HDF5 version 1.8.0 released on Tue Feb 12 20:41:19 CST 2008 ================================================================================ INTRODUCTION ============ This document describes the differences between the HDF5-1.6.x release series and HDF5 1.8.0, and contains information on the platforms tested and known problems in HDF5-1.8.0. For more details, see the HISTORY-1_0-1_8_0_rc3.txt file in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.0 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.0 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.0 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in 1.8.0, 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 1.8.0 (current release) versus Release 1.6.x": 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 - Removed Feature - Support for new platforms and languages - Bug Fixes since HDF5-1.6.0 - Platforms Tested - Supported Configuration Features Summary - Known Problems New Features ============ HDF5 Release 1.8.0 is a major release with many changes and new features. New format and interface features discussed in the "What's New in HDF5 1.8.0" document include the following: Enhanced group object management Enhanced attribute management and more efficient meta data handling Expanded datatype features Creation order tracking and indexing Improved meta data caching and cache control UTF-8 encoding New I/O filters: n-bit and scale+offset compression New link (H5L) and object (H5O) interfaces and features External and user-defined links New high-level APIs: HDF5 Packet Table (H5PT) and HDF5 Dimension Scale (H5DS) C++ and Fortran interfaces for older high-level APIs: H5Lite (H5LT), H5Image (H5IM), and H5Table (H5TB) New and improved tools And more... http://hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html New APIs associated with these features, other interface changes (e.g., ENUM and struct definitions), and new library configuration flags are listed in the "Release 1.8.0 (current release) versus Release 1.6.x" section of "HDF5 Software Changes from Release to Release." http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html Compatibility ------------- Many HDF5 users and user communities have existing applications that they may wish to port to Release 1.8.0. Alternatively, some users may wish to take advantage of Release 1.8.0's improved performance without having to port such applications. To facilitate managing application compatibility and porting applications from release to release, the HDF Team has implemented the following features: Individually-configurable macros that selectively map common interface names to the old and new interfaces Library configuration options to configure the macro mappings Two related documents accompany this release: "API Compatibility Macros in HDF5" discusses the specifics of the new individually-configurable macros and library configuration options. http://hdfgroup.org/HDF5/doc/RM/APICompatMacros.html "New Features in HDF5 Release 1.8.0 and Backward/Forward Format Compatibility Issues" discusses each new feature with regard to its impact on format compatibility. http://hdfgroup.org/HDF5/doc/ADGuide/CompatFormat180.html Referenced documents -------------------- http://hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html "What's New in HDF5 1.8.0" http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html The "Release 1.8.0 (current release) versus Release 1.6.x " section in "HDF5 Software Changes from Release to Release" http://hdfgroup.org/HDF5/doc/RM/APICompatMacros.html "API Compatibility Macros in HDF5" http://hdfgroup.org/HDF5/doc/ADGuide/CompatFormat180.html "New Features in HDF5 Release 1.8.0 and Backward/Forward Format Compatibility Issues" Removed Feature =============== The stream virtual file driver (H5FD_STREAM) have been removed in this release. This affects the functions H5Pset_fapl_stream and H5Pget_fapl_stream and the constant H5FD_STREAM. This virtual file driver will be available at http://hdf5-addons.origo.ethz.ch/. Note that at the time of this release, the transition is still in progress; the necessary integration tools may not be available when HDF5 Release 1.8.0 first comes out. Support for New Platforms, Languages, and Compilers =================================================== - Support for Open VMS 7.3 was added. Bug Fixes since HDF5-1.6.0 ========================== This release contains numerous bug fixes. For details, see the "Changes from 1.6.0 to 1.8.0-rc3" section of the HISTORY.txt file for this release. Platforms Tested ================ The following platforms and compilers have been tested for for this release. AIX 5.2 (32/64 bit) xlc 8.0.0.11 xlC 8.0 xlf 10.01.0000.0 mpcc_r 6.0.0.8 mpxlf_r 8.1.1.7 FreeBSD 6.2-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 (duty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.2.1 20080123 g++ 4.2.1 20080123 gfortran 4.2.1 20070620 FreeBSD 6.2-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 (liberty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.2.1 20080123 g++ 4.2.1 20080123 gfortran 4.2.1 20080123 IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m F90 MIPSpro 7.4.4m C++ MIPSpro cc 7.4.4m Linux 2.6.9 (RHEL4) Intel 10.0 compilers (abe.ncsa.uiuc.edu) Linux 2.4.21-47 gcc 3.2.3 20030502 (osage) Linux 2.6.9-42.0.10 gcc 3.4.6 20060404 (kagiso) PGI 7.0-7 (pgcc, pgf90, pgCC) Intel 9.1 (icc, ifort, icpc) Linux 2.6.16.27 x86_64 AMD gcc 4.1.0 (SuSE Linux), g++ 4.1.0, (smirom) g95 (GCC 4.0.3) PGI 6.2-5 (pgcc, pgf90, pgCC) Intel 9.1 (icc, iort, icpc) Linux 2.6.5-7.252.1-rtgfx #1 Intel(R) C++ Version 9.0 SMP ia64 Intel(R) Fortran Itanium(R) Version 9.0 (cobalt) SGI MPI SunOS 5.8 32,46 Sun WorkShop 6 update 2 C 5.3 (Solaris 2.8) Sun WorkShop 6 update 2 Fortran 95 6.2 Sun WorkShop 6 update 2 C++ 5.3 SunOS 5.10 cc: Sun C 5.8 (linew) f90: Sun Fortran 95 8.2 CC: Sun C++ 5.8 Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre (tungsten) gcc 3.2.2 20030222 Intel(R) C++ Version 9.0 Intel(R) Fortran Compiler Version 9.0 IA-64 Linux 2.4.21.SuSE_292.til1 ia64 (NCSA tg-login) gcc 3.2.2 Intel(R) C++ Version 8.1 Intel(R) Fortran Compiler Version 8.1 mpich-gm-1.2.5..10-intel-r2 Windows XP Visual Studio .NET Visual Studio 2005 w/ Intel Fortran 9.1 Cygwin(native gcc compiler and g95) MinGW(native gcc compiler and g95) Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 Windows Vista Visual Studio 2005 MAC OS 10.4 (Intel) gcc i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 G95 (GCC 4.0.3 (g95 0.91!) Nov 21 2006) Alpha Open VMS 7.3 Compaq C V6.5-001-48BCD HP Fortran V7.6-3276 Compaq C++ V6.5-004 Supported Configuration Features Summary ======================================== In the tables below 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 = testing incomplete on this feature or platform Platform C F90 F90 C++ zlib SZIP parallel parallel SunOS5.8 64-bit n y n y y y SunOS5.8 32-bit n y n y y y SunOS5.10 64-bit y(1) y n y y y SunOS5.10 32-bit y(1) y n y y y IRIX64_6.5 64-bit n y y y y y IRIX64_6.5 32-bit n n n n y y AIX-5.2 32-bit y y y y y y AIX-5.2 64-bit y y y y y y Windows XP n y(15) n(15) y y y Windows XP x64 n y(15) n(15) y y y Windows Vista n n n y y y Mac OS X 10.4 PowerPC n n Mac OS X 10.4 Intel n y n y y y FreeBSD 4.11 n n n y y y RedHat EL3 W (3) y(1a) y(10) y(1a) y y y RedHat EL3 W Intel (3) n y n y y n RedHat EL3 W PGI (3) n y n y y n SuSe x86_64 gcc (3,12) y(1a) y(11) n y y y SuSe x86_64 Int (3,12) n y(13) n y y n SuSe x86_64 PGI (3,12) n y(8) n y y y Linux 2.4 Xeon C Lustre Intel (3,6) n y n y y n Linux 2.6 SuSE ia64 C Intel (3,7) y y y y y n Linux 2.6 SGI Altix ia64 Intel (3) y y y y y y Alpha OpenVMS 7.3.2 n y n y n n Platform Shared Shared Shared static- Thread- C libs F90 libs C++ libs exec safe Solaris2.8 64-bit y y y x y Solaris2.8 32-bit y y y x y Solaris2.10 64-bit y x y Solaris2.10 32-bit y x y IRIX64_6.5 64-bit y y n y y IRIX64_6.5 32-bit y dna y y y AIX-5.2 & 5.3 32-bit n n n y n AIX-5.2 & 5.3 64-bit n n n y n Windows XP y y(15) y y y Windows XP x64 y y(15) y y y Windows Vista y n n y y Mac OS X 10.3 y y n FreeBSD 4.11 y n y y y RedHat EL3 W (3) y y(10) y y y RedHat EL3 W Intel (3) y y y y n RedHat EL3 W PGI (3) y y y y n SuSe x86_64 W GNU (3,12) y y y y y SuSe x86_64 W Int (3,12) y y y y(14) n SuSe x86_64 W PGI (3,12) y y y y(14) n Linux 2.4 Xeon C Lustre Intel (6) y y y y n Linux 2.4 SuSE ia64 C Intel (7) y y y y n Linux 2.4 SGI Altix ia64 Intel y y n Alpha OpenVMS 7.3.2 n n n y n Notes: (1) Using mpich 1.2.6. (1a) Using mpich2 1.0.6. (2) Using mpt and mpich 1.2.6. (3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated. W or C indicates workstation or cluster, respectively. (6) Linux 2.4.21-32.0.1. Xeon cluster with ELsmp_perfctr_lustre and Intel compilers (7) Linux 2.4.21, SuSE_292.till. Ia64 cluster with Intel compilers (8) pgf90 (9) With Compaq Visual Fortran 6.6c compiler. (10) With PGI and Absoft compilers. (11) PGI and Intel compilers for both C and Fortran (12) AMD Opteron x86_64 (13) ifort (14) Yes with C and Fortran, but not with C++ (15) Using Visual Studio 2005 or Cygwin (16) Not tested for this release. Compiler versions for each platform are listed in the preceding "Platforms Tested" table. Known Problems ============== * We have discovered two problems when running collective IO parallel HDF5 tests with chunking storage on 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. These issues arise only when turning on collective IO with chunking storage with some complex selections. We have not found these problems on other MPI-IO compilers. If you encounter these problems, you may use independent IO instead. To avoid this behavior, 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 * For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel tests failed with MPI-IO file locking message. AKC - 2007/6/25 * 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. * For SNL, Red Storm: Only parallel HDF5 is supported. The serial tests pass when run against the parallel library; the parallel tests also pass, but with lots of non-fatal error messages. * For LLNL, uP: both serial and parallel tests pass. Zeus: Serial tests pass but parallel tests fail with a known problem in MPI. ubgl: Serial tests pass but parallel tests fail. * On SUN 5.10 C++, testing fails in the "Testing Shared Datatypes with Attributes" test. * Configuring with --enable-debug=all produces compiler errors on most platforms: Users who want to run HDF5 in debug mode should use --enable-debug rather than --enable-debug=all to enable debugging information on most modules. * On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long double to (unsigned) long long and from (unsigned) long long to long double. * On Altix SGI with Intel 9.0, testmeta.c would not compile with -O3 optimization flag. * On VAX, the Scaleoffset filter is not supported. The filter cannot be applied to HDF5 data generated on VAX. The Scaleoffset filter only supports the IEEE standard for floating-point data. * On Cray X1, a lone colon on the command line of h5dump --xml (as in the testh5dumpxml.sh script) is misinterpereted by the operating system and causes an error. * 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. * On IRIX6.5, when the C compiler version is greater than 7.4, complicated MPI derived datatype code will work. However, the user should increase the value of the MPI_TYPE_MAX environment variable to some appropriate value to use collective irregular selection code. For example, the current parallel HDF5 test needs to raise MPI_TYPE_MAX to 200,000 to pass the test. * 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 calculating code 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 * For version 6 (6.02 and 6.04) of the Portland Group compiler on the AMD Opteron processor, there is 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. * 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 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 do not use this option on these platforms during configuration. * With the gcc 2.95.2 compiler, HDF5 uses the `-ansi' flag during compilation. The ANSI version of the compiler complains about not being able to handle the `long long' datatype with the warning: warning: ANSI C does not support `long long' This warning is innocuous and can be safely ignored. * The ./dsets tests fail on 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. * Not all platforms behave correctly with Szip's shared libraries. Szip is disabled in these cases, and a message is relayed at configure time. Static libraries should be working on all systems that support Szip and should be used when shared libraries are unavailable. There is also a configure error on Altix machines that incorrectly reports when a version of Szip without an encoder is being used. * On some platforms that use Intel and Absoft compilers to build the HDF5 Fortran library, compilation may fail for fortranlib_test.f90, fflush1.f90 and fflush2.f90 complaining about the exit subroutine. Comment out the line IF (total_error .ne. 0) CALL exit (total_error). * Information about building with PGI and Intel compilers is available in the INSTALL file sections 4.7 and 4.8. * 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 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 scipts 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. * H5Ocopy() does not copy reg_ref attributes correctly when shared-message is turn on. The value of the reference in the destination attriubte is wrong. This H5Ocopy problem will affect the h5copy tool.