2279 lines
102 KiB
Plaintext
2279 lines
102 KiB
Plaintext
HDF5 History
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============
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This file contains development history of HDF5 1.8 branch
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4. Release Information for hdf5-1.8.3
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3. Release Information for hdf5-1.8.2
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2. Release Information for hdf5-1.8.1
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1. Release Information for hdf5-1.8.0
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[Search on the string '%%%%' for per-release section breaks.]
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%%%%1.8.3%%%%
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HDF5 version 1.8.3 released on Mon May 4 09:21:00 CDT 2009
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================================================================================
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INTRODUCTION
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============
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This document describes the differences between HDF5-1.8.2 and
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HDF5 1.8.3, and contains information on the platforms tested and
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known problems in HDF5-1.8.3.
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For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
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and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
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Links to the HDF5 1.8.3 source code, documentation, and additional materials
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can be found on the HDF5 web page at:
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http://www.hdfgroup.org/products/hdf5/
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The HDF5 1.8.3 release can be obtained from:
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http://www.hdfgroup.org/HDF5/release/obtain5.html
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User documentation for 1.8.3 can be accessed directly at this location:
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http://www.hdfgroup.org/HDF5/doc/
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New features in the HDF5-1.8.x release series, including brief general
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descriptions of some new and modified APIs, are described in the "What's New
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in 1.8.0?" document:
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http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
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All new and modified APIs are listed in detail in the "HDF5 Software Changes
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from Release to Release" document, in the section "Release 1.8.3 (current
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release) versus Release 1.8.2":
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http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
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If you have any questions or comments, please send them to the HDF Help Desk:
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help@hdfgroup.org
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CONTENTS
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========
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- New Features
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- Support for New Platforms, Languages, and Compilers
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- Bug Fixes since HDF5-1.8.2
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- Platforms Tested
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- Supported Configuration Features Summary
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- Known Problems
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New Features
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============
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Configuration
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-------------
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- Added libtool version numbers to generated c++, fortran, and
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hl libraries. MAM 2009/04/19.
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- Regenerated Makefile.ins using Automake 1.10.2. MAM 2009/04/19.
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- Added a Make target of check-all-install to test the correctness of
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installing via the prefix= or $DESTDIR options. AKC - 2009/04/14
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Library
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-------
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- Embed the content of libhdf5.settings into the hdf5 executables
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so that an "orphaned" executables can display (via the Unix
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strings command, for example) the library settings used to build
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the executables. This is a prototype implementation. Improvement will
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be added in next release. AKC - 2009/04/20
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- Separated "factory" free list class from block free lists. These free
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lists are dynamically created and manage blocks of a fixed size.
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H5set_free_list_limits() will use the same settings specified for block
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free lists for factory free lists. NAF - 2009/04/08
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- Added support for dense attributes to H5Ocopy. XCao/NAF - 2009/01/29
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- Added H5Pset_elink_cb and H5Pget_elink_cb functions to support a
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user-defined callback function for external link traversal.
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NAF - 2009/01/08
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- Added H5Pset_elink_acc_flags and H5Pget_elink_acc_flags functions to
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allow the user to specify the file access flags used to open the target
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file of an external link. NAF - 2009/01/08
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- Added H5Pset_chunk_cache() and H5Pget_chunk_cache() functions to allow
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individual rdcc configuration for each dataset. Added
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H5Dget_access_plist() function to retrieve a dataset access property
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list from a dataset. NAF - 2008/11/12
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- Added H5Iis_valid() function to check if an id is valid without
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producing an error message. NAF - 2008/11/5
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- Added code to maintain a min_clean_fraction in the metadata cache when
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in serial mode. MAM - 2009/01/9
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Parallel Library
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----------------
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- Modified parallel tests to run with arbitrary number of processes. The
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modified tests are testphdf5 (parallel dataset access), t_chunk_alloc
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(chunk allocation), and t_posix_compliant (posix compliance). The rest of
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the parallel tests already use in the code the number of processes
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available in the communicator. (CMC - 2009/04/28)
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Tools
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-----
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- h5diff new flag, -c, --compare, list objects that are not comparable.
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PVN - 2009/4/2 - 1368
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- h5diff new flag, -N, --nan, avoids NaNs detection. PVN - 2009/4/2
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- h5dump correctly specifies XML dtd / schema urls ADB - 2009/4/3 - 1519
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- h5repack now handles group creation order. PVN - 2009/4/2 - 1402
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- h5repack: When user doesn't specify a chunk size, h5repack now
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defines a default chunk size as the same size of the size of the
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hyperslab used to read the chunks. The size of the hyperslabs are
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defined as the size of each dimension or a predefined constant,
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whatever is smaller. This assures that the chunk read fits in the
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chunk cache. PVN - 2008/11/21
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High-Level APIs
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---------------
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- Table: In version 3.0 of Table, the writing of the "NROWS" attribute
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(used to store number of records) was deprecated. PVN - 2008/11/24
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F90 API
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-------
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- Added for the C APIs the Fortran wrappers:
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h5dget_access_plist_f
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h5iis_valid_f
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h5pset_chunk_cache_f
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h5pget_chunk_cache_f
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MSB - 2009/04/17
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C++ API
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-------
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- None
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Support for New Platforms, Languages, and Compilers
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===================================================
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Bug Fixes since HDF5-1.8.2
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==========================
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Configuration
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-------------
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- The --includedir=DIR configuration option now works as intended, and
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can be used to specify the location to install C header files. The
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default location remains unchanged, residing at ${prefix}/include.
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MAM - 2009/03/10 - BZ #1381
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- Configure no longer removes the '-g' flag from CFLAGS when in production
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mode if it has been explicitly set in the CFLAGS environment variable
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prior to configuration. MAM - 2009/03/09 - BZ #1401
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Library
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-------
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- Added versioning to H5Z_class_t struct to allow compatibility with 1.6
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API. NAF - 2009/04/20 - 1533
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- Fixed a problem with using data transforms with non-native types in the
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file. NAF - 2009/04/20 - 1548
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- Added direct.h include file to windows section of H5private.h
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to fix _getcwd() warning. ADB - 2009/04/14 - 1536
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- Fixed a bug that prevented external links from working after calling
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H5close(). NAF - 2009/04/10 - 1539
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- Modified library to write cached symbol table information to the
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superblock, to allow library versions 1.3.0 to 1.6.3 to read files created
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by this version. NAF - 2009/04/08 - 1423
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- Changed skip lists to use a deterministic algorithm. The library should
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now never call rand() or srand(). NAF - 2009/04/08 - 503
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- Fixed a bug where H5Lcopy and H5Lmove wouldn't create intermediate groups
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when that property was set. NAF - 2009/04/07 - 1526
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- Fixed a bug that caused files with a user block to grow by the size of the
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user block every time they were opened. NAF - 2009/03/26 - 1499
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- Fixed a rare problem that could occur with files using the old (pre 1.4)
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array datatype. NAF - 2009/03/23
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- Modified library to be able to open files with corrupt root group symbol
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table messages, and correct these errors if they are found. Such files
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can only be successfully opened with write access. NAF - 2009/03/23 - 1189
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- Removed the long_long #define and replaced all instances with
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"long long". This caused problems with third party products. All
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currently supported compliers support the type. ADB - 2009/03/05
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- Fixed various bugs that could prevent the fill value from being written
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in certain rare cases. NAF - 2009/02/26 - 1469
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- Fixed a bug that prevented more than one dataset chunk from being cached
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at a time. NAF - 2009/02/12 - 1015
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- Fixed an assertion failure caused by opening an attribute multiple times
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through multiple file handles. NAF - 2009/02/12 - 1420
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- Fixed a problem that could prevent the user from adding attributes (or any
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object header message) in some circumstances. NAF - 2009/02/12 - 1427
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- Fixed a bug that could cause problems when an attribute was added to a
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committed datatype using the committed datatype's datatype.
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NAF - 2009/02/12
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- Fixed a bug that could cause problems when copying an object with a shared
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message in its own object header. NAF - 2009/01/29
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- Changed H5Tset_order to properly reject H5T_ORDER_NONE for most datatypes.
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NAF - 2009/01/27 - 1443
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- Fixed a bug where H5Tpack wouldn't remove trailing space from an otherwise
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packed compound type. NAF - 2009/01/14
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- Fixed up some old v2 btree assertions that get run in debug mode that
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were previously failing on compilation, and removed some of the
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more heavily outdated and non-rewritable ones. MAM - 2008/12/15
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- Fixed a bug that could cause problems when "automatically" unmounting
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multiple files. NAF - 2008/11/17
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- H5Dset_extent: when shrinking dimensions, some chunks were not deleted.
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PVN - 2009/01/8
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Parallel Library
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----------------
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- None
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Tools
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-----
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- Fixed many problems that could occur when using h5repack with named
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datatypes. NAF - 2009/4/20 - 1516/1466
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- h5dump, h5diff, h5repack were not reading (by hyperslabs) datasets
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that have a datatype datum size greater than H5TOOLS_BUFSIZE, a constant
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defined as 1024Kb, such as array types with large dimensions.
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PVN - 2009/4/1 - 1501
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- h5import: By selecting a compression type, a big endian byte order
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was being selected. PVN - 2009/3/11 - 1462
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- zip_perf.c had missing argument on one of the open() calls. Fixed.
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AKC - 2008/12/9
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F90 API
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------
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- None
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C++ API
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------
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- None
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High-Level APIs:
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------
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- Dimension scales: The scale index return value in H5DSiterate_scales
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was not always incremented. PVN - 2009/4/8 - 1538
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Fortran High-Level APIs:
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------
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- Lite: The h5ltget_dataset_info_f function (gets information about
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a dataset) was not correctly returning the dimension array
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PVN - 2009/3/23
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Platforms Tested
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================
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The following platforms and compilers have been tested for this release.
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AIX 5.3 xlc 7.0.0.8
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(LLNL Up) xlf 09.01.0000.0008
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xlC 7.0.0.8
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mpcc_r 7.0.0.8
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mpxlf_r 09.01.0000.0008
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Cray XT3 (2.0.41) cc (pgcc) 7.1-4
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(SNL red storm) ftn (pgf90) 7.1-4
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CC (pgCC) 7.1-4
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FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305
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(duty) g++ 3.4.6 [FreeBSD] 20060305
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gcc 4.3.4 20090419
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g++ 4.3.4 20090419
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gfortran 4.3.4 20090419
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FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
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(liberty) g++ 3.4.6 [FreeBSD] 20060305
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gcc 4.4.1 20090421
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g++ 4.4.1 20090421
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gfortran 4.4.1 20090421
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IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m
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F90 MIPSpro 7.4.4m
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C++ MIPSpro cc 7.4.4m
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Linux 2.6.18-128.1.6.el5xen gcc (GCC) 4.1.2
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#1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009)
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(jam) PGI C, Fortran, C++ 7.2-1 32-bit
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PGI C, Fortran, C++ 8.0-1 32-bit
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Intel(R) C Compiler for 32-bit
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applications, Versions 10.1, 11.0
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Intel(R) C++ Compiler for 32-bit
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applications, Version 10.1, 11.0
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Intel(R) Fortran Compiler for 32-bit
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applications, Version 10.1, 11.0
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Absoft 32-bit Fortran 95 10.0.7
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MPICH mpich2-1.0.8 compiled with
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gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!)
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Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6
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SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009)
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(kagiso) MPICH mpich2-1.0.8 compiled with
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gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!)
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Linux 2.6.16.60-0.37-smp #1 gcc 4.1.2
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SMP x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009)
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(smirom) Intel(R) C, C++, Fortran Compilers for
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applications running on Intel(R) 64,
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Versions 10.1, 11.0.
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PGI C, Fortran, C++ Version 7.2-1, 8.0-1
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for 64-bit target on x86-64
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gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!)
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MPICH mpich2-1.0.8 compiled with
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gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!)
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tested for both 32- and 64-bit binaries
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Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 10.1.017
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SGI Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017
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(cobalt) SGI MPI 1.38
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SunOS 5.10 32- and 64-bit Sun WorkShop 6 update 2 C 5.9 Patch 124867-09
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(linew) Sun WorkShop 6 update 2 Fortran 95 8.3
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Patch 127000-07
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Sun WorkShop 6 update 2 C++ 5.8
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Patch 124863-11
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Intel Xeon Linux 2.6.18- gcc 3.4.6 20060404
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92.1.10.el5_lustre.1.6.6smp- Intel(R) C++ Version 10.0.026
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perfctr #2 SMP Intel(R) Fortran Compiler Version 10.0.026
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(abe) Open MPI 1.2.2
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MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2
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compiled with icc v10.0.026 and ifort 10.0.026
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IA-64 Linux 2.4.21-309.tg1 gcc (GCC) 3.2.2
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#1 SMP ia64 Intel(R) C++ Version 8.1.037
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(NCSA tg-login) Intel(R) Fortran Compiler Version 8.1.033
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mpich-gm-1.2.7p1..16-intel-8.1.037-r1
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Linux 2.6.9-55.0.9.EL_lustre Intel(R) C, C++, Fortran Compilers for
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.1.4.11.1smp #1 SMP applications running on Intel(R) 64,
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SMP x86_64 GNU/Linux Versions 9.1.
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(SNL Spirit)
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Linux 2.6.9-55.0.9.EL_lustre Intel(R) C, C++, Fortran Compilers for
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.1.4.11.1smp #1 SMP applications running on Intel(R) 64,
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SMP x86_64 GNU/Linux Versions 10.1.
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(SNL Thunderbird)
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Linux 2.6.18-63chaos #1 SMP Intel(R) C, C++, Fortran Compilers for
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SMP x86_64 GNU/Linux applications running on Intel(R) 64,
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(SNL Glory) Versions 10.1.
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Linux 2.6.18-63chaos #1 SMP Intel(R) C, C++, Fortran Compilers for
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SMP x86_64 GNU/Linux applications running on Intel(R) 64,
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(LLNL Zeus) Versions 9.1.
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gcc/gfortran/g++ (GCC) 4.1.2.
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Windows XP Visual Studio .NET
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Visual Studio 2005 w/ Intel Fortran 9.1
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Cygwin(native gcc compiler and g95)
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Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1
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Windows Vista Visual Studio 2005
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MAC OS 10.5.6 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1
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GNU Fortran (GCC) 4.3.0 20070810
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G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008)
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Intel C, C++ and Fortran compilers 10.1
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Supported Configuration Features Summary
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========================================
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In the tables below
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y = tested and supported
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n = not supported or not tested in this release
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C = Cluster
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W = Workstation
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x = not working in this release
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dna = does not apply
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( ) = footnote appears below second table
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<blank> = testing incomplete on this feature or platform
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Platform C F90 F90 C++ zlib SZIP
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parallel parallel
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Solaris2.10 32-bit n y n y y y
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Solaris2.10 64-bit n y n y y y
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IRIX64_6.5 32-bit n n n n y y
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IRIX64_6.5 64-bit n y y y y y
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Windows XP n y(4) n(4) y y y
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Windows XP x64 n y(4) n(4) y y y
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Windows Vista n n n y y y
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Mac OS X 10.5 Intel n y n y y y
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AIX 5.3 32- and 64-bit n y n y y n
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FreeBSD 6.3-STABLE 32&64 bit n y n y y y
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RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y y y
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RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y y y
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RedHat EL5 2.6.18-128 i686 Intel W n y n y y n
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RedHat EL5 2.6.18-128 i686 PGI W n y n y y n
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SuSe Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y
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SuSe Linux 2.6.16 x86_64 Intel W n y n y y n
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SuSe Linux 2.6.16 x86_64 PGI W n y n y y y
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SuSe Linux 2.6.16 SGI Altix ia64 C y y y y y y
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RedHat EL4 2.6.18 Xeon Lustre C y y y y y n
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SuSe Linux 2.4.21 ia64 Intel C y y y y y n
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Cray XT3 2.0.41 y y y y y n
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Platform Shared Shared Shared Thread-
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C libs F90 libs C++ libs safe
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Solaris2.10 32-bit y y y y
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Solaris2.10 64-bit y y y y
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IRIX64_6.5 32-bit y dna y y
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IRIX64_6.5 64-bit y y n y
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Windows XP y y(4) y y
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Windows XP x64 y y(4) y y
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Windows Vista y n n y
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Mac OS X 10.5 y n y n
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AIX 5.3 32- and 64-bit n n n n
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FreeBSD 6.3-STABLE 32&64 bit y n y y
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RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y
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RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y
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RedHat EL5 2.6.18-128 i686 Intel W y y y n
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RedHat EL5 2.6.18-128 i686 PGI W y y y n
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SuSe Linux 2.6.16 x86_64 GNU (1) W y y y y
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SuSe Linux 2.6.16 x86_64 Intel W y y y n
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SuSe Linux 2.6.16 x86_64 PGI W y y y n
|
|
SuSe Linux 2.6.16 SGI Altix ia64 C y n
|
|
RedHat EL4 2.6.18 Xeon Lustre C y y y n
|
|
SuSe Linux 2.4.21 ia64 Intel C y y y n
|
|
Cray XT3 2.0.41 n n n n
|
|
|
|
(1) Fortran compiled with g95.
|
|
(2) With PGI and Absoft compilers.
|
|
(3) With PGI compiler for Fortran.
|
|
(4) Using Visual Studio 2005 or Cygwin
|
|
Compiler versions for each platform are listed in the preceding
|
|
"Platforms Tested" table.
|
|
|
|
|
|
Known Problems
|
|
==============
|
|
* Parallel tests failed with 16 processes with data inconsistency at testphdf5
|
|
/ dataset_readAll. Parallel tests also failed with 32 and 64 processes with
|
|
collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
|
|
with MPI IO. CMC - 2009/04/28
|
|
|
|
* There is a known issue in which HDF5 will change the timestamp on a file
|
|
simply by opening it with read/write permissions, even if the file is not
|
|
modified in any way. This is due to the way in which HDF5 manages the file
|
|
superblock. A fix is currently underway and should be included in the 1.8.4
|
|
release of HDF5. MAM - 2009/04/28
|
|
|
|
* For gcc v4.3 and v4.4, with production mode, if -O3 is used, H5Tinit.c
|
|
would fail to compile. Actually bad H5Tinit.c is produced. If -O (same
|
|
as -O1) is used, H5Tinit.c compiled okay but test/dt_arith would fail.
|
|
When -O0 (no optimizatio) is used, H5Tinit.c compilete okay and all
|
|
tests passed. Therefore, -O0 is imposed for v4.3 and v4.4 of gcc.
|
|
AKC - 2009/04/20
|
|
|
|
* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and
|
|
tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests
|
|
are expected to fail and should exit with a non-zero code but the yod
|
|
command does not propagate the exit code of the executables. Yod always
|
|
returns 0 if it can launch the executable. The test suite shell expects
|
|
a non-zero for this particular test, therefore it concludes the test has
|
|
failed when it receives 0 from yod. Skip all the "failing" test for now
|
|
by changing them as following.
|
|
|
|
======== Original tools/h5ls/testh5ls.sh =========
|
|
TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
|
|
======== Change to ===============================
|
|
echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
|
|
==================================================
|
|
|
|
======== Original tools/h5copy/testh5copy.sh =========
|
|
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
|
|
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
|
|
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
|
|
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
|
|
H5LSTEST $FILEOUT
|
|
======== Change to ===============================
|
|
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
|
|
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
|
|
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
|
|
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
|
|
echo SKIP H5LSTEST $FILEOUT
|
|
==================================================
|
|
AKC - 2008/11/10
|
|
|
|
* For Red Storm, a Cray XT3 system, the yod command sometimes gives the
|
|
message, "yod allocation delayed for node recovery". This interferes with
|
|
test suites that do not expect seeing this message. See the section of "Red
|
|
Storm" in file INSTALL_parallel for a way to deal with this problem.
|
|
AKC - 2008/05/28
|
|
|
|
* We have discovered two problems when running collective IO parallel HDF5
|
|
tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a
|
|
Linux cluster at NCSA.
|
|
|
|
Under some complex selection cases:
|
|
1) MPI_Get_element returns the wrong value.
|
|
2) MPI_Type_struct also generates the wrong derived datatype and corrupt
|
|
data may be generated.
|
|
These issues arise only when turning on collective IO with chunking storage
|
|
with some complex selections. We have not found these problems on other
|
|
MPI-IO compilers. If you encounter these problems, you may use independent
|
|
IO instead.
|
|
|
|
To avoid this behavior, change the following line in your code
|
|
H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
|
|
to
|
|
H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT);
|
|
KY - 2007/08/24
|
|
|
|
* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
|
|
use -mp -O1 compilation flags to build the libraries. A higher level of
|
|
optimization causes failures in several HDF5 library tests.
|
|
|
|
* For LLNL, uP: both serial and parallel tests pass.
|
|
Zeus: Serial tests pass but parallel tests fail with a known problem in MPI.
|
|
ubgl: Serial tests pass but parallel tests fail.
|
|
|
|
* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and
|
|
the application asks to do collective IO, we have found that when using 4
|
|
processors, a simple collective write will sometimes be hung. This can be
|
|
verified with t_mpi test under testpar.
|
|
|
|
* On IRIX6.5, when the C compiler version is greater than 7.4, complicated
|
|
MPI derived datatype code will work. However, the user should increase
|
|
the value of the MPI_TYPE_MAX environment variable to some appropriate value
|
|
to use collective irregular selection code. For example, the current
|
|
parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test.
|
|
|
|
* A dataset created or rewritten with a v1.6.3 library or after cannot be read
|
|
with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
|
|
There was a bug in the calculation of the Fletcher32 checksum in the
|
|
library before v1.6.3; the checksum value was not consistent between big-
|
|
endian and little-endian systems. This bug was fixed in Release 1.6.3.
|
|
However, after fixing the bug, the checksum value was no longer the same as
|
|
before on little-endian system. Library releases after 1.6.4 can still read
|
|
datasets created or rewritten with an HDF5 library of v1.6.2 or before.
|
|
SLU - 2005/6/30
|
|
|
|
* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
|
|
messages like "INFO: 0031-XXX ...". This is from the command `poe'.
|
|
Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
|
|
and run the tests again.
|
|
|
|
The tests may fail with messages like "The socket name is already in use",
|
|
but HDF5 does not use sockets. This failure is due to problems with the
|
|
poe command trying to set up the debug socket. To resolve this problem,
|
|
check to see whether there are many old /tmp/s.pedb.* files staying around.
|
|
These are sockets used by the poe command and left behind due to failed
|
|
commands. First, ask your system administrator to clean them out.
|
|
Lastly, request IBM to provide a means to run poe without the debug socket.
|
|
|
|
* 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 IBM SP2 platforms for serial mode. The parallel mode works fine with
|
|
this option.
|
|
|
|
It is suggested that you do not use this option on these platforms
|
|
during configuration.
|
|
|
|
* There is also a configure error on Altix machines that incorrectly reports
|
|
when a version of Szip without an encoder is being used.
|
|
|
|
* Information about building with PGI and Intel compilers is available in
|
|
the INSTALL file sections 4.7 and 4.8.
|
|
|
|
|
|
%%%%1.8.2%%%%
|
|
|
|
|
|
HDF5 version 1.8.2 released on Mon Nov 10 15:43:09 CST 2008
|
|
================================================================================
|
|
|
|
INTRODUCTION
|
|
============
|
|
|
|
This document describes the differences between HDF5-1.8.1 and HDF5 1.8.2,
|
|
and contains information on the platforms tested and known problems in
|
|
HDF5-1.8.2. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
|
|
and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
|
|
|
|
Links to the HDF5 1.8.2 source code, documentation, and additional materials
|
|
can be found on the HDF5 web page at:
|
|
|
|
http://www.hdfgroup.org/products/hdf5/
|
|
|
|
The HDF5 1.8.2 release can be obtained from:
|
|
|
|
http://www.hdfgroup.org/HDF5/release/obtain5.html
|
|
|
|
User documentation for 1.8.2 can be accessed directly at this location:
|
|
|
|
http://www.hdfgroup.org/HDF5/doc/
|
|
|
|
New features in the HDF5-1.8.x release series, including brief general
|
|
descriptions of some new and modified APIs, are described in the "What's New
|
|
in 1.8.0?" document:
|
|
|
|
http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
|
|
|
|
All new and modified APIs are listed in detail in the "HDF5 Software Changes
|
|
from Release to Release" document, in the section "Release 1.8.2 (current
|
|
release) versus Release 1.8.1":
|
|
|
|
http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
|
|
|
|
If you have any questions or comments, please send them to the HDF Help Desk:
|
|
|
|
help@hdfgroup.org
|
|
|
|
|
|
CONTENTS
|
|
========
|
|
|
|
- New Features
|
|
- Support for new platforms and languages
|
|
- Bug Fixes since HDF5-1.8.1
|
|
- Platforms Tested
|
|
- Supported Configuration Features Summary
|
|
- Known Problems
|
|
|
|
|
|
New Features
|
|
============
|
|
|
|
Configuration
|
|
-------------
|
|
- Upgraded libtool to version 2.2.6a. (MAM - 2008/10/15).
|
|
|
|
Library
|
|
-------
|
|
- Added two new public routines: H5Pget_elink_fapl() and
|
|
H5Pset_elink_fapl(). (see bug #1247) (VC - 2008/10/13)
|
|
- Improved free space tracking in file to be faster. (QAK - 2008/10/06)
|
|
- Added 'mounted' field to H5G_info_t struct. (QAK - 2008/07/15)
|
|
|
|
Parallel Library
|
|
----------------
|
|
- None
|
|
|
|
Tools
|
|
-----
|
|
- h5repack: added new options -u and -b to add a userblock to an HDF5
|
|
file during the repack. (PVN - 2008/08/26)
|
|
- h5repack: added options -t and -a to call H5Pset_alignment while
|
|
creating a repacked file. (PVN - 2008/08/29)
|
|
- h5ls: added capability to traverse through external links when the -r
|
|
(recursive) flag is given. (NAF - 2008/09/16)
|
|
- h5ls: added -E option to enable traversal of external links.
|
|
h5ls will not traverse external links without this flag being set.
|
|
(NAF - 2008/10/06)
|
|
- h5dump: when -b flag is used without a keyword after it, binary
|
|
output defaults to NATIVE. MEMORY keyword was deprecated
|
|
and replaced by NATIVE keyword. (PVN - 2008/10/30)
|
|
- h5diff: returns 1 when file graphs differ by any object.
|
|
Error return code was changed to 2 from -1. (PVN - 2008/10/30)
|
|
- h5import: TEXTFPE (scientific format) was deprecated. Use TEXTFP
|
|
instead (PVN - 2008/10/30)
|
|
|
|
|
|
|
|
F90 API
|
|
------
|
|
- Added optional parameter 'mounted' to H5Gget_info_f,
|
|
H5Gget_info_by_idx_f, H5Gget_info_by_name_f (MSB - 2008/09/24)
|
|
- Added H5Tget_native_type_f (MSB - 2008/09/30)
|
|
|
|
|
|
C++ API
|
|
------
|
|
- These member functions were added as wrapper for H5Rdereference to
|
|
replace the incorrect IdComponent::dereference().
|
|
void H5Object::dereference(H5Object& obj, void* ref,
|
|
H5R_type_t ref_type=H5R_OBJECT)
|
|
void H5Object::dereference(H5File& h5file, void* ref,
|
|
H5R_type_t ref_type=H5R_OBJECT)
|
|
void H5Object::dereference(Attribute& obj, void* ref,
|
|
H5R_type_t ref_type=H5R_OBJECT)
|
|
|
|
In addition, these constructors were added to create the associated
|
|
objects by way of dereference:
|
|
DataSet(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
|
|
DataSet(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT)
|
|
DataSet(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT)
|
|
Group(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
|
|
Group(H5File& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
|
|
Group(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT)
|
|
DataType(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
|
|
DataType(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT)
|
|
DataType(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT)
|
|
(BMR - 2008/10/29)
|
|
|
|
|
|
Support for New Platforms, Languages, and Compilers
|
|
===================================================
|
|
- Intel 10.1 is supported on Mac OS X 10.5.4.
|
|
Note:
|
|
When Fortran is enabled, configure automatically
|
|
disables the build of shared libraries (i.e., only
|
|
static C and C++ HDF5 libraries will be built
|
|
along with the static HDF5 Fortran library).
|
|
Intel 10.1 C and C++ compilers require
|
|
"-no-multibyte-chars" compilation flag due to the known
|
|
bug in the compilers.
|
|
(EIP - 2008/10/30)
|
|
|
|
|
|
Bug Fixes since HDF5-1.8.1
|
|
==========================
|
|
|
|
Configuration
|
|
-------------
|
|
- Fixed error with 'make check install' failing due to h5dump
|
|
needing other tools built first. (MAM - 2008/10/15).
|
|
- When using shared szip, it is no longer necessary to specify
|
|
the path to the shared szip libraries in LD_LIBRARY_PATH.
|
|
(MAM - 2008/10/15).
|
|
- The file libhdf5_fortran.settings is not installed since its content
|
|
is included in libhdf5.settings now. (AKC - 2008/10/21)
|
|
- "make DESTDIR=xxx install" failed to install some tools and files
|
|
(e.g., h5cc and fortran modules). Fixed. (AKC - 2008/10/8).
|
|
|
|
Library
|
|
-------
|
|
- H5Ovisit and H5Ovisit_by_name will now properly terminate when the
|
|
callback function returns a positive value on the starting object.
|
|
(NAF - 2008/11/03)
|
|
- Fixed an error where a null message could be created that was larger
|
|
than could be written to the file. (NAF - 2008/10/23)
|
|
- Corrected error with family/split/multi VFD not updating driver info
|
|
when "latest" version of the file format used. (QAK - 2008/10/14)
|
|
- Corrected alignment+threshold errors to work correctly when metadata
|
|
aggregation is enabled. (QAK - 2008/10/06)
|
|
- Changed H5Fget_obj_count and H5Fget_obj_ids to ignore objects
|
|
registered by the library for internal library use.
|
|
(NAF - 2008/10/06)
|
|
- Fixed potential memory leak during compound conversion.
|
|
(NAF - 2008/10/06)
|
|
- Changed the return value of H5Fget_obj_count from INT to SSIZE_T.
|
|
Also changed the return value of H5Fget_obj_ids from HERR_T to
|
|
SSIZE_T and the type of the parameter MAX_OBJS from INT to SIZE_T.
|
|
(SLU - 2008/09/26)
|
|
- Fixed an issue that could cause data to be improperly overwritten
|
|
during compound type conversion. (NAF - 2008/09/19)
|
|
- Fixed pointer alignment violations that could occur during vlen
|
|
conversion. (NAF - 2008/09/16)
|
|
- Fixed problem where library could cause a segmentation fault when
|
|
an invalid location ID was given to H5Giterate(). (QAK - 2008/08/19)
|
|
- Fixed improper shutdown when objects have reference count > 1. The
|
|
library now tracks reference count due to the application separately
|
|
from that due to internal library routines. (NAF - 2008/08/19)
|
|
- Fixed assertion failure caused by incorrect array datatype version.
|
|
(NAF - 2008/08/08)
|
|
- Fixed an issue where mount point traversal would fail when using
|
|
multiple handles for the child. (NAF - 2008/08/07)
|
|
- Fixed an issue where mount points were inaccessible when using
|
|
multiple file handles for the parent. The mount table is now in
|
|
the shared file structure (the parent pointer is still in the
|
|
top structure). (NAF - 2008/08/07)
|
|
- Fixed assertion failure caused by incorrect array datatype version.
|
|
(NAF - 2008/08/04)
|
|
- Fixed issue where a group could have a file mounted on it twice.
|
|
(QAK - 2008/07/15)
|
|
- When an attribute was opened twice and data was written with
|
|
one of the handles, the file didn't have the data. It happened
|
|
because each handle had its own object structure, and the empty
|
|
one overwrote the data with fill value. This is fixed by making
|
|
some attribute information like the data be shared in the
|
|
attribute structure. (SLU - 2008/07/07)
|
|
- Fixed a Windows-specific issue in the ohdr test which was causing
|
|
users in some timezones to get false errors. This a deficiency in
|
|
the Windows mktime() function, and has been handled properly.
|
|
(SJW - 2008/06/19)
|
|
|
|
Parallel Library
|
|
----------------
|
|
- None
|
|
|
|
Tools
|
|
-----
|
|
- h5dump now checks for uniqueness of committed datatypes.
|
|
(NAF - 2008/10/15)
|
|
- Fixed unnecessary indentation of committed datatypes in h5dump.
|
|
(NAF - 2008/10/15)
|
|
- Fixed bugs in h5stat: segmemtation fault when printing groups and
|
|
print warning message when traversal of objects is unsuccessful.
|
|
(see bug #1253) (VC- 2008/10/13)
|
|
- Fixed bug in h5ls that prevented relative group listings (like
|
|
"h5ls foo.h5/bar") from working correctly (QAK - 2008/06/03)
|
|
- h5dump: when doing binary output (-b), the stdout printing of
|
|
attributes was done incorrectly. Removed printing of attributes
|
|
when doing binary output. (PVN - 2008/06/05)
|
|
|
|
|
|
F90 API
|
|
------
|
|
- h5sselect_elements_f: Added additional operators H5S_SELECT_APPEND
|
|
and H5S_SELECT_PREPEND (MSB - 2008/09/30)
|
|
- h5sget_select_elem_pointlist: Fixed list of returned points by
|
|
rearranging the point list correctly by accounting for C
|
|
conventions. (MSB - 2008/09/30)
|
|
- h5sget_select_hyper_blocklist_f: Fixed error in transposed dimension
|
|
of arrays.(MSB - 2008/9/30)
|
|
- h5sget_select_bounds_f: Swapped array bounds to account for C and
|
|
Fortran reversed array notation (MSB - 2008/9/30)
|
|
- Changed to initializing string to a blank character instead of a
|
|
null type in tH5P.f90 to fix compiling error using AIX 5.3.0
|
|
(MSB - 2008/7/29)
|
|
- Fixed missing commas in H5test_kind.f90 detected by NAG compiler
|
|
(MSB - 2008/7/29)
|
|
- Fixed passing and array to a scalar in tH5A_1_8.f90 detected by
|
|
NAG compiler (MSB - 2008/7/29)
|
|
- Added the ability of the test programs to use the status of
|
|
HDF5_NOCLEANUP to determine if the *.h5 files should be removed
|
|
or not after the tests are completed (MSB - 2008/10/1)
|
|
- In nh5tget_offset_c: (MSB 9/12/2008)
|
|
If offset was equal to 0 it returned the error code of -1,
|
|
this was changed to return an error code of -1 when the offset
|
|
value is < 0.
|
|
- Uses intrinsic Fortran function SIZEOF if available when detecting
|
|
type of INTEGERs and REALs in H5test_kind.f90 (MSB - 2008/9/3)
|
|
- Put the DOUBLE PRECISION interfaces in a separate module and
|
|
added a USE statement for the module. The interfaces are
|
|
included/excluded depending on the state of FORTRAN_DEFAULT_REAL
|
|
is DBLE_F which detects if the default REAL is DOUBLE PRECISION.
|
|
This allows the library to be compiled with -r8 Fortran flag
|
|
without the user needing to edit the source code.
|
|
(MSB - 200/8/27)
|
|
- Enable building shared library for fortran by adding the flag -fPIC
|
|
to the compile flags for versions of Intel Fortran compiler >=9
|
|
(MSB - 2008/8/26)
|
|
|
|
C++ API
|
|
------
|
|
- Fixed a design bug which allowed an Attribute object to create/modify
|
|
attributes (bugzilla #1068). The API class hierarchy was revised
|
|
to address the problem. Classes AbstractDS and Attribute are moved
|
|
out of H5Object. Class Attribute now multiply inherits from
|
|
IdComponent and AbstractDs and class DataSet from H5Object and
|
|
AbstractDs. In addition, the data member IdComponent::id was
|
|
moved into subclasses: Attribute, DataSet, DataSpace, DataType,
|
|
H5File, Group, and PropList. (BMR - 2008/05/20)
|
|
- IdComponent::dereference was incorrect and replaced as described
|
|
in "New Features" section.
|
|
(BMR - 2008/10/29)
|
|
|
|
|
|
Platforms Tested
|
|
================
|
|
The following platforms and compilers have been tested for this release.
|
|
|
|
AIX 5.3 xlc 7.0.0.8
|
|
xlf 09.01.0000.0008
|
|
xlC 7.0.0.8
|
|
mpcc_r 7.0.0.8
|
|
mpxlf_r 09.01.0000.0008
|
|
|
|
Cray XT3 (2.0.41) cc (pgcc) 7.1-4
|
|
(red storm) ftn (pgf90) 7.1-4
|
|
CC (pgCC) 7.1-4
|
|
|
|
FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305
|
|
(duty) g++ 3.4.6 [FreeBSD] 20060305
|
|
gcc 4.2.5 20080702
|
|
g++ 4.2.5 20080702
|
|
gfortran 4.2.5 20080702
|
|
|
|
FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
|
|
(liberty) g++ 3.4.6 [FreeBSD] 20060305
|
|
gcc 4.2.5 20080702
|
|
g++ 4.2.5 20080702
|
|
gfortran 4.2.5 20080702
|
|
|
|
IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m
|
|
F90 MIPSpro 7.4.4m
|
|
C++ MIPSpro cc 7.4.4m
|
|
|
|
Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6
|
|
SMP i686 i386 G95 (GCC 4.0.3 (g95 0.92!) April 18 2007)
|
|
(kagiso) PGI C, Fortran, C++ 7.2-1 32-bit
|
|
Intel(R) C Compiler for 32-bit
|
|
applications, Version 10.1
|
|
Intel(R) C++ Compiler for 32-bit
|
|
applications, Version 10.1
|
|
Intel(R) Fortran Compiler for 32-bit
|
|
applications, Version 10.1
|
|
Absoft 32-bit Fortran 95 10.0.4
|
|
MPICH mpich-1.2.7 compiled with
|
|
gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!)
|
|
MPICH mpich2-1.0.6p1 compiled with
|
|
gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!)
|
|
|
|
Linux 2.6.16.46-0.14-smp #1 Intel(R) C++ for Intel(R) EM64T
|
|
SMP x86_64 GNU/Linux Ver. 10.1.013
|
|
(smirom) Intel(R) Fortran Intel(R) EM64T
|
|
Ver. 10.1.013
|
|
PGI C, Fortran, C++ Version 7.2-1
|
|
for 64-bit target on x86-64
|
|
MPICH mpich-1.2.7 compiled with
|
|
gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!)
|
|
MPICH mpich2-1.0.7 compiled with
|
|
gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!)
|
|
tested for both 32- and 64-bit binaries
|
|
|
|
Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 10.1.017
|
|
Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017
|
|
(cobalt) SGI MPI 1.16
|
|
|
|
SunOS 5.10 32- and 64-bit Sun WorkShop 6 update 2 C 5.8
|
|
(linew) Sun WorkShop 6 update 2 Fortran 95 8.2
|
|
Sun WorkShop 6 update 2 C++ 5.8
|
|
Patch 121019-06
|
|
|
|
Xeon Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp
|
|
(abe) Intel(R) C++ Version 10.0.026
|
|
Intel(R) Fortran Compiler Version 10.0.026
|
|
Open MPI 1.2.2
|
|
MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2
|
|
compiled with icc v10.0.026 and
|
|
ifort 10.0.026
|
|
|
|
IA-64 Linux 2.4.21-309.tg1 #1 SMP
|
|
ia64 gcc (GCC) 3.2.2
|
|
(NCSA tg-login) Intel(R) C++ Version 8.1.037
|
|
Intel(R) Fortran Compiler Version 8.1.033
|
|
mpich-gm-1.2.7p1..16-intel-8.1.037-r1
|
|
|
|
Intel 64 Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp
|
|
(abe) gcc 3.4.6 20060404
|
|
Intel(R) C++ Version 10.0
|
|
Intel (R) Fortran Compiler Version 10.0
|
|
mvapich2-0.9.8p2patched-intel-ofed-1.2
|
|
|
|
Windows XP Visual Studio .NET
|
|
Visual Studio 2005 w/ Intel Fortran 9.1
|
|
Cygwin(native gcc compiler and g95)
|
|
|
|
Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1
|
|
|
|
Windows Vista Visual Studio 2005
|
|
|
|
MAC OS 10.5.4 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1
|
|
GNU Fortran (GCC) 4.3.0 20070810
|
|
G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008)
|
|
Intel C, C++ and Fortran compilers 10.1
|
|
|
|
|
|
Supported Configuration Features Summary
|
|
========================================
|
|
|
|
In the tables below
|
|
y = tested and supported
|
|
n = not supported or not tested in this release
|
|
x = not working in this release
|
|
dna = does not apply
|
|
( ) = footnote appears below second table
|
|
<blank> = testing incomplete on this feature or platform
|
|
|
|
Platform C F90 F90 C++ zlib SZIP
|
|
parallel parallel
|
|
Solaris2.10 32-bit n y n y y y
|
|
Solaris2.10 64-bit n y n y y y
|
|
IRIX64_6.5 32-bit n n n n y y
|
|
IRIX64_6.5 64-bit n y y y y y
|
|
Windows XP n y(15) n(15) y y y
|
|
Windows XP x64 n y(15) n(15) y y y
|
|
Windows Vista n n n y y y
|
|
Mac OS X 10.5 Intel n y n y y y
|
|
AIX 5.3 32- and 64-bit n y n y y n
|
|
FreeBSD 6.3-STABLE
|
|
32&64 bit n y n y y y
|
|
RedHat EL4 (3) W y(1) y(10) y(1) y y y
|
|
RedHat EL4 Intel (3) W n y n y y n
|
|
RedHat EL4 PGI (3) W n y n y y n
|
|
SuSe x86_64 gcc(3,12) W y(2) y(11) y(2) y y y
|
|
SuSe x86_64 Int(3,12) W n y(13) n y y n
|
|
SuSe x86_64 PGI(3,12) W n y(8) n y y y
|
|
Linux 2.6 SuSE ia64 C
|
|
Intel (3,7) y y y y y n
|
|
Linux 2.6 SGI Altix
|
|
ia64 Intel (3) y y y y y y
|
|
Linux 2.6 RHEL C
|
|
Lustre Intel (5) y(4) y y(4) y y n
|
|
Cray XT3 2.0.41 y y y y y n
|
|
|
|
|
|
Platform Shared Shared Shared Thread-
|
|
C libs F90 libs C++ libs safe
|
|
Solaris2.10 32-bit y y y y
|
|
Solaris2.10 64-bit y y y y
|
|
IRIX64_6.5 32-bit y dna y y
|
|
IRIX64_6.5 64-bit y y n y
|
|
Windows XP y y(15) y y
|
|
Windows XP x64 y y(15) y y
|
|
Windows Vista y n n y
|
|
Mac OS X 10.5 y n y n
|
|
AIX 5.3 32- and 64-bit n n n n
|
|
FreeBSD 6.2 32&64 bit y n y y
|
|
RedHat EL4 (3) W y y(10) y y
|
|
RedHat EL4 Intel (3) W y y y n
|
|
RedHat EL4 PGI (3) W y y y n
|
|
SuSe x86_64 GNU(3,12) W y y y y
|
|
SuSe x86_64 Int(3,12) W y y y n
|
|
SuSe x86_64 PGI(3,12) W y y y n
|
|
Linux 2.4 SuSE C
|
|
ia64 C Intel (7) y y y n
|
|
Linux 2.4 SGI Altix C
|
|
ia64 Intel y n
|
|
Linux 2.6 RHEL C
|
|
Lustre Intel (5) y y y n
|
|
Cray XT3 2.0.41 n n n n
|
|
|
|
Notes: (1) Using mpich2 1.0.6.
|
|
(2) Using mpich2 1.0.7.
|
|
(3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated.
|
|
W or C indicates workstation or cluster, respectively.
|
|
(4) Using mvapich2 0.9.8.
|
|
(5) Linux 2.6.9-42.0.10. Xeon cluster with ELsmp_perfctr_lustre
|
|
and Intel compilers
|
|
(6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre
|
|
and Intel compilers
|
|
(7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel compilers
|
|
(8) pgf90
|
|
(9) With Compaq Visual Fortran 6.6c compiler.
|
|
(10) With PGI and Absoft compilers.
|
|
(11) PGI and Intel compilers for both C and Fortran
|
|
(12) AMD Opteron x86_64
|
|
(13) ifort
|
|
(14) Yes with C and Fortran, but not with C++
|
|
(15) Using Visual Studio 2005 or Cygwin
|
|
(16) Not tested for this release.
|
|
Compiler versions for each platform are listed in the preceding
|
|
"Platforms Tested" table.
|
|
|
|
|
|
Known Problems
|
|
==============
|
|
* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and
|
|
tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests
|
|
are expected to fail and should exit with a non-zero code but the yod
|
|
command does not propagate the exit code of the executables. Yod always
|
|
returns 0 if it can launch the executable. The test suite shell expects
|
|
a non-zero for this particular test, therefore it concludes the test has
|
|
failed when it receives 0 from yod. Skip all the "failing" test for now
|
|
by changing them as following.
|
|
|
|
======== Original tools/h5ls/testh5ls.sh =========
|
|
TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
|
|
======== Change to ===============================
|
|
echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
|
|
==================================================
|
|
|
|
======== Original tools/h5copy/testh5copy.sh =========
|
|
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
|
|
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
|
|
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
|
|
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
|
|
H5LSTEST $FILEOUT
|
|
======== Change to ===============================
|
|
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
|
|
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
|
|
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
|
|
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
|
|
echo SKIP H5LSTEST $FILEOUT
|
|
==================================================
|
|
AKC - 2008/11/10
|
|
|
|
* For Red Storm, a Cray XT3 system, the yod command sometimes gives the
|
|
message, "yod allocation delayed for node recovery". This interferes with
|
|
test suites that do not expect seeing this message. See the section of "Red
|
|
Storm" in file INSTALL_parallel for a way to deal with this problem.
|
|
AKC - 2008/05/28
|
|
|
|
* We have discovered two problems when running collective IO parallel HDF5
|
|
tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a
|
|
Linux cluster at NCSA.
|
|
|
|
Under some complex selection cases:
|
|
1) MPI_Get_element returns the wrong value.
|
|
2) MPI_Type_struct also generates the wrong derived datatype and corrupt
|
|
data may be generated.
|
|
These issues arise only when turning on collective IO with chunking storage
|
|
with some complex selections. We have not found these problems on other
|
|
MPI-IO compilers. If you encounter these problems, you may use independent
|
|
IO instead.
|
|
|
|
To avoid this behavior, change the following line in your code
|
|
H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
|
|
to
|
|
H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT);
|
|
|
|
KY - 2007/08/24
|
|
|
|
* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
|
|
use -mp -O1 compilation flags to build the libraries. A higher level of
|
|
optimization causes failures in several HDF5 library tests.
|
|
|
|
* For LLNL, uP: both serial and parallel tests pass.
|
|
Zeus: Serial tests pass but parallel tests fail with a known problem in MPI.
|
|
ubgl: Serial tests pass but parallel tests fail.
|
|
|
|
* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and
|
|
the application asks to do collective IO, we have found that when using 4
|
|
processors, a simple collective write will sometimes be hung. This can be
|
|
verified with t_mpi test under testpar.
|
|
|
|
* On IRIX6.5, when the C compiler version is greater than 7.4, complicated
|
|
MPI derived datatype code will work. However, the user should increase
|
|
the value of the MPI_TYPE_MAX environment variable to some appropriate value
|
|
to use collective irregular selection code. For example, the current
|
|
parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test.
|
|
|
|
* A dataset created or rewritten with a v1.6.3 library or after cannot be read
|
|
with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
|
|
There was a bug in the calculation of the Fletcher32 checksum in the
|
|
library before v1.6.3; the checksum value was not consistent between big-
|
|
endian and little-endian systems. This bug was fixed in Release 1.6.3.
|
|
However, after fixing the bug, the checksum value was no longer the same as
|
|
before on little-endian system. Library releases after 1.6.4 can still read
|
|
datasets created or rewritten with an HDF5 library of v1.6.2 or before.
|
|
SLU - 2005/6/30
|
|
|
|
* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
|
|
messages like "INFO: 0031-XXX ...". This is from the command `poe'.
|
|
Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
|
|
and run the tests again.
|
|
|
|
The tests may fail with messages like "The socket name is already in use",
|
|
but HDF5 does not use sockets. This failure is due to problems with the
|
|
poe command trying to set up the debug socket. To resolve this problem,
|
|
check to see whether there are many old /tmp/s.pedb.* files staying around.
|
|
These are sockets used by the poe command and left behind due to failed
|
|
commands. First, ask your system administrator to clean them out.
|
|
Lastly, request IBM to provide a means to run poe without the debug socket.
|
|
|
|
* 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 IBM SP2 platforms for serial mode. The parallel mode works fine with
|
|
this option.
|
|
|
|
It is suggested that you do not use this option on these platforms
|
|
during configuration.
|
|
|
|
* There is also a configure error on Altix machines that incorrectly reports
|
|
when a version of Szip without an encoder is being used.
|
|
|
|
* Information about building with PGI and Intel compilers is available in
|
|
the INSTALL file sections 4.7 and 4.8.
|
|
|
|
|
|
|
|
|
|
%%%%1.8.1%%%%
|
|
|
|
|
|
HDF5 version 1.8.1 released on Thu May 29 15:28:55 CDT 2008
|
|
================================================================================
|
|
|
|
INTRODUCTION
|
|
============
|
|
|
|
This document describes the differences between the HDF5-1.8.1 release
|
|
and HDF5 1.8.0, and contains information on the platforms tested and known
|
|
problems in HDF5-1.8.1. For more details, see the files
|
|
HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory
|
|
of the HDF5 source.
|
|
|
|
Links to the HDF5 1.8.1 source code, documentation, and additional materials
|
|
can be found on the HDF5 web page at:
|
|
|
|
http://www.hdfgroup.org/products/hdf5/
|
|
|
|
The HDF5 1.8.1 release can be obtained from:
|
|
|
|
http://www.hdfgroup.org/HDF5/release/obtain5.html
|
|
|
|
User documentation for 1.8.1 can be accessed directly at this location:
|
|
|
|
http://www.hdfgroup.org/HDF5/doc/
|
|
|
|
New features in the HDF5-1.8.x release series, including brief general
|
|
descriptions of some new and modified APIs, are described in the "What's New
|
|
in 1.8.0?" document:
|
|
|
|
http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
|
|
|
|
All new and modified APIs are listed in detail in the "HDF5 Software Changes
|
|
from Release to Release" document, in the section "Release 1.8.1 (current
|
|
release) versus Release 1.8.0":
|
|
|
|
http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
|
|
|
|
If you have any questions or comments, please send them to the HDF Help Desk:
|
|
|
|
help@hdfgroup.org
|
|
|
|
|
|
CONTENTS
|
|
========
|
|
|
|
- New Features
|
|
- Support for new platforms and languages
|
|
- Bug Fixes since HDF5-1.8.0
|
|
- Platforms Tested
|
|
- Supported Configuration Features Summary
|
|
- Known Problems
|
|
|
|
|
|
New Features
|
|
============
|
|
|
|
Configuration
|
|
-------------
|
|
- The lib/libhdf5.settings file contains much more configure
|
|
information. (AKC - 2008/05/18)
|
|
|
|
- The new configure option "--disable-sharedlib-rpath" disables
|
|
embedding the '-Wl,-rpath' information into executables when
|
|
shared libraries are produced, and instead solely relies on the
|
|
information in LD_LIBRARY_PATH. (MAM - 2008/05/15)
|
|
|
|
- Configuration suite now uses Autoconf 2.61, Automake 1.10.1, and
|
|
Libtool 2.2.2 (MAM - 2008/05/01)
|
|
|
|
Source code distribution
|
|
========================
|
|
|
|
Library
|
|
-------
|
|
- None
|
|
|
|
Parallel Library
|
|
----------------
|
|
- None
|
|
|
|
Tools
|
|
-----
|
|
- h5repack: Reinstated the -i and -o command line flags to specify
|
|
input and output files. h5repack now understands both the old
|
|
syntax (with -i and -o) and the new syntax introduced in Release
|
|
1.8.0. (PVN - 2008/05/23)
|
|
- h5dump: Added support for external links, displaying the object that
|
|
an external link points to. (PVN - 2008/05/12)
|
|
- h5dump: Added an option, -m, to allow user-defined formatting in the
|
|
output of floating point numbers. (PVN - 2008/05/06)
|
|
- h5dump, in output of the -p option: Added effective data compression
|
|
ratio to the dataset storage layout output when a compression filter
|
|
has been applied to a dataset. (PVN - 2008/05/01)
|
|
|
|
F90 API
|
|
------
|
|
New H5A, H5G, H5L, H5O, and H5P APIs to enable 1.8 features were
|
|
added. See "Release 1.8.1 (current release) versus Release 1.8.0" in
|
|
the document "HDF5 Software Changes from Release to Release"
|
|
(http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html) for the
|
|
complete list of the new APIs.
|
|
|
|
C++ API
|
|
------
|
|
- None
|
|
|
|
|
|
Support for New Platforms, Languages, and Compilers
|
|
===================================================
|
|
- Both serial and parallel HDF5 are supported for the Red Storm machine
|
|
which is a Cray XT3 system.
|
|
|
|
- The Fortran library will work correctly if compiled with the -i8
|
|
flag. This has been tested with the g95, PGI and Intel Fortran
|
|
compilers.
|
|
|
|
|
|
Bug Fixes since HDF5-1.8.0
|
|
==========================
|
|
|
|
Configuration
|
|
-------------
|
|
- None
|
|
|
|
Source code distribution
|
|
========================
|
|
|
|
Library
|
|
-------
|
|
- Chunking: Chunks greater than 4GB are disallowed.
|
|
(QAK - 2008/05/16)
|
|
- Fixed the problem with searching for a target file when following
|
|
an external link. The search pattern will depend on whether the
|
|
target file's pathname is an absolute or a relative path.
|
|
Please see the H5Lcreate_external description in the "HDF5
|
|
Reference Manual" (http://hdfgroup.org/HDF5/doc/RM/RM_H5L.html).
|
|
(VC - 2008/04/08)
|
|
- Fixed possible file corruption bug when encoding datatype
|
|
descriptions for compound datatypes whose size was between
|
|
256 and 511 bytes and the file was opened with the "use the
|
|
latest format" property enabled (with H5Pset_libver_bounds).
|
|
(QAK - 2008/03/13)
|
|
- Fixed bug in H5Aget_num_attrs() routine to correctly handle an
|
|
invalid location identifier. (QAK - 2008/03/11)
|
|
|
|
Parallel Library
|
|
----------------
|
|
- None
|
|
|
|
Tools
|
|
-----
|
|
- Fixed bug in h5diff that prevented datasets and attributes with
|
|
variable-length string elements from comparing correctly.
|
|
(QAK - 2008/02/28)
|
|
- Fixed bug in h5dump that caused binary output to be made only for
|
|
the first dataset, when several datasets were requested.
|
|
(PVN - 2008/04/07)
|
|
|
|
F90 API
|
|
------
|
|
- The h5tset(get)_fields subroutines were missing the parameter to
|
|
specify a sign position; fixed. (EIP - 2008/05/23)
|
|
- Many APIs were fixed to work with the 8-byte integers in Fortran vs.
|
|
4-byte integers in C. This change is trasparent to user applications.
|
|
|
|
C++ API
|
|
------
|
|
- The class hierarchy was revised to address the problem reported
|
|
in bugzilla #1068, Attribute should not be derived from base
|
|
class H5Object. Classes AbstractDS was moved out of H5Object.
|
|
Class Attribute now multiply inherits from IdComponent and
|
|
AbstractDs and class DataSet from H5Object and AbstractDs.
|
|
In addition, data member IdComponent::id was moved into subclasses:
|
|
Attribute, DataSet, DataSpace, DataType, H5File, Group, and PropList.
|
|
(BMR - 2008/05/20)
|
|
- IdComponent::dereference was incorrect; it was changed from:
|
|
void IdComponent::dereference(IdComponent& obj, void* ref)
|
|
to:
|
|
void H5Object::dereference(H5File& h5file, void* ref)
|
|
void H5Object::dereference(H5Object& obj, void* ref)
|
|
(BMR - 2008/05/20)
|
|
- Revised Attribute::write and Attribute::read wrappers to handle
|
|
memory allocation/deallocation properly. (bugzilla 1045)
|
|
(BMR - 2008/05/20)
|
|
|
|
|
|
Platforms Tested
|
|
================
|
|
The following platforms and compilers have been tested for this release.
|
|
|
|
Cray XT3 (2.0.41) cc (pgcc) 7.1-4
|
|
(red storm) ftn (pgf90) 7.1-4
|
|
CC (pgCC) 7.1-4
|
|
mpicc 1.0.2
|
|
mpif90 1.0.2
|
|
|
|
FreeBSD 6.2-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305
|
|
(duty) g++ 3.4.6 [FreeBSD] 20060305
|
|
gcc 4.2.1 20080123
|
|
g++ 4.2.1 20080123
|
|
gfortran 4.2.1 20070620
|
|
|
|
FreeBSD 6.2-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
|
|
(liberty) g++ 3.4.6 [FreeBSD] 20060305
|
|
gcc 4.2.1 20080123
|
|
g++ 4.2.1 20080123
|
|
gfortran 4.2.1 20080123
|
|
|
|
IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m
|
|
F90 MIPSpro 7.4.4m
|
|
C++ MIPSpro cc 7.4.4m
|
|
|
|
Linux 2.6.9 (RHEL4) Intel 10.0 compilers
|
|
(abe.ncsa.uiuc.edu)
|
|
|
|
Linux 2.4.21-47 gcc 3.2.3 20030502
|
|
(osage)
|
|
|
|
Linux 2.6.9-42.0.10 gcc,g++ 3.4.6 20060404, G95 (GCC 4.0.3)
|
|
(kagiso) PGI 7.1-6 (pgcc, pgf90, pgCC)
|
|
Intel 9.1 (icc, ifort, icpc)
|
|
|
|
Linux 2.6.16.27 x86_64 AMD gcc 4.1.0 (SuSE Linux), g++ 4.1.0,
|
|
(smirom) g95 (GCC 4.0.3)
|
|
PGI 7.1-6 (pgcc, pgf90, pgCC)
|
|
Intel 9.1 (icc, ifort, icpc)
|
|
|
|
Linux 2.6.5-7.252.1-rtgfx #1 Intel(R) C++ Version 9.0
|
|
SMP ia64 Intel(R) Fortran Itanium(R) Version 9.0
|
|
(cobalt) SGI MPI
|
|
|
|
SunOS 5.8 32,46 Sun WorkShop 6 update 2 C 5.3
|
|
(Solaris 2.8) Sun WorkShop 6 update 2 Fortran 95 6.2
|
|
Sun WorkShop 6 update 2 C++ 5.3
|
|
|
|
SunOS 5.10 cc: Sun C 5.8
|
|
(linew) f90: Sun Fortran 95 8.2
|
|
CC: Sun C++ 5.8
|
|
|
|
Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre
|
|
(tungsten) gcc 3.2.2 20030222
|
|
Intel(R) C++ Version 9.0
|
|
Intel(R) Fortran Compiler Version 9.0
|
|
|
|
IA-64 Linux 2.4.21.SuSE_309.tg1 ia64
|
|
(NCSA tg-login) gcc 3.2.2
|
|
Intel(R) C++ Version 8.1
|
|
Intel(R) Fortran Compiler Version 8.1
|
|
mpich-gm-1.2.6..14b-intel-r2
|
|
|
|
Intel 64 Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp
|
|
(abe) gcc 3.4.6 20060404
|
|
Intel(R) C++ Version 10.0
|
|
Intel (R) Fortran Compiler Version 10.0
|
|
mvapich2-0.9.8p2patched-intel-ofed-1.2
|
|
|
|
Windows XP Visual Studio .NET
|
|
Visual Studio 2005 w/ Intel Fortran 9.1
|
|
Cygwin(native gcc compiler and g95)
|
|
MinGW(native gcc compiler and g95)
|
|
|
|
Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1
|
|
|
|
Windows Vista Visual Studio 2005
|
|
|
|
MAC OS 10.5.2 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1
|
|
GNU Fortran (GCC) 4.3.0 20070810
|
|
G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008)
|
|
|
|
|
|
Supported Configuration Features Summary
|
|
========================================
|
|
|
|
In the tables below
|
|
y = tested and supported
|
|
n = not supported or not tested in this release
|
|
x = not working in this release
|
|
dna = does not apply
|
|
( ) = footnote appears below second table
|
|
<blank> = testing incomplete on this feature or platform
|
|
|
|
Platform C F90 F90 C++ zlib SZIP
|
|
parallel parallel
|
|
SunOS5.10 64-bit n y n y y y
|
|
SunOS5.10 32-bit n y n y y y
|
|
IRIX64_6.5 64-bit n y y y y y
|
|
IRIX64_6.5 32-bit n n n n y y
|
|
Windows XP n y(15) n(15) y y y
|
|
Windows XP x64 n y(15) n(15) y y y
|
|
Windows Vista n n n y y y
|
|
Mac OS X 10.5 Intel n y n y y y
|
|
FreeBSD 4.11 n n n y y y
|
|
RedHat EL3 W (3) y(1) y(10) y(1) y y y
|
|
RedHat EL3 W Intel (3) n y n y y n
|
|
RedHat EL3 W PGI (3) n y n y y n
|
|
SuSe x86_64 gcc (3,12) y(2) y(11) y(2) y y y
|
|
SuSe x86_64 Int (3,12) n y(13) n y y n
|
|
SuSe x86_64 PGI (3,12) n y(8) n y y y
|
|
Linux 2.4 Xeon C
|
|
Lustre Intel (3,6) n y n y y n
|
|
Linux 2.6 SuSE ia64 C
|
|
Intel (3,7) y y y y y n
|
|
Linux 2.6 SGI Altix
|
|
ia64 Intel (3) y y y y y y
|
|
Linux 2.6 RHEL C
|
|
Lustre Intel (5) y(4) y y(4) y y n
|
|
Cray XT3 2.0.41 y y y y y n
|
|
|
|
|
|
Platform Shared Shared Shared Thread-
|
|
C libs F90 libs C++ libs safe
|
|
Solaris2.10 64-bit y y y y
|
|
Solaris2.10 32-bit y y y y
|
|
IRIX64_6.5 64-bit y y n y
|
|
IRIX64_6.5 32-bit y dna y y
|
|
Windows XP y y(15) y y
|
|
Windows XP x64 y y(15) y y
|
|
Windows Vista y n n y
|
|
Mac OS X 10.3 y n
|
|
FreeBSD 4.11 y n y y
|
|
RedHat EL3 W (3) y y(10) y y
|
|
RedHat EL3 W Intel (3) y y y n
|
|
RedHat EL3 W PGI (3) y y y n
|
|
SuSe x86_64 W GNU (3,12) y y y y
|
|
SuSe x86_64 W Int (3,12) y y y n
|
|
SuSe x86_64 W PGI (3,12) y y y n
|
|
Linux 2.4 Xeon C
|
|
Lustre Intel (6) y y y n
|
|
Linux 2.4 SuSE
|
|
ia64 C Intel (7) y y y n
|
|
Linux 2.4 SGI Altix
|
|
ia64 Intel y n
|
|
Linux 2.6 RHEL C
|
|
Lustre Intel (5) y y y n
|
|
Cray XT3 2.0.41 n n n n n
|
|
|
|
Notes: (1) Using mpich2 1.0.6.
|
|
(2) Using mpich2 1.0.7.
|
|
(3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated.
|
|
W or C indicates workstation or cluster, respectively.
|
|
(4) Using mvapich2 0.9.8.
|
|
(5) Linux 2.6.9-42.0.10. Xeon cluster with ELsmp_perfctr_lustre
|
|
and Intel compilers
|
|
(6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre
|
|
and Intel compilers
|
|
(7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel compilers
|
|
(8) pgf90
|
|
(9) With Compaq Visual Fortran 6.6c compiler.
|
|
(10) With PGI and Absoft compilers.
|
|
(11) PGI and Intel compilers for both C and Fortran
|
|
(12) AMD Opteron x86_64
|
|
(13) ifort
|
|
(14) Yes with C and Fortran, but not with C++
|
|
(15) Using Visual Studio 2005 or Cygwin
|
|
(16) Not tested for this release.
|
|
Compiler versions for each platform are listed in the preceding
|
|
"Platforms Tested" table.
|
|
|
|
|
|
Known Problems
|
|
==============
|
|
* For Red Storm, a Cray XT3 system, the yod command sometimes gives the
|
|
message, "yod allocation delayed for node recovery". This interferes with
|
|
test suites that do not expect seeing this message. See the section of "Red
|
|
Storm" in file INSTALL_parallel for a way to deal with this problem.
|
|
AKC - 2008/05/28
|
|
|
|
* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh will fail on
|
|
the test "Testing h5ls -w80 -r -g tgroup.h5" fails. This test is
|
|
expected to fail and exit with a non-zero code but the yod command does
|
|
not propagate the exit code of the executables. Yod always returns 0 if it
|
|
can launch the executable. The test suite shell expects a non-zero for
|
|
this particular test, therefore it concludes the test has failed when it
|
|
receives 0 from yod. To bypass this problem for now, change the following
|
|
lines in the tools/h5ls/testh5ls.sh.
|
|
======== Original =========
|
|
# The following combination of arguments is expected to return an error message
|
|
# and return value 1
|
|
TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
|
|
======== Skip the test =========
|
|
echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
|
|
======== end of bypass ========
|
|
AKC - 2008/05/28
|
|
|
|
* We have discovered two problems when running collective IO parallel HDF5
|
|
tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a
|
|
Linux cluster at NCSA.
|
|
|
|
Under some complex selection cases:
|
|
1) MPI_Get_element returns the wrong value.
|
|
2) MPI_Type_struct also generates the wrong derived datatype and corrupt
|
|
data may be generated.
|
|
These issues arise only when turning on collective IO with chunking storage
|
|
with some complex selections. We have not found these problems on other
|
|
MPI-IO compilers. If you encounter these problems, you may use independent
|
|
IO instead.
|
|
|
|
To avoid this behavior, change the following line in your code
|
|
H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
|
|
to
|
|
H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT);
|
|
|
|
KY - 2007/08/24
|
|
|
|
* For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel
|
|
tests failed with MPI-IO file locking message. AKC - 2007/6/25
|
|
|
|
* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
|
|
use -mp -O1 compilation flags to build the libraries. A higher level of
|
|
optimization causes failures in several HDF5 library tests.
|
|
|
|
* For LLNL, uP: both serial and parallel tests pass.
|
|
Zeus: Serial tests pass but parallel tests fail with a known problem in MPI.
|
|
ubgl: Serial tests pass but parallel tests fail.
|
|
|
|
* Configuring with --enable-debug=all produces compiler errors on most
|
|
platforms: Users who want to run HDF5 in debug mode should use
|
|
--enable-debug rather than --enable-debug=all to enable debugging
|
|
information on most modules.
|
|
|
|
* On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long
|
|
double to (unsigned) long long and from (unsigned) long long to long double.
|
|
|
|
* On Altix SGI with Intel 9.0, testmeta.c would not compile with -O3
|
|
optimization flag.
|
|
|
|
* On VAX, the Scaleoffset filter is not supported. The Scaleoffset filter
|
|
supports only the IEEE standard for floating-point data; it cannot be applied
|
|
to HDF5 data generated on VAX.
|
|
|
|
* On Cray X1, a lone colon on the command line of h5dump --xml (as in
|
|
the testh5dumpxml.sh script) is misinterpereted by the operating system
|
|
and causes an error.
|
|
|
|
* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and
|
|
the application asks to do collective IO, we have found that when using 4
|
|
processors, a simple collective write will sometimes be hung. This can be
|
|
verified with t_mpi test under testpar.
|
|
|
|
* On IRIX6.5, when the C compiler version is greater than 7.4, complicated
|
|
MPI derived datatype code will work. However, the user should increase
|
|
the value of the MPI_TYPE_MAX environment variable to some appropriate value
|
|
to use collective irregular selection code. For example, the current
|
|
parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test.
|
|
|
|
* A dataset created or rewritten with a v1.6.3 library or after cannot be read
|
|
with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
|
|
There was a bug in the calculation of the Fletcher32 checksum in the
|
|
library before v1.6.3; the checksum value was not consistent between big-
|
|
endian and little-endian systems. This bug was fixed in Release 1.6.3.
|
|
However, after fixing the bug, the checksum value was no longer the same as
|
|
before on little-endian system. Library releases after 1.6.4 can still read
|
|
datasets created or rewritten with an HDF5 library of v1.6.2 or before.
|
|
SLU - 2005/6/30
|
|
|
|
* For version 6 (6.02 and 6.04) of the Portland Group compiler on the AMD
|
|
Opteron processor, there is a bug in the compiler for optimization(-O2).
|
|
The library failed in several tests, all related to the MULTI driver.
|
|
The problem has been reported to the vendor.
|
|
|
|
* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
|
|
messages like "INFO: 0031-XXX ...". This is from the command `poe'.
|
|
Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
|
|
and run the tests again.
|
|
|
|
The tests may fail with messages like "The socket name is already in use",
|
|
but HDF5 does not use sockets. This failure is due to problems with the
|
|
poe command trying to set up the debug socket. To resolve this problem,
|
|
check to see whether there are many old /tmp/s.pedb.* files staying around.
|
|
These are sockets used by the poe command and left behind due to failed
|
|
commands. First, ask your system administrator to clean them out.
|
|
Lastly, request IBM to provide a means to run poe without the debug socket.
|
|
|
|
* 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 IBM SP2 platforms for serial mode. The parallel mode works fine with
|
|
this option.
|
|
|
|
It is suggested that you do not use this option on these platforms
|
|
during configuration.
|
|
|
|
* With the gcc 2.95.2 compiler, HDF5 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.
|
|
|
|
* The ./dsets tests fail on 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.
|
|
|
|
* Not all platforms behave correctly with Szip's shared libraries. Szip is
|
|
disabled in these cases, and a message is relayed at configure time. Static
|
|
libraries should be working on all systems that support Szip and should be
|
|
used when shared libraries are unavailable.
|
|
|
|
There is also a configure error on Altix machines that incorrectly reports
|
|
when a version of Szip without an encoder is being used.
|
|
|
|
* On some platforms that use Intel and Absoft compilers to build the HDF5
|
|
Fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90
|
|
and fflush2.f90 complaining about the exit subroutine. Comment out the line
|
|
IF (total_error .ne. 0) CALL exit (total_error).
|
|
|
|
* Information about building with PGI and Intel compilers is available in
|
|
the INSTALL file sections 4.7 and 4.8.
|
|
|
|
* On at least one system, SDSC DataStar, the scheduler (in this case
|
|
LoadLeveler) sends job status updates to standard error when you run
|
|
any executable that was compiled with the parallel compilers.
|
|
|
|
This causes problems when running "make check" on parallel builds, as
|
|
many of the tool tests function by saving the output from test runs,
|
|
and comparing it to an exemplar.
|
|
|
|
The best solution is to reconfigure the target system so it no longer
|
|
inserts the extra text. However, this may not be practical.
|
|
|
|
In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to
|
|
the configure and build. This will cause "make check" to continue after
|
|
detecting errors in the tool tests. However, in the case of SDSC DataStar,
|
|
it also leaves you with some 150 "failed" tests to examine by hand.
|
|
|
|
A second solution is to write a script to run serial tests and filter
|
|
out the text added by the scheduler. A sample script used on SDSC
|
|
DataStar is given below, but you will probably have to customize it
|
|
for your installation.
|
|
|
|
Observe that the basic idea is to insert the script as the first item
|
|
on the command line which executes the the test. The script then
|
|
executes the test and filters out the offending text before passing
|
|
it on.
|
|
|
|
#!/bin/csh
|
|
|
|
set STDOUT_FILE=~/bin/serial_filter.stdout
|
|
set STDERR_FILE=~/bin/serial_filter.stderr
|
|
|
|
rm -f $STDOUT_FILE $STDERR_FILE
|
|
|
|
($* > $STDOUT_FILE) >& $STDERR_FILE
|
|
|
|
set RETURN_VALUE=$status
|
|
|
|
cat $STDOUT_FILE
|
|
|
|
tail +3 $STDERR_FILE
|
|
|
|
exit $RETURN_VALUE
|
|
|
|
You get the HDF5 make files and test scipts to execute your filter script
|
|
by setting the environment variable "RUNSERIAL" to the full path of the
|
|
script prior to running configure for parallel builds. Remember to
|
|
"unsetenv RUNSERIAL" before running configure for a serial build.
|
|
|
|
Note that the RUNSERIAL environment variable exists so that we can
|
|
prefix serial runs as necessary on the target system. On DataStar,
|
|
no prefix is necessary. However on an MPICH system, the prefix might
|
|
have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to
|
|
get the serial tests to run at all.
|
|
|
|
In such cases, you will have to include the regular prefix in your
|
|
filter script.
|
|
|
|
* H5Ocopy() does not copy reg_ref attributes correctly when shared-message
|
|
is turn on. The value of the reference in the destination attriubte is
|
|
wrong. This H5Ocopy problem will affect the h5copy tool.
|
|
|
|
* In the C++ API, it appears that there are bugs in Attribute::write/read
|
|
and DataSet::write/read for fixed- and variable-len strings. The problems
|
|
are being worked on and a patch will be provided when the fixes are
|
|
available.
|
|
|
|
|
|
%%%%1.8.0%%%%
|
|
|
|
|
|
HDF5 version 1.8.0 released on Tue Feb 12 20:41:19 CST 2008
|
|
================================================================================
|
|
|
|
INTRODUCTION
|
|
============
|
|
|
|
This document describes the differences between the HDF5-1.6.x release series
|
|
and HDF5 1.8.0, and contains information on the platforms tested and known
|
|
problems in HDF5-1.8.0. For more details, see the HISTORY-1_0-1_8_0_rc3.txt
|
|
file in the
|
|
release_docs/ directory of the HDF5 source.
|
|
|
|
Links to the HDF5 1.8.0 source code, documentation, and additional materials
|
|
can be found on the HDF5 web page at:
|
|
|
|
http://www.hdfgroup.org/products/hdf5/
|
|
|
|
The HDF5 1.8.0 release can be obtained from:
|
|
|
|
http://www.hdfgroup.org/HDF5/release/obtain5.html
|
|
|
|
User documentation for 1.8.0 can be accessed directly at this location:
|
|
|
|
http://www.hdfgroup.org/HDF5/doc/
|
|
|
|
New features in 1.8.0, including brief general descriptions of some new
|
|
and modified APIs, are described in the "What's New in 1.8.0?" document:
|
|
|
|
http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
|
|
|
|
All new and modified APIs are listed in detail in the "HDF5 Software Changes
|
|
from Release to Release" document, in the section "Release 1.8.0 (current
|
|
release) versus Release 1.6.x":
|
|
|
|
http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
|
|
|
|
If you have any questions or comments, please send them to the HDF Help Desk:
|
|
|
|
help@hdfgroup.org
|
|
|
|
|
|
CONTENTS
|
|
========
|
|
|
|
- New Features
|
|
- Removed Feature
|
|
- Support for new platforms and languages
|
|
- Bug Fixes since HDF5-1.6.0
|
|
- Platforms Tested
|
|
- Supported Configuration Features Summary
|
|
- Known Problems
|
|
|
|
|
|
New Features
|
|
============
|
|
|
|
HDF5 Release 1.8.0 is a major release with many changes and new features.
|
|
|
|
New format and interface features discussed in the "What's New in
|
|
HDF5 1.8.0" document include the following:
|
|
|
|
Enhanced group object management
|
|
Enhanced attribute management and more efficient meta data handling
|
|
Expanded datatype features
|
|
Creation order tracking and indexing
|
|
Improved meta data caching and cache control
|
|
UTF-8 encoding
|
|
New I/O filters: n-bit and scale+offset compression
|
|
New link (H5L) and object (H5O) interfaces and features
|
|
External and user-defined links
|
|
New high-level APIs:
|
|
HDF5 Packet Table (H5PT) and HDF5 Dimension Scale (H5DS)
|
|
C++ and Fortran interfaces for older high-level APIs:
|
|
H5Lite (H5LT), H5Image (H5IM), and H5Table (H5TB)
|
|
New and improved tools
|
|
And more...
|
|
|
|
http://hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
|
|
|
|
|
|
New APIs associated with these features, other interface changes
|
|
(e.g., ENUM and struct definitions), and new library configuration flags
|
|
are listed in the "Release 1.8.0 (current release) versus Release 1.6.x"
|
|
section of "HDF5 Software Changes from Release to Release."
|
|
|
|
http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html
|
|
|
|
Compatibility
|
|
-------------
|
|
Many HDF5 users and user communities have existing applications that
|
|
they may wish to port to Release 1.8.0. Alternatively, some users may
|
|
wish to take advantage of Release 1.8.0's improved performance without
|
|
having to port such applications. To facilitate managing application
|
|
compatibility and porting applications from release to release, the HDF
|
|
Team has implemented the following features:
|
|
Individually-configurable macros that selectively map common
|
|
interface names to the old and new interfaces
|
|
Library configuration options to configure the macro mappings
|
|
|
|
Two related documents accompany this release:
|
|
"API Compatibility Macros in HDF5" discusses the specifics of the
|
|
new individually-configurable macros and library configuration
|
|
options.
|
|
http://hdfgroup.org/HDF5/doc/RM/APICompatMacros.html
|
|
|
|
"New Features in HDF5 Release 1.8.0 and Backward/Forward Format
|
|
Compatibility Issues" discusses each new feature with regard to
|
|
its impact on format compatibility.
|
|
http://hdfgroup.org/HDF5/doc/ADGuide/CompatFormat180.html
|
|
|
|
Referenced documents
|
|
--------------------
|
|
http://hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
|
|
"What's New in HDF5 1.8.0"
|
|
|
|
http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html
|
|
The "Release 1.8.0 (current release) versus Release 1.6.x "
|
|
section in "HDF5 Software Changes from Release to Release"
|
|
|
|
http://hdfgroup.org/HDF5/doc/RM/APICompatMacros.html
|
|
"API Compatibility Macros in HDF5"
|
|
|
|
http://hdfgroup.org/HDF5/doc/ADGuide/CompatFormat180.html
|
|
"New Features in HDF5 Release 1.8.0 and Backward/Forward Format
|
|
Compatibility Issues"
|
|
|
|
|
|
Removed Feature
|
|
===============
|
|
The stream virtual file driver (H5FD_STREAM) have been removed in this
|
|
release. This affects the functions H5Pset_fapl_stream and H5Pget_fapl_stream
|
|
and the constant H5FD_STREAM.
|
|
|
|
This virtual file driver will be available at
|
|
http://hdf5-addons.origo.ethz.ch/. Note that at the time of this release,
|
|
the transition is still in progress; the necessary integration tools may
|
|
not be available when HDF5 Release 1.8.0 first comes out.
|
|
|
|
|
|
Support for New Platforms, Languages, and Compilers
|
|
===================================================
|
|
- Support for Open VMS 7.3 was added.
|
|
|
|
|
|
Bug Fixes since HDF5-1.6.0
|
|
==========================
|
|
This release contains numerous bug fixes. For details, see the
|
|
"Changes from 1.6.0 to 1.8.0-rc3" section of the HISTORY.txt file for
|
|
this release.
|
|
|
|
|
|
Platforms Tested
|
|
================
|
|
The following platforms and compilers have been tested for for this release.
|
|
|
|
AIX 5.2 (32/64 bit) xlc 8.0.0.11
|
|
xlC 8.0
|
|
xlf 10.01.0000.0
|
|
mpcc_r 6.0.0.8
|
|
mpxlf_r 8.1.1.7
|
|
|
|
FreeBSD 6.2-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305
|
|
(duty) g++ 3.4.6 [FreeBSD] 20060305
|
|
gcc 4.2.1 20080123
|
|
g++ 4.2.1 20080123
|
|
gfortran 4.2.1 20070620
|
|
|
|
FreeBSD 6.2-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
|
|
(liberty) g++ 3.4.6 [FreeBSD] 20060305
|
|
gcc 4.2.1 20080123
|
|
g++ 4.2.1 20080123
|
|
gfortran 4.2.1 20080123
|
|
|
|
IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m
|
|
F90 MIPSpro 7.4.4m
|
|
C++ MIPSpro cc 7.4.4m
|
|
|
|
Linux 2.6.9 (RHEL4) Intel 10.0 compilers
|
|
(abe.ncsa.uiuc.edu)
|
|
|
|
Linux 2.4.21-47 gcc 3.2.3 20030502
|
|
(osage)
|
|
|
|
Linux 2.6.9-42.0.10 gcc 3.4.6 20060404
|
|
(kagiso) PGI 7.0-7 (pgcc, pgf90, pgCC)
|
|
Intel 9.1 (icc, ifort, icpc)
|
|
|
|
Linux 2.6.16.27 x86_64 AMD gcc 4.1.0 (SuSE Linux), g++ 4.1.0,
|
|
(smirom) g95 (GCC 4.0.3)
|
|
PGI 6.2-5 (pgcc, pgf90, pgCC)
|
|
Intel 9.1 (icc, iort, icpc)
|
|
|
|
Linux 2.6.5-7.252.1-rtgfx #1 Intel(R) C++ Version 9.0
|
|
SMP ia64 Intel(R) Fortran Itanium(R) Version 9.0
|
|
(cobalt) SGI MPI
|
|
|
|
SunOS 5.8 32,46 Sun WorkShop 6 update 2 C 5.3
|
|
(Solaris 2.8) Sun WorkShop 6 update 2 Fortran 95 6.2
|
|
Sun WorkShop 6 update 2 C++ 5.3
|
|
|
|
SunOS 5.10 cc: Sun C 5.8
|
|
(linew) f90: Sun Fortran 95 8.2
|
|
CC: Sun C++ 5.8
|
|
|
|
Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre
|
|
(tungsten) gcc 3.2.2 20030222
|
|
Intel(R) C++ Version 9.0
|
|
Intel(R) Fortran Compiler Version 9.0
|
|
|
|
IA-64 Linux 2.4.21.SuSE_292.til1 ia64
|
|
(NCSA tg-login) gcc 3.2.2
|
|
Intel(R) C++ Version 8.1
|
|
Intel(R) Fortran Compiler Version 8.1
|
|
mpich-gm-1.2.5..10-intel-r2
|
|
|
|
Windows XP Visual Studio .NET
|
|
Visual Studio 2005 w/ Intel Fortran 9.1
|
|
Cygwin(native gcc compiler and g95)
|
|
MinGW(native gcc compiler and g95)
|
|
|
|
Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1
|
|
|
|
Windows Vista Visual Studio 2005
|
|
|
|
MAC OS 10.4 (Intel) gcc i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1
|
|
G95 (GCC 4.0.3 (g95 0.91!) Nov 21 2006)
|
|
|
|
Alpha Open VMS 7.3 Compaq C V6.5-001-48BCD
|
|
HP Fortran V7.6-3276
|
|
Compaq C++ V6.5-004
|
|
|
|
|
|
Supported Configuration Features Summary
|
|
========================================
|
|
|
|
In the tables below
|
|
y = tested and supported
|
|
n = not supported or not tested in this release
|
|
x = not working in this release
|
|
dna = does not apply
|
|
( ) = footnote appears below second table
|
|
<blank> = testing incomplete on this feature or platform
|
|
|
|
Platform C F90 F90 C++ zlib SZIP
|
|
parallel parallel
|
|
SunOS5.8 64-bit n y n y y y
|
|
SunOS5.8 32-bit n y n y y y
|
|
SunOS5.10 64-bit y(1) y n y y y
|
|
SunOS5.10 32-bit y(1) y n y y y
|
|
IRIX64_6.5 64-bit n y y y y y
|
|
IRIX64_6.5 32-bit n n n n y y
|
|
AIX-5.2 32-bit y y y y y y
|
|
AIX-5.2 64-bit y y y y y y
|
|
Windows XP n y(15) n(15) y y y
|
|
Windows XP x64 n y(15) n(15) y y y
|
|
Windows Vista n n n y y y
|
|
Mac OS X 10.4 PowerPC n n
|
|
Mac OS X 10.4 Intel n y n y y y
|
|
FreeBSD 4.11 n n n y y y
|
|
RedHat EL3 W (3) y(1a) y(10) y(1a) y y y
|
|
RedHat EL3 W Intel (3) n y n y y n
|
|
RedHat EL3 W PGI (3) n y n y y n
|
|
SuSe x86_64 gcc (3,12) y(1a) y(11) n y y y
|
|
SuSe x86_64 Int (3,12) n y(13) n y y n
|
|
SuSe x86_64 PGI (3,12) n y(8) n y y y
|
|
Linux 2.4 Xeon C
|
|
Lustre Intel (3,6) n y n y y n
|
|
Linux 2.6 SuSE ia64 C
|
|
Intel (3,7) y y y y y n
|
|
Linux 2.6 SGI Altix
|
|
ia64 Intel (3) y y y y y y
|
|
Alpha OpenVMS 7.3.2 n y n y n n
|
|
|
|
|
|
|
|
Platform Shared Shared Shared static- Thread-
|
|
C libs F90 libs C++ libs exec safe
|
|
Solaris2.8 64-bit y y y x y
|
|
Solaris2.8 32-bit y y y x y
|
|
Solaris2.10 64-bit y x y
|
|
Solaris2.10 32-bit y x y
|
|
IRIX64_6.5 64-bit y y n y y
|
|
IRIX64_6.5 32-bit y dna y y y
|
|
AIX-5.2 & 5.3 32-bit n n n y n
|
|
AIX-5.2 & 5.3 64-bit n n n y n
|
|
Windows XP y y(15) y y y
|
|
Windows XP x64 y y(15) y y y
|
|
Windows Vista y n n y y
|
|
Mac OS X 10.3 y y n
|
|
FreeBSD 4.11 y n y y y
|
|
RedHat EL3 W (3) y y(10) y y y
|
|
RedHat EL3 W Intel (3) y y y y n
|
|
RedHat EL3 W PGI (3) y y y y n
|
|
SuSe x86_64 W GNU (3,12) y y y y y
|
|
SuSe x86_64 W Int (3,12) y y y y(14) n
|
|
SuSe x86_64 W PGI (3,12) y y y y(14) n
|
|
Linux 2.4 Xeon C
|
|
Lustre Intel (6) y y y y n
|
|
Linux 2.4 SuSE
|
|
ia64 C Intel (7) y y y y n
|
|
Linux 2.4 SGI Altix
|
|
ia64 Intel y y n
|
|
Alpha OpenVMS 7.3.2 n n n y n
|
|
|
|
Notes: (1) Using mpich 1.2.6.
|
|
(1a) Using mpich2 1.0.6.
|
|
(2) Using mpt and mpich 1.2.6.
|
|
(3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated.
|
|
W or C indicates workstation or cluster, respectively.
|
|
|
|
(6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre
|
|
and Intel compilers
|
|
(7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel
|
|
compilers
|
|
(8) pgf90
|
|
(9) With Compaq Visual Fortran 6.6c compiler.
|
|
(10) With PGI and Absoft compilers.
|
|
(11) PGI and Intel compilers for both C and Fortran
|
|
(12) AMD Opteron x86_64
|
|
(13) ifort
|
|
(14) Yes with C and Fortran, but not with C++
|
|
(15) Using Visual Studio 2005 or Cygwin
|
|
(16) Not tested for this release.
|
|
Compiler versions for each platform are listed in the preceding
|
|
"Platforms Tested" table.
|
|
|
|
|
|
Known Problems
|
|
==============
|
|
* We have discovered two problems when running collective IO parallel HDF5
|
|
tests with chunking storage on the ChaMPIon MPI compiler on tungsten, a
|
|
Linux cluster at NCSA.
|
|
|
|
Under some complex selection cases:
|
|
1) MPI_Get_element returns the wrong value.
|
|
2) MPI_Type_struct also generates the wrong derived datatype and corrupt
|
|
data may be generated.
|
|
These issues arise only when turning on collective IO with chunking storage
|
|
with some complex selections. We have not found these problems on other
|
|
MPI-IO compilers. If you encounter these problems, you may use independent
|
|
IO instead.
|
|
|
|
To avoid this behavior, change the following line in your code
|
|
H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
|
|
|
|
to
|
|
H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT);
|
|
|
|
KY - 2007/08/24
|
|
|
|
* For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel
|
|
tests failed with MPI-IO file locking message. AKC - 2007/6/25
|
|
|
|
* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
|
|
use -mp -O1 compilation flags to build the libraries. A higher level of
|
|
optimization causes failures in several HDF5 library tests.
|
|
|
|
* For SNL, Red Storm: Only parallel HDF5 is supported. The serial tests pass
|
|
when run against the parallel library; the parallel tests also pass, but
|
|
with lots of non-fatal error messages.
|
|
|
|
* For LLNL, uP: both serial and parallel tests pass.
|
|
Zeus: Serial tests pass but parallel tests fail with a known problem in MPI.
|
|
ubgl: Serial tests pass but parallel tests fail.
|
|
|
|
* On SUN 5.10 C++, testing fails in the "Testing Shared Datatypes with
|
|
Attributes" test.
|
|
|
|
* Configuring with --enable-debug=all produces compiler errors on most
|
|
platforms: Users who want to run HDF5 in debug mode should use
|
|
--enable-debug rather than --enable-debug=all to enable debugging
|
|
information on most modules.
|
|
|
|
* On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long
|
|
double to (unsigned) long long and from (unsigned) long long to long double.
|
|
|
|
* On Altix SGI with Intel 9.0, testmeta.c would not compile with -O3
|
|
optimization flag.
|
|
|
|
* On VAX, the Scaleoffset filter is not supported. The filter cannot be
|
|
applied to HDF5 data generated on VAX. The Scaleoffset filter only supports
|
|
the IEEE standard for floating-point data.
|
|
|
|
* On Cray X1, a lone colon on the command line of h5dump --xml (as in
|
|
the testh5dumpxml.sh script) is misinterpereted by the operating system
|
|
and causes an error.
|
|
|
|
* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and
|
|
the application asks to do collective IO, we have found that when using 4
|
|
processors, a simple collective write will sometimes be hung. This can be
|
|
verified with t_mpi test under testpar.
|
|
|
|
* On IRIX6.5, when the C compiler version is greater than 7.4, complicated
|
|
MPI derived datatype code will work. However, the user should increase
|
|
the value of the MPI_TYPE_MAX environment variable to some appropriate value
|
|
to use collective irregular selection code. For example, the current
|
|
parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test.
|
|
|
|
* A dataset created or rewritten with a v1.6.3 library or after cannot be read
|
|
with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
|
|
There was a bug in the calculating code of the Fletcher32 checksum in the
|
|
library before v1.6.3; the checksum value was not consistent between big-
|
|
endian and little-endian systems. This bug was fixed in Release 1.6.3.
|
|
However, after fixing the bug, the checksum value was no longer the same as
|
|
before on little-endian system. Library releases after 1.6.4 can still read
|
|
datasets created or rewritten with an HDF5 library of v1.6.2 or before.
|
|
SLU - 2005/6/30
|
|
|
|
* For version 6 (6.02 and 6.04) of the Portland Group compiler on the AMD
|
|
Opteron processor, there is a bug in the compiler for optimization(-O2).
|
|
The library failed in several tests, all related to the MULTI driver.
|
|
The problem has been reported to the vendor.
|
|
|
|
* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
|
|
messages like "INFO: 0031-XXX ...". This is from the command `poe'.
|
|
Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
|
|
and run the tests again.
|
|
|
|
The tests may fail with messages like "The socket name is already in use",
|
|
but HDF5 does not use sockets. This failure is due to problems with the
|
|
poe command trying to set up the debug socket. To resolve this problem,
|
|
check to see whether there are many old /tmp/s.pedb.* files staying around.
|
|
These are sockets used by the poe command and left behind due to failed
|
|
commands. First, ask your system administrator to clean them out.
|
|
Lastly, request IBM to provide a means to run poe without the debug socket.
|
|
|
|
* 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 IBM SP2 platform for the serial mode. The parallel mode works fine with
|
|
this option.
|
|
|
|
It is suggested that you do not use this option on these platforms
|
|
during configuration.
|
|
|
|
* With the gcc 2.95.2 compiler, HDF5 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.
|
|
|
|
* The ./dsets tests fail on 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.
|
|
|
|
* Not all platforms behave correctly with Szip's shared libraries. Szip is
|
|
disabled in these cases, and a message is relayed at configure time. Static
|
|
libraries should be working on all systems that support Szip and should be
|
|
used when shared libraries are unavailable.
|
|
|
|
There is also a configure error on Altix machines that incorrectly reports
|
|
when a version of Szip without an encoder is being used.
|
|
|
|
* On some platforms that use Intel and Absoft compilers to build the HDF5
|
|
Fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90
|
|
and fflush2.f90 complaining about the exit subroutine. Comment out the line
|
|
IF (total_error .ne. 0) CALL exit (total_error).
|
|
|
|
* Information about building with PGI and Intel compilers is available in
|
|
the INSTALL file sections 4.7 and 4.8.
|
|
|
|
* On at least one system, SDSC DataStar, the scheduler (in this case
|
|
LoadLeveler) sends job status updates to standard error when you run
|
|
any executable that was compiled with the parallel compilers.
|
|
|
|
This causes problems when running "make check" on parallel builds, as
|
|
many of the tool tests function by saving the output from test runs,
|
|
and comparing it to an exemplar.
|
|
|
|
The best solution is to reconfigure the target system so it no longer
|
|
inserts the extra text. However, this may not be practical.
|
|
|
|
In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to
|
|
the configure and build. This will cause "make check" to continue after
|
|
detecting errors in the tool tests. However, in the case of SDSC DataStar,
|
|
it also leaves you with some 150 "failed" tests to examine by hand.
|
|
|
|
A second solution is to write a script to run serial tests and filter
|
|
out the text added by the scheduler. A sample script used on SDSC
|
|
DataStar is given below, but you will probably have to customize it
|
|
for your installation.
|
|
|
|
Observe that the basic idea is to insert the script as the first item
|
|
on the command line which executes the the test. The script then
|
|
executes the test and filters out the offending text before passing
|
|
it on.
|
|
|
|
#!/bin/csh
|
|
|
|
set STDOUT_FILE=~/bin/serial_filter.stdout
|
|
set STDERR_FILE=~/bin/serial_filter.stderr
|
|
|
|
rm -f $STDOUT_FILE $STDERR_FILE
|
|
|
|
($* > $STDOUT_FILE) >& $STDERR_FILE
|
|
|
|
set RETURN_VALUE=$status
|
|
|
|
cat $STDOUT_FILE
|
|
|
|
tail +3 $STDERR_FILE
|
|
|
|
exit $RETURN_VALUE
|
|
|
|
You get the HDF5 make files and test scipts to execute your filter script
|
|
by setting the environment variable "RUNSERIAL" to the full path of the
|
|
script prior to running configure for parallel builds. Remember to
|
|
"unsetenv RUNSERIAL" before running configure for a serial build.
|
|
|
|
Note that the RUNSERIAL environment variable exists so that we can
|
|
can prefix serial runs as necessary on the target system. On DataStar,
|
|
no prefix is necessary. However on an MPICH system, the prefix might
|
|
have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to
|
|
get the serial tests to run at all.
|
|
|
|
In such cases, you will have to include the regular prefix in your
|
|
filter script.
|
|
|
|
* H5Ocopy() does not copy reg_ref attributes correctly when shared-message
|
|
is turn on. The value of the reference in the destination attriubte is
|
|
wrong. This H5Ocopy problem will affect the h5copy tool.
|
|
|