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VersionHDF5 1.6.7
Release Date2008-01-31
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/ftp/HDF5/releases/hdf5-1.6/hdf5-1.6.7/

Release NotesRelease Notes

Release Notes:

HDF5 version 1.6.7 released on Thu Jan 31 21:09:10 CST 2008
================================================================================

INTRODUCTION
============
This document describes the differences between HDF5-1.6.6 and HDF5-1.6.7  
It contains information on the platforms tested and known problems in
HDF5-1.6.7. For more details, check the HISTORY.txt file in the HDF5 source.

HDF5 documentation can be found in the distributed release source code
in the subdirectory doc/html/ or on the THG (The HDF Group) FTP server: 

     ftp://ftp.hdfgroup.org/HDF5/docs/

Documentation for the current release in the HDF5 Release 1.6.x series is 
also on the HDF web site:

     http://hdfgroup.org/HDF5/doc1.6/

For more information, see the HDF5 home page:

     http://hdfgroup.org/products/hdf5/

If you have any questions or comments, please see the HDF Support page
for a list of available resources:

     http://hdfgroup.org/services/support.html


CONTENTS
========
- New Features
- Support for New Platforms, Languages and Compilers
- Bug Fixes since HDF5-1.6.6
- Documentation
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems


New Features
============
    Configuration:
    -------------------------
    '--enable-stream-vfd' and '--disable-stream-vfd' are no longer valid 
    configure options because the stream I/O driver has ben removed from
    the distribution.

    Source code distribution
    ========================
    Library:
    --------
    The stream I/O driver is not included with the HDF5 Library in this
    release.  The source code files hdf5/src/H5FDstream.c and
    hdf5/src/H5FDstream.h and the driver ENUM value H5FD_STREAM have been 
    removed.

    Parallel Library:
    -----------------
    None      

    Tools:
    ------
    None

    F90 API:
    --------
    None

    C++ API:
    --------
    None


Support for New Platforms, Languages and Compilers
==================================================

No new platorms, languages, or compilers are supported in this release.


Bug Fixes since HDF5-1.6.6 Release
==================================

    Library
    -------
        - H5Iget_name could not be used with an object identifier returned  
            by H5Rdereference; the function would not be able to determine 
            a valid object name.  It has been fixed.  SLU - 2008/1/30 
        - Changed library's behavior for reading files that might have
            corrupted object header information from a previous (buggy)
            version of the library.  By default, the library now rebuilds the
            correct object header information instead of issuing an error.
            Previous "strict" file format interpretation can be enabled with
            the "--enable-strict-format-checks" configure option.
            QAK - 2008/01/13
        - Fixed bug in H5Epush() which was clearing the error stack before
            pushing new error value.  QAK - 2007/08/23
        - Fixed bug in H5Ewalk() which was not passing back the return value
            from error stack walking callback.  QAK - 2007/08/23


    Configuration
    -------------
     None


    Performance
    -------------
     None
   

    Tools
    -----
     None


    Documentation 
    ------------- 
     None


    F90 API
    -------
     None

                                
    C++ API
    -------
     None


Documentation
=============
    HDF5 documentation can be found in the distributed release source 
    code in the subdirectory doc/html/ (start with index.html) or on the 
    THG (The HDF Group) FTP server: 

         ftp://ftp.hdfgroup.org/HDF5/docs/

    Online documentation for the current release in the HDF5 Release 1.6.x 
    series can be found on the THG web site:

         http://hdfgroup.org/HDF5/doc1.6/

    A listing of interface changes from release to release can be found
    in the document "HDF5 Software Changes from Release to Release":

         http://hdfgroup.org/HDF5/doc1.6/ADGuide/Changes.html
 
    Since the stream I/O driver is not included in this release, the 
    functions H5Pset_fapl_stream and H5Pget_fapl_stream and the stream 
    ENUM value H5FD_STREAM have been removed from the documentation.


Platforms Tested
================

    AIX 5.2 (32/64 bit)           xlc 8.0.0.11
    (datastar)                    xlC 8.0
                                  xlf 10.01.0000.0002

    FreeBSD 6.2 (32- and 64-bit)  gcc  and g++3.4.6
    (duty and liberty)            gcc and g++ 4.2.1

    IRIX64 6.5                    MIPSpro cc 7.4.4m
    (ucar mop1 64 & n32)          F90 MIPSpro 7.4.4m (64 only)
                                  C++ MIPSpro cc 7.4.4m

    Linux 2.4.21-47.ELsmp #1 SMP  gcc 3.2.3
        i686 i386 GNU/Linux
    (osage)

    Linux 2.6.9-42.0.10.ELsmp #1  gcc (GCC) 3.4.6
         SMP i686 i386             G95 (GCC 4.0.3 (g95 0.91!) April 18 2007)
    (kagiso)                      PGI C, Fortran, C++ 7.0-7 32-bit 
                                  Intel(R) C Compiler for 32-bit 
                                      applications, Version 9.1 
                                  Intel(R) C++ Compiler for 32-bit 
                                      applications, Version 9.1
                                  Intel(R) Fortran Compiler for 32-bit 
                                      applications, Version 9.1 
                                  Absoft 32-bit Fortran 95 10.0.4
                                  MPICH mpich2-1.0.6p1 compiled with  
                                  gcc 4.2.1 and G95 (GCC 4.0.3 (g95 0.91!) 

    Linux 2.6.16.46-0.12-debug #1 Intel(R) C++ Version 10.0.025
        SMP ia64 GNU/Linux        Intel(R) Fortran Itanium(R) Version 10.0.025
    (ucar hir1)                   

    Linux 2.6.16.46-0.14-smp #1   Intel(R) C++ for Intel(R) EM64T Ver. 9.1.037
        SMP x86_64 GNU/Linux      Intel(R) Fortran Intel(R) EM64T Ver. 9.1.031
    (smirom)                      PGI C, Fortran, C++ Version 7.0-7
                                         for 64-bit target on x86-64
                                  tested for both 32- and 64-bit binaries

    Linux 2.6.5-7.287.3-sn2 #1    Intel(R) C++ Version 9.0
        Altix SMP ia64            Intel(R) Fortran Itanium(R) Version 9.0
    (cobalt)                      SGI MPI

    SunOS 5.8 32- and 64-bit      Sun WorkShop 6 update 2 C 5.3
    (sol)                         Sun WorkShop 6 update 2 Fortran 95 6.2
                                  Sun WorkShop 6 update 2 C++ 5.3

    SunOS 5.10 32- and 64-bit     Sun WorkShop 6 update 2 C 5.8
    (linew)                       Sun WorkShop 6 update 2 Fortran 95 8.2
                                  Sun WorkShop 6 update 2 C++ 5.8
                                  Patch 121019-06 

    Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre
    (tungsten)                    Intel(R) C++ Version 9.0
                                  Intel(R) Fortran Compiler Version 9.0
                                  PGI C Version 6.0-5
                                  PGI C++ Version 6.0-5
                                  PGI Fortran Version 6.0-5
                                  gcc (GCC) 3.2.2 (Red Hat Linux 3.2.2-5)

    Xeon Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp
    (abe)                         Intel(R) C++ Version 10.0
                                  Intel(R) Fortran Compiler Version 10.0
                                  Open MPI 1.2.2

    IA-64 Linux 2.4.21-309.tg1 #1 SMP
        ia64                      gcc (GCC) 3.2.2
    (NCSA tg-login)               Intel(R) C++ Version 8.1
                                  Intel(R) Fortran Compiler Version 8.1
                                  mpich-gm-1.2.6..14-intel-r2

    Windows XP                    Visual Studio 6.0
                                  Visual Studio .NET (with Intel Fortran 9.1)
                                  Visual Studio 2005 (with Intel Fortran 9.1)
                                  cygwin (gcc 3.4.4)

    Windows Vista                 Visual studio 2005
    MAC OS X Intel                Darwin 8.10.1
                                  i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1
                                  g95 0.91


Supported Configuration Features Summary
========================================

Key:   y   = Tested and supported
       n   = Not supported or not tested in this release
       C   = Cluster
       W   = Workstation
       ( ) = Footnote appears below second table

Platform                              C        F90  F90      C++  zlib  SZIP
                                      parallel      parallel
Solaris2.8 32-bit                     n        y    n        y    n     y
Solaris2.8 64-bit                     n        y    n        n    y     y
Solaris2.10 32-bit                    n        y    n        y    y     y
Solaris2.10 64-bit                    n        y    n        n    y     y
IRIX64_6.5 32-bit                     n        n    n        n    y     y
IRIX64_6.5 64-bit                     n        y    n        n    y     y
WinXP Visual Studio 6.0               n        n    n        y    y     y
WinXP CYGWIN                          n        n    n        y    y     y
WinXP 2005                            n        y    n        y    y     y
WinXP .Net                            n        y    n        y    y     y
WinVista 2005                         n        n    n        y    y     y
Mac OS X 10.4.10                      n        y    n        y    y     y
AIX-5.2 & 5.3 32- and 64-bit          y        y    y        y    y     y
FreeBSD 6.2 32- and 64-bit            n        n    n        y    y     y
RedHat Linux 2.4.21              W    n        n    n        n    y     n
RedHat Linux 2.6.9-42 i686 GNU (1) W  y        y    y        y    y     y
RedHat Linux 2.6.9-42 i686 Intel   W  n        y    n        y    y     n
RedHat Linux 2.6.9-42 i686 PGI     W  n        y    n        y    y     n
SuSE Linux 2.6.16 x86_64 GNU (1) W    y        y    n        y    y     y
SuSE Linux 2.6.16 x86_64 Intel   W    n        y    n        y    y     n
SuSE Linux 2.6.16 x86_64 PGI     W    n        y    n        y    y     n
RHEL 4 Linux 2.6.9 Xeon Lustre   C    n        y    n        y    y     y
RedHat Linux 2.4 Xeon Lustre     C    n        y    n        y    y     n
SuSE Linux 2.4 ia64              C    y        y    y        y    y     y
SuSe Linux 2.6.5 SGI Altix ia64       n        y    n        y    y     y


Platform                              Shared        static-  Thread-  
                                      libraries(4)  exec     safe     
Solaris2.8 32- and 64-bit             y             n        y        
Solaris2.10 32- and 64-bit            y             n        y        
IRIX64_6.5 32-bit                     y             n        y        
IRIX64_6.5 64-bit                     y             n        y        
WinXP Visual Studio 6.0               y             n        n        
WinXP CYGWIN                          y             n        n        
WinXP 2005                            y             n        n        
WinXP .Net                            y             n        n        
WinVista 2005                         y             n        n        
Mac OS X 10.4.10                      y             n        n        
AIX-5.2 & 5.3 32- and 64-bit          n             n        n        
FreeBSD 6.2 32- and 64-bit            y             n        n        
RedHat Linux 2.4.21              W    y             n        n        
SuSE Linux 2.6.9-42 i686 GNU (1) W    y             n        y        
SuSE Linux 2.6.9-42 i686 Intel   W    y             n        n        
SuSE Linux 2.6.9-42 i686 PGI     W    n             n        n        
SuSE Linux 2.6.16 x86_64 GNU (1) W    y             n        y        
SuSE Linux 2.6.16 x86_64 Intel   W    y             n        n        
SuSE Linux 2.6.16 x86_64 PGI     W    n             n        n        
RHEL 4 Linux 2.6.9 Xeon Lustre   C    y             n        n        
RedHat Linux 2.4 Xeon Lustre     C    y             n        n        
SuSE Linux 2.4 ia64              C    y             n        n        
SuSe Linux 2.6.5 SGI Altix ia64       n             n        n        

Compiler versions for each platform are listed in the "Platforms Tested" 
table found elsewhere in this file (RELEASE.txt).  Unless otherwise noted, 
compilers used are the system compilers.

Footnotes:
(1) Fortran compiled with g95.


Known Problems
==============
* We discovered two problems when running collective IO parallel HDF5 tests
  with chunking storage with the ChaMPIon MPI compiler on tungsten, a Linux
  cluster at NCSA.
  Under some complex selection cases, 
  1) MPI_Get_element returns the wrong value.
  2) MPI_Type_struct also generates the wrong derived datatype and corrupt 
     data may be generated.
  This only happens when turning on collective IO with chunking storage
  with some complex selections. We haven't found these problems on other 
  MPI-IO compilers. If you encounter these problems, you may use Independent 
  IO instead.

  To avoid this problem, change the following line in your code:
  H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);

  to
  H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT);
 
  KY - 2007/08/24

* QSC (an HP alpha-based OSF1 cluster) does not create h5pfc correctly. It
  does not include the -lmpi properly.  This will be fixed in the next
  release.  AKC - 2007/08/07.

* On IRIX64 6.5 (UCAR SGI mop1), when testing HDF5 tools with an HDF5 shared
  library, especially for h5repacktst and h52gifgentst, the following (or a
  similar) error message may appear:
  "523648:lt-h5repacktst: rld: Fatal Error: Cannot Successfully map soname
  'libh5test.so.1' under any of the filenames .......(bunch of directories)
  "
  And the testing will fail. 

  We believe this is a libtool problem. One way to get rid of this is to
  add the paths of libh5test.so.1 and libh5.so.1 to the shared library path.

  For 32-bit:
  You may do this, under csh:
  setenv LD_LIBRARYN32_PATH .......(existing paths):[full path of HDF5
  directory/test/.libs]:[full path of HDF5 directory/src/.libs]

  For 64-bit:
  setenv LD_LIBRARY64_PATH ......(existing paths):[full path of HDF5
  directory/test/.libs]:[full path of HDF5 directory/src/.libs]

  NOTE: This problem ONLY affects the testing of the HDF5 library when you 
  build from source. It won't affect any applications that would like to link 
  with the HDF5 shared library since the shared library path needs to be set 
  anyway.  KY - 2007/8/2

* QSC (an HP alpha-based OSF1 cluster) failed the testpar/testphdf5 sub-test
  "calloc".  All other tests passed.  This indicates that a dataset using 
  chunked storage created by serial HDF5 may not work properly with parallel 
  HDF5.  The calloc test can be skipped by running "prun ... testphdf5 -x 
  calloc".  AKC - 2007/7/12.

* The Intel C Compiler for the Linux x86_64 platform (EM64T-based, v8.1) has
  an optimization error in the datatypes conversion code.  Before running
  configure, edit the file config/intel-flags by changing the setting of
  PROD_CFLAGS from -O3 to -O0.  Then run configure.  AKC - 2005/11/10.

* When testing parallel HDF5 with the C compiler version MIPSpro 7.4.3 on IRIX
  6.5, set the environment variable MPI_TYPE_MAX to be a bigger number, for 
  example 120000, in order to pass the complicated collective IO tests inside 
  the parallel HDF5 library. This is not a problem inside the parallel HDF5 
  library. You can always set a bigger number on your system.  KY - 2005/10/6

* A contiguous or chunked dataset created by a sequential version of HDF5 
  might not be able to be modified with a parallel version of the library. 
  Use the H5Pset_alloc_time function with H5D_ALLOC_TIME_EARLY to set up the 
  dataset creation property list to avoid the problem.  EIP - 2005/09/09

* A 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 (a 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.  HDF5 library releases 
  after 1.6.4 can still read datasets created or rewritten with an HDF5 
  library of v1.6.2 or before.  SLU - 2005/7/8

* For version 6 (6.02 and 6.04) of the Portland Group compiler on AMD Opteron
  processor, there's a bug in the compiler for optimization(-O2).  The library
  failed in several tests, all related to the multi driver.  The problem has 
  been reported to the vendor.  

* test/big fails sometimes with the message "Possible overlap with another
  region."  The test selects regions randomly, and this error occurs when
  two regions overlap each other; it is a bug in the test and not in
  HDF5.  Since the error is triggered by a random situation, it will
  usually disappear if the test is re-run.

* Newer SGI MIPSpro compilers (version 7.4.x) support C99 features but 
  have a "guard" statement in stdint.h that will #error and skip the rest
  of the header file if the C99 option is not used explicitly.  Hardsetting
  $CC to c99 will resolve the problem. AKC - 2004/12/13

* 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 also fail with messages like "The socket name is already
  in use".  HDF5 does not use sockets.  This is due to problems of the 
  poe command trying to set up the debug socket.  Check 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.  Ask your system 
  administrator to clean them out.  Lastly, request IBM to provide a means 
  to run poe without the debug socket.

* The h5dump tests may fail to match the expected output on some platforms
  (e.g. parallel jobs, Windows) where the error messages directed to
  "stderr" do not appear in the "right order" with output from stdout.
  This is not an error.

* The --enable-static-exec configure flag fails to compile for Solaris
  platforms. This is due to the fact that not all of the system
  libraries on Solaris are available in a static format.

  The --enable-static-exec configure flag also fails to correctly compile
  on the IBM SP2 platform for the serial mode. The parallel mode works fine
  with this option.

  The --enable-static-exec configure flag also fails to correctly compile
  on the HPUX 11.00.
  
  It is suggested that you don't use this option on these platforms
  during configuration.

* Use the --disable-shared configure flag if building with an Absoft Fortran
  compiler.

* Information about building with PGI and Intel compilers is available in
  INSTALL file sections 5.7 and 5.8.

* In LANL QSC, the new cc compiler has problems converting small values of
  long long (absolute values less than 1**-308) to double.  This triggers
  the test/dtypes to report failure in the following test:
      Testing random sw long double -> double conversions
  If -ieee is used, the converted doubles spread over the range 0.0 to 
  10**-308.  If -ieee is not used, the converted double values are mostly 
  0.0, but occasionally appear as 10**-308.  This has been reported to the 
  system staff.

  All other tests have passed.

* 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 test.  The script then
  executes the test and filters out the offending text before passing
  it on.

        #!/bin/csh

        set STDOUT_FILE=~/bin/serial_filter.stdout
        set STDERR_FILE=~/bin/serial_filter.stderr

        rm -f $STDOUT_FILE $STDERR_FILE

        ($* > $STDOUT_FILE) >& $STDERR_FILE

        set RETURN_VALUE=$status

        cat $STDOUT_FILE

        tail +3 $STDERR_FILE

        exit $RETURN_VALUE

  You get the HDF5 make files and test scripts to execute your filter script
  by setting the environment variable "RUNSERIAL" to the full path of the
  script prior to running configure for parallel builds.  Remember to
  "unsetenv RUNSERIAL" before running configure for a serial build.

  Note that the RUNSERIAL environment variable exists so that we can
  prefix serial runs as necessary on the target system.  On DataStar,
  no prefix is necessary.  However, on an MPICH system, the prefix might
  have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to
  get the serial tests to run at all.

  In such cases, you will have to include the regular prefix in your
  filter script.  JM - 2004/9/15

--- Last Modified: November 27, 2017 | 02:42 PM