690 lines
33 KiB
Plaintext
690 lines
33 KiB
Plaintext
HDF5 version 1.8.10-pre1 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 HDF5-1.8.9 and
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HDF5 1.8.10-*, and contains information on the platforms tested and
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known problems in HDF5-1.8.10-*.
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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 1.8.10 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 1.8.10 release can be obtained from:
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http://www.hdfgroup.org/HDF5/release/obtain5.html
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User documentation for 1.8.10 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 1.8.10 (current
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release) versus Release 1.8.9":
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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 HDF5-1.8.9
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- Platforms Tested
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- Supported Configuration Features Summary
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- Known Problems
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New Features
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============
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Configuration
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-------------
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- None
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Library
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-------
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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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- The data sieve buffer size was set 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 - 2012/4/11)
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Parallel Library
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----------------
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- Added the H5Pget_mpio_no_collective_cause() function that retrieves
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reasons 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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- Added H5Pget_mpio_actual_io_mode_f (MSB - 2012/09/27)
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Tools
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-----
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- h5import: Changed to allow the use of h5dump output as input files to
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h5import. h5dump must include the "-p" option to print the properties;
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configuration file is captured output of h5dump. The restrictions are
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that only one dataset with a simple datatype (integer, floating-point,
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or string) can be processed. Integers and floating-point imports from
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h5dump must use the "binary" option for the data file. The string version
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uses the h5dump "-y --width=1" options to disable the indexing printouts,
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print single columns, and obviously NOT use the "binary" option.
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(ADB - 2012/07/19 HDFFV-721)
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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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- Fixed a typo in return value of the nh5dread_f_c function (was 1
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instead of 0 on success); fixed the return value to make it consistent
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with other Fortran functions; cleaned debug statements from the code.
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(EIP - 2012/06/23)
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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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- None
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Bug Fixes since HDF5-1.8.9
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==========================
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Configuration
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-------------
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- Fixed AIX Fortran compiler flags to use appropriate settings for
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debugging, profiling, and optimization situations. HDFFV-8069.
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(AKC 2012/09/27)
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Library
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-------
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- Fixed a memory leak exposed when inserting/removing a property
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from a property list several times. HDFFV-8022. (MSC 2012/05/18)
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Parallel Library
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----------------
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- The MPI-POSIX VFD was updated to include the POSIX and Windows
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correctness features added that had already been added to the other VFDs.
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HDFFV-8058/7845. (DER 2012/09/17)
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Performance
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-------------
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- Removed program perform/benchpar from the enable-build-all list. The
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program will be retired or moved to another location. HDFFV-8156
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(AKC 2012/10/01)
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- Retired program perform/mpi-perf. Its purpose has been incorporated
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into h5perf. (AKC 2012/09/21)
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Tools
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-----
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- h5repack: "h5repack -f NONE file1.h5 out.h5" command failed if
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source file contains chunked dataset and a chunk dim is bigger than
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the dataset dim. Another issue is that the command changed max dims
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if chunk dim is smaller than the dataset dim. These issue occurred
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when dataset size is smaller than 64k (compact size limit) Fixed both.
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HDFFV-8012 (JKM 2012/09/24)
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- h5diff: Fixed not to accumulate attribute difference to dataset
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difference in verbose mode (-v, -r), which caused incorrect
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difference between dataset and group/datatype object if attribute
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exist with any differences. This also lead to fix inconsistent
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format indicating difference between dataset and group/datatype
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object. HDFFV-5919 (JKM 2012/09/10)
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- h5diff: Fixed the incorrect result when comparing attribute data
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values and the data type has the same class but different sizes.
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HDFFV-7942 (JKM 2012/08/15)
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- h5dump: Replaced single element fwrite with block writes.
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HDFFV-1208 (ADB 2012/08/13)
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- h5diff: Fixed test failure for "make check" due to failure of
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copying test files when performed in HDF5 source tree. Also applied
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to other tools. HDFFV-8107 (JKM 2012/08/01)
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- ph5diff: Fixed intermittent hang issue on a certain operation in
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parallel mode. It was detected by daily test for comparing
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non-comparable objects, but it could have occurred in other
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operations depending on machine condition. HDFFV-8003 (JKM 2012/08/01)
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- h5diff: Fixed the function COPY_TESTFILES_TO_TESTDIR() of testh5diff.sh
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to better report when there is an error in the file copying.
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HDFFV-8105 (AKC 2012/07/22)
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- h5dump: Fixed the sort by name display to maintain correct parent/child
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relationships between ascending/descending order.
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HDFFV-8095 (ADB 2012/07/12)
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- h5dump: Fixed the display by creation order when using option -n
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(print contents).
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HDFFV-5942 (ADB 2012/07/09)
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- h5dump: Changed to allow H5T_CSET_UTF8 to be displayed in h5dump output.
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Used technique similar to what was done in h5ls (matches library
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options).
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HDFFV-7999 (ADB 2012/05/23)
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- h5diff: Fixed not to check and display dangling link status without
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--follow-symlinks option. This also improved performance when
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comparing lots of external links without the --follow-symlinks
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option. HDFFV-7998 (JKM 2012/04/26)
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F90 API
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-------
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- Fixed a typo in return value of the nh5dread_f_c function (was 1
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instead of 0 on success); fixed the return value to make it consistent
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with other Fortran functions; cleaned debug statements from the code.
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(EIP - 2012/06/23)
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- Fixed a problem writing/reading control characters to a dataset; writing
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a string containing alerts, backspace, carriage_return, form_feed,
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horizontal_tab, vertical_tab, or new_line is now tested and working.
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(MSB - 2012/09/01)
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- Corrected the integer type of H5S_UNLIMITED_F to HSIZE_T (MSB - 2012/09/01)
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- Corrected the number of continuation lines in the src files
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to be less than 32 lines for F95 compliance. (MSB - 2012/10/01)
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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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- Fixed problem with H5TBdelete_record destroying all data following the
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deletion of a row. (MSB- 2012/7/26)
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- Fixed H5LTget_attribute_string not closing an object identifier when an
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error occurs. (MSB- 2012/7/21)
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- Corrected the return type of H5TBAget_fill from herr_t to htri_t to
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reflect that a return value of 1 indicates that a fill value is
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present, 0 indicates a fill value is not present, and <0 indicates an
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error.
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Fortran High-Level APIs:
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------
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- None
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Platforms Tested
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================
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The following platforms and compilers have been tested for this release.
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AIX 5.3 xlc 10.1.0.5
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(NASA G-ADA) xlC 10.1.0.5
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xlf90 12.1.0.6
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FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719
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(loyalty) g++ 4.2.1 [FreeBSD] 20070719
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gcc 4.6.1 20110422
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g++ 4.6.1 20110422
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gfortran 4.6.1 20110422
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FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719
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(freedom) g++ 4.2.1 [FreeBSD] 20070719
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gcc 4.6.1 20110422
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g++ 4.6.1 20110422
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gfortran 4.6.1 20110422
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Linux 2.6.18-194.3.1.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 4.1.2-52)
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Version 4.5.2
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PGI C, Fortran, C++ Compilers for 32-bit
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applications;
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Version 11.8-0
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Version 11.9-0
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Intel(R) C, C++, Fortran Compiler for 32-bit
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applications;
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Version 12.0
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Version 12.1
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MPICH mpich2-1.3.1 compiled with
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gcc 4.1.2 and gfortran 4.1.2
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Linux 2.6.18-308.1.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++)
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#1 SMP x86_64 GNU/Linux compilers for 32-bit applications;
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(koala) Version 4.1.2 20080704 (Red Hat 4.1.2-52)
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Version 4.5.2
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PGI C, Fortran, C++ for 64-bit target on
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x86-64;
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Version 11.9-0 (64-bit)
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Version 11.8-0 (32-bit)
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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 12.0
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Version 12.1
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MPICH mpich2-1.3.1 compiled with
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gcc 4.1.2 and gfortran 4.1.2
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Linux 2.6.32-220.7.1.el6.ppc64 gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3)
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#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.6 20110731
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(ostrich) GNU Fortran (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3)
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Linux 2.6.18-108chaos Intel C, C++, Fortran Compilers Version 11.1
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#1 SMP x86_64 GNU/Linux
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(LLNL Aztec)
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IBM Blue Gene/P XL C for Blue Gene/P, bgxlc V9.0
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(LLNL uDawn) XL C++ for Blue Gene/P, bgxlC V9.0
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XL Fortran for Blue Gene/P, bgxlf0 V11.1
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SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16
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(linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13
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Sun C++ 5.9 Sun OS_sparc Patch 124863-26
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Sun C 5.11 SunOS_sparc
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Sun Fortran 95 8.5 SunOS_sparc
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Sun C++ 5.11 SunOS_sparc
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SGI Altix UV Intel(R) C, Fortran Compilers
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SGI ProPack 7 Linux Version 11.1 20100806
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2.6.32.24-0.2.1.2230.2.PTF- SGI MPT 2.02
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default #1 SMP
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(NCSA ember)
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Dell NVIDIA Cluster Intel(R) C, Fortran Compilers
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Red Hat Enterprise Linux 6 Version 12.0.4 20110427
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2.6.32-131.4.1.el6.x86_64 mvapich2 1.7rc1-intel-12.0.4
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(NCSA forge)
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Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
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Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
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Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
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Visual Studio 2010 w/ Intel Fortran 12 (cmake)
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Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran)
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Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
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Visual Studio 2010 w/ Intel Fortran 12 (cmake)
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Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran)
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Mac OS X Snow Leopard 10.6.8 i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (gcc)
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Darwin Kernel Version 10.8.0 i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 (g++)
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Intel 64-bit (Apple Inc. build 5666) (dot 3)
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(fred) GNU Fortan (GCC) 4.6.1 (gfortran)
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Intel C (icc), Fortran (ifort), C++ (icpc)
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12.1.0.038 Build 20110811
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Mac OS X Snow Leopard 10.6.8 i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (gcc)
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Darwin Kernel Version 10.8.0 i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 (g++)
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Intel 32-bit (Apple Inc. build 5666) (dot 3)
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(tejeda) GNU Fortran (GCC) 4.6.1 (gfortran)
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Intel C (icc), Fortran (ifort), C++ (icpc)
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12.1.0.038 Build 20110811
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Mac OS X Lion 10.7.3 GCC 4.2.1 gcc
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32- and 64-bit GNU Fortran (GCC) 4.6.1 gfortran
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(duck) GCC 4.2.1. g++
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Mac OS X Mountain Lion 10.8.1 GCC 4.2.1 gcc
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(owl) GNU Fortran (GCC) 4.6.1 gfortran
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GCC 4.2.1. g++
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Apple clang version 4.0 (cc)
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Apple clang version 4.0 (c++)
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Debian6.0.3 2.6.32-5-686 #1 SMP i686 GNU/Linux
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gcc (Debian 4.4.5-8) 4.4.5
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GNU Fortran (Debian 4.4.5-8) 4.4.5
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Debian6.0.3 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux
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gcc (Debian 4.4.5-8) 4.4.5
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GNU Fortran (Debian 4.4.5-8) 4.4.5
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Fedora17 3.5.2-1.fc17.i6866 #1 SMP i686 i686 i386 GNU/Linux
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gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5)
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GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5)
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Fedora17 3.5.2-1.fc17.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
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gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5)
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GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5)
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SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux
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gcc (SUSE Linux) 4.7.1
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GNU Fortran (SUSE Linux) 4.7.1
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SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
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gcc (SUSE Linux) 4.7.1
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GNU Fortran (SUSE Linux) 4.7.1
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Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP i686 GNU/Linux
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gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
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GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
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Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP x86_64 GNU/Linux
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gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
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GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
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(Use optimization level -O1)
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Cray Linux Environment (CLE) PrgEnv-pgi 2.2.74
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hopper.nersc.gov pgcc 11.9-0 64-bit target on x86-64 Linux -tp k8e
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pgf90 11.9-0 64-bit target on x86-64 Linux -tp k8e
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pgCC 11.9-0 64-bit target on x86-64 Linux -tp k8e
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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 parallel
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Solaris2.10 32-bit n y n y y y
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Solaris2.10 64-bit n y n y y y
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Windows 7 y y n y y y
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Windows 7 x64 y y n y y y
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Mac OS X Snow Leopard 10.6.8 32-bit n y n y y n
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Mac OS X Snow Leopard 10.6.8 64-bit n y n y y y
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Mac OS X Lion 10.7.3 32-bit n y n y y n
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Mac OS X Lion 10.7.3 64-bit n y n y y y
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Mac OS X Mountain Lion 10.8.1 64-bit n y n y y n
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AIX 5.3 32- and 64-bit y y y y y y
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FreeBSD 8.2-STABLE 32&64 bit n x n x y y
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CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y y y
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CentOS 5.5 Linux 2.6.18-194 i686 Intel W n y n y y y
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CentOS 5.5 Linux 2.6.18-194 i686 PGI W n y n y y y
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CentOS 5.5 Linux 2.6.18 x86_64 GNU (1) W y y(3) y y y y
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CentOS 5.5 Linux 2.6.18 x86_64 Intel W n y n y y y
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CentOS 5.5 Linux 2.6.18 x86_64 PGI W n y n y y y
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Linux 2.6.32-220.7.1.el6.ppc64 n y n y y y
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SGI ProPack 7 Linux 2.6.32.24 y y y y y y
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Red Hat Enterprise Linux 6 y y y y y y
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CLE hopper.nersc.gov y y(3) y y y n
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Platform Shared Shared Shared Thread-
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C libs F90 libs C++ libs safe
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Solaris2.10 32-bit y y y y
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Solaris2.10 64-bit n n n n
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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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Mac OS X Snow Leopard 10.6.8 32-bit y n y n
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Mac OS X Snow Leopard 10.6.8 64-bit y n y n
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Mac OS X Lion 10.7.3 32-bit y n y y
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Mac OS X Lion 10.7.3 64-bit y n y y
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Mac OS X Mountain Lion 10.8.1 64-bit y n y y
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AIX 5.3 32- and 64-bit n n n y
|
|
FreeBSD 8.2-STABLE 32&64 bit y x x y
|
|
CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y
|
|
CentOS 5.5 Linux 2.6.18-194 i686 Intel W y y y n
|
|
CentOS 5.5 Linux 2.6.18-194 i686 PGI W y y y n
|
|
CentOS 5.5 Linux 2.6.18 x86_64 GNU (1) W y y y y
|
|
CentOS 5.5 Linux 2.6.18 x86_64 Intel W y y y n
|
|
CentOS 5.5 Linux 2.6.18 x86_64 PGI W y y y n
|
|
Linux 2.6.32-220.7.1.el6.ppc64 y y y n
|
|
SGI ProPack 7 Linux 2.6.32.24 y y y n
|
|
Red Hat Enterprise Linux 6 y y y n
|
|
CLE hopper.nersc.gov n n n n
|
|
|
|
(1) Fortran compiled with gfortran.
|
|
(2) With PGI and Absoft compilers.
|
|
(3) With PGI compiler for Fortran.
|
|
(4) Using Visual Studio 2008 w/ Intel Fortran 10.1 (Cygwin shared libraries are not supported)
|
|
(5) C and C++ shared libraries will not be built when Fortran is enabled.
|
|
Compiler versions for each platform are listed in the preceding
|
|
"Platforms Tested" table.
|
|
|
|
|
|
Known Problems
|
|
==============
|
|
* 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.
|
|
(SLU - 2012/06/12 - HDFFV-8017)
|
|
|
|
* The h5repacktst test fails on AIX 32-bit because the test uses more
|
|
memory than the default amount. The failure message typically looks like:
|
|
|
|
"time: 0551-010 The process was stopped abnormally. Try again."
|
|
|
|
This is an issue with the test only and does not represent a problem with
|
|
the library. To allow the test to pass, request more memory when testing
|
|
via appropriate command such as:
|
|
|
|
$ env LDR_CNRTL=MAXDATA=0x20000000@DSA make check
|
|
|
|
(AKC - 2012/05/09 - HDFFV-8016)
|
|
|
|
* The file_image test will fail in the "initial file image and callbacks in
|
|
the core VFD" sub-test if the source directory is read-only as the test
|
|
fails to create its test files in the build directory. This will be
|
|
resolved in a future release.
|
|
(AKC - 2012/05/05 - HDFFV-8009)
|
|
|
|
* The dt_arith test reports several errors involving "long double" on
|
|
Mac OS X 10.7 Lion when any level of optimization is enabled. The test does
|
|
not fail in debug mode. This will be addressed in a future release.
|
|
(SLU - 2012/05/08)
|
|
|
|
* The following h5dump test case fails in BG/P machines (and potentially other
|
|
machines that use a command script to launch executables):
|
|
|
|
h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0"
|
|
tno-subset.h5
|
|
|
|
This is due to the embedded spaces in the dataset name being interpreted
|
|
by the command script launcher as meta-characters, thus passing three
|
|
arguments to h5dump's -d flag. The command passes if run by hand, just
|
|
not via the test script.
|
|
(AKC - 2012/05/03)
|
|
|
|
* The ph5diff (parallel h5diff) tool can intermittently hang in parallel mode
|
|
when comparing two HDF5 files that contain objects with the same names but
|
|
with different object types.
|
|
(JKM - 2012/04/27)
|
|
|
|
* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set
|
|
to aprun -np X, because the H5lib_settings.c file was not generated
|
|
properly. Not setting those environment variables works, because
|
|
configure was able to automatically detect that it's a Cray system
|
|
and used the proper launch commands when necessary.
|
|
(MSC - 2012/04/18)
|
|
|
|
* 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 the
|
|
optimization level (-O1 or -O0) by defining CFLAGS in the command line of
|
|
"configure" like:
|
|
|
|
CFLAGS=-O1 ./configure
|
|
|
|
This will overwrite the library's default optimization level.
|
|
(SLU - 2012/02/07 - HDFFV-7829)
|
|
|
|
* The STDIO VFD does not work on some architectures, possibly due to 32/64
|
|
bit or large file issues. The basic STDIO VFD test is known to fail on
|
|
64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin
|
|
10.7.0. The STDIO VFD test has been disabled while we investigate and
|
|
a fix should appear in a future release.
|
|
(DER - 2011/10/14)
|
|
|
|
* h5diff can report inconsistent results when comparing datasets of enum type
|
|
that contain invalid values. This is due to how enum types are handled in
|
|
the library and will be addressed in a future release.
|
|
(DER - 2011/10/14 - HDFFV-7527)
|
|
|
|
* The links test can fail under the stdio VFD due to some issues with external
|
|
links. This will be investigated and fixed in a future release.
|
|
(DER - 2011/10/14 - HDFFV-7768)
|
|
|
|
* After the shared library support was fixed for some bugs, it was discovered
|
|
that "make prefix=XXX install" no longer works for shared libraries. It
|
|
still works correctly for static libraries. Therefore, if you want to
|
|
install the HDF5 shared libraries in a location such as /usr/local/hdf5,
|
|
you need to specify the location via the --prefix option during configure
|
|
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)
|
|
|
|
* The library's test dt_arith.c showed a compiler's rounding problem on
|
|
Cygwin when converting from unsigned long long to long double. The
|
|
library's own conversion works fine. We defined a macro for Cygwin to
|
|
skip this test until we can solve the problem.
|
|
(SLU - 2010/05/05 - HDFFV-1264)
|
|
|
|
* 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)
|
|
|
|
* MinGW has a missing libstdc++.dll.a library file and will not successfully link
|
|
C++ applications/tests. Do not use the enable-cxx configure option. Read all of
|
|
the INSTALL_MINGW.txt file for all restrictions.
|
|
(ADB - 2009/11/11)
|
|
|
|
* 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)
|
|
|
|
* The PathScale MPI implementation, accessing a Panasas file system, would
|
|
cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file does not
|
|
exist. This is due to the MPI_File_open() call failing if the mode has
|
|
the MPI_MODE_EXCL bit set.
|
|
(AKC - 2009/08/11 - HDFFV-988)
|
|
|
|
* 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 Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and
|
|
tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests
|
|
are expected to fail and should exit with a non-zero code but the yod
|
|
command does not propagate the exit code of the executables. Yod always
|
|
returns 0 if it can launch the executable. The test suite shell expects
|
|
a non-zero for this particular test, therefore it concludes the test has
|
|
failed when it receives 0 from yod. Skip all the "failing" test for now
|
|
by changing them as following.
|
|
|
|
======== Original tools/h5ls/testh5ls.sh =========
|
|
TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
|
|
======== Change to ===============================
|
|
echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
|
|
==================================================
|
|
|
|
======== Original tools/h5copy/testh5copy.sh =========
|
|
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
|
|
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
|
|
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
|
|
TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
|
|
H5LSTEST $FILEOUT
|
|
======== Change to ===============================
|
|
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename
|
|
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets
|
|
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
|
|
echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
|
|
echo SKIP H5LSTEST $FILEOUT
|
|
==================================================
|
|
(AKC - 2008/11/10)
|
|
|
|
* For Red Storm, a Cray XT3 system, the yod command sometimes gives the
|
|
message, "yod allocation delayed for node recovery". This interferes with
|
|
test suites that do not expect to see this message. See the section of "Red
|
|
Storm" in file INSTALL_parallel for a way to deal with this problem.
|
|
(AKC - 2008/05/28)
|
|
|
|
* 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.
|
|
|
|
* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and
|
|
the application asks to do collective IO, we have found that when using 4
|
|
processors, a simple collective write will sometimes be hung. This can be
|
|
verified with t_mpi test under testpar.
|
|
|
|
* 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)
|
|
|
|
* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
|
|
messages like "INFO: 0031-XXX ...". This is from the command `poe'.
|
|
Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
|
|
and run the tests again.
|
|
|
|
The tests may fail with messages like "The socket name is already in use",
|
|
but HDF5 does not use sockets. This failure is due to problems with the
|
|
poe command trying to set up the debug socket. To resolve this problem,
|
|
check to see whether there are many old /tmp/s.pedb.* files staying around.
|
|
These are sockets used by the poe command and left behind due to failed
|
|
commands. First, ask your system administrator to clean them out.
|
|
Lastly, request IBM to provide a means to run poe without the debug socket.
|
|
(AKC - 2004/12/08)
|