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bf01a42ab7
We updated these in the 1.14 branch first, so this just brings the changes over to develop.
2157 lines
99 KiB
Plaintext
2157 lines
99 KiB
Plaintext
HDF5 version 1.15.0 currently under development
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================================================================================
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INTRODUCTION
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============
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This document describes the differences between this release and the previous
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HDF5 release. It contains information on the platforms tested and known
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problems in this release. For more details check the HISTORY*.txt files in the
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HDF5 source.
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Note that documentation in the links below will be updated at the time of each
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final release.
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Links to HDF5 documentation can be found on:
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https://portal.hdfgroup.org/documentation/
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The official HDF5 releases can be obtained from:
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https://www.hdfgroup.org/downloads/hdf5/
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Changes from Release to Release and New Features in the HDF5-1.16.x release series
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can be found at:
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https://portal.hdfgroup.org/documentation/hdf5-docs/release_specific_info.html
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If you have any questions or comments, please send them to the HDF Help Desk:
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help@hdfgroup.org
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CONTENTS
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========
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- New Features
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- Support for new platforms and languages
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- Bug Fixes since HDF5-1.14.0
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- Platforms Tested
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- Known Problems
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- CMake vs. Autotools installations
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New Features
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============
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Configuration:
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-------------
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- Added configure options for enabling/disabling non-standard programming
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language features
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* Added a new configuration option that allows enabling or disabling of
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support for features that are extensions to programming languages, such
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as support for the _Float16 datatype:
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CMake: HDF5_ENABLE_NONSTANDARD_FEATURES (ON/OFF) (Default: ON)
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Autotools: --enable-nonstandard-features (yes/no) (Default: yes)
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When this option is enabled, configure time checks are still performed
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to ensure that a feature can be used properly, but these checks may not
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be sufficient when compiler support for a feature is incomplete or broken,
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resulting in library build failures. When set to OFF/no, this option
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provides a way to disable support for all non-standard features to avoid
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these issues. Individual features can still be re-enabled with their
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respective configuration options.
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* Added a new configuration option that allows enabling or disabling of
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support for the _Float16 C datatype:
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CMake: HDF5_ENABLE_NONSTANDARD_FEATURE_FLOAT16 (ON/OFF) (Default: ON)
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Autotools: --enable-nonstandard-feature-float16 (yes/no) (Default: yes)
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While support for the _Float16 C datatype can generally be detected and
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used properly, some compilers have incomplete support for the datatype
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and will pass configure time checks while still failing to build HDF5.
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This option provides a way to disable support for the _Float16 datatype
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when the compiler doesn't have the proper support for it.
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- Deprecate bin/cmakehdf5 script
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With the improvements made in CMake since version 3.23 and the addition
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of CMake preset files, this script is no longer necessary.
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See INSTALL_CMake.txt file, Section X: Using CMakePresets.json for compiling
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- Overhauled LFS support checks
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In 2024, we can assume that Large File Support (LFS) exists on all
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systems we support, though it may require flags to enable it,
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particularly when building 32-bit binaries. The HDF5 source does
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not use any of the 64-bit specific API calls (e.g., ftello64)
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or explicit 64-bit offsets via off64_t.
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Autotools
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* We now use AC_SYS_LARGEFILE to determine how to support LFS. We
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previously used a custom m4 script for this.
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CMake
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* The HDF_ENABLE_LARGE_FILE option (advanced) has been removed
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* We no longer run a test program to determine if LFS works, which
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will help with cross-compiling
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* On Linux we now unilaterally set -D_LARGEFILE_SOURCE and
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-D_FILE_OFFSET_BITS=64, regardless of 32/64 bit system. CMake
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doesn't offer a nice equivalent to AC_SYS_LARGEFILE and since
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those options do nothing on 64-bit systems, this seems safe and
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covers all our bases. We don't set -D_LARGEFILE64_SOURCE since
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we don't use any of the POSIX 64-bit specific API calls like
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ftello64, as noted above.
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* We didn't test for LFS support on non-Linux platforms. We've added
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comments for how LFS should probably be supported on AIX and Solaris,
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which seem to be alive, though uncommon. PRs would be appreciated if
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anyone wishes to test this.
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This overhaul also fixes GitHub #2395, which points out that the LFS flags
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used when building with CMake differ based on whether CMake has been
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run before. The LFS check program that caused this problem no longer exists.
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- The CMake HDF5_ENABLE_DEBUG_H5B option has been removed
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This enabled some additional version-1 B-tree checks. These have been
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removed so the option is no longer necessary.
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This option was CMake-only and marked as advanced.
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- New option for building with static CRT in Windows
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The following option has been added:
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HDF5_BUILD_STATIC_CRT_LIBS "Build With Static Windows CRT Libraries" OFF
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Because our minimum CMake is 3.18, the macro to change runtime flags no longer
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works as CMake changed the default behavior in CMake 3.15.
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Fixes GitHub issue #3984
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- Added support for the new MSVC preprocessor
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Microsoft added support for a new, standards-conformant preprocessor
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to MSVC, which can be enabled with the /Zc:preprocessor option. This
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preprocessor would trip over our HDopen() variadic function-like
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macro, which uses a feature that only works with the legacy preprocessor.
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ifdefs have been added that select the correct HDopen() form and
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allow building HDF5 with the /Zc:preprocessor option.
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The HDopen() macro is located in an internal header file and only
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affects building the HDF5 library from source.
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Fixes GitHub #2515
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- Renamed HDF5_ENABLE_USING_MEMCHECKER to HDF5_USING_ANALYSIS_TOOL
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The HDF5_USING_ANALYSIS_TOOL is used to indicate to test macros that
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an analysis tool is being used and that the tests should not use
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the runTest.cmake macros and it's variations. The analysis tools,
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like valgrind, test the macro code instead of the program under test.
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HDF5_ENABLE_USING_MEMCHECKER is still used for controlling the HDF5
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define, H5_USING_MEMCHECKER.
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- New option for building and naming tools in CMake
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The following option has been added:
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HDF5_BUILD_STATIC_TOOLS "Build Static Tools Not Shared Tools" OFF
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The default will build shared tools unless BUILD_SHARED_LIBS = OFF.
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Tools will no longer have "-shared" as only one set of tools will be created.
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- Incorporated HDF5 examples repository into HDF5 library.
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The HDF5Examples folder is equivalent to the hdf5-examples repository.
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This enables building and testing the examples
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during the library build process or after the library has been installed.
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Previously, the hdf5-examples archives were downloaded
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for packaging with the library. Now the examples can be built
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and tested without a packaged install of the library.
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However, to maintain the ability to use the HDF5Examples with an installed
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library, it is necessary to map the option names used by the library
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to those used by the examples. The typical pattern is:
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<example option> = <library option>
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HDF_BUILD_FORTRAN = ${HDF5_BUILD_FORTRAN}
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- Added new option for CMake to mark tests as SKIPPED.
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HDF5_DISABLE_TESTS_REGEX is a REGEX string that will be checked with
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test names and if there is a match then that test's property will be
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set to DISABLED. HDF5_DISABLE_TESTS_REGEX can be initialized on the
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command line: "-DHDF5_DISABLE_TESTS_REGEX:STRING=<regex>"
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See CMake documentation for regex-specification.
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- Added defaults to CMake for long double conversion checks
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HDF5 performs a couple of checks at build time to see if long double
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values can be converted correctly (IBM's Power architecture uses a
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special format for long doubles). These checks were performed using
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TRY_RUN, which is a problem when cross-compiling.
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These checks now use default values appropriate for most non-Power
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systems when cross-compiling. The cache values can be pre-set if
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necessary, which will preempt both the TRY_RUN and the default.
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Affected values:
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H5_LDOUBLE_TO_LONG_SPECIAL (default no)
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H5_LONG_TO_LDOUBLE_SPECIAL (default no)
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H5_LDOUBLE_TO_LLONG_ACCURATE (default yes)
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H5_LLONG_TO_LDOUBLE_CORRECT (default yes)
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H5_DISABLE_SOME_LDOUBLE_CONV (default no)
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Fixes GitHub #3585
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- Improved support for Intel oneAPI
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* Separates the old 'classic' Intel compiler settings and warnings
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from the oneAPI settings
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* Uses `-check nouninit` in debug builds to avoid false positives
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when building H5_buildiface with `-check all`
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* Both Autotools and CMake
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- Added new options for CMake and Autotools to control the Doxygen
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warnings as errors setting.
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* HDF5_ENABLE_DOXY_WARNINGS: ON/OFF (Default: ON)
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* --enable-doxygen-errors: enable/disable (Default: enable)
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The default will fail compile if the doxygen parsing generates warnings.
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The option can be disabled if certain versions of doxygen have parsing
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issues. i.e. 1.9.5, 1.9.8.
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Addresses GitHub issue #3398
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- Added support for AOCC and classic Flang w/ the Autotools
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* Adds a config/clang-fflags options file to support Flang
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* Corrects missing "-Wl," from linker options in the libtool wrappers
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when using Flang, the MPI Fortran compiler wrappers, and building
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the shared library. This would often result in unrecognized options
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like -soname.
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* Enable -nomp w/ Flang to avoid linking to the OpenMPI library.
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CMake can build the parallel, shared library w/ Fortran using AOCC
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and Flang, so no changes were needed for that build system.
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Fixes GitHub issues #3439, #1588, #366, #280
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- Converted the build of libaec and zlib to use FETCH_CONTENT with CMake.
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Using the CMake FetchContent module, the external filters can populate
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content at configure time via any method supported by the ExternalProject
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module. Whereas ExternalProject_Add() downloads at build time, the
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FetchContent module makes content available immediately, allowing the
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configure step to use the content in commands like add_subdirectory(),
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include() or file() operations.
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Removed HDF options for using FETCH_CONTENT explicitly:
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BUILD_SZIP_WITH_FETCHCONTENT:BOOL
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BUILD_ZLIB_WITH_FETCHCONTENT:BOOL
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- Thread-safety + static library disabled on Windows w/ CMake
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The thread-safety feature requires hooks in DllMain(), which is only
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present in the shared library.
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We previously just warned about this, but now any CMake configuration
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that tries to build thread-safety and the static library will fail.
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This cannot be overridden with ALLOW_UNSUPPORTED.
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Fixes GitHub issue #3613
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- Autotools builds now build the szip filter by default when an appropriate
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library is found
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Since libaec is prevalent and BSD-licensed for both encoding and
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decoding, we build the szip filter by default now.
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Both autotools and CMake build systems will process the szip filter the same as
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the zlib filter is processed.
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- Removed CMake cross-compiling variables
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* HDF5_USE_PREGEN
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* HDF5_BATCH_H5DETECT
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These were used to work around H5detect and H5make_libsettings and
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are no longer required.
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- Running H5make_libsettings is no longer required for cross-compiling
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The functionality of H5make_libsettings is now handled via template files,
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so H5make_libsettings has been removed.
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- Running H5detect is no longer required for cross-compiling
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The functionality of H5detect is now exercised at library startup,
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so H5detect has been removed.
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- Updated HDF5 API tests CMake code to support VOL connectors
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* Implemented support for fetching, building and testing HDF5
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VOL connectors during the library build process and documented
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the feature under doc/cmake-vols-fetchcontent.md
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* Implemented the HDF5_TEST_API_INSTALL option that enables
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installation of the HDF5 API tests on the system
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- Added new CMake options for building and running HDF5 API tests
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(Experimental)
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HDF5 API tests are an experimental feature, primarily targeted
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toward HDF5 VOL connector authors, that is currently being developed.
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These tests exercise the HDF5 API and are being integrated back
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into the HDF5 library from the HDF5 VOL tests repository
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(https://github.com/HDFGroup/vol-tests). To support this feature,
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the following new options have been added to CMake:
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* HDF5_TEST_API: ON/OFF (Default: OFF)
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Controls whether the HDF5 API tests will be built. These tests
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will only be run during testing of HDF5 if the HDF5_TEST_SERIAL
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(for serial tests) and HDF5_TEST_PARALLEL (for parallel tests)
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options are enabled.
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* HDF5_TEST_API_INSTALL: ON/OFF (Default: OFF)
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Controls whether the HDF5 API test executables will be installed
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on the system alongside the HDF5 library. This option is currently
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not functional.
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* HDF5_TEST_API_ENABLE_ASYNC: ON/OFF (Default: OFF)
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Controls whether the HDF5 Async API tests will be built. These
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tests will only be run if the VOL connector used supports Async
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operations.
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* HDF5_TEST_API_ENABLE_DRIVER: ON/OFF (Default: OFF)
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Controls whether to build the HDF5 API test driver program. This
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test driver program is useful for VOL connectors that use a
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client/server model where the server needs to be up and running
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before the VOL connector can function. This option is currently
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not functional.
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* HDF5_TEST_API_SERVER: String (Default: "")
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Used to specify a path to the server executable that the test
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driver program should execute.
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- Added support for CMake presets file.
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CMake supports two main files, CMakePresets.json and CMakeUserPresets.json,
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that allow users to specify common configure options and share them with others.
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HDF added a CMakePresets.json file of a typical configuration and support
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file, config/cmake-presets/hidden-presets.json.
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Also added a section to INSTALL_CMake.txt with very basic explanation of the
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process to use CMakePresets.
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- Deprecated and removed old SZIP library in favor of LIBAEC library
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LIBAEC library has been used in HDF5 binaries as the szip library of choice
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for a few years. We are removing the options for using the old SZIP library.
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Also removed the config/cmake/FindSZIP.cmake file.
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- Enabled instrumentation of the library by default in CMake for parallel
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debug builds
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HDF5 can be configured to instrument portions of the parallel library to
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aid in debugging. Autotools builds of HDF5 turn this capability on by
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default for parallel debug builds and off by default for other build types.
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CMake has been updated to match this behavior.
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- Added new option to build libaec and zlib inline with CMake.
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Using the CMake FetchContent module, the external filters can populate
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content at configure time via any method supported by the ExternalProject
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module. Whereas ExternalProject_Add() downloads at build time, the
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FetchContent module makes content available immediately, allowing the
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configure step to use the content in commands like add_subdirectory(),
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include() or file() operations.
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The HDF options (and defaults) for using this are:
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BUILD_SZIP_WITH_FETCHCONTENT:BOOL=OFF
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LIBAEC_USE_LOCALCONTENT:BOOL=OFF
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BUILD_ZLIB_WITH_FETCHCONTENT:BOOL=OFF
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ZLIB_USE_LOCALCONTENT:BOOL=OFF
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The CMake variables to control the path and file names:
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LIBAEC_TGZ_ORIGPATH:STRING
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LIBAEC_TGZ_ORIGNAME:STRING
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ZLIB_TGZ_ORIGPATH:STRING
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ZLIB_TGZ_ORIGNAME:STRING
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See the CMakeFilters.cmake and config/cmake/cacheinit.cmake files for usage.
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- Added the CMake variable HDF5_ENABLE_ROS3_VFD to the HDF5 CMake config
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file hdf5-config.cmake. This allows to easily detect if the library
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has been built with or without read-only S3 functionality.
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Library:
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--------
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- Relaxed behavior of H5Pset_page_buffer_size() when opening files
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This API call sets the size of a file's page buffer cache. This call
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was extremely strict about matching its parameters to the file strategy
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and page size used to create the file, requiring a separate open of the
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file to obtain these parameters.
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These requirements have been relaxed when using the fapl to open
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a previously-created file:
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* When opening a file that does not use the H5F_FSPACE_STRATEGY_PAGE
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strategy, the setting is ignored and the file will be opened, but
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without a page buffer cache. This was previously an error.
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* When opening a file that has a page size larger than the desired
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page buffer cache size, the page buffer cache size will be increased
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to the file's page size. This was previously an error.
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The behavior when creating a file using H5Pset_page_buffer_size() is
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unchanged.
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Fixes GitHub issue #3382
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- Added support for _Float16 16-bit half-precision floating-point datatype
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Support for the _Float16 C datatype has been added on platforms where:
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- The _Float16 datatype and its associated macros (FLT16_MIN, FLT16_MAX,
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FLT16_EPSILON, etc.) are available
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- A simple test program that converts between the _Float16 datatype and
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other datatypes with casts can be successfully compiled and run at
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configure time. Some compilers appear to be buggy or feature-incomplete
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in this regard and will generate calls to compiler-internal functions
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for converting between the _Float16 datatype and other datatypes, but
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will not link these functions into the build, resulting in build
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failures.
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The following new macros have been added:
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H5_HAVE__FLOAT16 - This macro is defined in H5pubconf.h and will have
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the value 1 if support for the _Float16 datatype is
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available. It will not be defined otherwise.
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H5_SIZEOF__FLOAT16 - This macro is defined in H5pubconf.h and will have
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a value corresponding to the size of the _Float16
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datatype, as computed by sizeof(). It will have the
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value 0 if support for the _Float16 datatype is not
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available.
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H5_HAVE_FABSF16 - This macro is defined in H5pubconf.h and will have the
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value 1 if the fabsf16 function is available for use.
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H5_LDOUBLE_TO_FLOAT16_CORRECT - This macro is defined in H5pubconf.h and
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will have the value 1 if the platform can
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correctly convert long double values to
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_Float16. Some compilers have issues with
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this.
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H5T_NATIVE_FLOAT16 - This macro maps to the ID of an HDF5 datatype representing
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the native C _Float16 datatype for the platform. If
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support for the _Float16 datatype is not available, the
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macro will map to H5I_INVALID_HID and should not be used.
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H5T_IEEE_F16BE - This macro maps to the ID of an HDF5 datatype representing
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a big-endian IEEE 754 16-bit floating-point datatype. This
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datatype is available regardless of whether _Float16 support
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is available or not.
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H5T_IEEE_F16LE - This macro maps to the ID of an HDF5 datatype representing
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a little-endian IEEE 754 16-bit floating-point datatype.
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This datatype is available regardless of whether _Float16
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support is available or not.
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The following new hard datatype conversion paths have been added, but
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will only be used when _Float16 support is available:
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|
|
H5T_NATIVE_SCHAR <-> H5T_NATIVE_FLOAT16 | H5T_NATIVE_UCHAR <-> H5T_NATIVE_FLOAT16
|
|
H5T_NATIVE_SHORT <-> H5T_NATIVE_FLOAT16 | H5T_NATIVE_USHORT <-> H5T_NATIVE_FLOAT16
|
|
H5T_NATIVE_INT <-> H5T_NATIVE_FLOAT16 | H5T_NATIVE_UINT <-> H5T_NATIVE_FLOAT16
|
|
H5T_NATIVE_LONG <-> H5T_NATIVE_FLOAT16 | H5T_NATIVE_ULONG <-> H5T_NATIVE_FLOAT16
|
|
H5T_NATIVE_LLONG <-> H5T_NATIVE_FLOAT16 | H5T_NATIVE_ULLONG <-> H5T_NATIVE_FLOAT16
|
|
H5T_NATIVE_FLOAT <-> H5T_NATIVE_FLOAT16 | H5T_NATIVE_DOUBLE <-> H5T_NATIVE_FLOAT16
|
|
H5T_NATIVE_LDOUBLE <-> H5T_NATIVE_FLOAT16
|
|
|
|
The H5T_NATIVE_LDOUBLE -> H5T_NATIVE_FLOAT16 hard conversion path will only
|
|
be available and used if H5_LDOUBLE_TO_FLOAT16_CORRECT has a value of 1. Otherwise,
|
|
the conversion will be emulated in software by the library.
|
|
|
|
Note that in the absence of any compiler flags for architecture-specific
|
|
tuning, the generated code for datatype conversions with the _Float16 type
|
|
may perform conversions by first promoting the type to float. Use of
|
|
architecture-specific tuning compiler flags may instead allow for the
|
|
generation of specialized instructions, such as AVX512-FP16 instructions,
|
|
if available.
|
|
|
|
- Made several improvements to the datatype conversion code
|
|
|
|
* The datatype conversion code was refactored to use pointers to
|
|
H5T_t datatype structures internally rather than IDs wrapping
|
|
the pointers to those structures. These IDs are needed if an
|
|
application-registered conversion function or conversion exception
|
|
function are involved during the conversion process. For simplicity,
|
|
the conversion code simply passed these IDs down and let the internal
|
|
code unwrap the IDs as necessary when needing to access the wrapped
|
|
H5T_t structures. However, this could cause a significant amount of
|
|
repeated ID lookups for compound datatypes and other container-like
|
|
datatypes. The code now passes down pointers to the datatype
|
|
structures and only creates IDs to wrap those pointers as necessary.
|
|
Quick testing showed an average ~3x to ~10x improvement in performance
|
|
of conversions on container-like datatypes, depending on the
|
|
complexity of the datatype.
|
|
|
|
* A conversion "context" structure was added to hold information about
|
|
the current conversion being performed. This allows conversions on
|
|
container-like datatypes to be optimized better by skipping certain
|
|
portions of the conversion process that remain relatively constant
|
|
when multiple elements of the container-like datatype are being
|
|
converted.
|
|
|
|
* After refactoring the datatype conversion code to use pointers
|
|
internally rather than IDs, several copies of datatypes that were
|
|
made by higher levels of the library were able to be removed. The
|
|
internal IDs that were previously registered to wrap those copied
|
|
datatypes were also able to be removed.
|
|
|
|
- Implemented optimized support for vector I/O in the Subfiling VFD
|
|
|
|
Previously, the Subfiling VFD would handle vector I/O requests by
|
|
breaking them down into individual I/O requests, one for each entry
|
|
in the I/O vectors provided. This could result in poor I/O performance
|
|
for features in HDF5 that utilize vector I/O, such as parallel I/O
|
|
to filtered datasets. The Subfiling VFD now properly handles vector
|
|
I/O requests in their entirety, resulting in fewer I/O calls, improved
|
|
vector I/O performance and improved vector I/O memory efficiency.
|
|
|
|
- Added a simple cache to the read-only S3 (ros3) VFD
|
|
|
|
The read-only S3 VFD now caches the first N bytes of a file stored
|
|
in S3 to avoid a lot of small I/O operations when opening files.
|
|
This cache is per-file and created when the file is opened.
|
|
|
|
N is currently 16 MiB or the size of the file, whichever is smaller.
|
|
|
|
Addresses GitHub issue #3381
|
|
|
|
- Added new API function H5Pget_actual_selection_io_mode()
|
|
|
|
This function allows the user to determine if the library performed
|
|
selection I/O, vector I/O, or scalar (legacy) I/O during the last HDF5
|
|
operation performed with the provided DXPL.
|
|
|
|
- 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.
|
|
|
|
- Changed 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 logged the error
|
|
and continue processing the list of paths to check.
|
|
|
|
- Implemented support for temporary security credentials for the Read-Only
|
|
S3 (ROS3) file driver.
|
|
|
|
When using temporary security credentials, one also needs to specify a
|
|
session/security token next to the access key id and secret access key.
|
|
This token can be specified by the new API function H5Pset_fapl_ros3_token().
|
|
The API function H5Pget_fapl_ros3_token() can be used to retrieve
|
|
the currently set token.
|
|
|
|
- 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.
|
|
|
|
- Added H5Pset_selection_io(), H5Pget_selection_io(), and
|
|
H5Pget_no_selection_io_cause() API functions to manage the selection I/O
|
|
feature. This can be used to enable collective I/O with type conversion,
|
|
or it can be used with custom VFDs that support vector or selection I/O.
|
|
|
|
- Added H5Pset_modify_write_buf() and H5Pget_modify_write_buf() API
|
|
functions to allow the library to modify the contents of write buffers, in
|
|
order to avoid malloc/memcpy. Currently only used for type conversion
|
|
with selection I/O.
|
|
|
|
|
|
Parallel Library:
|
|
-----------------
|
|
- Added optimized support for the parallel compression feature when
|
|
using the multi-dataset I/O API routines collectively
|
|
|
|
Previously, calling H5Dwrite_multi/H5Dread_multi collectively in parallel
|
|
with a list containing one or more filtered datasets would cause HDF5 to
|
|
break out of the optimized multi-dataset I/O mode and instead perform I/O
|
|
by looping over each dataset in the I/O request. The library has now been
|
|
updated to perform I/O in a more optimized manner in this case by first
|
|
performing I/O on all the filtered datasets at once and then performing
|
|
I/O on all the unfiltered datasets at once.
|
|
|
|
- Changed H5Pset_evict_on_close so that it can be called with a parallel
|
|
build of HDF5
|
|
|
|
Previously, H5Pset_evict_on_close would always fail when called from a
|
|
parallel build of HDF5, stating that the feature is not supported with
|
|
parallel HDF5. This failure would occur even if a parallel build of HDF5
|
|
was used with a serial HDF5 application. H5Pset_evict_on_close can now
|
|
be called regardless of the library build type and the library will
|
|
instead fail during H5Fcreate/H5Fopen if the "evict on close" property
|
|
has been set to true and the file is being opened for parallel access
|
|
with more than 1 MPI process.
|
|
|
|
|
|
Fortran Library:
|
|
----------------
|
|
|
|
- Added Fortran H5E APIs:
|
|
h5eregister_class_f, h5eunregister_class_f, h5ecreate_msg_f, h5eclose_msg_f
|
|
h5eget_msg_f, h5epush_f, h5eget_num_f, h5ewalk_f, h5eget_class_name_f,
|
|
h5eappend_stack_f, h5eget_current_stack_f, h5eset_current_stack_f, h5ecreate_stack_f,
|
|
h5eclose_stack_f, h5epop_f, h5eprint_f (C h5eprint v2 signature)
|
|
|
|
- Added API support for Fortran MPI_F08 module definitions:
|
|
Adds support for MPI's MPI_F08 module datatypes: type(MPI_COMM) and type(MPI_INFO) for HDF5 APIs:
|
|
H5PSET_FAPL_MPIO_F, H5PGET_FAPL_MPIO_F, H5PSET_MPI_PARAMS_F, H5PGET_MPI_PARAMS_F
|
|
Ref. #3951
|
|
|
|
- Added Fortran APIs:
|
|
H5FGET_INTENT_F, H5SSEL_ITER_CREATE_F, H5SSEL_ITER_GET_SEQ_LIST_F,
|
|
H5SSEL_ITER_CLOSE_F, H5S_mp_H5SSEL_ITER_RESET_F
|
|
|
|
- Added Fortran Parameters:
|
|
H5S_SEL_ITER_GET_SEQ_LIST_SORTED_F, H5S_SEL_ITER_SHARE_WITH_DATASPACE_F
|
|
|
|
- Added Fortran Parameters:
|
|
H5S_BLOCK_F and H5S_PLIST_F
|
|
|
|
- The configuration definitions file, H5config_f.inc, is now installed
|
|
and the HDF5 version number has been added to it.
|
|
|
|
- Added Fortran APIs:
|
|
h5fdelete_f
|
|
|
|
- Added Fortran APIs:
|
|
h5vlnative_addr_to_token_f and h5vlnative_token_to_address_f
|
|
|
|
- Fixed an uninitialized error return value for hdferr
|
|
to return the error state of the h5aopen_by_idx_f API.
|
|
|
|
- Added h5pget_vol_cap_flags_f and related Fortran VOL
|
|
capability definitions.
|
|
|
|
- Fortran async APIs H5A, H5D, H5ES, H5G, H5F, H5L and H5O were added.
|
|
|
|
- Added Fortran APIs:
|
|
h5pset_selection_io_f, h5pget_selection_io_f,
|
|
h5pget_actual_selection_io_mode_f,
|
|
h5pset_modify_write_buf_f, h5pget_modify_write_buf_f
|
|
|
|
- Added Fortran APIs:
|
|
h5get_free_list_sizes_f, h5dwrite_chunk_f, h5dread_chunk_f,
|
|
h5fget_info_f, h5lvisit_f, h5lvisit_by_name_f,
|
|
h5pget_no_selection_io_cause_f, h5pget_mpio_no_collective_cause_f,
|
|
h5sselect_shape_same_f, h5sselect_intersect_block_f,
|
|
h5pget_file_space_page_size_f, h5pset_file_space_page_size_f,
|
|
h5pget_file_space_strategy_f, h5pset_file_space_strategy_f
|
|
|
|
- Removed "-commons" linking option on Darwin, as COMMON and EQUIVALENCE
|
|
are no longer used in the Fortran source.
|
|
|
|
Fixes GitHub issue #3571
|
|
|
|
C++ Library:
|
|
------------
|
|
-
|
|
|
|
|
|
Java Library:
|
|
-------------
|
|
-
|
|
|
|
|
|
Tools:
|
|
------
|
|
-
|
|
|
|
|
|
High-Level APIs:
|
|
----------------
|
|
- Added Fortran HL API: h5doappend_f
|
|
|
|
|
|
C Packet Table API:
|
|
-------------------
|
|
-
|
|
|
|
|
|
Internal header file:
|
|
---------------------
|
|
-
|
|
|
|
|
|
Documentation:
|
|
--------------
|
|
-
|
|
|
|
|
|
Support for new platforms, languages and compilers
|
|
==================================================
|
|
-
|
|
|
|
Bug Fixes since HDF5-1.14.0 release
|
|
===================================
|
|
Configuration:
|
|
-------------
|
|
- Fix Autotools -Werror cleanup
|
|
|
|
The Autotools temporarily scrub -Werror(=whatever) from CFLAGS, etc.
|
|
so configure checks don't trip over warnings generated by configure
|
|
check programs. The sed line originally only scrubbed -Werror but not
|
|
-Werror=something, which would cause errors when the '=something' was
|
|
left behind in CFLAGS.
|
|
|
|
The sed line has been updated to handle -Werror=something lines.
|
|
|
|
Fixes one issue raised in #3872
|
|
|
|
Library
|
|
-------
|
|
- Fixed many (future) CVE issues
|
|
|
|
A partner organization corrected many potential security issues, which
|
|
were fixed and reported to us before submission to MITRE. These do
|
|
not have formal CVE issues assigned to them yet, so the numbers assigned
|
|
here are just placeholders. We will update the HDF5 1.14 CVE list (link
|
|
below) when official MITRE CVE tracking numbers are assigned.
|
|
|
|
These CVE issues are generally of the same form as other reported HDF5
|
|
CVE issues, and rely on the library failing while attempting to read
|
|
a malformed file. Most of them cause the library to segfault and will
|
|
probably be assigned "medium (~5/10)" scores by NIST, like the other
|
|
HDF5 CVE issues.
|
|
|
|
The issues that were reported to us have all been fixed in this release,
|
|
so HDF5 will continue to have no unfixed public CVE issues.
|
|
|
|
NOTE: HDF5 versions earlier than 1.14.4 should be considered vulnerable
|
|
to these issues and users should upgrade to 1.14.4 as soon as
|
|
possible. Note that it's possible to build the 1.14 library with
|
|
HDF5 1.8, 1.10, etc. API bindings for people who wish to enjoy
|
|
the benefits of a more secure library but don't want to upgrade
|
|
to the latest API. We will not be bringing the CVE fixes to earlier
|
|
versions of the library (they are no longer supported).
|
|
|
|
LIST OF CVE ISSUES FIXED IN THIS RELEASE:
|
|
|
|
* CVE-2024-0116-001
|
|
HDF5 library versions <=1.14.3 contain a heap buffer overflow in
|
|
H5D__scatter_mem resulting in causing denial of service or potential
|
|
code execution
|
|
|
|
* CVE-2024-0112-001
|
|
HDF5 library versions <=1.14.3 contain a heap buffer overflow in
|
|
H5S__point_deserialize resulting in the corruption of the
|
|
instruction pointer and causing denial of service or potential code
|
|
execution
|
|
|
|
* CVE-2024-0111-001
|
|
HDF5 library versions <=1.14.3 contain a heap buffer overflow in
|
|
H5T__conv_struct_opt resulting in causing denial of service or
|
|
potential code execution
|
|
|
|
* CVE-2023-1208-002
|
|
HDF5 library versions <=1.14.3 contain a heap buffer overflow in
|
|
H5O__mtime_new_encode resulting in the corruption of the instruction
|
|
pointer and causing denial of service or potential code execution
|
|
|
|
* CVE-2023-1208-001
|
|
HDF5 library versions <=1.14.3 contain a heap buffer overflow in
|
|
H5O__layout_encode resulting in the corruption of the instruction
|
|
pointer and causing denial of service or potential code execution
|
|
|
|
* CVE-2023-1207-001
|
|
HDF5 library versions <=1.14.3 contain a heap buffer overflow in
|
|
H5O__dtype_encode_helper causing denial of service or potential
|
|
code execution
|
|
|
|
* CVE-2023-1205-001
|
|
HDF5 library versions <=1.14.3 contain a heap buffer overflow in
|
|
H5VM_array_fill resulting in the corruption of the instruction
|
|
pointer and causing denial of service or potential code execution
|
|
|
|
* CVE-2023-1202-002
|
|
HDF5 library versions <=1.14.3 contain a heap buffer overflow in
|
|
H5T__get_native_type resulting in the corruption of the instruction
|
|
pointer and causing denial of service or potential code execution
|
|
|
|
* CVE-2023-1202-001
|
|
HDF5 library versions <=1.14.3 contain a heap buffer overflow in
|
|
H5T__ref_mem_setnull resulting in the corruption of the instruction
|
|
pointer and causing denial of service or potential code execution
|
|
|
|
* CVE-2023-1130-001
|
|
HDF5 library versions <=1.14.3 contain a heap buffer overflow in
|
|
H5T_copy_reopen resulting in the corruption of the instruction
|
|
pointer and causing denial of service or potential code execution
|
|
|
|
* CVE-2023-1125-001
|
|
HDF5 versions <= 1.14.3 contain a heap buffer overflow in
|
|
H5Z__nbit_decompress_one_byte caused by the earlier use of an
|
|
initialized pointer. This may result in Denial of Service or
|
|
potential code execution
|
|
|
|
* CVE-2023-1114-001
|
|
HDF5 library versions <=1.14.3 contain a heap buffer overflow in
|
|
H5HG_read resulting in the corruption of the instruction pointer
|
|
and causing denial of service or potential code execution
|
|
|
|
* CVE-2023-1113-002
|
|
HDF5 library versions <=1.14.3 contain a heap buffer overflow in
|
|
H5F_addr_decode_len resulting in the corruption of the instruction
|
|
pointer and causing denial of service or potential code execution
|
|
|
|
* CVE-2023-1113-001
|
|
HDF5 versions <= 1.14.3 contain a heap buffer overflow caused by
|
|
the unsafe use of strdup in H5MM_xstrdup, resulting in denial of
|
|
service or potential code execution
|
|
|
|
* CVE-2023-1108-001
|
|
HDF5 versions <= 1.14.3 contain a out-of-bounds read operation in
|
|
H5FL_arr_malloc resulting in denial of service or potential code
|
|
execution
|
|
|
|
* CVE-2023-1104-004
|
|
HDF5 versions <= 1.14.3 contain a out-of-bounds read operation in
|
|
H5T_close_real resulting in denial of service or potential code
|
|
execution
|
|
|
|
* CVE-2023-1104-003
|
|
HDF5 library versions <=1.14.3 contain a heap buffer overflow flaw
|
|
in the function H5HL__fl_deserialize resulting in denial of service
|
|
or potential code execution
|
|
|
|
* CVE-2023-1104-002
|
|
HDF5 library versions <=1.14.3 contain a heap buffer overflow in
|
|
H5HL__fl_deserialize resulting in the corruption of the instruction
|
|
pointer and causing denial of service or potential code execution
|
|
|
|
* CVE-2023-1104-001
|
|
HDF5 library versions <=1.14.3 contains a stack overflow in the
|
|
function H5E_printf_stack resulting in denial of service or
|
|
potential code execution
|
|
|
|
* CVE-2023-1023-001
|
|
HDF5 library versions <=1.14.3 heap buffer overflow in
|
|
H5VM_memcpyvv which may result in denial of service or code
|
|
execution
|
|
|
|
* CVE-2023-1019-001
|
|
HDF5 library versions <=1.14.3 contain a stack buffer overflow in
|
|
H5VM_memcpyvv resulting in the corruption of the instruction
|
|
pointer and causing denial of service or potential code execution
|
|
|
|
* CVE-2023-1018-001
|
|
HDF5 library versions <=1.14.3 contain a memory corruption in
|
|
H5A__close resulting in the corruption of the instruction pointer
|
|
and causing denial of service or potential code execution
|
|
|
|
* CVE-2023-1017-002
|
|
HDF5 library versions <=1.14.3 may use an uninitialized value
|
|
H5A__attr_release_table resulting in denial of service
|
|
|
|
* CVE-2023-1017-001
|
|
HDF5 library versions <=1.14.3 may attempt to dereference
|
|
uninitialized values in h5tools_str_sprint, which will lead to
|
|
denial of service
|
|
|
|
* CVE-2023-1013-004
|
|
HDF5 versions <= 1.13.3 contain a stack buffer overflow in
|
|
H5HG_read resulting in denial of service or potential code
|
|
execution
|
|
|
|
* CVE-2023-1013-003
|
|
HDF5 library versions <=1.14.3 contain a buffer overrun in
|
|
H5Z__filter_fletcher32 resulting in the corruption of the
|
|
instruction pointer and causing denial of service or potential
|
|
code execution
|
|
|
|
* CVE-2023-1013-002
|
|
HDF5 library versions <=1.14.3 contain a buffer overrun in
|
|
H5O__linfo_decode resulting in the corruption of the instruction
|
|
pointer and causing denial of service or potential code execution
|
|
|
|
* CVE-2023-1013-001
|
|
HDF5 library versions <=1.14.3 contain a buffer overrun in
|
|
H5Z__filter_scaleoffset resulting in the corruption of the
|
|
instruction pointer and causing denial of service or potential
|
|
code execution
|
|
|
|
* CVE-2023-1012-001
|
|
HDF5 library versions <=1.14.3 contain a stack buffer overflow in
|
|
H5R__decode_heap resulting in the corruption of the instruction
|
|
pointer and causing denial of service or potential code execution
|
|
|
|
* CVE-2023-1010-001
|
|
HDF5 library versions <=1.14.3 contain a stack buffer overflow in
|
|
H5FL_arr_malloc resulting in the corruption of the instruction
|
|
pointer and causing denial of service or potential code execution
|
|
|
|
* CVE-2023-1009-001
|
|
HDF5 library versions <=1.14.3 contain a stack buffer overflow in
|
|
H5FL_arr_malloc resulting in the corruption of the instruction
|
|
pointer and causing denial of service or potential code execution
|
|
|
|
* CVE-2023-1006-004
|
|
HDF5 library versions <=1.14.3 contain a heap buffer overflow in
|
|
H5A__attr_release_table resulting in the corruption of the
|
|
instruction pointer and causing denial of service or potential code
|
|
execution
|
|
|
|
* CVE-2023-1006-003
|
|
HDF5 library versions <=1.14.3 contain a heap buffer overflow in
|
|
H5T__bit_find resulting in the corruption of the instruction pointer
|
|
and causing denial of service or potential code execution.
|
|
|
|
* CVE-2023-1006-002
|
|
HDF5 library versions <=1.14.3 contain a heap buffer overflow in
|
|
H5HG_read resulting in the corruption of the instruction pointer
|
|
and causing denial of service or potential code execution
|
|
|
|
* CVE-2023-1006-001
|
|
HDF5 library versions <=1.14.3 contain a heap buffer overflow in
|
|
H5HG__cache_heap_deserialize resulting in the corruption of the
|
|
instruction pointer and causing denial of service or potential code
|
|
execution
|
|
|
|
FULL OFFICIAL HDF5 CVE list (from mitre.org):
|
|
|
|
https://cve.mitre.org/cgi-bin/cvekey.cgi?keyword=HDF5
|
|
|
|
1.14.x CVE tracking list:
|
|
|
|
https://github.com/HDFGroup/hdf5/blob/hdf5_1_14/CVE_list_1_14.md
|
|
|
|
HDF5 CVE regression test suite (includes proof-of-concept files):
|
|
|
|
https://github.com/HDFGroup/cve_hdf5
|
|
|
|
- Fixed a divide-by-zero issue when a corrupt file sets the page size to 0
|
|
|
|
If a corrupt file sets the page buffer size in the superblock to zero,
|
|
the library could attempt to divide by zero when allocating space in
|
|
the file. The library now checks for valid page buffer sizes when
|
|
reading the superblock message.
|
|
|
|
Fixes oss-fuzz issue 58762
|
|
|
|
- Fixed a bug when using array datatypes with certain parent types
|
|
|
|
Array datatype conversion would never use a background buffer, even if the
|
|
array's parent type (what the array is an array of) required a background
|
|
buffer for conversion. This resulted in crashes in some cases when using
|
|
an array of compound, variable length, or reference datatypes. Array types
|
|
now use a background buffer if needed by the parent type.
|
|
|
|
- Fixed potential buffer read overflows in H5PB_read
|
|
|
|
H5PB_read previously did not account for the fact that the size of the
|
|
read it's performing could overflow the page buffer pointer, depending
|
|
on the calculated offset for the read. This has been fixed by adjusting
|
|
the size of the read if it's determined that it would overflow the page.
|
|
|
|
- Fixed CVE-2017-17507
|
|
|
|
This CVE was previously declared fixed, but later testing with a static
|
|
build of HDF5 showed that it was not fixed.
|
|
|
|
When parsing a malformed (fuzzed) compound type containing variable-length
|
|
string members, the library could produce a segmentation fault, crashing
|
|
the library.
|
|
|
|
This was fixed after GitHub PR #4234
|
|
|
|
Fixes GitHub issue #3446
|
|
|
|
- Fixed a cache assert with very large metadata objects
|
|
|
|
If the library tries to load a metadata object that is above a
|
|
certain size, this would trip an assert in debug builds. This could
|
|
happen if you create a very large number of links in an old-style
|
|
group that uses local heaps.
|
|
|
|
There is no need for this assert. The library's metadata cache
|
|
can handle large objects. The assert has been removed.
|
|
|
|
Fixes GitHub #3762
|
|
|
|
- Fixed an issue with the Subfiling VFD and multiple opens of a
|
|
file
|
|
|
|
An issue with the way the Subfiling VFD handles multiple opens
|
|
of the same file caused the file structures for the extra opens
|
|
to occasionally get mapped to an incorrect subfiling context
|
|
object. The VFD now correctly maps the file structures for
|
|
additional opens of an already open file to the same context
|
|
object.
|
|
|
|
- Fixed a bug that causes the library to incorrectly identify
|
|
the endian-ness of 16-bit and smaller C floating-point datatypes
|
|
|
|
When detecting the endian-ness of an in-memory C floating-point
|
|
datatype, the library previously always assumed that the type
|
|
was at least 32 bits in size. This resulted in invalid memory
|
|
accesses and would usually cause the library to identify the
|
|
datatype as having an endian-ness of H5T_ORDER_VAX. This has
|
|
now been fixed.
|
|
|
|
- Fixed a bug that causes an invalid memory access issue when
|
|
converting 16-bit floating-point values to integers with the
|
|
library's software conversion function
|
|
|
|
The H5T__conv_f_i function previously always assumed that
|
|
floating-point values were at least 32 bits in size and would
|
|
access invalid memory when attempting to convert 16-bit
|
|
floating-point values to integers. To fix this, parts of the
|
|
H5T__conv_f_i function had to be rewritten, which also resulted
|
|
in a significant speedup when converting floating-point values
|
|
to integers where the library does not have a hard conversion
|
|
path. This is the case for any floating-point values with a
|
|
datatype not represented by H5T_NATIVE_FLOAT16 (if _Float16 is
|
|
supported), H5T_NATIVE_FLOAT, H5T_NATIVE_DOUBLE or
|
|
H5T_NATIVE_LDOUBLE.
|
|
|
|
- Fixed a bug that can cause incorrect data when overflows occur
|
|
while converting integer values to floating-point values with
|
|
the library's software conversion function
|
|
|
|
The H5T__conv_i_f function had a bug which previously caused it
|
|
to return incorrect data when an overflow occurs and an application's
|
|
conversion exception callback function decides not to handle the
|
|
overflow. Rather than return positive infinity, the library would
|
|
return truncated data. This has now been fixed.
|
|
|
|
- Corrected H5Soffset_simple() when offset is NULL
|
|
|
|
The reference manual states that the offset parameter of H5Soffset_simple()
|
|
can be set to NULL to reset the offset of a simple dataspace to 0. This
|
|
has never been true, and passing NULL was regarded as an error.
|
|
|
|
The library will now accept NULL for the offset parameter and will
|
|
correctly set the offset to zero.
|
|
|
|
Fixes HDFFV-9299
|
|
|
|
- Fixed an issue where the Subfiling VFD's context object cache could
|
|
grow too large
|
|
|
|
The Subfiling VFD keeps a cache of its internal context objects to
|
|
speed up access to a context object for a particular file, as well
|
|
as access to that object across multiple opens of the same file.
|
|
However, opening a large amount of files with the Subfiling VFD over
|
|
the course of an application's lifetime could cause this cache to grow
|
|
too large and result in the application running out of available MPI
|
|
communicator objects. On file close, the Subfiling VFD now simply
|
|
evicts context objects out of its cache and frees them. It is assumed
|
|
that multiple opens of a file will be a less common use case for the
|
|
Subfiling VFD, but this can be revisited if it proves to be an issue
|
|
for performance.
|
|
|
|
- Fixed error when overwriting certain nested variable length types
|
|
|
|
Previously, when using a datatype that included a variable length type
|
|
within a compound or array within another variable length type, and
|
|
overwriting data with a shorter (top level) variable length sequence, an
|
|
error could occur. This has been fixed.
|
|
|
|
- Take user block into account in H5Dchunk_iter() and H5Dget_chunk_info()
|
|
|
|
The address reported by the following functions did not correctly
|
|
take the user block into account:
|
|
|
|
* H5Dchunk_iter() <-- addr passed to callback
|
|
* H5Dget_chunk_info() <-- addr parameter
|
|
* H5Dget_chunk_info_by_coord() <-- addr parameter
|
|
|
|
This means that these functions reported logical HDF5 file addresses,
|
|
which would only be equal to the physical addresses when there is no
|
|
user block prepended to the HDF5 file. This is unfortunate, as the
|
|
primary use of these functions is to get physical addresses in order
|
|
to directly access the chunks.
|
|
|
|
The listed functions now correctly take the user block into account,
|
|
so they will emit physical addresses that can be used to directly
|
|
access the chunks.
|
|
|
|
Fixes #3003
|
|
|
|
- Fixed asserts raised by large values of H5Pset_est_link_info() parameters
|
|
|
|
If large values for est_num_entries and/or est_name_len were passed
|
|
to H5Pset_est_link_info(), the library would attempt to create an
|
|
object header NIL message to reserve enough space to hold the links in
|
|
compact form (i.e., concatenated), which could exceed allowable object
|
|
header message size limits and trip asserts in the library.
|
|
|
|
This bug only occurred when using the HDF5 1.8 file format or later and
|
|
required the product of the two values to be ~64k more than the size
|
|
of any links written to the group, which would cause the library to
|
|
write out a too-large NIL spacer message to reserve the space for the
|
|
unwritten links.
|
|
|
|
The library now inspects the phase change values to see if the dataset
|
|
is likely to be compact and checks the size to ensure any NIL spacer
|
|
messages won't be larger than the library allows.
|
|
|
|
Fixes GitHub #1632
|
|
|
|
- Fixed a bug where H5Tset_fields does not account for any offset
|
|
set for a floating-point datatype when determining if values set
|
|
for spos, epos, esize, mpos and msize make sense for the datatype
|
|
|
|
Previously, H5Tset_fields did not take datatype offsets into account
|
|
when determining if the values set make sense for the datatype.
|
|
This would cause the function to fail when the precision for a
|
|
datatype is correctly set such that the offset bits are not included.
|
|
This has now been fixed.
|
|
|
|
- Fixed H5Fget_access_plist so that it returns the file locking
|
|
settings for a file
|
|
|
|
When H5Fget_access_plist (and the internal H5F_get_access_plist)
|
|
is called on a file, the returned File Access Property List has
|
|
the library's default file locking settings rather than any
|
|
settings set for the file. This causes two problems:
|
|
|
|
- Opening an HDF5 file through an external link using H5Gopen,
|
|
H5Dopen, etc. with H5P_DEFAULT for the Dataset/Group/etc.
|
|
Access Property List will cause the external file to be opened
|
|
with the library's default file locking settings rather than
|
|
inheriting them from the parent file. This can be surprising
|
|
when a file is opened with file locking disabled, but its
|
|
external files are opened with file locking enabled.
|
|
|
|
- An application cannot make use of the H5Pset_elink_fapl
|
|
function to match file locking settings between an external
|
|
file and its parent file without knowing the correct setting
|
|
ahead of time, as calling H5Fget_access_plist on the parent
|
|
file will not return the correct settings.
|
|
|
|
This has been fixed by copying a file's file locking settings
|
|
into the newly-created File Access Property List in H5F_get_access_plist.
|
|
|
|
This fix partially addresses GitHub issue #4011
|
|
|
|
- Memory usage growth issue
|
|
|
|
Starting with the HDF5 1.12.1 release, an issue (GitHub issue #1256)
|
|
was observed where running a simple program that has a loop of opening
|
|
a file, reading from an object with a variable-length datatype and
|
|
then closing the file would result in the process fairly quickly
|
|
running out of memory. Upon further investigation, it was determined
|
|
that this memory was being kept around in the library's datatype
|
|
conversion pathway cache that is used to speed up datatype conversions
|
|
which are repeatedly used within an HDF5 application's lifecycle. For
|
|
conversions involving variable-length or reference datatypes, each of
|
|
these cached pathway entries keeps a reference to its associated file
|
|
for later use. Since the file was being closed and reopened on each
|
|
loop iteration, and since the library compares for equality between
|
|
instances of opened files (rather than equality of the actual files)
|
|
when determining if it can reuse a cached conversion pathway, it was
|
|
determining that no cached conversion pathways could be reused and was
|
|
creating a new cache entry on each loop iteration during I/O. This
|
|
would lead to constant growth of that cache and the memory it consumed,
|
|
as well as constant growth of the memory consumed by each cached entry
|
|
for the reference to its associated file.
|
|
|
|
To fix this issue, the library now removes any cached datatype
|
|
conversion path entries for variable-length or reference datatypes
|
|
associated with a particular file when that file is closed.
|
|
|
|
Fixes GitHub #1256
|
|
|
|
- Suppressed floating-point exceptions in H5T init code
|
|
|
|
The floating-point datatype initialization code in H5Tinit_float.c
|
|
could raise FE_INVALID exceptions while munging bits and performing
|
|
comparisons that might involve NaN. This was not a problem when the
|
|
initialization code was executed in H5detect at compile time (prior
|
|
to 1.14.3), but now that the code is executed at library startup
|
|
(1.14.3+), these exceptions can be caught by user code, as is the
|
|
default in the NAG Fortran compiler.
|
|
|
|
Starting in 1.14.4, we now suppress floating-point exceptions while
|
|
initializing the floating-point types and clear FE_INVALID before
|
|
restoring the original environment.
|
|
|
|
Fixes GitHub #3831
|
|
|
|
- Fixed a file handle leak in the core VFD
|
|
|
|
When opening a file with the core VFD and a file image, if the file
|
|
already exists, the file check would leak the POSIX file handle.
|
|
|
|
Fixes GitHub issue #635
|
|
|
|
- Fixed some issues with chunk index metadata not getting read
|
|
collectively when collective metadata reads are enabled
|
|
|
|
When looking up dataset chunks during I/O, the parallel library
|
|
temporarily disables collective metadata reads since it's generally
|
|
unlikely that the application will read the same chunks from all
|
|
MPI ranks. Leaving collective metadata reads enabled during
|
|
chunk lookups can lead to hangs or other bad behavior depending
|
|
on the chunk indexing structure used for the dataset in question.
|
|
However, due to the way that dataset chunk index metadata was
|
|
previously loaded in a deferred manner, this could mean that
|
|
the metadata for the main chunk index structure or its
|
|
accompanying pieces of metadata (e.g., fixed array data blocks)
|
|
could end up being read independently if these chunk lookup
|
|
operations are the first chunk index-related operation that
|
|
occurs on a dataset. This behavior is generally observed when
|
|
opening a dataset for which the metadata isn't in the metadata
|
|
cache yet and then immediately performing I/O on that dataset.
|
|
This behavior is not generally observed when creating a dataset
|
|
and then performing I/O on it, as the relevant metadata will
|
|
usually be in the metadata cache as a side effect of creating
|
|
the chunk index structures during dataset creation.
|
|
|
|
This issue has been fixed by adding callbacks to the different
|
|
chunk indexing structure classes that allow more explicit control
|
|
over when chunk index metadata gets loaded. When collective
|
|
metadata reads are enabled, the necessary index metadata will now
|
|
get loaded collectively by all MPI ranks at the start of dataset
|
|
I/O to ensure that the ranks don't unintentionally read this
|
|
metadata independently further on. These changes fix collective
|
|
loading of the main chunk index structure, as well as v2 B-tree
|
|
root nodes, extensible array index blocks and fixed array data
|
|
blocks. There are still pieces of metadata that cannot currently
|
|
be loaded collectively, however, such as extensible array data
|
|
blocks, data block pages and super blocks, as well as fixed array
|
|
data block pages. These pieces of metadata are not necessarily
|
|
read in by all MPI ranks since this depends on which chunks the
|
|
ranks have selected in the dataset. Therefore, reading of these
|
|
pieces of metadata remains an independent operation.
|
|
|
|
- Fixed potential hangs in parallel library during collective I/O with
|
|
independent metadata writes
|
|
|
|
When performing collective parallel writes to a dataset where metadata
|
|
writes are requested as (or left as the default setting of) independent,
|
|
hangs could potentially occur during metadata cache sync points. This
|
|
was due to incorrect management of the internal state tracking whether
|
|
an I/O operation should be collective or not, causing the library to
|
|
attempt collective writes of metadata when they were meant to be
|
|
independent writes. During the metadata cache sync points, if the number
|
|
of cache entries being flushed was a multiple of the number of MPI ranks
|
|
in the MPI communicator used to access the HDF5 file, an equal amount of
|
|
collective MPI I/O calls were made and the dataset write call would be
|
|
successful. However, when the number of cache entries being flushed was
|
|
NOT a multiple of the number of MPI ranks, the ranks with more entries
|
|
than others would get stuck in an MPI_File_set_view call, while other
|
|
ranks would get stuck in a post-write MPI_Barrier call. This issue has
|
|
been fixed by correctly switching to independent I/O temporarily when
|
|
writing metadata independently during collective dataset I/O.
|
|
|
|
- Dropped support for MPI-2
|
|
|
|
The MPI-2 supporting artifacts have been removed due to the cessation
|
|
of MPI-2 maintenance and testing since version HDF5 1.12.
|
|
|
|
- Fixed a bug with the way the Subfiling VFD assigns I/O concentrators
|
|
|
|
During a file open operation, the Subfiling VFD determines the topology
|
|
of the application and uses that to select a subset of MPI ranks that
|
|
I/O will be forwarded to, called I/O concentrators. The code for this
|
|
had previously assumed that the parallel job launcher application (e.g.,
|
|
mpirun, srun, etc.) would distribute MPI ranks sequentially among a node
|
|
until all processors on that node have been assigned before going on to
|
|
the next node. When the launcher application mapped MPI ranks to nodes
|
|
in a different fashion, such as round-robin, this could cause the Subfiling
|
|
VFD to incorrectly map MPI ranks as I/O concentrators, leading to missing
|
|
subfiles.
|
|
|
|
- Fixed performance regression with some compound type conversions
|
|
|
|
In-place type conversion was introduced for most use cases in 1.14.2.
|
|
While being able to use the read buffer for type conversion potentially
|
|
improves performance by performing the entire I/O at once, it also
|
|
disables the optimized compound type conversion used when the destination
|
|
is a subset of the source. Disabled in-place type conversion when using
|
|
this optimized conversion and there is no benefit in terms of the I/O
|
|
size.
|
|
|
|
- Fixed an assertion in a previous fix for CVE-2016-4332
|
|
|
|
An assert could fail when processing corrupt files that have invalid
|
|
shared message flags (as in CVE-2016-4332).
|
|
|
|
The assert statement in question has been replaced with pointer checks
|
|
that don't raise errors. Since the function is in cleanup code, we do
|
|
our best to close and free things, even when presented with partially
|
|
initialized structs.
|
|
|
|
Fixes CVE-2016-4332 and HDFFV-9950 (confirmed via the cve_hdf5 repo)
|
|
|
|
- Fixed a file space allocation bug in the parallel library for chunked
|
|
datasets
|
|
|
|
With the addition of support for incremental file space allocation for
|
|
chunked datasets with filters applied to them that are created/accessed
|
|
in parallel, a bug was introduced to the library's parallel file space
|
|
allocation code. This could cause file space to not be allocated correctly
|
|
for datasets without filters applied to them that are created with serial
|
|
file access and later opened with parallel file access. In turn, this could
|
|
cause parallel writes to those datasets to place incorrect data in the file.
|
|
|
|
- Fixed an assertion failure in Parallel HDF5 when a file can't be created
|
|
due to an invalid library version bounds setting
|
|
|
|
An assertion failure could occur in H5MF_settle_raw_data_fsm when a file
|
|
can't be created with Parallel HDF5 due to specifying the use of a paged,
|
|
persistent file free space manager
|
|
(H5Pset_file_space_strategy(..., H5F_FSPACE_STRATEGY_PAGE, 1, ...)) with
|
|
an invalid library version bounds combination
|
|
(H5Pset_libver_bounds(..., H5F_LIBVER_EARLIEST, H5F_LIBVER_V18)). This
|
|
has now been fixed.
|
|
|
|
- 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.
|
|
|
|
- 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 H5Pget_vol_cap_flags and H5Pget_vol_id to accept H5P_DEFAULT
|
|
|
|
H5Pget_vol_cap_flags and H5Pget_vol_id were updated to correctly
|
|
accept H5P_DEFAULT for the 'plist_id' FAPL parameter. Previously,
|
|
they would fail if provided with H5P_DEFAULT as the FAPL.
|
|
|
|
- Fixed ROS3 VFD anonymous credential usage with h5dump and h5ls
|
|
|
|
ROS3 VFD anonymous credential functionality became broken in h5dump
|
|
and h5ls in the HDF5 1.14.0 release with the added support for VFD
|
|
plugins, which changed the way that the tools handled setting of
|
|
credential information that the VFD uses. The tools could be
|
|
provided the command-line option of "--s3-cred=(,,)" as a workaround
|
|
for anonymous credential usage, but the documentation for this
|
|
option stated that anonymous credentials could be used by simply
|
|
omitting the option. The latter functionality has been restored.
|
|
|
|
Fixes GitHub issue #2406
|
|
|
|
- Fixed memory leaks when processing malformed object header continuation messages
|
|
|
|
Malformed object header continuation messages can result in a too-small
|
|
buffer being passed to the decode function, which could lead to reading
|
|
past the end of the buffer. Additionally, errors in processing these
|
|
malformed messages can lead to allocated memory not being cleaned up.
|
|
|
|
This fix adds bounds checking and cleanup code to the object header
|
|
continuation message processing.
|
|
|
|
Fixes GitHub issue #2604
|
|
|
|
- Fixed memory leaks, aborts, and overflows in H5O EFL decode
|
|
|
|
The external file list code could call assert(), read past buffer
|
|
boundaries, and not properly clean up resources when parsing malformed
|
|
external data files messages.
|
|
|
|
This fix cleans up allocated memory, adds buffer bounds checks, and
|
|
converts asserts to HDF5 error checking.
|
|
|
|
Fixes GitHub issue #2605
|
|
|
|
- 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.
|
|
|
|
Fixes GitHub issue #2603
|
|
|
|
- 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 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 potential heap buffer overrun in group info header decoding from malformed file
|
|
|
|
H5O__ginfo_decode could sometimes read past allocated memory when parsing a
|
|
group info message from the header of a malformed file.
|
|
|
|
It now checks buffer size before each read to properly throw an error in these cases.
|
|
|
|
Fixes GitHub issue #2601
|
|
|
|
- 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
|
|
|
|
- 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.
|
|
|
|
- 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 #2458
|
|
|
|
- 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
|
|
|
|
- Fixed buffer overflow error in image decoding function.
|
|
|
|
The error occurred in the function for decoding address from the specified
|
|
buffer, which is called many times from the function responsible for image
|
|
decoding. The length of the buffer is known in the image decoding function,
|
|
but no checks are produced, so the buffer overflow can occur in many places,
|
|
including callee functions for address decoding.
|
|
|
|
The error was fixed by inserting corresponding checks for buffer overflow.
|
|
|
|
Fixes GitHub issue #2432
|
|
|
|
- Reading a H5std_string (std::string) via a C++ DataSet previously
|
|
truncated the string at the first null byte as if reading a C string.
|
|
Fixed length datasets are now read into H5std_string as a fixed length
|
|
string of the appropriate size. Variable length datasets will still be
|
|
truncated at the first null byte.
|
|
|
|
Fixes Github issue #3034
|
|
|
|
- Fixed write buffer overflow in H5O__alloc_chunk
|
|
|
|
The overflow was found by OSS-Fuzz https://bugs.chromium.org/p/oss-fuzz/issues/detail?id=58658
|
|
|
|
- Fixed a segfault when using a user-defined conversion function between compound datatypes
|
|
|
|
During type info initialization for compound datatype conversion, the library checked if the
|
|
datatypes are subsets of one another in order to perform special conversion handling.
|
|
This check uses information that is only defined if a library conversion function is in use.
|
|
The library now skips this check for user-defined conversion functions.
|
|
|
|
Fixes Github issue #3840
|
|
|
|
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
|
|
-------------
|
|
- Changed default of 'Error on HDF5 doxygen warnings' DOXYGEN_WARN_AS_ERROR option.
|
|
|
|
The default setting of DOXYGEN_WARN_AS_ERROR to 'FAIL_ON_WARNINGS' has been changed
|
|
to 'NO'. It was decided that the setting was too aggressive and should be a user choice.
|
|
The github actions and scripts have been updated to reflect this.
|
|
|
|
* HDF5_ENABLE_DOXY_WARNINGS: ON/OFF (Default: OFF)
|
|
* --enable-doxygen-errors: enable/disable (Default: disable)
|
|
|
|
- Removed an Autotools configure hack that causes problems on MacOS
|
|
|
|
A sed line in configure.ac was added in the past to paper over some
|
|
problems with older versions of the Autotools that would add incorrect
|
|
linker flags. This hack is not needed with recent versions of the
|
|
Autotools and the sed line errors on MacOS (though this was a silent
|
|
error that didn't break the build) so the hack has been removed.
|
|
|
|
Fixes GitHub issue #3843
|
|
|
|
- Fixed an issue where the h5tools_test_utils test program was being
|
|
installed on the system for Autotools builds of HDF5
|
|
|
|
The h5tools_test_utils test program was mistakenly added to bin_PROGRAMS
|
|
in its Makefile.am configuration file, causing the executable to be
|
|
installed on the system. The executable is now added to noinst_PROGRAMS
|
|
instead and will no longer be installed on the system for Autotools builds
|
|
of HDF5. The CMake configuration code already avoids installing the
|
|
executable on the system.
|
|
|
|
- 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.
|
|
|
|
- Fixes the ordering of INCLUDES when building with CMake
|
|
|
|
Include directories in the source or build tree should come before other
|
|
directories to prioritize headers in the sources over installed ones.
|
|
|
|
Fixes GitHub #1027
|
|
|
|
- The accum test now passes on macOS 12+ (Monterey) w/ CMake
|
|
|
|
Due to changes in the way macOS handles LD_LIBRARY_PATH, the accum test
|
|
started failing on macOS 12+ when building with CMake. CMake has been
|
|
updated to set DYLD_LIBRARY_PATH on macOS and the test now passes.
|
|
|
|
Fixes GitHub #2994, #2261, and #1289
|
|
|
|
- Changed the default settings used by CMake for the GZIP filter
|
|
|
|
The default for the option HDF5_ENABLE_Z_LIB_SUPPORT was OFF. Now the default is ON.
|
|
This was done to match the defaults used by the autotools configure.ac.
|
|
In addition, the CMake message level for not finding a suitable filter library was
|
|
changed from FATAL_ERROR (which would halt the build process) to WARNING (which
|
|
will print a message to stderr). Associated files and documentation were changed to match.
|
|
|
|
In addition, the default settings in the config/cmake/cacheinit.cmake file were changed to
|
|
allow CMake to disable building the filters if the tgz file could not be found. The option
|
|
to allow CMake to download the file from the original Github location requires setting
|
|
the ZLIB_USE_LOCALCONTENT option to OFF for gzip. And setting the LIBAEC_USE_LOCALCONTENT
|
|
option to OFF for libaec (szip).
|
|
|
|
Fixes GitHub issue #2926
|
|
|
|
- Fixed syntax of generator expressions used by CMake
|
|
|
|
Add 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
|
|
|
|
- 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 issue #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
|
|
|
|
- Force lowercase Fortran module file names
|
|
|
|
The Cray Fortran compiler uses uppercase Fortran module file names, which
|
|
caused CMake installs to fail. A compiler option was added to use lowercase
|
|
instead.
|
|
|
|
|
|
Tools
|
|
-----
|
|
|
|
- Renamed h5fuse.sh to h5fuse
|
|
|
|
Addresses Discussion #3791
|
|
|
|
|
|
- Fixed an issue with unmatched MPI messages in ph5diff
|
|
|
|
The "manager" MPI rank in ph5diff was unintentionally sending "program end"
|
|
messages to its workers twice, leading to an error from MPICH similar to the
|
|
following:
|
|
|
|
Abort(810645519) on node 1 (rank 1 in comm 0): Fatal error in internal_Finalize: Other MPI error, error stack:
|
|
internal_Finalize(50)...........: MPI_Finalize failed
|
|
MPII_Finalize(394)..............:
|
|
MPIR_Comm_delete_internal(1224).: Communicator (handle=44000000) being freed has 1 unmatched message(s)
|
|
MPIR_Comm_release_always(1250)..:
|
|
MPIR_finalize_builtin_comms(154):
|
|
|
|
- Fixed an issue in h5repack for variable-length typed datasets
|
|
|
|
When repacking datasets into a new file, h5repack tries to determine 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 allocate 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.
|
|
|
|
- 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.
|
|
|
|
Fixes GitHub issue #2682
|
|
|
|
- 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
|
|
-----------
|
|
- Fixed: HDF5 fails to compile with -Werror=lto-type-mismatch
|
|
|
|
Removed the use of the offending C stub wrapper.
|
|
|
|
Fixes GitHub issue #3987
|
|
|
|
|
|
High-Level Library
|
|
------------------
|
|
- Fixed a memory leak in H5LTopen_file_image with H5LT_FILE_IMAGE_DONT_COPY flag
|
|
|
|
When the H5LT_FILE_IMAGE_DONT_COPY flag is passed to H5LTopen_file_image, the
|
|
internally-allocated udata structure gets leaked as the core file driver doesn't
|
|
have a way to determine when or if it needs to call the "udata_free" callback.
|
|
This has been fixed by freeing the udata structure when the "image_free" callback
|
|
gets made during file close, where the file is holding the last reference to the
|
|
udata structure.
|
|
|
|
Fixes GitHub issue #827
|
|
|
|
|
|
Fortran High-Level APIs
|
|
-----------------------
|
|
-
|
|
|
|
|
|
Documentation
|
|
-------------
|
|
-
|
|
|
|
|
|
F90 APIs
|
|
--------
|
|
-
|
|
|
|
|
|
C++ APIs
|
|
--------
|
|
-
|
|
|
|
|
|
Testing
|
|
-------
|
|
- Fixed a bug in the dt_arith test when H5_WANT_DCONV_EXCEPTION is not
|
|
defined
|
|
|
|
The dt_arith test program's test_particular_fp_integer sub-test tries
|
|
to ensure that the library correctly raises a datatype conversion
|
|
exception when converting a floating-point value to an integer overflows.
|
|
However, this test would run even when H5_WANT_DCONV_EXCEPTION isn't
|
|
defined, causing the test to fail due to the library not raising
|
|
datatype conversion exceptions. This has now been fixed by not running
|
|
the test when H5_WANT_DCONV_EXCEPTION is not defined.
|
|
|
|
- Disabled running of MPI Atomicity tests for OpenMPI major versions < 5
|
|
|
|
Support for MPI atomicity operations is not implemented for major
|
|
versions of OpenMPI less than version 5. This would cause the MPI
|
|
atomicity tests for parallel HDF5 to sporadically fail when run
|
|
with OpenMPI. Testphdf5 now checks if OpenMPI is being used and will
|
|
skip running the atomicity tests if the major version of OpenMPI is
|
|
< 5.
|
|
|
|
- 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.
|
|
|
|
- Fixed Fortran 2003 test with gfortran-v13, optimization levels O2,O3
|
|
|
|
Fixes failing Fortran 2003 test with gfortran, optimization level O2,O3
|
|
with -fdefault-real-16. Fixes GH #2928.
|
|
|
|
|
|
Platforms Tested
|
|
===================
|
|
|
|
- HDF5 supports the latest macOS versions, including the current and two
|
|
preceding releases. As new major macOS versions become available, HDF5
|
|
will discontinue support for the oldest version and add the latest
|
|
version to its list of compatible systems, along with the previous two
|
|
releases.
|
|
|
|
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 5.19.0-1027-aws GNU gcc (GCC) 11.3.0-1ubuntu1
|
|
#36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.3.0-1ubuntu1
|
|
Ubuntu 22.04 Intel oneAPI DPC++/C++ Compiler, IFX 2023.1.0
|
|
Ubuntu clang version 14.0.0-1ubuntu1
|
|
(cmake and autotools)
|
|
|
|
Linux 5.15.0-1037-aws GNU gcc (GCC) 9.4.0-1ubuntu1
|
|
#36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.4.0-1ubuntu1
|
|
Ubuntu 20.04 Intel oneAPI DPC++/C++ Compiler, IFX 2023.1.0
|
|
Ubuntu clang version 10.0.0-4ubuntu1
|
|
(cmake and autotools)
|
|
|
|
Linux 5.14.21-cray_shasta_c cray-mpich/8.1.25
|
|
#1 SMP x86_64 GNU/Linux cce 15.0.1
|
|
(perlmutter) GCC 12.2.0
|
|
intel-oneapi/2023.1.0
|
|
nvidia/22.7
|
|
(cmake)
|
|
|
|
Linux 5.14.21-cray_shasta_c cray-mpich/8.1.23
|
|
#1 SMP x86_64 GNU/Linux cce 15.0.1
|
|
(crusher) GCC 12.2.0
|
|
(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)
|
|
IBM XL C for Linux, V13.1
|
|
IBM XL Fortran for Linux, V15.1
|
|
|
|
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 3.3 compiled with GCC 7.2.0
|
|
MPICH 4.0.3 compiled with GCC 7.2.0
|
|
OpenMPI 3.1.3 compiled with GCC 7.2.0
|
|
OpenMPI 4.1.2 compiled with GCC 9.1.0
|
|
PGI C, Fortran, C++ for 64-bit target on
|
|
x86_64;
|
|
Version 19.10-0
|
|
NVIDIA C, Fortran, C++ for 64-bit target on
|
|
x86_64;
|
|
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
|
|
|
|
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
|
|
|
|
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
|
|
==============
|
|
|
|
- When building with the NAG Fortran compiler using the Autotools and libtool
|
|
2.4.2 or earlier, the -shared flag will be missing '-Wl,', which will cause
|
|
compilation to fail. This is due to a bug in libtool that was fixed in 2012
|
|
and released in 2.4.4 in 2014.
|
|
|
|
- When the library detects and builds in support for the _Float16 datatype, an
|
|
issue has been observed on at least one MacOS 14 system where the library
|
|
fails to initialize due to not being able to detect the byte order of the
|
|
_Float16 type (https://github.com/HDFGroup/hdf5/issues/4310):
|
|
|
|
#5: H5Tinit_float.c line 308 in H5T__fix_order(): failed to detect byte order
|
|
major: Datatype
|
|
minor: Unable to initialize object
|
|
|
|
If this issue is encountered, support for the _Float16 type can be disabled
|
|
with a configuration option:
|
|
|
|
CMake: HDF5_ENABLE_NONSTANDARD_FEATURE_FLOAT16=OFF
|
|
Autotools: --disable-nonstandard-feature-float16
|
|
|
|
- When HDF5 is compiled with NVHPC versions 23.5 - 23.9 (additional versions may
|
|
also be applicable) and with -O2 (or higher) and -DNDEBUG, test failures occur
|
|
in the following tests:
|
|
|
|
H5PLUGIN-filter_plugin
|
|
H5TEST-flush2
|
|
H5TEST-testhdf5-base
|
|
MPI_TEST_t_filters_parallel
|
|
|
|
Sporadic failures (even with lower -O levels):
|
|
Java JUnit-TestH5Pfapl
|
|
Java JUnit-TestH5D
|
|
|
|
Also, NVHPC will fail to compile the test/tselect.c test file with a compiler
|
|
error of 'use of undefined value' when the optimization level is -O2 or higher.
|
|
|
|
This is confirmed to be a bug in the nvc compiler that has been fixed as of
|
|
23.11. If you are using an affected version of the NVidia compiler, the
|
|
work-around is to set the optimization level to -O1.
|
|
|
|
https://forums.developer.nvidia.com/t/hdf5-no-longer-compiles-with-nv-23-9/269045
|
|
|
|
- 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.
|
|
|
|
- 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.
|
|
|
|
- The subsetting option in ph5diff currently will fail and should be avoided.
|
|
The subsetting option works correctly in serial h5diff.
|
|
|
|
- Flang Fortran compilation will fail (last check version 17) due to not yet
|
|
implemented: (1) derived type argument passed by value (H5VLff.F90),
|
|
and (2) support for REAL with KIND = 2 in intrinsic SPACING used in testing.
|
|
|
|
- Fortran tests HDF5_1_8.F90 and HDF5_F03.F90 will fail with Cray compilers
|
|
greater than version 16.0 due to a compiler bug. The latest version verified
|
|
as failing was version 17.0.
|
|
|
|
- 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.
|
|
|
|
- File space may not be released when overwriting or deleting certain nested
|
|
variable length or reference types.
|
|
|
|
- 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
|