path: root/RELEASE

 
                       HDF5 Release 1.4-Beta3


INTRODUCTION

This document describes the differences between HDF5-1.2.0 and
HDF5-1.4-Beta3, and contains information on the platforms tested and
known problems in HDF5-1.4-Beta3. For more details check the HISTORY 
file in the HDF5 source.

The HDF5 documentation can be found on the NCSA ftp server
(ftp.ncsa.uiuc.edu) in the directory:

     /HDF/HDF5/docs/

For more information look at the HDF5 home page at:
   
    http://hdf.ncsa.uiuc.edu/HDF5/

If you have any questions or comments, please send them to:

    hdfhelp@ncsa.uiuc.edu


CONTENTS

- New Features
- h4toh5 Utility 
- F90 Support
- C++ Support
- Bug Fixes since HDF5-1.2.0 
- Bug Fixes since HDF5-1.4.0-beta2
- Platforms Tested
- Known Problems

New Features
============
   * The Virtual File Layer, VFL, was added to replace the old file
     drivers. It also provides an API for user defined file drivers.
   * New features added to snapshots. Use 'snapshot help' to see a
     complete list of features.
   * Improved configure to detect if MPIO routines are available when
     parallel mode is requested.
   * Added Thread-Safe support. Phase I implemented.
   * Added data sieve buffering to raw data I/O path. This is enabled
     for all VFL drivers except the mpio & core drivers. Setting the
     sieve buffer size is controlled with the new API function,
     H5Pset_sieve_buf_size(), and retrieved with H5Pget_sieve_buf_size().
   * Added new Virtual File Driver, Stream VFD, to send/receive entire
     HDF5 files via socket connections.
   * As parts of VFL, HDF-GASS and HDF-SRB are also added to this
     release. To find out details, please read INSTALL_VFL file. 
   * Increased maximum number of dimensions for a dataset (H5S_MAX_RANK)
     from 31 to 32 to align with HDF4 & netCDF.
   * Added 'query' function to VFL drivers.  Also added 'type' parameter to
     VFL 'read' & 'write' calls, so they are aware of the type of data
     being accessed in the file.  Updated the VFL document also.
   * A new h4toh5 uitlity, to convert HDF4 files to analogous HDF5 files.
   * Added a new array datatype to the datatypes which can be created.  Removed
     "array fields" from compound datatypes (use an array datatype instead).
   * Parallel HDF5 works correctly with mpich-1.2.1 on Solaris, SGI, Linux.

h4toh5 Utility 
==============

    The h4toh5 utility is a new utility that converts an HDF4 file to an 
    HDF5 file.  For details, see the document, "Mapping HDF4 Objects to 
    HDF5 Objects":
       http://hdf.ncsa.uiuc.edu/HDF5/papers/H4-H5MappingGuidelines.pdf

    Known Limitations of the h4toh5 beta release
    ---------------------------------------------

    1. Error Handling

    Error reporting is minimal.

    2. String Datatype

    HDF4 has no 'string' type. String valued data are usually defined as
    an array of 'char' in HDF4. The h4toh5 utility will generally map
    these to HDF5 'String' types rather than array of char, with the
    following additional rules:

       * For the data of an HDF4 SDS, image, and palette, if the data is
	 declared 'DFNT_CHAR8' it will be assumed to be integer and
	 will be an H5T_INTEGER type.
       * For attributes of any HDF4 object, data of type 'DFNT_CHAR8'
	 will be converted to an HDF5 'H5T_STRING' type.
       * For an HDF4 Vdata, it is difficult to determine whether data 
	 of type 'DFNT_CHAR8' is intended to be bytes or characters.
	 The h4toh5 utility will consider them to be C characters, and
	 will convert them to an HDF5 'H5T_STRING' type.


    3. Compression, Chunking and External Storage

    Chunking is supported, but compression and external storage is not.

    An HDF4 object that uses chunking will be converted to an HDF5 file
    with analogous chunked storage.

    An HDF4 object that uses compression will be converted to an
    uncompressed HDF5 object.  

    An HDF4 object that uses external storage will be converted to an
    HDF5 object without external storage.  

    4. Memory Use

    The beta version of the h4toh5 utility copies data from HDF4 objects
    in a single read followed by a single write to the HDF5 object. For
    large objects, this requires a very large amount of memory, which may
    be extremely slow or fail on some platforms.

    Note that a dataset that has only been partly written will
    be read completely, including uninitialized data, and all the
    data will be written to the HDF5 object.

    5. Platforms

    The h4toh5 utility requires HDF5.1.4 and HDF4r1.4

    The beta h4toh5 utility has been tested on Solaris 2.6, Solaris 2.5,
    Irix 6.5, HPUX 11.0, DEC Unix, FreeBSD, Windows 2000(NT5.0),Windows NT 
    and Windows 98.

F90 Support
===========
 
    This is the first release of the HDF5 Library with fully integrated 
    F90 API support.  The Fortran Library is created when the 
    --enable-fortran flag is specified during configuration.

    Not all F90 subroutines are implemented. Please refer to the HDF5 
    Reference Manual for more details.
   
    F90 APIs are available for the Solaris 2.6 and 2.7, Linux, DEC UNIX, 
    T3E, J90 and O2K (64 bit option only) platforms. The Parallel version of 
    the HDF5 F90 Library is supported on the O2K and T3E platforms.

    Changes since the last prototype release (July 2000)
    ----------------------------------------------------

       * h5open_f and h5close_f must be called instead of h5init_types and 
         h5close_types.

       * The following subroutines are no longer available: 
             h5pset_xfer_f
             h5pget_xfer_f
             h5pset_mpi_f
             h5pget_mpi_f
             h5pset_stdio_f
             h5pget_stdio_f
             h5pset_sec2_f
             h5pget_sec2_f
             h5pset_core_f
             h5pget_core_f
             h5pset_family_f
             h5pget_family_f
             
       * The following functions have been added:
             h5pset_fapl_mpio_f
             h5pget_fapl_mpio_f
             h5pset_dxpl_mpio_f
             h5pget_dxpl_mpio_f
        
       * In the previous HDF5 F90 releases, the implementation of object 
         references and dataset region references was not portable. This 
         release introduces a portable implementation, but it also introduces 
         changes to the read/write APIs that handle references.  If object or 
         dataset region references are written or read to/from an HDF5 file, 
         h5dwrite_f and h5dread_f must use the extra parameter, n, for the 
         buffer size:

            h5dwrite(read)_f(dset_id, mem_type_id, buf, n, hdferr, &
                                                       ^^^ 
                             mem_space_id, file_space_id, xfer_prp)

         For other datatypes the APIs were not changed. 
              
             
C++ Support
===========

        This is the first release of the HDF5 Library with fully integrated 
        C++ API support. The HDF5 C++ library is built when the --enable-cxx
        flag is specified during configuration.

        Check the HDF5 Reference Manual for available C++ documentation.

        C++ APIs are available for Solaris 2.6 and 2.7, Linux, and FreeBSD. 
 

Bug Fixes since HDF5-1.2.0
==========================

Library
-------

   * The function H5Pset_mpi is renamed as H5Pset_fapl_mpio.
   * Corrected a floating point number conversion error for the Cray J90
     platform. The error did not convert the value 0.0 correctly.
   * Error was fixed which was not allowing dataset region references to
     have their regions retrieved correctly.
   * Corrected a bug that caused non-parallel file drivers to fail in
     the parallel version.
   * Added internal free-lists to reduce memory required by the library
     and H5garbage_collect API function
   * Fixed error in H5Giterate which was not updating the "index"
     parameter correctly.
   * Fixed error in hyperslab iteration which was not walking through the
     correct sequence of array elements if hyperslabs were staggered in a
     certain pattern
   * Fixed several other problems in hyperslab iteration code.
   * Fixed another H5Giterate bug which was causes groups with large
     numbers of objects in them to misbehave when the callback function
     returned non-zero values.
   * Changed return type of H5Aiterate and H5A_operator_t typedef to be
     herr_t, to align them with the dataset and group iterator functions.
   * Changed H5Screate_simple and H5Sset_extent_simple to not allow
     dimensions of size 0 with out the same dimension being unlimited.
   * QAK - 4/19/00 - Improved metadata hashing & caching algorithms to
     avoid many hash flushes and also remove some redundant I/O when
     moving metadata blocks in the file.
   * The "struct(opt)" type conversion function which gets invoked for
     certain compound datatype conversions was fixed for nested compound
     types. This required a small change in the datatype conversion
     function API.
   * Re-wrote lots of the hyperslab code to speed it up quite a bit.
   * Added bounded garbage collection for the free lists when they run
     out of memory and also added H5set_free_list_limits API call to
     allow users to put an upper limit on the amount of memory used for
     free lists.
   * Checked for non-existent or deleted objects when dereferencing one
     with object or region references and disallow dereference.
   * "Time" datatypes (H5T_UNIX_D*) were not being stored and retrieved
     from object headers correctly, fixed now.
   * Fixed H5Dread or H5Dwrite calls with H5FD_MPIO_COLLECTIVE requests
     that may hang because not all processes are transfer the same amount
     of data. (A.K.A. prematured collective return when zero amount data
     requested.) Collective calls that may cause hanging is done via the
     corresponding MPI-IO independent calls.
   * If configure with --enable-debug=all, couple functions would issue
     warning messages to "stderr" that the operation is expensive time-wise.
     This messed up applications (like testings) that did not expect the
     extra output. It is changed so that the warning will be printed only
     if the corresponding Debug key is set.

Configuration
-------------

   * The hdf5.h include file was fixed to allow the HDF5 Library to be
     compiled with other libraries/applications that use GNU autoconf. 
   * Configuration for parallel HDF5 was improved. Configure now attempts
     to link with libmpi.a and/or libmpio.a as the MPI libraries by
     default. It also uses "mpirun" to launch MPI tests by default. It
     tests to link MPIO routines during the configuration stage, rather
     than failing later as before. One can just do "./configure
     --enable-parallel" if the MPI library is in the system library.
   * Added support for pthread library and thread-safe option.
   * The libhdf5.settings file shows the correct machine byte-sex.
   * Added option "--enable-stream-vfd" to configure w/o the Stream VFD.
     For Solaris, added -lsocket to the LIBS list of libraries.

Tools
-----
    * h5dump now accepts both short and long command-line parameters:
          -h, --help          Print a usage message and exit
          -B, --bootblock     Print the content of the boot block
          -H, --header        Print the header only; no data is displayed
          -i, --object-ids    Print the object ids
          -V, --version       Print version number and exit
          -a P, --attribute=P Print the specified attribute
          -d P, --dataset=P   Print the specified dataset
          -g P, --group=P     Print the specified group and all members
          -l P, --soft-link=P Print the value(s) of the specified soft link
          -o F, --output=F    Output raw data into file F
          -t T, --datatype=T  Print the specified named data type
          -w #, --width=#     Set the number of columns

      P - is the full path from the root group to the object.
      T - is the name of the data type.
      F - is a filename.
      # - is an integer greater than 1.
    * A change from the old way command line parameters were interpreted
      is that multiple attributes, datasets, groups, soft-links, and
      object-ids cannot be specified with just one flag but you have to
      use a flag with each object. I.e., instead of doing this:

        h5dump -a /attr1 /attr2 foo.h5

      do this:

        h5dump -a /attr1 -a /attr2 foo.h5

      The cases are similar for the other object types.
    * h5dump correctly displays compound datatypes.
    * Corrected an error in h5toh4 which did not convert the 32bits
      int from HDF5 to HDF4 corectly for the T3E platform.
    * h5dump correctly displays the committed copy of predefined types
      correctly.
    * Added an option, -V, to show the version information of h5dump.
    * Fixed a core dumping bug of h5toh4 when executed on platforms like 
      TFLOPS.
    * The test script for h5toh4 used to not able to detect the hdp
      dumper command was not valid.  It now detects and reports the
      failure of hdp execution.
    * Merged the tools with the 1.2.2 branch. Required adding new
      macros, VERSION12 and VERSION13, used in conditional compilation.
      Updated the Windows project files for the tools.            
    * h5dump displays opaque and bitfield data correctly.
    * h5dump and h5ls can browse files created with the Stream VFD
      (eg. "h5ls <hostname>:<port>").
    * h5dump has a new feature "-o <filename>" which outputs the raw data
      of the dataset into ascii text file <filename>.
    * h5toh4 used to converts hdf5 strings type to hdf4 DFNT_INT8 type.
      Corrected to produce hdf4 DFNT_CHAR type instead.
    * h5dump and h5ls displays array data correctly.

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

    * User's Guide and Reference Manual were updated. 
      See doc/html/PSandPDF/index.html for more details. 

   
Bug Fixes since HDF5-1.4.0-beta2
================================

    * Corrected configuration error which was not including compression support
        correctly.
    * Cleaned up lots of warnings.
    * Changed a few h5dump command line switches and added long versions of
        the switches.
    * Changed parameters for H5Tconvert, H5Pset_bufer and H5Pget_buffer from
        size_t to hsize_t
    * Fixed fairly obscure bug in hyperslab I/O which could (in rare cases)
        not copy all the data during a transfer.
    * Removed ragged array code from library.
    * F90 library and module files are installed properly now on all supported platforms.

Platforms Tested
================

 Note: Due to the nature of the bug fixes, only static versions of the
       library and tools were tested.


  AIX 4.3.2 (IBM SP)            mpcc_r 3.6.6
  Cray T3E sn6711 2.0.5.43      Cray Standard C Version 6.4.0.0
                                Cray Fortran Version 3.4.0.2
  FreeBSD 4.2                   gcc 2.95.2
                                g++ 2.95.2
  HP-UX B.10.20                 HP C  HP92453-01 A.10.32.30
  HP-UX B.11.00                 HP C  HP92453-01 A.11.00.13
  IRIX 6.5                      MIPSpro cc 7.30
  IRIX64 6.5 (64 & n32)         MIPSpro cc 7.3.1m
                                mpt.1.4.0.2
                                mpich-1.2.1
  Linux 2.2.16-3smp             gcc-2.95.2
                                g++ 2.95.2
                                pgf90 3.1-3
  OSF1 V4.0                     DEC-V5.2-040
                                Digital Fortran 90 V4.1-270
  SunOS 5.6                     WorkShop Compilers 5.0 98/12/15 C 5.0 
  (Solaris 2.6)                 WorkShop Compilers 5.0 99/10/25 Fortran 90
                                       2.0 Patch 107356-04
                                Workshop Compilers 5.0 98/12/15 C++ 5.0
  SunOS 5.7                     WorkShop Compilers 5.0 98/12/15 C 5.0
  (Solaris 2.7)                 WorkShop Compilers 5.0 99/10/25 Fortran 90
                                       2.0 Patch 107356-04
                                Workshop Compilers 5.0 98/12/15 C++ 5.0
  TFLOPS 3.3                    mpich-1.2.0 with local changes
  Windows NT4.0, 2000 (NT5.0)   MSVC++ 6.0
  Windows 98                    MSVC++ 6.0

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

* The --enable-static-exec configure flag fails to compile for Solaris
  platforms. This is due to the fact that not all of the system
  libraries on Solaris are available in a static format.

  The --enable-static-exec configure flag also fails to correctly compile
  on Linux platforms using the gcc-2.95.2 compiler.
  
  It is suggested that you don't use this option on these platforms
  during configuration.

* With the gcc 2.95.2 compiler, HDF 5 uses the `-ansi' flag during
  compilation. The ANSI version of the compiler complains about not being
  able to handle the `long long' datatype with the warning:

        warning: ANSI C does not support `long long'
  
  This warning is innocuous and can be safely ignored.

* SunOS 5.6 with C WorkShop Compilers 4.2:  Hyperslab selections will 
  fail if library is compiled using optimization of any level.

* When building hdf5 tools and applications on windows platform, a linking
warning: defaultlib "LIBC" conflicts with use of other libs will appear
on debug version when running VC++6.0. This warning doesn't affect building
and testing hdf5 applications. We are investigating this now.
* The Stream VFD was not tested yet under Windows.
  It is not supported in the TFLOPS machine.

* Shared library option is broken for IBM SP and some Origin 2000 platforms.
  One needs to run ./configure with '--disable-shared'

* The ./dsets tests failed in the TFLOPS machine if the test program,
  dsets.c, is compiled with the -O option.  The hdf5 library still works
  correctly with the -O option.  The test program works fine if it is
  compiled with -O1 or -O0.  Only -O (same as -O2) causes the test
  program to fail.

* Certain platforms give false negatives when testing h5ls:
    - Solaris x86 2.5.1, Cray T3E and Cray J90 give errors during testing
        when displaying object references in certain files.  These are benign 
        differences due to the difference in sizes of the objects created on
        those platforms.  h5ls appears to be dumping object references
        correctly.
    - Cray J90 (and Cray T3E?) give errors during testing when displaying
        some floating-point values.  These are benign differences due to the
        different precision in the values displayed and h5ls appears to be
        dumping floating-point numbers correctly.

* Before building HDF5 F90 Library from source on Crays (T3E and J90) 
  replace H5Aff.f90, H5Dff.f90 and H5Pff.f90 files in the fortran/src subdirectory 
  in the top level directory with the Cray-specific files from the 
  ftp://hdf.ncsa.uiuc.edu/pub/ougoing/hdf5/hdf5-1.4.0-beta/F90_source_for_Crays
  directory.