path: root/release_docs/RELEASE.txt

HDF5 version 1.8.7-snap1 currently under development
================================================================================

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

This document describes the differences between HDF5-1.8.6 and 
HDF5 1.8.7-*, and contains information on the platforms tested and 
known problems in HDF5-1.8.7-*. 
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 1.8.7 source code, documentation, and additional materials
can be found on the HDF5 web page at:

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

The HDF5 1.8.7 release can be obtained from:

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

User documentation for 1.8.7 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 1.8.7 (current 
release) versus Release 1.8.6":

     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 HDF5-1.8.6
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems


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

    Configuration
    -------------
    - Added mpicc and mpif90 as the default C and Fortran compilers for Linux
      systems when --enable-parallel is specified but no $CC or $FC is defined.
      (AKC - 2011/2/7)
    - Added a new configure option, "--enable-unsupported", which can
      be used to stop configure from preventing the use of unsupported
      configure option combinations, such as c++ in parallel or fortran
      with threadsafe. Use at your own risk, as it may result in a 
      library that won't compile or run as expected!
      (MAM - 2010/11/17 - Bug 2061)

    Library
    -------
    - Finished implementing all options for 'log' VFD.  (QAK - 2011/1/25)
    - Removed all old code for Metraowerks compilers, bracketed by
      __MWERKS__). Metraowerks compiler is long gone. (AKC - 2010/11/17) 

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

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

    F90 API
    -------
     - None

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


Support for New Platforms, Languages, and Compilers
===================================================
    - Intel V11.1 uses now -O3 optimization in production mode (EIP - 2010/10/08)
             


Bug Fixes since HDF5-1.8.6
==========================

    Configuration
    -------------
    - None

    Library
    -------
    - None

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

    Tools
    -----
    - Fixed h5diff for the segfault when compares compound datasets
      with combination of fixed length string types and vlen string types 
      in certain orders. bug#2089 (JKM 2010/12/28)
    - Improve h5diff performance. 1) use HDmemcmp() before comparing each 
      elements. 2) replace expensive H5Tequals() calls 3) retrieve datatype
      information at dataset level not each element level for compound 
      datasets
    - Fixed h5ls to display nested compound type with curly bracket 
      when -S (--simple) option is used with -l (--label), so it shows  
      which member (in curly bracket) belong to which nested compound type 
      and make the output make sense.  bug#1979 (JKM 2010/11/09)
    - Fixed h5diff to handle variable-length strings in a compound dataset 
      correctly. (also variable-length string array in a compound dataset)
      Garbage values were displayed when h5diff compared multiple 
      variable-length strings in a compound type dataset. 
      Bug#1989 (JKM 2010/10/28)
    - Fixed h5copy to fail gracefully when copying object to non-exist
          group without -p option. Bug#2040 (JKM 2010/10/18)

    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 5.3                       xlc 7.0.0.9, 8.0.0.20, 9.0.0.4
    (LLNL Up)                     xlC 7.0.0.9, 8.0.0.20, 9.0.0.4
                                  xlf 9.1.0.8, 10.1.0.9, 11.1.0.7
                                  mpcc_r 7.0.0.9
                                  mpxlf_r 9.1.0.8

    AIX 6.1                       xlc 11.1.0.3
    (NCSA BP)                     xlC 11.1.0.3
                                  xlf 13.1.0.3
                                  mpcc_r 11.1.0.3
                                  mpxlf_r 13.1.0.3

    FreeBSD 6.3-STABLE i386       gcc 3.4.6 [FreeBSD] 20060305
    (duty)                        g++ 3.4.6 [FreeBSD] 20060305
                                  gcc 4.3.4 20090419
                                  g++ 4.3.4 20090419
                                  gfortran 4.3.4 20090419

    FreeBSD 6.3-STABLE amd64      gcc 3.4.6 [FreeBSD] 20060305
    (liberty)                     g++ 3.4.6 [FreeBSD] 20060305
                                  gcc 4.4.1 20090421
                                  g++ 4.4.1 20090421
                                  gfortran 4.4.1 20090421

    Linux 2.6.18-128.1.6.el5xen   gcc (GCC) 4.1.2
    #1 SMP i686 i686 i386         G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009)
    (jam)                         GNU Fortran (GCC) 4.1.2 20080704 
                                  (Red Hat 4.1.2-46)
                                  PGI C, Fortran, C++ 7.2-1 32-bit
                                  PGI C, Fortran, C++ 8.0-1 32-bit
                                  Intel(R) C Compiler for 32-bit
                                      applications, Versions 10.1, 11.0
                                  Intel(R) C++ Compiler for 32-bit
                                      applications, Version 10.1, 11.0
                                  Intel(R) Fortran Compiler for 32-bit
                                      applications, Version 10.1, 11.0
                                  Absoft 32-bit Fortran 95 10.0.7
                                  MPICH mpich2-1.3.1 compiled with
                                      gcc 4.1.2 and gfortran 4.1.2

    Linux 2.6.18-164.el5 #1 SMP   gcc 4.1.2 20080704
    x86_64 GNU/Linux              G95 (GCC 4.0.3 (g95 0.92!) Jun 24 2009)
    (amani)                           tested for both 32- and 64-bit binaries
                                  GNU Fortran (GCC) 4.1.2 20080704
                                      (Red Hat 4.1.2-46)
                                  Intel(R) C, C++, Fortran Compilers for 
                                      applications running on Intel(R) 64, 
                                      Versions 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

    Linux 2.6.16.54-0.2.5 #1      Intel(R) C++ Version 11.0.074
    SGI Altix SMP ia64            Intel(R) Fortran Itanium(R) Version 11.0.074
    (cobalt)                      SGI MPI 1.38

    SunOS 5.10 32- and 64-bit     Sun WorkShop 6 update 2 C 5.9 Patch 124867-09
    (linew)                       Sun WorkShop 6 update 2 Fortran 95 8.3 
                                  Patch 127000-07
                                  Sun WorkShop 6 update 2 C++ 5.9 
                                  Patch 124863-16 2009/09/15 

    Intel Xeon Linux 2.6.18-      gcc 3.4.6 20060404
    92.1.10.el5_lustre.1.6.6smp-  Intel(R) C++ Version 10.0.026
    perfctr #2 SMP                Intel(R) Fortran Compiler Version 10.0.026
    (abe)                         Open MPI 1.2.2
                                  MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2
                                  compiled with icc v10.0.026 and ifort 10.0.026

    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(1.7.7 native gcc(4.3.4) 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(1.7.7 native gcc(4.3.4) compiler and gfortran)

    Windows Vista                 Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
                                  Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)

    Windows Vista x64             Visual Studio 2008 w/ Intel Fortran 10.1 (project files)
                                  Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)

    Windows 7                     Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
                                  Visual Studio 2010 (cmake)

    Windows 7 x64                 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
                                  Visual Studio 2010 (cmake)

    MAC OS  10.5.6 (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
          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(4)     y     y     y
Windows XP x64                       n        y(4)   n(4)     y     y     y
Windows Vista                        n        y(4)   n(4)     y     y     y
Windows Vista x64                    n        y(4)   n(4)     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
AIX 6.1 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 2.6.9-42 i686 GNU (1)  W  y        y      y        y     y     y
RedHat EL5 2.6.18-128 i686 GNU (1)W  y        y(2)   y        y     y     y
RedHat EL5 2.6.18-128 i686 Intel  W  n        y      n        y     y     n
RedHat EL5 2.6.18-128 i686 PGI    W  n        y      n        y     y     n
SuSe Linux 2.6.16 x86_64 GNU (1)  W  y        y(3)   y        y     y     y
SuSe Linux 2.6.16 x86_64 Intel    W  n        y      n        y     y     n
SuSe Linux 2.6.16 x86_64 PGI      W  n        y      n        y     y     y
SuSe Linux 2.6.16 SGI Altix ia64  C  y        y      y        y     y     y
RedHat EL4 2.6.18 Xeon Lustre     C  y        y      y        y     y     n
SuSe Linux 2.4.21 ia64 Intel      C  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        
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        
Mac OS X 10.5                        y       n         y         n        
AIX 5.3 32- and 64-bit               n       n         n         n        
AIX 6.1 32- and 64-bit               n       n         n         n        
FreeBSD 6.3-STABLE 32&64 bit         y       n         y         y        
RedHat EL4 2.6.9-42 i686 GNU (1)  W  y       y         y         y        
RedHat EL5 2.6.18-128 i686 GNU (1)W  y       y(2)      y         y        
RedHat EL5  2.6.18-128 i686 Intel W  y       y         y         n        
RedHat EL5 2.6.18-128 i686 PGI    W  y       y         y         n        
SuSe Linux 2.6.16 x86_64 GNU (1)  W  y       y         y         y        
SuSe Linux 2.6.16 x86_64 Intel    W  y       y         y         n        
SuSe Linux 2.6.16 x86_64 PGI      W  y       y         y         n        
SuSe Linux 2.6.16 SGI Altix ia64  C  y                           n        
RedHat EL4 2.6.18 Xeon Lustre     C  y       y         y         n
SuSe Linux 2.4.21 ia64 Intel      C  y       y         y         n        

           (1) Fortran compiled with g95.
           (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)
    Compiler versions for each platform are listed in the preceding
    "Platforms Tested" table.


Known Problems
==============
* 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 filesystems.

  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 AIX --enable-shared does not quite work. It can produce shared library
  but there cannot be more than one shared libraries that interlinking with
  each other. That means only C-API without High-level can work. Not very
  usefule. We hope to have a solution in the next release. (AKC - 2010/10/15)

* 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 is not
  existing. This is due to the MPI_File_open() call failing if the amode 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 gcc v4.3 and v4.4, with production mode, if -O3 is used, H5Tinit.c
  would fail to compile. Actually bad H5Tinit.c is produced.  If -O (same
  as -O1) is used, H5Tinit.c compiled okay but test/dt_arith would fail.
  When -O0 (no optimizatio) is used, H5Tinit.c compilete okay and all
  tests passed. Therefore, -O0 is imposed for v4.3 and v4.4 of gcc.
  AKC - 2009/04/20

* 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

* 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. 

* 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