path: root/release_docs/RELEASE.txt

HDF5 version 1.8.6-pre1 currently under development
================================================================================

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

This document describes the differences between HDF5-1.8.5 and 
HDF5 1.8.6-*, and contains information on the platforms tested and 
known problems in HDF5-1.8.6-*. 
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 1.8.6 source code, documentation, and additional materials
can be found on the HDF5 web page at:

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

The HDF5 1.8.6 release can be obtained from:

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

User documentation for 1.8.6 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 1.8.6 (current 
release) versus Release 1.8.5":

     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 HDF5-1.8.5
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems


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

    Configuration
    -------------
    - Changed configure default setting to --disable-production (was
      --enable-production). This affects all unoffical releases such as
      snapshot releases. It will be set to --enable-production for all
      official releases.  (AKC  - 2010/05/28)

    Library
    -------
    - Added support for threadsafety on windows using the windows threads
      library. Use the HDF5_ENABLE_THREADSAFE option in CMake while on a 
      windows platform to enable this functionality. This is supported on 
      Windows Vista and newer Windows operating systems. (MAM - 2010/09/10)
    - H5Tset_order and H5Tget_order now support all data types.  A new byte 
      order H5T_ORDER_MIXED has been added specifically for compound datatype
      and its derived type.  Please see bug #1934. (SLU - 2010/8/23)
    - Improved performance of metadata I/O by changing the default algorithm
      to perform I/O from all processes (instead of just process 0) when using
      parallel I/O drivers. (QAK - 2010/07/19)
    - Improved performance of I/O on datasets with the same shape, but
      different rank. (QAK - 2010/07/19)
    - Improved performance of the chunk cache by avoiding unnecessary b-tree
      lookups of chunks already in cache. (NAF - 2010/06/15) 

    Parallel Library
    ----------------
    - None
 
    Tools
    -----
    - h5diff: Add a new flag --exclude-path. Specified path to an object will
              be excluded from comparing the two files or two groups. If group
              is specified all the member objects will be excluded.  
              (JKM - 2010/09/16).
    - h5ls: Add new flag --no-dangling-links. (refer to --help for details)
      (JKM - 2010/06/15)
    - h5ls: Add new flag --follow-symlinks. (refer to --help for details)
      (JKM - 2010/05/25)

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

    F90 API
    -------
     - None

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


Support for New Platforms, Languages, and Compilers
===================================================
    - Sun C and C++ 5.10 and Sun Fortran 95 8.4.


Bug Fixes since HDF5-1.8.5
==========================

    Configuration
    -------------
    - Removed recognition of the parallel compilers of LAM(hcc) and
      ChMPIon(cmpicc) since we have no access to these two MPI implementations
      and cannot verify their correctness. (AKC - 2010/07/14 - Bug 1921)
    - PHDF5 changed to use "mpiexec", instead of mpirun, as the default MPI
      applications startup command as defined in the MPI-2 definition, section
      4.1. (AKC - 2010/06/11 - Bug 1921)

    Library
    -------
    - H5Eset_auto causes a seg fault when an application uses -DH5_USE_16_API
      to compile with the library. The problem is fixed and the behavior
      of H5Eget_auto is modified (Bug #1707). (SLU - 2010/9/21)
    - Modified library to always cache symbol table information.  Libraries
      version 1.6.3 have a bug which causes them to require this information for
      some operations. (NAF - 2010/09/21 - 1864)
    - Fixed a bug where the library could generate an assertion/core dump when
      a file that had been created with H5Pset_libver_bounds(fapl,
      H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) but didn't have a superblock
      extension was later reopened.  (QAK - 2010/09/16 - Bug 1968)
    - Fixed a bug that could occur when getting information for a new-style
      group that was previously opened through a file handle that was later
      closed. (NAF - 2010/09/15)
    - Added define check in H5public.h if stdint.h is supported by the C++
      compiler. This define is only available on Windows with VS2010 and using
      CMake to build the library. (ADB - 2010/09/13 - Bug 1938)
    - When a mandatory filter failed to write data chunks, the dataset
      couldn't close (bug 1260).  The fix releases all resources and closes
      the dataset but returns a failure. (SLU - 2010/09/08) 
    - H5Eset_current_stack now also closes the error stack to be set as the
      default.  This is to avoid a potential problem (Bug 1799). 
      (SLU - 2010/09/07)
    - Corrected situation where 1-D chunked dataset could get created by an
      application without calling H5Pset_chunk().  H5Pset_chunk is now
      required for creating all chunked datasets.  (QAK - 2010/09/02)
    - Fixed many memory issues that valgrind exposed.  (QAK - 2010/08/24)
    - Fixed the bug in the filter's public CAN_APPLY function.  The return
      value should be htri_t not herr_t (Bug #1239). (SLU - 2010/08/05)
    - Fixed a bug in the direct I/O driver that could render files with certain
      kinds of unaligned data unreadable or corrupt them. (NAF - 2010/07/28)
    - valgrind reported an error of copying data to itself when a new attribute 
      is written (Bug #1956).  I fixed it by taking out the memcpy step in the
      attribute code. (SLU - 2010/07/28)
    - Corrected various issues in the MPI datatype creation code which could
      cause resource leaks or incorrect behavior (and may improve the
      performance as well).  (QAK - 2010/07/19)
    - Fixed a bug that could cause file corruption when using non-default sizes
      of addresses and/or lengths.  This bug could also cause uncorrupted files
      with this property to be unreadable.  This bug was introduced in 1.8.5.
      (NAF - 2010/07/16 - Bug 1951)

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

    Tools
    -----
    - Fixed to compare member objects and groups recursively when two 
      files or groups are specified to be compared. Bug#1975
      (JKM 2010/9/16)
    - Make h5repack be able to convert a layout to COMPACT for small size
      dataset as default.  bug#1896 (JKM 2010/09/15)
    - Change h5ls not to manipulate special characters in object name or 
      attribute name for smart display. (JKM 2010/06/28 - Bug 1784)


    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 9.1.0.9, 10.1.0.9, 11.1.0.7
                                  mpcc_r 7.0.0.9
                                  mpxlf_r 09.01.0000.0008

    AIX 6.1                       xlc 10.1.0.6
    (NCSA BP)                     xlC 10.1.0.6
                                  xlf 12.1.0.7

    Cray XT3 (2.1.56)             cc (pgcc) 10.0-0
    (SNL red storm)               ftn (pgf90) 10.0-0
                                  CC (pgCC) 10.0-0

    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 mpich2-1.0.8 compiled with
                                  gcc 4.1.2 and G95  (GCC 4.0.3 (g95 0.92!)

    Linux 2.6.9-42.0.10.ELsmp #1  gcc (GCC) 3.4.6
    SMP i686 i686 i386            G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009)
    (kagiso)                      MPICH mpich2-1.0.8 compiled with
                                  gcc 3.4.6 and G95  (GCC 4.0.3 (g95 0.92!)

    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
                                  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
                                  gcc 4.1.2 and G95  (GCC 4.0.3 (g95 0.92!)
                                  MPICH mpich2-1.0.8 compiled with
                                  gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!)
                                  GNU Fortran (GCC) 4.1.2 20080704
                                  (Red Hat 4.1.2-46)


    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

    Linux 2.6.18-76chaos #1 SMP   Intel(R) C, C++, Fortran Compilers for 
    SMP x86_64 GNU/Linux          applications running on Intel(R) 64, 
    (SNL Glory)                   Versions 11.1.
    
    Windows XP                    Visual Studio 2008 w/ Intel Fortran 11.1
                                  Cygwin(1.7.5 native gcc(4.3.4) compiler and gfortran)

    Windows XP x64                Visual Studio 2008 w/ Intel Fortran 11.1

    Windows Vista                 Visual Studio 2008 w/ Intel Fortran 11.1

    Windows Vista x64             Visual Studio 2008 w/ Intel Fortran 11.1

    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
Cray XT3 2.1.56                      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         n        
Windows Vista x64                    y       y(4)      y         n        
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        
Cray XT3 2.1.56                      n       n         n         n

           (1) Fortran compiled with g95.
           (2) With PGI and Absoft compilers.
           (3) With PGI compiler for Fortran.
           (4) Using Visual Studio 2008 (Cygwin shared libraries are not supported)
    Compiler versions for each platform are listed in the preceding
    "Platforms Tested" table.


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
  
* Some tests in tools/h5repack may fail in AIX systems when -q32 mode is used.
  The error is due to insufficient memory requested. Request a large amount
  of runtime memory by setting the following environment variable for more
  memory.
     LDR_CNTRL=MAXDATA=0x20000000@DSA
  AKC - 2009/10/31

* 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