HDF5 version 1.10.10 released on 2023-03-31 ================================================================================ 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/Release+Specific+Information 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 HDF5-1.10.9 - Platforms Tested - Known Problems - CMake vs. Autotools installations New Features ============ Configuration: ------------- - Removal of dmalloc support The ability to build with dmalloc support has been removed along with the following configure options: Autotools: --with-dmalloc= CMake: HDF5_ENABLE_USING_DMALLOC (DER - 2023/03/17) - Allow parallel and threadsafe to be built In the past, we required --enable-unsupported (Autotools) or ALLOW_UNSUPPORTED (CMake) in order to build the parallel library with thread-safety support. The parallel, thread-safe library can now be built without these options. (DER - 2023/03/17) - Added new option to build libaec and zlib inline with CMake. Using the CMake FetchContent module, the external filters can populate content at configure time via any method supported by the ExternalProject module. Whereas ExternalProject_Add() downloads at build time, the FetchContent module makes content available immediately, allowing the configure step to use the content in commands like add_subdirectory(), include() or file() operations. The HDF options (and defaults) for using this are: BUILD_SZIP_WITH_FETCHCONTENT:BOOL=OFF LIBAEC_USE_LOCALCONTENT:BOOL=OFF BUILD_ZLIB_WITH_FETCHCONTENT:BOOL=OFF ZLIB_USE_LOCALCONTENT:BOOL=OFF The CMake variables to control the path and file names: LIBAEC_TGZ_ORIGPATH:STRING LIBAEC_TGZ_ORIGNAME:STRING ZLIB_TGZ_ORIGPATH:STRING ZLIB_TGZ_ORIGNAME:STRING See the CMakeFilters.cmake and config/cmake/cacheinit.cmake files for usage. (ADB - 2023/02/21) - 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) Library: -------- - Parallel Library: ----------------- - Fortran Library: ---------------- - C++ Library: ------------ - Java Library: ------------- - HDF5GroupInfo class has been deprecated. This class assumes that an object can contain four values which uniquely identify an object among those HDF5 files which are open. This is no longer valid in future HDF5 releases. (ADB - 2023/03/27) - Added version of H5Rget_name to return the name as a Java string. Other functions that get_name process the get_size then get the name within the JNI implementation. Now H5Rget_name has a H5Rget_name_string. (ADB - 2022/07/12) - Added reference support to H5A and H5D read write vlen JNI functions. Added the implementation to handle VL references as an Array of Lists of byte arrays. The JNI wrappers translate the Array of Lists to/from the hvl_t vlen structures. The wrappers use the specified datatype arguments for the List type translation, it is expected that the Java type is correct. (ADB - 2022/07/11, HDFFV-11318) - H5A and H5D read write vlen JNI functions were incorrect. Corrected the vlen function implementations for the basic primitive types. The VLStrings functions now correctly use the implementation that had been the VL functions. (VLStrings functions did not have an implementation.) The new VL functions implementation now expect an Array of Lists between Java and the JNI wrapper. The JNI wrappers translate the Array of Lists to/from the hvl_t vlen structures. The wrappers use the specified datatype arguments for the List type translation, it is expected that the Java type is correct. (ADB - 2022/07/07, HDFFV-11310) - H5A and H5D read write JNI functions had flawed vlen datatype check. Adapted tools function for JNI utils file. This reduced multiple calls to a single check and variable. The variable can then be used to call the H5Treclaim function. Adjusted existing test and added new test. (ADB - 2022/06/22) Tools: ------ - Building h5perf/h5perf_serial in "standalone mode" has been removed Building h5perf separately from the library was added circa 2008 in HDF5 1.6.8. It's unclear what purpose this serves and the current implementation is currently broken. The existing files require H5private.h and the symbols we use to determine how the copied platform-independence scheme should be used come from H5pubconf.h, which may not match the compiler being used to build standalone h5perf. Due to the maintenance overhead and lack of a clear use case, support for building h5perf and h5perf_serial separately from the HDF5 library has been removed. (DER - 2023/03/20) - The perf tool has been removed The small `perf` tool didn't really do anything special and the name conflicts with gnu's perf tool. (DER - 2023/03/20, GitHub #1787) High-Level APIs: ---------------- - C Packet Table API: ------------------- - Internal header file: --------------------- - Documentation: -------------- - Support for new platforms, languages and compilers ================================================== - Bug Fixes since HDF5-1.10.9 release =================================== Library ------- - Fixed a memory corruption issue that can occur when reading from a dataset using a hyperslab selection in the file dataspace and a point selection in the memory dataspace When reading from a dataset using a hyperslab selection in the dataset's file dataspace and a point selection in the dataset's memory dataspace where the file dataspace's "rank" is greater than the memory dataspace's "rank", memory corruption could occur due to an incorrect number of selection points being copied when projecting the point selection onto the hyperslab selection's dataspace. (JTH - 2023/03/23) - Fix CVE-2021-37501 / GHSA-rfgw-5vq3-wrjf Check for overflow when calculating on-disk attribute data size. A bogus hdf5 file may contain dataspace messages with sizes which lead to the on-disk data sizes to exceed what is addressable. When calculating the size, make sure, the multiplication does not overflow. The test case was crafted in a way that the overflow caused the size to be 0. (EFE - 2023/02/11 GH-2458) - 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) - Fixed an issue with hyperslab selections Previously, when combining hyperslab selections, it was possible for the library to produce an incorrect combined selection. (NAF - 2022/09/25) - 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 - 2022/08/22, GitHub #2016) - Modified H5Fstart_swmr_write() to preserve DAPL properties Internally, H5Fstart_swmr_write() closes and reopens the file in question as part of its process for making the file SWMR-safe. Previously, when the library reopened the file it would simply use the default access properties. Modified the library to instead save these properties and use them when reopening the file. (NAF - 2022/07/18, HDFFV-11308) - Converted an assertion on (possibly corrupt) file contents to a normal error check Previously, the library contained an assertion check that a read superblock doesn't contain a superblock extension message when the superblock version < 2. When a corrupt HDF5 file is read, this assertion can be triggered in debug builds of HDF5. In production builds, this situation could cause either a library error or a crash, depending on the platform. (JTH - 2022/07/08, HDFFV-11316, HDFFV-11317) - 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) Java Library ------------ - Configuration ------------- - Correct the CMake generated pkg-config file The pkg-config file generated by CMake had the order and placement of the libraries wrong. Also added support for debug library names. Changed the order of Libs.private libraries so that dependencies come after dependents. Did not move the compression libraries into Requires.private because there was not a way to determine if the compression libraries had supported pkconfig files. Still recommend that the CMake config file method be used for building projects with CMake. (ADB - 2023/02/16 GH-1546,GH-2259) - Remove Javadoc generation The use of doxygen now supersedes the requirement to build javadocs. We do not have the resources to continue to support two documentation methods and have chosen doxygen as our standard. (ADB - 2022/12/19) - Change the default for building the high-level tools The gif2hdf5 and hdf2gif high-level tools are deprecated and will be removed in a future release. The default build setting for them have been changed from enabled to disabled. A user can enable the build of these tools if needed. autotools: --enable-hlgiftools cmake: HDF5_BUILD_HL_GIF_TOOLS=ON (ADB - 2022/12/16) - 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 - 2022/20/27) Tools ----- - Fix h5repack to only print output when verbose option is selected When timing option was added to h5repack, the check for verbose was incorrectly implemented. (ADB - 2022/12/02, GH #2270) Performance ------------- - Fortran API ----------- - High-Level Library ------------------ - Fortran High-Level APIs ----------------------- - Documentation ------------- - Doxygen updated with recent Fortran changes. (ADB - 2022/09/09) F90 APIs -------- - C++ APIs -------- - Testing ------- - 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, 10.2.0 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 NVIDIA C, Fortran, C++ for 64-bit target on x86_64 Linux -tp haswell; Version 22.5-0 (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 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 ============== The function prototype for H5Treclaim was mistakenly added to code for HDF5 1.10.9; however no implementation code was added. This prototype has been removed, resulting in a source incompatibility for shared library versions between HDF5 versions 1.10.10 and 1.10.9, but not binary incompatibility since the function was not implemented. 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