path: root/release_docs/RELEASE.txt

HDF5 version 1.10.2-snap3 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:
    -------------
    - Removed version-specific gcc/gfortran flags for version 4.0 (inclusive)
      and earlier.

      The config/gnu-flags file, which is sourced as a part of the configure
      process, adds version-specific flags for use when building HDF5. Most of
      these flags control warnings and do not affect the final product.

      Flags for older versions of the compiler were consolidated into the
      common flags section. Moving these flags simplifies maintenance of
      the file.

      The upshot of this is that building with ancient versions of gcc
      (<= 4.0) will possibly no longer work without hand-hacking the file
      to remove the flags not understood by that version of the compiler.
      Nothing should change when building with gcc >= 4.1.

      (HDFFV-9937, DER, 2017/05/31)

    - -fno-omit-frame-pointer was added when building with debugging symbols
      enabled.

      Debugging symbols can be enabled independently of the overall build
      mode in both the autotools and CMake. This allows (limited) debugging
      of optimized code. Since many debuggers rely on the frame pointer,
      we've disabled this optimization when debugging symbols are requested
      (e.g.: via building with --enable-symbols).

      (HDFFV-10226, DER, 2017/05/31)

    Library:
    --------
    - H5FDdriver_query() API call added to the C library.

      This new library call allows the user to query a virtual file driver
      (VFD) for the feature flags it supports (listed in H5FDpublic.h).
      This can be useful to determine if a VFD supports SWMR, for example.

      Note that some VFDs have feature flags that may only be present
      after a file has been created or opened (e.g.: the core VFD will
      have the H5FD_FEAT_POSIX_COMPAT_HANDLE flag set if the backing
      store is switched on). Since the new API call queries a generic VFD
      unassociated with a file, these flags will never be returned.

      (HDFFV-10215, DER, 2017/05/31)


    - H5FD_FEAT_DEFAULT_VFD_COMPATIBLE VFD feature flag added to the C library.

      This new feature flag indicates that the VFD is compatible with the
      default VFD. VFDs that set this flag create single files that follow
      the canonical HDF5 file format.

      (HDFFV-10214, DER, 2017/05/31)

    - The H5I_REFERENCE value in the H5I_type_t enum (defined in H5Ipublic.h)
      has been marked as deprectated.

      This ID type value is not used in the C library. i.e.: There are no
      hid_t values that are of ID type H5I_REFERENCE.

      This enum value will be removed in a future major version of the library.
      The code will remain unchanged in the HDF5 1.10.x branches.

      (HDFFV-10252, DER, 2017/04/05)

    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:
    -------------

    - The H5I_REFERENCE value in the H5I_type_t enum (defined in H5Ipublic.h)
      has been marked as deprectated.

      JNI code which refers to this value will be removed in a future
      major version of the library. The code will remain unchanged in the
      1.10.x branches.

      See the C library section, above, for further information.

      (HDFFV-10252, DER, 2017/04/05)


    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
    -------
    - 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)

    - Fix H5HL_offset_into()

      (1) Fix H5HL_offset_into() to return error when offset exceeds heap data
          block size.
      (2) Fix other places in the library that call this routine to detect
          error routine.
        
      (HDFFV-10216, VC, 2017/08/30)

    - Fixes for paged aggregation

      Skip test in test/fheap.c when:
      (1) multi/split drivers and
      (2) persisting free-space or using paged aggregation strategy

      (VC, 2017/07/10)

    - Fixes for paged aggregation

      Changes made based on RFC review comments:
      (1) Add maximum value for file space page size
      (2) Drop check for page end metadata threshold
      (3) Remove "can_shrink" and "shrink" callbacks for small section class

      (VC, 2017/06/09)

    - Fix for infinite loop in H5VM_power2up().

      The function H5VM_power2up() returns the next power of 2
      for n. When n exceeds 2^63, it overflows and becomes 0 causing
      the infinite looping. 

      The fix ensures that the function checks for n >= 2^63
      and returns 0.

      (HDFFV-10217, VC, 2017/07/10)

    - Fix for H5Ocopy doesn't work with open identifiers

      Changes made so that raw data for dataset objects are copied from
      cached info when possible instead of flushing objects to file and
      read them back in again.

      (HDFFV-7853, VC, 2017/07/05)

    Configuration
    -------------
    - Corrected FORTRAN_HAVE_C_LONG_DOUBLE processing in the autotools.

      A bug in the autotools Fortran processing code always set the
      FORTRAN_HAVE_C_LONG_DOUBLE variable to be true regardless of
      whether or not a C long double type was present.

      This would cause compilation failures on platforms where a C
      long double type was not available and the Fortran wrappers
      were being built.

      (HDFFV-10247, DER, 2017/07/05)

    - The deprecated --enable-production and --enable-debug configure options
      failed to emit errors when passed an empty string
      (e.g.: --enable-debug="").

      Due to the way we checked for these options being set, it was possible
      to avoid the error message and continue configuration if an empty string
      was passed to the option.

      Any use of --enable-production or --enable-debug will now halt the
      configuration step and emit a helpful error message
      (use --enable-build-mode=debug|production instead).

      (HDFFV-10248, DER, 2017/07/05)

    - 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
    --------
    -

    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.

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

    - 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-10276)

    - 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)

    - h5repack

      Add tests to h5repack.sh.in to verify options added for paged 
      aggregation work as expected.

      (VC, 2017/08/03)

    - 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:
    ------
    - Fixed a bug in the H5DOwrite_chunk() API call where overwriting a chunk
      with no filters caused an assert to trip (with assertions enabled /
      debug builds) or additional chunks to be inserted instead of overwriting
      the data (without assertions enabled / production builds).

      (HDFFV-10187, DER, 2017/05/11)

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

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

    F90 APIs
    --------
    -

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

    Testing
    -------
    -

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

    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     y
Mac OS X Yosemite 10.10.5 64-bit        n        y/y    n        y    y     y
Mac OS X El Capitan 10.11.6 64-bit      n        y/y    n        y    y     y
CentOS 7.2 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/y    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 7.2 Linux 2.6.32 x86_64 PGI         y       y         y         n
CentOS 7.2 Linux 2.6.32 x86_64 GNU         y       y         y         y
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.