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d2232a345f
Bug Fix & Feature
Description:
The selection offset was being ignored for optimized hyperslab selection
I/O operations.
Additionally, I've found that the restrictions on optimized selection
I/O operations were too strict and found a way to allow more hyperslabs
to use the optimized I/O routines.
Solution:
Incorporate the selection offset into the selection location when performing
optimized I/O operations.
Allow optimized I/O on any single hyperslab selection and also allow
hyperslab operations on chunked datasets.
Platforms tested:
FreeBSD 4.5 (sleipnir)
366 lines
18 KiB
Plaintext
366 lines
18 KiB
Plaintext
HDF5 version 1.5.24 currently under development
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================================================================================
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INTRODUCTION
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This document describes the differences between HDF5-1.4.0 and
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HDF5-1.5-snap0, and contains information on the platforms tested and
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known problems in HDF5-1.5-snap0. For more details check the HISTORY.txt
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file in the HDF5 source.
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The HDF5 documentation can be found on the NCSA ftp server
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(ftp.ncsa.uiuc.edu) in the directory:
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/HDF/HDF5/docs/
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For more information look at the HDF5 home page at:
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http://hdf.ncsa.uiuc.edu/HDF5/
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If you have any questions or comments, please send them to:
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hdfhelp@ncsa.uiuc.edu
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CONTENTS
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- New Features
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- Bug Fixes since HDF5-1.4.0
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- Platforms Tested
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- Known Problems
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Bug Fixes since HDF5-1.4.2
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==========================
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Library
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-------
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* Fixed bug where selection offset was being ignored for certain hyperslab
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selections when optimized I/O was being performed. QAK - 2002/04/02
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* Added serial multi-gigabyte file size test. "test/big -h" shows
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the help page. AKC - 2002/03/29
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* Fixed bug where variable-length string type doesn't behave as
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string. SLU - 2002/03/28
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* Fixed bug in H5Gget_objinfo() which was not setting the 'fileno'
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of the H5G_stat_t struct. QAK - 2002/03/27
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* Fixed data corruption bug in hyperslab routines when contiguous
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hyperslab that spans entire dimension and is larger than type
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conversion buffer is attempted to be read. QAK - 2002/03/26
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* Fixed bug where non-zero fill-value was not being read correctly from
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certain chunked datasets when using an "all" or contiguous hyperslab
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selection. QAK - 2002/02/14
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* Fixed bug where a preempted chunk in the chunk data could still be
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used by an internal pointer and cause an assertion failure or core
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dump. QAK - 2002/02/13
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* Fixed bug where raw data re-allocated from the free-list would sometimes
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overlap with the metadata accumulator and get corrupted. QAK - 2002/01/23
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* Fixed bug where variable-length datatypes for attributes was not working
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correctly.
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* Retired the DPSS virtual file driver (--with-gridstorage configure
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option).
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* Corrected behavior of H5Tinsert to not allow compound datatype fields to
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be inserted past the end of the datatype.
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* Fixed the internal macros used to encode & decode file metadata, to avoid
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an unaligned access warning on IA64 machines.
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* Fixed an off-by-one error in H5Sselect_valid when hyperslab selections
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which would allow hyperslab selections which overlapped the edge of the
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selection by one element as valid.
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* Fixed a bug in internal B-tree code where a B-tree was not being copied
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correctly.
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* Fixed a bug in the 'big' test where quota limits weren't being detected
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properly if they caused close() to fail.
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* Fixed a bug where 'or'ing a hyperslab with a 'none' selection would
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fail. Now adds that hyperslab as the first hyperlab in the selection.
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* Fixed a bug where appending a point selection to the current selection
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would not actually append the point when there were no points defined
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currently.
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* Fixed a bug where reading or writing chunked data which needed datatype
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conversion could result in data values getting corrupted.
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* Fixed a bug where reading an entire dataset wasn't being handled
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optimally when the dataset had unlimited dimensions. Dataset is read
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in a single low-level I/O now, instead of being broken into separate
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pieces internally.
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* Fixed a bug when reading chunked datasets where the edge of the dataset
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would be incorrectly detected and generate an assertion failure.
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* Added new parallel hdf5 tests in t_mpi. The new test checks if the
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filesystem or the MPI-IO can really handle greater than 2GB files.
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If it fails, it prints information message only without failing the
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test.
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* Fixed a bug in H5FD_mpio_flush() that might result in negative file seek
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if both MPIO and Split-file drivers are used together.
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* Fixed H5FDmpio.h to be C++ friendly by making Parallel HDF5 API's to be
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external to C++.
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* Fixed a bug of H5pubconf.h causing repeated definitions if it is included
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more than once. hdf5.h now includes H5public.h which includes
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H5pubconf.h. Applications should #include hdf5.h which handles multiple
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inclusion correctly.
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* Tweaked a few API functions to use 'size_t' instead of 'unsigned' or
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'hsize_t', which may cause errors in some cases.
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* Changed behavior of H5Tget_member_type to correctly emulate HDF5 v1.2.x
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when --enable-hdf5v1_2 configure flag is enabled.
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* Removed limitation that the data transfer buffer size needed to be
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set for datasets whose dimensions were too large for the 'all' selection
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code to handle. Any size dimensioned datasets should be handled
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correctly now.
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* The allocation by alignment (H5Pset_alignment) feature code somehow
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got dropped in some 1.3.x version. Re-implemented it with "new and
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improved" algorithm. It keeps track of "wasted" file-fragment in
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the free-list too.
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* IMPORTANT: Fixed file metadata corruption bug which could cause metadata
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data loss in certain situations.
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* Fixed build on Linux systems with --enable-static-exec flag. It now
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works correctly.
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* Fixed bug with non-zero userblock sizes causing raw data to not write
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correctly.
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* The RCSID string in H5public.h was causing the C++ compiling problem
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because when it was included multiple times, C++ did not like multiple
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definitions of the same static variable. All occurance of RCSID
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definition are removed since we have not used it consistently before.
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* Fixed bug where non-aligned hyperslab I/O on chunked datasets was
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causing errors during I/O
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* Fixed bug with contiguous hyperslabs not being detected, causing
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slower I/O than necessary.
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Configuration
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-------------
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* Can use just enable-threadsafe if the C compiler has builtin pthreads
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support.
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* Require HDF (a.k.a. hdf4) software that consists of a newer version
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of zlib library which consists of the compress2() function. Versions
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HDF version 4.1r3 and newer meets this requirement. The compress2
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uses a newer compression algorithm used by the HDF5 library. Also,
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4.1r3 has an hdp tool that can handle "loops" in Vgroups.
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* Added --enable-linux-lfs flag to allow more control over whether to enable
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or disable large file support on Linux.
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* Basic port to Compaq (nee DEC) Alpha OSF 5.
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* Changed the default value of $NPROCS from 2 to 3 since 3 processes
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have a much bigger chance catching parallel errors than just 2.
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Tools
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-----
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* Fixed limitation in h5dumper with object names which reached over 1024
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characters in length. We can now handle arbitrarily larger sizes for
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object names. BW - 2002/02/27
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* Fixed so that the "-i" flag works correctly with the h5dumper.
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* Fixed segfault when "-v" flag was used with the h5dumper.
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Documentation
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-------------
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New Features
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============
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* Improved performance of single hyperslab I/O when datatype conversion is
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unneccessary. QAK - 2002/04/02
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* Added new "H5Sget_select_type" API function to determine which type of
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selection is defined for a dataspace ("all", "none", "hyperslab" or
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"point"). QAK - 2002/02/7
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* Added support to read/write portions of chunks directly, if they are
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uncompressed and too large to cache. This should speed up I/O on chunked
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datasets for a few more cases. QAK - 2002/01/31
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* Parallel HDF5 is now supported on HP-UX 11.00 platforms.
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* Added H5Rget_obj_type() API function, which performs the same functionality
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as H5Rget_object_type(), but requires the reference type as a parameter
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in order to correctly handle dataset region references. Moved
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H5Rget_object_type() to be only compiled into the library when v1.4
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compatibility is enabled.
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* Changed internal error handling macros to reduce code size of library by
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about 10-20%.
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* Added a new file access property, file close degree, to control file
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close behavior. It has four values, H5F_CLOSE_WEAK, H5F_CLOSE_SEMI,
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H5F_CLOSE_STRONG, and H5F_CLOSE_DEFAULT. Two correspont functions
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H5Pset_fclose_degree and H5Pget_fclose_degree are also provided. Two
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new functions H5Fget_obj_count and H5Fget_obj_ids are offerted to assist
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this new feature. For full details, please refer to the reference
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manual under the description of H5Fcreate, H5Fopen, H5Fclose and the
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functions mentioned above.
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* Removed H5P(get|set)_hyper_cache API function, since the property is no
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longer used.
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* Improved performance of non-contiguous hyperslabs (built up with
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several hyperslab selection calls).
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* Improved performance of single, contiguous hyperslabs when reading or
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writing.
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* As part of the transition to using generic properties everywhere, the
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parameter of H5Pcreate changed from H5P_class_t to hid_t, as well
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the return type of H5Pget_class changed from H5P_class_t to hid_t.
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Further changes are still necessary and will be documented here as they
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are made.
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* Added a new test to verify the information provided by the configure
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command.
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* The H5Pset_fapl_split() accepts raw and meta file names similar to the
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syntax of H5Pset_fapl_multi() in addition to what it used to accept.
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* Added perform programs to test the HDF5 library performance. Programs
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are installed in directory perform/.
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* Added new checking in H5check_version() to verify the five HDF5 version
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information macros (H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE,
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H5_VERS_SUBRELEASE and H5_VERS_INFO) are consistent.
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* Added a new public macro, H5_VERS_INFO, which is a string holding
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the HDF5 library version information. This string is also compiled
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into all HDF5 binary code which helps to identify the version
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information of the binary code. One may use the Unix strings
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command on the binary file and looks for the pattern "HDF5 library
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version".
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* Added a parallel HDF5 example examples/ph5example.c to illustrate
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the basic way of using parallel HDF5.
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* Added two simple parallel performance tests as mpi-perf.c (MPI
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performance) and perf.c (PHDF5 performance) in testpar.
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* Improved regular hyperslab I/O by about a factor of 6 or so.
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* Modified the Pablo build procedure to permit building of the instrumented
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library to link either with the Trace libraries as before or with the
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Pablo Performance Caputure Facility.
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* Verified correct operation of library on Solaris 2.8 in both 64-bit and
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32-bit compilation modes. See INSTALL document for instructions on
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compiling the distribution with 64-bit support.
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* Parallel HDF5 now runs on the HP V2500 and HP N4000 machines.
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* H5 <-> GIF convertor has been added. This is available under
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tools/gifconv. The convertor supports the ability to create animated
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gifs as well.
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* Added a global string variable H5_lib_vers_info_g which holds the
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HDF5 library version information. This can be used to identify
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an hdf5 library or hdf5 application binary.
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Also added a verification of the consistency between H5_lib_vers_info_g
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and other version information in the source code.
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* File sizes greater than 2GB are now supported on Linux systems with
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version 2.4.x or higher kernels.
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* F90 APIs are available on HPUX 11.00 and IBM SP platforms.
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* F90 static library is available on Windows platforms. See
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INSTALL_Windows.txt for details.
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* F90 API:
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- Added aditional parameter "dims" to the h5dread/h5dwrite and
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h5aread/h5awrite subroutines. This parameter is 1D array of size
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7 and contains the sizes of the data buffer dimensions.
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* C++ API:
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- Added two new member functions: Exception::getFuncName() and
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Exception::getCFuncName() to provide the name of the member
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function, where an exception is thrown.
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- IdComponent::operator= becomes a virtual function because
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DataType, DataSpace, and PropList provide their own
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implementation. The new operator= functions invoke H5Tcopy,
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H5Scopy, and H5Pcopy to make a copy of a datatype, dataspace,
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and property list, respectively.
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* A helper script called ``h5cc'', which helps compilation of HDF5
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programs, is now distributed with HDF5. See the reference manual
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for information on how to use this feature.
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Platforms Tested
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================
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AIX 4.3.3.0 (IBM SP powerpc) mpcc_r 3.6.6
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Cray T3E sn6711 2.0.5.45 Cray Standard C Version 6.4.0.0
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Cray Fortran Version 3.4.0.2
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Cray SV1 sn9605 10.0.0.7 Cray Standard C Version 6.4.0.0
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Cray Fortran Version 3.4.0.2
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FreeBSD 4.3 gcc 2.95.2
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g++ 2.95.2
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HP-UX B.10.20 HP C HP92453-01 A.10.32.30
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HP-UX B.11.00 HP C HP92453-01 A.11.00.13
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HP C HP92453-01 A.11.01.20
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IRIX 6.5 MIPSpro cc 7.30
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IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1m
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mpt.1.4.0.2
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mpich-1.2.1
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Linux 2.4.4 gcc-2.95.3
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g++ 2.95.3
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Linux 2.2.16-3smp gcc-2.95.2
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g++ 2.95.2
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pgf90 3.1-3
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OSF1 V4.0 DEC-V5.2-040
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Digital Fortran 90 V4.1-270
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SunOS 5.6 WorkShop Compilers 5.0 98/12/15 C 5.0
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(Solaris 2.6) WorkShop Compilers 5.0 99/10/25 Fortran 90
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2.0 Patch 107356-04
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Workshop Compilers 5.0 98/12/15 C++ 5.0
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SunOS 5.7 WorkShop Compilers 5.0 98/12/15 C 5.0
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(Solaris 2.7) WorkShop Compilers 5.0 99/10/25 Fortran 90
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2.0 Patch 107356-04
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Workshop Compilers 5.0 98/12/15 C++ 5.0
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TFLOPS r1.0.4 v4.0 mpich-1.2.1 with local changes
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Windows NT4.0, 2000 (NT5.0) MSVC++ 6.0
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Windows 98 MSVC++ 6.0
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Known Problems
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==============
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* Datasets or attributes which have a variable-length string datatype are not
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printing correctly with h5dump and h5ls.
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* DLLs do not work on Windows 98
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* RELEASE DLLs will fail on some tests on Windows 2000 with Microsoft visual
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studio 6.0 due to memory allocation problems caused by compiler.
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Users are encouraged to go to microsoft site to find and install
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visual studio 6.0 service pack 5. After that, release dlls will work.
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* The stream-vfd test uses ip port 10007 for testing. If another
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application is already using that port address, the test will hang
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indefinitely and has to be terminated by the kill command. To try the
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test again, change the port address in test/stream_test.c to one not
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being used in the host.
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* The --enable-static-exec configure flag fails to compile for Solaris
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platforms. This is due to the fact that not all of the system
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libraries on Solaris are available in a static format.
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The --enable-static-exec configure flag also fails to correctly compile
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on IBM SP2 platform for the serial mode. The parallel mode works fine
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with this option.
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It is suggested that you don't use this option on these platforms
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during configuration.
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* With the gcc 2.95.2 compiler, HDF 5 uses the `-ansi' flag during
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compilation. The ANSI version of the compiler complains about not being
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able to handle the `long long' datatype with the warning:
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warning: ANSI C does not support `long long'
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This warning is innocuous and can be safely ignored.
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* SunOS 5.6 with C WorkShop Compilers 4.2: Hyperslab selections will
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fail if library is compiled using optimization of any level.
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* h5toh4 converter fails two cases (tstr.h5 and tmany.h5) for release dll
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version on windows 2000 and NT. The reason is possibly due to windows
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NT DLL convention on freeing memory. It seems that memory cannot be
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free across library or DLL. It is still under investigated.
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* The Stream VFD was not tested yet under Windows. It is not supported
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in the TFLOPS machine.
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* Shared library option is broken for IBM SP and some Origin 2000
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platforms. One needs to run ./configure with '--disable-shared'
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* The ./dsets tests failed in the TFLOPS machine if the test program,
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dsets.c, is compiled with the -O option. The hdf5 library still works
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correctly with the -O option. The test program works fine if it is
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compiled with -O1 or -O0. Only -O (same as -O2) causes the test
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program to fail.
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* Certain platforms give false negatives when testing h5ls:
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- Solaris x86 2.5.1, Cray T3E and Cray J90 give errors during testing
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when displaying object references in certain files. These are
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benign differences due to the difference in sizes of the objects
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created on those platforms. h5ls appears to be dumping object
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references correctly.
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- Cray J90 (and Cray T3E?) give errors during testing when displaying
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some floating-point values. These are benign differences due to
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the different precision in the values displayed and h5ls appears to
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be dumping floating-point numbers correctly.
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* Before building HDF5 F90 Library from source on Crays (T3E and J90)
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replace H5Aff.f90, H5Dff.f90 and H5Pff.f90 files in the fortran/src
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subdirectory in the top level directory with the Cray-specific files
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from the site:
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ftp://hdf.ncsa.uiuc.edu/pub/ougoing/hdf5/hdf5-1.4.0-beta/F90_source_for_Crays
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