HDF5 version 1.8.23 released on 2023-02-08 ================================================================================ 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 HDF5-1.8.x release series can be found at: https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide If you have any questions or comments, please send them to the HDF Help Desk: help@hdfgroup.org CONTENTS ======== - New Features - Support for New Platforms and Languages - Bug Fixes since HDF5-1.8.22 - Platforms Tested - Known Problems - CMake vs. Autotools installations New Features ============ Configuration: ------------- - Add new CMake configuration variable HDF5_USE_GNU_DIRS HDF5_USE_GNU_DIRS (default OFF) selects the use of GNU Coding Standard install directory variables by including the CMake module, GNUInstallDirs(see CMake documentation for details). The HDF_DIR_PATHS macro in the HDFMacros.cmake file sets various PATH variables for use during the build, test and install processes. By default, the historical settings for these variables will be used. (ADB - 2022/10/21, GH-2175, GH-1716) - Correct the usage of CMAKE_Fortran_MODULE_DIRECTORY and where to install Fortran mod files. The Fortran modules files, ending in .mod are files describing a Fortran 90 (and above) module API and ABI. These are not like C header files describing an API, they are compiler dependent and arch dependent, and not easily readable by a human being. They are nevertheless searched for in the includes directories by gfortran (in directories specified with -I). Autotools configure uses the -fmoddir option to specify the folder. CMake will use "mod" folder by default unless overridden by the CMake variable; HDF5_INSTALL_MODULE_DIR. (ADB - 2022/07/21) - Added new option to the h5cc scripts produced by CMake. Add -showconfig option to h5cc scripts to cat the libhdf5-settings to the standard output. (ADB - 2022/03/11) - Changed autotools and CMake configurations to derive both compilation warnings-as-errors and warnings-only-warn configurations from the same files, 'config/*/*error*'. Removed redundant files 'config/*/*noerror*'. (DCY - 2021/09/29) - Added new option to control the build of High-Level tools that default ON/enabled. Add configure options (autotools - CMake): enable-hltools HDF5_BUILD_HL_TOOLS (ADB - 2021/09/16, HDFFV-11266) - 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) - 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) - 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 - 2021/02/16, 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 - 2021/02/16, 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 - 2021/02/16, HDFFV-11189) - 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, https://github.com/HDFGroup/hdf5/issues/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) Library: -------- - H5Epush_ret() now requires a trailing semi-colon H5Epush_ret() is a function-like macro that has been changed to contain a `do {} while(0)` loop. Consequently, a trailing semi-colon 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) Fortran Library: ---------------- - H5Fget_name_f fixed to handle correctly trailing whitespaces and newly allocated buffers. (MSB - 2021/08/30, github-826,972) Tools: ------ - 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 - 2021/02/16, HDFFV-11099) - h5repack added options to control how external links are handled. Currently h5repack preserves external links and cannot copy and merge data from the external files. Two options, merge and prune, were added to control how to merge data from an external link into the resulting file. --merge Follow external soft link recursively and merge data. --prune Do not follow external soft links and remove link. --merge --prune Follow external link, merge data and remove dangling link. (ADB - 2021/02/16, HDFFV-9984) Bug Fixes since HDF5-1.8.22 =========================== Configuration ------------- - Change the settings of the *pc files to use the correct format The pkg-config files generated by CMake uses incorrect syntax for the 'Requires' settings. Changing the set to use 'lib-name = version' instead 'lib-name-version' fixes the issue (ADB - 2022/12/06 HDFFV-11355) - Move MPI libraries link from PRIVATE to PUBLIC The install dependencies were not including the need for MPI libraries when an application or library was built with the C library. Also updated the CMake target link command to use the newer style MPI::MPI_C link variable. (ADB - 2022/10/27) - Reworked 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 setting the HDF5_ROOT variable failed to locate the configuration files. The build variable HDF5_INSTALL_CMAKE_DIR is now set to the /cmake folder. The location of the configuration files can still be specified by the "HDF5_DIR" variable. (ADB - 2022/03/11) - 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) - 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 - 2021/02/16, 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 - 2021/02/16, HDFFV-11201) Library ------- - Fixed an issue with variable length attributes Previously, if a variable length attribute was held open while its file was opened through another handle, the same attribute was opened through the second file handle, and the second file and attribute handles were closed, attempting to write to the attribute through the first handle would cause an error. (NAF - 2022/10/24) - Memory leak A memory leak was observed with variable-length fill value in H5O_fill_convert() function in H5Ofill.c. The leak is manifested by running valgrind on test/set_extent.c. Previously, fill->buf is used for datatype conversion if it is large enough and the variable-length information is therefore lost. A buffer is now allocated regardless so that the element in fill->buf can later be reclaimed. (VC - 2022/10/10, HDFFV-10840) - Fixed an issue with attribute type conversion with compound datatypes Previously, when performing type conversion for attribute I/O with a compound datatype, the library would not fill the background buffer with the contents of the destination, potentially causing data to be lost when only writing to a subset of the compound fields. (NAF - 2022/09/12, GitHub #2016) - Issue #1436 identified a problem with the H5_VERS_RELEASE check in the H5check_version function. Investigating the original fix, #812, we discovered some inconsistencies with a new block added to check H5_VERS_RELEASE for incompatibilities. This new block was not using the new warning text dealing with the H5_VERS_RELEASE check and would cause the warning to be duplicated. By removing the H5_VERS_RELEASE argument in the first check for H5_VERS_MAJOR and H5_VERS_MINOR, the second check would only check the H5_VERS_RELEASE for incompatible release versions. This adheres to the statement that except for the develop branch, all release versions in a major.minor maintenance branch should be compatible. The prerequisite is that an application will not use any APIs not present in all release versions. (ADB - 2022/03/11, #1438) 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 - 2021/02/16, HDFFV-11106) - The tools library was updated by standardizing the error stack process. General sequence is: h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); h5tools_init(); ... process the command-line (check for error-stack enable) ... h5tools_error_report(); ... (do work) ... h5diff_exit(ret); (ADB - 2021/02/16, HDFFV-11066) - h5diff fixed a command line parsing error. h5diff would ignore the argument to -d (delta) if it is smaller than DBL_EPSILON. The macro H5_DBL_ABS_EQUAL was removed and a direct value comparision was used. (ADB - 2021/02/16, HDFFV-10897) - h5diff added a command line option to ignore attributes. h5diff would ignore all objects with a supplied path if the exclude-path argument is used. Adding the exclude-attribute argument will only eclude attributes, with the supplied path, from comparision. (ADB - 2021/02/16, HDFFV-5935) - h5diff added another level to the verbose argument to print filenames. Added verbose level 3 that is level 2 plus the filenames. The levels are: 0 : Identical to '-v' or '--verbose' 1 : All level 0 information plus one-line attribute status summary 2 : All level 1 information plus extended attribute status report 3 : All level 2 information plus file names (ADB - 2021/02/16, HDFFV-10005) - h5repack was fixed to repack the reference attributes properly. The code line that checks if the update of reference inside a compound datatype is misplaced outside the code block loop that carries out the check. In consequence, the next attribute that is not the reference type was repacked again as the reference type and caused the failure of repacking. The fix is to move the corresponding code line to the correct code block. (KY -2021/02/16, HDFFV-11014) Packet Table APIs: ------------------ - Fixed HL_test_packet, test for packet table vlen of vlen. Incorrect length assignment. (ADB - 2021/10/14) Support for New Platforms and Languages ======================================= - Added support for IBM Power 8 GNU/Linux 3.10.0 ppc64be with GCC 4.8.5, xlc/xlC 13.1 and xlf 15.1 - Added support for Ubuntu 22.04 GNU/Linux5.15.0-1026-aws with GCC 11.3.0, clang 14.0.0 - Added support for CentOS8 GNU/Linux 4.18.0-348.7.1.el8_5 with GCC 8.5.0, clang 12.0.1 - Added support for macOS Apple M1 11.6 with Apple clang 12.0.5, GNU Fortran 11.1.0, Intel icc/icpc/ifort 2021.3.0 - Added support for macOS Big Sur 11.3.1 with Apple clang 12.0.5, GNU Fortran 10.2.0, Intel icc/icpc/ifort version 2021.2.0 - Added support for Visual Studio 2022 w/ clang 15.0.1 with MSVC-like command-line (C/C++ only - cmake), Intel C/C++/Fortran oneAPI 2022 (cmake) Platforms Tested ================ Linux 5.15.0-1026-aws gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 #30-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 Ubuntu 22.04 Ubuntu clang version 14.0.0-1ubuntu1 (cmake and autotools) Linux 5.13.0-1031-aws GNU gcc (GCC) 9.4.0-1ubuntu1 #35-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.4.0-1ubuntu1 Ubuntu 20.04 clang version 10.0.0-4ubuntu1 (cmake and autotools) Linux 4.18.0-348.7.1.el8_5 gcc (GCC) 8.5.0 20210514 (Red Hat 8.5.0-4) #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 8.5.0 20210514 (Red Hat 8.5.0-4) CentOS8 clang version 12.0.1 (Red Hat 12.0.1) (cmake and autotools) Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release #1 SMP ppc64le GNU/Linux clang 12.0.1, 14.0.5 (lassen) GCC 8.3.1 XL 16.1.1.2, 2021.09.22, 2022.08.05 (cmake) Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) #1 SMP ppc64 GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) IBM XL C/C++ V13.1 IBM XL Fortran V15.1 Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP x86_64 GNU/Linux compilers: (jelly/kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-39) Versions 4.9.3, 5.3.0, 6.3.0, 7.2.0 8.3.0, 9.1.0, 10.1.0 Intel(R) C (icc), C++ (icpc), Fortran (icc) compilers: Version 17.0.0.098 Build 20160721 MPICH 3.1.4 built with GCC 4.9.3, 3.3 built with GCC 7.2.0 OpenMPI 3.1.3, 4.0.0 compiled with GCC 7.2.0 NAG Fortran Compiler Release 7.0(Yurakuchho) Build 7011 PGI C, Fortran, C++ for 64-bit target on x86_64; Version 19.10-0 (autotools and cmake) Linux-3.10.0-1160.0.0.1chaos openmpi-4.1.2 #1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1 (quartz) GCC 7.3.0, 8.1.0 Intel 19.0.4, 2022.2, oneapi.2022.2 Linux-3.10.0-1160.59.1.1chaos openmpi/4.1 #1 SMP x86_64 GNU/Linux Intel/19.1, 21.3.0, 22.2.0 (chama) (cmake) 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: (platypus) Version 4.4.7 20120313 Versions 4.9.3, 5.3.0, 6.2.0 MPICH 3.1.4 compiled with GCC 4.9.3 PGI C, Fortran, C++ for 64-bit target on x86-64; Version 19.10-0 Windows 10 x64 Visual Studio 2015 w/ Intel C/C++/Fortran 18 (cmake) Visual Studio 2017 w/ Intel C/C++/Fortran 19 (cmake) Visual Studio 2019 w/ clang 12.0.0 with MSVC-like command-line (C/C++ only - cmake) Visual Studio 2019 w/ Intel C/C++/Fortran oneAPI 2022 (cmake) Visual Studio 2022 w/ clang 15.0.1 with MSVC-like command-line (C/C++ only - cmake) Visual Studio 2022 w/ Intel C/C++/Fortran oneAPI 2022 (cmake) Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake) Known Problems ============== MacOS using CMake to build HDF5 with ifort versions 2021.2.0 or 2021.3.0 has a test failure that does not occur when using Autotools to build it. All tests also pass using CMake with ifort version 2021.8.0 on macOS13. This failure may not indicate any particular problem with the build. It can be avoided by building with clang and gfortran for CMake builds or by using Autotools to build with ifort on macOS. 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 The dynamically loaded plugin test libraries require undefined references to HDF5 functions to be resolved at runtime in order to function properly. With autotools on CYGWIN this results in build errors, and we have not found a solution that satisfies both. Therefore the dynamically loaded plugin tests have been disabled on CYGWIN. 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.