HDF5 version 1.8.6-pre3 currently under development ================================================================================ 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(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 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 n y n 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".