hdf5/RELEASE

 
                       HDF5 Release 1.3.x
    			Under Development


INTRODUCTION

This document describes the differences between HDF5-1.2.0 and
HDF5-1.3.x, and contains information on the platforms where HDF5-1.3.x
was tested (????? careful, under construction) and known problems in
HDF5-1.3.x. 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
- New h4toh5 utility
- F90 Support
- C++ Support
- Bug fixes since HDF5-1.2.0 
- Platforms Tested
- Known Problems

New features
============
   * The Virtual File Layer, VFL, is 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 new API functions:
     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).

Release Notes for h4toh5 beta
=============================

    The h4toh5 utility converts an HDF4 file to an HDF5 file.  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 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 Vdata of HDF4, it is difficult to determine whether data 
	 of type 'DFNT_CHAR8' is intended to be bytes or charaters.
	 The h4toh5 utility will consider them as C character, 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 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.

    The beta h4toh5 utility has been tested on Solaris 2.6, Solaris 2.5,
    Irix 6.5, HPUX 11.0, DEC Unix, FreeBSD, and Windows 2000.

F90 support
============
 
    This is the first release of the HDF5 Library wil 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. Parallel version of the HDF5 F90 Library
    is supported on the O2K and T3E platforms.

    Changes since last prototype release (July 2000).

       * h5open_f and h5close_f must be called instead of h5init_types and h5close_types.
       * The following subroutines cannot be used anymore: 
             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, implementation of object references 
         and dataset region references was not portable. This release introduces
         portable implementation, but it also introduces changes to read/write APIs
         that handles references.
         If object or dataset region references are written or read to/from
         an HDF5 file, h5dwrite_f and h5dread_f must use extra parameter n - buffer size, i.e

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

         For other datatypes APIs were not changed. 
              
             
C++ support
============

        This is the first release of the HDF5 Library with fully integrated 
        C++ APIs 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.

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 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. 

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


  AIX 4.3.2 (IBM SP)            3.6.6
  Cray T3E 2.0.4.81             cc 6.3.0.1
                                mpt.1.3
  FreeBSD 3.3-STABLE            gcc 2.95.2
  HP-UX B.10.20                 HP C  HP92453-01 A.10.32
  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.1.3 (SGI MPI 3.2.0.0)

  Linux 2.2.10 SuSE             egcs-2.91.66               configured with
  (i686-pc-linux-gnu)                                      --disable-hsizet
                                mpich-1.2.0 egcs-2.91.66 19990314/Linux 
  Linux 2.2.16 RedHat		gcc-2.95.2

  OSF1 V4.0                     DEC-V5.2-040
  SunOS 5.6                     cc WorkShop Compilers 4.2  no optimization
  SunOS 5.7                     cc WorkShop Compilers 5.0
  TFLOPS 3.3                    mpich-1.2.0 with local changes
  Windows NT4.0 sp5             MSVC++ 6.0

Known Problems:
==============

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

* The Stream VFD was not tested yet under Windows.
  It is not supported in the TFLOPS machine.

* Shared library (--enable-shared) option does not work with Pacific
  Blue, Mountain Blue.  It is not supported in the TFLOPS machine.

* 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.