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hdf5/release_docs/RELEASE.txt
jhendersonHDF 7b426bf3ea
CMake - Match Autotools behavior for library instrumentation (#2648) 
Enable library instrumentation by default for parallel debug builds
2023-03-31 22:38:15 -05:00

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HDF5 version 1.15.0 currently under development
================================================================================
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 HDF5-1.16.x release series
can be found at:
https://portal.hdfgroup.org/display/HDF5/Release+Specific+Information
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 HDF5-1.14.0
- Platforms Tested
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- Enabled instrumentation of the library by default in CMake for parallel
debug builds
HDF5 can be configured to instrument portions of the parallel library to
aid in debugging. Autotools builds of HDF5 turn this capability on by
default for parallel debug builds and off by default for other build types.
CMake has been updated to match this behavior.
(JTH - 2023/03/29)
- Added new option to build libaec and zlib inline with CMake.
Using the CMake FetchContent module, the external filters can populate
content at configure time via any method supported by the ExternalProject
module. Whereas ExternalProject_Add() downloads at build time, the
FetchContent module makes content available immediately, allowing the
configure step to use the content in commands like add_subdirectory(),
include() or file() operations.
The HDF options (and defaults) for using this are:
BUILD_SZIP_WITH_FETCHCONTENT:BOOL=OFF
LIBAEC_USE_LOCALCONTENT:BOOL=OFF
BUILD_ZLIB_WITH_FETCHCONTENT:BOOL=OFF
ZLIB_USE_LOCALCONTENT:BOOL=OFF
The CMake variables to control the path and file names:
LIBAEC_TGZ_ORIGPATH:STRING
LIBAEC_TGZ_ORIGNAME:STRING
ZLIB_TGZ_ORIGPATH:STRING
ZLIB_TGZ_ORIGNAME:STRING
See the CMakeFilters.cmake and config/cmake/cacheinit.cmake files for usage.
(ADB - 2023/02/21)
Library:
--------
- Added a Subfiling VFD configuration file prefix environment variable
The Subfiling VFD now checks for values set in a new environment
variable "H5FD_SUBFILING_CONFIG_FILE_PREFIX" to determine if the
application has specified a pathname prefix to apply to the file
path for its configuration file. For example, this can be useful
for cases where the application wishes to write subfiles to a
machine's node-local storage while placing the subfiling configuration
file on a file system readable by all machine nodes.
(JTH - 2023/02/22)
Parallel Library:
-----------------
-
Fortran Library:
----------------
-
C++ Library:
------------
-
Java Library:
-------------
-
Tools:
------
-
High-Level APIs:
----------------
-
C Packet Table API:
-------------------
-
Internal header file:
---------------------
-
Documentation:
--------------
-
Support for new platforms, languages and compilers
==================================================
-
Bug Fixes since HDF5-1.13.3 release
===================================
Library
-------
- Fixed a memory corruption issue that can occur when reading
from a dataset using a hyperslab selection in the file
dataspace and a point selection in the memory dataspace
When reading from a dataset using a hyperslab selection in
the dataset's file dataspace and a point selection in the
dataset's memory dataspace where the file dataspace's "rank"
is greater than the memory dataspace's "rank", memory corruption
could occur due to an incorrect number of selection points
being copied when projecting the point selection onto the
hyperslab selection's dataspace.
(JTH - 2023/03/23)
- Fixed issues in the Subfiling VFD when using the SELECT_IOC_EVERY_NTH_RANK
or SELECT_IOC_TOTAL I/O concentrator selection strategies
Multiple bugs involving these I/O concentrator selection strategies
were fixed, including:
* A bug that caused the selection strategy to be altered when
criteria for the strategy was specified in the
H5FD_SUBFILING_IOC_SELECTION_CRITERIA environment variable as
a single value, rather than in the old and undocumented
'integer:integer' format
* Two bugs which caused a request for 'N' I/O concentrators to
result in 'N - 1' I/O concentrators being assigned, which also
lead to issues if only 1 I/O concentrator was requested
Also added a regression test for these two I/O concentrator selection
strategies to prevent future issues.
(JTH - 2023/03/15)
- Fix CVE-2021-37501 / GHSA-rfgw-5vq3-wrjf
Check for overflow when calculating on-disk attribute data size.
A bogus hdf5 file may contain dataspace messages with sizes
which lead to the on-disk data sizes to exceed what is addressable.
When calculating the size, make sure, the multiplication does not
overflow.
The test case was crafted in a way that the overflow caused the
size to be 0.
(EFE - 2023/02/11 GH-2458)
- Fixed an issue with collective metadata writes of global heap data
New test failures in parallel netCDF started occurring with debug
builds of HDF5 due to an assertion failure and this was reported in
GitHub issue #2433. The assertion failure began happening after the
collective metadata write pathway in the library was updated to use
vector I/O so that parallel-enabled HDF5 Virtual File Drivers (other
than the existing MPI I/O VFD) can support collective metadata writes.
The assertion failure was fixed by updating collective metadata writes
to treat global heap metadata as raw data, as done elsewhere in the
library.
(JTH - 2023/02/16, GH #2433)
Java Library
------------
-
Configuration
-------------
- Correct the CMake generated pkg-config file
The pkg-config file generated by CMake had the order and placement of the
libraries wrong. Also added support for debug library names.
Changed the order of Libs.private libraries so that dependencies come after
dependents. Did not move the compression libraries into Requires.private
because there was not a way to determine if the compression libraries had
supported pkconfig files. Still recommend that the CMake config file method
be used for building projects with CMake.
(ADB - 2023/02/16 GH-1546,GH-2259)
Tools
-----
-
Performance
-------------
-
Fortran API
-----------
-
High-Level Library
------------------
-
Fortran High-Level APIs
-----------------------
-
Documentation
-------------
-
F90 APIs
--------
-
C++ APIs
--------
-
Testing
-------
-
Platforms Tested
===================
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
#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 5.3.18-150300-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 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 12.0.1, 14.0.5
(lassen) GCC 8.3.1
XL 16.1.1.2, 2021,09.22, 2022.08.05
(cmake)
Linux-4.12.14-197.99-default cray-mpich/7.7.14
#1 SMP x86_64 GNU/Linux cce 12.0.3
(theta) GCC 11.2.0
llvm 9.0
Intel 19.1.2
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
(autotools and cmake)
Linux-3.10.0-1160.0.0.1chaos openmpi-4.1.2
#1 SMP x86_64 GNU/Linux clang 6.0.0, 11.0.1
(quartz) GCC 7.3.0, 8.1.0
Intel 19.0.4, 2022.2, oneapi.2022.2
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
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 C/C++/Fortran oneAPI 2022 (cmake)
Visual Studio 2022 w/ clang 15.0.1
with MSVC-like command-line (C/C++ only - cmake)
Visual Studio 2022 w/ Intel C/C++/Fortran oneAPI 2022 (cmake)
Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake)
Known Problems
==============
************************************************************
* _ *
* (_) *
* __ ____ _ _ __ _ __ _ _ __ __ _ *
* \ \ /\ / / _` | '__| '_ \| | '_ \ / _` | *
* \ V V / (_| | | | | | | | | | | (_| | *
* \_/\_/ \__,_|_| |_| |_|_|_| |_|\__, | *
* __/ | *
* |___/ *
* *
* Please refrain from running any program (including *
* HDF5 tests) which uses the subfiling VFD on Perlmutter *
* at the National Energy Research Scientific Computing *
* Center, NERSC. *
* Doing so may cause a system disruption due to subfiling *
* crashing Lustre. The sytem's Lustre bug is expected *
* to be resolved by 2023. *
* *
************************************************************
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.
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.
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 are avoided by not building
the gif tool by default. Enable building the High-Level tools with these options:
autotools: --enable-hltools
cmake: HDF5_BUILD_HL_TOOLS=ON
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