527 lines
23 KiB
Plaintext
527 lines
23 KiB
Plaintext
HDF5 version 1.8.15-snap8 currently under development
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================================================================================
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INTRODUCTION
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============
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This document describes the differences between HDF5-1.8.14 and
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HDF5-1.8.15-*, and contains information on the platforms tested and
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known problems in HDF5-1.8.15-*.
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For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
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and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
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Links to the HDF5 1.8.14 source code, documentation, and additional materials
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can be found on the HDF5 web page at:
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http://www.hdfgroup.org/products/hdf5/
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The HDF5 1.8.14 release can be obtained from:
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http://www.hdfgroup.org/HDF5/release/obtain5.html
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User documentation for 1.8.14 can be accessed directly at this location:
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http://www.hdfgroup.org/HDF5/doc/
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New features in the HDF5-1.8.x release series, including brief general
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descriptions of some new and modified APIs, are described in the "What's New
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in 1.8.0?" document:
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http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
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All new and modified APIs are listed in detail in the "HDF5 Software Changes
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from Release to Release" document, in the section "Release 1.8.15 (current
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release) versus Release 1.8.14
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http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
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If you have any questions or comments, please send them to the HDF Help Desk:
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help@hdfgroup.org
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CONTENTS
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========
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- New Features
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- Support for New Platforms, Languages, and Compilers
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- Bug Fixes since HDF5-1.8.14
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- Supported Platforms
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- Supported 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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- 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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Library
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-------
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- None
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Parallel Library
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----------------
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- None
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Tools
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-----
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- None
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High-Level APIs
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---------------
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- None
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Fortran API
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-----------
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- None
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C++ API
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-------
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- None
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Support for New Platforms, Languages, and Compilers
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===================================================
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- Support for AIX 6.1 added and AIX 5.3 is retired. (AKC - 2015/01/09)
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Bug Fixes since HDF5-1.8.14
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===========================
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Configuration
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-------------
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- Windows installer incorrect display of PATH environment variable.
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In the Windows installer, the dialog box where the user can elect to
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add the product's bin path to the %PATH% environment variable displayed
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an incorrect path. This path was missing the C:\Program Files part
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and used the POSIX file separator '/' before the bin (<path>/bin,
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instead of <path>\bin).
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The dialog box text was changed to simply say that the product's bin
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path would be added instead of explicitly displaying the path.
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This is in line with most installers. The reason for not fixing the
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displayed path instead is that it is difficult to pass the correct
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path from CPack to the NSIS installer for display.
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Note that this was never a code issue - it was just a display
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problem. The installer always did the right thing when updating the
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environment variable.
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(DER - 2014/11/14, HDFFV-9016)
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Library
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-------
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- Incorrect usage of list in CMake COMPILE_DEFINITIONS set_property
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The CMake command, set_property with COMPILE_DEFINITIONS property
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needs a quoted semi-colon separated list of values. CMake will
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transform the list to a series of -D{value} for the compile.
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(ADB - 2014/12/09, HDFV-9041)
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Parallel Library
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----------------
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- None
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Performance
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-------------
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- None
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Tools
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-----
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- Benchpar.c in perform is retired. (AKC - 2014/12/19, HDFFV-8156)
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- The perform directory is moved to tools/perform for easier maintenance.
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(AKC - 2014/12/17, HDFFV-9046)
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F90 API
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-------
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- None
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C++ API
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------
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- None
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High-Level APIs:
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------
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- None
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Fortran High-Level APIs:
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------
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- None
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Testing
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-------
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- None
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Supported Platforms
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===================
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The following platforms are supported and have been tested for this release.
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They are built with the configure process unless specified otherwise.
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AIX 6.1 xlc/xlc_r 10.1.0.5
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(NASA G-ADA) xlC/xlC_r 10.1.0.5
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xlf90/xlf90_r 12.1.0.6
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Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++)
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#1 SMP i686 i686 i386 compilers for 32-bit applications;
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(jam) Version 4.1.2 20080704 (Red Hat 4.1.2-54)
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Version 4.8.2
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PGI C, Fortran, C++ Compilers for 32-bit
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applications;
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Version 13.7-0
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Intel(R) C, C++, Fortran Compiler for 32-bit
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applications;
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Version 14.0.2 (Build 20140120)
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Linux 2.6.18-371.6.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++)
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#1 SMP x86_64 GNU/Linux compilers for 64-bit applications;
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(koala) Version 4.1.2 20080704 (Red Hat 4.1.2-54)
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Version 4.8.2
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Intel(R) C, C++, Fortran Compilers for
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applications running on Intel(R) 64;
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Version 14.0.2 (Build 20140120)
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Linux 2.6.32-431.11.2.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
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#1 SMP x86_64 GNU/Linux compilers:
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(platypus) Version 4.4.7 20120313
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Version 4.8.2
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PGI C, Fortran, C++ for 64-bit target on
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x86-64;
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Version 13.7-0
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Intel(R) C (icc), C++ (icpc), Fortran (icc)
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compilers:
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Version 14.0.2 (Build 20140120)
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Linux 2.6.32-431.29.2.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
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#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
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(ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
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IBM XL C/C++ V13.1
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IBM XL Fortran V15.1
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SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
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(emu) Sun Fortran 95 8.6 SunOS_sparc
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Sun C++ 5.12 SunOS_sparc
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Windows 7 Visual Studio 2008 (cmake)
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Visual Studio 2010 w/ Intel Fortran 14 (cmake)
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Visual Studio 2012 w/ Intel Fortran 14 (cmake)
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Visual Studio 2013 w/ Intel Fortran 14 (cmake)
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Cygwin(CYGWIN_NT-6.1 1.7.32(0.274/5/3) gcc(4.8.3) compiler and gfortran)
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(cmake and autotools)
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Windows 7 x64 Visual Studio 2008 (cmake)
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Visual Studio 2010 w/ Intel Fortran 14 (cmake)
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Visual Studio 2012 w/ Intel Fortran 14 (cmake)
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Visual Studio 2013 w/ Intel Fortran 14 (cmake)
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Windows 8.1 Visual Studio 2012 w/ Intel Fortran 14 (cmake)
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Visual Studio 2013 w/ Intel Fortran 14 (cmake)
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Windows 8.1 x64 Visual Studio 2012 w/ Intel Fortran 14 (cmake)
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Visual Studio 2013 w/ Intel Fortran 14 (cmake)
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Mac OS X Lion 10.7.5 Apple clang/clang++ version 3.0 from Xcode 4.6.1
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64-bit gfortran GNU Fortran (GCC) 4.8.2
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(duck) Intel icc/icpc/ifort version 13.0.3
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Mac OS X Mt. Lion 10.8.5 Apple clang/clang++ version 5.1 from Xcode 5.1
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64-bit gfortran GNU Fortran (GCC) 4.8.2
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(swallow/kite) Intel icc/icpc/ifort version 14.0.2
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Mac OS X Mavericks 10.9.5 Apple clang/clang++ version 6.0 from Xcode 6.0.1
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64-bit gfortran GNU Fortran (GCC) 4.8.2
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(wren) Intel icc/icpc/ifort version 14.0.2
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Tested Configuration Features Summary
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=====================================
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In the tables below
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y = tested
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n = not tested in this release
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C = Cluster
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W = Workstation
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x = not working in this release
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dna = does not apply
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( ) = footnote appears below second table
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<blank> = testing incomplete on this feature or platform
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Platform C F90/ F90 C++ zlib SZIP
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parallel F2003 parallel
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Solaris2.11 32-bit n y/y n y y y
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Solaris2.11 64-bit n y/y n y y y
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Windows 7 y y/y n y y y
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Windows 7 x64 y y/y n y y y
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Windows 7 Cygwin n y/y n y y n
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Windows 8.1 n y/y n y y y
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Windows 8.1 x64 n y/y n y y y
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Mac OS X Lion 10.7.5 64-bit n y/y n y y y
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Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y
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Mac OS X Mavericks 10.9.5 64-bit n y/y n y y ?
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AIX 6.1 32- and 64-bit n y/n n y y y
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CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y
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CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y
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CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y
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CentOS 5.9 Linux 2.6.18 x86_64 GNU n y/y n y y y
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CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y
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CentOS 6.4 Linux 2.6.32 x86_64 GNU y y/y y y y y
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CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y
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CentOS 6.4 Linux 2.6.32 x86_64 PGI n y/y n y y y
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Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y
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Platform Shared Shared Shared Thread-
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C libs F90 libs C++ libs safe
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Solaris2.11 32-bit y y y y
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Solaris2.11 64-bit y y y y
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Windows 7 y y y y
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Windows 7 x64 y y y y
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Windows 7 Cygwin n n n y
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Windows 8.1 y y y y
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Windows 8.1 x64 y y y y
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Mac OS X Lion 10.7.5 64-bit y n y y
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Mac OS X Mountain Lion 10.8.5 64-bit y n y y
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Mac OS X Mavericks 10.9.5 64-bit y n y y
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AIX 6.1 32- and 64-bit y n n y
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CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y
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CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n
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CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n
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CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y
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CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n
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CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n
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CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n
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CentOS 6.4 Linux 2.6.32 x86_64 PGI y y y n
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Linux 2.6.32-431.11.2.el6.ppc64 y y y n
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Compiler versions for each platform are listed in the preceding
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"Supported Platforms" table.
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More Tested Platforms
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=====================
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The following platforms are not supported but have been tested for this release.
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Linux 2.6.18-308.13.1.el5PAE MPICH mpich 3.1.2 compiled with
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#1 SMP i686 i686 i386 gcc 4.9.1 and gfortran 4.9.1
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(jam) g95 (GCC 4.0.3 (g95 0.94!)
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Linux 2.6.18-431.11.2.el6 MPICH mpich 3.1.2 compiled with
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#1 SMP x86_64 GNU/Linux gcc 4.9.1 and gfortran 4.9.1
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(platypus) g95 (GCC 4.0.3 (g95 0.94!)
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FreeBSD 8.2-STABLE i386 gcc 4.5.4 [FreeBSD] 20110526
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(loyalty) gcc 4.6.1 20110527
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g++ 4.6.1 20110527
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gfortran 4.6.1 20110527
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FreeBSD 8.2-STABLE amd64 gcc 4.5.4 [FreeBSD] 20110526
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(freedom) gcc 4.6.1 20110527
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g++ 4.6.1 20110527
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gfortran 4.6.1 20110527
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Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux
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gcc (Debian 4.7.2-5) 4.7.2
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GNU Fortran (Debian 4.7.2-5) 4.7.2
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(cmake and autotools)
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Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
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gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
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GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
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(cmake and autotools)
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SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
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gcc (SUSE Linux) 4.8.1
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GNU Fortran (SUSE Linux) 4.8.1
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(cmake and autotools)
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Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux
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gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
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GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
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(cmake and autotools)
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Cray Linux Environment (CLE) PrgEnv-pgi/4.2.34
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hopper.nersc.gov pgcc 13.6-0 64-bit target on x86-64 Linux -tp istanbul
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pgf90 13.6-0 64-bit target on x86-64 Linux -tp istanbul
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pgCC 13.6-0 64-bit target on x86-64 Linux -tp istanbul
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Known Problems
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==============
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* On windows platforms in debug configurations, the VFD flush1 tests will fail
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with the split and multi VFD drivers. These tests will display a modal debug
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dialog which must be answered or wait for the test timeout to expire.
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(ADB - 2014/06/23 - HDFFV-8851)
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* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv
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catches some undefined behavior in the alignment algorithm of the macro DETECT_I
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in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment
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of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for
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H5detect.c. In the future, we can separate flags for H5detect.c from the rest of
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the library. (SLU - 2013/10/16)
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* Make provided by Solaris fails in "make check". Solaris users should use
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gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534)
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* The h5dump and h5diff utilities occasionally produce different output
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between Linux and Windows systems. This is caused by lower-level library
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routines that fail to write fill values to the user's buffer when reading
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unallocated chunks from datasets that have a fill value set to
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H5D_FILL_VALUE_DEFAULT. Due to platform differences the return of
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spurious data values has only been encountered on Windows 32-bit systems.
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(Issue HDFFV-8247; JP - 2013/03/27)
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* The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp. It
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complains with this message:
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"/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined.
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The reason is that __func__ is a predefined identifier in C99 standard. The
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HDF5 C library uses it in H5private.h. The test ttypes.cpp includes
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H5private.h (H5Tpkg.h<-H5Fprivate.h<-H5Vprivate.h<-H5private.h). Sun's 5.9
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C++ compiler doesn't support __func__, thus fails to compile the C++ test.
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But Sun's 5.11 C++ compiler does. To check whether your Sun C++ compiler
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knows this identifier, try to compile the following simple C++ program:
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#include<stdio.h>
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int main(void)
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{
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printf("%s\n", __func__);
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return 0;
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}
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(SLU - 2012/11/5)
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* The C++ and FORTRAN bindings are not currently working on FreeBSD with the
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native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the
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ports (and probably gcc releases after that).
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(QAK - 2012/10/19)
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* The following h5dump test case fails in BG/P machines (and potentially other
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machines that use a command script to launch executables):
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h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0"
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tno-subset.h5
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This is due to the embedded spaces in the dataset name being interpreted
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by the command script launcher as meta-characters, thus passing three
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arguments to h5dump's -d flag. The command passes if run by hand, just
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not via the test script.
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(AKC - 2012/05/03)
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* The data conversion test dt_arith.c fails in "long double" to integer
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conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library
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is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernal
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(3.2.2 on Fedora) doesn't have the problem. Users should lower the
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optimization level (-O1 or -O0) by defining CFLAGS in the command line of
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"configure" like:
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CFLAGS=-O1 ./configure
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This will overwrite the library's default optimization level.
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(SLU - 2012/02/07 - HDFFV-7829)
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This issue is no longer present on Ubuntu 12.10 (3.5.0 kernel) with
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gcc 4.7.2.
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* The STDIO VFD does not work on some architectures, possibly due to 32/64
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bit or large file issues. The basic STDIO VFD test is known to fail on
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64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin
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10.7.0. The STDIO VFD test has been disabled while we investigate and
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a fix should appear in a future release.
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(DER - 2011/10/14 - HDFFV-8235)
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* h5diff can report inconsistent results when comparing datasets of enum type
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that contain invalid values. This is due to how enum types are handled in
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the library and will be addressed in a future release.
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(DER - 2011/10/14 - HDFFV-7527)
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* The links test can fail under the stdio VFD due to some issues with external
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links. This will be investigated and fixed in a future release.
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(DER - 2011/10/14 - HDFFV-7768)
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* After the shared library support was fixed for some bugs, it was discovered
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that "make prefix=XXX install" no longer works for shared libraries. It
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still works correctly for static libraries. Therefore, if you want to
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install the HDF5 shared libraries in a location such as /usr/local/hdf5,
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you need to specify the location via the --prefix option during configure
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time. E.g, ./configure --prefix=/usr/local/hdf5 ...
|
|
(AKC - 2011/05/07 - HDFFV-7583)
|
|
|
|
* The parallel test, t_shapesame, in testpar/, may run for a long time and may
|
|
be terminated by the alarm signal. If that happens, one can increase the
|
|
alarm seconds (default is 1200 seconds = 20 minutes) by setting the
|
|
environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600
|
|
(60 minutes). Note that the t_shapesame test may fail in some systems
|
|
(see the "While working on the 1.8.6 release..." problem below). If
|
|
it does, it will waste more time if $HDF5_ALARM_SECONDS is set
|
|
to a larger value.
|
|
(AKC - 2011/05/07)
|
|
|
|
* The C++ and FORTRAN bindings are not currently working on FreeBSD.
|
|
(QAK - 2011/04/26)
|
|
|
|
* Shared Fortran libraries are not quite working on AIX. While they are
|
|
generated when --enable-shared is specified, the fortran and hl/fortran
|
|
tests fail. We are looking into the issue. HL and C++ shared libraries
|
|
should now be working as intended, however.
|
|
(MAM - 2011/04/20)
|
|
|
|
* The --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 file systems.
|
|
|
|
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/
|
|
(NAF - 2011/01/19)
|
|
|
|
* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the
|
|
structure H5FD_class_t changed in 1.8. There is new parameter added to
|
|
get_eoa and set_eoa callback functions. A new callback function
|
|
get_type_map was added in. The public function H5FDrealloc was taken
|
|
out in 1.8. The problem only happens when users define their own driver
|
|
for 1.6 and try to plug in 1.8 library. Because there's only one user
|
|
complaining about it, we (Elena, Quincey, and I) decided to leave it as
|
|
it is (see bug report #1279). Quincey will make a plan for 1.10.
|
|
(SLU - 2010/02/02)
|
|
|
|
* 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.
|
|
(MAM - 2009/11/04)
|
|
|
|
* 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)
|
|
|
|
* On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers,
|
|
use -mp -O1 compilation flags to build the libraries. A higher level of
|
|
optimization causes failures in several HDF5 library tests.
|
|
|
|
* A dataset created or rewritten with a v1.6.3 library or after cannot be read
|
|
with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
|
|
There was a bug in the calculation of the Fletcher32 checksum in the
|
|
library before v1.6.3; the checksum value was not consistent between big-
|
|
endian and little-endian systems. This bug was fixed in Release 1.6.3.
|
|
However, after fixing the bug, the checksum value was no longer the same as
|
|
before on little-endian system. Library releases after 1.6.4 can still read
|
|
datasets created or rewritten with an HDF5 library of v1.6.2 or before.
|
|
(SLU - 2005/06/30)
|