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hdf5/release_docs/RELEASE.txt
Allen Byrne f4dbb810c1
Add msys2 workflow for CMake (#4991) 
Also updates CMake configure checks to build HDF5 w/ MSYS2
2024-10-28 16:28:29 -07:00

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HDF5 version 2.0.0 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:
https://support.hdfgroup.org/releases/hdf5/latest-docs.html
The official HDF5 releases can be obtained from:
https://support.hdfgroup.org/downloads/index.html
Changes from Release to Release and New Features in the HDF5-2.x.y release series
can be found at:
https://support.hdfgroup.org/releases/hdf5/documentation/release_specific_info.md
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 HDF5-2.0.0
- Platforms Tested
- Known Problems
- CMake vs. Autotools installations
New Features
============
Configuration:
-------------
- Added support for MinGW + MSYS2 when building with CMake
We previously added support for this to the Autotools and the appropriate
configure-time checks have been added to CMake.
CMake + MinGW + MSYS2 is now tested with the following environments:
* mingw32
* mingw64
* ucrt64
* clang64
- Added CMake build mode flags to the libhdf5.settings file
Flags from the CMake build mode (e.g., optimization) are not a part of
CMAKE_<language>_FLAGS and were not exported to the libhdf5.settings file. This
has been fixed and the C, Fortran, and C++ build mode flags are now exported to
the file.
This also affects the text output of H5check_version() and the libhdf5.settings
string stored in the library (for those who use strings(1), etc. to get
build info from the binary).
- CMake: Split compiler specific flags into separate files
The compiler specific flags have been split into separate files to make
it easier to maintain and add new compiler flags. The flags for NVHPC,
Intel, GNU and Clang compilers are now in separate files included from
the current compiler flags files; HDFCompiler<language>Flags.cmake.
- Added a configuration option for internal threading/concurrency support:
CMake: HDF5_ENABLE_THREADS (ON/OFF) (Default: ON)
Autotools: --enable-threads (yes/no) (Default: yes)
This option enables support for threading and concurrency algorithms
within the HDF5 library. It is required for, but separate from, the
'threadsafe' configure option, which makes the HDF5 API safe to call from
multiple threads. It is possible to enable the 'threads' option and
disable the 'threadsafe' option, but not vice versa. The 'threads' option
must be on to enable the subfiling VFD.
- Added support for native zlib-ng compression.
Changed the zlib-ng CMake logic to prefer the native zlib-ng library. Added
#ifdef around the compression function calls. Added including the correct
header file with the same #ifdef.
- Renamed remaining HDF5 library CMake options except for CMake BUILD* variables
DEFAULT_API_VERSION to HDF5_DEFAULT_API_VERSION
DISABLE_PDB_FILES to HDF5_DISABLE_PDB_FILES
ONLY_SHARED_LIBS to HDF5_ONLY_SHARED_LIBS
ALLOW_UNSUPPORTED to HDF5_ALLOW_UNSUPPORTED
TEST_SHELL_SCRIPTS to HDF5_TEST_SHELL_SCRIPTS
All other HDF5 library CMake options are prefixed with HDF5_
- bin/cmakehdf5 has been removed
This was an unsupported build script that made building HDF5 via CMake
work like building HDF5 via the Autotools. It has been unmaintained
for a long time, has been marked deprecated, and is being removed.
- Generated files in src are now checked into version control
These files are infrequently updated and generating them adds a
dependency on Perl. The listed files are now checked in and do
not need to be recreated when checking out development branches.
* H5Edefin.h
* H5Einit.h
* H5Emajdef.h
* H5Emindef.h
* H5Epubgen.h
* H5Eterm.h
* H5overflow.h
* H5version.h
- Dropped some old Solaris Studio work-arounds
Solaris Studio no longer seems to be maintained and the last version
(12.4, circa 2015) doesn't seem to fully support C11. We've removed
some hacks that work around things like __attribute__() support.
- Dropped support for the traditional MSVC preprocessor
Visual Studio has recently started using a standards-compliant
preprocessor (In VS2019+) and this is the default in C11.
https://learn.microsoft.com/en-us/cpp/preprocessor/preprocessor-experimental-overview?view=msvc-170
Because of this, we've dropped support for the traditional
MSVC preprocessor.
- The standard for building the library is now C11
We have updated the build files to set the C standard to C11, though
some platforms use gnu11 to get some GNU things to work.
Library:
--------
- The H5VLstart_lib_state / H5VLfinish_lib_state API routines for pass-
through connector authors now require a parameter that can be used to
store the library's context.
- Removed H5FDperform_init API routine. Virtual File Driver (VFD)
developers who wish to provide an ID for their driver should create
a routine specific to their individual implementation.
- H5Pset_external() now uses HDoff_t, which is always a 64-bit type
The H5Pset_external() call took an off_t parameter in HDF5 1.14.x and
earlier. On POSIX systems, off_t is specified as a 64-bit type via
POSIX large-file support (LFS). On Windows, however, off_t is defined
as a 32-bit type, even on 64-bit Windows.
HDoff_t has been added to H5public.h and is defined to be int64_t on
Windows and the library has been updated to use HDoff_t in place of
off_t throughout. The H5Pset_external() offset parameter has also been
updated to be HDoff_t.
There is no API compatibility wrapper for this change.
Fixes GitHub issue #3506
Parallel Library:
-----------------
-
Fortran Library:
----------------
-
C++ Library:
------------
-
Java Library:
-------------
-
Tools:
------
- Remove the high-level GIF tools
The high-level GIF tools, h52gif and gif2h5, have unfixed CVE issues
(with no proof-of-concept files). They are not critical tools, are not
well maintained, and are an odd fit for building with the library.
Because of this, they have been removed. We may move them to a separate
repository in the future.
This also removes the following configure options:
Autotools: --(dis|en)able-hlgiftools
CMake: HDF5_BUILD_HL_GIF_TOOLS
High-Level APIs:
----------------
-
C Packet Table API:
-------------------
-
Internal header file:
---------------------
-
Documentation:
--------------
- The COPYING file has been renamed to LICENSE
This is where most people will expect to find license information. The
COPYING_LBNL_HDF5 file has also been renamed to LICENSE_LBNL_HDF5.
The licenses are unchanged.
Support for new platforms, languages and compilers
==================================================
-
Bug Fixes since HDF5-2.0.0 release
===================================
Library
-------
- Fixed a bug in the H5Oexists and H5Oexists_by_name API routines that
would cause those routines to return FAIL instead of FALSE when checking
the existence of a non-existent object with a file ID instead of a
group ID.
- Only clear FE_INVALID when that symbol is present on the system
When we initialize the floating-point types at library startup, it's
possible to raise floating-point exceptions when we check which things
are supported. Normally, we clear these floating-point exceptions via
feclearexcept(FE_INVALID), but FE_INVALID may not be present on all
systems. Specifically, this was reported as being a problem when using
Emscripten 3.1.68 to compile HDF5 1.14.5 to WebAssembly.
We've added an #ifdef FE_INVALID block around the exception clearing
code to correct this.
Fixes GitHub issue #4952
Java Library
------------
-
Configuration
-------------
- Changed name of libhdf5hl_fortran installed by autotools to libhdf5_hl_fortran. The
new name is consistent with the name of the lib when installed by CMake and with the
other hl libs.
Fixes GitHub issue #4811
Tools
-----
-
Performance
-------------
-
Fortran API
-----------
-
High-Level Library
------------------
-
Fortran High-Level APIs
-----------------------
-
Documentation
-------------
-
F90 APIs
--------
-
C++ APIs
--------
-
Testing
-------
Platforms Tested
===================
- HDF5 is tested with the two latest macOS versions that are available
on github runners. As new major macOS versions become available, HDF5
will discontinue support for the older version and add the new latest
version to its list of compatible systems, along with the previous
version.
Linux 6.8.0-1010-aws GNU gcc, gfortran, g++
#10-Ubuntu SMP 2024 x86_64 (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU/Linux Ubuntu 24.04 Ubuntu clang version 18.1.3 (1ubuntu1)
Intel(R) oneAPI DPC++/C++ Compiler 2024.2.0
ifx (IFX) 2024.2.0 20240602
(cmake and autotools)
Linux 6.5.0-1018-aws GNU gcc, gfortran, g++
#18-Ubuntu SMP x86_64 GNU/Linux (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Ubuntu 22.04 Ubuntu clang version 14.0.0-1ubuntu1
Intel(R) oneAPI DPC++/C++ Compiler 2024.0.2
ifx (IFX) 2024.0.2 20231213
(cmake and autotools)
Linux 5.14.21-cray_shasta_c cray-mpich/8.1.28
#1 SMP x86_64 GNU/Linux cce/15.0.0
(frontier) gcc/13.2
(cmake)
Linux 5.14.0-427.24.1.el9_4 GNU gcc, gfortran, g++ (Red Hat 11.4.1-3)
#1 SMP x86_64 GNU/Linux clang version 17.0.6
Rocky 9 Intel(R) oneAPI DPC++/C++ Compiler 2024.2.0
ifx (IFX) 2024.2.0
(cmake and autotools)
Linux-4.18.0-553.16.1.1toss.t4 openmpi/4.1.2
#1 SMP x86_64 GNU/Linux clang 14.0.6
(corona, dane) GCC 12.1.1
Intel(R) oneAPI DPC++/C++ Compiler 2023.2.1
ifx (IFX) 2023.2.1
Linux-4.18.0-553.5.1.1toss.t4 openmpi/4.1/4.1.6
#1 SMP x86_64 GNU/Linux clang 16.0.6
(eclipse) GCC 12.3.0
Intel(R) oneAPI DPC++/C++ Compiler 2024.0.2
ifx (IFX) 2024.0.2
(cmake)
Linux 4.14.0-115.35.1.3chaos spectrum-mpi/rolling-release
#1 SMP ppc64le GNU/Linux clang 17.0.6
(vortex) GCC 12.2.1
nvhpc 24.1
XL 2023.06.28
(cmake)
Linux-4.14.0-115.35.1 spectrum-mpi/rolling-release
#1 SMP ppc64le GNU/Linux clang 14.0.5, 15.0.6
(lassen) GCC 8.3.1
XL 2021.09.22, 2022.08.05
(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 3.10.0-1160.80.1.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 7.2.0, Version 8.3.0,
Version 9.1.0, Version 10.2.0
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 7.1(Hanzomon)
Intel(R) C (icc) and C++ (icpc) 17.0.0.098 compilers
with NAG Fortran Compiler Release 7.1(Hanzomon)
MPICH 3.1.4 compiled with GCC 4.9.3
MPICH 3.3 compiled with GCC 7.2.0
OpenMPI 3.1.3 compiled with GCC 7.2.0 and 4.1.2
compiled with GCC 9.1.0
PGI C, Fortran, C++ for 64-bit target on
x86_64;
Versions 18.4.0 and 19.10-0
NVIDIA nvc, nvfortran and nvc++ version 22.5-0
(autotools and cmake)
Linux-3.10.0-1160.119.1.1chaos openmpi/4.1.4
#1 SMP x86_64 GNU/Linux clang 16.0.6
(skybridge) Intel(R) oneAPI DPC++/C++ Compiler 2023.2.0
ifx (IFX) 2023.2.0
(cmake)
Linux-3.10.0-1160.90.1.1chaos openmpi/4.1
#1 SMP x86_64 GNU/Linux clang 16.0.6
(attaway) GCC 12.1.0
Intel(R) oneAPI DPC++/C++ Compiler 2024.0.2
ifx (IFX) 2024.0.2
(cmake)
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 2019 w/ clang 12.0.0
with MSVC-like command-line (C/C++ only - cmake)
Visual Studio 2019 w/ Intel (C/C++ only - cmake)
Visual Studio 2022 w/ clang 17.0.3
with MSVC-like command-line (C/C++ only - cmake)
Visual Studio 2022 w/ Intel C/C++ oneAPI 2023 (cmake)
Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake)
Known Problems
==============
- When building with the NAG Fortran compiler using the Autotools and libtool
2.4.2 or earlier, the -shared flag will be missing '-Wl,', which will cause
compilation to fail. This is due to a bug in libtool that was fixed in 2012
and released in 2.4.4 in 2014.
- When the library detects and builds in support for the _Float16 datatype, an
issue has been observed on at least one MacOS 14 system where the library
fails to initialize due to not being able to detect the byte order of the
_Float16 type (https://github.com/HDFGroup/hdf5/issues/4310):
#5: H5Tinit_float.c line 308 in H5T__fix_order(): failed to detect byte order
major: Datatype
minor: Unable to initialize object
If this issue is encountered, support for the _Float16 type can be disabled
with a configuration option:
CMake: HDF5_ENABLE_NONSTANDARD_FEATURE_FLOAT16=OFF
Autotools: --disable-nonstandard-feature-float16
- When HDF5 is compiled with NVHPC versions 23.5 - 23.9 (additional versions may
also be applicable) and with -O2 (or higher) and -DNDEBUG, test failures occur
in the following tests:
H5PLUGIN-filter_plugin
H5TEST-flush2
H5TEST-testhdf5-base
MPI_TEST_t_filters_parallel
Sporadic failures (even with lower -O levels):
Java JUnit-TestH5Pfapl
Java JUnit-TestH5D
Also, NVHPC will fail to compile the test/tselect.c test file with a compiler
error of 'use of undefined value' when the optimization level is -O2 or higher.
This is confirmed to be a bug in the nvc compiler that has been fixed as of
23.11. If you are using an affected version of the NVidia compiler, the
work-around is to set the optimization level to -O1.
https://forums.developer.nvidia.com/t/hdf5-no-longer-compiles-with-nv-23-9/269045
- 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.
- 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.
- The subsetting option in ph5diff currently will fail and should be avoided.
The subsetting option works correctly in serial h5diff.
- Flang Fortran compilation will fail (last check version 17) due to not yet
implemented: (1) derived type argument passed by value (H5VLff.F90),
and (2) support for REAL with KIND = 2 in intrinsic SPACING used in testing.
- Fortran tests HDF5_1_8.F90 and HDF5_F03.F90 will fail with Cray compilers
greater than version 16.0 due to a compiler bug. The latest version verified
as failing was version 17.0.
- 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.
- File space may not be released when overwriting or deleting certain nested
variable length or reference types.
- 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
LICENSE 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-hlgiftools
cmake: HDF5_BUILD_HL_GIF_TOOLS=ON
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