Release information for hdf5-1.2.0beta ------------------------------------ CHANGES SINCE VERSION 1.0.1 Documentation ------------- * More examples * Updated user guide, reference manual, and format specification. * Self-contained documentation for installations isolated from the Internet. 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. * Support for Cray T3E and Windows/NT. Debugging --------- * Improved control and redirection of debugging and tracing messages. 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 currently supported only as variable length arrays of 1-byte integers. Data Spaces ----------- * New query functions for selections. * I/O operations bypass the stripmining loop and go directly to storage for certain contiguous selections in the absense 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 are implemented. Parallel Support ---------------- * Improved parallel I/O performance. * Supported new platforms: Cray T3E, Linux, DEC Cluster. * Use vendor supported version of MPIO on SGI O2K and Cray platforms. * Improved the algorithm that translates an HDF5 hyperslab selection into an MPI type for better collective I/O performance. 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. CHANGES SINCE THE Version 1.0.0 RELEASE * [Improvement]: configure sets up the Makefile in the parallel tests suit (testpar/) correctly. * [Bug-Fix]: Configure failed for all IRIX versions other than 6.3. It now configures correctly for all IRIX 6.x version. CHANGES SINCE THE BETA RELEASE * Added fill values for datasets. For contiguous datasets fill value performance may be quite poor since the fill value is written to the entire dataset when the dataset is created. This will be remedied in a future version. Chunked datasets using fill values do not incur any additional overhead. See H5Pset_fill_value(). * Multiple hdf5 files can be "mounted" on one another to create a larger virtual file. See H5Fmount(). * Object names can be removed or changed but objects are never actually removed from the file yet. See H5Gunlink() and H5Gmove(). * Added a tuning mechanism for B-trees to insure that sequential writes to chunked datasets use less overhead. See H5Pset_btree_ratios(). * Various optimizations and bug fixes. CHANGES SINCE THE SECOND ALPHA * Strided hyperslab selections in dataspaces now working. * The compression API has been replaced with a more general filter API. See doc/html/Filters.html for details. * Alpha-quality 2d ragged arrays are implemented as a layer built on top of other hdf5 objects. The API and storage format will almost certainly change. * More debugging support including API tracing. See Debugging.html. * C and Fortran style 8-bit fixed-length character string types are supported with space or null padding or null termination and translations between them. * Added function H5Fflush() to write all cached data immediately to the file. * Datasets maintain a modification time which can be retrieved with H5Gstat(). * The h5ls tool can display much more information, including all the values of a dataset. CHANGES SINCE THE FIRST ALPHA * Two of the packages have been renamed. The data space API has been renamed from `H5P' to `H5S' and the property list (template) API has been renamed from `H5C' to `H5P'. * The new attribute API `H5A' has been added. An attribute is a small dataset which can be attached to some other object (for instance, a 4x4 transformation matrix attached to a 3-dimensional dataset, or an English abstract attached to a group). * The error handling API `H5E' has been completed. By default, when an API function returns failure an error stack is displayed on the standard error stream. The H5Eset_auto() controls the automatic printing and H5E_BEGIN_TRY/H5E_END_TRY macros can temporarily disable the automatic error printing. * Support for large files and datasets (>2GB) has been added. There is an html document that describes how it works. Some of the types for function arguments have changed to support this: all arguments pertaining to sizes of memory objects are `size_t' and all arguments pertaining to file sizes are `hsize_t'. * More data type conversions have been added although none of them are fine tuned for performance. There are new converters from integer to integer and float to float, but not between integers and floating points. A bug has been fixed in the converter between compound types. * The numbered types have been removed from the API: int8, uint8, int16, uint16, int32, uint32, int64, uint64, float32, and float64. Use standard C types instead. Similarly, the numbered types were removed from the H5T_NATIVE_* architecture; use unnumbered types which correspond to the standard C types like H5T_NATIVE_INT. * More debugging support was added. If tracing is enabled at configuration time (the default) and the HDF5_TRACE environment variable is set to a file descriptor then all API calls will emit the function name, argument names and values, and return value on that file number. There is an html document that describes this. If appropriate debugging options are enabled at configuration time, some packages will display performance information on stderr. * Data types can be stored in the file as independent objects and multiple datasets can share a data type. * The raw data I/O stream has been implemented and the application can control meta and raw data caches, so I/O performance should be improved from the first alpha release. * Group and attribute query functions have been implemented so it is now possible to find out the contents of a file with no prior knowledge. * External raw data storage allows datasets to be written by other applications or I/O libraries and described and accessed through HDF5. * Hard and soft (symbolic) links are implemented which allow groups to share objects. Dangling and recursive symbolic links are supported. * User-defined data compression is implemented although we may generalize the interface to allow arbitrary user-defined filters which can be used for compression, checksums, encryption, performance monitoring, etc. The publicly-available `deflate' method is predefined if the GNU libz.a can be found at configuration time. * The configuration scripts have been modified to make it easier to build debugging vs. production versions of the library. * The library automatically checks that the application was compiled with the correct version of header files. Parallel HDF5 Changes * Parallel support for fixed dimension datasets with contiguous or chunked storages. Also, support unlimited dimension datasets which must use chunk storage. No parallel support for compressed datasets. * Collective data transfer for H5Dread/H5Dwrite. Collective access support for datasets with contiguous storage only, thus only fixed dimension datasets for now. * H5Pset_mpi and H5Pget_mpi no longer have the access_mode argument. It is taken over by the data-transfer property list of H5Dread/H5Dwrite. * New functions H5Pset_xfer and H5Pget_xfer to handle the specification of independent or collective data transfer_mode in the dataset transfer properties list. The properties list can be used to specify data transfer mode in the H5Dwrite and H5Dread function calls. * Added parallel support for datasets with chunked storage layout. When a dataset is extend in a PHDF5 file, all processes that open the file must collectively call H5Dextend with identical new dimension sizes. LIST OF API FUNCTIONS The following functions are implemented. Errors are returned if an attempt is made to use some feature which is not implemented and printing the error stack will show `not implemented yet'. Library H5check - check that lib version matches header version H5open - initialize library (happens automatically) H5close - shut down the library (happens automatically) H5dont_atexit - don't call H5close on exit H5get_libversion - retrieve library version info H5check_version - check for specific library version Property Lists H5Pclose - release template resources H5Pcopy - copy a template H5Pcreate - create a new template H5Pget_chunk - get chunked storage properties H5Pset_chunk - set chunked storage properties H5Pget_class - get template class H5Pget_istore_k - get chunked storage properties H5Pset_istore_k - set chunked storage properties H5Pget_layout - get raw data layout class H5Pset_layout - set raw data layout class H5Pget_sizes - get address and size sizes H5Pset_sizes - set address and size sizes H5Pget_sym_k - get symbol table storage properties H5Pset_sym_k - set symbol table storage properties H5Pget_userblock - get user-block size H5Pset_userblock - set user-block size H5Pget_version - get file version numbers H5Pget_alignment - get data alignment properties H5Pset_alignment - set data alignment properties H5Pget_external_count- get count of external data files H5Pget_external - get information about an external data file H5Pset_external - add a new external data file to the list H5Pget_driver - get low-level file driver class H5Pget_stdio - get properties for stdio low-level driver H5Pset_stdio - set properties for stdio low-level driver H5Pget_sec2 - get properties for sec2 low-level driver H5Pset_sec2 - set properties for sec2 low-level driver H5Pget_core - get properties for core low-level driver H5Pset_core - set properties for core low-level driver H5Pget_split - get properties for split low-level driver H5Pset_split - set properties for split low-level driver H5P_get_family - get properties for family low-level driver H5P_set_family - set properties for family low-level driver H5Pget_cache - get meta- and raw-data caching properties H5Pset_cache - set meta- and raw-data caching properties H5Pget_buffer - get raw-data I/O pipe buffer properties H5Pset_buffer - set raw-data I/O pipe buffer properties H5Pget_preserve - get type conversion preservation properties H5Pset_preserve - set type conversion preservation properties H5Pget_nfilters - get number of raw data filters H5Pget_filter - get raw data filter properties H5Pset_filter - set raw data filter properties H5Pset_deflate - set deflate compression filter properties H5Pget_mpi - get MPI-IO properties H5Pset_mpi - set MPI-IO properties H5Pget_xfer - get data transfer properties H5Pset_xfer - set data transfer properties Datasets H5Dclose - release dataset resources H5Dcreate - create a new dataset H5Dget_space - get data space H5Dget_type - get data type H5Dget_create_plist - get dataset creation properties H5Dopen - open an existing dataset H5Dread - read raw data H5Dwrite - write raw data H5Dextend - extend a dataset Attributes H5Acreate - create a new attribute H5Aopen_name - open an attribute by name H5Aopen_idx - open an attribute by number H5Awrite - write values into an attribute H5Aread - read values from an attribute H5Aget_space - get attribute data space H5Aget_type - get attribute data type H5Aget_name - get attribute name H5Anum_attrs - return the number of attributes for an object H5Aiterate - iterate over an object's attributes H5Adelete - delete an attribute H5Aclose - close an attribute Errors H5Eclear - clear the error stack H5Eprint - print an error stack H5Eget_auto - get automatic error reporting settings H5Eset_auto - set automatic error reporting H5Ewalk - iterate over the error stack H5Ewalk_cb - the default error stack iterator function H5Eget_major - get the message for the major error number H5Eget_minor - get the message for the minor error number Files H5Fclose - close a file and release resources H5Fcreate - create a new file H5Fget_create_plist - get file creation property list H5Fget_access_plist - get file access property list H5Fis_hdf5 - determine if a file is an hdf5 file H5Fopen - open an existing file Groups H5Gclose - close a group and release resources H5Gcreate - create a new group H5Gopen - open an existing group H5Gpop - pop a group from the cwg stack H5Gpush - push a group onto the cwg stack H5Gset - set the current working group (cwg) H5Giterate - iterate over the contents of a group H5Gmove - change the name of some object H5Glink - create a hard or soft link to an object H5Gunlink - break the link between a name and an object H5Gget_objinfo - get information about a group entry H5Gget_linkval - get the value of a soft link H5Gget_comment - get the comment string for an object H5Gset_comment - set the comment string for an object Dataspaces H5Screate - create a new data space H5Scopy - copy a data space H5Sclose - release data space H5Screate_simple - create a new simple data space H5Sset_space - set simple data space extents H5Sis_simple - determine if data space is simple H5Sset_extent_simple - set simple data space dimensionality and size H5Sget_simple_extent_npoints - get number of points in simple extent H5Sget_simple_extent_ndims - get simple data space dimensionality H5Sget_simple_extent_dims - get simple data space size H5Sget_simple_extent_type - get type of simple extent H5Sset_extent_none - reset extent to be empty H5Sextent_copy - copy the extent from one data space to another H5Sget_select_npoints - get number of points selected for I/O H5Sselect_hyperslab - set hyperslab dataspace selection H5Sselect_elements - set element sequence dataspace selection H5Sselect_all - select entire extent for I/O H5Sselect_none - deselect all elements of extent H5Soffset_simple - set selection offset H5Sselect_valid - determine if selection is valid for extent Datatypes H5Tclose - release data type resources H5Topen - open a named data type H5Tcommit - name a data type H5Tcommitted - determine if a type is named H5Tcopy - copy a data type H5Tcreate - create a new data type H5Tequal - compare two data types H5Tlock - lock type to prevent changes H5Tfind - find a data type conversion function H5Tconvert - convert data from one type to another H5Tregister_hard - register specific type conversion function H5Tregister_soft - register general type conversion function H5Tunregister - remove a type conversion function H5Tget_overflow - get function that handles overflow conv. cases H5Tset_overflow - set function to handle overflow conversion cases H5Tget_class - get data type class H5Tget_cset - get character set H5Tget_ebias - get exponent bias H5Tget_fields - get floating point fields H5Tget_inpad - get inter-field padding H5Tget_member_dims - get struct member dimensions H5Tget_member_name - get struct member name H5Tget_member_offset - get struct member byte offset H5Tget_member_type - get struct member type H5Tget_nmembers - get number of struct members H5Tget_norm - get floating point normalization H5Tget_offset - get bit offset within type H5Tget_order - get byte order H5Tget_pad - get padding type H5Tget_precision - get precision in bits H5Tget_sign - get integer sign type H5Tget_size - get size in bytes H5Tget_strpad - get string padding H5Tinsert - insert scalar struct member H5Tinsert_array - insert array struct member H5Tpack - pack struct members H5Tset_cset - set character set H5Tset_ebias - set exponent bias H5Tset_fields - set floating point fields H5Tset_inpad - set inter-field padding H5Tset_norm - set floating point normalization H5Tset_offset - set bit offset within type H5Tset_order - set byte order H5Tset_pad - set padding type H5Tset_precision - set precision in bits H5Tset_sign - set integer sign type H5Tset_size - set size in bytes H5Tset_strpad - set string padding Filters H5Tregister - register a new filter method Ragged Arrays (alpha) H5Rcreate - create a new ragged array H5Ropen - open an existing array H5Rclose - close a ragged array H5Rwrite - write to an array H5Rread - read from an array PLATFORMS SUPPORTED ------------------- Operating systems listed below with compiler information and MPI library, if applicable, are systems that HDF5 1.2.0beta was tested. Compiler & libraries Platform Information Comment -------- ---------- -------- AIX 4.3.2 (IBM SP) FreeBSD 3.2 gcc 2.8.1 HP-UX 10.20 cc A.10.32.03 IRIX 6.5 cc 7.2.1 IRIX64 6.5 (64 & n32) cc 7.30 mpt.1.3 (SGI MPI 3.2.0.0) Linux (SuSE and RedHat) egcs-1.1.2 configured with --disable-hsizet OSF1 V4.0 DEC-V5.2-033 SunOS 5.6 cc 4.2 no optimization gcc 2.8.1 SunOS 5.5.1 gcc 2.7.2 configured with --disable-hsizet TFLOPS O/S 1.0.4 cicc (pgcc Rel 1.7-6i) mpich-1.1.2 with local changes Unicos 2.0.4.61 (T3E) cc 6.2.1.0 mpt.1.3 Windows/NT 4.0/SP3 MSVC++ 5.0 and 6.0 Cygwin gcc egcs-2.91.57