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1743 lines
95 KiB
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1743 lines
95 KiB
Plaintext
HDF5 HISTORY
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=============
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INTRODUCTION
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This document describes the development history between the HDF5-1.8.0 and
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HDF5 1.10.0 releases. For more iformation see the SVN log.
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Information about supported and tested platforms is provided for historical
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reasons only and may not be accurate.
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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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- Supported Platforms
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- Tested Configuration Features Summary
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- More Tested Platforms
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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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- Java JNI library API wrappers and supporting files added as HDF_JAVA language
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option. Both configure and CMake disable this option by default.
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HDFFV-9552 (ADB 2016/02.28)
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- CMake minimum is now 3.1.0. (ADB 2015/11/14)
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- cmakehdf5: configure options added to enable or disable the building of
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different API's and testings. See "cmakehdf5 --help" for details.
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(AKC - 2014/12/09 HDFFV-8932)
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- Autotools: Automake updated to 1.14.1 (ADB - 2014/04/08)
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- CMake: Moved minimum CMake version to 2.8.11 which enables better library
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include processing. (ADB - 2014/03/26)
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- New configuration option added to change the default plugin path.
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configure option is --with-default-plugin=location
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cmake option is -DH5_DEFAULT_PLUGINDIR:PATH=location
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HDFFV-8513. (ADB 2013/09/04)
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- Rename FFLAGS to FCFLAGS in configure (ADB 2013/08/13)
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- CMake minimum is now 2.8.10. (ADB 2013/01/14)
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- A new tool, cmakehdf5, which is a build command script similar to
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buildhdf5 is added and is available in the bin directory.
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(AKC - 2012/12/12)
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- Fixed AIX Fortran compiler flags to use appropriate settings for
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debugging, profiling, optimization situations. HDFFV-8069. (AKC
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2012/09/27)
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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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- 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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- 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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- 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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- 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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- 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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- 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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- 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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- 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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- Configuration suite now uses Automake 1.11 and Autoconf 2.64.
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MAM 2009/08/11.
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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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- Added libtool version numbers to generated c++, fortran, and
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hl libraries. MAM 2009/04/19.
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- Regenerated Makefile.ins using Automake 1.10.2. MAM 2009/04/19.
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- Added a Make target of check-all-install to test the correctness of
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installing via the prefix= or $DESTDIR options. AKC - 2009/04/14
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- 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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- Virtual Dataset feature was added
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(NAF - 2015-10-05, VDS-193)
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- H5F_ACC_DEBUG labeled "deprecated"
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The symbol was originally used to emit some extra debugging
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informationi in the multi VFD. The underlying functionality
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was removed due to disuse in HDF5 1.8.16 though the symbol
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remained defined since it was visible in H5Fpublic.h.
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In this release, the symbol has been labeled deprecated and will
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not be defined when H5_NO_DEPRECATED_SYMBOLS is defined.
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(DER - 2015-04-30, HDFFV-1074)
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- The library can load filter libraries dynamically during runtime. Users
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can set the search path through environment variable HDF5_PLUGIN_PATH
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and call H5Pset_filter to enable a dynamic filter. (SLU - 2013/04/08)
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- Added new API functions H5Dscatter and H5Dgather to scatter data to and
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and gather data from a selection within a memory buffer.
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(NAF - 2013/02/05)
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- The library now supports the data conversion from enumeration to numeric
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(integer and floating-point number) datatypes. See Issue 8221.
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(SLU - 2012/10/23)
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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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- 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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- H5Tcreate now supports string type (fixed-length and variable-length).
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(SLU - 2011/05/20)
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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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H5Pget_elink_file_cache_size(), and H5Fclear_elink_file_cache().
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(NAF - 2011/02/17)
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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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- 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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- 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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- 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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- 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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- Greatly improved performance of extending a dataset with early
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allocation. (NAF - 2010/03/24 - 1637)
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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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- 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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print a warning and allows the program to continue. (AKC - 2009/9/28)
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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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during configure. (AKC - 2009/9/15)
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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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- Separated "factory" free list class from block free lists. These free
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lists are dynamically created and manage blocks of a fixed size.
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H5set_free_list_limits() will use the same settings specified for block
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free lists for factory free lists. (NAF - 2009/04/08)
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- Added support for dense attributes to H5Ocopy. (XCao/NAF - 2009/01/29)
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- Added H5Pset_elink_cb and H5Pget_elink_cb functions to support a
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user-defined callback function for external link traversal.
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(NAF - 2009/01/08)
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- Added H5Pset_elink_acc_flags and H5Pget_elink_acc_flags functions to
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allow the user to specify the file access flags used to open the target
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file of an external link. (NAF - 2009/01/08)
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- Added H5Pset_chunk_cache() and H5Pget_chunk_cache() functions to allow
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individual rdcc configuration for each dataset. Added
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H5Dget_access_plist() function to retrieve a dataset access property
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list from a dataset. (NAF - 2008/11/12)
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- Added H5Iis_valid() function to check if an id is valid without producing
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an error message. (NAF - 2008/11/5)
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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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- 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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- 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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- 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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Fortran Library:
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----------------
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- Added parallel routine H5Pget_mpio_actual_io_mode_f (MSB - 2012/09/27)
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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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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:
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h5aread_f
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h5awrite_f
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h5dread_f
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h5dwrite_f
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- New subroutines
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h5dvlen_reclaim_f
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h5literate_by_name_f
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h5literate_f
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h5ovisit_f
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h5tconvert_f
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- Subroutines with additional optional parameters:
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h5pcreate_class_f
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(EIP - 2011/10/14)
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- Added for the C APIs the Fortran wrappers:
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h5dget_access_plist_f
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h5iis_valid_f
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h5pset_chunk_cache_f
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h5pget_chunk_cache_f
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(MSB - 2009/04/17)
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C++ Library:
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------------
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- New member function added
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The assignment operator ArrayType::operator= is added because ArrayType
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has pointer data members.
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(BMR, 2016/03/07, HDFFV-9562)
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- New member functions
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+ Overloaded CommonFG::getObjnameByIdx to take char* for name
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+ Overloaded CommonFG::getObjTypeByIdx to return type name as a char*.
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(BMR - 2010/05/02)
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+ DataSet::getInMemDataSize() to simplify getting the dataset's
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data size in memory. (BMR - 2009/07/26)
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- These member functions were added as wrapper for H5Rdereference to
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replace the incorrect IdComponent::dereference().
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void H5Object::dereference(H5File& h5file, void* ref)
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void H5Object::dereference(H5Object& obj, void* ref)
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In addition, these constructors were added to create the associated
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objects by way of dereference:
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Attribute(H5Object& obj, void* ref);
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Attribute(H5File& file, void* ref);
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DataSet(H5Object& obj, void* ref);
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DataSet(H5File& file, void* ref);
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DataType(H5Object& obj, void* ref);
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DataType(H5File& file, void* ref);
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Group(H5Object& obj, void* ref);
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Group(H5File& obj, void* ref);
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(BMR - 2008/08/10)
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Tools:
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------
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- h5repack: Added ability to use plugin filters. HDFFV-8345 (ADB - 2013/09/04).
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- h5dump: Added option -N --any_path, which searches the file for paths that
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match the search path. HDFFV-7989 (ADB - 2013/08/12).
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- h5dump: Added optional arg 0 to -A, which excludes attributes from display.
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HDFFV-8134 (ADB - 2013/08/01).
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- h5dump: Fixed displaying compression ratio for unknown or user-defined
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filters. HDFFV-8344 (XCAO 2013/03/19)
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- h5dump: Changed UNKNOWN_FILTER to USER_DEFINED_FILTER for user defined filter.
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HDFFV-8346 (XCAO 2013/03/19)
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- h5dump: Added capability for "-a" option to show attributes containing "/"
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by using an escape character. For example, for a dataset "/dset"
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containing attribute "speed(m/h)", use "h5dump -a "/dset/speed(\/h)"
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to show the content of the attribute. See details at HDFFV-7523
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(PC -- 2012/03/12)
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- h5dump: Added ability to apply command options across multiple files using a
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wildcard in the filename. Example; "h5dump -H -d Dataset1 tarr*.h5".
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HDFFV-7876 (ADB - 2012/03/12).
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- h5repack: Improved performance for big chunked datasets (size > 128MB)
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when used with layout (-l) or compression (-f) option.
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It would perform much better prior to the improvement,
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especially for cases that chunk dimentions looks like
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"1024x5x1" (compare to "1x5x1024"). When bigger numbers
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are toward front and smaller number is toward back in chunk
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dimentions. HDFFV-7862 (JKM - 2012/03/01)
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- h5dump: Added new option --no-compact-subset. This option will not
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interpret the '[' character as starting the compact form of
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subsetting. This is useful when the "h5dump error: unable to
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open dataset "datset_name"" message is output because a dataset
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name contains a '[' character. HDFFV-7689 (ADB - 2012/01/31)
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- h5dump: Corrected schema location:
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<hdf5:HDF5-File
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xmlns:hdf5="http://hdfgroup.org/HDF5/XML/schema/HDF5-File"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://hdfgroup.org/HDF5/XML/schema/HDF5-File
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http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd">
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(ADB - 2011/08/10)
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- h5diff: Added new level for -v (verbose) option. The new levels are
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1 and 2. So -v1 and -v2 can be specified to view more
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information about attributes differences.
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Bug#2121 (JKM 2011/3/23)
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- h5dump: Added new option --enable-error-stack. This option will display
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error stack information in the output stream. This is useful
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when the "h5dump: Unable to print data" message is output.
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(ADB - 2011/02/24)
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- h5diff: Add a new flag --exclude-path. Specified path to an object will
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be excluded from comparing the two files or two groups. If group
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is specified all the member objects will be excluded.
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(JKM - 2010/09/16).
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- h5ls: Add new flag --no-dangling-links. (refer to --help for details)
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(JKM - 2010/06/15)
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- h5ls: Add new flag --follow-symlinks. (refer to --help for details)
|
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(JKM - 2010/05/25)
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- h5diff: Add new flag --no-dangling-links. (refer to --help for details)
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(JKM - 2010/02/10)
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- h5diff: Add new flag --follow-symlinks. (refer to --help for details)
|
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(JKM - 2010/01/25)
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- h5diff: fix for displaying garbage value on LE machine for BE data.
|
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(JKM - 2009/11/20)
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- h5dump: subsetting now allows default for count. Also trailing ; in short form
|
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can be omitted after last specified value.
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(ADB - 2009/09/04)
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- h5dump/h5ls: now can display data in region references
|
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using new -R, --region flag.
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(ADB - 2009/09/04)
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- h5diff: new flag, -c, --compare, list objects that are not comparable.
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(PVN - 2009/4/10 - 1368)
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- h5diff new flag, -N, --nan, avoids NaNs detection. (PVN - 2009/4/10)
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- h5dump correctly specifies XML dtd / schema urls (ADB - 2009/4/3 - 1519)
|
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- h5repack now handles group creation order. (PVN - 2009/4/2 - 1402)
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- h5dump: added a printing of the compression ratio of uncompressed and compressed
|
||
sizes for cases where compression filters are present. (PVN - 2008/05/01)
|
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- h5dump: added an option to allow a user defined formatting string for printf
|
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regarding floating point numbers. (PVN - 2008/05/06)
|
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- h5dump: support for external links, display the object that the external link
|
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points to. (PVN - 2008/05/12)
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- h5repack: add a userblock to an HDF5 file during the repack. (PVN - 2008/08/26)
|
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- h5repack: add 2 options that call H5Pset_alignment in the repacked file. (PVN - 2008/08/29)
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- h5ls: added capability to traverse through external links when the -r
|
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(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)
|
||
- 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)
|
||
- 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)
|
||
- h5diff: add option "--use-system-epsilon" to print difference if (|a-b| > EPSILON)
|
||
Change default to use strict equality (PC -- 2009/09/12)
|
||
|
||
|
||
High-Level APIs:
|
||
---------------
|
||
|
||
C Packet Table API
|
||
------------------
|
||
- Replacement of a public function
|
||
|
||
The existing function H5PTcreate_fl limits applications to deflate
|
||
compression only. The public function H5PTcreate is added to replace
|
||
H5PTcreate_fl. H5PTcreate takes a property list ID to provide
|
||
flexibility on creation properties.
|
||
|
||
hid_t H5PTcreate(hid_t loc_id, const char *dset_name,
|
||
hid_t dtype_id, hsize_t chunk_size, hid_t plist_id);
|
||
(BMR, 2016/03/04, HDFFV-8623)
|
||
|
||
- New public functions
|
||
|
||
Two accessor functions were added per HDFFV-8623/patch 003.
|
||
/* Returns the ID of the dataset associated with the packet table */
|
||
hid_t H5PTget_dataset(hid_t table_id);
|
||
|
||
/* Returns the ID of the datatype the packet table uses */
|
||
hid_t H5PTget_type(hid_t table_id);
|
||
(BMR, 2016/03/04, HDFFV-8623)
|
||
|
||
- Regarding #ifdef VLPT_REMOVED
|
||
|
||
The #ifdef VLPT_REMOVED blocks are removed from the PT library source
|
||
except the following cases:
|
||
+ H5PTis_varlen() is made available again.
|
||
+ H5PTfree_vlen_readbuff() now became H5PTfree_vlen_buff()
|
||
(BMR, 2016/03/04, HDFFV-442)
|
||
|
||
C++ Packet Table API
|
||
--------------------
|
||
- New constructor
|
||
|
||
An overloaded constructor is added to FL_PacketTable and takes a property
|
||
list ID to provide flexibility on creation properties.
|
||
|
||
FL_PacketTable(hid_t fileID, hid_t plist_id, const char* name, hid_t dtypeID, hsize_t chunkSize);
|
||
(BMR, 2016/03/08, HDFFV-8623)
|
||
|
||
- New public functions
|
||
|
||
Two accessor wrappers to class PacketTable, per HDFFV-8623/patch 004.
|
||
/* Returns the ID of the dataset associated with the packet table */
|
||
hid_t PacketTable::GetDataset()
|
||
|
||
/* Returns the ID of the datatype the packet table uses */
|
||
hid_t PacketTable::GetDataset()
|
||
(BMR, 2016/03/04, HDFFV-8623)
|
||
|
||
- Member functions having "char*" as an argument
|
||
|
||
Overloaded functions were added to provide "const char*" argument, the
|
||
existing version will be deprecated.
|
||
(BMR, 2016/03/04)
|
||
|
||
- Regarding #ifdef VLPT_REMOVED
|
||
|
||
The #ifdef VLPT_REMOVED blocks are removed from the PT library source
|
||
except the following cases:
|
||
+ VL_PacketTable::IsVariableLength() is moved to PacketTable
|
||
+ VL_PacketTable::FreeReadBuff() now became PacketTable::FreeBuff()
|
||
|
||
(BMR, 2016/03/04, HDFFV-442)
|
||
|
||
|
||
Internal header file
|
||
--------------------
|
||
- A new API function H5DOwrite_chunk. It writes a data chunk directly
|
||
into a file bypassing hyperslab selection, data conversion, and
|
||
filter pipeline. The user must be careful with the function and
|
||
clearly understand the I/O process of the library.
|
||
(SLU - 2013/2/11)
|
||
- New API: h5ltpath_valid (Fortran: h5ltpath_valid_f) which checks
|
||
if a path is correct and determines if a link resolves to a valid
|
||
object and checks that the link does not dangle. (MSB- 2012/3/15)
|
||
|
||
- 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)
|
||
|
||
- Table: In version 3.0 of Table, "NROWS" (used to store number of records) was
|
||
deprecated (PVN - 2008/11/24)
|
||
|
||
Documentation
|
||
-------------
|
||
|
||
Support for new platforms, languages and compilers.
|
||
=======================================
|
||
- Intel V11.1 uses now -O3 optimization in production mode (EIP - 2010/10/08)
|
||
- PathScale compilers are recognized and can build the HDF5 library
|
||
properly. AKC - 2009/7/28 -
|
||
- SunOS 5.11 (emu) 32-bit and 64-bit with Sun C/C++ 5.12 compiler and
|
||
Sun Fortran 95 8.6 compiler. (SLU - 2013/04/15)
|
||
|
||
Bug Fixes since HDF5-1.8.0 release
|
||
==================================
|
||
|
||
Library
|
||
-------
|
||
- Incorrect usage of list in CMake COMPILE_DEFINITIONS set_property
|
||
|
||
The CMake command, set_property with COMPILE_DEFINITIONS property
|
||
needs a quoted semi-colon separated list of values. CMake will
|
||
transform the list to a series of -D{value} for the compile.
|
||
|
||
(ADB - 2014/12/09, HDFV-9041)
|
||
|
||
- H5Z.c: H5Zfilter_avail(H5Z_filter_t id)
|
||
Added else block if the call to the internal H5Z_filter_avail(id) does not
|
||
fail and returns FALSE. This block calls the H5PL_load(H5PL_TYPE_FILTER, (int)id)
|
||
function to attempt to dynamically load the filter plugin.
|
||
(ADB - 2014/03/03 HDFFV-8629)
|
||
- Added const qualifier to source buffer parameters in H5Dgather and
|
||
H5D_scatter_func_t (H5Dscatter callback). (NAF - 2013/7/02)
|
||
- Fixed an error involving failure to write fill values to the user's
|
||
buffer when reading unallocated chunks from datasets that have a
|
||
fill value set to H5D_FILL_VALUE_DEFAULT. A consequence of this
|
||
was the reporting of spurious data values in h5dump and h5diff
|
||
output.
|
||
(HDFFV-8247; JP - 2013/05/03)
|
||
- Fixed an error that could occur when calling H5Ocopy within an
|
||
H5Literate callback (and possibly other situations).
|
||
(NAF - 2012/7/25 - HDFFV-5853)
|
||
- Fixed an error that would occur when copying an object with attribute
|
||
creation order tracked and indexed. (NAF - 2012/3/28 - HDFFV-7762)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- Fixed rare corruption bugs that could occur when using the new object
|
||
header format. (NAF - 2012/3/15 - HDFFV-7879)
|
||
- Creating a dataset in a read-only file caused seg fault when the file
|
||
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)
|
||
- Fixed a seg fault that could occur when shrinking a dataset with chunks
|
||
larger than 1 MB. (NAF - 2011/11/30 - HDFFV-7833)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- #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.
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- 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
|
||
by any machine after this patch. (NAF - 2010/02/02 - Bug 2131)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- Fixed a file corruption bug that could happen when shrinking a
|
||
compressed dataset. (NAF - 2010/05/20)
|
||
- Fixed some memory leaks in VL datatype conversion when strings are
|
||
used as fill values. (MAM - 2010/05/12 - BZ# 1826)
|
||
- Fixed a bug when copying objects with NULL references with the
|
||
H5O_COPY_EXPAND_REFERENCE_FLAG flag set. (NAF - 2010/04/08 - 1815)
|
||
- 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)
|
||
- 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)
|
||
- Fixed a bug where the library, when traversing an external link, would
|
||
reopen the source file if nothing else worked. (NAF - 2010/03/05)
|
||
- 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)
|
||
- 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)
|
||
- 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.
|
||
(NAF - 2009/10/27 - 1483)
|
||
- Fixed incorrect return value for H5Pget_preserve. (AKC - 2009/10/08 - 1628)
|
||
- Fixed an assertion failure that occurred when H5Ocopy was called on a
|
||
dataset using a vlen inside a compound. (NAF - 2009/10/02 - 1597)
|
||
- Fixed incorrect return value for H5Pget_filter_by_id1/2 in H5Ppublic.h.
|
||
(NAF - 2009/09/25 - 1620)
|
||
- Fixed a bug where properties weren't being compared with the registered
|
||
compare callback. (NAF - 2009/09/25 - 1555)
|
||
- Fixed a bug where H5Pget_fitler_by_id would succeed when called for a
|
||
filter that wasn't present. (NAF - 2009/06/25 - 1250)
|
||
- Fixed an issue with committed compound datatypes containing a vlen.
|
||
Also fixed memory leaks involving committed datatypes.
|
||
(NAF - 2009/06/10 - 1593)
|
||
- Added versioning to H5Z_class_t struct to allow compatibility with 1.6
|
||
API. (NAF - 2009/04/20 - 1533)
|
||
- Fixed a problem with using data transforms with non-native types in the
|
||
file. (NAF - 2009/04/20 - 1548)
|
||
- Added direct.h include file to windows section of H5private.h
|
||
to fix _getcwd() warning. (ADB - 2009/04/14 - 1536)
|
||
- Fixed a bug that prevented external links from working after calling
|
||
H5close(). (NAF - 2009/04/10 - 1539)
|
||
- 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
|
||
created by this version. (NAF - 2009/04/08 - 1423)
|
||
- Changed skip lists to use a deterministic algorithm. The library should
|
||
now never call rand() or srand(). (NAF - 2009/04/08 - 503)
|
||
- Fixed a bug where H5Lcopy and H5Lmove wouldn't create intermediate
|
||
groups when that property was set. (NAF - 2009/04/07 - 1526)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- Fixed various bugs that could prevent the fill value from being written
|
||
in certain rare cases. (NAF - 2009/02/26 - 1469)
|
||
- Fixed a bug that prevented more than one dataset chunk from being cached
|
||
at a time. (NAF - 2009/02/12 - 1015)
|
||
- Fixed an assertion failure caused by opening an attribute multiple times
|
||
through multiple file handles. (NAF - 2009/02/12 - 1420)
|
||
- Fixed a problem that could prevent the user from adding attributes (or
|
||
any object header message) in some circumstances.
|
||
(NAF - 2009/02/12 - 1427)
|
||
- 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)
|
||
- Changed H5Tset_order to properly reject H5T_ORDER_NONE for most
|
||
datatypes. (NAF - 2009/01/27 - 1443)
|
||
- Fixed a bug where H5Tpack wouldn't remove trailing space from an
|
||
otherwise packed compound type. (NAF - 2009/01/14)
|
||
- 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
|
||
multiple files. (NAF - 2008/11/17)
|
||
- H5Ovisit and H5Ovisit_by_name will now properly terminate when the
|
||
callback function returns a positive value on the starting object.
|
||
(NAF - 2008/11/03)
|
||
- Fixed an error where a null message could be created that was larger
|
||
than could be written to the file. (NAF - 2008/10/23)
|
||
- Corrected error with family/split/multi VFD not updating driver info
|
||
when "latest" version of the file format used. (QAK - 2008/10/14)
|
||
- Corrected alignment+threshold errors to work correctly when metadata
|
||
aggregation is enabled. (QAK - 2008/10/06)
|
||
- Changed H5Fget_obj_count and H5Fget_obj_ids to ignore objects registered
|
||
by the library for internal library use. (NAF - 2008/10/06)
|
||
- Fixed potential memory leak during compound conversion.
|
||
(NAF - 2008/10/06)
|
||
- Changed the return value of H5Fget_obj_count from INT to SSIZE_T. Also
|
||
changed the return value of H5Fget_obj_ids from HERR_T to SSIZE_T and
|
||
the type of the parameter MAX_OBJS from INT to SIZE_T. (SLU - 2008/09/26)
|
||
- Fixed an issue that could cause data to be improperly overwritten
|
||
during compound type conversion. (NAF - 2008/09/19)
|
||
- Fixed pointer alignment violations that could occur during vlen
|
||
conversion. (NAF - 2008/09/16)
|
||
- Fixed problem where library could cause a segmentation fault when
|
||
an invalid location ID was given to H5Giterate(). (QAK - 2008/08/19)
|
||
- Fixed improper shutdown when objects have reference count > 1. The
|
||
library now tracks reference count due to the application separately
|
||
from that due to internal library routines. (NAF - 2008/08/19)
|
||
- Fixed assertion failure caused by incorrect array datatype version.
|
||
(NAF - 2008/08/08)
|
||
- Fixed an issue where mount point traversal would fail when using
|
||
multiple handles for the child. (NAF - 2008/08/07)
|
||
- Fixed an issue where mount points were inaccessible when using multiple
|
||
file handles for the parent. The mount table is now in the shared
|
||
file structure (the parent pointer is still in the top structure).
|
||
(NAF - 2008/08/07)
|
||
- 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().
|
||
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)
|
||
- 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)
|
||
- H5Dset_extent: when shrinking dimensions, some chunks were not deleted.
|
||
(PVN - 2009/01/8)
|
||
- Added code to maintain a min_clean_fraction in the metadata cache when
|
||
in serial mode. (MAM - 2009/01/9)
|
||
|
||
|
||
|
||
Configuration
|
||
-------------
|
||
- CMake: When CMake commands are executed individually on the command line
|
||
and the external filters are being built, the CMAKE_BUILD_TYPE define
|
||
must be set to the same value as the configuration
|
||
(-DCMAKE_BUILD_TYPE:STRING=Release if using -C Release). This is needed
|
||
by the the szip and zlib filter build commands. (ADB - HDFFV-8695)
|
||
- CMake: Remove use of XLATE_UTILITY program. (ADB - 2014/03/28 HDFFV-8640)
|
||
- CMake: Added missing quotes in setting the CMAKE_EXE_LINKER_FLAGS for the
|
||
MPI option. (ADB - 2014/02/27 HDFFV-8674)
|
||
- Modified H5detect.c to scan floating point types for padding bits before
|
||
analyzing the type further. This should fix problems with gcc 4.8
|
||
(NAF - 2013/09/19 - HDFFV-8523/HDFFV-8500)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
|
||
- 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)
|
||
- Removed config/ibm-aix6.x. All IBM-AIX settings are in one file,
|
||
ibm-aix. (AKC - 2011/4/14)
|
||
- 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).
|
||
- 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)
|
||
- 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
|
||
- Support for TFLOPS, config/intel-osf1, is removed since the TFLOPS
|
||
machine has long retired. AKC - 2009/10/06.
|
||
- 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
|
||
- 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
|
||
- 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 -
|
||
- 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
|
||
- 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
|
||
- 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.
|
||
- Fixed error with 'make check install' failing due to h5dump
|
||
needing other tools built first. MAM - 2008/10/24.
|
||
- Wpen using shared szip, it is no longer necessary to specify
|
||
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.
|
||
- Autotools: An export of LD_LIBRARY_PATH=<szip library location> was
|
||
removed from configure and make installcheck was revised to run
|
||
scripts installed in share/hdf5_examples to use the installed h5cc, etc.
|
||
to compile and run example source files also installed there. Make
|
||
installcheck will now fail when a shared szip or other external lib file
|
||
cannot be found in the same manner that executables compiled and linked
|
||
with h5cc will fail to run when those lib files cannot be found after
|
||
install. Make installcheck should pass after setting LD_LIBRARY_PATH to the
|
||
szip location.
|
||
(LRK - 2014/04/16)
|
||
|
||
Performance
|
||
-------------
|
||
- Removed program perform/benchpar from the enable-build-all list. The
|
||
program will be retired or moved to another location. HDFFV-8156
|
||
(AKC 2012/10/01)
|
||
- Retired program perform/mpi-perf. Its purpose has been incorporated
|
||
into h5perf before. (AKC 2012/09/20)
|
||
- ifdefs added to tests around include unistd.h and function to simulate
|
||
getlogin() on Windows.
|
||
(ADB - 2011/08/15)
|
||
- perf_serial test added to Windows projects and check batch file.
|
||
(ADB - 2009/06/11)
|
||
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)
|
||
|
||
- Fixed problem writing/reading control characters to a dataset; writing
|
||
a string containing: alerts, backspace, carriage_return, form_feed,
|
||
horizontal_tab, vertical_tab, new_line is now tested and working.
|
||
(MSB - 2012/09/01)
|
||
|
||
- Corrected the integer type of H5S_UNLIMITED_F to HSIZE_T (MSB - 2012/09/01)
|
||
|
||
- Corrected the number of continuation lines in the src files
|
||
to be less then 32 lines for F95 compliance. (MSB - 2012/10/01)
|
||
|
||
Tools
|
||
-----
|
||
- h5dump subsetting fixed for dims greater then two
|
||
When a dataset has more then two dimensions, subsetting would incorrectly
|
||
calculate the data that needed to be displayed.
|
||
Added in block and stride calculation that account for dimensions greater
|
||
then two. NOTE: lines that have line breaks inserted because of display
|
||
length calculations, may have index info that is incorrect until the next
|
||
dimension break. (ADB, 2016/03/04, HDFFV-9698)
|
||
- h5repack: h5repack would not attempt to remove UD filters. Added a
|
||
check to h5repack for UD filters that checks if the filter can
|
||
be dynamically loaded. This will require a change in the library to
|
||
add the H5PL_load() to the H5Zfilter_avail(). (ADB - 2014/03/03 HDFFV-8629)
|
||
- h5repack: Fixed failure for converting a layout of small chunked dataset
|
||
(size < 1K) to contiguous layout. HDFFV-8214 (JKM 2013/03/18)
|
||
- h5diff: Fixed to return correct exit code 1 when detect unique extra
|
||
attribute. Prior to this fix, h5diff returned exit code 0 indicating
|
||
two files are identical. HDFFV-7643 (JKM 2013/02/15)
|
||
- h5diff: Improved speed when comparing HDF5 files with lots of
|
||
attributes. Much slower performance was identified with release
|
||
version from 1.8.7 to 1.8.10 compared to 1.8.6. (JKM 2012/10/19)
|
||
- h5repack: "h5repack -f NONE file1.h5 out.h5" command failed if
|
||
source file contains chunked dataset and a chunk dim is bigger than
|
||
the dataset dim. Another issue is that the command changed max dims
|
||
if chunk dim is smaller than the dataset dim.
|
||
These issue occurred when dataset size is smaller than 64k (compact
|
||
size limit) Fixed both.
|
||
HDFFV-8012 (JKM 2012/09/24)
|
||
- 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)
|
||
- h5diff: Fixed the incorrect result when comparing attribute data
|
||
values and the data type has same class but different size.
|
||
HDFFV-7942 (JKM 2012/08/15)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- h5unjam: Fixed sefgault when used -V (show version) option.
|
||
HDFFV-8001 (JKM 2012/04/19)
|
||
- h5repack: Fixed a failure when change the chunk size of a specified
|
||
chunked dataset with unlimited max dims. HDFFV-7993 (JKM 2012/04/11)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- h5dump: Refactored code to remove duplicated functions. Split XML
|
||
functions from DDL functions. Corrected indentation and formatting
|
||
errors. Also fixed subsetting counting overflow (HDFFV-5874). Verified
|
||
all tools call tools_init() in main.
|
||
HDFFV-7560 (ADB 2012/02/17)
|
||
- 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)
|
||
- h5repack: fixed memory leak for handling variable length string in
|
||
attribute. HDFFV-7840 (JKM 2012/01/06)
|
||
- h5ls: fixed segfault when access region reference data in an
|
||
attribute. HDFFV-7838 (JKM 2011/12/29)
|
||
- 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
|
||
- h5diff: fixed segfault over dataset with container types
|
||
(array,lven) with multiple nested compound types.
|
||
(ex: compound->array->compound, compound->vlen->compound)
|
||
HDFFV-7712 JKM (2011/09/01)
|
||
- h5repack: added macro to handle failure in H5Dread/write when memory
|
||
allocation failed inside the library. (PC -- 2011/08/19)
|
||
- Fixed h5jam not to allow specifying an HDF5 formatted file as input
|
||
file for -u (user block file) option, because the original HDF5 file
|
||
will not be accessible if allows. HDFFV-5941 (JKM 2011/08/15)
|
||
- Revised command help pages of h5jam and h5unjam. The descriptions
|
||
were not up to date and some were missing.
|
||
HDFFV-7515 (JKM 2011/08/15)
|
||
- 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)
|
||
- Fixed h5diff to display instructive error message and exit with 1
|
||
when mutually exclusive options (-d, -p and --use-system-epsilon)
|
||
are used together. HDFFV-7600 (JKM 2011/07/07)
|
||
- 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).
|
||
Bug #HDFFV-5878 (JKM 2011/06/15)
|
||
- Fixed h5dump to display correct value for H5T_STD_I8LE dataset
|
||
on a system (ppc64, linux, Big-Endian, clustering).
|
||
Bug #HDFFV-7594 (ABERT & JKM 2011/05/12)
|
||
- 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
|
||
or attributes) Bug #HDFFV-5928 (XCAO & JKM 2011/05/06)
|
||
- Updated h5dump test case script to prevent entire test failure upon
|
||
source directory is read-only. Bug# HDFFV-4342 (JKM 2011/4/12)
|
||
- Fixed h5dump displaying incorrect values for H5T_STD_I8BE type data in
|
||
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.
|
||
Bug #HDFFV-4358 (JKM 2011/04/08)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- Fixed memory leak for h5diff when accessing symbolic links with
|
||
--follow-symlink option. Bug#2214 (JKM 2011/3/18)
|
||
- Fixed memory leak for h5diff when access variable length string
|
||
data. Bug#2216 (JKM 2011/3/18)
|
||
- Fixed and improved help page for -a option of h5ls.
|
||
Bug#1904 (JKM 2011/3/11)
|
||
- 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)
|
||
- 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)
|
||
- 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)
|
||
- 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).
|
||
- 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)
|
||
- 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
|
||
- 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)
|
||
- 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)
|
||
- Fixed h5copy to fail gracefully when copying object to non-exist
|
||
group without -p option. Bug#2040 (JKM 2010/10/18)
|
||
- Fixed to compare member objects and groups recursively when two
|
||
files or groups are specified to be compared. Bug#1975
|
||
(JKM 2010/9/16)
|
||
- Make h5repack be able to convert a layout to COMPACT for small size
|
||
dataset as default. bug#1896 (JKM 2010/09/15)
|
||
- Change h5ls not to manipulate special characters in object name or
|
||
attribute name for smart display. bug#1784 (JKM 2010/06/28)
|
||
- 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)
|
||
- h5diff: fixed incorrect behavior (hang) in parallel mode when
|
||
specify invalid options (ex: -v and -q) (JKM 2010/02/17)
|
||
- h5dump/h5ls display buffer resize fixed in tools library.
|
||
(ADB - 2009/07/21 - 1520)
|
||
- Fixed many problems that could occur when using h5repack with named
|
||
datatypes. (NAF - 2009/4/20 - 1516/1466)
|
||
- h5dump, h5diff, h5repack were not reading (by hyperslabs) datasets
|
||
that have a datatype datum size greater than H5TOOLS_BUFSIZE, a
|
||
constant defined as 1024Kb, such as array types with large
|
||
dimensions (PVN - 2009/4/1 - 1501)
|
||
- h5import: By selecting a compression type, a big endian byte order was being
|
||
selected (PVN - 2009/3/11 - 1462)
|
||
- 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)
|
||
- Fixed bugs in h5stat:segmemtation fault when printing groups and
|
||
print warning message when traversal of objects is unsuccessful.
|
||
(see bug #1253) (VC- 2008/10/13)
|
||
- Fixed bug in h5ls that prevented relative group listings (like
|
||
"h5ls foo.h5/bar") from working correctly (QAK - 2008/06/03)
|
||
- 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
|
||
|
||
|
||
High-Level APIs:
|
||
------
|
||
- Packet Table is updated.
|
||
|
||
In the Packet Table C API, there are changes with the following functions,
|
||
which had been ifdef'ed out with VLPT_REMOVED since 2006
|
||
* H5PTcreate_vl, is removed from this release
|
||
* H5PTfree_vlen_readbuff, is renamed to H5PTfree_vlen_buff
|
||
* H5PTis_varlen, is made available again
|
||
|
||
Various cleanup: replacing 0/-1 with SUCCEED/FAIL and H5I_BADID with
|
||
H5I_INVALID_HID. (BMR, 2016/03/04, HDFFV-442)
|
||
|
||
- Fixed problem with H5DSget_scale_name including the NULL terminator in
|
||
the size calculation returned by the function. The API does not
|
||
include the NULL terminator in the size returned (MSB- 2013/2/10)
|
||
|
||
- Fixed problem with H5TBdelete_record destroying all data following the deletion
|
||
of a row. (MSB- 2012/7/26)
|
||
|
||
- Fixed H5LTget_attribute_string not closing an object identifier when an
|
||
error occurs. (MSB- 2012/7/21)
|
||
|
||
- Fixed the H5LTdtype_to_text function. It had some memory problems when
|
||
dealing with some complicated data types. HDFFVI-7701 (SLU - 2011/10/19)
|
||
|
||
- 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.
|
||
(EIP - 2010/05/22 -1851)
|
||
- 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)
|
||
- Fixed a bug where the H5TB API would forget the order of fields when
|
||
added out of offset order. (NAF - 2009/10/27 - 1582)
|
||
- H5DSis_attached failed to account for different platform types. Added a
|
||
get native type call. (ADB - 2009/9/29 - 1562)
|
||
- Dimension scales: The scale index return value in H5DSiterate_scales was not always
|
||
incremented. (PVN - 2009/4/8 - 1538)
|
||
|
||
Fortran High-Level APIs:
|
||
------
|
||
|
||
- 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)
|
||
- Lite: The h5ltget_dataset_info_f function (gets information about a dataset)
|
||
was not correctly returning the dimension array. (PVN - 2009/3/23)
|
||
- Lite: the h5ltread_dataset_string_f and h5ltget_attribute_string_f functions
|
||
had memory problems with the g95 fortran compiler. (PVN <20> 5/13/2009) 1522
|
||
|
||
|
||
|
||
|
||
|
||
Documentation
|
||
-------------
|
||
|
||
|
||
F90 APIs
|
||
--------
|
||
- 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)
|
||
|
||
|
||
C++ APIs
|
||
--------
|
||
- 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)
|
||
- 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)
|
||
|
||
Testing
|
||
-------
|
||
- tools/h5diff/testh5diff.sh is run in every "make check", even after it
|
||
has passed in the previous run. It should not run again if there is no
|
||
code changes. Fixed. (AKC - 2013/07/19 HDFFV-8392)
|
||
- In some Mac system, testlibinfo.sh failed with this error:
|
||
Check file ../src/.libs/libhdf5.7.dylib
|
||
strings: object: ../src/.libs/libhdf5.7.dylib malformed object \
|
||
(unknown load command 15)
|
||
The strings command of Mac inspects library files and older
|
||
versions of strings may not know newer library format, resulting
|
||
in errors. Fixed by sending the library file as stdin to the strings
|
||
coommand to avoid this problem. (AKC - 2013/03/08 HDFFV-8305)
|
||
|
||
- Fixed a typo in the ERROR macro in test/testhdf5.h. It segmentation
|
||
faulted when used before. (AKC - 2013/02/12 HDFFV-8267)
|
||
|
||
|
||
Supported Platforms
|
||
===================
|
||
AIX 6.1 xlc 10.1.0.5
|
||
(NASA G-ADA) xlC 10.1.0.5
|
||
xlf90 12.1.0.6
|
||
|
||
Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++)
|
||
#1 SMP i686 i686 i386 compilers for 32-bit applications;
|
||
(jam) Version 4.1.2 20080704 (Red Hat 4.1.2-54)
|
||
Version 4.8.2
|
||
PGI C, Fortran, C++ Compilers for 32-bit
|
||
applications;
|
||
Version 13.7-0
|
||
Intel(R) C, C++, Fortran Compiler for 32-bit
|
||
applications;
|
||
Version 14.0.2 (Build 20140120)
|
||
|
||
Linux 2.6.18-371.6.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++)
|
||
#1 SMP x86_64 GNU/Linux compilers for 64-bit applications;
|
||
(koala) Version 4.1.2 20080704 (Red Hat 4.1.2-54)
|
||
Version 4.8.2
|
||
Intel(R) C, C++, Fortran Compilers for
|
||
applications running on Intel(R) 64;
|
||
Version 14.0.2 (Build 20140120)
|
||
|
||
Linux 2.6.32-431.11.2.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
|
||
#1 SMP x86_64 GNU/Linux compilers:
|
||
(platypus) Version 4.4.7 20120313
|
||
Version 4.8.2
|
||
PGI C, Fortran, C++ for 64-bit target on
|
||
x86-64;
|
||
Version 13.7-0
|
||
Intel(R) C (icc), C++ (icpc), Fortran (icc)
|
||
compilers:
|
||
Version 14.0.2 (Build 20140120)
|
||
|
||
Linux 2.6.32-431.29.2.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
|
||
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
|
||
(ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
|
||
IBM XL C/C++ V13.1
|
||
IBM XL Fortran V15.1
|
||
|
||
Linux 2.6.32-220.23.1.1chaos Intel C, C++, Fortran Compilers
|
||
ch5.x86_64 GNU/Linux Version 12.1.5.339
|
||
(LLNL Aztec)
|
||
|
||
IBM Blue Gene/P XL C for Blue Gene/P, bgxlc V9.0
|
||
(LLNL uDawn) XL C++ for Blue Gene/P, bgxlC V9.0
|
||
XL Fortran for Blue Gene/P, bgxlf90 V11.1
|
||
|
||
SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
|
||
(emu) Sun Fortran 95 8.6 SunOS_sparc
|
||
Sun C++ 5.12 SunOS_sparc
|
||
|
||
Windows 7 Visual Studio 2008 (cmake)
|
||
Visual Studio 2010 w/ Intel Fortran 14 (cmake)
|
||
Visual Studio 2012 w/ Intel Fortran 15 (cmake)
|
||
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
|
||
Visual Studio 2015 (cmake)
|
||
Cygwin(CYGWIN_NT-6.1 1.7.34(0.285/5/3) gcc(4.9.2) compiler and gfortran)
|
||
(cmake and autotools)
|
||
|
||
Windows 7 x64 Visual Studio 2008 (cmake)
|
||
Visual Studio 2010 w/ Intel Fortran 14 (cmake)
|
||
Visual Studio 2012 w/ Intel Fortran 15 (cmake)
|
||
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
|
||
Visual Studio 2015 (cmake)
|
||
|
||
Windows 8.1 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
|
||
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
|
||
|
||
Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
|
||
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
|
||
|
||
Mac OS X Lion 10.7.3 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.2.1
|
||
32- and 64-bit g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.2.1
|
||
(duck) gfortran GNU Fortran (GCC) 4.6.2
|
||
|
||
Mac OS X Mountain Lion 10.8.1 cc Apple clang version 4.0 from Xcode 4.5.1
|
||
(owl) c++ Apple clang version 4.0 from Xcode 4.5.1
|
||
gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.5.1
|
||
g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.5.1
|
||
gfortran GNU Fortran (GCC) 4.6.2
|
||
|
||
|
||
Tested Configuration Features Summary
|
||
=====================================
|
||
|
||
In the tables below
|
||
y = tested
|
||
n = not tested in this release
|
||
C = Cluster
|
||
W = Workstation
|
||
x = not working in this release
|
||
dna = does not apply
|
||
( ) = footnote appears below second table
|
||
<blank> = testing incomplete on this feature or platform
|
||
|
||
Platform C F90/ F90 C++ zlib SZIP
|
||
parallel F2003 parallel
|
||
Solaris2.11 32-bit n y/y n y y y
|
||
Solaris2.11 64-bit n y/n n y y y
|
||
Windows 7 y y/y n y y y
|
||
Windows 7 x64 y y/y n y y y
|
||
Windows 7 Cygwin n y/n n y y y
|
||
Windows 7 x64 Cygwin n y/n n y y y
|
||
Windows 8 y y/y n y y y
|
||
Windows 8 x64 y y/y n y y y
|
||
Mac OS X Lion 10.7.3 32-bit n y/y n y y n
|
||
Mac OS X Lion 10.7.3 64-bit n y/y n y y y
|
||
Mac OS X Mountain Lion 10.8.1 64-bit n y/y n y y y
|
||
Mac OS X Mavericks 10.9.1 64-bit n y/y n y y ?
|
||
AIX 6.1 32- and 64-bit n y/n n y y y
|
||
CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y
|
||
CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y
|
||
CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y
|
||
CentOS 5.9 Linux 2.6.18 x86_64 GNU n y/y n y y y
|
||
CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y
|
||
CentOS 6.4 Linux 2.6.32 x86_64 GNU y y/y y y y y
|
||
CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y
|
||
CentOS 6.4 Linux 2.6.32 x86_64 PGI n y/y n y y y
|
||
Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y
|
||
|
||
|
||
Platform Shared Shared Shared Thread-
|
||
C libs F90 libs C++ libs safe
|
||
Solaris2.11 32-bit y y y y
|
||
Solaris2.11 64-bit y y y y
|
||
Windows 7 y y y y
|
||
Windows 7 x64 y y y y
|
||
Windows 7 Cygwin n n n y
|
||
Windows 7 x64 Cygwin n n n y
|
||
Windows 8 y y y y
|
||
Windows 8 x64 y y y y
|
||
Mac OS X Lion 10.7.3 32-bit y n y y
|
||
Mac OS X Lion 10.7.3 64-bit y n y y
|
||
Mac OS X Mountain Lion 10.8.1 64-bit y n y y
|
||
Mac OS X Mavericks 10.9.1 64-bit y n y y
|
||
AIX 6.1 32- and 64-bit y n n y
|
||
CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y
|
||
CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n
|
||
CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n
|
||
CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y
|
||
CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n
|
||
CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n
|
||
CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n
|
||
CentOS 6.4 Linux 2.6.32 x86_64 PGI y y y n
|
||
Linux 2.6.32-431.11.2.el6.ppc64 y y y n
|
||
|
||
Compiler versions for each platform are listed in the preceding
|
||
"Supported Platforms" table.
|
||
|
||
|
||
More Tested Platforms
|
||
=====================
|
||
The following platforms are not supported but have been tested for this release.
|
||
|
||
Linux 2.6.18-308.13.1.el5PAE MPICH mpich 3.1.2 compiled with
|
||
#1 SMP i686 i686 i386 gcc 4.9.1 and gfortran 4.9.1
|
||
(jam) g95 (GCC 4.0.3 (g95 0.94!)
|
||
|
||
Linux 2.6.18-431.11.2.el6 MPICH mpich 3.1.2 compiled with
|
||
#1 SMP x86_64 GNU/Linux gcc 4.9.1 and gfortran 4.9.1
|
||
(platypus) g95 (GCC 4.0.3 (g95 0.94!)
|
||
|
||
FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719
|
||
(loyalty) gcc 4.6.1 20110422
|
||
g++ 4.6.1 20110422
|
||
gfortran 4.6.1 20110422
|
||
|
||
FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719
|
||
(freedom) gcc 4.6.1 20110422
|
||
g++ 4.6.1 20110422
|
||
gfortran 4.6.1 20110422
|
||
|
||
Debian7.5.0 3.2.0-4-686 #1 SMP Debian 3.2.51-1 i686 GNU/Linux
|
||
gcc (Debian 4.7.2-5) 4.7.2
|
||
GNU Fortran (Debian 4.7.2-5) 4.7.2
|
||
(cmake and autotools)
|
||
|
||
Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux
|
||
gcc (Debian 4.7.2-5) 4.7.2
|
||
GNU Fortran (Debian 4.7.2-5) 4.7.2
|
||
(cmake and autotools)
|
||
|
||
Fedora20 3.15.3-200.fc20.i6866 #1 SMP i686 i686 i386 GNU/Linux
|
||
gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
|
||
GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
|
||
(cmake and autotools)
|
||
|
||
Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
|
||
gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
|
||
GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
|
||
(cmake and autotools)
|
||
|
||
SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT i686 athlon i386 GNU/Linux
|
||
gcc (SUSE Linux) 4.8.1
|
||
GNU Fortran (SUSE Linux) 4.8.1
|
||
(cmake and autotools)
|
||
|
||
SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
|
||
gcc (SUSE Linux) 4.8.1
|
||
GNU Fortran (SUSE Linux) 4.8.1
|
||
(cmake and autotools)
|
||
|
||
Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP i686 GNU/Linux
|
||
gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
|
||
GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
|
||
(cmake and autotools)
|
||
|
||
Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux
|
||
gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
|
||
GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
|
||
(cmake and autotools)
|
||
|
||
Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46
|
||
hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai
|
||
pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai
|
||
pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai
|
||
|
||
|
||
Known Problems
|
||
==============
|
||
* "make check" fails on CYGWIN when building shared lib files is enabled. The
|
||
default on Cygwin has been changed to disable shared. It can be enabled with
|
||
the --enable-shared configure option but is likely to fail "make check"
|
||
with GCC compilers. (LK -2015/04/16)
|
||
|
||
* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv
|
||
catches some undefined behavior in the alignment algorithm of the macro DETECT_I
|
||
in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment
|
||
of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for
|
||
H5detect.c. In the future, we can separate flags for H5detect.c from the rest of
|
||
the library. (SLU - 2013/10/16)
|
||
|
||
* The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp. It
|
||
complains with this message:
|
||
"/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined.
|
||
|
||
The reason is that __func__ is a predefined identifier in C99 standard. The
|
||
HDF5 C library uses it in H5private.h. The test ttypes.cpp includes
|
||
H5private.h (H5Tpkg.h<-H5Fprivate.h<-H5Vprivate.h<-H5private.h). Sun's 5.9
|
||
C++ compiler doesn't support __func__, thus fails to compile the C++ test.
|
||
But 5.11 C++ compiler does. To check whether your Sun C++ compiler knows this
|
||
identifier, try to compile the following simple C++ program:
|
||
#include<stdio.h>
|
||
|
||
int main(void)
|
||
{
|
||
printf("%s\n", __func__);
|
||
return 0;
|
||
}
|
||
(SLU - 2012/11/5)
|
||
|
||
* The C++ and FORTRAN bindings are not currently working on FreeBSD with the
|
||
native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the
|
||
ports (and probably gcc releases after that).
|
||
(QAK - 2012/10/19)
|
||
|
||
* 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)
|
||
|
||
* 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)
|
||
|
||
* --with-mpe configure option does not work with Mpich2. AKC - 2011/03/10)
|
||
|
||
* 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/
|
||
|
||
* Parallel mode in AIX will fail some of the testcheck_version.sh tests where
|
||
it treats "exit(134) the same as if process 0 had received an abort signal.
|
||
This is fixed and will be available in the next release. AKC - 2009/11/3
|
||
|
||
* The PathScale MPI implementation, accessing a Panasas file system, would
|
||
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
|
||
|
||
* Parallel tests failed with 16 processes with data inconsistency at testphdf5
|
||
/ dataset_readAll. Parallel tests also failed with 32 and 64 processes with
|
||
collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
|
||
with MPI IO. (CMC - 2009/04/28)
|
||
|
||
* 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.
|
||
|
||
* The C++ library's tests fails when compiling with PGI C++ compiler. The
|
||
workaround until the problem is correctly handled is to use the
|
||
flag "--instantiate=local" prior to the configure and build steps, as:
|
||
setenv CXX "pgCC --instantiate=local" for pgCC 5.02 and higher
|
||
|
||
|
||
* The stream-vfd test uses ip port 10007 for testing. If another
|
||
application is already using that port address, the test will hang
|
||
indefinitely and has to be terminated by the kill command. To try the
|
||
test again, change the port address in test/stream_test.c to one not
|
||
being used in the host.
|
||
|
||
* The --enable-static-exec configure flag will only statically link libraries
|
||
if the static version of that library is present. If only the shared version
|
||
of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
|
||
for example, only have shared versions), the flag should still result in a
|
||
successful compilation, but note that the installed executables will not be
|
||
fully static. Thus, the only guarantee on these systems is that the
|
||
executable is statically linked with just the HDF5 library.
|
||
|
||
* With the gcc 2.95.2 compiler, HDF 5 uses the `-ansi' flag during
|
||
compilation. The ANSI version of the compiler complains about not being
|
||
able to handle the `long long' datatype with the warning:
|
||
|
||
warning: ANSI C does not support `long long'
|
||
|
||
This warning is innocuous and can be safely ignored.
|
||
|
||
* Certain platforms give false negatives when testing h5ls:
|
||
- Cray J90 and Cray T90IEEE give errors during testing when displaying
|
||
some floating-point values. These are benign differences due to
|
||
the different precision in the values displayed and h5ls appears to
|
||
be dumping floating-point numbers correctly.
|
||
|
||
* Not all platforms behave correctly with szip's shared libraries. Szip is
|
||
disabled in these cases, and a message is relayed at configure time. Static
|
||
libraries should be working on all systems that support szip, and should be
|
||
used when shared libraries are unavailable. There is also a configure error
|
||
on Altix machines that incorrectly reports when a version of szip without
|
||
an encoder is being used.
|
||
|
||
* On some platforms that use Intel and Absoft compilers to build HDF5 fortran library,
|
||
compilation may fail for fortranlib_test.f90, fflush1.f90 and fflush2.f90
|
||
complaining about exit subroutine. Comment out the line
|
||
IF (total_error .ne. 0) CALL exit (total_error)
|
||
|
||
* Information about building with PGI and Intel compilers is available in
|
||
INSTALL file sections 5.7 and 5.8
|
||
|
||
* On at least one system, (SDSC DataStar), the scheduler (in this case
|
||
LoadLeveler) sends job status updates to standard error when you run
|
||
any executable that was compiled with the parallel compilers.
|
||
|
||
This causes problems when running "make check" on parallel builds, as
|
||
many of the tool tests function by saving the output from test runs,
|
||
and comparing it to an exemplar.
|
||
|
||
The best solution is to reconfigure the target system so it no longer
|
||
inserts the extra text. However, this may not be practical.
|
||
|
||
In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to
|
||
the configure and build. This will cause "make check" to continue after
|
||
detecting errors in the tool tests. However, in the case of SDSC DataStar,
|
||
it also leaves you with some 150 "failed" tests to examine by hand.
|
||
|
||
A second solution is to write a script to run serial tests and filter
|
||
out the text added by the scheduler. A sample script used on SDSC
|
||
DataStar is given below, but you will probably have to customize it
|
||
for your installation.
|
||
|
||
Observe that the basic idea is to insert the script as the first item
|
||
on the command line which executes the the test. The script then
|
||
executes the test and filters out the offending text before passing
|
||
it on.
|
||
|
||
#!/bin/csh
|
||
|
||
set STDOUT_FILE=~/bin/serial_filter.stdout
|
||
set STDERR_FILE=~/bin/serial_filter.stderr
|
||
|
||
rm -f $STDOUT_FILE $STDERR_FILE
|
||
|
||
($* > $STDOUT_FILE) >& $STDERR_FILE
|
||
|
||
set RETURN_VALUE=$status
|
||
|
||
cat $STDOUT_FILE
|
||
|
||
tail +3 $STDERR_FILE
|
||
|
||
exit $RETURN_VALUE
|
||
|
||
You get the 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
|
||
have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to
|
||
get the serial tests to run at all.
|
||
|
||
In such cases, you will have to include the regular prefix in your
|
||
filter script.
|
||
|
||
* H5Ocopy() does not copy reg_ref attributes correctly when shared-message
|
||
is turn on. The value of the reference in the destination attriubte is
|
||
wrong. This H5Ocopy problem will affect h5copy tool
|
||
|