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VersionHDF5 1.6.8
Release Date2008-11-10
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/ftp/HDF5/releases/hdf5-1.6/hdf5-1.6.8/

Release NotesRelease Notes

Release Notes:

HDF5 version 1.6.8 released on Mon Nov 10 15:36:46 CST 2008
================================================================================

INTRODUCTION
============
This document describes the differences between HDF5-1.6.7 and HDF5-1.6.8.  
It contains information on the platforms tested and known problems in
HDF5-1.6.8. 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 HDF5-1.6.7
- Documentation
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems


New Features
============
    Configuration:
    -------------------------
	- Added no-repeat test feature from v1.8 to this branch.  What it does
	  is that if a test has passed in previous "make check", it will not
	  run again unless its executable has changed. This can be overridden
	  by "make check-clean" which removes all check-success markers and
	  let all tests run again. AKC - 2008/2/22.

    Library:
    --------
     - Added support for $(DESTDIR) to the install feature. AKC - 2008/10/13.
     - Added version compatibility macros for functions changed in 1.8.  For
           example, H5Gcreate1 will work the same in both 1.6 and 1.8.
           NAF - 2008/10/11

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

    Tools:
    ------
     - h5repack and h5diff changed command line parameter syntax to be
           similar to h5dump, adding also long switch names. PVN - 2008/2/13
     - h5repack now supports adding multiple filters to all objects. 
	     PVN - 2008/2/13
     - h5import imports string (text) data.  PVN - 2008/2/19
     - h5dump: add a printing of the compression ratio of uncompressed and 
       compressed sizes for cases where compression  filters are present. 
             PVN - 2008/05/01
     - h5dump: added an option to allow a user defined formatting string for 
       printf regarding floating point numbers.  PVN - 2008/05/06
     - h5repack: add a userblock to an HDF5 file during the repack. 
             PVN - 2008/08/26
     - h5repack: copy userblock from HDF5 file during the repack. 
             PVN - 2008/08/26
     - h5diff: return 1 for file differences when both file graphs differ by 
       any object. Error return code was changed to 2 from -1. 
             PVN - 2008/10/30
     - h5import: TEXTFPE (scientific format) was deprecated. Use TEXTFP 
       instead.  PVN - 2008/10/30
    

    

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

    C++ API:
    --------
        - These member functions were added as wrapper for H5Rdereference to
          replace the incorrect IdComponent::dereference().
             void H5Object::dereference(H5Object& obj, void* ref, 
                                        H5R_type_t ref_type=H5R_OBJECT)
             void H5Object::dereference(H5File& h5file, void* ref, 
                                        H5R_type_t ref_type=H5R_OBJECT)
             void H5Object::dereference(Attribute& obj, void* ref, 
                                        H5R_type_t ref_type=H5R_OBJECT)

          In addition, these constructors were added to create the associated
          objects by way of dereference:
            DataSet(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
            DataSet(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT)
            DataSet(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT)
            Group(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
            Group(H5File& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
            Group(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT)
            DataType(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
            DataType(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT)
            DataType(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT)
          BMR - 2008/10/29


Support for New Platforms, Languages and Compilers
==================================================
    None

Bug Fixes since HDF5-1.6.7 Release
==================================

    Library
    -------
     - Changed the return value of H5Fget_obj_count from INT to SSIZE_T. Also
       changed the return value of H5Fget_obj_ids from HERR_T to SSIZE_T and
       the type of the parameter MAX_OBJS from INT to SIZE_T. 
       SLU - 2008/09/26

    Configuration
    -------------
     - Fixed error with 'make check install' failing due to h5dump
       needing other tools built first. MAM - 2008/10/22.
     - Fixed error with exampples/ph5example getting built even in serial
       mode. Will now only get built and tested if parallel is enabled.
       MAM - 2008/09/18
     - The file libhdf5_fortran.settings is not installed since its content
       is included in libhdf5.settings now. AKC - 2008/10/21
     - The GASS and SRB virtual file drivers have been retired and removed
       from the HDF5 library. AKC - 2008/9/26


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

    Tools
    -----
     - h5import bug on Windows w/binary datasets. fread in windows needs a 
       binary file to be open with 'rb' instead of 'r' otherwise it terminates 
       execution if an end of file character is found on the input file. 
       Besides that the binary file generated needs to be open with 'wb', 
       otherwise an end of line character is read twice. PVN - 2008/2/19
     - Fixed h5diff regarding the display of NaN (Not a Number) values. 
       PVN - 2008/03/04
     - Fixed h5dump regarding the display of array indices and block 
       selections in subsetting. PVN - 2008/03/10 
     - Fixed bug in h5dump that caused binary output to be made only for 
       the first dataset, when several datasets were requested. 
       PVN - 2008/04/07
     - h5dump: when doing binary output (-b), the stdout printing of attributes 
       was done incorrectly. Removed printing of attributes when doing binary 
       output. PVN - 2008/06/05

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


    F90 API
    -------
     None

                                
    C++ API
    -------
        - Fixed a design bug which allowed an Attribute object to create/modify
          attributes (bugzilla #1068).  The API class hierarchy was revised
          to address the problem.  Classes AbstractDS and Attribute are moved
          out of H5Object.  Class Attribute now multiply inherits from
          IdComponent and AbstractDs and class DataSet from H5Object and
          AbstractDs.  In addition, the data member IdComponent::id was
          moved into subclasses: Attribute, DataSet, DataSpace, DataType,
          H5File, Group, and PropList. BMR - 2008/08/10
        - IdComponent::dereference was incorrect and replaced as described
          in "New Features" section.
          BMR - 2008/08/10


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 5.3			  xlc 7.0.0.8
				  xlf 09.01.0000.0008
				  xlC 7.0.0.8
				  mpcc_r 7.0.0.8
				  mpxlf_r 09.01.0000.0008

    FreeBSD 6.3-STABLE i386       gcc 3.4.6 [FreeBSD] 20060305
    (duty)                        g++ 3.4.6 [FreeBSD] 20060305
                                  gcc 4.2.5 20080702 
                                  g++ 4.2.5 20080702 
                                  gfortran 4.2.5 20080702

    FreeBSD 6.3-STABLE amd64      gcc 3.4.6 [FreeBSD] 20060305
    (liberty)                     g++ 3.4.6 [FreeBSD] 20060305
                                  gcc 4.2.5 20080702 
                                  g++ 4.2.5 20080702 
                                  gfortran 4.2.5 20080702

    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 2.6.9-42.0.10.ELsmp #1  gcc (GCC) 3.4.6
         SMP i686 i386            G95 (GCC 4.0.3 (g95 0.92!) April 18 2007)
    (kagiso)                      PGI C, Fortran, C++ 7.2-1 32-bit 
                                  Intel(R) C Compiler for 32-bit 
                                      applications, Version 10.1 
                                  Intel(R) C++ Compiler for 32-bit 
                                      applications, Version 10.1
                                  Intel(R) Fortran Compiler for 32-bit 
                                      applications, Version 10.1 
                                  Absoft 32-bit Fortran 95 10.0.4
                                  MPICH mpich-1.2.7 compiled with  
                                  gcc 3.4.6 and G95  (GCC 4.0.3 (g95 0.92!) 
                                  MPICH mpich2-1.0.6p1 compiled with  
                                  gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!)

    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. 10.1.013
        SMP x86_64 GNU/Linux      Intel(R) Fortran Intel(R) EM64T Ver. 10.1.013
    (smirom)                      PGI C, Fortran, C++ Version 7.2-1
                                         for 64-bit target on x86-64
                                  MPICH mpich-1.2.7 compiled with  
                                  gcc 4.1.2 and G95  (GCC 4.0.3 (g95 0.92!) 
                                  MPICH mpich2-1.0.7 compiled with  
                                  gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) 
                                  tested for both 32- and 64-bit binaries

    Linux 2.6.16.54-0.2.5 #1      Intel(R) C++ Version 10.1.017
        Altix SMP ia64            Intel(R) Fortran Itanium(R) Version 10.1.017
    (cobalt)                      SGI MPI 1.16

    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 2.6.9-42.0.10.EL_lustre-1.4.10.1smp
    (abe)                         Intel(R) C++ Version 10.0.026
                                  Intel(R) Fortran Compiler Version 10.0.026
                                  Open MPI 1.2.2
                                  MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2
                                  compiled with icc v10.0.026 and ifort 10.0.026

    IA-64 Linux 2.4.21-309.tg1 #1 SMP
        ia64                      gcc (GCC) 3.2.2
    (NCSA tg-login)               Intel(R) C++ Version 8.1.037
                                  Intel(R) Fortran Compiler Version 8.1.033
                                  mpich-gm-1.2.7p1..16-intel-8.1.037-r1

    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 10.5.4         i686-apple-darwin9-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
Solaris2.10 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 5.3 32-bit                	      n        y    n        y    y     n
FreeBSD 6.3 32- and 64-bit            n        n    n        y    y     y
RedHat EL4 2.6.9-42 i686 GNU (1)  W   y        y    y        y    y     y
RedHat EL4 2.6.9-42 i686 Intel    W   n        y    n        y    y     n
RedHat EL4 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
RedHat EL 4 2.6.9 Xeon Lustre     C   n        y    n        y    y     y
SuSE Linux 2.4.21 ia64            C   y        y    y        y    y     y
SuSe Linux 2.6.16 SGI Altix ia64  C   n        y    n        y    y     y


Platform                              Shared        static-  Thread-  
                                      libraries(4)  exec     safe     
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 5.3 32-bit                        n             n        n        
FreeBSD 6.3 32- and 64-bit            y             n        n        
RedHat EL4 2.6.9-42 i686 GNU (1)  W   y             n        y        
RedHat EL4 2.6.9-42 i686 Intel    W   y             n        n        
RedHat EL4 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        
RedHat EL4 2.6.9 Xeon Lustre      C   y             n        n        
SuSE Linux 2.4.21 ia64            C   y             n        n        
SuSe Linux 2.6.16 SGI Altix ia64  C   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.

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

  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.

* 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

* 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.


--- Last Modified: November 27, 2017 | 02:41 PM