HDF5 version 1.10.9 released on 2022-05-25 ================================================================================ INTRODUCTION ============ This document describes the differences between this release and the previous HDF5 release in the same series. 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/Software+Changes+from+Release+to+Release+for+HDF5-1.10 Please send any questions or comments to the HDF Help Desk: help@hdfgroup.org CONTENTS ======== - New Features - Support for new platforms and languages - Bug Fixes since HDF5-1.10.8 - Platforms Tested - Known Problems - CMake vs. Autotools installations New Features ============ Configuration: ------------- - 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) - HDF5 memory allocation sanity checking is now off by default for Autotools debug builds HDF5 can be configured to perform sanity checking on internal memory allocations by adding heap canaries to these allocations. However, enabling this option can cause issues with external filter plugins when working with (reallocating/freeing/allocating and passing back) buffers. Previously, this option was off by default for all CMake build types, but only off by default for non-debug Autotools builds. Since debug is the default build mode for HDF5 when built from source with Autotools, this can result in surprising segfaults that don't occur when an application is built against a release version of HDF5. Therefore, this option is now off by default for all build types across both CMake and Autotools. (JTH - 2022/03/01) - Refactored the utils folder. Added subfolder test and moved the 'swmr_check_compat_vfd.c file' from test into utils/test. Deleted the duplicate swmr_check_compat_vfd.c file in hl/tools/h5watch folder. Also fixed vfd check options. (ADB - 2021/10/18) - 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) Library: -------- - Several improvements to parallel compression feature, including: * Improved support for collective I/O (for both writes and reads) * Significant reduction of memory usage for the feature as a whole * Reduction of copying of application data buffers passed to H5Dwrite * Addition of support for incremental file space allocation for filtered datasets created in parallel. Incremental file space allocation is the default for these types of datasets (early file space allocation is also still supported), while early file space allocation is still the default (and only supported allocation time) for unfiltered datasets created in parallel. Incremental file space allocation should help with parallel HDF5 applications that wish to use fill values on filtered datasets, but would typically avoid doing so since dataset creation in parallel would often take an excessive amount of time. Since these datasets previously used early file space allocation, HDF5 would allocate space for and write fill values to every chunk in the dataset at creation time, leading to noticeable overhead. Instead, with incremental file space allocation, allocation of file space for chunks and writing of fill values to those chunks will be delayed until each individual chunk is initially written to. * Addition of support for HDF5's "don't filter partial edge chunks" flag (https://portal.hdfgroup.org/display/HDF5/H5P_SET_CHUNK_OPTS) * Addition of proper support for HDF5 fill values with the feature * Addition of 'H5_HAVE_PARALLEL_FILTERED_WRITES' macro to H5pubconf.h so HDF5 applications can determine at compile-time whether the feature is available * Addition of simple examples (ph5_filtered_writes.c and ph5_filtered_writes_no_sel.c) under examples directory to demonstrate usage of the feature * Improved coverage of regression testing for the feature (JTH - 2022/2/23) Fortran Library: ---------------- - None C++ Library: ------------ - None Java Library: ------------- - None Tools: ------ - h5repack added an optional verbose value for reporting R/W timing. In addition to adding timing capture around the read/write calls in h5repack, added help text to indicate how to show timing for read/write; -v N, --verbose=N Verbose mode, print object information. N - is an integer greater than 1, 2 displays read/write timing (ADB - 2022/04/01) High-Level APIs: ---------------- - None C Packet Table API: ------------------- - None Internal header file: --------------------- - None Documentation: -------------- - None New platforms, languages and compilers tested ================================================== - macOS Apple M1 11.6 Darwin 20.6.0 arm64 with Apple clang version 12.0.5 - Fedora35 Linux 5.16.14-200.fc35 with GCC 11.2.1 and clang version 13.0.0 Bug Fixes since HDF5-1.10.8 release =================================== Library ------- - Fixed a metadata cache bug when resizing a pinned/protected cache entry When resizing a pinned/protected cache entry, the metadata cache code previously would wait until after resizing the entry to attempt to log the newly-dirtied entry. This would cause H5C_resize_entry to mark the entry as dirty and make H5AC_resize_entry think that it doesn't need to add the newly-dirtied entry to the dirty entries skiplist. Thus, a subsequent H5AC__log_moved_entry would think it needs to allocate a new entry for insertion into the dirty entry skip list, since the entry doesn't exist on that list. This causes an assertion failure, as the code to allocate a new entry assumes that the entry is not dirty. (JRM - 2022/02/28) - 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) - Unified handling of collective metadata reads to correctly fix old bugs Due to MPI-related issues occurring in HDF5 from mismanagement of the status of collective metadata reads, they were forced to be disabled during chunked dataset raw data I/O in the HDF5 1.10.5 release. This wouldn't generally have affected application performance because HDF5 already disables collective metadata reads during chunk lookup, since it is generally unlikely that the same chunks will be read by all MPI ranks in the I/O operation. However, this was only a partial solution that wasn't granular enough. This change now unifies the handling of the file-global flag and the API context-level flag for collective metadata reads in order to simplify querying of the true status of collective metadata reads. Thus, collective metadata reads are once again enabled for chunked dataset raw data I/O, but manually controlled at places where some processing occurs on MPI rank 0 only and would cause issues when collective metadata reads are enabled. (JTH - 2021/11/16, HDFFV-10501/HDFFV-10562) - Fixed several potential MPI deadlocks in library failure conditions In the parallel library, there were several places where MPI rank 0 could end up skipping past collective MPI operations when some failure occurs in rank 0-specific processing. This would lead to deadlocks where rank 0 completes an operation while other ranks wait in the collective operation. These places have been rewritten to have rank 0 push an error and try to cleanup after the failure, then continue to participate in the collective operation to the best of its ability. (JTH - 2021/11/09) - Fixed an issue with collective metadata reads being permanently disabled after a dataset chunk lookup operation. This would usually cause a mismatched MPI_Bcast and MPI_ERR_TRUNCATE issue in the library for simple cases of H5Dcreate() -> H5Dwrite() -> H5Dcreate(). (JTH - 2021/11/08, HDFFV-11090) Java Library ------------ - None Configuration ------------- - 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) Tools ----- - None Fortran API ----------- - None High-Level Library ------------------ - Fixed HL_test_packet, test for packet table vlen of vlen. Incorrect length assignment. (ADB - 2021/10/14) Fortran High-Level APIs ----------------------- - None Documentation ------------- - None F90 APIs -------- - None C++ APIs -------- - None Testing ------- - None 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-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 2019.02.07 (cmake) Linux-5.3.18-24.96-default cray-mpich/7.7.19 #1 SMP x86_64 GNU/Linux GCC 8.3.0, 11.2.0 (cori) Intel (R) Version 19.1.3.304 (cmake) Linux-4.12.14-197.86-default cray-mpich/7.7.16 # 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 3.10.0-1160.49.1.1chaos openmpi-intel/4.1 #1 SMP x86_64 GNU/Linux Intel (R) Version 18.0.5, 19.1.2 (chama) 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 Version 10.2.0 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-3.10.0-1160.53.1.1chaos openmpi-4.1.2 #1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1 (quartz) GCC 8.3.1, 10.2.1 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 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 2021(cmake) Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake) Known Problems ============== 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. 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