HDF5 version 1.14.1-1 currently under development ================================================================================ INTRODUCTION ============ This document describes the differences between this release and the previous HDF5 release. It contains information on the platforms tested and known 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: ------------- - 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. Parallel Library: ----------------- - Fortran Library: ---------------- - 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 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. - 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 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 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 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 Java Library ------------ - Configuration ------------- - 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 Tools ----- - 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 ============== ************************************************************ * _ * * (_) * * __ ____ _ _ __ _ __ _ _ __ __ _ * * \ \ /\ / / _` | '__| '_ \| | '_ \ / _` | * * \ V V / (_| | | | | | | | | | | (_| | * * \_/\_/ \__,_|_| |_| |_|_|_| |_|\__, | * * __/ | * * |___/ * * * * Please refrain from running any program (including * * HDF5 tests) which uses the subfiling VFD on Perlmutter * * at the National Energy Research Scientific Computing * * Center, NERSC. * * Doing so may cause a system disruption due to subfiling * * crashing Lustre. The sytem's Lustre bug is expected * * to be resolved by 2023. * * * ************************************************************ 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