HDF5 version 1.6.1 released on Thu Oct 16 21:42:02 CDT 2003 ================================================================================ INTRODUCTION This document describes the differences between HDF5-1.6.0 and HDF5-1.6.1, and contains information on the platforms tested and known problems in HDF5-1.6.1. 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 HDF5-1.6.0 - Documentation - Platforms Tested - Known Problems New Features ============ Configuration: -------------- Library: -------- - Added new fields to the H5G_stat_t for more information about an object's object header. QAK 2003/10/06 - Added new H5Fget_freespace() routine to query the free space in a given file. QAK 2003/10/06 Parallel Library: ----------------- Tools: ------ C++ API: -------- - Added overloaded functions read and write to H5::Attribute. BMR - 2003/04/21 - Added an overloaded constructor H5::StrType so the need to separately set the length of the string type can be eliminated. BMR - 2003/04/21 - Added overloaded functions read and write to H5::DataSet. BMR - 2003/04/27 The following items were added but not documented in previous releases: - On windows, any application, that uses the C++ API dll, must include the name HDF5CPP_USEDLL in its project setting. (Feb 17, 2002) BMR - 2003/10/10 - Added missing default constructor H5::H5File. (Apr 26, 2002) BMR - 2003/10/10 - Added new member function H5::DataSet::fillMemBuf per the new C API H5Dfill, which fills the elements in a selection for a memory buffer with a fill value. (May 16, 2002) BMR - 2003/10/10 - Added the new member function getMemberIndex to H5::EnumType and H5::CompType to match the new C API H5Tget_member_index. Given the name of a member of an enumeration or compound datatype, this new function queries the index of the member. (May 16, 2002) BMR - 2003/10/10 - Added these member functions to H5::Group per the new C functions H5Gget_num_objs, H5Gget_objname_by_idx and H5Gget_objtype_by_idx: + getNumObjs: Returns the number of objects in the group. + getObjnameByIdx: Retrieves the name of an object in a group, given an index + getObjTypeByIdx: Returns the type of an object in a group, given an index (Jan 20, 2003) BMR - 2003/10/10 Support for new platforms, languages and compilers. ======================================= - gcc 3.3.1 is supported on Linux. Bug Fixes since HDF5-1.6.0 release ================================== Library ------- - Fixed incorrect datatype of the third parameter to the Fortran90 h5pset(get)_cache_f functions (INTEGER to INTEGER(SIZE_T)) EIP - 2003/10/13 - Fixed problems with accessing variable-length data datatypes on Crays. QAK - 2003/10/10 - Fixed potential file corruption bug when too many object header messages (probably attributes, from a user perspective) were inserted into an object header and certain other conditions were met. QAK - 2003/10/08 - Changed implementation of internal ID searching algorithm to avoid O(n) behavior for many common cases. QAK - 2003/10/06 - Allow partial parallel writing to compact datasets. QAK - 2003/10/06 - Correctly create reference to shared datatype in attribute, instead of making a copy of the shared datatype in the attribute. QAK - 2003/10/01 - Revert changes which caused files >2GB to fail when created with MPI-I/O file driver on certain platforms. QAK - 2003/09/16 - Allow compound datatypes to grow in size. SLU - 2003/09/10 - Detect if a type is already packed before attempting to pack it again or check if it is locked. SLU - 2003/09/10 - Corrected bug when opening a file twice with read-only permission for one open and then closing the read-only access file ID would generate an error. QAK - 2003/09/10 - Corrected bug in repeated calls to H5Pget_access_plist() which would incorrectly manage reference counts of internal information and eventually blow up. QAK - 2003/09/02 - Return rank of the array datatype on successful call to H5Tget_array_dims(). QAK - 2003/08/30 - Corrected bug in H5Tdetect_class which was not correctly detecting datatype classes of fields in nested compound datatypes in some circumstances. QAK - 2003/08/30 - Corrected bug in sieve buffer code which could cause loss of data when a small dataset was created and deleted in quick succession. QAK - 2003/08/27 - Corrected bug in H5Gget_objname_by_idx which was not allowing NULL for the name when just querying for the object name's length. QAK - 2003/08/25 - Corrected bug in variable-length string handling which could generate a core dump on writing variable-length strings as part of a compound datatype on certain architectures. QAK - 2003/08/25 - Corrected bug in H5Tget_native_type which would incorrectly compute the size of certain compound datatypes and also incorrectly compute the offset of the last field for those compound datatypes. QAK - 2003/08/25 - Corrected bug in H5Tget_native_type which would drop string datatype metadata (padding, etc.) QAK - 2003/08/25 - Corrected bugs in H5Gget_num_objs, H5Gget_objname_by_idx and H5Gget_objtype_by_idx to allow them to accept location IDs, not just group IDs. QAK - 2003/08/21 - Corrected bug when using scalar dataspace for memory selection and operating on chunked dataset. QAK - 2003/08/18 - Corrected bugs with multiple '/' characters in names for H5Glink and H5Gunlink. QAK - 2003/08/16 - Corrected bug with user blocks that didn't allow a user block to be inserted in front of a file after the file was created. QAK - 2003/08/13 - Corrected errors with using point selections to access data in chunked datasets. QAK - 2003/07/23 - Corrected error with variable-length datatypes and chunked datasets which caused H5Dwrite to fail sometimes. QAK - 2003/07/19 - Modified library and file format to support storing indexed storage (chunked dataset) B-tree's with non-default internal 'K' values. QAK - 2003/07/15 - Returned H5T_BKG_TEMP support to library after it was accidentally removed. QAK - 2003/07/14 Configuration ------------- - Fixed the error that caused "make install" to fail because of the macro definition syntax of "prefix?=..." AKC - 2003/07/22 Performance ------------- Tools ----- - Fixed a segmentation fault of h5diff when percentage option is used. AKC - 2003/08/27 - Switched away from tools using internal "fixtype" function(s) to use H5Tget_native_type() internally. QAK - 2003/08/25 Documentation ------------- - Added two missing Fortran APIs (h5pget_fapl_mpiposix_f and h5pset_fapl_mpiposix_f) to the reference manual. FMB - 2003/10/15 - Corrected the reference manual descriptions of H5open/h5open_f and H5close/h5close_f to indicate that these calls are required in Fortran90 applications. FMB - 2003/10/15 Documentation ============= Fortran90 APIs are being integrated into the main body of the HDF5 Reference Manual (RM). This process is complete in all RM sections except H5P. A PDF version of the RM will be posted on the HDF5 website (at http://hdf.ncsa.uiuc.edu/HDF5/doc/PSandPDF/) approximately one week after the release. Platforms Tested ================ AIX 5.1 (32 and 64-bit) xlc 6.0.0.2 xlf 8.1.0.3 xlC 6.0.0.4 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 poe 3.2.0.10 Cray T3E sn6606 2.0.6.08 Cray Standard C Version 6.6.0.2 Cray Fortran Version 3.6.0.2 Cray SV1 sn9617 10.0.1.2 Cray Standard C Version 6.6.0.2 Cray Fortran Version 3.6.0.2 Cray T90IEEE 10.0.1.01y Cray Standard C Version 6.4.0.2.3 Cray Fortran Version 3.4.0.3 FreeBSD 4.9 gcc 2.95.4 g++ 2.95.4 HP-UX B.11.00 HP C HP92453-01 A.11.01.20 HP F90 v2.4 HP ANSI C++ B3910B A.03.13 HP MPI 01.07.00.00 IRIX 6.5 MIPSpro cc 7.3.1.2m IRIX64 6.5 (64 & n32) MIPSpro cc 7.3.1.3m F90 MIPSpro 7.3.1.3m (64 only) MPIch 1.2.4 Linux 2.4.18 gcc 2.96, 3.2.2, 3.3.1 g++ 3.2.2, 3.2.3 Intel(R) C++ Version 7.1 Intel(R) Fortran Compiler Version 7.1 PGI compilers (pgcc, pgf90, pgCC) version 4.0-2 MPIch 1.2.4 Linux 2.4.20-8 gcc 3.2.2 OSF1 V5.1 Compaq C V6.4-014 Compaq C V6.3-027 Compaq Fortran V5.5-2602 Compaq C++ V6.5-030 MPI_64bit_R5 g++ version 3.0 for C++ SunOS 5.7(32 and 64 bit) WorkShop Compilers 5.0 98/12/15 C 5.0 (Solaris 2.7) WorkShop Compilers 5.0 98/12/15 C++ 5.0 WorkShop Compilers 5.0 98/10/25 FORTRAN 90 2.0 Patch 107356-04 SunOS 5.8(32 and 64 bit) 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 TFLOPS r1.0.4 v4.4.0 i386 pgcc Rel 3.1-4i with mpich-1.2.4 with local modifications IA-32 Linux 2.4.9 gcc 2.96 Intel(R) C++ Version 7.0 Intel(R) Fortran Compiler Version 7.0 IA-64 Linux 2.4.16 ia64 gcc version 2.96 20000731 Intel(R) C++ Version 7.0 Intel(R) Fortran Compiler Version 7.0 Windows 2000 (NT5.0) MSVC++ 6.0 DEC Visual Fortran 6.0 Intel C and F90 compilers version 7.1 Code Warrior 8.0 Windows XP MSVC++.NET MAC OS X Darwin 6.8 gcc and g++ Apple Computer, Inc. GCC version 1175, based on gcc version 3.1 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 Platform C C F90 F90 C++ Shared zlib parallel parallel libraries (4) Solaris2.7 64-bit y y (1) y y (1) y y y Solaris2.7 32-bit y y (1) y y (1) y y y Solaris2.8 64-bit y y (1) y y (1) y y y Solaris2.8 32-bit y y y y (1) y y y IRIX6.5 y y (1) n n n y y IRIX64_6.5 64-bit y y (2) y y y y y IRIX64_6.5 32-bit y y (2) n n n y y HPUX11.00 y y (1) y y y y y OSF1 v5.1 y y y y y y y T3E y y (5) y y (5) n n y SV1 y y (5) y y (5) n n y T90 IEEE y y (5) y y (5) n n y TFLOPS n y (1) n n n n y AIX-5.1 32-bit y y y y y n y AIX-5.1 64-bit y y y y y n y WinXP (6) y n n n y y y WinXP Intel y n n n y y y Win2000 y n y n y y y Win2000 Intel y n y n y y y WinNT CW y n n n n n y Mac OS X 10.2 y n n n y y y FreeBSD y y (1) n n y y y Linux 2.4 gcc (3) y y (1) y (PGI) n y y y Linux 2.4 Intel (3) y n y n y n y Linux 2.4 PGI (3) y n y n y n y Linux 2.4 IA32 Intel y n y n y n y Linux 2.4 IA64 Intel y n y n y n y ASCII Table 2 -- for RELEASE.txt Platform static- Thread- SZIP GASS STREAM- High-level H4/H5 exec safe VFD APIs tools (7) Solaris2.7 64-bit x y y n y y n Solaris2.7 32-bit x y y n y y y Solaris2.8 64-bit x y y n y y n Solaris2.8 32-bit x y y n y y y IRIX6.5 x n y n y y y IRIX64_6.5 64-bit x y y y y y y IRIX64_6.5 32-bit x y y y y y y HPUX11.00 x n y n y y y OSF1 v5.1 y n y n y y y T3E y n n n y y y SV1 y n n n y y y T90 IEEE y n n n y y n TFLOPS y n n n n n n AIX-5.1 32-bit y n y n y y y AIX-5.1 64-bit y n y n y y y WinXP (6) y n y n n y y WinXP Intel y n y n n y y Win2000 y n y n n y y Win2000 Intel y n y n n y y WinNT CW y n y n n y y Mac OS X 10.2 y n y n y y n FreeBSD y y y n y y y Linux 2.4 gcc (3) y y y n y y y Linux 2.4 Intel (3) y n y n y n n Linux 2.4 PGI (3) y n y n y n n Linux 2.4 IA32 Intel y n y n y y y Linux 2.4 IA64 Intel y n y n y y y Notes: (1) Using mpich 1.2.4. (2) Using mpt and mpich 1.2.4. (3) Linux 2.4 with GNU, Intel, and PGI compilers, 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) Binaries only; source code for this platform is not being released at this time. (7) Includes the H4toH5 Library and the h4toh5 and h5toh4 utilities. Compiler versions for each platform are listed in the preceding "Platforms Tested" table. Known Problems ============== * Fortran subroutine h5pget_driver_f doesn't return a correct driver information. The fix willl be available in the 1.6.2 release. * 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. * With the gcc 2.95.2 compiler, HDF 5 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 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 J90 and 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 and 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: * On some platforms that use Intel 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) ftp://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/hdf5-1.6.0/F90_source_for_Crays * On IA32 and IA64 systems, if you use a compiler other than GCC (such as Intel's ecc or icc compilers), you will need to modify the generated "libtool" program after configuration is finished. On or around line 104 of the libtool file, there are lines which look like: # How to pass a linker flag through the compiler. wl="" change these lines to this: # How to pass a linker flag through the compiler. wl="-Wl," UPDATE: This is now done automatically by the configure script. However, if you still experience a problem, you may want to check this line in the libtool file and make sure that it has the correct value. * Information about building with PGI and Intel compilers is available in INSTALL file sections 5.7 and 5.8