HDF5 version 1.6.3 released on Wed Sep 22 11:30:11 CDT 2004 ================================================================================ INTRODUCTION This document describes the differences between HDF5-1.6.2 and HDF5-1.6.3, and contains information on the platforms tested and known problems in HDF5-1.6.3. 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 HDF5-1.6.2 - Documentation - Platforms Tested - Supported Configuration Features Summary - Known Problems New Features ============ Configuration: -------------- - Added some initial support for making purify (or similar memory checking products) happier by initializing buffers to zero and disabling the internal free list code. To take advantage of this, define 'H5_USING_PURIFY' in your CFLAGS when building the library. QAK - 2004/07/23 - WINDOWS building,testing and installing improvements - On Windows, FORTRAN,C++ and C projects are merged into one zip file, users can choose an option to build either FORTRAN or C++ or both with basic C library.For detailed information, please read INSTALL_Windows.txt. - On Windows, szip compression library with or without encoder can be easily turned off or on when building HDF5. For detailed information, please read INSTALL_Windows.txt, especially section V. - On Windows, an optional procedure for building,testing and installing HDF5 from command line is provided. This procedure is supposed to be convenient for experienced users, please read INSTALL_windows_From_Command_Line.txt for details. - On Windows, an alternative short instruction document for building, testing and installing HDF5 is provided. This instruction is supposed to be convenient for general users, please read INSTALL_Windows_Short.txt for details. - On Windows, h5repack,h5diff,h5ls and h5import tool tests have been added. KY - 2004/9/16 Library: -------- - Modified the way how HDF5 calculates 'pixels_per_scanline' parameter for SZIP compression. Now there is no restriction on the size and shape of the chunk except that the total number of elements in the chunk cannot be bigger than 'pixels_per_block' parameter provided by the user. EIP - 2004/07/21 - HDF5 can now link to SZIP with or without szip's encoder. The new API function H5Zget_filter_info can be used to check szip's status. Attempting to assign szip to a dataset property list or attempting to write with szip will generate an error if szip's encoder is disabled. JL/NF - 2004/6/30 - SZIP always uses K13 compression. This flag no longer needs to be set when calling H5Pset_szip. If the flag for CHIP compression is set, it will be ignored (since the two are mutually exclusive). JL/NF - 2004/6/30 - A new API function H5Fget_name was added. It returns the name of the file by object(file, group, data set, named data type, attribute) ID. SLU - 2004/06/29 - A new API function H5Fget_filesize was added. It returns the actual file size of the opened file. SLU - 2004/06/24 - Added option that if $HDF5_DISABLE_VERSION_CHECK is set to 2, will suppress all library version mismatch warning messages. AKC - 2004/4/14 Parallel Library: ----------------- Tools: ------ - h5repack was added to the tools suite. h5repack regenerates an HDF5 file from another HDF5 file, optionally applying HDF5 filters (compression) and/or chunking to the copied file. The filters options are read from the command line. See /doc/html/Tools.html for more details. PVN - 2004/9/13 - h5dump includes new features: 1) Printing of dataset filters, storage layout and fill value information. 2) Print a list of the file contents. 3) Escape non printing characters. 4) Print the content of the boot block. 5) Print array indices with the data (the default). These options are all switch controlled. See /doc/html/Tools.html for more details. PVN - 2004/9/13 F90 API: -------- - added new subroutines: h5fget_filesize_f h5iget_file_id_f h5premove_filter_f h5zget_filter_info_f EIP 2004/9/21 - added new h5fget_name_f and h5fget_filesize_f subroutines EIP 2004/07/08 C++ API: -------- - Added wrappers for array and variable length datatypes APIs - Added wrappers for newly added APIs from H5T, H5F, and H5I - Added many wrappers that were missing from the H5P API - Added the ability to reference HDF5 objects to these classes: DataSet, DataType, Group, and H5File (wrappers for H5R APIs) BMR 2004/08/04 Support for new platforms, languages and compilers. ======================================= - Added PGI Fortran support for Linux64 (x86_64) systems EIP - 2004/08/19 - Absoft compiler f95 v9.0 is supported on Linux 2.4 32bit EIP - 2004/07/29 - HDF5 Fortran APIs are supported on Mac OSX with IBM XL Fortran compiler version 8.1. This is a default compiler. - HDF5 Fortran APIs are supported on MAC OSX with Absoft F95 compiler version 8.2; set F9X environment variable to f95, for example setenv F9X f95 Use --disable-shared --enable-static configure flags when Absoft compiler is used. EIP - 2004/07/27 Bug Fixes since HDF5-1.6.2 release ================================== Library ------- - Fixed parallel bug in which some processes attempted collective I/O while others did independent I/O. Bug appeared when some processes used point selections, and others didn't. JRM - 2004/9/15 - Corrected error where dataset region references were written in an incorrect way on Cray machines. PVN & QAK - 2004/09/13 - The H5Tget_native_type now determines the native type for integers based on the precision. This is to avoid cases of wrongly converting an int to a short in machines that have a short of 8 bytes but with 32bit precision (e.g Cray SV1). PVN - 2004/09/07 - Changed H5Dread() to not overwrite data in an application's buffer with garbage when accessing a chunked dataset with an undefined fill value and an unwritten chunk is uncountered. QAK - 2004/08/25 - Fixed error which could cause a core dump when a type conversion routine was registered after a compound datatype had been converted and then an equivalent compound datatype was converted again. QAK - 2004/08/07 - Fixed memory overwrite when encoding "multi" file driver information for file's superblock. QAK - 2004/08/05 - Fixed obscure bug where a filter which failed during chunk allocation could allow library to write uncompressed data to disk but think the data was compressed. QAK - 2004/07/29 - Fixed bug where I/O to an extendible chunked dataset with zero-sized dimensions would cause library to fail an assertion. QAK - 2004/07/27 - Fixed bug where chunked datasets which have filters defined, allocation time set to "late" and whose chunks don't align with the dataspace bounds could have incorrect data stored when overwriting the entire dataset on the first write. QAK - 2004/07/27 - Added check to ensure that dataspaces have extents set. JML-2004/07/26 - Fixed bug on some Solaris systems where HDF5 would try to use gettimeofday() when that function didn't work properly. JML - 2004/07/23 - Fixed bug in H5Sset_extent_simple where setting maximum size to non-zero, then to zero would cause an error. JML - 2004/07/20 - Allow NULL pointer for buffer parameter to H5Dread & H5Dwrite when not writing data ("none" selection or hyperslab or point selection with no elements defined). QAK - 2004/07/20 - Calling H5Gcreate() on "/" or "." throws an error instead of failing quietly. JML - 2004/07/19 - Fixed bug where setting file address size to be very small could trigger an assert if the file grew to more than 64 KB. Now throws an error and data can be recovered. JL/NF - 2004/07/14 - Fixed bug where "resurrecting" a dataset was failing. QAK - 2004/07/14 - Fixed bug where incorrect data could be read from a chunked dataset after it was extended. QAK - 2004/07/12 - After compound datatype with variable-length string in the fields is committed to file, the size is messed up when it's read back. Fixed. SLU - 2004/06/11 - Fixed potential file corruption bug when a block of metadata could overlap the end of the internal metadata accumulator buffer and the buffer would be extended correctly, but would incorrectly change it's starting address. QAK - 2004/06/09 - Opaque datatype with no tag failed for some operations. Fixed. SLU - 2004/6/3 - Fixed potential file corruption bug where dimensions that were too large (a value greater than could be represented in 32-bits) could cause the incorrect amount of space to be allocated in a file for the raw data for the dataset. QAK - 2004/06/01 - Fixed dtypes "sw long double -> double" failure in QSC class machines. AKC - 2004/4/16 Configuration ------------- - Fixed the long compile time of H5detect.c when v7.x Intel Compiler is used with optimization NOT off. AKC - 2004/05/20 Performance ------------- Tools ----- - On SGI h5dump displayed only part of the data due to the bug in the system printf; fixed. EIP - 2004/09/21 Documentation ------------- - Several descriptive errors have been fixed throughout the documentation, particularly in the reference manual (RM). A selection particularly worthy of note would be these: - The H5Pset_szip description in the RM has been expanded and corrected to facilitate use of SZIP compression. - A note has been added to the H5Dcreate description that an unexplained failure is likely to be due to a property list error that is detected only at the time of dataset creation. - FMB - 2004/09/21 F90 API ------- Fortran functions h5dwrite/read_f and h5awrite/read_f do not accept dims parameter of INTEGER type anymore. Code was removed. 2004/04/15 C++ API ------- - H5::Exception's and its subclasses' constructors that were overloaded to take char pointers are removed and constructors that passed in reference of 'string' are changed to pass by value. In addition, the default value of the data member H5::Exception::detailMessage is changed from 0/NULL to DEFAULT_MSG ("No detailed information provided".) - Prototype for DSetCreatPropList::setLayout is changed: 1st parameter is removed because it was there only by mistake. BMR 2004/08/04 Documentation ============= HDF5 Library documentation -------------------------- - HDF5 C++ API Reference Manual This document has been added to the HDF5 document set. The predecessor document, "HDF5 C++ Interfaces," has been removed. - HDF5 C++ API Design Specification A first draft of this document has been added to the HDF5 document set. The draft has been posted on the HDF5 website and a link has been added to the HDF5 documents index (index.html at the top level of the document set). - Parallel HDF5 In prior releases, the HDF5 document set included two parallel HDF5 documents. Those documents have been deleted and the HDF5 documents index (index.html) now links to a "Parallel HDF5" page on the HDF5 website (http://hdf.ncsa.uiuc.edu/HDF5/PHDF5/). - HDF5 High Level APIs Links to the HDF5 High Level APIs and to the HDF5 High Level Reference Manual have been added to the HDF5 documents index (index.html). - HDF5 Reference Manual Tools: h5repack -- A description of the new h5repack tool has been added to the Tools page. Tools: h5dump -- Several new options have been added to h5dump. New functions -- All new functions have been added to the RM. API changes -- Relevant function descriptions have been updated in instances where programming interfaces have changed. FMB - 2004/09/21 Windows installation documentation ---------------------------------- - INSTALL_Windows.txt has been enhanced to include instructions building HDF5 with FORTRAN and C++. - Two optional installation documents have been added. They are INSTALL_Windows_Short.txt and INSTALL_Windows_From_Command_Line.txt. INSTALL_Windows_Short.txt is supposed to help general users who only want to build,test and install HDF5 in a quick way. INSTALL_Windows_From_Command_Line.txt is supposed to help users who would like to compile,test and install HDF5 in command line environment. - INSTALL_Windows_withcpp.txt and INSTALL_Windows_withF90.txt became obsolete. Files are deleted from the release_docs directory. KY 2004/09/16, EIP 2004/9/21 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 xlc 6.0.0.8 xlC 6.0.0.8 xlf 8.1.1.6 mpcc_r 6.0.0.8 mpxlf_r 8.1.1.6 Cray T90 sn7001 10.0.0md Cray Standard C Version 6.4.0.3 Cray Fortran Version 3.4.0.0 Cray T3E sn6606 2.0.6.08 Cray Standard C Version 6.6.0.3 Cray Fortran Version 3.6.0.3 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 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 (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 2.4.18 gcc 2.96, 3.3.2 g++ 3.3.2 Intel(R) C++ Version 7.1 Intel(R) Fortran Compiler Version 7.1 PGI compilers (pgcc, pgf90, pgCC) version 5.0-2 MPIch 1.2.4 Absoft Fortran compiler v9.0 Linux 2.4.20-8 gcc 3.3.2 PGI compilers (pgcc, pgf90, pgCC) version 5.0-2 MPIch 1.2.4 Linux 2.4.21-2.9.5ws #3 gcc 3.2.3 (Red Hat Linux 3.2.3-16) SMP x86_64 g++ 3.2.3 Linux 2.4.21-4.ELsmp Intel(R) C++ 32-bit Version 8.0 Intel(R) Fortran 32-bit Version 8.0 gcc 3.4.0 MPICH 1..5.2 Inmel 8.0 Linux 2.4.19-SMP x86_64 gcc (GCC) 3.2.2 (SuSE Linux) g++ 3.2.2 Linux 2.6.4-52smp x86_64 gcc 3.3.3 (SuSE Linux 9.1 AMD64)) PGI 5.2-1 C and F90 Linux 2.4.21-sgi Altix SMP ia64 Intel(R) C++ Version 8.0 Intel(R) Fortran Itanium(R) Version 8.0 SGI MPI OSF1 V5.1 Compaq C V6.5-303 HP Fortran V5.5A-3548 Compaq C++ V6.5-040 MPI_64bit_R13 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 v4.4.3 i386 pgcc Rel 3.1-4i with mpich-1.2.4 with local modifications IA-32 Linux 2.4.18 gcc 2.96 Intel(R) C++ Version 7.0 Intel(R) Fortran Compiler Version 7.0 Xeon Linux 2.4.20-31.9smp_perfctr_lustre Intel(R) C++ Version 8.0 Intel(R) Fortran Compiler Version 8.0 IA-64 Linux 2.4.16 ia64 gcc version 3.0.4 Intel(R) C++ Version 7.1 Intel(R) Fortran Compiler Version 7.1 IA-64 Linux 2.4.21.SuSE_128.bef1 ia64 Intel(R) C++ Version 8.0 Intel(R) Fortran Compiler Version 8.0 mpich-gm-1.2.5..intel Windows 2000 (NT5.0) MSVC++ 6.0 MSVC++ .NET DEC Visual Fortran 6.0 Intel C and F90 compilers version 7.1 Code Warrior 8.0 Windows XP MSVC++.NET MSVC++ 6.0 DEC Visual Fortran 6.0 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 Solaris2.7 64-bit y (1) y y (1) y y y Solaris2.7 32-bit y (1) y y (1) y y y Solaris2.8 64-bit y (1) y y (1) y y y Solaris2.8 32-bit y 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 T3E y (5) y y (5) 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 y y WinXP Code Warrior n n n n y y Win2000 Visual Studio 6.0 n y (10) n y y y Win2000 Visual Studio Intel (6) n y n y y y Win2000 .Net n n n y y y Mac OS X 10.3 n y (11) n y y y FreeBSD 4.9 y (1) n n y y y RedHat 7 W (3) y (1) y (12) 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 RedHat 8 & SuSe x86_64 gcc (3) n y (13) n y y y Linux 2.4 Xeon C Lustre Intel (3,7) n y n y y y Linux 2.4 SuSE ia64 C Intel (3,8) 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 Solaris2.7 64-bit y x y y Solaris2.7 32-bit y x y y Solaris2.8 64-bit y x y y Solaris2.8 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 T3E 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 WinXP Code Warrior n y n n Win2000 Visual Studio 6.0 y y n n Win2000 Visual Studio Intel (6) y y n n Win2000 .Net y y n n Mac OS X 10.3 y y n y FreeBSD 4.9 y y y y RedHat 7 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 RedHat 8 & SuSe x86_64 gcc (3) n y n y Linux 2.4 Xeon C Lustre Intel (3,7) y y n y Linux 2.4 SuSE ia64 C Intel (3,8) 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 1.2.4 (2) Using mpt and mpich 1.2.4 (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) Intel 7.1 compilers in Visual Studio 6.0 environment (7) Linux 2.4.20-31.9. Xeon cluster with smp_perfctr_lustre and Intel compilers (8) Linux 2.4.21, SuSE_128.befl. Ia64 cluster with Intel compilers (9) DEC Visual Fortran 6.0 and Intel 7.1 (10) DEC Visual Fortran 6.0 (11) IBM XLF and Absoft (12) PGI, Absoft (13) PGI FMB/EIP - 2004/09/21 Known Problems ============== * h5fc and h5c++ compilation scripts have a bug: object files (*.o) cannot be created when source code is compiled using h5fc or h5c++. We will provide a fix. Please check ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/src/patches/ for the patches. * Fortran subroutine h5pget_driver_f doesn't return a correct driver information. * 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 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: 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) * 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 * 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. * 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.