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:
    -------------
    - 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.

    - 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.

    - 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.

    - 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.


    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.

    - 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.

    - 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.

      Fixes Jira issue 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.

      Fixes Jira issue 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.


    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. 


    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.


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


Bug Fixes since HDF5-1.12.2 release
===================================
    Library
    -------
    - Fixed potential heap buffer overflow in decoding of link info message

      Detections of buffer overflow were added for decoding version, index
      flags, link creation order value, and the next three addresses.  The
      checkings will remove the potential invalid read of any of these
      values that could be triggered by a malformed file.

      (GH-2603 - 2023/04/16)

    - Fixed potential buffer overrun issues in some object header decode routines

      Several checks were added to H5O__layout_decode and H5O__sdspace_decode to
      ensure that memory buffers don't get overrun when decoding buffers read from
      a (possibly corrupted) HDF5 file.

    - Fixed a heap buffer overflow that occurs when reading from
      a dataset with a compact layout within a malformed HDF5 file

      During opening of a dataset that has a compact layout, the
      library allocates a buffer that stores the dataset's raw data.
      The dataset's object header that gets written to the file
      contains information about how large of a buffer the library
      should allocate. If this object header is malformed such that
      it causes the library to allocate a buffer that is too small
      to hold the dataset's raw data, future I/O to the dataset can
      result in heap buffer overflows. To fix this issue, an extra
      check is now performed for compact datasets to ensure that
      the size of the allocated buffer matches the expected size
      of the dataset's raw data (as calculated from the dataset's
      dataspace and datatype information). If the two sizes do not
      match, opening of the dataset will fail.

      Fixes GitHub issue #2606

    - 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.

      Fixes Jira issue HDFFV-10712, CVE-2019-8396, GitHub issue #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.

      Fixes GitHub issue #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.

      - 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.

      Fixes GitHub issue #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.

      Fixes Jira issue 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.

    - Fixed an issue with hyperslab selections

      Previously, when combining hyperslab selections, it was possible for the
      library to produce an incorrect combined selection.

    - 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.

      Fixes GitHub issue #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.

      Fixes Jira issue 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.

      Fixes Jira issues 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.

      Fixes Jira issue 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.

      Fixes GitHub issues #1546 & #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

      Fixes Jira issue 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.


    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.

      Fixes GitHub issue #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.

      Fixes GitHub issue #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