2022-12-22 02:07:25 +08:00
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HDF5 version 1.15.0 currently under development
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2009-01-06 22:58:21 +08:00
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================================================================================
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INTRODUCTION
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2021-02-26 05:12:57 +08:00
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============
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2009-01-06 22:58:21 +08:00
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2018-04-04 05:57:26 +08:00
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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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2009-01-06 22:58:21 +08:00
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2018-04-04 05:57:26 +08:00
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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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2009-01-06 22:58:21 +08:00
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2018-04-04 05:57:26 +08:00
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Links to HDF5 documentation can be found on The HDF5 web page:
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2017-02-01 06:05:20 +08:00
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2018-04-04 05:57:26 +08:00
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https://portal.hdfgroup.org/display/HDF5/HDF5
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2017-03-21 02:32:26 +08:00
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2018-04-04 05:57:26 +08:00
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The official HDF5 releases can be obtained from:
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2017-02-01 06:05:20 +08:00
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2018-04-04 05:57:26 +08:00
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https://www.hdfgroup.org/downloads/hdf5/
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2017-03-21 02:32:26 +08:00
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2023-03-23 09:41:00 +08:00
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Changes from Release to Release and New Features in the HDF5-1.16.x release series
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2018-04-04 05:57:26 +08:00
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can be found at:
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2009-01-06 22:58:21 +08:00
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2022-11-02 05:14:52 +08:00
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https://portal.hdfgroup.org/display/HDF5/Release+Specific+Information
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2009-01-06 22:58:21 +08:00
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If you have any questions or comments, please send them to the HDF Help Desk:
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2018-04-04 05:57:26 +08:00
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help@hdfgroup.org
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2009-01-06 22:58:21 +08:00
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CONTENTS
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2021-01-27 21:56:28 +08:00
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========
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2009-01-06 22:58:21 +08:00
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- New Features
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- Support for new platforms and languages
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2023-03-23 09:41:00 +08:00
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- Bug Fixes since HDF5-1.14.0
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2021-09-29 03:35:19 +08:00
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- Platforms Tested
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2009-01-06 22:58:21 +08:00
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- Known Problems
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2018-07-31 04:09:50 +08:00
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- CMake vs. Autotools installations
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2009-01-06 22:58:21 +08:00
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New Features
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============
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Configuration:
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-------------
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2023-06-13 23:16:41 +08:00
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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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2023-05-27 04:29:02 +08:00
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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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2023-05-04 05:11:38 +08:00
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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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2023-04-27 06:56:57 +08:00
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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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2023-04-24 04:11:17 +08:00
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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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2023-05-06 00:07:16 +08:00
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Also removed the config/cmake/FindSZIP.cmake file.
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2023-04-01 11:38:15 +08:00
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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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2023-02-27 07:06:14 +08:00
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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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2018-12-12 23:12:50 +08:00
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2009-01-06 22:58:21 +08:00
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Library:
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--------
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2023-02-27 02:12:00 +08:00
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- Added a Subfiling VFD configuration file prefix environment variable
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The Subfiling VFD now checks for values set in a new environment
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variable "H5FD_SUBFILING_CONFIG_FILE_PREFIX" to determine if the
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application has specified a pathname prefix to apply to the file
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path for its configuration file. For example, this can be useful
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for cases where the application wishes to write subfiles to a
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machine's node-local storage while placing the subfiling configuration
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file on a file system readable by all machine nodes.
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2023-04-29 07:58:25 +08:00
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- Added H5Pset_selection_io(), H5Pget_selection_io(), and
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H5Pget_no_selection_io_cause() API functions to manage the selection I/O
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feature. This can be used to enable collective I/O with type conversion,
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or it can be used with custom VFDs that support vector or selection I/O.
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- Added H5Pset_modify_write_buf() and H5Pget_modify_write_buf() API
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functions to allow the library to modify the contents of write buffers, in
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order to avoid malloc/memcpy. Currently only used for type conversion
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with selection I/O.
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2019-08-28 23:33:31 +08:00
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2018-11-15 05:37:31 +08:00
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Parallel Library:
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2009-01-06 22:58:21 +08:00
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-----------------
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2022-03-07 22:31:58 +08:00
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-
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2022-02-25 00:04:59 +08:00
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2009-01-06 22:58:21 +08:00
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Fortran Library:
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----------------
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2023-06-06 00:59:51 +08:00
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- Added h5pget_vol_cap_flags_f and related Fortran VOL
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capability definitions.
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2023-05-02 06:21:47 +08:00
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- Fortran async APIs H5A, H5D, H5ES, H5G, H5F, H5L and H5O were added.
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2020-08-04 00:11:27 +08:00
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2023-05-02 06:21:47 +08:00
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- Added Fortran APIs:
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h5pset_selection_io_f, h5pget_selection_io_f
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h5pset_modify_write_buf_f, h5pget_modify_write_buf_f
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2020-08-04 00:11:27 +08:00
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2009-01-06 22:58:21 +08:00
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C++ Library:
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------------
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2022-08-18 21:35:21 +08:00
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-
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2020-08-04 00:11:27 +08:00
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2018-03-16 23:42:33 +08:00
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2017-07-06 05:37:11 +08:00
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Java Library:
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2021-02-26 05:12:57 +08:00
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-------------
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2022-08-18 21:35:21 +08:00
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-
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2020-08-04 00:11:27 +08:00
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2018-12-09 00:14:05 +08:00
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2016-03-07 02:15:05 +08:00
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Tools:
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------
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2022-08-18 21:35:21 +08:00
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-
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2019-06-24 20:27:32 +08:00
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2016-03-08 00:01:53 +08:00
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2009-01-06 22:58:21 +08:00
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High-Level APIs:
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2021-02-26 05:12:57 +08:00
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----------------
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2022-10-28 23:10:02 +08:00
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-
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2021-09-09 04:53:15 +08:00
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2016-03-09 21:56:58 +08:00
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2021-02-26 05:12:57 +08:00
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C Packet Table API:
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-------------------
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2017-05-27 00:17:44 +08:00
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-
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2016-03-07 02:15:05 +08:00
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2022-03-02 04:48:12 +08:00
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2021-02-26 05:12:57 +08:00
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Internal header file:
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---------------------
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2022-08-18 21:35:21 +08:00
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-
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2017-03-21 02:32:26 +08:00
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2022-03-02 04:48:12 +08:00
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2021-02-26 05:12:57 +08:00
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Documentation:
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--------------
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2023-03-23 09:41:00 +08:00
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-
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2009-01-06 22:58:21 +08:00
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2022-03-02 04:48:12 +08:00
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2021-02-26 05:12:57 +08:00
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Support for new platforms, languages and compilers
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==================================================
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2017-03-21 02:32:26 +08:00
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-
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2022-12-08 06:14:40 +08:00
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2023-04-14 05:35:45 +08:00
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Bug Fixes since HDF5-1.14.0 release
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2021-02-26 05:12:57 +08:00
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===================================
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2009-01-06 22:58:21 +08:00
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Library
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-------
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2023-06-13 03:14:25 +08:00
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- Fixed a potential bug when copying empty enum datatypes
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Copying an empty enum datatype (including implicitly, as when an enum
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is a part of a compound datatype) would fail in an assert in debug
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mode and could fail in release mode depending on how the platform
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handles undefined behavior regarding size 0 memory allocations and
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using memcpy with a NULL src pointer.
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The library is now more more careful about using memory operations when
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copying empty enum datatypes and will not error or raise an assert.
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2023-05-27 04:29:02 +08:00
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- Added an AAPL check to H5Acreate
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A check was added to H5Acreate to ensure that a failure is correctly
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returned when an invalid Attribute Access Property List is passed
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in to the function. The HDF5 API tests were failing for certain
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build types due to this condition not being checked previously.
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2023-04-27 06:57:22 +08:00
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- Fixed a bug in H5Ocopy that could generate invalid HDF5 files
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H5Ocopy was missing a check to determine whether the new object's
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object header version is greater than version 1. Without this check,
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copying of objects with object headers that are smaller than a
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certain size would cause H5Ocopy to create an object header for the
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new object that has a gap in the header data. According to the
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HDF5 File Format Specification, this is not allowed for version
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1 of the object header format.
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Fixes GitHub issue #2653
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2023-04-26 01:04:17 +08:00
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- Fixed H5Pget_vol_cap_flags and H5Pget_vol_id to accept H5P_DEFAULT
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H5Pget_vol_cap_flags and H5Pget_vol_id were updated to correctly
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accept H5P_DEFAULT for the 'plist_id' FAPL parameter. Previously,
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they would fail if provided with H5P_DEFAULT as the FAPL.
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2023-04-25 00:12:30 +08:00
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- Fixed ROS3 VFD anonymous credential usage with h5dump and h5ls
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ROS3 VFD anonymous credential functionality became broken in h5dump
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and h5ls in the HDF5 1.14.0 release with the added support for VFD
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plugins, which changed the way that the tools handled setting of
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credential information that the VFD uses. The tools could be
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provided the command-line option of "--s3-cred=(,,)" as a workaround
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for anonymous credential usage, but the documentation for this
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option stated that anonymous credentials could be used by simply
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omitting the option. The latter functionality has been restored.
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Fixes GitHub issue #2406
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2023-04-15 06:17:24 +08:00
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- Fixed memory leaks when processing malformed object header continuation messages
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Malformed object header continuation messages can result in a too-small
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buffer being passed to the decode function, which could lead to reading
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past the end of the buffer. Additionally, errors in processing these
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malformed messages can lead to allocated memory not being cleaned up.
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This fix adds bounds checking and cleanup code to the object header
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continuation message processing.
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2023-04-17 00:09:41 +08:00
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Fixes GitHub issue #2604
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2023-04-15 06:17:24 +08:00
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2023-04-14 05:34:50 +08:00
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|
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- 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.
|
|
|
|
|
2023-04-17 00:09:41 +08:00
|
|
|
Fixes GitHub issue #2605
|
2023-04-12 12:06:29 +08:00
|
|
|
|
2023-04-14 05:35:45 +08:00
|
|
|
- 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.
|
|
|
|
|
2023-04-17 00:09:41 +08:00
|
|
|
Fixes GitHub issue #2603
|
2023-04-14 05:35:45 +08:00
|
|
|
|
2023-04-12 12:06:29 +08:00
|
|
|
- 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.
|
|
|
|
|
2023-04-17 00:09:41 +08:00
|
|
|
Fixes GitHub issue #2599
|
2023-04-12 12:06:29 +08:00
|
|
|
|
2023-04-12 05:09:05 +08:00
|
|
|
- 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.
|
|
|
|
|
2023-04-17 00:09:41 +08:00
|
|
|
Fixes GitHub issue #2602
|
2023-04-12 05:09:05 +08:00
|
|
|
|
2023-04-12 04:22:11 +08:00
|
|
|
- Fixed potential heap buffer overrun in group info header decoding from malformed file
|
|
|
|
|
2023-04-15 06:17:24 +08:00
|
|
|
H5O__ginfo_decode could sometimes read past allocated memory when parsing a
|
|
|
|
group info message from the header of a malformed file.
|
2023-04-12 04:22:11 +08:00
|
|
|
|
|
|
|
It now checks buffer size before each read to properly throw an error in these cases.
|
|
|
|
|
2023-04-17 00:09:41 +08:00
|
|
|
Fixes GitHub issue #2601
|
2023-04-12 04:22:11 +08:00
|
|
|
|
2023-04-12 03:47:51 +08:00
|
|
|
- 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.
|
|
|
|
|
2023-04-12 03:08:46 +08:00
|
|
|
- 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.
|
|
|
|
|
2023-04-17 00:09:41 +08:00
|
|
|
Fixes GitHub issue #2606
|
2023-04-12 03:08:46 +08:00
|
|
|
|
2023-03-24 11:55:34 +08:00
|
|
|
- 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.
|
|
|
|
|
2023-03-18 04:45:07 +08:00
|
|
|
- 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.
|
|
|
|
|
2023-03-03 01:17:49 +08:00
|
|
|
- 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.
|
|
|
|
|
2023-04-17 00:09:41 +08:00
|
|
|
Fixes GitHub #2458
|
2023-03-03 01:17:49 +08:00
|
|
|
|
2023-02-20 22:49:34 +08:00
|
|
|
- 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.
|
|
|
|
|
2023-04-17 00:09:41 +08:00
|
|
|
Fixes GitHub issue #2433
|
2023-02-20 22:49:34 +08:00
|
|
|
|
2023-04-14 05:37:10 +08:00
|
|
|
- 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.
|
|
|
|
|
2023-04-17 00:09:41 +08:00
|
|
|
Fixes GitHub issue #2432
|
2023-04-14 05:37:10 +08:00
|
|
|
|
2022-12-08 06:14:40 +08:00
|
|
|
|
2021-02-26 05:12:57 +08:00
|
|
|
Java Library
|
|
|
|
------------
|
2023-06-14 07:12:14 +08:00
|
|
|
- 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
|
2018-10-05 05:48:34 +08:00
|
|
|
|
|
|
|
|
2018-08-28 04:13:54 +08:00
|
|
|
Configuration
|
|
|
|
-------------
|
2023-05-25 22:53:15 +08:00
|
|
|
- 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
|
|
|
|
|
2023-05-19 05:05:20 +08:00
|
|
|
- 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.
|
|
|
|
|
2023-05-23 07:04:48 +08:00
|
|
|
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).
|
|
|
|
|
2023-05-19 05:05:20 +08:00
|
|
|
Fixes GitHub issue #2926
|
|
|
|
|
2023-05-06 04:57:40 +08:00
|
|
|
- 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
|
|
|
|
|
2023-04-12 03:31:25 +08:00
|
|
|
- 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.
|
|
|
|
|
2023-04-17 00:09:41 +08:00
|
|
|
Fixes GitHub issue #2621
|
2023-04-12 03:31:25 +08:00
|
|
|
|
2023-02-18 06:17:17 +08:00
|
|
|
- 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.
|
|
|
|
|
2023-04-17 00:09:41 +08:00
|
|
|
Fixes GitHub issues #1546 and #2259
|
2023-02-18 06:17:17 +08:00
|
|
|
|
2023-05-04 11:03:58 +08:00
|
|
|
- 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.
|
|
|
|
|
2018-08-28 04:13:54 +08:00
|
|
|
|
2021-01-27 21:56:28 +08:00
|
|
|
Tools
|
|
|
|
-----
|
2023-04-19 02:21:18 +08:00
|
|
|
- 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
|
|
|
|
|
2023-04-08 01:35:51 +08:00
|
|
|
- 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.
|
|
|
|
|
2023-04-17 00:09:41 +08:00
|
|
|
Fixes GitHub issue #2598
|
2016-03-05 04:49:15 +08:00
|
|
|
|
2017-04-04 00:33:01 +08:00
|
|
|
|
2021-01-27 21:56:28 +08:00
|
|
|
Performance
|
|
|
|
-------------
|
|
|
|
-
|
|
|
|
|
|
|
|
|
|
|
|
Fortran API
|
2021-02-26 05:12:57 +08:00
|
|
|
-----------
|
2022-08-18 21:35:21 +08:00
|
|
|
-
|
2022-04-20 07:31:09 +08:00
|
|
|
|
2021-01-27 21:56:28 +08:00
|
|
|
High-Level Library
|
2021-02-26 05:12:57 +08:00
|
|
|
------------------
|
2022-06-09 21:35:33 +08:00
|
|
|
-
|
2016-03-05 03:50:52 +08:00
|
|
|
|
2020-11-24 02:04:49 +08:00
|
|
|
|
2021-02-26 05:12:57 +08:00
|
|
|
Fortran High-Level APIs
|
|
|
|
-----------------------
|
2017-03-21 02:32:26 +08:00
|
|
|
-
|
2016-03-07 02:15:05 +08:00
|
|
|
|
2021-01-27 21:56:28 +08:00
|
|
|
|
2016-03-08 00:01:53 +08:00
|
|
|
Documentation
|
|
|
|
-------------
|
2017-05-05 06:14:38 +08:00
|
|
|
-
|
2009-01-06 22:58:21 +08:00
|
|
|
|
2021-01-27 21:56:28 +08:00
|
|
|
|
2009-01-06 22:58:21 +08:00
|
|
|
F90 APIs
|
|
|
|
--------
|
2017-03-21 02:32:26 +08:00
|
|
|
-
|
2016-03-08 00:01:53 +08:00
|
|
|
|
2021-01-27 21:56:28 +08:00
|
|
|
|
2009-01-06 22:58:21 +08:00
|
|
|
C++ APIs
|
|
|
|
--------
|
2022-03-02 04:48:12 +08:00
|
|
|
-
|
2019-03-27 03:00:27 +08:00
|
|
|
|
2009-01-06 22:58:21 +08:00
|
|
|
|
2022-06-09 21:35:33 +08:00
|
|
|
Testing
|
|
|
|
-------
|
2023-05-27 04:29:02 +08:00
|
|
|
- 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.
|
2022-06-09 21:35:33 +08:00
|
|
|
|
|
|
|
|
2021-09-29 03:35:19 +08:00
|
|
|
Platforms Tested
|
2012-11-15 02:10:03 +08:00
|
|
|
===================
|
2017-03-21 02:32:26 +08:00
|
|
|
|
2022-08-18 21:35:21 +08:00
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|
Linux 5.16.14-200.fc35 GNU gcc (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9)
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|
#1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9)
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|
Fedora35 clang version 13.0.0 (Fedora 13.0.0-3.fc35)
|
2020-11-24 02:04:49 +08:00
|
|
|
(cmake and autotools)
|
|
|
|
|
2021-09-29 03:35:19 +08:00
|
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|
Linux 5.11.0-34-generic GNU gcc (GCC) 9.3.0-17ubuntu1
|
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|
#36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.3.0-17ubuntu1
|
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|
Ubuntu 20.04 Ubuntu clang version 10.0.0-4
|
2021-05-21 11:44:36 +08:00
|
|
|
(cmake and autotools)
|
|
|
|
|
2022-08-18 21:35:21 +08:00
|
|
|
Linux 5.3.18-150300-cray_shasta_c cray-mpich/8.1.16
|
|
|
|
#1 SMP x86_64 GNU/Linux Cray clang 14.0.0
|
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|
|
(crusher) GCC 11.2.0
|
|
|
|
(cmake)
|
2016-03-08 00:01:53 +08:00
|
|
|
|
2022-08-18 21:35:21 +08:00
|
|
|
Linux 4.14.0-115.35.1.1chaos openmpi 4.0.5
|
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|
|
#1 SMP aarch64 GNU/Linux GCC 9.2.0 (ARM-build-5)
|
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|
|
(stria) GCC 7.2.0 (Spack GCC)
|
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|
|
(cmake)
|
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|
|
|
|
|
|
Linux 4.14.0-115.35.1.3chaos spectrum-mpi/rolling-release
|
|
|
|
#1 SMP ppc64le GNU/Linux clang 12.0.1
|
|
|
|
(vortex) GCC 8.3.1
|
|
|
|
XL 16.1.1
|
|
|
|
(cmake)
|
2021-02-03 21:57:04 +08:00
|
|
|
|
2021-09-29 03:35:19 +08:00
|
|
|
Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release
|
2022-10-28 23:10:02 +08:00
|
|
|
#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
|
2021-09-29 03:35:19 +08:00
|
|
|
(cmake)
|
|
|
|
|
2022-10-28 23:10:02 +08:00
|
|
|
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
|
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|
|
llvm 9.0
|
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|
|
Intel 19.1.2
|
2021-09-29 03:35:19 +08:00
|
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|
|
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)
|
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|
|
Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
|
|
|
|
|
|
|
|
Linux 3.10.0-1160.24.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
|
|
|
|
#1 SMP x86_64 GNU/Linux compilers:
|
|
|
|
Centos7 Version 4.8.5 20150623 (Red Hat 4.8.5-4)
|
|
|
|
(jelly/kituo/moohan) Version 4.9.3, Version 5.3.0, Version 6.3.0,
|
|
|
|
Version 7.2.0, Version 8.3.0, Version 9.1.0
|
|
|
|
Intel(R) C (icc), C++ (icpc), Fortran (icc)
|
|
|
|
compilers:
|
|
|
|
Version 17.0.0.098 Build 20160721
|
|
|
|
GNU C (gcc) and C++ (g++) 4.8.5 compilers
|
|
|
|
with NAG Fortran Compiler Release 6.1(Tozai)
|
|
|
|
Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers
|
|
|
|
with NAG Fortran Compiler Release 6.1(Tozai)
|
|
|
|
MPICH 3.1.4 compiled with GCC 4.9.3
|
|
|
|
MPICH 3.3 compiled with GCC 7.2.0
|
|
|
|
OpenMPI 2.1.6 compiled with icc 18.0.1
|
|
|
|
OpenMPI 3.1.3 and 4.0.0 compiled with GCC 7.2.0
|
|
|
|
PGI C, Fortran, C++ for 64-bit target on
|
|
|
|
x86_64;
|
|
|
|
Version 19.10-0
|
2022-08-18 21:35:21 +08:00
|
|
|
(autotools and cmake)
|
2021-09-29 03:35:19 +08:00
|
|
|
|
2022-10-28 23:10:02 +08:00
|
|
|
Linux-3.10.0-1160.0.0.1chaos openmpi-4.1.2
|
2021-09-29 03:35:19 +08:00
|
|
|
#1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1
|
|
|
|
(quartz) GCC 7.3.0, 8.1.0
|
2022-10-28 23:10:02 +08:00
|
|
|
Intel 19.0.4, 2022.2, oneapi.2022.2
|
2021-09-29 03:35:19 +08:00
|
|
|
|
2022-08-18 21:35:21 +08:00
|
|
|
Linux-3.10.0-1160.71.1.1chaos openmpi/4.1
|
|
|
|
#1 SMP x86_64 GNU/Linux GCC 7.2.0
|
|
|
|
(skybridge) Intel/19.1
|
|
|
|
(cmake)
|
|
|
|
|
|
|
|
Linux-3.10.0-1160.66.1.1chaos openmpi/4.1
|
|
|
|
#1 SMP x86_64 GNU/Linux GCC 7.2.0
|
|
|
|
(attaway) Intel/19.1
|
|
|
|
(cmake)
|
|
|
|
|
|
|
|
Linux-3.10.0-1160.59.1.1chaos openmpi/4.1
|
|
|
|
#1 SMP x86_64 GNU/Linux Intel/19.1
|
|
|
|
(chama) (cmake)
|
|
|
|
|
2021-09-29 03:35:19 +08:00
|
|
|
macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11)
|
|
|
|
Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0
|
|
|
|
(macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609
|
|
|
|
|
|
|
|
macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9)
|
|
|
|
Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0
|
|
|
|
(bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228
|
|
|
|
|
|
|
|
macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4)
|
|
|
|
64-bit gfortran GNU Fortran (GCC) 6.3.0
|
|
|
|
(bear) Intel icc/icpc/ifort version 19.0.4.233 20190416
|
|
|
|
|
|
|
|
macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2)
|
|
|
|
64-bit gfortran GNU Fortran (GCC) 7.4.0
|
|
|
|
(kite) Intel icc/icpc/ifort version 17.0.2
|
|
|
|
|
|
|
|
Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3
|
|
|
|
64-bit gfortran GNU Fortran (GCC) 5.2.0
|
|
|
|
(osx1011test) Intel icc/icpc/ifort version 16.0.2
|
|
|
|
|
|
|
|
|
|
|
|
Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
|
|
|
|
#1 SMP x86_64 GNU/Linux compilers:
|
|
|
|
Centos6 Version 4.4.7 20120313
|
|
|
|
(platypus) Version 4.9.3, 5.3.0, 6.2.0
|
|
|
|
MPICH 3.1.4 compiled with GCC 4.9.3
|
|
|
|
PGI C, Fortran, C++ for 64-bit target on
|
|
|
|
x86_64;
|
|
|
|
Version 19.10-0
|
|
|
|
|
|
|
|
Windows 10 x64 Visual Studio 2015 w/ Intel C/C++/Fortran 18 (cmake)
|
|
|
|
Visual Studio 2017 w/ Intel C/C++/Fortran 19 (cmake)
|
|
|
|
Visual Studio 2019 w/ clang 12.0.0
|
|
|
|
with MSVC-like command-line (C/C++ only - cmake)
|
2022-12-14 22:58:20 +08:00
|
|
|
Visual Studio 2019 w/ Intel C/C++/Fortran oneAPI 2022 (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 2022 (cmake)
|
2021-09-29 03:35:19 +08:00
|
|
|
Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake)
|
|
|
|
|
2017-03-21 02:32:26 +08:00
|
|
|
|
2009-01-06 22:58:21 +08:00
|
|
|
Known Problems
|
|
|
|
==============
|
2022-10-29 00:01:06 +08:00
|
|
|
|
2019-05-07 23:03:10 +08:00
|
|
|
CMake files do not behave correctly with paths containing spaces.
|
|
|
|
Do not use spaces in paths because the required escaping for handling spaces
|
|
|
|
results in very complex and fragile build files.
|
|
|
|
ADB - 2019/05/07
|
2007-04-14 02:53:50 +08:00
|
|
|
|
2017-05-05 06:14:38 +08:00
|
|
|
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.
|
|
|
|
|
2020-12-17 01:59:51 +08:00
|
|
|
CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA
|
|
|
|
issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler.
|
|
|
|
|
2021-06-24 03:11:07 +08:00
|
|
|
The subsetting option in ph5diff currently will fail and should be avoided.
|
|
|
|
The subsetting option works correctly in serial h5diff.
|
|
|
|
|
2022-08-18 21:35:21 +08:00
|
|
|
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.
|
|
|
|
|
2017-05-05 06:14:38 +08:00
|
|
|
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.
|
|
|
|
|
2018-07-31 04:09:50 +08:00
|
|
|
|
|
|
|
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
|
2018-07-31 22:41:11 +08:00
|
|
|
creates dynamic versions of the tools with the suffix "-shared". Autotools
|
|
|
|
installs one set of tools depending on the "--enable-shared" configuration
|
|
|
|
option.
|
2018-07-31 04:09:50 +08:00
|
|
|
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
|
2018-07-31 22:41:11 +08:00
|
|
|
CMake produces a tools library, the header files for tools will appear in
|
2018-07-31 04:09:50 +08:00
|
|
|
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
|
2018-07-31 22:41:11 +08:00
|
|
|
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
|
2018-07-31 22:56:12 +08:00
|
|
|
installs the tools library. The names of the szip libraries are different
|
|
|
|
between the build systems.
|
2018-07-31 04:09:50 +08:00
|
|
|
|
|
|
|
The share folder will have the most differences because CMake builds include
|
2018-07-31 22:28:17 +08:00
|
|
|
a number of CMake specific files for support of CMake's find_package and support
|
2018-07-31 04:09:50 +08:00
|
|
|
for the HDF5 Examples CMake project.
|
|
|
|
|
2021-10-22 05:08:05 +08:00
|
|
|
The issues with the gif tool are:
|
|
|
|
HDFFV-10592 CVE-2018-17433
|
|
|
|
HDFFV-10593 CVE-2018-17436
|
|
|
|
HDFFV-11048 CVE-2020-10809
|
2022-12-17 11:56:07 +08:00
|
|
|
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-hltools
|
|
|
|
cmake: HDF5_BUILD_HL_TOOLS=ON
|