HDF5 version 1.6.4-post6 released on Sun Jul 24 20:08:54 CDT 2005 ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.6.4 and HDF5-1.6.4-post*, and contains information on the platforms tested and known problems in HDF5-1.6.4. For more details check the HISTORY.txt file in the HDF5 source. The HDF5 documentation can be found on the NCSA ftp server (ftp.ncsa.uiuc.edu) in the directory: /HDF/HDF5/docs/ For more information look at the HDF5 home page at: http://hdf.ncsa.uiuc.edu/HDF5/ If you have any questions or comments, please send them to: hdfhelp@ncsa.uiuc.edu CONTENTS ======== - New Features - Support for new platforms and languages - Bug Fixes since HDF5-1.6.4 - Documentation - Platforms Tested - Supported Configuration Features Summary - Known Problems New Features ============ Source code distribution: ------------------------- Library: -------- - Added H5F_OBJ_LOCAL flag to H5Fget_obj_count() & H5Fget_obj_ids(), to allow querying for objects in file that were opened with a particular file ID, instead of all objects opened in file with any file ID. QAK - 2005/06/01 Parallel Library: ----------------- Tools: ------ F90 API: -------- - Added missing h5tget_member_class_f function EIP 2005/04/06 C++ API: -------- Support for new platforms, languages and compilers. ======================================= Configuration ------------- Bug Fixes since HDF5-1.6.4 release ================================== Library ------- - Fixed a bug with named datatypes where a copy of a named datatype used to create a dataset would accidentally use the original named datatype for the dataset's datatype. QAK - 2005/07/23 - Made H5Fget_name() be consistent and always return name of actual file the ID is in. (Instead of the name of the top file in a file mounting hierarchy). QAK - 2005/07/19 - Reworked internal file mounting semantics to hopefully eliminate mounting problems. We now require that files that are mounting together all have the same "file close degree". QAK - 2005/07/19 - More bug fixes on holding open files that are mounted and have IDs open. QAK - 2005/07/14 - More bug fixes on holding open files that are mounted and have IDs open. QAK - 2005/07/14 - Dataset sieve buffer cache was inadvertantly disabled - re-enable it. QAK - 2005/07/08 - Don't unmount child files until the parent file actually closes. (Previously, if an object is holding open a file, the child files would get unmounted too early). QAK - 2005/07/05 - Fixed bug where unmounted files could cause the library to go into an infinite loop when shutting down. QAK - 2005/06/30 - Fixed bug with hyperslab selections that use selection offsets and operate on chunked datasets going into infinite loop or dumping core. QAK - 2005/06/17 - Corrected memory leak and possible corruption when opening a group. QAK - 2005/06/17 - Added check for opaque datatype tags being too long (check against H5T_OPAQUE_TAG_MAX, currently set to 256). QAK - 2005/06/14 - Fixed various errors in maintaining names for open objects in the face of unusual mount & unmount operations. QAK - 2005/06/08 - "SEMI" and "STRONG" file close degree settings now apply only to the particular file ID being closed, instead of operating on all open file IDs for a given file. QAK - 2005/06/01 - Fixed error in opening object in group that was opened in mounted file which has been unmounted. QAK - 2005/03/17 Configuration ------------- Performance ------------- - Optimized I/O for enumerated datatypes that are a superset of source enumerated datatype. QAK - 2005/03/19 Tools ----- Documentation ------------- F90 API ------- - h5pget_driver_f was returning information that could not be interpreted by fortran application program; fixed. EIP - 2005/04/10 C++ API ------- Documentation ============= Platforms Tested ================ AIX 5.1 (32 and 64-bit) xlc 6.0.0.6 xlf 8.1.1.3 xlC 6.0.0.6 mpcc_r 6.0.0.6 mpxlf_r 8.1.1.3 xlc 5.0.2.5 xlf 7.1.1.2 xlC 5.0.2.5 mpcc_r 5.0.2.5 mpxlf_r 7.1.1.2 AIX 5.2 (32/64 bit) xlc 6.0.0.8 xlC 6.0.0.9 xlf 8.1.1.7 mpcc_r 6.0.0.8 mpxlf_r 8.1.1.7 AIX 5.2 (32/64 bit, LLNL frost) xlc 6.0.0.8 xlC 6.0.0.8 xlf 8.1.1.7 mpcc_r 6.0.0.8 mpxlf_r 8.1.1.7 Cray T90 sn7001 10.0.0md Cray Standard C Version 6.4.0.3 Cray Fortran Version 3.4.0.0 Cray SV1 sn9617 10.0.1.2 Cray Standard C Version 6.6.0.3.6 Cray Fortran Version 3.6.0.3.1 FreeBSD 4.9 gcc 2.95.4 g++ 2.95.4 gcc 3.2.3, 3.3.6, 3.4.4, 4.0.0 HP-UX B.11.00 HP C HP92453-01 A.11.01.20 HP F90 v2.4 HP ANSI C++ B3910B A.03.13 MPIch 1.2.4 IRIX64 6.5 (tesla -64) MIPSpro cc 7.4.2m F90 MIPSpro 7.4.2m C++ MIPSpro cc 7.4.2m IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1.3m F90 MIPSpro 7.3.1.3m (64 only) C++ MIPSpro cc 7.3.1.3m mpt 1.6 Linux 2.4.20-28.7 gcc 2.96 (eirene, verbena) gcc 3.3.2 PGI compilers (pgcc, pgf90, pgCC) version 5.2-1 Absoft Fortran compiler v9.0 Intel(R) C++ 32-bit Version 8.1 Intel(R) Fortran 32-bit Version 8.1 MPIch 1.2.6 Linux 2.4.21-268-smp x86_64 gcc 3.3.1 (SuSE Linux, AMD) (mir) PGI 5.2-1 C and F90 (with k3-32) Intel(R) C++ 32-bit Version 8.1 Intel(R) Fortran 32-bit Version 8.1 Linux 2.4.21-sgi303r2 Altix SMP ia64 Intel(R) C++ Version 8.1 (cobalt) Intel(R) Fortran Itanium(R) Version 8.1 SGI MPI OSF1 V5.1 (QSC) Compaq C V6.5-011 HP Fortran V5.5A-3548 Compaq C++ V6.5-036 MPIX200_64_r13.4 OSF1 V5.1 (PSC) Compaq C V6.5-303 HP Fortran V5.5A-3548 Compaq C++ V6.5-040 MPIX200_64_r13.4 FORTRAN 90 2.0 Patch 107356-04 SunOS 5.8 32,46 Sun WorkShop 6 update 2 C 5.3 (Solaris 2.8) Sun WorkShop 6 update 2 Fortran 90 Sun WorkShop 6 update 2 C++ 5.3 SunOS 5.9 32,64 Sun C 5.6 2004/07/15 (Solaris 2.9) Sun Fortran 95 8.0 2004/07/15 Sun C++ 5.6 2004/07/15 TFLOPS r1.0.4 v4.5.2 i386 pgcc Rel 3.1-4i with mpich-1.2.4 with local modifications Xeon Linux 2.4.20-31.9smp_perfctr_lustre (tungsten) Intel(R) C++ Version 8.0 Intel(R) Fortran Compiler Version 8.0 IA-64 Linux 2.4.21.SuSE_128.bef1 ia64 (NCSA tg-login) Intel(R) C++ Version 8.0 Intel(R) Fortran Compiler Version 8.0 mpich-gm-1.2.5..intel Windows XP MSVC++.NET MSVC++ 6.0 Compaq Visual Fortran 6.6C Intel 8.1 C++ MAC OS X Darwin 7.5 gcc and g++ Apple Computer, Inc. GCC version 1175, based on gcc version 3.3.2 IBM XL Fortran version 8.1 Absoft Fortran compiler v8.2 Supported Configuration Features Summary ======================================== Key: y = tested and supported n = not supported or not tested in this release x = not working in this release dna = does not apply ( ) = footnote appears below second table Platform C F90 F90 C++ zlib SZIP parallel parallel Solaris2.8 64-bit y y y(1) y y y Solaris2.8 32-bit y y y(1) y y y Solaris2.9 64-bit y(1) y y(1) y y y Solaris2.9 32-bit y(1) y y(1) y y y IRIX64_6.5 64-bit y(2) y y y y y IRIX64_6.5 32-bit y(2) n n n y y HPUX11.00 y(1) y y y y y OSF1 v5.1 y y y y y y T90 IEEE n y n n y n SV1 y(5) y y(5) n y n TFLOPS y(1) n n n y n AIX-5.1 & 5.2 32-bit y y y y y y AIX-5.1 & 5.2 64-bit y y y y y y WinXP Visual Studio 6.0 n y(9) n y y y WinXP .Net n n n y(8) y y Mac OS X 10.3 n y(10) n y y y FreeBSD 4.9 y(1) n n y y y RedHat 7.3 W (3) y(1) y(11) n y y y RedHat 7.3 W Intel (3) n y n y y y RedHat 7.3 W PGI (3) n y n y y y SuSe x86_64 gcc (3,13) n y(12) n y y y SuSe x86_64 icc (3,13) n y(14) n y y y Linux 2.4 Xeon C Lustre Intel (3,6) n y n y y y Linux 2.4 SuSE ia64 C Intel (3,7) y y y y y y Linux 2.4 SGI Altix ia64 Intel (3) y y y y y y Platform Shared static- Thread- STREAM- libraries(4) exec safe VFD Solaris2.8 64-bit y x y y Solaris2.8 32-bit y x y y Solaris2.9 64-bit y x y y Solaris2.9 32-bit y x y y IRIX64_6.5 64-bit y y y y IRIX64_6.5 32-bit y y y y HPUX11.00 y x n y OSF1 v5.1 y y n y T90 IEEE n y n y SV1 n y n y TFLOPS n y n n AIX-5.1 & 5.2 32-bit n y n y AIX-5.1 & 5.2 64-bit n y n y WinXP Visual Studio 6.0 y y n n WinXP .Net y y n n Mac OS X 10.3 y y n y FreeBSD 4.9 y y y y RedHat 7.3 W (3) y y y y RedHat 7.3 W Intel (3) n y n y RedHat 7.3 W PGI (3) n y n y SuSe x86_64 gcc (3,13) n y n y SuSe x86_64 icc (3,13) y y(15) n y Linux 2.4 Xeon C Lustre Intel (3,6) y y n y Linux 2.4 SuSE ia64 C Intel (3,7) y y n n Linux 2.4 SGI Altix ia64 Intel (3) y y n y 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) Using mpich 1.2.6 (2) Using mpt and mpich 1.2.6. (3) Linux 2.4 with GNU, Intel, and PGI compilers, as indicated. W or C indicates workstation or cluster, respectively. (4) Shared libraries are provided only for the C library, except on Windows where they are provided for C and C++. (5) Using mpt. (6) Linux 2.4.20-31.9. Xeon cluster with smp_perfctr_lustre and Intel compilers (7) Linux 2.4.21, SuSE_128.befl. Ia64 cluster with Intel compilers (8) Intel 8.1 (9) Compaq Visual Fortran 6.6C (10) IBM XLF and Absoft (11) PGI, Absoft. No shared libraries with Absoft; use '--disable-shared'. (12) PGI and Intel compilers for both C and Fortran (13) AMD Opteron x86_64 (14) ifort (15) Yes with C and Fortran, but not with C++ FMB/EIP - 2005/03/15 Known Problems ============== * The 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(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. The library release after 1.6.4 can still read the dataset created or rewritten with the library of v1.6.2 or before. SLU - 2005/7/8 * For the version 6(6.02 and 6.04) of Portland Group compiler on AMD Opteron processor, there's a bug in the compiler for optimization(-O2). The library failed in several tests but all related to 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 an 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. * Cray SV1 fails to correctly convert between floating-point and "long double" for software conversion. Problem is being investigated. SLU - 2005/03/04 * Newer SGI MIPSpro compilers (version 7.4.x) support C99 features but it has a "guard" statement in stdint.h that will #error and skip the rest of the header file if C99 option is not used explicitly. Hardset $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 fail with messages like "The socket name is already in use". HDF5 does not use sockets (except for stream-VFD). This is due to problems of the poe command trying to set up the debug socket. Check if there are many old /tmp/s.pedb.* 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 mean to run poe without the debug socket. * There are two h5dump xml tests(h5dump --xml thlink.h5 and h5dump --xml tmany.h5) failed on windows xp with .NET for debug and debug dll. Release and Release dll work fine. * 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 stream-vfd test uses ip port 10007 for testing. If another application is already using that port address, the test will hang indefinitely and has to be terminated by the kill command. To try the test again, change the port address in test/stream_test.c to one not being used in the host. * 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 IBM SP2 platform for the serial mode. The parallel mode works fine with this option. It is suggested that you don't use this option on these platforms during configuration. * The Stream VFD was not tested yet under Windows. It is not supported in the TFLOPS machine. * The ./dsets tests failed in the TFLOPS machine if the test program, dsets.c, is compiled with the -O option. The hdf5 library still works correctly with the -O option. The test program works fine if it is compiled with -O1 or -O0. Only -O (same as -O2) causes the test program to fail. * Certain platforms give false negatives when testing h5ls: - Cray T90IEEE give errors during testing when displaying some floating-point values. These are benign differences due to the different precision in the values displayed. h5ls appears to be dumping floating-point numbers correctly. * Before building HDF5 F90 Library from source on Crays replace H5Aff.f90, H5Dff.f90 and H5Pff.f90 files in the fortran/src subdirectory in the top level directory with the Cray-specific files from the site: ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/src/patches/ * On some platforms that use Intel and Absoft compilers to build HDF5 fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90 and fflush2.f90 complaining about exit subroutine. Comment out the line IF (total_error .ne. 0) CALL exit (total_error) * Use --disable-shared configure flag if building with 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 Testing random sw long double -> double conversions If -ieee is used, the converted doubles spread over the range 0.0 to 1**-308. If -ieee is not used, the converted double values are mostly 0.0 but occasionally as 1**-308. This has been reported to the system staff. All other tests have passed. * The C++ library's tests fails when compiling with PGI C++ compiler. The workaround until the problem is correctly handled is to use the flag "--instantiate=local" prior to the configure and build steps, as: setenv CXX "pgCC --instantiate=local" for pgCC 5.02 and higher setenv CXX "pgCC -tlocal" for others * Fortran release DLL randomly failed with compaq visual fortran 6.6c on windows. * Fortran DLL built with Intel 8.1 in .NET environment crushed the compiler, To build Fortran Static library with Intel 8.1 in .NET environment needs manually setting the project file, please contact to hdfhelp@ncsa.uiuc.edu if you need to build fortran static library with Intel 8.1 with .NET environment. * 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 HDF 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 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.