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)