HDF5 History ============ This file contains development history of HDF5 1.8 branch 13. Release Information for hdf5-1.8.11 12. Release Information for hdf5-1.8.10-patch1 11. Release Information for hdf5-1.8.10 10. Release Information for hdf5-1.8.9 09. Release Information for hdf5-1.8.8 08. Release Information for hdf5-1.8.7 07. Release Information for hdf5-1.8.6 06. Release Information for hdf5-1.8.5 05. Release Information for hdf5-1.8.4 04. Release Information for hdf5-1.8.3 03. Release Information for hdf5-1.8.2 02. Release Information for hdf5-1.8.1 01. Release Information for hdf5-1.8.0 [Search on the string '%%%%' for section breaks of each release.] %%%%1.8.11%%%% HDF5 version 1.8.11 released on 2013-05-08 ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.10 and HDF5-1.8.11-*, and contains information on the platforms tested and known problems in HDF5-1.8.11-*. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.11 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.11 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.11 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in the HDF5-1.8.x release series, 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 1.8.11 (current release) versus Release 1.8.10": 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 - Support for New Platforms, Languages, and Compilers - Bug Fixes since HDF5-1.8.10 - Supported Platforms - Supported Configuration Features Summary - More Tested Platforms - Known Problems New Features ============ Configuration ------------- - Libtool version number is changed to 8.0.0 because there are API changes. See below for details. (AKC - 2013/05/07 HDFFV-8435) - Mac OS X 10.7 (Lion) and 10.8 (Mountain Lion) uses clang/clang++ as the default C and C++ compilers. (AKC - 2013/04/19 HDFFV-8245) - CMake minimum is now 2.8.10. (ADB 2013/1/14) - A new tool, cmakehdf5, which is a build command script similar to buildhdf5 is added and is available in the bin directory. (AKC - 2013/01/16 HDFFV-8336) Library ------- - The library can load filter libraries dynamically during runtime. Users can set the search path through environment variable HDF5_PLUGIN_PATH and call H5Pset_filter to enable a dynamic filter. (SLU - 2013/04/08) - Added new API functions H5Dscatter and H5Dgather to scatter data to and and gather data from a selection within a memory buffer. (NAF - 2013/02/05) - The library now supports the data conversion from enumeration to numeric (integer and floating-point number) datatypes. See Issue HDFFV-8221. (SLU - 2012/10/23) Parallel Library ---------------- - None Tools ----- - h5dump: added new option -O or -ddl to output the ddl text to a file. This is a complement to the -o or --output option, which redirects the data to a file. HDFFV-8229 (ADB - 2013/2/25) High-Level APIs --------------- - A new API function, H5DOwrite_chunk. This function writes a data chunk directly into a file, bypassing hyperslab selection, data conversion, and the filter pipeline. The user must be careful with the function and clearly understand the I/O process of the library. (SLU - 2013/2/11) Fortran API ----------- - New API functions added (MSB - 2013/3/23): h5odecr_refcount_f, h5oexists_by_name_f, h5oget_comment_f, h5oget_comment_by_name_f, h5oincr_refcount_f, h5oopen_by_idx_f, h5oset_comment_f, h5oset_comment_by_name_f, h5oset_comment_by_name_f F2003: h5oget_info_f, h5oget_info_by_idx_f, h5ovisit_by_name_f C++ API ------- - None Support for New Platforms, Languages, and Compilers =================================================== - SunOS 5.11 (emu) 32-bit and 64-bit with Sun C/C++ 5.12 compiler and Sun Fortran 95 8.6 compiler. - Visual Studio 2012 w/ Intel Fortran 13 on Windows 7 - g95 released new version recently and is tested in this release. Bug Fixes since HDF5-1.8.10 ========================== Configuration ------------- - Fixed Thread-safe configure failure for the AIX platform. (AKC - 2013/04/19 HDFFV-8390) - Configure will check the result of header searches before searching for the library. Fixes HDFFV-8257 (ADB 2013/03/04) - HDF does not support building SHARED Fortran libraries on OSX. Added CMake code to check for this condition. Fixes HDFFV-8227 (ADB 2013/03/04) - CMake builds on Windows will no longer use legacy naming for libraries. The "dll" tag will no longer be added to the name of *.lib and *.dll. The option HDF_LEGACY_NAMING is now OFF by default. Fixes HDFFV-8292 (ADB 2013/01/30) Library ------- - The library now behaves correctly when performing large I/O operations on Mac OS-X. Previously, single I/O operations > 2 GB would fail since the Darwin read/write calls cannot handle the number of bytes that their parameter types imply. Fixes HDFFV-7975 and HDFFV-8240 (DER 2013/01/07) - Fixed a bug in the core VFD that causes failures when opening files > 2 GB. Fixes HDFFV-8124 and HDFFV-8158 (DER 2013/01/07) - Fixed a bug where unintialized memory was read during variable-length type conversion. This caused segfaults in netCDF. Fixes HDFFV-8159. (DER 2013/03/30) - Removed the H5Pset/get_dxpl_multi functions from the library. The intended functionality for them was never fully implemented, and they have always been fundamentally broken. NOTE: This does not affect setting the multi VFD or any expected VFD functionality. Multi VFD usage remains unchanged. Fixes HDFFV-8296. (DER 2013/03/30) Parallel Library ---------------- - None Performance ------------- - None Tools ----- - h5redeploy is changed to do this by default: Installation directories: prefix architecture-independent files. exec_prefix architecture-dependent files, default is . libdir libraries, default is /lib. includedir header files, default is . This allows users to just change the first line of prefix=<...> and the effect will change libdir and includedir too. (AKC 2013/04/05 HDFFV-8358) - h5repack: Fixed failure to convert the layout of a small chunked dataset (size < 1K) to contiguous layout. HDFFV-8214 (JKM 2013/03/26) - h5dump: Fixed displaying compression ratio for unknown or user-defined filters. HDFFV-8344 (XCAO 2013/03/19) - h5dump: Changed UNKNOWN_FILTER to USER_DEFINED_FILTER for user defined filter. HDFFV-8346 (XCAO 2013/03/19) - h5diff: Fixed to return the correct exit code 1 when the program detects a unique extra attribute. Prior to this fix, h5diff returned exit code 0 indicating the two files are identical. HDFFV-7643 (JKM 2013/02/15) - h5dump: Fixed writing nulls to a binary file when exporting a dataset with compound string datatype. HDFFV-8169 (ADB 2013/1/31) - The following h5stat test case failed in BG/P machines (and potentially other machines that display extra output if an MPI task returns with a non-zero code.) Testing h5stat notexist.h5 The test script was fixed to ignore the extra output. HDFFV-8233 (AKC - 2012/11/30) - h5diff: Improved speed when comparing HDF5 files with lots of attributes. Much slower performance was identified with release versions from 1.8.7 to 1.8.10 compared to 1.8.6. (JKM 2012/10/19) F90 API ------- - The integer type of the 'offset' argument in h5pset_external_f and h5pget_external_f was changed to INTEGER(KIND=OFF_T) to support 8-byte integers, matching the C type definition of off_t. (MSB - 2013/3/23) - h5fc updated to recognize .f95, .f03 and .f08 file extensions. C++ API ------ - The C++ wrappers DSetMemXferPropList::setMulti/getMulti were removed because the C functions H5Pset/get_dxpl_multi functions are removed from the library. Fixes HDFFV-8296 by DER. (BMR 2013/03/30) - An exception thrown by an internal function was not propagating to the test program during stack unwinding, so it couldn't be caught by the test, and the program terminated "without an active exception." It seemed that the problem happened when c_str() was used to generate an equivalent const char* from a std::string and the resulting string was passed to the internal function. As a work-around, we added a try/catch around the the call to the internal function and when the exception is caught there, it is re-thrown. Fixes HDFFV-8067. (BMR 2013/03/30) High-Level APIs: ------ - Fixed a problem with H5DSget_scale_name including the NULL terminator in the size calculation returned by the function. The API was changed to NOT include the NULL terminator in the size of name returned (MSB- 2013/2/10) Fortran High-Level APIs: ------ - None Testing ------- - In some Mac systems, testlibinfo.sh failed with this error: Check file ../src/.libs/libhdf5.7.dylib strings: object: ../src/.libs/libhdf5.7.dylib malformed object \ (unknown load command 15) The strings command of Mac systems inspects library files, and older versions of strings may not know newer library formats, resulting in errors. Fixed by sending the library file as stdin to the strings command to avoid this problem. (AKC - 2013/03/08 HDFFV-8305) - Fixed a typo in the ERROR macro in test/testhdf5.h. It segmentation faulted when used before. (AKC - 2013/02/12 HDFFV-8267) Supported Platforms =================== The following platforms are supported and have been tested for this release. They are built with the configure process unless specified otherwise. AIX 5.3 xlc 10.1.0.5 (NASA G-ADA) xlC 10.1.0.5 xlf90 12.1.0.6 Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP i686 i686 i386 compilers for 32-bit applications; (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-54) Version 4.6.3 PGI C, Fortran, C++ Compilers for 32-bit applications; Version 11.9-0 Version 12.5-0 Intel(R) C, C++, Fortran Compiler for 32-bit applications; Version 12.1 (Build 20110811) Version 12.1 (Build 20120212) Linux 2.6.18-308.16.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP x86_64 GNU/Linux compilers for 64-bit applications; (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-52) Version 4.6.3 PGI C, Fortran, C++ for 64-bit target on x86-64; Version 11.9-0 Version 12.5-0 Intel(R) C, C++, Fortran Compilers for applications running on Intel(R) 64; Version 12.1 (Build 20110811) Version 12.1 (Build 20120212) Linux 2.6.32-358.2.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP x86_64 GNU/Linux compilers: (platypus) Version 4.4.7 20120313 Intel(R) C (icc), C++ (icpc), Fortran (icc) compilers: Version 12.1 20120212 Linux 2.6.32-358.2.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) IBM XL C/C++ V11.1 IBM XL Fortran V13.1 SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc (emu) Sun Fortran 95 8.6 SunOS_sparc Sun C++ 5.12 SunOS_sparc Windows 7 Visual Studio 2008 w/ Intel Fortran 11 (cmake) Visual Studio 2010 w/ Intel Fortran 12 (cmake) Visual Studio 2012 w/ Intel Fortran 13 (cmake) Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) (cmake and autotools) Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11 (cmake) Visual Studio 2010 w/ Intel Fortran 12 (cmake) Visual Studio 2012 w/ Intel Fortran 13 (cmake) Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) (cmake and autotools) Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 64-bit gfortran GNU Fortran (GCC) 4.6.2 (fred) Intel C (icc), Fortran (ifort), C++ (icpc) 12.1 Build 20120928 Mac OS X Lion 10.7.3 Apple clang/clang++ version 3.0 from Xcode 4.6.1 64-bit gfortran GNU Fortran (GCC) 4.6.2 (duck) Intel icc/icpc/ifort version 13.0 Mac OS X Mountain Lion 10.8.1 Apple clang/clang++ version 4.2 from Xcode 4.6.1 64-bit gfortran GNU Fortran (GCC) 4.6.2 (wren) Intel icc/icpc/ifort version 13.0.1.119 Tested Configuration Features Summary ===================================== In the tables below y = tested n = not tested in this release C = Cluster W = Workstation 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 F2003 parallel Solaris2.11 32-bit n y/y n y y y Solaris2.11 64-bit n y/n n y y y Windows 7 y y/y n y y y Windows 7 x64 y y/y n y y y Windows 7 Cygwin n y/n n y y y Windows 7 x64 Cygwin n y/n n y y y Mac OS X Snow Leopard 10.6.8 64-bit n y/y n y y y Mac OS X Lion 10.7.3 64-bit n y/y n y y y Mac OS X Mountain Lion 10.8.1 64-bit n y/y n y y y AIX 5.3 32- and 64-bit n y/n n y y y CentOS 5.9 Linux 2.6.18-308 i686 GNU y y/y y y y y CentOS 5.9 Linux 2.6.18-308 i686 Intel n y/y n y y y CentOS 5.9 Linux 2.6.18-308 i686 PGI n y/y n y y y CentOS 5.9 Linux 2.6.18 x86_64 GNU y y/y y y y y CentOS 5.9 Linux 2.6.18 x86_64 Intel n y/y n y y y CentOS 5.9 Linux 2.6.18 x86_64 PGI n y/y n y y y CentOS 6.4 Linux 2.6.32 x86_64 GNU n y/n n y y y CentOS 6.4 Linux 2.6.32 x86_64 Intel n y/y n y y y Linux 2.6.32-358.2.1.el6.ppc64 n y/n n y y y Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Solaris2.11 32-bit y y y y Solaris2.11 64-bit y y y y Windows 7 y y y y Windows 7 x64 y y y y Windows 7 Cygwin n n n y Windows 7 x64 Cygwin n n n y Mac OS X Snow Leopard 10.6.8 64-bit y n y n Mac OS X Lion 10.7.3 64-bit y n y y Mac OS X Mountain Lion 10.8.1 64-bit y n y y AIX 5.3 32- and 64-bit y n n y CentOS 5.9 Linux 2.6.18-308 i686 GNU y y y y CentOS 5.9 Linux 2.6.18-308 i686 Intel y y y n CentOS 5.9 Linux 2.6.18-308 i686 PGI y y y n CentOS 5.9 Linux 2.6.18 x86_64 GNU y y y y CentOS 5.9 Linux 2.6.18 x86_64 Intel y y y n CentOS 5.9 Linux 2.6.18 x86_64 PGI y y y n CentOS 6.4 Linux 2.6.32 x86_64 GNU y y y n CentOS 6.4 Linux 2.6.32 x86_64 Intel y y y n Linux 2.6.32-358.2.1.el6.ppc64 y y y n Compiler versions for each platform are listed in the preceding "Supported Platforms" table. More Tested Platforms ===================== The following platforms are not supported but have been tested for this release. Linux 2.6.18-308.13.1.el5PAE MPICH mpich2-1.4.1p1 compiled with #1 SMP i686 i686 i386 gcc 4.1.2 and gfortran 4.1.2 (jam) g95 (GCC 4.0.3 (g95 0.94!) Linux 2.6.18-308.16.1.el5 MPICH mpich2-1.4.1p1 compiled with #1 SMP x86_64 GNU/Linux gcc 4.1.2 and gfortran 4.1.2 (koala) g95 (GCC 4.0.3 (g95 0.94!) FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 (loyalty) gcc 4.6.1 20110422 g++ 4.6.1 20110422 gfortran 4.6.1 20110422 FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 (freedom) gcc 4.6.1 20110422 g++ 4.6.1 20110422 gfortran 4.6.1 20110422 Debian6.0.7 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux gcc (Debian 4.4.5-8) 4.4.5 GNU Fortran (Debian 4.4.5-8) 4.4.5 (cmake and autotools) Fedora18 3.7.9-205.fc18.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux gcc (GCC) 4.7.2 20121109 (Red Hat 4.7.2-8) GNU Fortran (GCC) 4.7.2 20120507 (Red Hat 4.7.2-8) (cmake and autotools) SUSE 12.3 3.7.10-1.1-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux gcc (SUSE Linux) 4.7.2 GNU Fortran (SUSE Linux) 4.7.2 (cmake and autotools) Ubuntu 12.10 3.5.0-25-generic #39-Ubuntu SMP x86_64 GNU/Linux gcc (Ubuntu/Linaro 4.7.2-2ubuntu1) 4.7.2 GNU Fortran (Ubuntu/Linaro 4.7.2-2ubuntu1) 4.7.2 (cmake and autotools) Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46 hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai Known Problems ============== * When building using the Cray compilers on Cray machines, HDF5 configure mistakenly thinks the compiler is an intel compiler and sets the -std=c99 flag which breaks configure on Cray. To build HDF5 properly on a Cray machine, please consult with the instructions in INSTALL_parallel for building on Hopper. (MSC - 2013/04/26 - HDFFV-8429) * The h5dump and h5diff utilities occasionally produce different output between Linux and Windows systems. This is caused by lower-level library routines that fail to write fill values to the user's buffer when reading unallocated chunks from datasets that have a fill value set to H5D_FILL_VALUE_DEFAULT. Due to platform differences the return of spurious data values has only been encountered on Windows 32-bit systems. (Issue HDFFV-8247; JP - 2013/03/27) * The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp. It complains with this message: "/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined. The reason is that __func__ is a predefined identifier in C99 standard. The HDF5 C library uses it in H5private.h. The test ttypes.cpp includes H5private.h (H5Tpkg.h<-H5Fprivate.h<-H5Vprivate.h<-H5private.h). Sun's 5.9 C++ compiler doesn't support __func__, thus fails to compile the C++ test. But Sun's 5.11 C++ compiler does. To check whether your Sun C++ compiler knows this identifier, try to compile the following simple C++ program: #include int main(void) { printf("%s\n", __func__); return 0; } (SLU - 2012/11/5) * The C++ and FORTRAN bindings are not currently working on FreeBSD with the native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the ports (and probably gcc releases after that). (QAK - 2012/10/19) * The following h5dump test case fails in BG/P machines (and potentially other machines that use a command script to launch executables): h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" tno-subset.h5 This is due to the embedded spaces in the dataset name being interpreted by the command script launcher as meta-characters, thus passing three arguments to h5dump's -d flag. The command passes if run by hand, just not via the test script. (AKC - 2012/05/03) * On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set to aprun -np X, because the H5lib_settings.c file was not generated properly. Not setting those environment variables works, because configure was able to automatically detect that it's a Cray system and used the proper launch commands when necessary. (MSC - 2012/04/18) * The data conversion test dt_arith.c fails in "long double" to integer conversion on Ubuntu 11.10 (3.0.0.13 kernel) with GCC 4.6.1 if the library is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernal (3.2.2 on Fedora) doesn't have the problem. Users should lower the optimization level (-O1 or -O0) by defining CFLAGS in the command line of "configure" like: CFLAGS=-O1 ./configure This will overwrite the library's default optimization level. (SLU - 2012/02/07 - HDFFV-7829) This issue is no longer present on Ubuntu 12.10 (3.5.0 kernel) with gcc 4.7.2. * The STDIO VFD does not work on some architectures, possibly due to 32/64 bit or large file issues. The basic STDIO VFD test is known to fail on 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin 10.7.0. The STDIO VFD test has been disabled while we investigate and a fix should appear in a future release. (DER - 2011/10/14 - HDFFV-8235) * h5diff can report inconsistent results when comparing datasets of enum type that contain invalid values. This is due to how enum types are handled in the library and will be addressed in a future release. (DER - 2011/10/14 - HDFFV-7527) * The links test can fail under the stdio VFD due to some issues with external links. This will be investigated and fixed in a future release. (DER - 2011/10/14 - HDFFV-7768) * After the shared library support was fixed for some bugs, it was discovered that "make prefix=XXX install" no longer works for shared libraries. It still works correctly for static libraries. Therefore, if you want to install the HDF5 shared libraries in a location such as /usr/local/hdf5, you need to specify the location via the --prefix option during configure time. E.g, ./configure --prefix=/usr/local/hdf5 ... (AKC - 2011/05/07 - HDFFV-7583) * The parallel test, t_shapesame, in testpar/, may run for a long time and may be terminated by the alarm signal. If that happens, one can increase the alarm seconds (default is 1200 seconds = 20 minutes) by setting the environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 (60 minutes). Note that the t_shapesame test may fail in some systems (see the "While working on the 1.8.6 release..." problem below). If it does, it will waste more time if $HDF5_ALARM_SECONDS is set to a larger value. (AKC - 2011/05/07) * The C++ and FORTRAN bindings are not currently working on FreeBSD. (QAK - 2011/04/26) * Shared Fortran libraries are not quite working on AIX. While they are generated when --enable-shared is specified, the fortran and hl/fortran tests fail. We are looking into the issue. HL and C++ shared libraries should now be working as intended, however. (MAM - 2011/04/20) * The --with-mpe configure option does not work with Mpich2. (AKC - 2011/03/10) * While working on the 1.8.6 release of HDF5, a bug was discovered that can occur when reading from a dataset in parallel shortly after it has been written to collectively. The issue was exposed by a new test in the parallel HDF5 test suite, but had existed before that. We believe the problem lies with certain MPI implementations and/or file systems. We have provided a pure MPI test program, as well as a standalone HDF5 program, that can be used to determine if this is an issue on your system. They should be run across multiple nodes with a varying number of processes. These programs can be found at: http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ (NAF - 2011/01/19) * The library's test dt_arith.c showed a compiler's rounding problem on Cygwin when converting from unsigned long long to long double. The library's own conversion works fine. We defined a macro for Cygwin to skip this test until we can solve the problem. (SLU - 2010/05/05 - HDFFV-1264) * All the VFL drivers aren't backward compatible. In H5FDpublic.h, the structure H5FD_class_t changed in 1.8. There is new parameter added to get_eoa and set_eoa callback functions. A new callback function get_type_map was added in. The public function H5FDrealloc was taken out in 1.8. The problem only happens when users define their own driver for 1.6 and try to plug in 1.8 library. Because there's only one user complaining about it, we (Elena, Quincey, and I) decided to leave it as it is (see bug report #1279). Quincey will make a plan for 1.10. (SLU - 2010/02/02) * The --enable-static-exec configure flag will only statically link libraries if the static version of that library is present. If only the shared version of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, for example, only have shared versions), the flag should still result in a successful compilation, but note that the installed executables will not be fully static. Thus, the only guarantee on these systems is that the executable is statically linked with just the HDF5 library. (MAM - 2009/11/04) * Parallel tests failed with 16 processes with data inconsistency at testphdf5 / dataset_readAll. Parallel tests also failed with 32 and 64 processes with collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks with MPI IO. (CMC - 2009/04/28) * On an 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. * 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 calculation 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 - 2005/06/30) %%%%1.8.10-patch1%%%% HDF5 version 1.8.10-patch1 released on 2013-01-22 ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.9 and HDF5 1.8.10, and contains information on the platforms tested and known problems in HDF5-1.8.10. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.10 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.10 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.10 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in the HDF5-1.8.x release series, 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 1.8.10 (current release) versus Release 1.8.9": 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 - Support for New Platforms, Languages, and Compilers - Bug Fixes since HDF5-1.8.10 - Bug Fixes since HDF5-1.8.9 - Supported Platforms - Supported Configuration Features Summary - More Tested Platforms - Known Problems New Features ============ Configuration ------------- - A new tool, cmakehdf5, which is a build command script similar to buildhdf5 is added and is available in the bin directory. (AKC - 2013/01/21) Library ------- - Updated to latest autotools and changed all hard *.sh scripts to configure managed *.sh.in files. Removed overloading of autotools TESTS variable by examples and tests. Renamed configure.in to configure.ac. (ADB - 2012/08/23 - HDFFV-8129) - The data sieve buffer size was set for all the datasets in the file. It could waste memory if any dataset size is smaller than the sieve buffer size. Now the library picks the smaller one between the dataset size and the sieve buffer size from the file access property. See Issue 7934. (SLU - 2012/4/11) Parallel Library ---------------- - Added the H5Pget_mpio_no_collective_cause() function that retrieves reasons why the collective I/O was broken during read/write IO access. (JKM - 2012/08/30 HDFFV-8143) - Added H5Pget_mpio_actual_io_mode_f (MSB - 2012/09/27) Tools ----- - h5import: Changed to allow the use of h5dump output as input files to h5import. h5dump must include the "-p" option to print the properties; configuration file is captured output of h5dump. The restrictions are that only one dataset with a simple datatype (integer, floating-point, or string) can be processed. Integers and floating-point imports from h5dump must use the "binary" option for the data file. The string version uses the h5dump "-y --width=1" options to disable the indexing printouts, print single columns, and obviously NOT use the "binary" option. (ADB - 2012/07/19 HDFFV-721) High-Level APIs --------------- - None Fortran API ----------- - Fixed a typo in return value of the nh5dread_f_c function (was 1 instead of 0 on success); fixed the return value to make it consistent with other Fortran functions; cleaned debug statements from the code. (EIP - 2012/06/23) C++ API ------- - None Support for New Platforms, Languages, and Compilers =================================================== - None Bug Fixes since HDF5-1.8.10 =========================== Library ------- - The library now behaves correctly when performing large I/O operations on Mac OS-X. Previously, single I/O operations > 2 GB would fail since the Darwin read/write calls cannot handle the number of bytes that their parameter types imply. Fixes HDFFV-7975 and HDFFV-8240 (DER - 07 JAN 2013) - Fixed a bug in the core VFD that cause failures when opening files > 2 GB. Fixes HDFFV-8124 and HDFFV-8158 (DER - 07 JAN 2013) Tools ----- - The following h5stat test case failed in BG/P machines (and potentially other machines that display extra output if an MPI task returns with a non-zero code.) Testing h5stat notexist.h5 The test script was fixed to ignore the extra output. HDFFV-8233 (AKC - 2012/12/17) - h5diff: Fixed slowness when comparing HDF5 files with many attributes. Much slower performance was identified with later release version (from 1.8.7 to 1.8.10) compared to 1.8.6. The issue was introduced from fixing an attribute related bug for 1.8.7 release in the past. HDFFV-8145 (JKM 2012/12/13) Testing ------- - None Bug Fixes since HDF5-1.8.9 ========================== Configuration ------------- - Fixed configure --enable-production to not use -O optimization for Lion and Mountain Lion systems when gcc (i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1) is used. Somehow the -O optimization will cause some of the hard conversion code in test/dt_arith.c to fail. HDFFV-8017. (AKC - 2012/10/10) - Fixed AIX Fortran compiler flags to use appropriate settings for debugging, profiling, and optimization situations. HDFFV-8069. (AKC 2012/09/27) Library ------- - Fixed a memory leak exposed when inserting/removing a property from a property list several times. HDFFV-8022. (MSC 2012/05/18) - The file_image test will fail in the "initial file image and callbacks in the core VFD" sub-test if the source directory is read-only as the test fails to create its test files in the build directory. This has been fixed. HDFFV-8009 (AKC - 2012/07/06) Parallel Library ---------------- - The MPI-POSIX VFD was updated to include the POSIX and Windows correctness features added that had already been added to the other VFDs. HDFFV-8058/7845. (DER 2012/09/17) Performance ------------- - Removed program perform/benchpar from the enable-build-all list. The program will be retired or moved to another location. HDFFV-8156 (AKC 2012/10/01) - Retired program perform/mpi-perf. Its purpose has been incorporated into h5perf. (AKC 2012/09/21) Tools ----- - h5repack: "h5repack -f NONE file1.h5 out.h5" command failed if source file contains chunked dataset and a chunk dim is bigger than the dataset dim. Another issue is that the command changed max dims if chunk dim is smaller than the dataset dim. These issue occurred when dataset size is smaller than 64k (compact size limit) Fixed both. HDFFV-8012 (JKM 2012/09/24) - h5diff: Fixed the counter in verbose mode (-v, -r) so that it will no longer add together the differences between datasets and the differences between attributes of those datasets. This change makes the output of verbose mode consistent for datasets, groups, and committed datatypes. HDFFV-5919 (JKM 2012/09/10) - h5diff: Fixed the incorrect result when comparing attribute data values and the data type has the same class but different sizes. HDFFV-7942 (JKM 2012/08/15) - h5dump: Replaced single element fwrite with block writes. HDFFV-1208 (ADB 2012/08/13) - h5diff: Fixed test failure for "make check" due to failure of copying test files when performed in HDF5 source tree. Also applied to other tools. HDFFV-8107 (JKM 2012/08/01) - ph5diff: Fixed intermittent hang issue on a certain operation in parallel mode. It was detected by daily test for comparing non-comparable objects, but it could have occurred in other operations depending on machine condition. HDFFV-8003 (JKM 2012/08/01) - h5diff: Fixed the function COPY_TESTFILES_TO_TESTDIR() of testh5diff.sh to better report when there is an error in the file copying. HDFFV-8105 (AKC 2012/07/22) - h5dump: Fixed the sort by name display to maintain correct parent/child relationships between ascending/descending order. HDFFV-8095 (ADB 2012/07/12) - h5dump: Fixed the display by creation order when using option -n (print contents). HDFFV-5942 (ADB 2012/07/09) - h5dump: Changed to allow H5T_CSET_UTF8 to be displayed in h5dump output. Used technique similar to what was done in h5ls (matches library options). HDFFV-7999 (ADB 2012/05/23) - h5diff: Fixed the tool so that it will not check and display the status of dangling links without setting the --follow-symlinks option. This also improved performance when comparing lots of external links without the --follow-symlinks option. HDFFV-7998 (JKM 2012/04/26) F90 API ------- - Fixed a typo in return value of the nh5dread_f_c function (was 1 instead of 0 on success); fixed the return value to make it consistent with other Fortran functions; cleaned debug statements from the code. (EIP - 2012/06/23) - Fixed a problem writing/reading control characters to a dataset; writing a string containing alerts, backspace, carriage_return, form_feed, horizontal_tab, vertical_tab, or new_line is now tested and working. (MSB - 2012/09/01) - Corrected the integer type of H5S_UNLIMITED_F to HSIZE_T (MSB - 2012/09/01) - Corrected the number of continuation lines in the src files to be less than 32 lines for F95 compliance. (MSB - 2012/10/01) C++ API ------ - None High-Level APIs: ------ - Fixed problem with H5TBdelete_record destroying all data following the deletion of a row. (MSB- 2012/7/26) - Fixed H5LTget_attribute_string not closing an object identifier when an error occurs. (MSB- 2012/7/21) - Corrected the return type of H5TBAget_fill from herr_t to htri_t to reflect that a return value of 1 indicates that a fill value is present, 0 indicates a fill value is not present, and <0 indicates an error. Fortran High-Level APIs: ------ - None Supported Platforms =================== AIX 5.3 xlc 10.1.0.5 (NASA G-ADA) xlC 10.1.0.5 xlf90 12.1.0.6 Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP i686 i686 i386 compilers for 32-bit applications; (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-52) Version 4.6.3 PGI C, Fortran, C++ Compilers for 32-bit applications; Version 11.9-0 Intel(R) C, C++, Fortran Compiler for 32-bit applications; Version 12.1 MPICH mpich2-1.4.1p1 compiled with gcc 4.1.2 and gfortran 4.1.2 Linux 2.6.18-308.16.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP x86_64 GNU/Linux compilers for 32-bit applications; (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-52) Version 4.6.3 PGI C, Fortran, C++ for 64-bit target on x86-64; Version 11.9-0 Version 12.5-0 Intel(R) C, C++, Fortran Compilers for applications running on Intel(R) 64; Version 12.1 (Build 20110811) Version 12.1 (Build 20120212) MPICH mpich2-1.4.1p1 compiled with gcc 4.1.2 and gfortran 4.1.2 Linux 2.6.32-220.7.1.el6.ppc64 gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.6 20110731 (ostrich) GNU Fortran (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) Linux 2.6.32-220.23.1.1chaos Intel C, C++, Fortran Compilers ch5.x86_64 GNU/Linux Version 12.1.5.339 (LLNL Aztec) IBM Blue Gene/P XL C for Blue Gene/P, bgxlc V9.0 (LLNL uDawn) XL C++ for Blue Gene/P, bgxlC V9.0 XL Fortran for Blue Gene/P, bgxlf90 V11.1 SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16 (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13 Sun C++ 5.9 Sun OS_sparc Patch 124863-26 Sun C 5.11 SunOS_sparc Sun Fortran 95 8.5 SunOS_sparc Sun C++ 5.11 SunOS_sparc Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Visual Studio 2010 w/ Intel Fortran 12 (cmake) Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) (cmake and autotools) Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Visual Studio 2010 w/ Intel Fortran 12 (cmake) Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) (cmake and autotools) Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 (fred) gfortran GNU Fortran (GCC) 4.6.2 Intel C (icc), Fortran (ifort), C++ (icpc) 12.1.0.038 Build 20110811 Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 Intel 32-bit gfortran GNU Fortran (GCC) 4.6.1 (tejeda) Intel C (icc), Fortran (ifort), C++ (icpc) 12.1.0.038 Build 20110811 Mac OS X Lion 10.7.3 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.2.1 32- and 64-bit g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.2.1 (duck) gfortran GNU Fortran (GCC) 4.6.2 Mac OS X Mountain Lion 10.8.1 cc Apple clang version 4.0 from Xcode 4.5.1 (owl) c++ Apple clang version 4.0 from Xcode 4.5.1 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.5.1 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.5.1 gfortran GNU Fortran (GCC) 4.6.2 Tested Configuration Features Summary ===================================== In the tables below y = tested n = not tested in this release C = Cluster W = Workstation 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 F2003 parallel Solaris2.10 32-bit n y/y n y y y Solaris2.10 64-bit n y/n n y y y Windows 7 y y/n n y y y Windows 7 x64 y y/n n y y y Mac OS X Snow Leopard 10.6.8 32-bit n y/y n y y n Mac OS X Snow Leopard 10.6.8 64-bit n y/y n y y y Mac OS X Lion 10.7.3 32-bit n y/y n y y n Mac OS X Lion 10.7.3 64-bit n y/y n y y y Mac OS X Mountain Lion 10.8.1 64-bit n y/n n y y n AIX 5.3 32- and 64-bit y y/n y y y y CentOS 5.5 Linux 2.6.18-308 i686 GNU y y/y y y y y CentOS 5.5 Linux 2.6.18-308 i686 Intel n y/y n y y y CentOS 5.5 Linux 2.6.18-308 i686 PGI n y/y n y y y CentOS 5.5 Linux 2.6.18 x86_64 GNU y y/y y y y y CentOS 5.5 Linux 2.6.18 x86_64 Intel n y/y n y y y CentOS 5.5 Linux 2.6.18 x86_64 PGI n y/y n y y y Linux 2.6.32-220.7.1.el6.ppc64 n y/n n y y y Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Solaris2.10 32-bit y y y y Solaris2.10 64-bit n n n n Windows 7 y y y y Windows 7 x64 y y y y Mac OS X Snow Leopard 10.6.8 32-bit y n y n Mac OS X Snow Leopard 10.6.8 64-bit y n y n Mac OS X Lion 10.7.3 32-bit y n y y Mac OS X Lion 10.7.3 64-bit y n y y Mac OS X Mountain Lion 10.8.1 64-bit y n y y AIX 5.3 32- and 64-bit n n n y CentOS 5.5 Linux 2.6.18-308 i686 GNU y y y y CentOS 5.5 Linux 2.6.18-308 i686 Intel y y y n CentOS 5.5 Linux 2.6.18-308 i686 PGI y y y n CentOS 5.5 Linux 2.6.18 x86_64 GNU y y y y CentOS 5.5 Linux 2.6.18 x86_64 Intel y y y n CentOS 5.5 Linux 2.6.18 x86_64 PGI y y y n Linux 2.6.32-220.7.1.el6.ppc64 y y y n Compiler versions for each platform are listed in the preceding "Supported Platforms" table. More Tested Platforms ===================== The following platforms are not supported but have been tested for this release. FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 (loyalty) gcc 4.6.1 20110422 g++ 4.6.1 20110422 gfortran 4.6.1 20110422 FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 (freedom) gcc 4.6.1 20110422 g++ 4.6.1 20110422 gfortran 4.6.1 20110422 Debian6.0.3 2.6.32-5-686 #1 SMP i686 GNU/Linux gcc (Debian 4.4.5-8) 4.4.5 GNU Fortran (Debian 4.4.5-8) 4.4.5 (cmake and autotools) Debian6.0.3 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux gcc (Debian 4.4.5-8) 4.4.5 GNU Fortran (Debian 4.4.5-8) 4.4.5 (cmake and autotools) Fedora17 3.5.2-1.fc17.i6866 #1 SMP i686 i686 i386 GNU/Linux gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) (cmake and autotools) Fedora17 3.5.2-1.fc17.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) (cmake and autotools) SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux gcc (SUSE Linux) 4.7.1 GNU Fortran (SUSE Linux) 4.7.1 (cmake and autotools) SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux gcc (SUSE Linux) 4.7.1 GNU Fortran (SUSE Linux) 4.7.1 (cmake and autotools) Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP i686 GNU/Linux gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 (cmake and autotools) Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP x86_64 GNU/Linux gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 (cmake and autotools) (Use optimization level -O1) Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46 hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai Known Problems ============== * The C++ and FORTRAN bindings are not currently working on FreeBSD with the native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the ports (and probably gcc releases after that). (QAK - 2012/10/19) * The following h5dump test case fails in BG/P machines (and potentially other machines that use a command script to launch executables): h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" tno-subset.h5 This is due to the embedded spaces in the dataset name being interpreted by the command script launcher as meta-characters, thus passing three arguments to h5dump's -d flag. The command passes if run by hand, just not via the test script. (AKC - 2012/05/03) * On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set to aprun -np X, because the H5lib_settings.c file was not generated properly. Not setting those environment variables works, because configure was able to automatically detect that it's a Cray system and used the proper launch commands when necessary. (MSC - 2012/04/18) * The data conversion test dt_arith.c fails in "long double" to integer conversion on Ubuntu 11.10 (3.0.0.13 kernal) with GCC 4.6.1 if the library is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernal (3.2.2 on Fedora) doesn't have the problem. Users should lower the optimization level (-O1 or -O0) by defining CFLAGS in the command line of "configure" like: CFLAGS=-O1 ./configure This will overwrite the library's default optimization level. (SLU - 2012/02/07 - HDFFV-7829) * The STDIO VFD does not work on some architectures, possibly due to 32/64 bit or large file issues. The basic STDIO VFD test is known to fail on 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin 10.7.0. The STDIO VFD test has been disabled while we investigate and a fix should appear in a future release. (DER - 2011/10/14 - HDFFV-8235) * h5diff can report inconsistent results when comparing datasets of enum type that contain invalid values. This is due to how enum types are handled in the library and will be addressed in a future release. (DER - 2011/10/14 - HDFFV-7527) * The links test can fail under the stdio VFD due to some issues with external links. This will be investigated and fixed in a future release. (DER - 2011/10/14 - HDFFV-7768) * After the shared library support was fixed for some bugs, it was discovered that "make prefix=XXX install" no longer works for shared libraries. It still works correctly for static libraries. Therefore, if you want to install the HDF5 shared libraries in a location such as /usr/local/hdf5, you need to specify the location via the --prefix option during configure time. E.g, ./configure --prefix=/usr/local/hdf5 ... (AKC - 2011/05/07 - HDFFV-7583) * The parallel test, t_shapesame, in testpar/, may run for a long time and may be terminated by the alarm signal. If that happens, one can increase the alarm seconds (default is 1200 seconds = 20 minutes) by setting the environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 (60 minutes). Note that the t_shapesame test may fail in some systems (see the "While working on the 1.8.6 release..." problem below). If it does, it will waste more time if $HDF5_ALARM_SECONDS is set to a larger value. (AKC - 2011/05/07) * The C++ and FORTRAN bindings are not currently working on FreeBSD. (QAK - 2011/04/26) * Shared Fortran libraries are not quite working on AIX. While they are generated when --enable-shared is specified, the fortran and hl/fortran tests fail. We are looking into the issue. HL and C++ shared libraries should now be working as intended, however. (MAM - 2011/04/20) * The --with-mpe configure option does not work with Mpich2. (AKC - 2011/03/10) * While working on the 1.8.6 release of HDF5, a bug was discovered that can occur when reading from a dataset in parallel shortly after it has been written to collectively. The issue was exposed by a new test in the parallel HDF5 test suite, but had existed before that. We believe the problem lies with certain MPI implementations and/or file systems. We have provided a pure MPI test program, as well as a standalone HDF5 program, that can be used to determine if this is an issue on your system. They should be run across multiple nodes with a varying number of processes. These programs can be found at: http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ (NAF - 2011/01/19) * The library's test dt_arith.c showed a compiler's rounding problem on Cygwin when converting from unsigned long long to long double. The library's own conversion works fine. We defined a macro for Cygwin to skip this test until we can solve the problem. (SLU - 2010/05/05 - HDFFV-1264) * All the VFL drivers aren't backward compatible. In H5FDpublic.h, the structure H5FD_class_t changed in 1.8. There is new parameter added to get_eoa and set_eoa callback functions. A new callback function get_type_map was added in. The public function H5FDrealloc was taken out in 1.8. The problem only happens when users define their own driver for 1.6 and try to plug in 1.8 library. Because there's only one user complaining about it, we (Elena, Quincey, and I) decided to leave it as it is (see bug report #1279). Quincey will make a plan for 1.10. (SLU - 2010/02/02) * The --enable-static-exec configure flag will only statically link libraries if the static version of that library is present. If only the shared version of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, for example, only have shared versions), the flag should still result in a successful compilation, but note that the installed executables will not be fully static. Thus, the only guarantee on these systems is that the executable is statically linked with just the HDF5 library. (MAM - 2009/11/04) * Parallel tests failed with 16 processes with data inconsistency at testphdf5 / dataset_readAll. Parallel tests also failed with 32 and 64 processes with collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks with MPI IO. (CMC - 2009/04/28) * On an 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. * 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 calculation 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 - 2005/06/30) %%%%1.8.10%%%% HDF5 version 1.8.10 released on 2012-10-26 ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.9 and HDF5 1.8.10, and contains information on the platforms tested and known problems in HDF5-1.8.10. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.10 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.10 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.10 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in the HDF5-1.8.x release series, 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 1.8.10 (current release) versus Release 1.8.9": 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 - Support for New Platforms, Languages, and Compilers - Bug Fixes since HDF5-1.8.9 - Supported Platforms - Supported Configuration Features Summary - More Tested Platforms - Known Problems New Features ============ Configuration ------------- - None Library ------- - Updated to latest autotools and changed all hard *.sh scripts to configure managed *.sh.in files. Removed overloading of autotools TESTS variable by examples and tests. Renamed configure.in to configure.ac. (ADB - 2012/08/23 - HDFFV-8129) - The data sieve buffer size was set for all the datasets in the file. It could waste memory if any dataset size is smaller than the sieve buffer size. Now the library picks the smaller one between the dataset size and the sieve buffer size from the file access property. See Issue 7934. (SLU - 2012/4/11) Parallel Library ---------------- - Added the H5Pget_mpio_no_collective_cause() function that retrieves reasons why the collective I/O was broken during read/write IO access. (JKM - 2012/08/30 HDFFV-8143) - Added H5Pget_mpio_actual_io_mode_f (MSB - 2012/09/27) Tools ----- - h5import: Changed to allow the use of h5dump output as input files to h5import. h5dump must include the "-p" option to print the properties; configuration file is captured output of h5dump. The restrictions are that only one dataset with a simple datatype (integer, floating-point, or string) can be processed. Integers and floating-point imports from h5dump must use the "binary" option for the data file. The string version uses the h5dump "-y --width=1" options to disable the indexing printouts, print single columns, and obviously NOT use the "binary" option. (ADB - 2012/07/19 HDFFV-721) High-Level APIs --------------- - None Fortran API ----------- - Fixed a typo in return value of the nh5dread_f_c function (was 1 instead of 0 on success); fixed the return value to make it consistent with other Fortran functions; cleaned debug statements from the code. (EIP - 2012/06/23) C++ API ------- - None Support for New Platforms, Languages, and Compilers =================================================== - None Bug Fixes since HDF5-1.8.9 ========================== Configuration ------------- - Fixed configure --enable-production to not use -O optimization for Lion and Mountain Lion systems when gcc (i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1) is used. Somehow the -O optimization will cause some of the hard conversion code in test/dt_arith.c to fail. HDFFV-8017. (AKC - 2012/10/10) - Fixed AIX Fortran compiler flags to use appropriate settings for debugging, profiling, and optimization situations. HDFFV-8069. (AKC 2012/09/27) Library ------- - Fixed a memory leak exposed when inserting/removing a property from a property list several times. HDFFV-8022. (MSC 2012/05/18) - The file_image test will fail in the "initial file image and callbacks in the core VFD" sub-test if the source directory is read-only as the test fails to create its test files in the build directory. This has been fixed. HDFFV-8009 (AKC - 2012/07/06) Parallel Library ---------------- - The MPI-POSIX VFD was updated to include the POSIX and Windows correctness features added that had already been added to the other VFDs. HDFFV-8058/7845. (DER 2012/09/17) Performance ------------- - Removed program perform/benchpar from the enable-build-all list. The program will be retired or moved to another location. HDFFV-8156 (AKC 2012/10/01) - Retired program perform/mpi-perf. Its purpose has been incorporated into h5perf. (AKC 2012/09/21) Tools ----- - h5repack: "h5repack -f NONE file1.h5 out.h5" command failed if source file contains chunked dataset and a chunk dim is bigger than the dataset dim. Another issue is that the command changed max dims if chunk dim is smaller than the dataset dim. These issue occurred when dataset size is smaller than 64k (compact size limit) Fixed both. HDFFV-8012 (JKM 2012/09/24) - h5diff: Fixed the counter in verbose mode (-v, -r) so that it will no longer add together the differences between datasets and the differences between attributes of those datasets. This change makes the output of verbose mode consistent for datasets, groups, and committed datatypes. HDFFV-5919 (JKM 2012/09/10) - h5diff: Fixed the incorrect result when comparing attribute data values and the data type has the same class but different sizes. HDFFV-7942 (JKM 2012/08/15) - h5dump: Replaced single element fwrite with block writes. HDFFV-1208 (ADB 2012/08/13) - h5diff: Fixed test failure for "make check" due to failure of copying test files when performed in HDF5 source tree. Also applied to other tools. HDFFV-8107 (JKM 2012/08/01) - ph5diff: Fixed intermittent hang issue on a certain operation in parallel mode. It was detected by daily test for comparing non-comparable objects, but it could have occurred in other operations depending on machine condition. HDFFV-8003 (JKM 2012/08/01) - h5diff: Fixed the function COPY_TESTFILES_TO_TESTDIR() of testh5diff.sh to better report when there is an error in the file copying. HDFFV-8105 (AKC 2012/07/22) - h5dump: Fixed the sort by name display to maintain correct parent/child relationships between ascending/descending order. HDFFV-8095 (ADB 2012/07/12) - h5dump: Fixed the display by creation order when using option -n (print contents). HDFFV-5942 (ADB 2012/07/09) - h5dump: Changed to allow H5T_CSET_UTF8 to be displayed in h5dump output. Used technique similar to what was done in h5ls (matches library options). HDFFV-7999 (ADB 2012/05/23) - h5diff: Fixed the tool so that it will not check and display the status of dangling links without setting the --follow-symlinks option. This also improved performance when comparing lots of external links without the --follow-symlinks option. HDFFV-7998 (JKM 2012/04/26) F90 API ------- - Fixed a typo in return value of the nh5dread_f_c function (was 1 instead of 0 on success); fixed the return value to make it consistent with other Fortran functions; cleaned debug statements from the code. (EIP - 2012/06/23) - Fixed a problem writing/reading control characters to a dataset; writing a string containing alerts, backspace, carriage_return, form_feed, horizontal_tab, vertical_tab, or new_line is now tested and working. (MSB - 2012/09/01) - Corrected the integer type of H5S_UNLIMITED_F to HSIZE_T (MSB - 2012/09/01) - Corrected the number of continuation lines in the src files to be less than 32 lines for F95 compliance. (MSB - 2012/10/01) C++ API ------ - None High-Level APIs: ------ - Fixed problem with H5TBdelete_record destroying all data following the deletion of a row. (MSB- 2012/7/26) - Fixed H5LTget_attribute_string not closing an object identifier when an error occurs. (MSB- 2012/7/21) - Corrected the return type of H5TBAget_fill from herr_t to htri_t to reflect that a return value of 1 indicates that a fill value is present, 0 indicates a fill value is not present, and <0 indicates an error. Fortran High-Level APIs: ------ - None Supported Platforms =================== AIX 5.3 xlc 10.1.0.5 (NASA G-ADA) xlC 10.1.0.5 xlf90 12.1.0.6 Linux 2.6.18-308.13.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP i686 i686 i386 compilers for 32-bit applications; (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-52) Version 4.6.3 PGI C, Fortran, C++ Compilers for 32-bit applications; Version 11.9-0 Intel(R) C, C++, Fortran Compiler for 32-bit applications; Version 12.1 MPICH mpich2-1.4.1p1 compiled with gcc 4.1.2 and gfortran 4.1.2 Linux 2.6.18-308.16.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP x86_64 GNU/Linux compilers for 32-bit applications; (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-52) Version 4.6.3 PGI C, Fortran, C++ for 64-bit target on x86-64; Version 11.9-0 Version 12.5-0 Intel(R) C, C++, Fortran Compilers for applications running on Intel(R) 64; Version 12.1 (Build 20110811) Version 12.1 (Build 20120212) MPICH mpich2-1.4.1p1 compiled with gcc 4.1.2 and gfortran 4.1.2 Linux 2.6.32-220.7.1.el6.ppc64 gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.6 20110731 (ostrich) GNU Fortran (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) Linux 2.6.32-220.23.1.1chaos Intel C, C++, Fortran Compilers ch5.x86_64 GNU/Linux Version 12.1.5.339 (LLNL Aztec) IBM Blue Gene/P XL C for Blue Gene/P, bgxlc V9.0 (LLNL uDawn) XL C++ for Blue Gene/P, bgxlC V9.0 XL Fortran for Blue Gene/P, bgxlf90 V11.1 SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16 (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13 Sun C++ 5.9 Sun OS_sparc Patch 124863-26 Sun C 5.11 SunOS_sparc Sun Fortran 95 8.5 SunOS_sparc Sun C++ 5.11 SunOS_sparc Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Visual Studio 2010 w/ Intel Fortran 12 (cmake) Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) (cmake and autotools) Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Visual Studio 2010 w/ Intel Fortran 12 (cmake) Cygwin(CYGWIN_NT-6.1 1.7.15(0.260/5/3) gcc(4.5.3) compiler and gfortran) (cmake and autotools) Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 (fred) gfortran GNU Fortran (GCC) 4.6.2 Intel C (icc), Fortran (ifort), C++ (icpc) 12.1.0.038 Build 20110811 Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 Intel 32-bit gfortran GNU Fortran (GCC) 4.6.1 (tejeda) Intel C (icc), Fortran (ifort), C++ (icpc) 12.1.0.038 Build 20110811 Mac OS X Lion 10.7.3 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.2.1 32- and 64-bit g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.2.1 (duck) gfortran GNU Fortran (GCC) 4.6.2 Mac OS X Mountain Lion 10.8.1 cc Apple clang version 4.0 from Xcode 4.5.1 (owl) c++ Apple clang version 4.0 from Xcode 4.5.1 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.5.1 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.5.1 gfortran GNU Fortran (GCC) 4.6.2 Tested Configuration Features Summary ===================================== In the tables below y = tested n = not tested in this release C = Cluster W = Workstation 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 F2003 parallel Solaris2.10 32-bit n y/y n y y y Solaris2.10 64-bit n y/n n y y y Windows 7 y y/n n y y y Windows 7 x64 y y/n n y y y Mac OS X Snow Leopard 10.6.8 32-bit n y/y n y y n Mac OS X Snow Leopard 10.6.8 64-bit n y/y n y y y Mac OS X Lion 10.7.3 32-bit n y/y n y y n Mac OS X Lion 10.7.3 64-bit n y/y n y y y Mac OS X Mountain Lion 10.8.1 64-bit n y/n n y y n AIX 5.3 32- and 64-bit y y/n y y y y CentOS 5.5 Linux 2.6.18-308 i686 GNU y y/y y y y y CentOS 5.5 Linux 2.6.18-308 i686 Intel n y/y n y y y CentOS 5.5 Linux 2.6.18-308 i686 PGI n y/y n y y y CentOS 5.5 Linux 2.6.18 x86_64 GNU y y/y y y y y CentOS 5.5 Linux 2.6.18 x86_64 Intel n y/y n y y y CentOS 5.5 Linux 2.6.18 x86_64 PGI n y/y n y y y Linux 2.6.32-220.7.1.el6.ppc64 n y/n n y y y Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Solaris2.10 32-bit y y y y Solaris2.10 64-bit n n n n Windows 7 y y y y Windows 7 x64 y y y y Mac OS X Snow Leopard 10.6.8 32-bit y n y n Mac OS X Snow Leopard 10.6.8 64-bit y n y n Mac OS X Lion 10.7.3 32-bit y n y y Mac OS X Lion 10.7.3 64-bit y n y y Mac OS X Mountain Lion 10.8.1 64-bit y n y y AIX 5.3 32- and 64-bit n n n y CentOS 5.5 Linux 2.6.18-308 i686 GNU y y y y CentOS 5.5 Linux 2.6.18-308 i686 Intel y y y n CentOS 5.5 Linux 2.6.18-308 i686 PGI y y y n CentOS 5.5 Linux 2.6.18 x86_64 GNU y y y y CentOS 5.5 Linux 2.6.18 x86_64 Intel y y y n CentOS 5.5 Linux 2.6.18 x86_64 PGI y y y n Linux 2.6.32-220.7.1.el6.ppc64 y y y n Compiler versions for each platform are listed in the preceding "Supported Platforms" table. More Tested Platforms ===================== The following platforms are not supported but have been tested for this release. FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 (loyalty) gcc 4.6.1 20110422 g++ 4.6.1 20110422 gfortran 4.6.1 20110422 FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 (freedom) gcc 4.6.1 20110422 g++ 4.6.1 20110422 gfortran 4.6.1 20110422 Debian6.0.3 2.6.32-5-686 #1 SMP i686 GNU/Linux gcc (Debian 4.4.5-8) 4.4.5 GNU Fortran (Debian 4.4.5-8) 4.4.5 (cmake and autotools) Debian6.0.3 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux gcc (Debian 4.4.5-8) 4.4.5 GNU Fortran (Debian 4.4.5-8) 4.4.5 (cmake and autotools) Fedora17 3.5.2-1.fc17.i6866 #1 SMP i686 i686 i386 GNU/Linux gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) (cmake and autotools) Fedora17 3.5.2-1.fc17.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux gcc (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) GNU Fortran (GCC) 4.7.0 20120507 (Red Hat 4.7.0-5) (cmake and autotools) SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux gcc (SUSE Linux) 4.7.1 GNU Fortran (SUSE Linux) 4.7.1 (cmake and autotools) SUSE 12.2 3.4.6-2.10-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux gcc (SUSE Linux) 4.7.1 GNU Fortran (SUSE Linux) 4.7.1 (cmake and autotools) Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP i686 GNU/Linux gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 (cmake and autotools) Ubuntu 12.04 3.2.0-29-generic #46-Ubuntu SMP x86_64 GNU/Linux gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 (cmake and autotools) (Use optimization level -O1) Cray Linux Environment (CLE) PrgEnv-pgi/4.0.46 hopper.nersc.gov pgcc 12.5-0 64-bit target on x86-64 Linux -tp shanghai pgf90 12.5-0 64-bit target on x86-64 Linux -tp shanghai pgCC 12.5-0 64-bit target on x86-64 Linux -tp shanghai Known Problems ============== * The following h5stat test case fails in BG/P machines (and potentially other machines that display extra output if an MPI task returns with a non-zero code.) Testing h5stat notexist.h5 The test actually runs and passes as expected. It is the extra output from the MPI process that causes the test script to fail. This will be fixed in the next release. (AKC - 2012/10/25 - HDFFV-8233) * The C++ and FORTRAN bindings are not currently working on FreeBSD with the native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the ports (and probably gcc releases after that). (QAK - 2012/10/19) * The following h5dump test case fails in BG/P machines (and potentially other machines that use a command script to launch executables): h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" tno-subset.h5 This is due to the embedded spaces in the dataset name being interpreted by the command script launcher as meta-characters, thus passing three arguments to h5dump's -d flag. The command passes if run by hand, just not via the test script. (AKC - 2012/05/03) * On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set to aprun -np X, because the H5lib_settings.c file was not generated properly. Not setting those environment variables works, because configure was able to automatically detect that it's a Cray system and used the proper launch commands when necessary. (MSC - 2012/04/18) * The data conversion test dt_arith.c fails in "long double" to integer conversion on Ubuntu 11.10 (3.0.0.13 kernal) with GCC 4.6.1 if the library is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernal (3.2.2 on Fedora) doesn't have the problem. Users should lower the optimization level (-O1 or -O0) by defining CFLAGS in the command line of "configure" like: CFLAGS=-O1 ./configure This will overwrite the library's default optimization level. (SLU - 2012/02/07 - HDFFV-7829) * The STDIO VFD does not work on some architectures, possibly due to 32/64 bit or large file issues. The basic STDIO VFD test is known to fail on 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin 10.7.0. The STDIO VFD test has been disabled while we investigate and a fix should appear in a future release. (DER - 2011/10/14 - HDFFV-8235) * h5diff can report inconsistent results when comparing datasets of enum type that contain invalid values. This is due to how enum types are handled in the library and will be addressed in a future release. (DER - 2011/10/14 - HDFFV-7527) * The links test can fail under the stdio VFD due to some issues with external links. This will be investigated and fixed in a future release. (DER - 2011/10/14 - HDFFV-7768) * After the shared library support was fixed for some bugs, it was discovered that "make prefix=XXX install" no longer works for shared libraries. It still works correctly for static libraries. Therefore, if you want to install the HDF5 shared libraries in a location such as /usr/local/hdf5, you need to specify the location via the --prefix option during configure time. E.g, ./configure --prefix=/usr/local/hdf5 ... (AKC - 2011/05/07 - HDFFV-7583) * The parallel test, t_shapesame, in testpar/, may run for a long time and may be terminated by the alarm signal. If that happens, one can increase the alarm seconds (default is 1200 seconds = 20 minutes) by setting the environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 (60 minutes). Note that the t_shapesame test may fail in some systems (see the "While working on the 1.8.6 release..." problem below). If it does, it will waste more time if $HDF5_ALARM_SECONDS is set to a larger value. (AKC - 2011/05/07) * The C++ and FORTRAN bindings are not currently working on FreeBSD. (QAK - 2011/04/26) * Shared Fortran libraries are not quite working on AIX. While they are generated when --enable-shared is specified, the fortran and hl/fortran tests fail. We are looking into the issue. HL and C++ shared libraries should now be working as intended, however. (MAM - 2011/04/20) * The --with-mpe configure option does not work with Mpich2. (AKC - 2011/03/10) * While working on the 1.8.6 release of HDF5, a bug was discovered that can occur when reading from a dataset in parallel shortly after it has been written to collectively. The issue was exposed by a new test in the parallel HDF5 test suite, but had existed before that. We believe the problem lies with certain MPI implementations and/or file systems. We have provided a pure MPI test program, as well as a standalone HDF5 program, that can be used to determine if this is an issue on your system. They should be run across multiple nodes with a varying number of processes. These programs can be found at: http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ (NAF - 2011/01/19) * The library's test dt_arith.c showed a compiler's rounding problem on Cygwin when converting from unsigned long long to long double. The library's own conversion works fine. We defined a macro for Cygwin to skip this test until we can solve the problem. (SLU - 2010/05/05 - HDFFV-1264) * All the VFL drivers aren't backward compatible. In H5FDpublic.h, the structure H5FD_class_t changed in 1.8. There is new parameter added to get_eoa and set_eoa callback functions. A new callback function get_type_map was added in. The public function H5FDrealloc was taken out in 1.8. The problem only happens when users define their own driver for 1.6 and try to plug in 1.8 library. Because there's only one user complaining about it, we (Elena, Quincey, and I) decided to leave it as it is (see bug report #1279). Quincey will make a plan for 1.10. (SLU - 2010/02/02) * The --enable-static-exec configure flag will only statically link libraries if the static version of that library is present. If only the shared version of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, for example, only have shared versions), the flag should still result in a successful compilation, but note that the installed executables will not be fully static. Thus, the only guarantee on these systems is that the executable is statically linked with just the HDF5 library. (MAM - 2009/11/04) * Parallel tests failed with 16 processes with data inconsistency at testphdf5 / dataset_readAll. Parallel tests also failed with 32 and 64 processes with collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks with MPI IO. (CMC - 2009/04/28) * On an 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. * 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 calculation 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 - 2005/06/30) %%%%1.8.9%%%% HDF5 version 1.8.9 released on 2012-05-09 ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.8 and HDF5 1.8.9. It also contains information on the platforms tested and known problems in HDF5-1.8.9. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.9 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.9 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.9 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in the HDF5-1.8.x release series, 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 1.8.9 (current release) versus Release 1.8.8": 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 - Support for New Platforms, Languages, and Compilers - Bug Fixes since HDF5-1.8.8 - Platforms Tested - Supported Configuration Features Summary - Known Problems New Features ============ Configuration ------------- - None Library ------- - Added new feature to merge committed datatypes when copying objects, using new H5O_COPY_MERGE_COMMITTED_DTYPE_FLAG, modified by new API routines: H5Padd_merge_committed_dtype_path(), H5Pfree_merge_committed_dtype_paths(), H5Pset_mcdt_search_cb() and H5Pget_mcdt_search_cb(). (QAK - 2012/03/30) - Added new feature which allows working with files in memory in the same ways files are worked with on disk. New API routines include H5Pset_file_image, H5Pget_file_image, H5Pset_file_image_callbacks, H5Pget_file_image_callbacks, H5Fget_file_image, and H5LTopen_file_image. (QAK - 2012/04/17) Parallel Library ---------------- - Corrected memory allocation error in MPI datatype construction code. (QAK - 2012/04/23) - Add two new routines to set/get the atomicity parameter in the MPI library to perform atomic operations. Some file systems (for example PVFS2) do not support atomic updates, so those routines would not be supported. (MSC - 2012/03/27 - HDFFV-7961) Tools ----- - h5repack: Added ability to set the metadata block size of the output file, with the '-M'/'--metadata_block_size' command line parameter. (QAK - 2012/03/30) - h5stat: Added ability to display a summary of the file space usage for a file, with the '-S'/'--summary' command line parameter. (QAK - 2012/03/28) - h5dump: Added capability for "-a" option to show attributes containing "/" by using an escape character. For example, for a dataset "/dset" containing attribute "speed(m/h)", use "h5dump -a "/dset/speed(\/h)" to show the content of the attribute. (PC - 2012/03/12 - HDFFV-7523) - h5dump: Added ability to apply command options across multiple files using a wildcard in the filename. Unix example; "h5dump -H -d Dataset1 tarr*.h5". Cross platform example; "h5dump -H -d Dataset1 tarray1.h5 tarray2.h5 tarray3.h5". (ADB - 2012/03/12 - HDFFV-7876). - h5dump: Added new option --no-compact-subset. This option will not interpret the '[' character as starting the compact form of subsetting. This is useful when the "h5dump error: unable to open dataset "datset_name"" message is output because a dataset name contains a '[' character. (ADB - 2012/03/05 - HDFFV-7689). - h5repack: Improved performance for big chunked datasets (size > 128MB) when used with the layout (-l) or compression (-f) options. Before this change, repacking datasets with chunks with a large first dimension would take extremely long. For example, repacking a dataset with chunk dimensions of 1024x5x1 might take many hours to process while changing a dataset with chunk dimensions set to 1x5x1024 might take under an hour. After this change, processing the dataset with chunk dimensions of 1024x5x1 takes about 15 minutes, and processing a dataset with chunk dimensions of 1x5x1024 takes about 14 minutes. (JKM - 2012/03/01 - HDFFV-7862) High-Level APIs --------------- - New API: H5LTpath_valid (Fortran: h5ltpath_valid_f) checks if a path is correct, determines if a link resolves to a valid object, and checks that the link does not dangle. (MSB - 2012/03/15) Fortran API ----------- - Added for the C API the Fortran wrapper: h5ocopy_f (MSB - 2012/03/22) C++ API ------- - None Support for New Platforms, Languages, and Compilers =================================================== - None Bug Fixes since HDF5-1.8.8 ========================== Configuration ------------- - Fixed Makefile issue in which "-Wl," was not properly specified prior to -rpath when building parallel Fortran libraries with an Intel compiler. (MAM - 2012/03/26) - Makefiles generated by other packages using h5cc as the compiler no longer error when 'make' is invoked more than once in order to 'rebuild' after changes to source. (MAM - 2012/03/26) - Added code to display the version information of XL Fortran and C++ in the summary of configure. (AKC - 2012/02/28 - HDFFV-7793) - Updated all CMakeLists.txt files to indicate the minimum CMake version is the current standard of 2.8.6 (ADB - 2011/12/05 - HDFFV-7854) Library ------- - Windows and STDIO correctness changes have been propagated from the SEC2 and old Windows drivers to the STDIO VFD. (DER - 2012/03/30 - HDFFV-7917) - Fixed an error that would occur when copying an object with attribute creation order tracked and indexed. (NAF - 2012/03/28 - HDFFV-7762) - Fixed a bug in H5Ocopy(): When copying an opened object, call the object's flush class action to ensure that cached data is flushed so that H5Ocopy will get the correct data. (VC - 2012/03/27 - HDFFV-7853) - The istore test will now skip the sparse 50x50x50 test when the VFD does not support sparse files on that platform. The most important platforms on which this will be skipped are Windows (NTFS sparse files are not supported) and Mac OS-X (HFS sparse files are not supported). This fixes CTest timeout issues on Windows. (DER - 2012/03/27 - HDFFV-7769) - Windows and POSIX correctness changes have been propagated from the SEC2 VFD to the Core VFD. This mainly affects file operations on the driver's backing store and fixes a problem on Windows where large files could not be read. (DER - 2012/03/27 - HDFFV-7916 - HDFFV-7603) - When an application tries to write or read many small data chunks and runs out of memory, the library had a segmentation fault. The fix is to return the error stack with proper information. (SLU - 2012/03/23 - HDFFV-7785) - H5Pset_data_transform had a segmentation fault in some cases like x*-100. It works correctly now and handles other cases like 100-x or 2/x. (SLU - 2012/03/15 - HDFFV-7922) - Fixed rare corruption bugs that could occur when using the new object header format. (NAF - 2012/03/15 - HDFFV-7879) - Fixed an error that occurred when creating a contiguous dataset with a zero-sized dataspace and space allocation time set to 'early'. (QAK - 2012/03/12) - Changed Windows thread creation to use _beginthread() instead of CreateThread(). Threads created by the latter can be killed in low-memory situations. (DER - 2012/02/10 - HDFFV-7780) - Creating a dataset in a read-only file caused a segmentation fault when the file is closed. It's fixed. The attempt to create a dataset will fail with an error indicating the file is read-only. (SLU - 2012/01/25 - HDFFV-7756) - Fixed a segmentation fault that could occur when shrinking a dataset with chunks larger than 1 MB. (NAF - 2011/11/30 - HDFFV-7833) - Fixed a bug that could cause H5Oget_info to return the wrong address after copying a committed (named) datatype. (NAF - 2011/11/14) - The library allowed the conversion of strings between ASCII and UTF8 We have corrected it to report an error under this situation. (SLU - 2011/11/8 - HDFFV-7582) - Fixed a segmentation fault when the library tried to shrink the size of a compound datatype through H5Tset_size immediately after the datatype was created. (SLU - 2011/11/4 - HDFFV-7618) Parallel Library ---------------- - None Tools ----- - h5unjam: Fixed a segmentation fault that occurred when h5unjam was used with the -V (show version) option. (JKM - 2012/04/19 - HDFFV-8001) - h5repack: Fixed a failure that occurred when repacking the chunk size of a specified chunked dataset with unlimited max dims. (JKM - 2012/04/11 - HDFFV-7993) - h5diff: Fixed a failure when comparing groups. Before the fix, if an object in a group was compared with an object in another group where both had the same name but the object type was different, then h5diff would fail. After the fix, h5diff detects such cases as non-comparable and displays appropriate error messages. (JKM - 2012/03/28 - HDFFV-7644) - h5diff: If unique objects exist only in one file and if h5diff is set to exclude the unique objects with the --exclude-path option, then h5diff might miss excluding some objects. This was fixed to correctly exclude objects. (JKM - 2012/03/20 - HDFFV-7837) - h5diff: When two symbolic dangling links are compared with the --follow-symlinks option, the result should be the same. This worked when comparing two files, but didn't work when comparing two objects. h5diff now works when comparing two objects. (JKM - 2012/03/09 - HDFFV-7835) - h5dump: Added the tools library error stack to properly catch error information generated within the library. (ADB - 2012/03/12 - HDFFV-7958) - h5dump: Changed the process where an open link used to fail. Now dangling links no longer throw error messages. (ADB - 2012/03/12 - HDFFV-7839) - h5dump: Refactored code to remove duplicated functions. Split XML functions from DDL functions. Corrected indentation and formatting errors. Also fixed subsetting counting overflow (HDFFV-5874). Verified all tools call tools_init() in main. The USER_BLOCK data now correctly displays within the SUPER_BLOCK info. NOTE: WHITESPACE IN THE OUTPUT HAS CHANGED. (ADB - 2012/02/17 - HDFFV-7560) - h5diff: Fixed to prevent from displaying error stack message when comparing two dangling symbolic links with the follow-symlinks option. (JKM - 2012/01/13 - HDFFV-7836) - h5repack: Fixed a memory leak that occurred with the handling of variable length strings in attributes. (JKM - 2012/01/10 - HDFFV-7840) - h5ls: Fixed a segmentation fault that occurred when accessing region reference data in an attribute. (JKM - 2012/01/06 - HDFFV-7838) F90 API ------- - None C++ API ------ - None High-Level APIs: ------ - None Fortran High-Level APIs: ------ - h5ltget_attribute_string_f: The h5ltget_attribute_string_f used to return the C NULL character in the returned character buffer. The returned charactor buffer now does not return the C NULL character; the buffer is blank-padded if needed. (MSB - 2012/03/23) Platforms Tested ================ The following platforms and compilers have been tested for this release. AIX 5.3 xlc 10.1.0.5 (NASA G-ADA) xlC 10.1.0.5 xlf90 12.1.0.6 FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 (loyalty) g++ 4.2.1 [FreeBSD] 20070719 gcc 4.6.1 20110422 g++ 4.6.1 20110422 gfortran 4.6.1 20110422 FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 (freedom) g++ 4.2.1 [FreeBSD] 20070719 gcc 4.6.1 20110422 g++ 4.6.1 20110422 gfortran 4.6.1 20110422 Linux 2.6.18-194.3.1.el5PAE GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP i686 i686 i386 compilers for 32-bit applications; (jam) Version 4.1.2 20080704 (Red Hat 4.1.2-52) Version 4.5.2 PGI C, Fortran, C++ Compilers for 32-bit applications; Version 11.8-0 Version 11.9-0 Intel(R) C, C++, Fortran Compiler for 32-bit applications; Version 12.0 Version 12.1 MPICH mpich2-1.3.1 compiled with gcc 4.1.2 and gfortran 4.1.2 Linux 2.6.18-308.1.1.el5 GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP x86_64 GNU/Linux compilers for 32-bit applications; (koala) Version 4.1.2 20080704 (Red Hat 4.1.2-52) Version 4.5.2 PGI C, Fortran, C++ for 64-bit target on x86-64; Version 11.9-0 (64-bit) Version 11.8-0 (32-bit) Intel(R) C, C++, Fortran Compilers for applications running on Intel(R) 64; Version 12.0 Version 12.1 MPICH mpich2-1.3.1 compiled with gcc 4.1.2 and gfortran 4.1.2 Linux 2.6.32-220.7.1.el6.ppc64 gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.6 20110731 (ostrich) GNU Fortran (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) Linux 2.6.18-108chaos Intel C, C++, Fortran Compilers Version 11.1 #1 SMP x86_64 GNU/Linux (LLNL Aztec) IBM Blue Gene/P XL C for Blue Gene/P, bgxlc V9.0 (LLNL uDawn) XL C++ for Blue Gene/P, bgxlC V9.0 XL Fortran for Blue Gene/P, bgxlf0 V11.1 SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16 (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13 Sun C++ 5.9 Sun OS_sparc Patch 124863-26 Sun C 5.11 SunOS_sparc Sun Fortran 95 8.5 SunOS_sparc Sun C++ 5.11 SunOS_sparc SGI Altix UV Intel(R) C, Fortran Compilers SGI ProPack 7 Linux Version 11.1 20100806 2.6.32.24-0.2.1.2230.2.PTF- SGI MPT 2.02 default #1 SMP (NCSA ember) Dell NVIDIA Cluster Intel(R) C, Fortran Compilers Red Hat Enterprise Linux 6 Version 12.0.4 20110427 2.6.32-131.4.1.el6.x86_64 mvapich2 1.7rc1-intel-12.0.4 (NCSA forge) Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Visual Studio 2010 w/ Intel Fortran 12 (cmake) Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Visual Studio 2010 w/ Intel Fortran 12 (cmake) Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Visual Studio 2010 w/ Intel Fortran 12 (cmake) Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran) Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Visual Studio 2010 w/ Intel Fortran 12 (cmake) Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran) Mac OS X Snow Leopard 10.6.8 i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (gcc) Darwin Kernel Version 10.8.0 i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 (g++) Intel 64-bit (Apple Inc. build 5666) (dot 3) (fred) GNU Fortan (GCC) 4.6.1 (gfortran) Intel C (icc), Fortran (ifort), C++ (icpc) 12.1.0.038 Build 20110811 Mac OS X Snow Leopard 10.6.8 i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (gcc) Darwin Kernel Version 10.8.0 i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 (g++) Intel 32-bit (Apple Inc. build 5666) (dot 3) (tejeda) GNU Fortran (GCC) 4.6.1 (gfortran) Intel C (icc), Fortran (ifort), C++ (icpc) 12.1.0.038 Build 20110811 Mac OS X Lion 10.7.3 GCC 4.2.1 gcc 32- and 64-bit GNU Fortran (GCC) 4.6.1 gfortran (duck) GCC 4.2.1. g++ Debian6.0.3 2.6.32-5-686 #1 SMP i686 GNU/Linux gcc (Debian 4.4.5-8) 4.4.5 GNU Fortran (Debian 4.4.5-8) 4.4.5 Debian6.0.3 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux gcc (Debian 4.4.5-8) 4.4.5 GNU Fortran (Debian 4.4.5-8) 4.4.5 Fedora16 3.2.9-2.fc16.i6866 #1 SMP i686 i686 i386 GNU/Linux gcc (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1) GNU Fortran (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1) Fedora16 3.2.9-2.fc16.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux gcc (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1) GNU Fortran (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1) SUSE 12.1 3.1.9-1.4-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux gcc (SUSE Linux) 4.6.2 GNU Fortran (SUSE Linux) 4.6.2 SUSE 12.1 3.1.9-1.4-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux gcc (SUSE Linux) 4.6.2 GNU Fortran (SUSE Linux) 4.6.2 Ubuntu 11.10 3.0.0-16-generic #29-Ubuntu SMP i686 GNU/Linux gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 GNU Fortran (Ubuntu/Linaro 4.6.4-9ubuntu3) 4.6.1 Ubuntu 11.10 3.0.0-16-generic #29-Ubuntu SMP x86_64 GNU/Linux gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 GNU Fortran (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 Cray Linux Environment (CLE) PrgEnv-pgi 2.2.74 hopper.nersc.gov pgcc 11.9-0 64-bit target on x86-64 Linux -tp k8e pgf90 11.9-0 64-bit target on x86-64 Linux -tp k8e pgCC 11.9-0 64-bit target on x86-64 Linux -tp k8e Tested Configuration Features Summary ===================================== In the tables below y = tested n = not tested in this release C = Cluster W = Workstation 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 Solaris2.10 32-bit n y n y y y Solaris2.10 64-bit n y n y y y Windows XP n y(4) n y y y Windows XP x64 n y(4) n y y y Windows Vista n y(4) n y y y Windows Vista x64 n y(4) n y y y Mac OS X Snow Leopard 10.6.8 32-bit n y n y y n Mac OS X Snow Leopard 10.6.8 64-bit n y n y y y Mac OS X Lion 10.7.3 32-bit n y n y y n Mac OS X Lion 10.7.3 64-bit n y n y y y AIX 5.3 32- and 64-bit y y y y y y FreeBSD 8.2-STABLE 32&64 bit n x n x y y CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y y y CentOS 5.5 Linux 2.6.18-194 i686 Intel W n y n y y y CentOS 5.5 Linux 2.6.18-194 i686 PGI W n y n y y y CentOS 5.5 Linux 2.6.18 x86_64 GNU (1) W y y(3) y y y y CentOS 5.5 Linux 2.6.18 x86_64 Intel W n y n y y y CentOS 5.5 Linux 2.6.18 x86_64 PGI W n y n y y y Linux 2.6.32-220.7.1.el6.ppc64 n y n y y y SGI ProPack 7 Linux 2.6.32.24 y y y y y y Red Hat Enterprise Linux 6 y y y y y y CLE hopper.nersc.gov y y(3) y y y n Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Solaris2.10 32-bit y y y y Solaris2.10 64-bit n n n n Windows XP y y(4) y n Windows XP x64 y y(4) y n Windows Vista y y(4) y y Windows Vista x64 y y(4) y y Mac OS X Snow Leopard 10.6.8 32-bit y n y n Mac OS X Snow Leopard 10.6.8 64-bit y n y n Mac OS X Lion 10.7.3 32-bit y n y y Mac OS X Lion 10.7.3 64-bit y n y y AIX 5.3 32- and 64-bit n n n y FreeBSD 8.2-STABLE 32&64 bit y x x y CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y CentOS 5.5 Linux 2.6.18-194 i686 Intel W y y y n CentOS 5.5 Linux 2.6.18-194 i686 PGI W y y y n CentOS 5.5 Linux 2.6.18 x86_64 GNU (1) W y y y y CentOS 5.5 Linux 2.6.18 x86_64 Intel W y y y n CentOS 5.5 Linux 2.6.18 x86_64 PGI W y y y n Linux 2.6.32-220.7.1.el6.ppc64 y y y n SGI ProPack 7 Linux 2.6.32.24 y y y n Red Hat Enterprise Linux 6 y y y n CLE hopper.nersc.gov n n n n (1) Fortran compiled with gfortran. (2) With PGI and Absoft compilers. (3) With PGI compiler for Fortran. (4) Using Visual Studio 2008 w/ Intel Fortran 10.1 (Cygwin shared libraries are not supported) (5) C and C++ shared libraries will not be built when Fortran is enabled. Compiler versions for each platform are listed in the preceding "Platforms Tested" table. Known Problems ============== * The h5repacktst test fails on AIX 32-bit because the test uses more memory than the default amount. The failure message typically looks like: "time: 0551-010 The process was stopped abnormally. Try again." This is an issue with the test only and does not represent a problem with the library. To allow the test to pass, request more memory when testing via appropriate command such as: $ env LDR_CNRTL=MAXDATA=0x20000000@DSA make check (AKC - 2012/05/09 - HDFFV-8016) * The file_image test will fail in the "initial file image and callbacks in the core VFD" sub-test if the source directory is read-only as the test fails to create its test files in the build directory. This will be resolved in a future release. (AKC - 2012/05/05 - HDFFV-8009) * The dt_arith test reports several errors involving "long double" on Mac OS X 10.7 Lion when any level of optimization is enabled. The test does not fail in debug mode. This will be addressed in a future release. (SLU - 2012/05/08) * The following h5dump test case fails in BG/P machines (and potentially other machines that use a command script to launch executables): h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" tno-subset.h5 This is due to the embedded spaces in the dataset name being interpreted by the command script launcher as meta-characters, thus passing three arguments to h5dump's -d flag. The command passes if run by hand, just not via the test script. (AKC - 2012/05/03) * The ph5diff (parallel h5diff) tool can intermittently hang in parallel mode when comparing two HDF5 files that contain objects with the same names but with different object types. (JKM - 2012/04/27) * On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set to aprun -np X, because the H5lib_settings.c file was not generated properly. Not setting those environment variables works, because configure was able to automatically detect that it's a Cray system and used the proper launch commands when necessary. (MSC - 2012/04/18) * The data conversion test dt_arith.c fails in "long double" to integer conversion on Ubuntu 11.10 (3.0.0.13 kernal) with GCC 4.6.1 if the library is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernal (3.2.2 on Fedora) doesn't have the problem. Users should lower the optimization level (-O1 or -O0) by defining CFLAGS in the command line of "configure" like: CFLAGS=-O1 ./configure This will overwrite the library's default optimization level. (SLU - 2012/02/07 - HDFFV-7829) * The STDIO VFD does not work on some architectures, possibly due to 32/64 bit or large file issues. The basic STDIO VFD test is known to fail on 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin 10.7.0. The STDIO VFD test has been disabled while we investigate and a fix should appear in a future release. (DER - 2011/10/14) * h5diff can report inconsistent results when comparing datasets of enum type that contain invalid values. This is due to how enum types are handled in the library and will be addressed in a future release. (DER - 2011/10/14 - HDFFV-7527) * The links test can fail under the stdio VFD due to some issues with external links. This will be investigated and fixed in a future release. (DER - 2011/10/14 - HDFFV-7768) * After the shared library support was fixed for some bugs, it was discovered that "make prefix=XXX install" no longer works for shared libraries. It still works correctly for static libraries. Therefore, if you want to install the HDF5 shared libraries in a location such as /usr/local/hdf5, you need to specify the location via the --prefix option during configure time. E.g, ./configure --prefix=/usr/local/hdf5 ... (AKC - 2011/05/07 - HDFFV-7583) * The parallel test, t_shapesame, in testpar/, may run for a long time and may be terminated by the alarm signal. If that happens, one can increase the alarm seconds (default is 1200 seconds = 20 minutes) by setting the environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 (60 minutes). Note that the t_shapesame test may fail in some systems (see the "While working on the 1.8.6 release..." problem below). If it does, it will waste more time if $HDF5_ALARM_SECONDS is set to a larger value. (AKC - 2011/05/07) * The C++ and FORTRAN bindings are not currently working on FreeBSD. (QAK - 2011/04/26) * Shared Fortran libraries are not quite working on AIX. While they are generated when --enable-shared is specified, the fortran and hl/fortran tests fail. We are looking into the issue. HL and C++ shared libraries should now be working as intended, however. (MAM - 2011/04/20) * The --with-mpe configure option does not work with Mpich2. (AKC - 2011/03/10) * While working on the 1.8.6 release of HDF5, a bug was discovered that can occur when reading from a dataset in parallel shortly after it has been written to collectively. The issue was exposed by a new test in the parallel HDF5 test suite, but had existed before that. We believe the problem lies with certain MPI implementations and/or file systems. We have provided a pure MPI test program, as well as a standalone HDF5 program, that can be used to determine if this is an issue on your system. They should be run across multiple nodes with a varying number of processes. These programs can be found at: http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ (NAF - 2011/01/19) * The library's test dt_arith.c showed a compiler's rounding problem on Cygwin when converting from unsigned long long to long double. The library's own conversion works fine. We defined a macro for Cygwin to skip this test until we can solve the problem. (SLU - 2010/05/05 - HDFFV-1264) * All the VFL drivers aren't backward compatible. In H5FDpublic.h, the structure H5FD_class_t changed in 1.8. There is new parameter added to get_eoa and set_eoa callback functions. A new callback function get_type_map was added in. The public function H5FDrealloc was taken out in 1.8. The problem only happens when users define their own driver for 1.6 and try to plug in 1.8 library. Because there's only one user complaining about it, we (Elena, Quincey, and I) decided to leave it as it is (see bug report #1279). Quincey will make a plan for 1.10. (SLU - 2010/02/02) * MinGW has a missing libstdc++.dll.a library file and will not successfully link C++ applications/tests. Do not use the enable-cxx configure option. Read all of the INSTALL_MINGW.txt file for all restrictions. (ADB - 2009/11/11) * The --enable-static-exec configure flag will only statically link libraries if the static version of that library is present. If only the shared version of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, for example, only have shared versions), the flag should still result in a successful compilation, but note that the installed executables will not be fully static. Thus, the only guarantee on these systems is that the executable is statically linked with just the HDF5 library. (MAM - 2009/11/04) * The PathScale MPI implementation, accessing a Panasas file system, would cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file does not exist. This is due to the MPI_File_open() call failing if the mode has the MPI_MODE_EXCL bit set. (AKC - 2009/08/11 - HDFFV-988) * Parallel tests failed with 16 processes with data inconsistency at testphdf5 / dataset_readAll. Parallel tests also failed with 32 and 64 processes with collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks with MPI IO. (CMC - 2009/04/28) * For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests are expected to fail and should exit with a non-zero code but the yod command does not propagate the exit code of the executables. Yod always returns 0 if it can launch the executable. The test suite shell expects a non-zero for this particular test, therefore it concludes the test has failed when it receives 0 from yod. Skip all the "failing" test for now by changing them as following. ======== Original tools/h5ls/testh5ls.sh ========= TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ======== Change to =============================== echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ================================================== ======== Original tools/h5copy/testh5copy.sh ========= TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested H5LSTEST $FILEOUT ======== Change to =============================== echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested echo SKIP H5LSTEST $FILEOUT ================================================== (AKC - 2008/11/10) * For Red Storm, a Cray XT3 system, the yod command sometimes gives the message, "yod allocation delayed for node recovery". This interferes with test suites that do not expect to see this message. See the section of "Red Storm" in file INSTALL_parallel for a way to deal with this problem. (AKC - 2008/05/28) * On an 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. * 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. * 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 calculation 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 - 2005/06/30) * 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. (AKC - 2004/12/08) %%%%1.8.8%%%% HDF5 version 1.8.8 released on 2011-11-15 ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.7 and HDF5 1.8.8, and contains information on the platforms tested and known problems in HDF5-1.8.8. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.8 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.8 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.8 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in the HDF5-1.8.x release series, 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 1.8.8 (current release) versus Release 1.8.7": 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 - Support for New Platforms, Languages, and Compilers - Bug Fixes since HDF5-1.8.7 - Platforms Tested - Supported Configuration Features Summary - Known Problems New Features ============ Configuration ------------- - Added the --enable-fortran2003 flag to enable Fortran2003 support in the HDF5 Fortran library. The flag should be used along with the --enable-fortran flag and takes affect only when the Fortran compiler is Fortran2003 compliant. (EIP - 2011/11/14) - Added checks for clock_gettime and mach/mach_time.h to both configure and CMake. This will support the move from gettimeofday to clock_gettime's monotonic timer in the profiling code in a future release. (DER - 2011/10/12) Library ------- - The Windows VFD code has been removed with the exception of the functions which set it (H5Pset_fapl_windows, for example). Setting the Windows VFD now really sets the SEC2 VFD. The WINDOWS_MAX_BUF and WINDOWS_USE_STDIO configuration options and #defines have also been removed. NOTE: Since the Windows VFD was a clone of the SEC2 VFD, this change should be transparent to users. (DER - 2011/10/12 - HDFFV-7740, HDFFV-7744) - H5Tcreate now supports the string type (fixed-length and variable- length). (SLU - 2011/05/20) Parallel Library ---------------- - Added new H5Pget_mpio_actual_chunk_opt_mode and H5Pget_mpio_actual_io_mode API routines for querying whether/how a collective I/O operation completed. (QAK - 2011/10/12) Tools ----- - None High-Level APIs --------------- - Added the following Fortran wrappers for the Dimension Scale APIs: h5dsset_scale_f h5dsattach_scale_f h5dsdetach_scale_f h5dsis_attached_f h5dsis_scale_f h5dsset_label_f h5dsget_label_f h5dsget_scale_name_f h5dsget_num_scales_f (EIP for SB - 2011/10/13 - HDFFV-3797) Fortran API ----------- - The HDF5 Fortran library was enhanced to support the Fortran 2003 standard. The following features are available when the HDF5 library is configured using the --enable-fortran and --enable-fortran2003 configure flags AND if the Fortran compiler is Fortran 2003 compliant: - Subroutines overloaded with the C_PTR derived type: h5pget_f h5pget_fill_value_f h5pinsert_f h5pregister_f h5pset_f h5pset_fill_value_f h5rcreate_f h5rderefrence_f h5rget_name_f h5rget_obj_type_f - Subroutines overloaded with the C_PTR derived type and simplified signatures: h5aread_f h5awrite_f h5dread_f h5dwrite_f - New subroutines h5dvlen_reclaim_f h5literate_by_name_f h5literate_f h5ovisit_f h5tconvert_f h5pset_nbit_f h5pset_scaleoffset_f - Subroutines with additional optional parameters: h5pcreate_class_f (EIP - 2011/10/14) C++ API ------- - None Support for New Platforms, Languages, and Compilers =================================================== - None Bug Fixes since HDF5-1.8.7 ========================== Configuration ------------- - Changed the size of H5_SIZEOF_OFF_T to 4 bytes (was 8) in the VMS h5pubconf.h based on the output of a test program. (DER - 2011/10/12) - The Windows and VMS versions of H5pubconf.h were brought into sync with the linux/posix version. (DER - 2011/10/12) - Fixed a bug in the bin/trace Perl script where API functions that take a variable number of arguments were not processed for trace statement fixup. (DER - 2011/08/25) - The --enable-h5dump-packed-bits configure option has been removed. The h5dump code that this option conditionally enabled is now always compiled into h5dump. Please refer to the h5dump reference manual for usage of the packed bits feature. (MAM - 2011/06/23 - HDFFV-7592) - Configure now uses the same flags and symbols in its tests that are used to build the library. (DER - 2011/05/24) Library ------- - Corrected the error when copying attributes between files which are using different versions of the file format. (QAK - 2011/10/20 - HDFFV-7718) - Corrected the error when loading local heaps from the file, which could cause the size of the local heap's data block to increase dramatically. (QAK - 2011/10/14 - HDFFV-7767) - An application does not need to do H5O_move_msgs_forward() when writing attributes. Tests were checked into the performance suite. (VC - 2011/10/13 - HDFFV-7640) - Fixed a bug that occurred when using H5Ocopy on a committed datatype containing an attribute using that committed datatype. (NAF - 2011/10/13 - HDFFV-5854) - Added generic VFD I/O types to the SEC2 and log VFDs to ensure correct I/O sizes (and remove compiler warnings) between Windows and true POSIX systems. (DER - 2011/10/12) - Corrected some Windows behavior in the SEC2 and log VFDs. This mainly involved datatype correctness fixes, Windows API call error checks, and adding the volume serial number to the VFD cmp functions. (DER - 2011/10/12) - Converted post-checks for the appropriate POSIX I/O sizes to pre-checks in order to avoid platform-specific or undefined behavior. (DER - 2011/10/12) - #ifdef _WIN32 instances have been changed to #ifdef H5_HAVE_WIN32_API. H5_HAVE_VISUAL_STUDIO checks have been added where necessary. This is in CMake only as configure never sets _WIN32. (ADB - 2011/09/12) - CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv discovered 3 problems in tests and tools' library: 1. In dsets.c, left shifting an unsigned int for 32 bits or more caused undefined behavior. 2. In dt_arith.c, the INIT_INTEGER macro definition has an overflow when the value is a negative minimal and is being subtracted from one. 3. In tools/lib/h5tools_str.c, right shifting an int value for 32 bits or more caused undefined behavior. All the problems have been corrected. (SLU - 2011/09/02 - HDFFV-7674) - H5Epush2() now has the correct trace functionality (this is related to the bin/trace Perl script bug noted in the configure section). (DER - 2011/08/25) - Corrected mismatched function name typo of h5pget_dxpl_mpio_c and h5pfill_value_defined_c. (AKC - 2011/08/22 - HDFFV-7641) - Corrected an internal error in the library where objects that use committed (named) datatypes and were accessed from two different file IDs could confuse the two and cause erroneous failures. (QAK - 2011/07/18 - HDFFV-7638) - In v1.6 of the library, there was an EOA for the whole MULTI file saved in the super block. We took it out in v1.8 of the library because it's meaningless for the MULTI file. v1.8 of the library saves the EOA for the metadata file instead, but this caused a backward compatibility problem. A v1.8 library couldn't open the file created with the v1.6 library. We fixed the problem by checking the EOA value to detect the file created with v1.6 library. (SLU - 2011/06/22) - When a dataset had filters and reading data failed, the error message didn't say which filter wasn't registered. It's fixed now. (SLU - 2011/06/03) Parallel Library ---------------- - The Special Collective IO (IO when some processes do not contribute to the IO) and the Complex Derived Datatype MPI functionalities are no longer conditionally enabled in the library by configure. They are always enabled in order to take advantage of performance boosts from these behaviors. Older MPI implementations that do not allow for these functionalities can no longer by used by HDF5. (MAM - 2011/07/08 - HDFFV-7639). Tools ----- - h5diff: fixed segfault over non-comparable attribute with different dimention or rank, along with '-c' option to display details. (JKM - 2011/10/24 - HDFFV-7770) - Fixed h5diff to display all the comparable objects and attributes regardless of detecting non-comparables. (JKM - 2011/09/16 - HDFFV-7693) - Fixed h5repack to update the values of references(object and region) of attributes in h5repack for 1) references, 2) arrays of references, 3) variable-length references, and 4) compound references. (PC - 2011/09/14 - HDFFV-5932) - h5diff: fixed a segfault over a dataset with container types array and variable-length (vlen) along with multiple nested compound types. Example: compound->array->compound, compound->vlen->compound. (JKM - 2011/09/01 - HDFFV-7712) - h5repack: added macro to handle a failure in H5Dread/write when memory allocation failed inside the library. (PC - 2011/08/19) - Fixed h5jam to not to allow the specifying of an HDF5 formatted file as an input file for the -u (user block file) option. The original HDF5 file would not be accessible if this behavior was allowed. (JKM - 2011/08/19 - HDFFV-5941) - Revised the command help pages of h5jam and h5unjam. The descriptions were not up to date and some were missing. (JKM - 2011/08/15 - HDFFV-7515) - Fixed h5dump to correct the schema location: (ADB - 2011/08/10) - h5repack: h5repack failed to copy a dataset if the layout is changed from chunked with unlimited dimensions to contiguous. (PC - 2011/07/15 - HDFFV-7649) - Fixed h5diff: the "--delta" option considers two NaN of the same type are different. This is wrong based on the h5diff description in the Reference Manual. (PC - 2011/07/15 - HDFFV-7656) - Fixed h5diff to display an instructive error message and exit with an instructive error message when mutually exclusive options (-d, -p and --use-system-epsilon) are used together. (JKM - 2011/07/07 - HDFFV-7600) - Fixed h5dump so that it displays the first line of each element in correct position for multiple dimention array types. Before this fix, the first line of each element in an array was displayed after the last line of previous element without moving to the next line (+indentation). (JKM - 2011/06/15 - HDFFV-5878) - Fixed h5dump so that it will display the correct value for H5T_STD_I8LE datasets on the Blue-gene system (ppc64, linux, Big-Endian, clustering). (AKC & JKM - 2011/05/12 - HDFFV-7594) - Fixed h5diff to compare a file to itself correctly. Previously h5diff reported either the files were different or not compatible in certain cases even when comparing a file to itself. This fix also improves performance when comparing the same target objects through verifying the object and file addresses before comparing the details in the objects. Examples of details are datasets and attributes. (XCAO & JKM - 2011/05/06 - HDFFV-5928) F90 API ------- - Modified the h5open_f and h5close_f subroutines to not to call H5open and H5close correspondingly. While the H5open call just adds overhead, the H5close call called by a Fortran application shuts down the HDF5 library. This makes the library inaccessible to the application. (EIP & SB - 2011/10/13 - HDFFV-915) - Fixed h5tget_tag_f where the length of the C string was used to repack the C string into the Fortran string. This lead to memory corruption in the calling program. (SB - 2011/07/26) - Added defined constants: H5T_ORDER_MIXED_F (HDFFV-2767) H5Z_SO_FLOAT_DSCALE_F H5Z_SO_FLOAT_ESCALE_F H5Z_SO_INT_F H5Z_SO_INT_MINBITS_DEFAULT_F H5O_TYPE_UNKNOWN_F H5O_TYPE_GROUP_F H5O_TYPE_DATASET_F H5O_TYPE_NAMED_DATATYPE_F H5O_TYPE_NTYPES_F C++ API ------ - None High-Level APIs: ------ - Fixed the H5LTdtype_to_text function. It had some memory problems when dealing with some complicated data types. (SLU - 2011/10/19 - HDFFV-7701) - Fixed H5DSset_label seg faulting when retrieving the length of a dimension label that was not set. (SB - 2011/08/07 - HDFFV-7673) - Fixed a dimension scale bug where if you create a dimscale, attach two datasets to it, and then unattach them, you get an error if they are unattached in order, but no error if you unattach them in reverse order. (SB - 2011/06/07 - HDFFV-7605) Fortran High-Level APIs: ------ - None Platforms Tested ================ The following platforms and compilers have been tested for this release. AIX 5.3 xlc 10.1.0.5 (NASA G-ADA) xlC 10.1.0.5 xlf90 12.1.0.6 FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 (loyalty) g++ 4.2.1 [FreeBSD] 20070719 gcc 4.6.1 20110422 g++ 4.6.1 20110422 gfortran 4.6.1 20110422 FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 (freedom) g++ 4.2.1 [FreeBSD] 20070719 gcc 4.6.1 20110422 g++ 4.6.1 20110422 gfortran 4.6.1 20110422 IBM Blue Gene/P bgxlc 9.0.0.9 (LLNL uDawn) bgxlf90 11.1.0.7 bgxlC 9.0.0.9 Linux 2.6.16.60-0.54.5-smp Intel(R) C, C++, Fortran Compilers x86_64 Version 11.1 20090630 (INL Icestorm) Linux 2.6.18-194.el5 x86_64 Intel(R) C, C++, Fortran Compilers (INL Fission) Version 12.0.2 20110112 Linux 2.6.18-108chaos x86_64 Intel(R) C, C++, Fortran Compilers (LLNL Aztec) Version 11.1 20090630 Linux 2.6.18-194.3.1.el5PAE gcc (GCC) 4.1.2 and 4.4.2 #1 SMP i686 i686 i386 GNU Fortran (GCC) 4.1.2 20080704 (jam) (Red Hat 4.1.2-48) and 4.4.2 PGI C, Fortran, C++ 10.4-0 32-bit PGI C, Fortran, C++ 10.6-0 32-bit Intel(R) C Compiler for 32-bit applications, Version 11.1 Intel(R) C++ Compiler for 32-bit applications, Version 11.1 Intel(R) Fortran Compiler for 32-bit applications, Version 11.1 MPICH mpich2-1.3.1 compiled with gcc 4.1.2 and gfortran 4.1.2 Linux 2.6.18-238.12.1.el5 gcc 4.1.2 and 4.4.2 #1 SMP x86_64 GNU/Linux GNU Fortran (GCC) 4.1.2 20080704 (koala) (Red Hat 4.1.2-46) and 4.4.2 tested for both 32- and 64-bit binaries Intel(R) C, C++, Fortran Compilers for applications running on Intel(R) 64, Version 11.1. PGI C, Fortran, C++ Version 9.0-4 for 64-bit target on x86-64 MPICH mpich2-1.3.1 compiled with gcc 4.1.2 and gfortran 4.1.2 SGI Altix UV Intel(R) C, Fortran Compilers SGI ProPack 7 Linux Version 11.1 20100806 2.6.32.24-0.2.1.2230.2.PTF- SGI MPT 2.02 default #1 SMP (NCSA ember) Dell NVIDIA Cluster Intel(R) C, Fortran Compilers Red Hat Enterprise Linux 6 Version 12.0.4 20110427 2.6.32-131.4.1.el6.x86_64 mvapich2 1.7rc1-intel-12.0.4 (NCSA forge) SunOS 5.10 32- and 64-bit Sun C 5.11 SunOS_sparc 2010/08/13 Sun Fortran 95 8.5 SunOS_sparc 2010/08/13 Sun C++ 5.11 SunOS_sparc 2010/08/13 Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Visual Studio 2010 (cmake) Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran) Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Visual Studio 2010 (cmake) Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran) Windows Vista Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Windows Vista x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Mac OS X 10.8.0 (Intel 64-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) Darwin Kernel Version 10.8.0 GNU Fortran (GCC) 4.6.1 Intel C, C++ and Fortran compilers 12.1.0 Mac OS X 10.8.0 (Intel 32-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) Darwin Kernel Version 10.8.0 GNU Fortran (GCC) version 4.6.1 Intel C, C++ and Fortran compilers 12.1.0 Fedora 12 2.6.32.16-150.fc12.ppc64 #1 SMP ppc64 GNU/Linux gcc (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10) GNU Fortran (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10) Debian6.0.3 2.6.32-5-686 #1 SMP i686 GNU/Linux gcc (Debian 4.4.5-8) 4.4.5 GNU Fortran (Debian 4.4.5-8) 4.4.5 Debian6.0.3 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux gcc (Debian 4.4.5-8) 4.4.5 GNU Fortran (Debian 4.4.5-8) 4.4.5 Fedora15 2.6.40.6-0.fc15.i686.PAE #1 SMP i686 i686 i386 GNU/Linux gcc (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9) GNU Fortran (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9) Fedora15 2.6.40.6-0.fc15.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux gcc (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9) GNU Fortran (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9) SUSE 11.4 2.6.37.6-0.7-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux gcc (SUSE Linux) 4.5.1 20101208 GNU Fortran (SUSE Linux) 4.5.1 20101208 SUSE 11.4 2.6.37.6-0.7-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux gcc (SUSE Linux) 4.5.1 20101208 GNU Fortran (SUSE Linux) 4.5.1 20101208 Ubuntu 11.10 3.0.0-12-generic #20-Ubuntu SMP i686 GNU/Linux gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 GNU Fortran (Ubuntu/Linaro 4.6.4-9ubuntu3) 4.6.1 Ubuntu 11.10 3.0.0-12-generic #20-Ubuntu SMP x86_64 GNU/Linux gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 GNU Fortran (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 OpenVMS Alpha 8.3 HP C V7.3-009 HP Fortran V8.2-104679-48H9K HP C++ V7.3-009 Cray Linux Environment (CLE) PrgEnv-pgi 2.2.74 hopper.nersc.gov pgcc 11.7-0 64-bit target on x86-64 Linux -tp k8e franklin.nersc.gov pgf90 11.7-0 64-bit target on x86-64 Linux -tp k8e pgCC 11.7-0 64-bit target on x86-64 Linux -tp k8e Tested Configuration Features Summary ===================================== In the tables below y = tested n = not tested in this release C = Cluster W = Workstation 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 Solaris2.10 32-bit n y n y y y Solaris2.10 64-bit n y n y y y Windows XP n y(4) n y y y Windows XP x64 n y(4) n y y y Windows Vista n y(4) n y y y Windows Vista x64 n y(4) n y y y OpenVMS Alpha n y n y y n Mac OS X 10.8 Intel 32-bit n y n y y y Mac OS X 10.8 Intel 64-bit n y n y y y AIX 5.3 32- and 64-bit n y n y y y FreeBSD 8.2-STABLE 32&64 bit n x n x y y CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y y y CentOS 5.5 Linux 2.6.18-194 i686 Intel W n y n y y n CentOS 5.5 Linux 2.6.18-194 i686 PGI W n y n y y n CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y CentOS 5.5 Linux 2.6.16 x86_64 Intel W n y n y y n CentOS 5.5 Linux 2.6.16 x86_64 PGI W n y n y y y Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 n y n y y y SGI ProPack 7 Linux 2.6.32.24 y y y y y y Red Hat Enterprise Linux 6 y y y y y y CLE hopper.nersc.gov y y(3) y y y n CLE franklin.nersc.gov y y(3) y y y n Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Solaris2.10 32-bit y y y y Solaris2.10 64-bit y y y y Windows XP y y(4) y n Windows XP x64 y y(4) y n Windows Vista y y(4) y y Windows Vista x64 y y(4) y y OpenVMS Alpha n n n n Mac OS X 10.8 Intel 32-bit y(5) n y n Mac OS X 10.8 Intel 64-bit y(5) n y n AIX 5.3 32- and 64-bit n n n y FreeBSD 8.2-STABLE 32&64 bit y x x y CentOS 5.5 Linux 2.6.18-128 i686 GNU (1)W y y(2) y y CentOS 5.5 Linux 2.6.18-128 i686 Intel W y y y n CentOS 5.5 Linux 2.6.18-128 i686 PGI W y y y n CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y y y CentOS 5.5 Linux 2.6.16 x86_64 Intel W y y y n CentOS 5.5 Linux 2.6.16 x86_64 PGI W y y y n Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 y y y y SGI ProPack 7 Linux 2.6.32.24 y y y n Red Hat Enterprise Linux 6 y y y n CLE hopper.nersc.gov n n n n CLE franklin.nersc.gov n n n n (1) Fortran compiled with gfortran. (2) With PGI and Absoft compilers. (3) With PGI compiler for Fortran. (4) Using Visual Studio 2008 w/ Intel Fortran 10.1 (Cygwin shared libraries are not supported) (5) C and C++ shared libraries will not be built when Fortran is enabled. Compiler versions for each platform are listed in the preceding "Platforms Tested" table. Known Problems ============== * The STDIO VFD does not work on some architectures, possibly due to 32/64 bit or large file issues. The basic STDIO VFD test is known to fail on 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin 10.7.0. The STDIO VFD test has been disabled while we investigate and a fix should appear in a future release, possibly 1.8.9. (DER - 2011/10/14) * h5diff can report inconsistent results when comparing datasets of enum type that contain invalid values. This is due to how enum types are handled in the library and will be addressed in the next release. (DER - 2011/10/14 - HDFFV-7527) * The links test can fail under the stdio VFD due to some issues with external links. This will be investigated and fixed in a future release. (DER - 2011/10/14 - HDFFV-7768) * After the shared library support was fixed for some bugs, it was discovered that "make prefix=XXX install" no longer works for shared libraries. It still works correctly for static libraries. Therefore, if you want to install the HDF5 shared libraries in a location such as /usr/local/hdf5, you need to specify the location via the --prefix option during configure time. E.g, ./configure --prefix=/usr/local/hdf5 ... (AKC - 2011/05/07 - HDFFV-7583) * The parallel test, t_shapesame, in testpar/, may run for a long time and may be terminated by the alarm signal. If that happens, one can increase the alarm seconds (default is 1200 seconds = 20 minutes) by setting the environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 (60 minutes). Note that the t_shapesame test may fail in some systems (see the "While working on the 1.8.6 release..." problem below). If it does, it will waste more time if $HDF5_ALARM_SECONDS is set to a larger value. (AKC - 2011/05/07) * The C++ and FORTRAN bindings are not currently working on FreeBSD. (QAK - 2011/04/26) * Shared Fortran libraries are not quite working on AIX. While they are generated when --enable-shared is specified, the fortran and hl/fortran tests fail. We are looking into the issue. HL and C++ shared libraries should now be working as intended, however. (MAM - 2011/04/20) * The --with-mpe configure option does not work with Mpich2. (AKC - 2011/03/10) * While working on the 1.8.6 release of HDF5, a bug was discovered that can occur when reading from a dataset in parallel shortly after it has been written to collectively. The issue was exposed by a new test in the parallel HDF5 test suite, but had existed before that. We believe the problem lies with certain MPI implementations and/or file systems. We have provided a pure MPI test program, as well as a standalone HDF5 program, that can be used to determine if this is an issue on your system. They should be run across multiple nodes with a varying number of processes. These programs can be found at: http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ (NAF - 2011/01/19) * The library's test dt_arith.c showed a compiler's rounding problem on Cygwin when converting from unsigned long long to long double. The library's own conversion works fine. We defined a macro for Cygwin to skip this test until we can solve the problem. (SLU - 2010/05/05 - HDFFV-1264) * All the VFL drivers aren't backward compatible. In H5FDpublic.h, the structure H5FD_class_t changed in 1.8. There is new parameter added to get_eoa and set_eoa callback functions. A new callback function get_type_map was added in. The public function H5FDrealloc was taken out in 1.8. The problem only happens when users define their own driver for 1.6 and try to plug in 1.8 library. Because there's only one user complaining about it, we (Elena, Quincey, and I) decided to leave it as it is (see bug report #1279). Quincey will make a plan for 1.10. (SLU - 2010/02/02) * MinGW has a missing libstdc++.dll.a library file and will not successfully link C++ applications/tests. Do not use the enable-cxx configure option. Read all of the INSTALL_MINGW.txt file for all restrictions. (ADB - 2009/11/11) * The --enable-static-exec configure flag will only statically link libraries if the static version of that library is present. If only the shared version of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, for example, only have shared versions), the flag should still result in a successful compilation, but note that the installed executables will not be fully static. Thus, the only guarantee on these systems is that the executable is statically linked with just the HDF5 library. (MAM - 2009/11/04) * The PathScale MPI implementation, accessing a Panasas file system, would cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file does not exist. This is due to the MPI_File_open() call failing if the mode has the MPI_MODE_EXCL bit set. (AKC - 2009/08/11 - HDFFV-988) * Parallel tests failed with 16 processes with data inconsistency at testphdf5 / dataset_readAll. Parallel tests also failed with 32 and 64 processes with collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks with MPI IO. (CMC - 2009/04/28) * For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests are expected to fail and should exit with a non-zero code but the yod command does not propagate the exit code of the executables. Yod always returns 0 if it can launch the executable. The test suite shell expects a non-zero for this particular test, therefore it concludes the test has failed when it receives 0 from yod. Skip all the "failing" test for now by changing them as following. ======== Original tools/h5ls/testh5ls.sh ========= TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ======== Change to =============================== echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ================================================== ======== Original tools/h5copy/testh5copy.sh ========= TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested H5LSTEST $FILEOUT ======== Change to =============================== echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested echo SKIP H5LSTEST $FILEOUT ================================================== (AKC - 2008/11/10) * For Red Storm, a Cray XT3 system, the yod command sometimes gives the message, "yod allocation delayed for node recovery". This interferes with test suites that do not expect to see this message. See the section of "Red Storm" in file INSTALL_parallel for a way to deal with this problem. (AKC - 2008/05/28) * On an 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. * 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. * 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 calculation 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 - 2005/06/30) * 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. (AKC - 2004/12/08) %%%%1.8.7%%%% HDF5 version 1.8.7 released on Tue May 10 09:24:44 CDT 2011 ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.6 and HDF5 1.8.7, and contains information on the platforms tested and known problems in HDF5-1.8.7. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.7 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.7 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.7 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in the HDF5-1.8.x release series, 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 1.8.7 (current release) versus Release 1.8.6": 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 - Support for New Platforms, Languages, and Compilers - Bug Fixes since HDF5-1.8.6 - Platforms Tested - Supported Configuration Features Summary - Known Problems New Features ============ Configuration ------------- - Configure now generates Makefiles that build in "silent make mode" by default in which compile and link lines are significantly simplified for clarity. To override this and view actual compile and link lines during building, the --disable-silent-rules flag can be used at configure time, or the 'make' command can be followed by V=1, to indicate a "verbose" make. (MAM - 2011/4/14). - Added mpicc and mpif90 as the default C and Fortran compilers for Linux systems when --enable-parallel is specified but no $CC or $FC is defined. (AKC - 2011/2/7) - Added a new configure option, "--enable-unsupported", which can be used to stop configure from preventing the use of unsupported configure option combinations, such as c++ in parallel or Fortran with threadsafe. Use at your own risk, as it may result in a library that won't compile or run as expected! (MAM - 2010/11/17 - Bug 2061) Library ------- - The library allows the dimension size of a dataspace to be zero. In the past, the library would allow this only if the maximal dimension size was unlimited. Now there is no such restriction, but no data can be written to this kind of dataset. (SLU - 2011/4/20) - We added two new macros, H5_VERSION_GE and H5_VERSION_LE, to let users compare certain version numbers with the library being used. (SLU - 2011/4/20) - Added ability to cache files opened through external links. Added new public functions H5Pset_elink_file_cache_size(), H5Pget_elink_file_cache_size(), and H5Fclear_elink_file_cache(). (NAF - 2011/02/17) - Finished implementing all options for 'log' VFD. (QAK - 2011/1/25) - Removed all old code for Metrowerks compilers, bracketed by __MWERKS__). Metrowerks compiler is long gone. (AKC - 2010/11/17) Parallel Library ---------------- - None Tools ----- - h5diff: Added new "verbose with levels" option, '-vN, --verbose=N'. The old '-v, --verbose' option is deprecated but remains available; it is exactly equivalent to '-v0, --verbose=0'. The new levels 1 ('-v1' or '--verbose=1') and 2 ('-v2' or '--verbose=2') can be specified to view more information regarding attributes differences. Bug #2121 (JKM 2011/3/23) - h5dump: Added new option --enable-error-stack. This option will display error stack information in the output stream. This is useful when the "h5dump: Unable to print data" message is output. (ADB - 2011/03/03) High-Level APIs --------------- - Fortran LT make datasets routines (H5LTmake_dataset_f, h5ltmake_dataset_int_f, h5ltmake_dataset_float_f, h5ltmake_dataset_double_f) and LT read datasets routines (h5ltread_dataset_f,h5ltread_dataset_int_f, h5ltread_dataset_float_f, 5ltread_dataset_double_f) can now handle 4-dimensional to 7-dimensional rank datasets. HDFFV-1217 (MSB-2011/4/24/2011) F90 API ------- - None C++ API ------- - None Support for New Platforms, Languages, and Compilers =================================================== - Intel V11.1 uses now -O3 optimization in production mode (EIP - 2010/10/08) Bug Fixes since HDF5-1.8.6 ========================== Configuration ------------- - Shared C++ and HL libraries on AIX should now be working correctly. Note that Fortran shared libraries are still not working on AIX. (See the Known Problems section, below). (MAM - 2011/4/20) - Removed config/ibm-aix6.x. All IBM-AIX settings are in one file, ibm-aix. (AKC - 2011/4/14) - Shared C libraries are no longer disabled on Mac when Fortran is enabled. Shared Fortran libraries are still not supported on Mac, so configure will disable them by default, but this is overrideable with the new --enable-unsupported configure option. The configure summary has been updated to reflect the fact that the shared-ness of the C++/Fortran wrapper libraries may not align with the C library. (MAM - 2011/04/11 - HDFFV-4353). Library ------- - Changed assertion failure when decoding a compound datatype with no fields into a normal error failure. Also prohibit using this sort of datatype for creating an attribute (as is already the case for datasets and committed (named) datatypes). (QAK - 2011/04/15, Jira issue #HDFFV-2766) - Tell the VFL flush call that the file will be closing, allowing the VFDs to avoid sync'ing the file (particularly valuable in parallel). (QAK - 2011/03/09) - The datatype handler created with H5Tencode/decode used to have the reference count 0 (zero); it now has the reference count 1 (one). (SLU - 2011/2/18) - Fixed the definition of H5_HAVE_GETTIMEOFDAY on Windows so that HDgettimeofday() is defined and works properly. Bug HDFFV-5931 (DER - 2011/04/14) - Added basic VFD tests for the Windows, STDIO and log VFD tests. (DER - 2011/04/11) Parallel Library ---------------- - None Tools ----- - Updated h5dump test case script to prevent entire test failure when source directory is read-only. Bug #HDFFV-4342 (JKM 2011/4/12) - Fixed h5dump displaying incorrect values for H5T_STD_I8BE type data in attribute on Big-Endian machine. H5T_STD_I8BE is unsigned 8bit type, so h5dump is supposed to display -2 instead of 254. It worked correctly on Little-Endian system , but not on Big-Endian system. Bug #HDFFV-4358 (JKM 04/08/2011) - Updated some HDF5 tools to standardize the option name as '--enable-error-stack' for printing HDF5 error stack messages. h5ls and h5dump have been updated. For h5ls, this replaces "-e/--errors" option, which is deprecated. For h5dump, this is a new option. Bug #2182 (JKM 2011/3/30) - Fixed the h5diff --use-system-epsilon option. The formula used in the calculation was changed from ( |a - b| / b ) to ( |a - b| ). This was done to improve performance. Bug #2184 (JKM 2011/3/24) - Fixed output for H5T_REFERENCE in h5dump. According to the BNF document the output of a H5T_REFERENCE should be followed by the type; ::= H5T_REFERENCE { } ::= H5T_STD_REF_OBJECT | H5T_STD_REF_DSETREG Previously this was only displayed if the -R option was used. Bug #1725 (ADB 2011/3/28) - Fixed two h5diff issues. 1) h5diff compared attributes correctly only when two objects had the same number of attributes and the attribute names were identical. 2) h5diff did not display useful information about attribute differences. Bug #2121 (JKM 2011/3/17) - Fixed a memory leak in h5diff that occurred when accessing symbolic links with the --follow-symlink option. Bug #2214 (JKM 2011/3/18) - Fixed a memory leak in h5diff that occurred when accessing variable length string data. Bug #2216 (JKM 2011/3/18) - Fixed and improved the help page for h5ls -a, --address option. Bug #1904 (JKM 2011/3/11) - Fixed h5copy to enable copying an object into the same HDF5 file. Previously h5copy displayed an error message when the target file was the same as the source file. (XCAO 2011/3/8) - Fixed an h5dump problem that caused the tool to skip some data elements in large datasets with a large array datatype on Windows. This issue arose only on Windows due to the different return behavior of the _vsnprintf() function. Bug #2161 (JKM 2011/3/3) - Fixed h5dump which was skipping some array indices in large datasets with a relatively large array datatype. The interval of skipped indices varied according to the size of the array. Bug #2092 (JKM 2011/2/15) - Fixed h5diff which was segfaulting when comparing compound datasets with a combination of fixed-length string datatypes and variable-length string datatypes in certain orders. Bug #2089 (JKM 2010/12/28) - Improved h5diff performance. 1) Now use HDmemcmp() before comparing two elements. 2) Replace expensive H5Tequals() calls. 3) Retrieve datatype information at dataset level, not at each element level for compound datasets. HDFFV-7516 (JKM 2011/4/18) - Fixed h5ls to display nested compound types with curly brackets when -S (--simple) option is used with -l (--label), so it shows which members (in curly brackets) belong to which nested compound type, making the output clearer. Bug #1979 (JKM 2010/11/09) - Fixed h5diff to handle variable-length strings in a compound dataset and variable-length string arrays in a compound dataset correctly. Garbage values were previously displayed when h5diff compared multiple variable-length strings in a compound type dataset. Bug #1989 (JKM 2010/10/28) - Fixed h5copy to fail gracefully when copying an object to a non- existing group without the -p option. Bug #2040 (JKM 2010/10/18) F90 API ------ - None C++ API ------ - None High-Level APIs: ------ - None Fortran High-Level APIs: ------ - h5tbmake_table_f: Fixed error in passing an array of characters with different length field names. - h5tget_field_info_f: Fixed error with packing the C strings into a Fortran array of strings. Added optional argument called 'maxlen_out' which returns the maximum string character length in a field name element. Bug HDFFV-1255 (MSB- 4/17/2011) Platforms Tested ================ The following platforms and compilers have been tested for this release. AIX 6.1 xlc 11.1.0.3 (NCSA BP) xlC 11.1.0.3 xlf90 13.1.0.3 mpcc_r 11.1.0.3 mpxlf90_r 13.1.0.3 FreeBSD 8.2-STABLE i386 gcc 4.2.1 [FreeBSD] 20070719 (loyalty) g++ 4.2.1 [FreeBSD] 20070719 gcc 4.6.1 20110422 g++ 4.6.1 20110422 gfortran 4.6.1 20110422 FreeBSD 8.2-STABLE amd64 gcc 4.2.1 [FreeBSD] 20070719 (freedom) g++ 4.2.1 [FreeBSD] 20070719 gcc 4.6.1 20110422 g++ 4.6.1 20110422 gfortran 4.6.1 20110422 Linux 2.6.18-194.3.1.el5PAE gcc (GCC) 4.1.2 and 4.4.2 #1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010) (jam) GNU Fortran (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48) and 4.4.2 PGI C, Fortran, C++ 10.4-0 32-bit PGI C, Fortran, C++ 10.6-0 32-bit Intel(R) C Compiler for 32-bit applications, Version 11.1 Intel(R) C++ Compiler for 32-bit applications, Version 11.1 Intel(R) Fortran Compiler for 32-bit applications, Version 11.1 Absoft 32-bit Fortran 95 10.0.7 MPICH mpich2-1.3.1 compiled with gcc 4.1.2 and gfortran 4.1.2 Linux 2.6.18-194.17.1.el5 gcc 4.1.2 and 4.4.2 #1 SMP x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010) (amani) tested for both 32- and 64-bit binaries GNU Fortran (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46) and 4.4.2 Intel(R) C, C++, Fortran Compilers for applications running on Intel(R) 64, Version 11.1. PGI C, Fortran, C++ Version 9.0-4 for 64-bit target on x86-64 MPICH mpich2-1.3.1 compiled with gcc 4.1.2 and gfortran 4.1.2 SGI ProPack 7 Linux Intel(R) C++ Version 11.1 20100806 2.6.32.24-0.2.1.2230.2.PTF- Intel(R) Fortran Version 11.1 20100806 default #1 SMP SGI MPT 2.01 SGI Altix UV (NCSA ember) SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16 (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13 Sun C++ 5.9 Sun OS_sparc Patch 124863-26 Sun C 5.10 SunOS_sparc Patch 141861-07 Sun Fortran 95 8.4 SunOS_sparc Patch 128231-06 Sun C++ 5.10 SunOS_sparc 128228-11 Intel Xeon Linux 2.6.18- gcc 4.2.4 92.1.10.el5_lustre.1.6.6smp- Intel(R) C++ Version 10.1.017 perfctr #8 SMP Intel(R) Fortran Compiler Version 10.1.017 (NCSA abe) Open MPI 1.3.2 MVAPICH2-1.5.1_pgi-10.8 Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Visual Studio 2010 (cmake) Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran) Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Visual Studio 2010 (cmake) Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran) Windows Vista Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Windows Vista x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Mac OS X 10.7.0 (Intel 64-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 Darwin Kernel Version 10.7.0 GNU Fortran (GCC) 4.6.0 20101106 (experimental) Intel C, C++ and Fortran compilers 12.0.1.122 20101110 Mac OS X 10.7.0 (Intel 32-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) Darwin Kernel Version 10.7.0 GNU Fortran (GCC) version 4.4.0 20090123 (experimental) [trunk revision 143587] Fedora 12 2.6.32.16-150.fc12.ppc64 #1 SMP ppc64 GNU/Linux gcc (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10) GNU Fortran (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10) Debian6.01 2.6.32-5-686 #1 SMP i686 GNU/Linux gcc (Debian 4.4.5-8) 4.4.5 GNU Fortran (Debian 4.4.5-8) 4.4.5 Debian6.01 2.6.32-5-amd64 #1 SMP x86_64 GNU/Linux gcc (Debian 4.4.5-8) 4.4.5 GNU Fortran (Debian 4.4.5-8) 4.4.5 Fedora14 2.6.35.12-88.fc14.i686.PAE #1 SMP i686 i686 i386 GNU/Linux gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) GNU Fortran (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) Fedora14 2.6.35.12-88.fc14.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) GNU Fortran (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) SUSE 11.4 2.6.37.1-1.2-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux gcc (SUSE Linux) 4.5.1 20101208 GNU Fortran (SUSE Linux) 4.5.1 20101208 SUSE 11.4 2.6.37.1-1.2-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux gcc (SUSE Linux) 4.5.1 20101208 GNU Fortran (SUSE Linux) 4.5.1 20101208 Ubuntu 10.10 2.6.35-28-generic #50-Ubuntu SMP i686 GNU/Linux gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 GNU Fortran (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 Ubuntu 10.10 2.6.35-28-generic #50-Ubuntu SMP x86_64 GNU/Linux gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 GNU Fortran (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 OpenVMS Alpha 8.3 HP C V7.3-009 HP Fortran V8.2-104679-48H9K HP C++ V7.3-009 Tested Configuration Features Summary ======================================== In the tables below y = tested n = not tested in this release C = Cluster W = Workstation 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 Solaris2.10 32-bit n y n y y y Solaris2.10 64-bit n y n y y y Windows XP n y(4) n y y y Windows XP x64 n y(4) n y y y Windows Vista n y(4) n y y y Windows Vista x64 n y(4) n y y y OpenVMS Alpha n y n y y n Mac OS X 10.7 Intel 32-bit n y n y y y Mac OS X 10.7 Intel 64-bit n y n y y y AIX 6.1 32- and 64-bit y y y y y y FreeBSD 8.2-STABLE 32&64 bit n x n x y y CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y y y CentOS 5.5 Linux 2.6.18-194 i686 Intel W n y n y y n CentOS 5.5 Linux 2.6.18-194 i686 PGI W n y n y y n CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y CentOS 5.5 Linux 2.6.16 x86_64 Intel W n y n y y n CentOS 5.5 Linux 2.6.16 x86_64 PGI W n y n y y y RedHat EL4 2.6.18 Xeon Lustre C y y y y y n Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 n y n y y y SGI Linux 2.6.32.19 y y y y y y Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Solaris2.10 32-bit y y y y Solaris2.10 64-bit y y y y Windows XP y y(4) y n Windows XP x64 y y(4) y n Windows Vista y y(4) y y Windows Vista x64 y y(4) y y OpenVMS Alpha n n n n Mac OS X 10.7 Intel 32-bit y(5) n y n Mac OS X 10.7 Intel 64-bit y(5) n y n AIX 6.1 32- and 64-bit n n n y FreeBSD 8.2-STABLE 32&64 bit y x x y CentOS 5.5 Linux 2.6.18-128 i686 GNU (1)W y y(2) y y CentOS 5.5 Linux 2.6.18-128 i686 Intel W y y y n CentOS 5.5 Linux 2.6.18-128 i686 PGI W y y y n CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y y y CentOS 5.5 Linux 2.6.16 x86_64 Intel W y y y n CentOS 5.5 Linux 2.6.16 x86_64 PGI W y y y n RedHat EL4 2.6.18 Xeon Lustre C y y y n Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 y y y y SGI Linux 2.6.32.19 y y y y (1) Fortran compiled with gfortran. (2) With PGI and Absoft compilers. (3) With PGI compiler for Fortran. (4) Using Visual Studio 2008 w/ Intel Fortran 10.1 (Cygwin shared libraries are not supported) (5) C and C++ shared libraries will not be built when Fortran is enabled. Compiler versions for each platform are listed in the preceding "Platforms Tested" table. Known Problems ============== * After the shared library support was fixed for some bugs, it was discovered that "make prefix=XXX install" no longer works for shared libraries. It still works correctly for static libraries. Therefore, if you want to install the HDF5 shared libraries in a location such as /usr/local/hdf5, you need to specify the location via the --prefix option during configure time. E.g, ./configure --prefix=/usr/local/hdf5 ... (AKC - 2011/05/07 HDFFV-7583) * The parallel test, t_shapesame, in testpar/, may run for a long time and may be terminated by the alarm signal. If that happens, one can increase the alarm seconds (default is 1200 seconds = 20 minutes) by setting the environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 (60 minutes). Note that the t_shapesame test may fail in some systems (see the "While working on the 1.8.6 release..." problem below). If it does, it will waste more time if $HDF5_ALARM_SECONDS is set to a larger value. (AKC - 2011/05/07) * The C++ and FORTRAN bindings are not currently working on FreeBSD. (QAK - 2011/04/26) * Shared Fortran libraries are not quite working on AIX. While they are generated when --enable-shared is specified, the fortran and hl/fortran tests fail. We are looking into the issue. HL and C++ shared libraries should now be working as intended, however. (MAM - 2011/04/20) * The --with-mpe configure option does not work with Mpich2. AKC - 2011/03/10 * If parallel gmake (e.g., gmake -j 4) is used, the "gmake clean" command sometimes fails in the perform directory due to the attempt to remove the executable of h5perf or h5perf_serial by two "parallel" commands. This error has no consequence on the functionality of the HDF5 library or install. It is fixed in the next release. AKC - 2011/01/25 * While working on the 1.8.6 release of HDF5, a bug was discovered that can occur when reading from a dataset in parallel shortly after it has been written to collectively. The issue was exposed by a new test in the parallel HDF5 test suite, but had existed before that. We believe the problem lies with certain MPI implementations and/or file systems. We have provided a pure MPI test program, as well as a standalone HDF5 program, that can be used to determine if this is an issue on your system. They should be run across multiple nodes with a varying number of processes. These programs can be found at: http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ * The library's test dt_arith.c showed a compiler's rounding problem on Cygwin when converting from unsigned long long to long double. The library's own conversion works fine. We defined a macro for Cygwin to skip this test until we can solve the problem. Please see bug #1813. SLU - 2010/5/5 * All the VFL drivers aren't backward compatible. In H5FDpublic.h, the structure H5FD_class_t changed in 1.8. There is new parameter added to get_eoa and set_eoa callback functions. A new callback function get_type_map was added in. The public function H5FDrealloc was taken out in 1.8. The problem only happens when users define their own driver for 1.6 and try to plug in 1.8 library. Because there's only one user complaining about it, we (Elena, Quincey, and I) decided to leave it as it is (see bug report #1279). Quincey will make a plan for 1.10. SLU - 2010/2/2 * MinGW has a missing libstdc++.dll.a library file and will not successfully link C++ applications/tests. Do not use the enable-cxx configure option. Read all of the INSTALL_MINGW.txt file for all restrictions. ADB - 2009/11/11 * The PathScale MPI implementation, accessing a Panasas file system, would cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file does not exist. This is due to the MPI_File_open() call failing if the mode has the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11 * Parallel tests failed with 16 processes with data inconsistency at testphdf5 / dataset_readAll. Parallel tests also failed with 32 and 64 processes with collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks with MPI IO. CMC - 2009/04/28 * For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests are expected to fail and should exit with a non-zero code but the yod command does not propagate the exit code of the executables. Yod always returns 0 if it can launch the executable. The test suite shell expects a non-zero for this particular test, therefore it concludes the test has failed when it receives 0 from yod. Skip all the "failing" test for now by changing them as following. ======== Original tools/h5ls/testh5ls.sh ========= TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ======== Change to =============================== echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ================================================== ======== Original tools/h5copy/testh5copy.sh ========= TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested H5LSTEST $FILEOUT ======== Change to =============================== echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested echo SKIP H5LSTEST $FILEOUT ================================================== AKC - 2008/11/10 * For Red Storm, a Cray XT3 system, the yod command sometimes gives the message, "yod allocation delayed for node recovery". This interferes with test suites that do not expect to see this message. See the section of "Red Storm" in file INSTALL_parallel for a way to deal with this problem. AKC - 2008/05/28 * On an 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. * 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. * 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 calculation 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 * 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 will only statically link libraries if the static version of that library is present. If only the shared version of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, for example, only have shared versions), the flag should still result in a successful compilation, but note that the installed executables will not be fully static. Thus, the only guarantee on these systems is that the executable is statically linked with just the HDF5 library. * There is also a configure error on Altix machines that incorrectly reports when a version of Szip without an encoder is being used. * On cobalt, an SGI Altix SMP ia64 system, Intel compiler version 10.1 (which is the default on that system) does not work properly and results in failures during make check (in a static build) and make installcheck (during a shared build). This appears to be a compiler optimization problem. Reducing optimization by setting CFLAGS to -O1 or below resolves the issue. Alternatively, using a newer version of the compiler (11.0) also works as intended. MAM - 2010/06/01 * h5diff will not report enum value differences when one or both of the values is not a valid enumeration value. The source of this bug has been identified and it will be fixed in 1.8.8. DER - 2011/04/27 %%%%1.8.6%%%% HDF5 version 1.8.6 released on Mon Feb 14 10:26:30 CST 2011 ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.5 and HDF5 1.8.6, and contains information on the platforms tested and known problems in HDF5-1.8.6. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.6 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.6 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.6 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in the HDF5-1.8.x release series, 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 1.8.6 (current release) versus Release 1.8.5": 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 - Support for New Platforms, Languages, and Compilers - Bug Fixes since HDF5-1.8.5 - Platforms Tested - Supported Configuration Features Summary - Known Problems New Features ============ Configuration ------------- - CMake: Improved CPack packaging, added parallel commands, improved configuration options (better similarity to configure), added more tests, better support for use in external cmake projects. (ADB - 2010/10/07) - The default configuration setting for official releases is --enable-production. For unofficial releases, the default configuration setting has been --disable-production. (AKC - 2010/05/28) Library ------- - Added support for thread safety on Windows using the Windows threads library. Use the HDF5_ENABLE_THREADSAFE option in CMake on a Windows platform to enable this functionality. This is supported on Windows Vista and newer Windows operating systems. (MAM - 2010/09/10) - H5Tset_order and H5Tget_order now support all datatypes. A new byte order, H5T_ORDER_MIXED, has been added specifically for a compound datatype and its derived type. (SLU - 2010/8/23) - Improved performance of metadata I/O by changing the default algorithm to perform I/O from all processes (instead of just process 0) when using parallel I/O drivers. (QAK - 2010/07/19) - Improved performance of I/O on datasets with the same shape, but different rank. (QAK - 2010/07/19) - Improved performance of the chunk cache by avoiding unnecessary b-tree lookups of chunks already in cache. (NAF - 2010/06/15) Parallel Library ---------------- - None Tools ----- - h5diff: Added a new flag: --exclude-path. The specified path to an object will be excluded when comparing two files or two groups. If a group is specified to be excluded, all member objects of that group will be excluded. (JKM - 2010/09/16). - h5ls: Added a new flag: --no-dangling-links. See --help output for details. (JKM - 2010/06/15) - h5ls: Added a new flag --follow-symlinks. See --help output for details. (JKM - 2010/05/25) High-Level APIs --------------- - None F90 API ------- - None C++ API ------- - None Support for New Platforms, Languages, and Compilers =================================================== - Sun C and C++ 5.10 and Sun Fortran 95 8.4. - Mac OS X 10.6.4 with gcc 4.2.1 and gfortran 4.6 Bug Fixes since HDF5-1.8.5 ========================== Configuration ------------- - The default number of MPI processes for testing purposes has been changed from 3 to 6. (AKC - 2010/11/11) - Some tests in tools/h5repack may fail in AIX systems when -q32 mode is used. The error is caused by not requesting enough memory in default. Added "env LDR_CNTRL=MAXDATA=0x20000000@DSA" into the $RUNSERIAL and $RUNPARALLE in the AIX config file so that executables are tested with more memory. (AKC - 2010/11/11) - Removed recognition of the parallel compilers of LAM(hcc) and ChMPIon(cmpicc) since we have no access to these two MPI implementations and cannot verify their correctness. (AKC - 2010/07/14 - Bug 1921) - PHDF5 was changed to use "mpiexec" instead of mpirun as the default MPI applications startup command as defined in the MPI-2 definition, section 4.1. (AKC - 2010/06/11 - Bug 1921) Library ------- - Fixed a bug that caused big endian machines to generate corrupt files when using the scale-offset filter with floating point data or fill values. Note that such datasets will no longer be readable by any by any machine after this patch. (NAF - 2010/02/02 - Bug 2131) - Retrieving a link's name by index in the case where the link is external and the file that the link refers to doesn't exist will now fail gracefully rather than cause a segmentation fault. (MAM - 2010/11/17) - Modified metadata accumulator to better track accumulated dirty metadata in an effort to reduce unnecessary I/O in certain situations and to fix some other corner cases which were prone to error. (MAM - 2010/10/15) - Added a new set of unit tests that are run during 'make check' to verify the behavior of the metadata accumulator. (MAM - 2010/10/15) - Modified library to always cache symbol table information. Libraries from version 1.6.3 and earler have a bug which causes them to require this information for some operations. (NAF - 2010/09/21 - Bug 1864) - Fixed a bug where the library could generate an assertion/core dump when a file that had been created with H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) but didn't have a superblock extension was later reopened. (QAK - 2010/09/16 - Bug 1968) - Fixed a bug that could occur when getting information for a new-style group that was previously opened through a file handle that was later closed. (NAF - 2010/09/15) - Added define check in H5public.h if stdint.h is supported by the C++ compiler. This define is only available on Windows with VS2010 and using CMake to build the library. (ADB - 2010/09/13 - Bug 1938) - When a mandatory filter failed to write data chunks, the dataset couldn't close (bug 1260). The fix releases all resources and closes the dataset but returns a failure. (SLU - 2010/09/08) - H5Eset_current_stack now also closes the error stack set as the default. This is to avoid a potential problem. (SLU - 2010/09/07 - Bug 1799) - Corrected situation where 1-D chunked dataset could get created by an application without calling H5Pset_chunk(). H5Pset_chunk is now required for creating all chunked datasets. (QAK - 2010/09/02) - Fixed many memory issues that valgrind exposed. (QAK - 2010/08/24) - Fixed the bug in the filter's public CAN_APPLY function. The return value should be htri_t not herr_t. (SLU - 2010/08/05 - Bug 1239) - Fixed the STDIO VFD to use fseeko64 instead of fseek64 for 64-bit I/O support. (AKC - 2010/7/30) - Fixed a bug in the direct I/O driver that could render files with certain kinds of unaligned data unreadable or corrupt them. (NAF - 2010/07/28) - valgrind reported an error of copying data to itself when a new attribute is written. Fixed by taking out the memcpy step in the attribute code. (SLU - 2010/07/28 - Bug 1956) - Corrected various issues in the MPI datatype creation code which could cause resource leaks or incorrect behavior (and may improve the performance as well). (QAK - 2010/07/19) - Fixed a bug that could cause file corruption when using non-default sizes of addresses and/or lengths. This bug could also cause uncorrupted files with this property to be unreadable. This bug was introduced in 1.8.5. (NAF - 2010/07/16 - Bug 1951) Parallel Library ---------------- - None Tools ----- - Fixed h5diff to compare member objects and groups recursively when two files or groups are compared. (JKM - 2010/9/16 - Bug 1975) - Fixed h5repack to be able to convert a dataset to COMPACT layout. (JKM - 2010/09/15 - Bug 1896) - Changed h5ls to not interpret special characters in object or attribute names for output. (JKM - 2010/06/28 - Bug 1784) - Revised the order of arguments for h5cc, h5fc, h5c++, h5pcc and h5pfc. CPPFLAGS, CFLAGS, LDFLAGS, and LIBS have been duplicated with an H5BLD_ prefix to put the flags and paths from the hdf5 build in the correct places and allow the script user to add entries in CPPFLAGS, CFLAGS, LDFLAGS, and LIBS that will take precedence over those from the hdf5 build. The user can make these entries persistent by editing CFLAGSBASE, CPPFLAGSBASE, LDFLAGSBASE, and LIBSBASE near the top of the script or temporary by setting HDF5_CFLAGS, HDF5_CPPFLAGS, HDF5_LDFLAGS, or HDF5_LIBS in the environment. The new order of arguments in these scripts is $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args $shared_link. (LRK - 2010/10/25 - Bug 1973) F90 API ------ - None C++ API ------ - None High-Level APIs: ------ - None Fortran High-Level APIs: ------ - None Platforms Tested ================ The following platforms and compilers have been tested for this release. AIX 6.1 xlc 11.1.0.3 (NCSA BP) xlC 11.1.0.3 xlf 13.1.0.3 mpcc_r 11.1.0.3 mpxlf_r 13.1.0.3 FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 (duty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.4.5 20100803 g++ 4.4.5 20100803 gfortran 4.4.5 20100803 FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 (liberty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.4.5 20100803 g++ 4.4.5 20100803 gfortran 4.4.5 20100803 Linux 2.6.18-194.3.1.el5PAE gcc (GCC) 4.1.2 and 4.4.2 #1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010) (jam) GNU Fortran (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48) and 4.4.2 PGI C, Fortran, C++ 10.4-0 32-bit PGI C, Fortran, C++ 10.6-0 32-bit Intel(R) C Compiler for 32-bit applications, Version 11.1 Intel(R) C++ Compiler for 32-bit applications, Version 11.1 Intel(R) Fortran Compiler for 32-bit applications, Version 11.1 Absoft 32-bit Fortran 95 10.0.7 MPICH mpich2-1.3.1 compiled with gcc 4.1.2 and gfortran 4.1.2 Linux 2.6.18-194.17.1.el5 gcc 4.1.2 and 4.4.2 #1 SMP x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010) (amani) tested for both 32- and 64-bit binaries GNU Fortran (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46) and 4.4.2 Intel(R) C, C++, Fortran Compilers for applications running on Intel(R) 64, Version 11.1. PGI C, Fortran, C++ Version 9.0-4 for 64-bit target on x86-64 MPICH mpich2-1.3.1 compiled with gcc 4.1.2 and gfortran 4.1.2 SGI ProPack 7 Linux Intel(R) C++ Version 11.1 20100806 2.6.32.19-0.3.1.1982.0.PTF- Intel(R) Fortran Version 11.1 20100806 default #1 SMP SGI MPT 2.01 SGI Altix UV (NCSA ember) SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16 (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13 Sun C++ 5.9 Sun OS_sparc Patch 124863-62 Sun C 5.10 SunOS_sparc Patch 141861-07 Sun Fortran 95 8.4 SunOS_sparc Patch 128231-06 Sun C++ 5.10 SunOS_sparc 128228-11 Intel Xeon Linux 2.6.18- gcc 4.2.4 92.1.10.el5_lustre.1.6.6smp- Intel(R) C++ Version 10.1.017 perfctr #8 SMP Intel(R) Fortran Compiler Version 10.1.017 (NCSA abe) Open MPI 1.3.2 MVAPICH2-1.5.1_pgi-10.8 Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Visual Studio 2010 (cmake) Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran) Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Visual Studio 2010 (cmake) Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran) Windows Vista Visual Studio 2008 w/ Intel Fortran 10.1 (project files) Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Windows Vista x64 Visual Studio 2008 w/ Intel Fortran 10.1 (project files) Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Windows 7 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Windows 7 x64 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake) Mac OS X 10.6.3 (Intel 64-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 Darwin Kernel Version 10.3.1 GNU Fortran (GCC) 4.5.0 20090910 Intel C, C++ and Fortran compilers 11.1 20100806 Mac OS X 10.6.4 (Intel 32-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 Darwin Kernel Version 10.4.0 GNU Fortran (GCC) 4.6.0 20101106 Intel C, C++ and Fortran compilers 12.0.0 20101110 Mac OS X 10.6.4 (Intel 64-bit) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5659) Darwin Kernel Version 10.6.0 GNU Fortran (GCC) 4.5.0 20090910 Intel C, C++ and Fortran compilers 11.1 20100806 Fedora 12 2.6.32.16-150.fc12.ppc64 #1 SMP ppc64 GNU/Linux gcc (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10) GNU Fortran (GCC) 4.4.4 20100630 (Red Hat 4.4.4-10) Debian5.06 2.6.26-2-686 #1 SMP i686 GNU/Linux gcc (Debian 4.3.2-1.1) 4.3.2 GNU Fortran (Debian 4.3.2-1.1) 4.3.2 Debian5.06 2.6.26-2-amd64 #1 SMP x86_64 GNU/Linux gcc (Debian 4.3.2-1.1) 4.3.2 GNU Fortran (Debian 4.3.2-1.1) 4.3.2 Fedora14 2.6.35.6-48.fc14.i686.PAE #1 SMP i686 i686 i386 GNU/Linux gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) GNU Fortran (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) Fedora14 2.6.35.6-48.fc14.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) GNU Fortran (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) SUSE 11.3 2.6.34.7-0.7-desktop #1 SMP PREEMPT i686 i686 i386 GNU/Linux gcc (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292] GNU Fortran (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292] SUSE 11.3 2.6.34.7-0.7-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux gcc (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292] GNU Fortran (SUSE Linux) 4.5.0 20100604 [gcc-4_5-branch revision 160292] Ubuntu 10.10 2.6.35-25-generic #44-Ubuntu SMP i686 GNU/Linux gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 GNU Fortran (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 Ubuntu 10.10 2.6.35-25-generic #44-Ubuntu SMP x86_64 GNU/Linux gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 GNU Fortran (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5 OpenVMS Alpha 8.3 HP C V7.3-009 HP Fortran V8.2-104679-48H9K HP C++ V7.3-009 Tested Configuration Features Summary ======================================== In the tables below y = tested n = not tested in this release C = Cluster W = Workstation 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 Solaris2.10 32-bit n y n y y y Solaris2.10 64-bit n y n y y y Windows XP n y(4) n y y y Windows XP x64 n y(4) n y y y Windows Vista n y(4) n y y y Windows Vista x64 n y(4) n y y y OpenVMS Alpha n y n y y n Mac OS X 10.6 Intel n y n y y y AIX 6.1 32- and 64-bit y y y y y y FreeBSD 6.3-STABLE 32&64 bit n y n y y y CentOS 5.5 Linux 2.6.18-194 i686 GNU (1)W y y(2) y y y y CentOS 5.5 Linux 2.6.18-194 i686 Intel W n y n y y n CentOS 5.5 Linux 2.6.18-194 i686 PGI W n y n y y n CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y(3) y y y y CentOS 5.5 Linux 2.6.16 x86_64 Intel W n y n y y n CentOS 5.5 Linux 2.6.16 x86_64 PGI W n y n y y y RedHat EL4 2.6.18 Xeon Lustre C y y y y y n Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 n y n y y y SGI Linux 2.6.32.19 y y y y y y Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Solaris2.10 32-bit y y y y Solaris2.10 64-bit y y y y Windows XP y y(4) y n Windows XP x64 y y(4) y n Windows Vista y y(4) y y Windows Vista x64 y y(4) y y OpenVMS Alpha n n n n Mac OS X 10.6 y(5) n y n AIX 6.1 32- and 64-bit n n n y FreeBSD 6.3-STABLE 32&64 bit y n y y CentOS 5.5 Linux 2.6.18-128 i686 GNU (1)W y y(2) y y CentOS 5.5 Linux 2.6.18-128 i686 Intel W y y y n CentOS 5.5 Linux 2.6.18-128 i686 PGI W y y y n CentOS 5.5 Linux 2.6.16 x86_64 GNU (1) W y y y y CentOS 5.5 Linux 2.6.16 x86_64 Intel W y y y n CentOS 5.5 Linux 2.6.16 x86_64 PGI W y y y n RedHat EL4 2.6.18 Xeon Lustre C y y y n Fedora 12 Linux 2.6.32.16-150.fc12.ppc64 y y y y SGI Linux 2.6.32.19 y y y y (1) Fortran compiled with gfortran. (2) With PGI and Absoft compilers. (3) With PGI compiler for Fortran. (4) Using Visual Studio 2008 w/ Intel Fortran 10.1 (Cygwin shared libraries are not supported) (5) C and C++ shared libraries will not be built when Fortran is enabled. Compiler versions for each platform are listed in the preceding "Platforms Tested" table. Known Problems ============== * examples/run-all-ex.sh does not work on Cygwin. (NAF - 2011/02/11) * Parallel test, t_shapesame in testpar, is rather unstable as it continues to have occasional errors in AIX and quite often in NCSA Abe. It is being built but it is not run automatically in the "make check" command. One would have to run it by hand to see if it works in a particular machine. AKC - 2011/01/28 * Although OpenVMS Alpha is supported, there are several problems with the C test suite - getname.c, lheap.c, lheap.c, mtime.c, and stab.c. The test suite for h5diff also fails. These failures are from the tests, not the library. We have fixed these failures. But it's too late to put the fixes into this release. If you install the 1.8.6 library, it should still work despite of these test failures. If you want the working copy without any test failure, you can request it from us. SLU - 2011/01/26 * If parallel gmake (e.g., gmake -j 4) is used, the "gmake clean" command sometimes fails in the perform directory due to the attempt to remove the executable of h5perf or h5perf_serial by two "parallel" commands. This error has no consequence on the functionality of the HDF5 library or install. It is fixed in the next release. AKC - 2011/01/25 * While working on the 1.8.6 release of HDF5, a bug was discovered that can occur when reading from a dataset in parallel shortly after it has been written to collectively. The issue was exposed by a new test in the parallel HDF5 test suite, but had existed before that. We believe the problem lies with certain MPI implementations and/or filesystems. We have provided a pure MPI test program, as well as a standalone HDF5 program, that can be used to determine if this is an issue on your system. They should be run across multiple nodes with a varying number of processes. These programs can be found at: http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ * The h5diff tool can display garbage values when variable-length strings in a compound type dataset are compared. This also occurs with variable-length string arrays in a compound type dataset. See bug #1989. This will be fixed in the next release. JKM - 2010/11/05 * The AIX --enable-shared setting does not quite work. It can produce a shared library, but there cannot be more than one shared library that is interlinked. This means that the high level APIs will not work which is not very useful. We hope to have a solution in the next release. (AKC - 2010/10/15) * H5Eset_auto can cause a seg fault for a library API call if the application compiles with -DH5_USE_16_API (see bug 1707). It will be fixed in the next release. SLU - 2010/10/5 * The library's test dt_arith.c showed a compiler's rounding problem on Cygwin when converting an unsigned long long to a long double. The library's own conversion works fine. We defined a macro for Cygwin to skip this test until we can solve the problem. Please see bug #1813. SLU - 2010/5/5 * All the VFL drivers aren't backwardly compatible. In H5FDpublic.h, the structure H5FD_class_t changed in 1.8. A new parameter was added to the get_eoa and set_eoa callback functions, and a new callback function get_type_map was added. The public function H5FDrealloc was taken out in 1.8. The problem only happens when users define their own driver for 1.6 and try to plug in a 1.8 library. This will be fixed in 1.10. SLU - 2010/2/2 * MinGW has a missing libstdc++.dll.a library file and will not successfully link C++ applications/tests. Do not use the enable-cxx configure option. Read all of the INSTALL_MINGW.txt file for all restrictions. ADB - 2009/11/11 * The PathScale MPI implementation, accessing a Panasas file system, would cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file does not exist. This is due to the MPI_File_open() call failing if the amode has the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11 * Parallel tests failed with 16 processes with data inconsistency at testphdf5 / dataset_readAll. Parallel tests also failed with 32 and 64 processes with collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks with MPI IO. CMC - 2009/04/28 * For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and tools/h5copy/testh5copy.sh will fail some of their sub-tests. These sub-tests are expected to fail and should exit with a non-zero code but the yod command does not propagate the exit code of the executables. Yod always returns 0 if it can launch the executable. The test suite shell expects a non-zero for this particular test. Therefore, it concludes the test has failed when it receives 0 from yod. To skip all the "failing" tests for now, change them as shown below. ======== Original tools/h5ls/testh5ls.sh ========= TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ======== Change to =============================== echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ================================================== ======== Original tools/h5copy/testh5copy.sh ========= TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested H5LSTEST $FILEOUT ======== Change to =============================== echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested echo SKIP H5LSTEST $FILEOUT ================================================== AKC - 2008/11/10 * For Red Storm, a Cray XT3 system, the yod command sometimes gives the message "yod allocation delayed for node recovery." This interferes with test suites that do not expect to see this message. See the "Red Storm" section in file INSTALL_parallel for a way to deal with this problem. AKC - 2008/05/28 * On an Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers, use the -mp -O1 compilation flags to build the libraries. A higher level of optimization causes failures in several HDF5 library tests. * On mpich 1.2.5 and 1.2.6 on a system using four processors, if more than two processes contribute no I/O and the application asks to do collective I/O, we have found that a simple collective write will sometimes hang. This can be verified with the t_mpi test under testpar. * A dataset created or rewritten with a v1.6.3 or later library cannot be read with the v1.6.2 or earlier library when the Fletcher32 EDC filter is enabled. There was a bug in the calculation 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 earlier. SLU - 2005/6/30 * On IBM AIX systems, parallel HDF5 mode will fail some tests with error messages like "INFO: 0031-XXX ...". This is from the command `poe'. To work around this, 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 any old /tmp/s.pedb.* files around. These are sockets used by the poe command and left behind if the command failed at some point. To resolve this, ask your system administrator to remove the old/tmp/s.pedb.* files, and then ask IBM to provide a means to run poe without the debug socket. * The --enable-static-exec configure flag will only statically link libraries if the static version of that library is present. If only the shared version of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, for example, only have shared versions), the flag should still result in a successful compilation, but note that the installed executables will not be fully static. Thus, the only guarantee on these systems is that the executable is statically linked with just the HDF5 library. * On an SGI Altix SMP ia64 system, the Intel compiler version 10.1 (which is the default on that system) does not work properly and results in failures during the make check (in a static build) and the make installcheck (in a shared build). This appears to be a compiler optimization problem. Reducing the optimization by setting CFLAGS to -O1 or below resolves the issue. Using a newer version of the compiler (11.0) avoids the issue. MAM - 2010/06/01 * On solaris systems, when running the examples with the scripts installed in .../share/hdf5_examples, two of the c tests, h5_extlink and h5_elink_unix2win may fail or generate HDF5 errors because the script commands in c/run-c-ex.sh fail to create test directories red, blue, and u2w. Moving the '!' in lines 67, 70, 73 of run-c-ex.sh will fix the problem. For example the script command "if ! test -d red; then" will work on solaris if changed to "if test ! -d red; then". %%%%1.8.5%%%% HDF5 version 1.8.5 released on Fri Jun 4 13:27:31 CDT 2010 ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.4 and HDF5 1.8.5, and contains information on the platforms tested and known problems in HDF5-1.8.5. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.5 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.5 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.5 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in the HDF5-1.8.x release series, 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 1.8.5 (current release) versus Release 1.8.4": 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 - Support for New Platforms, Languages, and Compilers - Bug Fixes since HDF5-1.8.4 - Platforms Tested - Supported Configuration Features Summary - Known Problems New Features ============ Configuration ------------- - CMake Early Access: This release adds support for building HDF5 using the CMake system. Initial work has targeted Windows, but other platforms can be used. See the CMake.TXT file for more information. Version 2.8.1 of CMake is required. - Configure now adds appropriate defines for supporting large (64-bit) files on all systems, where supported, by default, instead of only Linux. This large file support is controllable with the --enable-largefile configure option. The Linux-specific --enable-linux-lfs option has been deprecated in favor of this new option. Please note that specifying --disable-large does NOT attempt to "turn off" largefile support if it is natively supported by the compiler, but rather just disables configure from actively trying to add any additional compiler flags. (MAM - 2010/05/05 - Bug # 1772/1434) - Fixed an signal handling mask error in H5detect that might result in SIGBUS or SIGSEGV failures in some platforms such as Linux on Sparc. (AKC - 2010/4/28 - Bug # 1764) - Fixed various "strict aliasing" problems, allowing higher levels of compiler optimization (in particular, allowing '-O3' to work with recent versions of GCC). (QAK - 2010/04/26) - Upgraded versions of autotools used to generate configuration suite. We now use Automake 1.11.1, Autoconf 2.65, and Libtool 2.2.6b. (MAM - 2010/04/15) - Added the xlc-* and mpcc_r-* BASENAME patterns to be recognized as IBM compilers so that the IBM compiler options can be added properly. This allows non-system-default compiler command names (e.g. xlc-m.n.k.l) be recognized. (AKC - 2009/11/26) Library ------- - Performance is substantially improved when extending a dataset with early allocation. (NAF - 2010/03/24 - Bug # 1637) - Added support for filtering densely stored groups. Many of the API functions related to filters have been extended to support dense groups as well as datasets. Pipeline messages can now be stored in a group's object header. (NAF/QAK - 2009/11/3) Parallel Library ---------------- - None Tools ----- - h5dump: Added the new packed bits feature which prints packed bits stored in an integer dataset. (AKC/ADB - 2010/5/7) - h5diff: Fixed incorrect behavior (hang) in parallel mode when specifying invalid options (ex: -v and -q). (JKM - 2010/02/17) - h5diff: Added new flag --no-dangling-links (see --help for details). (JKM - 2010/02/10) - h5diff: Added new flag --follow-symlinks (see --help for details). (JKM - 2010/01/25) - h5diff: Added a fix to correct the display of garbage values when displaying big-endian data on a little-endian machine. (JKM - 2009/11/20) High-Level APIs --------------- - None F90 API ------- - None C++ API ------- - New member functions + Overloaded CommonFG::getObjnameByIdx to take char* for name. + Overloaded CommonFG::getObjTypeByIdx to return type name as a char*. (BMR - 2010/05/10) + Added DataSet::getInMemDataSize() to simplify getting the dataset's data size in memory. (BMR - 2009/07/26) Support for New Platforms, Languages, and Compilers =================================================== - AIX 6.1 has been added. (AKC - 2010/1/4) Bug Fixes since HDF5-1.8.4 ========================== Configuration ------------- - Fixed various "strict aliasing" problems, allowing higher levels of compiler optimization (in particular, allowing '-O3' to work with recent versions of GCC). (QAK - 2010/04/26) Library ------- - Fixed a file corruption bug that could happen when shrinking a compressed dataset. (NAF - 2010/05/20) - Fixed some memory leaks in VL datatype conversion when strings are used as fill values. (MAM - 2010/05/12 - Bug # 1826) - Fixed an H5Rcreate failure when passing in a -1 for the dataspace identifier. (ADB - 2010/4/28) - Fixed a bug when copying objects with NULL references with the H5O_COPY_EXPAND_REFERENCE_FLAG flag set. (NAF - 2010/04/08 - Bug # 1815) - Added a mechanism to the H5I interface to save returned object identifier structures for immediate re-use if needed. This addresses a potential performance issue by delaying the case when the next identifier to be registered has grown so large that it wraps around and needs to be checked to see whether it is available for distribution. (MAM - 2010/03/15 - Bug # 1730) - Files can now be concurrently opened more than once using the core file driver, as long as the backing store is used. (NAF - 2010/03/09) - Added support for H5O_COPY_EXPAND_EXT_LINK_FLAG to H5Ocopy. External links will now be expanded if this flag is set. (NAF - 2010/03/05 - Bug # 1733) - Fixed a bug where the library, when traversing an external link, would reopen the source file if nothing else worked. (NAF - 2010/03/05) - Fixed a bug where fractal heap identifiers for attributes and shared object header messages could be incorrectly encoded in the file for files created on big-endian platforms. Please see http://www.hdfgroup.org/HDF5/release/known_problems if you suspect you have a file with this problem. (QAK - 2010/02/23 - Bug # 1755) - Fixed an intermittent bug in the b-tree code which could be triggered by expanding and shrinking chunked datasets in certain ways. (NAF - 2010/02/16) - H5Tdetect_class said a VL string is a string type. But when it's in a compound type, it said it's a VL type. THis has been fixed to be consistent; it now always returns a string type. (SLU - 2009/12/10 - Bug # 1584) - Allow "child" files from external links to be correctly located when relative to a "parent" file that is opened through a symbolic link. (QAK - 2009/12/01) Parallel Library ---------------- - Parallel mode in AIX will fail some of the testcheck_version.sh tests where it treats "exit(134) the same as if process 0 had received an abort signal. Fixed. (AKC - 2009/11/3) Tools ----- - Fixed h5ls to return exit code 1 (error) when a non-existent file is specified. (JKM - 2010/04/27 - Bug # 1793) - Fixed h5copy failure when copying a dangling link that is specified directly. (JKM - 2010/04/22 - Bug # 1817) - Fixed an h5repack failure that lost attributes from a dataset of reference type. (JKM - 2010/3/25 - Bug # 1726) - Fixed h5repack error that set NULL for object reference values for datasets, groups, or named datatypes. (JKM - 2010/03/19 - Bug # 1814) F90 API ------ - None C++ API ------ - The constructor PropList::PropList(id) was fixed to act properly according to the nature of 'id'. When 'id' is a property class identifier, a new property list will be created. When 'id' is a property list identifier, a copy of the property list will be made. (BMR - 2010/5/9) - The parameters 'size' and 'bufsize' in CommonFG::getLinkval and CommonFG::getComment, respectively, now have default values for the user's convenience. (BMR - 2009/10/23) - NULL pointer accessing was fixed. (BMR - 2009/10/05 - Bug # 1061) - Read/write methods of DataSet and Attribute classes were fixed to handle string correctly. (BMR - 2009/07/26) High-Level APIs: ------ - Fixed a bug in H5DSattach_scale, H5DSis_attached, and H5DSdetach_scale caused by using the H5Tget_native_type function to determine the native type for reading the REFERENCE_LIST attribute. This bug was exposed on Mac PPC. (EIP - 2010/05/22 - Bug # 1851) - Fixed a bug in the H5DSdetach_scale function when 0 bytes were allocated after the last reference to a dimension scale was removed from the list of references in a VL element of the DIMENSION_LIST attribute. Modified the function to comply with the specification: the DIMENSION_LIST attribute is now deleted when no dimension scales are left attached. (EIP - 2010/05/14 - Bug # 1822) Fortran High-Level APIs: ------ - None Platforms Tested ================ The following platforms and compilers have been tested for this release. AIX 5.3 xlc 7.0.0.9, 8.0.0.20, 9.0.0.4 (LLNL Up) xlC 7.0.0.9, 8.0.0.20, 9.0.0.4 xlf 9.1.0.9, 10.1.0.9, 11.1.0.7 mpcc_r 7.0.0.9 mpxlf_r 09.01.0000.0008 AIX 6.1 xlc 10.1.0.6 (NCSA BP) xlC 10.1.0.6 xlf 12.1.0.7 Cray XT3 (2.1.56) cc (pgcc) 10.0-0 (SNL red storm) ftn (pgf90) 10.0-0 CC (pgCC) 10.0-0 FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 (duty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.3.4 20090419 g++ 4.3.4 20090419 gfortran 4.3.4 20090419 FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 (liberty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.4.1 20090421 g++ 4.4.1 20090421 gfortran 4.4.1 20090421 Linux 2.6.18-128.1.6.el5xen gcc (GCC) 4.1.2 20080704 and 4.4.2 #1 SMP i686 i686 i386 GNU Fortran (GCC) 4.1.2 20080704 and 4.4.2 (jam) g++ (GCC) 4.1.2 20080704 and 4.4.2 G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010) Absoft 32-bit Fortran 95 10.0.7 PGI C, Fortran, C++ 10.4-0 32-bit Intel(R) C, C++, Fortran Compilers for 32-bit applications, Version 11.1 Build 20090827 MPICH mpich2-1.0.8 compiled with gcc 4.1.2 and GNU Fortran (GCC) 4.1.2 Linux 2.6.18-164.el5 #1 SMP gcc 4.1.2 20080704 and gcc 4.4.2 x86_64 GNU/Linux GNU Fortran (GCC) 4.1.2 20080704 and 4.4.2 (amani) g++ (GCC) 4.1.2 20080704 and 4.4.2 G95 (GCC 4.0.3 (g95 0.93!) Apr 21 2010) Intel(R) C, C++, Fortran Compilers for applications running on Intel(R) 64, Version 11.1 Build 20090827. PGI C, Fortran, C++ Version 10.4-0 for 32 & 64-bit target on x86-64 MPICH mpich2-1.0.8 compiled with gcc 4.1.2 and GNU Fortran (GCC) 4.1.2 Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 11.0.074 SGI Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 11.0.074 (cobalt) SGI MPI 1.38 SunOS 5.10 32- and 64-bit Sun C 5.9 SunOS_sparc Patch 124867-14 (linew) Sun Fortran 95 8.3 SunOS_sparc Patch 127000-13 Sun C++ 5.9 SunOS_sparc Patch 124863-23 Intel Xeon Linux 2.6.18- Intel(R) C++ Version 10.0.026 92.1.10.el5_lustre.1.6.6smp- Intel(R) Fortran Compiler Version 10.0.026 perfctr #7 SMP Open MPI 1.2.2 (abe) MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2 compiled with icc v10.0.026 and ifort 10.0.026 Linux 2.6.18-76chaos #1 SMP Intel(R) C, C++, Fortran Compilers for SMP x86_64 GNU/Linux applications running on Intel(R) 64, (SNL Glory) Versions 11.1. Windows XP Visual Studio 2008 w/ Intel Fortran 10.1 Cygwin(1.7.5 native gcc(4.3.4) compiler and gfortran) Windows XP x64 Visual Studio 2008 w/ Intel Fortran 10.1 Windows Vista Visual Studio 2008 w/ Intel Fortran 10.1 Windows Vista x64 Visual Studio 2008 w/ Intel Fortran 10.1 MAC OS 10.6.3 (Intel) i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (pahra) GNU Fortran (GCC) 4.5.0 20090910 i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 Intel C, C++ and Fortran compilers 11.1 MAC OS 10.5.8 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (tejeda) MAC OS 10.5 (PPC) powerpc-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (juniper-w) OpenVMS Alpha V8.3 HP C V7.3-009 HP C++ V7.3-009 HP Fortran V8.0-1-104669-48GBT Supported Configuration Features Summary ======================================== In the tables below y = tested and supported n = not supported or not tested in this release C = Cluster W = Workstation 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 Solaris2.10 32-bit n y n y y y Solaris2.10 64-bit n y n y y y Windows XP n y(4) n(4) y y y Windows XP x64 n y(4) n(4) y y y Windows Vista n y(4) n(4) y y y Windows Vista x64 n y(4) n(4) y y y Mac OS X 10.5 PPC n n n n y n Mac OS X 10.5 Intel n y n y y y Mac OS X 10.6 Intel n y n y y y AIX 5.3 32- and 64-bit n y n y y n AIX 6.1 32- and 64-bit n y n y y n FreeBSD 6.3-STABLE 32&64 bit n y n y y y RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y y y RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y y y RedHat EL5 2.6.18-128 i686 Intel W n y n y y n RedHat EL5 2.6.18-128 i686 PGI W n y n y y n SuSe Linux 2.6.16 x86_64 GNU (1) W y y(3) y 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 y SuSe Linux 2.6.16 SGI Altix ia64 C y y y y y y RedHat EL4 2.6.18 Xeon Lustre C y y y y y n Cray XT3 2.1.56 y y y y y n OpenVMS Alpha V8.3 n y n y y n Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Solaris2.10 32-bit y y y y Solaris2.10 64-bit y y y y Windows XP y y(4) y n Windows XP x64 y y(4) y n Windows Vista y y(4) y n Windows Vista x64 y y(4) y n Mac OS X 10.5 PPC y n n n Mac OS X 10.5 (Intel) y(5) n y n Mac OS X 10.6 (Intel) y(5) n y n AIX 5.3 32- and 64-bit n n n n AIX 6.1 32- and 64-bit n n n n FreeBSD 6.3-STABLE 32&64 bit y n y y RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y RedHat EL5 2.6.18-128 i686 Intel W y y y n RedHat EL5 2.6.18-128 i686 PGI W y y y n SuSe Linux 2.6.16 x86_64 GNU (1) W y y y y SuSe Linux 2.6.16 x86_64 Intel W y y y n SuSe Linux 2.6.16 x86_64 PGI W y y y n SuSe Linux 2.6.16 SGI Altix ia64 C y n RedHat EL4 2.6.18 Xeon Lustre C y y y n Cray XT3 2.1.56 n n n n OpenVMS Alpha V8.3 n n n n (1) Fortran compiled with g95. (2) With PGI and Absoft compilers. (3) With PGI compiler for Fortran. (4) Using Visual Studio 2008. (Cygwin shared libraries are not supported.) (5) Shared C and C++ are disabled when Fortran is configured in. Compiler versions for each platform are listed in the preceding "Platforms Tested" table. Known Problems ============== * The library's test dt_arith.c exposed a compiler's rounding problem on Cygwin when converting from unsigned long long to long double. The library's own conversion works correctly. A macro is defined for Cygwin to skip this test until we can solve the problem. (Please see bug #1813.) SLU - 2010/5/5 * All the VFL drivers aren't backward compatible. In H5FDpublic.h, the structure H5FD_class_t changed in 1.8. There is a new parameter added to get_eoa and set_eoa callback functions. A new callback function get_type_map was added. The public function H5FDrealloc was taken out in 1.8. The problem only happens when users define their own driver for 1.6 and try to plug it into a 1.8 library. This affects a very small number of users. (See bug report #1279.) SLU - 2010/2/2 * MinGW has a missing libstdc++.dll.a library file and will not successfully link C++ applications/tests. Do not use the enable-cxx configure option. Read all of the INSTALL_MINGW.txt file for all restrictions. ADB - 2009/11/11 * Some tests in tools/h5repack may fail in AIX systems when -q32 mode is used. The error is due to insufficient memory requested. Request a large amount of runtime memory by setting the following environment variable for more memory. LDR_CNTRL=MAXDATA=0x20000000@DSA AKC - 2009/10/31 * The PathScale MPI implementation, accessing a Panasas file system, would cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file is not existing. This is due to the MPI_File_open() call failing if the amode has the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11 * Parallel tests failed with 16 processes with data inconsistency at testphdf5 / dataset_readAll. Parallel tests also failed with 32 and 64 processes with collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks with MPI IO. CMC - 2009/04/28 * For gcc v4.3 and v4.4, with production mode, if -O3 is used, H5Tinit.c would fail to compile. Actually bad H5Tinit.c is produced. If -O (same as -O1) is used, H5Tinit.c compiled okay but test/dt_arith would fail. When -O0 (no optimizatio) is used, H5Tinit.c compilete okay and all tests passed. Therefore, -O0 is imposed for v4.3 and v4.4 of gcc. AKC - 2009/04/20 * For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests are expected to fail and should exit with a non-zero code but the yod command does not propagate the exit code of the executables. Yod always returns 0 if it can launch the executable. The test suite shell expects a non-zero for this particular test, therefore it concludes the test has failed when it receives 0 from yod. Skip all the "failing" test for now by changing them as following. ======== Original tools/h5ls/testh5ls.sh ========= TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ======== Change to =============================== echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ================================================== ======== Original tools/h5copy/testh5copy.sh ========= TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested H5LSTEST $FILEOUT ======== Change to =============================== echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested echo SKIP H5LSTEST $FILEOUT ================================================== AKC - 2008/11/10 * For Red Storm, a Cray XT3 system, the yod command sometimes gives the message, "yod allocation delayed for node recovery". This interferes with test suites that do not expect seeing this message. See the section of "Red Storm" in file INSTALL_parallel for a way to deal with this problem. AKC - 2008/05/28 * 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. * 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. * 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 calculation 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 * 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 will only statically link libraries if the static version of that library is present. If only the shared version of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, for example, only have shared versions), the flag should still result in a successful compilation, but note that the installed executables will not be fully static. Thus, the only guarantee on these systems is that the executable is statically linked with just the HDF5 library. * There is also a configure error on Altix machines that incorrectly reports when a version of Szip without an encoder is being used. * On FREE-BSD systems when shared libraries are disabled, make install fails in install-examples with the error '"Makefile", line 635: Need an operator'. When this error occurs removing or commenting out the line "export LD_LIBRARY_PATH=$(LL_PATH)" (line 635 in examples/Makefile) will allow make install to finish installing examples. The problem will be fixed in the next release. LRK - 2010/05/26 * On cobalt, an SGI Altix SMP ia64 system, Intel compiler version 10.1 (which is the default on that system) does not work properly and results in failures during make check (in a static build) and make installcheck (during a shared build). This appears to be a compiler optimization problem. Reducing optimization by setting CFLAGS to -O1 or below resolves the issue. Alternatively, using a newer version of the compiler (11.0) also works as intended. MAM - 2010/06/01 %%%%1.8.4%%%% HDF5 version 1.8.4 released on Tue Nov 10 15:33:14 CST 2009 ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.3 and HDF5 1.8.4, and contains information on the platforms tested and known problems in HDF5-1.8.4 For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.4 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.4 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.4 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in the HDF5-1.8.x release series, 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 1.8.4 (current release) versus Release 1.8.3": 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 - Support for New Platforms, Languages, and Compilers - Bug Fixes since HDF5-1.8.3 - Platforms Tested - Supported Configuration Features Summary - Known Problems New Features ============ Configuration ------------- - Configuration suite now uses Automake 1.11 and Autoconf 2.64. MAM 2009/08/31. - Changed default Gnu fortran compiler from g95 to gfortran since gfortran is more likely installed with gcc now. -AKC 2009/07/19- Library ------- - The embedded library information is displayed by H5check_version() if a version mismatch is detected. Also changed H5check_version() to suppress the warning message totally if $HDF5_DISABLE_VERSION_CHECK is 2 or higher. (Old behavior treated 3 or higher the same as 1, that is print a warning and allows the program to continue. (AKC - 2009/9/28) - If a user does not care for the extra library information insert in the executables, he may turn it off by --disable-embedded-libinfo during configure. (AKC - 2009/9/15) Parallel Library ---------------- - None Tools ----- - h5diff: h5diff treats two INFINITY values different. Fixed by checking (value==expect) before call ABS(...) at h5diff_array.c. This will make that (INF==INF) is true (INF is treated as an number instead of NaN) (PC -- 2009/07/28) - h5diff: add option "--use-system-epsilon" to print difference if (|a-b| > EPSILON). Change default to use strict equality (PC -- 2009/09/12) High-Level APIs --------------- - None F90 API ------- - Added H5Oopen_by_addr_f MSB - 9/14/09 C++ API ------- - None Support for New Platforms, Languages, and Compilers =================================================== - PathScale compilers are recognized and can build the HDF5 library properly. AKC - 2009/7/28 - Bug Fixes since HDF5-1.8.3 ========================== Configuration ------------- - Removed the following config files, as we no longer support them: config/dec-osf*, config/hpux11.00, config/irix5.x, config/powerpc-ibm-aix4.x config/rs6000-ibm-aix5.x config/unicos* MAM - 2009/10/08 - Modified configure and make process to properly preserve user's CFLAGS (and company) environment variables. Build will now properly use automake's AM_CFLAGS for any compiler flags set by the configure process. Configure will no longer modify CFLAGS directly, nor will setting CFLAGS during make completely replace what configure has set up. MAM - 2009/10/08 - Support for TFLOPS, config/intel-osf1, is removed since the TFLOPS machine has long retired. AKC - 2009/10/06. - Added $(EXEEXT) extension to H5detect when it's executed in the src/Makefile to generate H5Tinit.c so it works correctly on platforms that require the full extension when running executables. MAM - 2009/10/01 - BZ #1613 - Configure will now set FC and CXX to "no" when fortran and c++ are not being compiled, respectively, so configure will not run some of the compiler tests for these languages when they are not being used. MAM - 2009/10/01 - The --enable-static-exec flag will now properly place the -static flag on the link line of all installed executables. This will force the executable to link with static libraries over shared libraries, provided the static libraries are available. MAM - 2009/08/31 - BZ #1583 - The PathScale compiler (v3.2) was mistaken as gcc v4.2.0 but it fails to recognize some gcc options. Fixed. (see bug 1301). AKC - 2009/7/28 - Library ------- - Fixed a bug where writing and deleting many global heap objects (i.e. variable length data) would render the file unreadable. Previously created files exhibiting this problem should now be readable. NAF - 2009/10/27 - 1483 - Fixed error in library's internal caching mechanisms which could cause an assertion failure (and attendent core dump) when encountering an unusually formatted file. (QAK - 2009/10/13) - Fixed incorrect return value for H5Pget_preserve. AKC - 2009/10/08 - 1628 - Fixed an assertion failure that occurred when H5Ocopy was called on a dataset using a vlen inside a compound. NAF - 2009/10/02 - 1597 - Fixed incorrect return value for H5Pget_filter_by_id1/2 in H5Ppublic.h. NAF - 2009/09/25 - 1620 - Fixed a bug where properties weren't being compared with the registered compare callback. NAF - 2009/09/25 - 1555 - Corrected problem where library would re-write the superblock in a file opened for R/W access, even when no changes were made to the file. (QAK - 2009/08/20, Bz#1473) - Fixed a bug where H5Pget_filter_by_id would succeed when called for a filter that wasn't present. NAF - 2009/06/25 - 1250 - Fixed an issue with committed compound datatypes containing a vlen. Also fixed memory leaks involving committed datatypes. NAF - 2009/06/10 - 1593 Parallel Library ---------------- - None Tools ----- - h5dump/h5ls display buffer resize fixed in tools library. ADB - 2009/7/21 - 1520 - perf_serial test added to Windows projects and check batch file. ADB - 2009/06/11 -1504 F90 API ------ - Fixed bug in h5lget_info_by_idx_f by adding missing arguments, consequently changing the API. New API is: SUBROUTINE h5lget_info_by_idx_f(loc_id, group_name, index_field, order, n, & link_type, f_corder_valid, corder, cset, address, val_size, hdferr, lapl_id) MSB - 2009/9/17 - 1652 - Corrected the values for the H5L_flags FORTRAN constants: H5L_LINK_ERROR_F, H5L_LINK_HARD_F, H5L_LINK_SOFT_F, H5L_LINK_EXTERNAL_F MSB - 2009-09-17 - 1653 - Added FORTRAN equivalent of C constant H5T_ORDER_NONE: H5T_ORDER_NONE_F MSB - 2009-9-24 - 1471 C++ API ------ - None High-Level APIs: ------ - Fixed a bug where the H5TB API would forget the order of fields when added out of offset order. NAF - 2009/10/27 - 1582 - H5DSis_attached failed to account for different platform types. Added a get native type call. ADB - 2009/9/29 - 1562 Fortran High-Level APIs: ------ - Lite: the h5ltread_dataset_string_f and h5ltget_attribute_string_f functions had memory problems with the g95 fortran compiler. (PVN � 5/13/2009) 1522 Platforms Tested ================ The following platforms and compilers have been tested for this release. AIX 5.3 xlc 7.0.0.8 (LLNL Up) xlf 09.01.0000.0008 xlC 7.0.0.8 mpcc_r 7.0.0.8 mpxlf_r 09.01.0000.0008 Cray XT3 (2.0.41) cc (pgcc) 7.1-4 (SNL red storm) ftn (pgf90) 7.1-4 CC (pgCC) 7.1-4 FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 (duty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.3.5 20091004 g++ 4.3.5 20091004 gfortran 4.3.5 20091004 FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 (liberty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.4.2 20091006 g++ 4.4.2 20091006 gfortran 4.4.2 20091006 Linux 2.6.18-164.el5 gcc (GCC) 4.1.2 20080704 #1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Jun 24 2009) (jam) GNU Fortran (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46) PGI C, Fortran, C++ 8.0-5 32-bit PGI C, Fortran, C++ 8.0-1 32-bit Intel(R) C Compiler for 32-bit applications, Versions 11.0, 11.1 Intel(R) C++ Compiler for 32-bit applications, Version 11.0, 11.1 Intel(R) Fortran Compiler for 32-bit applications, Version 11.0, 11.1 Absoft 32-bit Fortran 95 10.0.7 MPICH mpich2-1.0.8 compiled with gcc (GCC) 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) Linux 2.6.18-164.el5 #1 SMP gcc 4.1.2 20080704 x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.92!) Jun 24 2009) (amani) tested for both 32- and 64-bit binaries Intel(R) C, C++, Fortran Compilers for applications running on Intel(R) 64, Versions 11.1. PGI C, Fortran, C++ Version 9.0-4 for 64-bit target on x86-64 gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) MPICH mpich2-1.0.8 compiled with gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) GNU Fortran (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46) Linux 2.6.16.60-0.42.5 #1 Intel(R) C++ Version 10.1.017 SGI Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017 (cobalt) SGI MPI 1.38 SunOS 5.10 32- and 64-bit Sun C 5.9 SunOS_sparc Patch 124867-11 2009/04/30 (linew) Sun Fortran 95 8.3 SunOS_sparc Patch 127000-11 2009/10/06 Sun C++ 5.9 SunOS_sparc Patch 124863-16 2009/09/15 Intel Xeon Linux 2.6.18- Intel(R) C++ Version 10.0.026 92.1.10.el5_lustre.1.6.6smp- Intel(R) Fortran Compiler Version 10.0.026 perfctr #6 SMP Open MPI 1.2.2 (abe) MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2 compiled with icc v10.0.026 and ifort 10.0.026 IA-64 Linux 2.4.21-309.tg1 gcc (GCC) 3.2.2 #1 SMP ia64 Intel(R) C++ Version 8.1.037 (NCSA tg-login) Intel(R) Fortran Compiler Version 8.1.033 mpich-gm-1.2.7p1..16-intel-8.1.037-r1 Linux 2.6.9-55.0.9.EL_lustre Intel(R) C, C++, Fortran Compilers for .1.4.11.1smp #1 SMP applications running on Intel(R) 64, SMP x86_64 GNU/Linux Versions 10.1. (SNL Thunderbird) Linux 2.6.18-76chaos #1 SMP Intel(R) C, C++, Fortran Compilers for SMP x86_64 GNU/Linux applications running on Intel(R) 64, (SNL Glory) Versions 10.1. Windows XP Visual Studio 2005 w/ Intel Fortran 9.1 Cygwin(native gcc compiler and g95) Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 Windows Vista Visual Studio 2005 w/ Intel Fortran 9.1 Windows Vista x64 Visual Studio 2005 w/ Intel Fortran 9.1 MAC OS 10.5.6 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 GNU Fortran (GCC) 4.3.0 20070810 G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008) Intel C, C++ and Fortran compilers 10.1 Supported Configuration Features Summary ======================================== In the tables below y = tested and supported n = not supported or not tested in this release C = Cluster W = Workstation 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 Solaris2.10 32-bit n y n y y y Solaris2.10 64-bit n y n y y y Windows XP n y(4) n(4) y y y Windows XP x64 n y(4) n(4) y y y Windows Vista n n n y y y Mac OS X 10.5 Intel n y n y y y AIX 5.3 32- and 64-bit n y n y y n FreeBSD 6.3-STABLE 32&64 bit n y n y y y RedHat EL5 2.6.18-164 i686 GNU (1)W y y(2) y y y y RedHat EL5 2.6.18-164 i686 Intel W n y n y y n RedHat EL5 2.6.18-164 i686 PGI W n y n y y n RedHat EL5 2.6.18-164 x86_64 GNU(1)W y y(3) y y y y RedHat EL5 2.6.18-164 x86_64 IntelW n y n y y n RedHat EL5 2.6.18-164 x86_64 PGI W n y n y y y SuSe Linux 2.6.16 SGI Altix ia64 C y y y y y y RedHat EL4 2.6.18 Xeon Lustre C y y y y y n SuSe Linux 2.4.21 ia64 Intel C y y y y y n Cray XT3 2.0.62 y y y y y n Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Solaris2.10 32-bit y y y y Solaris2.10 64-bit y y y y Windows XP y y(4) y y Windows XP x64 y y(4) y y Windows Vista y n n y Mac OS X 10.5 y n y n AIX 5.3 32- and 64-bit n n n n FreeBSD 6.3-STABLE 32&64 bit y y y y RedHat EL5 2.6.18-164 i686 GNU (1)W y y(2) y y RedHat EL5 2.6.18-164 i686 Intel W y y y n RedHat EL5 2.6.18-164 i686 PGI W y y y n RedHat EL5 2.6.18-164 x86_64 GNU(1)W y y y y RedHat EL5 2.6.18-164 x86_64 IntelW y y y n RedHat EL5 2.6.18-164 x86_64 PGI W y y y n SuSe Linux 2.6.16 SGI Altix ia64 C y n RedHat EL4 2.6.18 Xeon Lustre C y y y n SuSe Linux 2.4.21 ia64 Intel C y y y n Cray XT3 2.0.62 n n n n (1) Fortran compiled with g95. (2) With PGI and Absoft compilers. (3) With PGI compiler for Fortran. (4) Using Visual Studio 2005 or Cygwin Compiler versions for each platform are listed in the preceding "Platforms Tested" table. Known Problems ============== * Parallel mode in AIX will fail some of the testcheck_version.sh tests where it treats "exit(134) the same as if process 0 had received an abort signal. This is fixed and will be available in the next release. AKC - 2009/11/3 * Some tests in tools/h5repack may fail in AIX systems when -q32 mode is used. The error is due to insufficient memory requested. Request a large amount of runtime memory by setting the following environment variable for more memory. LDR_CNTRL=MAXDATA=0x20000000@DSA AKC - 2009/10/31 * The PathScale MPI implementation, accessing a Panasas file system, would cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file is not existing. This is due to the MPI_File_open() call failing if the amode has the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11 * Parallel tests failed with 16 processes with data inconsistency at testphdf5 / dataset_readAll. Parallel tests also failed with 32 and 64 processes with collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks with MPI IO. CMC - 2009/04/28 * There is a known issue in which HDF5 will change the timestamp on a file simply by opening it with read/write permissions, even if the file is not modified in any way. This is due to the way in which HDF5 manages the file superblock. A fix is currently underway and should be included in the 1.8.4 release of HDF5. MAM - 2009/04/28 * For gcc v4.3 and v4.4, with production mode, if -O3 is used, H5Tinit.c would fail to compile. Actually bad H5Tinit.c is produced. If -O (same as -O1) is used, H5Tinit.c compiled okay but test/dt_arith would fail. When -O0 (no optimizatio) is used, H5Tinit.c compilete okay and all tests passed. Therefore, -O0 is imposed for v4.3 and v4.4 of gcc. AKC - 2009/04/20 * For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests are expected to fail and should exit with a non-zero code but the yod command does not propagate the exit code of the executables. Yod always returns 0 if it can launch the executable. The test suite shell expects a non-zero for this particular test, therefore it concludes the test has failed when it receives 0 from yod. Skip all the "failing" test for now by changing them as following. ======== Original tools/h5ls/testh5ls.sh ========= TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ======== Change to =============================== echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ================================================== ======== Original tools/h5copy/testh5copy.sh ========= TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested H5LSTEST $FILEOUT ======== Change to =============================== echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested echo SKIP H5LSTEST $FILEOUT ================================================== AKC - 2008/11/10 * For Red Storm, a Cray XT3 system, the yod command sometimes gives the message, "yod allocation delayed for node recovery". This interferes with test suites that do not expect seeing this message. See the section of "Red Storm" in file INSTALL_parallel for a way to deal with this problem. AKC - 2008/05/28 * 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. * 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. * 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 calculation 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 * 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 will only statically link libraries if the static version of that library is present. If only the shared version of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, for example, only have shared versions), the flag should still result in a successful compilation, but note that the installed executables will not be fully static. Thus, the only guarantee on these systems is that the executable is statically linked with just the HDF5 library. * There is also a configure error on Altix machines that incorrectly reports when a version of Szip without an encoder is being used. %%%%1.8.3%%%% HDF5 version 1.8.3 released on Mon May 4 09:21:00 CDT 2009 ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.2 and HDF5 1.8.3, and contains information on the platforms tested and known problems in HDF5-1.8.3. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.3 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.3 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.3 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in the HDF5-1.8.x release series, 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 1.8.3 (current release) versus Release 1.8.2": 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 - Support for New Platforms, Languages, and Compilers - Bug Fixes since HDF5-1.8.2 - Platforms Tested - Supported Configuration Features Summary - Known Problems New Features ============ Configuration ------------- - Added libtool version numbers to generated c++, fortran, and hl libraries. MAM 2009/04/19. - Regenerated Makefile.ins using Automake 1.10.2. MAM 2009/04/19. - Added a Make target of check-all-install to test the correctness of installing via the prefix= or $DESTDIR options. AKC - 2009/04/14 Library ------- - Embed the content of libhdf5.settings into the hdf5 executables so that an "orphaned" executables can display (via the Unix strings command, for example) the library settings used to build the executables. This is a prototype implementation. Improvement will be added in next release. AKC - 2009/04/20 - Separated "factory" free list class from block free lists. These free lists are dynamically created and manage blocks of a fixed size. H5set_free_list_limits() will use the same settings specified for block free lists for factory free lists. NAF - 2009/04/08 - Added support for dense attributes to H5Ocopy. XCao/NAF - 2009/01/29 - Added H5Pset_elink_cb and H5Pget_elink_cb functions to support a user-defined callback function for external link traversal. NAF - 2009/01/08 - Added H5Pset_elink_acc_flags and H5Pget_elink_acc_flags functions to allow the user to specify the file access flags used to open the target file of an external link. NAF - 2009/01/08 - Added H5Pset_chunk_cache() and H5Pget_chunk_cache() functions to allow individual rdcc configuration for each dataset. Added H5Dget_access_plist() function to retrieve a dataset access property list from a dataset. NAF - 2008/11/12 - Added H5Iis_valid() function to check if an id is valid without producing an error message. NAF - 2008/11/5 - Added code to maintain a min_clean_fraction in the metadata cache when in serial mode. MAM - 2009/01/9 Parallel Library ---------------- - Modified parallel tests to run with arbitrary number of processes. The modified tests are testphdf5 (parallel dataset access), t_chunk_alloc (chunk allocation), and t_posix_compliant (posix compliance). The rest of the parallel tests already use in the code the number of processes available in the communicator. (CMC - 2009/04/28) Tools ----- - h5diff new flag, -c, --compare, list objects that are not comparable. PVN - 2009/4/2 - 1368 - h5diff new flag, -N, --nan, avoids NaNs detection. PVN - 2009/4/2 - h5dump correctly specifies XML dtd / schema urls ADB - 2009/4/3 - 1519 - h5repack now handles group creation order. PVN - 2009/4/2 - 1402 - h5repack: When user doesn't specify a chunk size, h5repack now defines a default chunk size as the same size of the size of the hyperslab used to read the chunks. The size of the hyperslabs are defined as the size of each dimension or a predefined constant, whatever is smaller. This assures that the chunk read fits in the chunk cache. PVN - 2008/11/21 High-Level APIs --------------- - Table: In version 3.0 of Table, the writing of the "NROWS" attribute (used to store number of records) was deprecated. PVN - 2008/11/24 F90 API ------- - Added for the C APIs the Fortran wrappers: h5dget_access_plist_f h5iis_valid_f h5pset_chunk_cache_f h5pget_chunk_cache_f MSB - 2009/04/17 C++ API ------- - None Support for New Platforms, Languages, and Compilers =================================================== Bug Fixes since HDF5-1.8.2 ========================== Configuration ------------- - The --includedir=DIR configuration option now works as intended, and can be used to specify the location to install C header files. The default location remains unchanged, residing at ${prefix}/include. MAM - 2009/03/10 - BZ #1381 - Configure no longer removes the '-g' flag from CFLAGS when in production mode if it has been explicitly set in the CFLAGS environment variable prior to configuration. MAM - 2009/03/09 - BZ #1401 Library ------- - Added versioning to H5Z_class_t struct to allow compatibility with 1.6 API. NAF - 2009/04/20 - 1533 - Fixed a problem with using data transforms with non-native types in the file. NAF - 2009/04/20 - 1548 - Added direct.h include file to windows section of H5private.h to fix _getcwd() warning. ADB - 2009/04/14 - 1536 - Fixed a bug that prevented external links from working after calling H5close(). NAF - 2009/04/10 - 1539 - Modified library to write cached symbol table information to the superblock, to allow library versions 1.3.0 to 1.6.3 to read files created by this version. NAF - 2009/04/08 - 1423 - Changed skip lists to use a deterministic algorithm. The library should now never call rand() or srand(). NAF - 2009/04/08 - 503 - Fixed a bug where H5Lcopy and H5Lmove wouldn't create intermediate groups when that property was set. NAF - 2009/04/07 - 1526 - Fixed a bug that caused files with a user block to grow by the size of the user block every time they were opened. NAF - 2009/03/26 - 1499 - Fixed a rare problem that could occur with files using the old (pre 1.4) array datatype. NAF - 2009/03/23 - Modified library to be able to open files with corrupt root group symbol table messages, and correct these errors if they are found. Such files can only be successfully opened with write access. NAF - 2009/03/23 - 1189 - Removed the long_long #define and replaced all instances with "long long". This caused problems with third party products. All currently supported compliers support the type. ADB - 2009/03/05 - Fixed various bugs that could prevent the fill value from being written in certain rare cases. NAF - 2009/02/26 - 1469 - Fixed a bug that prevented more than one dataset chunk from being cached at a time. NAF - 2009/02/12 - 1015 - Fixed an assertion failure caused by opening an attribute multiple times through multiple file handles. NAF - 2009/02/12 - 1420 - Fixed a problem that could prevent the user from adding attributes (or any object header message) in some circumstances. NAF - 2009/02/12 - 1427 - Fixed a bug that could cause problems when an attribute was added to a committed datatype using the committed datatype's datatype. NAF - 2009/02/12 - Fixed a bug that could cause problems when copying an object with a shared message in its own object header. NAF - 2009/01/29 - Changed H5Tset_order to properly reject H5T_ORDER_NONE for most datatypes. NAF - 2009/01/27 - 1443 - Fixed a bug where H5Tpack wouldn't remove trailing space from an otherwise packed compound type. NAF - 2009/01/14 - Fixed up some old v2 btree assertions that get run in debug mode that were previously failing on compilation, and removed some of the more heavily outdated and non-rewritable ones. MAM - 2008/12/15 - Fixed a bug that could cause problems when "automatically" unmounting multiple files. NAF - 2008/11/17 - H5Dset_extent: when shrinking dimensions, some chunks were not deleted. PVN - 2009/01/8 Parallel Library ---------------- - None Tools ----- - Fixed many problems that could occur when using h5repack with named datatypes. NAF - 2009/4/20 - 1516/1466 - h5dump, h5diff, h5repack were not reading (by hyperslabs) datasets that have a datatype datum size greater than H5TOOLS_BUFSIZE, a constant defined as 1024Kb, such as array types with large dimensions. PVN - 2009/4/1 - 1501 - h5import: By selecting a compression type, a big endian byte order was being selected. PVN - 2009/3/11 - 1462 - zip_perf.c had missing argument on one of the open() calls. Fixed. AKC - 2008/12/9 F90 API ------ - None C++ API ------ - None High-Level APIs: ------ - Dimension scales: The scale index return value in H5DSiterate_scales was not always incremented. PVN - 2009/4/8 - 1538 Fortran High-Level APIs: ------ - Lite: The h5ltget_dataset_info_f function (gets information about a dataset) was not correctly returning the dimension array PVN - 2009/3/23 Platforms Tested ================ The following platforms and compilers have been tested for this release. AIX 5.3 xlc 7.0.0.8 (LLNL Up) xlf 09.01.0000.0008 xlC 7.0.0.8 mpcc_r 7.0.0.8 mpxlf_r 09.01.0000.0008 Cray XT3 (2.0.41) cc (pgcc) 7.1-4 (SNL red storm) ftn (pgf90) 7.1-4 CC (pgCC) 7.1-4 FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 (duty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.3.4 20090419 g++ 4.3.4 20090419 gfortran 4.3.4 20090419 FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 (liberty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.4.1 20090421 g++ 4.4.1 20090421 gfortran 4.4.1 20090421 IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m F90 MIPSpro 7.4.4m C++ MIPSpro cc 7.4.4m Linux 2.6.18-128.1.6.el5xen gcc (GCC) 4.1.2 #1 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009) (jam) PGI C, Fortran, C++ 7.2-1 32-bit PGI C, Fortran, C++ 8.0-1 32-bit Intel(R) C Compiler for 32-bit applications, Versions 10.1, 11.0 Intel(R) C++ Compiler for 32-bit applications, Version 10.1, 11.0 Intel(R) Fortran Compiler for 32-bit applications, Version 10.1, 11.0 Absoft 32-bit Fortran 95 10.0.7 MPICH mpich2-1.0.8 compiled with gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6 SMP i686 i686 i386 G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009) (kagiso) MPICH mpich2-1.0.8 compiled with gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!) Linux 2.6.16.60-0.37-smp #1 gcc 4.1.2 SMP x86_64 GNU/Linux G95 (GCC 4.0.3 (g95 0.92!) Feb 4 2009) (smirom) Intel(R) C, C++, Fortran Compilers for applications running on Intel(R) 64, Versions 10.1, 11.0. PGI C, Fortran, C++ Version 7.2-1, 8.0-1 for 64-bit target on x86-64 gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) MPICH mpich2-1.0.8 compiled with gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) tested for both 32- and 64-bit binaries Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 10.1.017 SGI Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017 (cobalt) SGI MPI 1.38 SunOS 5.10 32- and 64-bit Sun WorkShop 6 update 2 C 5.9 Patch 124867-09 (linew) Sun WorkShop 6 update 2 Fortran 95 8.3 Patch 127000-07 Sun WorkShop 6 update 2 C++ 5.8 Patch 124863-11 Intel Xeon Linux 2.6.18- gcc 3.4.6 20060404 92.1.10.el5_lustre.1.6.6smp- Intel(R) C++ Version 10.0.026 perfctr #2 SMP Intel(R) Fortran Compiler Version 10.0.026 (abe) Open MPI 1.2.2 MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2 compiled with icc v10.0.026 and ifort 10.0.026 IA-64 Linux 2.4.21-309.tg1 gcc (GCC) 3.2.2 #1 SMP ia64 Intel(R) C++ Version 8.1.037 (NCSA tg-login) Intel(R) Fortran Compiler Version 8.1.033 mpich-gm-1.2.7p1..16-intel-8.1.037-r1 Linux 2.6.9-55.0.9.EL_lustre Intel(R) C, C++, Fortran Compilers for .1.4.11.1smp #1 SMP applications running on Intel(R) 64, SMP x86_64 GNU/Linux Versions 9.1. (SNL Spirit) Linux 2.6.9-55.0.9.EL_lustre Intel(R) C, C++, Fortran Compilers for .1.4.11.1smp #1 SMP applications running on Intel(R) 64, SMP x86_64 GNU/Linux Versions 10.1. (SNL Thunderbird) Linux 2.6.18-63chaos #1 SMP Intel(R) C, C++, Fortran Compilers for SMP x86_64 GNU/Linux applications running on Intel(R) 64, (SNL Glory) Versions 10.1. Linux 2.6.18-63chaos #1 SMP Intel(R) C, C++, Fortran Compilers for SMP x86_64 GNU/Linux applications running on Intel(R) 64, (LLNL Zeus) Versions 9.1. gcc/gfortran/g++ (GCC) 4.1.2. Windows XP Visual Studio .NET Visual Studio 2005 w/ Intel Fortran 9.1 Cygwin(native gcc compiler and g95) Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 Windows Vista Visual Studio 2005 MAC OS 10.5.6 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 GNU Fortran (GCC) 4.3.0 20070810 G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008) Intel C, C++ and Fortran compilers 10.1 Supported Configuration Features Summary ======================================== In the tables below y = tested and supported n = not supported or not tested in this release C = Cluster W = Workstation 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 Solaris2.10 32-bit n y n y y y Solaris2.10 64-bit n y n y y y IRIX64_6.5 32-bit n n n n y y IRIX64_6.5 64-bit n y y y y y Windows XP n y(4) n(4) y y y Windows XP x64 n y(4) n(4) y y y Windows Vista n n n y y y Mac OS X 10.5 Intel n y n y y y AIX 5.3 32- and 64-bit n y n y y n FreeBSD 6.3-STABLE 32&64 bit n y n y y y RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y y y RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y y y RedHat EL5 2.6.18-128 i686 Intel W n y n y y n RedHat EL5 2.6.18-128 i686 PGI W n y n y y n SuSe Linux 2.6.16 x86_64 GNU (1) W y y(3) y 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 y SuSe Linux 2.6.16 SGI Altix ia64 C y y y y y y RedHat EL4 2.6.18 Xeon Lustre C y y y y y n SuSe Linux 2.4.21 ia64 Intel C y y y y y n Cray XT3 2.0.41 y y y y y n Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Solaris2.10 32-bit y y y y Solaris2.10 64-bit y y y y IRIX64_6.5 32-bit y dna y y IRIX64_6.5 64-bit y y n y Windows XP y y(4) y y Windows XP x64 y y(4) y y Windows Vista y n n y Mac OS X 10.5 y n y n AIX 5.3 32- and 64-bit n n n n FreeBSD 6.3-STABLE 32&64 bit y n y y RedHat EL4 2.6.9-42 i686 GNU (1) W y y y y RedHat EL5 2.6.18-128 i686 GNU (1)W y y(2) y y RedHat EL5 2.6.18-128 i686 Intel W y y y n RedHat EL5 2.6.18-128 i686 PGI W y y y n SuSe Linux 2.6.16 x86_64 GNU (1) W y y y y SuSe Linux 2.6.16 x86_64 Intel W y y y n SuSe Linux 2.6.16 x86_64 PGI W y y y n SuSe Linux 2.6.16 SGI Altix ia64 C y n RedHat EL4 2.6.18 Xeon Lustre C y y y n SuSe Linux 2.4.21 ia64 Intel C y y y n Cray XT3 2.0.41 n n n n (1) Fortran compiled with g95. (2) With PGI and Absoft compilers. (3) With PGI compiler for Fortran. (4) Using Visual Studio 2005 or Cygwin Compiler versions for each platform are listed in the preceding "Platforms Tested" table. Known Problems ============== * Parallel tests failed with 16 processes with data inconsistency at testphdf5 / dataset_readAll. Parallel tests also failed with 32 and 64 processes with collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks with MPI IO. CMC - 2009/04/28 * There is a known issue in which HDF5 will change the timestamp on a file simply by opening it with read/write permissions, even if the file is not modified in any way. This is due to the way in which HDF5 manages the file superblock. A fix is currently underway and should be included in the 1.8.4 release of HDF5. MAM - 2009/04/28 * For gcc v4.3 and v4.4, with production mode, if -O3 is used, H5Tinit.c would fail to compile. Actually bad H5Tinit.c is produced. If -O (same as -O1) is used, H5Tinit.c compiled okay but test/dt_arith would fail. When -O0 (no optimizatio) is used, H5Tinit.c compilete okay and all tests passed. Therefore, -O0 is imposed for v4.3 and v4.4 of gcc. AKC - 2009/04/20 * For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests are expected to fail and should exit with a non-zero code but the yod command does not propagate the exit code of the executables. Yod always returns 0 if it can launch the executable. The test suite shell expects a non-zero for this particular test, therefore it concludes the test has failed when it receives 0 from yod. Skip all the "failing" test for now by changing them as following. ======== Original tools/h5ls/testh5ls.sh ========= TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ======== Change to =============================== echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ================================================== ======== Original tools/h5copy/testh5copy.sh ========= TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested H5LSTEST $FILEOUT ======== Change to =============================== echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested echo SKIP H5LSTEST $FILEOUT ================================================== AKC - 2008/11/10 * For Red Storm, a Cray XT3 system, the yod command sometimes gives the message, "yod allocation delayed for node recovery". This interferes with test suites that do not expect seeing this message. See the section of "Red Storm" in file INSTALL_parallel for a way to deal with this problem. AKC - 2008/05/28 * 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 * 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 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 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 calculation 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 * 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 platforms for 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. * There is also a configure error on Altix machines that incorrectly reports when a version of Szip without an encoder is being used. * Information about building with PGI and Intel compilers is available in the INSTALL file sections 4.7 and 4.8. %%%%1.8.2%%%% HDF5 version 1.8.2 released on Mon Nov 10 15:43:09 CST 2008 ================================================================================ INTRODUCTION ============ This document describes the differences between HDF5-1.8.1 and HDF5 1.8.2, and contains information on the platforms tested and known problems in HDF5-1.8.2. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.2 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.2 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.2 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in the HDF5-1.8.x release series, 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 1.8.2 (current release) versus Release 1.8.1": 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 - Support for new platforms and languages - Bug Fixes since HDF5-1.8.1 - Platforms Tested - Supported Configuration Features Summary - Known Problems New Features ============ Configuration ------------- - Upgraded libtool to version 2.2.6a. (MAM - 2008/10/15). Library ------- - Added two new public routines: H5Pget_elink_fapl() and H5Pset_elink_fapl(). (see bug #1247) (VC - 2008/10/13) - Improved free space tracking in file to be faster. (QAK - 2008/10/06) - Added 'mounted' field to H5G_info_t struct. (QAK - 2008/07/15) Parallel Library ---------------- - None Tools ----- - h5repack: added new options -u and -b to add a userblock to an HDF5 file during the repack. (PVN - 2008/08/26) - h5repack: added options -t and -a to call H5Pset_alignment while creating a repacked file. (PVN - 2008/08/29) - h5ls: added capability to traverse through external links when the -r (recursive) flag is given. (NAF - 2008/09/16) - h5ls: added -E option to enable traversal of external links. h5ls will not traverse external links without this flag being set. (NAF - 2008/10/06) - h5dump: when -b flag is used without a keyword after it, binary output defaults to NATIVE. MEMORY keyword was deprecated and replaced by NATIVE keyword. (PVN - 2008/10/30) - h5diff: returns 1 when file graphs differ by any object. Error return code was changed to 2 from -1. (PVN - 2008/10/30) - h5import: TEXTFPE (scientific format) was deprecated. Use TEXTFP instead (PVN - 2008/10/30) F90 API ------ - Added optional parameter 'mounted' to H5Gget_info_f, H5Gget_info_by_idx_f, H5Gget_info_by_name_f (MSB - 2008/09/24) - Added H5Tget_native_type_f (MSB - 2008/09/30) C++ API ------ - These member functions were added as wrapper for H5Rdereference to replace the incorrect IdComponent::dereference(). void H5Object::dereference(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) void H5Object::dereference(H5File& h5file, void* ref, H5R_type_t ref_type=H5R_OBJECT) void H5Object::dereference(Attribute& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) In addition, these constructors were added to create the associated objects by way of dereference: DataSet(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) DataSet(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT) DataSet(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT) Group(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) Group(H5File& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) Group(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT) DataType(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) DataType(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT) DataType(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT) (BMR - 2008/10/29) Support for New Platforms, Languages, and Compilers =================================================== - Intel 10.1 is supported on Mac OS X 10.5.4. Note: When Fortran is enabled, configure automatically disables the build of shared libraries (i.e., only static C and C++ HDF5 libraries will be built along with the static HDF5 Fortran library). Intel 10.1 C and C++ compilers require "-no-multibyte-chars" compilation flag due to the known bug in the compilers. (EIP - 2008/10/30) Bug Fixes since HDF5-1.8.1 ========================== Configuration ------------- - Fixed error with 'make check install' failing due to h5dump needing other tools built first. (MAM - 2008/10/15). - When using shared szip, it is no longer necessary to specify the path to the shared szip libraries in LD_LIBRARY_PATH. (MAM - 2008/10/15). - The file libhdf5_fortran.settings is not installed since its content is included in libhdf5.settings now. (AKC - 2008/10/21) - "make DESTDIR=xxx install" failed to install some tools and files (e.g., h5cc and fortran modules). Fixed. (AKC - 2008/10/8). Library ------- - H5Ovisit and H5Ovisit_by_name will now properly terminate when the callback function returns a positive value on the starting object. (NAF - 2008/11/03) - Fixed an error where a null message could be created that was larger than could be written to the file. (NAF - 2008/10/23) - Corrected error with family/split/multi VFD not updating driver info when "latest" version of the file format used. (QAK - 2008/10/14) - Corrected alignment+threshold errors to work correctly when metadata aggregation is enabled. (QAK - 2008/10/06) - Changed H5Fget_obj_count and H5Fget_obj_ids to ignore objects registered by the library for internal library use. (NAF - 2008/10/06) - Fixed potential memory leak during compound conversion. (NAF - 2008/10/06) - Changed the return value of H5Fget_obj_count from INT to SSIZE_T. Also changed the return value of H5Fget_obj_ids from HERR_T to SSIZE_T and the type of the parameter MAX_OBJS from INT to SIZE_T. (SLU - 2008/09/26) - Fixed an issue that could cause data to be improperly overwritten during compound type conversion. (NAF - 2008/09/19) - Fixed pointer alignment violations that could occur during vlen conversion. (NAF - 2008/09/16) - Fixed problem where library could cause a segmentation fault when an invalid location ID was given to H5Giterate(). (QAK - 2008/08/19) - Fixed improper shutdown when objects have reference count > 1. The library now tracks reference count due to the application separately from that due to internal library routines. (NAF - 2008/08/19) - Fixed assertion failure caused by incorrect array datatype version. (NAF - 2008/08/08) - Fixed an issue where mount point traversal would fail when using multiple handles for the child. (NAF - 2008/08/07) - Fixed an issue where mount points were inaccessible when using multiple file handles for the parent. The mount table is now in the shared file structure (the parent pointer is still in the top structure). (NAF - 2008/08/07) - Fixed assertion failure caused by incorrect array datatype version. (NAF - 2008/08/04) - Fixed issue where a group could have a file mounted on it twice. (QAK - 2008/07/15) - When an attribute was opened twice and data was written with one of the handles, the file didn't have the data. It happened because each handle had its own object structure, and the empty one overwrote the data with fill value. This is fixed by making some attribute information like the data be shared in the attribute structure. (SLU - 2008/07/07) - Fixed a Windows-specific issue in the ohdr test which was causing users in some timezones to get false errors. This a deficiency in the Windows mktime() function, and has been handled properly. (SJW - 2008/06/19) Parallel Library ---------------- - None Tools ----- - h5dump now checks for uniqueness of committed datatypes. (NAF - 2008/10/15) - Fixed unnecessary indentation of committed datatypes in h5dump. (NAF - 2008/10/15) - Fixed bugs in h5stat: segmemtation fault when printing groups and print warning message when traversal of objects is unsuccessful. (see bug #1253) (VC- 2008/10/13) - Fixed bug in h5ls that prevented relative group listings (like "h5ls foo.h5/bar") from working correctly (QAK - 2008/06/03) - h5dump: when doing binary output (-b), the stdout printing of attributes was done incorrectly. Removed printing of attributes when doing binary output. (PVN - 2008/06/05) F90 API ------ - h5sselect_elements_f: Added additional operators H5S_SELECT_APPEND and H5S_SELECT_PREPEND (MSB - 2008/09/30) - h5sget_select_elem_pointlist: Fixed list of returned points by rearranging the point list correctly by accounting for C conventions. (MSB - 2008/09/30) - h5sget_select_hyper_blocklist_f: Fixed error in transposed dimension of arrays.(MSB - 2008/9/30) - h5sget_select_bounds_f: Swapped array bounds to account for C and Fortran reversed array notation (MSB - 2008/9/30) - Changed to initializing string to a blank character instead of a null type in tH5P.f90 to fix compiling error using AIX 5.3.0 (MSB - 2008/7/29) - Fixed missing commas in H5test_kind.f90 detected by NAG compiler (MSB - 2008/7/29) - Fixed passing and array to a scalar in tH5A_1_8.f90 detected by NAG compiler (MSB - 2008/7/29) - Added the ability of the test programs to use the status of HDF5_NOCLEANUP to determine if the *.h5 files should be removed or not after the tests are completed (MSB - 2008/10/1) - In nh5tget_offset_c: (MSB 9/12/2008) If offset was equal to 0 it returned the error code of -1, this was changed to return an error code of -1 when the offset value is < 0. - Uses intrinsic Fortran function SIZEOF if available when detecting type of INTEGERs and REALs in H5test_kind.f90 (MSB - 2008/9/3) - Put the DOUBLE PRECISION interfaces in a separate module and added a USE statement for the module. The interfaces are included/excluded depending on the state of FORTRAN_DEFAULT_REAL is DBLE_F which detects if the default REAL is DOUBLE PRECISION. This allows the library to be compiled with -r8 Fortran flag without the user needing to edit the source code. (MSB - 200/8/27) - Enable building shared library for fortran by adding the flag -fPIC to the compile flags for versions of Intel Fortran compiler >=9 (MSB - 2008/8/26) C++ API ------ - Fixed a design bug which allowed an Attribute object to create/modify attributes (bugzilla #1068). The API class hierarchy was revised to address the problem. Classes AbstractDS and Attribute are moved out of H5Object. Class Attribute now multiply inherits from IdComponent and AbstractDs and class DataSet from H5Object and AbstractDs. In addition, the data member IdComponent::id was moved into subclasses: Attribute, DataSet, DataSpace, DataType, H5File, Group, and PropList. (BMR - 2008/05/20) - IdComponent::dereference was incorrect and replaced as described in "New Features" section. (BMR - 2008/10/29) Platforms Tested ================ The following platforms and compilers have been tested for this release. AIX 5.3 xlc 7.0.0.8 xlf 09.01.0000.0008 xlC 7.0.0.8 mpcc_r 7.0.0.8 mpxlf_r 09.01.0000.0008 Cray XT3 (2.0.41) cc (pgcc) 7.1-4 (red storm) ftn (pgf90) 7.1-4 CC (pgCC) 7.1-4 FreeBSD 6.3-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 (duty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.2.5 20080702 g++ 4.2.5 20080702 gfortran 4.2.5 20080702 FreeBSD 6.3-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305 (liberty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.2.5 20080702 g++ 4.2.5 20080702 gfortran 4.2.5 20080702 IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m F90 MIPSpro 7.4.4m C++ MIPSpro cc 7.4.4m Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6 SMP i686 i386 G95 (GCC 4.0.3 (g95 0.92!) April 18 2007) (kagiso) PGI C, Fortran, C++ 7.2-1 32-bit Intel(R) C Compiler for 32-bit applications, Version 10.1 Intel(R) C++ Compiler for 32-bit applications, Version 10.1 Intel(R) Fortran Compiler for 32-bit applications, Version 10.1 Absoft 32-bit Fortran 95 10.0.4 MPICH mpich-1.2.7 compiled with gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!) MPICH mpich2-1.0.6p1 compiled with gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.92!) Linux 2.6.16.46-0.14-smp #1 Intel(R) C++ for Intel(R) EM64T SMP x86_64 GNU/Linux Ver. 10.1.013 (smirom) Intel(R) Fortran Intel(R) EM64T Ver. 10.1.013 PGI C, Fortran, C++ Version 7.2-1 for 64-bit target on x86-64 MPICH mpich-1.2.7 compiled with gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) MPICH mpich2-1.0.7 compiled with gcc 4.1.2 and G95 (GCC 4.0.3 (g95 0.92!) tested for both 32- and 64-bit binaries Linux 2.6.16.54-0.2.5 #1 Intel(R) C++ Version 10.1.017 Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 10.1.017 (cobalt) SGI MPI 1.16 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 2.6.9-42.0.10.EL_lustre-1.4.10.1smp (abe) Intel(R) C++ Version 10.0.026 Intel(R) Fortran Compiler Version 10.0.026 Open MPI 1.2.2 MVAPICH2-0.9.8p28p2patched-intel-ofed-1.2 compiled with icc v10.0.026 and ifort 10.0.026 IA-64 Linux 2.4.21-309.tg1 #1 SMP ia64 gcc (GCC) 3.2.2 (NCSA tg-login) Intel(R) C++ Version 8.1.037 Intel(R) Fortran Compiler Version 8.1.033 mpich-gm-1.2.7p1..16-intel-8.1.037-r1 Intel 64 Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp (abe) gcc 3.4.6 20060404 Intel(R) C++ Version 10.0 Intel (R) Fortran Compiler Version 10.0 mvapich2-0.9.8p2patched-intel-ofed-1.2 Windows XP Visual Studio .NET Visual Studio 2005 w/ Intel Fortran 9.1 Cygwin(native gcc compiler and g95) Windows XP x64 Visual Studio 2005 w/ Intel Fortran 9.1 Windows Vista Visual Studio 2005 MAC OS 10.5.4 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 GNU Fortran (GCC) 4.3.0 20070810 G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008) Intel C, C++ and Fortran compilers 10.1 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 = testing incomplete on this feature or platform Platform C F90 F90 C++ zlib SZIP parallel parallel Solaris2.10 32-bit n y n y y y Solaris2.10 64-bit n y n y y y IRIX64_6.5 32-bit n n n n y y IRIX64_6.5 64-bit n 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 10.5 Intel n y n y y y AIX 5.3 32- and 64-bit n y n y y n FreeBSD 6.3-STABLE 32&64 bit n y n y y y RedHat EL4 (3) W y(1) y(10) y(1) y y y RedHat EL4 Intel (3) W n y n y y n RedHat EL4 PGI (3) W n y n y y n SuSe x86_64 gcc(3,12) W y(2) y(11) y(2) y y y SuSe x86_64 Int(3,12) W n y(13) n y y n SuSe x86_64 PGI(3,12) W n y(8) n y y y 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 Linux 2.6 RHEL C Lustre Intel (5) y(4) y y(4) y y n Cray XT3 2.0.41 y y y y y n Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Solaris2.10 32-bit y y y y Solaris2.10 64-bit y y y y IRIX64_6.5 32-bit y dna y y IRIX64_6.5 64-bit y y n y Windows XP y y(15) y y Windows XP x64 y y(15) y y Windows Vista y n n y Mac OS X 10.5 y n y n AIX 5.3 32- and 64-bit n n n n FreeBSD 6.2 32&64 bit y n y y RedHat EL4 (3) W y y(10) y y RedHat EL4 Intel (3) W y y y n RedHat EL4 PGI (3) W y y y n SuSe x86_64 GNU(3,12) W y y y y SuSe x86_64 Int(3,12) W y y y n SuSe x86_64 PGI(3,12) W y y y n Linux 2.4 SuSE C ia64 C Intel (7) y y y n Linux 2.4 SGI Altix C ia64 Intel y n Linux 2.6 RHEL C Lustre Intel (5) y y y n Cray XT3 2.0.41 n n n n Notes: (1) Using mpich2 1.0.6. (2) Using mpich2 1.0.7. (3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated. W or C indicates workstation or cluster, respectively. (4) Using mvapich2 0.9.8. (5) Linux 2.6.9-42.0.10. Xeon cluster with ELsmp_perfctr_lustre and Intel compilers (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 ============== * For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh and tools/h5copy/testh5copy.sh will fail some of its sub-tests. These sub-tests are expected to fail and should exit with a non-zero code but the yod command does not propagate the exit code of the executables. Yod always returns 0 if it can launch the executable. The test suite shell expects a non-zero for this particular test, therefore it concludes the test has failed when it receives 0 from yod. Skip all the "failing" test for now by changing them as following. ======== Original tools/h5ls/testh5ls.sh ========= TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ======== Change to =============================== echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ================================================== ======== Original tools/h5copy/testh5copy.sh ========= TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested H5LSTEST $FILEOUT ======== Change to =============================== echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d grp_rename echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -v -s grp_dsets -d /grp_rename/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_dsets -d /E/F/grp_dsets echo SKIP TOOLTEST_FAIL -i $TESTFILE -o $FILEOUT -vp -s /grp_nested -d /G/H/grp_nested echo SKIP H5LSTEST $FILEOUT ================================================== AKC - 2008/11/10 * For Red Storm, a Cray XT3 system, the yod command sometimes gives the message, "yod allocation delayed for node recovery". This interferes with test suites that do not expect seeing this message. See the section of "Red Storm" in file INSTALL_parallel for a way to deal with this problem. AKC - 2008/05/28 * 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 * 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 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 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 calculation 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 * 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 platforms for 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. * There is also a configure error on Altix machines that incorrectly reports when a version of Szip without an encoder is being used. * Information about building with PGI and Intel compilers is available in the INSTALL file sections 4.7 and 4.8. %%%%1.8.1%%%% HDF5 version 1.8.1 released on Thu May 29 15:28:55 CDT 2008 ================================================================================ INTRODUCTION ============ This document describes the differences between the HDF5-1.8.1 release and HDF5 1.8.0, and contains information on the platforms tested and known problems in HDF5-1.8.1. For more details, see the files HISTORY-1_0-1_8_0_rc3.txt and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source. Links to the HDF5 1.8.1 source code, documentation, and additional materials can be found on the HDF5 web page at: http://www.hdfgroup.org/products/hdf5/ The HDF5 1.8.1 release can be obtained from: http://www.hdfgroup.org/HDF5/release/obtain5.html User documentation for 1.8.1 can be accessed directly at this location: http://www.hdfgroup.org/HDF5/doc/ New features in the HDF5-1.8.x release series, 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 1.8.1 (current release) versus Release 1.8.0": 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 - Support for new platforms and languages - Bug Fixes since HDF5-1.8.0 - Platforms Tested - Supported Configuration Features Summary - Known Problems New Features ============ Configuration ------------- - The lib/libhdf5.settings file contains much more configure information. (AKC - 2008/05/18) - The new configure option "--disable-sharedlib-rpath" disables embedding the '-Wl,-rpath' information into executables when shared libraries are produced, and instead solely relies on the information in LD_LIBRARY_PATH. (MAM - 2008/05/15) - Configuration suite now uses Autoconf 2.61, Automake 1.10.1, and Libtool 2.2.2 (MAM - 2008/05/01) Source code distribution ======================== Library ------- - None Parallel Library ---------------- - None Tools ----- - h5repack: Reinstated the -i and -o command line flags to specify input and output files. h5repack now understands both the old syntax (with -i and -o) and the new syntax introduced in Release 1.8.0. (PVN - 2008/05/23) - h5dump: Added support for external links, displaying the object that an external link points to. (PVN - 2008/05/12) - h5dump: Added an option, -m, to allow user-defined formatting in the output of floating point numbers. (PVN - 2008/05/06) - h5dump, in output of the -p option: Added effective data compression ratio to the dataset storage layout output when a compression filter has been applied to a dataset. (PVN - 2008/05/01) F90 API ------ New H5A, H5G, H5L, H5O, and H5P APIs to enable 1.8 features were added. See "Release 1.8.1 (current release) versus Release 1.8.0" in the document "HDF5 Software Changes from Release to Release" (http://hdfgroup.org/HDF5/doc/ADGuide/Changes.html) for the complete list of the new APIs. C++ API ------ - None Support for New Platforms, Languages, and Compilers =================================================== - Both serial and parallel HDF5 are supported for the Red Storm machine which is a Cray XT3 system. - The Fortran library will work correctly if compiled with the -i8 flag. This has been tested with the g95, PGI and Intel Fortran compilers. Bug Fixes since HDF5-1.8.0 ========================== Configuration ------------- - None Source code distribution ======================== Library ------- - Chunking: Chunks greater than 4GB are disallowed. (QAK - 2008/05/16) - Fixed the problem with searching for a target file when following an external link. The search pattern will depend on whether the target file's pathname is an absolute or a relative path. Please see the H5Lcreate_external description in the "HDF5 Reference Manual" (http://hdfgroup.org/HDF5/doc/RM/RM_H5L.html). (VC - 2008/04/08) - Fixed possible file corruption bug when encoding datatype descriptions for compound datatypes whose size was between 256 and 511 bytes and the file was opened with the "use the latest format" property enabled (with H5Pset_libver_bounds). (QAK - 2008/03/13) - Fixed bug in H5Aget_num_attrs() routine to correctly handle an invalid location identifier. (QAK - 2008/03/11) Parallel Library ---------------- - None Tools ----- - Fixed bug in h5diff that prevented datasets and attributes with variable-length string elements from comparing correctly. (QAK - 2008/02/28) - Fixed bug in h5dump that caused binary output to be made only for the first dataset, when several datasets were requested. (PVN - 2008/04/07) F90 API ------ - The h5tset(get)_fields subroutines were missing the parameter to specify a sign position; fixed. (EIP - 2008/05/23) - Many APIs were fixed to work with the 8-byte integers in Fortran vs. 4-byte integers in C. This change is trasparent to user applications. C++ API ------ - The class hierarchy was revised to address the problem reported in bugzilla #1068, Attribute should not be derived from base class H5Object. Classes AbstractDS was moved out of H5Object. Class Attribute now multiply inherits from IdComponent and AbstractDs and class DataSet from H5Object and AbstractDs. In addition, data member IdComponent::id was moved into subclasses: Attribute, DataSet, DataSpace, DataType, H5File, Group, and PropList. (BMR - 2008/05/20) - IdComponent::dereference was incorrect; it was changed from: void IdComponent::dereference(IdComponent& obj, void* ref) to: void H5Object::dereference(H5File& h5file, void* ref) void H5Object::dereference(H5Object& obj, void* ref) (BMR - 2008/05/20) - Revised Attribute::write and Attribute::read wrappers to handle memory allocation/deallocation properly. (bugzilla 1045) (BMR - 2008/05/20) Platforms Tested ================ The following platforms and compilers have been tested for this release. Cray XT3 (2.0.41) cc (pgcc) 7.1-4 (red storm) ftn (pgf90) 7.1-4 CC (pgCC) 7.1-4 mpicc 1.0.2 mpif90 1.0.2 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,g++ 3.4.6 20060404, G95 (GCC 4.0.3) (kagiso) PGI 7.1-6 (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 7.1-6 (pgcc, pgf90, pgCC) Intel 9.1 (icc, ifort, 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_309.tg1 ia64 (NCSA tg-login) gcc 3.2.2 Intel(R) C++ Version 8.1 Intel(R) Fortran Compiler Version 8.1 mpich-gm-1.2.6..14b-intel-r2 Intel 64 Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp (abe) gcc 3.4.6 20060404 Intel(R) C++ Version 10.0 Intel (R) Fortran Compiler Version 10.0 mvapich2-0.9.8p2patched-intel-ofed-1.2 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 10.5.2 (Intel) i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 GNU Fortran (GCC) 4.3.0 20070810 G95 (GCC 4.0.3 (g95 0.91!) Apr 24 2008) 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 SunOS5.10 64-bit n y n y y y SunOS5.10 32-bit n 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 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 10.5 Intel n y n y y y FreeBSD 4.11 n n n y y y RedHat EL3 W (3) y(1) y(10) y(1) 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(2) y(11) y(2) 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 Linux 2.6 RHEL C Lustre Intel (5) y(4) y y(4) y y n Cray XT3 2.0.41 y y y y y n Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe Solaris2.10 64-bit y y y y Solaris2.10 32-bit y y y y IRIX64_6.5 64-bit y y n y IRIX64_6.5 32-bit y dna y y Windows XP y y(15) y y Windows XP x64 y y(15) y y Windows Vista y n n y Mac OS X 10.3 y n FreeBSD 4.11 y n y y RedHat EL3 W (3) y y(10) y y RedHat EL3 W Intel (3) y y y n RedHat EL3 W PGI (3) y y y n SuSe x86_64 W GNU (3,12) y y y y SuSe x86_64 W Int (3,12) y y y n SuSe x86_64 W PGI (3,12) y y y n Linux 2.4 Xeon C Lustre Intel (6) y y y n Linux 2.4 SuSE ia64 C Intel (7) y y y n Linux 2.4 SGI Altix ia64 Intel y n Linux 2.6 RHEL C Lustre Intel (5) y y y n Cray XT3 2.0.41 n n n n n Notes: (1) Using mpich2 1.0.6. (2) Using mpich2 1.0.7. (3) Linux 2.6 with GNU, Intel, and PGI compilers, as indicated. W or C indicates workstation or cluster, respectively. (4) Using mvapich2 0.9.8. (5) Linux 2.6.9-42.0.10. Xeon cluster with ELsmp_perfctr_lustre and Intel compilers (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 ============== * For Red Storm, a Cray XT3 system, the yod command sometimes gives the message, "yod allocation delayed for node recovery". This interferes with test suites that do not expect seeing this message. See the section of "Red Storm" in file INSTALL_parallel for a way to deal with this problem. AKC - 2008/05/28 * For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh will fail on the test "Testing h5ls -w80 -r -g tgroup.h5" fails. This test is expected to fail and exit with a non-zero code but the yod command does not propagate the exit code of the executables. Yod always returns 0 if it can launch the executable. The test suite shell expects a non-zero for this particular test, therefore it concludes the test has failed when it receives 0 from yod. To bypass this problem for now, change the following lines in the tools/h5ls/testh5ls.sh. ======== Original ========= # The following combination of arguments is expected to return an error message # and return value 1 TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ======== Skip the test ========= echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ======== end of bypass ======== AKC - 2008/05/28 * 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 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. * 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 Scaleoffset filter supports only the IEEE standard for floating-point data; it cannot be applied to HDF5 data generated on VAX. * 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 calculation 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 platforms for 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 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. * In the C++ API, it appears that there are bugs in Attribute::write/read and DataSet::write/read for fixed- and variable-len strings. The problems are being worked on and a patch will be provided when the fixes are available. %%%%1.8.0%%%% 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.