HDF5 History ============ This file contains development history of HDF5 1.8 branch 3. Release Information for hdf5-1.8.2 2. Release Information for hdf5-1.8.1 1. Release Information for hdf5-1.8.0 [Search on the string '%%%%' for per-release section breaks.] %%%%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.