2022-10-27 00:07:17 +08:00
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HDF5 version 1.13.4-1 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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2020-02-27 03:54:34 +08:00
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Changes from Release to Release and New Features in the HDF5-1.13.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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2022-10-28 23:10:02 +08:00
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- Bug Fixes since HDF5-1.13.3
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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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2022-11-10 03:06:26 +08:00
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- Removal of MPE support
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The ability to build with MPE instrumentation has been removed along with
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the following configure options:
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Autotools:
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--with-mpe=
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CMake has never supported building with MPE support.
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(DER - 2022/11/08)
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- Removal of dmalloc support
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2022-11-10 01:22:14 +08:00
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The ability to build with dmalloc support has been removed along with
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the following configure options:
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Autotools:
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--with-dmalloc=
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CMake:
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HDF5_ENABLE_USING_DMALLOC
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(DER - 2022/11/08)
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2022-11-04 07:30:08 +08:00
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- Removal of memory allocation sanity checks configure options
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With the removal of the memory allocation sanity checks feature, the
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following configure options are no longer necessary and have been
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removed:
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Autotools:
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--enable-memory-alloc-sanity-check
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CMake:
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HDF5_MEMORY_ALLOC_SANITY_CHECK
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HDF5_ENABLE_MEMORY_STATS
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2022-09-03 08:31:29 +08:00
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2022-11-04 07:30:08 +08:00
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(DER - 2022/11/03)
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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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2022-11-10 09:03:55 +08:00
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- Fix for CVE-2019-8396
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Malformed HDF5 files may have truncated content which does not match
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the expected size. When H5O__pline_decode() attempts to decode these it
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may read past the end of the allocated space leading to heap overflows
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as bounds checking is incomplete.
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The fix ensures each element is within bounds before reading.
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(2022/11/09 - HDFFV-10712, CVE-2019-8396, GitHub #2209)
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2022-11-04 07:30:08 +08:00
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- Removal of memory allocation sanity checks feature
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This feature added heap canaries and statistics tracking for internal
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library memory operations. Unfortunately, the heap canaries caused
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problems when library memory operations were mixed with standard C
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library memory operations (such as in the filter pipeline, where
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buffers may have to be reallocated). Since any platform with a C
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compiler also usually has much more sophisticated memory sanity
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checking tools than the HDF5 library provided (e.g., valgrind), we
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have decided to to remove the feature entirely.
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In addition to the configure changes described above, this also removes
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the following from the public API:
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H5get_alloc_stats()
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H5_alloc_stats_t
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2022-01-20 21:34:43 +08:00
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2022-11-04 07:30:08 +08:00
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(DER - 2022/11/03)
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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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2022-10-28 23:10:02 +08:00
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-
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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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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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2022-10-28 23:10:02 +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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2009-01-06 22:58:21 +08:00
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2022-03-02 04:48:12 +08:00
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2022-10-28 23:10:02 +08:00
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Bug Fixes since HDF5-1.13.3 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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2022-11-11 13:01:45 +08:00
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- Fix CVE-2018-17439 / GHSA-vcxv-vp43-rch7
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H5IMget_image_info(): Make sure to not exceed local array size
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Malformed hdf5 files may provide more dimensions than the array dim[] in
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H5IMget_image_info() is able to hold. Check number of elements first by calling
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H5Sget_simple_extent_dims() with NULL for both 'dims' and 'maxdims' arguments.
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This will cause the function to return only the number of dimensions.
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The fix addresses a stack overflow on write.
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(EFE - 2022/09/27 HDFFV-10589, GH-2226)
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2019-08-28 23:33:31 +08:00
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2021-02-26 05:12:57 +08:00
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Java Library
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------------
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2022-10-28 23:10:02 +08:00
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-
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2018-10-05 05:48:34 +08:00
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2018-08-28 04:13:54 +08:00
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Configuration
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-------------
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2022-11-02 05:03:13 +08:00
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- Move MPI libraries link from PRIVATE to PUBLIC
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The install dependencies were not including the need for MPI libraries when
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an application or library was built with the C library. Also updated the
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CMake target link command to use the newer style MPI::MPI_C link variable.
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2022-11-04 07:30:08 +08:00
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(ADB - 2022/10/27)
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2021-06-22 20:01:22 +08:00
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2018-08-28 04:13:54 +08:00
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2021-01-27 21:56:28 +08:00
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Tools
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-----
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2022-06-09 21:35:33 +08:00
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-
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2016-03-05 04:49:15 +08:00
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2017-04-04 00:33:01 +08:00
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2021-01-27 21:56:28 +08:00
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Performance
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-------------
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-
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Fortran API
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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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2022-04-20 07:31:09 +08:00
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2021-01-27 21:56:28 +08:00
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High-Level Library
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2021-02-26 05:12:57 +08:00
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------------------
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2022-06-09 21:35:33 +08:00
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-
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2016-03-05 03:50:52 +08:00
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2020-11-24 02:04:49 +08:00
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2021-02-26 05:12:57 +08:00
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Fortran High-Level APIs
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-----------------------
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2017-03-21 02:32:26 +08:00
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-
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2016-03-07 02:15:05 +08:00
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2021-01-27 21:56:28 +08:00
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2016-03-08 00:01:53 +08:00
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Documentation
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-------------
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2017-05-05 06:14:38 +08:00
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-
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2009-01-06 22:58:21 +08:00
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2021-01-27 21:56:28 +08:00
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2009-01-06 22:58:21 +08:00
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F90 APIs
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--------
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2017-03-21 02:32:26 +08:00
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-
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2016-03-08 00:01:53 +08:00
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2021-01-27 21:56:28 +08:00
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2009-01-06 22:58:21 +08:00
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C++ APIs
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--------
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2022-03-02 04:48:12 +08:00
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-
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2019-03-27 03:00:27 +08:00
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2009-01-06 22:58:21 +08:00
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2022-06-09 21:35:33 +08:00
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Testing
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-------
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-
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2021-09-29 03:35:19 +08:00
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Platforms Tested
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2012-11-15 02:10:03 +08:00
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===================
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2017-03-21 02:32:26 +08:00
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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)
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2020-11-24 02:04:49 +08:00
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(cmake and autotools)
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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
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2021-05-21 11:44:36 +08:00
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(cmake and autotools)
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2022-08-18 21:35:21 +08:00
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Linux 5.3.18-150300-cray_shasta_c cray-mpich/8.1.16
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#1 SMP x86_64 GNU/Linux Cray clang 14.0.0
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(crusher) GCC 11.2.0
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(cmake)
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2016-03-08 00:01:53 +08:00
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2022-08-18 21:35:21 +08:00
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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
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#1 SMP ppc64le GNU/Linux clang 12.0.1
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(vortex) GCC 8.3.1
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XL 16.1.1
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(cmake)
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2021-02-03 21:57:04 +08:00
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2021-09-29 03:35:19 +08:00
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Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release
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2022-10-28 23:10:02 +08:00
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#1 SMP ppc64le GNU/Linux clang 12.0.1, 14.0.5
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(lassen) GCC 8.3.1
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XL 16.1.1.2, 2021,09.22, 2022.08.05
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2021-09-29 03:35:19 +08:00
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(cmake)
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2022-10-28 23:10:02 +08:00
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Linux-4.12.14-197.99-default cray-mpich/7.7.14
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#1 SMP x86_64 GNU/Linux cce 12.0.3
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(theta) GCC 11.2.0
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llvm 9.0
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Intel 19.1.2
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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)
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#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)
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Linux 3.10.0-1160.24.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
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#1 SMP x86_64 GNU/Linux compilers:
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Centos7 Version 4.8.5 20150623 (Red Hat 4.8.5-4)
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(jelly/kituo/moohan) Version 4.9.3, Version 5.3.0, Version 6.3.0,
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Version 7.2.0, Version 8.3.0, Version 9.1.0
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Intel(R) C (icc), C++ (icpc), Fortran (icc)
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compilers:
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Version 17.0.0.098 Build 20160721
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GNU C (gcc) and C++ (g++) 4.8.5 compilers
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with NAG Fortran Compiler Release 6.1(Tozai)
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Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers
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with NAG Fortran Compiler Release 6.1(Tozai)
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MPICH 3.1.4 compiled with GCC 4.9.3
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MPICH 3.3 compiled with GCC 7.2.0
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OpenMPI 2.1.6 compiled with icc 18.0.1
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OpenMPI 3.1.3 and 4.0.0 compiled with GCC 7.2.0
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PGI C, Fortran, C++ for 64-bit target on
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x86_64;
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Version 19.10-0
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2022-08-18 21:35:21 +08:00
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(autotools and cmake)
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2021-09-29 03:35:19 +08:00
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2022-10-28 23:10:02 +08:00
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Linux-3.10.0-1160.0.0.1chaos openmpi-4.1.2
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2021-09-29 03:35:19 +08:00
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#1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1
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(quartz) GCC 7.3.0, 8.1.0
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2022-10-28 23:10:02 +08:00
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Intel 19.0.4, 2022.2, oneapi.2022.2
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2021-09-29 03:35:19 +08:00
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2022-08-18 21:35:21 +08:00
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Linux-3.10.0-1160.71.1.1chaos openmpi/4.1
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#1 SMP x86_64 GNU/Linux GCC 7.2.0
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(skybridge) Intel/19.1
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(cmake)
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Linux-3.10.0-1160.66.1.1chaos openmpi/4.1
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#1 SMP x86_64 GNU/Linux GCC 7.2.0
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(attaway) Intel/19.1
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(cmake)
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Linux-3.10.0-1160.59.1.1chaos openmpi/4.1
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#1 SMP x86_64 GNU/Linux Intel/19.1
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(chama) (cmake)
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2021-09-29 03:35:19 +08:00
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macOS Apple M1 11.6 Apple clang version 12.0.5 (clang-1205.0.22.11)
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Darwin 20.6.0 arm64 gfortran GNU Fortran (Homebrew GCC 11.2.0) 11.1.0
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(macmini-m1) Intel icc/icpc/ifort version 2021.3.0 202106092021.3.0 20210609
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macOS Big Sur 11.3.1 Apple clang version 12.0.5 (clang-1205.0.22.9)
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Darwin 20.4.0 x86_64 gfortran GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0
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(bigsur-1) Intel icc/icpc/ifort version 2021.2.0 20210228
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macOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang-1000.10.44.4)
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64-bit gfortran GNU Fortran (GCC) 6.3.0
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(bear) Intel icc/icpc/ifort version 19.0.4.233 20190416
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macOS Sierra 10.12.6 Apple LLVM version 9.0.0 (clang-900.39.2)
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64-bit gfortran GNU Fortran (GCC) 7.4.0
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(kite) Intel icc/icpc/ifort version 17.0.2
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Mac OS X El Capitan 10.11.6 Apple clang version 7.3.0 from Xcode 7.3
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64-bit gfortran GNU Fortran (GCC) 5.2.0
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(osx1011test) Intel icc/icpc/ifort version 16.0.2
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Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
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#1 SMP x86_64 GNU/Linux compilers:
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Centos6 Version 4.4.7 20120313
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(platypus) Version 4.9.3, 5.3.0, 6.2.0
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MPICH 3.1.4 compiled with GCC 4.9.3
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PGI C, Fortran, C++ for 64-bit target on
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x86_64;
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Version 19.10-0
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Windows 10 x64 Visual Studio 2015 w/ Intel C/C++/Fortran 18 (cmake)
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Visual Studio 2017 w/ Intel C/C++/Fortran 19 (cmake)
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Visual Studio 2019 w/ clang 12.0.0
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with MSVC-like command-line (C/C++ only - cmake)
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2022-05-21 07:41:39 +08:00
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Visual Studio 2019 w/ Intel C/C++/Fortran oneAPI 2021 (cmake)
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2021-09-29 03:35:19 +08:00
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Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake)
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2017-03-21 02:32:26 +08:00
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2009-01-06 22:58:21 +08:00
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Known Problems
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==============
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2022-10-29 00:01:06 +08:00
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************************************************************
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* _ *
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* (_) *
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* __ ____ _ _ __ _ __ _ _ __ __ _ *
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* \ \ /\ / / _` | '__| '_ \| | '_ \ / _` | *
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* \ V V / (_| | | | | | | | | | | (_| | *
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* \_/\_/ \__,_|_| |_| |_|_|_| |_|\__, | *
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* __/ | *
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* |___/ *
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* *
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* Please refrain from running any program (including *
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* HDF5 tests) which uses the subfiling VFD on Perlmutter *
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* at the National Energy Research Scientific Computing *
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* Center, NERSC. *
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* Doing so may cause a system disruption due to subfiling *
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* crashing Lustre. The sytem's Lustre bug is expected *
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* to be resolved by 2023. *
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* *
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************************************************************
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2019-05-07 23:03:10 +08:00
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CMake files do not behave correctly with paths containing spaces.
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Do not use spaces in paths because the required escaping for handling spaces
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results in very complex and fragile build files.
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ADB - 2019/05/07
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2007-04-14 02:53:50 +08:00
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2017-05-05 06:14:38 +08:00
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At present, metadata cache images may not be generated by parallel
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applications. Parallel applications can read files with metadata cache
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images, but since this is a collective operation, a deadlock is possible
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if one or more processes do not participate.
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2020-12-17 01:59:51 +08:00
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CPP ptable test fails on both VS2017 and VS2019 with Intel compiler, JIRA
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issue: HDFFV-10628. This test will pass with VS2015 with Intel compiler.
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2021-06-24 03:11:07 +08:00
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The subsetting option in ph5diff currently will fail and should be avoided.
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The subsetting option works correctly in serial h5diff.
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2022-08-18 21:35:21 +08:00
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Several tests currently fail on certain platforms:
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MPI_TEST-t_bigio fails with spectrum-mpi on ppc64le platforms.
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MPI_TEST-t_subfiling_vfd and MPI_TEST_EXAMPLES-ph5_subfiling fail with
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cray-mpich on theta and with XL compilers on ppc64le platforms.
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MPI_TEST_testphdf5_tldsc fails with cray-mpich 7.7 on cori and theta.
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2017-05-05 06:14:38 +08:00
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Known problems in previous releases can be found in the HISTORY*.txt files
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in the HDF5 source. Please report any new problems found to
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help@hdfgroup.org.
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2018-07-31 04:09:50 +08:00
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CMake vs. Autotools installations
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=================================
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While both build systems produce similar results, there are differences.
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Each system produces the same set of folders on linux (only CMake works
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on standard Windows); bin, include, lib and share. Autotools places the
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COPYING and RELEASE.txt file in the root folder, CMake places them in
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the share folder.
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The bin folder contains the tools and the build scripts. Additionally, CMake
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2018-07-31 22:41:11 +08:00
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creates dynamic versions of the tools with the suffix "-shared". Autotools
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installs one set of tools depending on the "--enable-shared" configuration
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option.
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2018-07-31 04:09:50 +08:00
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build scripts
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-------------
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Autotools: h5c++, h5cc, h5fc
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CMake: h5c++, h5cc, h5hlc++, h5hlcc
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The include folder holds the header files and the fortran mod files. CMake
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places the fortran mod files into separate shared and static subfolders,
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while Autotools places one set of mod files into the include folder. Because
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2018-07-31 22:41:11 +08:00
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CMake produces a tools library, the header files for tools will appear in
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2018-07-31 04:09:50 +08:00
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the include folder.
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The lib folder contains the library files, and CMake adds the pkgconfig
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subfolder with the hdf5*.pc files used by the bin/build scripts created by
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2018-07-31 22:41:11 +08:00
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the CMake build. CMake separates the C interface code from the fortran code by
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creating C-stub libraries for each Fortran library. In addition, only CMake
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2018-07-31 22:56:12 +08:00
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installs the tools library. The names of the szip libraries are different
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between the build systems.
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2018-07-31 04:09:50 +08:00
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The share folder will have the most differences because CMake builds include
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2018-07-31 22:28:17 +08:00
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a number of CMake specific files for support of CMake's find_package and support
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2018-07-31 04:09:50 +08:00
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for the HDF5 Examples CMake project.
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2021-10-22 05:08:05 +08:00
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The issues with the gif tool are:
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HDFFV-10592 CVE-2018-17433
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HDFFV-10593 CVE-2018-17436
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HDFFV-11048 CVE-2020-10809
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These CVE issues have not yet been addressed and can be avoided by not building
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the gif tool. Disable building the High-Level tools with these options:
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autotools: --disable-hltools
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cmake: HDF5_BUILD_HL_TOOLS=OFF
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