hdf5/release_docs/RELEASE.txt

HDF5 version 1.11.1 currently under development
================================================================================


INTRODUCTION

This document describes the differences between HDF5-1.10.1 and HDF5 1.10.2, and
contains information on the platforms tested and known problems in HDF5-1.10.1.
For more details check the HISTORY*.txt files in the HDF5 source.


Links to HDF5 1.10.1 source code, documentation, and additional materials can be found on The HDF5 web page at:

     https://support.hdfgroup.org/HDF5/

The HDF5 1.10.1 release can be obtained from:

     https://support.hdfgroup.org/HDF5/release/obtain5.html

User documentation for the snapshot can be accessed directly at this location:

     https://support.hdfgroup.org/HDF5/doc/

New features in the HDF5-1.10.x release series, including brief general
descriptions of some new and modified APIs, are described in the "New Features
in HDF5 1.10" document:

https://support.hdfgroup.org/HDF5/docNewFeatures/index.html

All new and modified APIs are listed in detail in the "HDF5 Software Changes
from Release to Release" document, in the section "Release 1.10.1 (current
release) versus Release 1.10.0

     https://support.hdfgroup.org/HDF5/doc/ADGuide/Changes.html

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 HDF5-1.10.1
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems


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

    Configuration:
    -------------
    -

    Library:
    --------
    - Add prefix option to VDS files.

      Currently, VDS source files must be in the active directory to be
      found by the virtual file. Adding the option of a prefix to be set
      on the virtual file, using a data access property list (DAPL),
      allows the source files to located at an absolute or relative path
      to the virtual file.

      New public APIs:
            herr_t H5Pset_virtual_prefix(hid_t dapl_id, const char* prefix);
            ssize_t H5Pget_virtual_prefix(hid_t dapl_id, char* prefix /*out*/, size_t size);
      The prefix can also be set with an environment variable, HDF5_VDS_PREFIX.

      (ADB - 2017/12/12, HDFFV-9724)


    Parallel Library:
    -----------------
    - Optimize parallel open/location of the HDF5 super-block

      Previous releases of PHDF5 required all parallel ranks to
      search for the HDF5 superblock signature when opening the
      file. As this is accomplished more or less as a synchronous
      operation, a large number of processes can experience a
      slowdown in the file open due to filesystem contention.

      As a first step in improving the startup/file-open performance,
      we allow MPI rank 0 of the associated MPI communicator to locate
      the base offset of the super-block and then broadcast that result
      to the remaining ranks in the parallel group.  Note that this
      approach is utilized ONLY during file opens which employ the MPIO
      file driver in HDF5 by previously having called H5Pset_fapl_mpio().

      HDF5 parallel file operations which do not employ multiple ranks
      e.g. specifiying MPI_COMM_SELF (whose MPI_Comm_size == 1)
      as opposed to MPI_COMM_WORLD, will not be affected by this
      optimization.  Conversely, parallel file operations on subgroups
      of MPI_COMM_WORLD are allowed to be run in parallel with each
      subgroup operating as an independant collection of processes.

      (RAW - 2017/10/10, HDFFV-10294)


    - Large MPI-IO transfers

      Previous releases of PHDF5 would fail when attempting to
      read or write greater than 2GB of data in a single IO operation.
      This issue stems principally from an MPI API whose definitions
      utilize 32 bit integers to describe the number of data elements
      and datatype that MPI should use to effect a data transfer.
      Historically, HDF5 has invoked MPI-IO with the number of
      elements in a contiguous buffer represented as the length
      of that buffer in bytes.

      Resolving the issue and thus enabling larger MPI-IO transfers
      is accomplished first, by detecting when a user IO request would
      exceed the 2GB limit as described above.  Once a transfer request
      is identified as requiring special handling, PHDF5 now creates a
      derived datatype consisting of a vector of fixed sized blocks
      which is in turn wrapped within a single MPI_Type_struct to
      contain the vector and any remaining data.   The newly created
      datatype is then used in place of MPI_BYTE and can be used to
      fulfill the original user request without encountering API
      errors.

      (RAW - 2017/07/11, HDFFV-8839)

    Fortran Library:
    ----------------
    -

    C++ Library:
    ------------
    -

    Java Library:
    ----------------
    - Wrappers added for the following APIs:
      H5Pset_evict_on_close
      H5Pget_evict_on_close
      H5Pset_chunk_opts
      H5Pget_chunk_opts
      H5Pset_efile_prefix
      H5Pget_efile_prefix
      H5Pset_virtual_prefix
      H5Pget_virtual_prefix

      (ADB - 2017/12/20)

    Tools:
    ------
    - h5diff

      h5diff has new option enable-error-stack.

      Updated h5diff with the --enable-error-stack argument, which
      enables the display of the hdf5 error stack. This completes the
      improvement to the main tools; h5copy, h5diff, h5dump, h5ls and
      h5repack.

      (ADB - 2017/08/30, HDFFV-9774)

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

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

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

    Documentation
    -------------
    -

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

Bug Fixes since HDF5-1.10.1 release
==================================

    Library
    -------
    - filter plugin handling in H5PL.c and H5Z.c

      It was discovered that the dynamic loading process used by
      filter plugins had issues with library dependencies.

      CMake build process changed to use LINK INTERFACE keywords, which
      allowed HDF5 C library to make dependent libraries private. The
      filter plugin libraries no longer require dependent libraries
      (such as szip or zlib) to be available.
             (ADB - 2017/11/16, HDFFV-10328)

    - H5Zfilter_avail in H5Z.c

      The public function checked for plugins, while the private
      function did not.

      Modified H5Zfilter_avail and private function, H5Z_filter_avail.
      Moved check for plugin from public to private function. Updated
      H5P__set_filter due to change in H5Z_filter_avail. Updated tests.

      (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319)

    - An uninitialized struct could cause a memory access error when using
      variable-length or reference types in a compressed, chunked dataset.

      A struct containing a callback function pointer and a pointer to some
      associated data was used before initialization. This could cause a
      memory access error and system crash. This could only occur under
      unusual conditions when using variable-lenth and reference types in
      a compressed, chunked dataset.

      On recent versions of Visual Studio, when built in debug mode, the
      debug heap will complain and cause a crash if the code in question
      is executed (this will cause the objcopy test to fail).

      (DER - 2017/11/21, HDFFV-10330)

    Configuration
    -------------
    - cmake

      The hdf5 library used shared szip and zlib, which needlessly required
      applications to link with the same szip and zlib libraries.

      Changed the target_link_libraries commands to use the static libs.
      Removed improper link duplication of szip and zlib.
      Adjusted the link dependencies and the link interface values of
      the target_link_libraries commands.

      (ADB - 2017/11/14, HDFFV-10329)

    - cmake MPI

      CMake implementation for MPI was problematic and would create incorrect
      MPI library references in the hdf5 libraries.

      Reworked the CMake MPI code to properly create CMake targets. Also merged
      the latest CMake FindMPI.cmake changes to the local copy. This is necessary
      until HDF changes the CMake minimum to 3.9 or greater.

      (ADB - 2017/11/02, HDFFV-10321)

    - cmake

      Too many commands for POST_BUILD step caused command line to be
      too big on windows.

      Changed foreach of copy command to use a custom command with the
      use of the HDFTEST_COPY_FILE macro.

      (ADB - 2017/07/12, HDFFV-10254)

    Performance
    -------------
    -

    Fortran
    --------
    - Fixed compilation errors when using Intel 18 Fortran compilers
      (MSB - 2017/11/3, HDFFV-10322)

    Tools
    -----
    - h5repack

      h5repack failed to copy a dataset with existing filter.

      Reworked code for h5repack and h5diff code in tools library. Added
      improved error handling, cleanup of resources and checks of calls.
      Modified H5Zfilter_avail and private function, H5Z_filter_avail.
      Moved check for plugin from public to private function. Updated
      H5P__set_filter due to change in H5Z_filter_avail. Updated tests.
      Note, h5repack output display has changed to clarify the individual
      steps of the repack process. The output indicates if an operation
      applies to all objects. Lines with notation and no information
      have been removed.

      (ADB - 2017/10/10, HDFFV-10297, HDFFV-10319)

    - h5repack

      h5repack always set the User Defined filter flag to H5Z_FLAG_MANDATORY.

      Added another parameter to the 'UD=' option to set the flag by default
      to '0' or H5Z_FLAG_MANDATORY, the other choice is '1' or H5Z_FLAG_OPTIONAL.

      (ADB - 2017/08/31, HDFFV-10269)

    - h5ls

      h5ls generated error on stack when it encountered a H5S_NULL
      dataspace.

      Adding checks for H5S_NULL before calling H5Sis_simple (located
      in the h5tools_dump_mem function) fixed the issue.

      (ADB - 2017/08/17, HDFFV-10188)

    - h5dump

      h5dump segfaulted on output of XML file.

      Function that escape'd strings used the full buffer length
      instead of just the length of the replacement string in a
      strncpy call. Using the correct length fixed the issue.

      (ADB - 2017/08/01, HDFFV-10256)

    - h5diff

      h5diff segfaulted on compare of a  NULL variable length string.

      Improved h5diff compare of strings by adding a check for
      NULL strings and setting the lengths to zero.

      (ADB - 2017/07/25, HDFFV-10246)

    - h5import

      h5import crashed trying to import data from a subset of a dataset.

      Improved h5import by adding the SUBSET keyword. h5import understands
      to use the Count times the Block as the size of the dimensions.
      Added INPUT_B_ORDER keyword to old-style configuration files.
      The import from h5dump function expects the binary files to use native
      types (FILE '-b' option) in the binary file.

      (ADB - 2017/06/15, HDFFV-10219)

    - h5repack

      h5repack did not maintain the creation order flag of the root
      group.

      Improved h5repack by reading the creation order and applying the
      flag to the new root group. Also added arguments to set the
      order and index direction, which applies to the traversing of the
      original file, on the command line.

      (ADB - 2017/05/26, HDFFV-8611)

    - h5diff

      h5diff failed to account for strpad type and null terminators
      of char strings. Also, h5diff failed to account for string length
      differences and would give a different result depending on file
      order in the command line.

      Improved h5diff compare of strings and arrays by adding a check for
      string lengths and if the strpad was null filled.

      (ADB - 2017/05/18, HDFFV-9055, HDFFV-10128)

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

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

    Documentation
    -------------
    -

    F90 APIs
    --------
    -

    C++ APIs
    --------
    -

    Testing
    -------
    -

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

    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 4.8.4
                                  PGI C, Fortran, C++ for 64-bit target on
                                  x86-64;
                                      Version 16.10-0
                                  Intel(R) C (icc), C++ (icpc), Fortran (icc)
                                  compilers:
                                     Version 15.0.3.187 (Build 20150407)
                                  MPICH 3.1.4 compiled with GCC 4.9.3

    Linux 2.6.32-573.18.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
    #1 SMP ppc64 GNU/Linux        g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
    (ostrich)                     GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
                                  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, Version 5.2.0
                                  Intel(R) C (icc), C++ (icpc), Fortran (icc)
                                  compilers:
                                     Version 15.0.3.187 Build 20150407
                                  MPICH 3.1.4 compiled with GCC 4.9.3

    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                     Visual Studio 2012 w/ Intel Fortran 15 (cmake)
                                  Visual Studio 2013 w/ Intel Fortran 15 (cmake)
                                  Visual Studio 2015 w/ Intel Fortran 16 (cmake)

    Windows 7 x64                 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
                                  Visual Studio 2013 w/ Intel Fortran 15 (cmake)
                                  Visual Studio 2015 w/ Intel Fortran 16 (cmake)
                                  Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake)
                                  Visual Studio 2015 w/ MSMPI 8 (cmake)
                                  Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3)
                                      gcc and gfortran compilers (GCC 5.4.0)
                                      (cmake and autotools)

    Windows 10                    Visual Studio 2015 w/ Intel Fortran 16 (cmake)
                                  Cygwin(CYGWIN_NT-6.1 2.8.0(0.309/5/3)
                                      gcc and gfortran compilers (GCC 5.4.0)
                                      (cmake and autotools)

    Windows 10 x64                Visual Studio 2015 w/ Intel Fortran 16 (cmake)

    Mac OS X Mt. Lion 10.8.5      Apple clang/clang++ version 5.1 from Xcode 5.1
    64-bit                        gfortran GNU Fortran (GCC) 4.8.2
    (swallow/kite)                Intel icc/icpc/ifort version 15.0.3

    Mac OS X Mavericks 10.9.5     Apple clang/clang++ version 6.0 from Xcode 6.2
    64-bit                        gfortran GNU Fortran (GCC) 4.9.2
    (wren/quail)                  Intel icc/icpc/ifort version 15.0.3

    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
    (osx1010dev/osx1010test)      Intel icc/icpc/ifort version 16.0.2


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 4.8.4
                                  PGI C, Fortran, C++ for 64-bit target on
                                  x86-64;
                                      Version 16.10-0
                                  Intel(R) C (icc), C++ (icpc), Fortran (icc)
                                  compilers:
                                     Version 15.0.3.187 (Build 20150407)
                                  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)
                                  Intel(R) C (icc) and C++ (icpc) compilers
                                     Version 15.0.3.187 (Build 20150407)
                                  with NAG Fortran Compiler Release 6.1(Tozai)

    Linux 2.6.32-573.18.1.el6.ppc64  MPICH mpich 3.1.4 compiled with
    #1 SMP ppc64 GNU/Linux           IBM XL C/C++ for Linux, V13.1
    (ostrich)                        and IBM XL Fortran for Linux, V15.1

    Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux
                                  gcc, g++ (Debian 4.9.2-10) 4.9.2
                                  GNU Fortran (Debian 4.9.2-10) 4.9.2
                                  (cmake and autotools)

    Fedora 24  4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
                                  gcc, g++ (GCC) 6.1.1 20160621
                                      (Red Hat 6.1.1-3)
                                  GNU Fortran (GCC) 6.1.1 20160621
                                      (Red Hat 6.1.1-3)
                                  (cmake and autotools)

    Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux
                                  gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2)
                                      5.4.0 20160609
                                  GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2)
                                      5.4.0 20160609
                                  (cmake and autotools)


Known Problems
==============

    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.