Page tree

The license could not be verified: License Certificate has expired!

VersionHDF5 1.8.4-patch1
Release Date2010-02-23


Release NotesRelease Notes

Release Notes:

HDF5 version 1.8.4-patch1 released on Tue Feb 23 11:31:09 CST 2010


This document describes the differences between HDF5-1.8.3 and 
HDF5 1.8.4, and contains information on the platforms tested and 
known problems in HDF5-1.8.4
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 1.8.4 source code, documentation, and additional materials
can be found on the HDF5 web page at:

The HDF5 1.8.4 release can be obtained from:

User documentation for 1.8.4 can be accessed directly at this location:

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:

All new and modified APIs are listed in detail in the "HDF5 Software Changes 
from Release to Release" document, in the section "Release 1.8.4 (current 
release) versus Release 1.8.3":

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


- New Features
- Support for New Platforms, Languages, and Compilers
- Bug Fixes since HDF5-1.8.4
- Bug Fixes since HDF5-1.8.3
- Platforms Tested
- Supported Configuration Features Summary
- Known Problems

New Features

    - Configuration suite now uses Automake 1.11 and Autoconf 2.64.
      MAM 2009/08/31.
    - Changed default Gnu fortran compiler from g95 to gfortran since
      gfortran is more likely installed with gcc now. -AKC 2009/07/19- 

    - The embedded library information is displayed by H5check_version() if a
      version mismatch is detected.  Also changed H5check_version() to
      suppress the warning message totally if $HDF5_DISABLE_VERSION_CHECK is 2
      or higher. (Old behavior treated 3 or higher the same as 1, that is
      print a warning and allows the program to continue. (AKC - 2009/9/28)
    - If a user does not care for the extra library information insert
      in the executables, he may turn it off by --disable-embedded-libinfo
      during configure. (AKC - 2009/9/15)

    Parallel Library
    - None
    - h5diff: h5diff treats two INFINITY values different. Fixed by checking
      (value==expect) before call ABS(...) at h5diff_array.c. This will make 
      that (INF==INF) is true (INF is treated as an number instead of NaN) 
      (PC -- 2009/07/28)
    - h5diff: add option "--use-system-epsilon" to print difference if 
      (|a-b| > EPSILON).
      Change default to use strict equality (PC -- 2009/09/12)

    High-Level APIs
    - None

    F90 API
     - Added H5Oopen_by_addr_f MSB - 9/14/09

    C++ API
    - None

Support for New Platforms, Languages, and Compilers
    - PathScale compilers are recognized and can build the HDF5 library
      properly. AKC - 2009/7/28 -

Bug Fixes since HDF5-1.8.4

    - Fixed a bug where fractal heap IDs for attributes and shared object
      header messages could be incorrectly encoded in the file for files
      created on big-endian platforms.  
      Please see if you 
      suspect you have a file with this problem.  QAK - 2010/02/23 - 1755

Bug Fixes since HDF5-1.8.3

    - Removed the following config files, as we no longer support them:
        config/dec-osf*, config/hpux11.00, config/irix5.x, 
        config/powerpc-ibm-aix4.x config/rs6000-ibm-aix5.x config/unicos*
      MAM - 2009/10/08
    - Modified configure and make process to properly preserve user's CFLAGS
      (and company) environment variables. Build will now properly use
      automake's AM_CFLAGS for any compiler flags set by the configure
      process. Configure will no longer modify CFLAGS directly, nor will 
      setting CFLAGS during make completely replace what configure has set up.
      MAM - 2009/10/08
    - Support for TFLOPS, config/intel-osf1, is removed since the TFLOPS
      machine has long retired. AKC - 2009/10/06.
    - Added $(EXEEXT) extension to H5detect when it's executed in the
      src/Makefile to generate H5Tinit.c so it works correctly on platforms 
      that require the full extension when running executables.
      MAM - 2009/10/01 - BZ #1613
    - Configure will now set FC and CXX to "no" when fortran and c++
      are not being compiled, respectively, so configure will not run
      some of the compiler tests for these languages when they are not 
      being used. MAM - 2009/10/01
    - The --enable-static-exec flag will now properly place the -static flag
      on the link line of all installed executables. This will force the 
      executable to link with static libraries over shared libraries, provided
      the static libraries are available. MAM - 2009/08/31 - BZ #1583
    - The PathScale compiler (v3.2) was mistaken as gcc v4.2.0 but it fails to
      recognize some gcc options. Fixed. (see bug 1301). AKC - 2009/7/28 -

    - Fixed a bug where writing and deleting many global heap objects (i.e.
      variable length data) would render the file unreadable.  Previously
      created files exhibiting this problem should now be readable.
      NAF - 2009/10/27 - 1483
    - Fixed error in library's internal caching mechanisms which could cause
      an assertion failure (and attendent core dump) when encountering an
      unusually formatted file.  (QAK - 2009/10/13)
    - Fixed incorrect return value for H5Pget_preserve. AKC - 2009/10/08 - 1628
    - Fixed an assertion failure that occurred when H5Ocopy was called on a
      dataset using a vlen inside a compound. NAF - 2009/10/02 - 1597
    - Fixed incorrect return value for H5Pget_filter_by_id1/2 in H5Ppublic.h.
      NAF - 2009/09/25 - 1620
    - Fixed a bug where properties weren't being compared with the registered
      compare callback. NAF - 2009/09/25 - 1555
    - Corrected problem where library would re-write the superblock in a file
      opened for R/W access, even when no changes were made to the file.
      (QAK - 2009/08/20, Bz#1473)
    - Fixed a bug where H5Pget_filter_by_id would succeed when called for a
      filter that wasn't present. NAF - 2009/06/25 - 1250
    - Fixed an issue with committed compound datatypes containing a vlen. Also
      fixed memory leaks involving committed datatypes. NAF - 2009/06/10 - 1593

    Parallel Library
    - None

    - h5dump/h5ls display buffer resize fixed in tools library.
      ADB - 2009/7/21 - 1520
    - perf_serial test added to Windows projects and check batch file. 
      ADB - 2009/06/11 -1504

    F90 API
    - Fixed bug in h5lget_info_by_idx_f by adding missing arguments, 
      consequently changing the API. New API is:

      SUBROUTINE h5lget_info_by_idx_f(loc_id, group_name, index_field, order, n, &
        link_type, f_corder_valid, corder, cset, address, val_size, hdferr, lapl_id)

        MSB - 2009/9/17 - 1652

    - Corrected the values for the H5L_flags FORTRAN constants: 
        MSB - 2009-09-17 - 1653

    - Added FORTRAN equivalent of C constant H5T_ORDER_NONE: H5T_ORDER_NONE_F
        MSB - 2009-9-24 - 1471

    C++ API
    - None

    High-Level APIs:
    - Fixed a bug where the H5TB API would forget the order of fields when added
      out of offset order. NAF - 2009/10/27 - 1582
    - H5DSis_attached failed to account for different platform types. Added a
      get native type call. ADB - 2009/9/29 - 1562

    Fortran High-Level APIs:
    - Lite: the h5ltread_dataset_string_f and h5ltget_attribute_string_f functions 
           had memory problems with the g95 fortran compiler. (PVN � 5/13/2009) 1522

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

    AIX 5.3                       xlc
    (LLNL Up)                     xlf 09.01.0000.0008
                                  mpxlf_r 09.01.0000.0008

    Cray XT3 (2.0.41)             cc (pgcc) 7.1-4
    (SNL 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 4.3.5 20091004
                                  g++ 4.3.5 20091004
                                  gfortran 4.3.5 20091004

    FreeBSD 6.3-STABLE amd64      gcc 3.4.6 [FreeBSD] 20060305
    (liberty)                     g++ 3.4.6 [FreeBSD] 20060305
                                  gcc 4.4.2 20091006
                                  g++ 4.4.2 20091006
                                  gfortran 4.4.2 20091006

    Linux 2.6.18-164.el5          gcc (GCC) 4.1.2 20080704
    #1 SMP i686 i686 i386         G95 (GCC 4.0.3 (g95 0.92!) Jun 24 2009)
    (jam)                         GNU Fortran (GCC) 4.1.2 20080704 
                                  (Red Hat 4.1.2-46)
                                  PGI C, Fortran, C++ 8.0-5 32-bit
                                  PGI C, Fortran, C++ 8.0-1 32-bit
                                  Intel(R) C Compiler for 32-bit
                                      applications, Versions 11.0, 11.1
                                  Intel(R) C++ Compiler for 32-bit
                                      applications, Version 11.0, 11.1
                                  Intel(R) Fortran Compiler for 32-bit
                                      applications, Version 11.0, 11.1
                                  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 2.6.18-164.el5 #1 SMP   gcc 4.1.2 20080704
    x86_64 GNU/Linux              G95 (GCC 4.0.3 (g95 0.92!) Jun 24 2009)
    (amani)                       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!)
                                  tested for both 32- and 64-bit binaries
                                  GNU Fortran (GCC) 4.1.2 20080704
                                  (Red Hat 4.1.2-46)

    Linux #1     Intel(R) C++ Version 10.1.017
    SGI Altix SMP ia64            Intel(R) Fortran Itanium(R) Version 10.1.017
    (cobalt)                      SGI MPI 1.38

    SunOS 5.10 32- and 64-bit     Sun C 5.9 SunOS_sparc Patch 124867-11 2009/04/30
    (linew)                       Sun Fortran 95 8.3 SunOS_sparc 
                                  Patch 127000-11 2009/10/06
                                  Sun C++ 5.9 SunOS_sparc 
                                  Patch 124863-16 2009/09/15 

    Intel Xeon Linux 2.6.18-      Intel(R) C++ Version 10.0.026
    92.1.10.el5_lustre.1.6.6smp-  Intel(R) Fortran Compiler Version 10.0.026
    perfctr #6 SMP                Open MPI 1.2.2
    (abe)                         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    gcc (GCC) 3.2.2
    #1 SMP ia64                   Intel(R) C++ Version 8.1.037
    (NCSA tg-login)               Intel(R) Fortran Compiler Version 8.1.033

    Linux 2.6.9-55.0.9.EL_lustre  Intel(R) C, C++, Fortran Compilers for 
    . #1 SMP           applications running on Intel(R) 64, 
    SMP x86_64 GNU/Linux          Versions 10.1.
    (SNL Thunderbird)             
    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 10.1.
    Windows XP                    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 w/ Intel Fortran 9.1

    Windows Vista x64             Visual Studio 2005 w/ Intel Fortran 9.1

    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
    OpenVMS V8.3                  HP C V7.3-009 on OpenVMS Alpha V8.3
                                  HP Fortran V8.0-1-104669-48GBT
                                  HP C++ V7.3-009 for OpenVMS Alpha V8.3

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        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 EL5 2.6.18-164 i686 GNU (1)W  y        y(2)   y        y     y     y
RedHat EL5 2.6.18-164 i686 Intel  W  n        y      n        y     y     n
RedHat EL5 2.6.18-164 i686 PGI    W  n        y      n        y     y     n
RedHat EL5 2.6.18-164 x86_64 GNU(1)W y        y(3)   y        y     y     y
RedHat EL5 2.6.18-164 x86_64 IntelW  n        y      n        y     y     n
RedHat EL5 2.6.18-164 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 2.0.62                      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         y        
Windows XP x64                       y       y(4)      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 6.3-STABLE 32&64 bit         y       y         y         y        
RedHat EL5 2.6.18-164 i686 GNU (1)W  y       y(2)      y         y        
RedHat EL5 2.6.18-164 i686 Intel  W  y       y         y         n        
RedHat EL5 2.6.18-164 i686 PGI    W  y       y         y         n        
RedHat EL5 2.6.18-164 x86_64 GNU(1)W y       y         y         y        
RedHat EL5 2.6.18-164 x86_64 IntelW  y       y         y         n        
RedHat EL5 2.6.18-164 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 2.0.62                      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 2005 or Cygwin
    Compiler versions for each platform are listed in the preceding
    "Platforms Tested" table.

Known Problems
* Parallel mode in AIX will fail some of the tests where
  it treats "exit(134) the same as if process 0 had received an abort signal.
  This is fixed and will be available in the next release. AKC - 2009/11/3

* 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
  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

* There is a known issue in which HDF5 will change the timestamp on a file 
  simply by opening it with read/write permissions, even if the file is not
  modified in any way. This is due to the way in which HDF5 manages the file 
  superblock. A fix is currently underway and should be included in the 1.8.4
  release of HDF5. MAM - 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/ and
  tools/h5copy/ 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/ =========
  TOOLTEST 1 -w80 -r -g tgroup.h5
  ======== Change to ===============================
  echo SKIP TOOLTEST 1 -w80 -r -g tgroup.h5

  ======== Original tools/h5copy/ =========
  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
  ======== 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
  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.

--- Last Modified: November 27, 2017 | 02:33 PM