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|
HDF5 version 1.12.3-1 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 HDF5-1.12.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 HDF5-1.12.2
- 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)
- Add new CMake configuration variable HDF5_USE_GNU_DIRS
HDF5_USE_GNU_DIRS (default OFF) selects the use of GNU Coding Standard install
directory variables by including the CMake module, GNUInstallDirs(see CMake
documentation for details). The HDF_DIR_PATHS macro in the HDFMacros.cmake file
sets various PATH variables for use during the build, test and install processes.
By default, the historical settings for these variables will be used.
(ADB - 2022/10/21, GH-2175, GH-1716)
- 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)
Library:
--------
-
Parallel Library:
-----------------
-
Fortran Library:
----------------
-
C++ Library:
------------
-
Java Library:
-------------
- HDF5GroupInfo class has been deprecated.
This class assumes that an object can contain four values which uniquely identify an
object among those HDF5 files which are open. This is no longer valid in future
HDF5 releases.
(ADB - 2023/03/27)
- 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:
------
- 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:
----------------
-
C Packet Table API:
-------------------
-
Internal header file:
---------------------
-
Documentation:
--------------
- Doxygen User Guide documentation is available when configured and generated.
The resulting documentation files will be in the share/html subdirectory
of the HDF5 install directory.
(ADB - 2022/08/09)
Support for new platforms, languages and compilers
==================================================
-
Bug Fixes since HDF5-1.12.1 release
===================================
Library
-------
- Fix for CVE-2019-8396
Malformed HDF5 files may have truncated content which does not match
the expected size. When H5O__pline_decode() attempts to decode these it
may read past the end of the allocated space leading to heap overflows
as bounds checking is incomplete.
The fix ensures each element is within bounds before reading.
(2023/04/13 - HDFFV-10712, CVE-2019-8396, GitHub #2209)
- Memory leak
Memory leak was detected when running h5dump with "pov". The memory was allocated
via H5FL__malloc() in hdf5/src/H5FL.c
The fuzzed file "pov" was an HDF5 file containing an illegal continuation message.
When deserializing the object header chunks for the file, memory is allocated for the
array of continuation messages (cont_msg_info->msgs) in continuation message info struct.
As error is encountered in loading the illegal message, the memory allocated for
cont_msg_info->msgs needs to be freed.
(VC - 2023/04/11 GH-2599)
- 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)
- 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)
- Seg fault on file close
h5debug fails at file close with core dump on a file that has an
illegal file size in its cache image. In H5F_dest(), the library
performs all the closing operations for the file and keeps track of
the error encountered when reading the file cache image.
At the end of the routine, it frees the file's file structure and
returns error. Due to the error return, the file object is not removed
from the ID node table. This eventually causes assertion failure in
H5VL__native_file_close() when the library finally exits and tries to
access that file object in the table for closing.
The closing routine, H5F_dest(), will not free the file structure if
there is error, keeping a valid file structure in the ID node table.
It will be freed later in H5VL__native_file_close() when the
library exits and terminates the file package.
(VC - 2022/12/14, HDFFV-11052, CVE-2020-10812)
- Fixed an issue with variable length attributes
Previously, if a variable length attribute was held open while its file
was opened through another handle, the same attribute was opened through
the second file handle, and the second file and attribute handles were
closed, attempting to write to the attribute through the first handle
would cause an error.
(NAF - 2022/10/24)
- Fixed an issue with hyperslab selections
Previously, when combining hyperslab selections, it was possible for the
library to produce an incorrect combined selection.
(NAF - 2022/09/25)
- Fixed an issue with attribute type conversion with compound datatypes
Previously, when performing type conversion for attribute I/O with a
compound datatype, the library would not fill the background buffer with
the contents of the destination, potentially causing data to be lost when
only writing to a subset of the compound fields.
(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, HDFFV-11316, HDFFV-11317)
- Memory leak
A memory leak was observed with variable-length fill value in
H5O_fill_convert() function in H5Ofill.c. The leak is
manifested by running valgrind on test/set_extent.c.
Previously, fill->buf is used for datatype conversion
if it is large enough and the variable-length information
is therefore lost. A buffer is now allocated regardless
so that the element in fill->buf can later be reclaimed.
(VC - 2022/10/10, HDFFV-10840)
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)
- Change the settings of the *pc files to use the correct format
The pkg-config files generated by CMake uses incorrect syntax for the 'Requires'
settings. Changing the set to use 'lib-name = version' instead 'lib-name-version'
fixes the issue
(ADB - 2022/12/06 HDFFV-11355)
- Move MPI libraries link from PRIVATE to PUBLIC
The install dependencies were not including the need for MPI libraries when
an application or library was built with the C library. Also updated the
CMake target link command to use the newer style MPI::MPI_C link variable.
(ADB - 2022/20/27)
Tools
-----
- In the tools traverse function - an error in either visit call
will bypass the cleanup of the local data variables.
Replaced the H5TOOLS_GOTO_ERROR with just H5TOOLS_ERROR.
(ADB - 2023/04/06 GH-2598)
- Fix h5repack to only print output when verbose option is selected
When timing option was added to h5repack, the check for verbose was
incorrectly implemented.
(ADB - 2022/12/02, GH #2270)
Performance
-------------
-
Fortran API
-----------
-
High-Level Library
------------------
-
Fortran High-Level APIs
-----------------------
-
Documentation
-------------
-
F90 APIs
--------
-
C++ APIs
--------
-
Testing
-------
-
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-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 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 2021 (cmake)
Visual Studio 2019 w/ MSMPI 10.1 (C only - cmake)
Known Problems
==============
testflushrefresh.sh will fail when run with "make check-passthrough-vol"
on centos7, with 3 Errors/Segmentation faults. These will not occur when
run with "make check". See https://github.com/HDFGroup/hdf5/issues/673
for details.
The t_bigio test fails on several HPC platforms, generally by timeout with
OpenMPI 4.0.0 or with this error from spectrum-mpi:
*** on communicator MPI_COMM_WORLD
*** MPI_ERR_COUNT: invalid count argument
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
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