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Release updates (#2033)

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* Update HISTORy-1_13.txt and clean RELEASE.txt entries after 1.13.2 release.
This commit is contained in:
Larry Knox
2022-08-18 08:35:21 -05:00
committed by GitHub
parent a3fd350483
commit 9dfcca0bbb
2 changed files with 611 additions and 189 deletions
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244
release_docs/RELEASE.txt
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@@ -36,7 +36,7 @@ CONTENTS
- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.13.1
- Bug Fixes since HDF5-1.13.2
- Platforms Tested
- Known Problems
- CMake vs. Autotools installations
@@ -47,83 +47,12 @@ New Features
Configuration:
-------------
- Correct the usage of CMAKE_Fortran_MODULE_DIRECTORY and where to
install Fortran mod files.
The Fortran modules files, ending in .mod are files describing a
Fortran 90 (and above) module API and ABI. These are not like C
header files describing an API, they are compiler dependent and
arch dependent, and not easily readable by a human being. They are
nevertheless searched for in the includes directories by gfortran
(in directories specified with -I).
Autotools configure uses the -fmoddir option to specify the folder.
CMake will use "mod" folder by default unless overridden by the CMake
variable; HDF5_INSTALL_MODULE_DIR.
(ADB - 2022/07/21)
- HDF5 memory allocation sanity checking is now off by default for
Autotools debug builds
HDF5 can be configured to perform sanity checking on internal memory
allocations by adding heap canaries to these allocations. However,
enabling this option can cause issues with external filter plugins
when working with (reallocating/freeing/allocating and passing back)
buffers.
Previously, this option was off by default for all CMake build types,
but only off by default for non-debug Autotools builds. Since debug
is the default build mode for HDF5 when built from source with
Autotools, this can result in surprising segfaults that don't occur
when an application is built against a release version of HDF5.
Therefore, this option is now off by default for all build types
across both CMake and Autotools.
(JTH - 2022/03/01)
-
Library:
--------
- Subfiling VFD
The HDF5 Subfiling VFD is a new MPI-based file driver that allows an
HDF5 application to distribute an HDF5 file across a collection of
"sub-files" in equal-sized data segment "stripes". I/O to the logical
HDF5 file is then directed to the appropriate "sub-file" according to
the Subfiling configuration and a system of I/O concentrators, which
are MPI ranks operating worker threads.
By allowing a configurable stripe size, number of I/O concentrators and
method for selecting MPI ranks as I/O concentrators, the Subfiling VFD
aims to enable an HDF5 application to find a middle ground between the
single shared file and file-per-process approaches to parallel file I/O
for the particular machine the application is running on. In general, the
goal is to avoid some of the complexity of the file-per-process approach
while also minimizing the locking issues of the single shared file approach
on a parallel file system.
Also included with the Subfiling VFD is a new h5fuse.sh script which
reads a Subfiling configuration file and then combines the various
sub-files back into a single HDF5 file. By default, the h5fuse.sh script
looks in the current directory for the Subfiling configuration file,
but can also be pointed to the configuration file with a command-line
option.
The Subfiling VFD can be used by calling H5Pset_fapl_subfiling() on a
File Access Property List and using that FAPL for file operations. Note
that the Subfiling VFD currently has the following limitations:
* Does not currently support HDF5 collective I/O, other than collective
metadata writes and reads as set by H5Pset_coll_metadata_write() and
H5Pset_all_coll_metadata_ops()
* The Subfiling VFD should not currently be used with an HDF5 library
that has been built with thread-safety enabled. This can cause deadlocks
when failures occur due to interactions between the VFD's internal
threads and HDF5's global lock.
(JTH - 2022/07/22)
-
Parallel Library:
@@ -138,85 +67,17 @@ New Features
C++ Library:
------------
- Added two new constructors to H5::H5File class
Two new constructors were added to allow opening a file with non-default
access property list.
-
Java Library:
-------------
- Added version of H5Rget_name to return the name as a Java string.
Other functions that get_name process the get_size then get the name
within the JNI implementation. Now H5Rget_name has a H5Rget_name_string.
(ADB - 2022/07/12)
- Added reference support to H5A and H5D read write vlen JNI functions.
Added the implementation to handle VL references as an Array of Lists
of byte arrays.
The JNI wrappers translate the Array of Lists to/from the hvl_t vlen
structures. The wrappers use the specified datatype arguments for the
List type translation, it is expected that the Java type is correct.
(ADB - 2022/07/11, HDFFV-11318)
- H5A and H5D read write vlen JNI functions were incorrect.
Corrected the vlen function implementations for the basic primitive types.
The VLStrings functions now correctly use the implementation that had been
the VL functions. (VLStrings functions did not have an implementation.)
The new VL functions implementation now expect an Array of Lists between
Java and the JNI wrapper.
The JNI wrappers translate the Array of Lists to/from the hvl_t vlen
structures. The wrappers use the specified datatype arguments for the
List type translation, it is expected that the Java type is correct.
(ADB - 2022/07/07, HDFFV-11310)
- H5A and H5D read write JNI functions had flawed vlen datatype check.
Adapted tools function for JNI utils file. This reduced multiple calls
to a single check and variable. The variable can then be used to call
the H5Treclaim function. Adjusted existing test and added new test.
(ADB - 2022/06/22)
-
Tools:
------
- Building h5perf/h5perf_serial in "standalone mode" has been removed
Building h5perf separately from the library was added circa 2008
in HDF5 1.6.8. It's unclear what purpose this serves and the current
implementation is currently broken. The existing files require
H5private.h and the symbols we use to determine how the copied
platform-independence scheme should be used come from H5pubconf.h,
which may not match the compiler being used to build standalone h5perf.
Due to the maintenance overhead and lack of a clear use case, support
for building h5perf and h5perf_serial separately from the HDF5 library
has been removed.
(DER - 2022/07/15)
- The perf tool has been removed
The small `perf` tool didn't really do anything special and the name
conflicts with gnu's perf tool.
(DER - 2022/07/15, GitHub #1787)
- 1.10 References in containers were not displayed properly by h5dump.
Ported 1.10 tools display function to provide ability to inspect and
display 1.10 reference data.
(ADB - 2022/06/22)
-
High-Level APIs:
@@ -231,7 +92,7 @@ New Features
Internal header file:
---------------------
- All the #defines named H5FD_CTL__* were renamed to H5FD_CTL_*, i.e. the double underscore was reduced to a single underscore.
-
Documentation:
@@ -244,7 +105,7 @@ Support for new platforms, languages and compilers
-
Bug Fixes since HDF5-1.13.1 release
Bug Fixes since HDF5-1.13.2 release
===================================
Library
-------
@@ -257,27 +118,6 @@ Bug Fixes since HDF5-1.13.1 release
(NAF - 2022/08/22, GitHub #2016)
- Modified H5Fstart_swmr_write() to preserve DAPL properties
Internally, H5Fstart_swmr_write() closes and reopens the file in question
as part of its process for making the file SWMR-safe. Previously, when
the library reopened the file it would simply use the default access
properties. Modified the library to instead save these properties and use
them when reopening the file.
(NAF - 2022/07/18, HDFFV-11308)
- Converted an assertion on (possibly corrupt) file contents to a normal
error check
Previously, the library contained an assertion check that a read superblock
doesn't contain a superblock extension message when the superblock
version < 2. When a corrupt HDF5 file is read, this assertion can be triggered
in debug builds of HDF5. In production builds, this situation could cause
either a library error or a crash, depending on the platform.
(JTH - 2022/07/08)
Java Library
------------
@@ -301,11 +141,7 @@ Bug Fixes since HDF5-1.13.1 release
Fortran API
-----------
- h5open_f and h5close_f fixes
* Fixed it so both h5open_f and h5close_f can be called multiple times.
* Fixed an issue with open objects remaining after h5close_f was called.
* Added additional tests.
(MSB, 2022/04/19, HDFFV-11306)
-
High-Level Library
@@ -341,9 +177,9 @@ Bug Fixes since HDF5-1.13.1 release
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)
Linux 5.16.14-200.fc35 GNU gcc (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9)
#1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9)
Fedora35 clang version 13.0.0 (Fedora 13.0.0-3.fc35)
(cmake and autotools)
Linux 5.11.0-34-generic GNU gcc (GCC) 9.3.0-17ubuntu1
@@ -351,15 +187,27 @@ Platforms Tested
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 5.3.18-150300-cray_shasta_c cray-mpich/8.1.16
#1 SMP x86_64 GNU/Linux Cray clang 14.0.0
(crusher) GCC 11.2.0
(cmake)
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 5.3.18-24-cray_shasta_c cray-mpich/8.1.12
#1 SMP x86_64 GNU/Linux Cray clang 13.0.0
(spock) AMD clang 13.0.0
GCC 8.2.0, 11.2.0
(cmake)
Linux 4.14.0-115.35.1.1chaos openmpi 4.0.5
#1 SMP aarch64 GNU/Linux GCC 9.2.0 (ARM-build-5)
(stria) GCC 7.2.0 (Spack GCC)
(cmake)
Linux 4.14.0-115.35.1.3chaos spectrum-mpi/rolling-release
#1 SMP ppc64le GNU/Linux clang 12.0.1
(vortex) GCC 8.3.1
XL 16.1.1
(cmake)
Linux-4.14.0-115.21.2 spectrum-mpi/rolling-release
#1 SMP ppc64le GNU/Linux clang 8.0.1, 11.0.1
@@ -372,11 +220,6 @@ Platforms Tested
(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)
@@ -400,12 +243,27 @@ Platforms Tested
PGI C, Fortran, C++ for 64-bit target on
x86_64;
Version 19.10-0
(autotools and cmake)
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
Linux-3.10.0-1160.71.1.1chaos openmpi/4.1
#1 SMP x86_64 GNU/Linux GCC 7.2.0
(skybridge) Intel/19.1
(cmake)
Linux-3.10.0-1160.66.1.1chaos openmpi/4.1
#1 SMP x86_64 GNU/Linux GCC 7.2.0
(attaway) Intel/19.1
(cmake)
Linux-3.10.0-1160.59.1.1chaos openmpi/4.1
#1 SMP x86_64 GNU/Linux Intel/19.1
(chama) (cmake)
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
@@ -466,6 +324,14 @@ Known Problems
The subsetting option in ph5diff currently will fail and should be avoided.
The subsetting option works correctly in serial h5diff.
Several tests currently fail on certain platforms:
MPI_TEST-t_bigio fails with spectrum-mpi on ppc64le platforms.
MPI_TEST-t_subfiling_vfd and MPI_TEST_EXAMPLES-ph5_subfiling fail with
cray-mpich on theta and with XL compilers on ppc64le platforms.
MPI_TEST_testphdf5_tldsc fails with cray-mpich 7.7 on cori and theta.
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.