HDF5 version 1.14.1-2 released on 2023-05-11 ================================================================================ HDF5 1.14.1-2 is a patch release for HDF5 1.14.1. The only change in the patch release is that Autoconf 2.71 was used to generate the Autotools build files, which allows building with Intel's oneAPI. 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 HDF5-1.14.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 HDF5-1.14.0 - Platforms Tested - Known Problems - CMake vs. Autotools installations New Features ============ Configuration: ------------- - Added new CMake options for building and running HDF5 API tests (Experimental) HDF5 API tests are an experimental feature, primarily targeted toward HDF5 VOL connector authors, that is currently being developed. These tests exercise the HDF5 API and are being integrated back into the HDF5 library from the HDF5 VOL tests repository (https://github.com/HDFGroup/vol-tests). To support this feature, the following new options have been added to CMake: * HDF5_TEST_API: ON/OFF (Default: OFF) Controls whether the HDF5 API tests will be built. These tests will only be run during testing of HDF5 if the HDF5_TEST_SERIAL (for serial tests) and HDF5_TEST_PARALLEL (for parallel tests) options are enabled. * HDF5_TEST_API_INSTALL: ON/OFF (Default: OFF) Controls whether the HDF5 API test executables will be installed on the system alongside the HDF5 library. This option is currently not functional. * HDF5_TEST_API_ENABLE_ASYNC: ON/OFF (Default: OFF) Controls whether the HDF5 Async API tests will be built. These tests will only be run if the VOL connector used supports Async operations. * HDF5_TEST_API_ENABLE_DRIVER: ON/OFF (Default: OFF) Controls whether to build the HDF5 API test driver program. This test driver program is useful for VOL connectors that use a client/server model where the server needs to be up and running before the VOL connector can function. This option is currently not functional. * HDF5_TEST_API_SERVER: String (Default: "") Used to specify a path to the server executable that the test driver program should execute. - Added support for CMake presets file. CMake supports two main files, CMakePresets.json and CMakeUserPresets.json, that allow users to specify common configure options and share them with others. HDF added a CMakePresets.json file of a typical configuration and support file, config/cmake-presets/hidden-presets.json. Also added a section to INSTALL_CMake.txt with very basic explanation of the process to use CMakePresets. - Deprecated and removed old SZIP library in favor of LIBAEC library LIBAEC library has been used in HDF5 binaries as the szip library of choice for a few years. We are removing the options for using the old SZIP library. Also removed the config/cmake/FindSZIP.cmake file. - Enabled instrumentation of the library by default in CMake for parallel debug builds HDF5 can be configured to instrument portions of the parallel library to aid in debugging. Autotools builds of HDF5 turn this capability on by default for parallel debug builds and off by default for other build types. CMake has been updated to match this behavior. - 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. Library: -------- - Added a Subfiling VFD configuration file prefix environment variable The Subfiling VFD now checks for values set in a new environment variable "H5FD_SUBFILING_CONFIG_FILE_PREFIX" to determine if the application has specified a pathname prefix to apply to the file path for its configuration file. For example, this can be useful for cases where the application wishes to write subfiles to a machine's node-local storage while placing the subfiling configuration file on a file system readable by all machine nodes. - Added H5Pset_selection_io(), H5Pget_selection_io(), and H5Pget_no_selection_io_cause() API functions to manage the selection I/O feature. This can be used to enable collective I/O with type conversion, or it can be used with custom VFDs that support vector or selection I/O. - Added H5Pset_modify_write_buf() and H5Pget_modify_write_buf() API functions to allow the library to modify the contents of write buffers, in order to avoid malloc/memcpy. Currently only used for type conversion with selection I/O. Parallel Library: ----------------- - Fortran Library: ---------------- - Fortran async APIs H5A, H5D, H5ES, H5G, H5F, H5L and H5O were added. - Added Fortran APIs: h5pset_selection_io_f, h5pget_selection_io_f h5pset_modify_write_buf_f, h5pget_modify_write_buf_f C++ Library: ------------ - Java Library: ------------- - Tools: ------ - High-Level APIs: ---------------- - C Packet Table API: ------------------- - Internal header file: --------------------- - Documentation: -------------- - Ported the existing VOL Connector Author Guide document to doxygen. Added new dox file, VOLConnGuide.dox. Support for new platforms, languages and compilers ================================================== - Bug Fixes since HDF5-1.14.0 release =================================== Library ------- - Fixed a bug in H5Ocopy that could generate invalid HDF5 files H5Ocopy was missing a check to determine whether the new object's object header version is greater than version 1. Without this check, copying of objects with object headers that are smaller than a certain size would cause H5Ocopy to create an object header for the new object that has a gap in the header data. According to the HDF5 File Format Specification, this is not allowed for version 1 of the object header format. Fixes GitHub issue #2653 - Fixed H5Pget_vol_cap_flags and H5Pget_vol_id to accept H5P_DEFAULT H5Pget_vol_cap_flags and H5Pget_vol_id were updated to correctly accept H5P_DEFAULT for the 'plist_id' FAPL parameter. Previously, they would fail if provided with H5P_DEFAULT as the FAPL. - Fixed ROS3 VFD anonymous credential usage with h5dump and h5ls ROS3 VFD anonymous credential functionality became broken in h5dump and h5ls in the HDF5 1.14.0 release with the added support for VFD plugins, which changed the way that the tools handled setting of credential information that the VFD uses. The tools could be provided the command-line option of "--s3-cred=(,,)" as a workaround for anonymous credential usage, but the documentation for this option stated that anonymous credentials could be used by simply omitting the option. The latter functionality has been restored. Fixes GitHub issue #2406 - Fixed memory leaks when processing malformed object header continuation messages Malformed object header continuation messages can result in a too-small buffer being passed to the decode function, which could lead to reading past the end of the buffer. Additionally, errors in processing these malformed messages can lead to allocated memory not being cleaned up. This fix adds bounds checking and cleanup code to the object header continuation message processing. Fixes GitHub issue #2604 - Fixed memory leaks, aborts, and overflows in H5O EFL decode The external file list code could call assert(), read past buffer boundaries, and not properly clean up resources when parsing malformed external data files messages. This fix cleans up allocated memory, adds buffer bounds checks, and converts asserts to HDF5 error checking. Fixes GitHub issue #2605 - Fixed potential heap buffer overflow in decoding of link info message Detections of buffer overflow were added for decoding version, index flags, link creation order value, and the next three addresses. The checkings will remove the potential invalid read of any of these values that could be triggered by a malformed file. Fixes GitHub issue #2603 - Memory leak Memory leak was detected when running h5dump with "pov". The memory was allocated via H5FL__malloc() in hdf5/src/H5FL.c The fuzzed file "pov" was an HDF5 file containing an illegal continuation message. When deserializing the object header chunks for the file, memory is allocated for the array of continuation messages (cont_msg_info->msgs) in continuation message info struct. As error is encountered in loading the illegal message, the memory allocated for cont_msg_info->msgs needs to be freed. Fixes GitHub issue #2599 - Fixed memory leaks that could occur when reading a dataset from a malformed file When attempting to read layout, pline, and efl information for a dataset, memory leaks could occur if attempting to read pline/efl information threw an error, which is due to the memory that was allocated for pline and efl not being properly cleaned up on error. Fixes GitHub issue #2602 - Fixed potential heap buffer overrun in group info header decoding from malformed file H5O__ginfo_decode could sometimes read past allocated memory when parsing a group info message from the header of a malformed file. It now checks buffer size before each read to properly throw an error in these cases. Fixes GitHub issue #2601 - Fixed potential buffer overrun issues in some object header decode routines Several checks were added to H5O__layout_decode and H5O__sdspace_decode to ensure that memory buffers don't get overrun when decoding buffers read from a (possibly corrupted) HDF5 file. - Fixed issues in the Subfiling VFD when using the SELECT_IOC_EVERY_NTH_RANK or SELECT_IOC_TOTAL I/O concentrator selection strategies Multiple bugs involving these I/O concentrator selection strategies were fixed, including: * A bug that caused the selection strategy to be altered when criteria for the strategy was specified in the H5FD_SUBFILING_IOC_SELECTION_CRITERIA environment variable as a single value, rather than in the old and undocumented 'integer:integer' format * Two bugs which caused a request for 'N' I/O concentrators to result in 'N - 1' I/O concentrators being assigned, which also lead to issues if only 1 I/O concentrator was requested Also added a regression test for these two I/O concentrator selection strategies to prevent future issues. - Fixed a heap buffer overflow that occurs when reading from a dataset with a compact layout within a malformed HDF5 file During opening of a dataset that has a compact layout, the library allocates a buffer that stores the dataset's raw data. The dataset's object header that gets written to the file contains information about how large of a buffer the library should allocate. If this object header is malformed such that it causes the library to allocate a buffer that is too small to hold the dataset's raw data, future I/O to the dataset can result in heap buffer overflows. To fix this issue, an extra check is now performed for compact datasets to ensure that the size of the allocated buffer matches the expected size of the dataset's raw data (as calculated from the dataset's dataspace and datatype information). If the two sizes do not match, opening of the dataset will fail. Fixes GitHub issue #2606 - 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. - Fixed an issue with collective metadata writes of global heap data New test failures in parallel netCDF started occurring with debug builds of HDF5 due to an assertion failure and this was reported in GitHub issue #2433. The assertion failure began happening after the collective metadata write pathway in the library was updated to use vector I/O so that parallel-enabled HDF5 Virtual File Drivers (other than the existing MPI I/O VFD) can support collective metadata writes. The assertion failure was fixed by updating collective metadata writes to treat global heap metadata as raw data, as done elsewhere in the library. Fixes GitHub issue #2433 - 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. Fixes GitHub issue #2458 - Fixed buffer overflow error in image decoding function. The error occurred in the function for decoding address from the specified buffer, which is called many times from the function responsible for image decoding. The length of the buffer is known in the image decoding function, but no checks are produced, so the buffer overflow can occur in many places, including callee functions for address decoding. The error was fixed by inserting corresponding checks for buffer overflow. Fixes GitHub issue #2432 Java Library ------------ - Configuration ------------- - Fixed syntax of generator expressions used by CMake Add quotes around the generator expression should allow CMake to correctly parse the expression. Generator expressions are typically parsed after command arguments. If a generator expression contains spaces, new lines, semicolons or other characters that may be interpreted as command argument separators, the whole expression should be surrounded by quotes when passed to a command. Failure to do so may result in the expression being split and it may no longer be recognized as a generator expression. Fixes GitHub issue #2906 - Fixed improper include of Subfiling VFD build directory With the release of the Subfiling Virtual File Driver feature, compiler flags were added to the Autotools build's CPPFLAGS and AM_CPPFLAGS variables to always include the Subfiling VFD source code directory, regardless of whether the VFD is enabled and built or not. These flags are needed because the header files for the VFD contain macros that are assumed to always be available, such as H5FD_SUBFILING_NAME, so the header files are unconditionally included in the HDF5 library. However, these flags are only needed when building HDF5, so they belong in the H5_CPPFLAGS variable instead. Inclusion in the CPPFLAGS and AM_CPPFLAGS variables would export these flags to the h5cc and h5c++ wrapper scripts, as well as the libhdf5.settings file, which would break builds of software that use HDF5 and try to use or parse information out of these files after deleting temporary HDF5 build directories. Fixes GitHub issues #2422 and #2621 - 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. Fixes GitHub issues #1546 and #2259 - Force lowercase Fortran module file names The Cray Fortran compiler uses uppercase Fortran module file names, which caused CMake installs to fail. A compiler option was added to use lowercase instead. Tools ----- - Names of objects with square brackets will have trouble without the special argument, --no-compact-subset, on the h5dump command line. h5diff did not have this option and now it has been added. Fixes GitHub issue #2682 - In the tools traverse function - an error in either visit call will bypass the cleanup of the local data variables. Replaced the H5TOOLS_GOTO_ERROR with just H5TOOLS_ERROR. Fixes GitHub issue #2598 Performance ------------- - Fortran API ----------- - High-Level Library ------------------ - Fortran High-Level APIs ----------------------- - Documentation ------------- - F90 APIs -------- - C++ APIs -------- - Testing ------- - Platforms Tested =================== Linux 5.16.14-200.fc35 GNU gcc (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9) #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9) Fedora35 clang version 13.0.0 (Fedora 13.0.0-3.fc35) (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 5.3.18-150300-cray_shasta_c cray-mpich/8.1.16 #1 SMP x86_64 GNU/Linux Cray clang 14.0.0 (crusher) GCC 11.2.0 (cmake) Linux 4.14.0-115.35.1.1chaos openmpi 4.0.5 #1 SMP aarch64 GNU/Linux GCC 9.2.0 (ARM-build-5) (stria) GCC 7.2.0 (Spack GCC) (cmake) Linux 4.14.0-115.35.1.3chaos spectrum-mpi/rolling-release #1 SMP ppc64le GNU/Linux clang 12.0.1 (vortex) GCC 8.3.1 XL 16.1.1 (cmake) 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-4.12.14-197.99-default cray-mpich/7.7.14 #1 SMP x86_64 GNU/Linux cce 12.0.3 (theta) GCC 11.2.0 llvm 9.0 Intel 19.1.2 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 (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-3.10.0-1160.71.1.1chaos openmpi/4.1 #1 SMP x86_64 GNU/Linux GCC 7.2.0 (skybridge) Intel/19.1 (cmake) Linux-3.10.0-1160.66.1.1chaos openmpi/4.1 #1 SMP x86_64 GNU/Linux GCC 7.2.0 (attaway) Intel/19.1 (cmake) Linux-3.10.0-1160.59.1.1chaos openmpi/4.1 #1 SMP x86_64 GNU/Linux Intel/19.1 (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: Centos6 Version 4.4.7 20120313 (platypus) Version 4.9.3, 5.3.0, 6.2.0 MPICH 3.1.4 compiled with GCC 4.9.3 PGI C, Fortran, C++ for 64-bit target on x86_64; Version 19.10-0 Windows 10 x64 Visual Studio 2015 w/ Intel C/C++/Fortran 18 (cmake) Visual Studio 2017 w/ Intel C/C++/Fortran 19 (cmake) Visual Studio 2019 w/ clang 12.0.0 with MSVC-like command-line (C/C++ only - cmake) Visual Studio 2019 w/ Intel 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 ============== CMake files do not behave correctly with paths containing spaces. Do not use spaces in paths because the required escaping for handling spaces results in very complex and fragile build files. ADB - 2019/05/07 At present, metadata cache images may not be generated by parallel applications. Parallel applications can read files with metadata cache images, but since this is a collective operation, a deadlock is possible if one or more processes do not participate. CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler. The subsetting option in ph5diff currently will fail and should be avoided. The subsetting option works correctly in serial h5diff. Several tests currently fail on certain platforms: MPI_TEST-t_bigio fails with spectrum-mpi on ppc64le platforms. MPI_TEST-t_subfiling_vfd and MPI_TEST_EXAMPLES-ph5_subfiling fail with cray-mpich on theta and with XL compilers on ppc64le platforms. MPI_TEST_testphdf5_tldsc fails with cray-mpich 7.7 on cori and theta. 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 are avoided by not building the gif tool by default. Enable building the High-Level tools with these options: autotools: --enable-hlgiftools cmake: HDF5_BUILD_HL_GIF_TOOLS=ON