HDF5 version 1.10.9 released on 2022-05-25
================================================================================


INTRODUCTION
============

This document describes the differences between this release and the previous
HDF5 release in the same series. 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/Software+Changes+from+Release+to+Release+for+HDF5-1.10

Please send any questions or comments to the HDF Help Desk:

     help@hdfgroup.org


CONTENTS
========

- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.10.8
- Platforms Tested
- Known Problems
- CMake vs. Autotools installations


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

    Configuration:
    -------------
    - Added new option to the h5cc scripts produced by CMake.

      Add -showconfig option to h5cc scripts to cat the 
      libhdf5-settings to the standard output.

      (ADB - 2022/03/11)

    - HDF5 memory allocation sanity checking is now off by default for
      Autotools debug builds

      HDF5 can be configured to perform sanity checking on internal memory
      allocations by adding heap canaries to these allocations. However,
      enabling this option can cause issues with external filter plugins
      when working with (reallocating/freeing/allocating and passing back)
      buffers.

      Previously, this option was off by default for all CMake build types,
      but only off by default for non-debug Autotools builds. Since debug
      is the default build mode for HDF5 when built from source with
      Autotools, this can result in surprising segfaults that don't occur
      when an application is built against a release version of HDF5.
      Therefore, this option is now off by default for all build types
      across both CMake and Autotools.

      (JTH - 2022/03/01)

    - Refactored the utils folder.

      Added subfolder test and moved the 'swmr_check_compat_vfd.c file'
      from test into utils/test. Deleted the duplicate swmr_check_compat_vfd.c
      file in hl/tools/h5watch folder. Also fixed vfd check options.

      (ADB - 2021/10/18)

    - Changed autotools and CMake configurations to derive both
      compilation warnings-as-errors and warnings-only-warn configurations
      from the same files, 'config/*/*error*'.  Removed redundant files
      'config/*/*noerror*'.

      (DCY - 2021/09/29)


    Library:
    --------
    - Several improvements to parallel compression feature, including:

      * Improved support for collective I/O (for both writes and reads)

      * Significant reduction of memory usage for the feature as a whole

      * Reduction of copying of application data buffers passed to H5Dwrite

      * Addition of support for incremental file space allocation for filtered
        datasets created in parallel. Incremental file space allocation is the
        default for these types of datasets (early file space allocation is
        also still supported), while early file space allocation is still the
        default (and only supported allocation time) for unfiltered datasets
        created in parallel. Incremental file space allocation should help with
        parallel HDF5 applications that wish to use fill values on filtered
        datasets, but would typically avoid doing so since dataset creation in
        parallel would often take an excessive amount of time. Since these
        datasets previously used early file space allocation, HDF5 would
        allocate space for and write fill values to every chunk in the dataset
        at creation time, leading to noticeable overhead. Instead, with
        incremental file space allocation, allocation of file space for chunks
        and writing of fill values to those chunks will be delayed until each
        individual chunk is initially written to.

      * Addition of support for HDF5's "don't filter partial edge chunks" flag
        (https://portal.hdfgroup.org/display/HDF5/H5P_SET_CHUNK_OPTS)

      * Addition of proper support for HDF5 fill values with the feature

      * Addition of 'H5_HAVE_PARALLEL_FILTERED_WRITES' macro to H5pubconf.h
        so HDF5 applications can determine at compile-time whether the feature
        is available

      * Addition of simple examples (ph5_filtered_writes.c and
        ph5_filtered_writes_no_sel.c) under examples directory to demonstrate
        usage of the feature

      * Improved coverage of regression testing for the feature

      (JTH - 2022/2/23)

    Fortran Library:
    ----------------
    - None 


    C++ Library:
    ------------
    - None


    Java Library:
    -------------
    - None


    Tools:
    ------
    - h5repack added an optional verbose value for reporting R/W timing.

      In addition to adding timing capture around the read/write calls in
      h5repack, added help text to indicate how to show timing for read/write;
           -v N, --verbose=N       Verbose mode, print object information.
              N - is an integer greater than 1, 2 displays read/write timing
      (ADB - 2022/04/01)


    High-Level APIs:
    ----------------
    - None


    C Packet Table API:
    -------------------
    - None


    Internal header file:
    ---------------------
    - None


    Documentation:
    --------------
    - None


New platforms, languages and compilers tested
==================================================
    - macOS Apple M1 11.6 Darwin 20.6.0 arm64 with Apple clang version 12.0.5

    - Fedora35 Linux 5.16.14-200.fc35 with GCC 11.2.1 and clang version 13.0.0


Bug Fixes since HDF5-1.10.8 release
===================================
    Library
    -------
    - Fixed a metadata cache bug when resizing a pinned/protected cache entry

      When resizing a pinned/protected cache entry, the metadata
      cache code previously would wait until after resizing the
      entry to attempt to log the newly-dirtied entry. This would
      cause H5C_resize_entry to mark the entry as dirty and make
      H5AC_resize_entry think that it doesn't need to add the
      newly-dirtied entry to the dirty entries skiplist.

      Thus, a subsequent H5AC__log_moved_entry would think it
      needs to allocate a new entry for insertion into the dirty
      entry skip list, since the entry doesn't exist on that list.
      This causes an assertion failure, as the code to allocate a
      new entry assumes that the entry is not dirty.

      (JRM - 2022/02/28)

    - Issue #1436 identified a problem with the H5_VERS_RELEASE check in the
      H5check_version function.

      Investigating the original fix, #812, we discovered some inconsistencies
      with a new block added to check H5_VERS_RELEASE for incompatibilities.
      This new block was not using the new warning text dealing with the
      H5_VERS_RELEASE check and would cause the warning to be duplicated.

      By removing the H5_VERS_RELEASE argument in the first check for 
      H5_VERS_MAJOR and H5_VERS_MINOR, the second check would only check
      the H5_VERS_RELEASE for incompatible release versions. This adheres
      to the statement that except for the develop branch, all release versions
      in a major.minor maintenance branch should be compatible. The prerequisite
      is that an application will not use any APIs not present in all release versions.

      (ADB - 2022/03/11, #1438)

    - Unified handling of collective metadata reads to correctly fix old bugs

      Due to MPI-related issues occurring in HDF5 from mismanagement of the
      status of collective metadata reads, they were forced to be disabled
      during chunked dataset raw data I/O in the HDF5 1.10.5 release. This
      wouldn't generally have affected application performance because HDF5
      already disables collective metadata reads during chunk lookup, since
      it is generally unlikely that the same chunks will be read by all MPI
      ranks in the I/O operation. However, this was only a partial solution
      that wasn't granular enough.

      This change now unifies the handling of the file-global flag and the
      API context-level flag for collective metadata reads in order to
      simplify querying of the true status of collective metadata reads. Thus,
      collective metadata reads are once again enabled for chunked dataset
      raw data I/O, but manually controlled at places where some processing
      occurs on MPI rank 0 only and would cause issues when collective
      metadata reads are enabled.

      (JTH - 2021/11/16, HDFFV-10501/HDFFV-10562)

    - Fixed several potential MPI deadlocks in library failure conditions

      In the parallel library, there were several places where MPI rank 0
      could end up skipping past collective MPI operations when some failure
      occurs in rank 0-specific processing. This would lead to deadlocks
      where rank 0 completes an operation while other ranks wait in the
      collective operation. These places have been rewritten to have rank 0
      push an error and try to cleanup after the failure, then continue to
      participate in the collective operation to the best of its ability.

      (JTH - 2021/11/09)

    - Fixed an issue with collective metadata reads being permanently disabled
      after a dataset chunk lookup operation. This would usually cause a
      mismatched MPI_Bcast and MPI_ERR_TRUNCATE issue in the library for
      simple cases of H5Dcreate() -> H5Dwrite() -> H5Dcreate().

      (JTH - 2021/11/08, HDFFV-11090)

    Java Library
    ------------
    - None


    Configuration
    -------------
    - Reworked corrected path searched by CMake find_package command

      The install path for cmake find_package files had been changed to use
        "share/cmake"
      for all platforms. However setting the HDF5_ROOT variable failed to locate
      the configuration files. The build variable HDF5_INSTALL_CMAKE_DIR is now
      set to the <INSTALL_DIR>/cmake folder. The location of the configuration 
      files can still be specified by the "HDF5_DIR" variable.

      (ADB - 2022/03/11)


    Tools
    -----
    - None


    Fortran API
    -----------
    - None


    High-Level Library
    ------------------
    - Fixed HL_test_packet, test for packet table vlen of vlen.

      Incorrect length assignment.

      (ADB - 2021/10/14)


    Fortran High-Level APIs
    -----------------------
    - None


    Documentation
    -------------
    - None


    F90 APIs
    --------
    - None


    C++ APIs
    --------
    - None


    Testing
    -------
    - None


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-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 2019.02.07
                                     (cmake)

    Linux-5.3.18-24.96-default       cray-mpich/7.7.19
    #1 SMP x86_64 GNU/Linux              GCC 8.3.0, 11.2.0
    (cori)                               Intel (R) Version 19.1.3.304
                                     (cmake)

    Linux-4.12.14-197.86-default     cray-mpich/7.7.16
    # 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 3.10.0-1160.49.1.1chaos    openmpi-intel/4.1
    #1 SMP x86_64 GNU/Linux              Intel (R) Version 18.0.5, 19.1.2
    (chama)

    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
                                         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 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-3.10.0-1160.53.1.1chaos    openmpi-4.1.2
    #1 SMP x86_64 GNU/Linux              clang 6.0.0, 11.0.1
    (quartz)                             GCC 8.3.1, 10.2.1
                                         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.

    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
