diff options
| author | Allen Byrne <50328838+byrnHDF@users.noreply.github.com> | 2020-11-23 18:04:49 (GMT) |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2020-11-23 18:04:49 (GMT) |
| commit | ecbcb4356c2bbdad7ad801f9c61fe695082a6b25 (patch) | |
| tree | 6118c67abd35585376b0b8e822b89cd010fa970d /release_docs/RELEASE.txt | |
| parent | 5ff09ae971cdb8a85c596520666c8dc178541e4a (diff) | |
| download | hdf5-ecbcb4356c2bbdad7ad801f9c61fe695082a6b25.zip hdf5-ecbcb4356c2bbdad7ad801f9c61fe695082a6b25.tar.gz hdf5-ecbcb4356c2bbdad7ad801f9c61fe695082a6b25.tar.bz2 | |
Update release text files (#109)
* Update release text files
* spelling correction
* Update list
Diffstat (limited to 'release_docs/RELEASE.txt')
| -rw-r--r-- | release_docs/RELEASE.txt | 1652 |
1 files changed, 394 insertions, 1258 deletions
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 639dbe7..1b6a097 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -34,8 +34,7 @@ CONTENTS - New Features - Support for new platforms and languages -- Bug Fixes since HDF5-1.10.3 -- Bug Fixes since HDF5-1.10.2 +- Bug Fixes since HDF5-1.12.0 - Supported Platforms - Tested Configuration Features Summary - More Tested Platforms @@ -50,150 +49,199 @@ New Features ------------- - Autotools and CMake target added to produce doxygen generated documentation - The default is OFF or disabled. - Autoconf option is '--enable-doxygen' + The default is OFF or disabled. + Autoconf option is '--enable-doxygen' autotools make target is 'doxygen' and will build all doxygen targets - CMake configure option is 'HDF5_BUILD_DOC'. + CMake configure option is 'HDF5_BUILD_DOC'. CMake target is 'doxygen' for all available doxygen targets CMake target is 'hdf5lib_doc' for the src subdirectory - (ADB - 2020/11/03) + (ADB - 2020/11/03) - CMake option to use MSVC naming conventions with MinGW - HDF5_MSVC_NAMING_CONVENTION option enable to use MSVC naming conventions - when using a MinGW toolchain + HDF5_MSVC_NAMING_CONVENTION option enable to use MSVC naming conventions + when using a MinGW toolchain - (xan - 2020/10/30) + (xan - 2020/10/30) - CMake option to statically link gcc libs with MinGW - HDF5_MINGW_STATIC_GCC_LIBS allows to statically link libg/libstdc++ - with the MinGW toolchain + HDF5_MINGW_STATIC_GCC_LIBS allows to statically link libg/libstdc++ + with the MinGW toolchain - (xan - 2020/10/30) + (xan - 2020/10/30) - CMake option to build the HDF filter plugins project as an external project - The HDF filter plugins project is a collection of registered compression - filters that can be dynamically loaded when needed to access data stored - in a hdf5 file. This CMake-only option allows the plugins to be built and - distributed with the hdf5 library and tools. Like the options for szip and - zlib, either a tgz file or a git repository can be specified for the source. + The HDF filter plugins project is a collection of registered compression + filters that can be dynamically loaded when needed to access data stored + in a hdf5 file. This CMake-only option allows the plugins to be built and + distributed with the hdf5 library and tools. Like the options for szip and + zlib, either a tgz file or a git repository can be specified for the source. - The necessary options are (see the INSTALL_CMake.txt file): + The necessary options are (see the INSTALL_CMake.txt file): HDF5_ENABLE_PLUGIN_SUPPORT PLUGIN_TGZ_NAME or PLUGIN_GIT_URL - There are more options necessary for various filters and the plugin project - documents should be referenced. + There are more options necessary for various filters and the plugin project + documents should be referenced. - (ADB - 2020/09/27, OESS-98) + (ADB - 2020/09/27, OESS-98) - Added CMake option to format source files - HDF5_ENABLE_FORMATTERS option will enable creation of targets using the - pattern - HDF5_*_SRC_FORMAT - where * corresponds to the source folder - or tool folder. All sources can be formatted by executing the format target; - make format + HDF5_ENABLE_FORMATTERS option will enable creation of targets using the + pattern - HDF5_*_SRC_FORMAT - where * corresponds to the source folder + or tool folder. All sources can be formatted by executing the format target; + make format - (ADB - 2020/08/24) + (ADB - 2020/08/24) + + - Add file locking configure and CMake options + + HDF5 1.10.0 introduced a file locking scheme, primarily to help + enforce SWMR setup. Formerly, the only user-level control of the scheme + was via the HDF5_USE_FILE_LOCKING environment variable. + + This change introduces configure-time options that control whether + or not file locking will be used and whether or not the library + ignores errors when locking has been disabled on the file system + (useful on some HPC Lustre installations). + + In both the Autotools and CMake, the settings have the effect of changing + the default property list settings (see the H5Pset/get_file_locking() + entry, below). + + The yes/no/best-effort file locking configure setting has also been + added to the libhdf5.settings file. + + Autotools: + + An --enable-file-locking=(yes|no|best-effort) option has been added. + + yes: Use file locking. + no: Do not use file locking. + best-effort: Use file locking and ignore "disabled" errors. + + CMake: + + Two self-explanatory options have been added: + + HDF5_USE_FILE_LOCKING + HDF5_IGNORE_DISABLED_FILE_LOCKS + + Setting both of these to ON is the equivalent to the Autotools' + best-effort setting. + + NOTE: + The precedence order of the various file locking control mechanisms is: + + 1) HDF5_USE_FILE_LOCKING environment variable (highest) + + 2) H5Pset_file_locking() + + 3) configure/CMake options (which set the property list defaults) + + 4) library defaults (currently best-effort) + + (DER - 2020/07/30, HDFFV-11092) - CMake option to link the generated Fortran MOD files into the include directory. - The Fortran generation of MOD files by a Fortran compile can produce - different binary files between SHARED and STATIC compiles with different - compilers and/or different platforms. Note that it has been found that - different versions of Fortran compilers will produce incompatible MOD - files. Currently, CMake will locate these MOD files in subfolders of - the include directory and add that path to the Fortran library target - in the CMake config file, which can be used by the CMake find library - process. For other build systems using the binary from a CMake install, - a new CMake configuration can be used to copy the pre-chosen version - of the Fortran MOD files into the install include directory. - - The default will depend on the configuration of - BUILD_STATIC_LIBS and BUILD_SHARED_LIBS: + The Fortran generation of MOD files by a Fortran compile can produce + different binary files between SHARED and STATIC compiles with different + compilers and/or different platforms. Note that it has been found that + different versions of Fortran compilers will produce incompatible MOD + files. Currently, CMake will locate these MOD files in subfolders of + the include directory and add that path to the Fortran library target + in the CMake config file, which can be used by the CMake find library + process. For other build systems using the binary from a CMake install, + a new CMake configuration can be used to copy the pre-chosen version + of the Fortran MOD files into the install include directory. + + The default will depend on the configuration of + BUILD_STATIC_LIBS and BUILD_SHARED_LIBS: YES YES Default to SHARED YES NO Default to STATIC NO YES Default to SHARED NO NO Default to SHARED - The defaults can be overriden by setting the config option - HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC + The defaults can be overriden by setting the config option + HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC - (ADB - 2020/07/9, HDFFV-11116) + (ADB - 2020/07/09, HDFFV-11116) - CMake option to use AEC (open source SZip) library instead of SZip - The open source AEC library is a replacement library for SZip. In - order to use it for hdf5 the libaec CMake source was changed to add - "-fPIC" and exclude test files. Autotools does not build the - compression libraries within hdf5 builds. New option USE_LIBAEC is - required to compensate for the different files produced by AEC build. + The open source AEC library is a replacement library for SZip. In + order to use it for hdf5 the libaec CMake source was changed to add + "-fPIC" and exclude test files. Autotools does not build the + compression libraries within hdf5 builds. New option USE_LIBAEC is + required to compensate for the different files produced by AEC build. - (ADB - 2020/04/22, OESS-65) + (ADB - 2020/04/22, OESS-65) - CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER - Some handcrafted tests in HDFTests.c has been removed and the CMake - CHECK_STRUCT_HAS_MEMBER module has been used. + Some handcrafted tests in HDFTests.c has been removed and the CMake + CHECK_STRUCT_HAS_MEMBER module has been used. - (ADB - 2020/03/24, TRILAB-24) + (ADB - 2020/03/24, TRILAB-24) - Both build systems use same set of warnings flags - GNU C, C++ and gfortran warnings flags were moved to files in a config - sub-folder named gnu-warnings. Flags that only are available for a specific - version of the compiler are in files named with that version. - Clang C warnings flags were moved to files in a config sub-folder - named clang-warnings. - Intel C, Fortran warnings flags were moved to files in a config sub-folder - named intel-warnings. + GNU C, C++ and gfortran warnings flags were moved to files in a config + sub-folder named gnu-warnings. Flags that only are available for a specific + version of the compiler are in files named with that version. + Clang C warnings flags were moved to files in a config sub-folder + named clang-warnings. + Intel C, Fortran warnings flags were moved to files in a config sub-folder + named intel-warnings. - There are flags in named "error-xxx" files with warnings that may - be promoted to errors. Some source files may still need fixes. + There are flags in named "error-xxx" files with warnings that may + be promoted to errors. Some source files may still need fixes. - There are also pairs of files named "developer-xxx" and "no-developer-xxx" - that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the - configure option:--enable-developer-warnings. + There are also pairs of files named "developer-xxx" and "no-developer-xxx" + that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the + configure option:--enable-developer-warnings. - In addition, CMake no longer applies these warnings for examples. + In addition, CMake no longer applies these warnings for examples. - (ADB - 2020/03/24, TRILAB-192) + (ADB - 2020/03/24, TRILAB-192) - Added test script for file size compare - if CMake minimum version is at least 3.14, the fileCompareTest.cmake - script will compare file sizes. + If CMake minimum version is at least 3.14, the fileCompareTest.cmake + script will compare file sizes. - (ADB - 2020/02/24, HDFFV-11036) + (ADB - 2020/02/24, HDFFV-11036) - Update CMake minimum version to 3.12 - Updated CMake minimum version to 3.12 and added version checks - for Windows features. + Updated CMake minimum version to 3.12 and added version checks + for Windows features. - (ADB - 2020/02/05, TRILABS-142) + (ADB - 2020/02/05, TRILABS-142) - Fixed CMake include properties for Fortran libraries - Corrected the library properties for Fortran to use the - correct path for the Fortran module files. + Corrected the library properties for Fortran to use the + correct path for the Fortran module files. - (ADB - 2020/02/04, HDFFV-11012) + (ADB - 2020/02/04, HDFFV-11012) - Added common warnings files for gnu and intel - Added warnings files to use one common set of flags - during configure for both autotools and CMake build - systems. The initial implementation only affects a - general set of flags for gnu and intel compilers. + Added warnings files to use one common set of flags + during configure for both autotools and CMake build + systems. The initial implementation only affects a + general set of flags for gnu and intel compilers. - (ADB - 2020/01/17) + (ADB - 2020/01/17) - Added new options to CMake for control of testing - Added CMake options (default ON); + Added CMake options (default ON); HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL combined with: HDF5_TEST_TOOLS @@ -203,13 +251,13 @@ New Features HDF5_TEST_CPP HDF5_TEST_JAVA - (ADB - 2020/01/15, HDFFV-11001) + (ADB - 2020/01/15, HDFFV-11001) - Added Clang sanitizers to CMake for analyzer support if compiler is clang. - Added CMake code and files to execute the Clang sanitizers if - HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option - is set to one of the following: + Added CMake code and files to execute the Clang sanitizers if + HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option + is set to one of the following: Address Memory MemoryWithOrigins @@ -218,640 +266,267 @@ New Features Leak 'Address;Undefined' - (ADB - 2019/12/12, TRILAB-135) + (ADB - 2019/12/12, TRILAB-135) - Update CMake for VS2019 support - CMake added support for VS2019 in version 3.15. Changes to the CMake - generator setting required changes to scripts. Also updated version - references in CMake files as necessary. + CMake added support for VS2019 in version 3.15. Changes to the CMake + generator setting required changes to scripts. Also updated version + references in CMake files as necessary. - (ADB - 2019/11/18, HDFFV-10962) + (ADB - 2019/11/18, HDFFV-10962) - Update CMake options to match new autotools options - Add configure options (autotools - CMake): + Add configure options (autotools - CMake): enable-asserts HDF5_ENABLE_ASSERTS enable-symbols HDF5_ENABLE_SYMBOLS enable-profiling HDF5_ENABLE_PROFILING enable-optimization HDF5_ENABLE_OPTIMIZATION - In addition NDEBUG is no longer forced defined and relies on the CMake - process. - - (ADB - 2019/10/07, HDFFV-100901, HDFFV-10637, TRILAB-97) - - - Update CMake tests to use FIXTURES - - CMake test fixtures allow setup/cleanup tests and other dependency - requirements as properties for tests. This is more flexible for - modern CMake code. - - (ADB - 2019/07/23, HDFFV-10529) - - - Windows PDB files are always installed - - There are build configuration or flag settings for Windows that may not - generate PDB files. If those files are not generated then the install - utility will fail because those PDB files are not found. An optional - variable, DISABLE_PDB_FILES, was added to not install PDB files. - - (ADB - 2019/07/17, HDFFV-10424) - - - Add mingw CMake support with a toolchain file - - There has been a number of mingw issues that has been linked under - HDFFV-10845. It has been decided to implement the CMake cross-compiling - technique of toolchain files. We will use a linux platform with the mingw - compiler stack for testing. Only the C language is fully supported, and - the error tests are skipped. The C++ language works for static but shared - builds has a shared library issue with the mingw Standard Exception Handling - library, which is not available on Windows. Fortran has a common cross-compile - problem with the fortran configure tests. - - (ADB - 2019/07/12, HDFFV-10845, HDFFV-10595) - - - Windows PDB files are installed incorrectly - - For static builds, the PDB files for windows should be installed next - to the static libraries in the lib folder. Also the debug versions of - libraries and PDB files are now correctly built using the default - CMAKE_DEBUG_POSTFIX setting. - - (ADB - 2019/07/09, HDFFV-10581) - - - Add option to build only shared libs - - A request was made to prevent building static libraries and only build - shared. A new option was added to CMake, ONLY_SHARED_LIBS, which will - skip building static libraries. Certain utility functions will build with - static libs but are not published. Tests are adjusted to use the correct - libraries depending on SHARED/STATIC settings. - - (ADB - 2019/06/12, HDFFV-10805) - - - Add options to enable or disable building tools and tests - - Configure options --enable-tests and --enable-tools were added for - autotools configure. These options are enabled by default, and can be - disabled with either --disable-tests (or tools) or --enable-tests=no - (or --enable-tools=no). Build time is reduced ~20% when tools are - disabled, 35% when tests are disabled, 45% when both are disabled. - Reenabling them after the initial build requires running configure - again with the option(s) enabled. - - (LRK - 2019/06/12, HDFFV-9976) - - - Change tools test that test the error stack - - There are some use cases which can cause the error stack of tools to be - different then the expected output. These tests now use grepTest.cmake, - this was changed to allow the error file to be searched for an expected string. - - (ADB - 2019/04/15, HDFFV-10741) - - - Keep stderr and stdout separate in tests - - Changed test handling of output capture. Tests now keep the stderr - output separate from the stdout output. It is up to the test to decide - which output to check against a reference. Also added the option - to grep for a string in either output. - - (ADB - 2018/12/12, HDFFV-10632) - - - Add toolchain and cross-compile support - - Added info on using a toolchain file to INSTALL_CMAKE.txt. A - toolchain file is also used in cross-compiling, which requires - CMAKE_CROSSCOMPILING_EMULATOR to be set. To help with cross-compiling - the fortran configure process, the HDF5UseFortran.cmake file macros - were improved. Fixed a Fortran configure file issue that incorrectly - used #cmakedefine instead of #define. - - (ADB - 2018/10/04, HDFFV-10594) + In addition NDEBUG is no longer forced defined and relies on the CMake + process. - - Add warning flags for Intel compilers - - Identified Intel compiler specific warnings flags that should be used - instead of GNU flags. - - (ADB - 2018/10/04, TRILABS-21) - - - Add default rpath to targets - - Default rpaths should be set in shared executables and - libraries to allow the use of loading dependent libraries - without requiring LD_LIBRARY_PATH to be set. The default - path should be relative using @rpath on osx and $ORIGIN - on linux. Windows is not affected. - - (ADB - 2018/09/26, HDFFV-10594) - - - Add missing USE_110_API_DEFAULT option. - - Option USE_110_API_DEFAULT sets the default version of - versioned APIs. The bin/makevers perl script did not set - the maxidx variable correctly when the 1.10 branch was - created. This caused the versioning process to always use - the latest version of any API. - - (ADB - 2018/08/17, HDFFV-10552) - - - Added configuration checks for the following MPI functions: - - MPI_Mprobe - Used for the Parallel Compression feature - MPI_Imrecv - Used for the Parallel Compression feature - - MPI_Get_elements_x - Used for the "big Parallel I/O" feature - MPI_Type_size_x - Used for the "big Parallel I/O" feature - - (JTH - 2018/08/02, HDFFV-10512) - - - Added section to the libhdf5.settings file to indicate - the status of the Parallel Compression and "big Parallel I/O" - features. - - (JTH - 2018/08/02, HDFFV-10512) - - - Add option to execute swmr shell scripts from CMake. - - Option TEST_SHELL_SCRIPTS redirects processing into a - separate ShellTests.cmake file for UNIX types. The tests - execute the shell scripts if a SH program is found. - - (ADB - 2018/07/16) - - - Add file locking configure and CMake options - - HDF5 1.10.0 introduced a file locking scheme, primarily to help - enforce SWMR setup. Formerly, the only user-level control of the scheme - was via the HDF5_USE_FILE_LOCKING environment variable. - - This change introduces configure-time options that control whether - or not file locking will be used and whether or not the library - ignores errors when locking has been disabled on the file system - (useful on some HPC Lustre installations). - - In both the Autotools and CMake, the settings have the effect of changing - the default property list settings (see the H5Pset/get_file_locking() - entry, below). - - The yes/no/best-effort file locking configure setting has also been - added to the libhdf5.settings file. - - Autotools: - - An --enable-file-locking=(yes|no|best-effort) option has been added. - - yes: Use file locking. - no: Do not use file locking. - best-effort: Use file locking and ignore "disabled" errors. - - CMake: - - Two self-explanatory options have been added: - - HDF5_USE_FILE_LOCKING - HDF5_IGNORE_DISABLED_FILE_LOCKS - - Setting both of these to ON is the equivalent to the Autotools' - best-effort setting. - - NOTE: - The precedence order of the various file locking control mechanisms is: - - 1) HDF5_USE_FILE_LOCKING environment variable (highest) - - 2) H5Pset_file_locking() - - 3) configure/CMake options (which set the property list defaults) - - 4) library defaults (currently best-effort) - - (DER - 2020/07/30, HDFFV-11092) + (ADB - 2019/10/07, HDFFV-100901, HDFFV-10637, TRILAB-97) Library: -------- - Add new public function H5Ssel_iter_reset - This function resets a dataspace selection iterator back to an - initial state so that it may be used for iteration once more. - This can be useful when needing to iterate over a selection - multiple times without having to repeatedly create/destroy - a selection iterator for that dataspace selection. + This function resets a dataspace selection iterator back to an + initial state so that it may be used for iteration once more. + This can be useful when needing to iterate over a selection + multiple times without having to repeatedly create/destroy + a selection iterator for that dataspace selection. - (JTH - 2020/09/18) + (JTH - 2020/09/18) - Remove HDFS VFD stubs - The original implementation of the HDFS VFD included non-functional - versions of the following public API calls when the HDFS VFD is - not built as a part of the HDF5 library: + The original implementation of the HDFS VFD included non-functional + versions of the following public API calls when the HDFS VFD is + not built as a part of the HDF5 library: - * H5FD_hdfs_init() - * H5Pget_fapl_hdfs() - * H5Pset_fapl_hdfs() + * H5FD_hdfs_init() + * H5Pget_fapl_hdfs() + * H5Pset_fapl_hdfs() - They will remain present in HDF5 1.10 and HDF5 1.12 releases - for binary compatibility purposes but have been removed as of 1.14.0. + They will remain present in HDF5 1.10 and HDF5 1.12 releases + for binary compatibility purposes but have been removed as of 1.14.0. - Note that this has nothing to do with the real HDFS VFD API calls - that are fully functional when the HDFS VFD is configured and built. + Note that this has nothing to do with the real HDFS VFD API calls + that are fully functional when the HDFS VFD is configured and built. - We simply changed: + We simply changed: - #ifdef LIBHDFS - <real API call> - #else - <useless stub> - #endif + #ifdef LIBHDFS + <real API call> + #else + <useless stub> + #endif - to: + to: - #ifdef LIBHDFS - <real API call> - #endif + #ifdef LIBHDFS + <real API call> + #endif - Which is how the other optional VFDs are handled. + Which is how the other optional VFDs are handled. - (DER - 2020/08/27) + (DER - 2020/08/27) - Add Mirror VFD - Use TCP/IP sockets to perform write-only (W/O) file I/O on a remote - machine. Must be used in conjunction with the Splitter VFD. + Use TCP/IP sockets to perform write-only (W/O) file I/O on a remote + machine. Must be used in conjunction with the Splitter VFD. - (JOS - 2020/03/13, TBD) + (JOS - 2020/03/13, TBD) - Add Splitter VFD - Maintain separate R/W and W/O channels for "concurrent" file writes - to two files using a single HDF5 file handle. + Maintain separate R/W and W/O channels for "concurrent" file writes + to two files using a single HDF5 file handle. - (JOS - 2020/03/13, TBD) + (JOS - 2020/03/13, TBD) - Refactored public exposure of haddr_t type in favor of "object tokens" - To better accommodate HDF5 VOL connectors where "object addresses in a file" - may not make much sense, the following changes were made to the library: - - * Introduced new H5O_token_t "object token" type, which represents a - unique and permanent identifier for referencing an HDF5 object within - a container; these "object tokens" are meant to replace object addresses. - Along with the new type, a new H5Oopen_by_token API call was introduced - to open an object by a token, similar to how object addresses were - previously used with H5Oopen_by_addr. - - * Introduced new H5Lget_info2, H5Lget_info_by_idx2, H5Literate2, H5Literate_by_name2, - H5Lvisit2 and H5Lvisit_by_name2 API calls, along with their associated H5L_info2_t - struct and H5L_iterate2_t callback function, which work with the newly-introduced - object tokens, instead of object addresses. The original functions have been - renamed to version 1 functions and are deprecated in favor of the new version 2 - functions. The H5L_info_t and H5L_iterate_t types have been renamed to version 1 - types and are now deprecated in favor of their version 2 counterparts. For each of - the functions and types, compatibility macros take place of the original symbols. - - * Introduced new H5Oget_info3, H5Oget_info_by_name3, H5Oget_info_by_idx3, - H5Ovisit3 and H5Ovisit_by_name3 API calls, along with their associated H5O_info2_t - struct and H5O_iterate2_t callback function, which work with the newly-introduced - object tokens, instead of object addresses. The version 2 functions are now - deprecated in favor of the version 3 functions. The H5O_info_t and H5O_iterate_t - types have been renamed to version 1 types and are now deprecated in favor of their - version 2 counterparts. For each, compatibility macros take place of the original - symbols. - - * Introduced new H5Oget_native_info, H5Oget_native_info_by_name and - H5Oget_native_info_by_idx API calls, along with their associated H5O_native_info_t - struct, which are used to retrieve the native HDF5 file format-specific information - about an object. This information (such as object header info and B-tree/heap info) - has been removed from the new H5O_info2_t struct so that the more generic - H5Oget_info(_by_name/_by_idx)3 routines will not try to retrieve it for non-native - VOL connectors. - - * Added new H5Otoken_cmp, H5Otoken_to_str and H5Otoken_from_str routines to compare - two object tokens, convert an object token into a nicely-readable string format and - to convert an object token string back into a real object token, respectively. - - (DER, QAK, JTH - 2020/01/16) + To better accommodate HDF5 VOL connectors where "object addresses in a file" + may not make much sense, the following changes were made to the library: + + * Introduced new H5O_token_t "object token" type, which represents a + unique and permanent identifier for referencing an HDF5 object within + a container; these "object tokens" are meant to replace object addresses. + Along with the new type, a new H5Oopen_by_token API call was introduced + to open an object by a token, similar to how object addresses were + previously used with H5Oopen_by_addr. + + * Introduced new H5Lget_info2, H5Lget_info_by_idx2, H5Literate2, H5Literate_by_name2, + H5Lvisit2 and H5Lvisit_by_name2 API calls, along with their associated H5L_info2_t + struct and H5L_iterate2_t callback function, which work with the newly-introduced + object tokens, instead of object addresses. The original functions have been + renamed to version 1 functions and are deprecated in favor of the new version 2 + functions. The H5L_info_t and H5L_iterate_t types have been renamed to version 1 + types and are now deprecated in favor of their version 2 counterparts. For each of + the functions and types, compatibility macros take place of the original symbols. + + * Introduced new H5Oget_info3, H5Oget_info_by_name3, H5Oget_info_by_idx3, + H5Ovisit3 and H5Ovisit_by_name3 API calls, along with their associated H5O_info2_t + struct and H5O_iterate2_t callback function, which work with the newly-introduced + object tokens, instead of object addresses. The version 2 functions are now + deprecated in favor of the version 3 functions. The H5O_info_t and H5O_iterate_t + types have been renamed to version 1 types and are now deprecated in favor of their + version 2 counterparts. For each, compatibility macros take place of the original + symbols. + + * Introduced new H5Oget_native_info, H5Oget_native_info_by_name and + H5Oget_native_info_by_idx API calls, along with their associated H5O_native_info_t + struct, which are used to retrieve the native HDF5 file format-specific information + about an object. This information (such as object header info and B-tree/heap info) + has been removed from the new H5O_info2_t struct so that the more generic + H5Oget_info(_by_name/_by_idx)3 routines will not try to retrieve it for non-native + VOL connectors. + + * Added new H5Otoken_cmp, H5Otoken_to_str and H5Otoken_from_str routines to compare + two object tokens, convert an object token into a nicely-readable string format and + to convert an object token string back into a real object token, respectively. + + (DER, QAK, JTH - 2020/01/16) - Add new public function H5Sselect_adjust. - This function shifts a dataspace selection by a specified logical offset - within the dataspace extent. This can be useful for VOL developers to - implement chunked datasets. + This function shifts a dataspace selection by a specified logical offset + within the dataspace extent. This can be useful for VOL developers to + implement chunked datasets. - (NAF - 2019/11/18) + (NAF - 2019/11/18) - Add new public function H5Sselect_project_intersection. - This function computes the intersection between two dataspace selections - and projects that intersection into a third selection. This can be useful - for VOL developers to implement chunked or virtual datasets. + This function computes the intersection between two dataspace selections + and projects that intersection into a third selection. This can be useful + for VOL developers to implement chunked or virtual datasets. - (NAF - 2019/11/13, ID-148) + (NAF - 2019/11/13, ID-148) - Add new public function H5VLget_file_type. - This function returns a datatype equivalent to the supplied datatype but - with the location set to be in the file. This datatype can then be used - with H5Tconvert to convert data between file and in-memory representation. - This funcition is intended for use only by VOL connector developers. - - (NAF - 2019/11/08, ID-127) - - - Add S3 and HDFS VFDs to HDF5 maintenance - - Fix windows requirements and java tests. Windows requires CMake 3.13. - Install openssl library (with dev files); - from "Shining Light Productions". msi package preferred. - - PATH should have been updated with the installation dir. - set ENV variable OPENSSL_ROOT_DIR to the installation dir. - set ENV variable OPENSSL_CONF to the cfg file, likely %OPENSSL_ROOT_DIR%\bin\openssl.cfg - Install libcurl library (with dev files); - download the latest released version using git: https://github.com/curl/curl.git - - Open a Visual Studio Command prompt - change to the libcurl root folder - run the "buildconf.bat" batch file - change to the winbuild directory - nmake /f Makefile.vc mode=dll MACHINE=x64 - copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl (installation dir) - set ENV variable CURL_ROOT to C:\curl (installation dir) - update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir). - the aws credentials file should be in %USERPROFILE%\.aws folder - set the ENV variable "HDF5_ROS3_TEST_BUCKET_URL=https://s3.us-east-2.amazonaws.com/hdf5ros3" - - (ADB - 2019/09/12, HDFFV-10854) - - - Added new chunk query functions - - The following public functions were added to discover information about - the chunks in an HDF5 file. - herr_t H5Dget_num_chunks(dset_id, fspace_id, *nchunks) - herr_t H5Dget_chunk_info_by_coord(dset_id, *coord, *filter_mask, *addr, *size) - herr_t H5Dget_chunk_info(dset_id, fspace_id, index, *coord, *filter_mask, *addr, *size) - - (BMR - 2019/06/11, HDFFV-10677) - - - Improved the performance of virtual dataset I/O + This function returns a datatype equivalent to the supplied datatype but + with the location set to be in the file. This datatype can then be used + with H5Tconvert to convert data between file and in-memory representation. + This funcition is intended for use only by VOL connector developers. - Refactored the internal dataspace routines used by the virtual dataset - code to improve performance, especially when one of the selections - involved is very long and non-contiguous. + (NAF - 2019/11/08, ID-127) - (NAF - 2019/05/31, HDFFV-10693) - - - Added the ability to open files with UTF-8 file names on Windows. - - The POSIX open(2) API call on Windows is limited to ASCII - file names. The library has been updated to convert incoming file - names to UTF-16 (via MultiByteToWideChar(CP_UTF8, ...) and use - _wopen() instead. - - (DER - 2019/03/15, HDFFV-2714, HDFFV-3914, HDFFV-3895, HDFFV-8237, HDFFV-10413, HDFFV-10691) - - - Add new API H5M for map objects. Currently not supported by native - library, can be supported by VOL connectors. - - (NAF - 2019/03/01) - - - Add new H5R_ref_t type for object, dataset region and _attribute_ - references. This new type will deprecate the current hobj_ref_t - and hdset_reg_ref_t types for references. Added H5T_REF datatype - to read and write new reference types. As opposed to previous - reference types, reference creation no longer modifies existing - files. New reference types also now support references to external - files. - - (JS - 2019/10/08) - - - Remove H5I_REFERENCE from the library - - This ID class was never used by the library and has been removed. - - (DER - 2018/12/08, HDFFV-10252) - - - Allow pre-generated H5Tinit.c and H5make_libsettings.c to be used. - - Rather than always running H5detect and generating H5Tinit.c and - H5make_libsettings.c, supply a location for those files. - - (ADB - 2018/09/18, HDFFV-10332) - - - Fix shutdown failure when using H5VLregister_connector_by_name/value - - When using H5VLregister_connector_by_name/value to dynamically load a - VOL connector plugin, the library can experience segmentation faults - when the library is closed. This is due to the library unloading - the plugin interface before the virtual object layer. Then, when the - VOL shutdown occurs, it will attempt to close the VOL connector, - however this will fail since the plugin will already have been unloaded. - - (DER - 2020/03/18, HDFFV-11057) - - - Add BEST_EFFORT value to HDF5_USE_FILE_LOCKING environment variable - - This change adds a BEST_EFFORT to the TRUE/FALSE, 1/0 settings that - were previously accepted. This option turns on file locking but - ignores locking errors when the library detects that file locking - has been disabled on a file system (useful on some HPC Lustre - installations). - - The capitalization of BEST_EFFORT is mandatory. - - See the configure option discussion for HDFFV-11092 (above) for more - information on the file locking feature and how it's controlled. - - (DER - 2020/07/30, HDFFV-11092) - - - - Add H5Pset/get_file_locking() API calls - - This change adds new API calls which can be used to set or get the - file locking parameters. The single API call sets both the "use file - locking" flag and the "ignore disabled file locking" flag. - - See the configure option discussion for HDFFV-11092 (above) for more - information on the file locking feature and how it's controlled. - - (DER - 2020/07/30, HDFFV-11092) Parallel Library: ----------------- - - Changed the default behavior in parallel when reading the same dataset in its entirely - (i.e. H5S_ALL dataset selection) which is being read by all the processes collectively. - The dataset mush be contiguous, less than 2GB, and of an atomic datatype. - The new behavior is the HDF5 library will use an MPI_Bcast to pass the data read from - the disk by the root process to the remain processes in the MPI communicator associated - with the HDF5 file. + - - (MSB - 2019/01/02, HDFFV-10652) Fortran Library: ---------------- - - Added new Fortran derived type, c_h5o_info_t, which is interoperable with - C's h5o_info_t. This is needed for callback functions which - pass C's h5o_info_t data type definition. - - (MSB, 2019/01/08, HDFFV-10443) - - - Added new Fortran API, H5gmtime, which converts (C) 'time_t' structure - to Fortran DATE AND TIME storage format. - - (MSB, 2019/01/08, HDFFV-10443) - - - Added new Fortran 'fields' optional parameter to: h5ovisit_f, h5oget_info_by_name_f, - h5oget_info, h5oget_info_by_idx and h5ovisit_by_name_f. - - (MSB, 2019/01/08, HDFFV-10443) - - Add wrappers for H5Pset/get_file_locking() API calls - h5pget_file_locking_f() - h5pset_file_locking_f() + h5pget_file_locking_f() + h5pset_file_locking_f() - See the configure option discussion for HDFFV-11092 (above) for more - information on the file locking feature and how it's controlled. + See the configure option discussion for HDFFV-11092 (above) for more + information on the file locking feature and how it's controlled. - (DER - 2020/07/30, HDFFV-11092) + (DER - 2020/07/30, HDFFV-11092) C++ Library: ------------ - - Added new wrappers for H5Pset/get_create_intermediate_group() - LinkCreatPropList::getCreateIntermediateGroup() - LinkCreatPropList::setCreateIntermediateGroup() - - (BMR - 2019/04/22, HDFFV-10622) - - - Added new wrapper for H5Ovisit2() - H5Object::visit() - - (BMR - 2019/02/14, HDFFV-10532) - - Add wrappers for H5Pset/get_file_locking() API calls - FileAccPropList::setFileLocking() - FileAccPropList::getFileLocking() + FileAccPropList::setFileLocking() + FileAccPropList::getFileLocking() - See the configure option discussion for HDFFV-11092 (above) for more - information on the file locking feature and how it's controlled. + See the configure option discussion for HDFFV-11092 (above) for more + information on the file locking feature and how it's controlled. - (DER - 2020/07/30, HDFFV-11092) + (DER - 2020/07/30, HDFFV-11092) Java Library: ---------------- - Added new H5S functions. - H5Sselect_copy, H5Sselect_shape_same, H5Sselect_adjust, - H5Sselect_intersect_block, H5Sselect_project_intersection, - H5Scombine_hyperslab, H5Smodify_select, H5Scombine_select - wrapper functions added. - - (ADB - 2020/10/27, HDFFV-10868) - - - Added ability to test java library with VOLs. - - Created new CMake script that combines the java and vol test scripts. - - (ADB - 2020/02/03, HDFFV-10996) - - - Tests fail for non-English locale. - - In the JUnit tests with a non-English locale, only the part before - the decimal comma is replaced by XXXX and this leads to a comparison - error. Changed the regex for the Time substitution. - - (ADB - 2020/01/09, HDFFV-10995) - - - Fix a failure in JUnit-TestH5P on 32-bit architectures + H5Sselect_copy, H5Sselect_shape_same, H5Sselect_adjust, + H5Sselect_intersect_block, H5Sselect_project_intersection, + H5Scombine_hyperslab, H5Smodify_select, H5Scombine_select + wrapper functions added. - (JTH - 2019/04/30) + (ADB - 2020/10/27, HDFFV-10868) - - Duplicate the data read/write functions of Datasets for Attributes. + - Add wrappers for H5Pset/get_file_locking() API calls - Region references could not be displayed for attributes as they could - for datasets. Datasets had overloaded read and write functions for different - datatypes that were not available for attributes. After adding similar - functions, attribute region references work normally. + H5Pset_file_locking() + H5Pget_use_file_locking() + H5Pget_ignore_disabled_file_locking() - (ADB - 2018/12/12, HDFVIEW-4) + Unlike the C++ and Fortran wrappers, there are separate getters for the + two file locking settings, each of which returns a boolean value. - - Removed H5I_REFERENCE from the Java wrappers + See the configure option discussion for HDFFV-11092 (above) for more + information on the file locking feature and how it's controlled. - This ID class was never used by the library and has been removed - from the Java wrappers. + (DER - 2020/07/30, HDFFV-11092) - (DER - 2018/12/08, HDFFV-10252) + - Added ability to test java library with VOLs. - - Add wrappers for H5Pset/get_file_locking() API calls + Created new CMake script that combines the java and vol test scripts. - H5Pset_file_locking() - H5Pget_use_file_locking() - H5Pget_ignore_disabled_file_locking() + (ADB - 2020/02/03, HDFFV-10996) - Unlike the C++ and Fortran wrappers, there are separate getters for the - two file locking settings, each of which returns a boolean value. + - Tests fail for non-English locale. - See the configure option discussion for HDFFV-11092 (above) for more - information on the file locking feature and how it's controlled. + In the JUnit tests with a non-English locale, only the part before + the decimal comma is replaced by XXXX and this leads to a comparison + error. Changed the regex for the Time substitution. - (DER - 2020/07/30, HDFFV-11092) + (ADB - 2020/01/09, HDFFV-10995) Tools: ------ - h5repack added options to control how external links are handled. - Currently h5repack preserves external links and cannot copy and merge - data from the external files. Two options, merge and prune, were added to - control how to merge data from an external link into the resulting file. - --merge Follow external soft link recursively and merge data. - --prune Do not follow external soft links and remove link. - --merge --prune Follow external link, merge data and remove dangling link. + Currently h5repack preserves external links and cannot copy and merge + data from the external files. Two options, merge and prune, were added to + control how to merge data from an external link into the resulting file. + --merge Follow external soft link recursively and merge data. + --prune Do not follow external soft links and remove link. + --merge --prune Follow external link, merge data and remove dangling link. - (ADB - 2020/08/05, HDFFV-9984) + (ADB - 2020/08/05, HDFFV-9984) - h5repack was fixed to repack the reference attributes properly. - The code line that checks if the update of reference inside a compound - datatype is misplaced outside the code block loop that carries out the - check. In consequence, the next attribute that is not the reference - type was repacked again as the reference type and caused the failure of - repacking. The fix is to move the corresponding code line to the correct - code block. + The code line that checks if the update of reference inside a compound + datatype is misplaced outside the code block loop that carries out the + check. In consequence, the next attribute that is not the reference + type was repacked again as the reference type and caused the failure of + repacking. The fix is to move the corresponding code line to the correct + code block. - (KY -2020/02/07, HDFFV-11014) + (KY -2020/02/07, HDFFV-11014) - h5diff was updated to use the new reference APIs. - h5diff uses the new reference APIs to compare references. - Attribute references can also be compared. + h5diff uses the new reference APIs to compare references. + Attribute references can also be compared. - (ADB - 2019/12/19, HDFFV-10980) + (ADB - 2019/12/19, HDFFV-10980) - h5dump and h5ls were updated to use the new reference APIs. - The tools library now use the new reference APIs to inspect a - file. Also the DDL spec was updated to reflect the format - changes produced with the new APIs. The export API and support - functions in the JNI were updated to match. - - (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877) - - - h5repack was fixed to repack datasets with external storage - to other types of storage. + The tools library now use the new reference APIs to inspect a + file. Also the DDL spec was updated to reflect the format + changes produced with the new APIs. The export API and support + functions in the JNI were updated to match. - New test added to repack files and verify the correct data using h5diff. - - (JS - 2019/09/25, HDFFV-10408) - (ADB - 2019/10/02, HDFFV-10918) - - - h5dump was fixed for 128-bit floats, but was missing a test. - - New test greps for the first 15 numbers of the 128-bit value. - - (ADB - 2019/06/23, HDFFV-9407) + (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877) High-Level APIs: @@ -874,431 +549,130 @@ Support for new platforms, languages and compilers. ======================================= - -Bug Fixes since HDF5-1.10.3 release +Bug Fixes since HDF5-1.12.0 release ================================== Library ------- - Creation of dataset with optional filter - When the combination of type, space, etc doesn't work for filter - and the filter is optional, it was supposed to be skipped but it was - not skipped and the creation failed. + When the combination of type, space, etc doesn't work for filter + and the filter is optional, it was supposed to be skipped but it was + not skipped and the creation failed. - Allowed the creation of the dataset in such situation. + Allowed the creation of the dataset in such situation. - (BMR - 2020/8/13, HDFFV-10933) + (BMR - 2020/08/13, HDFFV-10933) - Explicitly declared dlopen to use RTLD_LOCAL - dlopen documentation states that if neither RTLD_GLOBAL nor - RTLD_LOCAL are specified, then the default behavior is unspecified. - The default on linux is usually RTLD_LOCAL while macos will default - to RTLD_GLOBAL. - - (ADB - 2020/08/12, HDFFV-11127) - - - Fixed issues CVE-2018-13870 and CVE-2018-13869 - - When a buffer overflow occurred because a name length was corrupted - and became very large, h5dump crashed on memory access violation. - - A check for reading pass the end of the buffer was added to multiple - locations to prevent the crashes and h5dump now simply fails with an - error message when this error condition occurs. - - (BMR - 2020/07/22, HDFFV-11120 and HDFFV-11121) - - - Fixed the segmentation fault when reading attributes with multiple threads - - It was reported that the reading of attributes with variable length string - datatype will crash with segmentation fault particularly when the number of - threads is high (>16 threads). The problem was due to the file pointer that - was set in the variable length string datatype for the attribute. That file - pointer was already closed when the attribute was accessed. - - The problem was fixed by setting the file pointer to the current opened file pointer - when the attribute was accessed. Similar patch up was done before when reading - dataset with variable length string datatype. - - (VC - 2020/07/13, HDFFV-11080) - - - Fixed CVE-2020-10810 - - The tool h5clear produced a segfault during an error recovery in - the superblock decoding. An internal pointer was reset to prevent - further accessing when it is not assigned with a value. - - (BMR - 2020/6/29, HDFFV-11053) - - - Fixed CVE-2018-17435 - - The tool h52gif produced a segfault when the size of an attribute - message was corrupted and caused a buffer overflow. - - The problem was fixed by verifying the attribute message's size - against the buffer size before accessing the buffer. h52gif was - also fixed to display the failure instead of silently exiting - after the segfault was eliminated. - - (BMR - 2020/6/19, HDFFV-10591) - - - Improved peformance when creating a large number of small datasets by - retrieving default property values from the API context instead of doing - skip list searches. - - (CJH - 2019/12/10, HDFFV-10658) - - - Fixed user-created data access properties not existing in the property list - returned by H5Dget_access_plist. Thanks to Steven Varga for submitting a - reproducer and a patch. - - (CJH - 2019/12/9, HDFFV-10934) - - - Fixed an assertion failure in the parallel library when collectively - filling chunks. As it is required that chunks be written in - monotonically non-decreasing order of offset in the file, this assertion - was being triggered when the list of chunk file space allocations being - passed to the collective chunk filling routine was not sorted according - to this particular requirement. - - The addition of a sort of the out of order chunks trades a bit of - performance for the elimination of this assertion and of any complaints - from MPI implementations about the file offsets used being out of order. - - (JTH - 2019/10/07, HDFFV-10792) - - - Fixed the iteration error in test_versionbounds() in test/dtypes.c - - The test was supposed to loop through all valid combinations of - low and high bounds in the array versions[], but they were set to - H5F_LIBVER_EARLIEST always without changing. - - The problem was fixed by indexing low and high into the array versions[]. - - (VC - 2019/09/30) - - - Fixed the slowness of regular hyperslab selection in a chunked dataset - - It was reported that the selection of every 10th element from a 20G - chunked dataset was extremely slow and sometimes could hang the system. - The problem was due to the iteration and the building of the span tree - for all the selected elements in file space. - - As the selected elements are going to a 1-d contiguous single block - memory space, the problem was fixed by building regular hyperslab selections - in memory space for the selected elements in file space. - - (VC - 2019/09/26, HDFFV-10585) - - - Fixed a bug caused by bad tag value when condensing object header - messages + dlopen documentation states that if neither RTLD_GLOBAL nor + RTLD_LOCAL are specified, then the default behavior is unspecified. + The default on linux is usually RTLD_LOCAL while macos will default + to RTLD_GLOBAL. - There was an assertion failure when moving meessages from running a - user test program with library release hdf5.1.10.4. It was because - the tag value (object header's address) was not set up when entering - the library routine H5O__chunk_update_idx(), which will eventually - verifies the metadata tag value when protecting the object header. + (ADB - 2020/08/12, HDFFV-11127) - The problem was fixed by replacing FUNC_ENTER_PACKAGE in H5O__chunk_update_idx() - with FUNC_ENTER_PACKAGE_TAG(oh->cache_info.addr) to set up the metadata tag. - - (VC - 2019/08/23, HDFFV-10873) - - - Fixed the test failure from test_metadata_read_retry_info() in - test/swmr.c - - The test failure is due to the incorrect number of bins returned for - retry info (info.nbins). The # of bins expected for 101 read attempts - is 3 instead of 2. The routine H5F_set_retries() in src/H5Fint.c - calculates the # of bins by first obtaining the log10 value for - (read attempts - 1). For PGI/19, the log10 value for 100 read attempts - is 1.9999999999999998 instead of 2.00000. When casting the log10 value - to unsigned later on, the decimal part is chopped off causing the test - failure. - - This was fixed by obtaining the rounded integer value (HDceil) for the - log10 value of read attempts first before casting the result to unsigned. - - (VC - 2019/8/14, HDFFV-10813) - - - Fixed an issue where creating a file with non-default file space info - together with library high bound setting to H5F_LIBVER_V18. - - When setting non-default file space info in fcpl via - H5Pset_file_space_strategy() and then creating a file with - both high and low library bounds set to - H5F_LIBVER_V18 in fapl, the library succeeds in creating the file. - File creation should fail because the feature of setting non-default - file space info does not exist in library release 1.8 or earlier. - - This was fixed by setting and checking the proper version in the - file space info message based on the library low and high bounds - when creating and opening the HDF5 file. - - (VC - 2019/6/25, HDFFV-10808) - - - When iterating over an old-style group (i.e., when not using the latest - file format) of size 0, a NULL pointer representing the empty links - table would be sent to qsort(3) for sorting, which is undefined behavior. - - Iterating over an empty group is explicitly tested in the links test. - This has not caused any failures to date and was flagged by gcc's - -fsanitize=undefined. - - The library no longer attempts to sort an empty array. - - (DER - 2019/06/18, HDFFV-10829) - - - Fixed an issue where copying a version 1.8 dataset between files using - H5Ocopy fails due to an incompatible fill version - - When using the HDF5 1.10.x H5Ocopy() API call to copy a version 1.8 - dataset to a file created with both high and low library bounds set to - H5F_LIBVER_V18, the H5Ocopy() call will fail with the error stack indicating - that the fill value version is out of bounds. - - This was fixed by changing the fill value message version to H5O_FILL_VERSION_3 - (from H5O_FILL_VERSION_2) for H5F_LIBVER_V18. - - (VC - 2019/6/14, HDFFV-10800) - - - Some oversights in the index iterating area of the library caused - a callback function to continue iterating even though it's supposed - to stop. - - Added the returned value check to the for loop's conditions in - H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate(). The - iteration now stops when it should. - - (BMR - 2019/06/11, HDFFV-10661) - - - Fixed a bug that would cause an error or cause fill values to be - incorrectly read from a chunked dataset using the "single chunk" index if - the data was held in cache and there was no data on disk. - - (NAF - 2019/03/06) - - - Fixed a bug that could cause an error or cause fill values to be - incorrectly read from a dataset that was written to using H5Dwrite_chunk - if the dataset was not closed after writing. - - (NAF - 2019/03/06, HDFFV-10716) - - - Fixed memory leak in scale offset filter - - In a special case where the MinBits is the same as the number of bits in - the datatype's precision, the filter's data buffer was not freed, causing - the memory usage to grow. In general the buffer was freed correctly. The - Minbits are the minimal number of bits to store the data values. Please - see the reference manual for H5Pset_scaleoffset for the detail. - - (RL - 2019/3/4, HDFFV-10705) - - - Fix hangs with collective metadata reads during chunked dataset I/O - - In the parallel library, it was discovered that when a particular - sequence of operations following a pattern of: - - "write to chunked dataset" -> "flush file" -> "read from dataset" - - occurred with collective metadata reads enabled, hangs could be - observed due to certain MPI ranks not participating in the collective - metadata reads. - - To fix the issue, collective metadata reads are now disabled during - chunked dataset raw data I/O. - - (JTH - 2019/02/11, HDFFV-10563, HDFFV-10688) - - - Performance issue when closing an object - - The slow down is due to the search of the "tag_list" to find - out the "corked" status of an object and "uncork" it if so. - - Improve porformance by skipping the search of the "tag_list" - if there are no "corked" objects when closing an object. - - (VC - 2019/2/6) - - - Fixed a potential invalid memory access and failure that could occur when - decoding an unknown object header message (from a future version of the - library). - - (NAF - 2019/01/07) - - - Deleting attributes in dense storage - - The library aborts with "infinite loop closing library" after - attributes in dense storage are created and then deleted. - - When deleting the attribute nodes from the name index v2 B-tree, - if an attribute is found in the intermediate B-tree nodes, - which may be merged/redistributed in the process, we need to - free the dynamically allocated spaces for the intermediate - decoded attribute. - - (VC - 2018/12/26, HDFFV-10659) - - - Allow H5detect and H5make_libsettings to take a file as an argument. - - Rather than only writing to stdout, add a command argument to name - the file that H5detect and H5make_libsettings will use for output. - Without an argument, stdout is still used, so backwards compatibility - is maintained. + - H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which + causes asserts/errors when passed to other dataspace API calls. - (ADB - 2018/09/05, HDFFV-9059) + H5S_NO_CLASS is an internal class value that should not have been + exposed via a public API call. - - A bug was discovered in the parallel library where an application - would hang if a collective read/write of a chunked dataset occurred - when collective metadata reads were enabled and some of the ranks - had no selection in the dataset's dataspace. The ranks which had no - selection in the dataset's dataspace called H5D__chunk_addrmap() to - retrieve the lowest chunk address in the dataset. This is because we - require reads/writes to be performed in strictly non-decreasing order - of chunk address in the file. + In debug builds of the library, this can cause asserts to trip. In + non-debug builds, it will produce normal library errors. - When the chunk index used was a version 1 or 2 B-tree, these - non-participating ranks would issue a collective MPI_Bcast() call - that the participating ranks would not issue, causing the hang. Since - the non-participating ranks are not actually reading/writing anything, - the H5D__chunk_addrmap() call can be safely removed and the address used - for the read/write can be set to an arbitrary number (0 was chosen). + The new library behavior is for H5Sset_extent_none() to convert + the dataspace into one of type H5S_NULL, which is better handled + by the library and easier for developers to reason about. - (JTH - 2018/08/25, HDFFV-10501) + (DER - 2020/07/27, HDFFV-11027) - - fcntl(2)-based file locking incorrectly passed the lock argument struct - instead of a pointer to the struct, causing errors on systems where - flock(2) is not available. + - Fixed issues CVE-2018-13870 and CVE-2018-13869 - File locking is used when files are opened to enforce SWMR semantics. A - lock operation takes place on all file opens unless the - HDF5_USE_FILE_LOCKING environment variable is set to the string "FALSE". - flock(2) is preferentially used, with fcntl(2) locks as a backup if - flock(2) is unavailable on a system (if neither is available, the lock - operation fails). On these systems, the file lock will often fail, which - causes HDF5 to not open the file and report an error. + When a buffer overflow occurred because a name length was corrupted + and became very large, h5dump crashed on memory access violation. - This bug only affects POSIX systems. Win32 builds on Windows use a no-op - locking call which always succeeds. Systems which exhibit this bug will - have H5_HAVE_FCNTL defined but not H5_HAVE_FLOCK in the configure output. + A check for reading pass the end of the buffer was added to multiple + locations to prevent the crashes and h5dump now simply fails with an + error message when this error condition occurs. - This bug affects HDF5 1.10.0 through 1.10.5. + (BMR - 2020/07/22, HDFFV-11120 and HDFFV-11121) - fcntl(2)-based file locking now correctly passes the struct pointer. + - Fixed the segmentation fault when reading attributes with multiple threads - (DER - 2019/08/27, HDFFV-10892) + It was reported that the reading of attributes with variable length string + datatype will crash with segmentation fault particularly when the number of + threads is high (>16 threads). The problem was due to the file pointer that + was set in the variable length string datatype for the attribute. That file + pointer was already closed when the attribute was accessed. - - Torn pread/pwrite I/O would result in read and write corruption. + The problem was fixed by setting the file pointer to the current opened file pointer + when the attribute was accessed. Similar patch up was done before when reading + dataset with variable length string datatype. - In the sec2, log, and core (with backing store) virtual file drivers - (VFDs), the read and write calls incorrectly reset the offset parameter - on torn pread and pwrite operations (i.e., I/O operations which fail to - be written atomically by the OS). For this bug to occur, pread/pwrite - have to be configured (this is the default if they are present on the - system) and the pread/pwrite operation has to fail to transfer all - the bytes, resulting in a multiple pread/pwrite calls. + (VC - 2020/07/13, HDFFV-11080) - This feature was initially enabled in HDF5 1.10.5 so the bug is - limited to that version. + - Fixed CVE-2020-10810 - (DER - 2019/12/09, HDFFV-10945) + The tool h5clear produced a segfault during an error recovery in + the superblock decoding. An internal pointer was reset to prevent + further accessing when it is not assigned with a value. - - H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which - causes asserts/errors when passed to other dataspace API calls. + (BMR - 2020/06/29, HDFFV-11053) - H5S_NO_CLASS is an internal class value that should not have been - exposed via a public API call. + - Fixed CVE-2018-17435 - In debug builds of the library, this can cause asserts to trip. In - non-debug builds, it will produce normal library errors. + The tool h52gif produced a segfault when the size of an attribute + message was corrupted and caused a buffer overflow. - The new library behavior is for H5Sset_extent_none() to convert - the dataspace into one of type H5S_NULL, which is better handled - by the library and easier for developers to reason about. + The problem was fixed by verifying the attribute message's size + against the buffer size before accessing the buffer. h52gif was + also fixed to display the failure instead of silently exiting + after the segfault was eliminated. - (DER - 2020/07/27, HDFFV-11027) + (BMR - 2020/06/19, HDFFV-10591) Java Library: ---------------- - - JNI native library dependencies - - The build for the hdf5_java native library used the wrong - hdf5 target library for CMake builds. Correcting the hdf5_java - library to build with the shared hdf5 library required testing - paths to change also. - - (ADB - 2018/08/31, HDFFV-10568) - - Java iterator callbacks - - Change global callback object to a small stack structure in order - to fix a runtime crash. This crash was discovered when iterating - through a file with nested group members. The global variable - visit_callback is overwritten when recursion starts. When recursion - completes, visit_callback will be pointing to the wrong callback method. - - (ADB - 2018/08/15, HDFFV-10536) + - Added ability to test java library with VOLs. - - Java HDFLibraryException class + Created new CMake script that combines the java and vol test scripts. - Change parent class from Exception to RuntimeException. + (ADB - 2020/02/03, HDFFV-10996) - (ADB - 2018/07/30, HDFFV-10534) + - Tests fail for non-English locale. - - JNI Read and Write + In the JUnit tests with a non-English locale, only the part before + the decimal comma is replaced by XXXX and this leads to a comparison + error. Changed the regex for the Time substitution. - Refactored variable-length functions, H5DreadVL and H5AreadVL, - to correct dataset and attribute reads. New write functions, - H5DwriteVL and H5AwriteVL, are under construction. + (ADB - 2020/01/09, HDFFV-10995) - (ADB - 2018/06/02, HDFFV-10519) Configuration ------------- - - Correct option for default API version - - CMake options for default API version are not mutually exclusive. - Change the multiple BOOL options to a single STRING option with the - strings; v16, v18, v110, v112. + - - (ADB - 2019/08/12, HDFFV-10879) Performance ------------- - + Fortran -------- - - Added symbolic links libhdf5_hl_fortran.so to libhdf5hl_fortran.so and - libhdf5_hl_fortran.a to libhdf5hl_fortran.a in hdf5/lib directory for - autotools installs. These were added to match the name of the files - installed by cmake and the general pattern of hl lib files. We will - change the names of the installed lib files to the matching name in - the next major release. - - (LRK - 2019/01/04, HDFFV-10596) - - - Made Fortran specific subroutines PRIVATE in generic procedures. - - Effected generic procedures were functions in H5A, H5D, H5P, H5R and H5T. - - (MSB, 2018/12/04, HDFFV-10511) - - - Fixed issue with Fortran not returning h5o_info_t field values - meta_size%attr%index_size and meta_size%attr%heap_size. - - (MSB, 2018/1/8, HDFFV-10443) - - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f. - (MSB - 2020/2/18, HDFFV-11029) + (MSB - 2020/02/18, HDFFV-11029) + Tools ----- - The tools library was updated by standardizing the error stack process. - General sequence is: + General sequence is: h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); h5tools_init(); @@ -1307,292 +681,66 @@ Bug Fixes since HDF5-1.10.3 release ... (do work) ... h5diff_exit(ret); - (ADB - 2020/07/20, HDFFV-11066) + (ADB - 2020/07/20, HDFFV-11066) - h5diff fixed a command line parsing error. - h5diff would ignore the argument to -d (delta) if it is smaller than DBL_EPSILON. - The macro H5_DBL_ABS_EQUAL was removed and a direct value comparision was used. + h5diff would ignore the argument to -d (delta) if it is smaller than DBL_EPSILON. + The macro H5_DBL_ABS_EQUAL was removed and a direct value comparision was used. - (ADB - 2020/07/20, HDFFV-10897) + (ADB - 2020/07/20, HDFFV-10897) - h5diff added a command line option to ignore attributes. - h5diff would ignore all objects with a supplied path if the exclude-path argument is used. - Adding the exclude-attribute argument will only eclude attributes, with the supplied path, - from comparision. + h5diff would ignore all objects with a supplied path if the exclude-path argument is used. + Adding the exclude-attribute argument will only eclude attributes, with the supplied path, + from comparision. - (ADB - 2020/07/20, HDFFV-5935) + (ADB - 2020/07/20, HDFFV-5935) - h5diff added another level to the verbose argument to print filenames. - Added verbose level 3 that is level 2 plus the filenames. The levels are: + Added verbose level 3 that is level 2 plus the filenames. The levels are: 0 : Identical to '-v' or '--verbose' 1 : All level 0 information plus one-line attribute status summary 2 : All level 1 information plus extended attribute status report 3 : All level 2 information plus file names - (ADB - 2020/07/20, HDFFV-10005) - - High-Level APIs: - ------ - - The H5DSis_scale function was updated to return "not a dimension scale" (0) - instead of failing (-1), when CLASS or DIMENSION_SCALE attributes are - not written according to Dimension Scales Specification. - - (EIP - 2020/08/12, HDFFV-10436) - - Fortran High-Level APIs: - ------ - - - - Documentation - ------------- - - - - F90 APIs - -------- - - - - C++ APIs - -------- - - - - Testing - ------- - - Stopped java/test/junit.sh.in installing libs for testing under ${prefix} - - Lib files needed are now copied to a subdirectory in the java/test - directory, and on Macs the loader path for libhdf5.xxxs.so is changed - in the temporary copy of libhdf5_java.dylib. - - (LRK, 2020/7/2, HDFFV-11063) - - - Fixed a test failure in testpar/t_dset.c caused by - the test trying to use the parallel filters feature - on MPI-2 implementations. - - (JTH, 2019/2/7) - -Bug Fixes since HDF5-1.10.2 release -================================== - - Library - ------- - - Java HDF5LibraryException class - - The error minor and major values would be lost after the - constructor executed. - - Created two local class variables to hold the values obtained during - execution of the constructor. Refactored the class functions to retrieve - the class values rather then calling the native functions. - The native functions were renamed and called only during execution - of the constructor. - Added error checking to calling class constructors in JNI classes. - - (ADB - 2018/08/06, HDFFV-10544) - - - Added checks of the defined MPI_VERSION to guard against usage of - MPI-3 functions in the Parallel Compression and "big Parallel I/O" - features when HDF5 is built with MPI-2. Previously, the configure - step would pass but the build itself would fail when it could not - locate the MPI-3 functions used. - - As a result of these new checks, HDF5 can again be built with MPI-2, - but the Parallel Compression feature will be disabled as it relies - on the MPI-3 functions used. - - (JTH - 2018/08/02, HDFFV-10512) - - - User's patches: CVEs - - The following patches have been applied: - - CVE-2018-11202 - NULL pointer dereference was discovered in - H5S_hyper_make_spans in H5Shyper.c (HDFFV-10476) - https://security-tracker.debian.org/tracker/CVE-2018-11202 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11202 - - CVE-2018-11203 - A division by zero was discovered in - H5D__btree_decode_key in H5Dbtree.c (HDFFV-10477) - https://security-tracker.debian.org/tracker/CVE-2018-11203 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11203 - - CVE-2018-11204 - A NULL pointer dereference was discovered in - H5O__chunk_deserialize in H5Ocache.c (HDFFV-10478) - https://security-tracker.debian.org/tracker/CVE-2018-11204 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11204 - - CVE-2018-11206 - An out of bound read was discovered in - H5O_fill_new_decode and H5O_fill_old_decode in H5Ofill.c - (HDFFV-10480) - https://security-tracker.debian.org/tracker/CVE-2018-11206 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11206 - - CVE-2018-11207 - A division by zero was discovered in - H5D__chunk_init in H5Dchunk.c (HDFFV-10481) - https://security-tracker.debian.org/tracker/CVE-2018-11207 - https://cve.mitre.org/cgi-bin/cvename.cgi?name=3DCVE-2018-11207 - - (BMR - 2018/7/22, PR#s: 1134 and 1139, - HDFFV-10476, HDFFV-10477, HDFFV-10478, HDFFV-10480, HDFFV-10481) - - - H5Adelete - - H5Adelete failed when deleting the last "large" attribute that - is stored densely via fractal heap/v2 b-tree. - - After removing the attribute, update the ainfo message. If the - number of attributes goes to zero, remove the message. - - (VC - 2018/07/20, HDFFV-9277) - - - A bug was discovered in the parallel library which caused partial - parallel reads of filtered datasets to return incorrect data. The - library used the incorrect dataspace for each chunk read, causing - the selection used in each chunk to be wrong. - - The bug was not caught during testing because all of the current - tests which do parallel reads of filtered data read all of the data - using an H5S_ALL selection. Several tests were added which exercise - partial parallel reads. - - (JTH - 2018/07/16, HDFFV-10467) - - - A bug was discovered in the parallel library which caused parallel - writes of filtered datasets to trigger an assertion failure in the - file free space manager. - - This occurred when the filter used caused chunks to repeatedly shrink - and grow over the course of several dataset writes. The previous chunk - information, such as the size of the chunk and the offset in the file, - was being cached and not updated after each write, causing the next write - to the chunk to retrieve the incorrect cached information and run into - issues when reallocating space in the file for the chunk. - - (JTH - 2018/07/16, HDFFV-10509) - - - A bug was discovered in the parallel library which caused the - H5D__mpio_array_gatherv() function to allocate too much memory. - - When the function is called with the 'allgather' parameter set - to a non-true value, the function will receive data from all MPI - ranks and gather it to the single rank specied by the 'root' - parameter. However, the bug in the function caused memory for - the received data to be allocated on all MPI ranks, not just the - singular rank specified as the receiver. In some circumstances, - this would cause an application to fail due to the large amounts - of memory being allocated. - - (JTH - 2018/07/16, HDFFV-10467) - - - Error checks in h5stat and when decoding messages - - h5stat exited with seg fault/core dumped when - errors are encountered in the internal library. - - Add error checks and --enable-error-stack option to h5stat. - Add range checks when decoding messages: old fill value, old - layout and refcount. - - (VC - 2018/07/11, HDFFV-10333) - - - If an HDF5 file contains a malformed compound datatype with a - suitably large offset, the type conversion code can run off - the end of the type conversion buffer, causing a segmentation - fault. - - This issue was reported to The HDF Group as issue #CVE-2017-17507. - - NOTE: The HDF5 C library cannot produce such a file. This condition - should only occur in a corrupt (or deliberately altered) file - or a file created by third-party software. + (ADB - 2020/07/20, HDFFV-10005) - THE HDF GROUP WILL NOT FIX THIS BUG AT THIS TIME - - Fixing this problem would involve updating the publicly visible - H5T_conv_t function pointer typedef and versioning the API calls - which use it. We normally only modify the public API during - major releases, so this bug will not be fixed at this time. - - (DER - 2018/02/26, HDFFV-10356) - - - Inappropriate linking with deprecated MPI C++ libraries - - HDF5 does not define *_SKIP_MPICXX in the public headers, so applications - can inadvertently wind up linking to the deprecated MPI C++ wrappers. - - MPICH_SKIP_MPICXX and OMPI_SKIP_MPICXX have both been defined in H5public.h - so this should no longer be an issue. HDF5 makes no use of the deprecated - MPI C++ wrappers. - - (DER - 2019/09/17, HDFFV-10893) - - - - Configuration - ------------- - - Applied patches to address Cywin build issues - - There were three issues for Cygwin builds: - - Shared libs were not built. - - The -std=c99 flag caused a SIG_SETMASK undeclared error. - - Undefined errors when buildbing test shared libraries. - - Patches to address these issues were received and incorporated in this version. - - (LRK - 2018/07/18, HDFFV-10475) - - - Moved the location of gcc attribute. - - The gcc attribute(no_sanitize), named as the macro HDF_NO_UBSAN, - was located after the function name. Builds with GCC 7 did not - indicate any problem, but GCC 8 issued errors. Moved the - attribute before the function name, as required. - - (ADB - 2018/05/22, HDFFV-10473) - - - Reworked java test suite into individual JUnit tests. + - h5repack was fixed to repack the reference attributes properly. - Testing the whole suite of java unit tests in a single JUnit run - made it difficult to determine actual failures when tests would fail. - Running each file set of tests individually, allows individual failures - to be diagnosed easier. A side benefit is that tests for optional components - of the library can be disabled if not configured. + The code line that checks if the update of reference inside a compound + datatype is misplaced outside the code block loop that carries out the + check. In consequence, the next attribute that is not the reference + type was repacked again as the reference type and caused the failure of + repacking. The fix is to move the corresponding code line to the correct + code block. - (ADB - 2018/05/16, HDFFV-9739) + (KY -2020/02/10, HDFFV-11014) - - Converted CMake global commands ADD_DEFINITIONS and INCLUDE_DIRECTORIES - to use target_* type commands. This change modernizes the CMake usage - in the HDF5 library. + - h5diff was updated to use the new reference APIs. - In addition, there is the intention to convert to generator expressions, - where possible. The exception is Fortran FLAGS on Windows Visual Studio. - The HDF macros TARGET_C_PROPERTIES and TARGET_FORTRAN_PROPERTIES have - been removed with this change in usage. + h5diff uses the new reference APIs to compare references. + Attribute references can also be compared. - The additional language (C++ and Fortran) checks have also been localized - to only be checked when that language is enabled. + (ADB - 2019/12/19, HDFFV-10980) - (ADB - 2018/05/08) + - h5dump and h5ls were updated to use the new reference APIs. - Performance - ------------- - - + The tools library now use the new reference APIs to inspect a + file. Also the DDL spec was updated to reflect the format + changes produced with the new APIs. The export API and support + functions in the JNI were updated to match. - Fortran - -------- - - + (ADB - 2019/12/06, HDFFV-10876 and HDFFV-10877) - Tools - ----- - - High-Level APIs: ------ - + Fortran High-Level APIs: ------ - @@ -1607,36 +755,18 @@ Bug Fixes since HDF5-1.10.2 release C++ APIs -------- - - Adding default arguments to existing functions - - Added the following items: - + Two more property list arguments are added to H5Location::createDataSet: - const DSetAccPropList& dapl = DSetAccPropList::DEFAULT - const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT - - + One more property list argument is added to H5Location::openDataSet: - const DSetAccPropList& dapl = DSetAccPropList::DEFAULT - - (BMR - 2018/07/21, PR# 1146) - - - Improvement C++ documentation - - Replaced the table in main page of the C++ documentation from mht to htm format - for portability. - - (BMR - 2018/07/17, PR# 1141) + - Testing ------- - - The dt_arith test failed on IBM Power8 and Power9 machines when testing - conversions from or to long double types, especially when special values - such as infinity or NAN were involved. In some cases the results differed - by extremely small amounts from those on other machines, while some other - tests resulted in segmentation faults. These conversion tests with long - double types have been disabled for ppc64 machines until the problems are - better understood and can be properly addressed. + - Stopped java/test/junit.sh.in installing libs for testing under ${prefix} + + Lib files needed are now copied to a subdirectory in the java/test + directory, and on Macs the loader path for libhdf5.xxxs.so is changed + in the temporary copy of libhdf5_java.dylib. + + (LRK, 2020/07/02, HDFFV-11063) - (SRL - 2019/01/07, TRILAB-98) Supported Platforms =================== @@ -1773,9 +903,15 @@ The following platforms are not supported but have been tested for this release. #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1 (ostrich) and IBM XL Fortran for Linux, V15.1 - Fedora30 5.3.11-200.fc30.x86_64 - #1 SMP x86_64 GNU/Linux GNU gcc (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827) - GNU Fortran (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827) + Fedora32 5.8.18-200.fc32.x86_64 + #1 SMP x86_64 GNU/Linux GNU gcc (GCC) 10.2.1 20201016 (Red Hat 10.2.1-6) + GNU Fortran (GCC) 10.2.1 20201016 (Red Hat 10.2.1-6) + clang version 10.0.1 (Fedora 10.0.1-3.fc32) + (cmake and autotools) + + Ubuntu20.10 -5.8.0-29-generic-x86_64 + #31-Ubuntu SMP x86_64 GNU/Linux GNU gcc (GCC) 10.2.0-13ubuntu1 + GNU Fortran (GCC) 10.2.0-13ubuntu1 (cmake and autotools) |