From f86004dbde46d4aff365cc7d0a5c503ff60d3416 Mon Sep 17 00:00:00 2001 From: Dana Robinson <43805+derobins@users.noreply.github.com> Date: Fri, 28 May 2021 08:48:51 -0700 Subject: Normalization with develop (#704) --- config/clang-cxxflags | 14 +- config/cmake/H5pubconf.h.in | 15 - config/cmake/HDFCXXCompilerFlags.cmake | 2 +- config/cmake_ext_mod/ConfigureChecks.cmake | 20 +- config/cmake_ext_mod/HDFTests.c | 8 - config/cmake_ext_mod/HDFUseCXX.cmake | 11 - config/gnu-cxxflags | 2 +- configure.ac | 10 +- release_docs/INSTALL | 24 +- release_docs/INSTALL_CMake.txt | 133 ++- release_docs/INSTALL_Warnings.txt | 2 - release_docs/README_HDF5_CMake | 1 + release_docs/README_HPC | 2 +- release_docs/RELEASE.txt | 1786 +++++++++++++--------------- src/H5FDmpio.c | 24 +- src/H5private.h | 12 - src/H5public.h | 31 +- test/cache.c | 13 - test/cache_common.c | 12 - tools/test/perform/chunk.c | 2 - tools/test/perform/direct_write_perf.c | 5 +- tools/test/perform/overhead.c | 2 - tools/test/perform/perf.c | 2 - tools/test/perform/pio_engine.c | 2 - tools/test/perform/pio_standalone.h | 5 - tools/test/perform/sio_engine.c | 2 - tools/test/perform/sio_standalone.h | 5 - 27 files changed, 974 insertions(+), 1173 deletions(-) diff --git a/config/clang-cxxflags b/config/clang-cxxflags index e7ab6d8..c585ce7 100644 --- a/config/clang-cxxflags +++ b/config/clang-cxxflags @@ -113,19 +113,7 @@ if test "X-clang" = "X-$cxx_vendor" -o "X-Apple LLVM" = "X-$cxx_vendor"; then ;; esac - case "$host_os-$host_cpu" in - # cygwin needs the "-std=c99" flag removed, so make - # a specific case for Cygwin without the flag and a default - # case to add the flag everywhere else - cygwin-*) - ;; - - *) - H5_CXXFLAGS="$H5_CXXFLAGS -std=c++11" - ;; - esac - - H5_CXXFLAGS="$H5_CXXFLAGS $arch" + H5_CXXFLAGS="$H5_CXXFLAGS $arch -std=c++11" ############## # Production # diff --git a/config/cmake/H5pubconf.h.in b/config/cmake/H5pubconf.h.in index d757158..dd7fa21 100644 --- a/config/cmake/H5pubconf.h.in +++ b/config/cmake/H5pubconf.h.in @@ -198,9 +198,6 @@ optimization operation */ #cmakedefine H5_HAVE_INSTRUMENTED_LIBRARY @H5_HAVE_INSTRUMENTED_LIBRARY@ -/* Define to 1 if you have the header file. */ -#cmakedefine H5_HAVE_INTTYPES_H @H5_HAVE_INTTYPES_H@ - /* Define to 1 if you have the `ioctl' function. */ #cmakedefine H5_HAVE_IOCTL @H5_HAVE_IOCTL@ @@ -346,18 +343,9 @@ /* Define if `struct stat' has the `st_blocks' field */ #cmakedefine H5_HAVE_STAT_ST_BLOCKS @H5_HAVE_STAT_ST_BLOCKS@ -/* Define to 1 if you have the header file. */ -#cmakedefine H5_HAVE_STDBOOL_H @H5_HAVE_STDBOOL_H@ - /* Define to 1 if you have the header file. */ #cmakedefine H5_HAVE_STDDEF_H @H5_HAVE_STDDEF_H@ -/* Define to 1 if you have the header file. */ -#cmakedefine H5_HAVE_STDINT_H @H5_HAVE_STDINT_H@ - -/* Define to 1 if you have the header file for Cplusplus. */ -#cmakedefine H5_HAVE_STDINT_H_CXX @H5_HAVE_STDINT_H_CXX@ - /* Define to 1 if you have the header file. */ #cmakedefine H5_HAVE_STDLIB_H @H5_HAVE_STDLIB_H@ @@ -704,9 +692,6 @@ /* The size of `__int64', as computed by sizeof. */ #define H5_SIZEOF___INT64 @H5_SIZEOF___INT64@ -/* Define to 1 if you have the ANSI C header files. */ -#cmakedefine H5_STDC_HEADERS @H5_STDC_HEADERS@ - /* Define if strict file format checks are enabled */ #cmakedefine H5_STRICT_FORMAT_CHECKS @H5_STRICT_FORMAT_CHECKS@ diff --git a/config/cmake/HDFCXXCompilerFlags.cmake b/config/cmake/HDFCXXCompilerFlags.cmake index 757692c..e2904ca 100644 --- a/config/cmake/HDFCXXCompilerFlags.cmake +++ b/config/cmake/HDFCXXCompilerFlags.cmake @@ -9,7 +9,7 @@ # If you do not have access to either file, you may request a copy from # help@hdfgroup.org. # -set(CMAKE_CXX_STANDARD 98) +set(CMAKE_CXX_STANDARD 11) set(CMAKE_CXX_STANDARD_REQUIRED TRUE) set(CMAKE_CXX_EXTENSIONS OFF) diff --git a/config/cmake_ext_mod/ConfigureChecks.cmake b/config/cmake_ext_mod/ConfigureChecks.cmake index 105e0e7..366cf16 100644 --- a/config/cmake_ext_mod/ConfigureChecks.cmake +++ b/config/cmake_ext_mod/ConfigureChecks.cmake @@ -120,7 +120,6 @@ CHECK_INCLUDE_FILE_CONCAT ("features.h" ${HDF_PREFIX}_HAVE_FEATURES_H) CHECK_INCLUDE_FILE_CONCAT ("dirent.h" ${HDF_PREFIX}_HAVE_DIRENT_H) CHECK_INCLUDE_FILE_CONCAT ("setjmp.h" ${HDF_PREFIX}_HAVE_SETJMP_H) CHECK_INCLUDE_FILE_CONCAT ("stddef.h" ${HDF_PREFIX}_HAVE_STDDEF_H) -CHECK_INCLUDE_FILE_CONCAT ("stdint.h" ${HDF_PREFIX}_HAVE_STDINT_H) CHECK_INCLUDE_FILE_CONCAT ("unistd.h" ${HDF_PREFIX}_HAVE_UNISTD_H) # Windows @@ -146,12 +145,9 @@ CHECK_INCLUDE_FILE_CONCAT ("strings.h" ${HDF_PREFIX}_HAVE_STRINGS_H) CHECK_INCLUDE_FILE_CONCAT ("stdlib.h" ${HDF_PREFIX}_HAVE_STDLIB_H) CHECK_INCLUDE_FILE_CONCAT ("memory.h" ${HDF_PREFIX}_HAVE_MEMORY_H) CHECK_INCLUDE_FILE_CONCAT ("dlfcn.h" ${HDF_PREFIX}_HAVE_DLFCN_H) -CHECK_INCLUDE_FILE_CONCAT ("inttypes.h" ${HDF_PREFIX}_HAVE_INTTYPES_H) CHECK_INCLUDE_FILE_CONCAT ("netinet/in.h" ${HDF_PREFIX}_HAVE_NETINET_IN_H) CHECK_INCLUDE_FILE_CONCAT ("netdb.h" ${HDF_PREFIX}_HAVE_NETDB_H) CHECK_INCLUDE_FILE_CONCAT ("arpa/inet.h" ${HDF_PREFIX}_HAVE_ARPA_INET_H) -# _Bool type support -CHECK_INCLUDE_FILE_CONCAT (stdbool.h ${HDF_PREFIX}_HAVE_STDBOOL_H) ## Check for non-standard extenstion quadmath.h @@ -238,11 +234,6 @@ macro (HDF_FUNCTION_TEST OTHER_TEST) endmacro () #----------------------------------------------------------------------------- -# Check for these functions before the time headers are checked -#----------------------------------------------------------------------------- -HDF_FUNCTION_TEST (STDC_HEADERS) - -#----------------------------------------------------------------------------- # Check for large file support #----------------------------------------------------------------------------- @@ -416,13 +407,9 @@ HDF_CHECK_TYPE_SIZE (time_t ${HDF_PREFIX}_SIZEOF_TIME_T) # Extra C99 types #----------------------------------------------------------------------------- -# _Bool type support -if (HAVE_STDBOOL_H) - set (CMAKE_EXTRA_INCLUDE_FILES stdbool.h) - HDF_CHECK_TYPE_SIZE (bool ${HDF_PREFIX}_SIZEOF_BOOL) -else () - HDF_CHECK_TYPE_SIZE (_Bool ${HDF_PREFIX}_SIZEOF_BOOL) -endif () +# Size of bool +set (CMAKE_EXTRA_INCLUDE_FILES stdbool.h) +HDF_CHECK_TYPE_SIZE (_Bool ${HDF_PREFIX}_SIZEOF_BOOL) if (MINGW OR NOT WINDOWS) #----------------------------------------------------------------------------- @@ -556,7 +543,6 @@ if (MINGW OR NOT WINDOWS) foreach (other_test HAVE_ATTRIBUTE HAVE_C99_FUNC -# STDC_HEADERS HAVE_FUNCTION HAVE_C99_DESIGNATED_INITIALIZER SYSTEM_SCOPE_THREADS diff --git a/config/cmake_ext_mod/HDFTests.c b/config/cmake_ext_mod/HDFTests.c index 2d7e1b4..0c3b7b7 100644 --- a/config/cmake_ext_mod/HDFTests.c +++ b/config/cmake_ext_mod/HDFTests.c @@ -88,14 +88,6 @@ int main(void) } #endif -#ifdef STDC_HEADERS -#include -#include -#include -#include -int main() { return 0; } -#endif /* STDC_HEADERS */ - #ifdef HAVE_ATTRIBUTE diff --git a/config/cmake_ext_mod/HDFUseCXX.cmake b/config/cmake_ext_mod/HDFUseCXX.cmake index 580c409..423f74a 100644 --- a/config/cmake_ext_mod/HDFUseCXX.cmake +++ b/config/cmake_ext_mod/HDFUseCXX.cmake @@ -32,17 +32,6 @@ endif () include (CheckIncludeFileCXX) include (TestForSTDNamespace) -# IF the c compiler found stdint, check the C++ as well. On some systems this -# file will be found by C but not C++, only do this test IF the C++ compiler -# has been initialized (e.g. the project also includes some c++) -if (${HDF_PREFIX}_HAVE_STDINT_H AND CMAKE_CXX_COMPILER_LOADED) - CHECK_INCLUDE_FILE_CXX ("stdint.h" ${HDF_PREFIX}_HAVE_STDINT_H_CXX) - if (NOT ${HDF_PREFIX}_HAVE_STDINT_H_CXX) - set (${HDF_PREFIX}_HAVE_STDINT_H "" CACHE INTERNAL "Have includes HAVE_STDINT_H") - set (USE_INCLUDES ${USE_INCLUDES} "stdint.h") - endif () -endif () - # For other CXX specific tests, use this MACRO. macro (HDF_CXX_FUNCTION_TEST OTHER_TEST) if (NOT DEFINED ${OTHER_TEST}) diff --git a/config/gnu-cxxflags b/config/gnu-cxxflags index cba8298..0a7c63e 100644 --- a/config/gnu-cxxflags +++ b/config/gnu-cxxflags @@ -119,7 +119,7 @@ if test "X-g++" = "X-$cxx_vendor"; then esac # C++-specific - H5_CXXFLAGS="$H5_CXXFLAGS $arch" + H5_CXXFLAGS="$H5_CXXFLAGS $arch -std=c++11" ############## # Production # diff --git a/configure.ac b/configure.ac index d6dc7b3..09da906 100644 --- a/configure.ac +++ b/configure.ac @@ -1251,8 +1251,6 @@ AC_CHECK_HEADERS([sys/resource.h sys/time.h unistd.h sys/ioctl.h sys/stat.h]) AC_CHECK_HEADERS([sys/socket.h sys/types.h sys/file.h]) AC_CHECK_HEADERS([stddef.h setjmp.h features.h]) AC_CHECK_HEADERS([dirent.h]) -AC_CHECK_HEADERS([stdint.h], [C9x=yes]) -AC_CHECK_HEADERS([stdbool.h]) AC_CHECK_HEADERS([netdb.h netinet/in.h arpa/inet.h]) ## Darwin @@ -1417,11 +1415,7 @@ AC_CHECK_SIZEOF([off_t]) if test "X$C9x" = "Xyes"; then cat >>confdefs.h <<\EOF -#ifdef HAVE_STDBOOL_H -#include /* for bool definition */ -#else -#define bool _Bool -#endif +#include EOF AC_CHECK_SIZEOF([bool]) fi @@ -1932,10 +1926,8 @@ if test "x$HAVE_PTHREAD" = "xyes"; then AC_CACHE_VAL([hdf5_cv_system_scope_threads], [AC_RUN_IFELSE( [AC_LANG_PROGRAM([ - #if STDC_HEADERS #include #include - #endif ],[ pthread_attr_t attribute; int ret; diff --git a/release_docs/INSTALL b/release_docs/INSTALL index fcf9602..c9f7d4c 100644 --- a/release_docs/INSTALL +++ b/release_docs/INSTALL @@ -351,15 +351,18 @@ CONTENTS so it can be debugged with gdb, dbx, ddd, etc., or it can be compiled with various optimizations. To compile for symbolic debugging (the default for snapshots), say - `--enable-build-mode=production'; to compile with optimizations + `--enable-build-mode=debug'; to compile with optimizations (the default for supported public releases), - say `--enable-build-mode=production'. On some systems the + say `--enable-build-mode=production'. For a 'clean slate' configuration + with optimization disabled and nothing turned on, + say `--enable-build-mode=clean'. On some systems the library can also be compiled for profiling with gprof by saying - `--enable-production=profile'. + `--enable-profiling'. $ ./configure --enable-build-mode=debug #symbolic debugging $ ./configure --enable-build-mode=production #optimized code - $ ./configure --enable-production=profile #for use with gprof + $ ./configure --enable-build-mode=clean #'clean slate' + $ ./configure --enable-profiling #for use with gprof Regardless of whether support for symbolic debugging is enabled, the library can also perform runtime debugging of certain packages @@ -447,6 +450,19 @@ CONTENTS $ make -j -l6 +4.4. Building doxygen + One can optionally build the doxygen files for the HDF5 C library. + By default, this option is disabled. To build the html files, specify + '--enable-doxygen'. + + $ ./configure --enable-doxygen + + Configuration will halt if the required applications are not available. + To build: + + $ make doxygen + + 4.5. Testing HDF5 comes with various test suites, all of which can be run by specifying: diff --git a/release_docs/INSTALL_CMake.txt b/release_docs/INSTALL_CMake.txt index 89cd9f8..5d11957 100644 --- a/release_docs/INSTALL_CMake.txt +++ b/release_docs/INSTALL_CMake.txt @@ -65,6 +65,9 @@ External compression szip and zlib libraries: SZip.tar.gz ZLib.tar.gz +External compression plugin libraries: + hdf5_plugins.tar.gz + Examples Source package: HDF5Examples-1.14.x-Source.tar.gz @@ -306,9 +309,28 @@ IV. Further considerations TGZPATH:STRING="some_location" where "some_location" is the URL or full path to the compressed file and ext is the type of compression file. Also set CMAKE_BUILD_TYPE - to the configuration type during configuration + to the configuration type during configuration. See the settings in the + config/cmake/cacheinit.cmake file HDF uses for testing. + + 3. If you plan to use compression plugins: + A. Use source packages from an GIT server by adding the following CMake + options: + HDF5_ALLOW_EXTERNAL_SUPPORT:STRING="GIT" + PLUGIN_GIT_URL:STRING="http://some_location/plugins" + where "some_location" is the URL to the GIT repository. Also set + CMAKE_BUILD_TYPE to the configuration type. - 3. If you are building on Apple Darwin platforms, you should add the + B. Use source packages from a compressed file by adding the following + CMake options: + HDF5_ALLOW_EXTERNAL_SUPPORT:STRING="TGZ" + PLUGIN_TGZ_NAME:STRING="plugin_src.ext" + TGZPATH:STRING="some_location" + where "some_location" is the URL or full path to the compressed + file and ext is the type of compression file. Also set CMAKE_BUILD_TYPE + to the configuration type during configuration. See the settings in the + config/cmake/cacheinit.cmake file HDF uses for testing. + + 4. If you are building on Apple Darwin platforms, you should add the following options: Compiler choice - use xcode by setting the ENV variables of CC and CXX Shared fortran is not supported, build static: @@ -318,11 +340,11 @@ IV. Further considerations CTEST_USE_LAUNCHERS:BOOL=ON CMAKE_BUILD_WITH_INSTALL_RPATH:BOOL=OFF - 4. Windows developers should install NSIS or WiX to create an install image with CPack. + 5. Windows developers should install NSIS or WiX to create an install image with CPack. Visual Studio Express users will not be able to package HDF5 into an install image executable. - 5. Developers can copy the config/cmake/cacheinit.cmake file and alter the + 6. Developers can copy the config/cmake/cacheinit.cmake file and alter the the settings for the developers' environment. Then the only options needed on the command line are those options that are different. Example using HDF default cache file: @@ -330,7 +352,7 @@ IV. Further considerations -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF \ -DCMAKE_BUILD_TYPE:STRING=Release .. - 6. CMake uses a toolchain of utilities to compile, link libraries and + 7. CMake uses a toolchain of utilities to compile, link libraries and create archives, and other tasks to drive the build. The toolchain utilities available are determined by the languages enabled. In normal builds, CMake automatically determines the toolchain for host builds @@ -481,6 +503,87 @@ These five steps are described in detail below. set (ZLIB_PACKAGE_NAME "zlib" CACHE STRING "Name of 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) + ####################### + # filter plugin options + ####################### + set (PLUGIN_TGZ_NAME "hdf5_plugins.tar.gz" CACHE STRING "Use PLUGINS from compressed file" FORCE) + set (PLUGIN_PACKAGE_NAME "pl" CACHE STRING "Name of PLUGIN package" FORCE) + ############ + # bitshuffle + ########### + set (BSHUF_GIT_URL "https://git@bitbucket.hdfgroup.org/scm/test/bitshuffle.git" CACHE STRING "Use BSHUF from HDF repository" FORCE) + set (BSHUF_GIT_BRANCH "master" CACHE STRING "" FORCE) + set (BSHUF_TGZ_NAME "bitshuffle.tar.gz" CACHE STRING "Use BSHUF from compressed file" FORCE) + set (BSHUF_PACKAGE_NAME "bshuf" CACHE STRING "Name of BSHUF package" FORCE) + ####### + # blosc + ####### + set (BLOSC_GIT_URL "https://github.com/Blosc/c-blosc.git" CACHE STRING "Use BLOSC from Github" FORCE) + set (BLOSC_GIT_BRANCH "master" CACHE STRING "" FORCE) + set (BLOSC_TGZ_NAME "c-blosc.tar.gz" CACHE STRING "Use BLOSC from compressed file" FORCE) + 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 (ZLIB_TGZ_NAME "ZLib.tar.gz" CACHE STRING "Use ZLib from compressed file" FORCE) + set (ZLIB_PACKAGE_NAME "zlib" CACHE STRING "Name of ZLIB package" FORCE) + ####### + # bzip2 + ###### + # + set (BZ2_GIT_URL "https://git@bitbucket.hdfgroup.org/scm/test/bzip2.git" CACHE STRING "Use BZ2 from HDF repository" FORCE) + set (BZ2_GIT_BRANCH "master" CACHE STRING "" FORCE) + set (BZ2_TGZ_NAME "BZ2.tar.gz" CACHE STRING "Use BZ2 from compressed file" FORCE) + set (BZ2_PACKAGE_NAME "bz2" CACHE STRING "Name of BZ2 package" FORCE) + ####### + # fpzip + ####### + set (FPZIP_GIT_URL "https://https://github.com/LLNL/fpzip" CACHE STRING "Use FPZIP from github repository" FORCE) + set (FPZIP_GIT_BRANCH "master" CACHE STRING "" FORCE) + set (FPZIP_TGZ_NAME "fpzip.tar.gz" CACHE STRING "Use FPZIP from compressed file" FORCE) + set (FPZIP_PACKAGE_NAME "fpzip" CACHE STRING "Name of FPZIP package" FORCE) + ###### + # jpeg + ###### + set (JPEG_GIT_URL "https://git@bitbucket.hdfgroup.org/scm/test/jpeg.git" CACHE STRING "Use JPEG from HDF repository" FORCE) + set (JPEG_GIT_BRANCH "jpeg9c" CACHE STRING "" FORCE) + #set (JPEG_TGZ_NAME "JPEG9c.tar.gz" CACHE STRING "Use JPEG from compressed file" FORCE) + set (JPEG_TGZ_NAME "JPEG.tar.gz" CACHE STRING "Use JPEG from compressed file" FORCE) + set (JPEG_PACKAGE_NAME "jpeg" CACHE STRING "Name of JPEG package" FORCE) + ###### + # lz4 + ###### + set (BUILD_LZ4_LIBRARY_SOURCE ON CACHE BOOL "build the lz4 library within the plugin" FORCE) + set (LZ4_GIT_URL "https://git@bitbucket.hdfgroup.org/scm/test/lz4.git" CACHE STRING "Use LZ4 from HDF repository" FORCE) + set (LZ4_GIT_BRANCH "master" CACHE STRING "" FORCE) + set (LZ4_TGZ_NAME "lz4.tar.gz" CACHE STRING "Use LZ4 from compressed file" FORCE) + set (LZ4_PACKAGE_NAME "lz4" CACHE STRING "Name of LZ4 package" FORCE) + ###### + # lzf + ###### + set (LZF_GIT_URL "https://git@bitbucket.hdfgroup.org/scm/test/lzf.git" CACHE STRING "Use LZF from HDF repository" FORCE) + set (LZF_GIT_BRANCH "master" CACHE STRING "" FORCE) + set (LZF_TGZ_NAME "lzf.tar.gz" CACHE STRING "Use LZF from compressed file" FORCE) + set (LZF_PACKAGE_NAME "lzf" CACHE STRING "Name of LZF package" FORCE) + ######## + # mafisc + ######## + #set (BUILD_MAFISC_LIBRARY_SOURCE OFF CACHE BOOL "build the mafisc library within the plugin" FORCE) + #set (MAFISC_PACKAGE_NAME "mafisc" CACHE STRING "Name of MAFISC package" FORCE) + ###### + # szf + ###### + 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 (SZF_TGZ_NAME "szf.tar.gz" CACHE STRING "Use SZ from compressed file" FORCE) + set (SZF_PACKAGE_NAME "szf" CACHE STRING "Name of SZ package" FORCE) + ###### + # zfp + ###### + set (ZFP_GIT_URL "https://github.com/LLNL/zfp.git" CACHE STRING "Use ZFP from Github" FORCE) + set (ZFP_GIT_BRANCH "master" CACHE STRING "" FORCE) + set (ZFP_TGZ_NAME "zfp.tar.gz" CACHE STRING "Use ZFP from compressed file" FORCE) + set (ZFP_PACKAGE_NAME "zfp" CACHE STRING "Name of ZFP package" FORCE) + 2. Configure the cache settings @@ -532,7 +635,7 @@ These five steps are described in detail below. file in your build directory. Be sure to select either Debug or Release and build the solution. - 3.2.1 The external libraries (zlib and szip) can be configured + 3.2.1 The external libraries (zlib, szip and plugins) can be configured to allow building the libraries by downloading from a GIT repository. The option is 'HDF5_ALLOW_EXTERNAL_SUPPORT'; by adding the following configuration option: @@ -541,10 +644,11 @@ These five steps are described in detail below. The options to control the GIT URL (config/cmake/cacheinit.cmake file) are: ZLIB_GIT_URL:STRING="http://${git_url}/zlib" SZIP_GIT_URL:STRING="http://${git_url}/szip" + PLUGIN_GIT_URL:STRING="http://${git_url}/plugin" ${git_url} should be changed to your location. Also define CMAKE_BUILD_TYPE to be the configuration type. - 3.2.2 Or the external libraries (zlib and szip) can be configured + 3.2.2 Or the external libraries (zlib, szip and plugins) can be configured to allow building the libraries by using a compressed file. The option is 'HDF5_ALLOW_EXTERNAL_SUPPORT' and is enabled by adding the following configuration option: @@ -554,7 +658,8 @@ These five steps are described in detail below. file) are: ZLIB_TGZ_NAME:STRING="zlib_src.ext" SZIP_TGZ_NAME:STRING="szip_src.ext" - LIBAEC_TGZ_NAME:STRING="liaec_src.ext" + LIBAEC_TGZ_NAME:STRING="libaec_src.ext" + PLUGIN_TGZ_NAME:STRING="plugin_src.ext" TGZPATH:STRING="some_location" where "some_location/xxxx_src.ext" is the URL or full path to the compressed file and where ext is the type of the compression @@ -629,7 +734,7 @@ BUILD_STATIC_EXECS "Build Static Executables" OFF BUILD_TESTING "Build HDF5 Unit Testing" ON ---------------- HDF5 Build Options --------------------- -HDF5_BUILD_CPP_LIB "Build HDF5 C++ Library" ON +HDF5_BUILD_CPP_LIB "Build HDF5 C++ Library" OFF HDF5_BUILD_EXAMPLES "Build HDF5 Library Examples" ON HDF5_BUILD_FORTRAN "Build FORTRAN support" OFF HDF5_BUILD_JAVA "Build JAVA support" OFF @@ -648,7 +753,6 @@ HDF5_ENABLE_DEBUG_APIS "Turn on extra debug output in all packages" HDF5_ENABLE_DEPRECATED_SYMBOLS "Enable deprecated public API symbols" ON HDF5_ENABLE_DIRECT_VFD "Build the Direct I/O Virtual File Driver" OFF HDF5_ENABLE_EMBEDDED_LIBINFO "embed library info into executables" ON -HDF5_ENABLE_HSIZET "Enable datasets larger than memory" ON HDF5_ENABLE_PARALLEL "Enable parallel build (requires MPI)" OFF HDF5_ENABLE_PREADWRITE "Use pread/pwrite in sec2/log/core VFDs in place of read/write (when available)" ON HDF5_ENABLE_TRACE "Enable API tracing capability" OFF @@ -672,6 +776,8 @@ HDF5_USE_FOLDERS "Enable folder grouping of projects in IDEs." HDF5_WANT_DATA_ACCURACY "IF data accuracy is guaranteed during data conversions" ON HDF5_WANT_DCONV_EXCEPTION "exception handling functions is checked during data conversions" ON HDF5_ENABLE_THREADSAFE "Enable Threadsafety" OFF +HDF5_MSVC_NAMING_CONVENTION "Use MSVC Naming conventions for Shared Libraries" OFF +HDF5_MINGW_STATIC_GCC_LIBS "Statically link libgcc/libstdc++" OFF if (APPLE) HDF5_BUILD_WITH_INSTALL_NAME "Build with library install_name set to the installation path" OFF if (CMAKE_BUILD_TYPE MATCHES Debug) @@ -684,11 +790,18 @@ if (HDF5_BUILD_FORTRAN) if (BUILD_SHARED_LIBS AND NOT BUILD_STATIC_LIBS) default HDF5_INSTALL_MOD_FORTRAN is SHARED if (NOT BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS) default HDF5_INSTALL_MOD_FORTRAN is STATIC if (NOT BUILD_SHARED_LIBS AND NOT BUILD_STATIC_LIBS) default HDF5_INSTALL_MOD_FORTRAN is SHARED +HDF5_BUILD_DOC "Build documentation" OFF +HDF5_ENABLE_ANALYZER_TOOLS "enable the use of Clang tools" OFF +HDF5_ENABLE_SANITIZERS "execute the Clang sanitizer" OFF +HDF5_ENABLE_FORMATTERS "format source files" OFF +TEST_SHELL_SCRIPTS "Enable shell script tests" ON ---------------- External Library Options --------------------- HDF5_ALLOW_EXTERNAL_SUPPORT "Allow External Library Building (NO GIT TGZ)" "NO" +HDF5_ENABLE_PLUGIN_SUPPORT "Enable PLUGIN Filters" OFF HDF5_ENABLE_SZIP_SUPPORT "Use SZip Filter" OFF HDF5_ENABLE_Z_LIB_SUPPORT "Enable Zlib Filters" OFF +PLUGIN_USE_EXTERNAL "Use External Library Building for PLUGINS" 0 ZLIB_USE_EXTERNAL "Use External Library Building for ZLIB" 0 SZIP_USE_EXTERNAL "Use External Library Building for SZIP" 0 if (HDF5_ENABLE_SZIP_SUPPORT) diff --git a/release_docs/INSTALL_Warnings.txt b/release_docs/INSTALL_Warnings.txt index 97b3f76..97981be 100644 --- a/release_docs/INSTALL_Warnings.txt +++ b/release_docs/INSTALL_Warnings.txt @@ -60,7 +60,6 @@ Autotools UNIX warnings added to H5_CFLAGS -Wcast-align -Wcast-qual -Wconversion - -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal -Wformat=2 @@ -291,7 +290,6 @@ IF GNU GCC -Wcast-align -Wcast-qual -Wconversion - -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal -Wformat=2 diff --git a/release_docs/README_HDF5_CMake b/release_docs/README_HDF5_CMake index 0584037..cf0ab6f 100644 --- a/release_docs/README_HDF5_CMake +++ b/release_docs/README_HDF5_CMake @@ -9,6 +9,7 @@ This tar file contains hdf5-1.13.0 HDF5 1.13.0 source LIBAEC.tar.gz source for building SZIP replacement ZLib.tar.gz source for building ZLIB + hdf5_plugins.tar.gz source for building compression plugins For more information about building HDF5 with CMake, see USING_HDF5_CMake.txt in hdf5-1.13.0/release_docs, or diff --git a/release_docs/README_HPC b/release_docs/README_HPC index 513064c..6b31ce6 100644 --- a/release_docs/README_HPC +++ b/release_docs/README_HPC @@ -32,7 +32,7 @@ II. Obtain HDF5 source Obtain HDF5 source code from the HDF5 repository using a git command or from a release tar file in a working directory: - git clone https://git@bitbucket.hdfgroup.org/scm/hdffv/hdf5.git + git clone https://github.com/HDFGroup/hdf5.git [-b branch] [source directory] If no branch is specified, then the 'develop' version will be checked out. diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 3d662c7..20d561c 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -3,6 +3,7 @@ HDF5 version 1.13.0 currently under development INTRODUCTION +============ This document describes the differences between this release and the previous HDF5 release. It contains information on the platforms tested and known @@ -31,11 +32,11 @@ If you have any questions or comments, please send them to the HDF Help Desk: CONTENTS +======== - New Features - Support for new platforms and languages -- Bug Fixes since HDF5-1.10.3 -- Bug Fixes since HDF5-1.10.2 +- Bug Fixes since HDF5-1.12.0 - Supported Platforms - Tested Configuration Features Summary - More Tested Platforms @@ -48,1349 +49,1156 @@ New Features Configuration: ------------- - - CMake option to link the generated Fortran MOD files into the include - directory. + - A C++11-compliant compiler is now required to build the C++ wrappers - 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 overriden by setting the config option - HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC + 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. - (ADB - 2020/07/9, HDFFV-11116) + (DER - 2021/05/27) - - 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. + - CMake will now run the shell script tests in test/ by default - (ADB - 2020/04/22, OESS-65) + 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. - - CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER + (DER - 2021/05/23) - Some handcrafted tests in HDFTests.c has been removed and the CMake - CHECK_STRUCT_HAS_MEMBER module has been used. + - Removed unused HDF5_ENABLE_HSIZET option from CMake - (ADB - 2020/03/24, TRILAB-24) + This has been unused for some time and has no effect. - - Both build systems use same set of warnings flags + (DER - 2021/05/23) - 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. + - CMake no longer builds the C++ library by default - There are flags in named "error-xxx" files with warnings that may - be promoted to errors. Some source files may still need fixes. + HDF5_BUILD_CPP_LIB now defaults to OFF, which is in line with the + Autotools build defaults. - 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. + (DER - 2021/04/20) - In addition, CMake no longer applies these warnings for examples. + - Removal of pre-VS2015 work-arounds - (ADB - 2020/03/24, TRILAB-192) + HDF5 now requires Visual Studio 2015 or greater, so old work-around + code and definitions have been removed, including: - - Added test script for file size compare + * + * snprintf and vsnprintf + * llround, llroundf, lround, lroundf, round, roundf + * strtoll and strtoull + * va_copy + * struct timespec - if CMake minimum version is at least 3.14, the fileCompareTest.cmake - script will compare file sizes. + (DER - 2021/03/22) - (ADB - 2020/02/24, HDFFV-11036) + - Add CMake variable HDF5_LIB_INFIX - - Update CMake minimum version to 3.12 + 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) - Updated CMake minimum version to 3.12 and added version checks - for Windows features. + (barcode - 2021/03/22) - (ADB - 2020/02/05, TRILABS-142) + - On macOS, Universal Binaries can now be built, allowing native execution on + both Intel and Apple Silicon (ARM) based Macs. - - Fixed CMake include properties for Fortran libraries + To do so, set CMAKE_OSX_ARCHITECTURES="x86_64;arm64" - Corrected the library properties for Fortran to use the - correct path for the Fortran module files. + (SAM - 2021/02/07, https://github.com/HDFGroup/hdf5/issues/311) - (ADB - 2020/02/04, HDFFV-11012) + - Added a configure-time option to control certain compiler warnings + diagnostics - - Added common warnings files for gnu and intel + 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. - 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. + 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. - (ADB - 2020/01/17) + Autotools: --enable-diags - - Added new options to CMake for control of testing + CMake: HDF5_ENABLE_BUILD_DIAGS - 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 - 2021/02/05, HDFFV-11213) - (ADB - 2020/01/15, HDFFV-11001) + - CMake option to build the HDF filter plugins project as an external project - - Added Clang sanitizers to CMake for analyzer support if compiler is clang. + 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. - 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' + 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 - 2019/12/12, TRILAB-135) + (ADB - 2020/12/10, OESS-98) - - Update CMake for VS2019 support + - FreeBSD Autotools configuration now defaults to 'cc' and 'c++' compilers - 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. + 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'). - (ADB - 2019/11/18, HDFFV-10962) + 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). - - Update CMake options to match new autotools options + (DER - 2020/11/28, HDFFV-11193) - 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) - - - Update CMake tests to use FIXTURES - - CMake test fixtures allow setup/cleanup tests and other dependency - requirements as properties for tests. This is more flexible for - modern CMake code. - - (ADB - 2019/07/23, HDFFV-10529) - - - Windows PDB files are always installed - - There are build configuration or flag settings for Windows that may not - generate PDB files. If those files are not generated then the install - utility will fail because those PDB files are not found. An optional - variable, DISABLE_PDB_FILES, was added to not install PDB files. - - (ADB - 2019/07/17, HDFFV-10424) - - - Add mingw CMake support with a toolchain file + - Fixed POSIX problems when building w/ gcc on Solaris - There has been a number of mingw issues that has been linked under - HDFFV-10845. It has been decided to implement the CMake cross-compiling - technique of toolchain files. We will use a linux platform with the mingw - compiler stack for testing. Only the C language is fully supported, and - the error tests are skipped. The C++ language works for static but shared - builds has a shared library issue with the mingw Standard Exception Handling - library, which is not available on Windows. Fortran has a common cross-compile - problem with the fortran configure tests. + 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. - (ADB - 2019/07/12, HDFFV-10845, HDFFV-10595) + 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. - - Windows PDB files are installed incorrectly + (DER - 2020/11/25, HDFFV-11191) - For static builds, the PDB files for windows should be installed next - to the static libraries in the lib folder. Also the debug versions of - libraries and PDB files are now correctly built using the default - CMAKE_DEBUG_POSTFIX setting. + - Added a configure-time option to consider certain compiler warnings + as errors - (ADB - 2019/07/09, HDFFV-10581) + 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. - - Add option to build only shared libs + 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. - A request was made to prevent building static libraries and only build - shared. A new option was added to CMake, ONLY_SHARED_LIBS, which will - skip building static libraries. Certain utility functions will build with - static libs but are not published. Tests are adjusted to use the correct - libraries depending on SHARED/STATIC settings. + Autotools: --enable-warnings-as-errors - (ADB - 2019/06/12, HDFFV-10805) + CMake: HDF5_ENABLE_WARNINGS_AS_ERRORS - - Add options to enable or disable building tools and tests + (DER - 2020/11/23, HDFFV-11189) - Configure options --enable-tests and --enable-tools were added for - autotools configure. These options are enabled by default, and can be - disabled with either --disable-tests (or tools) or --enable-tests=no - (or --enable-tools=no). Build time is reduced ~20% when tools are - disabled, 35% when tests are disabled, 45% when both are disabled. - Reenabling them after the initial build requires running configure - again with the option(s) enabled. + - Autotools and CMake target added to produce doxygen generated documentation - (LRK - 2019/06/12, HDFFV-9976) + 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 - - Change tools test that test the error stack + (ADB - 2020/11/03) - There are some use cases which can cause the error stack of tools to be - different then the expected output. These tests now use grepTest.cmake, - this was changed to allow the error file to be searched for an expected string. + - CMake option to use MSVC naming conventions with MinGW - (ADB - 2019/04/15, HDFFV-10741) + HDF5_MSVC_NAMING_CONVENTION option enable to use MSVC naming conventions + when using a MinGW toolchain - - Keep stderr and stdout separate in tests + (xan - 2020/10/30) - Changed test handling of output capture. Tests now keep the stderr - output separate from the stdout output. It is up to the test to decide - which output to check against a reference. Also added the option - to grep for a string in either output. + - CMake option to statically link gcc libs with MinGW - (ADB - 2018/12/12, HDFFV-10632) + HDF5_MINGW_STATIC_GCC_LIBS allows to statically link libg/libstdc++ + with the MinGW toolchain - - Add toolchain and cross-compile support + (xan - 2020/10/30) - Added info on using a toolchain file to INSTALL_CMAKE.txt. A - toolchain file is also used in cross-compiling, which requires - CMAKE_CROSSCOMPILING_EMULATOR to be set. To help with cross-compiling - the fortran configure process, the HDF5UseFortran.cmake file macros - were improved. Fixed a Fortran configure file issue that incorrectly - used #cmakedefine instead of #define. + - CMake option to build the HDF filter plugins project as an external project - (ADB - 2018/10/04, HDFFV-10594) + 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. - - Add warning flags for Intel compilers + 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. - Identified Intel compiler specific warnings flags that should be used - instead of GNU flags. + (ADB - 2020/09/27, OESS-98) - (ADB - 2018/10/04, TRILABS-21) + - Added CMake option to format source files - - Add default rpath to targets + 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 - Default rpaths should be set in shared executables and - libraries to allow the use of loading dependent libraries - without requiring LD_LIBRARY_PATH to be set. The default - path should be relative using @rpath on osx and $ORIGIN - on linux. Windows is not affected. + (ADB - 2020/08/24) - (ADB - 2018/09/26, HDFFV-10594) + - Add file locking configure and CMake options - - Add missing USE_110_API_DEFAULT option. + 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. - Option USE_110_API_DEFAULT sets the default version of - versioned APIs. The bin/makevers perl script did not set - the maxidx variable correctly when the 1.10 branch was - created. This caused the versioning process to always use - the latest version of any API. + 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). - (ADB - 2018/08/17, HDFFV-10552) + 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). - - Added configuration checks for the following MPI functions: + The yes/no/best-effort file locking configure setting has also been + added to the libhdf5.settings file. - MPI_Mprobe - Used for the Parallel Compression feature - MPI_Imrecv - Used for the Parallel Compression feature + Autotools: - MPI_Get_elements_x - Used for the "big Parallel I/O" feature - MPI_Type_size_x - Used for the "big Parallel I/O" feature + An --enable-file-locking=(yes|no|best-effort) option has been added. - (JTH - 2018/08/02, HDFFV-10512) + yes: Use file locking. + no: Do not use file locking. + best-effort: Use file locking and ignore "disabled" errors. - - Added section to the libhdf5.settings file to indicate - the status of the Parallel Compression and "big Parallel I/O" - features. + CMake: - (JTH - 2018/08/02, HDFFV-10512) + Two self-explanatory options have been added: - - Add option to execute swmr shell scripts from CMake. + HDF5_USE_FILE_LOCKING + HDF5_IGNORE_DISABLED_FILE_LOCKS - Option TEST_SHELL_SCRIPTS redirects processing into a - separate ShellTests.cmake file for UNIX types. The tests - execute the shell scripts if a SH program is found. + Setting both of these to ON is the equivalent to the Autotools' + best-effort setting. - (ADB - 2018/07/16) + NOTE: + The precedence order of the various file locking control mechanisms is: + 1) HDF5_USE_FILE_LOCKING environment variable (highest) - Library: - -------- - - Add Mirror VFD + 2) H5Pset_file_locking() - 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. + 3) configure/CMake options (which set the property list defaults) - (JOS - 2020/03/13, TBD) + 4) library defaults (currently best-effort) - - Add Splitter VFD + (DER - 2020/07/30, HDFFV-11092) - Maintain separate R/W and W/O channels for "concurrent" file writes - to two files using a single HDF5 file handle. + - CMake option to link the generated Fortran MOD files into the include + directory. - (JOS - 2020/03/13, TBD) + 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 - - Refactored public exposure of haddr_t type in favor of "object tokens" + (ADB - 2020/07/09, HDFFV-11116) - 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) + - CMake option to use AEC (open source SZip) library instead of SZip - - Add new public function H5Sselect_adjust. + 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. - 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. + (ADB - 2020/04/22, OESS-65) - (NAF - 2019/11/18) + - CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER - - Add new public function H5Sselect_project_intersection. + Some handcrafted tests in HDFTests.c has been removed and the CMake + CHECK_STRUCT_HAS_MEMBER module has been used. - 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. + (ADB - 2020/03/24, TRILAB-24) - (NAF - 2019/11/13, ID-148) + - Both build systems use same set of warnings flags - - Add new public function H5VLget_file_type. + 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. - 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 funcition is intended for use only by VOL connector developers. + There are flags in named "error-xxx" files with warnings that may + be promoted to errors. Some source files may still need fixes. - (NAF - 2019/11/08, ID-127) + 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. - - Add S3 and HDFS VFDs to HDF5 maintenance + In addition, CMake no longer applies these warnings for examples. - Fix windows requirements and java tests. Windows requires CMake 3.13. - Install openssl library (with dev files); - from "Shining Light Productions". msi package preferred. + (ADB - 2020/03/24, TRILAB-192) - PATH should have been updated with the installation dir. - set ENV variable OPENSSL_ROOT_DIR to the installation dir. - set ENV variable OPENSSL_CONF to the cfg file, likely %OPENSSL_ROOT_DIR%\bin\openssl.cfg - Install libcurl library (with dev files); - download the latest released version using git: https://github.com/curl/curl.git + - Added test script for file size compare - Open a Visual Studio Command prompt - change to the libcurl root folder - run the "buildconf.bat" batch file - change to the winbuild directory - nmake /f Makefile.vc mode=dll MACHINE=x64 - copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl (installation dir) - set ENV variable CURL_ROOT to C:\curl (installation dir) - update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir). - the aws credentials file should be in %USERPROFILE%\.aws folder - set the ENV variable "HDF5_ROS3_TEST_BUCKET_URL=https://s3.us-east-2.amazonaws.com/hdf5ros3" + If CMake minimum version is at least 3.14, the fileCompareTest.cmake + script will compare file sizes. - (ADB - 2019/09/12, HDFFV-10854) + (ADB - 2020/02/24, HDFFV-11036) - - Added new chunk query functions + - Update CMake minimum version to 3.12 - The following public functions were added to discover information about - the chunks in an HDF5 file. - herr_t H5Dget_num_chunks(dset_id, fspace_id, *nchunks) - herr_t H5Dget_chunk_info_by_coord(dset_id, *coord, *filter_mask, *addr, *size) - herr_t H5Dget_chunk_info(dset_id, fspace_id, index, *coord, *filter_mask, *addr, *size) + Updated CMake minimum version to 3.12 and added version checks + for Windows features. - (BMR - 2019/06/11, HDFFV-10677) + (ADB - 2020/02/05, TRILABS-142) - - Improved the performance of virtual dataset I/O + - Fixed CMake include properties for Fortran libraries - Refactored the internal dataspace routines used by the virtual dataset - code to improve performance, especially when one of the selections - involved is very long and non-contiguous. + Corrected the library properties for Fortran to use the + correct path for the Fortran module files. - (NAF - 2019/05/31, HDFFV-10693) + (ADB - 2020/02/04, HDFFV-11012) - - Added the ability to open files with UTF-8 file names on Windows. + - Added common warnings files for gnu and intel - The POSIX open(2) API call on Windows is limited to ASCII - file names. The library has been updated to convert incoming file - names to UTF-16 (via MultiByteToWideChar(CP_UTF8, ...) and use - _wopen() instead. + 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. - (DER - 2019/03/15, HDFFV-2714, HDFFV-3914, HDFFV-3895, HDFFV-8237, HDFFV-10413, HDFFV-10691) + (ADB - 2020/01/17) - - Add new API H5M for map objects. Currently not supported by native - library, can be supported by VOL connectors. + - Added new options to CMake for control of testing - (NAF - 2019/03/01) + 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 - - Add new H5R_ref_t type for object, dataset region and _attribute_ - references. This new type will deprecate the current hobj_ref_t - and hdset_reg_ref_t types for references. Added H5T_REF datatype - to read and write new reference types. As opposed to previous - reference types, reference creation no longer modifies existing - files. New reference types also now support references to external - files. + (ADB - 2020/01/15, HDFFV-11001) - (JS - 2019/10/08) + - Added Clang sanitizers to CMake for analyzer support if compiler is clang. - - Remove H5I_REFERENCE from the library + 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' - This ID class was never used by the library and has been removed. + (ADB - 2019/12/12, TRILAB-135) - (DER - 2018/12/08, HDFFV-10252) + - Update CMake for VS2019 support - - Allow pre-generated H5Tinit.c and H5make_libsettings.c to be used. + 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. - Rather than always running H5detect and generating H5Tinit.c and - H5make_libsettings.c, supply a location for those files. + (ADB - 2019/11/18, HDFFV-10962) - (ADB - 2018/09/18, HDFFV-10332) + - Update CMake options to match new autotools options - - Fix shutdown failure when using H5VLregister_connector_by_name/value + 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. - When using H5VLregister_connector_by_name/value to dynamically load a - VOL connector plugin, the library can experience segmentation faults - when the library is closed. This is due to the library unloading - the plugin interface before the virtual object layer. Then, when the - VOL shutdown occurs, it will attempt to close the VOL connector, - however this will fail since the plugin will already have been unloaded. + (ADB - 2019/10/07, HDFFV-100901, HDFFV-10637, TRILAB-97) - (DER - 2020/03/18, HDFFV-11057) + Library: + -------- + - H5Gcreate1() now rejects size_hint parameters larger than UINT32_MAX - Parallel Library: - ----------------- - - Changed the default behavior in parallel when reading the same dataset in its entirely - (i.e. H5S_ALL dataset selection) which is being read by all the processes collectively. - The dataset mush be contiguous, less than 2GB, and of an atomic datatype. - The new behavior is the HDF5 library will use an MPI_Bcast to pass the data read from - the disk by the root process to the remain processes in the MPI communicator associated - with the HDF5 file. + 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. - (MSB - 2019/01/02, HDFFV-10652) + 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. - Fortran Library: - ---------------- - - Added new Fortran derived type, c_h5o_info_t, which is interoperable with - C's h5o_info_t. This is needed for callback functions which - pass C's h5o_info_t data type definition. + The Doxygen documentation has been updated and passing values larger + than UINT32_MAX for size_hint will now produce a normal HDF5 error. - (MSB, 2019/01/08, HDFFV-10443) + (DER - 2021/04/29, HDFFV-11241) - - Added new Fortran API, H5gmtime, which converts (C) 'time_t' structure - to Fortran DATE AND TIME storage format. - (MSB, 2019/01/08, HDFFV-10443) + - H5Pset_fapl_log() no longer crashes when passed an invalid fapl ID - - Added new Fortran 'fields' optional parameter to: h5ovisit_f, h5oget_info_by_name_f, - h5oget_info, h5oget_info_by_idx and h5ovisit_by_name_f. + 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. - (MSB, 2019/01/08, HDFFV-10443) + The pointer is now correctly initialized and the API call now + produces a normal HDF5 error when fed an invalid fapl ID. - C++ Library: - ------------ - - Added new wrappers for H5Pset/get_create_intermediate_group() - LinkCreatPropList::setCreateIntermediateGroup() - LinkCreatPropList::getCreateIntermediateGroup() + (DER - 2021/04/28, HDFFV-11240) - (BMR - 2019/04/22, HDFFV-10622) + - Fixes a segfault when H5Pset_mdc_log_options() is called multiple times - - Added new wrapper for H5Ovisit2() - H5Object::visit() + 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. - (BMR - 2019/02/14, HDFFV-10532) + The string is now handled properly and the segfault no longer occurs. + (DER - 2021/04/27, HDFFV-11239) - Java Library: - ---------------- - - Added ability to test java library with VOLs. + - HSYS_GOTO_ERROR now emits the results of GetLastError() on Windows - Created new CMake script that combines the java and vol test scripts. + 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. - (ADB - 2020/02/03, HDFFV-10996) + 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. - - Tests fail for non-English locale. + The format string on Windows has been changed from: - 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. + "%s, errno = %d, error message = '%s'" - (ADB - 2020/01/09, HDFFV-10995) + to: - - Fix a failure in JUnit-TestH5P on 32-bit architectures + "%s, errno = %d, error message = '%s', Win32 GetLastError() = %"PRIu32"" - (JTH - 2019/04/30) + for those inclined to parse it for error values. - - Duplicate the data read/write functions of Datasets for Attributes. + (DER - 2021/03/21) - Region references could not be displayed for attributes as they could - for datasets. Datasets had overloaded read and write functions for different - datatypes that were not available for attributes. After adding similar - functions, attribute region references work normally. + - File locking now works on Windows - (ADB - 2018/12/12, HDFVIEW-4) + 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. - - Removed H5I_REFERENCE from the Java wrappers + 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. - This ID class was never used by the library and has been removed - from the Java wrappers. + 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 - 2018/12/08, HDFFV-10252) + (DER - 2021/03/19, HDFFV-10191) + - H5Epush_ret() now requires a trailing semicolon - Tools: - ------ - - 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. + 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. - (KY -2020/02/07, HDFFV-11014) + (SAM - 2021/03/03) - - h5diff was updated to use the new reference APIs. + - Improved performance of H5Sget_select_elem_pointlist - h5diff uses the new reference APIs to compare references. - Attribute references can also be compared. + 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. - (ADB - 2019/12/19, HDFFV-10980) + (NAF - 2021/01/19) - - h5dump and h5ls were updated to use the new reference APIs. + - Replaced H5E_ATOM with H5E_ID in H5Epubgen.h - 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. + 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. - (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877) + (DER - 2020/11/24, HDFFV-11190) - - h5repack was fixed to repack datasets with external storage - to other types of storage. + - Add a new public function H5Ssel_iter_reset - New test added to repack files and verify the correct data using h5diff. + 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. - (JS - 2019/09/25, HDFFV-10408) - (ADB - 2019/10/02, HDFFV-10918) + (JTH - 2020/09/18) - - h5dump was fixed for 128-bit floats, but was missing a test. + - Remove HDFS VFD stubs - New test greps for the first 15 numbers of the 128-bit value. + 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: - (ADB - 2019/06/23, HDFFV-9407) + * 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. - High-Level APIs: - --------------- - - + 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. - C Packet Table API - ------------------ - - + We simply changed: - Internal header file - -------------------- - - + #ifdef LIBHDFS + + #else + + #endif - Documentation - ------------- - - + to: -Support for new platforms, languages and compilers. -======================================= - - + #ifdef LIBHDFS + + #endif -Bug Fixes since HDF5-1.10.3 release -================================== + Which is how the other optional VFDs are handled. - Library - ------- - - Fixed issues CVE-2018-13870 and CVE-2018-13869 + (DER - 2020/08/27) - When a buffer overflow occurred because a name length was corrupted - and became very large, h5dump crashed on memory access violation. + - Add Mirror VFD - 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. + 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. - (BMR - 2020/7/22, HDFFV-11120 and HDFFV-11121) + (JOS - 2020/03/13, TBD) - - Fixed the segmentation fault when reading attributes with multiple threads + - Add Splitter VFD - 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. + Maintain separate R/W and W/O channels for "concurrent" file writes + to two files using a single HDF5 file handle. - 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. + (JOS - 2020/03/13, TBD) - (VC - 2020/07/13, HDFFV-11080) + - Refactored public exposure of haddr_t type in favor of "object tokens" - - Fixed CVE-2020-10810 + 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) - 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. + - Add new public function H5Sselect_adjust. - (BMR - 2020/6/29, HDFFV-11053) + 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. - - Fixed CVE-2018-17435 + (NAF - 2019/11/18) - The tool h52gif produced a segfault when the size of an attribute - message was corrupted and caused a buffer overflow. + - Add new public function H5Sselect_project_intersection. - 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. + 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. - (BMR - 2020/6/19, HDFFV-10591) + (NAF - 2019/11/13, ID-148) - - Improved peformance when creating a large number of small datasets by - retrieving default property values from the API context instead of doing - skip list searches. + - Add new public function H5VLget_file_type. - (CJH - 2019/12/10, HDFFV-10658) + 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. - - Fixed user-created data access properties not existing in the property list - returned by H5Dget_access_plist. Thanks to Steven Varga for submitting a - reproducer and a patch. + (NAF - 2019/11/08, ID-127) - (CJH - 2019/12/9, HDFFV-10934) - - Fixed an assertion failure in the parallel library when collectively - filling chunks. As it is required that chunks be written in - monotonically non-decreasing order of offset in the file, this assertion - was being triggered when the list of chunk file space allocations being - passed to the collective chunk filling routine was not sorted according - to this particular requirement. + Parallel Library: + ----------------- + - - The addition of a sort of the out of order chunks trades a bit of - performance for the elimination of this assertion and of any complaints - from MPI implementations about the file offsets used being out of order. - (JTH - 2019/10/07) + Fortran Library: + ---------------- + - Add wrappers for H5Pset/get_file_locking() API calls - - Fixed the iteration error in test_versionbounds() in test/dtypes.c + h5pget_file_locking_f() + h5pset_file_locking_f() - The test was supposed to loop through all valid combinations of - low and high bounds in the array versions[], but they were set to - H5F_LIBVER_EARLIEST always without changing. + See the configure option discussion for HDFFV-11092 (above) for more + information on the file locking feature and how it's controlled. - The problem was fixed by indexing low and high into the array versions[]. + (DER - 2020/07/30, HDFFV-11092) - (VC - 2019/09/30) + C++ Library: + ------------ + - Add wrappers for H5Pset/get_file_locking() API calls - - Fixed the slowness of regular hyperslab selection in a chunked dataset + FileAccPropList::setFileLocking() + FileAccPropList::getFileLocking() - It was reported that the selection of every 10th element from a 20G - chunked dataset was extremely slow and sometimes could hang the system. - The problem was due to the iteration and the building of the span tree - for all the selected elements in file space. + See the configure option discussion for HDFFV-11092 (above) for more + information on the file locking feature and how it's controlled. - As the selected elements are going to a 1-d contiguous single block - memory space, the problem was fixed by building regular hyperslab selections - in memory space for the selected elements in file space. + (DER - 2020/07/30, HDFFV-11092) - (VC - 2019/09/26, HDFFV-10585) - - Fixed a bug caused by bad tag value when condensing object header - messages + Java Library: + ------------- + - Replaced HDF5AtomException with HDF5IdException - There was an assertion failure when moving meessages from running a - user test program with library release hdf5.1.10.4. It was because - the tag value (object header's address) was not set up when entering - the library routine H5O__chunk_update_idx(), which will eventually - verifies the metadata tag value when protecting the object header. + 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. - The problem was fixed by replacing FUNC_ENTER_PACKAGE in H5O__chunk_update_idx() - with FUNC_ENTER_PACKAGE_TAG(oh->cache_info.addr) to set up the metadata tag. + (See also the HDFFV-11190 note in the C library section) - (VC - 2019/08/23, HDFFV-10873) + (DER - 2020/11/24, HDFFV-11190) - - Fixed the test failure from test_metadata_read_retry_info() in - test/swmr.c + - Added new H5S functions. - The test failure is due to the incorrect number of bins returned for - retry info (info.nbins). The # of bins expected for 101 read attempts - is 3 instead of 2. The routine H5F_set_retries() in src/H5Fint.c - calculates the # of bins by first obtaining the log10 value for - (read attempts - 1). For PGI/19, the log10 value for 100 read attempts - is 1.9999999999999998 instead of 2.00000. When casting the log10 value - to unsigned later on, the decimal part is chopped off causing the test - failure. + H5Sselect_copy, H5Sselect_shape_same, H5Sselect_adjust, + H5Sselect_intersect_block, H5Sselect_project_intersection, + H5Scombine_hyperslab, H5Smodify_select, H5Scombine_select + wrapper functions added. - This was fixed by obtaining the rounded integer value (HDceil) for the - log10 value of read attempts first before casting the result to unsigned. + (ADB - 2020/10/27, HDFFV-10868) - (VC - 2019/8/14, HDFFV-10813) + - Add wrappers for H5Pset/get_file_locking() API calls - - Fixed an issue where creating a file with non-default file space info - together with library high bound setting to H5F_LIBVER_V18. + H5Pset_file_locking() + H5Pget_use_file_locking() + H5Pget_ignore_disabled_file_locking() - When setting non-default file space info in fcpl via - H5Pset_file_space_strategy() and then creating a file with - both high and low library bounds set to - H5F_LIBVER_V18 in fapl, the library succeeds in creating the file. - File creation should fail because the feature of setting non-default - file space info does not exist in library release 1.8 or earlier. + Unlike the C++ and Fortran wrappers, there are separate getters for the + two file locking settings, each of which returns a boolean value. - This was fixed by setting and checking the proper version in the - file space info message based on the library low and high bounds - when creating and opening the HDF5 file. + See the configure option discussion for HDFFV-11092 (above) for more + information on the file locking feature and how it's controlled. - (VC - 2019/6/25, HDFFV-10808) + (DER - 2020/07/30, HDFFV-11092) - - When iterating over an old-style group (i.e., when not using the latest - file format) of size 0, a NULL pointer representing the empty links - table would be sent to qsort(3) for sorting, which is undefined behavior. + - Added ability to test java library with VOLs. - Iterating over an empty group is explicitly tested in the links test. - This has not caused any failures to date and was flagged by gcc's - -fsanitize=undefined. + Created a new CMake script that combines the java and vol test scripts. - The library no longer attempts to sort an empty array. + (ADB - 2020/02/03, HDFFV-10996) - (DER - 2019/06/18, HDFFV-10829) + - Tests fail for non-English locales. - - Fixed an issue where copying a version 1.8 dataset between files using - H5Ocopy fails due to an incompatible fill version + 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. - When using the HDF5 1.10.x H5Ocopy() API call to copy a version 1.8 - dataset to a file created with both high and low library bounds set to - H5F_LIBVER_V18, the H5Ocopy() call will fail with the error stack indicating - that the fill value version is out of bounds. + (ADB - 2020/01/09, HDFFV-10995) - This was fixed by changing the fill value message version to H5O_FILL_VERSION_3 - (from H5O_FILL_VERSION_2) for H5F_LIBVER_V18. - (VC - 2019/6/14, HDFFV-10800) + Tools: + ------ + - h5repack added help text for user-defined filters. - - Some oversights in the index iterating area of the library caused - a callback function to continue iterating even though it's supposed - to stop. + 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 - Added the returned value check to the for loop's conditions in - H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate(). The - iteration now stops when it should. + (ADB - 2021/01/14, HDFFV-11099) - (BMR - 2019/06/11, HDFFV-10661) + - Added h5delete tool - - Fixed a bug that would cause an error or cause fill values to be - incorrectly read from a chunked dataset using the "single chunk" index if - the data was held in cache and there was no data on disk. + 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. - (NAF - 2019/03/06) + Note that the HDF5 library does currently have support for + H5Fdelete() in the native VOL connector. - - Fixed a bug that could cause an error or cause fill values to be - incorrectly read from a dataset that was written to using H5Dwrite_chunk - if the dataset was not closed after writing. + (DER - 2020/12/16) - (NAF - 2019/03/06, HDFFV-10716) + - h5repack added options to control how external links are handled. - - Fixed memory leak in scale offset filter + 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. - In a special case where the MinBits is the same as the number of bits in - the datatype's precision, the filter's data buffer was not freed, causing - the memory usage to grow. In general the buffer was freed correctly. The - Minbits are the minimal number of bits to store the data values. Please - see the reference manual for H5Pset_scaleoffset for the detail. + (ADB - 2020/08/05, HDFFV-9984) - (RL - 2019/3/4, HDFFV-10705) + - 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. - - Fix hangs with collective metadata reads during chunked dataset I/O + (KY -2020/02/07, HDFFV-11014) - In the parallel library, it was discovered that when a particular - sequence of operations following a pattern of: + - h5diff was updated to use the new reference APIs. - "write to chunked dataset" -> "flush file" -> "read from dataset" + h5diff uses the new reference APIs to compare references. + Attribute references can also be compared. - occurred with collective metadata reads enabled, hangs could be - observed due to certain MPI ranks not participating in the collective - metadata reads. + (ADB - 2019/12/19, HDFFV-10980) - To fix the issue, collective metadata reads are now disabled during - chunked dataset raw data I/O. + - h5dump and h5ls were updated to use the new reference APIs. - (JTH - 2019/02/11, HDFFV-10563, HDFFV-10688) + 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. - - Performance issue when closing an object + (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877) - The slow down is due to the search of the "tag_list" to find - out the "corked" status of an object and "uncork" it if so. - Improve porformance by skipping the search of the "tag_list" - if there are no "corked" objects when closing an object. + High-Level APIs: + ---------------- + - - (VC - 2019/2/6) + C Packet Table API: + ------------------- + - - - Fixed a potential invalid memory access and failure that could occur when - decoding an unknown object header message (from a future version of the - library). + Internal header file: + --------------------- + - - (NAF - 2019/01/07) + Documentation: + -------------- + - - - Deleting attributes in dense storage +Support for new platforms, languages and compilers +================================================== + - - The library aborts with "infinite loop closing library" after - attributes in dense storage are created and then deleted. +Bug Fixes since HDF5-1.12.0 release +=================================== + Library + ------- + - Fixed CVE-2018-14460 - When deleting the attribute nodes from the name index v2 B-tree, - if an attribute is found in the intermediate B-tree nodes, - which may be merged/redistributed in the process, we need to - free the dynamically allocated spaces for the intermediate - decoded attribute. + The tool h5repack produced a segfault when the rank in dataspace + message was corrupted, causing invalid read while decoding the + dimension sizes. - (VC - 2018/12/26, HDFFV-10659) + The problem was fixed by ensuring that decoding the dimension sizes + and max values will not go beyong the end of the buffer. - - Allow H5detect and H5make_libsettings to take a file as an argument. + (BMR - 2021/05/12, HDFFV-11223) - Rather than only writing to stdout, add a command argument to name - the file that H5detect and H5make_libsettings will use for output. - Without an argument, stdout is still used, so backwards compatibility - is maintained. + - Fixed CVE-2018-11206 - (ADB - 2018/09/05, HDFFV-9059) + The tool h5dump produced a segfault when the size of a fill value + message was corrupted and caused a buffer overflow. - - A bug was discovered in the parallel library where an application - would hang if a collective read/write of a chunked dataset occurred - when collective metadata reads were enabled and some of the ranks - had no selection in the dataset's dataspace. The ranks which had no - selection in the dataset's dataspace called H5D__chunk_addrmap() to - retrieve the lowest chunk address in the dataset. This is because we - require reads/writes to be performed in strictly non-decreasing order - of chunk address in the file. + The problem was fixed by verifying the fill value's size + against the buffer size before attempting to access the buffer. - When the chunk index used was a version 1 or 2 B-tree, these - non-participating ranks would issue a collective MPI_Bcast() call - that the participating ranks would not issue, causing the hang. Since - the non-participating ranks are not actually reading/writing anything, - the H5D__chunk_addrmap() call can be safely removed and the address used - for the read/write can be set to an arbitrary number (0 was chosen). + (BMR - 2021/03/15, HDFFV-10480) - (JTH - 2018/08/25, HDFFV-10501) + - Fixed CVE-2018-14033 (same issue as CVE-2020-10811) - - fcntl(2)-based file locking incorrectly passed the lock argument struct - instead of a pointer to the struct, causing errors on systems where - flock(2) is not available. + The tool h5dump produced a segfault when the storage size message + was corrupted and caused a buffer overflow. - File locking is used when files are opened to enforce SWMR semantics. A - lock operation takes place on all file opens unless the - HDF5_USE_FILE_LOCKING environment variable is set to the string "FALSE". - flock(2) is preferentially used, with fcntl(2) locks as a backup if - flock(2) is unavailable on a system (if neither is available, the lock - operation fails). On these systems, the file lock will often fail, which - causes HDF5 to not open the file and report an error. + The problem was fixed by verifying the storage size against the + buffer size before attempting to access the buffer. - This bug only affects POSIX systems. Win32 builds on Windows use a no-op - locking call which always succeeds. Systems which exhibit this bug will - have H5_HAVE_FCNTL defined but not H5_HAVE_FLOCK in the configure output. + (BMR - 2021/03/15, HDFFV-11159/HDFFV-11049) - This bug affects HDF5 1.10.0 through 1.10.5. + - Remove underscores on header file guards - fcntl(2)-based file locking now correctly passes the struct pointer. + Header file guards used a variety of underscores at the beginning of the define. - (DER - 2019/08/27, HDFFV-10892) + Removed all leading (some trailing) underscores from header file guards. - - Torn pread/pwrite I/O would result in read and write corruption. + (ADB - 2021/03/03, #361) - In the sec2, log, and core (with backing store) virtual file drivers - (VFDs), the read and write calls incorrectly reset the offset parameter - on torn pread and pwrite operations (i.e., I/O operations which fail to - be written atomically by the OS). For this bug to occur, pread/pwrite - have to be configured (this is the default if they are present on the - system) and the pread/pwrite operation has to fail to transfer all - the bytes, resulting in a multiple pread/pwrite calls. + - Fixed issue with MPI communicator and info object not being + copied into new FAPL retrieved from H5F_get_access_plist - This feature was initially enabled in HDF5 1.10.5 so the bug is - limited to that version. + 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. - (DER - 2019/12/09, HDFFV-10945) + (JTH - 2021/02/15, HDFFV-11109) - - H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which - causes asserts/errors when passed to other dataspace API calls. + - Fixed problems with vlens and refs inside compound using + H5VLget_file_type() - H5S_NO_CLASS is an internal class value that should not have been - exposed via a public API call. + 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. - In debug builds of the library, this can cause asserts to trip. In - non-debug builds, it will produce normal library errors. + (NAF - 2021/01/22) - 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. + - Creation of dataset with optional filter - (DER - 2020/07/27, HDFFV-11027) + 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. - Java Library: - ---------------- - - JNI native library dependencies + (BMR - 2020/08/13, HDFFV-10933) - The build for the hdf5_java native library used the wrong - hdf5 target library for CMake builds. Correcting the hdf5_java - library to build with the shared hdf5 library required testing - paths to change also. + - Explicitly declared dlopen to use RTLD_LOCAL - (ADB - 2018/08/31, HDFFV-10568) - - Java iterator callbacks + 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. - Change global callback object to a small stack structure in order - to fix a runtime crash. This crash was discovered when iterating - through a file with nested group members. The global variable - visit_callback is overwritten when recursion starts. When recursion - completes, visit_callback will be pointing to the wrong callback method. + (ADB - 2020/08/12, HDFFV-11127) - (ADB - 2018/08/15, HDFFV-10536) + - H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which + causes asserts/errors when passed to other dataspace API calls. - - Java HDFLibraryException class + H5S_NO_CLASS is an internal class value that should not have been + exposed via a public API call. - Change parent class from Exception to RuntimeException. + In debug builds of the library, this can cause assert() function to + trip. In non-debug builds, it will produce normal library errors. - (ADB - 2018/07/30, HDFFV-10534) + 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. - - JNI Read and Write + (DER - 2020/07/27, HDFFV-11027) - Refactored variable-length functions, H5DreadVL and H5AreadVL, - to correct dataset and attribute reads. New write functions, - H5DwriteVL and H5AwriteVL, are under construction. + - Fixed issues CVE-2018-13870 and CVE-2018-13869 - (ADB - 2018/06/02, HDFFV-10519) + When a buffer overflow occurred because a name length was corrupted + and became very large, h5dump crashed on memory access violation. - Configuration - ------------- - - Correct option for default API version + 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. - CMake options for default API version are not mutually exclusive. - Change the multiple BOOL options to a single STRING option with the - strings; v16, v18, v110, v112. + (BMR - 2020/07/22, HDFFV-11120 and HDFFV-11121) - (ADB - 2019/08/12, HDFFV-10879) + - Fixed the segmentation fault when reading attributes with multiple threads - Performance - ------------- - - + 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. - Fortran - -------- - - Added symbolic links libhdf5_hl_fortran.so to libhdf5hl_fortran.so and - libhdf5_hl_fortran.a to libhdf5hl_fortran.a in hdf5/lib directory for - autotools installs. These were added to match the name of the files - installed by cmake and the general pattern of hl lib files. We will - change the names of the installed lib files to the matching name in - the next major release. + 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. - (LRK - 2019/01/04, HDFFV-10596) + (VC - 2020/07/13, HDFFV-11080) - - Made Fortran specific subroutines PRIVATE in generic procedures. + - Fixed CVE-2020-10810 - Effected generic procedures were functions in H5A, H5D, H5P, H5R and H5T. + 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. - (MSB, 2018/12/04, HDFFV-10511) + (BMR - 2020/06/29, HDFFV-11053) - - Fixed issue with Fortran not returning h5o_info_t field values - meta_size%attr%index_size and meta_size%attr%heap_size. + - Fixed CVE-2018-17435 - (MSB, 2018/1/8, HDFFV-10443) + The tool h52gif produced a segfault when the size of an attribute + message was corrupted and caused a buffer overflow. - - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f. + 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. - (MSB - 2020/2/18, HDFFV-11029) + (BMR - 2020/06/19, HDFFV-10591) - Tools - ----- - - 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); + Java Library + ------------ + - JNI utility function does not handle new references. - (ADB - 2020/07/20, HDFFV-11066) + 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. - - h5diff fixed a command line parsing error. + (ADB - 2021/02/16, HDFFV-11212) - 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 comparision was used. + - 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. - (ADB - 2020/07/20, HDFFV-10897) + 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. - - h5diff added a command line option to ignore attributes. + (PGT,ADB - 2020/12/13, HDFFV-10865) - h5diff would ignore all objects with a supplied path if the exclude-path argument is used. - Adding the exclude-attribute argument will only eclude attributes, with the supplied path, - from comparision. + - Added ability to test java library with VOLs. - (ADB - 2020/07/20, HDFFV-5935) + Created a new CMake script that combines the java and vol test scripts. - - h5diff added another level to the verbose argument to print filenames. + (ADB - 2020/02/03, HDFFV-10996) - 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 + - Tests fail for non-English locales. - (ADB - 2020/07/20, HDFFV-10005) + 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. - High-Level APIs: - ------ - - + (ADB - 2020/01/09, HDFFV-10995) - Fortran High-Level APIs: - ------ - - - Documentation + Configuration ------------- - - - - F90 APIs - -------- - - - - C++ APIs - -------- - - - - 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, 2020/7/2, HDFFV-11063) - - - Fixed a test failure in testpar/t_dset.c caused by - the test trying to use the parallel filters feature - on MPI-2 implementations. - - (JTH, 2019/2/7) - -Bug Fixes since HDF5-1.10.2 release -================================== + - Remove arbitrary warning flag groups from CMake builds - Library - ------- - - Java HDF5LibraryException class - - The error minor and major values would be lost after the - constructor executed. - - Created two local class variables to hold the values obtained during - execution of the constructor. Refactored the class functions to retrieve - the class values rather then calling the native functions. - The native functions were renamed and called only during execution - of the constructor. - Added error checking to calling class constructors in JNI classes. - - (ADB - 2018/08/06, HDFFV-10544) + 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. - - Added checks of the defined MPI_VERSION to guard against usage of - MPI-3 functions in the Parallel Compression and "big Parallel I/O" - features when HDF5 is built with MPI-2. Previously, the configure - step would pass but the build itself would fail when it could not - locate the MPI-3 functions used. + Visual Studio warnings C4100, C4706, and C4127 have been moved to + developer warnings, HDF5_ENABLE_DEV_WARNINGS, and are disabled for normal builds. - As a result of these new checks, HDF5 can again be built with MPI-2, - but the Parallel Compression feature will be disabled as it relies - on the MPI-3 functions used. + (ADB - 2021/03/22, HDFFV-11228) - (JTH - 2018/08/02, HDFFV-10512) + - Reclassify CMake messages, to allow new modes and --log-level option - - User's patches: CVEs + 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. - The following patches have been applied: + (ADB - 2021/01/11, HDFFV-11144) - CVE-2018-11202 - NULL pointer dereference was discovered in - H5S_hyper_make_spans in H5Shyper.c (HDFFV-10476) - https://security-tracker.debian.org/tracker/CVE-2018-11202 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11202 + - Fixes Autotools determination of the stat struct having an st_blocks field - CVE-2018-11203 - A division by zero was discovered in - H5D__btree_decode_key in H5Dbtree.c (HDFFV-10477) - https://security-tracker.debian.org/tracker/CVE-2018-11203 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11203 + 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. - CVE-2018-11204 - A NULL pointer dereference was discovered in - H5O__chunk_deserialize in H5Ocache.c (HDFFV-10478) - https://security-tracker.debian.org/tracker/CVE-2018-11204 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11204 + (DER - 2021/01/07, HDFFV-11201) - CVE-2018-11206 - An out of bound read was discovered in - H5O_fill_new_decode and H5O_fill_old_decode in H5Ofill.c - (HDFFV-10480) - https://security-tracker.debian.org/tracker/CVE-2018-11206 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11206 - CVE-2018-11207 - A division by zero was discovered in - H5D__chunk_init in H5Dchunk.c (HDFFV-10481) - https://security-tracker.debian.org/tracker/CVE-2018-11207 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11207 - - (BMR - 2018/7/22, PR#s: 1134 and 1139, - HDFFV-10476, HDFFV-10477, HDFFV-10478, HDFFV-10480, HDFFV-10481) - - - H5Adelete - - H5Adelete failed when deleting the last "large" attribute that - is stored densely via fractal heap/v2 b-tree. + Tools + ----- + - Changed how h5dump and h5ls identify long double. - After removing the attribute, update the ainfo message. If the - number of attributes goes to zero, remove the message. + 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. - (VC - 2018/07/20, HDFFV-9277) + (ADB - 2021/03/24, HDFFV-11229) - - A bug was discovered in the parallel library which caused partial - parallel reads of filtered datasets to return incorrect data. The - library used the incorrect dataspace for each chunk read, causing - the selection used in each chunk to be wrong. + - Fixed tools argument parsing. - The bug was not caught during testing because all of the current - tests which do parallel reads of filtered data read all of the data - using an H5S_ALL selection. Several tests were added which exercise - partial parallel reads. + 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. - (JTH - 2018/07/16, HDFFV-10467) + (ADB - 2021/01/19, HDFFV-11106) - - A bug was discovered in the parallel library which caused parallel - writes of filtered datasets to trigger an assertion failure in the - file free space manager. + - The tools library was updated by standardizing the error stack process. - This occurred when the filter used caused chunks to repeatedly shrink - and grow over the course of several dataset writes. The previous chunk - information, such as the size of the chunk and the offset in the file, - was being cached and not updated after each write, causing the next write - to the chunk to retrieve the incorrect cached information and run into - issues when reallocating space in the file for the chunk. + 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); - (JTH - 2018/07/16, HDFFV-10509) + (ADB - 2020/07/20, HDFFV-11066) - - A bug was discovered in the parallel library which caused the - H5D__mpio_array_gatherv() function to allocate too much memory. + - h5diff fixed a command line parsing error. - When the function is called with the 'allgather' parameter set - to a non-true value, the function will receive data from all MPI - ranks and gather it to the single rank specied by the 'root' - parameter. However, the bug in the function caused memory for - the received data to be allocated on all MPI ranks, not just the - singular rank specified as the receiver. In some circumstances, - this would cause an application to fail due to the large amounts - of memory being allocated. + 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 comparision was used. - (JTH - 2018/07/16, HDFFV-10467) + (ADB - 2020/07/20, HDFFV-10897) - - Error checks in h5stat and when decoding messages + - h5diff added a command line option to ignore attributes. - h5stat exited with seg fault/core dumped when - errors are encountered in the internal library. + 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. - Add error checks and --enable-error-stack option to h5stat. - Add range checks when decoding messages: old fill value, old - layout and refcount. + (ADB - 2020/07/20, HDFFV-5935) - (VC - 2018/07/11, HDFFV-10333) + - h5diff added another level to the verbose argument to print filenames. - - If an HDF5 file contains a malformed compound datatype with a - suitably large offset, the type conversion code can run off - the end of the type conversion buffer, causing a segmentation - fault. + 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 - This issue was reported to The HDF Group as issue #CVE-2017-17507. + (ADB - 2020/07/20, HDFFV-10005) - NOTE: The HDF5 C library cannot produce such a file. This condition - should only occur in a corrupt (or deliberately altered) file - or a file created by third-party software. + - h5repack was fixed to repack the reference attributes properly. - THE HDF GROUP WILL NOT FIX THIS BUG AT THIS TIME + 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. - Fixing this problem would involve updating the publicly visible - H5T_conv_t function pointer typedef and versioning the API calls - which use it. We normally only modify the public API during - major releases, so this bug will not be fixed at this time. + (KY -2020/02/10, HDFFV-11014) - (DER - 2018/02/26, HDFFV-10356) + - h5diff was updated to use the new reference APIs. - - Inappropriate linking with deprecated MPI C++ libraries + h5diff uses the new reference APIs to compare references. + Attribute references can also be compared. - HDF5 does not define *_SKIP_MPICXX in the public headers, so applications - can inadvertently wind up linking to the deprecated MPI C++ wrappers. + (ADB - 2019/12/19, HDFFV-10980) - MPICH_SKIP_MPICXX and OMPI_SKIP_MPICXX have both been defined in H5public.h - so this should no longer be an issue. HDF5 makes no use of the deprecated - MPI C++ wrappers. + - h5dump and h5ls were updated to use the new reference APIs. - (DER - 2019/09/17, HDFFV-10893) + 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) - Configuration + Performance ------------- - - Applied patches to address Cywin build issues - - There were three issues for Cygwin builds: - - Shared libs were not built. - - The -std=c99 flag caused a SIG_SETMASK undeclared error. - - Undefined errors when buildbing test shared libraries. - - Patches to address these issues were received and incorporated in this version. - - (LRK - 2018/07/18, HDFFV-10475) - - - Moved the location of gcc attribute. - - The gcc attribute(no_sanitize), named as the macro HDF_NO_UBSAN, - was located after the function name. Builds with GCC 7 did not - indicate any problem, but GCC 8 issued errors. Moved the - attribute before the function name, as required. - - (ADB - 2018/05/22, HDFFV-10473) - - - Reworked java test suite into individual JUnit tests. - - Testing the whole suite of java unit tests in a single JUnit run - made it difficult to determine actual failures when tests would fail. - Running each file set of tests individually, allows individual failures - to be diagnosed easier. A side benefit is that tests for optional components - of the library can be disabled if not configured. - - (ADB - 2018/05/16, HDFFV-9739) + - - - Converted CMake global commands ADD_DEFINITIONS and INCLUDE_DIRECTORIES - to use target_* type commands. This change modernizes the CMake usage - in the HDF5 library. - In addition, there is the intention to convert to generator expressions, - where possible. The exception is Fortran FLAGS on Windows Visual Studio. - The HDF macros TARGET_C_PROPERTIES and TARGET_FORTRAN_PROPERTIES have - been removed with this change in usage. + Fortran API + ----------- + - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f. - The additional language (C++ and Fortran) checks have also been localized - to only be checked when that language is enabled. + (MSB - 2020/02/18, HDFFV-11029) - (ADB - 2018/05/08) - Performance - ------------- + High-Level Library + ------------------ - - Fortran - -------- - - - Tools - ----- + Fortran High-Level APIs + ----------------------- - - High-Level APIs: - ------ - - - - Fortran High-Level APIs: - ------ - - Documentation ------------- - + F90 APIs -------- - + C++ APIs -------- - - Adding default arguments to existing functions - - Added the following items: - + Two more property list arguments are added to H5Location::createDataSet: - const DSetAccPropList& dapl = DSetAccPropList::DEFAULT - const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT - - + One more property list argument is added to H5Location::openDataSet: - const DSetAccPropList& dapl = DSetAccPropList::DEFAULT + - Added DataSet::operator= - (BMR - 2018/07/21, PR# 1146) + Some compilers complain if the copy constructor is given explicitly + but the assignment operator is implicitly set to default. - - Improvement C++ documentation + (2021/05/19) - Replaced the table in main page of the C++ documentation from mht to htm format - for portability. - - (BMR - 2018/07/17, PR# 1141) Testing ------- - - The dt_arith test failed on IBM Power8 and Power9 machines when testing - conversions from or to long double types, especially when special values - such as infinity or NAN were involved. In some cases the results differed - by extremely small amounts from those on other machines, while some other - tests resulted in segmentation faults. These conversion tests with long - double types have been disabled for ppc64 machines until the problems are - better understood and can be properly addressed. + - 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) - (SRL - 2019/01/07, TRILAB-98) Supported Platforms =================== @@ -1414,12 +1222,10 @@ Supported Platforms (emu) Sun Fortran 95 8.6 SunOS_sparc Sun C++ 5.12 SunOS_sparc - Windows 7 x64 Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake) - Visual Studio 2015 w/ MSMPI 10 (cmake) - Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake) Visual Studio 2017 w/ Intel Fortran 19 (cmake) Visual Studio 2019 w/ Intel Fortran 19 (cmake) + Visual Studio 2019 w/ MSMPI 10.1 (cmake) Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0 64-bit gfortran GNU Fortran (GCC) 4.9.2 @@ -1451,10 +1257,6 @@ Platform C F90/ F90 C++ zlib SZIP parallel F2003 parallel Solaris2.11 32-bit n y/y n y y y Solaris2.11 64-bit n y/n n y y y -Windows 7 y y/y n y y y -Windows 7 x64 y y/y y y y y -Windows 7 Cygwin n y/n n y y y -Windows 7 x64 Cygwin n y/n n y y y Windows 10 y y/y n y y y Windows 10 x64 y y/y n y y y Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y @@ -1473,10 +1275,6 @@ Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Solaris2.11 32-bit y y y y Solaris2.11 64-bit y y y y -Windows 7 y y y y -Windows 7 x64 y y y y -Windows 7 Cygwin n n n y -Windows 7 x64 Cygwin n n n y Windows 10 y y y y Windows 10 x64 y y y y Mac OS X Mountain Lion 10.8.5 64-bit y n y y @@ -1527,9 +1325,28 @@ The following platforms are not supported but have been tested for this release. #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1 (ostrich) and IBM XL Fortran for Linux, V15.1 - Fedora30 5.3.11-200.fc30.x86_64 - #1 SMP x86_64 GNU/Linux GNU gcc (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827) - GNU Fortran (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827) + Fedora33 5.11.18-200.fc33.x86_64 + #1 SMP x86_64 GNU/Linux GNU gcc (GCC) 10.3.1 20210422 (Red Hat 10.3.1-1) + GNU Fortran (GCC) 10.3.1 20210422 (Red Hat 10.3.1-1) + clang version 11.0.0 (Fedora 11.0.0-2.fc33) + (cmake and autotools) + + Ubuntu20.04 5.8.0-53-generic-x86_64 + #60~20.04-Ubuntu SMP x86_64 GNU/Linux GNU gcc (GCC) 9.3.0-17ubuntu1 + GNU Fortran (GCC) 9.3.0-17ubuntu1 + clang version 10.0.0-4ubuntu1 + (cmake and autotools) + + Ubuntu20.10 5.8.0-53-generic-x86_64 + #60-Ubuntu SMP x86_64 GNU/Linux GNU gcc (GCC) 10.2.0-13ubuntu1 + GNU Fortran (GCC) 10.2.0-13ubuntu1 + Ubuntu clang version 11.0.0-2 + (cmake and autotools) + + SUSE15sp2 5.3.18-22-default + #1 SMP x86_64 GNU/Linux GNU gcc (SUSE Linux) 7.5.0 + GNU Fortran (SUSE Linux) 7.5.0 + clang version 7.0.1 (tags/RELEASE_701/final 349238) (cmake and autotools) @@ -1545,6 +1362,9 @@ Known Problems 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. + 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. diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c index b229207..5f1caa8 100644 --- a/src/H5FDmpio.c +++ b/src/H5FDmpio.c @@ -1196,12 +1196,6 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU if ((hsize_t)size_i != size) HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "can't convert from size to size_i") -#ifdef H5FDmpio_DEBUG - if (H5FD_mpio_debug_r_flag) - HDfprintf(stderr, "%s: (%d) mpi_off = %ld size_i = %d\n", FUNC, file->mpi_rank, (long)mpi_off, - size_i); -#endif - /* Only look for MPI views for raw data transfers */ if (type == H5FD_MEM_DRAW) { H5FD_mpio_xfer_t xfer_mode; /* I/O transfer mode */ @@ -1350,6 +1344,12 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU if (bytes_read < 0 || bytes_read > io_size) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed") +#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); +#endif + /* * This gives us zeroes beyond end of physical MPI file. */ @@ -1437,12 +1437,6 @@ H5FD__mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, h HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "can't convert from haddr to MPI off") size_i = (int)size; -#ifdef H5FDmpio_DEBUG - if (H5FD_mpio_debug_w_flag) - HDfprintf(stderr, "%s: (%d) mpi_off = %ld size_i = %d\n", FUNC, file->mpi_rank, (long)mpi_off, - size_i); -#endif - /* Get the transfer mode from the API context */ if (H5CX_get_io_xfer_mode(&xfer_mode) < 0) HGOTO_ERROR(H5E_VFL, H5E_CANTGET, FAIL, "can't get MPI-I/O transfer mode") @@ -1567,6 +1561,12 @@ H5FD__mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, h if (bytes_written != io_size || bytes_written < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed") +#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); +#endif + /* Each process will keep track of its perceived EOF value locally, and * ultimately we will reduce this value to the maximum amongst all * processes, but until then keep the actual eof at HADDR_UNDEF just in diff --git a/src/H5private.h b/src/H5private.h index 75b94bd..2d8d437 100644 --- a/src/H5private.h +++ b/src/H5private.h @@ -41,10 +41,6 @@ #endif /* H5_HAVE_WIN32_API */ #endif /* H5_HAVE_THREADSAFE */ -/* - * Include ANSI-C header files. - */ -#ifdef H5_STDC_HEADERS #include #include #include @@ -56,7 +52,6 @@ #include #include #include -#endif /* * If _POSIX_VERSION is defined in unistd.h then this system is Posix.1 @@ -71,14 +66,7 @@ #include #endif -/* - * C9x integer types - */ -#ifndef __cplusplus -#ifdef H5_HAVE_STDINT_H #include -#endif -#endif /* * The `struct stat' data type for stat() and fstat(). This is a Posix file diff --git a/src/H5public.h b/src/H5public.h index ada15a7..33f8b37 100644 --- a/src/H5public.h +++ b/src/H5public.h @@ -34,28 +34,21 @@ #ifdef H5_HAVE_FEATURES_H #include /* For setting POSIX, BSD, etc. compatibility */ #endif + #ifdef H5_HAVE_SYS_TYPES_H #include #endif -#ifdef H5_STDC_HEADERS + #include /* For H5T_NATIVE_CHAR defn in H5Tpublic.h */ #include /* For variadic functions in H5VLpublic.h */ -#endif -#ifndef __cplusplus -#ifdef H5_HAVE_STDINT_H -#include /* For C9x types */ -#endif -#else -#ifdef H5_HAVE_STDINT_H_CXX -#include /* For C9x types (when included from C++) */ -#endif -#endif -#ifdef H5_HAVE_INTTYPES_H + +#include /* For C9x types */ #include /* C99/POSIX.1 header for uint64_t, PRIu64 */ -#endif + #ifdef H5_HAVE_STDDEF_H #include #endif + #ifdef H5_HAVE_PARALLEL /* Don't link against MPI C++ bindings */ #define MPICH_SKIP_MPICXX 1 @@ -220,19 +213,7 @@ typedef int herr_t; * } * \endcode */ -#ifdef H5_HAVE_STDBOOL_H #include -#else /* H5_HAVE_STDBOOL_H */ -#ifndef __cplusplus -#if defined(H5_SIZEOF_BOOL) && (H5_SIZEOF_BOOL != 0) -#define bool _Bool -#else -#define bool unsigned int -#endif -#define true 1 -#define false 0 -#endif /* __cplusplus */ -#endif /* H5_HAVE_STDBOOL_H */ typedef bool hbool_t; typedef int htri_t; diff --git a/test/cache.c b/test/cache.c index e83dd14..abbfaff 100644 --- a/test/cache.c +++ b/test/cache.c @@ -8060,19 +8060,6 @@ check_flush_cache__flush_op_test(H5F_t *file_ptr, int test_num, unsigned int flu if ((check[i].entry_num != i) || (check[i].entry_type < 0) || (check[i].entry_type >= NUMBER_OF_ENTRY_TYPES) || (check[i].entry_index < 0) || (check[i].entry_index > max_indices[check[i].entry_type]) || -#ifndef H5_HAVE_STDBOOL_H - /* Check for nonsense values if hbool_t is an integral - * type instead of a real Boolean. - */ - ((check[i].in_cache != TRUE) && (check[i].in_cache != FALSE)) || - ((check[i].at_main_addr != TRUE) && (check[i].at_main_addr != FALSE)) || - ((check[i].is_dirty != TRUE) && (check[i].is_dirty != FALSE)) || - ((check[i].is_protected != TRUE) && (check[i].is_protected != FALSE)) || - ((check[i].is_pinned != TRUE) && (check[i].is_pinned != FALSE)) || - ((check[i].expected_deserialized != TRUE) && (check[i].expected_deserialized != FALSE)) || - ((check[i].expected_serialized != TRUE) && (check[i].expected_serialized != FALSE)) || - ((check[i].expected_destroyed != TRUE) && (check[i].expected_destroyed != FALSE)) || -#endif /* H5_HAVE_STDBOOL_H */ (check[i].expected_size <= (size_t)0)) { pass = FALSE; diff --git a/test/cache_common.c b/test/cache_common.c index 807f264..9a65051 100644 --- a/test/cache_common.c +++ b/test/cache_common.c @@ -1499,12 +1499,6 @@ add_flush_op(int target_type, int target_idx, int op_code, int type, int idx, hb HDassert((0 <= type) && (type < NUMBER_OF_ENTRY_TYPES)); HDassert((0 <= idx) && (idx <= max_indices[type])); HDassert(new_size <= VARIABLE_ENTRY_SIZE); -#ifndef H5_HAVE_STDBOOL_H - /* Check for TRUE or FALSE if we're using an integer type instead - * of a real Boolean type. - */ - HDassert((flag == TRUE) || (flag == FALSE)); -#endif /* H5_HAVE_STDBOOL_H */ if (pass) { @@ -1710,12 +1704,6 @@ execute_flush_op(H5F_t *file_ptr, struct test_entry_t *entry_ptr, struct flush_o HDassert((0 <= op_ptr->type) && (op_ptr->type < NUMBER_OF_ENTRY_TYPES)); HDassert((0 <= op_ptr->idx) && (op_ptr->idx <= max_indices[op_ptr->type])); HDassert(flags_ptr != NULL); -#ifndef H5_HAVE_STDBOOL_H - /* Check for TRUE or FALSE if we're using an integer type instead - * of a real Boolean type. - */ - HDassert((op_ptr->flag == FALSE) || (op_ptr->flag == TRUE)); -#endif /* H5_HAVE_STDBOOL_H */ if (pass) { diff --git a/tools/test/perform/chunk.c b/tools/test/perform/chunk.c index 1b6793a..1b08e95 100644 --- a/tools/test/perform/chunk.c +++ b/tools/test/perform/chunk.c @@ -24,12 +24,10 @@ #undef NDEBUG #include "hdf5.h" -#ifdef H5_STDC_HEADERS #include #include #include #include -#endif /* Solaris Studio defines attribute, but for the attributes we need */ #if !defined(H5_HAVE_ATTRIBUTE) || defined __cplusplus || defined(__SUNPRO_C) diff --git a/tools/test/perform/direct_write_perf.c b/tools/test/perform/direct_write_perf.c index b3ae54d..6537215 100644 --- a/tools/test/perform/direct_write_perf.c +++ b/tools/test/perform/direct_write_perf.c @@ -23,14 +23,11 @@ #if !defined(WIN32) && !defined(__MINGW32__) -#include - -#ifdef H5_STDC_HEADERS #include #include +#include #include #include -#endif #ifdef H5_HAVE_UNISTD_H #include diff --git a/tools/test/perform/overhead.c b/tools/test/perform/overhead.c index dba8220..345c5c8 100644 --- a/tools/test/perform/overhead.c +++ b/tools/test/perform/overhead.c @@ -23,13 +23,11 @@ #include "hdf5.h" #include "H5private.h" -#ifdef H5_STDC_HEADERS #include #include #include #include #include -#endif #ifdef H5_HAVE_IO_H #include diff --git a/tools/test/perform/perf.c b/tools/test/perform/perf.c index bf4b2a9..a06fb77 100644 --- a/tools/test/perform/perf.c +++ b/tools/test/perform/perf.c @@ -26,13 +26,11 @@ #ifdef H5_HAVE_PARALLEL -#ifdef H5_STDC_HEADERS #include #include #include #include #include -#endif #ifdef H5_HAVE_UNISTD_H #include diff --git a/tools/test/perform/pio_engine.c b/tools/test/perform/pio_engine.c index 65194b0..cac36d7 100644 --- a/tools/test/perform/pio_engine.c +++ b/tools/test/perform/pio_engine.c @@ -16,12 +16,10 @@ #include "hdf5.h" -#ifdef H5_STDC_HEADERS #include #include #include #include -#endif #ifdef H5_HAVE_UNISTD_H #include diff --git a/tools/test/perform/pio_standalone.h b/tools/test/perform/pio_standalone.h index 35a5217..82fabdc 100644 --- a/tools/test/perform/pio_standalone.h +++ b/tools/test/perform/pio_standalone.h @@ -21,10 +21,6 @@ #include "H5public.h" /* Include Public Definitions */ -/* - * Include ANSI-C header files. - */ -#ifdef H5_STDC_HEADERS #include #include #include @@ -37,7 +33,6 @@ #include #include #include -#endif /* * Redefine all the POSIX functions. We should never see a POSIX diff --git a/tools/test/perform/sio_engine.c b/tools/test/perform/sio_engine.c index e5a0ec8..f67a7a6 100644 --- a/tools/test/perform/sio_engine.c +++ b/tools/test/perform/sio_engine.c @@ -16,12 +16,10 @@ #include "hdf5.h" -#ifdef H5_STDC_HEADERS #include #include #include #include -#endif #ifdef H5_HAVE_UNISTD_H #include diff --git a/tools/test/perform/sio_standalone.h b/tools/test/perform/sio_standalone.h index d8b6412..54e82fa 100644 --- a/tools/test/perform/sio_standalone.h +++ b/tools/test/perform/sio_standalone.h @@ -21,10 +21,6 @@ #include "H5public.h" /* Include Public Definitions */ -/* - * Include ANSI-C header files. - */ -#ifdef H5_STDC_HEADERS #include #include #include @@ -37,7 +33,6 @@ #include #include #include -#endif /* maximum of two, three, or four values */ #undef MAX -- cgit v0.12