path: root/release_docs/RELEASE.txt

HDF5 version 1.8.2-post13 currently under development
================================================================================

INTRODUCTION
============

This document describes the differences between HDF5-1.8.2 and 
HDF5 1.8.2-snap*, and contains information on the platforms tested and 
known problems in HDF5-1.8.2-snap*. 
For more details, see the files HISTORY-1_0-1_8_0_rc3.txt 
and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.

Links to the HDF5 1.8.2 source code, documentation, and additional materials
can be found on the HDF5 web page at:

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

The HDF5 1.8.2 release can be obtained from:

     http://www.hdfgroup.org/HDF5/release/obtain5.html

User documentation for 1.8.2 can be accessed directly at this location: 

     http://www.hdfgroup.org/HDF5/doc/

New features in the HDF5-1.8.x release series, including brief general 
descriptions of some new and modified APIs, are described in the "What's New 
in 1.8.0?" document:

     http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html

All new and modified APIs are listed in detail in the "HDF5 Software Changes 
from Release to Release" document, in the section "Release 1.8.2 (current 
release) versus Release 1.8.1":

     http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html

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 HDF5-1.8.2
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems


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

    Configuration
    -------------
    - Added a Make target of check-all-install to test the correctness of
      installing via the prefix= or $DESTDIR options. AKC - 2009/04/14
    - Add description here. Do not exceed 80 characters per line.
      EIP - 2008/11/12

    Library
    -------
    - Separated "factory" free list class from block free lists. These free
      lists are dynamically created and manage blocks of a fixed size.
      H5set_free_list_limits() will use the same settings specified for block
      free lists for factory free lists. NAF - 2009/04/08
    - Added support for dense attributes to H5Ocopy. XCao/NAF - 2009/01/29
    - Added H5Pset_elink_cb and H5Pget_elink_cb functions to support a
      user-defined callback function for external link traversal.
      NAF - 2009/01/08
    - Added H5Pset_elink_acc_flags and H5Pget_elink_acc_flags functions to
      allow the user to specify the file access flags used to open the target
      file of an external link. NAF - 2009/01/08
    - Added H5Pset_chunk_cache() and H5Pget_chunk_cache() functions to allow
      individual rdcc configuration for each dataset.  Added
      H5Dget_access_plist() function to retrieve a dataset access property
      list from a dataset. NAF - 2008/11/12
    - Added H5Iis_valid() function to check if an id is valid without
      producing an error message. NAF - 2008/11/5
    - Added code to maintain a min_clean_fraction in the metadata cache when
      in serial mode. MAM - 2009/01/9

    Parallel Library
    ----------------

    Tools
    -----
    - h5diff new flag, -c, --compare, list objects that are not comparable.
        PVN - 2009/4/2 - 1368
    - h5diff new flag, -N, --nan, avoids NaNs detection. PVN - 2009/4/2
    - h5dump correctly specifies XML dtd / schema urls ADB - 2009/4/3 - 1519
    - h5repack now handles group creation order. PVN - 2009/4/2 - 1402
    - h5repack: When user doesn't specify a chunk size, h5repack now defines a default 
            chunk size as the same size of the size of the hyperslab used to read the chunks. 
            The size of the hyperslabs are defined as the size of each dimension or a 
            predefined constant, whatever is smaller. This assures that the chunk 
            read fits in the chunk cache. PVN - 2008/11/21

    High-Level APIs:
    ------
    - Table: In version 3.0 of Table, the writing of the "NROWS" attribute (used to store 
            number of records)was deprecated. PVN - 2008/11/24


    F90 API
    ------

        - Added for the C APIs the Fortran wrappers:
            H5D_h5dget_access_plist_f
            H5I_h5iis_valid_f
            H5P_h5pset_chunk_cache_f
            H5P_h5pget_chunk_cache_f
          (MSB - 2009/04/17)
     
     
    C++ API
    ------


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


Bug Fixes since HDF5-1.8.2
==========================

    Configuration
    -------------
    - The --includedir=DIR configuration option now works as intended, and 
      can be used to specify the location to install C header files. The
      default location remains unchanged, residing at ${prefix}/include.
      MAM - 2009/03/10 - BZ #1381
    - Configure no longer removes the '-g' flag from CFLAGS when in production
      mode if it has been explicitly set in the CFLAGS environment variable 
      prior to configuration. MAM - 2009/03/09 - BZ #1401

    Library
    -------
    - Added direct.h include file to windows section of H5private.h 
      to fix _getcwd() warning. ADB - 2009/04/14 - 1536
    - Fixed a bug that prevented external links from working after calling
      H5close(). NAF - 2009/04/10 - 1539
    - Modified library to write cached symbol table information to the
      superblock, to allow library versions 1.3.0 to 1.6.3 to read files created
      by this version. NAF - 2009/04/08 - 1423
    - Changed skip lists to use a deterministic algorithm.  The library should
      now never call rand() or srand(). NAF - 2009/04/08 - 503
    - Fixed a bug where H5Lcopy and H5Lmove wouldn't create intermediate groups
      when that property was set. NAF - 2009/04/07 - 1526
    - Fixed a bug that caused files with a user block to grow by the size of the
      user block every time they were opened. NAF - 2009/03/26 - 1499
    - Fixed a rare problem that could occur with files using the old (pre 1.4)
      array datatype. NAF - 2009/03/23
    - Modified library to be able to open files with corrupt root group symbol
      table messages, and correct these errors if they are found.  Such files
      can only be successfully opened with write access. NAF - 2009/03/23 - 1189
    - Removed the long_long #define and replaced all instances with 
      "long long". This caused problems with third party products. All 
      currently supported compliers support the type. (ADB - 2009/03/05)
    - Fixed various bugs that could prevent the fill value from being written
      in certain rare cases. NAF - 2009/02/26 - 1469
    - Fixed a bug that prevented more than one dataset chunk from being cached
      at a time. NAF - 2009/02/12 - 1015
    - Fixed an assertion failure caused by opening an attribute multiple times
      through multiple file handles. NAF - 2009/02/12 - 1420
    - Fixed a problem that could prevent the user from adding attributes (or any
      object header message) in some circumstances. NAF - 2009/02/12 - 1427
    - Fixed a bug that could cause problems when an attribute was added to a
      committed datatype using the committed datatype's datatype.
      NAF - 2009/02/12
    - Fixed a bug that could cause problems when copying an object with a shared
      message in its own object header. NAF - 2009/01/29
    - Changed H5Tset_order to properly reject H5T_ORDER_NONE for most datatypes.
      NAF - 2009/01/27 - 1443
    - Fixed a bug where H5Tpack wouldn't remove trailing space from an otherwise
      packed compound type. NAF - 2009/01/14
    - Fixed up some old v2 btree assertions that get run in debug mode that
      were previously failing on compilation, and removed some of the 
      more heavily outdated and non-rewritable ones. MAM - 2008/12/15
    - Fixed a bug that could cause problems when "automatically" unmounting
      multiple files. NAF - 2008/11/17
    - H5Dset_extent: when shrinking dimensions, some chunks were not deleted.  
            PVN - 2009/01/8 


    Parallel Library
    ----------------

    Tools
    -----
     - h5dump, h5diff, h5repack were not reading (by hyperslabs) datasets 
            that have a datatype datum size greater than H5TOOLS_BUFSIZE, a 
            constant defined as 1024Kb, such as array types with large 
            dimensions. PVN - 2009/4/1 - 1501
     - h5import: By selecting a compression type, a big endian byte order was being 
            selected. PVN - 2009/3/11 - 1462
     - zip_perf.c had missing argument on one of the open() calls. Fixed.
      AKC - 2008/12/9

    F90 API
    ------

    C++ API
    ------

    High-Level APIs:
    ------
     - Dimension scales: The scale index return value in H5DSiterate_scales was not always 
          incremented. (PVN - 2009/4/8 - 1538)

   Fortran High-Level APIs:
    ------
     - Lite: The h5ltget_dataset_info_f function (gets information about a dataset) 
           was not correctly returning the dimension array (PVN - 2009/3/23)



Platforms Tested
================
The following platforms and compilers have been tested for this release.

    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

    Cray XT3 (2.0.41)             cc (pgcc) 7.1-4
    (red storm)                   ftn (pgf90) 7.1-4
				  CC (pgCC) 7.1-4

    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 (64 & n32)         MIPSpro cc 7.4.4m
                                  F90 MIPSpro 7.4.4m 
                                  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 2.6.16.46-0.14-smp #1   Intel(R) C++ for Intel(R) EM64T 
    SMP x86_64 GNU/Linux          Ver.  10.1.013
    (smirom)                      Intel(R) Fortran Intel(R) EM64T 
                                  Ver.  10.1.013
                                  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

    Intel 64 Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp
    (abe)                         gcc 3.4.6 20060404
                                  Intel(R) C++ Version 10.0
                                  Intel (R) Fortran Compiler Version 10.0
                                  mvapich2-0.9.8p2patched-intel-ofed-1.2

    Windows XP                    Visual Studio .NET
                                  Visual Studio 2005 w/ Intel Fortran 9.1
                                  Cygwin(native gcc compiler and g95)

    Windows XP x64                Visual Studio 2005 w/ Intel Fortran 9.1

    Windows Vista                 Visual Studio 2005

    MAC OS  10.5.4 (Intel)        i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1
                                  GNU Fortran (GCC) 4.3.0 20070810
                                  G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008)
                                  Intel C, C++ and Fortran compilers 10.1
                                  

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
          dna = does not apply
          ( ) = footnote appears below second table
          <blank> = testing incomplete on this feature or platform 

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        y     y     y
IRIX64_6.5 32-bit        n        n      n        n     y     y
IRIX64_6.5 64-bit        n        y      y        y     y     y
Windows XP               n        y(15)  n(15)    y     y     y
Windows XP x64           n        y(15)  n(15)    y     y     y
Windows Vista            n        n      n        y     y     y
Mac OS X 10.5 Intel      n        y      n        y     y     y
AIX 5.3 32- and 64-bit   n        y      n        y     y     n
FreeBSD 6.3-STABLE 
32&64 bit                n        y      n        y     y     y
RedHat EL4       (3)  W  y(1)     y(10)  y(1)     y     y     y
RedHat EL4 Intel (3)  W  n        y      n        y     y     n
RedHat EL4 PGI   (3)  W  n        y      n        y     y     n
SuSe x86_64 gcc(3,12) W  y(2)     y(11)  y(2)     y     y     y
SuSe x86_64 Int(3,12) W  n        y(13)  n        y     y     n
SuSe x86_64 PGI(3,12) W  n        y(8)   n        y     y     y
Linux 2.6 SuSE ia64   C 
    Intel       (3,7)    y        y      y        y     y     n
Linux 2.6 SGI Altix 
    ia64 Intel    (3)    y        y      y        y     y     y
Linux 2.6 RHEL        C
    Lustre Intel  (5)    y(4)     y      y(4)     y     y     n
Cray XT3 2.0.41          y        y      y        y     y     n


Platform                 Shared  Shared    Shared    Thread-  
                         C libs  F90 libs  C++ libs  safe     
Solaris2.10 32-bit       y       y         y         y        
Solaris2.10 64-bit       y       y         y         y        
IRIX64_6.5 32-bit        y       dna       y         y        
IRIX64_6.5 64-bit        y       y         n         y        
Windows XP               y       y(15)     y         y        
Windows XP x64           y       y(15)     y         y        
Windows Vista            y       n         n         y        
Mac OS X 10.5            y       n         y         n        
AIX 5.3 32- and 64-bit   n       n         n         n        
FreeBSD 6.2 32&64 bit    y       n         y         y        
RedHat EL4       (3)  W  y       y(10)     y         y        
RedHat EL4 Intel (3)  W  y       y         y         n        
RedHat EL4 PGI   (3)  W  y       y         y         n        
SuSe x86_64 GNU(3,12) W  y       y         y         y        
SuSe x86_64 Int(3,12) W  y       y         y         n        
SuSe x86_64 PGI(3,12) W  y       y         y         n        
Linux 2.4 SuSE        C
    ia64 C Intel (7)     y       y         y         n        
Linux 2.4 SGI Altix   C
    ia64 Intel           y                           n        
Linux 2.6 RHEL        C
    Lustre Intel (5)     y       y         y         n
Cray XT3 2.0.41          n       n         n         n

    Notes: (1)  Using mpich2 1.0.6.
           (2)  Using mpich2 1.0.7.
           (3)  Linux 2.6 with GNU, Intel, and PGI compilers, as indicated.  
                  W or C indicates workstation or cluster, respectively.
           (4)  Using mvapich2 0.9.8.
           (5)  Linux 2.6.9-42.0.10.  Xeon cluster with ELsmp_perfctr_lustre 
                  and Intel compilers
           (6)  Linux 2.4.21-32.0.1.  Xeon cluster with ELsmp_perfctr_lustre 
                  and Intel compilers
           (7)  Linux 2.4.21, SuSE_292.till.  Ia64 cluster with Intel compilers
           (8)  pgf90
           (9)  With Compaq Visual Fortran 6.6c compiler.
           (10) With PGI and Absoft compilers.
           (11) PGI and Intel compilers for both C and Fortran
           (12) AMD Opteron x86_64
           (13) ifort
           (14) Yes with C and Fortran, but not with C++
           (15) Using Visual Studio 2005 or Cygwin
           (16) Not tested for this release.
    Compiler versions for each platform are listed in the preceding
    "Platforms Tested" table.


Known Problems
==============
* For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and
  tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests
  are expected to fail and should exit with a non-zero code but the yod
  command does not propagate the exit code of the executables. Yod always
  returns 0 if it can launch the executable.  The test suite shell expects
  a non-zero for this particular test, therefore it concludes the test has
  failed when it receives 0 from yod.  Skip all the "failing" test for now
  by changing them as following.

  ======== Original tools/h5ls/testh5ls.sh =========
  TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
  ======== Change to ===============================
  echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
  ==================================================

  ======== Original tools/h5copy/testh5copy.sh =========
  TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets  -d grp_rename
  TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets  -d /grp_rename/grp_dsets
  TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
  TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
  H5LSTEST $FILEOUT
  ======== Change to ===============================
  echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets  -d grp_rename
  echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets  -d /grp_rename/grp_dsets
  echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets
  echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested
  echo SKIP H5LSTEST $FILEOUT
  ==================================================
  AKC - 2008/11/10

* For Red Storm, a Cray XT3 system, the yod command sometimes gives the
  message,  "yod allocation delayed for node recovery".  This interferes with
  test suites that do not expect seeing this message.  See the section of "Red
  Storm" in file INSTALL_parallel for a way to deal with this problem.
  AKC - 2008/05/28

* We have discovered two problems when running collective IO parallel HDF5 
  tests with chunking storage on 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.
  These issues arise only when turning on collective IO with chunking storage 
  with some complex selections. We have not found these problems on other 
  MPI-IO compilers. If you encounter these problems, you may use independent 
  IO instead.

  To avoid this behavior, 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

* 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. A higher level of 
  optimization causes failures in several HDF5 library tests. 

* For LLNL, uP: both serial and parallel tests pass.  
  Zeus: Serial tests pass but parallel tests fail with a known problem in MPI.
  ubgl: Serial tests pass but parallel tests fail. 

* On mpich 1.2.5 and 1.2.6, if more than two processes contribute no IO and 
  the application asks to do collective IO, we have found that when using 4 
  processors, a simple collective write will sometimes be hung. This can be 
  verified with t_mpi test under testpar.

* On IRIX6.5, when the C compiler version is greater than 7.4, complicated
  MPI derived datatype code will work. However, the user should increase
  the value of the MPI_TYPE_MAX environment variable to some appropriate value 
  to use collective irregular selection code.  For example, the current 
  parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test. 

* A dataset created or rewritten with a v1.6.3 library or after cannot be read 
  with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
  There was a bug in the calculation of the Fletcher32 checksum in the 
  library before v1.6.3; the checksum value was not consistent between big-
  endian and little-endian systems.  This bug was fixed in Release 1.6.3.  
  However, after fixing the bug, the checksum value was no longer the same as 
  before on little-endian system.  Library releases after 1.6.4 can still read 
  datasets created or rewritten with an HDF5 library of v1.6.2 or before.  
  SLU - 2005/6/30

* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
  messages like "INFO: 0031-XXX ...".  This is from the command `poe'.
  Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
  and run the tests again.

  The tests may fail with messages like "The socket name is already in use",  
  but HDF5 does not use sockets.  This failure is due to problems with the 
  poe command trying to set up the debug socket.  To resolve this problem, 
  check to see whether there are many old /tmp/s.pedb.* files staying around.  
  These are sockets used by the poe command and left behind due to failed 
  commands.  First, ask your system administrator to clean them out.  
  Lastly, request IBM to provide a means to run poe without the debug socket.

* 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 platforms for serial mode. The parallel mode works fine with 
  this option.
  
  It is suggested that you do not use this option on these platforms
  during configuration.

* There is also a configure error on Altix machines that incorrectly reports 
  when a version of Szip without an encoder is being used.

* Information about building with PGI and Intel compilers is available in
  the INSTALL file sections 4.7 and 4.8.