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HDF Newsletter 45

CONTENTS

    ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/

    http://hdf.ncsa.uiuc.edu/HDF5/

    ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/docs/

Datatypes

• Optimizations to compound datatype conversions and I/O operations.
• Added nearly 100 optimized conversion functions for native datatypes including support for non-aligned data.
• Added support for bitfield, opaque, and enumeration types.
• Added distinctions between signed and unsigned char types to the list of predefined native hdf5 datatypes.
• Added HDF5 type definitions for C9x types like int32_t.
• Application-defined type conversion functions can handle non-packed data.
• Changed the H5Tunregister() function to use wildcards when matching conversion functions. H5Tregister_hard() and H5Tregister_soft() were combined into H5Tregister().
• Support for variable-length datatypes (arrays of varying length per dataset element). Variable length strings are currently supported only as variable length arrays of 1-byte integers.

Dataspaces

• New query functions for selections.
• I/O operations bypass the stripmining loop and go directly to storage for certain contiguous selections in the absence of type conversions. In other cases the stripmining buffers are used more effectively.
• Reduced the number of I/O requests under certain circumstances, improving performance on systems with high I/O latency.

Persistent Pointers

• Object (serial and parallel) and dataset region (serial only) references were implemented.

Parallel Support

• Improved parallel I/O performance.
• Supports new platforms: Cray T3E, Linux, DEC Cluster.
• Uses vendor supported version of MPIO on SGI O2K and Cray platforms.
• Improved algorithm for translating an HDF5 hyperslab selection into an MPI type for better collective I/O performance.

Debugging

• Improved control and redirection of debugging and tracing messages.

Configuration

• Better detection and support for MPI-IO.
• Recognition of compilers with known code generation problems.
• Support for various compilers on a single architecture (e.g., the native compiler and the GNU compilers).
• Ability to build from read-only media and with different compilers and/or options concurrently.
• Added a libhdf5.settings file which summarizes the configuration information and is installed along with the library.
• Builds a shared library on most systems that support it.

Documentation

• More examples.
• Updated User's Guide, Reference Manual, and Format Specification.
• HDF5 Tutorial was added to the documentation.
• Documentation available in PDF and Postscript. (NOTE: This is not quite ready but should be available in the near future.)

Tools

• Enhancements to the h5ls tool including the ability to list objects from more than one file, to display raw hexadecimal data, to show file addresses for raw data, to format output more reasonably, to show object attributes, and to perform a recursive listing,
• Enhancements to h5dump: support new data types added since previous versions.
• h5toh4: An hdf5 to hdf4 converter.

New API functions

  Property List Interface:
  ------------------------

  H5Pset_xfer          - set data transfer properties
  H5Pset_preserve      - set dataset transfer property list status 
  H5Pget_preserve      - get dataset transfer property list status
  H5Pset_hyper_cache   - indicates whether to cache hyperslab blocks during I/O
  H5Pget_hyper_cache   - returns information regarding the caching of 
                         hyperslab blocks during I/O
  H5Pget_btree_ratios  - sets B-tree split ratios for a dataset 
                         transfer property list
  H5Pset_btree_ratios  - gets B-tree split ratios for a dataset
                         transfer property list
  H5Pset_vlen_mem_manager - sets the memory manager for variable-length 
                            datatype allocation
  H5Pget_vlen_mem_manager - sets the memory manager for variable-length
                            datatype allocation

  Dataset Interface:
  ------------------

  H5Diterate           - iterate over all selected elements in a dataspace
  H5Dget_storage_size  - return the amount of storage required for a dataset
  H5Dvlen_reclaim      - reclaim VL datatype memory buffers

  Dataspace Interface:
  --------------------
  H5Sget_select_hyper_nblocks   - get number of hyperslab blocks
  H5Sget_select_hyper_blocklist - get the list of hyperslab blocks 
                                  currently selected
  H5Sget_select_elem_npoints    - get the number of element points 
                                  in the current selection
  H5Sget_select_elem_pointlist  - get the list of element points 
                                  currently selected
  H5Sget_select_bounds          - gets the bounding box containing 
                                  the current selection

  Datatype Interface:
  -------------------
  H5Tget_super         - return the base datatype from which a 
                         datatype is derived
  H5Tvlen_create       - creates a new variable-length dataype
  H5Tenum_create       - creates a new enumeration datatype
  H5Tenum_insert       - inserts a new enumeration datatype member
  H5Tenum_nameof       - returns the symbol name corresponding to a 
                         specified member of an enumeration datatype
  H5Tvalueof           - return the value corresponding to a 
                         specified member of an enumeration datatype 
  H5Tget_member_value  - return the value of an enumeration datatype member
  H5Tset_tag           - tags an opaque datatype
  H5Tget_tag           - gets the tag associated with an opaque datatype

  Identifier Interface:
  ---------------------
  H5Iget_type          - retrieve the type of an object

  Reference Interface:
  --------------------
  H5Rcreate            - creates a reference
  H5Rdereference       - open the HDF5 object referenced
  H5Rget_region        - retrieve a dataspace with the specified region selected
  H5Rget_object_type   - retrieve the type of object that an 
                         object reference points to

  Ragged Arrays (alpha) (names of those API functions were changed):
  ------------------------------------------------------------------
  H5RAcreate	       - create a new ragged array (old name was H5Rcreate)
  H5RAopen	       - open an existing array    (old name was H5Ropen)
  H5RAclose	       - close a ragged array      (old name was H5Rclose)
  H5RAwrite	       - write to an array         (old name was H5Rwrite)
  H5RAread	       - read from an array        (old name was H5Rread)

  AIX 4.3.2 (IBM SP)            3.6.6
  Cray J90 10.0.0.6             cc 6.3.0.0
  Cray T3E 2.0.4.61             cc 6.2.1.0
                                mpt.1.3
  FreeBSD 3.2                   gcc 2.95.1
  HP-UX B.10.20                 HP C  HP92453-01 A.10.32
                                gcc 2.8.1
  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                  egcs-2.91.66               configured with
                                                         --disable-hsizet
                                                           lbraries: glibc2
  OSF1 V4.0                     DEC-V5.2-040
  SunOS 5.6                     cc WorkShop Compilers 4.2  no optimization
                                gcc 2.8.1
  SunOS 5.7                     cc WorkShop Compilers 5.0
                                gcc 2.8.1
  TFLOPS 2.7.1                  cicc (pgcc Rel 3.0-4i)
                                mpich-1.1.2 with local changes
  Windows NT4.0 intel           MSVC++ 5.0 and 6.0
  Windows NT alpha 4.0          MSVC++ 5.0
  Windows 98                    MSVC++ 5.0

• NT alpha 4.0: The dumper utility, h5dump, fails if linked with DLL.
• SunOS 5.6 with C WorkShop Compilers 4.2: Hyperslab selections will fail if library is compiled using optimization of any level.