HDF5 version 1.13.2 released on 2022-08-15 ================================================================================ 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 HDF5-1.13.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 HDF5-1.13.1 - Platforms Tested - Known Problems - CMake vs. Autotools installations New Features ============ Configuration: ------------- - 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) - 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) Library: -------- - Onion VFD The onion VFD allows creating "versioned" HDF5 files. File open/close operations after initial file creation will add changes to an external "onion" file (.onion extension by default) instead of the original file. Each written revision can be opened independently. To open a file with the onion VFD, use the H5Pset_fapl_onion() API call (does not need to be used for the initial creation of the file). The options for the H5FD_onion_fapl_info_t struct are described in H5FDonion.h. The H5FDonion_get_revision_count() API call can be used to query a file to find out how many revisions have been created. (DER - 2022/08/02) - Subfiling VFD The HDF5 Subfiling VFD is a new MPI-based file driver that allows an HDF5 application to distribute an HDF5 file across a collection of "sub-files" in equal-sized data segment "stripes". I/O to the logical HDF5 file is then directed to the appropriate "sub-file" according to the Subfiling configuration and a system of I/O concentrators, which are MPI ranks operating worker threads. By allowing a configurable stripe size, number of I/O concentrators and method for selecting MPI ranks as I/O concentrators, the Subfiling VFD aims to enable an HDF5 application to find a middle ground between the single shared file and file-per-process approaches to parallel file I/O for the particular machine the application is running on. In general, the goal is to avoid some of the complexity of the file-per-process approach while also minimizing the locking issues of the single shared file approach on a parallel file system. Also included with the Subfiling VFD is a new h5fuse.sh script which reads a Subfiling configuration file and then combines the various sub-files back into a single HDF5 file. By default, the h5fuse.sh script looks in the current directory for the Subfiling configuration file, but can also be pointed to the configuration file with a command-line option. The Subfiling VFD can be used by calling H5Pset_fapl_subfiling() on a File Access Property List and using that FAPL for file operations. Note that the Subfiling VFD currently has the following limitations: * Does not currently support HDF5 collective I/O, other than collective metadata writes and reads as set by H5Pset_coll_metadata_write() and H5Pset_all_coll_metadata_ops() * The Subfiling VFD should not currently be used with an HDF5 library that has been built with thread-safety enabled. This can cause deadlocks when failures occur due to interactions between the VFD's internal threads and HDF5's global lock. (JTH - 2022/07/22) Parallel Library: ----------------- - Fortran Library: ---------------- - C++ Library: ------------ - Added two new constructors to H5::H5File class Two new constructors were added to allow opening a file with non-default access property list. Java Library: ------------- - 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 - 2022/07/15) - 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 - 2022/07/15, GitHub #1787) - 1.10 References in containers were not displayed properly by h5dump. Ported 1.10 tools display function to provide ability to inspect and display 1.10 reference data. (ADB - 2022/06/22) High-Level APIs: ---------------- - C Packet Table API: ------------------- - Internal header file: --------------------- - All the #defines named H5FD_CTL__* were renamed to H5FD_CTL_*, i.e. the double underscore was reduced to a single underscore. Documentation: -------------- - Support for new platforms, languages and compilers ================================================== - Bug Fixes since HDF5-1.13.1 release =================================== Library ------- - The offset parameter in H5Dchunk_iter() is now scaled properly In earlier HDF5 1.13.x versions, the chunk offset was not scaled by the chunk dimensions. This offset parameter in the callback now matches that of H5Dget_chunk_info(). (@mkitti - 2022/08/06, GitHub #1419) - 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) Java Library ------------ - Configuration ------------- - Tools ----- - Performance ------------- - Fortran API ----------- - h5open_f and h5close_f fixes * Fixed it so both h5open_f and h5close_f can be called multiple times. * Fixed an issue with open objects remaining after h5close_f was called. * Added additional tests. (MSB, 2022/04/19, HDFFV-11306) 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 5.3.18-24-cray_shasta_c cray-mpich/8.1.12 #1 SMP x86_64 GNU/Linux Cray clang 13.0.0 (spock) AMD clang 13.0.0 GCC 8.2.0, 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 8.0.1, 11.0.1 (lassen) GCC 7.3.1 XL 16.1.1.2 (cmake) Linux-4.12.14-150.75-default cray-mpich/7.7.10 #1 SMP x86_64 GNU/Linux GCC 7.3.0, 8.2.0 (cori) Intel (R) Version 19.0.3.199 (cmake) 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-3.10.0-1160.71.1.1chaos openmpi-4.0.0 #1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1 (quartz) GCC 7.3.0, 8.1.0 Intel 16.0.4, 18.0.2, 19.0.4 (cmake) 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 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. 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 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