0, "H5Dset_extent succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); + } + + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + } + + if (data) + HDfree(data); + if (read_buf) + HDfree(read_buf); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); + VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); + + return; +} + +/* + * Tests parallel write of filtered data in the case where + * a dataset has a single unlimited dimension and each + * MPI rank writes to a portion of each chunk in the dataset. + * On each iteration, the dataset is extended in its extensible + * dimension by two chunks and the new chunks are written to + * by all ranks, then read back and verified. + */ +static void +test_write_filtered_dataset_single_unlim_dim_overlap(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) +{ + C_DATATYPE *data = NULL; + C_DATATYPE *read_buf = NULL; + hsize_t dataset_dims[WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS]; + hsize_t max_dims[WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS]; + hsize_t chunk_dims[WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS]; + hsize_t sel_dims[WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS]; + hsize_t start[WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS]; + hsize_t stride[WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS]; + hsize_t count[WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS]; + hsize_t block[WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS]; + size_t i, data_size; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID; + + if (MAINPROCESS) + HDputs("Testing write to shared filtered chunks w/ single unlimited dimension"); + + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); + VRFY((file_id >= 0), "Test file open succeeded"); + + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + + /* Create the dataspace for the dataset */ + dataset_dims[0] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_NROWS; + dataset_dims[1] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_NCOLS; + max_dims[0] = dataset_dims[0]; + max_dims[1] = H5S_UNLIMITED; + chunk_dims[0] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_CH_NROWS; + chunk_dims[1] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_CH_NCOLS; + sel_dims[0] = (hsize_t)DIM0_SCALE_FACTOR; + sel_dims[1] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_CH_NCOLS * (hsize_t)DIM1_SCALE_FACTOR; + + filespace = H5Screate_simple(WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS, dataset_dims, max_dims); + VRFY((filespace >= 0), "File dataspace creation succeeded"); + + /* Create chunked dataset */ + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); + + VRFY((H5Pset_chunk(plist_id, WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS, chunk_dims) >= 0), + "Chunk size set"); + + /* Add test filter to the pipeline */ + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); + + dset_id = H5Dcreate2(group_id, WRITE_SHARED_ONE_UNLIM_DIM_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, + H5P_DEFAULT, plist_id, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset creation succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + + /* Fill data buffer */ + data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); + + data = (C_DATATYPE *)HDcalloc(1, data_size); + VRFY((NULL != data), "HDcalloc succeeded"); + + read_buf = (C_DATATYPE *)HDcalloc(1, data_size); + VRFY((NULL != read_buf), "HDcalloc succeeded"); + + for (i = 0; i < data_size / sizeof(*data); i++) + data[i] = (C_DATATYPE)GEN_DATA(i); + + for (i = 0; i < (size_t)WRITE_SHARED_ONE_UNLIM_DIM_NLOOPS; i++) { + /* Select hyperslab in the file */ + filespace = H5Dget_space(dset_id); + VRFY((filespace >= 0), "File dataspace retrieval succeeded"); + + /* Each process defines the dataset selection in memory and writes + * it to the hyperslab in the file + */ + count[0] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_NROWS / (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_CH_NROWS; + count[1] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_NCOLS / (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_CH_NCOLS; + stride[0] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_CH_NROWS; + stride[1] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_CH_NCOLS; + block[0] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_CH_NROWS / (hsize_t)mpi_size; + block[1] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_CH_NCOLS; + start[0] = (hsize_t)mpi_rank * block[0]; + start[1] = i * count[1] * block[1]; + + if (VERBOSE_MED) { + HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE + ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE + ", %" PRIuHSIZE " ]\n", + mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], + block[1]); + HDfflush(stdout); + } + + VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), + "Hyperslab selection succeeded"); + + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), + "Dataset write succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + dset_id = H5Dopen2(group_id, WRITE_SHARED_ONE_UNLIM_DIM_DATASET_NAME, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset open succeeded"); + + HDmemset(read_buf, 255, data_size); + + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + /* Verify correct data was written */ + VRFY((0 == HDmemcmp(read_buf, data, data_size)), "Data verification succeeded"); + + if (i < (size_t)WRITE_SHARED_ONE_UNLIM_DIM_NLOOPS - 1) { + /* Extend the dataset by count[1] chunks in the extensible dimension */ + dataset_dims[1] += count[1] * block[1]; + VRFY(H5Dset_extent(dset_id, dataset_dims) >= 0, "H5Dset_extent succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); + } + + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + } + + if (data) + HDfree(data); + if (read_buf) + HDfree(read_buf); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); + VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); + + return; +} + +/* + * Tests parallel write of filtered data in the case where + * a dataset has two unlimited dimensions and each + * MPI rank writes to its own separate chunks. On each + * iteration, the dataset is extended in its first + * extensible dimension by the size of one chunk per rank + * and in its second extensible dimension by the size of + * one chunk. Then, all chunks are written to, read back + * and verified. + */ +static void +test_write_filtered_dataset_multi_unlim_dim_no_overlap(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) +{ + C_DATATYPE *data = NULL; + C_DATATYPE *read_buf = NULL; + hsize_t dataset_dims[WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS]; + hsize_t max_dims[WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS]; + hsize_t chunk_dims[WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS]; + hsize_t sel_dims[WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS]; + hsize_t start[WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS]; + hsize_t stride[WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS]; + hsize_t count[WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS]; + hsize_t block[WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS]; + size_t i, data_size; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID; + + if (MAINPROCESS) + HDputs("Testing write to unshared filtered chunks w/ two unlimited dimensions"); + + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); + VRFY((file_id >= 0), "Test file open succeeded"); + + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + + /* Create the dataspace for the dataset */ + dataset_dims[0] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_NROWS; + dataset_dims[1] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_NCOLS; + max_dims[0] = H5S_UNLIMITED; + max_dims[1] = H5S_UNLIMITED; + chunk_dims[0] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NROWS; + chunk_dims[1] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NCOLS; + sel_dims[0] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NROWS; + sel_dims[1] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_NCOLS; + + filespace = H5Screate_simple(WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS, dataset_dims, max_dims); + VRFY((filespace >= 0), "File dataspace creation succeeded"); + + /* Create chunked dataset */ + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); + + VRFY((H5Pset_chunk(plist_id, WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS, chunk_dims) >= 0), + "Chunk size set"); + + /* Add test filter to the pipeline */ + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); + + dset_id = H5Dcreate2(group_id, WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, + H5P_DEFAULT, plist_id, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset creation succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + + for (i = 0; i < (size_t)WRITE_UNSHARED_TWO_UNLIM_DIM_NLOOPS; i++) { + C_DATATYPE *tmp_realloc = NULL; + size_t j; + + /* Set selected dimensions */ + sel_dims[0] = (i + 1) * WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NROWS; + sel_dims[1] = (i + 1) * WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NCOLS; + + /* Fill data buffer */ + data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); + + tmp_realloc = (C_DATATYPE *)HDrealloc(data, data_size); + VRFY((NULL != tmp_realloc), "HDrealloc succeeded"); + data = tmp_realloc; + + tmp_realloc = (C_DATATYPE *)HDrealloc(read_buf, data_size); + VRFY((NULL != tmp_realloc), "HDrealloc succeeded"); + read_buf = tmp_realloc; + + for (j = 0; j < data_size / sizeof(*data); j++) + data[j] = (C_DATATYPE)GEN_DATA(j); + + /* Select hyperslab in the file */ + filespace = H5Dget_space(dset_id); + VRFY((filespace >= 0), "File dataspace retrieval succeeded"); + + /* Each process defines the dataset selection in memory and writes + * it to the hyperslab in the file + */ + count[0] = (i + 1); + count[1] = (i + 1); + stride[0] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NROWS; + stride[1] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NCOLS; + block[0] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NROWS; + block[1] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NCOLS; + start[0] = ((hsize_t)mpi_rank * block[0] * count[0]); + start[1] = 0; + + if (VERBOSE_MED) { + HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE + ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE + ", %" PRIuHSIZE " ]\n", + mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], + block[1]); + HDfflush(stdout); + } + + VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), + "Hyperslab selection succeeded"); + + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), + "Dataset write succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + dset_id = H5Dopen2(group_id, WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_NAME, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset open succeeded"); + + HDmemset(read_buf, 255, data_size); + + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + /* Verify the correct data was written */ + VRFY((0 == HDmemcmp(read_buf, data, data_size)), "Data verification succeeded"); + + if (i < (size_t)WRITE_UNSHARED_TWO_UNLIM_DIM_NLOOPS - 1) { + /* + * Extend the dataset by the size of one chunk per rank + * in the first extensible dimension. Extend the dataset + * by the size of chunk in the second extensible dimension. + */ + dataset_dims[0] += (hsize_t)mpi_size * block[0]; + dataset_dims[1] += block[1]; + VRFY(H5Dset_extent(dset_id, dataset_dims) >= 0, "H5Dset_extent succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); + } + + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + } + + if (data) + HDfree(data); + if (read_buf) + HDfree(read_buf); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); + VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); + + return; +} + +/* + * Tests parallel write of filtered data in the case where + * a dataset has two unlimited dimensions and each MPI + * rank writes to a portion of each chunk in the dataset. + * On each iteration, the dataset is extended in its extensible + * dimensions by the size of a chunk and then all chunks are + * written to by all ranks, then read back and verified. + */ +static void +test_write_filtered_dataset_multi_unlim_dim_overlap(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) +{ + C_DATATYPE *data = NULL; + C_DATATYPE *read_buf = NULL; + hsize_t dataset_dims[WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS]; + hsize_t max_dims[WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS]; + hsize_t chunk_dims[WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS]; + hsize_t sel_dims[WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS]; + hsize_t start[WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS]; + hsize_t stride[WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS]; + hsize_t count[WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS]; + hsize_t block[WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS]; + size_t i, data_size; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID; + + if (MAINPROCESS) + HDputs("Testing write to shared filtered chunks w/ two unlimited dimensions"); + + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); + VRFY((file_id >= 0), "Test file open succeeded"); + + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + + /* Create the dataspace for the dataset */ + dataset_dims[0] = (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_NROWS; + dataset_dims[1] = (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_NCOLS; + max_dims[0] = H5S_UNLIMITED; + max_dims[1] = H5S_UNLIMITED; + chunk_dims[0] = (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_CH_NROWS; + chunk_dims[1] = (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_CH_NCOLS; + sel_dims[0] = (hsize_t)DIM0_SCALE_FACTOR; + sel_dims[1] = (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_CH_NCOLS * (hsize_t)DIM1_SCALE_FACTOR; + + filespace = H5Screate_simple(WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS, dataset_dims, max_dims); + VRFY((filespace >= 0), "File dataspace creation succeeded"); + + /* Create chunked dataset */ + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); + + VRFY((H5Pset_chunk(plist_id, WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS, chunk_dims) >= 0), + "Chunk size set"); + + /* Add test filter to the pipeline */ + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); + + dset_id = H5Dcreate2(group_id, WRITE_SHARED_TWO_UNLIM_DIM_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, + H5P_DEFAULT, plist_id, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset creation succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + + for (i = 0; i < (size_t)WRITE_SHARED_TWO_UNLIM_DIM_NLOOPS; i++) { + C_DATATYPE *tmp_realloc = NULL; + size_t j; + + /* Set selected dimensions */ + sel_dims[0] = (i + 1); + sel_dims[1] = (i + 1) * (size_t)WRITE_SHARED_TWO_UNLIM_DIM_CH_NCOLS; + + /* Fill data buffer */ + data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); + + tmp_realloc = (C_DATATYPE *)HDrealloc(data, data_size); + VRFY((NULL != tmp_realloc), "HDrealloc succeeded"); + data = tmp_realloc; + + tmp_realloc = (C_DATATYPE *)HDrealloc(read_buf, data_size); + VRFY((NULL != tmp_realloc), "HDrealloc succeeded"); + read_buf = tmp_realloc; + + for (j = 0; j < data_size / sizeof(*data); j++) + data[j] = (C_DATATYPE)GEN_DATA(j); + + /* Select hyperslab in the file */ + filespace = H5Dget_space(dset_id); + VRFY((filespace >= 0), "File dataspace retrieval succeeded"); + + /* Each process defines the dataset selection in memory and writes + * it to the hyperslab in the file + */ + count[0] = (i + 1); + count[1] = (i + 1); + stride[0] = (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_CH_NROWS; + stride[1] = (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_CH_NCOLS; + block[0] = 1; + block[1] = (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_CH_NROWS; + start[0] = (hsize_t)mpi_rank; + start[1] = 0; + + if (VERBOSE_MED) { + HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE + ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE + ", %" PRIuHSIZE " ]\n", + mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], + block[1]); + HDfflush(stdout); + } + + VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), + "Hyperslab selection succeeded"); + + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), + "Dataset write succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + dset_id = H5Dopen2(group_id, WRITE_SHARED_TWO_UNLIM_DIM_DATASET_NAME, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset open succeeded"); + + HDmemset(read_buf, 255, data_size); + + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + /* Verify correct data was written */ + VRFY((0 == HDmemcmp(read_buf, data, data_size)), "Data verification succeeded"); + + if (i < (size_t)WRITE_SHARED_TWO_UNLIM_DIM_NLOOPS - 1) { + /* Extend the dataset by the size of a chunk in each extensible dimension */ + dataset_dims[0] += (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_CH_NROWS; + dataset_dims[1] += (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_CH_NCOLS; + VRFY(H5Dset_extent(dset_id, dataset_dims) >= 0, "H5Dset_extent succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); + } + + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + } + + if (data) + HDfree(data); + if (read_buf) + HDfree(read_buf); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -669,7 +1660,8 @@ test_write_filtered_dataset_overlap(void) * 02/01/2017 */ static void -test_write_filtered_dataset_single_no_selection(void) +test_write_filtered_dataset_single_no_selection(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; @@ -683,27 +1675,18 @@ test_write_filtered_dataset_single_no_selection(void) hsize_t block[WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; size_t i, data_size, correct_buf_size; size_t segment_length; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to filtered chunks with a single process having no selection"); - CHECK_CUR_FILTER_AVAIL(); - - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NROWS; @@ -723,20 +1706,22 @@ test_write_filtered_dataset_single_no_selection(void) VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, + dset_id = H5Dcreate2(group_id, WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes @@ -774,15 +1759,17 @@ test_write_filtered_dataset_single_no_selection(void) data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); - data = (C_DATATYPE *)HDcalloc(1, data_size); - VRFY((NULL != data), "HDcalloc succeeded"); + if (mpi_rank != WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NO_SELECT_PROC) { + data = (C_DATATYPE *)HDcalloc(1, data_size); + VRFY((NULL != data), "HDcalloc succeeded"); + + for (i = 0; i < data_size / sizeof(*data); i++) + data[i] = (C_DATATYPE)GEN_DATA(i); + } correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); - for (i = 0; i < data_size / sizeof(*data); i++) - data[i] = (C_DATATYPE)GEN_DATA(i); - for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = (C_DATATYPE)((i % (dataset_dims[0] / (hsize_t)mpi_size * dataset_dims[1])) + (i / (dataset_dims[0] / (hsize_t)mpi_size * dataset_dims[1]))); @@ -793,15 +1780,12 @@ test_write_filtered_dataset_single_no_selection(void) ((size_t)WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NO_SELECT_PROC * segment_length), 0, segment_length * sizeof(*data)); - /* Create property list for collective dataset write */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - - VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, data) >= 0), + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); + /* Verify space allocation status - data should only have been written if MPI size > 1 */ + verify_space_alloc_status(dset_id, plist_id, (mpi_size > 1 ? SOME_CHUNKS_WRITTEN : NO_CHUNKS_WRITTEN)); + if (data) HDfree(data); @@ -811,10 +1795,10 @@ test_write_filtered_dataset_single_no_selection(void) read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - dset_id = H5Dopen2(file_id, "/" WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); @@ -824,10 +1808,11 @@ test_write_filtered_dataset_single_no_selection(void) if (read_buf) HDfree(read_buf); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -847,7 +1832,8 @@ test_write_filtered_dataset_single_no_selection(void) * 02/02/2017 */ static void -test_write_filtered_dataset_all_no_selection(void) +test_write_filtered_dataset_all_no_selection(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; @@ -856,27 +1842,18 @@ test_write_filtered_dataset_all_no_selection(void) hsize_t chunk_dims[WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t sel_dims[WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; size_t i, data_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to filtered chunks with all processes having no selection"); - CHECK_CUR_FILTER_AVAIL(); - - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_NROWS; @@ -892,20 +1869,22 @@ test_write_filtered_dataset_all_no_selection(void) VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, + dset_id = H5Dcreate2(group_id, WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); filespace = H5Dget_space(dset_id); @@ -926,15 +1905,12 @@ test_write_filtered_dataset_all_no_selection(void) for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); - /* Create property list for collective dataset write */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - - VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, data) >= 0), + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); + /* Verify space allocation status - no ranks should have written any data */ + verify_space_alloc_status(dset_id, plist_id, NO_CHUNKS_WRITTEN); + if (data) HDfree(data); @@ -944,10 +1920,10 @@ test_write_filtered_dataset_all_no_selection(void) read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - dset_id = H5Dopen2(file_id, "/" WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); @@ -957,10 +1933,11 @@ test_write_filtered_dataset_all_no_selection(void) if (read_buf) HDfree(read_buf); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -974,7 +1951,8 @@ test_write_filtered_dataset_all_no_selection(void) * 02/02/2017 */ static void -test_write_filtered_dataset_point_selection(void) +test_write_filtered_dataset_point_selection(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *correct_buf = NULL; @@ -985,27 +1963,18 @@ test_write_filtered_dataset_point_selection(void) hsize_t sel_dims[WRITE_POINT_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; size_t i, j, data_size, correct_buf_size; size_t num_points; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to filtered chunks with point selection"); - CHECK_CUR_FILTER_AVAIL(); - - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_POINT_SELECTION_FILTERED_CHUNKS_NROWS; @@ -1022,20 +1991,22 @@ test_write_filtered_dataset_point_selection(void) VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_POINT_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, WRITE_POINT_SELECTION_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, + dset_id = H5Dcreate2(group_id, WRITE_POINT_SELECTION_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Set up point selection */ @@ -1075,15 +2046,12 @@ test_write_filtered_dataset_point_selection(void) (dataset_dims[1] * (i / ((hsize_t)mpi_size * dataset_dims[1]))) + (i % dataset_dims[1]) + (((i % ((hsize_t)mpi_size * dataset_dims[1])) / dataset_dims[1]) % dataset_dims[1])); - /* Create property list for collective dataset write */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - - VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, data) >= 0), + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + if (data) HDfree(data); @@ -1093,10 +2061,10 @@ test_write_filtered_dataset_point_selection(void) read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - dset_id = H5Dopen2(file_id, "/" WRITE_POINT_SELECTION_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, WRITE_POINT_SELECTION_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); @@ -1108,10 +2076,11 @@ test_write_filtered_dataset_point_selection(void) if (read_buf) HDfree(read_buf); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -1129,7 +2098,8 @@ test_write_filtered_dataset_point_selection(void) * 02/02/2017 */ static void -test_write_filtered_dataset_interleaved_write(void) +test_write_filtered_dataset_interleaved_write(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; @@ -1142,27 +2112,18 @@ test_write_filtered_dataset_interleaved_write(void) hsize_t count[INTERLEAVED_WRITE_FILTERED_DATASET_DIMS]; hsize_t block[INTERLEAVED_WRITE_FILTERED_DATASET_DIMS]; size_t i, data_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing interleaved write to filtered chunks"); - CHECK_CUR_FILTER_AVAIL(); - - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)INTERLEAVED_WRITE_FILTERED_DATASET_NROWS; @@ -1179,20 +2140,22 @@ test_write_filtered_dataset_interleaved_write(void) VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, INTERLEAVED_WRITE_FILTERED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, INTERLEAVED_WRITE_FILTERED_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, + dset_id = H5Dcreate2(group_id, INTERLEAVED_WRITE_FILTERED_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes @@ -1251,15 +2214,12 @@ test_write_filtered_dataset_interleaved_write(void) + ((hsize_t)INTERLEAVED_WRITE_FILTERED_DATASET_NCOLS * (i / (hsize_t)(mpi_size * INTERLEAVED_WRITE_FILTERED_DATASET_NCOLS)))); - /* Create property list for collective dataset write */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - - VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, data) >= 0), + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + if (data) HDfree(data); @@ -1269,10 +2229,10 @@ test_write_filtered_dataset_interleaved_write(void) read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - dset_id = H5Dopen2(file_id, "/" INTERLEAVED_WRITE_FILTERED_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, INTERLEAVED_WRITE_FILTERED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); @@ -1282,10 +2242,11 @@ test_write_filtered_dataset_interleaved_write(void) if (read_buf) HDfree(read_buf); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -1308,7 +2269,8 @@ test_write_filtered_dataset_interleaved_write(void) * 08/20/2021 */ static void -test_write_transformed_filtered_dataset_no_overlap(void) +test_write_transformed_filtered_dataset_no_overlap(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; @@ -1321,27 +2283,18 @@ test_write_transformed_filtered_dataset_no_overlap(void) hsize_t count[WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t block[WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS]; size_t i, data_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to unshared transformed and filtered chunks"); - CHECK_CUR_FILTER_AVAIL(); - - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_NROWS; @@ -1358,19 +2311,22 @@ test_write_transformed_filtered_dataset_no_overlap(void) VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, - filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); + dset_id = H5Dcreate2(group_id, WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_NAME, + HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); @@ -1419,11 +2375,9 @@ test_write_transformed_filtered_dataset_no_overlap(void) correct_buf[i] = (C_DATATYPE)((i % (dataset_dims[0] / (hsize_t)mpi_size * dataset_dims[1])) + (i / (dataset_dims[0] / (hsize_t)mpi_size * dataset_dims[1]))); - /* Create property list for collective dataset write and data transform */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); + /* Create property list for data transform */ + plist_id = H5Pcopy(dxpl_id); + VRFY((plist_id >= 0), "DXPL copy succeeded"); /* Set data transform expression */ VRFY((H5Pset_data_transform(plist_id, "x") >= 0), "Set data transform expression succeeded"); @@ -1440,7 +2394,7 @@ test_write_transformed_filtered_dataset_no_overlap(void) read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - dset_id = H5Dopen2(file_id, "/" WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, plist_id, read_buf) >= 0), @@ -1448,6 +2402,13 @@ test_write_transformed_filtered_dataset_no_overlap(void) VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + + /* Verify space allocation status */ + plist_id = H5Dget_create_plist(dset_id); + VRFY((plist_id >= 0), "H5Dget_create_plist succeeded"); + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + if (correct_buf) HDfree(correct_buf); if (read_buf) @@ -1457,6 +2418,7 @@ test_write_transformed_filtered_dataset_no_overlap(void) VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -1471,7 +2433,8 @@ test_write_transformed_filtered_dataset_no_overlap(void) * 02/06/2017 */ static void -test_write_3d_filtered_dataset_no_overlap_separate_pages(void) +test_write_3d_filtered_dataset_no_overlap_separate_pages(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; @@ -1484,27 +2447,18 @@ test_write_3d_filtered_dataset_no_overlap_separate_pages(void) hsize_t count[WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS]; hsize_t block[WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS]; size_t i, data_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to unshared filtered chunks on separate pages in 3D dataset"); - CHECK_CUR_FILTER_AVAIL(); - - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_NROWS; @@ -1524,20 +2478,22 @@ test_write_3d_filtered_dataset_no_overlap_separate_pages(void) VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_NAME, HDF5_DATATYPE_NAME, - filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); + dset_id = H5Dcreate2(group_id, WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_NAME, + HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes @@ -1591,15 +2547,12 @@ test_write_3d_filtered_dataset_no_overlap_separate_pages(void) for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = (C_DATATYPE)((i % (hsize_t)mpi_size) + (i / (hsize_t)mpi_size)); - /* Create property list for collective dataset write */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - - VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, data) >= 0), + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + if (data) HDfree(data); @@ -1609,10 +2562,10 @@ test_write_3d_filtered_dataset_no_overlap_separate_pages(void) read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - dset_id = H5Dopen2(file_id, "/" WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); @@ -1622,10 +2575,11 @@ test_write_3d_filtered_dataset_no_overlap_separate_pages(void) if (read_buf) HDfree(read_buf); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -1641,7 +2595,8 @@ test_write_3d_filtered_dataset_no_overlap_separate_pages(void) * 02/06/2017 */ static void -test_write_3d_filtered_dataset_no_overlap_same_pages(void) +test_write_3d_filtered_dataset_no_overlap_same_pages(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; @@ -1654,27 +2609,18 @@ test_write_3d_filtered_dataset_no_overlap_same_pages(void) hsize_t count[WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS]; hsize_t block[WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS]; size_t i, data_size, correct_buf_size; - hid_t file_id, dset_id, plist_id; - hid_t filespace, memspace; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to unshared filtered chunks on the same pages in 3D dataset"); - CHECK_CUR_FILTER_AVAIL(); - - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_NROWS; @@ -1695,20 +2641,22 @@ test_write_3d_filtered_dataset_no_overlap_same_pages(void) VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_NAME, + dset_id = H5Dcreate2(group_id, WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes @@ -1762,15 +2710,12 @@ test_write_3d_filtered_dataset_no_overlap_same_pages(void) correct_buf[i] = (C_DATATYPE)((i % (dataset_dims[0] * dataset_dims[1])) + (i / (dataset_dims[0] * dataset_dims[1]))); - /* Create property list for collective dataset write */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - - VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, data) >= 0), + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + if (data) HDfree(data); @@ -1780,10 +2725,10 @@ test_write_3d_filtered_dataset_no_overlap_same_pages(void) read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - dset_id = H5Dopen2(file_id, "/" WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); @@ -1793,10 +2738,11 @@ test_write_3d_filtered_dataset_no_overlap_same_pages(void) if (read_buf) HDfree(read_buf); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -1812,7 +2758,8 @@ test_write_3d_filtered_dataset_no_overlap_same_pages(void) * 02/06/2017 */ static void -test_write_3d_filtered_dataset_overlap(void) +test_write_3d_filtered_dataset_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; @@ -1825,27 +2772,18 @@ test_write_3d_filtered_dataset_overlap(void) hsize_t count[WRITE_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS]; hsize_t block[WRITE_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS]; size_t i, data_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to shared filtered chunks in 3D dataset"); - CHECK_CUR_FILTER_AVAIL(); - - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_3D_NROWS; @@ -1865,20 +2803,22 @@ test_write_3d_filtered_dataset_overlap(void) VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, WRITE_SHARED_FILTERED_CHUNKS_3D_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, - H5P_DEFAULT, plist_id, H5P_DEFAULT); + dset_id = H5Dcreate2(group_id, WRITE_SHARED_FILTERED_CHUNKS_3D_DATASET_NAME, HDF5_DATATYPE_NAME, + filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes @@ -1943,15 +2883,12 @@ test_write_3d_filtered_dataset_overlap(void) (i / (hsize_t)(mpi_size * WRITE_SHARED_FILTERED_CHUNKS_3D_DEPTH * WRITE_SHARED_FILTERED_CHUNKS_3D_NCOLS)))); - /* Create property list for collective dataset write */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - - VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, data) >= 0), + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + if (data) HDfree(data); @@ -1961,10 +2898,10 @@ test_write_3d_filtered_dataset_overlap(void) read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - dset_id = H5Dopen2(file_id, "/" WRITE_SHARED_FILTERED_CHUNKS_3D_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, WRITE_SHARED_FILTERED_CHUNKS_3D_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); @@ -1974,10 +2911,11 @@ test_write_3d_filtered_dataset_overlap(void) if (read_buf) HDfree(read_buf); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -1992,7 +2930,8 @@ test_write_3d_filtered_dataset_overlap(void) * 02/10/2017 */ static void -test_write_cmpd_filtered_dataset_no_conversion_unshared(void) +test_write_cmpd_filtered_dataset_no_conversion_unshared(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { COMPOUND_C_DATATYPE *data = NULL; COMPOUND_C_DATATYPE *read_buf = NULL; @@ -2005,28 +2944,27 @@ test_write_cmpd_filtered_dataset_no_conversion_unshared(void) hsize_t count[WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t block[WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS]; size_t i, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1, memtype = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID, + memtype = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to unshared filtered chunks in Compound Datatype dataset without Datatype " "conversion"); - CHECK_CUR_FILTER_AVAIL(); - - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); + /* SZIP and ScaleOffset filters don't support compound types */ + if (filter_id == H5Z_FILTER_SZIP || filter_id == H5Z_FILTER_SCALEOFFSET) { + if (MAINPROCESS) + SKIPPED(); + return; + } - file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_NROWS; @@ -2045,15 +2983,15 @@ test_write_cmpd_filtered_dataset_no_conversion_unshared(void) VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); /* Create the compound type for memory. */ memtype = H5Tcreate(H5T_COMPOUND, sizeof(COMPOUND_C_DATATYPE)); @@ -2066,11 +3004,13 @@ test_write_cmpd_filtered_dataset_no_conversion_unshared(void) VRFY((H5Tinsert(memtype, "LongData", HOFFSET(COMPOUND_C_DATATYPE, field3), H5T_NATIVE_LONG) >= 0), "Datatype insertion succeeded"); - dset_id = H5Dcreate2(file_id, WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_NAME, memtype, - filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); + dset_id = H5Dcreate2(group_id, WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_NAME, + memtype, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes @@ -2124,13 +3064,10 @@ test_write_cmpd_filtered_dataset_no_conversion_unshared(void) correct_buf[i].field3 = (long)((i % dataset_dims[1]) + (i / dataset_dims[1])); } - /* Create property list for collective dataset write */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); + VRFY((H5Dwrite(dset_id, memtype, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); - VRFY((H5Dwrite(dset_id, memtype, memspace, filespace, plist_id, data) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); if (data) HDfree(data); @@ -2141,11 +3078,11 @@ test_write_cmpd_filtered_dataset_no_conversion_unshared(void) read_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - dset_id = H5Dopen2(file_id, "/" WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_NAME, - H5P_DEFAULT); + dset_id = + H5Dopen2(group_id, WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); - VRFY((H5Dread(dset_id, memtype, H5S_ALL, H5S_ALL, plist_id, read_buf) >= 0), "Dataset read succeeded"); + VRFY((H5Dread(dset_id, memtype, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); @@ -2154,11 +3091,12 @@ test_write_cmpd_filtered_dataset_no_conversion_unshared(void) if (read_buf) HDfree(read_buf); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Tclose(memtype) >= 0), "Datatype close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -2173,7 +3111,8 @@ test_write_cmpd_filtered_dataset_no_conversion_unshared(void) * 02/10/2017 */ static void -test_write_cmpd_filtered_dataset_no_conversion_shared(void) +test_write_cmpd_filtered_dataset_no_conversion_shared(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { COMPOUND_C_DATATYPE *data = NULL; COMPOUND_C_DATATYPE *read_buf = NULL; @@ -2186,28 +3125,27 @@ test_write_cmpd_filtered_dataset_no_conversion_shared(void) hsize_t count[WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS]; hsize_t block[WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS]; size_t i, correct_buf_size; - hid_t file_id, dset_id, plist_id, memtype; - hid_t filespace, memspace; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID, + memtype = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to shared filtered chunks in Compound Datatype dataset without Datatype " "conversion"); - CHECK_CUR_FILTER_AVAIL(); - - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); + /* SZIP and ScaleOffset filters don't support compound types */ + if (filter_id == H5Z_FILTER_SZIP || filter_id == H5Z_FILTER_SCALEOFFSET) { + if (MAINPROCESS) + SKIPPED(); + return; + } - file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_NROWS; @@ -2226,15 +3164,15 @@ test_write_cmpd_filtered_dataset_no_conversion_shared(void) VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); /* Create the compound type for memory. */ memtype = H5Tcreate(H5T_COMPOUND, sizeof(COMPOUND_C_DATATYPE)); @@ -2247,11 +3185,13 @@ test_write_cmpd_filtered_dataset_no_conversion_shared(void) VRFY((H5Tinsert(memtype, "LongData", HOFFSET(COMPOUND_C_DATATYPE, field3), H5T_NATIVE_LONG) >= 0), "Datatype insertion succeeded"); - dset_id = H5Dcreate2(file_id, WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_NAME, memtype, + dset_id = H5Dcreate2(group_id, WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_NAME, memtype, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes @@ -2311,13 +3251,10 @@ test_write_cmpd_filtered_dataset_no_conversion_shared(void) (((i % ((hsize_t)mpi_size * dataset_dims[1])) / dataset_dims[1]) % dataset_dims[1])); } - /* Create property list for collective dataset write */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); + VRFY((H5Dwrite(dset_id, memtype, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); - VRFY((H5Dwrite(dset_id, memtype, memspace, filespace, plist_id, data) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); if (data) HDfree(data); @@ -2329,10 +3266,10 @@ test_write_cmpd_filtered_dataset_no_conversion_shared(void) VRFY((NULL != read_buf), "HDcalloc succeeded"); dset_id = - H5Dopen2(file_id, "/" WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_NAME, H5P_DEFAULT); + H5Dopen2(group_id, WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); - VRFY((H5Dread(dset_id, memtype, H5S_ALL, H5S_ALL, plist_id, read_buf) >= 0), "Dataset read succeeded"); + VRFY((H5Dread(dset_id, memtype, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); @@ -2341,11 +3278,12 @@ test_write_cmpd_filtered_dataset_no_conversion_shared(void) if (read_buf) HDfree(read_buf); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Tclose(memtype) >= 0), "Datatype close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -2356,16 +3294,18 @@ test_write_cmpd_filtered_dataset_no_conversion_shared(void) * chunks using a compound datatype which requires a * datatype conversion. * - * NOTE: This test currently should fail because the - * datatype conversion causes the parallel library to - * break to independent I/O and this isn't allowed when - * there are filters in the pipeline. + * NOTE: This test currently should fail for mpi_size > 1 + * because the datatype conversion causes the parallel + * library to break to independent I/O and this isn't + * allowed when there are filters in the pipeline, + * unless there is only one MPI rank. * * Programmer: Jordan Henderson * 02/07/2017 */ static void -test_write_cmpd_filtered_dataset_type_conversion_unshared(void) +test_write_cmpd_filtered_dataset_type_conversion_unshared(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { COMPOUND_C_DATATYPE *data = NULL; COMPOUND_C_DATATYPE *read_buf = NULL; @@ -2378,28 +3318,33 @@ test_write_cmpd_filtered_dataset_type_conversion_unshared(void) hsize_t count[WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t block[WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS]; size_t i, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1, filetype = -1, memtype = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID, + filetype = H5I_INVALID_HID, memtype = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to unshared filtered chunks in Compound Datatype dataset with Datatype " "conversion"); - CHECK_CUR_FILTER_AVAIL(); - - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); + /* Skip for MPI communicator size of 1 */ + if (mpi_size == 1) { + SKIPPED(); + return; + } - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); + /* SZIP and ScaleOffset filters don't support compound types */ + if (filter_id == H5Z_FILTER_SZIP || filter_id == H5Z_FILTER_SCALEOFFSET) { + if (MAINPROCESS) + SKIPPED(); + return; + } - file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_NROWS; @@ -2418,15 +3363,15 @@ test_write_cmpd_filtered_dataset_type_conversion_unshared(void) VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); /* Create the compound type for memory. */ memtype = H5Tcreate(H5T_COMPOUND, sizeof(COMPOUND_C_DATATYPE)); @@ -2447,11 +3392,13 @@ test_write_cmpd_filtered_dataset_type_conversion_unshared(void) VRFY((H5Tinsert(filetype, "IntData", 8, H5T_STD_I64BE) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(filetype, "LongData", 16, H5T_STD_I64BE) >= 0), "Datatype insertion succeeded"); - dset_id = H5Dcreate2(file_id, WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_NAME, + dset_id = H5Dcreate2(group_id, WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_NAME, filetype, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes @@ -2497,20 +3444,16 @@ test_write_cmpd_filtered_dataset_type_conversion_unshared(void) data[i].field3 = (long)GEN_DATA(i); } - /* Create property list for collective dataset write */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - /* Ensure that this test currently fails since type conversions break collective mode */ H5E_BEGIN_TRY { - VRFY((H5Dwrite(dset_id, memtype, memspace, filespace, plist_id, data) < 0), - "Dataset write succeeded"); + VRFY((H5Dwrite(dset_id, memtype, memspace, filespace, dxpl_id, data) < 0), "Dataset write succeeded"); } H5E_END_TRY; + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, NO_CHUNKS_WRITTEN); + if (data) HDfree(data); @@ -2520,11 +3463,11 @@ test_write_cmpd_filtered_dataset_type_conversion_unshared(void) read_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - dset_id = H5Dopen2(file_id, "/" WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_NAME, - H5P_DEFAULT); + dset_id = + H5Dopen2(group_id, WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); - VRFY((H5Dread(dset_id, memtype, H5S_ALL, H5S_ALL, plist_id, read_buf) >= 0), "Dataset read succeeded"); + VRFY((H5Dread(dset_id, memtype, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); @@ -2533,12 +3476,13 @@ test_write_cmpd_filtered_dataset_type_conversion_unshared(void) if (read_buf) HDfree(read_buf); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Tclose(filetype) >= 0), "File datatype close succeeded"); VRFY((H5Tclose(memtype) >= 0), "Memory datatype close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -2549,16 +3493,18 @@ test_write_cmpd_filtered_dataset_type_conversion_unshared(void) * chunks using a compound datatype which requires * a datatype conversion. * - * NOTE: This test currently should fail because the - * datatype conversion causes the parallel library to - * break to independent I/O and this isn't allowed when - * there are filters in the pipeline. + * NOTE: This test currently should fail for mpi_size > 1 + * because the datatype conversion causes the parallel + * library to break to independent I/O and this isn't + * allowed when there are filters in the pipeline, + * unless there is only one MPI rank. * * Programmer: Jordan Henderson * 02/10/2017 */ static void -test_write_cmpd_filtered_dataset_type_conversion_shared(void) +test_write_cmpd_filtered_dataset_type_conversion_shared(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { COMPOUND_C_DATATYPE *data = NULL; COMPOUND_C_DATATYPE *read_buf = NULL; @@ -2571,28 +3517,33 @@ test_write_cmpd_filtered_dataset_type_conversion_shared(void) hsize_t count[WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS]; hsize_t block[WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS]; size_t i, correct_buf_size; - hid_t file_id, dset_id, plist_id, filetype, memtype; - hid_t filespace, memspace; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t filetype = H5I_INVALID_HID, memtype = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs( "Testing write to shared filtered chunks in Compound Datatype dataset with Datatype conversion"); - CHECK_CUR_FILTER_AVAIL(); - - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); + /* Skip for MPI communicator size of 1 */ + if (mpi_size == 1) { + SKIPPED(); + return; + } - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); + /* SZIP and ScaleOffset filters don't support compound types */ + if (filter_id == H5Z_FILTER_SZIP || filter_id == H5Z_FILTER_SCALEOFFSET) { + if (MAINPROCESS) + SKIPPED(); + return; + } - file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_NROWS; @@ -2611,15 +3562,15 @@ test_write_cmpd_filtered_dataset_type_conversion_shared(void) VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); /* Create the compound type for memory. */ memtype = H5Tcreate(H5T_COMPOUND, sizeof(COMPOUND_C_DATATYPE)); @@ -2640,11 +3591,13 @@ test_write_cmpd_filtered_dataset_type_conversion_shared(void) VRFY((H5Tinsert(filetype, "IntData", 8, H5T_STD_I64BE) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(filetype, "LongData", 16, H5T_STD_I64BE) >= 0), "Datatype insertion succeeded"); - dset_id = H5Dcreate2(file_id, WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_NAME, + dset_id = H5Dcreate2(group_id, WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_NAME, filetype, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes @@ -2690,20 +3643,16 @@ test_write_cmpd_filtered_dataset_type_conversion_shared(void) data[i].field3 = (long)GEN_DATA(i); } - /* Create property list for collective dataset write */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - /* Ensure that this test currently fails since type conversions break collective mode */ H5E_BEGIN_TRY { - VRFY((H5Dwrite(dset_id, memtype, memspace, filespace, plist_id, data) < 0), - "Dataset write succeeded"); + VRFY((H5Dwrite(dset_id, memtype, memspace, filespace, dxpl_id, data) < 0), "Dataset write succeeded"); } H5E_END_TRY; + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, NO_CHUNKS_WRITTEN); + if (data) HDfree(data); @@ -2713,11 +3662,11 @@ test_write_cmpd_filtered_dataset_type_conversion_shared(void) read_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - dset_id = H5Dopen2(file_id, "/" WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_NAME, - H5P_DEFAULT); + dset_id = + H5Dopen2(group_id, WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); - VRFY((H5Dread(dset_id, memtype, H5S_ALL, H5S_ALL, plist_id, read_buf) >= 0), "Dataset read succeeded"); + VRFY((H5Dread(dset_id, memtype, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); @@ -2726,12 +3675,13 @@ test_write_cmpd_filtered_dataset_type_conversion_shared(void) if (read_buf) HDfree(read_buf); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Tclose(filetype) >= 0), "File datatype close succeeded"); VRFY((H5Tclose(memtype) >= 0), "Memory datatype close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -2751,7 +3701,8 @@ test_write_cmpd_filtered_dataset_type_conversion_shared(void) * 05/14/2018 */ static void -test_read_one_chunk_filtered_dataset(void) +test_read_one_chunk_filtered_dataset(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; @@ -2765,16 +3716,15 @@ test_read_one_chunk_filtered_dataset(void) hsize_t block[READ_ONE_CHUNK_FILTERED_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int * recvcounts = NULL; int * displs = NULL; if (MAINPROCESS) HDputs("Testing read from one-chunk filtered dataset"); - CHECK_CUR_FILTER_AVAIL(); - dataset_dims[0] = (hsize_t)READ_ONE_CHUNK_FILTERED_DATASET_NROWS; dataset_dims[1] = (hsize_t)READ_ONE_CHUNK_FILTERED_DATASET_NCOLS; @@ -2802,6 +3752,9 @@ test_read_one_chunk_filtered_dataset(void) VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_ONE_CHUNK_FILTERED_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); @@ -2810,44 +3763,43 @@ test_read_one_chunk_filtered_dataset(void) chunk_dims[0] = (hsize_t)READ_ONE_CHUNK_FILTERED_DATASET_CH_NROWS; chunk_dims[1] = (hsize_t)READ_ONE_CHUNK_FILTERED_DATASET_CH_NCOLS; - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_ONE_CHUNK_FILTERED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, READ_ONE_CHUNK_FILTERED_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, + dset_id = H5Dcreate2(group_id, READ_ONE_CHUNK_FILTERED_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); - dset_id = H5Dopen2(file_id, "/" READ_ONE_CHUNK_FILTERED_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, READ_ONE_CHUNK_FILTERED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_ONE_CHUNK_FILTERED_DATASET_NROWS / (hsize_t)mpi_size; @@ -2887,18 +3839,12 @@ test_read_one_chunk_filtered_dataset(void) VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); - /* Create property list for collective dataset read */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); @@ -2937,7 +3883,7 @@ test_read_one_chunk_filtered_dataset(void) VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -2956,7 +3902,8 @@ test_read_one_chunk_filtered_dataset(void) * 05/15/2018 */ static void -test_read_filtered_dataset_no_overlap(void) +test_read_filtered_dataset_no_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; @@ -2970,16 +3917,15 @@ test_read_filtered_dataset_no_overlap(void) hsize_t block[READ_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int * recvcounts = NULL; int * displs = NULL; if (MAINPROCESS) HDputs("Testing read from unshared filtered chunks"); - CHECK_CUR_FILTER_AVAIL(); - dataset_dims[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_NCOLS; @@ -3006,6 +3952,9 @@ test_read_filtered_dataset_no_overlap(void) VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); @@ -3014,44 +3963,43 @@ test_read_filtered_dataset_no_overlap(void) chunk_dims[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_CH_NCOLS; - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, READ_UNSHARED_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, + dset_id = H5Dcreate2(group_id, READ_UNSHARED_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); - dset_id = H5Dopen2(file_id, "/" READ_UNSHARED_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, READ_UNSHARED_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_CH_NROWS; @@ -3091,18 +4039,12 @@ test_read_filtered_dataset_no_overlap(void) VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); - /* Create property list for collective dataset read */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); @@ -3141,7 +4083,7 @@ test_read_filtered_dataset_no_overlap(void) VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -3161,7 +4103,8 @@ test_read_filtered_dataset_no_overlap(void) * 05/15/2018 */ static void -test_read_filtered_dataset_overlap(void) +test_read_filtered_dataset_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; @@ -3175,16 +4118,15 @@ test_read_filtered_dataset_overlap(void) hsize_t block[READ_SHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int * recvcounts = NULL; int * displs = NULL; if (MAINPROCESS) HDputs("Testing read from shared filtered chunks"); - CHECK_CUR_FILTER_AVAIL(); - dataset_dims[0] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_NCOLS; @@ -3211,6 +4153,9 @@ test_read_filtered_dataset_overlap(void) VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_SHARED_FILTERED_CHUNKS_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); @@ -3219,44 +4164,43 @@ test_read_filtered_dataset_overlap(void) chunk_dims[0] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_CH_NCOLS; - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_SHARED_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, READ_SHARED_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, - H5P_DEFAULT, plist_id, H5P_DEFAULT); + dset_id = H5Dcreate2(group_id, READ_SHARED_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, + filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); - dset_id = H5Dopen2(file_id, "/" READ_SHARED_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, READ_SHARED_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)DIM0_SCALE_FACTOR; @@ -3296,18 +4240,12 @@ test_read_filtered_dataset_overlap(void) VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); - /* Create property list for collective dataset read */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); @@ -3362,7 +4300,7 @@ test_read_filtered_dataset_overlap(void) VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -3382,7 +4320,8 @@ test_read_filtered_dataset_overlap(void) * 05/15/2018 */ static void -test_read_filtered_dataset_single_no_selection(void) +test_read_filtered_dataset_single_no_selection(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; @@ -3397,16 +4336,15 @@ test_read_filtered_dataset_single_no_selection(void) hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; size_t segment_length; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int * recvcounts = NULL; int * displs = NULL; if (MAINPROCESS) HDputs("Testing read from filtered chunks with a single process having no selection"); - CHECK_CUR_FILTER_AVAIL(); - dataset_dims[0] = (hsize_t)READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NCOLS; @@ -3437,6 +4375,9 @@ test_read_filtered_dataset_single_no_selection(void) VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, dataset_dims, NULL); @@ -3446,44 +4387,43 @@ test_read_filtered_dataset_single_no_selection(void) chunk_dims[0] = (hsize_t)READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NCOLS; - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, + dset_id = H5Dcreate2(group_id, READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); - dset_id = H5Dopen2(file_id, "/" READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NROWS; @@ -3530,19 +4470,19 @@ test_read_filtered_dataset_single_no_selection(void) VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); - /* Create property list for collective dataset read */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, read_buf) >= 0), - "Dataset read succeeded"); + if (mpi_rank == READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NO_SELECT_PROC) { + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, NULL) >= 0), + "Dataset read succeeded"); + } + else { + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + } global_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != global_buf), "HDcalloc succeeded"); @@ -3588,7 +4528,7 @@ test_read_filtered_dataset_single_no_selection(void) VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -3609,7 +4549,8 @@ test_read_filtered_dataset_single_no_selection(void) * 05/15/2018 */ static void -test_read_filtered_dataset_all_no_selection(void) +test_read_filtered_dataset_all_no_selection(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; @@ -3617,14 +4558,13 @@ test_read_filtered_dataset_all_no_selection(void) hsize_t chunk_dims[READ_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t sel_dims[READ_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; size_t read_buf_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing read from filtered chunks with all processes having no selection"); - CHECK_CUR_FILTER_AVAIL(); - dataset_dims[0] = (hsize_t)READ_ALL_NO_SELECTION_FILTERED_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)READ_ALL_NO_SELECTION_FILTERED_CHUNKS_NCOLS; @@ -3646,6 +4586,9 @@ test_read_filtered_dataset_all_no_selection(void) VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); @@ -3654,44 +4597,43 @@ test_read_filtered_dataset_all_no_selection(void) chunk_dims[0] = (hsize_t)READ_ALL_NO_SELECTION_FILTERED_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)READ_ALL_NO_SELECTION_FILTERED_CHUNKS_CH_NCOLS; - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, READ_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, + dset_id = H5Dcreate2(group_id, READ_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); - dset_id = H5Dopen2(file_id, "/" READ_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, READ_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = sel_dims[1] = 0; @@ -3705,20 +4647,16 @@ test_read_filtered_dataset_all_no_selection(void) VRFY((H5Sselect_none(filespace) >= 0), "Select none succeeded"); - /* Create property list for collective dataset read */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - read_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); + VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); + if (read_buf) HDfree(read_buf); if (correct_buf) @@ -3727,7 +4665,7 @@ test_read_filtered_dataset_all_no_selection(void) VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -3747,7 +4685,8 @@ test_read_filtered_dataset_all_no_selection(void) * 05/15/2018 */ static void -test_read_filtered_dataset_point_selection(void) +test_read_filtered_dataset_point_selection(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *correct_buf = NULL; C_DATATYPE *read_buf = NULL; @@ -3759,16 +4698,15 @@ test_read_filtered_dataset_point_selection(void) hsize_t flat_dims[1]; size_t i, j, read_buf_size, correct_buf_size; size_t num_points; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int * recvcounts = NULL; int * displs = NULL; if (MAINPROCESS) HDputs("Testing read from filtered chunks with point selection"); - CHECK_CUR_FILTER_AVAIL(); - dataset_dims[0] = (hsize_t)READ_POINT_SELECTION_FILTERED_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)READ_POINT_SELECTION_FILTERED_CHUNKS_NCOLS; @@ -3795,6 +4733,9 @@ test_read_filtered_dataset_point_selection(void) VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_POINT_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); @@ -3803,44 +4744,43 @@ test_read_filtered_dataset_point_selection(void) chunk_dims[0] = (hsize_t)READ_POINT_SELECTION_FILTERED_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)READ_POINT_SELECTION_FILTERED_CHUNKS_CH_NCOLS; - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_POINT_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, READ_POINT_SELECTION_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, + dset_id = H5Dcreate2(group_id, READ_POINT_SELECTION_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); - dset_id = H5Dopen2(file_id, "/" READ_POINT_SELECTION_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, READ_POINT_SELECTION_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_POINT_SELECTION_FILTERED_CHUNKS_NROWS / (hsize_t)mpi_size; @@ -3871,18 +4811,12 @@ test_read_filtered_dataset_point_selection(void) VRFY((H5Sselect_elements(filespace, H5S_SELECT_SET, (hsize_t)num_points, (const hsize_t *)coords) >= 0), "Point selection succeeded"); - /* Create property list for collective dataset read */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); @@ -3941,7 +4875,7 @@ test_read_filtered_dataset_point_selection(void) VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -3964,7 +4898,8 @@ test_read_filtered_dataset_point_selection(void) * 05/15/2018 */ static void -test_read_filtered_dataset_interleaved_read(void) +test_read_filtered_dataset_interleaved_read(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; @@ -3978,16 +4913,15 @@ test_read_filtered_dataset_interleaved_read(void) hsize_t block[INTERLEAVED_READ_FILTERED_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int * recvcounts = NULL; int * displs = NULL; if (MAINPROCESS) HDputs("Testing interleaved read from filtered chunks"); - CHECK_CUR_FILTER_AVAIL(); - dataset_dims[0] = (hsize_t)INTERLEAVED_READ_FILTERED_DATASET_NROWS; dataset_dims[1] = (hsize_t)INTERLEAVED_READ_FILTERED_DATASET_NCOLS; @@ -4023,6 +4957,9 @@ test_read_filtered_dataset_interleaved_read(void) VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + /* Create the dataspace for the dataset */ filespace = H5Screate_simple(INTERLEAVED_READ_FILTERED_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); @@ -4031,44 +4968,43 @@ test_read_filtered_dataset_interleaved_read(void) chunk_dims[0] = (hsize_t)INTERLEAVED_READ_FILTERED_DATASET_CH_NROWS; chunk_dims[1] = (hsize_t)INTERLEAVED_READ_FILTERED_DATASET_CH_NCOLS; - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, INTERLEAVED_READ_FILTERED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, INTERLEAVED_READ_FILTERED_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, + dset_id = H5Dcreate2(group_id, INTERLEAVED_READ_FILTERED_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); - dset_id = H5Dopen2(file_id, "/" INTERLEAVED_READ_FILTERED_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, INTERLEAVED_READ_FILTERED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)(INTERLEAVED_READ_FILTERED_DATASET_NROWS / mpi_size); @@ -4110,18 +5046,12 @@ test_read_filtered_dataset_interleaved_read(void) VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); - /* Create property list for collective dataset read */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); @@ -4176,7 +5106,7 @@ test_read_filtered_dataset_interleaved_read(void) VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -4196,7 +5126,8 @@ test_read_filtered_dataset_interleaved_read(void) * 05/16/2018 */ static void -test_read_3d_filtered_dataset_no_overlap_separate_pages(void) +test_read_3d_filtered_dataset_no_overlap_separate_pages(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { MPI_Datatype vector_type; MPI_Datatype resized_vector_type; @@ -4212,14 +5143,13 @@ test_read_3d_filtered_dataset_no_overlap_separate_pages(void) hsize_t block[READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing read from unshared filtered chunks on separate pages in 3D dataset"); - CHECK_CUR_FILTER_AVAIL(); - dataset_dims[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_NROWS; dataset_dims[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_NCOLS; dataset_dims[2] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DEPTH; @@ -4245,6 +5175,9 @@ test_read_3d_filtered_dataset_no_overlap_separate_pages(void) VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS, dataset_dims, NULL); @@ -4255,45 +5188,44 @@ test_read_3d_filtered_dataset_no_overlap_separate_pages(void) chunk_dims[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_CH_NCOLS; chunk_dims[2] = 1; - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY( (H5Pset_chunk(plist_id, READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_NAME, + dset_id = H5Dcreate2(group_id, READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); - dset_id = H5Dopen2(file_id, "/" READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_NROWS; @@ -4340,18 +5272,12 @@ test_read_3d_filtered_dataset_no_overlap_separate_pages(void) VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); - /* Create property list for collective dataset read */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); @@ -4392,7 +5318,7 @@ test_read_3d_filtered_dataset_no_overlap_separate_pages(void) VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -4419,7 +5345,8 @@ test_read_3d_filtered_dataset_no_overlap_separate_pages(void) * 08/20/2021 */ static void -test_read_transformed_filtered_dataset_no_overlap(void) +test_read_transformed_filtered_dataset_no_overlap(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; @@ -4433,16 +5360,15 @@ test_read_transformed_filtered_dataset_no_overlap(void) hsize_t block[READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int * recvcounts = NULL; int * displs = NULL; if (MAINPROCESS) HDputs("Testing read from unshared transformed and filtered chunks"); - CHECK_CUR_FILTER_AVAIL(); - dataset_dims[0] = (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_NCOLS; @@ -4469,6 +5395,9 @@ test_read_transformed_filtered_dataset_no_overlap(void) VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS, dataset_dims, NULL); @@ -4478,20 +5407,23 @@ test_read_transformed_filtered_dataset_no_overlap(void) chunk_dims[0] = (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NCOLS; - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY( (H5Pset_chunk(plist_id, READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_NAME, + dset_id = H5Dcreate2(group_id, READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); @@ -4505,26 +5437,26 @@ test_read_transformed_filtered_dataset_no_overlap(void) VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, plist_id, correct_buf) >= 0), "Dataset write succeeded"); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + + /* Verify space allocation status */ + plist_id = H5Dget_create_plist(dset_id); + VRFY((plist_id >= 0), "H5Dget_create_plist succeeded"); + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); - dset_id = H5Dopen2(file_id, "/" READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NROWS; @@ -4565,11 +5497,9 @@ test_read_transformed_filtered_dataset_no_overlap(void) VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); - /* Create property list for collective dataset read and data transform */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); + /* Create property list for data transform */ + plist_id = H5Pcopy(dxpl_id); + VRFY((plist_id >= 0), "DXPL copy succeeded"); /* Set data transform expression */ VRFY((H5Pset_data_transform(plist_id, "x") >= 0), "Set data transform expression succeeded"); @@ -4619,6 +5549,7 @@ test_read_transformed_filtered_dataset_no_overlap(void) VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -4639,7 +5570,8 @@ test_read_transformed_filtered_dataset_no_overlap(void) * 05/16/2018 */ static void -test_read_3d_filtered_dataset_no_overlap_same_pages(void) +test_read_3d_filtered_dataset_no_overlap_same_pages(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; @@ -4653,16 +5585,15 @@ test_read_3d_filtered_dataset_no_overlap_same_pages(void) hsize_t block[READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; - hid_t file_id, dset_id, plist_id; - hid_t filespace, memspace; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int * recvcounts = NULL; int * displs = NULL; if (MAINPROCESS) HDputs("Testing read from unshared filtered chunks on the same pages in 3D dataset"); - CHECK_CUR_FILTER_AVAIL(); - dataset_dims[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_NROWS; dataset_dims[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_NCOLS; dataset_dims[2] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DEPTH; @@ -4689,6 +5620,9 @@ test_read_3d_filtered_dataset_no_overlap_same_pages(void) VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS, dataset_dims, NULL); @@ -4699,45 +5633,44 @@ test_read_3d_filtered_dataset_no_overlap_same_pages(void) chunk_dims[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NCOLS; chunk_dims[2] = 1; - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_NAME, + dset_id = H5Dcreate2(group_id, READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); - dset_id = H5Dopen2(file_id, "/" READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NROWS; @@ -4783,18 +5716,12 @@ test_read_3d_filtered_dataset_no_overlap_same_pages(void) VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); - /* Create property list for collective dataset read */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); @@ -4833,7 +5760,7 @@ test_read_3d_filtered_dataset_no_overlap_same_pages(void) VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -4854,7 +5781,8 @@ test_read_3d_filtered_dataset_no_overlap_same_pages(void) * 05/16/2018 */ static void -test_read_3d_filtered_dataset_overlap(void) +test_read_3d_filtered_dataset_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id) { MPI_Datatype vector_type; MPI_Datatype resized_vector_type; @@ -4870,14 +5798,13 @@ test_read_3d_filtered_dataset_overlap(void) hsize_t block[READ_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing read from shared filtered chunks in 3D dataset"); - CHECK_CUR_FILTER_AVAIL(); - dataset_dims[0] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_3D_NROWS; dataset_dims[1] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_3D_NCOLS; dataset_dims[2] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_3D_DEPTH; @@ -4916,6 +5843,9 @@ test_read_3d_filtered_dataset_overlap(void) VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); @@ -4925,44 +5855,43 @@ test_read_3d_filtered_dataset_overlap(void) chunk_dims[1] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_3D_CH_NCOLS; chunk_dims[2] = 1; - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, READ_SHARED_FILTERED_CHUNKS_3D_DATASET_NAME, HDF5_DATATYPE_NAME, + dset_id = H5Dcreate2(group_id, READ_SHARED_FILTERED_CHUNKS_3D_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); - dset_id = H5Dopen2(file_id, "/" READ_SHARED_FILTERED_CHUNKS_3D_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, READ_SHARED_FILTERED_CHUNKS_3D_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)(READ_SHARED_FILTERED_CHUNKS_3D_NROWS / mpi_size); @@ -5007,18 +5936,12 @@ test_read_3d_filtered_dataset_overlap(void) VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); - /* Create property list for collective dataset read */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); @@ -5068,7 +5991,7 @@ test_read_3d_filtered_dataset_overlap(void) VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -5088,7 +6011,8 @@ test_read_3d_filtered_dataset_overlap(void) * 05/17/2018 */ static void -test_read_cmpd_filtered_dataset_no_conversion_unshared(void) +test_read_cmpd_filtered_dataset_no_conversion_unshared(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { COMPOUND_C_DATATYPE *read_buf = NULL; COMPOUND_C_DATATYPE *correct_buf = NULL; @@ -5102,16 +6026,23 @@ test_read_cmpd_filtered_dataset_no_conversion_unshared(void) hsize_t block[READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1, memtype = -1; - hid_t filespace = -1, memspace = -1; - int * recvcounts = NULL; - int * displs = NULL; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID, + memtype = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; + int * recvcounts = NULL; + int * displs = NULL; if (MAINPROCESS) HDputs("Testing read from unshared filtered chunks in Compound Datatype dataset without Datatype " "conversion"); - CHECK_CUR_FILTER_AVAIL(); + /* SZIP and ScaleOffset filters don't support compound types */ + if (filter_id == H5Z_FILTER_SZIP || filter_id == H5Z_FILTER_SCALEOFFSET) { + if (MAINPROCESS) + SKIPPED(); + return; + } dataset_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_NROWS; dataset_dims[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_NCOLS; @@ -5153,6 +6084,9 @@ test_read_cmpd_filtered_dataset_no_conversion_unshared(void) VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS, dataset_dims, NULL); @@ -5162,46 +6096,45 @@ test_read_cmpd_filtered_dataset_no_conversion_unshared(void) chunk_dims[0] = READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_CH_NROWS; chunk_dims[1] = READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_CH_NCOLS; - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_NAME, + dset_id = H5Dcreate2(group_id, READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_NAME, memtype, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = - H5Dopen2(file_id, "/" READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_NAME, H5P_DEFAULT); + H5Dopen2(group_id, READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_CH_NROWS; @@ -5241,18 +6174,12 @@ test_read_cmpd_filtered_dataset_no_conversion_unshared(void) VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); - /* Create property list for collective dataset read */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - VRFY((H5Dread(dset_id, memtype, memspace, filespace, plist_id, read_buf) >= 0), "Dataset read succeeded"); + VRFY((H5Dread(dset_id, memtype, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != global_buf), "HDcalloc succeeded"); @@ -5291,7 +6218,7 @@ test_read_cmpd_filtered_dataset_no_conversion_unshared(void) VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Tclose(memtype) >= 0), "Memory datatype close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -5311,7 +6238,8 @@ test_read_cmpd_filtered_dataset_no_conversion_unshared(void) * 05/17/2018 */ static void -test_read_cmpd_filtered_dataset_no_conversion_shared(void) +test_read_cmpd_filtered_dataset_no_conversion_shared(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { COMPOUND_C_DATATYPE *read_buf = NULL; COMPOUND_C_DATATYPE *correct_buf = NULL; @@ -5325,16 +6253,23 @@ test_read_cmpd_filtered_dataset_no_conversion_shared(void) hsize_t block[READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; - hid_t file_id, dset_id, plist_id, memtype; - hid_t filespace, memspace; - int * recvcounts = NULL; - int * displs = NULL; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID, + memtype = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; + int * recvcounts = NULL; + int * displs = NULL; if (MAINPROCESS) HDputs("Testing read from shared filtered chunks in Compound Datatype dataset without Datatype " "conversion"); - CHECK_CUR_FILTER_AVAIL(); + /* SZIP and ScaleOffset filters don't support compound types */ + if (filter_id == H5Z_FILTER_SZIP || filter_id == H5Z_FILTER_SCALEOFFSET) { + if (MAINPROCESS) + SKIPPED(); + return; + } dataset_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_NROWS; dataset_dims[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_NCOLS; @@ -5382,6 +6317,9 @@ test_read_cmpd_filtered_dataset_no_conversion_shared(void) VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS, dataset_dims, NULL); @@ -5391,46 +6329,45 @@ test_read_cmpd_filtered_dataset_no_conversion_shared(void) chunk_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_CH_NROWS; chunk_dims[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_CH_NCOLS; - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_NAME, + dset_id = H5Dcreate2(group_id, READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_NAME, memtype, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = - H5Dopen2(file_id, "/" READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_NAME, H5P_DEFAULT); + H5Dopen2(group_id, READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_CH_NROWS / (hsize_t)mpi_size; @@ -5470,18 +6407,12 @@ test_read_cmpd_filtered_dataset_no_conversion_shared(void) VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); - /* Create property list for collective dataset read */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - VRFY((H5Dread(dset_id, memtype, memspace, filespace, plist_id, read_buf) >= 0), "Dataset read succeeded"); + VRFY((H5Dread(dset_id, memtype, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != global_buf), "HDcalloc succeeded"); @@ -5520,7 +6451,7 @@ test_read_cmpd_filtered_dataset_no_conversion_shared(void) VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Tclose(memtype) >= 0), "Memory datatype close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -5540,7 +6471,8 @@ test_read_cmpd_filtered_dataset_no_conversion_shared(void) * 05/17/2018 */ static void -test_read_cmpd_filtered_dataset_type_conversion_unshared(void) +test_read_cmpd_filtered_dataset_type_conversion_unshared(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { COMPOUND_C_DATATYPE *read_buf = NULL; COMPOUND_C_DATATYPE *correct_buf = NULL; @@ -5554,8 +6486,10 @@ test_read_cmpd_filtered_dataset_type_conversion_unshared(void) hsize_t block[READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1, filetype = -1, memtype = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t filetype = H5I_INVALID_HID, memtype = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int * recvcounts = NULL; int * displs = NULL; @@ -5563,7 +6497,12 @@ test_read_cmpd_filtered_dataset_type_conversion_unshared(void) HDputs("Testing read from unshared filtered chunks in Compound Datatype dataset with Datatype " "conversion"); - CHECK_CUR_FILTER_AVAIL(); + /* SZIP and ScaleOffset filters don't support compound types */ + if (filter_id == H5Z_FILTER_SZIP || filter_id == H5Z_FILTER_SCALEOFFSET) { + if (MAINPROCESS) + SKIPPED(); + return; + } dataset_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_NROWS; dataset_dims[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_NCOLS; @@ -5613,6 +6552,9 @@ test_read_cmpd_filtered_dataset_type_conversion_unshared(void) VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS, dataset_dims, NULL); @@ -5622,46 +6564,45 @@ test_read_cmpd_filtered_dataset_type_conversion_unshared(void) chunk_dims[0] = READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_CH_NROWS; chunk_dims[1] = READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_CH_NCOLS; - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_NAME, + dset_id = H5Dcreate2(group_id, READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_NAME, filetype, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); - dset_id = H5Dopen2(file_id, "/" READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_NAME, - H5P_DEFAULT); + dset_id = + H5Dopen2(group_id, READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_CH_NROWS; @@ -5701,18 +6642,12 @@ test_read_cmpd_filtered_dataset_type_conversion_unshared(void) VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); - /* Create property list for collective dataset read */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - VRFY((H5Dread(dset_id, memtype, memspace, filespace, plist_id, read_buf) >= 0), "Dataset read succeeded"); + VRFY((H5Dread(dset_id, memtype, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != global_buf), "HDcalloc succeeded"); @@ -5752,7 +6687,7 @@ test_read_cmpd_filtered_dataset_type_conversion_unshared(void) VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Tclose(filetype) >= 0), "File datatype close succeeded"); VRFY((H5Tclose(memtype) >= 0), "Memory datatype close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -5772,7 +6707,8 @@ test_read_cmpd_filtered_dataset_type_conversion_unshared(void) * 05/17/2018 */ static void -test_read_cmpd_filtered_dataset_type_conversion_shared(void) +test_read_cmpd_filtered_dataset_type_conversion_shared(const char *parent_group, H5Z_filter_t filter_id, + hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { COMPOUND_C_DATATYPE *read_buf = NULL; COMPOUND_C_DATATYPE *correct_buf = NULL; @@ -5786,8 +6722,10 @@ test_read_cmpd_filtered_dataset_type_conversion_shared(void) hsize_t block[READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; - hid_t file_id, dset_id, plist_id, filetype, memtype; - hid_t filespace, memspace; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t filetype = H5I_INVALID_HID, memtype = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int * recvcounts = NULL; int * displs = NULL; @@ -5795,7 +6733,12 @@ test_read_cmpd_filtered_dataset_type_conversion_shared(void) HDputs( "Testing read from shared filtered chunks in Compound Datatype dataset with Datatype conversion"); - CHECK_CUR_FILTER_AVAIL(); + /* SZIP and ScaleOffset filters don't support compound types */ + if (filter_id == H5Z_FILTER_SZIP || filter_id == H5Z_FILTER_SCALEOFFSET) { + if (MAINPROCESS) + SKIPPED(); + return; + } dataset_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_NROWS; dataset_dims[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_NCOLS; @@ -5851,6 +6794,9 @@ test_read_cmpd_filtered_dataset_type_conversion_shared(void) VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS, dataset_dims, NULL); @@ -5860,46 +6806,45 @@ test_read_cmpd_filtered_dataset_type_conversion_shared(void) chunk_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_CH_NROWS; chunk_dims[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_CH_NCOLS; - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_NAME, + dset_id = H5Dcreate2(group_id, READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_NAME, filetype, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = - H5Dopen2(file_id, "/" READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_NAME, H5P_DEFAULT); + H5Dopen2(group_id, READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_CH_NROWS / (hsize_t)mpi_size; @@ -5939,18 +6884,12 @@ test_read_cmpd_filtered_dataset_type_conversion_shared(void) VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); - /* Create property list for collective dataset read */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); - VRFY((H5Dread(dset_id, memtype, memspace, filespace, plist_id, read_buf) >= 0), "Dataset read succeeded"); + VRFY((H5Dread(dset_id, memtype, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != global_buf), "HDcalloc succeeded"); @@ -5989,7 +6928,7 @@ test_read_cmpd_filtered_dataset_type_conversion_shared(void) VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Tclose(memtype) >= 0), "Memory datatype close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -6006,7 +6945,8 @@ test_read_cmpd_filtered_dataset_type_conversion_shared(void) * 08/03/2017 */ static void -test_write_serial_read_parallel(void) +test_write_serial_read_parallel(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; @@ -6014,14 +6954,13 @@ test_write_serial_read_parallel(void) hsize_t dataset_dims[WRITE_SERIAL_READ_PARALLEL_DATASET_DIMS]; hsize_t chunk_dims[WRITE_SERIAL_READ_PARALLEL_DATASET_DIMS]; size_t i, data_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write file serially; read file in parallel"); - CHECK_CUR_FILTER_AVAIL(); - dataset_dims[0] = (hsize_t)WRITE_SERIAL_READ_PARALLEL_NROWS; dataset_dims[1] = (hsize_t)WRITE_SERIAL_READ_PARALLEL_NCOLS; dataset_dims[2] = (hsize_t)WRITE_SERIAL_READ_PARALLEL_DEPTH; @@ -6040,6 +6979,9 @@ test_write_serial_read_parallel(void) VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + /* Create the dataspace for the dataset */ chunk_dims[0] = (hsize_t)WRITE_SERIAL_READ_PARALLEL_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_SERIAL_READ_PARALLEL_CH_NCOLS; @@ -6049,20 +6991,22 @@ test_write_serial_read_parallel(void) VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_SERIAL_READ_PARALLEL_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, WRITE_SERIAL_READ_PARALLEL_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, + dset_id = H5Dcreate2(group_id, WRITE_SERIAL_READ_PARALLEL_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); data_size = dataset_dims[0] * dataset_dims[1] * dataset_dims[2] * sizeof(*data); @@ -6076,10 +7020,15 @@ test_write_serial_read_parallel(void) VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, data) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + if (data) HDfree(data); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } @@ -6095,28 +7044,16 @@ test_write_serial_read_parallel(void) correct_buf[i] = (long)i; /* All ranks open the file and verify their "portion" of the dataset is correct */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); - dset_id = H5Dopen2(file_id, "/" WRITE_SERIAL_READ_PARALLEL_DATASET_NAME, H5P_DEFAULT); + dset_id = H5Dopen2(group_id, WRITE_SERIAL_READ_PARALLEL_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - - VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, plist_id, read_buf) >= 0), + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); @@ -6127,13 +7064,13 @@ test_write_serial_read_parallel(void) HDfree(read_buf); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } -#if MPI_VERSION >= 3 +#ifdef H5_HAVE_PARALLEL_FILTERED_WRITES /* * Tests parallel write of filtered data * to a dataset. After the write has @@ -6145,7 +7082,8 @@ test_write_serial_read_parallel(void) * 08/03/2017 */ static void -test_write_parallel_read_serial(void) +test_write_parallel_read_serial(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, + hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; @@ -6158,27 +7096,18 @@ test_write_parallel_read_serial(void) hsize_t block[WRITE_PARALLEL_READ_SERIAL_DATASET_DIMS]; hsize_t offset[WRITE_PARALLEL_READ_SERIAL_DATASET_DIMS]; size_t i, data_size, correct_buf_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write file in parallel; read serially"); - CHECK_CUR_FILTER_AVAIL(); - - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_PARALLEL_READ_SERIAL_NROWS; @@ -6198,20 +7127,22 @@ test_write_parallel_read_serial(void) VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_PARALLEL_READ_SERIAL_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, WRITE_PARALLEL_READ_SERIAL_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, + dset_id = H5Dcreate2(group_id, WRITE_PARALLEL_READ_SERIAL_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes @@ -6256,22 +7187,20 @@ test_write_parallel_read_serial(void) for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); - /* Create property list for collective dataset write */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - - VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, data) >= 0), + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + if (data) HDfree(data); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); if (MAINPROCESS) { @@ -6286,7 +7215,10 @@ test_write_parallel_read_serial(void) VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); - dset_id = H5Dopen2(file_id, "/" WRITE_PARALLEL_READ_SERIAL_DATASET_NAME, H5P_DEFAULT); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + + dset_id = H5Dopen2(group_id, WRITE_PARALLEL_READ_SERIAL_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); correct_buf_size = dataset_dims[0] * dataset_dims[1] * dataset_dims[2] * sizeof(*correct_buf); @@ -6307,6 +7239,7 @@ test_write_parallel_read_serial(void) VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); HDfree(correct_buf); @@ -6326,9 +7259,11 @@ test_write_parallel_read_serial(void) * 06/04/2018 */ static void -test_shrinking_growing_chunks(void) +test_shrinking_growing_chunks(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, + hid_t dxpl_id) { - double *data = NULL; + double *data = NULL; + double *read_buf = NULL; hsize_t dataset_dims[SHRINKING_GROWING_CHUNKS_DATASET_DIMS]; hsize_t chunk_dims[SHRINKING_GROWING_CHUNKS_DATASET_DIMS]; hsize_t sel_dims[SHRINKING_GROWING_CHUNKS_DATASET_DIMS]; @@ -6337,27 +7272,18 @@ test_shrinking_growing_chunks(void) hsize_t count[SHRINKING_GROWING_CHUNKS_DATASET_DIMS]; hsize_t block[SHRINKING_GROWING_CHUNKS_DATASET_DIMS]; size_t i, data_size; - hid_t file_id = -1, dset_id = -1, plist_id = -1; - hid_t filespace = -1, memspace = -1; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing continually shrinking/growing chunks"); - CHECK_CUR_FILTER_AVAIL(); - - /* Set up file access property list with parallel I/O access */ - plist_id = H5Pcreate(H5P_FILE_ACCESS); - VRFY((plist_id >= 0), "FAPL creation succeeded"); - - VRFY((H5Pset_fapl_mpio(plist_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); - - file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)SHRINKING_GROWING_CHUNKS_NROWS; @@ -6374,19 +7300,21 @@ test_shrinking_growing_chunks(void) VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ - plist_id = H5Pcreate(H5P_DATASET_CREATE); - VRFY((plist_id >= 0), "DCPL creation succeeded"); + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, SHRINKING_GROWING_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ - VRFY((set_dcpl_filter(plist_id) >= 0), "Filter set"); + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); - dset_id = H5Dcreate2(file_id, SHRINKING_GROWING_CHUNKS_DATASET_NAME, H5T_NATIVE_DOUBLE, filespace, + dset_id = H5Dcreate2(group_id, SHRINKING_GROWING_CHUNKS_DATASET_NAME, H5T_NATIVE_DOUBLE, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* @@ -6417,39 +7345,1302 @@ test_shrinking_growing_chunks(void) VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); - /* Create property list for collective dataset write */ - plist_id = H5Pcreate(H5P_DATASET_XFER); - VRFY((plist_id >= 0), "DXPL creation succeeded"); - - VRFY((H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE) >= 0), "Set DXPL MPIO succeeded"); - data_size = sel_dims[0] * sel_dims[1] * sizeof(double); data = (double *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); + read_buf = (double *)HDcalloc(1, data_size); + VRFY((NULL != read_buf), "HDcalloc succeeded"); + for (i = 0; i < SHRINKING_GROWING_CHUNKS_NLOOPS; i++) { /* Continually write random float data, followed by zeroed-out data */ - if ((i % 2)) + if (i % 2) HDmemset(data, 0, data_size); else { size_t j; for (j = 0; j < data_size / sizeof(*data); j++) { - data[j] = (float)(rand() / (double)(RAND_MAX / (double)1.0L)); + data[j] = (rand() / (double)(RAND_MAX / (double)1.0L)); } } - VRFY((H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, memspace, filespace, plist_id, data) >= 0), + VRFY((H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + if (i % 2) { + HDmemset(read_buf, 255, data_size); + } + else { + HDmemset(read_buf, 0, data_size); + } + + VRFY((H5Dread(dset_id, H5T_NATIVE_DOUBLE, memspace, filespace, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + VRFY((0 == HDmemcmp(read_buf, data, data_size)), "data verification succeeded"); } + if (read_buf) + HDfree(read_buf); if (data) HDfree(data); + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); - VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); + VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); + + return; +} + +/* + * Tests that filtered and unfiltered partial edge chunks can be + * written to and read from correctly in parallel when only one MPI + * rank writes to a particular partial edge chunk in the dataset. + * + * The dataset contains partial edge chunks in the second dimension. + * Each MPI rank selects a hyperslab in the shape of a single chunk + * that is offset to cover the whole edge chunk and part of the + * full chunk next to the edge chunk. + */ +static void +test_edge_chunks_no_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, + hid_t dxpl_id) +{ + C_DATATYPE *data = NULL; + C_DATATYPE *read_buf = NULL; + hsize_t dataset_dims[WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; + hsize_t chunk_dims[WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; + hsize_t sel_dims[WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; + hsize_t start[WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; + hsize_t stride[WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; + hsize_t count[WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; + hsize_t block[WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; + size_t i, data_size; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID; + + if (MAINPROCESS) + HDputs("Testing write to unshared filtered edge chunks"); + + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); + VRFY((file_id >= 0), "Test file open succeeded"); + + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + + /* Create the dataspace for the dataset */ + dataset_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_NROWS; + dataset_dims[1] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_NCOLS; + chunk_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NROWS; + chunk_dims[1] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; + sel_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NROWS; + sel_dims[1] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; + + filespace = H5Screate_simple(WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS, dataset_dims, NULL); + VRFY((filespace >= 0), "File dataspace creation succeeded"); + + /* Create chunked dataset */ + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); + + VRFY((H5Pset_chunk(plist_id, WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), + "Chunk size set"); + + /* Add test filter to the pipeline */ + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); + + dset_id = H5Dcreate2(group_id, WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, + filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset creation succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + + /* Each process defines the dataset selection in memory and writes + * it to the hyperslab in the file + */ + count[0] = 1; + count[1] = 1; + stride[0] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NROWS; + stride[1] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; + block[0] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NROWS; + block[1] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; + start[0] = ((hsize_t)mpi_rank * (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NROWS); + start[1] = + (hsize_t)(WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_NCOLS - WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS); + + if (VERBOSE_MED) { + HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE + ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE + ", %" PRIuHSIZE " ]\n", + mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); + HDfflush(stdout); + } + + /* Select hyperslab in the file */ + filespace = H5Dget_space(dset_id); + VRFY((filespace >= 0), "File dataspace retrieval succeeded"); + + VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), + "Hyperslab selection succeeded"); + + /* Fill data buffer */ + data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); + + data = (C_DATATYPE *)HDcalloc(1, data_size); + VRFY((NULL != data), "HDcalloc succeeded"); + + read_buf = (C_DATATYPE *)HDcalloc(1, data_size); + VRFY((NULL != read_buf), "HDcalloc succeeded"); + + for (i = 0; i < data_size / sizeof(*data); i++) + data[i] = (C_DATATYPE)GEN_DATA(i); + + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), + "Dataset write succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, (mpi_size > 1) ? SOME_CHUNKS_WRITTEN : ALL_CHUNKS_WRITTEN); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + /* Verify the correct data was written */ + dset_id = H5Dopen2(group_id, WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset open succeeded"); + + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + VRFY((0 == HDmemcmp(read_buf, data, data_size)), "Data verification succeeded"); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + /* Repeat the previous, but set option to not filter partial edge chunks */ + if (MAINPROCESS) + HDputs("Testing write to unshared unfiltered edge chunks"); + + H5Pset_chunk_opts(plist_id, H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS); + + dset_id = H5Dcreate2(group_id, WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME2, HDF5_DATATYPE_NAME, + filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset creation succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + + /* Each process defines the dataset selection in memory and writes + * it to the hyperslab in the file + */ + count[0] = 1; + count[1] = 1; + stride[0] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NROWS; + stride[1] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; + block[0] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NROWS; + block[1] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; + start[0] = ((hsize_t)mpi_rank * (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NROWS); + start[1] = + (hsize_t)(WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_NCOLS - WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS); + + if (VERBOSE_MED) { + HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE + ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE + ", %" PRIuHSIZE " ]\n", + mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); + HDfflush(stdout); + } + + /* Select hyperslab in the file */ + filespace = H5Dget_space(dset_id); + VRFY((filespace >= 0), "File dataspace retrieval succeeded"); + + VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), + "Hyperslab selection succeeded"); + + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), + "Dataset write succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, (mpi_size > 1) ? SOME_CHUNKS_WRITTEN : ALL_CHUNKS_WRITTEN); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + /* Verify the correct data was written */ + dset_id = H5Dopen2(group_id, WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME2, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset open succeeded"); + + HDmemset(read_buf, 255, data_size); + + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + VRFY((0 == HDmemcmp(read_buf, data, data_size)), "Data verification succeeded"); + + if (data) + HDfree(data); + if (read_buf) + HDfree(read_buf); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); + VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); + + return; +} + +/* + * Tests that filtered and unfiltered partial edge chunks can be + * written to and read from correctly in parallel when every MPI + * rank writes to every partial edge chunk in the dataset. + * + * The dataset contains partial edge chunks in the second dimension. + * Each MPI rank selects a hyperslab in the shape of one row of each + * chunk that is offset in the second dimension to cover the whole + * edge chunk and part of the full chunk next to the edge chunk. + */ +static void +test_edge_chunks_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, + hid_t dxpl_id) +{ + C_DATATYPE *data = NULL; + C_DATATYPE *read_buf = NULL; + hsize_t dataset_dims[WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; + hsize_t chunk_dims[WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; + hsize_t sel_dims[WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; + hsize_t start[WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; + hsize_t stride[WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; + hsize_t count[WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; + hsize_t block[WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; + size_t i, data_size; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID; + + if (MAINPROCESS) + HDputs("Testing write to shared filtered edge chunks"); + + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); + VRFY((file_id >= 0), "Test file open succeeded"); + + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + + /* Create the dataspace for the dataset */ + dataset_dims[0] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_NROWS; + dataset_dims[1] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_NCOLS; + chunk_dims[0] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NROWS; + chunk_dims[1] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; + sel_dims[0] = (hsize_t)DIM0_SCALE_FACTOR; + sel_dims[1] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; + + filespace = H5Screate_simple(WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS, dataset_dims, NULL); + VRFY((filespace >= 0), "File dataspace creation succeeded"); + + /* Create chunked dataset */ + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); + + VRFY((H5Pset_chunk(plist_id, WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), + "Chunk size set"); + + /* Add test filter to the pipeline */ + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); + + dset_id = H5Dcreate2(group_id, WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, + filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset creation succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + + /* Each process defines the dataset selection in memory and writes + * it to the hyperslab in the file + */ + count[0] = + (hsize_t)(WRITE_SHARED_FILTERED_EDGE_CHUNKS_NROWS / WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NROWS); + count[1] = 1; + stride[0] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NROWS; + stride[1] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; + block[0] = (hsize_t)1; + block[1] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; + start[0] = (hsize_t)mpi_rank; + start[1] = + (hsize_t)(WRITE_SHARED_FILTERED_EDGE_CHUNKS_NCOLS - WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS); + + if (VERBOSE_MED) { + HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE + ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE + ", %" PRIuHSIZE " ]\n", + mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); + HDfflush(stdout); + } + + /* Select hyperslab in the file */ + filespace = H5Dget_space(dset_id); + VRFY((filespace >= 0), "File dataspace retrieval succeeded"); + + VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), + "Hyperslab selection succeeded"); + + /* Fill data buffer */ + data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); + + data = (C_DATATYPE *)HDcalloc(1, data_size); + VRFY((NULL != data), "HDcalloc succeeded"); + + read_buf = (C_DATATYPE *)HDcalloc(1, data_size); + VRFY((NULL != read_buf), "HDcalloc succeeded"); + + for (i = 0; i < data_size / sizeof(*data); i++) + data[i] = (C_DATATYPE)GEN_DATA(i); + + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), + "Dataset write succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + /* Verify the correct data was written */ + dset_id = H5Dopen2(group_id, WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset open succeeded"); + + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + VRFY((0 == HDmemcmp(read_buf, data, data_size)), "Data verification succeeded"); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + /* Repeat the previous, but set option to not filter partial edge chunks */ + if (MAINPROCESS) + HDputs("Testing write to shared unfiltered edge chunks"); + + H5Pset_chunk_opts(plist_id, H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS); + + dset_id = H5Dcreate2(group_id, WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME2, HDF5_DATATYPE_NAME, + filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset creation succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + + /* Each process defines the dataset selection in memory and writes + * it to the hyperslab in the file + */ + count[0] = + (hsize_t)(WRITE_SHARED_FILTERED_EDGE_CHUNKS_NROWS / WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NROWS); + count[1] = 1; + stride[0] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NROWS; + stride[1] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; + block[0] = (hsize_t)1; + block[1] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; + start[0] = (hsize_t)mpi_rank; + start[1] = + (hsize_t)(WRITE_SHARED_FILTERED_EDGE_CHUNKS_NCOLS - WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS); + + if (VERBOSE_MED) { + HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE + ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE + ", %" PRIuHSIZE " ]\n", + mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); + HDfflush(stdout); + } + + /* Select hyperslab in the file */ + filespace = H5Dget_space(dset_id); + VRFY((filespace >= 0), "File dataspace retrieval succeeded"); + + VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), + "Hyperslab selection succeeded"); + + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), + "Dataset write succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + /* Verify the correct data was written */ + dset_id = H5Dopen2(group_id, WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME2, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset open succeeded"); + + HDmemset(read_buf, 255, data_size); + + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + VRFY((0 == HDmemcmp(read_buf, data, data_size)), "Data verification succeeded"); + + if (data) + HDfree(data); + if (read_buf) + HDfree(read_buf); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); + VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); + + return; +} + +/* + * Tests that filtered and unfiltered partial edge chunks can be + * written to and read from correctly in parallel when only one + * MPI rank writes to a particular edge chunk in the dataset and + * only performs a partial write to the edge chunk. + * + * The dataset contains partial edge chunks in the second dimension. + * Each MPI rank selects a hyperslab in the shape of part of a single + * edge chunk and writes to just a portion of the edge chunk. + */ +static void +test_edge_chunks_partial_write(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, + hid_t dxpl_id) +{ + /* TODO */ +} + +/* + * Tests that the parallel compression feature correctly handles + * writing fill values to a dataset and reading fill values from + * unallocated parts of a dataset. + */ +static void +test_fill_values(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, + hid_t dxpl_id) +{ + C_DATATYPE *data = NULL; + C_DATATYPE *read_buf = NULL; + C_DATATYPE *correct_buf = NULL; + C_DATATYPE fill_value; + hsize_t dataset_dims[FILL_VALUES_TEST_DATASET_DIMS]; + hsize_t chunk_dims[FILL_VALUES_TEST_DATASET_DIMS]; + hsize_t sel_dims[FILL_VALUES_TEST_DATASET_DIMS]; + hsize_t start[FILL_VALUES_TEST_DATASET_DIMS]; + hsize_t stride[FILL_VALUES_TEST_DATASET_DIMS]; + hsize_t count[FILL_VALUES_TEST_DATASET_DIMS]; + hsize_t block[FILL_VALUES_TEST_DATASET_DIMS]; + size_t i, data_size, read_buf_size; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID; + int * recvcounts = NULL; + int * displs = NULL; + + if (MAINPROCESS) + HDputs("Testing fill values"); + + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); + VRFY((file_id >= 0), "Test file open succeeded"); + + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + + /* Create the dataspace for the dataset */ + dataset_dims[0] = (hsize_t)FILL_VALUES_TEST_NROWS; + dataset_dims[1] = (hsize_t)FILL_VALUES_TEST_NCOLS; + chunk_dims[0] = (hsize_t)FILL_VALUES_TEST_CH_NROWS; + chunk_dims[1] = (hsize_t)FILL_VALUES_TEST_CH_NCOLS; + sel_dims[0] = (hsize_t)DIM0_SCALE_FACTOR; + sel_dims[1] = (hsize_t)FILL_VALUES_TEST_CH_NCOLS * (hsize_t)DIM1_SCALE_FACTOR; + + filespace = H5Screate_simple(FILL_VALUES_TEST_DATASET_DIMS, dataset_dims, NULL); + VRFY((filespace >= 0), "File dataspace creation succeeded"); + + /* Create chunked dataset */ + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); + + VRFY((H5Pset_chunk(plist_id, FILL_VALUES_TEST_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); + + /* Add test filter to the pipeline */ + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); + + /* Set a fill value */ + fill_value = FILL_VALUES_TEST_FILL_VAL; + VRFY((H5Pset_fill_value(plist_id, HDF5_DATATYPE_NAME, &fill_value) >= 0), "Fill Value set"); + + dset_id = H5Dcreate2(group_id, FILL_VALUES_TEST_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, + plist_id, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset creation succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + + /* Allocate buffer for reading entire dataset */ + read_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*read_buf); + + read_buf = HDcalloc(1, read_buf_size); + VRFY((NULL != read_buf), "HDcalloc succeeded"); + + correct_buf = HDcalloc(1, read_buf_size); + VRFY((NULL != correct_buf), "HDcalloc succeeded"); + + /* Read entire dataset and verify that the fill value is returned */ + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + for (i = 0; i < read_buf_size / sizeof(*read_buf); i++) + correct_buf[i] = FILL_VALUES_TEST_FILL_VAL; + + VRFY((0 == HDmemcmp(read_buf, correct_buf, read_buf_size)), "Data verification succeeded"); + + /* + * Write to part of the first chunk in the dataset with + * all ranks, then read the whole dataset and ensure that + * the fill value is returned for the unwritten part of + * the chunk, as well as for the rest of the dataset that + * hasn't been written to yet. + */ + count[0] = 1; + count[1] = 1; + stride[0] = (hsize_t)FILL_VALUES_TEST_CH_NROWS; + stride[1] = (hsize_t)FILL_VALUES_TEST_CH_NCOLS; + block[0] = 1; + block[1] = (hsize_t)(FILL_VALUES_TEST_CH_NCOLS - 1); + start[0] = (hsize_t)mpi_rank; + start[1] = 0; + + if (VERBOSE_MED) { + HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE + ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE + ", %" PRIuHSIZE " ]\n", + mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); + HDfflush(stdout); + } + + /* Select hyperslab in the file */ + filespace = H5Dget_space(dset_id); + VRFY((filespace >= 0), "File dataspace retrieval succeeded"); + + VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), + "Hyperslab selection succeeded"); + + /* Fill data buffer */ + data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); + + data = (C_DATATYPE *)HDcalloc(1, data_size); + VRFY((NULL != data), "HDcalloc succeeded"); + + for (i = 0; i < data_size / sizeof(*data); i++) + data[i] = (C_DATATYPE)GEN_DATA(i); + + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), + "Dataset write succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + /* Verify correct data was written */ + dset_id = H5Dopen2(group_id, FILL_VALUES_TEST_DATASET_NAME, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset open succeeded"); + + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + /* + * Each MPI rank communicates their written piece of data + * into each other rank's correctness-checking buffer + */ + recvcounts = HDcalloc(1, (size_t)mpi_size * sizeof(*recvcounts)); + VRFY((NULL != recvcounts), "HDcalloc succeeded"); + + displs = HDcalloc(1, (size_t)mpi_size * sizeof(*displs)); + VRFY((NULL != displs), "HDcalloc succeeded"); + + for (i = 0; i < (size_t)mpi_size; i++) { + recvcounts[i] = (int)(count[1] * block[1]); + displs[i] = (int)(i * dataset_dims[1]); + } + + VRFY((MPI_SUCCESS == MPI_Allgatherv(data, recvcounts[mpi_rank], C_DATATYPE_MPI, correct_buf, recvcounts, + displs, C_DATATYPE_MPI, comm)), + "MPI_Allgatherv succeeded"); + + VRFY((0 == HDmemcmp(read_buf, correct_buf, read_buf_size)), "Data verification succeeded"); + + /* + * Write to whole dataset and ensure fill value isn't returned + * after reading whole dataset back + */ + + /* Each process defines the dataset selection in memory and writes + * it to the hyperslab in the file + */ + count[0] = (hsize_t)FILL_VALUES_TEST_NROWS / (hsize_t)FILL_VALUES_TEST_CH_NROWS; + count[1] = (hsize_t)FILL_VALUES_TEST_NCOLS / (hsize_t)FILL_VALUES_TEST_CH_NCOLS; + stride[0] = (hsize_t)FILL_VALUES_TEST_CH_NROWS; + stride[1] = (hsize_t)FILL_VALUES_TEST_CH_NCOLS; + block[0] = (hsize_t)FILL_VALUES_TEST_CH_NROWS / (hsize_t)mpi_size; + block[1] = (hsize_t)FILL_VALUES_TEST_CH_NCOLS; + start[0] = (hsize_t)mpi_rank * block[0]; + start[1] = 0; + + if (VERBOSE_MED) { + HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE + ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE + ", %" PRIuHSIZE " ]\n", + mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); + HDfflush(stdout); + } + + VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), + "Hyperslab selection succeeded"); + + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), + "Dataset write succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + /* Verify correct data was written */ + dset_id = H5Dopen2(group_id, FILL_VALUES_TEST_DATASET_NAME, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset open succeeded"); + + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + for (i = 0; i < read_buf_size / sizeof(*read_buf); i++) + VRFY((read_buf[i] != FILL_VALUES_TEST_FILL_VAL), "Data verification succeeded"); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + /******************************************************************** + * Set the fill time to H5D_FILL_TIME_ALLOC and repeat the previous * + ********************************************************************/ + + VRFY((H5Pset_fill_time(plist_id, H5D_FILL_TIME_ALLOC) >= 0), "H5Pset_fill_time succeeded"); + + dset_id = H5Dcreate2(group_id, FILL_VALUES_TEST_DATASET_NAME2, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, + plist_id, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset creation succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + + /* Read entire dataset and verify that the fill value is returned */ + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + for (i = 0; i < read_buf_size / sizeof(*read_buf); i++) + correct_buf[i] = FILL_VALUES_TEST_FILL_VAL; + + VRFY((0 == HDmemcmp(read_buf, correct_buf, read_buf_size)), "Data verification succeeded"); + + /* + * Write to part of the first chunk in the dataset with + * all ranks, then read the whole dataset and ensure that + * the fill value is returned for the unwritten part of + * the chunk, as well as for the rest of the dataset that + * hasn't been written to yet. + */ + count[0] = 1; + count[1] = 1; + stride[0] = (hsize_t)FILL_VALUES_TEST_CH_NROWS; + stride[1] = (hsize_t)FILL_VALUES_TEST_CH_NCOLS; + block[0] = 1; + block[1] = (hsize_t)(FILL_VALUES_TEST_CH_NCOLS - 1); + start[0] = (hsize_t)mpi_rank; + start[1] = 0; + + if (VERBOSE_MED) { + HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE + ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE + ", %" PRIuHSIZE " ]\n", + mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); + HDfflush(stdout); + } + + /* Select hyperslab in the file */ + filespace = H5Dget_space(dset_id); + VRFY((filespace >= 0), "File dataspace retrieval succeeded"); + + VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), + "Hyperslab selection succeeded"); + + for (i = 0; i < data_size / sizeof(*data); i++) + data[i] = (C_DATATYPE)GEN_DATA(i); + + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), + "Dataset write succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + /* Verify correct data was written */ + dset_id = H5Dopen2(group_id, FILL_VALUES_TEST_DATASET_NAME2, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset open succeeded"); + + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + for (i = 0; i < (size_t)mpi_size; i++) { + recvcounts[i] = (int)(count[1] * block[1]); + displs[i] = (int)(i * dataset_dims[1]); + } + + /* + * Each MPI rank communicates their written piece of data + * into each other rank's correctness-checking buffer + */ + VRFY((MPI_SUCCESS == MPI_Allgatherv(data, recvcounts[mpi_rank], C_DATATYPE_MPI, correct_buf, recvcounts, + displs, C_DATATYPE_MPI, comm)), + "MPI_Allgatherv succeeded"); + + VRFY((0 == HDmemcmp(read_buf, correct_buf, read_buf_size)), "Data verification succeeded"); + + /* + * Write to whole dataset and ensure fill value isn't returned + * after reading whole dataset back + */ + + /* Each process defines the dataset selection in memory and writes + * it to the hyperslab in the file + */ + count[0] = (hsize_t)FILL_VALUES_TEST_NROWS / (hsize_t)FILL_VALUES_TEST_CH_NROWS; + count[1] = (hsize_t)FILL_VALUES_TEST_NCOLS / (hsize_t)FILL_VALUES_TEST_CH_NCOLS; + stride[0] = (hsize_t)FILL_VALUES_TEST_CH_NROWS; + stride[1] = (hsize_t)FILL_VALUES_TEST_CH_NCOLS; + block[0] = (hsize_t)FILL_VALUES_TEST_CH_NROWS / (hsize_t)mpi_size; + block[1] = (hsize_t)FILL_VALUES_TEST_CH_NCOLS; + start[0] = (hsize_t)mpi_rank * block[0]; + start[1] = 0; + + if (VERBOSE_MED) { + HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE + ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE + ", %" PRIuHSIZE " ]\n", + mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); + HDfflush(stdout); + } + + VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), + "Hyperslab selection succeeded"); + + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), + "Dataset write succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + /* Verify correct data was written */ + dset_id = H5Dopen2(group_id, FILL_VALUES_TEST_DATASET_NAME2, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset open succeeded"); + + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + for (i = 0; i < read_buf_size / sizeof(*read_buf); i++) + VRFY((read_buf[i] != FILL_VALUES_TEST_FILL_VAL), "Data verification succeeded"); + + if (displs) + HDfree(displs); + if (recvcounts) + HDfree(recvcounts); + if (data) + HDfree(data); + if (read_buf) + HDfree(read_buf); + if (correct_buf) + HDfree(correct_buf); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); + VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); + + return; +} + +/* + * Tests that the parallel compression feature can handle + * an undefined fill value. Nothing is verified in this + * test since the fill value isn't defined. + */ +static void +test_fill_value_undefined(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, + hid_t dxpl_id) +{ + H5D_alloc_time_t alloc_time; + C_DATATYPE * data = NULL; + C_DATATYPE * read_buf = NULL; + hsize_t dataset_dims[FILL_VALUE_UNDEFINED_TEST_DATASET_DIMS]; + hsize_t chunk_dims[FILL_VALUE_UNDEFINED_TEST_DATASET_DIMS]; + hsize_t sel_dims[FILL_VALUE_UNDEFINED_TEST_DATASET_DIMS]; + hsize_t start[FILL_VALUE_UNDEFINED_TEST_DATASET_DIMS]; + hsize_t stride[FILL_VALUE_UNDEFINED_TEST_DATASET_DIMS]; + hsize_t count[FILL_VALUE_UNDEFINED_TEST_DATASET_DIMS]; + hsize_t block[FILL_VALUE_UNDEFINED_TEST_DATASET_DIMS]; + size_t i, data_size, read_buf_size; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID; + + if (MAINPROCESS) + HDputs("Testing undefined fill value"); + + VRFY((H5Pget_alloc_time(dcpl_id, &alloc_time) >= 0), "H5Pget_alloc_time succeeded"); + + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); + VRFY((file_id >= 0), "Test file open succeeded"); + + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + + /* Create the dataspace for the dataset */ + dataset_dims[0] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_NROWS; + dataset_dims[1] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_NCOLS; + chunk_dims[0] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NROWS; + chunk_dims[1] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NCOLS; + sel_dims[0] = (hsize_t)DIM0_SCALE_FACTOR; + sel_dims[1] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NCOLS * (hsize_t)DIM1_SCALE_FACTOR; + + filespace = H5Screate_simple(FILL_VALUE_UNDEFINED_TEST_DATASET_DIMS, dataset_dims, NULL); + VRFY((filespace >= 0), "File dataspace creation succeeded"); + + /* Create chunked dataset */ + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); + + VRFY((H5Pset_chunk(plist_id, FILL_VALUE_UNDEFINED_TEST_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); + + /* Add test filter to the pipeline */ + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); + + /* Set an undefined fill value */ + VRFY((H5Pset_fill_value(plist_id, HDF5_DATATYPE_NAME, NULL) >= 0), "Fill Value set"); + + dset_id = H5Dcreate2(group_id, FILL_VALUE_UNDEFINED_TEST_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, + H5P_DEFAULT, plist_id, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset creation succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + + /* Allocate buffer for reading entire dataset */ + read_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*read_buf); + + read_buf = HDcalloc(1, read_buf_size); + VRFY((NULL != read_buf), "HDcalloc succeeded"); + + /* + * Read entire dataset - nothing to verify since there's no fill value. + * If not using early space allocation, the read should fail since storage + * isn't allocated yet and no fill value is defined. + */ + if (alloc_time == H5D_ALLOC_TIME_EARLY) { + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + } + else { + H5E_BEGIN_TRY + { + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) < 0), + "Dataset read succeeded"); + } + H5E_END_TRY; + } + + /* + * Write to part of the first chunk in the dataset with + * all ranks, then read the whole dataset. Don't verify + * anything since there's no fill value defined. + */ + count[0] = 1; + count[1] = 1; + stride[0] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NROWS; + stride[1] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NCOLS; + block[0] = 1; + block[1] = (hsize_t)(FILL_VALUE_UNDEFINED_TEST_CH_NCOLS - 1); + start[0] = (hsize_t)mpi_rank; + start[1] = 0; + + if (VERBOSE_MED) { + HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE + ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE + ", %" PRIuHSIZE " ]\n", + mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); + HDfflush(stdout); + } + + /* Select hyperslab in the file */ + filespace = H5Dget_space(dset_id); + VRFY((filespace >= 0), "File dataspace retrieval succeeded"); + + VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), + "Hyperslab selection succeeded"); + + /* Fill data buffer */ + data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); + + data = (C_DATATYPE *)HDcalloc(1, data_size); + VRFY((NULL != data), "HDcalloc succeeded"); + + for (i = 0; i < data_size / sizeof(*data); i++) + data[i] = (C_DATATYPE)GEN_DATA(i); + + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), + "Dataset write succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + dset_id = H5Dopen2(group_id, FILL_VALUE_UNDEFINED_TEST_DATASET_NAME, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset open succeeded"); + + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + /* + * Write to whole dataset and ensure data is correct + * after reading whole dataset back + */ + + /* Each process defines the dataset selection in memory and writes + * it to the hyperslab in the file + */ + count[0] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_NROWS / (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NROWS; + count[1] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_NCOLS / (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NCOLS; + stride[0] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NROWS; + stride[1] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NCOLS; + block[0] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NROWS / (hsize_t)mpi_size; + block[1] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NCOLS; + start[0] = (hsize_t)mpi_rank * block[0]; + start[1] = 0; + + if (VERBOSE_MED) { + HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE + ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE + ", %" PRIuHSIZE " ]\n", + mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); + HDfflush(stdout); + } + + VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), + "Hyperslab selection succeeded"); + + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), + "Dataset write succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + /* Verify correct data was written */ + dset_id = H5Dopen2(group_id, FILL_VALUE_UNDEFINED_TEST_DATASET_NAME, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset open succeeded"); + + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + if (data) + HDfree(data); + if (read_buf) + HDfree(read_buf); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); + VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); + + return; +} + +/* + * Tests that the parallel compression feature correctly handles + * avoiding writing fill values to a dataset when the fill time + * is set as H5D_FILL_TIME_NEVER. + */ +static void +test_fill_time_never(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, + hid_t dxpl_id) +{ + C_DATATYPE *data = NULL; + C_DATATYPE *read_buf = NULL; + C_DATATYPE *fill_buf = NULL; + C_DATATYPE fill_value; + hsize_t dataset_dims[FILL_TIME_NEVER_TEST_DATASET_DIMS]; + hsize_t chunk_dims[FILL_TIME_NEVER_TEST_DATASET_DIMS]; + hsize_t sel_dims[FILL_TIME_NEVER_TEST_DATASET_DIMS]; + hsize_t start[FILL_TIME_NEVER_TEST_DATASET_DIMS]; + hsize_t stride[FILL_TIME_NEVER_TEST_DATASET_DIMS]; + hsize_t count[FILL_TIME_NEVER_TEST_DATASET_DIMS]; + hsize_t block[FILL_TIME_NEVER_TEST_DATASET_DIMS]; + size_t i, data_size, read_buf_size; + hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t filespace = H5I_INVALID_HID; + int * recvcounts = NULL; + int * displs = NULL; + + if (MAINPROCESS) + HDputs("Testing fill time H5D_FILL_TIME_NEVER"); + + /* + * Only run this test when incremental file space allocation is + * used, as HDF5's chunk allocation code always writes fill values + * when filters are in the pipeline, but parallel compression does + * incremental file space allocation differently. + */ + { + H5D_alloc_time_t alloc_time; + + VRFY((H5Pget_alloc_time(dcpl_id, &alloc_time) >= 0), "H5Pget_alloc_time succeeded"); + + if (alloc_time != H5D_ALLOC_TIME_INCR) { + if (MAINPROCESS) + SKIPPED(); + return; + } + } + + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); + VRFY((file_id >= 0), "Test file open succeeded"); + + group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gopen2 succeeded"); + + /* Create the dataspace for the dataset */ + dataset_dims[0] = (hsize_t)FILL_TIME_NEVER_TEST_NROWS; + dataset_dims[1] = (hsize_t)FILL_TIME_NEVER_TEST_NCOLS; + chunk_dims[0] = (hsize_t)FILL_TIME_NEVER_TEST_CH_NROWS; + chunk_dims[1] = (hsize_t)FILL_TIME_NEVER_TEST_CH_NCOLS; + sel_dims[0] = (hsize_t)DIM0_SCALE_FACTOR; + sel_dims[1] = (hsize_t)FILL_TIME_NEVER_TEST_CH_NCOLS * (hsize_t)DIM1_SCALE_FACTOR; + + filespace = H5Screate_simple(FILL_TIME_NEVER_TEST_DATASET_DIMS, dataset_dims, NULL); + VRFY((filespace >= 0), "File dataspace creation succeeded"); + + /* Create chunked dataset */ + plist_id = H5Pcopy(dcpl_id); + VRFY((plist_id >= 0), "DCPL copy succeeded"); + + VRFY((H5Pset_chunk(plist_id, FILL_TIME_NEVER_TEST_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); + + /* Add test filter to the pipeline */ + VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); + + /* Set a fill value */ + fill_value = FILL_VALUES_TEST_FILL_VAL; + VRFY((H5Pset_fill_value(plist_id, HDF5_DATATYPE_NAME, &fill_value) >= 0), "Fill Value set"); + + /* Set fill time of 'never' */ + VRFY((H5Pset_fill_time(plist_id, H5D_FILL_TIME_NEVER) >= 0), "H5Pset_fill_time succeeded"); + + dset_id = H5Dcreate2(group_id, FILL_TIME_NEVER_TEST_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, + H5P_DEFAULT, plist_id, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset creation succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); + + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + + /* Allocate buffer for reading entire dataset */ + read_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*read_buf); + + read_buf = HDcalloc(1, read_buf_size); + VRFY((NULL != read_buf), "HDcalloc succeeded"); + + fill_buf = HDcalloc(1, read_buf_size); + VRFY((NULL != fill_buf), "HDcalloc succeeded"); + + /* Read entire dataset and verify that the fill value isn't returned */ + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + for (i = 0; i < read_buf_size / sizeof(*read_buf); i++) + fill_buf[i] = FILL_TIME_NEVER_TEST_FILL_VAL; + + /* + * It should be very unlikely for the dataset's random + * values to all be the fill value, so this should be + * a safe comparison in theory. + */ + VRFY((0 != HDmemcmp(read_buf, fill_buf, read_buf_size)), "Data verification succeeded"); + + /* + * Write to part of the first chunk in the dataset with + * all ranks, then read the whole dataset and ensure that + * the fill value isn't returned for the unwritten part of + * the chunk, as well as for the rest of the dataset that + * hasn't been written to yet. + */ + count[0] = 1; + count[1] = 1; + stride[0] = (hsize_t)FILL_TIME_NEVER_TEST_CH_NROWS; + stride[1] = (hsize_t)FILL_TIME_NEVER_TEST_CH_NCOLS; + block[0] = 1; + block[1] = (hsize_t)(FILL_TIME_NEVER_TEST_CH_NCOLS - 1); + start[0] = (hsize_t)mpi_rank; + start[1] = 0; + + if (VERBOSE_MED) { + HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE + ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE + ", %" PRIuHSIZE " ]\n", + mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); + HDfflush(stdout); + } + + /* Select hyperslab in the file */ + filespace = H5Dget_space(dset_id); + VRFY((filespace >= 0), "File dataspace retrieval succeeded"); + + VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), + "Hyperslab selection succeeded"); + + /* Fill data buffer */ + data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); + + data = (C_DATATYPE *)HDcalloc(1, data_size); + VRFY((NULL != data), "HDcalloc succeeded"); + + for (i = 0; i < data_size / sizeof(*data); i++) + data[i] = (C_DATATYPE)GEN_DATA(i); + + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), + "Dataset write succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + /* Verify correct data was written */ + dset_id = H5Dopen2(group_id, FILL_TIME_NEVER_TEST_DATASET_NAME, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset open succeeded"); + + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + /* + * Each MPI rank communicates their written piece of data + * into each other rank's correctness-checking buffer + */ + recvcounts = HDcalloc(1, (size_t)mpi_size * sizeof(*recvcounts)); + VRFY((NULL != recvcounts), "HDcalloc succeeded"); + + displs = HDcalloc(1, (size_t)mpi_size * sizeof(*displs)); + VRFY((NULL != displs), "HDcalloc succeeded"); + + for (i = 0; i < (size_t)mpi_size; i++) { + recvcounts[i] = (int)(count[1] * block[1]); + displs[i] = (int)(i * dataset_dims[1]); + } + + VRFY((MPI_SUCCESS == MPI_Allgatherv(data, recvcounts[mpi_rank], C_DATATYPE_MPI, fill_buf, recvcounts, + displs, C_DATATYPE_MPI, comm)), + "MPI_Allgatherv succeeded"); + + /* + * It should be very unlikely for the dataset's random + * values to all be the fill value, so this should be + * a safe comparison in theory. + */ + VRFY((0 != HDmemcmp(read_buf, fill_buf, read_buf_size)), "Data verification succeeded"); + + /* + * Write to whole dataset and ensure fill value isn't returned + * after reading whole dataset back + */ + + /* Each process defines the dataset selection in memory and writes + * it to the hyperslab in the file + */ + count[0] = (hsize_t)FILL_TIME_NEVER_TEST_NROWS / (hsize_t)FILL_TIME_NEVER_TEST_CH_NROWS; + count[1] = (hsize_t)FILL_TIME_NEVER_TEST_NCOLS / (hsize_t)FILL_TIME_NEVER_TEST_CH_NCOLS; + stride[0] = (hsize_t)FILL_TIME_NEVER_TEST_CH_NROWS; + stride[1] = (hsize_t)FILL_TIME_NEVER_TEST_CH_NCOLS; + block[0] = (hsize_t)FILL_TIME_NEVER_TEST_CH_NROWS / (hsize_t)mpi_size; + block[1] = (hsize_t)FILL_TIME_NEVER_TEST_CH_NCOLS; + start[0] = (hsize_t)mpi_rank * block[0]; + start[1] = 0; + + if (VERBOSE_MED) { + HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE + ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE + ", %" PRIuHSIZE " ]\n", + mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); + HDfflush(stdout); + } + + VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), + "Hyperslab selection succeeded"); + + VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), + "Dataset write succeeded"); + + /* Verify space allocation status */ + verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); + + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + + /* Verify correct data was written */ + dset_id = H5Dopen2(group_id, FILL_TIME_NEVER_TEST_DATASET_NAME, H5P_DEFAULT); + VRFY((dset_id >= 0), "Dataset open succeeded"); + + VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), + "Dataset read succeeded"); + + for (i = 0; i < read_buf_size / sizeof(*read_buf); i++) + VRFY((read_buf[i] != FILL_TIME_NEVER_TEST_FILL_VAL), "Data verification succeeded"); + + if (displs) + HDfree(displs); + if (recvcounts) + HDfree(recvcounts); + if (data) + HDfree(data); + if (read_buf) + HDfree(read_buf); + if (fill_buf) + HDfree(fill_buf); + + VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); + VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); + VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); + VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; @@ -6459,8 +8650,14 @@ test_shrinking_growing_chunks(void) int main(int argc, char **argv) { - size_t i; - hid_t file_id = -1, fapl = -1; + size_t cur_filter_idx = 0; + size_t num_filters = 0; + hid_t file_id = H5I_INVALID_HID; + hid_t fcpl_id = H5I_INVALID_HID; + hid_t group_id = H5I_INVALID_HID; + hid_t fapl_id = H5I_INVALID_HID; + hid_t dxpl_id = H5I_INVALID_HID; + hid_t dcpl_id = H5I_INVALID_HID; int mpi_code; /* Initialize MPI */ @@ -6487,7 +8684,7 @@ main(int argc, char **argv) if (MAINPROCESS) { HDprintf("==========================\n"); - HDprintf("Parallel Filters tests\n"); + HDprintf(" Parallel Filters tests\n"); HDprintf("==========================\n\n"); } @@ -6496,72 +8693,161 @@ main(int argc, char **argv) TestAlarmOn(); - /* Create test file */ - fapl = H5Pcreate(H5P_FILE_ACCESS); - VRFY((fapl >= 0), "FAPL creation succeeded"); + num_filters = ARRAY_SIZE(filterIDs); - VRFY((H5Pset_fapl_mpio(fapl, comm, info) >= 0), "Set FAPL MPIO succeeded"); + /* Set up file access property list with parallel I/O access, + * collective metadata reads/writes and the latest library + * version bounds */ + fapl_id = H5Pcreate(H5P_FILE_ACCESS); + VRFY((fapl_id >= 0), "FAPL creation succeeded"); - VRFY((H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); + VRFY((H5Pset_fapl_mpio(fapl_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); + VRFY((H5Pset_all_coll_metadata_ops(fapl_id, TRUE) >= 0), "H5Pset_all_coll_metadata_ops succeeded"); + VRFY((H5Pset_coll_metadata_write(fapl_id, TRUE) >= 0), "H5Pset_coll_metadata_write succeeded"); - VRFY((h5_fixname(FILENAME[0], fapl, filenames[0], sizeof(filenames[0])) != NULL), - "Test file name created"); - - file_id = H5Fcreate(filenames[0], H5F_ACC_TRUNC, H5P_DEFAULT, fapl); - VRFY((file_id >= 0), "Test file creation succeeded"); - - VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); - - for (i = 0; i < ARRAY_SIZE(tests); i++) { - if (MPI_SUCCESS == (mpi_code = MPI_Barrier(comm))) { - (*tests[i])(); - } - else { - if (MAINPROCESS) - MESG("MPI_Barrier failed"); - nerrors++; - } - } + VRFY((H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), + "Set libver bounds succeeded"); /* - * Increment the filter index to switch to the checksum filter - * and re-run the tests. + * Set up Paged and Persistent Free Space Management */ - cur_filter_idx++; - - h5_clean_files(FILENAME, fapl); + fcpl_id = H5Pcreate(H5P_FILE_CREATE); + VRFY((fcpl_id >= 0), "FCPL creation succeeded"); - fapl = H5Pcreate(H5P_FILE_ACCESS); - VRFY((fapl >= 0), "FAPL creation succeeded"); + VRFY((H5Pset_file_space_strategy(fcpl_id, H5F_FSPACE_STRATEGY_PAGE, TRUE, 1) >= 0), + "H5Pset_file_space_strategy succeeded"); - VRFY((H5Pset_fapl_mpio(fapl, comm, info) >= 0), "Set FAPL MPIO succeeded"); - - VRFY((H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), - "Set libver bounds succeeded"); + VRFY((h5_fixname(FILENAME[0], fapl_id, filenames[0], sizeof(filenames[0])) != NULL), + "Test file name created"); - file_id = H5Fcreate(filenames[0], H5F_ACC_TRUNC, H5P_DEFAULT, fapl); + file_id = H5Fcreate(filenames[0], H5F_ACC_TRUNC, fcpl_id, fapl_id); VRFY((file_id >= 0), "Test file creation succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); + file_id = H5I_INVALID_HID; - if (MAINPROCESS) { - HDprintf("\n=================================================================\n"); - HDprintf("Re-running Parallel Filters tests with Fletcher32 checksum filter\n"); - HDprintf("=================================================================\n\n"); - } - - for (i = 0; i < ARRAY_SIZE(tests); i++) { - if (MPI_SUCCESS == (mpi_code = MPI_Barrier(comm))) { - (*tests[i])(); - } - else { - if (MAINPROCESS) - MESG("MPI_Barrier failed"); - nerrors++; + /* Create property list for collective dataset write */ + dxpl_id = H5Pcreate(H5P_DATASET_XFER); + VRFY((dxpl_id >= 0), "DXPL creation succeeded"); + + VRFY((H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE) >= 0), "H5Pset_dxpl_mpio succeeded"); + + /* Create DCPL for dataset creation */ + dcpl_id = H5Pcreate(H5P_DATASET_CREATE); + VRFY((dcpl_id >= 0), "DCPL creation succeeded"); + + /* Run tests with all available filters */ + for (cur_filter_idx = 0; cur_filter_idx < num_filters; cur_filter_idx++) { + H5FD_mpio_chunk_opt_t chunk_opt; + H5Z_filter_t cur_filter = filterIDs[cur_filter_idx]; + + /* Run tests with both linked-chunk and multi-chunk I/O */ + for (chunk_opt = H5FD_MPIO_CHUNK_ONE_IO; chunk_opt <= H5FD_MPIO_CHUNK_MULTI_IO; chunk_opt++) { + H5D_alloc_time_t space_alloc_time; + + /* Run tests with all available space allocation times */ + for (space_alloc_time = H5D_ALLOC_TIME_EARLY; space_alloc_time <= H5D_ALLOC_TIME_INCR; + space_alloc_time++) { + const char *alloc_time; + unsigned filter_config; + htri_t filter_avail; + size_t i; + char group_name[512]; + + switch (space_alloc_time) { + case H5D_ALLOC_TIME_EARLY: + alloc_time = "Early"; + break; + case H5D_ALLOC_TIME_LATE: + alloc_time = "Late"; + break; + case H5D_ALLOC_TIME_INCR: + alloc_time = "Incremental"; + break; + default: + alloc_time = "Unknown"; + } + + if (MAINPROCESS) + HDprintf("== Running tests with filter '%s' using '%s' and '%s' allocation time ==\n\n", + filterNames[cur_filter_idx], + H5FD_MPIO_CHUNK_ONE_IO == chunk_opt ? "Linked-Chunk I/O" : "Multi-Chunk I/O", + alloc_time); + + /* Make sure current filter is available before testing with it */ + filter_avail = H5Zfilter_avail(cur_filter); + VRFY((filter_avail >= 0), "H5Zfilter_avail succeeded"); + + if (!filter_avail) { + if (MAINPROCESS) + HDprintf(" ** SKIPPED tests with filter '%s' - filter unavailable **\n\n", + filterNames[cur_filter_idx]); + continue; + } + + /* Get the current filter's info */ + VRFY((H5Zget_filter_info(cur_filter, &filter_config) >= 0), "H5Zget_filter_info succeeded"); + + /* Determine if filter is encode-enabled */ + if (0 == (filter_config & H5Z_FILTER_CONFIG_ENCODE_ENABLED)) { + if (MAINPROCESS) + HDprintf(" ** SKIPPED tests with filter '%s' - filter not encode-enabled **\n\n", + filterNames[cur_filter_idx]); + continue; + } + + /* Set space allocation time */ + VRFY((H5Pset_alloc_time(dcpl_id, space_alloc_time) >= 0), "H5Pset_alloc_time succeeded"); + + /* Set chunk I/O optimization method */ + VRFY((H5Pset_dxpl_mpio_chunk_opt(dxpl_id, chunk_opt) >= 0), + "H5Pset_dxpl_mpio_chunk_opt succeeded"); + + /* Create a group to hold all the datasets for this combination + * of filter and chunk optimization mode. Then, close the file + * again since some tests may need to open the file in a special + * way, like on rank 0 only */ + file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); + VRFY((file_id >= 0), "H5Fopen succeeded"); + + HDsnprintf(group_name, sizeof(group_name), "%s_%s_%s", filterNames[cur_filter_idx], + H5FD_MPIO_CHUNK_ONE_IO == chunk_opt ? "linked-chunk-io" : "multi-chunk-io", + alloc_time); + + group_id = H5Gcreate2(file_id, group_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + VRFY((group_id >= 0), "H5Gcreate2 succeeded"); + + VRFY((H5Gclose(group_id) >= 0), "H5Gclose failed"); + group_id = H5I_INVALID_HID; + + VRFY((H5Fclose(file_id) >= 0), "H5Fclose succeeded"); + file_id = H5I_INVALID_HID; + + for (i = 0; i < ARRAY_SIZE(tests); i++) { + test_func func = tests[i]; + + if (MPI_SUCCESS == (mpi_code = MPI_Barrier(comm))) { + func(group_name, cur_filter, fapl_id, dcpl_id, dxpl_id); + } + else { + if (MAINPROCESS) + MESG("MPI_Barrier failed"); + nerrors++; + } + } + + if (MAINPROCESS) + HDputs(""); + } } } + VRFY((H5Pclose(dcpl_id) >= 0), "DCPL close succeeded"); + dcpl_id = H5I_INVALID_HID; + + VRFY((H5Pclose(dxpl_id) >= 0), "DXPL close succeeded"); + dxpl_id = H5I_INVALID_HID; + if (nerrors) goto exit; @@ -6575,7 +8861,21 @@ exit: TestAlarmOff(); - h5_clean_files(FILENAME, fapl); + h5_clean_files(FILENAME, fapl_id); + fapl_id = H5I_INVALID_HID; + + if (dcpl_id >= 0) + VRFY((H5Pclose(dcpl_id) >= 0), "H5Pclose succeeded"); + if (dxpl_id >= 0) + VRFY((H5Pclose(dxpl_id) >= 0), "H5Pclose succeeded"); + if (fapl_id >= 0) + VRFY((H5Pclose(fapl_id) >= 0), "H5Pclose succeeded"); + if (fcpl_id >= 0) + VRFY((H5Pclose(fcpl_id) >= 0), "H5Pclose succeeded"); + if (group_id >= 0) + VRFY((H5Gclose(group_id) >= 0), "H5Gclose succeeded"); + if (file_id >= 0) + VRFY((H5Fclose(file_id) >= 0), "H5Fclose succeeded"); H5close(); diff --git a/testpar/t_filters_parallel.h b/testpar/t_filters_parallel.h index 7eb34ed..800604c 100644 --- a/testpar/t_filters_parallel.h +++ b/testpar/t_filters_parallel.h @@ -30,23 +30,23 @@ #include "stdlib.h" #include "testpar.h" +#define ARRAY_SIZE(a) sizeof(a) / sizeof(a[0]) + /* Used to load other filters than GZIP */ /* #define DYNAMIC_FILTER */ /* Uncomment and define the fields below to use a dynamically loaded filter */ + +#ifdef DYNAMIC_FILTER #define FILTER_NUM_CDVALUES 1 const unsigned int cd_values[FILTER_NUM_CDVALUES] = {0}; -H5Z_filter_t filter_id; -unsigned int flags = 0; -size_t cd_nelmts = FILTER_NUM_CDVALUES; - -/* Utility Macros */ -#define STRINGIFY(type) #type +unsigned int flags = 0; +size_t cd_nelmts = FILTER_NUM_CDVALUES; +#endif /* Common defines for all tests */ -#define C_DATATYPE long -#define C_DATATYPE_MPI MPI_LONG -#define COMPOUND_C_DATATYPE cmpd_filtered_t -#define C_DATATYPE_STR(type) STRINGIFY(type) -#define HDF5_DATATYPE_NAME H5T_NATIVE_LONG +#define C_DATATYPE long +#define C_DATATYPE_MPI MPI_LONG +#define COMPOUND_C_DATATYPE cmpd_filtered_t +#define HDF5_DATATYPE_NAME H5T_NATIVE_LONG /* Macro used to generate data for datasets for later verification */ #define GEN_DATA(i) INCREMENTAL_DATA(i) @@ -59,7 +59,7 @@ size_t cd_nelmts = FILTER_NUM_CDVALUES; #define RANK_DATA(i) \ (mpi_rank) /* Generates test data to visibly show which rank wrote to which parts of the dataset */ -#define DEFAULT_DEFLATE_LEVEL 6 +#define DEFAULT_DEFLATE_LEVEL 9 #define DIM0_SCALE_FACTOR 4 #define DIM1_SCALE_FACTOR 2 @@ -89,6 +89,14 @@ typedef struct { #define WRITE_UNSHARED_FILTERED_CHUNKS_CH_NROWS (WRITE_UNSHARED_FILTERED_CHUNKS_NROWS / mpi_size) #define WRITE_UNSHARED_FILTERED_CHUNKS_CH_NCOLS (WRITE_UNSHARED_FILTERED_CHUNKS_NCOLS / mpi_size) +/* Defines for the unshared filtered chunks partial write test */ +#define WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_NAME "unshared_filtered_chunks_partial_write" +#define WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_DIMS 2 +#define WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_NROWS (mpi_size * DIM0_SCALE_FACTOR) +#define WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_NCOLS (mpi_size * DIM1_SCALE_FACTOR) +#define WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NROWS (DIM0_SCALE_FACTOR) +#define WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NCOLS (DIM1_SCALE_FACTOR) + /* Defines for the shared filtered chunks write test */ #define WRITE_SHARED_FILTERED_CHUNKS_DATASET_NAME "shared_filtered_chunks_write" #define WRITE_SHARED_FILTERED_CHUNKS_DATASET_DIMS 2 @@ -97,6 +105,42 @@ typedef struct { #define WRITE_SHARED_FILTERED_CHUNKS_NROWS (WRITE_SHARED_FILTERED_CHUNKS_CH_NROWS * DIM0_SCALE_FACTOR) #define WRITE_SHARED_FILTERED_CHUNKS_NCOLS (WRITE_SHARED_FILTERED_CHUNKS_CH_NCOLS * DIM1_SCALE_FACTOR) +/* Defines for the unshared filtered chunks w/ single unlim. dimension write test */ +#define WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_NAME "unshared_filtered_chunks_single_unlim_dim_write" +#define WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS 2 +#define WRITE_UNSHARED_ONE_UNLIM_DIM_NROWS (mpi_size * DIM0_SCALE_FACTOR) +#define WRITE_UNSHARED_ONE_UNLIM_DIM_NCOLS (mpi_size * DIM1_SCALE_FACTOR) +#define WRITE_UNSHARED_ONE_UNLIM_DIM_CH_NROWS (WRITE_UNSHARED_ONE_UNLIM_DIM_NROWS / mpi_size) +#define WRITE_UNSHARED_ONE_UNLIM_DIM_CH_NCOLS (WRITE_UNSHARED_ONE_UNLIM_DIM_NCOLS / mpi_size) +#define WRITE_UNSHARED_ONE_UNLIM_DIM_NLOOPS 5 + +/* Defines for the shared filtered chunks w/ single unlim. dimension write test */ +#define WRITE_SHARED_ONE_UNLIM_DIM_DATASET_NAME "shared_filtered_chunks_single_unlim_dim_write" +#define WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS 2 +#define WRITE_SHARED_ONE_UNLIM_DIM_CH_NROWS (mpi_size) +#define WRITE_SHARED_ONE_UNLIM_DIM_CH_NCOLS (mpi_size) +#define WRITE_SHARED_ONE_UNLIM_DIM_NROWS (WRITE_SHARED_ONE_UNLIM_DIM_CH_NROWS * DIM0_SCALE_FACTOR) +#define WRITE_SHARED_ONE_UNLIM_DIM_NCOLS (WRITE_SHARED_ONE_UNLIM_DIM_CH_NCOLS * DIM1_SCALE_FACTOR) +#define WRITE_SHARED_ONE_UNLIM_DIM_NLOOPS 5 + +/* Defines for the unshared filtered chunks w/ two unlim. dimension write test */ +#define WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_NAME "unshared_filtered_chunks_two_unlim_dim_write" +#define WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS 2 +#define WRITE_UNSHARED_TWO_UNLIM_DIM_NROWS (mpi_size * DIM0_SCALE_FACTOR) +#define WRITE_UNSHARED_TWO_UNLIM_DIM_NCOLS (DIM1_SCALE_FACTOR) +#define WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NROWS (DIM0_SCALE_FACTOR) +#define WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NCOLS (DIM1_SCALE_FACTOR) +#define WRITE_UNSHARED_TWO_UNLIM_DIM_NLOOPS 5 + +/* Defines for the shared filtered chunks w/ two unlim. dimension write test */ +#define WRITE_SHARED_TWO_UNLIM_DIM_DATASET_NAME "shared_filtered_chunks_two_unlim_dim_write" +#define WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS 2 +#define WRITE_SHARED_TWO_UNLIM_DIM_CH_NROWS (mpi_size) +#define WRITE_SHARED_TWO_UNLIM_DIM_CH_NCOLS (mpi_size) +#define WRITE_SHARED_TWO_UNLIM_DIM_NROWS (mpi_size) +#define WRITE_SHARED_TWO_UNLIM_DIM_NCOLS (mpi_size) +#define WRITE_SHARED_TWO_UNLIM_DIM_NLOOPS 5 + /* Defines for the filtered chunks write test where a process has no selection */ #define WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME "single_no_selection_filtered_chunks_write" #define WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS 2 @@ -403,4 +447,53 @@ typedef struct { #define SHRINKING_GROWING_CHUNKS_CH_NCOLS (SHRINKING_GROWING_CHUNKS_NCOLS / mpi_size) #define SHRINKING_GROWING_CHUNKS_NLOOPS 20 +/* Defines for the unshared filtered edge chunks write test */ +#define WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME "unshared_filtered_edge_chunks_write" +#define WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME2 "unshared_filtered_edge_chunks_no_filter_write" +#define WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS 2 +#define WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NROWS (DIM0_SCALE_FACTOR) +#define WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS (DIM1_SCALE_FACTOR) +#define WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_NROWS (mpi_size * DIM0_SCALE_FACTOR) +#define WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_NCOLS \ + (mpi_size * DIM1_SCALE_FACTOR) + (WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS - 1) + +/* Defines for the shared filtered edge chunks write test */ +#define WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME "shared_filtered_edge_chunks_write" +#define WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME2 "shared_filtered_edge_chunks_no_filter_write" +#define WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS 2 +#define WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NROWS (mpi_size) +#define WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS (mpi_size) +#define WRITE_SHARED_FILTERED_EDGE_CHUNKS_NROWS \ + (WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NROWS * DIM0_SCALE_FACTOR) +#define WRITE_SHARED_FILTERED_EDGE_CHUNKS_NCOLS \ + ((WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS * DIM1_SCALE_FACTOR) + \ + (WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS - 1)) + +/* Defines for the fill values test */ +#define FILL_VALUES_TEST_DATASET_NAME "fill_value_test" +#define FILL_VALUES_TEST_DATASET_NAME2 "fill_value_alloc_test" +#define FILL_VALUES_TEST_DATASET_DIMS 2 +#define FILL_VALUES_TEST_FILL_VAL (-1) +#define FILL_VALUES_TEST_CH_NROWS (mpi_size) +#define FILL_VALUES_TEST_CH_NCOLS (mpi_size + 1) +#define FILL_VALUES_TEST_NROWS (FILL_VALUES_TEST_CH_NROWS * DIM0_SCALE_FACTOR) +#define FILL_VALUES_TEST_NCOLS (FILL_VALUES_TEST_CH_NCOLS * DIM1_SCALE_FACTOR) + +/* Defines for the undefined fill value test */ +#define FILL_VALUE_UNDEFINED_TEST_DATASET_NAME "fill_value_undefined_test" +#define FILL_VALUE_UNDEFINED_TEST_DATASET_DIMS 2 +#define FILL_VALUE_UNDEFINED_TEST_CH_NROWS (mpi_size) +#define FILL_VALUE_UNDEFINED_TEST_CH_NCOLS (mpi_size + 1) +#define FILL_VALUE_UNDEFINED_TEST_NROWS (FILL_VALUE_UNDEFINED_TEST_CH_NROWS * DIM0_SCALE_FACTOR) +#define FILL_VALUE_UNDEFINED_TEST_NCOLS (FILL_VALUE_UNDEFINED_TEST_CH_NCOLS * DIM1_SCALE_FACTOR) + +/* Defines for the fill time of 'never' test */ +#define FILL_TIME_NEVER_TEST_DATASET_NAME "fill_time_never_test" +#define FILL_TIME_NEVER_TEST_DATASET_DIMS 2 +#define FILL_TIME_NEVER_TEST_FILL_VAL (-1) +#define FILL_TIME_NEVER_TEST_CH_NROWS (mpi_size) +#define FILL_TIME_NEVER_TEST_CH_NCOLS (mpi_size + 1) +#define FILL_TIME_NEVER_TEST_NROWS (FILL_TIME_NEVER_TEST_CH_NROWS * DIM0_SCALE_FACTOR) +#define FILL_TIME_NEVER_TEST_NCOLS (FILL_TIME_NEVER_TEST_CH_NCOLS * DIM1_SCALE_FACTOR) + #endif /* TEST_PARALLEL_FILTERS_H_ */ diff --git a/testpar/t_pflush1.c b/testpar/t_pflush1.c index cc569f6..0500a2d 100644 --- a/testpar/t_pflush1.c +++ b/testpar/t_pflush1.c @@ -43,7 +43,7 @@ static int data_g[100][100]; *------------------------------------------------------------------------- */ static hid_t -create_test_file(char *name, hid_t fapl_id) +create_test_file(char *name, size_t name_length, hid_t fapl_id) { hid_t fid = H5I_INVALID_HID; hid_t dcpl_id = H5I_INVALID_HID; @@ -86,7 +86,7 @@ create_test_file(char *name, hid_t fapl_id) if ((top_level_gid = H5Gcreate2(fid, "some_groups", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) goto error; for (i = 0; i < N_GROUPS; i++) { - HDsprintf(name, "grp%02u", (unsigned)i); + HDsnprintf(name, name_length, "grp%02u", (unsigned)i); if ((gid = H5Gcreate2(top_level_gid, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) goto error; if (H5Gclose(gid) < 0) @@ -153,7 +153,7 @@ main(int argc, char *argv[]) /* Create the file */ h5_fixname(FILENAME[0], fapl_id, name, sizeof(name)); - if ((fid1 = create_test_file(name, fapl_id)) < 0) + if ((fid1 = create_test_file(name, sizeof(name), fapl_id)) < 0) goto error; /* Flush and exit without closing the library */ if (H5Fflush(fid1, H5F_SCOPE_GLOBAL) < 0) @@ -161,7 +161,7 @@ main(int argc, char *argv[]) /* Create the other file which will not be flushed */ h5_fixname(FILENAME[1], fapl_id, name, sizeof(name)); - if ((fid2 = create_test_file(name, fapl_id)) < 0) + if ((fid2 = create_test_file(name, sizeof(name), fapl_id)) < 0) goto error; if (mpi_rank == 0) diff --git a/testpar/t_pflush2.c b/testpar/t_pflush2.c index e782f8a..8cf40d0 100644 --- a/testpar/t_pflush2.c +++ b/testpar/t_pflush2.c @@ -43,7 +43,7 @@ static int data_g[100][100]; *------------------------------------------------------------------------- */ static herr_t -check_test_file(char *name, hid_t fapl_id) +check_test_file(char *name, size_t name_length, hid_t fapl_id) { hid_t fid = H5I_INVALID_HID; hid_t sid = H5I_INVALID_HID; @@ -89,7 +89,7 @@ check_test_file(char *name, hid_t fapl_id) if ((top_level_gid = H5Gopen2(fid, "some_groups", H5P_DEFAULT)) < 0) goto error; for (i = 0; i < N_GROUPS; i++) { - HDsprintf(name, "grp%02u", (unsigned)i); + HDsnprintf(name, name_length, "grp%02u", (unsigned)i); if ((gid = H5Gopen2(top_level_gid, name, H5P_DEFAULT)) < 0) goto error; if (H5Gclose(gid) < 0) @@ -182,7 +182,7 @@ main(int argc, char *argv[]) /* Check the case where the file was flushed */ h5_fixname(FILENAME[0], fapl_id1, name, sizeof(name)); - if (check_test_file(name, fapl_id1)) { + if (check_test_file(name, sizeof(name), fapl_id1)) { H5_FAILED() goto error; } @@ -199,7 +199,7 @@ main(int argc, char *argv[]) H5Eset_auto2(H5E_DEFAULT, NULL, NULL); h5_fixname(FILENAME[1], fapl_id2, name, sizeof(name)); - if (check_test_file(name, fapl_id2)) { + if (check_test_file(name, sizeof(name), fapl_id2)) { if (mpi_rank == 0) PASSED(); } diff --git a/testpar/t_prop.c b/testpar/t_prop.c index 5979c5d..606e100 100644 --- a/testpar/t_prop.c +++ b/testpar/t_prop.c @@ -556,7 +556,7 @@ external_links(void) /* test opening a group that is to an external link, the external linked file should inherit the source file's access properties */ - HDsprintf(link_path, "%s%s%s", group_path, "/", link_name); + HDsnprintf(link_path, sizeof(link_path), "%s%s%s", group_path, "/", link_name); group = H5Gopen2(fid, link_path, H5P_DEFAULT); VRFY((group >= 0), "H5Gopen succeeded"); ret = H5Gclose(group); diff --git a/testpar/testphdf5.h b/testpar/testphdf5.h index c692287..16f45d3 100644 --- a/testpar/testphdf5.h +++ b/testpar/testphdf5.h @@ -186,10 +186,6 @@ enum H5TEST_COLL_CHUNK_API { #define TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES 0x010 #define TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT 0x020 #define TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL 0x040 -#define TEST_FILTERS 0x080 -/* TEST_FILTERS will take place of this after supporting mpio + filter for - * H5Dcreate and H5Dwrite */ -#define TEST_FILTERS_READ 0x100 /* Don't erase these lines, they are put here for debugging purposes */ /* diff --git a/tools/lib/h5diff_array.c b/tools/lib/h5diff_array.c index 1b0d36f..a7156b5 100644 --- a/tools/lib/h5diff_array.c +++ b/tools/lib/h5diff_array.c @@ -204,7 +204,8 @@ diff_array(void *_mem1, void *_mem2, diff_opt_t *opts, hid_t container1_id, hid_ mcomp_t members; H5T_class_t type_class; - H5TOOLS_START_DEBUG(" - rank:%d hs_nelmts:%lld errstat:%d", opts->rank, opts->hs_nelmts, opts->err_stat); + H5TOOLS_START_DEBUG(" - rank:%d hs_nelmts:%" PRIuHSIZE " errstat:%d", opts->rank, opts->hs_nelmts, + opts->err_stat); opts->print_header = 1; /* enable print header */ /* get the size. */ @@ -388,7 +389,8 @@ diff_array(void *_mem1, void *_mem2, diff_opt_t *opts, hid_t container1_id, hid_ HDmemset(&members, 0, sizeof(mcomp_t)); get_member_types(opts->m_tid, &members); for (i = 0; i < opts->hs_nelmts; i++) { - H5TOOLS_DEBUG("opts->pos[%lld]:%lld - nelmts:%lld", i, opts->pos[i], opts->hs_nelmts); + H5TOOLS_DEBUG("opts->pos[%" PRIuHSIZE "]:%" PRIuHSIZE " - nelmts:%" PRIuHSIZE, i, + opts->pos[i], opts->hs_nelmts); nfound += diff_datum(mem1 + i * size, mem2 + i * size, i, opts, container1_id, container2_id, &members); if (opts->count_bool && nfound >= opts->count) @@ -396,7 +398,7 @@ diff_array(void *_mem1, void *_mem2, diff_opt_t *opts, hid_t container1_id, hid_ } /* i */ close_member_types(&members); } /* switch */ - H5TOOLS_ENDDEBUG(":%lld - errstat:%d", nfound, opts->err_stat); + H5TOOLS_ENDDEBUG(":%" PRIuHSIZE " - errstat:%d", nfound, opts->err_stat); return nfound; } @@ -452,7 +454,8 @@ diff_datum(void *_mem1, void *_mem2, hsize_t elemtno, diff_opt_t *opts, hid_t co hsize_t nfound = 0; /* differences found */ diff_err_t ret_value = opts->err_stat; - H5TOOLS_START_DEBUG("ph:%d elemtno:%lld - errstat:%d", opts->print_header, elemtno, opts->err_stat); + H5TOOLS_START_DEBUG("ph:%d elemtno:%" PRIuHSIZE " - errstat:%d", opts->print_header, elemtno, + opts->err_stat); type_size = H5Tget_size(opts->m_tid); type_class = H5Tget_class(opts->m_tid); @@ -702,8 +705,8 @@ diff_datum(void *_mem1, void *_mem2, hsize_t elemtno, diff_opt_t *opts, hid_t co H5TOOLS_DEBUG("H5T_ARRAY ph=%d", opts->print_header); arr_opts = *opts; - H5TOOLS_DEBUG("Check opts: hs_nelmts:%lld to %lld rank:%d to %d", opts->hs_nelmts, - arr_opts.hs_nelmts, opts->rank, arr_opts.rank); + H5TOOLS_DEBUG("Check opts: hs_nelmts:%" PRIuHSIZE " to %" PRIuHSIZE " rank:%d to %d", + opts->hs_nelmts, arr_opts.hs_nelmts, opts->rank, arr_opts.rank); /* get the array's base datatype for each element */ arr_opts.m_tid = H5Tget_super(opts->m_tid); size = H5Tget_size(arr_opts.m_tid); @@ -1051,8 +1054,8 @@ diff_datum(void *_mem1, void *_mem2, hsize_t elemtno, diff_opt_t *opts, hid_t co H5TOOLS_INFO("H5Rdestroy H5R_OBJECT1 failed"); if (H5Rdestroy(ref1_buf) < 0) H5TOOLS_INFO("H5Rdestroy H5R_OBJECT1 failed"); - H5TOOLS_DEBUG("H5T_REFERENCE - H5T_STD_REF complete nfound:%lld - errstat:%d", nfound, - ref_opts.err_stat); + H5TOOLS_DEBUG("H5T_REFERENCE - H5T_STD_REF complete nfound:%" PRIuHSIZE " - errstat:%d", + nfound, ref_opts.err_stat); } /*------------------------------------------------------------------------- * H5T_STD_REF_DSETREG @@ -1263,7 +1266,7 @@ diff_datum(void *_mem1, void *_mem2, hsize_t elemtno, diff_opt_t *opts, hid_t co done: opts->err_stat = opts->err_stat | ret_value; - H5TOOLS_ENDDEBUG(":%lld - errstat:%d", nfound, opts->err_stat); + H5TOOLS_ENDDEBUG(":%" PRIuHSIZE " - errstat:%d", nfound, opts->err_stat); return nfound; } @@ -1374,8 +1377,8 @@ diff_region(hid_t obj1_id, hid_t obj2_id, hid_t region1_id, hid_t region2_id, di npoints2 = H5Sget_select_elem_npoints(region2_id); } H5E_END_TRY; - H5TOOLS_DEBUG("blocks: 1=%lld-2=%lld", nblocks1, nblocks2); - H5TOOLS_DEBUG("points: 1=%lld-2=%lld", npoints1, npoints2); + H5TOOLS_DEBUG("blocks: 1=%" PRIdHSIZE "-2=%" PRIdHSIZE, nblocks1, nblocks2); + H5TOOLS_DEBUG("points: 1=%" PRIdHSIZE "-2=%" PRIdHSIZE, npoints1, npoints2); if (nblocks1 != nblocks2 || npoints1 != npoints2 || ndims1 != ndims2) { opts->not_cmp = 1; @@ -1518,10 +1521,10 @@ diff_region(hid_t obj1_id, hid_t obj2_id, hid_t region1_id, hid_t region2_id, di #if defined(H5DIFF_DEBUG) for (i = 0; i < npoints1; i++) { - parallel_print("%sPt%lu: ", i ? "," : "", (unsigned long)i); + parallel_print("%sPt%d: ", i ? "," : "", i); for (j = 0; j < ndims1; j++) - parallel_print("%s%lu", j ? "," : "(", (unsigned long)(ptdata1[i * ndims1 + j])); + parallel_print("%s%" PRIuHSIZE, j ? "," : "(", ptdata1[i * ndims1 + j]); parallel_print(")"); } @@ -1538,7 +1541,7 @@ diff_region(hid_t obj1_id, hid_t obj2_id, hid_t region1_id, hid_t region2_id, di ret_value = nfound_p + nfound_b; done: - H5TOOLS_ENDDEBUG(" with diffs:%lld", ret_value); + H5TOOLS_ENDDEBUG(" with diffs:%" PRIuHSIZE, ret_value); return ret_value; } @@ -1575,7 +1578,7 @@ character_compare(char *mem1, char *mem2, hsize_t elemtno, size_t u, diff_opt_t } nfound++; } - H5TOOLS_ENDDEBUG(": %lld", nfound); + H5TOOLS_ENDDEBUG(": %" PRIuHSIZE, nfound); return nfound; } @@ -1649,7 +1652,7 @@ character_compare_opt(unsigned char *mem1, unsigned char *mem2, hsize_t elemtno, nfound++; } - H5TOOLS_ENDDEBUG(": %lld zero:%d", nfound, both_zero); + H5TOOLS_ENDDEBUG(": %" PRIuHSIZE " zero:%d", nfound, both_zero); return nfound; } @@ -1830,7 +1833,7 @@ diff_float_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx, d } } - H5TOOLS_ENDDEBUG(": %lld zero:%d", nfound, both_zero); + H5TOOLS_ENDDEBUG(": %" PRIuHSIZE " zero:%d", nfound, both_zero); return nfound; } @@ -2001,7 +2004,7 @@ diff_double_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx, nfound++; } } - H5TOOLS_ENDDEBUG(":%lld - errstat:%d", nfound, opts->err_stat); + H5TOOLS_ENDDEBUG(":%" PRIuHSIZE " - errstat:%d", nfound, opts->err_stat); return nfound; } @@ -2063,7 +2066,7 @@ diff_ldouble_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx, opts->print_percentage = 0; print_pos(opts, elem_idx, 0); if (print_data(opts)) { - parallel_print(F_FORMAT, temp1_double, temp2_double, ABS(temp1_double - temp2_double)); + parallel_print(LD_FORMAT, temp1_double, temp2_double, ABS(temp1_double - temp2_double)); } nfound++; } @@ -2110,7 +2113,7 @@ diff_ldouble_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx, opts->print_percentage = 0; print_pos(opts, elem_idx, 0); if (print_data(opts)) { - parallel_print(F_FORMAT, temp1_double, temp2_double, ABS(temp1_double - temp2_double)); + parallel_print(LD_FORMAT, temp1_double, temp2_double, ABS(temp1_double - temp2_double)); } nfound++; } @@ -2157,7 +2160,7 @@ diff_ldouble_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx, opts->print_percentage = 0; print_pos(opts, elem_idx, 0); if (print_data(opts)) { - parallel_print(F_FORMAT, temp1_double, temp2_double, ABS(temp1_double - temp2_double)); + parallel_print(LD_FORMAT, temp1_double, temp2_double, ABS(temp1_double - temp2_double)); } nfound++; } @@ -2175,7 +2178,7 @@ diff_ldouble_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx, nfound++; } - H5TOOLS_ENDDEBUG(":%lld - errstat:%d", nfound, opts->err_stat); + H5TOOLS_ENDDEBUG(":%" PRIuHSIZE " - errstat:%d", nfound, opts->err_stat); return nfound; } @@ -2263,7 +2266,7 @@ diff_schar_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx, d nfound++; } - H5TOOLS_ENDDEBUG(":%lld - errstat:%d", nfound, opts->err_stat); + H5TOOLS_ENDDEBUG(":%" PRIuHSIZE " - errstat:%d", nfound, opts->err_stat); return nfound; } @@ -2351,7 +2354,7 @@ diff_uchar_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx, d nfound++; } - H5TOOLS_ENDDEBUG(":%lld - errstat:%d", nfound, opts->err_stat); + H5TOOLS_ENDDEBUG(":%" PRIuHSIZE " - errstat:%d", nfound, opts->err_stat); return nfound; } @@ -2439,7 +2442,7 @@ diff_short_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx, d nfound++; } - H5TOOLS_ENDDEBUG(":%lld - errstat:%d", nfound, opts->err_stat); + H5TOOLS_ENDDEBUG(":%" PRIuHSIZE " - errstat:%d", nfound, opts->err_stat); return nfound; } @@ -2531,7 +2534,7 @@ diff_ushort_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx, nfound++; } - H5TOOLS_ENDDEBUG(":%lld - errstat:%d", nfound, opts->err_stat); + H5TOOLS_ENDDEBUG(":%" PRIuHSIZE " - errstat:%d", nfound, opts->err_stat); return nfound; } @@ -2619,7 +2622,7 @@ diff_int_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx, dif nfound++; } - H5TOOLS_ENDDEBUG(":%lld - errstat:%d", nfound, opts->err_stat); + H5TOOLS_ENDDEBUG(":%" PRIuHSIZE " - errstat:%d", nfound, opts->err_stat); return nfound; } @@ -2707,7 +2710,7 @@ diff_uint_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx, di nfound++; } - H5TOOLS_ENDDEBUG(":%lld - errstat:%d", nfound, opts->err_stat); + H5TOOLS_ENDDEBUG(":%" PRIuHSIZE " - errstat:%d", nfound, opts->err_stat); return nfound; } @@ -2795,7 +2798,7 @@ diff_long_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx, di nfound++; } - H5TOOLS_ENDDEBUG(":%lld - errstat:%d", nfound, opts->err_stat); + H5TOOLS_ENDDEBUG(":%" PRIuHSIZE " - errstat:%d", nfound, opts->err_stat); return nfound; } @@ -2885,7 +2888,7 @@ diff_ulong_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx, d nfound++; } - H5TOOLS_ENDDEBUG(":%lld - errstat:%d", nfound, opts->err_stat); + H5TOOLS_ENDDEBUG(":%" PRIuHSIZE " - errstat:%d", nfound, opts->err_stat); return nfound; } @@ -2978,7 +2981,7 @@ diff_llong_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx, d } } - H5TOOLS_ENDDEBUG(":%lld - errstat:%d", nfound, opts->err_stat); + H5TOOLS_ENDDEBUG(":%" PRIuHSIZE " - errstat:%d", nfound, opts->err_stat); return nfound; } @@ -3078,7 +3081,7 @@ diff_ullong_element(unsigned char *mem1, unsigned char *mem2, hsize_t elem_idx, } } - H5TOOLS_ENDDEBUG(": %lld zero:%d", nfound, both_zero); + H5TOOLS_ENDDEBUG(": %" PRIuHSIZE " zero:%d", nfound, both_zero); return nfound; } @@ -3323,7 +3326,7 @@ print_header(diff_opt_t *opts) static void print_pos(diff_opt_t *opts, hsize_t idx, size_t u) { - H5TOOLS_START_DEBUG(" -- idx:%lld", idx); + H5TOOLS_START_DEBUG(" -- idx:%" PRIuHSIZE, idx); if (print_data(opts)) { hsize_t curr_pos = idx; @@ -3336,8 +3339,8 @@ print_pos(diff_opt_t *opts, hsize_t idx, size_t u) H5TOOLS_DEBUG("rank=%d", opts->rank); if (opts->rank > 0) { parallel_print("[ "); - H5TOOLS_DEBUG("do calc_acc_pos[%lld] nelmts:%lld - errstat:%d", idx, opts->hs_nelmts, - opts->err_stat); + H5TOOLS_DEBUG("do calc_acc_pos[%" PRIuHSIZE "] nelmts:%" PRIuHSIZE " - errstat:%d", idx, + opts->hs_nelmts, opts->err_stat); if (opts->sset[0] != NULL) { /* Subsetting is used - calculate total position */ hsize_t curr_idx = 0; /* current pos in the selection space for each dimension */ @@ -3364,33 +3367,36 @@ print_pos(diff_opt_t *opts, hsize_t idx, size_t u) j = opts->rank - i - 1; prev_total_dim_size *= prev_dim_size; dim_size = opts->dims[j]; - H5TOOLS_DEBUG("j=%d, dim_size=%lld, prev_dim_size=%lld, total_dim_size=%lld, " - "prev_total_dim_size=%lld", + H5TOOLS_DEBUG("j=%d, dim_size=%" PRIuHSIZE ", prev_dim_size=%" PRIuHSIZE + ", total_dim_size=%" PRIuHSIZE ", " + "prev_total_dim_size=%" PRIuHSIZE, j, dim_size, prev_dim_size, total_dim_size, prev_total_dim_size); count = opts->sset[0]->count.data[j]; block = opts->sset[0]->block.data[j]; stride = opts->sset[0]->stride.data[j]; - H5TOOLS_DEBUG("stride=%lld, count=%lld, block=%lld", stride, count, block); + H5TOOLS_DEBUG("stride=%" PRIuHSIZE ", count=%" PRIuHSIZE ", block=%" PRIuHSIZE, + stride, count, block); tmp = count * block; k0 = curr_idx / tmp; k1 = curr_idx % tmp; curr_pos += k1 * stride * prev_total_dim_size; - H5TOOLS_DEBUG("curr_idx=%lld, k0=%lld, k1=%lld, curr_pos=%lld", curr_idx, k0, k1, - curr_pos); + H5TOOLS_DEBUG("curr_idx=%" PRIuHSIZE ", k0=%" PRIuHSIZE ", k1=%" PRIuHSIZE + ", curr_pos=%" PRIuHSIZE, + curr_idx, k0, k1, curr_pos); if (k0 > 0) curr_idx = k0 * total_dim_size; - H5TOOLS_DEBUG("curr_idx=%lld, tmp=%lld", curr_idx, tmp); + H5TOOLS_DEBUG("curr_idx=%" PRIuHSIZE ", tmp=%" PRIuHSIZE, curr_idx, tmp); total_dim_size *= dim_size; /* if last calculation exists within in current dimension */ if (k0 == 0) break; - H5TOOLS_DEBUG("j=%d, curr_pos=%lld", j, curr_pos); + H5TOOLS_DEBUG("j=%d, curr_pos=%" PRIuHSIZE, j, curr_pos); prev_dim_size = dim_size; } /* check if there is a final calculation needed for slowest changing dimension */ if (k0 > 0) curr_pos += k0 * stride * prev_total_dim_size; - H5TOOLS_DEBUG("4:curr_idx=%lld, curr_pos=%lld", curr_idx, curr_pos); + H5TOOLS_DEBUG("4:curr_idx=%" PRIuHSIZE ", curr_pos=%" PRIuHSIZE, curr_idx, curr_pos); } } /* @@ -3400,11 +3406,11 @@ print_pos(diff_opt_t *opts, hsize_t idx, size_t u) calc_acc_pos((unsigned)opts->rank, curr_pos, opts->acc, opts->pos); for (int i = 0; i < opts->rank; i++) { - H5TOOLS_DEBUG("pos loop:%d with opts->pos=%lld opts->sm_pos=%lld", i, opts->pos[i], - opts->sm_pos[i]); + H5TOOLS_DEBUG("pos loop:%d with opts->pos=%" PRIuHSIZE " opts->sm_pos=%" PRIuHSIZE, i, + opts->pos[i], opts->sm_pos[i]); opts->pos[i] += (unsigned long)opts->sm_pos[i]; - H5TOOLS_DEBUG("pos loop:%d with opts->pos=%lld", i, opts->pos[i]); - parallel_print(HSIZE_T_FORMAT, (unsigned long long)opts->pos[i]); + H5TOOLS_DEBUG("pos loop:%d with opts->pos=%" PRIuHSIZE, i, opts->pos[i]); + parallel_print("%" PRIuHSIZE, opts->pos[i]); parallel_print(" "); } parallel_print("]"); diff --git a/tools/lib/h5diff_attr.c b/tools/lib/h5diff_attr.c index 5c1777a..63b6d8f 100644 --- a/tools/lib/h5diff_attr.c +++ b/tools/lib/h5diff_attr.c @@ -292,7 +292,7 @@ build_match_list_attrs(hid_t loc1_id, hid_t loc2_id, table_attrs_t **table_out, } if (opts->mode_verbose_level >= 1) - parallel_print("Attributes status: %d common, %d only in obj1, %d only in obj2\n", + parallel_print("Attributes status: %zu common, %zu only in obj1, %zu only in obj2\n", table_lp->nattrs - table_lp->nattrs_only1 - table_lp->nattrs_only2, table_lp->nattrs_only1, table_lp->nattrs_only2); diff --git a/tools/lib/h5diff_util.c b/tools/lib/h5diff_util.c index c40de9d..05f380a 100644 --- a/tools/lib/h5diff_util.c +++ b/tools/lib/h5diff_util.c @@ -39,11 +39,11 @@ print_dimensions(int rank, hsize_t *dims) else { parallel_print("["); for (i = 0; i < rank - 1; i++) { - parallel_print(HSIZE_T_FORMAT, dims[i]); + parallel_print("%" PRIuHSIZE, dims[i]); parallel_print("x"); } - parallel_print(HSIZE_T_FORMAT, dims[rank - 1]); + parallel_print("%" PRIuHSIZE, dims[rank - 1]); parallel_print("]"); } } diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c index db8df16..da55136 100644 --- a/tools/lib/h5tools.c +++ b/tools/lib/h5tools.c @@ -945,7 +945,7 @@ h5tools_fopen(const char *fname, unsigned flags, hid_t fapl_id, hbool_t use_spec * as TRUE, we should return failure now since the file couldn't be opened with * the VFL driver/VOL connector that was set on the FAPL by the caller. */ - if (fid < 0 && use_specific_driver) + if (use_specific_driver) H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "failed to open file using specified FAPL"); /* diff --git a/tools/lib/h5tools.h b/tools/lib/h5tools.h index cc6183a..d3501b3 100644 --- a/tools/lib/h5tools.h +++ b/tools/lib/h5tools.h @@ -29,9 +29,6 @@ #define START_OF_DATA 0x0001 #define END_OF_DATA 0x0002 -/* format for hsize_t */ -#define HSIZE_T_FORMAT "%" H5_PRINTF_LL_WIDTH "u" - #define H5TOOLS_DUMP_MAX_RANK H5S_MAX_RANK /* Stream macros */ diff --git a/tools/lib/h5tools_dump.c b/tools/lib/h5tools_dump.c index 0fc5d2d..78dd3ff 100644 --- a/tools/lib/h5tools_dump.c +++ b/tools/lib/h5tools_dump.c @@ -745,11 +745,11 @@ h5tools_dump_region_data_blocks(hid_t region_space, hid_t region_id, FILE *strea /* Start coordinates and opposite corner */ for (loop_indx = 0; loop_indx < ndims; loop_indx++) - h5tools_str_append(buffer, "%s" HSIZE_T_FORMAT, loop_indx ? "," : "(", + h5tools_str_append(buffer, "%s%" PRIuHSIZE, loop_indx ? "," : "(", ptdata[indx * 2 * ndims + loop_indx]); for (loop_indx = 0; loop_indx < ndims; loop_indx++) - h5tools_str_append(buffer, "%s" HSIZE_T_FORMAT, loop_indx ? "," : ")-(", + h5tools_str_append(buffer, "%s%" PRIuHSIZE, loop_indx ? "," : ")-(", ptdata[indx * 2 * ndims + loop_indx + ndims]); h5tools_str_append(buffer, ")"); @@ -1101,7 +1101,7 @@ h5tools_dump_region_data_points(hid_t region_space, hid_t region_id, FILE *strea (unsigned long)indx); for (loop_indx = 0; loop_indx < ndims; loop_indx++) - h5tools_str_append(buffer, "%s" HSIZE_T_FORMAT, loop_indx ? "," : "(", + h5tools_str_append(buffer, "%s%" PRIuHSIZE, loop_indx ? "," : "(", ptdata[indx * ndims + loop_indx]); h5tools_str_append(buffer, ")"); @@ -2486,7 +2486,7 @@ found_string_type: ctx->need_prefix = TRUE; h5tools_str_reset(buffer); - h5tools_str_append(buffer, "OPAQUE_SIZE \"%s\";", size); + h5tools_str_append(buffer, "OPAQUE_SIZE \"%zu\";", size); h5tools_render_element(stream, info, ctx, buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); } @@ -2608,7 +2608,7 @@ found_string_type: if (H5Tget_array_dims2(type, dims) >= 0) { /* Print array dimensions */ for (i = 0; i < ndims; i++) - h5tools_str_append(buffer, "[" HSIZE_T_FORMAT "]", dims[i]); + h5tools_str_append(buffer, "[%" PRIuHSIZE "]", dims[i]); h5tools_str_append(buffer, " "); } @@ -2683,12 +2683,12 @@ h5tools_print_dataspace(h5tools_str_t *buffer, hid_t space) case H5S_SIMPLE: /* simple dataspace */ - h5tools_str_append(buffer, "%s %s { %s " HSIZE_T_FORMAT, + h5tools_str_append(buffer, "%s %s { %s %" PRIuHSIZE, h5tools_dump_header_format->dataspacedescriptionbegin, S_SIMPLE, h5tools_dump_header_format->dataspacedimbegin, size[0]); for (i = 1; i < ndims; i++) - h5tools_str_append(buffer, ", " HSIZE_T_FORMAT, size[i]); + h5tools_str_append(buffer, ", %" PRIuHSIZE, size[i]); h5tools_str_append(buffer, " %s / ", h5tools_dump_header_format->dataspacedimend); @@ -2696,14 +2696,14 @@ h5tools_print_dataspace(h5tools_str_t *buffer, hid_t space) h5tools_str_append(buffer, "%s %s", h5tools_dump_header_format->dataspacedimbegin, "H5S_UNLIMITED"); else - h5tools_str_append(buffer, "%s " HSIZE_T_FORMAT, - h5tools_dump_header_format->dataspacedimbegin, maxsize[0]); + h5tools_str_append(buffer, "%s %" PRIuHSIZE, h5tools_dump_header_format->dataspacedimbegin, + maxsize[0]); for (i = 1; i < ndims; i++) if (maxsize[i] == H5S_UNLIMITED) h5tools_str_append(buffer, ", %s", "H5S_UNLIMITED"); else - h5tools_str_append(buffer, ", " HSIZE_T_FORMAT, maxsize[i]); + h5tools_str_append(buffer, ", %" PRIuHSIZE, maxsize[i]); h5tools_str_append(buffer, " %s }", h5tools_dump_header_format->dataspacedimend); break; @@ -2742,7 +2742,6 @@ h5tools_print_enum(FILE *stream, h5tools_str_t *buffer, const h5tool_format_t *i { char ** name = NULL; /*member names */ unsigned char *value = NULL; /*value array */ - unsigned char *copy = NULL; /*a pointer to value array */ unsigned i; unsigned nmembs = 0; /*number of members */ int snmembs; @@ -2834,16 +2833,16 @@ h5tools_print_enum(FILE *stream, h5tools_str_t *buffer, const h5tool_format_t *i h5tools_str_append(buffer, "%02x", value[i * dst_size + j]); } else if (H5T_SGN_NONE == H5Tget_sign(native)) { - /*On SGI Altix(cobalt), wrong values were printed out with "value+i*dst_size" - *strangely, unless use another pointer "copy".*/ - copy = value + i * dst_size; - h5tools_str_append(buffer, HSIZE_T_FORMAT, *((unsigned long long *)((void *)copy))); + unsigned long long copy; + + HDmemcpy(©, value + i * dst_size, sizeof(copy)); + h5tools_str_append(buffer, "%llu", copy); } else { - /*On SGI Altix(cobalt), wrong values were printed out with "value+i*dst_size" - *strangely, unless use another pointer "copy".*/ - copy = value + i * dst_size; - h5tools_str_append(buffer, "%" H5_PRINTF_LL_WIDTH "d", *((long long *)((void *)copy))); + long long copy; + + HDmemcpy(©, value + i * dst_size, sizeof(copy)); + h5tools_str_append(buffer, "%lld", copy); } h5tools_str_append(buffer, ";"); @@ -2996,7 +2995,7 @@ h5tools_dump_oid(FILE *stream, const h5tool_format_t *info, h5tools_context_t *c ctx->need_prefix = TRUE; h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "%s %s %d %s", OBJID, BEGIN, oid, END); + h5tools_str_append(&buffer, "%s %s %" PRId64 " %s", OBJID, BEGIN, oid, END); h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); h5tools_str_close(&buffer); @@ -3174,10 +3173,10 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info, h5tools_context_t * h5tools_str_append(&buffer, "%s ", CHUNKED); rank = H5Pget_chunk(dcpl_id, (int)NELMTS(chsize), chsize); - h5tools_str_append(&buffer, "%s " HSIZE_T_FORMAT, h5tools_dump_header_format->dataspacedimbegin, + h5tools_str_append(&buffer, "%s %" PRIuHSIZE, h5tools_dump_header_format->dataspacedimbegin, chsize[0]); for (i = 1; i < rank; i++) - h5tools_str_append(&buffer, ", " HSIZE_T_FORMAT, chsize[i]); + h5tools_str_append(&buffer, ", %" PRIuHSIZE, chsize[i]); h5tools_str_append(&buffer, " %s", h5tools_dump_header_format->dataspacedimend); h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); @@ -3219,17 +3218,17 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info, h5tools_context_t * if (storage_size != 0) ratio = (double)uncomp_size / (double)storage_size; - h5tools_str_append(&buffer, "SIZE " HSIZE_T_FORMAT " (%.3f:1 COMPRESSION)", storage_size, + h5tools_str_append(&buffer, "SIZE %" PRIuHSIZE " (%.3f:1 COMPRESSION)", storage_size, ratio); } else - h5tools_str_append(&buffer, "SIZE " HSIZE_T_FORMAT, storage_size); + h5tools_str_append(&buffer, "SIZE %" PRIuHSIZE, storage_size); H5Sclose(sid); H5Tclose(tid); } else { - h5tools_str_append(&buffer, "SIZE " HSIZE_T_FORMAT, storage_size); + h5tools_str_append(&buffer, "SIZE %" PRIuHSIZE, storage_size); } h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); @@ -3247,7 +3246,7 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info, h5tools_context_t * ctx->need_prefix = TRUE; h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "SIZE " HSIZE_T_FORMAT, storage_size); + h5tools_str_append(&buffer, "SIZE %" PRIuHSIZE, storage_size); h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); ctx->indent_level--; @@ -3283,7 +3282,7 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info, h5tools_context_t * ctx->need_prefix = TRUE; h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "FILENAME %s SIZE " HSIZE_T_FORMAT, name, size); + h5tools_str_append(&buffer, "FILENAME %s SIZE %" PRIuHSIZE, name, size); h5tools_str_append(&buffer, " OFFSET %ld", offset); h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); @@ -3313,7 +3312,7 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info, h5tools_context_t * ctx->need_prefix = TRUE; h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "SIZE " HSIZE_T_FORMAT, storage_size); + h5tools_str_append(&buffer, "SIZE %" PRIuHSIZE, storage_size); h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); @@ -3909,7 +3908,7 @@ h5tools_print_dims(h5tools_str_t *buffer, hsize_t *s, int dims) int i; for (i = 0; i < dims; i++) { - h5tools_str_append(buffer, HSIZE_T_FORMAT, s[i]); + h5tools_str_append(buffer, "%" PRIuHSIZE, s[i]); if (i + 1 != dims) h5tools_str_append(buffer, ", "); @@ -4330,7 +4329,7 @@ h5tools_dump_data(FILE *stream, const h5tool_format_t *info, h5tools_context_t * if (string_dataformat.pindex) { string_dataformat.idx_fmt = "(%s): "; - string_dataformat.idx_n_fmt = HSIZE_T_FORMAT; + string_dataformat.idx_n_fmt = "%" PRIuHSIZE; string_dataformat.idx_sep = ","; string_dataformat.line_pre = "%s"; } diff --git a/tools/lib/h5tools_str.c b/tools/lib/h5tools_str.c index 4e8dcc1..1fb2c68 100644 --- a/tools/lib/h5tools_str.c +++ b/tools/lib/h5tools_str.c @@ -300,11 +300,11 @@ h5tools_str_prefix(h5tools_str_t *str /*in,out*/, const h5tool_format_t *info, h if (i) h5tools_str_append(str, "%s", OPT(info->idx_sep, ",")); - h5tools_str_append(str, OPT(info->idx_n_fmt, HSIZE_T_FORMAT), (hsize_t)ctx->pos[i]); + h5tools_str_append(str, OPT(info->idx_n_fmt, "%" PRIuHSIZE), (hsize_t)ctx->pos[i]); } } else /* Scalar */ - h5tools_str_append(str, OPT(info->idx_n_fmt, HSIZE_T_FORMAT), (hsize_t)elmtno); + h5tools_str_append(str, OPT(info->idx_n_fmt, "%" PRIuHSIZE), (hsize_t)elmtno); H5TOOLS_DEBUG("str=%s", str->s); H5TOOLS_ENDDEBUG(" "); @@ -341,11 +341,11 @@ h5tools_str_region_prefix(h5tools_str_t *str /*in,out*/, const h5tool_format_t * if (i) h5tools_str_append(str, "%s", OPT(info->idx_sep, ",")); - h5tools_str_append(str, OPT(info->idx_n_fmt, HSIZE_T_FORMAT), (hsize_t)ctx->pos[i]); + h5tools_str_append(str, OPT(info->idx_n_fmt, "%" PRIuHSIZE), (hsize_t)ctx->pos[i]); } } else /* Scalar */ - h5tools_str_append(str, OPT(info->idx_n_fmt, HSIZE_T_FORMAT), (hsize_t)0); + h5tools_str_append(str, OPT(info->idx_n_fmt, "%" PRIuHSIZE), (hsize_t)0); H5TOOLS_DEBUG("str=%s", str->s); H5TOOLS_ENDDEBUG(" "); @@ -385,7 +385,7 @@ h5tools_str_dump_space_slabs(h5tools_str_t *str, hid_t rspace, const h5tool_form /* Start coordinates */ h5tools_str_append(str, "%s%s ", info->line_indent, START); for (j = 0; j < ndims; j++) - h5tools_str_append(str, "%s" HSIZE_T_FORMAT, j ? "," : "(", start[j]); + h5tools_str_append(str, "%s%" PRIuHSIZE, j ? "," : "(", start[j]); h5tools_str_append(str, ")"); h5tools_str_append(str, "%s", "\n"); h5tools_str_indent(str, info, ctx); @@ -393,7 +393,7 @@ h5tools_str_dump_space_slabs(h5tools_str_t *str, hid_t rspace, const h5tool_form /* Stride coordinates */ h5tools_str_append(str, "%s ", STRIDE); for (j = 0; j < ndims; j++) - h5tools_str_append(str, "%s" HSIZE_T_FORMAT, j ? "," : "(", stride[j]); + h5tools_str_append(str, "%s%" PRIuHSIZE, j ? "," : "(", stride[j]); h5tools_str_append(str, ")"); h5tools_str_append(str, "%s", "\n"); h5tools_str_indent(str, info, ctx); @@ -404,7 +404,7 @@ h5tools_str_dump_space_slabs(h5tools_str_t *str, hid_t rspace, const h5tool_form if (count[j] == H5S_UNLIMITED) h5tools_str_append(str, "%s%s", j ? "," : "(", "H5S_UNLIMITED"); else - h5tools_str_append(str, "%s" HSIZE_T_FORMAT, j ? "," : "(", count[j]); + h5tools_str_append(str, "%s%" PRIuHSIZE, j ? "," : "(", count[j]); } h5tools_str_append(str, ")"); h5tools_str_append(str, "%s", "\n"); @@ -416,7 +416,7 @@ h5tools_str_dump_space_slabs(h5tools_str_t *str, hid_t rspace, const h5tool_form if (block[j] == H5S_UNLIMITED) h5tools_str_append(str, "%s%s", j ? "," : "(", "H5S_UNLIMITED"); else - h5tools_str_append(str, "%s" HSIZE_T_FORMAT, j ? "," : "(", block[j]); + h5tools_str_append(str, "%s%" PRIuHSIZE, j ? "," : "(", block[j]); } h5tools_str_append(str, ")"); } @@ -468,11 +468,10 @@ h5tools_str_dump_space_blocks(h5tools_str_t *str, hid_t rspace, const h5tool_for /* Start coordinates and opposite corner */ for (v = 0; v < ndims; v++) - h5tools_str_append(str, "%s" HSIZE_T_FORMAT, v ? "," : "(", ptdata[u * 2 * ndims + v]); + h5tools_str_append(str, "%s%" PRIuHSIZE, v ? "," : "(", ptdata[u * 2 * ndims + v]); for (v = 0; v < ndims; v++) - h5tools_str_append(str, "%s" HSIZE_T_FORMAT, v ? "," : ")-(", - ptdata[u * 2 * ndims + v + ndims]); + h5tools_str_append(str, "%s%" PRIuHSIZE, v ? "," : ")-(", ptdata[u * 2 * ndims + v + ndims]); h5tools_str_append(str, ")"); } @@ -527,7 +526,7 @@ h5tools_str_dump_space_points(h5tools_str_t *str, hid_t rspace, const h5tool_for (unsigned long)u); for (v = 0; v < ndims; v++) - h5tools_str_append(str, "%s" HSIZE_T_FORMAT, v ? "," : "(", (ptdata[u * ndims + v])); + h5tools_str_append(str, "%s%" PRIuHSIZE, v ? "," : "(", (ptdata[u * ndims + v])); h5tools_str_append(str, ")"); } diff --git a/tools/lib/h5tools_str.h b/tools/lib/h5tools_str.h index eee87c9..f4610f0 100644 --- a/tools/lib/h5tools_str.h +++ b/tools/lib/h5tools_str.h @@ -26,7 +26,7 @@ typedef struct h5tools_str_t { H5TOOLS_DLL void h5tools_str_close(h5tools_str_t *str); H5TOOLS_DLL size_t h5tools_str_len(h5tools_str_t *str); -H5TOOLS_DLL char * h5tools_str_append(h5tools_str_t *str, const char *fmt, ...); +H5TOOLS_DLL char * h5tools_str_append(h5tools_str_t *str, const char *fmt, ...) H5_ATTR_FORMAT(printf, 2, 3); H5TOOLS_DLL char * h5tools_str_reset(h5tools_str_t *str); H5TOOLS_DLL char * h5tools_str_trunc(h5tools_str_t *str, size_t size); H5TOOLS_DLL char * h5tools_str_fmt(h5tools_str_t *str, size_t start, const char *fmt); diff --git a/tools/lib/h5tools_utils.h b/tools/lib/h5tools_utils.h index 3733742..4cf4e40 100644 --- a/tools/lib/h5tools_utils.h +++ b/tools/lib/h5tools_utils.h @@ -70,11 +70,11 @@ H5TOOLS_DLLVAR unsigned h5tools_nCols; /*max number of columns for outputting * /* Definitions of useful routines */ H5TOOLS_DLL void indentation(unsigned); H5TOOLS_DLL void print_version(const char *progname); -H5TOOLS_DLL void parallel_print(const char *format, ...); +H5TOOLS_DLL void parallel_print(const char *format, ...) H5_ATTR_FORMAT(printf, 1, 2); H5TOOLS_DLL herr_t parse_tuple(const char *start, int sep, char **cpy_out, unsigned *nelems, char ***ptrs_out); -H5TOOLS_DLL void error_msg(const char *fmt, ...); -H5TOOLS_DLL void warn_msg(const char *fmt, ...); +H5TOOLS_DLL void error_msg(const char *fmt, ...) H5_ATTR_FORMAT(printf, 1, 2); +H5TOOLS_DLL void warn_msg(const char *fmt, ...) H5_ATTR_FORMAT(printf, 1, 2); H5TOOLS_DLL void help_ref_msg(FILE *output); H5TOOLS_DLL void free_table(table_t *table); #ifdef H5DUMP_DEBUG diff --git a/tools/lib/h5trav.c b/tools/lib/h5trav.c index 1f4b0d6..cca36e4 100644 --- a/tools/lib/h5trav.c +++ b/tools/lib/h5trav.c @@ -53,11 +53,6 @@ typedef struct trav_path_op_data_t { const char *path; } trav_path_op_data_t; -/* format for hsize_t */ -#ifdef H5TRAV_PRINT_SPACE -#define HSIZE_T_FORMAT "%" H5_PRINTF_LL_WIDTH "u" -#endif /* H5TRAV_PRINT_SPACE */ - /*------------------------------------------------------------------------- * local functions *------------------------------------------------------------------------- @@ -856,7 +851,7 @@ trav_attr(hid_t /* simple dataspace */ HDprintf(" {"); for (i = 0; i < ndims; i++) { - HDprintf("%s" HSIZE_T_FORMAT, i ? ", " : "", size[i]); + HDprintf("%s%" PRIuHSIZE, i ? ", " : "", size[i]); } HDprintf("}\n"); break; diff --git a/tools/src/h5copy/h5copy.c b/tools/src/h5copy/h5copy.c index 4e9a25e..6f10fee 100644 --- a/tools/src/h5copy/h5copy.c +++ b/tools/src/h5copy/h5copy.c @@ -212,7 +212,7 @@ parse_flag(const char *s_flag, unsigned *flag) */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t fid_src = H5I_INVALID_HID; hid_t fid_dst = H5I_INVALID_HID; @@ -242,7 +242,7 @@ main(int argc, const char *argv[]) } /* end if */ /* parse command line options */ - while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) { + while ((opt = H5_get_option(argc, (const char *const *)argv, s_opts, l_opts)) != EOF) { switch ((char)opt) { case 'd': oname_dst = HDstrdup(H5_optarg); diff --git a/tools/src/h5diff/h5diff_common.c b/tools/src/h5diff/h5diff_common.c index ec41d21..77a6785 100644 --- a/tools/src/h5diff/h5diff_common.c +++ b/tools/src/h5diff/h5diff_common.c @@ -206,7 +206,7 @@ parse_subset_params(const char *dset) */ void -parse_command_line(int argc, const char *argv[], const char **fname1, const char **fname2, +parse_command_line(int argc, const char *const *argv, const char **fname1, const char **fname2, const char **objname1, const char **objname2, diff_opt_t *opts) { int i; diff --git a/tools/src/h5diff/h5diff_common.h b/tools/src/h5diff/h5diff_common.h index 83f4255..35e5dfb 100644 --- a/tools/src/h5diff/h5diff_common.h +++ b/tools/src/h5diff/h5diff_common.h @@ -23,7 +23,7 @@ extern "C" { #endif void usage(void); -void parse_command_line(int argc, const char *argv[], const char **fname1, const char **fname2, +void parse_command_line(int argc, const char *const *argv, const char **fname1, const char **fname2, const char **objname1, const char **objname2, diff_opt_t *opts); void h5diff_exit(int status); void print_info(diff_opt_t *opts); diff --git a/tools/src/h5diff/h5diff_main.c b/tools/src/h5diff/h5diff_main.c index 37c215b..2a43b56 100644 --- a/tools/src/h5diff/h5diff_main.c +++ b/tools/src/h5diff/h5diff_main.c @@ -65,7 +65,7 @@ */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { int ret; int i; @@ -86,7 +86,7 @@ main(int argc, const char *argv[]) * process the command-line *------------------------------------------------------------------------- */ - parse_command_line(argc, argv, &fname1, &fname2, &objname1, &objname2, &opts); + parse_command_line(argc, (const char *const *)argv, &fname1, &fname2, &objname1, &objname2, &opts); /* enable error reporting if command line option */ h5tools_error_report(); diff --git a/tools/src/h5diff/ph5diff_main.c b/tools/src/h5diff/ph5diff_main.c index ec78e49..8e5c3e8 100644 --- a/tools/src/h5diff/ph5diff_main.c +++ b/tools/src/h5diff/ph5diff_main.c @@ -44,7 +44,7 @@ static void ph5diff_worker(int); */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { int nID = 0; const char *fname1 = NULL; @@ -72,7 +72,7 @@ main(int argc, const char *argv[]) g_Parallel = 0; - parse_command_line(argc, argv, &fname1, &fname2, &objname1, &objname2, &opts); + parse_command_line(argc, (const char *const *)argv, &fname1, &fname2, &objname1, &objname2, &opts); h5diff(fname1, fname2, objname1, objname2, &opts); @@ -83,7 +83,8 @@ main(int argc, const char *argv[]) /* Have the manager process the command-line */ if (nID == 0) { - parse_command_line(argc, argv, &fname1, &fname2, &objname1, &objname2, &opts); + parse_command_line(argc, (const char *const *)argv, &fname1, &fname2, &objname1, &objname2, + &opts); h5diff(fname1, fname2, objname1, objname2, &opts); diff --git a/tools/src/h5dump/h5dump.c b/tools/src/h5dump/h5dump.c index a57b0e3..8c04bc7 100644 --- a/tools/src/h5dump/h5dump.c +++ b/tools/src/h5dump/h5dump.c @@ -828,7 +828,7 @@ free_handler(struct handler_t *hand, int len) *------------------------------------------------------------------------- */ static struct handler_t * -parse_command_line(int argc, const char *argv[]) +parse_command_line(int argc, const char *const *argv) { struct handler_t *hand = NULL; struct handler_t *last_dset = NULL; @@ -1329,7 +1329,7 @@ error: *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t fid = H5I_INVALID_HID; hid_t gid = H5I_INVALID_HID; @@ -1349,7 +1349,7 @@ main(int argc, const char *argv[]) /* Initialize h5tools lib */ h5tools_init(); - if ((hand = parse_command_line(argc, argv)) == NULL) { + if ((hand = parse_command_line(argc, (const char *const *)argv)) == NULL) { goto done; } diff --git a/tools/src/h5dump/h5dump_ddl.c b/tools/src/h5dump/h5dump_ddl.c index 8002ec2..b0bce0c 100644 --- a/tools/src/h5dump/h5dump_ddl.c +++ b/tools/src/h5dump/h5dump_ddl.c @@ -838,7 +838,7 @@ dump_group(hid_t gid, const char *name) type = H5Dget_type(dset); H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_tok_str); - HDsprintf(type_name, "#%s", obj_tok_str); + HDsnprintf(type_name, sizeof(type_name), "#%s", obj_tok_str); H5free_memory(obj_tok_str); dump_function_table->dump_named_datatype_function(type, type_name); @@ -1318,7 +1318,7 @@ attr_search(hid_t oid, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *a j = (int)HDstrlen(op_name) - 1; /* find the last / */ while (j >= 0) { - if (op_name[j] == '/' && (j == 0 || (j > 0 && op_name[j - 1] != '\\'))) + if (op_name[j] == '/' && (j == 0 || (op_name[j - 1] != '\\'))) break; j--; } @@ -1541,7 +1541,7 @@ handle_attributes(hid_t fid, const char *attr, void H5_ATTR_UNUSED *data, int H5 /* find the last / */ while (j >= 0) { - if (attr[j] == '/' && (j == 0 || (j > 0 && attr[j - 1] != '\\'))) + if (attr[j] == '/' && (j == 0 || (attr[j - 1] != '\\'))) break; j--; } @@ -1970,7 +1970,7 @@ handle_datatypes(hid_t fid, const char *type, void H5_ATTR_UNUSED *data, int pe, /* unnamed datatype */ H5Otoken_to_str(fid, &type_table->objs[idx].obj_token, &obj_tok_str); - HDsprintf(name, "/#%s", obj_tok_str); + HDsnprintf(name, sizeof(name), "/#%s", obj_tok_str); H5free_memory(obj_tok_str); if (!HDstrcmp(name, real_name)) diff --git a/tools/src/h5dump/h5dump_xml.c b/tools/src/h5dump/h5dump_xml.c index 8fec49c..827daf3 100644 --- a/tools/src/h5dump/h5dump_xml.c +++ b/tools/src/h5dump/h5dump_xml.c @@ -591,6 +591,8 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen if (outlen < 22) return 1; + H5_CHECK_OVERFLOW(outlen, int, size_t); + lookup_ret = ref_path_table_lookup(str, &obj_token); if (lookup_ret < 0) { if (HDstrlen(str) == 0) { @@ -600,7 +602,7 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen ref_path_table_gen_fake(str, &obj_token); H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str); - HDsprintf(outstr, "xid_%s", obj_tok_str); + HDsnprintf(outstr, (size_t)outlen, "xid_%s", obj_tok_str); H5free_memory(obj_tok_str); return 0; @@ -615,7 +617,7 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen ref_path_table_gen_fake(str, &obj_token); H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str); - HDsprintf(outstr, "xid_%s", obj_tok_str); + HDsnprintf(outstr, (size_t)outlen, "xid_%s", obj_tok_str); H5free_memory(obj_tok_str); return 0; @@ -627,7 +629,7 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen } H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str); - HDsprintf(outstr, "xid_%s", obj_tok_str); + HDsnprintf(outstr, (size_t)outlen, "xid_%s", obj_tok_str); H5free_memory(obj_tok_str); return 0; @@ -1777,8 +1779,7 @@ xml_dump_dataspace(hid_t space) /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, - "<%sDimension DimSize=\"%" H5_PRINTF_LL_WIDTH - "u\" MaxDimSize=\"UNLIMITED\"/>", + "<%sDimension DimSize=\"%" PRIuHSIZE "\" MaxDimSize=\"UNLIMITED\"/>", xmlnsprefix, size[i]); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); @@ -1788,10 +1789,9 @@ xml_dump_dataspace(hid_t space) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, - "<%sDimension DimSize=\"%" H5_PRINTF_LL_WIDTH - "u\" MaxDimSize=\"%" H5_PRINTF_LL_WIDTH "u\"/>", - xmlnsprefix, size[i], size[i]); + h5tools_str_append( + &buffer, "<%sDimension DimSize=\"%" PRIuHSIZE "\" MaxDimSize=\"%" PRIuHSIZE "\"/>", + xmlnsprefix, size[i], size[i]); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } @@ -1800,10 +1800,9 @@ xml_dump_dataspace(hid_t space) /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, - "<%sDimension DimSize=\"%" H5_PRINTF_LL_WIDTH - "u\" MaxDimSize=\"%" H5_PRINTF_LL_WIDTH "u\"/>", - xmlnsprefix, size[i], maxsize[i]); + h5tools_str_append( + &buffer, "<%sDimension DimSize=\"%" PRIuHSIZE "\" MaxDimSize=\"%" PRIuHSIZE "\"/>", + xmlnsprefix, size[i], maxsize[i]); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } @@ -2802,7 +2801,7 @@ xml_dump_group(hid_t gid, const char *name) type = H5Dget_type(dset); H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_tok_str); - HDsprintf(type_name, "#%s", obj_tok_str); + HDsnprintf(type_name, sizeof(type_name), "#%s", obj_tok_str); H5free_memory(obj_tok_str); dump_function_table->dump_named_datatype_function(type, type_name); @@ -2895,7 +2894,7 @@ xml_dump_group(hid_t gid, const char *name) type = H5Dget_type(dset); H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_tok_str); - HDsprintf(type_name, "#%s", obj_tok_str); + HDsnprintf(type_name, sizeof(type_name), "#%s", obj_tok_str); H5free_memory(obj_tok_str); dump_function_table->dump_named_datatype_function(type, type_name); @@ -3598,7 +3597,10 @@ xml_dump_fill_value(hid_t dcpl, hid_t type) h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "\""); for (i = 0; i < sz; i++) { - h5tools_str_append(&buffer, "%x ", *(unsigned int *)buf + (i * sizeof(unsigned int))); + unsigned long val = *(unsigned int *)buf + (i * sizeof(unsigned int)); + + H5_CHECK_OVERFLOW(val, unsigned long, unsigned); + h5tools_str_append(&buffer, "%x ", (unsigned)val); } h5tools_str_append(&buffer, "\""); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, @@ -3892,8 +3894,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED *ss /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, "<%sChunkDimension DimSize=\"%" H5_PRINTF_LL_WIDTH "u\" />", - xmlnsprefix, chsize[i]); + h5tools_str_append(&buffer, "<%sChunkDimension DimSize=\"%" PRIuHSIZE "\" />", xmlnsprefix, + chsize[i]); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } @@ -4524,12 +4526,16 @@ xml_print_enum(hid_t type) h5tools_str_append(&buffer, "%02x", value[i * dst_size + j]); } else if (H5T_SGN_NONE == H5Tget_sign(native)) { - h5tools_str_append(&buffer, "%" H5_PRINTF_LL_WIDTH "u", - *((unsigned long long *)((void *)(value + i * dst_size)))); + unsigned long long copy; + + HDmemcpy(©, value + i * dst_size, sizeof(copy)); + h5tools_str_append(&buffer, "%llu", copy); } else { - h5tools_str_append(&buffer, "%" H5_PRINTF_LL_WIDTH "d", - *((long long *)((void *)(value + i * dst_size)))); + long long copy; + + HDmemcpy(©, value + i * dst_size, sizeof(copy)); + h5tools_str_append(&buffer, "%lld", copy); } h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); diff --git a/tools/src/h5format_convert/h5format_convert.c b/tools/src/h5format_convert/h5format_convert.c index ddf129c..50d0f5d 100644 --- a/tools/src/h5format_convert/h5format_convert.c +++ b/tools/src/h5format_convert/h5format_convert.c @@ -94,7 +94,7 @@ usage(const char *prog) *------------------------------------------------------------------------- */ static int -parse_command_line(int argc, const char **argv) +parse_command_line(int argc, const char *const *argv) { int opt; @@ -127,7 +127,7 @@ parse_command_line(int argc, const char **argv) dname_g = HDstrdup(H5_optarg); if (dname_g == NULL) { h5tools_setstatus(EXIT_FAILURE); - error_msg("No dataset name\n", H5_optarg); + error_msg("No dataset name `%s`\n", H5_optarg); usage(h5tools_getprogname()); goto error; } @@ -383,7 +383,7 @@ error: *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t fid = H5I_INVALID_HID; @@ -394,7 +394,7 @@ main(int argc, const char *argv[]) h5tools_init(); /* Parse command line options */ - if (parse_command_line(argc, argv) < 0) + if (parse_command_line(argc, (const char *const *)argv) < 0) goto done; else if (verbose_g) HDfprintf(stdout, "Process command line options\n"); diff --git a/tools/src/h5import/h5import.c b/tools/src/h5import/h5import.c index 31fa7cf..317db81 100644 --- a/tools/src/h5import/h5import.c +++ b/tools/src/h5import/h5import.c @@ -3784,7 +3784,7 @@ setDefaultValues(struct Input *in, int count) in->path.count = 1; HDstrcpy(temp, "dataset"); - HDsprintf(num, "%d", count); + HDsnprintf(num, sizeof(num), "%d", count); HDstrcat(temp, num); HDstrcpy(in->path.group[0], temp); diff --git a/tools/src/h5jam/h5jam.c b/tools/src/h5jam/h5jam.c index 07140b5..45978bb 100644 --- a/tools/src/h5jam/h5jam.c +++ b/tools/src/h5jam/h5jam.c @@ -22,7 +22,7 @@ herr_t write_pad(int ofile, hsize_t old_where, hsize_t *new_where); hsize_t compute_user_block_size(hsize_t); hsize_t copy_some_to_file(int, int, hsize_t, hsize_t, ssize_t); -void parse_command_line(int, const char *[]); +void parse_command_line(int, const char *const *); int do_clobber = FALSE; char *output_file = NULL; @@ -104,7 +104,7 @@ leave(int ret) */ void -parse_command_line(int argc, const char *argv[]) +parse_command_line(int argc, const char *const *argv) { int opt = FALSE; @@ -149,7 +149,7 @@ parse_command_line(int argc, const char *argv[]) *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { int ufid = -1; int h5fid = -1; @@ -174,7 +174,7 @@ main(int argc, const char *argv[]) /* Initialize h5tools lib */ h5tools_init(); - parse_command_line(argc, argv); + parse_command_line(argc, (const char *const *)argv); /* enable error reporting if command line option */ h5tools_error_report(); diff --git a/tools/src/h5jam/h5unjam.c b/tools/src/h5jam/h5unjam.c index fa23b06..8ff354e 100644 --- a/tools/src/h5jam/h5unjam.c +++ b/tools/src/h5jam/h5unjam.c @@ -92,7 +92,7 @@ usage(const char *prog) *------------------------------------------------------------------------- */ static int -parse_command_line(int argc, const char *argv[]) +parse_command_line(int argc, const char *const *argv) { int opt = FALSE; @@ -172,7 +172,7 @@ leave(int ret) *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t ifile = H5I_INVALID_HID; hid_t plist = H5I_INVALID_HID; @@ -189,7 +189,7 @@ main(int argc, const char *argv[]) /* Initialize h5tools lib */ h5tools_init(); - if (EXIT_FAILURE == parse_command_line(argc, argv)) + if (EXIT_FAILURE == parse_command_line(argc, (const char *const *)argv)) goto done; /* enable error reporting if command line option */ diff --git a/tools/src/h5ls/h5ls.c b/tools/src/h5ls/h5ls.c index 17abf43..a27a8cc 100644 --- a/tools/src/h5ls/h5ls.c +++ b/tools/src/h5ls/h5ls.c @@ -78,9 +78,9 @@ static h5tool_format_t ls_dataformat = { ",", /*elmt_suf1 */ " ", /*elmt_suf2 */ - HSIZE_T_FORMAT, /*idx_n_fmt */ - ",", /*idx_sep */ - "(%s)", /*idx_fmt */ + "%" PRIuHSIZE, /*idx_n_fmt */ + ",", /*idx_sep */ + "(%s)", /*idx_fmt */ 65535, /*line_ncols */ /*standard default columns */ @@ -942,8 +942,7 @@ print_enum_type(h5tools_str_t *buffer, hid_t type, int ind) /* Print members */ for (i = 0; i < (unsigned)nmembs; i++) { - unsigned char *copy; /* a pointer to value array */ - int nchars; /* number of output characters */ + int nchars; /* number of output characters */ h5tools_str_append(buffer, "\n%*s", ind + 4, ""); nchars = print_string(buffer, name[i], TRUE); @@ -957,16 +956,16 @@ print_enum_type(h5tools_str_t *buffer, hid_t type, int ind) h5tools_str_append(buffer, "%02x", value[i * dst_size + j]); } else if (H5T_SGN_NONE == H5Tget_sign(native)) { - /*On SGI Altix(cobalt), wrong values were printed out with "value+i*dst_size" - *strangely, unless use another pointer "copy".*/ - copy = value + i * dst_size; - h5tools_str_append(buffer, HSIZE_T_FORMAT, *((unsigned long long *)((void *)copy))); + unsigned long long copy; + + HDmemcpy(©, value + i * dst_size, sizeof(copy)); + h5tools_str_append(buffer, "%llu", copy); } else { - /*On SGI Altix(cobalt), wrong values were printed out with "value+i*dst_size" - *strangely, unless use another pointer "copy".*/ - copy = value + i * dst_size; - h5tools_str_append(buffer, "%lld", *((long long *)((void *)copy))); + long long copy; + + HDmemcpy(©, value + i * dst_size, sizeof(copy)); + h5tools_str_append(buffer, "%lld", copy); } } @@ -1185,13 +1184,13 @@ print_array_type(h5tools_str_t *buffer, hid_t type, int ind) /* Print dimensions */ for (i = 0; i < ndims; i++) - h5tools_str_append(buffer, "%s" HSIZE_T_FORMAT, i ? "," : "[", dims[i]); + h5tools_str_append(buffer, "%s%" PRIuHSIZE, i ? "," : "[", dims[i]); h5tools_str_append(buffer, "]"); HDfree(dims); } else - h5tools_str_append(buffer, " [SCALAR]\n", rawoutstream); + h5tools_str_append(buffer, " [SCALAR]\n"); /* Print parent type */ h5tools_str_append(buffer, " "); @@ -1701,7 +1700,7 @@ list_attr(hid_t obj, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *ain /* simple dataspace */ h5tools_str_append(&buffer, " {"); for (i = 0; i < ndims; i++) { - h5tools_str_append(&buffer, "%s" HSIZE_T_FORMAT, i ? ", " : "", size[i]); + h5tools_str_append(&buffer, "%s%" PRIuHSIZE, i ? ", " : "", size[i]); nelmts *= size[i]; } h5tools_str_append(&buffer, "}\n"); @@ -1789,12 +1788,12 @@ dataset_list1(hid_t dset) ndims = H5Sget_simple_extent_dims(space, cur_size, max_size); h5tools_str_append(&buffer, " {"); for (i = 0; i < ndims; i++) { - h5tools_str_append(&buffer, "%s" HSIZE_T_FORMAT, i ? ", " : "", cur_size[i]); + h5tools_str_append(&buffer, "%s%" PRIuHSIZE, i ? ", " : "", cur_size[i]); if (max_size[i] == H5S_UNLIMITED) { h5tools_str_append(&buffer, "/%s", "Inf"); } else if (max_size[i] != cur_size[i] || verbose_g > 0) { - h5tools_str_append(&buffer, "/" HSIZE_T_FORMAT, max_size[i]); + h5tools_str_append(&buffer, "/%" PRIuHSIZE, max_size[i]); } } if (space_type == H5S_SCALAR) @@ -1868,10 +1867,10 @@ dataset_list2(hid_t dset, const char H5_ATTR_UNUSED *name) h5tools_str_append(&buffer, " %-10s {", "Chunks:"); total = H5Tget_size(type); for (i = 0; i < ndims; i++) { - h5tools_str_append(&buffer, "%s" HSIZE_T_FORMAT, i ? ", " : "", chsize[i]); + h5tools_str_append(&buffer, "%s%" PRIuHSIZE, i ? ", " : "", chsize[i]); total *= chsize[i]; } - h5tools_str_append(&buffer, "} " HSIZE_T_FORMAT " bytes\n", total); + h5tools_str_append(&buffer, "} %" PRIuHSIZE " bytes\n", total); } break; case H5D_COMPACT: break; @@ -1897,15 +1896,13 @@ dataset_list2(hid_t dset, const char H5_ATTR_UNUSED *name) if (H5Pget_external(dcpl, (unsigned)i, sizeof(f_name), f_name, &f_offset, &f_size) < 0) { h5tools_str_append( - &buffer, - " #%03d %10" H5_PRINTF_LL_WIDTH "u %10s %10s ***ERROR*** %s\n", i, + &buffer, " #%03d %10" PRIuHSIZE " %10s %10s ***ERROR*** %s\n", i, total, "", "", i + 1 < nf ? "Following addresses are incorrect" : ""); } else if (H5S_UNLIMITED == f_size) { h5tools_str_append(&buffer, - " #%03d %10" H5_PRINTF_LL_WIDTH - "u %10" H5_PRINTF_LL_WIDTH "u %10s ", - i, total, (hsize_t)f_offset, "INF"); + " #%03d %10" PRIuHSIZE " %10" PRIuHSIZE " %10s ", i, + total, (hsize_t)f_offset, "INF"); print_string(&buffer, f_name, TRUE); } else { @@ -1985,8 +1982,7 @@ dataset_list2(hid_t dset, const char H5_ATTR_UNUSED *name) case H5T_ARRAY: case H5T_NCLASSES: default: - h5tools_str_append(&buffer, - HSIZE_T_FORMAT " logical byte%s, " HSIZE_T_FORMAT " allocated byte%s", + h5tools_str_append(&buffer, "%" PRIuHSIZE " logical byte%s, %" PRIuHSIZE " allocated byte%s", total, 1 == total ? "" : "s", used, 1 == used ? "" : "s"); if (used > 0) { utilization = ((double)total * 100.0) / (double)used; @@ -2646,7 +2642,7 @@ leave(int ret) *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t file_id = H5I_INVALID_HID; char * fname = NULL, *oname = NULL, *x = NULL; diff --git a/tools/src/h5perf/pio_engine.c b/tools/src/h5perf/pio_engine.c index 3edc74a..e316245 100644 --- a/tools/src/h5perf/pio_engine.c +++ b/tools/src/h5perf/pio_engine.c @@ -282,7 +282,7 @@ do_pio(parameters param) /* Open file for write */ char base_name[256]; - HDsprintf(base_name, "#pio_tmp_%lu", nf); + HDsnprintf(base_name, sizeof(base_name), "#pio_tmp_%lu", nf); pio_create_filename(iot, base_name, fname, sizeof(fname)); if (pio_debug_level > 0) HDfprintf(output, "rank %d: data filename=%s\n", pio_mpi_rank_g, fname); @@ -898,7 +898,7 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets, off_t nby } /* end if */ } /* end else */ - HDsprintf(dname, "Dataset_%ld", ndset); + HDsnprintf(dname, sizeof(dname), "Dataset_%ld", ndset); h5ds_id = H5DCREATE(fd->h5fd, dname, ELMT_H5_TYPE, h5dset_space_id, h5dcpl); if (h5ds_id < 0) { @@ -1879,7 +1879,7 @@ do_read(results *res, file_descr *fd, parameters *parms, long ndsets, off_t nbyt break; case PHDF5: - HDsprintf(dname, "Dataset_%ld", ndset); + HDsnprintf(dname, sizeof(dname), "Dataset_%ld", ndset); h5ds_id = H5DOPEN(fd->h5fd, dname); if (h5ds_id < 0) { HDfprintf(stderr, "HDF5 Dataset open failed\n"); diff --git a/tools/src/h5perf/pio_perf.c b/tools/src/h5perf/pio_perf.c index bf5f62f..c233684 100644 --- a/tools/src/h5perf/pio_perf.c +++ b/tools/src/h5perf/pio_perf.c @@ -188,7 +188,7 @@ typedef struct _minmax { /* local functions */ static off_t parse_size_directive(const char *size); -static struct options *parse_command_line(int argc, char *argv[]); +static struct options *parse_command_line(int argc, const char *const *argv); static void run_test_loop(struct options *options); static int run_test(iotype iot, parameters parms, struct options *opts); static void output_all_info(minmax *mm, int count, int indent_level); @@ -260,7 +260,7 @@ main(int argc, char *argv[]) pio_comm_g = MPI_COMM_WORLD; h5_set_info_object(); - opts = parse_command_line(argc, argv); + opts = parse_command_line(argc, (const char *const *)argv); if (!opts) { exit_value = EXIT_FAILURE; @@ -1276,7 +1276,7 @@ report_parameters(struct options *opts) * Added 2D testing (Christian Chilan, 10. August 2005) */ static struct options * -parse_command_line(int argc, char *argv[]) +parse_command_line(int argc, const char *const *argv) { register int opt; struct options *cl_opts; @@ -1305,7 +1305,7 @@ parse_command_line(int argc, char *argv[]) cl_opts->h5_write_only = FALSE; /* Do both read and write by default */ cl_opts->verify = FALSE; /* No Verify data correctness by default */ - while ((opt = H5_get_option(argc, (const char **)argv, s_opts, l_opts)) != EOF) { + while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) { switch ((char)opt) { case 'a': cl_opts->h5_alignment = parse_size_directive(H5_optarg); diff --git a/tools/src/h5perf/sio_engine.c b/tools/src/h5perf/sio_engine.c index 98cb920..95ec3ce 100644 --- a/tools/src/h5perf/sio_engine.c +++ b/tools/src/h5perf/sio_engine.c @@ -1267,7 +1267,7 @@ done: static void do_cleanupfile(iotype iot, char *filename) { - char temp[2048]; + char temp[4096 + sizeof("-?.h5")]; int j; hid_t driver; diff --git a/tools/src/h5perf/sio_perf.c b/tools/src/h5perf/sio_perf.c index 0eb4508..87b9d65 100644 --- a/tools/src/h5perf/sio_perf.c +++ b/tools/src/h5perf/sio_perf.c @@ -164,7 +164,7 @@ typedef struct { /* local functions */ static hsize_t parse_size_directive(const char *size); -static struct options *parse_command_line(int argc, const char *argv[]); +static struct options *parse_command_line(int argc, const char *const *argv); static void run_test_loop(struct options *options); static int run_test(iotype iot, parameters parms, struct options *opts); static void output_all_info(minmax *mm, int count, int indent_level); @@ -185,7 +185,7 @@ static void report_parameters(struct options *opts); * Modifications: */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { int exit_value = EXIT_SUCCESS; struct options *opts = NULL; @@ -197,7 +197,7 @@ main(int argc, const char *argv[]) output = stdout; - opts = parse_command_line(argc, argv); + opts = parse_command_line(argc, (const char *const *)argv); if (!opts) { exit_value = EXIT_FAILURE; @@ -277,7 +277,7 @@ run_test_loop(struct options *opts) } /* print size information */ - output_report("Transfer Buffer Size (bytes): %d\n", buf_bytes); + output_report("Transfer Buffer Size (bytes): %zu\n", buf_bytes); output_report("File Size(MB): %.2f\n", ((double)parms.num_bytes) / ONE_MB); print_indent(0); @@ -817,7 +817,7 @@ report_parameters(struct options *opts) * Added multidimensional testing (Christian Chilan, April, 2008) */ static struct options * -parse_command_line(int argc, const char *argv[]) +parse_command_line(int argc, const char *const *argv) { int opt; struct options *cl_opts; diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c index 0a26500..4c88bd7 100644 --- a/tools/src/h5repack/h5repack_main.c +++ b/tools/src/h5repack/h5repack_main.c @@ -18,7 +18,7 @@ /* Name of tool */ #define PROGRAMNAME "h5repack" -static int parse_command_line(int argc, const char **argv, pack_opt_t *options); +static int parse_command_line(int argc, const char *const *argv, pack_opt_t *options); static void leave(int ret) H5_ATTR_NORETURN; /* module-scoped variables */ @@ -507,7 +507,7 @@ set_sort_order(const char *form) *------------------------------------------------------------------------- */ static int -parse_command_line(int argc, const char **argv, pack_opt_t *options) +parse_command_line(int argc, const char *const *argv, pack_opt_t *options) { h5tools_vol_info_t in_vol_info; h5tools_vol_info_t out_vol_info; @@ -701,7 +701,7 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options) case 'a': options->alignment = HDstrtoull(H5_optarg, NULL, 0); if (options->alignment < 1) { - error_msg("invalid alignment size\n", H5_optarg); + error_msg("invalid alignment size `%s`\n", H5_optarg); h5tools_setstatus(EXIT_FAILURE); ret_value = -1; goto done; @@ -721,7 +721,7 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options) else if (!HDstrcmp(strategy, "NONE")) options->fs_strategy = H5F_FSPACE_STRATEGY_NONE; else { - error_msg("invalid file space management strategy\n", H5_optarg); + error_msg("invalid file space management strategy `%s`\n", H5_optarg); h5tools_setstatus(EXIT_FAILURE); ret_value = -1; goto done; @@ -928,7 +928,7 @@ done: *------------------------------------------------------------------------- */ int -main(int argc, const char **argv) +main(int argc, char **argv) { pack_opt_t options; /*the global options */ int parse_ret; @@ -958,7 +958,7 @@ main(int argc, const char **argv) /* Initialize default indexing options */ sort_by = H5_INDEX_CRT_ORDER; - parse_ret = parse_command_line(argc, argv, &options); + parse_ret = parse_command_line(argc, (const char *const *)argv, &options); if (parse_ret < 0) { HDprintf("Error occurred while parsing command-line options\n"); h5tools_setstatus(EXIT_FAILURE); diff --git a/tools/src/h5stat/h5stat.c b/tools/src/h5stat/h5stat.c index 6b01e49..f1156f0 100644 --- a/tools/src/h5stat/h5stat.c +++ b/tools/src/h5stat/h5stat.c @@ -830,7 +830,7 @@ hand_free(struct handler_t *hand) *------------------------------------------------------------------------- */ static int -parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret) +parse_command_line(int argc, const char *const *argv, struct handler_t **hand_ret) { int opt; unsigned u; @@ -1677,7 +1677,7 @@ print_statistics(const char *name, const iter_t *iter) *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { iter_t iter; const char * fname = NULL; @@ -1693,7 +1693,7 @@ main(int argc, const char *argv[]) HDmemset(&iter, 0, sizeof(iter)); - if (parse_command_line(argc, argv, &hand) < 0) + if (parse_command_line(argc, (const char *const *)argv, &hand) < 0) goto done; /* enable error reporting if command line option */ diff --git a/tools/src/misc/h5clear.c b/tools/src/misc/h5clear.c index face2f0..15c170d 100644 --- a/tools/src/misc/h5clear.c +++ b/tools/src/misc/h5clear.c @@ -109,7 +109,7 @@ usage(const char *prog) *------------------------------------------------------------------------- */ static int -parse_command_line(int argc, const char **argv) +parse_command_line(int argc, const char *const *argv) { int opt; @@ -224,7 +224,7 @@ leave(int ret) *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { char * fname = NULL; /* File name */ hid_t fapl = H5I_INVALID_HID; /* File access property list */ @@ -240,7 +240,7 @@ main(int argc, const char *argv[]) h5tools_init(); /* Parse command line options */ - if (parse_command_line(argc, argv) < 0) + if (parse_command_line(argc, (const char *const *)argv) < 0) goto done; if (fname_g == NULL) diff --git a/tools/src/misc/h5delete.c b/tools/src/misc/h5delete.c index 3c4f8d5..20e81a1 100644 --- a/tools/src/misc/h5delete.c +++ b/tools/src/misc/h5delete.c @@ -29,7 +29,7 @@ usage(void) } int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hbool_t quiet = FALSE; const char *name = NULL; diff --git a/tools/src/misc/h5mkgrp.c b/tools/src/misc/h5mkgrp.c index 1e66fce..1b8b23d 100644 --- a/tools/src/misc/h5mkgrp.c +++ b/tools/src/misc/h5mkgrp.c @@ -131,7 +131,7 @@ usage(const char *prog) *------------------------------------------------------------------------- */ static int -parse_command_line(int argc, const char *argv[], mkgrp_opt_t *options) +parse_command_line(int argc, const char *const *argv, mkgrp_opt_t *options) { int opt; /* Option from command line */ size_t curr_group; /* Current group name to copy */ @@ -281,7 +281,7 @@ parse_command_line(int argc, const char *argv[], mkgrp_opt_t *options) *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { hid_t fid = H5I_INVALID_HID; /* HDF5 file ID */ hid_t lcpl_id = H5I_INVALID_HID; /* Link creation property list ID */ @@ -303,7 +303,7 @@ main(int argc, const char *argv[]) } /* Parse command line */ - if (parse_command_line(argc, argv, ¶ms_g) < 0) { + if (parse_command_line(argc, (const char *const *)argv, ¶ms_g) < 0) { error_msg("unable to parse command line arguments\n"); leave(EXIT_FAILURE); } diff --git a/tools/test/h5dump/binread.c b/tools/test/h5dump/binread.c index d6206ca..341a085 100644 --- a/tools/test/h5dump/binread.c +++ b/tools/test/h5dump/binread.c @@ -59,7 +59,7 @@ usage(void) */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { FILE * stream; size_t numread; diff --git a/tools/test/h5jam/getub.c b/tools/test/h5jam/getub.c index fd21d6c..4e67e98 100644 --- a/tools/test/h5jam/getub.c +++ b/tools/test/h5jam/getub.c @@ -15,7 +15,7 @@ #include "h5tools.h" #include "h5tools_utils.h" -void parse_command_line(int argc, const char *argv[]); +void parse_command_line(int argc, const char *const *argv); /* Name of tool */ #define PROGRAM_NAME "getub" @@ -52,7 +52,7 @@ usage(const char *prog) *------------------------------------------------------------------------- */ void -parse_command_line(int argc, const char *argv[]) +parse_command_line(int argc, const char *const *argv) { int opt; @@ -77,7 +77,7 @@ parse_command_line(int argc, const char *argv[]) } /* end parse_command_line() */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { int fd = H5I_INVALID_HID; unsigned size; @@ -91,7 +91,7 @@ main(int argc, const char *argv[]) /* Initialize h5tools lib */ h5tools_init(); - parse_command_line(argc, argv); + parse_command_line(argc, (const char *const *)argv); if (NULL == nbytes) { /* missing arg */ diff --git a/tools/test/h5jam/tellub.c b/tools/test/h5jam/tellub.c index e6769ec..f264d9b 100644 --- a/tools/test/h5jam/tellub.c +++ b/tools/test/h5jam/tellub.c @@ -56,7 +56,7 @@ usage(const char *prog) */ static void -parse_command_line(int argc, const char *argv[]) +parse_command_line(int argc, const char *const *argv) { int opt; @@ -98,7 +98,7 @@ leave(int ret) *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { char * ifname; hid_t ifile = H5I_INVALID_HID; @@ -113,7 +113,7 @@ main(int argc, const char *argv[]) /* Initialize h5tools lib */ h5tools_init(); - parse_command_line(argc, argv); + parse_command_line(argc, (const char *const *)argv); /* enable error reporting if command line option */ h5tools_error_report(); diff --git a/tools/test/h5repack/testfiles/h5repack_layout.h5-plugin_version_test.ddl b/tools/test/h5repack/testfiles/h5repack_layout.h5-plugin_version_test.ddl index 15ae813..0992a0c 100644 --- a/tools/test/h5repack/testfiles/h5repack_layout.h5-plugin_version_test.ddl +++ b/tools/test/h5repack/testfiles/h5repack_layout.h5-plugin_version_test.ddl @@ -11,7 +11,7 @@ GROUP "/" { USER_DEFINED_FILTER { FILTER_ID 260 COMMENT dynlib4 - PARAMS { 9 1 13 1 } + PARAMS { 9 1 13 2 } } } FILLVALUE { @@ -33,7 +33,7 @@ GROUP "/" { USER_DEFINED_FILTER { FILTER_ID 260 COMMENT dynlib4 - PARAMS { 9 1 13 1 } + PARAMS { 9 1 13 2 } } } FILLVALUE { @@ -55,7 +55,7 @@ GROUP "/" { USER_DEFINED_FILTER { FILTER_ID 260 COMMENT dynlib4 - PARAMS { 9 1 13 1 } + PARAMS { 9 1 13 2 } } } FILLVALUE { @@ -77,7 +77,7 @@ GROUP "/" { USER_DEFINED_FILTER { FILTER_ID 260 COMMENT dynlib4 - PARAMS { 9 1 13 1 } + PARAMS { 9 1 13 2 } } } FILLVALUE { @@ -99,7 +99,7 @@ GROUP "/" { USER_DEFINED_FILTER { FILTER_ID 260 COMMENT dynlib4 - PARAMS { 9 1 13 1 } + PARAMS { 9 1 13 2 } } } FILLVALUE { @@ -121,7 +121,7 @@ GROUP "/" { USER_DEFINED_FILTER { FILTER_ID 260 COMMENT dynlib4 - PARAMS { 9 1 13 1 } + PARAMS { 9 1 13 2 } } } FILLVALUE { @@ -143,7 +143,7 @@ GROUP "/" { USER_DEFINED_FILTER { FILTER_ID 260 COMMENT dynlib4 - PARAMS { 9 1 13 1 } + PARAMS { 9 1 13 2 } } } FILLVALUE { diff --git a/tools/test/misc/h5clear_gentest.c b/tools/test/misc/h5clear_gentest.c index 225fe16..97feabd 100644 --- a/tools/test/misc/h5clear_gentest.c +++ b/tools/test/misc/h5clear_gentest.c @@ -428,7 +428,7 @@ main(void) if ((my_fapl = H5Pcopy(fapl2)) < 0) goto error; /* Create the file */ - HDsprintf(fname, "%s%s", new_format ? "latest_" : "", FILENAME[0]); + HDsnprintf(fname, sizeof(fname), "%s%s", new_format ? "latest_" : "", FILENAME[0]); if ((fid = H5Fcreate(fname, H5F_ACC_TRUNC | (new_format ? 0 : H5F_ACC_SWMR_WRITE), H5P_DEFAULT, my_fapl)) < 0) goto error; @@ -453,7 +453,7 @@ main(void) goto error; /* Create the file */ - HDsprintf(fname, "%s%s", new_format ? "latest_" : "", FILENAME[1]); + HDsnprintf(fname, sizeof(fname), "%s%s", new_format ? "latest_" : "", FILENAME[1]); if ((fid = H5Fcreate(fname, H5F_ACC_TRUNC | (new_format ? 0 : H5F_ACC_SWMR_WRITE), H5P_DEFAULT, my_fapl)) < 0) goto error; diff --git a/tools/test/perform/perf_meta.c b/tools/test/perform/perf_meta.c index d8ed9ec..ad76711 100644 --- a/tools/test/perform/perf_meta.c +++ b/tools/test/perform/perf_meta.c @@ -304,7 +304,7 @@ create_dsets(hid_t file) * Create a dataset using the default dataset creation properties. */ for (i = 0; i < NUM_DSETS; i++) { - HDsprintf(dset_name, "dataset %d", i); + HDsnprintf(dset_name, sizeof(dset_name), "dataset %d", i); if ((dataset = H5Dcreate2(file, dset_name, H5T_NATIVE_DOUBLE, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) goto error; @@ -366,14 +366,14 @@ create_attrs_1(void) * Create all(user specifies the number) attributes for each dataset */ for (i = 0; i < NUM_DSETS; i++) { - HDsprintf(dset_name, "dataset %d", i); + HDsnprintf(dset_name, sizeof(dset_name), "dataset %d", i); open_t.start = retrieve_time(); if ((dataset = H5Dopen2(file, dset_name, H5P_DEFAULT)) < 0) goto error; perf(&open_t, open_t.start, retrieve_time()); for (j = 0; j < NUM_ATTRS; j++) { - HDsprintf(attr_name, "all attrs for each dset %d", j); + HDsnprintf(attr_name, sizeof(attr_name), "all attrs for each dset %d", j); attr_t.start = retrieve_time(); if ((attr = H5Acreate2(dataset, attr_name, H5T_NATIVE_DOUBLE, small_space, H5P_DEFAULT, H5P_DEFAULT)) < 0) @@ -468,7 +468,7 @@ create_attrs_2(void) * Create all(user specifies the number) attributes for each new dataset */ for (i = 0; i < NUM_DSETS; i++) { - HDsprintf(dset_name, "dataset %d", i); + HDsnprintf(dset_name, sizeof(dset_name), "dataset %d", i); create_t.start = retrieve_time(); if ((dataset = H5Dcreate2(file, dset_name, H5T_NATIVE_DOUBLE, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) @@ -476,7 +476,7 @@ create_attrs_2(void) perf(&create_t, create_t.start, retrieve_time()); for (j = 0; j < NUM_ATTRS; j++) { - HDsprintf(attr_name, "all attrs for each dset %d", j); + HDsnprintf(attr_name, sizeof(attr_name), "all attrs for each dset %d", j); attr_t.start = retrieve_time(); if ((attr = H5Acreate2(dataset, attr_name, H5T_NATIVE_DOUBLE, small_space, H5P_DEFAULT, H5P_DEFAULT)) < 0) @@ -579,14 +579,14 @@ create_attrs_3(void) for (i = 0; i < loop_num; i++) { for (j = 0; j < NUM_DSETS; j++) { - HDsprintf(dset_name, "dataset %d", j); + HDsnprintf(dset_name, sizeof(dset_name), "dataset %d", j); open_t.start = retrieve_time(); if ((dataset = H5Dopen2(file, dset_name, H5P_DEFAULT)) < 0) goto error; perf(&open_t, open_t.start, retrieve_time()); for (k = 0; k < BATCH_ATTRS; k++) { - HDsprintf(attr_name, "some attrs for each dset %d %d", i, k); + HDsnprintf(attr_name, sizeof(attr_name), "some attrs for each dset %d %d", i, k); attr_t.start = retrieve_time(); if ((attr = H5Acreate2(dataset, attr_name, H5T_NATIVE_DOUBLE, small_space, H5P_DEFAULT, H5P_DEFAULT)) < 0) diff --git a/tools/test/perform/pio_standalone.h b/tools/test/perform/pio_standalone.h index f1fb946..e64a765 100644 --- a/tools/test/perform/pio_standalone.h +++ b/tools/test/perform/pio_standalone.h @@ -461,7 +461,8 @@ struct h5_long_options { */ }; -extern int H5_get_option(int argc, const char **argv, const char *opt, const struct h5_long_options *l_opt); +extern int H5_get_option(int argc, const char *const *argv, const char *opt, + const struct h5_long_options *l_opt); extern int nCols; /*max number of columns for outputting */ diff --git a/tools/test/perform/sio_standalone.h b/tools/test/perform/sio_standalone.h index 99cca75..57180e5 100644 --- a/tools/test/perform/sio_standalone.h +++ b/tools/test/perform/sio_standalone.h @@ -476,7 +476,8 @@ struct h5_long_options { */ }; -extern int H5_get_option(int argc, const char **argv, const char *opt, const struct h5_long_options *l_opt); +extern int H5_get_option(int argc, const char *const *argv, const char *opt, + const struct h5_long_options *l_opt); extern int nCols; /*max number of columns for outputting */ diff --git a/tools/test/perform/zip_perf.c b/tools/test/perform/zip_perf.c index 37e69e2..74b1685 100644 --- a/tools/test/perform/zip_perf.c +++ b/tools/test/perform/zip_perf.c @@ -489,7 +489,7 @@ do_write_test(unsigned long file_size, unsigned long min_buf_size, unsigned long * Modifications: */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { unsigned long min_buf_size = 128 * ONE_KB, max_buf_size = ONE_MB; unsigned long file_size = 64 * ONE_MB; @@ -500,7 +500,7 @@ main(int argc, const char *argv[]) /* Initialize h5tools lib */ h5tools_init(); - while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) > 0) { + while ((opt = H5_get_option(argc, (const char *const *)argv, s_opts, l_opts)) > 0) { switch ((char)opt) { case '0': case '1': diff --git a/utils/mirror_vfd/mirror_remote.c b/utils/mirror_vfd/mirror_remote.c index f61580d..8bb9544 100644 --- a/utils/mirror_vfd/mirror_remote.c +++ b/utils/mirror_vfd/mirror_remote.c @@ -147,7 +147,7 @@ mirror_log_bytes(struct mirror_log_info *info, unsigned int level, size_t n_byte * ---------------------------------------------------------------------------- */ loginfo_t * -mirror_log_init(char *path, char *prefix, unsigned int verbosity) +mirror_log_init(char *path, const char *prefix, unsigned int verbosity) { loginfo_t *info = NULL; diff --git a/utils/mirror_vfd/mirror_remote.h b/utils/mirror_vfd/mirror_remote.h index 6f37b0b..9415f7f 100644 --- a/utils/mirror_vfd/mirror_remote.h +++ b/utils/mirror_vfd/mirror_remote.h @@ -42,7 +42,7 @@ typedef struct mirror_log_info { void mirror_log(loginfo_t *info, unsigned int level, const char *format, ...); void mirror_log_bytes(loginfo_t *info, unsigned int level, size_t n_bytes, const unsigned char *buf); -loginfo_t *mirror_log_init(char *path, char *prefix, unsigned int verbosity); +loginfo_t *mirror_log_init(char *path, const char *prefix, unsigned int verbosity); int mirror_log_term(loginfo_t *loginfo); herr_t run_writer(int socketfd, H5FD_mirror_xmit_open_t *xmit_open); diff --git a/utils/mirror_vfd/mirror_server.c b/utils/mirror_vfd/mirror_server.c index f6a8bfe..5381d95 100644 --- a/utils/mirror_vfd/mirror_server.c +++ b/utils/mirror_vfd/mirror_server.c @@ -94,14 +94,14 @@ * --------------------------------------------------------------------------- */ struct op_args { - uint32_t magic; - int help; - int main_port; - int verbosity; - int log_prepend_serv; - int log_prepend_type; - char log_path[PATH_MAX + 1]; - char writer_log_path[PATH_MAX + 1]; + uint32_t magic; + int help; + int main_port; + unsigned int verbosity; + int log_prepend_serv; + int log_prepend_type; + char log_path[PATH_MAX + 1]; + char writer_log_path[PATH_MAX + 1]; }; /* --------------------------------------------------------------------------- @@ -224,7 +224,7 @@ parse_args(int argc, char **argv, struct op_args *args_out) } /* end if port */ else if (!HDstrncmp(argv[i], "--verbosity=", 12)) { mirror_log(NULL, V_INFO, "parsing 'verbosity' (%s)", argv[i] + 12); - args_out->verbosity = HDatoi(argv[i] + 12); + args_out->verbosity = (unsigned int)HDatoi(argv[i] + 12); } /* end if verbosity */ else if (!HDstrncmp(argv[i], "--logpath=", 10)) { mirror_log(NULL, V_INFO, "parsing 'logpath' (%s)", argv[i] + 10); @@ -456,7 +456,7 @@ error: * --------------------------------------------------------------------------- */ static void -wait_for_child(int sig) +wait_for_child(int H5_ATTR_UNUSED sig) { while (HDwaitpid(-1, NULL, WNOHANG) > 0) ; @@ -476,7 +476,7 @@ handle_requests(struct server_run *run) { int connfd = -1; /**/ char mybuf[H5FD_MIRROR_XMIT_OPEN_SIZE]; /**/ - int ret; /* general-purpose error-checking */ + ssize_t ret; /* general-purpose error-checking */ int pid; /* process ID of fork */ struct sigaction sa; int ret_value = 0; @@ -521,14 +521,13 @@ handle_requests(struct server_run *run) /* Read handshake from port connection. */ - ret = (int)HDread(connfd, &mybuf, H5FD_MIRROR_XMIT_OPEN_SIZE); - if (-1 == ret) { + if ((ret = HDread(connfd, &mybuf, H5FD_MIRROR_XMIT_OPEN_SIZE)) < 0) { mirror_log(run->loginfo, V_ERR, "read:%d", ret); goto error; } mirror_log(run->loginfo, V_INFO, "received %d bytes", ret); mirror_log(run->loginfo, V_ALL, "```"); - mirror_log_bytes(run->loginfo, V_ALL, ret, (const unsigned char *)mybuf); + mirror_log_bytes(run->loginfo, V_ALL, (size_t)ret, (const unsigned char *)mybuf); mirror_log(run->loginfo, V_ALL, "```"); /* Respond to handshake message. diff --git a/utils/mirror_vfd/mirror_writer.c b/utils/mirror_vfd/mirror_writer.c index d3f12de..5726db5 100644 --- a/utils/mirror_vfd/mirror_writer.c +++ b/utils/mirror_vfd/mirror_writer.c @@ -788,8 +788,7 @@ do_write(struct mirror_session *session, const unsigned char *xmit_buf) */ sum_bytes_written = 0; do { - nbytes_in_packet = HDread(session->sockfd, buf, H5FD_MIRROR_DATA_BUFFER_MAX); - if (-1 == nbytes_in_packet) { + if ((nbytes_in_packet = HDread(session->sockfd, buf, H5FD_MIRROR_DATA_BUFFER_MAX)) < 0) { mirror_log(session->loginfo, V_ERR, "can't read into databuffer"); reply_error(session, "can't read data buffer"); return -1; @@ -798,7 +797,7 @@ do_write(struct mirror_session *session, const unsigned char *xmit_buf) mirror_log(session->loginfo, V_INFO, "received %zd bytes", nbytes_in_packet); if (HEXDUMP_WRITEDATA) { mirror_log(session->loginfo, V_ALL, "DATA:\n```"); - mirror_log_bytes(session->loginfo, V_ALL, nbytes_in_packet, (const unsigned char *)buf); + mirror_log_bytes(session->loginfo, V_ALL, (size_t)nbytes_in_packet, (const unsigned char *)buf); mirror_log(session->loginfo, V_ALL, "```"); } @@ -859,8 +858,7 @@ receive_communique(struct mirror_session *session, struct sock_comm *comm) mirror_log(session->loginfo, V_INFO, "ready to receive"); /* TODO */ - read_ret = HDread(session->sockfd, comm->raw, H5FD_MIRROR_XMIT_BUFFER_MAX); - if (-1 == read_ret) { + if ((read_ret = HDread(session->sockfd, comm->raw, H5FD_MIRROR_XMIT_BUFFER_MAX)) < 0) { mirror_log(session->loginfo, V_ERR, "read:%zd", read_ret); goto error; } diff --git a/utils/tools/h5dwalk/h5dwalk.c b/utils/tools/h5dwalk/h5dwalk.c index a1e66e0..5a22d75 100644 --- a/utils/tools/h5dwalk/h5dwalk.c +++ b/utils/tools/h5dwalk/h5dwalk.c @@ -1071,12 +1071,12 @@ run_command(int argc __attribute__((unused)), char **argv, char *cmdline, const if ((log_instance > 0) || processing_inputfile) { if (processing_inputfile) log_instance = current_input_index; - HDsprintf(logpath, "%s/%s_%s.log_%d", HDgetcwd(current_dir, sizeof(current_dir)), logbase, - thisapp, log_instance); + HDsnprintf(logpath, sizeof(logpath), "%s/%s_%s.log_%d", + HDgetcwd(current_dir, sizeof(current_dir)), logbase, thisapp, log_instance); } else { - HDsprintf(logpath, "%s/%s_%s.log", HDgetcwd(current_dir, sizeof(current_dir)), logbase, - thisapp); + HDsnprintf(logpath, sizeof(logpath), "%s/%s_%s.log", + HDgetcwd(current_dir, sizeof(current_dir)), logbase, thisapp); } } else { @@ -1085,15 +1085,17 @@ run_command(int argc __attribute__((unused)), char **argv, char *cmdline, const if (processing_inputfile) log_instance = current_input_index; if (txtlog[log_len - 1] == '/') - HDsprintf(logpath, "%s%s_%s.log_%d", txtlog, logbase, thisapp, log_instance); + HDsnprintf(logpath, sizeof(logpath), "%s%s_%s.log_%d", txtlog, logbase, thisapp, + log_instance); else - HDsprintf(logpath, "%s/%s_%s.log_%d", txtlog, logbase, thisapp, log_instance); + HDsnprintf(logpath, sizeof(logpath), "%s/%s_%s.log_%d", txtlog, logbase, thisapp, + log_instance); } else { if (txtlog[log_len - 1] == '/') - HDsprintf(logpath, "%s%s_%s.log", txtlog, logbase, thisapp); + HDsnprintf(logpath, sizeof(logpath), "%s%s_%s.log", txtlog, logbase, thisapp); else - HDsprintf(logpath, "%s/%s_%s.log", txtlog, logbase, thisapp); + HDsnprintf(logpath, sizeof(logpath), "%s/%s_%s.log", txtlog, logbase, thisapp); } } @@ -1204,7 +1206,7 @@ MFU_PRED_EXEC(mfu_flist flist, uint64_t idx, void *arg) } } - HDsprintf(cmdline, "\n---------\nCommand:"); + HDsnprintf(cmdline, sizeof(cmdline), "\n---------\nCommand:"); b_offset = strlen(cmdline); for (k = 0; k < count; k++) { HDsprintf(&cmdline[b_offset], " %s", argv[k]); @@ -1242,7 +1244,7 @@ static void add_executable(int argc, char **argv, char *cmdstring, int *f_index, int f_count __attribute__((unused))) { char cmdline[2048]; - HDsprintf(cmdline, "\n---------\nCommand: %s\n", cmdstring); + HDsnprintf(cmdline, sizeof(cmdline), "\n---------\nCommand: %s\n", cmdstring); argv[argc] = NULL; run_command(argc, argv, cmdline, argv[f_index[0]]); return; @@ -1322,7 +1324,7 @@ process_input_file(char *inputname, int myrank, int size) } int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { int i; int rc = 0; @@ -1352,7 +1354,7 @@ main(int argc, const char *argv[]) if (env_var) { int enable = HDatoi(env_var); if (enable) { - + } } #endif @@ -1392,7 +1394,7 @@ main(int argc, const char *argv[]) mfu_pred *pred_head = NULL; while (!tool_selected) { - opt = H5_get_option(argc, argv, s_opts, l_opts); + opt = H5_get_option(argc, (const char *const *)argv, s_opts, l_opts); switch ((char)opt) { default: usage(); |