path: root/release_docs/RELEASE.txt

HDF5 version 1.10.10-2 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 HDF5-1.10.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 HDF5-1.10.9
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools installations


New Features
============

    Configuration:
    -------------
    - Removal of dmalloc support

      The ability to build with dmalloc support has been removed along with
      the following configure options:

      Autotools:
          --with-dmalloc=

      CMake:
          HDF5_ENABLE_USING_DMALLOC

      (DER - 2023/03/17)
      
    - Allow parallel and threadsafe to be built

      In the past, we required --enable-unsupported (Autotools) or
      ALLOW_UNSUPPORTED (CMake) in order to build the parallel library with
      thread-safety support. The parallel, thread-safe library can now be
      built without these options.

      (DER - 2023/03/17)

    - 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:
    -------------
    - 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 - 2023/03/20)

    - 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 - 2023/03/20, GitHub #1787)


    High-Level APIs:
    ----------------
    -


    C Packet Table API:
    -------------------
    -


    Internal header file:
    ---------------------
    -


    Documentation:
    --------------
    -


Support for new platforms, languages and compilers
==================================================
    -


Bug Fixes since HDF5-1.10.9 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)

    - 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 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)

    - Remove Javadoc generation

      The use of doxygen now supersedes the requirement to build javadocs. We do not
      have the resources to continue to support two documentation methods and have
      chosen doxygen as our standard.

      (ADB - 2022/12/19)

    - Change the default for building the high-level tools

      The gif2hdf5 and hdf2gif high-level tools are deprecated and will be removed
      in a future release. The default build setting for them have been changed from enabled
      to disabled. A user can enable the build of these tools if needed.
          autotools:   --enable-hlgiftools
          cmake:       HDF5_BUILD_HL_GIF_TOOLS=ON

      (ADB - 2022/12/16)

    - 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
    -----
    - 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
    -------------
    - Doxygen updated with recent Fortran changes.

      (ADB - 2022/09/09)


    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
==============
    
    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.

    Two tests fail attempting collective writes with OpenMPI 3.0.0/GCC-7.2.0-2.29:
        testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio)
        t_shapesame (sscontig2)

    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