2012-09-16 22:27:43 +08:00
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HDF5 version 1.9.130 currently under development
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2009-01-06 22:58:21 +08:00
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================================================================================
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INTRODUCTION
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This document describes the differences between HDF5-1.9.0 and
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HDF5 1.9.x snapshot, and contains information on the platforms
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tested and known problems in HDF5-1.9.x.
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For more details check the HISTORY*.txt files in the HDF5 source.
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2009-01-23 04:53:59 +08:00
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Links to HDF5 1.9.x source code can be found on The HDF Group's
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development FTP server at the following location:
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2009-01-06 22:58:21 +08:00
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ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/snapshots
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User documentation for the snapshot can be accessed directly at this location:
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http://www.hdfgroup.uiuc.edu/HDF5/doc_dev_snapshot/H5_dev/
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For more information, see the HDF5 home page:
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http://www.hdfgroup.org/HDF5/
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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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- New Features
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- Support for new platforms and languages
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- Bug Fixes since HDF5-1.8.0
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- Platforms Tested
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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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2012-08-24 00:07:43 +08:00
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- Updated to latest autotools and changed all hard *.sh scripts to
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configure managed *.sh.in files. Removed overloading of autotools
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TESTS variable by examples and tests. Renamed configure.in to
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configure.ac. (ADB - 2012/08/23 - HDFFV-8129)
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2012-02-28 20:45:45 +08:00
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- Added code to display the version information of XL fortran and C++
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in the summary of configure. (AKC - 2012/02/28 - HDFFV-7793)
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2011-04-15 03:45:57 +08:00
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- Configure now generates Makefiles that build in "silent make mode"
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by default in which compile and link lines are significantly
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simplified for clarity. To override this and view actual compile and
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link lines during building, the --disable-silent-rules flag can be used
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at configure time, or the 'make' command can be followed by V=1, to
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indicate a "verbose" make. (MAM - 2011/4/14).
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2011-02-10 05:07:29 +08:00
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- Added mpicc and mpif90 as the default C and Fortran compilers for Linux
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systems when --enable-parallel is specified but no $CC or $FC is defined.
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(AKC - 2011/2/7)
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2010-11-18 02:07:51 +08:00
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- Added a new configure option, "--enable-unsupported", which can
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be used to stop configure from preventing the use of unsupported
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configure option combinations, such as c++ in parallel or parallel
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HDF5 with threadsafe. Use at your own risk, as it may result in a
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library that won't compile or run as expected!
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(MAM - 2010/11/17 - Bug 2061)
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2010-06-12 07:37:33 +08:00
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- PHDF5 changed to use "mpiexec", instead of mpirun, as the default MPI
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applications startup command as defined in the MPI-2 definition, section
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4.1. (AKC - 2010/6/11 - Bug 1921)
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2010-05-06 01:34:26 +08:00
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- Configure now adds appropriate defines for supporting large (64-bit)
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files on all systems, where supported, by default, instead of only linux.
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This largefile support is controllable with the --enable-largefile
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configure option. This is replacing the linux-specific --enable-linux-lfs
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option, which has been removed from configure.
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(MAM - 2010/05/05 - 1772/1434)
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2010-04-16 05:17:22 +08:00
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- Upgraded versions of autotools used to generate configuration suite.
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We now use Automake 1.11.1, Autoconf 2.65, and Libtool 2.2.6b.
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MAM 2010/04/15.
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2009-11-27 02:10:28 +08:00
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- Added the xlc-* and mpcc_r-* BASENAME patterns to be recognized as IBM
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compilers so that the ibm compiler options can be added properly. This
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allows non-system-default compiler command names (e.g. xlc-m.n.k.l) be
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recognized. AKC 2009/11/26.
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[svn-r17345] Purpose:
Updating autotools
Description:
Installed new autotools and used them to reconfigure HDF5.
- Automake upgraded to 1.11
- Autoconf upgraded to 2.64
- bin/reconfigure script edited to use new versions (on jam), and
run to generate new configure script and Makefile.in's.
- configure.in script edited to add "_cv_" to all AC_CACHE_VAL strings
(in order to comply with new autoconf standard).
Tested:
Tested on machines jam, smirom, liberty, linew.
Tested w/ features c++, fortran, parallel.
Tested w/ compilers gcc, pgcc, icc.
Further testing via Daily Tests should catch any other outliers. Upon
passing DT's, I'll propogate the new tools into 1.8, hdf4, et cetera.
2009-08-13 02:55:25 +08:00
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- Configuration suite now uses Automake 1.11 and Autoconf 2.64.
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MAM 2009/08/11.
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2009-07-20 07:47:30 +08:00
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- Changed default Gnu fortran compiler from g95 to gfortran since
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gfortran is more likely installed with gcc now. -AKC 2009/07/19-
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2009-04-20 14:00:11 +08:00
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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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2009-04-15 06:07:24 +08:00
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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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2009-01-06 22:58:21 +08:00
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- Configuration suite now uses Libtool 2.2.6a. MAM 2008/10/24
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- Configuration suite now uses Autoconf 2.61, Automake 1.10.1.
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MAM 2008/05/05.
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- The new configure option "--disable-sharedlib-rpath" disables
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embedding the '-Wl,-rpath' information into executables when
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shared libraries are produced, and instead solely relies on the
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information in LD_LIBRARY_PATH. (MAM - 2008/05/15)
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Library:
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--------
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2012-04-03 06:14:50 +08:00
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- The data sieve buffer size was for all the datasets in the file. It
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could waste memory if any dataset size is smaller than the sieve buffer
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size. Now the library picks the smaller one between the dataset size
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and the sieve buffer size from the file access property. See Issue 7934.
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(SLU - 2012/4/2)
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2011-07-19 05:23:02 +08:00
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- I added a new parameter of object access property list to the function
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H5Rdereference (Issue 2763). It's called H5Rdereference2 now. The former
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H5Rdereference function has been deprecated to H5Rdereference1. (SLU -
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2011/7/18)
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2011-05-21 00:14:33 +08:00
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- H5Tcreate now supports string type (fixed-length and variable-length).
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(SLU - 2011/05/20)
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2011-02-18 00:26:29 +08:00
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- Added ability to cache files opened through external links. Added new
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public functions H5Pset_elink_file_cache_size(),
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2011-04-14 05:03:30 +08:00
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H5Pget_elink_file_cache_size(), and H5Fclear_elink_file_cache().
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2011-02-18 00:26:29 +08:00
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(NAF - 2011/02/17)
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2010-11-18 07:25:56 +08:00
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- Removed all old code for Metraowerks compilers, bracketed by
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__MWERKS__). Metraowerks compiler is long gone. (AKC - 2010/11/17)
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2010-09-11 00:15:34 +08:00
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- Added support for threadsafety on windows using the windows threads
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library. Use the HDF5_ENABLE_THREADSAFE option in CMake while on a
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windows platform to enable this functionality. This is supported on
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Windows Vista and newer Windows operating systems. (MAM - 2010/09/10)
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2010-09-10 02:15:36 +08:00
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- When a mandatory filter failed to write data chunks, the dataset
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couldn't close (bug 1260). The fix releases all resources and closes
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the dataset but returns a failure. (SLU - 2010/9/8)
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2010-08-25 00:00:20 +08:00
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- H5Tset_order and H5Tget_order now support all data types. A new byte
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order H5T_ORDER_MIXED has been added specifically for compound datatype
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and its derived type. Please see bug #1934. (SLU - 2010/8/23)
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2010-06-16 05:21:03 +08:00
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- Improved performance of the chunk cache by avoiding unnecessary b-tree
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lookups of chunks already in cache. (NAF - 2010/06/15)
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2010-03-25 00:41:14 +08:00
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- Greatly improved performance of extending a dataset with early
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allocation. (NAF - 2010/03/24 - 1637)
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2009-11-04 00:33:30 +08:00
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- Added support for filtering densely stored groups. Many of the API
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functions related to filters have been extended to support dense groups
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as well as datasets. Pipeline messages can now be stored in a group's
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object header. (NAF/QAK - 2009/10/8)
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2009-09-29 12:43:22 +08:00
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- The embedded library information is displayed by H5check_version() if a
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version mismatch is detected. Also changed H5check_version() to
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suppress the warning message totally if $HDF5_DISABLE_VERSION_CHECK is 2
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or higher. (Old behavior treated 3 or higher the same as 1, that is
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2009-09-29 12:45:46 +08:00
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print a warning and allows the program to continue. (AKC - 2009/9/28)
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2009-09-30 00:49:34 +08:00
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- If a user does not care for the extra library information insert
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in the executables, he may turn it off by --disable-embedded-libinfo
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2009-09-29 12:43:22 +08:00
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during configure. (AKC - 2009/9/15)
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2009-08-21 03:17:51 +08:00
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- Corrected problem where library would re-write the superblock in a file
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opened for R/W access, even when no changes were made to the file.
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(QAK - 2009/08/20, Bz#1473)
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2009-04-17 05:06:37 +08:00
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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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2009-01-30 05:02:07 +08:00
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- Added support for dense attributes to H5Ocopy. (XCao/NAF - 2009/01/29)
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2009-01-09 02:16:31 +08:00
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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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2009-01-06 22:58:21 +08:00
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- Added H5Pset_chunk_cache() and H5Pget_chunk_cache() functions to allow
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2009-01-09 02:16:31 +08:00
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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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2009-01-06 22:58:21 +08:00
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- Added H5Iis_valid() function to check if an id is valid without producing
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2009-01-09 02:16:31 +08:00
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an error message. (NAF - 2008/11/5)
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2009-01-06 22:58:21 +08:00
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- Added two new public routines: H5Pget_elink_fapl() and
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H5Pset_elink_fapl(). (see bug #1247) (VC - 2008/10/13)
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- Improved free space tracking in file to be faster. (QAK - 2008/10/06)
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- Added 'mounted' field to H5G_info_t struct. (QAK - 2008/07/15)
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Parallel Library:
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-----------------
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2012-09-05 01:00:38 +08:00
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- Add H5Pget_mpio_no_collective_cause() function that retrive reasons
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why the collective I/O was broken during read/write IO access.
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(JKM - 2012/08/30 HDFFV-8143)
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[svn-r21101] HDFFV-7639
Purpose:
Remove H5_MPI_SPECIAL_COLLECTIVE_IO_WORKS and
H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS #defines from source.
Description:
Two advanced parallel functionalities, special collective IO and
complex derived datatypes, are not supported by older
implementations of mpi, and thus our code limits the use of these
features with #ifdefs and has checks in configure to set them (or
not). Unfortunately, configure can't actually run a parallel check
to see if these features are working (nor not) so it resorts to
looking in the config files where they are explicity enabled or
disabled based on versions of mpi, sytems being built on, or for
no documented reason at all (i.e. just set to on or off as some
'default'). Overriding these settings is easy if need be, provided
it is known that it needs to be done to get improved performance,
and oftentimes it is not.
Most new MPI implementations successfully handle the functionality
requested when these #defines are set, and many of the "turn these
features off" cases in the config files are for old (> 5 years)
versions of MPI and retired systems (such as NCSA's tungsten).
Therefore, the decision has been made to remove the support for
these old versions of MPI and systems that cannot handle these
behaviors. The #ifdefs and supporting setup in the config/ files
and configure script has been removed, and the code executed when
these options were not set removed from the source.
In passing, this commit also cleans up some whitespace issues in
both t_mpi.c and H5Dmpio.c. Furthermore, in t_mpi.c, the special
collective IO test was not getting regularly run due to it being
written to work only with four processes (we regularly test with
six, previously with three), and thus it failed when actually run
due to an out of bounds data buffer assignment. It has been
modified to run at any number of processes greater than four, and
the memory problem has been fixed so the test passes.
Tested:
jam, h5committest, ember
2011-07-15 04:33:21 +08:00
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- Special Collective IO (IO when some processes do not contribute to the
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IO) and Complex Derived Datatype MPI functionalities are no longer
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conditionally enabled in the library by configure. They are always
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enabled in order to take advantage of performance boosts from these
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behaviors. Older MPI implementations that do not allow for these
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functionalities can no longer by used by HDF5. (MAM - 2011/07/08).
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2009-04-29 14:39:10 +08:00
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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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2009-01-06 22:58:21 +08:00
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Fortran Library:
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----------------
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2012-03-26 12:30:48 +08:00
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- Added for the C API the Fortran wrapper:
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h5ocopy_f (MSB - 2012/03/22)
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2011-10-15 04:09:53 +08:00
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HDF5 Fortran library was enhanced to support Fortran 2003 standard.
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The following features are available when the HDF5 library is configured
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using --enable-fortran --enable-fortran2003 configure flags AND
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if fortran compiler is Fortran2003 compliant:
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- Subroutines overloaded with the C_PTR derived type:
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h5pget_f
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h5pget_fill_value_f
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h5pinsert_f
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h5pregister_f
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h5pset_f
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h5pset_fill_value_f
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h5rcreate_f
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h5rderefrence_f
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h5rget_name_f
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h5rget_obj_type_f
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- Subroutines overloaded with the C_PTR derived type
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|
|
|
|
and simplified signatures:
|
|
|
|
|
|
h5aread_f
|
|
|
|
|
|
h5awrite_f
|
|
|
|
|
|
h5dread_f
|
|
|
|
|
|
h5dwrite_f
|
|
|
|
|
|
- New subroutines
|
|
|
|
|
|
h5dvlen_reclaim_f
|
|
|
|
|
|
h5literate_by_name_f
|
|
|
|
|
|
h5literate_f
|
|
|
|
|
|
h5ovisit_f
|
|
|
|
|
|
h5tconvert_f
|
|
|
|
|
|
|
|
|
|
|
|
- Subroutines with additional optional parameters:
|
|
|
|
|
|
h5pcreate_class_f
|
|
|
|
|
|
(EIP - 2011/10/14)
|
2009-01-06 22:58:21 +08:00
|
|
|
|
|
2009-04-18 01:58:05 +08:00
|
|
|
|
- Added for the C APIs the Fortran wrappers:
|
2009-04-21 00:26:17 +08:00
|
|
|
|
h5dget_access_plist_f
|
|
|
|
|
|
h5iis_valid_f
|
|
|
|
|
|
h5pset_chunk_cache_f
|
|
|
|
|
|
h5pget_chunk_cache_f
|
2009-04-18 01:58:05 +08:00
|
|
|
|
(MSB - 2009/04/17)
|
|
|
|
|
|
|
|
|
|
|
|
|
2009-01-06 22:58:21 +08:00
|
|
|
|
C++ Library:
|
|
|
|
|
|
------------
|
2011-08-15 21:30:30 +08:00
|
|
|
|
- New member functions
|
|
|
|
|
|
+ Overloaded CommonFG::getObjnameByIdx to take char* for name
|
|
|
|
|
|
+ Overloaded CommonFG::getObjTypeByIdx to return type name as a char*.
|
2010-05-14 23:14:05 +08:00
|
|
|
|
(BMR - 2010/05/02)
|
2011-08-15 21:30:30 +08:00
|
|
|
|
+ DataSet::getInMemDataSize() to simplify getting the dataset's
|
2010-05-14 23:14:05 +08:00
|
|
|
|
data size in memory. (BMR - 2009/07/26)
|
2009-01-06 22:58:21 +08:00
|
|
|
|
- These member functions were added as wrapper for H5Rdereference to
|
|
|
|
|
|
replace the incorrect IdComponent::dereference().
|
|
|
|
|
|
void H5Object::dereference(H5File& h5file, void* ref)
|
|
|
|
|
|
void H5Object::dereference(H5Object& obj, void* ref)
|
|
|
|
|
|
In addition, these constructors were added to create the associated
|
|
|
|
|
|
objects by way of dereference:
|
|
|
|
|
|
Attribute(H5Object& obj, void* ref);
|
|
|
|
|
|
Attribute(H5File& file, void* ref);
|
|
|
|
|
|
DataSet(H5Object& obj, void* ref);
|
|
|
|
|
|
DataSet(H5File& file, void* ref);
|
|
|
|
|
|
DataType(H5Object& obj, void* ref);
|
|
|
|
|
|
DataType(H5File& file, void* ref);
|
|
|
|
|
|
Group(H5Object& obj, void* ref);
|
|
|
|
|
|
Group(H5File& obj, void* ref);
|
|
|
|
|
|
(BMR - 2008/08/10)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Tools:
|
|
|
|
|
|
------
|
2012-03-13 05:27:11 +08:00
|
|
|
|
- h5dump: Added capability for "-a" option to show attributes containing "/"
|
|
|
|
|
|
by using an escape character. For example, for a dataset "/dset"
|
|
|
|
|
|
containing attribute "speed(m/h)", use "h5dump -a "/dset/speed(\/h)"
|
|
|
|
|
|
to show the content of the attribute. See details at HDFFV-7523
|
|
|
|
|
|
(PC -- 2012/03/12)
|
2012-03-13 04:36:10 +08:00
|
|
|
|
- h5dump: Added ability to apply command options across multiple files using a
|
|
|
|
|
|
wildcard in the filename. Example; "h5dump -H -d Dataset1 tarr*.h5".
|
|
|
|
|
|
HDFFV-7876 (ADB - 2012/03/12).
|
2012-03-10 04:34:37 +08:00
|
|
|
|
- h5repack: Improved performance for big chunked datasets (size > 128MB)
|
|
|
|
|
|
when used with layout (-l) or compression (-f) option.
|
|
|
|
|
|
It would perform much better prior to the improvement,
|
|
|
|
|
|
especially for cases that chunk dimentions looks like
|
|
|
|
|
|
"1024x5x1" (compare to "1x5x1024"). When bigger numbers
|
2012-03-02 06:59:46 +08:00
|
|
|
|
are toward front and smaller number is toward back in chunk
|
2012-03-10 04:34:37 +08:00
|
|
|
|
dimentions. HDFFV-7862 (JKM - 2012/03/01)
|
2012-02-13 22:18:09 +08:00
|
|
|
|
- h5dump: Added new option --no-compact-subset. This option will not
|
|
|
|
|
|
interpret the '[' character as starting the compact form of
|
|
|
|
|
|
subsetting. This is useful when the "h5dump error: unable to
|
|
|
|
|
|
open dataset "datset_name"" message is output because a dataset
|
2012-03-13 04:36:10 +08:00
|
|
|
|
name contains a '[' character. HDFFV-7689 (ADB - 2012/01/31)
|
2011-08-15 21:30:30 +08:00
|
|
|
|
- h5dump: Corrected schema location:
|
|
|
|
|
|
<hdf5:HDF5-File
|
|
|
|
|
|
xmlns:hdf5="http://hdfgroup.org/HDF5/XML/schema/HDF5-File"
|
|
|
|
|
|
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
|
|
|
|
|
xsi:schemaLocation="http://hdfgroup.org/HDF5/XML/schema/HDF5-File
|
|
|
|
|
|
http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd">
|
|
|
|
|
|
(ADB - 2011/08/10)
|
2011-03-26 01:02:03 +08:00
|
|
|
|
- h5diff: Added new level for -v (verbose) option. The new levels are
|
|
|
|
|
|
1 and 2. So -v1 and -v2 can be specified to view more
|
|
|
|
|
|
information about attributes differences.
|
|
|
|
|
|
Bug#2121 (JKM 2011/3/23)
|
2011-03-10 21:54:21 +08:00
|
|
|
|
- h5dump: Added new option --enable-error-stack. This option will display
|
|
|
|
|
|
error stack information in the output stream. This is useful
|
|
|
|
|
|
when the "h5dump: Unable to print data" message is output.
|
|
|
|
|
|
(ADB - 2011/02/24)
|
2010-09-17 05:46:16 +08:00
|
|
|
|
- h5diff: Add a new flag --exclude-path. Specified path to an object will
|
|
|
|
|
|
be excluded from comparing the two files or two groups. If group
|
|
|
|
|
|
is specified all the member objects will be excluded.
|
|
|
|
|
|
(JKM - 2010/09/16).
|
2010-07-08 02:52:04 +08:00
|
|
|
|
- h5ls: Add new flag --no-dangling-links. (refer to --help for details)
|
|
|
|
|
|
(JKM - 2010/06/15)
|
2010-06-02 23:13:13 +08:00
|
|
|
|
- h5ls: Add new flag --follow-symlinks. (refer to --help for details)
|
|
|
|
|
|
(JKM - 2010/05/25)
|
2010-02-17 03:43:05 +08:00
|
|
|
|
- h5diff: Add new flag --no-dangling-links. (refer to --help for details)
|
|
|
|
|
|
(JKM - 2010/02/10)
|
2010-05-22 04:12:22 +08:00
|
|
|
|
- h5diff: Add new flag --follow-symlinks. (refer to --help for details)
|
2010-01-26 09:33:09 +08:00
|
|
|
|
(JKM - 2010/01/25)
|
2009-11-21 02:56:01 +08:00
|
|
|
|
- h5diff: fix for displaying garbage value on LE machine for BE data.
|
2011-08-15 21:30:30 +08:00
|
|
|
|
(JKM - 2009/11/20)
|
2011-03-10 21:54:21 +08:00
|
|
|
|
- h5dump: subsetting now allows default for count. Also trailing ; in short form
|
|
|
|
|
|
can be omitted after last specified value.
|
|
|
|
|
|
(ADB - 2009/09/04)
|
|
|
|
|
|
- h5dump/h5ls: now can display data in region references
|
|
|
|
|
|
using new -R, --region flag.
|
|
|
|
|
|
(ADB - 2009/09/04)
|
|
|
|
|
|
- h5diff: new flag, -c, --compare, list objects that are not comparable.
|
|
|
|
|
|
(PVN - 2009/4/10 - 1368)
|
2009-08-17 22:19:59 +08:00
|
|
|
|
- h5diff new flag, -N, --nan, avoids NaNs detection. (PVN - 2009/4/10)
|
2009-04-04 05:53:22 +08:00
|
|
|
|
- h5dump correctly specifies XML dtd / schema urls (ADB - 2009/4/3 - 1519)
|
2009-04-03 04:31:16 +08:00
|
|
|
|
- h5repack now handles group creation order. (PVN - 2009/4/2 - 1402)
|
2009-01-06 22:58:21 +08:00
|
|
|
|
- h5dump: added a printing of the compression ratio of uncompressed and compressed
|
|
|
|
|
|
sizes for cases where compression filters are present. (PVN - 2008/05/01)
|
|
|
|
|
|
- h5dump: added an option to allow a user defined formatting string for printf
|
|
|
|
|
|
regarding floating point numbers. (PVN - 2008/05/06)
|
|
|
|
|
|
- h5dump: support for external links, display the object that the external link
|
|
|
|
|
|
points to. (PVN - 2008/05/12)
|
|
|
|
|
|
- h5repack: add a userblock to an HDF5 file during the repack. (PVN - 2008/08/26)
|
|
|
|
|
|
- h5repack: add 2 options that call H5Pset_alignment in the 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)
|
|
|
|
|
|
- h5diff: added support for long double (PVN - 2008/10/28)
|
|
|
|
|
|
- h5dump: binary output defaults to NATIVE with -b optionally accepting
|
|
|
|
|
|
the form of binary output (NATIVE, FILE, BE, LE). (PVN - 2008/10/30)
|
|
|
|
|
|
- h5diff: return 1 for file differences when both 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)
|
2009-01-09 03:06:37 +08:00
|
|
|
|
- h5repack: When user doesn't specify a chunk size, h5repack now defines a default
|
|
|
|
|
|
chunk size as the same size of the size of the hyperslab used to read the chunks.
|
|
|
|
|
|
The size of the hyperslabs are defined as the size of each dimension or a
|
|
|
|
|
|
predefined constant, whatever is smaller. This assures that the chunk
|
|
|
|
|
|
read fits in the chunk cache. (PVN - 2008/11/21)
|
2009-08-12 07:14:40 +08:00
|
|
|
|
- h5diff: h5diff treats two INFINITY values different. Fixed by checking (value==expect)
|
|
|
|
|
|
before call ABS(...) at h5diff_array.c This will make that (INF==INF) is true
|
|
|
|
|
|
(INF is treated as an number instead of NaN) (PC -- 2009/07/28)
|
2009-10-09 03:40:42 +08:00
|
|
|
|
- h5diff: add option "--use-system-epsilon" to print difference if (|a-b| > EPSILON)
|
|
|
|
|
|
Change default to use strict equality (PC -- 2009/09/12)
|
|
|
|
|
|
|
2009-03-12 03:10:21 +08:00
|
|
|
|
|
2009-01-06 22:58:21 +08:00
|
|
|
|
High-Level APIs:
|
|
|
|
|
|
------
|
|
|
|
|
|
- Table: In version 3.0 of Table, "NROWS" (used to store number of records) was
|
|
|
|
|
|
deprecated (PVN - 2008/11/24)
|
2009-03-24 04:06:13 +08:00
|
|
|
|
|
2011-10-15 04:09:53 +08:00
|
|
|
|
- Added Fortran wrappers for Dimension Scale APIs. HDFFV-3797
|
|
|
|
|
|
h5dsset_scale_f
|
|
|
|
|
|
h5dsattach_scale_f
|
|
|
|
|
|
h5dsdetach_scale_f
|
|
|
|
|
|
h5dsis_attached_f
|
|
|
|
|
|
h5dsis_scale_f
|
|
|
|
|
|
h5dsset_label_f
|
|
|
|
|
|
h5dsget_label_f
|
|
|
|
|
|
h5dsget_scale_name_f
|
|
|
|
|
|
h5dsget_num_scales_f
|
|
|
|
|
|
(EIP for SB - 2011/10/13)
|
2012-03-16 12:24:55 +08:00
|
|
|
|
|
|
|
|
|
|
- New API: h5ltpath_valid (Fortran: h5ltpath_valid_f) which checks
|
|
|
|
|
|
if a path is correct and determines if a link resolves to a valid
|
2012-03-26 12:30:48 +08:00
|
|
|
|
object and checks that the link does not dangle. (MSB- 2012/3/15)
|
2009-01-06 22:58:21 +08:00
|
|
|
|
|
|
|
|
|
|
Documentation
|
|
|
|
|
|
-------------
|
|
|
|
|
|
|
|
|
|
|
|
Support for new platforms, languages and compilers.
|
|
|
|
|
|
=======================================
|
2010-10-09 04:57:17 +08:00
|
|
|
|
- Intel V11.1 uses now -O3 optimization in production mode (EIP - 2010/10/08)
|
2009-08-12 04:13:07 +08:00
|
|
|
|
- PathScale compilers are recognized and can build the HDF5 library
|
|
|
|
|
|
properly. AKC - 2009/7/28 -
|
2009-01-06 22:58:21 +08:00
|
|
|
|
|
|
|
|
|
|
Bug Fixes since HDF5-1.8.0 release
|
|
|
|
|
|
==================================
|
|
|
|
|
|
|
|
|
|
|
|
Library
|
|
|
|
|
|
-------
|
2012-07-26 05:50:22 +08:00
|
|
|
|
- Fixed an error that could occur when calling H5Ocopy within an
|
|
|
|
|
|
H5Literate callback (and possibly other situations).
|
|
|
|
|
|
(NAF - 2012/7/25 - HDFFV-5853)
|
2012-03-29 05:02:30 +08:00
|
|
|
|
- Fixed an error that would occur when copying an object with attribute
|
|
|
|
|
|
creation order tracked and indexed. (NAF - 2012/3/28 - HDFFV-7762)
|
2012-03-28 14:21:14 +08:00
|
|
|
|
- Fixed a bug in H5Ocopy(): When copying an opened object, call the
|
|
|
|
|
|
object's flush class action to ensure that cached data is flushed
|
|
|
|
|
|
so that H5Ocopy will get the correct data.
|
|
|
|
|
|
(VC - 2012/3/27 - HDFFV-7853)
|
2012-03-24 00:09:08 +08:00
|
|
|
|
- When an application tries to write or read many small data chunks and
|
|
|
|
|
|
runs out of memory, the library had a seg fault. The fix is to
|
|
|
|
|
|
return the error stack with proper information. (SLU - 2012/3/23.
|
|
|
|
|
|
Issue 7785)
|
2012-03-16 04:53:14 +08:00
|
|
|
|
- H5Pset_data_transform had seg fault in some cases like x*-100. It
|
|
|
|
|
|
works correctly now and handles other cases like 100-x or 2/x.
|
|
|
|
|
|
(SLU - 2012/3/15. Issue 7922)
|
2012-03-16 03:16:24 +08:00
|
|
|
|
- Fixed rare corruption bugs that could occur when using the new object
|
|
|
|
|
|
header format. (NAF - 2012/3/15 - HDFFV-7879)
|
2012-01-26 04:06:09 +08:00
|
|
|
|
- Creating a dataset in a read-only file caused seg fault when the file
|
2012-03-17 00:12:20 +08:00
|
|
|
|
is closed. It's fixed. The attemp to create a dataset will fail
|
|
|
|
|
|
with the error stack indicating the file is read-only. (SLU -
|
|
|
|
|
|
2012/1/25. Issue 7756)
|
2011-12-02 02:35:54 +08:00
|
|
|
|
- Fixed a seg fault that could occur when shrinking a dataset with chunks
|
|
|
|
|
|
larger than 1 MB. (NAF - 2011/11/30 - HDFFV-7833)
|
2012-03-29 03:45:49 +08:00
|
|
|
|
- Fixed a bug that could cause file corruption when copying named
|
|
|
|
|
|
datatypes to a file using shared messages. (NAF - 2011/11/14)
|
|
|
|
|
|
- Fixed a bug that could cause H5Oget_info to return the wrong address
|
|
|
|
|
|
after copying a named datatype. (NAF - 2011/11/14)
|
2011-11-09 06:34:00 +08:00
|
|
|
|
- The library allowed the conversion of strings between ASCII and UTF8
|
|
|
|
|
|
(Issue 7582). We have corrected it to report an error under this
|
|
|
|
|
|
situation. (SLU - 2011/11/8)
|
2011-10-26 22:25:16 +08:00
|
|
|
|
- The library had seg fault when it tried to shrink the size of compound type
|
|
|
|
|
|
through H5Tset_size immediately after the type was created (Issue
|
|
|
|
|
|
7618). It's fixed now. (SLU - 2011/10/26)
|
2011-10-21 06:06:38 +08:00
|
|
|
|
- Fixed a bug that occurred when using H5Ocopy on a committed datatype
|
|
|
|
|
|
containing an attribute using that committed datatype.
|
|
|
|
|
|
(NAF - 2011/10/13 - Issue 5854)
|
2011-09-07 00:50:32 +08:00
|
|
|
|
- #ifdef _WIN32 instances changed to #ifdef H5_HAVE_WIN32_API and added
|
|
|
|
|
|
H5_HAVE_VISUAL_STUDIO checks where necessary. CMake only as configure
|
|
|
|
|
|
never set _WIN32.
|
2011-09-02 23:54:06 +08:00
|
|
|
|
- CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv
|
|
|
|
|
|
discovered 3 problems in tests and tools' library (Issue 7674):
|
|
|
|
|
|
1. In dsets.c, left shifting an unsigned int for 32 bits or more
|
|
|
|
|
|
caused undefined behavior.
|
|
|
|
|
|
2. In dt_arith.c, the INIT_INTEGER macro definition has an overflow
|
|
|
|
|
|
when the value is negative minimal and is being subtracted one.
|
|
|
|
|
|
3. In tools/lib/h5tools_str.c, right shifting an int value for 32 bits
|
|
|
|
|
|
or more caused undefined behavior.
|
|
|
|
|
|
All the problems have been corrected. (SLU - 2011/9/2)
|
2011-06-22 23:47:57 +08:00
|
|
|
|
- In v1.6 library, there was EOA for the whole MULTI file saved in the
|
|
|
|
|
|
super block. We took it out in v1.8 library because it's meaningless
|
|
|
|
|
|
for the MULTI file. v1.8 library saves the EOA for the metadata file,
|
|
|
|
|
|
instead. But this caused some backward compatibility problem.
|
|
|
|
|
|
v1.8 library couldn't open the file created with v1.6 library. We
|
|
|
|
|
|
fixed the problem by checking the EOA value to detect the file
|
|
|
|
|
|
created with v1.6 library. (SLU - 2011/6/22)
|
2011-06-03 23:58:49 +08:00
|
|
|
|
- When a dataset had filters and reading data failed, the error message
|
|
|
|
|
|
didn't say which filter isn't registered. It's fixed now.
|
|
|
|
|
|
(SLU - 2011/6/3)
|
2011-02-19 03:01:34 +08:00
|
|
|
|
- The datatype handler created with H5Tencode/decode used to have the
|
|
|
|
|
|
reference count 0 (zero). I have fixed it. It is 1 (one) now.
|
|
|
|
|
|
(SLU - 2011/2/18)
|
2011-02-02 22:41:49 +08:00
|
|
|
|
- Fixed a bug that caused big endian machines to generate corrupt files
|
|
|
|
|
|
when using the scale-offset filter with floating point data or
|
|
|
|
|
|
fill values. Note that such datasets will no longer be readable
|
2011-02-02 23:05:03 +08:00
|
|
|
|
by any machine after this patch. (NAF - 2010/02/02 - Bug 2131)
|
2010-11-17 23:08:33 +08:00
|
|
|
|
- Retrieving a link's name by index in the case where the link is
|
|
|
|
|
|
external and the file that the link refers to doesn't exist will
|
|
|
|
|
|
now fail gracefully rather than cause a segmentation fault.
|
|
|
|
|
|
(MAM - 2010/11/17)
|
2010-09-22 01:52:12 +08:00
|
|
|
|
- Modified library to always cache symbol table information. Libraries
|
|
|
|
|
|
version 1.6.3 have a bug which causes them to require this
|
|
|
|
|
|
information for some operations. (NAF - 2010/09/21 - 1864)
|
2010-09-15 23:29:38 +08:00
|
|
|
|
- Fixed a bug that could occur when getting information for a new-style
|
|
|
|
|
|
group that was previously opened through a file handle that was
|
|
|
|
|
|
later closed. (NAF - 2010/09/15)
|
2010-09-13 23:54:55 +08:00
|
|
|
|
- Added define check in H5public.h if stdint.h is supported by the C++
|
|
|
|
|
|
compiler. This define is only available on Windows with VS2010 and
|
|
|
|
|
|
using CMake to build the library. (ADB - 2010/09/13 - Bug 1938)
|
2010-09-07 23:41:55 +08:00
|
|
|
|
- H5Eset_current_stack now also closes the error stack to be set as the
|
|
|
|
|
|
default. This is to avoid a potential problem (Bug 1799).
|
|
|
|
|
|
(SLU - 2010/9/7)
|
2010-08-06 01:14:39 +08:00
|
|
|
|
- Fixed the bug in the filter's public CAN_APPLY function. The return
|
|
|
|
|
|
value should be htri_t not herr_t (Bug #1239). (SLU - 2010/8/5)
|
2010-07-29 06:23:11 +08:00
|
|
|
|
- Fixed a bug in the direct I/O driver that could render files with
|
|
|
|
|
|
certain kinds of unaligned data unreadable or corrupt them.
|
|
|
|
|
|
(NAF - 2010/07/28)
|
2010-07-29 03:46:31 +08:00
|
|
|
|
- valgrind reported an error of copying data to itself when a new attribute
|
|
|
|
|
|
is written (Bug #1956). I fixed it by taking out the memcpy step in
|
|
|
|
|
|
the attribute code. (SLU - 2010/07/28)
|
2010-07-17 00:32:49 +08:00
|
|
|
|
- Fixed a bug that could cause file corruption when using non-default
|
|
|
|
|
|
sizes of addresses and/or lengths. This bug could also cause
|
|
|
|
|
|
uncorrupted files with this property to be unreadable. This bug
|
|
|
|
|
|
was introduced in 1.8.5. (NAF - 2010/07/16 - 1951)
|
2010-05-21 05:55:55 +08:00
|
|
|
|
- Fixed a file corruption bug that could happen when shrinking a
|
|
|
|
|
|
compressed dataset. (NAF - 2010/05/20)
|
2010-05-15 02:44:36 +08:00
|
|
|
|
- Fixed some memory leaks in VL datatype conversion when strings are
|
|
|
|
|
|
used as fill values. (MAM - 2010/05/12 - BZ# 1826)
|
2010-04-09 02:29:59 +08:00
|
|
|
|
- Fixed a bug when copying objects with NULL references with the
|
|
|
|
|
|
H5O_COPY_EXPAND_REFERENCE_FLAG flag set. (NAF - 2010/04/08 - 1815)
|
2010-03-10 02:19:42 +08:00
|
|
|
|
- Files can now be concurrently opened more than once using the core file
|
|
|
|
|
|
driver, as long as the backing store is used. (NAF - 2010/03/09)
|
2010-03-06 01:51:45 +08:00
|
|
|
|
- Added support for H5O_COPY_EXPAND_EXT_LINK_FLAG to H5Ocopy. External
|
|
|
|
|
|
links will now be expanded if this flag is set.
|
|
|
|
|
|
(NAF - 2010/03/05 - 1733)
|
2010-03-06 01:24:17 +08:00
|
|
|
|
- Fixed a bug where the library, when traversing an external link, would
|
|
|
|
|
|
reopen the source file if nothing else worked. (NAF - 2010/03/05)
|
2010-02-17 01:18:38 +08:00
|
|
|
|
- Fixed an intermittent bug in the b-tree code which could be triggered
|
|
|
|
|
|
by expanding and shrinking chunked datasets in certain ways.
|
|
|
|
|
|
(NAF - 2010/02/16)
|
2009-12-11 00:39:58 +08:00
|
|
|
|
- H5Tdetect_class said a VL string is a string type. But when it's
|
|
|
|
|
|
in a compound type, it said it's a VL type (Bug #1584). I fixed it
|
|
|
|
|
|
to be consistent. It always return string type. (SLU - 2009/12/10)
|
2009-10-28 10:52:05 +08:00
|
|
|
|
- Fixed a bug where writing and deleting many global heap objects (i.e.
|
|
|
|
|
|
variable length data) would render the file unreadable. Previously
|
|
|
|
|
|
created files exhibiting this problem should now be readable.
|
2009-12-11 00:39:58 +08:00
|
|
|
|
(NAF - 2009/10/27 - 1483)
|
|
|
|
|
|
- Fixed incorrect return value for H5Pget_preserve. (AKC - 2009/10/08 - 1628)
|
2009-10-03 04:40:01 +08:00
|
|
|
|
- Fixed an assertion failure that occurred when H5Ocopy was called on a
|
|
|
|
|
|
dataset using a vlen inside a compound. (NAF - 2009/10/02 - 1597)
|
2009-09-26 03:13:22 +08:00
|
|
|
|
- Fixed incorrect return value for H5Pget_filter_by_id1/2 in H5Ppublic.h.
|
|
|
|
|
|
(NAF - 2009/09/25 - 1620)
|
2009-09-26 03:08:41 +08:00
|
|
|
|
- Fixed a bug where properties weren't being compared with the registered
|
|
|
|
|
|
compare callback. (NAF - 2009/09/25 - 1555)
|
2009-06-26 02:56:00 +08:00
|
|
|
|
- Fixed a bug where H5Pget_fitler_by_id would succeed when called for a
|
2009-06-27 03:53:12 +08:00
|
|
|
|
filter that wasn't present. (NAF - 2009/06/25 - 1250)
|
2009-06-11 03:17:26 +08:00
|
|
|
|
- Fixed an issue with committed compound datatypes containing a vlen.
|
|
|
|
|
|
Also fixed memory leaks involving committed datatypes.
|
|
|
|
|
|
(NAF - 2009/06/10 - 1593)
|
2009-04-21 03:12:19 +08:00
|
|
|
|
- Added versioning to H5Z_class_t struct to allow compatibility with 1.6
|
|
|
|
|
|
API. (NAF - 2009/04/20 - 1533)
|
2009-04-21 00:54:52 +08:00
|
|
|
|
- Fixed a problem with using data transforms with non-native types in the
|
|
|
|
|
|
file. (NAF - 2009/04/20 - 1548)
|
2009-04-14 22:06:22 +08:00
|
|
|
|
- Added direct.h include file to windows section of H5private.h
|
|
|
|
|
|
to fix _getcwd() warning. (ADB - 2009/04/14 - 1536)
|
2009-04-11 04:07:14 +08:00
|
|
|
|
- Fixed a bug that prevented external links from working after calling
|
|
|
|
|
|
H5close(). (NAF - 2009/04/10 - 1539)
|
2009-04-09 05:53:31 +08:00
|
|
|
|
- Modified library to write cached symbol table information to the
|
|
|
|
|
|
superblock, to allow library versions 1.3.0 to 1.6.3 to read files
|
2009-04-09 06:17:48 +08:00
|
|
|
|
created by this version. (NAF - 2009/04/08 - 1423)
|
2009-04-09 01:02:09 +08:00
|
|
|
|
- Changed skip lists to use a deterministic algorithm. The library should
|
|
|
|
|
|
now never call rand() or srand(). (NAF - 2009/04/08 - 503)
|
2009-04-08 07:04:19 +08:00
|
|
|
|
- Fixed a bug where H5Lcopy and H5Lmove wouldn't create intermediate
|
|
|
|
|
|
groups when that property was set. (NAF - 2009/04/07 - 1526)
|
2009-03-26 23:31:27 +08:00
|
|
|
|
- Fixed a bug that caused files with a user block to grow by the size of
|
|
|
|
|
|
the user block every time they were opened.
|
|
|
|
|
|
(NAF - 2009/03/26 - 1499)
|
2009-03-24 03:17:12 +08:00
|
|
|
|
- Fixed a rare problem that could occur with files using the old (pre 1.4)
|
|
|
|
|
|
array datatype. (NAF - 2009/03/23)
|
|
|
|
|
|
- Modified library to be able to open files with corrupt root group symbol
|
|
|
|
|
|
table messages, and correct these errors if they are found. Such
|
|
|
|
|
|
files can only be successfully opened with write access.
|
|
|
|
|
|
(NAF - 2009/03/23 - 1189)
|
2009-03-05 21:48:54 +08:00
|
|
|
|
- Removed the long_long #define and replaced all instances with
|
|
|
|
|
|
"long long". This caused problems with third party products. All
|
|
|
|
|
|
currently supported compliers support the type. (ADB - 2009/03/05)
|
2009-02-28 01:01:00 +08:00
|
|
|
|
- Fixed various bugs that could prevent the fill value from being written
|
2009-03-26 23:31:27 +08:00
|
|
|
|
in certain rare cases. (NAF - 2009/02/26 - 1469)
|
2009-02-13 04:46:32 +08:00
|
|
|
|
- Fixed a bug that prevented more than one dataset chunk from being cached
|
2009-03-26 23:31:27 +08:00
|
|
|
|
at a time. (NAF - 2009/02/12 - 1015)
|
2009-02-13 03:06:37 +08:00
|
|
|
|
- Fixed an assertion failure caused by opening an attribute multiple times
|
2009-03-26 23:31:27 +08:00
|
|
|
|
through multiple file handles. (NAF - 2009/02/12 - 1420)
|
2009-02-13 02:59:11 +08:00
|
|
|
|
- Fixed a problem that could prevent the user from adding attributes (or
|
2009-03-26 23:31:27 +08:00
|
|
|
|
any object header message) in some circumstances.
|
|
|
|
|
|
(NAF - 2009/02/12 - 1427)
|
2009-02-13 02:47:04 +08:00
|
|
|
|
- Fixed a bug that could cause problems when an attribute was added to a
|
|
|
|
|
|
committed datatype using the committed datatype's datatype.
|
|
|
|
|
|
(NAF - 2009/02/12)
|
|
|
|
|
|
- Fixed a bug that could cause problems when copying an object with a
|
|
|
|
|
|
shared message in its own object header. (NAF - 2009/01/29)
|
2009-01-27 23:56:48 +08:00
|
|
|
|
- Changed H5Tset_order to properly reject H5T_ORDER_NONE for most
|
2009-03-26 23:31:27 +08:00
|
|
|
|
datatypes. (NAF - 2009/01/27 - 1443)
|
2009-01-14 23:30:51 +08:00
|
|
|
|
- Fixed a bug where H5Tpack wouldn't remove trailing space from an
|
|
|
|
|
|
otherwise packed compound type. (NAF - 2009/01/14)
|
2009-01-06 22:58:21 +08:00
|
|
|
|
- Fixed up some old v2 btree assertions that get run in debug mode that
|
|
|
|
|
|
were previously failing on compilation, and removed some of the
|
|
|
|
|
|
more heavily outdated and non-rewritable ones. (MAM - 2008/12/15)
|
|
|
|
|
|
- Fixed a bug that could cause problems when "automatically" unmounting
|
2009-01-14 23:30:51 +08:00
|
|
|
|
multiple files. (NAF - 2008/11/17)
|
2009-01-06 22:58:21 +08:00
|
|
|
|
- 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
|
2009-01-14 23:30:51 +08:00
|
|
|
|
than could be written to the file. (NAF - 2008/10/23)
|
2009-01-06 22:58:21 +08:00
|
|
|
|
- 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
|
2009-01-14 23:30:51 +08:00
|
|
|
|
by the library for internal library use. (NAF - 2008/10/06)
|
2009-01-06 22:58:21 +08:00
|
|
|
|
- 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
|
2009-01-14 23:30:51 +08:00
|
|
|
|
during compound type conversion. (NAF - 2008/09/19)
|
2009-01-06 22:58:21 +08:00
|
|
|
|
- Fixed pointer alignment violations that could occur during vlen
|
2009-01-14 23:30:51 +08:00
|
|
|
|
conversion. (NAF - 2008/09/16)
|
2009-01-06 22:58:21 +08:00
|
|
|
|
- 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
|
2009-01-14 23:30:51 +08:00
|
|
|
|
from that due to internal library routines. (NAF - 2008/08/19)
|
2009-01-06 22:58:21 +08:00
|
|
|
|
- Fixed assertion failure caused by incorrect array datatype version.
|
|
|
|
|
|
(NAF - 2008/08/08)
|
|
|
|
|
|
- Fixed an issue where mount point traversal would fail when using
|
2009-01-14 23:30:51 +08:00
|
|
|
|
multiple handles for the child. (NAF - 2008/08/07)
|
2009-01-06 22:58:21 +08:00
|
|
|
|
- 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)
|
|
|
|
|
|
- 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 - 2008/07/22
|
|
|
|
|
|
- Fixed issue where a group could have a file mounted on it twice.
|
|
|
|
|
|
(QAK - 2008/07/15)
|
|
|
|
|
|
- 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
|
|
|
|
|
|
- Fixed the problem with the searching of target file for H5Lcreate_external().
|
2011-08-15 21:30:30 +08:00
|
|
|
|
The searching pattern will depend on whether the target file's
|
|
|
|
|
|
pathname is an absolute or a relative path. Please see the description
|
|
|
|
|
|
in the RM for H5Lcreate_external(). (VC - 2008/04/08)
|
2009-01-06 22:58:21 +08:00
|
|
|
|
- Fixed possible file corruption bug when encoding datatype
|
|
|
|
|
|
descriptions for compound datatypes whose size was between
|
|
|
|
|
|
256 & 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 handle invalid location
|
|
|
|
|
|
ID correctly. (QAK - 2008/03/11)
|
2009-01-09 03:06:37 +08:00
|
|
|
|
- H5Dset_extent: when shrinking dimensions, some chunks were not deleted.
|
|
|
|
|
|
(PVN - 2009/01/8)
|
2009-01-10 03:53:30 +08:00
|
|
|
|
- Added code to maintain a min_clean_fraction in the metadata cache when
|
|
|
|
|
|
in serial mode. (MAM - 2009/01/9)
|
2009-01-09 03:06:37 +08:00
|
|
|
|
|
2009-01-06 22:58:21 +08:00
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Configuration
|
|
|
|
|
|
-------------
|
2012-03-27 04:26:06 +08:00
|
|
|
|
- Fixed Makefile issue in which "-Wl," was not properly specified
|
|
|
|
|
|
prior to -rpath when building parallel fortran libraries with
|
|
|
|
|
|
an Intel compiler. (MAM - 2012/03/26)
|
2012-03-27 03:34:42 +08:00
|
|
|
|
- Makefiles generated by other packages using h5cc as the compiler
|
|
|
|
|
|
no longer error when 'make' is invoked more than once in order
|
|
|
|
|
|
to 'rebuild' after changes to source. (MAM - 2012/03/26)
|
2011-10-15 04:09:53 +08:00
|
|
|
|
- Added --enable-fortran2003 flag to enable Fortran2003 support
|
|
|
|
|
|
in the HDF5 Fortran library. The flag should be used along with the
|
|
|
|
|
|
--enable-fortran flag and takes affect only when Fortran compiler
|
|
|
|
|
|
is Fortran2003 compliant. (EIP - 2011/11/14)
|
|
|
|
|
|
|
2011-10-05 01:50:49 +08:00
|
|
|
|
- In Windows platform, the default VFD, was Windows VFD, is restored back
|
|
|
|
|
|
to the SEC2, aka POSIX, VFD. The Windows VFD is deprecated. HDFFV-7740
|
|
|
|
|
|
(AKC 2011/09/26)
|
2011-04-16 04:10:47 +08:00
|
|
|
|
- Removed config/ibm-aix6.x. All IBM-AIX settings are in one file,
|
|
|
|
|
|
ibm-aix. (AKC - 2011/4/14)
|
[svn-r20475] Purpose:
- Revise shared Fortran library disabling scenarios in configure
- Improve configure output summary
Description:
Shared Fortran libraries are not supported on Mac, but were being
disabled by configure in a way that also forced the C libraries
to be static-only. This has been fixed, so now only shared Fortran
is disabled while shared C can remain.
This prompted two additional changes:
1. While working on the check that addresses whether or not
shared Fortran libraries are allowed, removed old and no
longer needed check(s) that disable shared Fortran
libraries with HP, Intel 8, PGI, and Absoft compilers.
(Essentially, Mac is the only situation in which Fortran
shared are disabled by configure.)
2. Having two different states of libraries (i.e. shared C
library with static-only Fortran library) was not apparent
in the configure summary, which labeled all libraries as
either shared and/or static. I've added lines to both the
C++ and Fortran output sections to list shared/static-ness
of these libraries specifically.
Additionally, I've made sure that the new --enable-unsupported
configure option correctly overrides configure if it tries to
disable a shared library.
Tested:
jam, fred, & h5committest
2011-04-12 05:00:38 +08:00
|
|
|
|
- Shared C libraries are no longer disabled on Mac when Fortran
|
|
|
|
|
|
is enabled. Shared Fortran libraries are still not supported on Mac,
|
|
|
|
|
|
so configure will disable them by default, but this is overridable
|
|
|
|
|
|
with the new --enable-unsupported configure option. The configure
|
|
|
|
|
|
summary has been updated to reflect the fact that the shared-ness of
|
|
|
|
|
|
the C++/Fortran wrapper libraries may not align with the C library.
|
|
|
|
|
|
(MAM - 04/11/2011 - HDFFV-4353).
|
2010-07-15 01:07:50 +08:00
|
|
|
|
- Removed recognition of the parallel compilers of LAM(hcc) and
|
|
|
|
|
|
ChMPIon(cmpicc) since we have no access to these two MPI implementations
|
|
|
|
|
|
and cannot verify their correctness. (AKC - 2010/7/14 - Bug 1921)
|
[svn-r17616] Purpose:
CFLAGS overhaul
Description:
Modified the way configure handles CFLAGS.
(note: all changes also apply to FCFLAGS, CXXFLAGS, CPPFLAGS, and LDFLAGS).
1. The configure process will now always preserve a user's CFLAGS
environment variable setup. Any additional flags necessary for compilation
added at configure time will be passed into the Makefiles as AM_CFLAGS,
which is an automake construct to be used in addition to CFLAGS.
This will allow a user to have the final say, as CFLAGS will always appear
later in the compile line than AM_CFLAGS. Additionally, setting CFLAGS
during make will no longer completely erase all flags set by configure,
since they're maintained in AM_CFLAGS.
2. Additionally, where possible, flags previously being assigned directly
into CFLAGS (and thus propagating into h5cc) have now been redirected into
H5_CFLAGS, so they're used ONLY for compiling hdf5, and not embedded into
the h5cc wrapper script as well.
*Note that H5_CFLAGS ultimately is assigned into AM_CFLAGS for use in the
Makefiles. Complete description of changes and build process will be
included in a Configure Document that Elena and I are working on.
3. Removed unsupported config files. This includes:
config/dec-osf*
config/hpux11.00
config/irix5.x
config/powerpc-ibm-aix4.x
config/rs6000-ibm-aix5.x
config/unicos*
4. Modified configure summary to display additional values. Specifically,
appropriate AM_* variables are being shown, as well as H5_FCFLAGS and
H5_CXXFLAGS, which were for some reason not already present.
Tested:
- H5committest
- Tested on all THG / NCSA machines, using several combinations of the more
prominent configure options (c++, fortran, szip, threadsafe, parallel,
et cetera). (Thanks to Quincey for rysnc testing setup!)
- With regards to new automated testing, anything *necessary* for
compilation will be caught by the daily tests as it stands now. (i.e.,
if LDFLAGS is not properly set when szip is used, linking will fail).
Additionally, with regards to which flags get into h5cc, if any
*necessary* flags have been improperly removed, then daily tests should
fail during make installcheck. Additional machine-specific desired
behaviors and/or checks may have to be set up separately within the
daily tests, so this is something to work on.
2009-10-08 23:17:30 +08:00
|
|
|
|
- Removed the following config files, as we no longer support them:
|
|
|
|
|
|
config/dec-osf*, config/hpux11.00, config/irix5.x,
|
|
|
|
|
|
config/powerpc-ibm-aix4.x config/rs6000-ibm-aix5.x config/unicos*
|
|
|
|
|
|
MAM - 2009/10/08
|
|
|
|
|
|
- Modified configure and make process to properly preserve user's CFLAGS
|
|
|
|
|
|
(and company) environment variables. Build will now properly use
|
|
|
|
|
|
automake's AM_CFLAGS for any compiler flags set by the configure
|
|
|
|
|
|
process. Configure will no longer modify CFLAGS directly, nor will
|
|
|
|
|
|
setting CFLAGS during make completely replace what configure has set up.
|
|
|
|
|
|
MAM - 2009/10/08
|
2009-10-07 13:08:05 +08:00
|
|
|
|
- Support for TFLOPS, config/intel-osf1, is removed since the TFLOPS
|
|
|
|
|
|
machine has long retired. AKC - 2009/10/06.
|
2009-10-02 03:51:57 +08:00
|
|
|
|
- Added $(EXEEXT) extension to H5detect when it's executed in the
|
|
|
|
|
|
src/Makfile to generate H5Tinit.c so it works correctly on platforms
|
|
|
|
|
|
that require the full extension when running executables.
|
|
|
|
|
|
MAM - 2009/10/01 - BZ #1613
|
2009-10-02 01:05:38 +08:00
|
|
|
|
- Configure will now set FC and CXX to "no" when fortran and c++
|
|
|
|
|
|
are not being compiled, respectively, so configure will not run
|
|
|
|
|
|
some of the compiler tests for these languages when they are not
|
|
|
|
|
|
being used. MAM - 2009/10/01
|
2009-08-12 04:13:07 +08:00
|
|
|
|
- The PathScale compiler (v3.2) was mistaken as gcc v4.2.0 but it fails to
|
|
|
|
|
|
recognize some gcc options. Fixed. (see bug 1301). AKC - 2009/7/28 -
|
2009-11-04 22:39:45 +08:00
|
|
|
|
- The --enable-static-exec flag will now properly place the -static flag
|
|
|
|
|
|
on the link line of all installed executables. This will force the
|
|
|
|
|
|
executable to link with static libraries over shared libraries, provided
|
|
|
|
|
|
the static libraries are available. MAM - 2009/08/31 - BZ #1583
|
2009-03-11 05:01:50 +08:00
|
|
|
|
- The --includedir=DIR configuration option now works as intended, and can
|
|
|
|
|
|
be used to specify the location to install C header files. The default
|
|
|
|
|
|
location remains unchanged, residing at ${prefix}/include.
|
|
|
|
|
|
MAM - 2009/03/10 - BZ #1381
|
2009-03-10 01:50:53 +08:00
|
|
|
|
- Configure no longer removes the '-g' flag from CFLAGS when in production
|
|
|
|
|
|
mode if it has been explicitly set in the CFLAGS environment variable
|
|
|
|
|
|
prior to configuration. MAM - 2009/03/09 - BZ #1401.
|
2009-01-06 22:58:21 +08:00
|
|
|
|
- Fixed error with 'make check install' failing due to h5dump
|
|
|
|
|
|
needing other tools built first. MAM - 2008/10/24.
|
2011-06-22 23:47:57 +08:00
|
|
|
|
- Wpen using shared szip, it is no longer necessary to specify
|
2009-01-06 22:58:21 +08:00
|
|
|
|
the path to the shared szip libraries in LD_LIBRARY_PATH. MAM -
|
|
|
|
|
|
2008/10/24.
|
|
|
|
|
|
- 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.
|
|
|
|
|
|
|
|
|
|
|
|
Performance
|
|
|
|
|
|
-------------
|
2012-09-23 03:44:14 +08:00
|
|
|
|
- Retired program perform/mpi-perf. Its purpose has been incorporated
|
|
|
|
|
|
into h5perf before. (AKC 2012/09/20)
|
2011-08-15 22:06:53 +08:00
|
|
|
|
- ifdefs added to tests around include unistd.h and function to simulate
|
|
|
|
|
|
getlogin() on Windows.
|
|
|
|
|
|
(ADB - 2011/08/15)
|
2009-06-12 03:29:54 +08:00
|
|
|
|
- perf_serial test added to Windows projects and check batch file.
|
|
|
|
|
|
(ADB - 2009/06/11)
|
2012-06-24 07:31:40 +08:00
|
|
|
|
Fortran
|
|
|
|
|
|
--------
|
|
|
|
|
|
- Fixed a typo in return value of the nh5dread_f_c function ( was 1
|
|
|
|
|
|
instead of 0 on success); fixed the return value to make it consistent
|
|
|
|
|
|
with other Fortran functions; cleaned the code from debug statements.
|
|
|
|
|
|
(EIP - 2012/06/23)
|
2009-01-06 22:58:21 +08:00
|
|
|
|
|
|
|
|
|
|
Tools
|
|
|
|
|
|
-----
|
2012-09-11 05:40:47 +08:00
|
|
|
|
- h5diff: Fixed not to accumulate attribute difference to dataset
|
|
|
|
|
|
difference in verbose mode (-v, -r), which caused incorrect
|
|
|
|
|
|
difference between dataset and group/datatype object if attribute
|
|
|
|
|
|
exist with any differences. This also lead to fix inconsistent
|
|
|
|
|
|
format indicating difference between dataset and group/datatype
|
|
|
|
|
|
object. HDFFV-5919 (JKM 2012/09/05)
|
2012-08-16 00:04:26 +08:00
|
|
|
|
- h5diff: Fixed the incorrect result when comparing attribute data
|
|
|
|
|
|
values and the data type has same class but different size.
|
2012-09-11 05:40:47 +08:00
|
|
|
|
HDFFV-7942 (JKM 2012/08/15)
|
2012-08-02 01:07:46 +08:00
|
|
|
|
- ph5diff: Fixed intermittent hang issue on a certain operation in
|
|
|
|
|
|
parallel mode. It was detected by daily test for comparing
|
|
|
|
|
|
non-comparable objects, but it could have occurred in other
|
|
|
|
|
|
operations depend on machine condition. HDFFV-8003 (JKM 2012/08/01)
|
2012-08-01 23:37:40 +08:00
|
|
|
|
- h5diff: Fixed test failure for "make check" due to failure of
|
|
|
|
|
|
copying test files when performed in HDF5 source tree. Also applied
|
|
|
|
|
|
to other tools.
|
|
|
|
|
|
HDFFV-8107 (JKM 2012/08/01)
|
2012-07-22 14:42:30 +08:00
|
|
|
|
- h5diff: Fixed the Function COPY_TESTFILES_TO_TESTDIR() of
|
|
|
|
|
|
testh5diff.sh to better report when there is an error in the file
|
|
|
|
|
|
copying. HDFFV-8105 (AKC -2012/07/22)
|
2012-04-26 23:56:16 +08:00
|
|
|
|
- h5diff: Fixed not to check and display dangling link status without
|
|
|
|
|
|
--follow-symlinks option. This also improved performance when
|
|
|
|
|
|
comparing lots of external links without the --follow-symlinks
|
|
|
|
|
|
option. HDFFV-7998 (JKM 2012/04/26)
|
2012-04-20 05:38:07 +08:00
|
|
|
|
- h5unjam: Fixed sefgault when used -V (show version) option.
|
|
|
|
|
|
HDFFV-8001 (JKM 2012/04/19)
|
2012-04-12 04:57:10 +08:00
|
|
|
|
- h5repack: Fixed a failure when change the chunk size of a specified
|
|
|
|
|
|
chunked dataset with unlimited max dims. HDFFV-7993 (JKM 2012/04/11)
|
[svn-r22176] Purpose:
Fix for HDFFV-7644 GMQS: h5diff - incorrect behaviors when comparing HDF5 files with different type of objects (dataset, group, type) as common objects
Description:
Fixed failure for comparing same named object with different object types in comparing groups. (common object comparison)
Prior to the fix, h5diff resulted in error. After the fix, h5diff detects such case as non-comparable and display messages accordingly.
Test cases were added and tagged with jira#.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
2012-03-29 06:09:38 +08:00
|
|
|
|
- h5diff: Fixed failure for comparing same named object with different
|
|
|
|
|
|
object types in comparing groups. Prior to the fix, h5diff resulted
|
|
|
|
|
|
in error. After the fix, h5diff detects such case as non-comparable
|
|
|
|
|
|
and display messages accordingly. HDFFV-7664 (JKM 2012/03/28)
|
2012-03-22 05:00:15 +08:00
|
|
|
|
- h5diff: If unique objects exists only in one file and try to exclude
|
|
|
|
|
|
the unique objects with --exclude-path option, h5diff missed
|
|
|
|
|
|
excluding some objects.
|
|
|
|
|
|
Fixed to exclude objects correctly in such case.
|
|
|
|
|
|
HDFFV-7837 (JKM 2012/03/20)
|
2012-03-13 04:36:10 +08:00
|
|
|
|
- h5dump: Added tools library error stack to properly catch error
|
|
|
|
|
|
information generated within the library.
|
|
|
|
|
|
HDFFV-7958 (ADB 2012/03/12)
|
|
|
|
|
|
- h5dump: Dangling links no longer throw error message, change process
|
|
|
|
|
|
when open link fails.
|
|
|
|
|
|
HDFFV-7839 (ADB 2012/03/12)
|
2012-03-10 04:34:37 +08:00
|
|
|
|
- h5diff: When two symbolic dangling links are compared with
|
|
|
|
|
|
--follow-symlinks option, the result should be same. It worked for
|
|
|
|
|
|
comparing two files, but didn't work for comparing two objects.
|
|
|
|
|
|
HDFFV-7835 (JKM 2012/03/09)
|
2012-02-18 05:50:40 +08:00
|
|
|
|
- h5dump: Refactored code to remove duplicated functions. Split XML
|
|
|
|
|
|
functions from DDL functions. Corrected indentation and formatting
|
2012-02-28 04:18:51 +08:00
|
|
|
|
errors. Also fixed subsetting counting overflow (HDFFV-5874). Verified
|
|
|
|
|
|
all tools call tools_init() in main.
|
2012-02-18 05:50:40 +08:00
|
|
|
|
HDFFV-7560 (ADB 2012/02/17)
|
2012-01-25 04:39:59 +08:00
|
|
|
|
- h5diff: fixed to prevent from displaying error stack message when
|
|
|
|
|
|
comparing the two dangling symlinks with follow-symlinks option.
|
|
|
|
|
|
HDFFV-7836 (JKM 2012/01/13)
|
2012-01-10 05:24:50 +08:00
|
|
|
|
- h5repack: fixed memory leak for handling variable length string in
|
|
|
|
|
|
attribute. HDFFV-7840 (JKM 2012/01/06)
|
2012-01-05 23:16:03 +08:00
|
|
|
|
- h5ls: fixed segfault when access region reference data in an
|
2012-01-10 05:24:50 +08:00
|
|
|
|
attribute. HDFFV-7838 (JKM 2011/12/29)
|
2011-10-25 05:50:13 +08:00
|
|
|
|
- h5diff: fixed segfault over non-comparable attribute with different
|
|
|
|
|
|
dimention or rank, along with '-c' option to display details.
|
|
|
|
|
|
HDFFV-7770 (JKM 2011/10/24)
|
|
|
|
|
|
- Fixed h5diff to display all the comparable object and attribute
|
|
|
|
|
|
regardless of non-comparables. HDFFV-7693 (JKM 2011/09/16)
|
|
|
|
|
|
- Fixed h5repack to update values of references(object and region) of
|
|
|
|
|
|
attributes in h5repack for 1) references, 2) ARRAY of references,
|
|
|
|
|
|
3) VLEN of references, and 4) COMPOUND of references.
|
|
|
|
|
|
(JIRA HDF5 5932) PC -2011/09/14
|
2011-09-03 00:29:45 +08:00
|
|
|
|
- h5diff: fixed segfault over dataset with container types
|
|
|
|
|
|
(array,lven) with multiple nested compound types.
|
|
|
|
|
|
(ex: compound->array->compound, compound->vlen->compound)
|
2011-10-25 05:50:13 +08:00
|
|
|
|
HDFFV-7712 JKM (2011/09/01)
|
2011-08-23 06:32:14 +08:00
|
|
|
|
- h5repack: added macro to handle failure in H5Dread/write when memory
|
|
|
|
|
|
allocation failed inside the library. (PC -- 2011/08/19)
|
2011-08-17 04:41:47 +08:00
|
|
|
|
- Fixed h5jam not to allow specifying an HDF5 formatted file as input
|
|
|
|
|
|
file for -u (user block file) option, because the original HDF5 file
|
2011-10-25 05:50:13 +08:00
|
|
|
|
will not be accessible if allows. HDFFV-5941 (JKM 2011/08/15)
|
2011-08-17 04:41:47 +08:00
|
|
|
|
- Revised command help pages of h5jam and h5unjam. The descriptions
|
|
|
|
|
|
were not up to date and some were missing.
|
2011-10-25 05:50:13 +08:00
|
|
|
|
HDFFV-7515 (JKM 2011/08/15)
|
2011-08-23 06:32:14 +08:00
|
|
|
|
- h5repack: h5repack failed to copy dataset if the layout is changed
|
|
|
|
|
|
from chunked with unlimited dims to contiguous. HDFFV-7649
|
|
|
|
|
|
(PC -- 2011/07/15)
|
|
|
|
|
|
- h5diff: "--delta" option considers two NaN of the same type are
|
|
|
|
|
|
different, which is wrong based on h5diff description in Reference
|
|
|
|
|
|
Manual. HDFFV-7656 (PC -- 2011/07/15)
|
2011-07-08 07:12:51 +08:00
|
|
|
|
- Fixed h5diff to display instructive error message and exit with 1
|
|
|
|
|
|
when mutually exclusive options (-d, -p and --use-system-epsilon)
|
2011-10-25 05:50:13 +08:00
|
|
|
|
are used together. HDFFV-7600 (JKM 2011/07/07)
|
2011-06-22 02:24:35 +08:00
|
|
|
|
- Fixed h5dump to display the first line of each element into correct
|
|
|
|
|
|
position for multiple dimention array type.
|
|
|
|
|
|
Before this fix, the first line of each element in array were
|
|
|
|
|
|
displayed after the last line of previous element without
|
|
|
|
|
|
moving to the next line (+indentation).
|
2011-10-25 05:50:13 +08:00
|
|
|
|
Bug #HDFFV-5878 (JKM 2011/06/15)
|
2011-05-13 07:12:29 +08:00
|
|
|
|
- Fixed h5dump to display correct value for H5T_STD_I8LE dataset
|
|
|
|
|
|
on a system (ppc64, linux, Big-Endian, clustering).
|
2011-10-25 05:50:13 +08:00
|
|
|
|
Bug #HDFFV-7594 (ABERT & JKM 2011/05/12)
|
2011-05-07 06:02:24 +08:00
|
|
|
|
- Fixed h5diff to compare file itself correctly. Previously h5diff
|
|
|
|
|
|
reported either different or not compatible in certain cases even
|
|
|
|
|
|
comparing file itself. This fix also improve performance when
|
|
|
|
|
|
comparing same target objects through verifying the obj&file
|
|
|
|
|
|
addresses before comparing the details in the objects (ex: datasets
|
2011-10-25 05:50:13 +08:00
|
|
|
|
or attributes) Bug #HDFFV-5928 (XCAO & JKM 2011/05/06)
|
2011-04-13 07:02:33 +08:00
|
|
|
|
- Updated h5dump test case script to prevent entire test failure upon
|
|
|
|
|
|
source directory is read-only. Bug# HDFFV-4342 (JKM 2011/4/12)
|
2011-04-27 02:36:03 +08:00
|
|
|
|
- Fixed h5dump displaying incorrect values for H5T_STD_I8BE type data in
|
2011-05-07 06:02:24 +08:00
|
|
|
|
attribute on Big-Endian machine. H5T_STD_I8BE is unsigned 8bit type,
|
|
|
|
|
|
so h5dump is supposed to display -2 instead of 254. It worked
|
|
|
|
|
|
correctly on Little-Endian system , but not on Big-Endian system.
|
2011-10-25 05:50:13 +08:00
|
|
|
|
Bug #HDFFV-4358 (JKM 2011/04/08)
|
[svn-r20378] Purpose:
Bug 2182 - h5ls and h5dump: update to use --enable-error-stack among tools, also update related descriptions
Description:
Decided to use --enable-error-stack long option name only to
display error stack messages from HDF5 lib among tools.
Updated to unify option name to '--enable-error-stack' for printing
HDF5 error stack messages for HDF5 tools. h5ls and h5dump for now.
For h5ls, this replaces "-e/--errors" option, which is deprecated.
For h5dump, remove -E from help page and RM , which was added by mistake
before release1.8.7.
Help page and RM got updated.
Updated test case.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE)
2011-03-31 00:06:14 +08:00
|
|
|
|
- Updated to unify option name to '--enable-error-stack' for printing
|
|
|
|
|
|
HDF5 error stack messages for HDF5 tools. h5ls and h5dump for now.
|
|
|
|
|
|
For h5ls, this replaces "-e/--errors" option, which is deprecated.
|
|
|
|
|
|
Bug#2182 (JKM 2011/3/30)
|
2011-04-01 05:43:46 +08:00
|
|
|
|
- Fix h5diff for --use-system-epsilon option: the calculation changed
|
|
|
|
|
|
from ( |a - b| / b ) to ( |a - b| ). This was decided for better
|
|
|
|
|
|
performance. Bug#2184 (JKM 2011/3/24)
|
2011-03-29 00:06:19 +08:00
|
|
|
|
- Fixed output for H5T_REFERENCE in h5dump. According to the BNF document
|
|
|
|
|
|
the output of a H5T_REFERENCE should be followed by the type;
|
|
|
|
|
|
<reference> ::= H5T_REFERENCE { <ref_type> }
|
|
|
|
|
|
<ref_type> ::= H5T_STD_REF_OBJECT | H5T_STD_REF_DSETREG
|
|
|
|
|
|
Previously this was only displayed if the -R option was used.
|
|
|
|
|
|
Bug#1725 (ADB 2011/3/28)
|
2011-03-22 23:47:07 +08:00
|
|
|
|
- Fix h5diff issues for #1: h5diff compared attributes correctly only
|
|
|
|
|
|
when two objects have the same number of attributes and attribute
|
|
|
|
|
|
names are identical, #2: didn't display useful information about
|
|
|
|
|
|
attribute difference. Bug#2121 (JKM 2011/3/17)
|
2011-03-19 04:13:16 +08:00
|
|
|
|
- Fixed memory leak for h5diff when accessing symbolic links with
|
|
|
|
|
|
--follow-symlink option. Bug#2214 (JKM 2011/3/18)
|
2011-03-19 02:50:19 +08:00
|
|
|
|
- Fixed memory leak for h5diff when access variable length string
|
|
|
|
|
|
data. Bug#2216 (JKM 2011/3/18)
|
2011-03-11 23:48:24 +08:00
|
|
|
|
- Fixed and improved help page for -a option of h5ls.
|
|
|
|
|
|
Bug#1904 (JKM 2011/3/11)
|
2011-03-10 21:38:42 +08:00
|
|
|
|
- Fixed h5dump not to include attribute values in the output file when
|
|
|
|
|
|
h5dump "-y -o output_file" options were used. The problem was introduced
|
|
|
|
|
|
in HDF5 1.8.6 by showing data pointed by region references. (XCAO 2011/3/9)
|
2011-03-09 04:17:17 +08:00
|
|
|
|
- Fixed h5copy to be able to copy any object into the same HDF5 file.
|
|
|
|
|
|
Previously h5copy displayed error message when target file is same
|
|
|
|
|
|
as source file. (XCAO 2011/3/8)
|
2011-03-05 00:21:26 +08:00
|
|
|
|
- Fixed h5dump for skipping some values for long array type dataset on
|
|
|
|
|
|
Windows. This issue only occurred on Windows due to the different
|
|
|
|
|
|
return behavior from _vsnprintf() funtion. Bug#2161 (JKM 2011/3/3)
|
2011-02-16 03:28:48 +08:00
|
|
|
|
- Fixed h5dump for skipping array indices every certain number
|
|
|
|
|
|
when the array type dataset is relatively big. The certain number
|
|
|
|
|
|
varies according to the size of array. Bug#2092 (JKM 2011/2/15).
|
[svn-r19892] Purpose:
Bug 2089 - GMQS: h5diff segfault on a compound dataset with fixed length +
vlen string type order
Description:
This is fix for the segfault when h5diff compares a compound dataset with
combination of fixed length string types and vlen string types in certain
orders. Optimized vlariable length string handling codes. The fix is
referred from h5dump handling vlen strings.
For testing, several compound datasets were added with various combinations.
Previous failed cases:
- Vlen string, Fixed length string, Vlen string, Fixed length string
- Fixed length string, Fixed length string, Vlen string, Vlen string
- Fixed length string, Vlen string, Fixed length string, Vlen string
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
2010-12-29 02:08:40 +08:00
|
|
|
|
- Fixed h5diff for the segfault when compares compound datasets
|
|
|
|
|
|
with combination of fixed length string types and vlen string types
|
|
|
|
|
|
in certain orders. bug#2089 (JKM 2010/12/28)
|
2010-11-11 23:23:44 +08:00
|
|
|
|
- Improve h5diff performance. 1) use HDmemcmp() before comparing each
|
|
|
|
|
|
elements. 2) replace expensive H5Tequals() calls 3) retrieve datatype
|
|
|
|
|
|
information at dataset level not each element level for compound
|
|
|
|
|
|
datasets
|
2010-11-10 05:13:53 +08:00
|
|
|
|
- Fixed h5ls to display nested compound type with curly bracket
|
|
|
|
|
|
when -S (--simple) option is used with -l (--label), so it shows
|
|
|
|
|
|
which member (in curly bracket) belong to which nested compound type
|
|
|
|
|
|
and make the output make sense. bug#1979 (JKM 2010/11/09)
|
2010-11-03 00:39:42 +08:00
|
|
|
|
- Fixed h5diff to handle variable-length strings in a compound dataset
|
|
|
|
|
|
correctly. (also variable-length string array in a compound dataset)
|
|
|
|
|
|
Garbage values were displayed when h5diff compared multiple
|
|
|
|
|
|
variable-length strings in a compound type dataset.
|
|
|
|
|
|
Bug#1989 (JKM 2010/10/28)
|
2010-10-19 07:06:53 +08:00
|
|
|
|
- Fixed h5copy to fail gracefully when copying object to non-exist
|
|
|
|
|
|
group without -p option. Bug#2040 (JKM 2010/10/18)
|
2010-09-17 01:48:06 +08:00
|
|
|
|
- Fixed to compare member objects and groups recursively when two
|
|
|
|
|
|
files or groups are specified to be compared. Bug#1975
|
|
|
|
|
|
(JKM 2010/9/16)
|
2010-09-16 02:32:07 +08:00
|
|
|
|
- Make h5repack be able to convert a layout to COMPACT for small size
|
|
|
|
|
|
dataset as default. bug#1896 (JKM 2010/09/15)
|
2010-06-29 04:34:32 +08:00
|
|
|
|
- Change h5ls not to manipulate special characters in object name or
|
|
|
|
|
|
attribute name for smart display. bug#1784 (JKM 2010/06/28)
|
2010-05-15 05:37:27 +08:00
|
|
|
|
- Fixed h5ls to return exit code 1 (error) when non-existent file is
|
|
|
|
|
|
specified. bug#1793. (JKM 2010/04/27)
|
|
|
|
|
|
- h5copy failed to copy dangling link when the link is specified
|
|
|
|
|
|
directly. bug#1817. (JKM 2010/04/22)
|
|
|
|
|
|
- h5repack lost attributes from a dataset of reference type. bug#1726.
|
|
|
|
|
|
(JKM 2010/3/25)
|
|
|
|
|
|
- h5repack sets NULL for object reference value for group or
|
|
|
|
|
|
named datatype. bug#1814. (JKM 2010/03/19)
|
2010-02-19 00:51:12 +08:00
|
|
|
|
- h5diff: fixed incorrect behavior (hang) in parallel mode when
|
|
|
|
|
|
specify invalid options (ex: -v and -q) (JKM 2010/02/17)
|
2009-09-05 04:38:40 +08:00
|
|
|
|
- h5dump/h5ls display buffer resize fixed in tools library.
|
|
|
|
|
|
(ADB - 2009/07/21 - 1520)
|
2009-04-21 00:37:47 +08:00
|
|
|
|
- Fixed many problems that could occur when using h5repack with named
|
|
|
|
|
|
datatypes. (NAF - 2009/4/20 - 1516/1466)
|
2009-04-02 00:33:01 +08:00
|
|
|
|
- h5dump, h5diff, h5repack were not reading (by hyperslabs) datasets
|
|
|
|
|
|
that have a datatype datum size greater than H5TOOLS_BUFSIZE, a
|
2009-04-02 03:02:18 +08:00
|
|
|
|
constant defined as 1024Kb, such as array types with large
|
2009-04-02 00:33:01 +08:00
|
|
|
|
dimensions (PVN - 2009/4/1 - 1501)
|
2009-04-02 03:02:18 +08:00
|
|
|
|
- h5import: By selecting a compression type, a big endian byte order was being
|
2009-04-02 00:33:01 +08:00
|
|
|
|
selected (PVN - 2009/3/11 - 1462)
|
2009-01-06 22:58:21 +08:00
|
|
|
|
- zip_perf.c had missing argument on one of the open() calls. Fixed.
|
|
|
|
|
|
(AKC - 2008/12/9)
|
|
|
|
|
|
- h5dump now checks for uniqueness of committed datatypes.
|
|
|
|
|
|
(NAF - 2008/10/15)
|
|
|
|
|
|
- Fixed unnecessary indentation of committed datatypes in h5dump.
|
|
|
|
|
|
(NAF - 2008/10/15)
|
2011-09-14 23:48:22 +08:00
|
|
|
|
- Fixed bugs in h5stat:segmemtation fault when printing groups and
|
2009-01-06 22:58:21 +08:00
|
|
|
|
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)
|
|
|
|
|
|
- Fixed bug in h5diff that prevented datasets & attributes with
|
|
|
|
|
|
variable-length string elements from comparing correctly.
|
|
|
|
|
|
(QAK - 2008/02/28)
|
|
|
|
|
|
- h5import bug on Windows w/binary datasets. fread in windows needs a
|
|
|
|
|
|
binary file to be open with 'rb' instead of 'r' otherwise it
|
|
|
|
|
|
terminates execution if an end of file character is found on the
|
|
|
|
|
|
input file. Besides that the binary file generated needs to be open
|
|
|
|
|
|
with 'wb' , otherwise an end of line character is read twice.
|
|
|
|
|
|
(PVN - 2008/02/19)
|
|
|
|
|
|
- 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)
|
|
|
|
|
|
- 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
|
2011-09-15 06:30:58 +08:00
|
|
|
|
|
2009-01-06 22:58:21 +08:00
|
|
|
|
|
2009-04-09 05:22:13 +08:00
|
|
|
|
High-Level APIs:
|
|
|
|
|
|
------
|
2011-10-26 05:18:41 +08:00
|
|
|
|
- Fixed the H5LTdtype_to_text function. It had some memory problems when
|
|
|
|
|
|
dealing with some complicated data types. HDFFVI-7701 (SLU - 2011/10/19)
|
|
|
|
|
|
|
2010-05-23 01:30:45 +08:00
|
|
|
|
- Fixed a bug in H5DSattach_scale, H5DSis_attached and H5DSdetach_scale
|
|
|
|
|
|
caused by using H5Tget_native_type function to determine the native
|
|
|
|
|
|
type for reading REFERENCE_LIST attribute. The bug was exposed
|
|
|
|
|
|
on Mac PPC.
|
2010-05-23 01:49:58 +08:00
|
|
|
|
(EIP - 2010/05/22 -1851)
|
2010-05-15 12:10:53 +08:00
|
|
|
|
- Fixed a bug in the H5DSdetach_scale function when 0 bytes
|
|
|
|
|
|
were allocated after the last reference to a dim. scale
|
|
|
|
|
|
was removed from the list of references in a VL element of the
|
|
|
|
|
|
DIMENSION_LIST attribute; modified the function to comply
|
|
|
|
|
|
with the Spec: DIMENSION_LIST attribute is deleted now when no
|
|
|
|
|
|
dimension scales left attached.
|
|
|
|
|
|
(EIP - 2010/05/14 -1822)
|
2009-10-28 06:23:49 +08:00
|
|
|
|
- Fixed a bug where the H5TB API would forget the order of fields when
|
2009-10-28 23:10:10 +08:00
|
|
|
|
added out of offset order. (NAF - 2009/10/27 - 1582)
|
2009-10-02 00:17:17 +08:00
|
|
|
|
- H5DSis_attached failed to account for different platform types. Added a
|
|
|
|
|
|
get native type call. (ADB - 2009/9/29 - 1562)
|
2009-04-09 05:22:13 +08:00
|
|
|
|
- Dimension scales: The scale index return value in H5DSiterate_scales was not always
|
|
|
|
|
|
incremented. (PVN - 2009/4/8 - 1538)
|
|
|
|
|
|
|
|
|
|
|
|
Fortran High-Level APIs:
|
|
|
|
|
|
------
|
2012-03-26 12:30:48 +08:00
|
|
|
|
|
|
|
|
|
|
- Lite: The h5ltget_attribute_string_f used to return the C NULL character in the
|
|
|
|
|
|
returned character buffer. The returned Fortran charactor buffer now does
|
|
|
|
|
|
not return the C NULL character. (MSB - 2012/3/23)
|
2009-04-09 05:22:13 +08:00
|
|
|
|
- Lite: The h5ltget_dataset_info_f function (gets information about a dataset)
|
2009-05-14 03:10:25 +08:00
|
|
|
|
was not correctly returning the dimension array. (PVN - 2009/3/23)
|
|
|
|
|
|
- Lite: the h5ltread_dataset_string_f and h5ltget_attribute_string_f functions
|
2009-06-12 03:29:54 +08:00
|
|
|
|
had memory problems with the g95 fortran compiler. (PVN <20> 5/13/2009) 1522
|
2009-04-09 05:22:13 +08:00
|
|
|
|
|
|
|
|
|
|
|
2009-01-06 22:58:21 +08:00
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Documentation
|
|
|
|
|
|
-------------
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
F90 APIs
|
|
|
|
|
|
--------
|
2011-10-14 04:25:32 +08:00
|
|
|
|
- Modified the h5open_f and h5close_f subroutines to not to call H5open
|
|
|
|
|
|
and H5close correspodningly. While the H5open call just adds overhead,
|
|
|
|
|
|
the H5close call called by an Fortran application shuts down the HDF5
|
|
|
|
|
|
library making it unaccessible to the application.
|
|
|
|
|
|
HDFFV-915 (EIP & SB - 2011/10/13)
|
|
|
|
|
|
|
2009-01-06 22:58:21 +08:00
|
|
|
|
|
|
|
|
|
|
C++ APIs
|
|
|
|
|
|
--------
|
2011-08-15 21:30:30 +08:00
|
|
|
|
- The constructor PropList::PropList(id) was fixed to act properly
|
|
|
|
|
|
according to the nature of 'id'. When 'id' is a property class id,
|
|
|
|
|
|
a new property list will be created. When 'id' id a property list id,
|
|
|
|
|
|
a copy of the property list will be made. (BMR - 2010/5/9)
|
|
|
|
|
|
- The parameters 'size' and 'bufsize' in CommonFG::getLinkval and
|
|
|
|
|
|
CommonFG::getComment, respectively, now have default values for
|
|
|
|
|
|
user's convenience. (BMR - 2009/10/23)
|
|
|
|
|
|
- NULL pointer accessing was fixed, bugzilla 1061. (BMR - 2009/10/05)
|
|
|
|
|
|
- read/write methods of DataSet and Attribute classes were fixed
|
|
|
|
|
|
to handle string correctly. (BMR - 2009/07/26)
|
2009-01-06 22:58:21 +08:00
|
|
|
|
- Fixed bug that caused segfaults in Attribute::read. (BMR - 2008/04/20)
|
|
|
|
|
|
- Fixed bug in PropList::getClassName to use portable HDfree instead
|
|
|
|
|
|
of free. (BMR - 2008/04/20)
|
|
|
|
|
|
- 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 - 2008/08/10)
|
|
|
|
|
|
- IdComponent::dereference was incorrect and replaced as described
|
|
|
|
|
|
in "New Features" section.
|
|
|
|
|
|
(BMR - 2008/08/10)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Platforms Tested
|
|
|
|
|
|
================
|
|
|
|
|
|
|
2012-02-28 20:45:45 +08:00
|
|
|
|
AIX 5.3 xlc 10.1.0.5
|
|
|
|
|
|
(NASA G-ADA) xlC 10.1.0.5
|
|
|
|
|
|
xlf90 12.1.0.6
|
|
|
|
|
|
|
2011-04-27 04:12:58 +08:00
|
|
|
|
FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719
|
|
|
|
|
|
(loyalty) g++ 4.2.1 [FreeBSD] 20070719
|
|
|
|
|
|
gcc 4.6.1 20110422
|
|
|
|
|
|
g++ 4.6.1 20110422
|
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gfortran 4.6.1 20110422
|
2011-07-24 06:15:13 +08:00
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2011-04-27 04:12:58 +08:00
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FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719
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(freedom) g++ 4.2.1 [FreeBSD] 20070719
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gcc 4.6.1 20110422
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g++ 4.6.1 20110422
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gfortran 4.6.1 20110422
|
2009-01-06 22:58:21 +08:00
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2011-07-24 06:15:13 +08:00
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Linux 2.6.18-194.3.1.el5PAE gcc (GCC) 4.1.2 and 4.4.2
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#1 SMP i686 i686 i386 GNU Fortran (GCC) 4.1.2 20080704
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(jam) (Red Hat 4.1.2-48) and 4.4.2
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PGI C, Fortran, C++ 10.4-0 32-bit
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PGI C, Fortran, C++ 10.6-0 32-bit
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Intel(R) C Compiler for 32-bit
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applications, Version 11.1
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Intel(R) C++ Compiler for 32-bit
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applications, Version 11.1
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Intel(R) Fortran Compiler for 32-bit
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applications, Version 11.1
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MPICH mpich2-1.3.1 compiled with
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gcc 4.1.2 and gfortran 4.1.2
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Linux 2.6.18-238.12.1.el5 gcc 4.1.2 and 4.4.2
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#1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 4.1.2 20080704
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(koala) (Red Hat 4.1.2-46) and 4.4.2
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tested for both 32- and 64-bit binaries
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Intel(R) C, C++, Fortran Compilers for
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applications running on Intel(R) 64,
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Version 11.1.
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PGI C, Fortran, C++ Version 9.0-4
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for 64-bit target on x86-64
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MPICH mpich2-1.3.1 compiled with
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gcc 4.1.2 and gfortran 4.1.2
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SGI ProPack 7 Linux Intel(R) C++ Version 11.1 20100806
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2.6.32.19-0.3.1.1982.0.PTF- Intel(R) Fortran Version 11.1 20100806
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default #1 SMP SGI MPT 2.01
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SGI Altix UV
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(NCSA ember)
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SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16
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(linew) Sun Fortran 95 8.3 Sun OS_sparc Patch
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127000-13
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Sun C++ 5.9 Sun OS_sparc Patch 124863-62
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Sun C 5.10 SunOS_sparc Patch 141861-07
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Sun Fortran 95 8.4 SunOS_sparc Patch
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128231-06
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Sun C++ 5.10 SunOS_sparc 128228-11
|
2010-06-02 04:34:26 +08:00
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2012-08-29 01:47:52 +08:00
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Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
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Visual Studio 2010 w/ Intel Fortran 12 (cmake)
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Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran)
|
2010-06-02 04:34:26 +08:00
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|
2012-08-29 01:47:52 +08:00
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Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
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Visual Studio 2010 w/ Intel Fortran 12 (cmake)
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Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran)
|
2009-01-06 22:58:21 +08:00
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|
2009-11-05 08:06:00 +08:00
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MAC OS 10.5 (Intel) gcc i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1
|
2009-01-06 22:58:21 +08:00
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G95 (GCC 4.0.3 (g95 0.91!) Nov 21 2006)
|
2009-11-05 08:06:00 +08:00
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GNU Fortran (GCC) 4.3.0 20070810
|
2009-01-06 22:58:21 +08:00
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Alpha Open VMS 7.3
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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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x = not working in this release
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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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W or C indicates workstation or cluster, respectively.
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Platform C F90 F90 C++ zlib SZIP
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parallel parallel
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SunOS5.10 64-bit n y n y y y
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SunOS5.10 32-bit n y n y y y
|
2012-08-29 01:47:52 +08:00
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Windows 7 y y n y y y
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Windows 7 x64 y y n y y y
|
2009-11-05 08:07:53 +08:00
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Mac OS X 10.5 Intel n y n y y y
|
2011-04-27 04:12:58 +08:00
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FreeBSD 8.2 32- and 64-bit n x n x y y
|
2009-01-06 22:58:21 +08:00
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|
RedHat EL4 2.6.9 i686 GNU W y(2) y(4) y(2) y y y
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RedHat EL4 2.6.9 i686 Intel W n y n y y n
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RedHat EL4 2.6.9 i686 PGI W n y n y y n
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|
SuSe Linux 2.6.16 x86_64 GNU (5) W y(2) y n y y y
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|
SuSe Linux 2.6.16 x86_64 Int (5) W n y n y n n
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SuSe Linux 2.6.16 x86_64 PGI (5) W n y n y n n
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RHL9 Linux 2.4 Xeon Lustre Intel C n y n y y n
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RHEL3 Linux 2.4 Xeon Intel W n y n n y n
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RHEL4 Linux 2.6 Xeon Lustre Int C n y n y y n
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SuSE Linux 2.4 ia64 Intel C y(1) y y y y y
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|
SuSe Linux 2.6.5
|
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|
SGI Altix ia64 Intel C n y n y n y
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|
Alpha OpenVMS 7.3.2 n y n y n n
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Platform Shared Shared Shared static- Thread-
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|
C libs F90 libs C++ libs exec safe
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|
SunOS 5.10 32-bit y y y x y
|
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|
|
SunOS 5.10 64-bit y y y x y
|
2010-06-02 04:34:26 +08:00
|
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|
Windows XP y y(3) y y n
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|
Windows XP x64 y y(3) y y n
|
2010-10-06 22:47:30 +08:00
|
|
|
|
Windows Vista y y(3) y y y
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|
Windows Vista x64 y y(3) y y y
|
2009-11-05 08:07:53 +08:00
|
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|
|
Mac OS X 10.5 Intel y y y x n
|
2011-04-27 04:12:58 +08:00
|
|
|
|
FreeBSD 8.2 32- and 64-bit y x x y y
|
2009-01-06 22:58:21 +08:00
|
|
|
|
RHEL4 2.6.9 i686 GNU W y y(4) y x y
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|
|
|
RHEL4 2.6.9 i686 Intel W y y y x n
|
|
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|
|
|
RHEL4 2.6.9 i686 PGI W y y y x n
|
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|
|
|
SuSE Linux 2.6.16 x86_64 GNU (5) W y y y x y
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|
|
SuSE Linux 2.6.16 x86_64 Intel(5) W y y y x n
|
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|
|
|
SuSE Linux 2.6.16 x86_64 PGI(5) W y y y x n
|
|
|
|
|
|
RHL9 Linux 2.4 Xeon Lustre Intel C y y y x n
|
|
|
|
|
|
RHEL3 Linux 2.4 Xeon Intel W y n n x n
|
|
|
|
|
|
RHEL4 Linux 2.6 Xeon Lustre Intel C y y y x n
|
|
|
|
|
|
SuSE Linux 2.4 ia64 Intel C y y y x n
|
|
|
|
|
|
SuSe Linux 2.6.5
|
|
|
|
|
|
SGI Altix ia64 Intel C n n n x n
|
|
|
|
|
|
|
|
|
|
|
|
Notes: (1) Using mpich 1.2.6.
|
|
|
|
|
|
(2) Using mpich2 1.0.6.
|
2010-06-02 04:34:26 +08:00
|
|
|
|
(3) Using Visual Studio 2008 (Cygwin shared libraries are not supported)
|
2009-01-06 22:58:21 +08:00
|
|
|
|
(4) With PGI and Absoft compilers.
|
|
|
|
|
|
(5) AMD Opteron x86_64
|
|
|
|
|
|
Compiler versions for each platform are listed in the preceding
|
|
|
|
|
|
"Platforms Tested" table.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Known Problems
|
|
|
|
|
|
==============
|
2012-06-13 04:55:52 +08:00
|
|
|
|
* The data conversion test dt_arith.c has failures (segmentation fault) from
|
|
|
|
|
|
"long double" to other datatypes during hard conversion when the library
|
|
|
|
|
|
is built with the default GCC 4.2.1 on Mac Lion system. It only happens
|
|
|
|
|
|
with optimization (-O3, -O2, and -O1). Some newer versions of GCC do not
|
|
|
|
|
|
have this problem. Users should disable optimization or try newer version
|
|
|
|
|
|
of GCC. (Issue 8017. SLU - 2012/6/12)
|
|
|
|
|
|
|
2012-02-08 05:42:32 +08:00
|
|
|
|
* The data conversion test dt_arith.c fails in "long double" to integer
|
|
|
|
|
|
conversion on Ubuntu 11.10 (3.0.0.13 kernal) with GCC 4.6.1 if the library
|
|
|
|
|
|
is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernal
|
|
|
|
|
|
(3.2.2 on Fedora) doesn't have the problem. Users should lower down the
|
|
|
|
|
|
optimization level (-O1 or -O0) by defining CFLAGS in the command line of
|
|
|
|
|
|
"configure" like:
|
|
|
|
|
|
|
|
|
|
|
|
CFLAGS=-O1 ./configure
|
|
|
|
|
|
|
|
|
|
|
|
It will overwrite the library's default optimization level. (Issue 7829.
|
|
|
|
|
|
SLU - 2012/2/7)
|
|
|
|
|
|
|
2011-03-11 03:11:02 +08:00
|
|
|
|
* --with-mpe configure option does not work with Mpich2. AKC - 2011/03/10)
|
|
|
|
|
|
|
2011-01-19 23:51:20 +08:00
|
|
|
|
* While working on the 1.8.6 release of HDF5, a bug was discovered that can
|
|
|
|
|
|
occur when reading from a dataset in parallel shortly after it has been
|
|
|
|
|
|
written to collectively. The issue was exposed by a new test in the parallel
|
|
|
|
|
|
HDF5 test suite, but had existed before that. We believe the problem lies with
|
|
|
|
|
|
certain MPI implementations and/or filesystems.
|
|
|
|
|
|
|
|
|
|
|
|
We have provided a pure MPI test program, as well as a standalone HDF5
|
|
|
|
|
|
program, that can be used to determine if this is an issue on your system.
|
|
|
|
|
|
They should be run across multiple nodes with a varying number of processes.
|
|
|
|
|
|
These programs can be found at:
|
|
|
|
|
|
http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
|
|
|
|
|
|
|
2009-11-04 12:32:18 +08:00
|
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|
|
* Parallel mode in AIX will fail some of the testcheck_version.sh tests where
|
|
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|
|
it treats "exit(134) the same as if process 0 had received an abort signal.
|
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|
|
This is fixed and will be available in the next release. AKC - 2009/11/3
|
|
|
|
|
|
|
2009-08-12 04:13:07 +08:00
|
|
|
|
* The PathScale MPI implementation, accessing a Panasas file system, would
|
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|
|
|
|
cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file is not
|
|
|
|
|
|
existing. This is due to the MPI_File_open() call failing if the amode has
|
|
|
|
|
|
the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11
|
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|
|
|
|
2009-04-29 14:39:10 +08:00
|
|
|
|
* Parallel tests failed with 16 processes with data inconsistency at testphdf5
|
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|
|
|
|
/ dataset_readAll. Parallel tests also failed with 32 and 64 processes with
|
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|
|
|
|
collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
|
|
|
|
|
|
with MPI IO. (CMC - 2009/04/28)
|
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|
|
|
|
|
2009-01-06 22:58:21 +08:00
|
|
|
|
* 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. Higher level of optimization
|
|
|
|
|
|
causes failures in several HDF5 library tests.
|
|
|
|
|
|
* For HPUX 11.23 many tools tests failed for 64-bit version when linked to the
|
|
|
|
|
|
shared libraries (tested for 1.8.0-beta2)
|
|
|
|
|
|
* For SNL, Red Storm: only paralle HDF5 is supported. The serial tests pass
|
|
|
|
|
|
and the parallel tests also pass with lots of non-fatal error messages.
|
|
|
|
|
|
* on SUN 5.10 C++ test 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, Scaleoffset filter isn't supported. The filter cannot be applied to
|
|
|
|
|
|
HDF5 data generated on VAX. Scaleoffset filter only supports 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, we found that if more than two processes
|
|
|
|
|
|
contribute no IO and the application asks to do IO with collective, we found
|
|
|
|
|
|
that when using 4 processors, a simple collective write will be hung
|
|
|
|
|
|
sometimes. This can be verified with t_mpi test under testpar.
|
|
|
|
|
|
* The dataset created or rewritten with the v1.6.3 library or after can't
|
|
|
|
|
|
be read with the v1.6.2 library or before when 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 wasn't 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 is no
|
|
|
|
|
|
longer the same as before on little-endian system. The library release
|
|
|
|
|
|
after 1.6.4 can still read the dataset created or rewritten with the library
|
|
|
|
|
|
of v1.6.2 or before. SLU - 2005/6/30
|
|
|
|
|
|
* For the version 6(6.02 and 6.04) of Portland Group compiler on AMD Opteron
|
|
|
|
|
|
processor, there's a bug in the compiler for optimization(-O2). The library
|
|
|
|
|
|
failed in several tests but all related to 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". HDF5 does not use sockets (except for stream-VFD). This is
|
|
|
|
|
|
due to problems of the poe command trying to set up the debug socket.
|
|
|
|
|
|
Check if there are many old /tmp/s.pedb.* staying around. These are
|
|
|
|
|
|
sockets used by the poe command and left behind due to failed commands.
|
|
|
|
|
|
Ask your system administrator to clean them out. Lastly, request IBM
|
|
|
|
|
|
to provide a mean to run poe without the debug socket.
|
|
|
|
|
|
|
|
|
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* The C++ library's tests fails when compiling with PGI C++ compiler. The
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workaround until the problem is correctly handled is to use the
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flag "--instantiate=local" prior to the configure and build steps, as:
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setenv CXX "pgCC --instantiate=local" for pgCC 5.02 and higher
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* The stream-vfd test uses ip port 10007 for testing. If another
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application is already using that port address, the test will hang
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indefinitely and has to be terminated by the kill command. To try the
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test again, change the port address in test/stream_test.c to one not
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being used in the host.
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2009-11-04 22:39:45 +08:00
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* The --enable-static-exec configure flag will only statically link libraries
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if the static version of that library is present. If only the shared version
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of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
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for example, only have shared versions), the flag should still result in a
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successful compilation, but note that the installed executables will not be
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fully static. Thus, the only guarantee on these systems is that the
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executable is statically linked with just the HDF5 library.
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2009-01-06 22:58:21 +08:00
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* With the gcc 2.95.2 compiler, HDF 5 uses the `-ansi' flag during
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compilation. The ANSI version of the compiler complains about not being
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able to handle the `long long' datatype with the warning:
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warning: ANSI C does not support `long long'
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This warning is innocuous and can be safely ignored.
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* Certain platforms give false negatives when testing h5ls:
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- Cray J90 and Cray T90IEEE give errors during testing when displaying
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some floating-point values. These are benign differences due to
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the different precision in the values displayed and h5ls appears to
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be dumping floating-point numbers correctly.
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* Not all platforms behave correctly with szip's shared libraries. Szip is
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disabled in these cases, and a message is relayed at configure time. Static
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libraries should be working on all systems that support szip, and should be
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used when shared libraries are unavailable. There is also a configure error
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on Altix machines that incorrectly reports when a version of szip without
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an encoder is being used.
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* On some platforms that use Intel and Absoft compilers to build HDF5 fortran library,
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|
compilation may fail for fortranlib_test.f90, fflush1.f90 and fflush2.f90
|
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|
|
complaining about exit subroutine. Comment out the line
|
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|
IF (total_error .ne. 0) CALL exit (total_error)
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* Information about building with PGI and Intel compilers is available in
|
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|
|
INSTALL file sections 5.7 and 5.8
|
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|
* On at least one system, (SDSC DataStar), the scheduler (in this case
|
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|
|
LoadLeveler) sends job status updates to standard error when you run
|
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|
|
any executable that was compiled with the parallel compilers.
|
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|
This causes problems when running "make check" on parallel builds, as
|
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|
|
many of the tool tests function by saving the output from test runs,
|
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|
|
and comparing it to an exemplar.
|
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|
|
The best solution is to reconfigure the target system so it no longer
|
|
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|
|
|
inserts the extra text. However, this may not be practical.
|
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|
|
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.
|
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|
|
|
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|
|
|
|
|
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) >& $STDERR_FILE
|
|
|
|
|
|
|
2011-08-15 21:30:30 +08:00
|
|
|
|
set RETURN_VALUE=$status
|
2009-01-06 22:58:21 +08:00
|
|
|
|
|
|
|
|
|
|
cat $STDOUT_FILE
|
|
|
|
|
|
|
|
|
|
|
|
tail +3 $STDERR_FILE
|
|
|
|
|
|
|
2011-08-15 21:30:30 +08:00
|
|
|
|
exit $RETURN_VALUE
|
2009-01-06 22:58:21 +08:00
|
|
|
|
|
|
|
|
|
|
You get the HDF 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
|
2004-09-15 02:52:05 +08:00
|
|
|
|
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.
|
2007-04-14 02:53:50 +08:00
|
|
|
|
|
|
|
|
|
|
* 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 h5copy tool
|
|
|
|
|
|
|
