HDF5 version 1.10.8 released on 2021-10-22 ================================================================================ INTRODUCTION ============ This document describes the differences between this release and the previous HDF5 release. It contains information on the platforms tested and known problems in this release. For more details check the HISTORY*.txt files in the HDF5 source. Note that documentation in the links below will be updated at the time of each final release. Links to HDF5 documentation can be found on The HDF5 web page: https://portal.hdfgroup.org/display/HDF5/HDF5 The official HDF5 releases can be obtained from: https://www.hdfgroup.org/downloads/hdf5/ Changes from Release to Release and New Features in the HDF5-1.10.x release series can be found at: https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide If you have any questions or comments, please send them to the HDF Help Desk: help@hdfgroup.org CONTENTS ======== - New Features - New platforms, languages and compilers tested - Bug Fixes since HDF5-1.10.7 - Platforms Tested - Configuration Options Tested - Known Problems - CMake vs. Autotools installations New Features ============ Configuration: ------------- - Added new option to control the build of High-Level tools with default ON/enabled. Add configure options (autotools - CMake): --enable-hltools HDF5_BUILD_HL_TOOLS Disabling this option prevents building the gif tool which contains the following CVEs: HDFFV-10592 CVE-2018-17433 HDFFV-10593 CVE-2018-17436 HDFFV-11048 CVE-2020-10809 (ADB - 2021/09/16, HDFFV-11266) - Adds C++ Autotools configuration file for Intel * Checks for icpc as the compiler * Copies most non-warning flags from intel-flags (DER - 2021/06/02) - Adds C++ Autotools configuration file for PGI * Checks for pgc++ as the compiler name (was: pgCC) * Other options basically match new C options (below) (DER - 2021/06/02) - Updates PGI C options * -Minform set to warn (was: inform) to suppress spurious messages * Sets -gopt -O2 as debug options * Sets -O4 as 'high optimization' option * Sets -O0 as 'no optimization' option * Removes specific settings for PGI 9 and 10 (DER - 2021/06/02) - CMake will now run the shell script tests in test/ by default The test directory includes several shell script tests that previously were not run by CMake. These are now run by default. TEST_SHELL_SCRIPTS has been set to ON and SH_PROGRAM has been set to bash (some test scripts use bash-isms). Platforms without bash (e.g., Windows) will ignore the script tests. (DER - 2021/05/23) - Removed unused HDF5_ENABLE_HSIZET option from CMake This has been unused for some time and has no effect. (DER - 2021/05/23) - CMake no longer builds the C++ library by default HDF5_BUILD_CPP_LIB now defaults to OFF, which is in line with the Autotools build defaults. (DER - 2021/04/20) - Removal of pre-VS2015 work-arounds HDF5 now requires Visual Studio 2015 or greater, so old work-around code and definitions have been removed, including: * * snprintf and vsnprintf * llround, llroundf, lround, lroundf, round, roundf * strtoll and strtoull * va_copy * struct timespec (DER - 2021/03/22) - Add CMake variable HDF5_LIB_INFIX This infix is added to all library names after 'hdf5'. e.g. the infix '_openmpi' results in the library name 'libhdf5_openmpi.so' This name is used in packages on debian based systems. (see https://packages.debian.org/jessie/amd64/libhdf5-openmpi-8/filelist) (barcode - 2021/03/22) - On macOS, Universal Binaries can now be built, allowing native execution on both Intel and Apple Silicon (ARM) based Macs. To do so, set CMAKE_OSX_ARCHITECTURES="x86_64;arm64" (SAM - 2021/02/07, github-311) - Added a configure-time option to control certain compiler warnings diagnostics A new configure-time option was added that allows some compiler warnings diagnostics to have the default operation. This is mainly intended for library developers and currently only works for gcc 10 and above. The diagnostics flags apply to C, C++ and Fortran compilers and will appear in "H5 C Flags", H5 C++ Flags" and H5 Fortran Flags, respectively. They will NOT be exported to h5cc, etc. The default is OFF, which will disable the warnings URL and color attributes for the warnings output. ON will not add the flags and allow default behavior. Autotools: --enable-diags CMake: HDF5_ENABLE_BUILD_DIAGS (ADB - 2021/02/05, HDFFV-11213) - CMake option to build the HDF filter plugins project as an external project The HDF filter plugins project is a collection of registered compression filters that can be dynamically loaded when needed to access data stored in a hdf5 file. This CMake-only option allows the plugins to be built and distributed with the hdf5 library and tools. Like the options for szip and zlib, either a tgz file or a git repository can be specified for the source. The option was refactored to use the CMake FetchContent process. This allows more control over the filter targets, but required external project command options to be moved to a CMake include file, HDF5PluginCache.cmake. Also enabled the filter examples to be used as tests for operation of the filter plugins. (ADB - 2020/12/10, OESS-98) - FreeBSD Autotools configuration now defaults to 'cc' and 'c++' compilers On FreeBSD, the autotools defaulted to 'gcc' as the C compiler and did not process C++ options. Since FreeBSD 10, the default compiler has been clang (via 'cc'). The default compilers have been set to 'cc' for C and 'c++' for C++, which will pick up clang and clang++ respectively on FreeBSD 10+. Additionally, clang options are now set correctly for both C and C++ and g++ options will now be set if that compiler is being used (an omission from the former functionality). (DER - 2020/11/28, HDFFV-11193) - Fixed POSIX problems when building w/ gcc on Solaris When building on Solaris using gcc, the POSIX symbols were not being set correctly, which could lead to issues like clock_gettime() not being found. The standard is now set to gnu99 when building with gcc on Solaris, which allows POSIX things to be #defined and linked correctly. This differs slightly from the gcc norm, where we set the standard to c99 and manually set POSIX #define symbols. (DER - 2020/11/25, HDFFV-11191) - Added a configure-time option to consider certain compiler warnings as errors A new configure-time option was added that converts some compiler warnings to errors. This is mainly intended for library developers and currently only works for gcc and clang. The warnings that are considered errors will appear in the generated libhdf5.settings file. These warnings apply to C and C++ code and will appear in "H5 C Flags" and H5 C++ Flags", respectively. They will NOT be exported to h5cc, etc. The default is OFF. Building with this option may fail when compiling on operating systems and with compiler versions not commonly used by the library developers. Compilation may also fail when headers not under the control of the library developers (e.g., mpi.h, hdfs.h) raise warnings. Autotools: --enable-warnings-as-errors CMake: HDF5_ENABLE_WARNINGS_AS_ERRORS (DER - 2020/11/23, HDFFV-11189) - Autotools and CMake target added to produce doxygen generated documentation The default is OFF or disabled. Autoconf option is '--enable-doxygen' autotools make target is 'doxygen' and will build all doxygen targets CMake configure option is 'HDF5_BUILD_DOC'. CMake target is 'doxygen' for all available doxygen targets CMake target is 'hdf5lib_doc' for the src subdirectory (ADB - 2020/11/13, HDFFV-11243) - CMake option to use MSVC naming conventions with MinGW HDF5_MSVC_NAMING_CONVENTION option enable to use MSVC naming conventions when using a MinGW toolchain (xan - 2020/10/30) - CMake option to statically link gcc libs with MinGW HDF5_MINGW_STATIC_GCC_LIBS allows to statically link libg/libstdc++ with the MinGW toolchain (xan - 2020/10/30) - CMake option to build the HDF filter plugins project as an external project The HDF filter plugins project is a collection of registered compression filters that can be dynamically loaded when needed to access data stored in a hdf5 file. This CMake-only option allows the plugins to be built and distributed with the hdf5 library and tools. Like the options for szip and zlib, either a tgz file or a git repository can be specified for the source. The necessary options are (see the INSTALL_CMake.txt file): HDF5_ENABLE_PLUGIN_SUPPORT PLUGIN_TGZ_NAME or PLUGIN_GIT_URL There are more options necessary for various filters and the plugin project documents should be referenced. (ADB - 2020/10/16, OESS-98) - Added CMake option to format source files HDF5_ENABLE_FORMATTERS option will enable creation of targets using the pattern - HDF5_*_SRC_FORMAT - where * corresponds to the source folder or tool folder. All sources can be formatted by executing the format target; make format (ADB - 2020/09/24) Library: -------- - Change how the release part of version, in major.minor.release is checked for compatibility The HDF5 library uses a function, H5check_version, to check that the version defined in the header files, which is used to compile an application is compatible with the version codified in the library, which the application loads at runtime. This previously required an exact match or the library would print a warning, dump the build settings and then abort or continue. An environment variable controlled the logic. Now the function first checks that the library release version, in major.minor.release, is not older than the version in the headers. Secondly, if the release version is different, it checks if either the library version or the header version is in the exception list, in which case the release part of version, in major.minor.release, must be exact. An environment variable still controls the logic. (ADB - 2021/07/27) - H5Gcreate1() now rejects size_hint parameters larger than UINT32_MAX The size_hint value is ultimately stored in a uint32_t struct field, so specifying a value larger than this on a 64-bit machine can cause undefined behavior including crashing the system. The documentation for this API call was also incorrect, stating that passing a negative value would cause the library to use a default value. Instead, passing a "negative" value actually passes a very large value, which is probably not what the user intends and can cause crashes on 64-bit systems. The Doxygen documentation has been updated and passing values larger than UINT32_MAX for size_hint will now produce a normal HDF5 error. (DER - 2021/04/29, HDFFV-11241) - H5Pset_fapl_log() no longer crashes when passed an invalid fapl ID When passed an invalid fapl ID, H5Pset_fapl_log() would usually segfault when attempting to free an uninitialized pointer in the error handling code. This behavior is more common in release builds or when the memory sanitization checks were not selected as a build option. The pointer is now correctly initialized and the API call now produces a normal HDF5 error when fed an invalid fapl ID. (DER - 2021/04/28, HDFFV-11240) - Fixes a segfault when H5Pset_mdc_log_options() is called multiple times The call incorrectly attempts to free an internal copy of the previous log location string, which causes a segfault. This only happens when the call is invoked multiple times on the same property list. On the first call to a given fapl, the log location is set to NULL so the segfault does not occur. The string is now handled properly and the segfault no longer occurs. (DER - 2021/04/27, HDFFV-11239) - HSYS_GOTO_ERROR now emits the results of GetLastError() on Windows HSYS_GOTO_ERROR is an internal macro that is used to produce error messages when system calls fail. These strings include errno and the the associated strerror() value, which are not particularly useful when a Win32 API call fails. On Windows, this macro has been updated to include the result of GetLastError(). When a system call fails on Windows, usually only one of errno and GetLastError() will be useful, however we emit both for the user to parse. The Windows error message is not emitted as it would be awkward to free the FormatMessage() buffer given the existing HDF5 error framework. Users will have to look up the error codes in MSDN. The format string on Windows has been changed from: "%s, errno = %d, error message = '%s'" to: "%s, errno = %d, error message = '%s', Win32 GetLastError() = %"PRIu32"" for those inclined to parse it for error values. (DER - 2021/03/21) - File locking now works on Windows Since version 1.10.0, the HDF5 library has used a file locking scheme to help enforce one reader at a time accessing an HDF5 file, which can be helpful when setting up readers and writers to use the single- writer/multiple-readers (SWMR) access pattern. In the past, this was only functional on POSIX systems where flock() or fcntl() were present. Windows used a no-op stub that always succeeded. HDF5 now uses LockFileEx() and UnlockFileEx() to lock the file using the same scheme as POSIX systems. We lock the entire file when we set up the locks (by passing DWORDMAX as both size parameters to LockFileEx()). (DER - 2021/03/19, HDFFV-10191) - H5Epush_ret() now requires a trailing semicolon H5Epush_ret() is a function-like macro that has been changed to contain a `do {} while(0)` loop. Consequently, a trailing semicolon is now required to end the `while` statement. Previously, a trailing semi would work, but was not mandatory. This change was made to allow clang-format to correctly format the source code. (SAM - 2021/03/03) - Improved performance of H5Sget_select_elem_pointlist Modified library to cache the point after the last block of points retrieved by H5Sget_select_elem_pointlist, so a subsequent call to the same function to retrieve the next block of points from the list can proceed immediately without needing to iterate over the point list. (NAF - 2021/01/19) Fortran Library: ---------------- - H5Fget_name_f fixed to handle correctly trailing whitespaces and newly allocated buffers. (MSB - 2021/08/30, github-826,972) Java Library: ------------- - Added new H5S functions. H5Sselect_copy, H5Sselect_shape_same, H5Sselect_adjust, H5Sselect_intersect_block, H5Sselect_project_intersection, H5Scombine_hyperslab, H5Smodify_select, H5Scombine_select wrapper functions added. (ADB - 2020/10/27, HDFFV-10868) Tools: ------ - Refactored the perform tools and removed dependencies on test library. Moved the perf and h5perf tools from tools/test/perform to tools/src/h5perf so that they can be installed. This required that the test library dependency be removed by copying the needed functions from h5test.c. The standalone scripts and other perform tools remain in the tools/test/perform folder. (ADB - 2021/08/10) - h5repack added help text for user-defined filters. Added help text line that states the valid values of the filter flag for user-defined filters; filter_flag: 1 is OPTIONAL or 0 is MANDATORY (ADB - 2021/01/14, HDFFV-11099) Documentation: -------------- - Doxygen documentation is available when configured and generated. The resulting documentation files will be in the share/html subdirectory of the HDF5 install directory. (LRK - 2021/10/06) New platforms, languages and compilers tested ============================================= - Linux 5.13.14-200.fc34 #1 SMP x86_64 GNU/Linux Fedora34 - Linux 5.11.0-34-generic #36-Ubuntu SMP x86_64 GNU/Linux Ubuntu 20.04 - Linux 5.3.18-22-default #1 SMP x86_64 GNU/Linux SUSE15sp2 - Linux-4.14.0-115.21.2 #1 SMP ppc64le GNU/Linux - Linux-4.12.14-150.75-default #1 SMP x86_64 GNU/Linux - macOS Apple M1 11.6 Darwin 20.6.0 arm64 - macOS Big Sur 11.3.1 Darwin 20.4.0 x86_64 - clang versions 11.0.1, 12.0.5 - Visual Studio 2019 w/ clang 12.0.0 with MSVC-like command-line Bug Fixes since HDF5-1.10.7 release =================================== Library ------- - Fixed CVE-2018-17432 The tool h5repack produced a segfault on a corrupted file which had invalid rank for scalar or NULL datatype. The problem was fixed by modifying the dataspace encode and decode functions to detect and report invalid rank. h5repack now fails with an error message for the corrupted file. (BMR - 2021/10/21, HDFFV-10590) - Fixed a segmentation fault A segmentation fault occurred with a corrupted file. A detection of accessing a null pointer was added to prevent the problem. (BMR - 2021/10/14, HDFFV-11150) - Detection of simple data transform function "x" In the case of the simple data transform function "x" the (parallel) library recognizes this is the same as not applying this data transform function. This improves the I/O performance. In the case of the parallel library, it also avoids breaking to independent I/O, which makes it possible to apply a filter when writing or reading data to or from the HDF5 file. (JWSB - 2021/09/13) - Fixed CVE-2020-10810 - an invalid read and memory leak when parsing corrupt file space info messages When the corrupt file from CVE-2020-10810 was parsed by the library, the code that imports the version 0 file space info object header message to the version 1 struct could read past the buffer read from the disk, causing an invalid memory read. Not catching this error would cause downstream errors that eventually resulted in a previously allocated buffer to be unfreed when the library shut down. In builds where the free lists are in use, this could result in an infinite loop and SIGABRT when the library shuts down. We now track the buffer size and raise an error on attempts to read past the end of it. (DER - 2021/08/12, HDFFV-11053) - Fixed CVE-2018-14460 The tool h5repack produced a segfault when the rank in dataspace message was corrupted, causing invalid read while decoding the dimension sizes. The problem was fixed by ensuring that decoding the dimension sizes and max values will not go beyong the end of the buffer. (BMR - 2021/05/12, HDFFV-11223) - Fixed CVE-2018-11206 The tool h5dump produced a segfault when the size of a fill value message was corrupted and caused a buffer overflow. The problem was fixed by verifying the fill value's size against the buffer size before attempting to access the buffer. (BMR - 2021/03/15, HDFFV-10480) - Fixed CVE-2018-14033 (same issue as CVE-2020-10811) The tool h5dump produced a segfault when the storage size message was corrupted and caused a buffer overflow. The problem was fixed by verifying the storage size against the buffer size before attempting to access the buffer. (BMR - 2021/03/15, HDFFV-11159/HDFFV-11049) - Remove underscores on header file guards Header file guards used a variety of underscores at the beginning of the define. Removed all leading (some trailing) underscores from header file guards. (ADB - 2021/03/03, #361) Java Library ------------ - The H5FArray.java class, in which virtually the entire execution time is spent using the HDFNativeData method that converts from an array of bytes to an array of the destination Java type. 1. Convert the entire byte array into a 1-d array of the desired type, rather than performing 1 conversion per row; 2. Use the Java Arrays method copyOfRange to grab the section of the array from (1) that is desired to be inserted into the destination array. (PGT,ADB - 2020/12/29, HDFFV-10865) Configuration ------------- - Corrected path searched by CMake find_package command The install path for cmake find_package files had been changed to use "share/cmake" for all platforms. However the trailing "hdf5" directory was not removed. This "hdf5" additional directory has been removed. (ADB - 2021/09/27) - Corrected pkg-config compile script It was discovered that the position of the "$@" argument for the command in the compile script may fail on some platforms and configurations. The position of the "$@"command argument was moved before the pkg-config sub command. (ADB - 2021/08/30) - Fixed CMake C++ compiler flags A recent refactoring of the C++ configure files accidently removed the file that executed the enable_language command for C++ needed by the HDFCXXCompilerFlags.cmake file. Also updated the intel warnings files, including adding support for windows platforms. (ADB - 2021/08/10) - Autotools clang debug optimization level change HDF5 1.10.7 erroneously sets the debug optimization level to "-g" when building with clang via the Autotools. This has now been set to: -Og clang 4+ or Xcode 9+ -O1 otherwise (DER - 2021/07/28, HDFFV-11192) - Better support for libaec (open-source Szip library) in CMake Implemented better support for libaec 1.0.5 (or later) library. This version of libaec contains improvements for better integration with HDF5. Furthermore, the variable USE_LIBAEC_STATIC has been introduced to allow to make use of static version of libaec library. Use libaec_DIR or libaec_ROOT to set the location in which libaec can be found. Be aware, the Szip library of libaec 1.0.4 depends on another library within libaec library. This dependency is not specified in the current CMake configuration which means that one can not use the static Szip library of libaec 1.0.4 when building HDF5. This has been resolved in libaec 1.0.5. (JWSB - 2021/06/22) - Refactor CMake configure for Fortran The Fortran configure tests for KINDs reused a single output file that was read to form the Integer and Real Kinds defines. However, if config was run more then once, the CMake completed variable prevented the tests from executing again and the last value saved in the file was used to create the define. Creating separate files for each KIND solved the issue. In addition the test for H5_PAC_C_MAX_REAL_PRECISION was not pulling in defines for proper operation and did not define H5_PAC_C_MAX_REAL_PRECISION correctly for a zero value. This was fixed by supplying the required defines. In addition it was moved from the Fortran specific HDF5UseFortran.camke file to the C centric ConfigureChecks.cmake file. (ADB - 2021/06/03) - Remove arbitrary warning flag groups from CMake builds The arbitrary groups were created to reduce the quantity of warnings being reported that overwhelmed testing report systems. Considerable work has been accomplished to reduce the warning count and these arbitrary groups are no longer needed. Also the default for all warnings, HDF5_ENABLE_ALL_WARNINGS, is now ON. Visual Studio warnings C4100, C4706, and C4127 have been moved to developer warnings, HDF5_ENABLE_DEV_WARNINGS, and are disabled for normal builds. (ADB - 2021/03/22, HDFFV-11228) - Reclassify CMake messages, to allow new modes and --log-level option CMake message commands have a mode argument. By default, STATUS mode was chosen for any non-error message. CMake version 3.15 added additional modes, NOTICE, VERBOSE, DEBUG and TRACE. All message commands with a mode of STATUS were reviewed and most were reclassified as VERBOSE. The new mode was protected by a check for a CMake version of at least 3.15. If CMake version 3.17 or above is used, the user can use the command line option of "--log-level" to further restrict which message commands are displayed. (ADB - 2021/01/11, HDFFV-11144) - Fixes Autotools determination of the stat struct having an st_blocks field A missing parenthesis in an autoconf macro prevented building the test code used to determine if the stat struct contains the st_blocks field. Now that the test functions correctly, the H5_HAVE_STAT_ST_BLOCKS #define found in H5pubconf.h will be defined correctly on both the Autotools and CMake. This #define is only used in the tests and does not affect the HDF5 C library. (DER - 2021/01/07, HDFFV-11201) Tools ----- - Changed how h5dump and h5ls identify long double. Long double support is not consistent across platforms. Tools will always identify long double as 128-bit [little/big]-endian float nn-bit precision. New test file created for datasets with attributes for float, double and long double. In addition any unknown integer or float datatype will now also show the number of bits for precision. These files are also used in the java tests. (ADB - 2021/03/24, HDFFV-11229) - Fixed tools argument parsing. Tools parsing used the length of the option from the long array to match the option from the command line. This incorrectly matched a shorter long name option that happened to be a subset of another long option. Changed to match whole names. (ADB - 2021/01/19, HDFFV-11106) Documentation ------------- - Updated doxygen comments with changes for release (ADB - 2021/05/17) C++ APIs -------- - Added DataSet::operator= Some compilers complain if the copy constructor is given explicitly but the assignment operator is implicitly set to default. (2021/05/19) Platforms Tested ================ Linux 5.13.14-200.fc34 GNU gcc (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1) #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1) Fedora34 clang version 12.0.1 (Fedora 12.0.1-1.fc34) (cmake and autotools) Linux 5.11.0-34-generic GNU gcc (GCC) 9.3.0-17ubuntu1 #36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.3.0-17ubuntu1 Ubuntu 20.04 Ubuntu clang version 10.0.0-4 (cmake and autotools) Linux 5.8.0-63-generic GNU gcc (GCC) 10.3.0-1ubuntu1 #71-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 10.3.0-1ubuntu1 Ubuntu20.10 Ubuntu clang version 11.0.0-2 (cmake and autotools) Linux 5.3.18-22-default GNU gcc (SUSE Linux) 7.5.0 #1 SMP x86_64 GNU/Linux GNU Fortran (SUSE Linux) 7.5.0 SUSE15sp2 clang version 7.0.1 (tags/RELEASE_701/final 349238) (cmake and autotools) Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release #1 SMP ppc64le GNU/Linux clang 8.0.1, 11.0.1 (lassen) GCC 7.3.1 XL 16.1.1.2 (cmake) Linux-4.12.14-150.75-default cray-mpich/7.7.10 #1 SMP x86_64 GNU/Linux GCC 7.3.0, 8.2.0 (cori) Intel (R) Version 19.0.3.199 (cmake) Linux-4.12.14-197.86-default cray-mpich/7.7.6 # 1SMP x86_64 GNU/Linux GCC 7.3.0, 9.3.0, 10.2.0 (mutrino) Intel (R) Version 17.0.4, 18.0.5, 19.1.3 (cmake) Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) #1 SMP ppc64be GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) Linux 3.10.0-1160.24.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP x86_64 GNU/Linux compilers: Centos7 Version 4.8.5 20150623 (Red Hat 4.8.5-4) (jelly/kituo/moohan) Version 4.9.3, Version 5.3.0, Version 6.3.0, Version 7.2.0, Version 8.3.0, Version 9.1.0 Intel(R) C (icc), C++ (icpc), Fortran (icc) compilers: Version 17.0.0.098 Build 20160721 GNU C (gcc) and C++ (g++) 4.8.5 compilers with NAG Fortran Compiler Release 6.1(Tozai) Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers with NAG Fortran Compiler Release 6.1(Tozai) MPICH 3.1.4 compiled with GCC 4.9.3 MPICH 3.3 compiled with GCC 7.2.0 OpenMPI 2.1.6 compiled with icc 18.0.1 OpenMPI 3.1.3 and 4.0.0 compiled with GCC 7.2.0 PGI C, Fortran, C++ for 64-bit target on x86_64; Version 19.10-0 Linux-3.10.0-1127.0.0.1chaos openmpi-4.0.0 #1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1 (quartz) GCC 7.3.0, 8.1.0 Intel 16.0.4, 18.0.2, 19.0.4 macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11) Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0 (macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609 macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9) Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0 (bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228 macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4) 64-bit gfortran GNU Fortran (GCC) 6.3.0 (bear) Intel icc/icpc/ifort version 19.0.4.233 20190416 macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2) 64-bit gfortran GNU Fortran (GCC) 7.4.0 (kite) Intel icc/icpc/ifort version 17.0.2 Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3 64-bit gfortran GNU Fortran (GCC) 5.2.0 (osx1011test) Intel icc/icpc/ifort version 16.0.2 Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP x86_64 GNU/Linux compilers: Centos6 Version 4.4.7 20120313 (platypus) Version 4.9.3, 5.3.0, 6.2.0 MPICH 3.1.4 compiled with GCC 4.9.3 Windows 10 x64 MSVC C/C++ 19.0.24215.1 w/ Visual Studio 2015 Intel C/C++/Fortran 18.0.5.20180823 (cmake) Windows 10 x64 MSVC C/C++ 19.16.27045.0 w/ Visual Studio 2017 Intel C/C++/Fortran 19.0.5.20190815 (cmake) Windows 10 x64 MSVC C/C++ 9.29.30133.0 w/ Visual Studio 2019 clang C/C++ 12.0.0 (cmake) IntelLLVM C/C++ 2021.3.0 with MSVC-like command-line Windows 10 x64 MSVC C/C++ is 19.29.30133.0 w/ Visual Studio 2019 MSMPI 10.1 (C only) (cmake) Configuration Options Tested on above platforms CMake option(=ON) Autotools option ============================ ========================= =================== C Library F90/F2003 HDF5_BUILD_FORTRAN --enable-fortran C++ HDF5_BUILD_CPP_LIB --enable-cxx Java HDF5_BUILD_JAVA --enable-java Zlib HDF5_ENABLE_Z_LIB_SUPPORT --with-zlib= SZIP(Libaec) HDF5_ENABLE_SZIP_SUPPORT --with-szlib= C/Fortran Parallel HDF5_ENABLE_PARALLEL --enable-parallel Shared C,C++,F90 BUILD_SHARED_LIBS --enable-shared(1) Threadsafe, C Library only HDF5_ENABLE_THREADSAFE --enable-threadsafe Other test configurations: clang sanitizers HDF5_ENABLE_SANITIZERS No sanitizer option for autotools Address USE_SANITIZER: Address Leak USE_SANITIZER: Leak Memory USE_SANITIZER: Memory Undefined USE_SANITIZER: Undefined VFDs: Direct HDF5_ENABLE_DIRECT_VFD --ennable-direct-vfd HDFS HDF5_ENABLE_HDFS --with-libhdfs=DIR Mirror HDF5_ENABLE_MIRROR_VFD --enable-mirror-vfd ROS3 HDF5_ENABLE_ROS3_VFD --enable-ros3-vfd ================================================================================ (1) enabled by default Known Problems ============== Corrupted files submitted with CVE-2019-08396 and CVE-2019-8398 that caused segmentation faults with h5repack in HDF5 versions before 1.10.8 are no longer segfaulting, but a specific fix for the problems has not yet been identified and is still under investigation in jira issues HDFFV-10710 and HDFFV-10712. A third corrupted file submitted with CVE-2019-9152 still causes a segmentation fault with h5repack; details in HDFFV-10719. Setting a variable-length dataset fill value will leak the memory allocated for the p field of the hvl_t struct. A fix is in progress for this. HDFFV-10840 CMake files do not behave correctly with paths containing spaces. Do not use spaces in paths because the required escaping for handling spaces results in very complex and fragile build files. ADB - 2019/05/07 At present, metadata cache images may not be generated by parallel applications. Parallel applications can read files with metadata cache images, but since this is a collective operation, a deadlock is possible if one or more processes do not participate. Two tests fail attempting collective writes with OpenMPI 3.0.0/GCC-7.2.0-2.29: testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio) t_shapesame (sscontig2) CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler. The subsetting option in ph5diff currently will fail and should be avoided. The subsetting option works correctly in serial h5diff. Known problems in previous releases can be found in the HISTORY*.txt files in the HDF5 source. Please report any new problems found to help@hdfgroup.org. CMake vs. Autotools installations ================================= While both build systems produce similar results, there are differences. Each system produces the same set of folders on linux (only CMake works on standard Windows); bin, include, lib and share. Autotools places the COPYING and RELEASE.txt file in the root folder, CMake places them in the share folder. The bin folder contains the tools and the build scripts. Additionally, CMake creates dynamic versions of the tools with the suffix "-shared". Autotools installs one set of tools depending on the "--enable-shared" configuration option. build scripts ------------- Autotools: h5c++, h5cc, h5fc CMake: h5c++, h5cc, h5hlc++, h5hlcc The include folder holds the header files and the fortran mod files. CMake places the fortran mod files into separate shared and static subfolders, while Autotools places one set of mod files into the include folder. Because CMake produces a tools library, the header files for tools will appear in the include folder. The lib folder contains the library files, and CMake adds the pkgconfig subfolder with the hdf5*.pc files used by the bin/build scripts created by the CMake build. CMake separates the C interface code from the fortran code by creating C-stub libraries for each Fortran library. In addition, only CMake installs the tools library. The names of the szip libraries are different between the build systems. The share folder will have the most differences because CMake builds include a number of CMake specific files for support of CMake's find_package and support for the HDF5 Examples CMake project. The issues with the gif tool are: HDFFV-10592 CVE-2018-17433 HDFFV-10593 CVE-2018-17436 HDFFV-11048 CVE-2020-10809 These CVE issues have not yet been addressed and can be avoided by not building the gif tool. Disable building the High-Level tools with these options: autotools: --disable-hltools cmake: HDF5_BUILD_HL_TOOLS=OFF