HDF5 version 1.10.11-1 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 HDF5-1.10.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 HDF5-1.10.10 - Supported Platforms - Tested Configuration Features Summary - More Tested Platforms - Known Problems - CMake vs. Autotools installations New Features ============ Configuration: ------------- - 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. - 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. Library: -------- - 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 ================================================== - Bug Fixes since HDF5-1.10.10 release =================================== Library ------- - Seg fault on file close h5debug fails at file close with core dump on a file that has an illegal file size in its cache image. In H5F__dest(), the library performs all the closing operations for the file and keeps track of the error encountered when reading the file cache image. At the end of the routine, it frees the file's file structure and returns error. Due to the error return, the file object is not removed from the ID node table. This eventually causes assertion failure in H5F__close_cb() when the library finally exits and tries to access that file object in the table for closing. The closing routine, H5F__dest(), will not free the file structure if there is error, keeping a valid file structure in the ID node table. It will be freed later in H5F__close_cb() when the library exits and terminates the file package. Fix for HDFFV-11052, CVE-2020-10812 - 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 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 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. (BMR - 2023/04/12 GH-2603) - 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 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 - Fix for CVE-2019-8396 Malformed HDF5 files may have truncated content which does not match the expected size. When H5O__pline_decode() attempts to decode these it may read past the end of the allocated space leading to heap overflows as bounds checking is incomplete. The fix ensures each element is within bounds before reading. Fix for Jira issue HDFFV-10712, CVE-2019-8396, GitHub issue #2209 - 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. Fix for GitHub issue #2599 Java Library ------------ - Configuration ------------- - Fixed syntax of generator expressions used by CMake Adding 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 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. Fix for GitHub issue #2682 Performance ------------- - Fortran API ----------- - High-Level Library ------------------ - Fortran High-Level APIs ----------------------- - Documentation ------------- - F90 APIs -------- - C++ APIs -------- - Testing ------- - Platforms Tested =================== Linux 5.13.14-200.fc34 GNU gcc (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1) #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1) Fedora34 clang version 12.0.1 (Fedora 12.0.1-1.fc34) (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 5.8.0-63-generic GNU gcc (GCC) 10.3.0-1ubuntu1 #71-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 10.3.0-1ubuntu1 Ubuntu20.10 Ubuntu clang version 11.0.0-2 (cmake and autotools) Linux 5.3.18-22-default GNU gcc (SUSE Linux) 7.5.0 #1 SMP x86_64 GNU/Linux GNU Fortran (SUSE Linux) 7.5.0 SUSE15sp2 clang version 7.0.1 (tags/RELEASE_701/final 349238) (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 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-4.12.14-197.86-default cray-mpich/7.7.6 # 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 3.10.0-1160.36.2.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 Linux-3.10.0-1127.0.0.1chaos 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 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. Two tests fail attempting collective writes with OpenMPI 3.0.0/GCC-7.2.0-2.29: testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio) t_shapesame (sscontig2) 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