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authorLarry Knox <lrknox@hdfgroup.org>2019-08-02 21:16:40 (GMT)
committerLarry Knox <lrknox@hdfgroup.org>2019-08-02 21:16:40 (GMT)
commitb9c948644d8e92ea9c90b593a3dfac3a4d45f44e (patch)
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parent2455d975c81b6b3da37fc9bf12a991d4f180b71f (diff)
downloadhdf5-b9c948644d8e92ea9c90b593a3dfac3a4d45f44e.zip
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Add contents of HDF5 1.10.5 RELEASE.txt to HISTORY-1_10.txt file.
Remove 1.10.5 entries from current RELEASE.txt and update version numbers.
Diffstat (limited to 'release_docs')
-rw-r--r--release_docs/HISTORY-1_10.txt706
-rw-r--r--release_docs/RELEASE.txt406
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diff --git a/release_docs/HISTORY-1_10.txt b/release_docs/HISTORY-1_10.txt
index ad8beb2..17678bb 100644
--- a/release_docs/HISTORY-1_10.txt
+++ b/release_docs/HISTORY-1_10.txt
@@ -3,15 +3,719 @@ HDF5 History
This file contains development history of the HDF5 1.10 branch
+07. Release Information for hdf5-1.10.5
06. Release Information for hdf5-1.10.4
05. Release Information for hdf5-1.10.3
04. Release Information for hdf5-1.10.2
03. Release Information for hdf5-1.10.1
-02. Release Information for hdf5-1.10.0-patch1
+02. Release Information for hdf5-1.10.0-patch1
01. Release Information for hdf5-1.10.0
[Search on the string '%%%%' for section breaks of each release.]
+%%%%1.10.5%%%%
+
+HDF5 version 1.10.5 released on 2019-02-25
+================================================================================
+
+
+INTRODUCTION
+
+This document describes the differences between this release and the previous
+HDF5 release. It contains information on the platforms tested and known
+problems in this release. For more details check the HISTORY*.txt files in the
+HDF5 source.
+
+Note that documentation in the links below will be updated at the time of each
+final release.
+
+Links to HDF5 documentation can be found on The HDF5 web page:
+
+ https://portal.hdfgroup.org/display/HDF5/HDF5
+
+The official HDF5 releases can be obtained from:
+
+ https://www.hdfgroup.org/downloads/hdf5/
+
+Changes from Release to Release and New Features in the HDF5-1.10.x release series
+can be found at:
+
+ https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide
+
+If you have any questions or comments, please send them to the HDF Help Desk:
+
+ help@hdfgroup.org
+
+
+CONTENTS
+
+- New Features
+- Support for new platforms and languages
+- Bug Fixes since HDF5-1.10.4
+- Supported Platforms
+- Tested Configuration Features Summary
+- More Tested Platforms
+- Known Problems
+- CMake vs. Autotools installations
+
+
+New Features
+============
+
+ Configuration:
+ -------------
+ - Cross compile on mutrino and other Cray XC40 systems.
+
+ Added support for CMake options to use CrayLinuxEnvironment, craype-mic-knl
+ module for building with craype-haswell module for configuration, and
+ batch scripts in bin/batch for use with sbatch or bsub to run tests in
+ batch jobs on compute nodes. An instruction file README_HPC describing
+ the use of these options was added in release_docs.
+
+ (LRK - 2019/02/18, TRILABS-34)
+
+ - Rework CMake command files to fix MPI testing.
+
+ Added setup fixture to remove any test generated files and added DEPENDS
+ to test properties to execute tests in order expected.
+
+ (ADB - 2019/02/14, TRILABS-111)
+
+ - Disable SZIP or ZLIB options if TGZ files are not available.
+
+ Changed the TGZ option for SZip and ZLib to disable the options
+ if the source tar.gz files are not found.
+
+ (ADB - 2019/02/05, HDFFV-10697)
+
+ - Added a new option to enable/disable using pread/pwrite instead of
+ read/write in the sec2, log, and core VFDs.
+
+ This option is enabled by default when pread/pwrite are detected.
+
+ Autotools: --enable-preadwrite
+ CMake: HDF5_ENABLE_PREADWRITE
+
+ (DER - 2019/02/03, HDFFV-10696)
+
+ - Rework CMake versioning for OSX platforms.
+
+ Changed the current_version and compatibility_version flags from optional
+ with HDF5_BUILD_WITH_INSTALL_NAME to always setting the flags for OSX.
+
+ (ADB - 2019/01/22, HDFFV-10685)
+
+ - Rework CMake command files to eliminate developer CMP005 warning
+
+ Use variables without quotes in if () statements.
+
+ (ADB - 2019/01/18, TILABS-105)
+
+ - Rework CMake configure files to eliminate developer CMP0075 warning
+
+ Renamed varname to HDF5_REQUIRED_LIBRARIES as the contents were not
+ required for configuration. Also moved check includes calls to top of
+ files.
+
+ (ADB - 2019/01/03, HDFFV-10546)
+
+ - Keep stderr and stdout separate in tests
+
+ Changed test handling of output capture. Tests now keep the stderr
+ output separate from the stdout output. It is up to the test to decide
+ which output to check against a reference. Also added the option
+ to grep for a string in either output.
+
+ (ADB - 2018/12/12, HDFFV-10632)
+
+ - Incorrectly installed private header files were removed from
+ CMake installs.
+
+ The CMake build files incorrectly flagged the following header files
+ as public and installed them. They are private and will no longer be
+ installed.
+
+ HDF5 library private package files (H5Xpkg.h)
+ H5Edefin.h
+ H5Einit.h
+ H5Eterm.h
+ H5LTparse.h
+ h5diff.h
+ h5tools_dump.h
+ h5tools.h
+ h5tools_ref.h
+ h5tools_str.h
+ h5tools_utils.h
+ h5trav.h
+
+ (DER - 2018/10/26, HDFFV-10614, 10609)
+
+ - Autotools installs now install H5FDwindows.h
+
+ This is simply to align the installed header files between the
+ autotools and CMake. H5FDwindows.h has no functionality on
+ non-Windows systems.
+
+ (DER - 2018/10/26, HDFFV-10614)
+
+
+ Library:
+ --------
+ - The sec2, log, and core VFDs can now use pread/pwrite instead of
+ read/write.
+
+ pread and pwrite do not change the file offset, a feature that was
+ requested by a user working with a multi-threaded application.
+
+ The option to configure this feature is described above.
+
+ (DER - 2019/02/03, HDFFV-10696)
+
+ - Add ability to minimze dataset object headers.
+
+ Creation of many, very small datasets resulted in extensive file bloat
+ due to extra space in the dataset object headers -- this space is
+ allocated by default to allow for the insertion of a small number of
+ attributes within the object header and not require a continuation
+ block, an unnecessary provision in the target use case.
+
+ Inform the library to expect no attributes on created datasets, and to
+ allocate the least space possible for the object headers.
+ NOTE: A continuation block is created if attributes are added to a
+ 'minimized' dataset, which can reduce performance.
+ NOTE: Some extra space is allocated for attributes essential to the
+ correct behavior of the object header (store creation times, e.g.). This
+ does not violate the design principle, as the space is calculated and
+ allocated as needed at the time of dataset object header creation --
+ unused space is not generated.
+ New API calls:
+ H5Fget_dset_no_attrs_hint
+ H5Fset_dset_no_attrs_hint
+ H5Pget_dset_no_attrs_hint
+ H5Pset_dset_no_attrs_hint
+
+ (JOS - 2019/01/04, TRILAB-45)
+
+ - Added new chunk query functions
+
+ The following public functions were added to discover information about
+ the chunks in an HDF5 file.
+ herr_t H5Dget_num_chunks(dset_id, fspace_id, *nchunks)
+ herr_t H5Dget_chunk_info_by_coord(dset_id, *coord, *filter_mask, *addr, *size)
+ herr_t H5Dget_chunk_info(dset_id, fspace_id, index, *coord, *filter_mask, *addr, *size)
+
+ (BMR - 2018/11/07, HDFFV-10615)
+
+ - Several empty public header files where removed from the distribution
+
+ The following files were empty placeholders. They are for internal
+ packages that are unlikely to ever have public functionality and have
+ thus been removed.
+
+ H5Bpublic.h
+ H5B2public.h
+ H5FSpublic.h
+ H5HFpublic.h
+ H5HGpublic.h
+ H5HLpublic.h
+
+ They were only installed in CMake builds.
+
+ (DER - 2018/10/26, HDFFV-10614)
+
+
+ Parallel Library:
+ -----------------
+ - Changed the default behavior in parallel when reading the same dataset in its entirety
+ (i.e. H5S_ALL dataset selection) which is being read by all the processes collectively.
+ The dataset must be contiguous, less than 2GB, and of an atomic datatype.
+ The new behavior is the HDF5 library will use an MPI_Bcast to pass the data read from
+ the disk by the root process to the remain processes in the MPI communicator associated
+ with the HDF5 file.
+
+ (MSB - 2019/01/02, HDFFV-10652)
+
+ - All MPI-1 API calls have been replaced with MPI-2 equivalents.
+
+ This was done to better support OpenMPI, as default builds no longer
+ include MPI-1 support (as of OpenMPI 4.0).
+
+ (DER - 2018/12/30, HDFFV-10566)
+
+ Fortran Library:
+ ----------------
+ - Added wrappers for dataset object header minimization calls.
+ (see the note for TRILAB-45, above)
+
+ New API calls:
+
+ h5fget_dset_no_attrs_hint_f
+ h5fset_dset_no_attrs_hint_f
+ h5pget_dset_no_attrs_hint_f
+ h5pset_dset_no_attrs_hint_f
+
+ (DER - 2019/01/09, TRILAB-45)
+
+ - Added new Fortran derived type, c_h5o_info_t, which is interoperable with
+ C's h5o_info_t. This is needed for callback functions which
+ pass C's h5o_info_t data type definition.
+
+ (MSB, 2019/01/08, HDFFV-10443)
+
+ - Added new Fortran API, H5gmtime, which converts (C) 'time_t' structure
+ to Fortran DATE AND TIME storage format.
+
+ (MSB, 2019/01/08, HDFFV-10443)
+
+ - Added new Fortran 'fields' optional parameter to: h5ovisit_f, h5oget_info_by_name_f,
+ h5oget_info, h5oget_info_by_idx and h5ovisit_by_name_f.
+
+ (MSB, 2019/01/08, HDFFV-10443)
+
+ C++ Library:
+ ------------
+ - Added new function to the C++ interface
+
+ Added wrapper for H5Ovisit2:
+ H5Object::visit()
+
+ (BMR - 2019/02/14, HDFFV-10532)
+
+
+ Java Library:
+ ----------------
+ - Rewrote the JNI error handling to be much cleaner
+
+ (JTH - 2019/02/12)
+
+ - Add new functions to java interface
+
+ Added wrappers for:
+ H5Fset_libver_bounds
+ H5Fget_dset_no_attrs_hint/H5Fset_dset_no_attrs_hint
+ H5Pget_dset_no_attrs_hint/H5Pset_dset_no_attrs_hint
+
+ (ADB - 2019/01/07, HDFFV-10664)
+
+ - Fix java unit tests when Time is a natural number
+
+ Time substitution in java/test/junit.sh.in doesn't
+ handle the case when Time is a natural number. Fixed
+ the regular expression.
+
+ (ADB - 2019/01/07, HDFFV-10674)
+
+ - Duplicate the data read/write functions of Datasets for Attributes.
+
+ Region references could not be displayed for attributes as they could
+ for datasets. Datasets had overloaded read and write functions for different
+ datatypes that were not available for attributes. After adding similar
+ functions, attribute region references work normally.
+
+ (ADB - 2018/12/12, HDFVIEW-4)
+
+
+ Tools:
+ ------
+ - The h5repart -family-to-sec2 argument was changed to -family-to-single
+
+ In order to better support other single-file VFDs which could work with
+ h5repart, the -family-to-sec2 argument was renamed to -family-to-single.
+ This is just a name change and the functionality of the argument has not
+ changed.
+
+ The -family-to-sec2 argument has been kept for backwards-compatibility.
+ This argument should be considered deprecated.
+
+ (DER - 2018/11/14, HDFFV-10633)
+
+
+Bug Fixes since HDF5-1.10.4 release
+==================================
+
+ Library
+ -------
+ - Fix hangs with collective metadata reads during chunked dataset I/O
+
+ In the parallel library, it was discovered that when a particular
+ sequence of operations following a pattern of:
+
+ "write to chunked dataset" -> "flush file" -> "read from dataset"
+
+ occurred with collective metadata reads enabled, hangs could be
+ observed due to certain MPI ranks not participating in the collective
+ metadata reads.
+
+ To fix the issue, collective metadata reads are now disabled during
+ chunked dataset raw data I/O.
+
+ (JTH - 2019/02/11, HDFFV-10563, HDFFV-10688)
+
+ - Performance issue when closing an object
+
+ The slow down is due to the search of the "tag_list" to find
+ out the "corked" status of an object and "uncork" it if so.
+
+ Improve performance by skipping the search of the "tag_list"
+ if there are no "corked" objects when closing an object.
+
+ (VC - 2019/02/06)
+
+ - Uninitialized bytes from a type conversion buffer could be written
+ to disk in H5Dwrite calls where type conversion takes place
+ and the type conversion buffer was created by the HDF5 library.
+
+ When H5Dwrite is called and datatype conversion must be performed,
+ the library will create a temporary buffer for type conversion if
+ one is not provided by the user via H5Pset_buffer. This internal
+ buffer is allocated via malloc and contains uninitialized data. In
+ some datatype conversions (float to long double, possibly others),
+ some of this uninitialized data could be written to disk.
+
+ This was flagged by valgrind in the dtransform test and does not
+ appear to be a common occurrence (it is flagged in one test out
+ of the entire HDF5 test suite).
+
+ Switching to calloc fixed the problem.
+
+ (DER - 2019/02/03, HDFFV-10694)
+
+ - There was missing protection against division by zero reported to
+ The HDF Group as issue #CVE-2018-17434.
+
+ Protection against division by zero was added to address the issue
+ #CVE-2018-17434.
+
+ (BMR - 2019/01/29, HDFFV-10586)
+
+ - The issue CVE-2018-17437 was reported to The HDF Group
+
+ Although CVE-2018-17437 reported a memory leak, the actual issue
+ was invalid read. It was found that the attribute name length
+ in an attribute message was corrupted, which caused the buffer
+ pointer to be advanced too far and later caused an invalid read.
+
+ A check was added to detect when the attribute name or its length
+ was corrupted and report the potential of data corruption.
+
+ (BMR - 2019/01/29, HDFFV-10588)
+
+ - H5Ewalk did not stop when it was supposed to
+
+ H5Ewalk was supposed to stop when the callback function stopped
+ even though the errors in the stack were not all visited, but it
+ did not. This problem is now fixed.
+
+ (BMR - 2019/01/29, HDFFV-10684)
+
+ - Revert H5Oget_info* and H5Ovisit* functions
+
+ In 1.10.3 new H5Oget_info*2 and H5Ovisit*2 functions were
+ added for performance. Inadvertently, the original functions;
+ H5Oget_info,
+ H5Oget_info_by_name,
+ H5Oget_info_by_idx,
+ H5Ovisit,
+ H5Ovisit_by_name
+ were versioned to H5Oget_info*1 and H5Ovisit*1. This
+ broke the API compatibility for a maintenance release. The
+ original functions have been restored.
+
+ (ADB - 2019/01/24, HDFFV-10686)
+
+ - Fixed a potential invalid memory access and failure that could occur when
+ decoding an unknown object header message (from a future version of the
+ library).
+
+ (NAF - 2019/01/07)
+
+ - Deleting attributes in dense storage
+
+ The library aborts with "infinite loop closing library" after
+ attributes in dense storage are created and then deleted.
+
+ When deleting the attribute nodes from the name index v2 B-tree,
+ if an attribute is found in the intermediate B-tree nodes,
+ which may be merged/redistributed in the process, we need to
+ free the dynamically allocated spaces for the intermediate
+ decoded attribute.
+
+ (VC - 2018/12/26, HDFFV-10659)
+
+ - There was missing protection against division by zero reported to
+ The HDF Group as issue #CVE-2018-17233.
+
+ Protection against division by zero was added to address the issue
+ #CVE-2018-17233. In addition, several similar occurrences in the same
+ file were fixed as well.
+
+ (BMR - 2018/12/23, HDFFV-10577)
+
+ - Fixed an issue where the parallel filters tests would fail
+ if zlib was not available on the system. Until support can
+ be added in the tests for filters beyond gzip/zlib, the tests
+ will be skipped if zlib is not available.
+
+ (JTH - 2018/12/05)
+
+ - A bug was discovered in the parallel library where an application
+ would eventually consume all of the available MPI communicators
+ when continually writing to a compressed dataset in parallel. This
+ was due to internal copies of an HDF5 File Access Property List,
+ which each contained a copy of the MPI communicator, not being
+ closed at the end of each write operation. This problem was
+ exacerbated by larger numbers of processors.
+
+ (JTH - 2018/12/05, HDFFV-10629)
+
+
+ Fortran
+ --------
+ - Fixed issue with Fortran not returning h5o_info_t field values
+ meta_size%attr%index_size and meta_size%attr%heap_size.
+
+ (MSB, 2019/01/08, HDFFV-10443)
+
+ - Added symbolic links libhdf5_hl_fortran.so to libhdf5hl_fortran.so and
+ libhdf5_hl_fortran.a to libhdf5hl_fortran.a in hdf5/lib directory for
+ autotools installs. These were added to match the name of the files
+ installed by cmake and the general pattern of hl lib files. We will
+ change the names of the installed lib files to the matching name in
+ the next major release.
+
+ (LRK - 2019/01/04, HDFFV-10596)
+
+ - Made Fortran specific subroutines PRIVATE in generic procedures.
+
+ Affected generic procedures were functions in H5A, H5D, H5P, H5R and H5T.
+
+ (MSB, 2018/12/04, HDFFV-10511)
+
+
+ Testing
+ -------
+ - Fixed a test failure in testpar/t_dset.c caused by
+ the test trying to use the parallel filters feature
+ on MPI-2 implementations.
+
+ (JTH, 2019/2/7)
+
+
+Supported Platforms
+===================
+
+ Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
+ #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
+ (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
+ IBM XL C/C++ V13.1
+ IBM XL Fortran V15.1
+
+ Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
+ #1 SMP x86_64 GNU/Linux compilers:
+ (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
+ Version 4.9.3, Version 5.2.0
+ Intel(R) C (icc), C++ (icpc), Fortran (icc)
+ compilers:
+ Version 17.0.0.098 Build 20160721
+ MPICH 3.1.4 compiled with GCC 4.9.3
+
+ SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
+ (emu) Sun Fortran 95 8.6 SunOS_sparc
+ Sun C++ 5.12 SunOS_sparc
+
+ Windows 7 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
+
+ Windows 7 x64 Visual Studio 2013
+ Visual Studio 2015 w/ Intel Fortran 16 (cmake)
+ Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake)
+ Visual Studio 2015 w/ MSMPI 8 (cmake)
+
+ Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
+
+ Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake)
+ Visual Studio 2017 w/ Intel Fortran 18 (cmake)
+
+ Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0
+ 64-bit gfortran GNU Fortran (GCC) 4.9.2
+ (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
+
+ Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3
+ 64-bit gfortran GNU Fortran (GCC) 5.2.0
+ (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
+
+ MacOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang/clang++-1000.10.44.4)
+ 64-bit gfortran GNU Fortran (GCC) 8.3.0
+
+
+Tested Configuration Features Summary
+=====================================
+
+ In the tables below
+ y = tested
+ n = not tested in this release
+ C = Cluster
+ W = Workstation
+ x = not working in this release
+ dna = does not apply
+ ( ) = footnote appears below second table
+ <blank> = testing incomplete on this feature or platform
+
+Platform C F90/ F90 C++ zlib SZIP
+ parallel F2003 parallel
+Solaris2.11 32-bit n y/y n y y y
+Solaris2.11 64-bit n y/n n y y y
+Windows 7 y y/y n y y y
+Windows 7 x64 y y/y y y y y
+Windows 7 Cygwin n y/n n y y y
+Windows 7 x64 Cygwin n y/n n y y y
+Windows 10 y y/y n y y y
+Windows 10 x64 y y/y n y y y
+Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y
+Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y
+MacOS High Sierra 10.13.6 64-bit n y/y n y y y
+CentOS 7.2 Linux 3.10.0 x86_64 PGI n y/y n y y y
+CentOS 7.2 Linux 3.10.0 x86_64 GNU y y/y y y y y
+CentOS 7.2 Linux 3.10.0 x86_64 Intel n y/y n y y y
+Linux 2.6.32-573.18.1.el6.ppc64 n y/y n y y y
+
+
+Platform Shared Shared Shared Thread-
+ C libs F90 libs C++ libs safe
+Solaris2.11 32-bit y y y y
+Solaris2.11 64-bit y y y y
+Windows 7 y y y y
+Windows 7 x64 y y y y
+Windows 7 Cygwin n n n y
+Windows 7 x64 Cygwin n n n y
+Windows 10 y y y y
+Windows 10 x64 y y y y
+Mac OS X Yosemite 10.10.5 64-bit y y y y
+Mac OS X El Capitan 10.11.6 64-bit y y y y
+MacOS High Sierra 10.13.6 64-bit y y y y
+CentOS 7.2 Linux 3.10.0 x86_64 PGI y y y n
+CentOS 7.2 Linux 3.10.0 x86_64 GNU y y y y
+CentOS 7.2 Linux 3.10.0 x86_64 Intel y y y n
+Linux 2.6.32-573.18.1.el6.ppc64 y y y n
+
+Compiler versions for each platform are listed in the preceding
+"Supported Platforms" table.
+
+
+More Tested Platforms
+=====================
+The following configurations are not supported but have been tested for this release.
+
+ Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
+ #1 SMP x86_64 GNU/Linux compilers:
+ (mayll/platypus) Version 4.4.7 20120313
+ Version 4.9.3, 5.3.0, 6.2.0
+ PGI C, Fortran, C++ for 64-bit target on
+ x86-64;
+ Version 17.10-0
+ Intel(R) C (icc), C++ (icpc), Fortran (icc)
+ compilers:
+ Version 17.0.4.196 Build 20170411
+ MPICH 3.1.4 compiled with GCC 4.9.3
+
+ Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers
+ #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4)
+ (jelly) with NAG Fortran Compiler Release 6.1(Tozai)
+ GCC Version 7.1.0
+ MPICH 3.2-GCC-4.9.3
+ MPICH 3.2.1-GCC-7.2.0-2.29
+ OpenMPI 2.1.5-GCC-7.2.0-2.29
+ Intel(R) C (icc) and C++ (icpc) compilers
+ Version 17.0.0.098 Build 20160721
+ with NAG Fortran Compiler Release 6.1(Tozai)
+
+ Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0
+ #1 SMP x86_64 GNU/Linux
+ (moohan)
+
+ Fedora 29 4.20.10-200.fc29.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
+ gcc, g++ (GCC) 8.2.1 20181215
+ (Red Hat 8.2.1-6)
+ GNU Fortran (GCC) 8.2.1 20181215
+ (Red Hat 8.2.1-6)
+ (cmake and autotools)
+
+ Windows 7 x64 Visual Studio 2008
+
+
+Known Problems
+==============
+
+ 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.
+
+ Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29:
+ testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio)
+ t_shapesame (sscontig2)
+ t_pflush1/fails on exit
+ The first two tests fail attempting collective writes.
+
+ CPP ptable test fails on VS2017 with Intel compiler, JIRA issue: HDFFV-10628.
+ This test will pass with VS2015 with Intel compiler.
+
+ Older MPI libraries such as OpenMPI 2.0.1 and MPICH 2.1.5 were tested
+ while attempting to resolve the Jira issue: HDFFV-10540.
+ The known problems of reading or writing > 2GBs when using MPI-2 was
+ partially resolved with the MPICH library. The proposed support recognizes
+ IO operations > 2GB and if the datatype is not a derived type, the library
+ breaks the IO into chunks which can be input or output with the existing
+ MPI 2 limitations, i.e. size reporting and function API size/count
+ arguments are restricted to be 32 bit integers. For derived types larger
+ than 2GB, MPICH 2.1.5 fails while attempting to read or write data.
+ OpenMPI in contrast, implements MPI-3 APIs even in the older releases
+ and thus does not suffer from the 32 bit size limitation described here.
+ OpenMPI releases prior to v3.1.3 appear to have other datatype issues however,
+ e.g. within a single parallel test (testphdf5) the subtests (cdsetr, eidsetr)
+ report data verfication errors before eventually aborting.
+ The most recent versions of OpenMPI (v3.1.3 or newer) have evidently
+ resolved these isses and parallel HDF5 testing does not currently report
+ errors though occasional hangs have been observed.
+
+ Known problems in previous releases can be found in the HISTORY*.txt files
+ in the HDF5 source. Please report any new problems found to
+ help@hdfgroup.org.
+
+
+CMake vs. Autotools installations
+=================================
+While both build systems produce similar results, there are differences.
+Each system produces the same set of folders on linux (only CMake works
+on standard Windows); bin, include, lib and share. Autotools places the
+COPYING and RELEASE.txt file in the root folder, CMake places them in
+the share folder.
+
+The bin folder contains the tools and the build scripts. Additionally, CMake
+creates dynamic versions of the tools with the suffix "-shared". Autotools
+installs one set of tools depending on the "--enable-shared" configuration
+option.
+ build scripts
+ -------------
+ Autotools: h5c++, h5cc, h5fc
+ CMake: h5c++, h5cc, h5hlc++, h5hlcc
+
+The include folder holds the header files and the fortran mod files. CMake
+places the fortran mod files into separate shared and static subfolders,
+while Autotools places one set of mod files into the include folder. Because
+CMake produces a tools library, the header files for tools will appear in
+the include folder.
+
+The lib folder contains the library files, and CMake adds the pkgconfig
+subfolder with the hdf5*.pc files used by the bin/build scripts created by
+the CMake build. CMake separates the C interface code from the fortran code by
+creating C-stub libraries for each Fortran library. In addition, only CMake
+installs the tools library. The names of the szip libraries are different
+between the build systems.
+
+The share folder will have the most differences because CMake builds include
+a number of CMake specific files for support of CMake's find_package and support
+for the HDF5 Examples CMake project.
+
%%%%1.10.4%%%%
HDF5 version 1.10.4 released on 2018-10-05
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 42dc6d2..a40f092 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -34,7 +34,7 @@ CONTENTS
- New Features
- Support for new platforms and languages
-- Bug Fixes since HDF5-1.10.4
+- Bug Fixes since HDF5-1.10.5
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
@@ -116,203 +116,14 @@ New Features
(ADB - 2019/04/15, HDFFV-10741)
- - Rework CMake command files to fix MPI testing.
-
- Added setup fixture to remove any test generated files and added DEPENDS
- to test properties to execute tests in order expected.
-
- (ADB - 2019/02/14, TRILABS-111)
-
- - Disable SZIP or ZLIB options if TGZ files are not available.
-
- Changed the TGZ option for SZip and ZLib to disable the options
- if the source tar.gz files are not found.
-
- (ADB - 2019/02/05, HDFFV-10697)
-
- - Added a new option to enable/disable using pread/pwrite instead of
- read/write in the sec2, log, and core VFDs.
-
- This option is enabled by default when pread/pwrite are detected.
-
- Autotools: --enable-preadwrite
- CMake: HDF5_ENABLE_PREADWRITE
-
- (DER - 2019/02/03, HDFFV-10696)
-
- - Rework CMake versioning for OSX platforms.
-
- Changed the current_version and compatibility_version flags from optional
- with HDF5_BUILD_WITH_INSTALL_NAME to always setting the flags for OSX.
-
- (ADB - 2019/01/22, HDFFV-10685)
-
- - Rework CMake command files to eliminate developer CMP005 warning
-
- Use variables without quotes in if () statements.
-
- (ADB - 2019/01/18, TILABS-105)
-
- - Rework CMake configure files to eliminate developer CMP0075 warning
-
- Renamed varname to HDF5_REQUIRED_LIBRARIES as the contents were not
- required for configuration. Also moved check includes calls to top of
- files.
-
- (ADB - 2019/01/03, HDFFV-10546)
-
- - Keep stderr and stdout separate in tests
-
- Changed test handling of output capture. Tests now keep the stderr
- output separate from the stdout output. It is up to the test to decide
- which output to check against a reference. Also added the option
- to grep for a string in either output.
-
- (ADB - 2018/12/12, HDFFV-10632)
-
- - Incorrectly installed private header files were removed from
- CMake installs.
-
- The CMake build files incorrectly flagged the following header files
- as public and installed them. They are private and will no longer be
- installed.
-
- HDF5 library private package files (H5Xpkg.h)
- H5Edefin.h
- H5Einit.h
- H5Eterm.h
- H5LTparse.h
- h5diff.h
- h5tools_dump.h
- h5tools.h
- h5tools_ref.h
- h5tools_str.h
- h5tools_utils.h
- h5trav.h
-
- (DER - 2018/10/26, HDFFV-10614, 10609)
-
- - Autotools installs now install H5FDwindows.h
-
- This is simply to align the installed header files between the
- autotools and CMake. H5FDwindows.h has no functionality on
- non-Windows systems.
-
- (DER - 2018/10/26, HDFFV-10614)
-
Library:
--------
- - The sec2, log, and core VFDs can now use pread/pwrite instead of
- read/write.
-
- pread and pwrite do not change the file offset, a feature that was
- requested by a user working with a multi-threaded application.
-
- The option to configure this feature is described above.
-
- (DER - 2019/02/03, HDFFV-10696)
-
- - Add ability to minimze dataset object headers.
-
- Creation of many, very small datasets resulted in extensive file bloat
- due to extra space in the dataset object headers -- this space is
- allocated by default to allow for the insertion of a small number of
- attributes within the object header and not require a continuation
- block, an unnecessary provision in the target use case.
-
- Inform the library to expect no attributes on created datasets, and to
- allocate the least space possible for the object headers.
- NOTE: A continuation block is created if attributes are added to a
- 'minimized' dataset, which can reduce performance.
- NOTE: Some extra space is allocated for attributes essential to the
- correct behavior of the object header (store creation times, e.g.). This
- does not violate the design principle, as the space is calculated and
- allocated as needed at the time of dataset object header creation --
- unused space is not generated.
- New API calls:
- H5Fget_dset_no_attrs_hint
- H5Fset_dset_no_attrs_hint
- H5Pget_dset_no_attrs_hint
- H5Pset_dset_no_attrs_hint
-
- (JOS - 2019/01/04, TRILAB-45)
-
- - Added new chunk query functions
-
- The following public functions were added to discover information about
- the chunks in an HDF5 file.
- herr_t H5Dget_num_chunks(dset_id, fspace_id, *nchunks)
- herr_t H5Dget_chunk_info_by_coord(dset_id, *coord, *filter_mask, *addr, *size)
- herr_t H5Dget_chunk_info(dset_id, fspace_id, index, *coord, *filter_mask, *addr, *size)
-
- (BMR - 2018/11/07, HDFFV-10615)
-
- - Several empty public header files where removed from the distribution
-
- The following files were empty placeholders. They are for internal
- packages that are unlikely to ever have public functionality and have
- thus been removed.
-
- H5Bpublic.h
- H5B2public.h
- H5FSpublic.h
- H5HFpublic.h
- H5HGpublic.h
- H5HLpublic.h
-
- They were only installed in CMake builds.
-
- (DER - 2018/10/26, HDFFV-10614)
-
+ -
Parallel Library:
-----------------
- - Changed the default behavior in parallel when reading the same dataset in its entirety
- (i.e. H5S_ALL dataset selection) which is being read by all the processes collectively.
- The dataset must be contiguous, less than 2GB, and of an atomic datatype.
- The new behavior is the HDF5 library will use an MPI_Bcast to pass the data read from
- the disk by the root process to the remain processes in the MPI communicator associated
- with the HDF5 file.
-
- (MSB - 2019/01/02, HDFFV-10652)
-
- - All MPI-1 API calls have been replaced with MPI-2 equivalents.
-
- This was done to better support OpenMPI, as default builds no longer
- include MPI-1 support (as of OpenMPI 4.0).
-
- (DER - 2018/12/30, HDFFV-10566)
-
- Fortran Library:
- ----------------
- - Added wrappers for dataset object header minimization calls.
- (see the note for TRILAB-45, above)
-
- New API calls:
-
- h5fget_dset_no_attrs_hint_f
- h5fset_dset_no_attrs_hint_f
- h5pget_dset_no_attrs_hint_f
- h5pset_dset_no_attrs_hint_f
-
- (DER - 2019/01/09, TRILAB-45)
-
- - Added new Fortran derived type, c_h5o_info_t, which is interoperable with
- C's h5o_info_t. This is needed for callback functions which
- pass C's h5o_info_t data type definition.
-
- (MSB, 2019/01/08, HDFFV-10443)
-
- - Added new Fortran API, H5gmtime, which converts (C) 'time_t' structure
- to Fortran DATE AND TIME storage format.
-
- (MSB, 2019/01/08, HDFFV-10443)
-
- - Added new Fortran 'fields' optional parameter to: h5ovisit_f, h5oget_info_by_name_f,
- h5oget_info, h5oget_info_by_idx and h5ovisit_by_name_f.
-
- (MSB, 2019/01/08, HDFFV-10443)
+ -
C++ Library:
------------
@@ -322,13 +133,6 @@ New Features
(BMR - 2019/04/22, HDFFV-10622)
- - Added new function to the C++ interface
-
- Added wrapper for H5Ovisit2:
- H5Object::visit()
-
- (BMR - 2019/02/14, HDFFV-10532)
-
Java Library:
----------------
@@ -336,50 +140,10 @@ New Features
(JTH - 2019/04/30)
- - Rewrote the JNI error handling to be much cleaner
-
- (JTH - 2019/02/12)
-
- - Add new functions to java interface
-
- Added wrappers for:
- H5Fset_libver_bounds
- H5Fget_dset_no_attrs_hint/H5Fset_dset_no_attrs_hint
- H5Pget_dset_no_attrs_hint/H5Pset_dset_no_attrs_hint
-
- (ADB - 2019/01/07, HDFFV-10664)
-
- - Fix java unit tests when Time is a natural number
-
- Time substitution in java/test/junit.sh.in doesn't
- handle the case when Time is a natural number. Fixed
- the regular expression.
-
- (ADB - 2019/01/07, HDFFV-10674)
-
- - Duplicate the data read/write functions of Datasets for Attributes.
-
- Region references could not be displayed for attributes as they could
- for datasets. Datasets had overloaded read and write functions for different
- datatypes that were not available for attributes. After adding similar
- functions, attribute region references work normally.
-
- (ADB - 2018/12/12, HDFVIEW-4)
-
Tools:
------
- - The h5repart -family-to-sec2 argument was changed to -family-to-single
-
- In order to better support other single-file VFDs which could work with
- h5repart, the -family-to-sec2 argument was renamed to -family-to-single.
- This is just a name change and the functionality of the argument has not
- changed.
-
- The -family-to-sec2 argument has been kept for backwards-compatibility.
- This argument should be considered deprecated.
-
- (DER - 2018/11/14, HDFFV-10633)
+ -
High-Level APIs:
---------------
@@ -401,7 +165,7 @@ Support for new platforms, languages and compilers.
=======================================
-
-Bug Fixes since HDF5-1.10.4 release
+Bug Fixes since HDF5-1.10.5 release
==================================
Library
@@ -457,139 +221,6 @@ Bug Fixes since HDF5-1.10.4 release
(RL - 2019/3/4, HDFFV-10705)
- - Fix hangs with collective metadata reads during chunked dataset I/O
-
- In the parallel library, it was discovered that when a particular
- sequence of operations following a pattern of:
-
- "write to chunked dataset" -> "flush file" -> "read from dataset"
-
- occurred with collective metadata reads enabled, hangs could be
- observed due to certain MPI ranks not participating in the collective
- metadata reads.
-
- To fix the issue, collective metadata reads are now disabled during
- chunked dataset raw data I/O.
-
- (JTH - 2019/02/11, HDFFV-10563, HDFFV-10688)
-
- - Performance issue when closing an object
-
- The slow down is due to the search of the "tag_list" to find
- out the "corked" status of an object and "uncork" it if so.
-
- Improve performance by skipping the search of the "tag_list"
- if there are no "corked" objects when closing an object.
-
- (VC - 2019/02/06)
-
- - Uninitialized bytes from a type conversion buffer could be written
- to disk in H5Dwrite calls where type conversion takes place
- and the type conversion buffer was created by the HDF5 library.
-
- When H5Dwrite is called and datatype conversion must be performed,
- the library will create a temporary buffer for type conversion if
- one is not provided by the user via H5Pset_buffer. This internal
- buffer is allocated via malloc and contains uninitialized data. In
- some datatype conversions (float to long double, possibly others),
- some of this uninitialized data could be written to disk.
-
- This was flagged by valgrind in the dtransform test and does not
- appear to be a common occurrence (it is flagged in one test out
- of the entire HDF5 test suite).
-
- Switching to calloc fixed the problem.
-
- (DER - 2019/02/03, HDFFV-10694)
-
- - There was missing protection against division by zero reported to
- The HDF Group as issue #CVE-2018-17434.
-
- Protection against division by zero was added to address the issue
- #CVE-2018-17434.
-
- (BMR - 2019/01/29, HDFFV-10586)
-
- - The issue CVE-2018-17437 was reported to The HDF Group
-
- Although CVE-2018-17437 reported a memory leak, the actual issue
- was invalid read. It was found that the attribute name length
- in an attribute message was corrupted, which caused the buffer
- pointer to be advanced too far and later caused an invalid read.
-
- A check was added to detect when the attribute name or its length
- was corrupted and report the potential of data corruption.
-
- (BMR - 2019/01/29, HDFFV-10588)
-
- - H5Ewalk did not stop when it was supposed to
-
- H5Ewalk was supposed to stop when the callback function stopped
- even though the errors in the stack were not all visited, but it
- did not. This problem is now fixed.
-
- (BMR - 2019/01/29, HDFFV-10684)
-
- - Revert H5Oget_info* and H5Ovisit* functions
-
- In 1.10.3 new H5Oget_info*2 and H5Ovisit*2 functions were
- added for performance. Inadvertently, the original functions;
- H5Oget_info,
- H5Oget_info_by_name,
- H5Oget_info_by_idx,
- H5Ovisit,
- H5Ovisit_by_name
- were versioned to H5Oget_info*1 and H5Ovisit*1. This
- broke the API compatibility for a maintenance release. The
- original functions have been restored.
-
- (ADB - 2019/01/24, HDFFV-10686)
-
- - Fixed a potential invalid memory access and failure that could occur when
- decoding an unknown object header message (from a future version of the
- library).
-
- (NAF - 2019/01/07)
-
- - Deleting attributes in dense storage
-
- The library aborts with "infinite loop closing library" after
- attributes in dense storage are created and then deleted.
-
- When deleting the attribute nodes from the name index v2 B-tree,
- if an attribute is found in the intermediate B-tree nodes,
- which may be merged/redistributed in the process, we need to
- free the dynamically allocated spaces for the intermediate
- decoded attribute.
-
- (VC - 2018/12/26, HDFFV-10659)
-
- - There was missing protection against division by zero reported to
- The HDF Group as issue #CVE-2018-17233.
-
- Protection against division by zero was added to address the issue
- #CVE-2018-17233. In addition, several similar occurrences in the same
- file were fixed as well.
-
- (BMR - 2018/12/23, HDFFV-10577)
-
- - Fixed an issue where the parallel filters tests would fail
- if zlib was not available on the system. Until support can
- be added in the tests for filters beyond gzip/zlib, the tests
- will be skipped if zlib is not available.
-
- (JTH - 2018/12/05)
-
- - A bug was discovered in the parallel library where an application
- would eventually consume all of the available MPI communicators
- when continually writing to a compressed dataset in parallel. This
- was due to internal copies of an HDF5 File Access Property List,
- which each contained a copy of the MPI communicator, not being
- closed at the end of each write operation. This problem was
- exacerbated by larger numbers of processors.
-
- (JTH - 2018/12/05, HDFFV-10629)
-
Java Library:
----------------
@@ -597,26 +228,7 @@ Bug Fixes since HDF5-1.10.4 release
Fortran
--------
- - Fixed issue with Fortran not returning h5o_info_t field values
- meta_size%attr%index_size and meta_size%attr%heap_size.
-
- (MSB, 2019/01/08, HDFFV-10443)
-
- - Added symbolic links libhdf5_hl_fortran.so to libhdf5hl_fortran.so and
- libhdf5_hl_fortran.a to libhdf5hl_fortran.a in hdf5/lib directory for
- autotools installs. These were added to match the name of the files
- installed by cmake and the general pattern of hl lib files. We will
- change the names of the installed lib files to the matching name in
- the next major release.
-
- (LRK - 2019/01/04, HDFFV-10596)
-
- - Made Fortran specific subroutines PRIVATE in generic procedures.
-
- Affected generic procedures were functions in H5A, H5D, H5P, H5R and H5T.
-
- (MSB, 2018/12/04, HDFFV-10511)
-
+ -
Tools
-----
@@ -644,11 +256,7 @@ Bug Fixes since HDF5-1.10.4 release
Testing
-------
- - Fixed a test failure in testpar/t_dset.c caused by
- the test trying to use the parallel filters feature
- on MPI-2 implementations.
-
- (JTH, 2019/2/7)
+ -
Supported Platforms