path: root/release_docs/RELEASE.txt

HDF5 version 1.12.1-3 currently under development
================================================================================


INTRODUCTION

This document describes the new features introduced in the HDF5 1.12.0 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 the
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/

More information about the new features can be found at:

     https://portal.hdfgroup.org/display/HDF5/New+Features+in+HDF5+Release+1.12

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 HDF5-1.12.0-alpha1
- Major Bug Fixes since HDF5-1.10.0
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems
- CMake vs. Autotools installations


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

    Configuration:
    -------------
    - CMake option to use MSVC naming conventions with MinGW

      HDF5_MSVC_NAMING_CONVENTION option enable to use MSVC naming conventions
      when using a MinGW toolchain

      (xan - 2020/10/30)

    - CMake option to statically link gcc libs with MinGW

      HDF5_MINGW_STATIC_GCC_LIBS allows to statically link libg/libstdc++
      with the MinGW toolchain

      (xan - 2020/10/30)

    - CMake option to build the HDF filter plugins project as an external project

      The HDF filter plugins project is a collection of registered compression
      filters that can be dynamically loaded when needed to access data stored
      in a hdf5 file. This CMake-only option allows the plugins to be built and
      distributed with the hdf5 library and tools. Like the options for szip and
      zlib, either a tgz file or a git repository can be specified for the source.

      The necessary options are (see the INSTALL_CMake.txt file):
          HDF5_ENABLE_PLUGIN_SUPPORT
          PLUGIN_TGZ_NAME or PLUGIN_GIT_URL
      There are more options necessary for various filters and the plugin project
      documents should be referenced.

      (ADB - 2020/10/16, OESS-98)

    - Added CMake option to format source files

      HDF5_ENABLE_FORMATTERS option will enable creation of targets using the
      pattern - HDF5_*_SRC_FORMAT - where * corresponds to the source folder
      or tool folder. All sources can be formatted by executing the format target;
         make format

      (ADB - 2020/09/24)

    - CMake option to link the generated Fortran MOD files into the include
      directory.

      The Fortran generation of MOD files by a Fortran compile can produce
      different binary files between SHARED and STATIC compiles with different
      compilers and/or different platforms. Note that it has been found that
      different versions of Fortran compilers will produce incompatible MOD
      files. Currently, CMake will locate these MOD files in subfolders of
      the include directory and add that path to the Fortran library target
      in the CMake config file, which can be used by the CMake find library
      process. For other build systems using the binary from a CMake install,
      a new CMake configuration can be used to copy the pre-chosen version
      of the Fortran MOD files into the install include directory.

      The default will depend on the configuration of
      BUILD_STATIC_LIBS and BUILD_SHARED_LIBS:
            YES                   YES         Default to SHARED
            YES                   NO          Default to STATIC
            NO                    YES         Default to SHARED
            NO                    NO          Default to SHARED
      The defaults can be overriden by setting the config option
         HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC

      (ADB - 2020/07/9, HDFFV-11116)

    - CMake option to use AEC (open source SZip) library instead of SZip

      The open source AEC library is a replacement library for SZip. In
      order to use it for hdf5 the libaec CMake source was changed to add
      "-fPIC" and exclude test files. Autotools does not build the
      compression libraries within hdf5 builds. New option USE_LIBAEC is
      required to compensate for the different files produced by AEC build.

      (ADB - 2020/04/22, OESS-65)

    - CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER

      Some handcrafted tests in HDFTests.c has been removed and the CMake
      CHECK_STRUCT_HAS_MEMBER module has been used.

      (ADB - 2020/03/24, TRILAB-24)

    - Both build systems use same set of warnings flags

      GNU C, C++ and gfortran warnings flags were moved to files in a config
      sub-folder named gnu-warnings. Flags that only are available for a specific
      version of the compiler are in files named with that version.
      Clang C warnings flags were moved to files in a config sub-folder
      named clang-warnings.
      Intel C, Fortran warnings flags were moved to files in a config sub-folder
      named intel-warnings.

      There are flags in named "error-xxx" files with warnings that may
      be promoted to errors. Some source files may still need fixes.

      There are also pairs of files named "developer-xxx" and "no-developer-xxx"
      that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the
      configure option:--enable-developer-warnings.

      In addition, CMake no longer applies these warnings for examples.

      (ADB - 2020/03/24, TRILAB-192)


    Library:
    --------
    - Added two new API routines for tracking library memory use:
        H5get_alloc_stats() and H5get_free_list_sizes().

      (QAK - 2020/03/25)

    Java Library:
    ----------------
    - Added new H5S functions.

      H5Sselect_copy, H5Sselect_shape_same, H5Sselect_adjust,
      H5Sselect_intersect_block, H5Sselect_project_intersection,
      H5Scombine_hyperslab, H5Smodify_select, H5Scombine_select
      wrapper functions added.

      (ADB - 2020/10/27, HDFFV-10868)


    Tools:
    ------
    - h5repack added options to control how external links are handled.

      Currently h5repack preserves external links and cannot copy and merge
      data from the external files. Two options, merge and prune, were added to
      control how to merge data from an external link into the resulting file.
       --merge             Follow external soft link recursively and merge data.
       --prune             Do not follow external soft links and remove link.
       --merge --prune     Follow external link, merge data and remove dangling link.

      (ADB - 2020/08/05, HDFFV-9984)


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


Bug Fixes since HDF5-1.12.0 release
==================================
    Library
    -------
    - Fix bug and simplify collective metadata write operation when some ranks
        have no entries to contribute.  This fixes parallel regression test
        failures with IBM SpectrumScale MPI on the Summit system at ORNL.

      (QAK - 2020/09/02)

    - Avoid setting up complex MPI types with 0-length vectors, which some
        MPI implementations don't handle well.  (In particular, IBM
        SpectrumScale MPI on the Summit system at ORNL)

      (QAK - 2020/08/21)

    - Explicitly declared dlopen to use RTLD_LOCAL

      dlopen documentation states that if neither RTLD_GLOBAL nor
      RTLD_LOCAL are specified, then the default behavior is unspecified.
      The default on linux is usually RTLD_LOCAL while macos will default
      to RTLD_GLOBAL.

      (ADB - 2020/08/12, HDFFV-11127)

    - Fixed the segmentation fault when reading attributes with multiple threads

      It was reported that the reading of attributes with variable length string
      datatype will crash with segmentation fault particularly when the number of
      threads is high (>16 threads).  The problem was due to the file pointer that
      was set in the variable length string datatype for the attribute.  That file
      pointer was already closed when the attribute was accessed.

      The problem was fixed by setting the file pointer to the current opened file pointer
      when the attribute was accessed.  Similar patch up was done before when reading
      dataset with variable length string datatype.

      (VC - 2020/07/13, HDFFV-11080)

    - Reduce overhead for H5open(), which is involved in public symbols like
        H5T_NATIVE_INT, etc.

      (QAK - 2020/06/18)

    - Cache last ID looked up for an ID type (dataset, datatype, file, etc),
        improving performance when accessing the same ID repeatedly.

      (QAK - 2020/06/11)

    - Streamline I/O to a single element, improving performance for record
        appends to chunked datasets.

      (QAK - 2020/06/11)

    - Remove redundant tagging of metadata cache entries for some chunked
        dataset operations, slightly improving performance for chunked
        datasets.

      (QAK - 2020/06/10)

    - Better detect selections with the same shape, improving performance for
        some uses of H5DOappend (and other situations).

      (QAK - 2020/06/07)

    - Don't allocate an empty (0-dimensioned) chunked dataset's chunk
        index, until the dataset's dimensions are increased.

      (QAK - 2020/05/07)

    - H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which
      causes asserts/errors when passed to other dataspace API calls.

      H5S_NO_CLASS is an internal class value that should not have been
      exposed via a public API call.

      In debug builds of the library, this can cause asserts to trip. In
      non-debug builds, it will produce normal library errors.

      The new library behavior is for H5Sset_extent_none() to convert
      the dataspace into one of type H5S_NULL, which is better handled
      by the library and easier for developers to reason about.

      (DER - 2020/07/27, HDFFV-11027)

    Tools:
    ------


    Fortran API
    -----------

    - Fixed configure issue when building HDF5 with NAG Fortran 7.0.

    HDF5 now accounts for the addition of half-precision floating-point
    in NAG 7.0 with a KIND=16.

    (MSB - 2020/02/28, HDFFV-11033)

    High-Level Library
    ------------------
    - Eliminated unnecessary code in H5DOappend(), improving its performance.

      (QAK - 2020/06/05)

    Testing
    -------
    - Stopped java/test/junit.sh.in installing libs for testing under ${prefix}

      Lib files needed are now copied to a subdirectory in the java/test
      directory, and on Macs the loader path for libhdf5.xxxs.so is changed
      in the temporary copy of libhdf5_java.dylib.

      (LRK, 2020/7/2, HDFFV-11063)


Supported Platforms
===================

    Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
    #1 SMP ppc64 GNU/Linux        g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
    (ostrich)                     GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
                                  IBM XL C/C++ V13.1
                                  IBM XL Fortran V15.1

    Linux 3.10.0-327.10.1.el7   GNU C (gcc), Fortran (gfortran), C++ (g++)
    #1 SMP x86_64 GNU/Linux       compilers:
    (kituo/moohan)                Version 4.8.5 20150623 (Red Hat 4.8.5-4)
                                    Version 4.9.3, 5.2.0, 7.1.0
                                  Intel(R) C (icc), C++ (icpc), Fortran (icc)
                                  compilers:
                                     Version 17.0.0.098 Build 20160721
                                  MPICH 3.1.4

    Linux-3.10.0-                 spectrum-mpi/rolling-release with cmake>3.10 and
    862.14.4.1chaos.ch6.ppc64le   clang/3.9,8.0
    #1 SMP ppc64le GNU/Linux      gcc/7.3
    (ray)                         xl/2016,2019

    Linux 3.10.0-                 openmpi/3.1,4.0 with cmake>3.10 and
    957.12.2.1chaos.ch6.x86_64    clang 5.0
    #1 SMP x86_64 GNU/Linux       gcc/7.3,8.2
    (serrano)                     intel/17.0,18.0/19.0

    Linux 3.10.0-                 openmpi/3.1/4.0 with cmake>3.10 and
    1062.1.1.1chaos.ch6.x86_64    clang/3.9,5.0,8.0
    #1 SMP x86_64 GNU/Linux       gcc/7.3,8.1,8.2
    (chama,quartz)                intel/16.0,18.0,19.0

    Linux 4.4.180-94.100-default  cray-mpich/7.7.6 with PrgEnv-*/6.0.5, cmake>3.10 and
    #1 SMP x86_64 GNU/Linux       gcc/7.2.0,8.2.0
    (mutrino)                     intel/17.0,18.0

    Linux 4.14.0-                 spectrum-mpi/rolling-release with cmake>3.10 and
    49.18.1.bl6.ppc64le           clang/6.0,8.0
    #1 SMP ppc64le GNU/Linux      gcc/7.3
    (lassen)                      xl/2019

    SunOS 5.11 32- and 64-bit     Sun C 5.12 SunOS_sparc
    (emu)                         Sun Fortran 95 8.6 SunOS_sparc
                                  Sun C++ 5.12 SunOS_sparc

    Windows 7 x64                 Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake)
                                  Visual Studio 2015 w/ MSMPI 10 (cmake)

    Windows 10 x64                Visual Studio 2015 w/ Intel Fortran 18 (cmake)
                                  Visual Studio 2017 w/ Intel Fortran 19 (cmake)
                                  Visual Studio 2019 w/ Intel Fortran 19 (cmake)

    Mac OS X Yosemite 10.10.5     Apple clang/clang++ version 6.1 from Xcode 7.0
    64-bit                        gfortran GNU Fortran (GCC) 4.9.2
    (osx1010dev/osx1010test)      Intel icc/icpc/ifort version 15.0.3

    Mac OS X El Capitan 10.11.6   Apple clang/clang++ version 7.3.0 from Xcode 7.3
    64-bit                        gfortran GNU Fortran (GCC) 5.2.0
    (osx1011dev/osx1011test)      Intel icc/icpc/ifort version 16.0.2

    Mac OS High Sierra 10.13.6    Apple LLVM version 10.0.0 (clang/clang++-1000.10.44.4)
    64-bit                        gfortran GNU Fortran (GCC) 6.3.0
    (bear)                        Intel icc/icpc/ifort version 19.0.4

    Mac OS Mojave 10.14.6         Apple LLVM version 10.0.1 (clang/clang++-1001.0.46.4)
    64-bit                        gfortran GNU Fortran (GCC) 6.3.0
    (bobcat)                      Intel icc/icpc/ifort version 19.0.4


Tested Configuration Features Summary
=====================================

    In the tables below
          y   = tested
          n   = not tested in this release
          C   = Cluster
          W   = Workstation
          x   = not working in this release
          dna = does not apply
          ( ) = footnote appears below second table
          <blank> = testing incomplete on this feature or platform

Platform                              C         F90/   F90      C++  zlib  SZIP
                                      parallel  F2003  parallel
Solaris2.11 32-bit                      n        y/y    n        y    y     y
Solaris2.11 64-bit                      n        y/n    n        y    y     y
Windows 7                               y        y/y    n        y    y     y
Windows 7 x64                           y        y/y    y        y    y     y
Windows 7 Cygwin                        n        y/n    n        y    y     y
Windows 7 x64 Cygwin                    n        y/n    n        y    y     y
Windows 10                              y        y/y    n        y    y     y
Windows 10 x64                          y        y/y    n        y    y     y
Mac OS X Mountain Lion 10.8.5 64-bit    n        y/y    n        y    y     y
Mac OS X Mavericks 10.9.5 64-bit        n        y/y    n        y    y     ?
Mac OS X Yosemite 10.10.5 64-bit        n        y/y    n        y    y     ?
Mac OS X El Capitan 10.11.6 64-bit      n        y/y    n        y    y     ?
CentOS 6.7 Linux 2.6.18 x86_64 GNU      n        y/y    n        y    y     y
CentOS 6.7 Linux 2.6.18 x86_64 Intel    n        y/y    n        y    y     y
CentOS 6.7 Linux 2.6.32 x86_64 PGI      n        y/y    n        y    y     y
CentOS 7.2 Linux 2.6.32 x86_64 GNU      y        y/y    y        y    y     y
CentOS 7.2 Linux 2.6.32 x86_64 Intel    n        y/y    n        y    y     y
Linux 2.6.32-573.18.1.el6.ppc64         n        y/n    n        y    y     y


Platform                                 Shared  Shared    Shared    Thread-
                                         C libs  F90 libs  C++ libs  safe
Solaris2.11 32-bit                         y       y         y         y
Solaris2.11 64-bit                         y       y         y         y
Windows 7                                  y       y         y         y
Windows 7 x64                              y       y         y         y
Windows 7 Cygwin                           n       n         n         y
Windows 7 x64 Cygwin                       n       n         n         y
Windows 10                                 y       y         y         y
Windows 10 x64                             y       y         y         y
Mac OS X Mountain Lion 10.8.5 64-bit       y       n         y         y
Mac OS X Mavericks 10.9.5 64-bit           y       n         y         y
Mac OS X Yosemite 10.10.5 64-bit           y       n         y         y
Mac OS X El Capitan 10.11.6 64-bit         y       n         y         y
CentOS 6.7 Linux 2.6.18 x86_64 GNU         y       y         y         y
CentOS 6.7 Linux 2.6.18 x86_64 Intel       y       y         y         n
CentOS 6.7 Linux 2.6.32 x86_64 PGI         y       y         y         n
CentOS 7.2 Linux 2.6.32 x86_64 GNU         y       y         y         n
CentOS 7.2 Linux 2.6.32 x86_64 Intel       y       y         y         n
Linux 2.6.32-573.18.1.el6.ppc64            y       y         y         n

Compiler versions for each platform are listed in the preceding
"Supported Platforms" table.


More Tested Platforms
=====================
The following platforms are not supported but have been tested for this release.

    Linux 2.6.32-573.22.1.el6    GNU C (gcc), Fortran (gfortran), C++ (g++)
    #1 SMP x86_64 GNU/Linux       compilers:
    (mayll/platypus)                 Version 4.4.7 20120313
                                     Version 4.9.3, 5.3.0, 6.2.0
                                  PGI C, Fortran, C++ for 64-bit target on
                                  x86-64;
                                      Version 17.10-0
                                  Intel(R) C (icc), C++ (icpc), Fortran (icc)
                                  compilers:
                                     Version 17.0.4.196 Build 20170411
                                  MPICH 3.1.4 compiled with GCC 4.9.3

    Linux 3.10.0-327.18.2.el7     GNU C (gcc) and C++ (g++) compilers
    #1 SMP x86_64 GNU/Linux          Version 4.8.5 20150623 (Red Hat 4.8.5-4)
    (jelly)                       with NAG Fortran Compiler Release 6.1(Tozai)
                                  GCC Version 7.1.0
                                  OpenMPI 3.0.0-GCC-7.2.0-2.29
                                  Intel(R) C (icc) and C++ (icpc) compilers
                                     Version 17.0.0.098 Build 20160721
                                  with NAG Fortran Compiler Release 6.1(Tozai)
                                  PGI C (pgcc), C++ (pgc++), Fortran (pgf90)
                                  compilers:
                                     Version 18.4, 19.4
                                  MPICH 3.3
                                  OpenMPI 2.1.5, 3.1.3, 4.0.0

   Fedora30 5.3.11-200.fc30.x86_64
   #1 SMP x86_64  GNU/Linux       GNU gcc (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827)
                                  GNU Fortran (GCC) 9.2.1 20190827 (Red Hat 9.2.1 20190827)
                                     (cmake and autotools)


Known Problems
==============
    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.

    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.