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Update HISTORY-1_13.txt and clean RELEASE.txt (#1471)

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* Committing clang-format changes

* Spelling of preceed was corrected to proceed, but should have been
corrected to precede.

* Correct spelling correction of 'preceed' incorrectly to 'proceed'.  It should be 'precede'.

* Update version to 1.13.2-1 after 1.13.1 release.
Add Makefile.in to MANIFEST for addition of utils/tools and h5dwalk.

* Update VERS_RELEASE_EXCEPTIONS with new incompatible release version.

* Add HDF5 1.13.1 RELEASE.txt to HISTORY-1_13.txt contents to
HISTORY-1_13.txt.
Clean entries from RELEASE.txt.

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release_docs/HISTORY-1_13.txt
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@ -5,6 +5,7 @@ This file contains development history of the HDF5 1.13 releases from
the develop branch
01. Release Information for hdf5-1.13.0
02. Release Information for hdf5-1.13.1
[Search on the string '%%%%' for section breaks of each release.]
@ -1756,3 +1757,393 @@ These CVE issues have not yet been addressed and can be avoided by not building
the gif tool. Disable building the High-Level tools with these options:
autotools: --disable-hltools
cmake: HDF5_BUILD_HL_TOOLS=OFF
%%%%1.13.1%%%%
HDF5 version 1.13.1 released on 2022-03-02
================================================================================
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 HDF5-1.13.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 HDF5-1.13.0
- Platforms Tested
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- CPack will now generate RPM/DEB packages.
Enabled the RPM and DEB CPack generators on linux. In addition to
generating STGZ and TGZ packages, CPack will try to package the
library for RPM and DEB packages. This is the initial attempt and
may change as issues are resolved.
(ADB - 2022/01/27)
- Added new option to the h5cc scripts produced by CMake.
Add -showconfig option to h5cc scripts to cat the
libhdf5.settings file to the standard output.
(ADB - 2022/01/25)
- CMake will now run the PowerShell script tests in test/ by default
on Windows.
The test directory includes several shell script tests that previously
were not run by CMake on Windows. These are now run by default.
If TEST_SHELL_SCRIPTS is ON and PWSH is found, the PowerShell scripts
will execute. Similar to the bash scripts on unix platforms.
(ADB - 2021/11/23)
Library:
--------
- Add a new public function, H5ESget_requests()
This function allows the user to retrieve request pointers from an event
set. It is intended for use primarily by VOL plugin developers.
(NAF - 2022/01/11)
Parallel Library:
-----------------
- Several improvements to parallel compression feature, including:
* Improved support for collective I/O (for both writes and reads)
* Significant reduction of memory usage for the feature as a whole
* Reduction of copying of application data buffers passed to H5Dwrite
* Addition of support for incremental file space allocation for filtered
datasets created in parallel. Incremental file space allocation is the
default for these types of datasets (early file space allocation is
also still supported), while early file space allocation is still the
default (and only supported at allocation time) for unfiltered datasets
created in parallel. Incremental file space allocation should help with
parallel HDF5 applications that wish to use fill values on filtered
datasets, but would typically avoid doing so since dataset creation in
parallel would often take an excessive amount of time. Since these
datasets previously used early file space allocation, HDF5 would
allocate space for and write fill values to every chunk in the dataset
at creation time, leading to noticeable overhead. Instead, with
incremental file space allocation, allocation of file space for chunks
and writing of fill values to those chunks will be delayed until each
individual chunk is initially written to.
* Addition of support for HDF5's "don't filter partial edge chunks" flag
(https://portal.hdfgroup.org/display/HDF5/H5P_SET_CHUNK_OPTS)
* Addition of proper support for HDF5 fill values with the feature
* Addition of 'H5_HAVE_PARALLEL_FILTERED_WRITES' macro to H5pubconf.h
so HDF5 applications can determine at compile-time whether the feature
is available
* Addition of simple examples (ph5_filtered_writes.c and
ph5_filtered_writes_no_sel.c) under examples directory to demonstrate
usage of the feature
* Improved coverage of regression testing for the feature
(JTH - 2022/2/23)
Support for new platforms, languages and compilers
==================================================
- None
Bug Fixes since HDF5-1.13.0 release
===================================
Library
-------
- Fixed a metadata cache bug when resizing a pinned/protected cache entry
When resizing a pinned/protected cache entry, the metadata
cache code previously would wait until after resizing the
entry to attempt to log the newly-dirtied entry. This
caused H5C_resize_entry to mark the entry as dirty and made
H5AC_resize_entry think that it didn't need to add the
newly-dirtied entry to the dirty entries skiplist.
Thus, a subsequent H5AC__log_moved_entry would think it
needed to allocate a new entry for insertion into the dirty
entry skip list, since the entry didGn't exist on that list.
This caused an assertion failure, as the code to allocate a
new entry assumes that the entry is not dirty.
(JRM - 2022/02/28)
- Issue #1436 identified a problem with the H5_VERS_RELEASE check in the
H5check_version function.
Investigating the original fix, #812, we discovered some inconsistencies
with a new block added to check H5_VERS_RELEASE for incompatibilities.
This new block was not using the new warning text dealing with the
H5_VERS_RELEASE check and would cause the warning to be duplicated.
By removing the H5_VERS_RELEASE argument in the first check for
H5_VERS_MAJOR and H5_VERS_MINOR, the second check would only check
the H5_VERS_RELEASE for incompatible release versions. This adheres
to the statement that except for the develop branch, all release versions
in a major.minor maintenance branch should be compatible. The prerequisite
is that an application will not use any APIs not present in all release versions.
(ADB - 2022/02/24, #1438)
- Unified handling of collective metadata reads to correctly fix old bugs
Due to MPI-related issues occurring in HDF5 from mismanagement of the
status of collective metadata reads, they were forced to be disabled
during chunked dataset raw data I/O in the HDF5 1.10.5 release. This
wouldn't generally have affected application performance because HDF5
already disables collective metadata reads during chunk lookup, since
it is generally unlikely that the same chunks will be read by all MPI
ranks in the I/O operation. However, this was only a partial solution
that wasn't granular enough.
This change now unifies the handling of the file-global flag and the
API context-level flag for collective metadata reads in order to
simplify querying of the true status of collective metadata reads. Thus,
collective metadata reads are once again enabled for chunked dataset
raw data I/O, but manually controlled at places where some processing
occurs on MPI rank 0 only and would cause issues when collective
metadata reads are enabled.
(JTH - 2021/11/16, HDFFV-10501/HDFFV-10562)
- Fixed several potential MPI deadlocks in library failure conditions
In the parallel library, there were several places where MPI rank 0
could end up skipping past collective MPI operations when some failure
occurs in rank 0-specific processing. This would lead to deadlocks
where rank 0 completes an operation while other ranks wait in the
collective operation. These places have been rewritten to have rank 0
push an error and try to cleanup after the failure, then continue to
participate in the collective operation to the best of its ability.
(JTH - 2021/11/09)
Platforms Tested
===================
Linux 5.13.14-200.fc34 GNU gcc (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1)
#1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 2021078 (Red Hat 11.2.1-1)
Fedora34 clang version 12.0.1 (Fedora 12.0.1-1.fc34)
(cmake and autotools)
Linux 5.11.0-34-generic GNU gcc (GCC) 9.3.0-17ubuntu1
#36-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 9.3.0-17ubuntu1
Ubuntu 20.04 Ubuntu clang version 10.0.0-4
(cmake and autotools)
Linux 5.8.0-63-generic GNU gcc (GCC) 10.3.0-1ubuntu1
#71-Ubuntu SMP x86_64 GNU/Linux GNU Fortran (GCC) 10.3.0-1ubuntu1
Ubuntu20.10 Ubuntu clang version 11.0.0-2
(cmake and autotools)
Linux 5.3.18-22-default GNU gcc (SUSE Linux) 7.5.0
#1 SMP x86_64 GNU/Linux GNU Fortran (SUSE Linux) 7.5.0
SUSE15sp2 clang version 7.0.1 (tags/RELEASE_701/final 349238)
(cmake and autotools)
Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release
#1 SMP ppc64le GNU/Linux clang 8.0.1, 11.0.1
(lassen) GCC 7.3.1
XL 16.1.1.2
(cmake)
Linux-3.10.0-1160.49.1 openmpi-intel/4.1
#1 SMP x86_64 GNU/Linux Intel(R) Version 18.0.5, 19.1.2
(chama) (cmake)
Linux-4.12.14-150.75-default cray-mpich/7.7.10
#1 SMP x86_64 GNU/Linux GCC 7.3.0, 8.2.0
(cori) Intel (R) Version 19.0.3.199
(cmake)
Linux-4.12.14-197.86-default cray-mpich/7.7.6
# 1SMP x86_64 GNU/Linux GCC 7.3.0, 9.3.0, 10.2.0
(mutrino) Intel (R) Version 17.0.4, 18.0.5, 19.1.3
(cmake)
Linux 3.10.0-1160.36.2.el7.ppc64 gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
#1 SMP ppc64be GNU/Linux g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
Power8 (echidna) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
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
Linux-3.10.0-1127.0.0.1chaos openmpi-4.0.0
#1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1
(quartz) GCC 7.3.0, 8.1.0
Intel 16.0.4, 18.0.2, 19.0.4
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)
Visual Studio 2019 w/ Intel Fortran 19 (cmake)
Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake)
Known Problems
==============
Setting a variable-length dataset fill value will leak the memory allocated
for the p field of the hvl_t struct. A fix is in progress for this.
HDFFV-10840
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
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.
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.
The subsetting option in ph5diff currently will fail and should be avoided.
The subsetting option works correctly in serial h5diff.
Known problems in previous releases can be found in the HISTORY*.txt files
in the HDF5 source. Please report any new problems found to
help@hdfgroup.org.
CMake vs. Autotools installations
=================================
While both build systems produce similar results, there are differences.
Each system produces the same set of folders on linux (only CMake works
on standard Windows); bin, include, lib and share. Autotools places the
COPYING and RELEASE.txt file in the root folder, CMake places them in
the share folder.
The bin folder contains the tools and the build scripts. Additionally, CMake
creates dynamic versions of the tools with the suffix "-shared". Autotools
installs one set of tools depending on the "--enable-shared" configuration
option.
build scripts
-------------
Autotools: h5c++, h5cc, h5fc
CMake: h5c++, h5cc, h5hlc++, h5hlcc
The include folder holds the header files and the fortran mod files. CMake
places the fortran mod files into separate shared and static subfolders,
while Autotools places one set of mod files into the include folder. Because
CMake produces a tools library, the header files for tools will appear in
the include folder.
The lib folder contains the library files, and CMake adds the pkgconfig
subfolder with the hdf5*.pc files used by the bin/build scripts created by
the CMake build. CMake separates the C interface code from the fortran code by
creating C-stub libraries for each Fortran library. In addition, only CMake
installs the tools library. The names of the szip libraries are different
between the build systems.
The share folder will have the most differences because CMake builds include
a number of CMake specific files for support of CMake's find_package and support
for the HDF5 Examples CMake project.
The issues with the gif tool are:
HDFFV-10592 CVE-2018-17433
HDFFV-10593 CVE-2018-17436
HDFFV-11048 CVE-2020-10809
These CVE issues have not yet been addressed and can be avoided by not building
the gif tool. Disable building the High-Level tools with these options:
autotools: --disable-hltools
cmake: HDF5_BUILD_HL_TOOLS=OFF

144
release_docs/RELEASE.txt
View File

@ -36,7 +36,7 @@ CONTENTS
- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.13.0
- Bug Fixes since HDF5-1.13.1
- Platforms Tested
- Known Problems
- CMake vs. Autotools installations
@ -66,85 +66,16 @@ New Features
(JTH - 2022/03/01)
- CPack will now generate RPM/DEB packages.
Enabled the RPM and DEB CPack generators on linux. In addition to
generating STGZ and TGZ packages, CPack will try to package the
library for RPM and DEB packages. This is the initial attempt and
may change as issues are resolved.
(ADB - 2022/01/27)
- Added new option to the h5cc scripts produced by CMake.
Add -showconfig option to h5cc scripts that cat the
libhdf5-settings to the standard output.
(ADB - 2022/01/25)
- CMake will now run the PowerShell script tests in test/ by default
on Windows.
The test directory includes several shell script tests that previously
were not run by CMake on Windows. These are now run by default.
If TEST_SHELL_SCRIPTS is ON and PWSH is found, the PowerShell scripts
will execute. Similar to the bash scripts on unix platforms.
(ADB - 2021/11/23)
Library:
--------
- Add a new public function, H5ESget_requests()
This function allows the user to retrieve request pointers from an event
set. It is intended for use primarily by VOL plug in developers.
(NAF - 2022/01/11)
-
Parallel Library:
-----------------
- Several improvements to parallel compression feature, including:
-
* Improved support for collective I/O (for both writes and reads)
* Significant reduction of memory usage for the feature as a whole
* Reduction of copying of application data buffers passed to H5Dwrite
* Addition of support for incremental file space allocation for filtered
datasets created in parallel. Incremental file space allocation is the
default for these types of datasets (early file space allocation is
also still supported), while early file space allocation is still the
default (and only supported allocation time) for unfiltered datasets
created in parallel. Incremental file space allocation should help with
parallel HDF5 applications that wish to use fill values on filtered
datasets, but would typically avoid doing so since dataset creation in
parallel would often take an excessive amount of time. Since these
datasets previously used early file space allocation, HDF5 would
allocate space for and write fill values to every chunk in the dataset
at creation time, leading to noticeable overhead. Instead, with
incremental file space allocation, allocation of file space for chunks
and writing of fill values to those chunks will be delayed until each
individual chunk is initially written to.
* Addition of support for HDF5's "don't filter partial edge chunks" flag
(https://portal.hdfgroup.org/display/HDF5/H5P_SET_CHUNK_OPTS)
* Addition of proper support for HDF5 fill values with the feature
* Addition of 'H5_HAVE_PARALLEL_FILTERED_WRITES' macro to H5pubconf.h
so HDF5 applications can determine at compile-time whether the feature
is available
* Addition of simple examples (ph5_filtered_writes.c and
ph5_filtered_writes_no_sel.c) under examples directory to demonstrate
usage of the feature
* Improved coverage of regression testing for the feature
(JTH - 2022/2/23)
Fortran Library:
----------------
@ -191,76 +122,11 @@ Support for new platforms, languages and compilers
-
Bug Fixes since HDF5-1.12.0 release
Bug Fixes since HDF5-1.13.1 release
===================================
Library
-------
- Fixed a metadata cache bug when resizing a pinned/protected cache entry
When resizing a pinned/protected cache entry, the metadata
cache code previously would wait until after resizing the
entry to attempt to log the newly-dirtied entry. This would
cause H5C_resize_entry to mark the entry as dirty and make
H5AC_resize_entry think that it doesn't need to add the
newly-dirtied entry to the dirty entries skiplist.
Thus, a subsequent H5AC__log_moved_entry would think it
needs to allocate a new entry for insertion into the dirty
entry skip list, since the entry doesn't exist on that list.
This causes an assertion failure, as the code to allocate a
new entry assumes that the entry is not dirty.
(JRM - 2022/02/28)
- Issue #1436 identified a problem with the H5_VERS_RELEASE check in the
H5check_version function.
Investigating the original fix, #812, we discovered some inconsistencies
with a new block added to check H5_VERS_RELEASE for incompatibilities.
This new block was not using the new warning text dealing with the
H5_VERS_RELEASE check and would cause the warning to be duplicated.
By removing the H5_VERS_RELEASE argument in the first check for
H5_VERS_MAJOR and H5_VERS_MINOR, the second check would only check
the H5_VERS_RELEASE for incompatible release versions. This adheres
to the statement that except for the develop branch, all release versions
in a major.minor maintenance branch should be compatible. The prerequisite
is that an application will not use any APIs not present in all release versions.
(ADB - 2022/02/24, #1438)
- Unified handling of collective metadata reads to correctly fix old bugs
Due to MPI-related issues occurring in HDF5 from mismanagement of the
status of collective metadata reads, they were forced to be disabled
during chunked dataset raw data I/O in the HDF5 1.10.5 release. This
wouldn't generally have affected application performance because HDF5
already disables collective metadata reads during chunk lookup, since
it is generally unlikely that the same chunks will be read by all MPI
ranks in the I/O operation. However, this was only a partial solution
that wasn't granular enough.
This change now unifies the handling of the file-global flag and the
API context-level flag for collective metadata reads in order to
simplify querying of the true status of collective metadata reads. Thus,
collective metadata reads are once again enabled for chunked dataset
raw data I/O, but manually controlled at places where some processing
occurs on MPI rank 0 only and would cause issues when collective
metadata reads are enabled.
(JTH - 2021/11/16, HDFFV-10501/HDFFV-10562)
- Fixed several potential MPI deadlocks in library failure conditions
In the parallel library, there were several places where MPI rank 0
could end up skipping past collective MPI operations when some failure
occurs in rank 0-specific processing. This would lead to deadlocks
where rank 0 completes an operation while other ranks wait in the
collective operation. These places have been rewritten to have rank 0
push an error and try to cleanup after the failure, then continue to
participate in the collective operation to the best of its ability.
(JTH - 2021/11/09)
-
Java Library