HDF5 version 1.6.7 released on Thu Jan 31 21:09:10 CST 2008 ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.6.6 and HDF5-1.6.7 It contains information on the platforms tested and known problems in HDF5-1.6.7. For more details, check the HISTORY.txt file in the HDF5 source. HDF5 documentation can be found in the distributed release source code in the subdirectory doc/html/ or on the THG (The HDF Group) FTP server: ftp://ftp.hdfgroup.org/HDF5/docs/ Documentation for the current release in the HDF5 Release 1.6.x series is also on the HDF web site: http://hdfgroup.org/HDF5/doc1.6/ For more information, see the HDF5 home page: http://hdfgroup.org/products/hdf5/ If you have any questions or comments, please see the HDF Support page for a list of available resources: http://hdfgroup.org/services/support.html CONTENTS ======== - New Features - Support for New Platforms, Languages and Compilers - Bug Fixes since HDF5-1.6.6 - Documentation - Platforms Tested - Supported Configuration Features Summary - Known Problems New Features ============ Configuration: ------------------------- '--enable-stream-vfd' and '--disable-stream-vfd' are no longer valid configure options because the stream I/O driver has ben removed from the distribution. Source code distribution ======================== Library: -------- The stream I/O driver is not included with the HDF5 Library in this release. The source code files hdf5/src/H5FDstream.c and hdf5/src/H5FDstream.h and the driver ENUM value H5FD_STREAM have been removed. Parallel Library: ----------------- None Tools: ------ None F90 API: -------- None C++ API: -------- None Support for New Platforms, Languages and Compilers ================================================== No new platorms, languages, or compilers are supported in this release. Bug Fixes since HDF5-1.6.6 Release ================================== Library ------- - H5Iget_name could not be used with an object identifier returned by H5Rdereference; the function would not be able to determine a valid object name. It has been fixed. SLU - 2008/1/30 - Changed library's behavior for reading files that might have corrupted object header information from a previous (buggy) version of the library. By default, the library now rebuilds the correct object header information instead of issuing an error. Previous "strict" file format interpretation can be enabled with the "--enable-strict-format-checks" configure option. QAK - 2008/01/13 - Fixed bug in H5Epush() which was clearing the error stack before pushing new error value. QAK - 2007/08/23 - Fixed bug in H5Ewalk() which was not passing back the return value from error stack walking callback. QAK - 2007/08/23 Configuration ------------- None Performance ------------- None Tools ----- None Documentation ------------- None F90 API ------- None C++ API ------- None Documentation ============= HDF5 documentation can be found in the distributed release source code in the subdirectory doc/html/ (start with index.html) or on the THG (The HDF Group) FTP server: ftp://ftp.hdfgroup.org/HDF5/docs/ Online documentation for the current release in the HDF5 Release 1.6.x series can be found on the THG web site: http://hdfgroup.org/HDF5/doc1.6/ A listing of interface changes from release to release can be found in the document "HDF5 Software Changes from Release to Release": http://hdfgroup.org/HDF5/doc1.6/ADGuide/Changes.html Since the stream I/O driver is not included in this release, the functions H5Pset_fapl_stream and H5Pget_fapl_stream and the stream ENUM value H5FD_STREAM have been removed from the documentation. Platforms Tested ================ AIX 5.2 (32/64 bit) xlc 8.0.0.11 (datastar) xlC 8.0 xlf 10.01.0000.0002 FreeBSD 6.2 (32- and 64-bit) gcc and g++3.4.6 (duty and liberty) gcc and g++ 4.2.1 IRIX64 6.5 MIPSpro cc 7.4.4m (ucar mop1 64 & n32) F90 MIPSpro 7.4.4m (64 only) C++ MIPSpro cc 7.4.4m Linux 2.4.21-47.ELsmp #1 SMP gcc 3.2.3 i686 i386 GNU/Linux (osage) Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6 SMP i686 i386 G95 (GCC 4.0.3 (g95 0.91!) April 18 2007) (kagiso) PGI C, Fortran, C++ 7.0-7 32-bit Intel(R) C Compiler for 32-bit applications, Version 9.1 Intel(R) C++ Compiler for 32-bit applications, Version 9.1 Intel(R) Fortran Compiler for 32-bit applications, Version 9.1 Absoft 32-bit Fortran 95 10.0.4 MPICH mpich2-1.0.6p1 compiled with gcc 4.2.1 and G95 (GCC 4.0.3 (g95 0.91!) Linux 2.6.16.46-0.12-debug #1 Intel(R) C++ Version 10.0.025 SMP ia64 GNU/Linux Intel(R) Fortran Itanium(R) Version 10.0.025 (ucar hir1) Linux 2.6.16.46-0.14-smp #1 Intel(R) C++ for Intel(R) EM64T Ver. 9.1.037 SMP x86_64 GNU/Linux Intel(R) Fortran Intel(R) EM64T Ver. 9.1.031 (smirom) PGI C, Fortran, C++ Version 7.0-7 for 64-bit target on x86-64 tested for both 32- and 64-bit binaries Linux 2.6.5-7.287.3-sn2 #1 Intel(R) C++ Version 9.0 Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 9.0 (cobalt) SGI MPI SunOS 5.8 32- and 64-bit Sun WorkShop 6 update 2 C 5.3 (sol) Sun WorkShop 6 update 2 Fortran 95 6.2 Sun WorkShop 6 update 2 C++ 5.3 SunOS 5.10 32- and 64-bit Sun WorkShop 6 update 2 C 5.8 (linew) Sun WorkShop 6 update 2 Fortran 95 8.2 Sun WorkShop 6 update 2 C++ 5.8 Patch 121019-06 Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre (tungsten) Intel(R) C++ Version 9.0 Intel(R) Fortran Compiler Version 9.0 PGI C Version 6.0-5 PGI C++ Version 6.0-5 PGI Fortran Version 6.0-5 gcc (GCC) 3.2.2 (Red Hat Linux 3.2.2-5) Xeon Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp (abe) Intel(R) C++ Version 10.0 Intel(R) Fortran Compiler Version 10.0 Open MPI 1.2.2 IA-64 Linux 2.4.21-309.tg1 #1 SMP ia64 gcc (GCC) 3.2.2 (NCSA tg-login) Intel(R) C++ Version 8.1 Intel(R) Fortran Compiler Version 8.1 mpich-gm-1.2.6..14-intel-r2 Windows XP Visual Studio 6.0 Visual Studio .NET (with Intel Fortran 9.1) Visual Studio 2005 (with Intel Fortran 9.1) cygwin (gcc 3.4.4) Windows Vista Visual studio 2005 MAC OS X Intel Darwin 8.10.1 i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 g95 0.91 Supported Configuration Features Summary ======================================== Key: y = Tested and supported n = Not supported or not tested in this release C = Cluster W = Workstation ( ) = Footnote appears below second table Platform C F90 F90 C++ zlib SZIP parallel parallel Solaris2.8 32-bit n y n y n y Solaris2.8 64-bit n y n n y y Solaris2.10 32-bit n y n y y y Solaris2.10 64-bit n y n n y y IRIX64_6.5 32-bit n n n n y y IRIX64_6.5 64-bit n y n n y y WinXP Visual Studio 6.0 n n n y y y WinXP CYGWIN n n n y y y WinXP 2005 n y n y y y WinXP .Net n y n y y y WinVista 2005 n n n y y y Mac OS X 10.4.10 n y n y y y AIX-5.2 & 5.3 32- and 64-bit y y y y y y FreeBSD 6.2 32- and 64-bit n n n y y y RedHat Linux 2.4.21 W n n n n y n RedHat Linux 2.6.9-42 i686 GNU (1) W y y y y y y RedHat Linux 2.6.9-42 i686 Intel W n y n y y n RedHat Linux 2.6.9-42 i686 PGI W n y n y y n SuSE Linux 2.6.16 x86_64 GNU (1) W y y n 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 n RHEL 4 Linux 2.6.9 Xeon Lustre C n y n y y y RedHat Linux 2.4 Xeon Lustre C n y n y y n SuSE Linux 2.4 ia64 C y y y y y y SuSe Linux 2.6.5 SGI Altix ia64 n y n y y y Platform Shared static- Thread- libraries(4) exec safe Solaris2.8 32- and 64-bit y n y Solaris2.10 32- and 64-bit y n y IRIX64_6.5 32-bit y n y IRIX64_6.5 64-bit y n y WinXP Visual Studio 6.0 y n n WinXP CYGWIN y n n WinXP 2005 y n n WinXP .Net y n n WinVista 2005 y n n Mac OS X 10.4.10 y n n AIX-5.2 & 5.3 32- and 64-bit n n n FreeBSD 6.2 32- and 64-bit y n n RedHat Linux 2.4.21 W y n n SuSE Linux 2.6.9-42 i686 GNU (1) W y n y SuSE Linux 2.6.9-42 i686 Intel W y n n SuSE Linux 2.6.9-42 i686 PGI W n n n SuSE Linux 2.6.16 x86_64 GNU (1) W y n y SuSE Linux 2.6.16 x86_64 Intel W y n n SuSE Linux 2.6.16 x86_64 PGI W n n n RHEL 4 Linux 2.6.9 Xeon Lustre C y n n RedHat Linux 2.4 Xeon Lustre C y n n SuSE Linux 2.4 ia64 C y n n SuSe Linux 2.6.5 SGI Altix ia64 n n n Compiler versions for each platform are listed in the "Platforms Tested" table found elsewhere in this file (RELEASE.txt). Unless otherwise noted, compilers used are the system compilers. Footnotes: (1) Fortran compiled with g95. Known Problems ============== * We discovered two problems when running collective IO parallel HDF5 tests with chunking storage with the ChaMPIon MPI compiler on tungsten, a Linux cluster at NCSA. Under some complex selection cases, 1) MPI_Get_element returns the wrong value. 2) MPI_Type_struct also generates the wrong derived datatype and corrupt data may be generated. This only happens when turning on collective IO with chunking storage with some complex selections. We haven't found these problems on other MPI-IO compilers. If you encounter these problems, you may use Independent IO instead. To avoid this problem, change the following line in your code: H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); to H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT); KY - 2007/08/24 * QSC (an HP alpha-based OSF1 cluster) does not create h5pfc correctly. It does not include the -lmpi properly. This will be fixed in the next release. AKC - 2007/08/07. * On IRIX64 6.5 (UCAR SGI mop1), when testing HDF5 tools with an HDF5 shared library, especially for h5repacktst and h52gifgentst, the following (or a similar) error message may appear: "523648:lt-h5repacktst: rld: Fatal Error: Cannot Successfully map soname 'libh5test.so.1' under any of the filenames .......(bunch of directories) " And the testing will fail. We believe this is a libtool problem. One way to get rid of this is to add the paths of libh5test.so.1 and libh5.so.1 to the shared library path. For 32-bit: You may do this, under csh: setenv LD_LIBRARYN32_PATH .......(existing paths):[full path of HDF5 directory/test/.libs]:[full path of HDF5 directory/src/.libs] For 64-bit: setenv LD_LIBRARY64_PATH ......(existing paths):[full path of HDF5 directory/test/.libs]:[full path of HDF5 directory/src/.libs] NOTE: This problem ONLY affects the testing of the HDF5 library when you build from source. It won't affect any applications that would like to link with the HDF5 shared library since the shared library path needs to be set anyway. KY - 2007/8/2 * QSC (an HP alpha-based OSF1 cluster) failed the testpar/testphdf5 sub-test "calloc". All other tests passed. This indicates that a dataset using chunked storage created by serial HDF5 may not work properly with parallel HDF5. The calloc test can be skipped by running "prun ... testphdf5 -x calloc". AKC - 2007/7/12. * The Intel C Compiler for the Linux x86_64 platform (EM64T-based, v8.1) has an optimization error in the datatypes conversion code. Before running configure, edit the file config/intel-flags by changing the setting of PROD_CFLAGS from -O3 to -O0. Then run configure. AKC - 2005/11/10. * When testing parallel HDF5 with the C compiler version MIPSpro 7.4.3 on IRIX 6.5, set the environment variable MPI_TYPE_MAX to be a bigger number, for example 120000, in order to pass the complicated collective IO tests inside the parallel HDF5 library. This is not a problem inside the parallel HDF5 library. You can always set a bigger number on your system. KY - 2005/10/6 * A contiguous or chunked dataset created by a sequential version of HDF5 might not be able to be modified with a parallel version of the library. Use the H5Pset_alloc_time function with H5D_ALLOC_TIME_EARLY to set up the dataset creation property list to avoid the problem. EIP - 2005/09/09 * A dataset created or rewritten with the v1.6.3 library or after can't be read with the v1.6.2 library or before when Fletcher32 EDC (a filter) is enabled. There was a bug in the calculating code of the Fletcher32 checksum in the library before v1.6.3. The checksum value wasn't 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 is no longer the same as before on little-endian system. HDF5 library releases after 1.6.4 can still read datasets created or rewritten with an HDF5 library of v1.6.2 or before. SLU - 2005/7/8 * For version 6 (6.02 and 6.04) of the Portland Group compiler on AMD Opteron processor, there's a bug in the compiler for optimization(-O2). The library failed in several tests, all related to the multi driver. The problem has been reported to the vendor. * test/big fails sometimes with the message "Possible overlap with another region." The test selects regions randomly, and this error occurs when two regions overlap each other; it is a bug in the test and not in HDF5. Since the error is triggered by a random situation, it will usually disappear if the test is re-run. * Newer SGI MIPSpro compilers (version 7.4.x) support C99 features but have a "guard" statement in stdint.h that will #error and skip the rest of the header file if the C99 option is not used explicitly. Hardsetting $CC to c99 will resolve the problem. AKC - 2004/12/13 * 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 also fail with messages like "The socket name is already in use". HDF5 does not use sockets. This is due to problems of the poe command trying to set up the debug socket. Check 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. Ask your system administrator to clean them out. Lastly, request IBM to provide a means to run poe without the debug socket. * The h5dump tests may fail to match the expected output on some platforms (e.g. parallel jobs, Windows) where the error messages directed to "stderr" do not appear in the "right order" with output from stdout. This is not an error. * The --enable-static-exec configure flag fails to compile for Solaris platforms. This is due to the fact that not all of the system libraries on Solaris are available in a static format. The --enable-static-exec configure flag also fails to correctly compile on the IBM SP2 platform for the serial mode. The parallel mode works fine with this option. The --enable-static-exec configure flag also fails to correctly compile on the HPUX 11.00. It is suggested that you don't use this option on these platforms during configuration. * Use the --disable-shared configure flag if building with an Absoft Fortran compiler. * Information about building with PGI and Intel compilers is available in INSTALL file sections 5.7 and 5.8. * In LANL QSC, the new cc compiler has problems converting small values of long long (absolute values less than 1**-308) to double. This triggers the test/dtypes to report failure in the following test: Testing random sw long double -> double conversions If -ieee is used, the converted doubles spread over the range 0.0 to 10**-308. If -ieee is not used, the converted double values are mostly 0.0, but occasionally appear as 10**-308. This has been reported to the system staff. All other tests have passed. * On at least one system, SDSC DataStar, the scheduler (in this case LoadLeveler) sends job status updates to standard error when you run any executable that was compiled with the parallel compilers. This causes problems when running "make check" on parallel builds, as many of the tool tests function by saving the output from test runs, and comparing it to an exemplar. The best solution is to reconfigure the target system so it no longer inserts the extra text. However, this may not be practical. In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to the configure and build. This will cause "make check" to continue after detecting errors in the tool tests. However, in the case of SDSC DataStar, it also leaves you with some 150 "failed" tests to examine by hand. A second solution is to write a script to run serial tests and filter out the text added by the scheduler. A sample script used on SDSC DataStar is given below, but you will probably have to customize it for your installation. Observe that the basic idea is to insert the script as the first item on the command line which executes the test. The script then executes the test and filters out the offending text before passing it on. #!/bin/csh set STDOUT_FILE=~/bin/serial_filter.stdout set STDERR_FILE=~/bin/serial_filter.stderr rm -f $STDOUT_FILE $STDERR_FILE ($* > $STDOUT_FILE) >& $STDERR_FILE set RETURN_VALUE=$status cat $STDOUT_FILE tail +3 $STDERR_FILE exit $RETURN_VALUE You get the HDF5 make files and test scripts to execute your filter script by setting the environment variable "RUNSERIAL" to the full path of the script prior to running configure for parallel builds. Remember to "unsetenv RUNSERIAL" before running configure for a serial build. Note that the RUNSERIAL environment variable exists so that we can prefix serial runs as necessary on the target system. On DataStar, no prefix is necessary. However, on an MPICH system, the prefix might have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to get the serial tests to run at all. In such cases, you will have to include the regular prefix in your filter script. JM - 2004/9/15