path: root/release_docs/RELEASE.txt

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:
    -------------
    - 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:
    ------
    - 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
    -------
    - 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)


    Java Library
    ------------
    -


    Configuration
    -------------
    -


    Tools
    -----
    -


    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