path: root/release_docs/RELEASE.txt

HDF5 version 1.8.9-snap8 currently under development
================================================================================

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

This document describes the differences between HDF5-1.8.8 and 
HDF5 1.8.9-*, and contains information on the platforms tested and 
known problems in HDF5-1.8.9-*. 
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 1.8.9 source code, documentation, and additional materials
can be found on the HDF5 web page at:

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

The HDF5 1.8.9 release can be obtained from:

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

User documentation for 1.8.9 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 1.8.9 (current 
release) versus Release 1.8.8":

     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, Languages, and Compilers
- Bug Fixes since HDF5-1.8.8
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems


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

    Configuration
    -------------
    - None
    
    Library
    -------
    - None
 
    Parallel Library
    ----------------
    - None
 
    Tools
    -----
    - None

    High-Level APIs
    ---------------
    - None

    Fortran API
    -----------
    - None

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


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

Bug Fixes since HDF5-1.8.8
==========================

    Configuration
    -------------
    - Updated all CMakeLists.txt files to indicate minimum CMake version is
      current standard of 2.8.6 (ADB -2011/12/05 - HDFFV-7854)

    Library
    -------
    - Fixed a seg fault that could occur when shrinking a dataset with chunks
      larger than 1 MB. (NAF - 2011/11/30 - HDFFV-7833)
    - The library allowed the conversion of strings between ASCII and UTF8
      (Issue 7582).  We have corrected it to report an error under this
      situation. (SLU - 2011/11/8)
    - The library had seg fault when it tried to shrink the size of compound
      type through H5Tset_size immediately after the type was created (Issue
      7618). It's fixed now. (SLU - 2011/11/4)

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

    Tools
    -----
    - h5diff: fixed to prevent from displaying error stack message when 
      comparing the two dangling symlinks with follow-symlinks option.
      HDFFV-7836 (JKM 2012/01/13)
    - h5repack: fixed memory leak for handling variable length string in 
      attribute.  HDFFV-7840 (JKM 2012/01/10)
    - h5ls: fixed segfault when access region reference data in an
      attribute. HDFFV-7838 (JKM 2012/01/06)

    F90 API
    -------
    - None

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

    High-Level APIs:
    ------
    - None

    Fortran High-Level APIs:
    ------
    - None


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

    AIX 6.1                       xlc 11.1.0.3
    (NCSA BP)                     xlC 11.1.0.3
                                  xlf90 13.1.0.3
                                  mpcc_r 11.1.0.3
                                  mpxlf90_r 13.1.0.3

    FreeBSD 8.2-STABLE i386       gcc 4.2.1 [FreeBSD] 20070719
    (loyalty)                     g++ 4.2.1 [FreeBSD] 20070719
                                  gcc 4.6.1 20110422
                                  g++ 4.6.1 20110422
                                  gfortran 4.6.1 20110422

    FreeBSD 8.2-STABLE amd64      gcc 4.2.1 [FreeBSD] 20070719
    (freedom)                     g++ 4.2.1 [FreeBSD] 20070719
                                  gcc 4.6.1 20110422
                                  g++ 4.6.1 20110422
                                  gfortran 4.6.1 20110422

    Linux 2.6.18-194.3.1.el5PAE   gcc (GCC) 4.1.2 and 4.4.2
    #1 SMP i686 i686 i386         GNU Fortran (GCC) 4.1.2 20080704
    (jam)                             (Red Hat 4.1.2-48) and 4.4.2 
                                  PGI C, Fortran, C++ 10.4-0 32-bit
                                  PGI C, Fortran, C++ 10.6-0 32-bit
                                  Intel(R) C Compiler for 32-bit
                                      applications, Version 11.1 
                                  Intel(R) C++ Compiler for 32-bit
                                      applications, Version 11.1
                                  Intel(R) Fortran Compiler for 32-bit
                                      applications, Version 11.1
                                  MPICH mpich2-1.3.1 compiled with
                                      gcc 4.1.2 and gfortran 4.1.2

    Linux 2.6.18-238.12.1.el5     gcc 4.1.2 and 4.4.2
    #1 SMP x86_64 GNU/Linux       GNU Fortran (GCC) 4.1.2 20080704
    (koala)                           (Red Hat 4.1.2-46) and 4.4.2
                                      tested for both 32- and 64-bit binaries
                                  Intel(R) C, C++, Fortran Compilers for 
                                      applications running on Intel(R) 64, 
                                      Version 11.1.
                                  PGI C, Fortran, C++ Version 9.0-4
                                      for 64-bit target on x86-64
                                  MPICH mpich2-1.3.1 compiled with
                                      gcc 4.1.2 and gfortran 4.1.2

    SGI ProPack 7 Linux           Intel(R) C++ Version 11.1 20100806
    2.6.32.24-0.2.1.2230.2.PTF-   Intel(R) Fortran Version 11.1 20100806
    default #1 SMP                SGI MPT 2.01
    SGI Altix UV
    (NCSA ember)

    SunOS 5.10 32- and 64-bit     Sun C 5.9 Sun OS_sparc Patch 124867-16
    (linew)                       Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13
                                  Sun C++ 5.9 Sun OS_sparc Patch 124863-62
                                  Sun C 5.10 SunOS_sparc Patch 141861-07
                                  Sun Fortran 95 8.4 SunOS_sparc Patch 128231-06
                                  Sun C++ 5.10 SunOS_sparc 128228-11

    Windows XP                    Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
                                  Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
                                  Visual Studio 2010 (cmake)
                                  Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran)

    Windows XP x64                Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
                                  Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
                                  Visual Studio 2010 (cmake)
                                  Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran)

    Windows Vista                 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)

    Windows Vista x64             Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)

    Windows 7                     Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)

    Windows 7 x64                 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)

    Mac OS X 10.7.0 (Intel 64-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1
    Darwin Kernel Version 10.7.0  GNU Fortran (GCC) 4.6.0 20101106 (experimental)
                                  Intel C, C++ and Fortran compilers 12.0.1.122 20101110

    Mac OS X 10.7.0 (Intel 32-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3)
    Darwin Kernel Version 10.7.0  GNU Fortran (GCC) version 4.4.0 20090123 (experimental) 
              [trunk revision 143587]

    Fedora 12 2.6.32.16-150.fc12.ppc64 #1 SMP ppc64 GNU/Linux
                                  gcc (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10)
                                  GNU Fortran (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10)

    Debian6.0.3 2.6.32-5-686 #1 SMP i686 GNU/Linux
                                  gcc (Debian 4.4.5-8) 4.4.5
                                  GNU Fortran (Debian 4.4.5-8) 4.4.5

    Debian6.0.3 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux
                                  gcc (Debian 4.4.5-8) 4.4.5
                                  GNU Fortran (Debian 4.4.5-8) 4.4.5

    Fedora15 2.6.40.6-0.fc15.i686.PAE #1 SMP i686 i686 i386 GNU/Linux
                                  gcc (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9)
                                  GNU Fortran (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9)

    Fedora15 2.6.40.6-0.fc15.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
                                  gcc (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9)
                                  GNU Fortran (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9)

    SUSE 11.4 2.6.37.6-0.7-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux
                                  gcc (SUSE Linux) 4.5.1 20101208
                                  GNU Fortran (SUSE Linux) 4.5.1 20101208

    SUSE 11.4 2.6.37.6-0.7-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
                                  gcc (SUSE Linux) 4.5.1 20101208
                                  GNU Fortran (SUSE Linux) 4.5.1 20101208

    Ubuntu 11.10 3.0.0-12-generic #20-Ubuntu SMP i686 GNU/Linux
                                  gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1
                                  GNU Fortran (Ubuntu/Linaro 4.6.4-9ubuntu3) 4.6.1

    Ubuntu 11.10 3.0.0-12-generic #20-Ubuntu SMP x86_64 GNU/Linux
                                  gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1
                                  GNU Fortran (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1
    
    OpenVMS Alpha 8.3             HP C V7.3-009
                                  HP Fortran V8.2-104679-48H9K
                                  HP C++ V7.3-009

Tested Configuration Features Summary
=====================================

    In the tables below
          y   = tested 
          n   = not tested in this release
          C   = Cluster
          W   = Workstation
          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
Windows XP                                 n        y(4)   n        y     y     y
Windows XP x64                             n        y(4)   n        y     y     y
Windows Vista                              n        y(4)   n        y     y     y
Windows Vista x64                          n        y(4)   n        y     y     y
OpenVMS Alpha                              n        y      n        y     y     n
Mac OS X 10.7 Intel 32-bit                 n        y      n        y     y     y
Mac OS X 10.7 Intel 64-bit                 n        y      n        y     y     y
AIX 6.1 32- and 64-bit                     y        y      y        y     y     y
FreeBSD 8.2-STABLE 32&64 bit               n        x      n        x     y     y
CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W  y        y(2)   y        y     y     y
CentOS 5.5 Linux 2.6.18-194 i686 Intel  W  n        y      n        y     y     n
CentOS 5.5 Linux 2.6.18-194 i686 PGI    W  n        y      n        y     y     n
CentOS 5.5 Linux 2.6.16 x86_64 GNU (1)  W  y        y(3)   y        y     y     y
CentOS 5.5 Linux 2.6.16 x86_64 Intel    W  n        y      n        y     y     n
CentOS 5.5 Linux 2.6.16 x86_64 PGI      W  n        y      n        y     y     y
Fedora 12 Linux 2.6.32.16-150.fc12.ppc64   n        y      n        y     y     y
SGI Linux 2.6.32.19                        y        y      y        y     y     y


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        
Windows XP                                 y       y(4)      y         n        
Windows XP x64                             y       y(4)      y         n        
Windows Vista                              y       y(4)      y         y
Windows Vista x64                          y       y(4)      y         y
OpenVMS Alpha                              n       n         n         n
Mac OS X 10.7 Intel 32-bit                 y(5)    n         y         n        
Mac OS X 10.7 Intel 64-bit                 y(5)    n         y         n        
AIX 6.1 32- and 64-bit                     n       n         n         y        
FreeBSD 8.2-STABLE 32&64 bit               y       x         x         y        
CentOS 5.5 Linux 2.6.18-128 i686 GNU (1)W  y       y(2)      y         y        
CentOS 5.5 Linux 2.6.18-128 i686 Intel  W  y       y         y         n        
CentOS 5.5 Linux 2.6.18-128 i686 PGI    W  y       y         y         n        
CentOS 5.5 Linux 2.6.16 x86_64 GNU (1)  W  y       y         y         y        
CentOS 5.5 Linux 2.6.16 x86_64 Intel    W  y       y         y         n        
CentOS 5.5 Linux 2.6.16 x86_64 PGI      W  y       y         y         n        
Fedora 12 Linux 2.6.32.16-150.fc12.ppc64   y       y         y         y 
SGI Linux 2.6.32.19                        y       y         y         y 

           (1) Fortran compiled with gfortran.
           (2) With PGI and Absoft compilers.
           (3) With PGI compiler for Fortran.
           (4) Using Visual Studio 2008 w/ Intel Fortran 10.1 (Cygwin shared libraries are not supported)
           (5) C and C++ shared libraries will not be built when Fortran is enabled.
    Compiler versions for each platform are listed in the preceding
    "Platforms Tested" table.


Known Problems
==============
* After the shared library support was fixed for some bugs, it was discovered
  that "make prefix=XXX install" no longer works for shared libraries. It
  still works correctly for static libraries. Therefore, if you want to
  install the HDF5 shared libraries in a location such as /usr/local/hdf5,
  you need to specify the location via the --prefix option during configure 
  time. E.g, ./configure --prefix=/usr/local/hdf5 ...
  (AKC - 2011/05/07 HDFFV-7583)

* The parallel test, t_shapesame, in testpar/, may run for a long time and may
  be terminated by the alarm signal.  If that happens, one can increase the
  alarm seconds (default is 1200 seconds = 20 minutes) by setting the
  environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600
  (60 minutes).  Note that the t_shapesame test may fail in some systems 
  (see the "While working on the 1.8.6 release..." problem below).  If 
  it does, it will waste more time if $HDF5_ALARM_SECONDS is set
  to a larger value. (AKC - 2011/05/07)

* The C++ and FORTRAN bindings are not currently working on FreeBSD.
  (QAK - 2011/04/26)

* Shared Fortran libraries are not quite working on AIX. While they are
  generated when --enable-shared is specified, the fortran and hl/fortran
  tests fail. We are looking into the issue. HL and C++ shared libraries
  should now be working as intended, however. (MAM - 2011/04/20)

* The --with-mpe configure option does not work with Mpich2. AKC - 2011/03/10

* If parallel gmake (e.g., gmake -j 4) is used, the "gmake clean" command
  sometimes fails in the perform directory due to the attempt to remove the
  executable of h5perf or h5perf_serial by two "parallel" commands. This error
  has no consequence on the functionality of the HDF5 library or install. It
  is fixed in the next release. AKC - 2011/01/25

* While working on the 1.8.6 release of HDF5, a bug was discovered that can
  occur when reading from a dataset in parallel shortly after it has been
  written to collectively. The issue was exposed by a new test in the parallel
  HDF5 test suite, but had existed before that. We believe the problem lies with
  certain MPI implementations and/or file systems.

  We have provided a pure MPI test program, as well as a standalone HDF5
  program, that can be used to determine if this is an issue on your system.
  They should be run across multiple nodes with a varying number of processes.
  These programs can be found at:
  http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/

* The library's test dt_arith.c showed a compiler's rounding problem on
  Cygwin when converting from unsigned long long to long double.  The 
  library's own conversion works fine.  We defined a macro for Cygwin to
  skip this test until we can solve the problem.  Please see bug #1813.
  SLU - 2010/5/5 

* All the VFL drivers aren't backward compatible.  In H5FDpublic.h, the
  structure H5FD_class_t changed in 1.8.  There is new parameter added to
  get_eoa and set_eoa callback functions.  A new callback function
  get_type_map was added in.  The public function H5FDrealloc was taken
  out in 1.8.  The problem only happens when users define their own driver
  for 1.6 and try to plug in 1.8 library.  Because there's only one user 
  complaining about it, we (Elena, Quincey, and I) decided to leave it as 
  it is (see bug report #1279).  Quincey will make a plan for 1.10.
  SLU - 2010/2/2

* MinGW has a missing libstdc++.dll.a library file and will not successfully link
  C++ applications/tests. Do not use the enable-cxx configure option. Read all of
  the INSTALL_MINGW.txt file for all restrictions. ADB - 2009/11/11
  
* The PathScale MPI implementation, accessing a Panasas file system, would
  cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file does not
  exist. This is due to the MPI_File_open() call failing if the mode has
  the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11
 
* Parallel tests failed with 16 processes with data inconsistency at testphdf5
  / dataset_readAll. Parallel tests also failed with 32 and 64 processes with
  collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
  with MPI IO. CMC - 2009/04/28

* 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
  
* The STDIO VFD does not work on some architectures, possibly due to 32/64
  bit or large file issues.  The basic STDIO VFD test is known to fail on
  64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin
  10.7.0.  The STDIO VFD test has been disabled while we investigate and
  a fix should appear in a future release, possibly 1.8.9.
  
* The links test can fail under the stdio VFD due to some issues with external
  links.  This will be investigated and fixed in a future release.  See JIRA
  issue HDFFV-7768 for more information.  DER - 10/14/2011
  
* h5diff can report inconsistent results when comparing datasets of enum type
  that contain invalid values.  This is due to how enum types are handled in
  the library and will be addressed in the next release.  See JIRA issue
  HDFFV-7527.  DER - 10/14/2011

* 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 to see this message.  See the section of "Red
  Storm" in file INSTALL_parallel for a way to deal with this problem.
  AKC - 2008/05/28

* On an 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. 

* 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.

* 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 will only statically link libraries
  if the static version of that library is present. If only the shared version
  of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
  for example, only have shared versions), the flag should still result in a 
  successful compilation, but note that the installed executables will not be 
  fully static. Thus, the only guarantee on these systems is that the 
  executable is statically linked with just the HDF5 library.

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

* On cobalt, an SGI Altix SMP ia64 system, Intel compiler version 10.1 (which
  is the default on that system) does not work properly and results in
  failures during make check (in a static build) and make installcheck (during
  a shared build). This appears to be a compiler optimization problem.
  Reducing optimization by setting CFLAGS to -O1 or below resolves the issue.
  Alternatively, using a newer version of the compiler (11.0) also works as
  intended. MAM - 2010/06/01