HDF5 version 1.10.0 released on 2016-03-30
================================================================================



INTRODUCTION

This document describes the differences between HDF5-1.8 series and
HDF5 1.10.0 releases, and contains information on the platforms
tested.

Links to HDF5 1.10.0 source code can be found on The HDF Group's
development FTP server at the following location:

    https://www.hdfgroup.org/HDF5/release/obtain5110.html

User documentation can be accessed directly at this location:

    https://www.hdfgroup.org/HDF5/docNewFeatures/

For more information, see the HDF5 home page:

    https://www.hdfgroup.org/HDF5/

If you have any questions or comments, please send them to the HDF
Help Desk:

    help@hdfgroup.org



CONTENTS

- New Features
- Issues Addressed in this Release
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems and Limitations



New Features
============
This release supports the following features:

    Configuration
    -------------
    - API Compatibility with HDF5 1.8 Flag Was Added

      The 1.10 version of the HDF5 Library can be configured to operate
      identically to the 1.8 library with the --with-default-api-version=v18
      configure flag. This allows existing code to be compiled with the 1.10
      library without requiring immediate changes to the application source
      code. For addtional configuration options and other details, see
      "API Compatibility Macros in HDF5" at
      https://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html.

    - Autotools Configuration Has Been Extensively Reworked

      The autotools configuration options have been updated to allow more
      fine-grained control of the build options and to correct some bugs.
      See configure --help for comprehensive information on each option.

      Specific changes:

      * --enable-debug and --enable-production are no longer accepted.
        Use --enable-build-mode=(debug | production) instead. These set
        appropriate defaults for symbols, optimizations, and other
        configuration options. These defaults can be overridden by the
        user.

      * Extra debug output messages are no longer enabled with
        --enable-debug=<package list>. Use --enable-internal-debug=<pkg list>
        instead.

      * A new --enable-symbols option allows symbols to be generated
        independently of the build mode. --disable-symbols can be used
        to strip symbols from the binary.

      * A new --enable-asserts option sets/unsets NDEBUG. This is
        independent of the build mode. This also enables some extra
        low-overhead debug checks in the library.

      * A new --enable-profiling option sets profiling flags. This is
        independent of the build mode.

      * A new --enable-optimization option sets the optimization level.
        This is independent of the build mode.

      * Many of these options can take a flags string that will be used
        to build the library. This can be useful for specifying custom
        optimization flags such as -Os and -Ofast.

      * gnu C++ and Fortran use configure sub-files that update the
        build flags and turn on warnings. The increase in warnings when
        building these wrapper libraries is due to these flag changes
        and not to a decrease in code quality.

      * The option to clear file buffers has been removed. Any buffer that
        will eventually be written to disk will now always be memset
        to zero. This prevents the previous contents of the buffer from
        being written to the disk if the buffer contents are not
        completely overwritten, which has security implications.

    - LFS Changes

      The way the autotools handle large file support (LFS) has been
      overhauled in this release.

      * We assume ftello and fseeko exist

      * We no longer explicitly use the *64 I/O functions. Instead, we
        rely on a mapping provided by _FILE_OFFSET_BITS or its equivalent.

      * _LARGEFILE(64)_SOURCE is no longer exported via AM_CPPFLAGS.



    Parallel Library
    -----------------
    - Collective Metadata I/O

      Calls for HDF5 metadata can result in many small reads and writes.
      On metadata reads, collective metadata I/O can improve performance
      by allowing the library to perform optimizations when reading the
      metadata by having one rank read the data and broadcasting it to
      all other ranks.

      Collective metadata I/O improves metadata write performance through
      the construction of an MPI derived datatype that is then written
      collectively in a single call. For more information, see
      https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesCollectiveMetadataIoDocs.html.



    Library
    --------
    - Concurrent Access to HDF5 Files - Single Writer/ Multple Reader (SWMR)

      The Single Writer/ Multiple Reader or SWMR feature enables users to
      read data concurrently while writing it. Communications between the
      processes and file locking are not required. The processes can run
      on the same or on different platforms as long as they share a common
      file system that is POSIX compliant. For more information, see the
      Single-Writer/Multiple-Reader (SWMR) documentation at
      https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html.

    - Virtual Dataset (VDS)

      The VDS feature enables data to be accessed across HDF5 files
      using standard HDF5 objects such as groups and datasets without
      rewriting or rearranging the data. An HDF5 virtual dataset (VDS)
      is an HDF5 dataset that is composed of source HDF5 datasets in
      a predefined mapping. VDS can be used with the SWMR feature. For
      documentation, check
      https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesVirtualDatasetDocs.html.

    - Persistent Free File Space Tracking

      Usage patterns when working with an HDF5 file sometimes result in
      wasted space within the file. This can also impair access times
      when working with the resulting files. The new file space management
      feature provides strategies for managing space in a file to improve
      performance in both of these areas. For more information, see
      https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesFileSpaceMgmtDocs.html.

    - Version 3 Metadata Cache

      The version 3 metadata cache moves management of metadata I/O from 
      the clients to the metadata cache proper.  This change is essential for
      SWMR and other features that have yet to be released.



    C++ Library
    ------------
    - New Member Function Added to H5::ArrayType

      The assignment operator ArrayType::operator= was added because
      ArrayType has pointer data members.

      (BMR - 2016/03/07, HDFFV-9562)



    Tools
    ------
    - h5watch

      The h5watch tool allows users to output new records appended to
      a dataset under SWMR access as it grows. The functionality is
      similar to the Unix user command "tail" with the follow option,
      which outputs appended data as the file grows. For more
      information, see
      https://www.hdfgroup.org/HDF5/docNewFeatures/NewFeaturesSwmrDocs.html#Tools.

    - h5format_convert

      The h5format_convert tool allows users to convert the indexing
      type of a chunked dataset made with a 1.10.x version of the HDF5
      Library when the latest file format is used to the 1.8.x version 1 B-tree indexing
      type. For example, datasets created using SWMR access, can be
      converted to be accessed by the HDF5 1.18 library and tools. The
      tool does not rewrite raw data, but it does rewrite HDF5 metadata.



    High-Level APIs
    ----------------
    - H5DOappend

      The function appends data to a dataset along a specified dimension.


    C Packet Table API
    ------------------
    - Replacement of a Public Function with H5PTcreate

      The existing function H5PTcreate_fl limits applications so they
      can use the deflate compression only. The public function
      H5PTcreate has been added to replace H5PTcreate_fl. H5PTcreate
      takes a property list identifier to provide flexibility on
      creation properties.

      (BMR - 2016/03/04, HDFFV-8623)

    - New Public Functions: H5PTget_dataset and H5PTget_type

      Two accessor functions have been added. H5PTget_dataset returns
      the identifier of the dataset associated with the packet table, 
      and H5PTget_type returns the identifier of the datatype used by
      the packet table.

      (BMR, 2016/03/04, HDFFV-8623)

    - Regarding #ifdef VLPT_REMOVED

      The #ifdef VLPT_REMOVED blocks have been removed from the packet
      table (PT) library source except for the following functions:
        + H5PTis_varlen() has been made available again
        + H5PTfree_vlen_readbuff() is now H5PTfree_vlen_buff()

      (BMR - 2016/03/04, HDFFV-442)

    C++ Packet Table API
    --------------------
    - New Constructor Added to FL_PacketTable

      An overloaded constructor has been added to FL_PacketTable and
      takes a property list identifier to provide flexibility on
      creation properties.

      (BMR - 2016/03/08, HDFFV-8623)

    - New Public Functions

      Two accessor wrappers are added to class PacketTable.
      PacketTable::GetDataset() returns the identifier of the dataset
      associated with the packet table, and PacketTable::GetDatatype()
      returns the identifier of the datatype that the packet table uses.

      (BMR - 2016/03/04, HDFFV-8623)

    - Member Functions with "char*" as an Argument

      Overloaded functions were added to provide the "const char*"
      argument; the existing version will be deprecated in future
      releases.

      (BMR - 2016/03/04, HDFFV-8623)

    - Regarding #ifdef VLPT_REMOVED

      The #ifdef VLPT_REMOVED blocks have been removed from the packet
      table library source code except for the following functions:
        + VL_PacketTable::IsVariableLength() was moved to PacketTable
        + VL_PacketTable::FreeReadBuff() is now PacketTable::FreeBuff()

      (BMR - 2016/03/04, HDFFV-442)



    Java Wrapper Library
    --------------------

    The Java HDF5 JNI library has been integrated into the HDF5 repository.
    The configure option is "--enable-java", and the CMake option is
    HDF5_BUILD_JAVA:BOOL=ON. The package hierarchy has changed from the
    HDF5 1.8 JNI, which was "ncsa.hdf.hdflib.hdf5", to HDF5 1.10,
    "hdf.hdflib.hdf5".

    A number of new APIs were added including some for VDS and SWMR.



    Other Important Changes
    -----------------------

    The hid_t type was changed from 32-bit to a 64-bit value.



Issues Addressed in this Release Since alpha1
=============================================

     - H5Pget_virtual_printf_gap, H5Pget_virtual_view, H5Pget_efile_prefix

       The correct access property list settings from the
       H5Pget_virtual_printf_gap, H5Pget_virtual_view, and
       H5Pget_efile_prefix function calls could not be retrieved
       using H5Dget_access_plist().

       Fixed.

       (DER and NAF - 2016/03/14, HDFFV-9716)

     - h5dump

       When h5dump was provided with the name of a non-existing file or
       when optional arguments were the last option on the command line,
       h5dump would segfault.

       Fixed.

       (ADB 2016/02/28 HDFFV-9639, HDFFV-9684)

     - No Error Message for Corrupt Metadata

       The HDF5 Library did not propagate an error when it encountered
       corrupt metadata in an HDF5 file. The issue was fixed for a
       specific file provided by a user. If you still see the problem,
       please contact help@hdfgroup.org

       Fixed.

       (MC - 2016/02/18, HDFFV-9670)

     - Problem Reading Chunked Datasets with a String Datatype Larger
       Than the Chunk Size in Bytes

       When the latest file format was used and when a chunked dataset
       was created with a datatype with the size bigger than a chunk
       size, the data could not be read back. The issue was reported
       for chunked datasets with a string datatype and was confirmed
       for other datatypes with the sizes bigger than the chunk size in
       bytes.

       Fixed.

       (JM - 2016/02/13, HDFFV-9672)

     - Control over the Location of External Files

       Users were unable to specify the locations of external files.

       Two APIs - H5Pget_efile_prefix and H5Pset_efile_prefix - were
       added so that users could specify the locations of external files.

       (DER - 2016/02/04, HDFFV-8740)



Issues Addressed in this Release Since alpha0
=============================================
    - h5format_convert

      The h5format_convert tool did not downgrade the version of the
      superblock.

      Fixed. The tool now will downgrade the version of the superblock.

      (EIP 2016/01/11)

    - Crashes with multiple threads: invalid pointers

      It was reported that alpha0 crashed when used with multiple
      threads. The issue exists in the HDF5 Library versions 1.8 and
      1.9. The problem is related to a shared file pointer used in some
      miscellaneous data structures. The thread-safe library exposed
      paths in the library where a file pointer became invalid.

      The alpha1 release contains the fixes for the specific use case
      as described in HDFFV-9643. We will keep working on identifying
      and fixing other paths in the library with similar problems.

      (EIP - 2016/01/15, HDFFV-9643)



Supported Platforms
===================
The following platforms are supported and have been tested for this release.
They are built with the configure process unless specified otherwise.

    AIX 6.1                       xlc/xlc_r 10.1.0.5
    (NASA G-ADA)                  xlC/xlC_r 10.1.0.5
                                  xlf90/xlf90_r 12.1.0.6

    Linux 2.6.32-573.18.1.el6    GNU C (gcc), Fortran (gfortran), C++ (g++)
    #1 SMP x86_64 GNU/Linux       compilers:
    (mayll/platypus)                 Version 4.4.7 20120313 (Red Hat 4.4.7-16)
                                     Version 4.9.3, Version 5.2.0
                                  PGI C, Fortran, C++ for 64-bit target on
                                  x86-64;
                                      Version 15.7-0
                                  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 2.6.32-504.8.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
    #1 SMP ppc64 GNU/Linux        g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
    (ostrich)                     GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
                                  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)
                                  Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran)
                                  (cmake and autotools)

    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)

    Windows 8.1                   Visual Studio 2012 w/ Intel Fortran 15 (cmake)
                                  Visual Studio 2013 w/ Intel Fortran 15 (cmake)

    Windows 8.1 x64               Visual Studio 2012 w/ Intel Fortran 15 (cmake)
                                  Visual Studio 2013 w/ Intel Fortran 15 (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 6.2.0
    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 6.0 from Xcode 7.0.0
    64-bit                  gfortran GNU Fortran (GCC) 4.9.2
    (osx1010dev/osx1010test)      Intel icc/icpc/ifort version 15.0.3

    Mac OS X El Capitan 10.11.3     Apple clang/clang++ version 7.0.2 from Xcode 7.0.2
    64-bit                  gfortran GNU Fortran (GCC) 5.2.0
    (osx1010dev/osx1010test)      Intel icc/icpc/ifort version 15.0.3



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
SunOS 5.11 32-bit                       n        y/y    n        y    y     y
SunOS 5.11 64-bit                       n        y/y    n        y    y     y
Windows 7                               y        y/y    n        y    y     y
Windows 7 x64                           y        y/y    n        y    y     y
Windows 7 Cygwin                        n        y/y    n        y    y     n
Windows 8.1                             n        y/y    n        y    y     y
Windows 8.1 x64                         n        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 Yosemeti 10.10.5 64-bit        n        y/y    n        y    y     y
AIX 6.1 32- and 64-bit                  n        y/n    n        y    y     y
CentOS 6.7 Linux 2.6.32 x86_64 GNU      y        y/y    y        y    y     y
CentOS 6.7 Linux 2.6.32 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 7.1 Linux 3.10.0 x86_64 GNU      y        y/y    y        y    y     y
CentOS 7.1 Linux 3.10.0 x86_64 Intel    n        y/y    n        y    y     y
Linux 2.6.32-431.11.2.el6.ppc64         n        y/n    n        y    y     y

Platform                                 Shared  Shared    Shared    Thread-
                                         C libs  F90 libs  C++ libs  safe
SunOS 5.11 32-bit                          y       y         y         y
SunOS 5.11 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 8.1                                y       y         y         y
Windows 8.1 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 Yosemeti 10.10.5 64-bit           y       n         y         y
AIX 6.1 32- and 64-bit                     y       n         n         y
CentOS 6.7 Linux 2.6.32 x86_64 GNU         y       y         y         y
CentOS 6.7 Linux 2.6.32 x86_64 Intel       y       y         y         y
CentOS 6.7 Linux 2.6.32 x86_64 PGI         y       y         y         y
CentOS 7.1 Linux 3.10.0 x86_64 GNU         y       y         y         y
CentOS 7.1 Linux 3.10.0 x86_64 Intel       y       y         y         y
Linux 2.6.32-431.11.2.el6.ppc64            y       y         y         y

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 2.6.18-431.11.2.el6     g95 (GCC 4.0.3 (g95 0.94!)
    #1 SMP x86_64 GNU/Linux
    (platypus)

    Windows 7                     Visual Studio 2008  (cmake)

    Windows 7 x64                 Visual Studio 2008  (cmake)

    Windows 7 x64                 Visual Studio 2010  (cmake) with SWMR using GPFS

    Windows 10                    Visual Studio 2013 w/ Intel Fortran 15 (cmake)

    Windows 10 x64                Visual Studio 2013 w/ Intel Fortran 15 (cmake)

    Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux
                                  gcc (Debian 4.7.2-5) 4.7.2
                                  GNU Fortran (Debian 4.7.2-5) 4.7.2
                                  (cmake and autotools)

    Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
                                  gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
                                  GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
                                  (cmake and autotools)

    SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
                                  gcc (SUSE Linux) 4.8.1
                                  GNU Fortran (SUSE Linux) 4.8.1
                                  (cmake and autotools)

    Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux
                                  gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
                                  GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
                                  (cmake and autotools)

    hopper.nersc.gov              PrgEnv-gnu/5.2.40
                                  gcc (GCC) 4.9.2 20141030 (Cray Inc.)
                                  GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.)
                                  g++ (GCC) 4.9.2 20141030 (Cray Inc.)



Known Problems and Limitations
==============================
This section contains the list of known problems and limitations introduced
in this release of HDF5.

Note: this list is not exhaustive of all known issues discovered in HDF5
software to date. For a list of significant problems and known workarounds
identified in past releases, please refer to:

https://www.hdfgroup.org/HDF5/release/known_problems/

The HDF Group also maintains a JIRA issue-tracking database which is used to
capture all known issues which are too numerous to reasonably list in this
document. The HDF Group is taking steps to make our JIRA issue database
open to the public, and this section will refer to that database in a future
release. In the meantime, please contact help@hdfgroup.org if you come across
an issue not listed here or at the link above, and we will provide any
information about known workarounds that we have or add it to our list of
known issues if it is a new issue.

 - The JUnit-interface test may fail on Solaris platforms. The result of
   a test for verifying the content of the error stack to stdout is
   in a different order on Solaris then other platforms. Use make -i option
   to test beyond the java/test folder.
   (ADB - 2016/03/22, HDFFV-9734)

 - The flush/refresh test occasionally fails on OS X platforms. This is
   being investigated but no fix or workaround is available at this time.
   (DER - 2016/03/22, HDFFV-9731)

 - The VDS/SWMR test will fail with a segmentation fault if the library
   is built with --enable-using-memchecker. The is due to a VDS shutdown
   procedure freeing a shared resource too early when the memory
   checker changes are built. This problem does not arise when the
   memory checker changes are not used since the internal library free
   lists behave differently. The memory checker configure option should
   normally only be used under special circumstances so this should not
   affect most users. Users should be aware that the --enable-using-memchecker
   + VDS combination may cause a segfault, however, so Valgrind et al. may
   have to be used with an HDF5 library built without the feature if this
   proves to be a problem.
   (DER - 2016/03/21, HDFFV-9732)

 - SWMR feature limitations
   The SWMR feature will only work if an HDF5 file under SWMR access resides
   on a file system that obeys POSIX write() ordering semantics. Because of
   this, SWMR will not work on  network file systems such as NFS or SMB/Windows
   file shares since those systems do not guarantee write odering. SWMR
   regression tests are likely to fail if run on a network file system. SWMR
   is currently not tested on Windows though it can be tested manually
   (some of the SWMR test programs are built by CMake), and there are no
   obvious reasons for it to not work on NTFS or GPFS.
   (EIP - 2016/03/20, HDFFV-9733)

 - VDS feature limitation
   Currently, the path to a VDS source file is interpreted as relative to the
   directory where the executable program runs and not to the HDF5 file with
   the VDS dataset unless a full path to the source file is specified during
   the mapping.
   (EIP - 2016/03/20, HDFFV-9724)

 - When building HDF5 with Java using CMake and specifying Debug for CMAKE_BUILD_TYPE,
   there is a missing command argument for the tests of the examples.

   This error can be avoided by not building Java with Debug, HDF5_BUILD_JAVA:BOOL=OFF, 
   or not building Examples, HDF5_BUILD_EXAMPLES:BOOL=OFF.
   (LRK - 2016/03/30, HDFFV-9743) 

 - The H5Lexists API changed behavior in HDF5-1.10 when used with a file handle 
   and root group name ("/"):

   H5Lexists(fileid, "/")

   In HDF5-1.8 it returns false (0) and in HDF5-1.10 it returns true (1). 
   The documentation will be updated with information regarding this change.
   (LRK - 2016/03/30, HDFFV-8746)

