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VersionHDF5 1.6.4
Release Date2005-03-15
Download

/ftp/HDF5/releases/hdf5-1.6/hdf5-1.6.4.tar.gz

Release NotesRelease Notes

Release Notes:

HDF5 version 1.6.4 released on Tue Mar 15 20:38:48 CST 2005
================================================================================

INTRODUCTION
============
This document describes the differences between HDF5-1.6.3 and
HDF5-1.6.4, and contains information on the platforms tested and
known problems in HDF5-1.6.4. For more details check the HISTORY.txt
file in the HDF5 source.

The HDF5 documentation can be found on the NCSA ftp server
(ftp.ncsa.uiuc.edu) in the directory:

     /HDF/HDF5/docs/

For more information look at the HDF5 home page at:
   
    http://hdf.ncsa.uiuc.edu/HDF5/

If you have any questions or comments, please send them to:

    hdfhelp@ncsa.uiuc.edu


CONTENTS
========
- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.6.3
- Documentation
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems


New Features
============
    Source code distribution:
    -------------------------

    The High-Level (HL) C APIs were added to the source code distribution.
    For HL documentation, see
    http://hdf.ncsa.uiuc.edu/HDF5/hdf5_hl/doc/RM_hdf5hl.html.

    The HL library, libhdf5_hl.a(so), is built and installed by default. 
    Use --disable-hl configure flag to disable the HL library.

    Library:
    --------
        - We recommend you to use SZIP v2.0 with this release. 
          For more information see
          http://hdf.ncsa.uiuc.edu/doc_resource/SZIP/ 
        - The compound datatype has been enhanced with a new feature of size 
            adjustment.  The size can be increased and decreased (without
            cutting the last member).  No API change is involved.  SLU - 
            2004/10/1
        - Removed PABLO support.  2005/01/20 EIP 

    Parallel Library:
    -----------------
        - Allow compressed, chunked datasets to be read in parallel.
            QAK - 2004/10/04

    Tools:
    ------
	- New tool, h5jam.  See HDF5 Reference Manual.  2004/10/08	      

    F90 API:
    --------
          No new features in this release.

    C++ API:
    --------
	- Started using C library's reference counting in place of the class
	  RefCounter, which existed before the C mechanism was available.  
	  As a result, RefCounter has been removed.  2005/03/12 BMR


Support for new platforms, languages and compilers.
=======================================

    Configuration
    -------------
	- Upgraded from GNU autoconf 2.53 to autoconf 2.59.  JML - 2005/01/31


Bug Fixes since HDF5-1.6.3 release
==================================

    Library
    -------
        - Fixed a racing condition in MPIPOSIX virtual file drive close
	  function.  Now all processes must completed the close before any
	  of them is returned.  This prevents some "faster" processes start
	  accessing the file for another purpose (e.g., open with truncate)
	  while other "slower" processes have not closed the same file with
	  the previous purpose.  AKC - 2005/03/01
	- H5Tget_member_value calls for enum datatype didn't return correct 
          value if H5Tenum_valueof was called first.  It's fixed.  SLU - 
          2005/02/08
        - For variable-length string, H5Tget_class returned H5T_STRING as its
          class.  But H5Tdetect_class and H5Tget_member_class considered it
          as H5T_VLEN.  This is fixed to let all these 3 functions treat it
          as H5T_STRING.  SLU - 2005/02/08
        - The byte order of all 1-byte integer types was fixed as
          little-endian even on a big-endian machine.  It's corrected.
          SLU - 2005/02/07
        - Fixed segmentation fault when calling H5Fflush with an attribute that
          hasn't had a value written to it open.  QAK - 2004/10/18
        - Backed out support for bitfield and time types in H5Tget_native_type.
          Leave it to future support.  The function simply returns error 
          message of "not support" for bitfield and time types. SLU - 2004/10/5
        - Fixed address check in Core VFL driver to avoid spurious address/size
          overflows for odd valued addresses and/or sizes.  QAK - 2004/09/27
        - Fixed problem where chunked datasets were not able to be deleted
          from a file under certain circumstances.  QAK - 2004/09/27/

    Configuration
    -------------
	- IRIX64 MIPSpro compiler of 7.4.x supports C99 features.  Default
	  to use the 'c99' compiler if available. AKC - 2004/12/13
	- Intel v8.0 compiler would infinite loop when compiling some test
	  code with -O3 option.  Changed enable-production default compiler
	  option to -O2. AKC - 2004/12/06
	- Long double is assumed to be a supported C data type.  It is a
	  standard C89 type. AKC - 2004/10/22

    Performance
    -------------
    Many changes were made to the library to improve performance,
    especially for the variable-length datatypes and metadata cache.
   
    Tools
    -----
        - h5fc and h5c++ work correctly when -c compiler flag
          is used.  EIP - 2005/03/14        
	- Fixed h5dump to print attributes data in ASCII if -r option is used.
	  AKC - 2004/11/18
        - Fixed space utilization reported in h5ls to correct error 
          in formula used.  QAK - 2004/10/22

    Documentation 
    ------------- 

    F90 API
    -------
       - On windows, previously Fortran DLL built and tested failed.
         Now Fortran DLL has been built and tested successfully
         with Dec Fortran 6.6c or Dec Fortran 6.0.

    C++ API
    -------


Documentation
=============

    HDF5 Library documentation
    --------------------------
    No substantive changes to the structure or types of content in the 
    HDF5 Library documentation.

    Windows installation documentation
    ----------------------------------
    1. On Windows zlib has been updated to 1.2.2. You may find the binary at
       either http://www.zlib.net/zlib122-dll.zip or
              ftp://hdf.ncsa.uiuc.edu/lib-external/zlib/bin/windows

    2. Only DLLs of external libraries (zlib and szip) are linked with the 
       HDF5 Library. We will no longer provide binary to link static library 
       with HDF5. For details, please check INSTALL_Windows in this directory.
        

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

    AIX 5.1  (32 and 64-bit)      xlc 6.0.0.6
                                  xlf 8.1.1.3
    				  xlC 6.0.0.6
				  mpcc_r 6.0.0.6
                                  mpxlf_r 8.1.1.3
				  xlc 5.0.2.5
				  xlf 7.1.1.2
				  xlC 5.0.2.5
				  mpcc_r 5.0.2.5
				  mpxlf_r 7.1.1.2
    AIX 5.2 (32/64 bit)           xlc 6.0.0.8
                                  xlC 6.0.0.9
                                  xlf 8.1.1.7
                                  mpcc_r 6.0.0.8
                                  mpxlf_r 8.1.1.7
    AIX 5.2 (32/64 bit, LLNL frost)    xlc 6.0.0.8
                                  xlC 6.0.0.8
                                  xlf 8.1.1.7
                                  mpcc_r 6.0.0.8
                                  mpxlf_r 8.1.1.7
    Cray T90 sn7001 10.0.0md      Cray Standard C Version 6.4.0.3
                                  Cray Fortran Version 3.4.0.0
    Cray SV1 sn9617 10.0.1.2      Cray Standard C Version 6.6.0.3.6
                                  Cray Fortran Version 3.6.0.3.1
    FreeBSD 4.9                   gcc 2.95.4
                                  g++ 2.95.4
                                  gcc 3.2.3, 3.3.6, 3.4.4, 4.0.0
    HP-UX B.11.00                 HP C  HP92453-01 A.11.01.20 
                                  HP F90 v2.4
                                  HP ANSI C++ B3910B A.03.13
                                  MPIch 1.2.4
    IRIX64 6.5 (tesla -64)        MIPSpro cc 7.4.2m
                                  F90 MIPSpro 7.4.2m
                                  C++ MIPSpro cc 7.4.2m
    IRIX64 6.5 (64 & n32)         MIPSpro cc 7.3.1.3m
                                  F90 MIPSpro 7.3.1.3m (64 only)
                                  C++ MIPSpro cc 7.3.1.3m
				  mpt 1.6
    Linux 2.4.20-28.7             gcc 2.96
    (eirene, verbena)             gcc 3.3.2
                                  PGI compilers (pgcc, pgf90, pgCC) 
                                  version 5.2-1
                                  Absoft Fortran compiler v9.0
                         	  Intel(R) C++ 32-bit Version 8.1
    				  Intel(R) Fortran 32-bit Version 8.1
                                  MPIch 1.2.6
    Linux 2.4.21-268-smp x86_64   gcc 3.3.1 (SuSE Linux, AMD)
    (mir)                         PGI 5.2-1 C and F90 (with k3-32) 
                         	  Intel(R) C++ 32-bit Version 8.1
    				  Intel(R) Fortran 32-bit Version 8.1
    Linux 2.4.21-sgi303r2 Altix 
          SMP ia64                Intel(R) C++ Version 8.1
    (cobalt)                      Intel(R) Fortran Itanium(R) Version 8.1
                                  SGI MPI
    OSF1 V5.1 (QSC)               Compaq C V6.5-011 
                                  HP Fortran V5.5A-3548
				  Compaq C++ V6.5-036  
				  MPIX200_64_r13.4
    OSF1 V5.1 (PSC)               Compaq C V6.5-303 
                                  HP Fortran V5.5A-3548
				  Compaq C++ V6.5-040  
				  MPIX200_64_r13.4
                                  FORTRAN 90 2.0 Patch 107356-04 
    SunOS 5.8 32,46               Sun WorkShop 6 update 2 C 5.3
     (Solaris 2.8)                Sun WorkShop 6 update 2 Fortran 90
                                  Sun WorkShop 6 update 2 C++ 5.3
    SunOS 5.9 32,64               Sun C 5.6 2004/07/15
     (Solaris 2.9)                Sun Fortran 95 8.0 2004/07/15
                                  Sun C++ 5.6 2004/07/15
    TFLOPS r1.0.4 v4.5.2 i386     pgcc Rel 3.1-4i with mpich-1.2.4 with
                                          local modifications
    Xeon Linux 2.4.20-31.9smp_perfctr_lustre
    (tungsten)	                  Intel(R) C++ Version 8.0
                                  Intel(R) Fortran Compiler Version 8.0
    IA-64 Linux 2.4.21.SuSE_128.bef1 ia64
    (NCSA tg-login)               Intel(R) C++ Version 8.0
                                  Intel(R) Fortran Compiler Version 8.0
				  mpich-gm-1.2.5..intel
    Windows XP                    MSVC++.NET
                                  MSVC++ 6.0
                                  Compaq Visual Fortran 6.6C
                                  Intel 8.1 C++
    MAC OS X                      Darwin 7.5
                                  gcc and g++ Apple Computer, Inc. GCC 
                                  version 1175, based on gcc version 3.3.2
                                  IBM XL Fortran version 8.1 
                                  Absoft Fortran compiler v8.2


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

Key:   y   = tested and supported
       n   = not supported or not tested in this release
       x   = not working in this release
       dna = does not apply
       ( ) = footnote appears below second table

Platform                             C        F90    F90      C++  zlib  SZIP
                                     parallel        parallel      
Solaris2.8 64-bit                    y        y      y(1)     y    y     y
Solaris2.8 32-bit                    y        y      y(1)     y    y     y
Solaris2.9 64-bit                    y(1)     y      y(1)     y    y     y
Solaris2.9 32-bit                    y(1)     y      y(1)     y    y     y
IRIX64_6.5 64-bit                    y(2)     y      y        y    y     y
IRIX64_6.5 32-bit                    y(2)     n      n        n    y     y
HPUX11.00                            y(1)     y      y        y    y     y
OSF1 v5.1                            y        y      y        y    y     y
T90 IEEE                             n        y      n        n    y     n
SV1                                  y(5)     y      y(5)     n    y     n
TFLOPS                               y(1)     n      n        n    y     n
AIX-5.1 & 5.2 32-bit                 y        y      y        y    y     y
AIX-5.1 & 5.2 64-bit                 y        y      y        y    y     y
WinXP Visual Studio 6.0              n        y(9)   n        y    y     y
WinXP .Net                           n        n      n        y(8) y     y
Mac OS X 10.3                        n        y(10)  n        y    y     y
FreeBSD 4.9                          y(1)     n      n        y    y     y
RedHat 7.3  W (3)                    y(1)     y(11)  n        y    y     y
RedHat 7.3  W Intel (3)              n        y      n        y    y     y
RedHat 7.3  W PGI (3)                n        y      n        y    y     y
SuSe x86_64 gcc (3,13)               n        y(12)  n        y    y     y
SuSe x86_64 icc (3,13)               n        y(14)  n        y    y     y
Linux 2.4 Xeon C Lustre Intel (3,6)  n        y      n        y    y     y
Linux 2.4 SuSE ia64 C Intel (3,7)    y        y      y        y    y     y
Linux 2.4 SGI Altix ia64 Intel (3)   y        y      y        y    y     y


Platform                             Shared        static-  Thread-  STREAM- 
                                     libraries(4)  exec     safe     VFD    
Solaris2.8 64-bit                    y              x       y        y
Solaris2.8 32-bit                    y              x       y        y
Solaris2.9 64-bit                    y              x       y        y
Solaris2.9 32-bit                    y              x       y        y
IRIX64_6.5 64-bit                    y              y       y        y
IRIX64_6.5 32-bit                    y              y       y        y
HPUX11.00                            y              x       n        y
OSF1 v5.1                            y              y       n        y
T90 IEEE                             n              y       n        y
SV1                                  n              y       n        y
TFLOPS                               n              y       n        n
AIX-5.1 & 5.2 32-bit                 n              y       n        y
AIX-5.1 & 5.2 64-bit                 n              y       n        y
WinXP Visual Studio 6.0              y              y       n        n
WinXP .Net                           y              y       n        n
Mac OS X 10.3                        y              y       n        y
FreeBSD 4.9                          y              y       y        y
RedHat 7.3   W (3)                   y              y       y        y
RedHat 7.3  W  Intel (3)             n              y       n        y
RedHat 7.3  W  PGI (3)               n              y       n        y
SuSe x86_64 gcc (3,13)               n              y       n        y
SuSe x86_64 icc (3,13)               y              y(15)   n        y
Linux 2.4 Xeon C Lustre Intel (3,6)  y              y       n        y
Linux 2.4 SuSE ia64 C Intel (3,7)    y              y       n        n
Linux 2.4 SGI Altix ia64 Intel  (3)  y              y       n        y


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) Using mpich 1.2.6
            (2) Using mpt and mpich 1.2.6.
            (3) Linux 2.4 with GNU, Intel, and PGI compilers, as indicated.  
                  W or C indicates workstation or cluster, respectively.
            (4) Shared libraries are provided only for the C library, 
                except on Windows where they are provided for C and C++.
            (5) Using mpt.
            (6) Linux 2.4.20-31.9.  Xeon cluster with smp_perfctr_lustre 
                and Intel compilers
            (7) Linux 2.4.21, SuSE_128.befl.  Ia64 cluster with Intel compilers
            (8) Intel 8.1
            (9) Compaq Visual Fortran 6.6C
           (10) IBM XLF and Absoft
           (11) PGI, Absoft.  No shared libraries with Absoft; 
                use '--disable-shared'.
           (12) PGI and Intel compilers for both C and Fortran
           (13) AMD Opteron x86_64
           (14) ifort
           (15) Yes with C and Fortran, but not with C++
       FMB/EIP - 2005/03/15


Known Problems
==============
* 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 an 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.

* Cray SV1 fails to correctly convert between floating-point and "long double"
  for software conversion.  Problem is being investigated. SLU - 2005/03/04

* Newer SGI MIPSpro compilers (version 7.4.x) support C99 features but it
  has a "guard" statement in stdint.h that will #error and skip the rest
  of the header file if C99 option is not used explicitly.  Hardset
  $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 fail with messages like "The socket name is already
  in use".  HDF5 does not use sockets (except for stream-VFD).  This is
  due to problems of the poe command trying to set up the debug socket.
  Check if there are many old /tmp/s.pedb.* staying around.  These are
  sockets used by the poe command and left behind due to failed commands.
  Ask your system administrator to clean them out.  Lastly, request IBM
  to provide a mean to run poe without the debug socket.

* Fortran subroutine h5pget_driver_f doesn't return a correct driver 
  information.

* There are two h5dump xml tests(h5dump --xml thlink.h5 and 
  h5dump --xml tmany.h5) failed on windows xp with .NET for debug and 
  debug dll. Release and Release dll work fine. 

* 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 stream-vfd test uses ip port 10007 for testing. If another
  application is already using that port address, the test will hang
  indefinitely and has to be terminated by the kill command. To try the
  test again, change the port address in test/stream_test.c to one not
  being used in the host.

* The --enable-static-exec configure flag 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 IBM SP2 platform for the serial mode. The parallel mode works fine
  with this option.
  
  It is suggested that you don't use this option on these platforms
  during configuration.

* The Stream VFD was not tested yet under Windows. It is not supported
  in the TFLOPS machine.

* The ./dsets tests failed in the TFLOPS machine if the test program,
  dsets.c, is compiled with the -O option.  The hdf5 library still works
  correctly with the -O option.  The test program works fine if it is
  compiled with -O1 or -O0.  Only -O (same as -O2) causes the test
  program to fail.

* Certain platforms give false negatives when testing h5ls:
    - Cray T90IEEE give errors during testing when displaying
      some floating-point values. These are benign differences due to
      the different precision in the values displayed.
      h5ls appears to be dumping floating-point numbers correctly.

* Before building HDF5 F90 Library from source on Crays 
  replace H5Aff.f90, H5Dff.f90 and H5Pff.f90 files in the fortran/src
  subdirectory in the top level directory with the Cray-specific files
  from the site:
  ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/src/patches/

* On some platforms that use Intel and Absoft compilers to build HDF5 fortran 
  library, compilation may fail for fortranlib_test.f90, fflush1.f90 and 
  fflush2.f90 complaining about exit subroutine. Comment out the line 
  IF (total_error .ne. 0) CALL exit (total_error)

* Use --disable-shared configure flag if building with 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
      Testing random sw long double -> double conversions
  If -ieee is used, the converted doubles spread over the range 0.0 to 1**-308.
  If -ieee is not used, the converted double values are mostly 0.0 but
  occasionally as 1**-308.  This has been reported to the system staff.
  All other tests have passed.

* The C++ library's tests fails when compiling with PGI C++ compiler.  The
  workaround until the problem is correctly handled is to use the
  flag "--instantiate=local" prior to the configure and build steps, as:
        setenv CXX "pgCC --instantiate=local"  for pgCC 5.02 and higher
        setenv CXX "pgCC -tlocal" for others

* Fortran release DLL randomly failed with compaq visual fortran 6.6c on
  windows. 

* Fortran DLL built with Intel 8.1 in .NET environment crushed the compiler,
  To build Fortran Static library with Intel 8.1 in .NET environment 
  needs manually setting the project file,
  please contact to hdfhelp@ncsa.uiuc.edu if you need to build
  fortran static library with Intel 8.1 with .NET environment.

* 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 HDF 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
  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.

--- Last Modified: November 27, 2017 | 02:46 PM