path: root/release_docs/RELEASE.txt

HDF5 version 1.9.11 currently under development
================================================================================


INTRODUCTION

This document describes the differences between HDF5-1.9.0 and
HDF5 1.9.x snapshot, and contains information on the platforms 
tested and known problems in HDF5-1.9.x. 
For more details check the HISTORY*.txt files in the HDF5 source.


Links to HDF5 1.9.x source code can be found on THG's development 
FTP server at the following location:
     ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/snapshots
User documentation for the snapshot can be accessed directly at this location: 
     http://www.hdfgroup.uiuc.edu/HDF5/doc_dev_snapshot/H5_dev/

For more information, see the HDF5 home page:
   
    http://www.hdfgroup.org/HDF5/

If you have any questions or comments, please send them to the HDF Help Desk:

    help@hdfgroup.org


CONTENTS

- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.8.0
- Platforms Tested
- Known Problems


New Features
============

    Configuration:
    -------------

    - Configuration suite now uses Autoconf 2.61, Automake 1.10.1, and 
      Libtool 2.2.2 (MAM - 2008/05/05)

    - The new configure option "--disable-sharedlib-rpath" disables
      embedding the '-Wl,-rpath' information into executables when
      shared libraries are produced, and instead solely relies on the
      information in LD_LIBRARY_PATH. (MAM - 2008/05/15)

    Library:
    --------
    - Added 'mounted' field to H5G_info_t struct. (QAK - 2008/07/15)

    Parallel Library:
    -----------------

    Fortran Library:
    ----------------

    C++ Library:
    ----------------


    Tools:
    ------

     - h5dump: added 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)
     - h5dump: support for external links, display the object that the external link 
         points to. (PVN - 2008/05/12)



    High-Level APIs:
    ------
    
    Documentation 
    ------------- 

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

Bug Fixes since HDF5-1.8.0 release
==================================

    Library
    -------
        - Fixed issue where a group could have a file mounted on it twice.
            (QAK - 2008/07/15)
	- Fixed the problem with the searching of target file for H5Lcreate_external().
	  The searching pattern will depend on whether the target file's
	  pathname is an absolute or a relative path. Please see the description
	  in the RM for H5Lcreate_external().  (VC - 2008/04/08)
      - Fixed possible file corruption bug when encoding datatype
            descriptions for compound datatypes whose size was between
            256 & 511 bytes and the file was opened with the "use the
            latest format" property enabled (with H5Pset_libver_bounds).
            (QAK - 2008/03/13)
      - Fixed bug in H5Aget_num_attrs() routine to handle invalid location
            ID correctly.  (QAK - 2008/03/11)


    Configuration
    -------------

    Performance
    -------------

    Tools
    -----
        - Fixed bug in h5ls that prevented relative group listings (like
            "h5ls foo.h5/bar") from working correctly (QAK - 2008/06/03)
        - Fixed bug in h5diff that prevented datasets & attributes with
            variable-length string elements from comparing correctly.
            (QAK - 2008/02/28)
        - 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 - 2008/02/19)
        - 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 
    ------------- 


    F90 APIs
    --------


    C++ APIs
    --------
        - Fixed bug that caused segfaults in Attribute::read. (BMR - 2008/04/20)
        - Fixed bug in PropList::getClassName to use portable HDfree instead
            of free. (BMR - 2008/04/20)


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

    AIX 5.2 (32/64 bit)           xlc 8.0.0.11
                                  xlC 8.0
                                  xlf 10.01.0000.0 
                                  mpcc_r 6.0.0.8
                                  mpxlf_r 8.1.1.7
    FreeBSD 6.2-STABLE i386       gcc 3.4.6 [FreeBSD] 20060305
    (duty)                        g++ 3.4.6 [FreeBSD] 20060305
                                  gcc 4.2.1 20080123
                                  g++ 4.2.1 20080123
                                  gfortran 4.2.1 20070620
    FreeBSD 6.2-STABLE amd64      gcc 3.4.6 [FreeBSD] 20060305
    (liberty)                     g++ 3.4.6 [FreeBSD] 20060305
                                  gcc 4.2.1 20080123
                                  g++ 4.2.1 20080123
                                  gfortran 4.2.1 20080123

    IRIX64 6.5 (64 & n32)         MIPSpro cc 7.4.4m
                                  F90 MIPSpro 7.4.4m 
                                  C++ MIPSpro cc 7.4.4m
				 
    Linux 2.6.9 (RHEL4)           Intel 10.0 compilers
    (abe.ncsa.uiuc.edu)
    Linux 2.4.21-47               gcc 3.2.3 20030502
    (osage)
    Linux 2.6.9-42.0.10           gcc 3.4.6 20060404
    (kagiso)                      PGI 7.0-7 (pgcc, pgf90, pgCC)
                                  Intel 9.1 (icc, ifort, icpc)
    Linux 2.6.16.27 x86_64 AMD    gcc 4.1.0 (SuSE Linux), g++ 4.1.0, g95 (GCC 4.0.3)
    (smirom)                      PGI 6.2-5 (pgcc, pgf90, pgCC)
                         	  Intel 9.1 (icc, iort, icpc)
    Linux 2.6.5-7.252.1-rtgfx #1 
          SMP ia64                Intel(R) C++ Version 9.0
    (cobalt)                      Intel(R) Fortran Itanium(R) Version 9.0 
                                  SGI MPI
    SunOS 5.8 32,46               Sun WorkShop 6 update 2 C 5.3
     (Solaris 2.8)                Sun WorkShop 6 update 2 Fortran 95 6.2
                                  Sun WorkShop 6 update 2 C++ 5.3
    SunOS 5.10                    cc: Sun C 5.8 
    (linew)                       f90: Sun Fortran 95 8.2 
                                  CC: Sun C++ 5.8 
    Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre
    (tungsten)	                  gcc 3.2.2 20030222
                                  Intel(R) C++ Version 9.0
                                  Intel(R) Fortran Compiler Version 9.0
    IA-64 Linux 2.4.21.SuSE_292.til1 ia64
    (NCSA tg-login)               gcc 3.2.2
                                  Intel(R) C++ Version 8.1
                                  Intel(R) Fortran Compiler Version 8.1
				  mpich-gm-1.2.5..10-intel-r2
    Windows XP                    
				  Visual Studio .NET
                                  Visual Studio 2005 w/ Intel Fortran 9.1
                                  Cygwin(native gcc compiler and g95)
				  MinGW(native gcc compiler and g95)
    Windows XP x64                
			          Visual Studio 2005 w/ Intel Fortran 9.1
    Windows Vista			
			          Visual Studio 2005

    MAC OS  10.4 (Intel)          gcc i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 
                                  G95 (GCC 4.0.3 (g95 0.91!) Nov 21 2006)
    Alpha Open VMS 7.3


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

    In the tables below
          y   = tested and supported
          n   = not supported or not tested in this release
          x   = not working in this release
          ( ) = footnote appears below second table
          <blank> = testing incomplete on this feature or platform
          W or C indicates workstation or cluster, respectively.

Platform                          C        F90    F90      C++   zlib  SZIP
                                  parallel        parallel
SunOS5.8 64-bit                    n        y      n        y     y     y
SunOS5.8 32-bit                    n        y      n        y     y     y
SunOS5.10 64-bit                   n        y      n        y     y     y
SunOS5.10 32-bit                   n        y      n        y     y     y
IRIX64_6.5 64-bit                  n        y      y        y     y     y
IRIX64_6.5 32-bit                  n        n      n        n     y     y
AIX-5.2  32-bit                    y        y      y        y     y     y
AIX-5.2  64-bit                    y        y      y        y     y     y
Cray XT3 (not tested
          for this release)        n        n      n        n     n     n
Windows XP                         n        y(3)   n(3)     y     y     y
Windows XP x64                     n        y(3)   n(3)     y     y     y
Windows Vista                      n        n      n        y     y     y
Mac OS X 10.4 PowerPC              n               n
Mac OS X 10.4 Intel                n        y      n        y     y     y
FreeBSD 6.2 32-bit                 n        n      n        y     y     y
FreeBSD 6.2 64-bit
RedHat EL4 2.6.9 i686 GNU        W y(2)     y(4)   y(2)     y     y     y
RedHat EL4 2.6.9 i686 Intel      W n        y      n        y     y     n
RedHat EL4 2.6.9 i686 PGI        W n        y      n        y     y     n
SuSe Linux 2.6.16 x86_64 GNU (5) W y(2)     y      n        y     y     y
SuSe Linux 2.6.16 x86_64 Int (5) W n        y      n        y     n     n
SuSe Linux 2.6.16 x86_64 PGI (5) W n        y      n        y     n     n
RHL9 Linux 2.4 Xeon Lustre Intel C n        y      n        y     y     n
RHEL3 Linux 2.4 Xeon Intel       W n        y      n        n     y     n
RHEL4 Linux 2.6 Xeon Lustre Int  C n        y      n        y     y     n
SuSE Linux 2.4 ia64 Intel        C y(1)     y      y        y     y     y
SuSe Linux 2.6.5
       SGI Altix ia64 Intel      C n        y      n        y     n     y
Alpha OpenVMS 7.3.2                n        y      n        y     n     n



Platform                          Shared   Shared    Shared    static-  Thread-
                                  C libs   F90 libs  C++ libs  exec     safe
SunOS 5.8 32-bit                    y        y         y         x        y
SunOS 5.8 64-bit                    y        y         y         x        y
SunOS 5.10 32-bit                   y        y         y         x        y
SunOS 5.10 64-bit                   y        y         y         x        y
IRIX64_6.5 32-bit                   y        n         y         x        y
IRIX64_6.5 64-bit                   y        y         n         x        y
AIX-5.2 32-bit                      n        n         n         x        n
AIX-5.2 64-bit                      n        n         n         x        n
Cray XT3 (not tested
          for this release)         n        n         n         x        n
Windows XP                          y        y(3)      y         y        y
Windows XP x64                      y        y(3)      y         y        y
Windows Vista                       y        n         n         y        y
Mac OS X 10.4 Intel Duo             y        y         y         x        n
FreeBSD 6.2 32-bit                  y        y         y         x        n
FreeBSD 6.2 64-bit                  y        y         y         x        n
RHEL4 2.6.9 i686 GNU              W y        y(4)      y         x        y
RHEL4 2.6.9 i686 Intel            W y        y         y         x        n
RHEL4 2.6.9 i686 PGI              W y        y         y         x        n
SuSE Linux 2.6.16 x86_64 GNU (5)  W y        y         y         x        y
SuSE Linux 2.6.16 x86_64 Intel(5) W y        y         y         x        n
SuSE Linux 2.6.16 x86_64 PGI(5)   W y        y         y         x        n
RHL9 Linux 2.4 Xeon Lustre Intel  C y        y         y         x        n
RHEL3 Linux 2.4 Xeon Intel        W y        n         n         x        n
RHEL4 Linux 2.6 Xeon Lustre Intel C y        y         y         x        n
SuSE Linux 2.4 ia64 Intel         C y        y         y         x        n
SuSe Linux 2.6.5
           SGI Altix ia64 Intel   C n        n         n         x        n

    Notes: (1)  Using mpich 1.2.6.
           (2) Using mpich2 1.0.6.
           (3) Using Visual Studio 2005 or Cygwin
           (4) With PGI and Absoft compilers.
           (5) AMD Opteron x86_64
    Compiler versions for each platform are listed in the preceding
    "Platforms Tested" table.



Known Problems
==============
* We discovered two problems when running collective IO parallel HDF5 tests 
  with chunking storage on  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 wrong derived data type 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.

  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

* For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel
  tests failed with MPI-IO file locking message. AKC - 2007/6/25.
* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers use
  -mp -O1 compilation flags to build the libraries. Higher level of optimization 
  causes failures in several HDF5 library tests. 
* For HPUX 11.23 many tools tests failed for 64-bit version when linked to the
  shared libraries (tested for 1.8.0-beta2)
* For SNL, Red Storm: only paralle HDF5 is supported.  The serial tests pass
  and the parallel tests also pass with lots of non-fatal error messages.
* For LLNL, uP: both serial and parallel pass.  Zeus: serial passes but
  parallel fails with a known proglem in MPI.  ubgl: serial passes but
  parallel fails. 
* on SUN 5.10 C++ test fails in the "Testing Shared Datatypes with Attributes" test 
* configuring with --enable-debug=all produces compiler errors on most
  platforms.  Users who want to run HDF5 in debug mode should use
  --enable-debug rather than --enable-debug=all to enable debugging
  information on most modules.
* On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long
  double to (unsigned) long long and from (unsigned)long long to long double. 
* On Altix SGI with Intel 9.0 testmeta.c would not compile with -O3
  optimization flag.
* On VAX, Scaleoffset filter isn't supported. The filter cannot be applied to
  HDF5 data generated on VAX. Scaleoffset filter only supports IEEE standard
  for floating-point data.
* On Cray X1, a lone colon on the command line of h5dump --xml (as in
  the testh5dumpxml.sh script) is misinterpereted by the operating system
  and causes an error.
* On mpich 1.2.5 and 1.2.6, we found that if more than two processes
  contribute no IO and the application asks to do IO with collective, we found
  that when using 4 processors, a simple collective write will be hung
  sometimes. This can be verified with t_mpi test under testpar.
* On IRIX6.5, when C compiler version >7.4, the complicate MPI derived data type
  code will work. However, the user should be aware to enlarge MPI_TYPE_MAX environment 
  variable to some certian value in order to use collective irregular selection code.
  For example, the current parallel HDF5 test needs to enlarge MPI_TYPE_MAX to 
  200,000 to make the test pass.
* The 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(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.  The library release 
  after 1.6.4 can still read the dataset created or rewritten with the library
  of v1.6.2 or before.  SLU - 2005/6/30
* For the version 6(6.02 and 6.04) of Portland Group compiler on AMD Opteron
  processor, there's a bug in the compiler for optimization(-O2).  The library
  failed in several tests but all related to multi driver.  The problem has 
  been reported to the vendor.  
* 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.

* 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


* 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.

* With the gcc 2.95.2 compiler, HDF 5 uses the `-ansi' flag during
  compilation. The ANSI version of the compiler complains about not being
  able to handle the `long long' datatype with the warning:

        warning: ANSI C does not support `long long'
  
  This warning is innocuous and can be safely ignored.


* 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 J90 and 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 and h5ls appears to
      be dumping floating-point numbers correctly.

* Not all platforms behave correctly with szip's shared libraries. Szip is
  disabled in these cases, and a message is relayed at configure time. Static
  libraries should be working on all systems that support szip, and should be
  used when shared libraries are unavailable. There is also a configure error
  on Altix machines that incorrectly reports when a version of szip without
  an encoder is being used.

* 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)

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

* 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 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 scipts 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.

* H5Ocopy() does not copy reg_ref attributes correctly when shared-message
  is turn on. The value of the reference in the destination attriubte is
  wrong. This H5Ocopy problem will affect h5copy tool