HDF5 version 1.14.2 released on 2023-08-11 ================================================================================ 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 HDF5-1.14.1 - Platforms Tested - Known Problems - CMake vs. Autotools installations New Features ============ Configuration: ------------- - Updated HDF5 API tests CMake code to support VOL connectors * Implemented support for fetching, building and testing HDF5 VOL connectors during the library build process and documented the feature under doc/cmake-vols-fetchcontent.md * Implemented the HDF5_TEST_API_INSTALL option that enables installation of the HDF5 API tests on the system Library: -------- - Added support for in-place type conversion in most cases In-place type conversion allows the library to perform type conversion without an intermediate type conversion buffer. This can improve performance by allowing I/O in a single operation over the entire selection instead of being limited by the size of the intermediate buffer. Implemented for I/O on contiguous and chunked datasets when the selection is contiguous in memory and when the memory datatype is not smaller than the file datatype. - Changed selection I/O to be on by default when using the MPIO file driver - Added support for selection I/O in the MPIO file driver Previously, only vector I/O operations were supported. Support for selection I/O should improve performance and reduce memory uses in some cases. - Change the error handling for a not found path in the find plugin process. While attempting to load a plugin the HDF5 library will fail if one of the directories in the plugin paths does not exist, even if there are more paths to check. Instead of exiting the function with an error, just log the error and continue processing the list of paths to check. Parallel Library: ----------------- - Fortran Library: ---------------- - C++ Library: ------------ - Java Library: ------------- - Tools: ------ - High-Level APIs: ---------------- - C Packet Table API: ------------------- - Internal header file: --------------------- - Documentation: -------------- - Support for new platforms, languages and compilers ================================================== - Linux 5.14.21-cray_shasta_c #1 SMP x86_64 GNU/Linux (frontier) Bug Fixes since HDF5-1.14.1 release =================================== Library ------- - Fixed bugs in selection I/O Previously, the library could fail in some cases when performing selection I/O with type conversion. - Fixed CVE-2018-13867 A corrupt file containing an invalid local heap datablock address could trigger an assert failure when the metadata cache attempted to load the datablock from storage. The local heap now verifies that the datablock address is valid when the local heap header information is parsed. - Fixed CVE-2018-11202 A malformed file could result in chunk index memory leaks. Under most conditions (i.e., when the --enable-using-memchecker option is NOT used), this would result in a small memory leak and and infinite loop and abort when shutting down the library. The infinite loop would be due to the "free list" package not being able to clear its resources so the library couldn't shut down. When the "using a memory checker" option is used, the free lists are disabled so there is just a memory leak with no abort on library shutdown. The chunk index resources are now correctly cleaned up when reading misparsed files and valgrind confirms no memory leaks. - Fixed an issue where an assert statement was converted to an incorrect error check statement An assert statement in the library dealing with undefined dataset data fill values was converted to an improper error check that would always trigger when a dataset's fill value was set to NULL (undefined). This has now been fixed. - Fixed an assertion failure when attempting to use the Subfiling IOC VFD directly The Subfiling feature makes use of two Virtual File Drivers, the Subfiling VFD and the IOC (I/O Concentrator) VFD. The two VFDs are intended to be stacked together such that the Subfiling VFD sits "on top" of the IOC VFD and routes I/O requests through it; using the IOC VFD alone is currently unsupported. The IOC VFD has been fixed so that an error message is displayed in this situation rather than causing an assertion failure. - Fixed a potential bug when copying empty enum datatypes Copying an empty enum datatype (including implicitly, as when an enum is a part of a compound datatype) would fail in an assert in debug mode and could fail in release mode depending on how the platform handles undefined behavior regarding size 0 memory allocations and using memcpy with a NULL src pointer. The library is now more careful about using memory operations when copying empty enum datatypes and will not error or raise an assert. - Added an AAPL check to H5Acreate A check was added to H5Acreate to ensure that a failure is correctly returned when an invalid Attribute Access Property List is passed in to the function. The HDF5 API tests were failing for certain build types due to this condition not being checked previously. Java Library ------------ - Fixed switch case 'L' block missing a break statement. The HDF5Array.arrayify method is missing a break statement in the case 'L': section which causes it to fall through and throw an HDF5JavaException when attempting to read an Array[Array[Long]]. The error was fixed by inserting a break statement at the end of the case 'L': sections. Fixes GitHub issue #3056 Configuration ------------- - Fixed a configuration issue that prevented building of the Subfiling VFD on macOS Checks were added to the CMake and Autotools code to verify that CLOCK_MONOTONIC_COARSE, PTHREAD_MUTEX_ADAPTIVE_NP and pthread_condattr_setclock() are available before attempting to use them in Subfiling VFD-related utility code. Without these checks, attempting to build the Subfiling VFD on macOS would fail. Tools ----- - Fixed an issue in h5repack for variable-length typed datasets When repacking datasets into a new file, h5repack tries to determines whether it can use H5Ocopy to copy each dataset into the new file, or if it needs to manually re-create the dataset, then read data from the old dataset and write it to the new dataset. H5repack was previously using H5Ocopy for datasets with variable-length datatypes, but this can be problematic if the global heap addresses involved do not match exactly between the old and new files. These addresses could change for a variety of reasons, such as the command-line options provided to h5repack, how h5repack allocates space in the repacked file, etc. Since H5Ocopy does not currently perform any translation when these addresses change, datasets that were repacked with H5Ocopy could become unreadable in the new file. H5repack has been fixed to repack variable-length typed datasets without using H5Ocopy to ensure that the new datasets always have the correct global heap addresses. Performance ------------- - Fortran API ----------- - High-Level Library ------------------ - Fortran High-Level APIs ----------------------- - Documentation ------------- - F90 APIs -------- - C++ APIs -------- - Testing ------- - Fixed a testing failure in testphdf5 on Cray machines On some Cray machines, what appears to be a bug in Cray MPICH was causing calls to H5Fis_accessible to create a 0-byte file with strange Unix permissions. This was causing an H5Fdelete file deletion test in the testphdf5 program to fail due to a just-deleted HDF5 file appearing to still be accessible on the file system. The issue in Cray MPICH has been worked around for the time being by resetting the MPI_Info object on the File Access Property List used to MPI_INFO_NULL before passing it to the H5Fis_accessible call. - A bug was fixed in the HDF5 API test random datatype generation code A bug in the random datatype generation code could cause test failures when trying to generate an enumeration datatype that has duplicated name/value pairs in it. This has now been fixed. - A bug was fixed in the HDF5 API test VOL connector registration checking code The HDF5 API test code checks to see if the VOL connector specified by the HDF5_VOL_CONNECTOR environment variable (if any) is registered with the library before attempting to run tests with it so that testing can be skipped and an error can be returned when a VOL connector fails to register successfully. Previously, this code didn't account for VOL connectors that specify extra configuration information in the HDF5_VOL_CONNECTOR environment variable and would incorrectly report that the specified VOL connector isn't registered due to including the configuration information as part of the VOL connector name being checked for registration status. This has now been fixed. Platforms Tested =================== Linux 5.19.0-1023-aws GNU gcc, gfortran, g++ #24-Ubuntu SMP x86_64 GNU/Linux (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 Ubuntu 22.04 Ubuntu clang version 14.0.0-1ubuntu1 Intel(R) oneAPI DPC++/C++ Compiler 2023.1.0 ifort (IFORT) 2021.9.0 20230302 (cmake and autotools) 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 5.14.21-cray_shasta_c cray-mpich/8.1.23 #1 SMP x86_64 GNU/Linux cce/15.0.0 (frontier) gcc/12.2.0 (cmake) Linux 5.11.0-34-generic GNU gcc (GCC) 9.4.0-1ubuntu1 #36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.4.0-1ubuntu1 Ubuntu 20.04 Ubuntu clang version 10.0.0-4ubuntu1 Intel(R) oneAPI DPC++/C++ Compiler 2023.1.0 ifort (IFORT) 2021.9.0 20230302 (cmake and autotools) Linux 4.14.0-115.35.1.1chaos aue/openmpi/4.1.4-arm-22.1.0.12 #1 SMP aarch64 GNU/Linux Arm C/C++/Fortran Compiler version 22.1 (stria) (based on LLVM 13.0.1) (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 2021.09.22 (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 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 7.1(Hanzomon) Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers with NAG Fortran Compiler Release 7.1(Hanzomon) MPICH 3.1.4 compiled with GCC 4.9.3 MPICH 3.3 compiled with GCC 7.2.0 OpenMPI 3.1.3 compiled with GCC 7.2.0 and 4.1.2 compiled with GCC 9.1.0 PGI C, Fortran, C++ for 64-bit target on x86_64; Versions 18.4.0 and 19.10-0 NVIDIA nvc, nvfortran and nvc++ 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-3.10.0-1160.90.1.1chaos openmpi/4.1 #1 SMP x86_64 GNU/Linux GCC 7.2.0 (skybridge) Intel/19.1 (cmake) Linux-3.10.0-1160.90.1.1chaos openmpi/4.1 #1 SMP x86_64 GNU/Linux GCC 7.2.0 (attaway) Intel/19.1 (cmake) Linux-3.10.0-1160.90.1.1chaos openmpi-intel/4.1 #1 SMP x86_64 GNU/Linux Intel/19.1.2, 21.3.0 and 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 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 2019 w/ clang 12.0.0 with MSVC-like command-line (C/C++ only - cmake) Visual Studio 2019 w/ Intel C/C++ only 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 2023 (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 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