diff options
Diffstat (limited to 'release_docs')
| -rw-r--r-- | release_docs/HISTORY-1_9.txt | 6 | ||||
| -rw-r--r-- | release_docs/HISTORY.txt (renamed from release_docs/HISTORY-1_0-1_8_0_rc3.txt) | 2550 | ||||
| -rw-r--r-- | release_docs/INSTALL | 1315 | ||||
| -rw-r--r-- | release_docs/INSTALL_Cygwin.txt | 55 | ||||
| -rw-r--r-- | release_docs/INSTALL_VMS.txt | 2 | ||||
| -rw-r--r-- | release_docs/INSTALL_Windows.txt | 22 | ||||
| -rw-r--r-- | release_docs/INSTALL_parallel | 35 | ||||
| -rw-r--r-- | release_docs/RELEASE.txt | 1168 |
8 files changed, 1743 insertions, 3410 deletions
diff --git a/release_docs/HISTORY-1_9.txt b/release_docs/HISTORY-1_9.txt deleted file mode 100644 index 8e7648a..0000000 --- a/release_docs/HISTORY-1_9.txt +++ /dev/null @@ -1,6 +0,0 @@ - HDF5 HISTORY - ============ - This file contains history of the HDF5 1.9 branch - - CONTENTS - diff --git a/release_docs/HISTORY-1_0-1_8_0_rc3.txt b/release_docs/HISTORY.txt index 964d374..1327827 100644 --- a/release_docs/HISTORY-1_0-1_8_0_rc3.txt +++ b/release_docs/HISTORY.txt @@ -1,14 +1,9 @@ HDF5 HISTORY ============ -This file contains history of the HDF5 libraries releases starting with -HDF5-1.0.0 and ending with HDF5-1.8.0-rc3 (the state of the code before i -the HDF5 1.8.0 release). +This file contains history of the HDF5 libraries releases CONTENTS -22. Changes from 1.6.0 to 1.8.0-rc3 -21. Release Information for hdf5-1.6.7 -20. Release Information for hdf5-1.6.6 19. Release Information for hdf5-1.6.5 18. Release Information for hdf5-1.6.4 17. Release Information for hdf5-1.6.3 @@ -32,2549 +27,6 @@ CONTENTS [Search on the string '%%%%' for per-release section breaks.] -%%%%1.8.0-rc3%%%% Changes from 1.6.0 to 1.8.0-rc3 - - -HDF5 version 1.8.0-rc3 -================================================================================ - - -INTRODUCTION - -This document describes the differences between HDF5-1.6.* and -Hdf5 1.8.0 release candidate "HDF5-1.8.0-rc3", and contains information -on the platforms tested and known problems in HDF5-1.8.0-rc3. -For more details check the HISTORY.txt file in the HDF5 source. - - -Links to HDF5 1.8.0-rc3 source code, documentation, and additional materials -can be found on THG's development server (www.hdfgroup.uiuc.edu) at the -following location: - http://www.hdfgroup.uiuc.edu/HDF5/release/beta/obtain518.html -User documentation for the beta can be accessed directly at this location: - http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/doc/ - -New features of the upcoming 1.8.0 release are described in -the "What's New in 1.8.0?" document: - http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/WhatsNew180.html - -New and modified APIs are described briefly in - http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/WhatsNew180.html -and will be listed in the "HDF5 Software Changes" document: - http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/doc/ADGuide/Changes.html - - - -For more information, see the HDF5 home page: - - http://www.hdfgroup.org/HDF5/ - -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 HDF5-1.6.0 -- Platforms Tested -- Known Problems - - -New Features -============ - - Configuration: - -------------- - - Removed stream-vfd from the HDF5 library. - AKC 2007/11/19. - - Updated versions of autotools. HDF5 now uses automake 1.10.0, - autoconf 2.61, and libtool 1.5.22. MAM - 2007/7/25. - - Changed default fortran compiler to g95 when gcc is used. - AKC - 2007/2/17. - - 'make check-vfd' can now be run from the top level directory. Not all - tests that 'make check' invokes work with certain Virtual File Drivers, - so those tests have been skipped. - MAM 2006/7/17 - - Added the variable HDF5TestExpress to control how long tests run. - Setting it to a value between 0 and 3 controls how thoroughly the - library is tested, with 0 being an "exhaustive run" and 3 being a - very quick "smoke test." 1 (a "full run") is the default. - -JML 2006/6/21 - - If both shared and static libraries are installed, now both will be - tested during 'make install'. -MAM 2006/06/21 - - Added support to explicity enable stream_vfd or shared libraries - when using parallel via the '--enable-stream_vfd' and - '--enable-shared' options, respectively. If not explicity defined, - These settings default to enabled when parallel is not used, - and disabled when parallel is used. -MAM 2006/06/17 - - Remove the flexible parallel code and the --enable-fphdf5 - configure option, it was never up to production standards - anyway. -QAK 2006/4/20 - - Added a macro hdf5_mpi_special_collective_io_works to filter out - some mpi-io packages that don't support collective IO for no IO - contributions in some processes. -KY 2006/2/16 - - Added -shlib option to link against installed shared libraries to - h5c++ and h5fc. -JML 2005/11/1 - - Added --enable-build-all option to configure, which only developers - should need to use. -JML 2005/10/24 - - Configure uses the 'TR' variable to let the user override the path - to the 'tr' utility. -JML 2005/10/17 - - Configure can recognize -lmpich as a form of MPI library. -AKC- - 2005/9/28. - - MD5 checksumming has been added to snapshot releases. Release - tarballs will be accompanied by .md5 checksum files, which can - be verified using the md5sum utility. -JML 2005/9/6 - - Some configure flags are incompatible (e.g., the C++ APIs cannot - be built using the parallel version of HDF5). configure will now - output errors when some common incompatible features are used - together. -JML 2005/9/6 - - A new API function, H5Tis_hard(), was added to the library. It - checks if a conversion function is a compiler (hard) conversion. - SLU - 2005/9/6 - - t_mpi will run the test_mpio_derived_dtype by default unless it is - known not working (indicated by macro H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS - not defined.) -AKC- 2005/8/23. - - Test execution has changed in a number of ways: - When make is invoked in parallel (using -j), sequential tests - are now executed as parallel make targets. This should make them - finish more quickly on machines with multiple processors. - Since test output is garbled when they are executed by parallel make, - tests now dump their output to foo.log files and foo.logsh files - (for test scripts). These logs are printed to the screen only - when a test fails or when all tests in the current directory have - completed successfully. - When tests pass, they will create a foo.chkexe file. - This prevents the test from executing again until the test or - main library changes. - All files generated by tests (*.chkexe, *.log, and any *.h5 files - created) can be removed by invoking 'make check-clean'. - Sequential and parallel library tests can now be invoked separately. - 'make check-s' will execute only sequential tests, and 'make check-p' - will execute only parallel tests. 'make check' will still execute - all tests. - -JML 2005/08/03 - - On windows, all.zip is deprecated. users should - read INSTALL_Windows.txt to know the details. - Reasons to deprecate all.zip: - 1. Avoid confliction for windows programmers - 2. Decrease size of CVS tree by adding all.zip - 3. Avoid using winzip as the intermediate step - --KY 2005/04/22 - - When HDF5 is created as a shared library, it now uses libtool's - shared library versioning scheme. -JML 2005/04/18 - - HDF5 now uses automake 1.9.5 to generate Makefiles.in. - This has a number of effects on users: - The Fortran compiler should be set using the environment - variable $FC, not $F9X. F9X still works, but is depreciated. - The output of make may be different. This should be only a - cosmetic effect. - make depened (or make dep) is no longer recognized, since automake - handles dependency tracking. - Some new configure options exist. --enable-dependency-tracking - and --disable-dependency-tracking are used to control automake's - dependency tracking. Dependencies are on by default *on most - platforms and compilers*. If --enable-dependency-tracking is - used, they will be enabled on any platform. However, this can - slow down builds or even cause build errors in some cases. - Likewise, --disable-dependency-tracking can speed up builds and - avoid some build errors. - Some make targets have alternate names. make check-install and - make installcheck do the same thing, for instance. - pmake on IRIX can be invoked from the root directory, but the - -V flag must be used to invoke it in any subdirectory or it - will give an error about undefined variables. - JML 2005/01 - 2005/03 - - Hardware conversion between long double and integers is also added. - SLU 2005/02/10 - - Started to support software conversion between long double and - integers. Hardware conversion will come very soon. SLU - 2005/1/6 - - Intel v8.0 compiler would infinite loop when compiling some test - code with -O3 option. Changed enable-production default compiler - option to -O2. AKC - 2004/12/06 - - Long double is assumed to be a supported C data type. It is a - stanadard C89 type. AKC - 2004/10/22 - - The IA64 will use ecc as the C++ compiler by default. - - Added some initial support for making valgrind/Purify (or similar - memory checking products) happier by initializing buffers to zero - and disabling the internal free list code. To take advantage of - this, use the "--enable-using-memchecker" configure option when - building the library. QAK - 2004/07/23 - - Fixed the long compile time of H5detect.c when v7.x Intel Compiler - is used with optimization NOT off. AKC - 2004/05/20 - - Fixed configure setting of C++ for OSF1 platform. AKC - 2004/01/06 - - Prefix default is changed from /usr/local to `pwd`/hdf5. - AKC - 2003/07/09 - - Library: - -------- - - Removed size restrictions on attributes, when using the "latest" - version of the file format. - QAK - 2007/02/21 - - Relaxed restrictions on attribute operations to allow a file ID to - be used as the "location ID". If a file ID is used, the attribute - operation will occur on the root group of the file. - - QAK - 2007/02/09 - - Enabled the CORE driver to read an existing file depending on - the setting of the backing_store for H5Pset_fapl_core and file - open flags. - SLU - 2006/11/30 - - Added new H5Gget_info_by_idx() routine to query the information about - a group according to the order within an index. - - QAK - 2006/11/27 - - Added new H5Gget_info() routine to query the information about a - group by name. - - QAK - 2006/11/27 - - Added new H5Oget_info_by_idx() routine to query the information about - an object in a group according to the order within an index. - - QAK - 2006/11/26 - - Added new H5Oget_info() routine to query the information about an - object in a group by name. - - QAK - 2006/11/26 - - Added new H5Oopen_by_idx() routine to open an object in a group - according to the order within an index. - - QAK - 2006/11/20 - - Added new H5Literate() routine to iterate over links in a group - according to the order within an index. - - QAK - 2006/11/20 - - Added new H5Ldelete_by_idx() routine to delete a link according to - the order within an index. - - QAK - 2006/11/13 - - Added new H5Lget_val_by_idx() routine to query the value of a soft link - according to the order within an index. - - QAK - 2006/11/13 - - Added new H5Lget_name_by_idx() routine to query the name of a link - according to the order within an index. - - QAK - 2006/11/12 - - Added new H5Rget_name() routine to determine the name of the object - that a reference points to, as long as the object is still - reachable in the group hierarchy. - - QAK - 2006/11/10 - - Added new H5Lget_info_by_idx() routine to query the link information - according to the order within an index. - - QAK - 2006/11/10 - - Added feature to H5Iget_name to allow retrieving the name of any - object's ID, as long as the object is still reachable in the - group hierarchy. - - LA - 2006/11/01 - - Added External and User-defined links. - External links are links from one HDF5 file to another; they - require both the name of the file and a path within that file. - User-defined links allow users to supply callback functions - for link traversals, allowing links to exhibit essentially - any behavior. - External links are a kind of user-defined link, so their default - behavior can be overridden by the user. - -JML 2006/8/23 - - Added H5Oopen and H5Oclose for opening objects of unknown type - (as link callback functions do). - -JML 2006/8/23 - - Added H5Oopen_by_addr, H5Oincr_refcount, and H5Odecr_refcount for - opening objects by address. Be very careful with these! - -JML 2006/8/23 - - Added H5Fget_intent to get the "intent" of a file (whether it - was opened with read-write access or read-only. - -JML 2006/8/23 - - Added Link Access Property Lists. They currently contain two - properties, nlinks (H5Pget/set_nlinks) and elink_prefix - (H5Pget/set_elink_prefix). nlinks controls how many soft and - user-defined traversals are allowed before HDF5 assumes it has - found a cycle (previously this defaulted to 16). - The elink_prefix is a filesystem path that is prefixed to the - names of any external link files opened using this LAPL. - -JML 2006/8/23 - - Add H5L link APIs. Old APIs (H5Glink, H5Gmove, etc.) are still - supported but deprecated. - New APIs are: - H5Llink - create a link to an object given its ID - H5Lmove - just like H5Gmove2 - H5Lcopy - copy a link without copying the underlying object - H5Lcreate_hard - like H5Glink2 for hard links - H5Lcreate_soft - like H5Glink2 for soft links - H5Ldelete - just like H5Gunlink - H5Lget_val - just like H5Gget_linkval - H5Lget_info - gets link-specific info (like H5Gget_objinfo) - - In addition, H5Gcreate_anon, H5Tcommit_anon, and H5Dcreate_anon - no longer create links to objects; objects must be manually linked - using H5Llink or they will be deleted when the ID is closed. - - Link Creation Property Lists can be used to pass character - encoding (ASCII or UTF-8) for link names and to set the Intermediate - Group Creation Flag: - H5Pset_char_encoding, H5Pget_char_encoding - H5Pset_copy_object, H5Pget_copy_object - -JML 2006/7/5 - - Added managements of collective IO supports for chunking storage - inside parallel HDF5 - 1) Implemented One IO with collective mode for all chunks in the - application by building one MPI derived datatype accross all - chunks. - 2) Implemented the decision-making support to do collective IO inside - MPI-IO per chunk. - 3) Added the decision-making support to do one IO accross all chunks - or to do multiple IOs with each IO per chunk. - 4) Added the support to handle the case some processes won't do any IOs in - collectively. - 5) Some MPI-IO package(mpich 1.2.6 or lower, e.g.) cannot handle - collective IO correctly for the case when some processes have no - contributions to IOs, a special macro is added to change - collective IO mode to independent IO mode inside HDF5 library. - - Currently we find that MPICH at Linux and vender MPI-IO package at NCSA - Altix cannot handle this case. - - "hdf5_mpi_special_collective_io_works=${hdf5_mpi_special_collective_io_works='no'}" - has been added at the end of file <ia64-linux-gnui> and - <linux-gnulibc1>. - - If MPI-IO packages at your Linux and Altix support this case, - please comment out the last line and report to us at - help@hdfgroup.org. We can tune in our configuration to - support this. - - KY - 2006/02/16 - - Added character encoding to attribute creation property lists. - JML - 2006/01/02 - - Added H5Gcopy() routine to copy objects between while keeping - data in compressed form. QAK - 2005/11/06 - - Added H5Sextent_equal() routine. QAK - 2005/11/06 - - Added HSYS_ERROR which retrieves the system error message and pushes - it to the error stack. This gives more information of the failed - system call. AKC - 2005/08/04 - - Added H5F_OBJ_LOCAL flag to H5Fget_obj_count() & H5Fget_obj_ids(), to - allow querying for objects in file that were opened with a particular - file ID, instead of all objects opened in file with any file ID. - QAK - 2005/06/01 - - Added H5T_CSET_UTF8 character set to mark datatypes that use the - UTF-8 Unicode character encoding. Added tests to ensure that - library handles UTF-8 object names, attributes, etc. -JL 2005/05/13 - - HDF5 supports collective MPI-IO for irregular selection with HDF5 - dataset. Irregular selection is when users use H5Sselect_hyperslab - more than once for the same dataset. - Currently, not all MPI-IO packages support complicated MPI derived - datatype used in the implementation of irregular - selection INSIDE HDF5. - 1) DEC 5.x is not supporting complicated derived datatype. - 2) For AIX 5.1, - if your poe version number is 3.2.0.19 or lower, - please edit powerpc-ibm-aix5.x under hdf5/config, - Find the line with - << hdf5_mpi_complex_derived_datatype_works>> - and UNCOMMENT this line before the configure. - check poe version with the following command: - lpp -l all | grep ppe.poe - 3) For Linux cluster, - if mpich version is 1.2.5 or lower, collective irregular selection - IO is not supported, internally independent IO is used. - 4) For IRIX 6.5, - if C compiler version is 7.3 or lower, collective irregular selection - IO is not supported, internally independent IO is used. - 5) For platforms which internally used mpich, if the - mpich version is 1.2.5 or lower, please find the - corresponding config file and add - hdf5_mpi_complex_derived_datatype_works='no' at the - end of the configuration file. For example, at NCSA - SGI Altix, the internal mpich library is 1.2.5. So - hdf5_mpi_complex_derived_datatype_works='no' should be - added at the end of the config file ia64-linux-gnu. - KY - 2005/09/12 - We also found not all MPI-IO packages support collective IO with one - or more processes to have no contributions to IO. - For mpich version 1.2.6 or lower and all IRIX machine, - if the library checks that there are no IO contributions for some - processes, collective IO request is replaced with - independent inside HDF5. - KY - 2006/05/04 - - - HDF5 N-bit filter - HDF5 support N-bit filter from this version, - The N-Bit filter is used effectively for compressing data of N-Bit - datatype as well as compound and array datatype with N-Bit fields. - KY - 2005/04/15 - - HDF5 scaleoffset filter - HDF5 supports scaleoffset filter for users to do data - compression through HDF5 library. - Scale-Offset compression performs a scale and/or offset operation - on each data value and truncates the resulting value to a minimum - number of bits and then stores the data. - Scaleoffset filter supports floating-point and integer datatype. - Please check the HDF5 reference manual for this. - KY - 2005/06/06 - - Retired SRB vfd (--with-srb). Functions H5Pset_fapl_srb and - H5Pget_fapl_srb were removed. EIP - 2005/04/07 - - Retired GASS vfd (--with-gass). Functions H5Pset_fapl_gass and - H5Pget_fapl_gass are removed too. AKC - 2005/3/3 - - Pablo was removed from the source code EIP - 2005/01/21 - - Modified registration of SZIP to dynamically detect the presence - or absence of the encoder. Changed configure and Makefiles, - and tests to dynamically detect encoder. BEM - 2004/11/02 - - Added function H5Pget_data_transform, together with the previously - added H5Pset_data_transform, to support the data transform - feature. AKC - 2004/10/26 - - Compound datatype has been enhanced with a new feature of size - adjustment. The size can be increased and decreased(without - cutting the last member) as long as it doesn't go down to zero. - No API change is involved. SLU - 2004/10/1 - - Put back 6 old error API functions to be backward compatible with - version 1.6. They are H5Epush, H5Eprint, H5Ewalk, H5Eclear, - H5Eset_auto, H5Eget_auto. Their new equivalent functions are - called H5Epush_stack, H5Eprint_stack, H5Ewalk_stack, - H5Eclear_stack, H5Eset_auto_stack, H5Eget_auto_stack. SLU - - 2004/9/2 - - 4 new API functions, H5Tencode, H5Tdecode, H5Sencode, H5Sdecode were - added to the library. Given object ID, these functions encode and - decode HDF5 objects(data type and space) information into and from - binary buffer. SLU - 2004/07/21 - - Modified the way how HDF5 calculates 'pixels_per_scanline' parameter for - SZIP compression. Now there is no restriction on the size and shape of the - chunk except that the total number of elements in the chunk cannot be - bigger than 'pixels_per_block' parameter provided by the user. - EIP - 2004/07/21 - - Added support for SZIP without encoder. Added H5Zget_filter_info - and changed H5Pget_filter and H5Pget_filter_by_id to support this - change. JL/NF - 2004/06/30 - - SZIP always uses K13 compression. This flag no longer needs to - be set when calling H5Pset_szip. If the flag for CHIP - compression is set, it will be ignored (since the two are mutually - exclusive). JL/NF - 2004/6/30 - - A new API function H5Fget_name was added. It returns the name - of the file by object(file, group, data set, named data type, - attribute) ID. SLU - 2004/06/29 - - Added support for user defined identifier types. NF/JL - 2004/06/29 - - A new API function H5Fget_filesize was added. It returns the - actual file size of the opened file. SLU - 2004/06/24 - - New Feature of Data transformation is added. AKC - 2004/05/03. - - New exception handler for datatype conversion is put in to - replace the old overflow callback function. This exception - handler is set through H5Pset_type_conv_cb function. - SLU - 2004/4/27 - - Added option that if $HDF5_DISABLE_VERSION_CHECK is set to 2, - will suppress all library version mismatch warning messages. - AKC - 2004/4/14 - - A new type of dataspace, null dataspace(dataspace without any - element) was added. SLU - 2004/3/24 - - Data type conversion(software) from integer to float was added. - SLU - 2004/3/13 - - Data type conversion(software) from float to integer was added. - Conversion from integer to float will be added later. - SLU -2004/2/4 - - Added new H5Premove_filter routine to remove I/O pipeline filters - from dataset creation property lists. PVN - 2004/01/26 - - Added new 'compare' callback parameter to H5Pregister & H5Pinsert - routines. QAK - 2004/01/07 - - Data type conversion(hardware) between integers and floats was added. - SLU 2003/11/21 - - New function H5Iget_file_id() was added. It returns file ID given - an object(dataset, group, or attribute) ID. SLU 2003/10/29 - - Added new fields to the H5G_stat_t for more information about an - object's object header. QAK 2003/10/06 - - Added new H5Fget_freespace() routine to query the free space in a - given file. QAK 2003/10/06 - - Added backward compatability with v1.6 for new Error API. SLU - - 2003/09/24 - - Changed 'objno' field in H5G_stat_t structure from 'unsigned long[2]' - to 'haddr_t'. QAK - 2003/08/08 - - Changed 'fileno' field in H5G_stat_t structure from 'unsigned long[2]' - to 'unsigned long'. QAK - 2003/08/08 - - Changed 'hobj_ref_t' type from structure with array field to 'haddr_t'. - QAK - 2003/08/08 - - Object references (hobj_ref_t) can now be compared with the 'objno' - field in the H5G_stat_t struct for testing if two objects are the - same within a file. QAK - 2003/08/08 - - Switched over to new error API. SLU - 2003/07/25 - - Parallel Library: - ----------------- - - Added mpich2 as a testing "platform" informally. AKC - 2005/9/28. - - A dataset created in serial mode with H5D_ALLOC_TIME_INCR allocation - setting was not extendible, either explicitly by H5Dextend or - implicitly by writing to unallocated chunks. Library now allocates - more space when needed or directed if the file is opened by parallel - mode, independent of what the dataset allocation mode is. - CC/AKC - 2005/08/29. - - Allow compressed, chunked datasets to be read in parallel. - QAK - 2004/10/04 - - Add options of using atomicity and file-sync to test_mpio_1wMr. - AKC - 2003/11/13 - - Added parallel test, test_mpio_1wMr, which tests if the - underlaying parallel I/O system is conforming to the POSIX - write/read requirement. AKC - 2003/11/12 - - Fortran Library: - ---------------- - - added support for shared Fortran libraries. -JML 2005/09/20 - - added missing h5tget_member_class_f function - EIP 2005/04/06 - - added new functions h5fget_name_f and h5fget_filesize_f - EIP 2004/07/08 - - h5dwrite/read_f and h5awrite/read_f functions only accept dims parameter - of the type INTEGER(HSIZE_T). - - added support for native integers of 8 bytes (i.e. when special - compiler flag is specified to set native fortran integers to 8 bytes, - for example, -i8 flag for PGI and Absoft Fortran compilers, - -qintsize=8 flag for IBM xlf compiler). - EIP 2005/06/20 - - added support for "big" REAL and DOUBLE PRECISION types - (usually the size is specified by compilers flags like - -r8, -r16, etc.) - Known problem: multi file test fails when REAL is 16 bytes. - EIP 2005/09/8 - - C++ Library: - ---------------- - - added support for shared C++ libraries. -JML 2005/09/20 - - Added missing member functions - H5::CompType::getMemberArrayType - H5::CompType::getMemberVarLenType - H5::AbstractDs::getArrayType - H5::AbstractDs::getVarLenType - H5::CommonFG::openArrayType - H5::CommonFG::openVarLenType - H5::PropList::copyProp -- this will replace the current - H5::PropList::copyProp in later releases due - to incorrect prototype. - H5::IdComponent::getHDFObjType - BMR - 2005/08/08 - - - Tools: - ------ - - h5repack and h5diff changed command line parameter syntax to be - similar to h5dump, adding also long switch names. PVN - 2008/1/16 - - h5repack now supports adding multiple filters to all objects. - PVN - 2008/1/16 - - h5dump lists groups and attributes in requested orders (by name and - creation order, both ascending and descending). PVN - 2007/10/5 - - h5import imports string (text) data. PVN - 2007/10/5 - - h52gif and gif2h5: Both these tools were revised to include the High - Level Image API support, and tests were added to /hl/tools/gif2h5. - PVN - 2007/04/13 - - h5dump: added support for double long type H5T_NATIVE_LDOUBLE. PVN - 2007/03/13 - - h5dump: added support for binary output, see usage. PVN 2007/03/13 - - h5repack: added support for the new nbit and scaleoffset filters. - PVN - 2007/05/07 - - h5repack: now uses the API function H5Ocopy (of the tool h5copy) to - recreate objects if there is not a user input for changes. PVN - - 2007/05/07 - - h5repack: added support for reading and repacking by hyperslabs for - large files. PVN - 2007/03/01 - - h5repack: a new option allows the copy using the file type (default) - instead of the previous conversion to native type. PVN - 2007/03/01 - - h5repack: output the percentage of compression used. PVN - 2007/03/01 - - h5diff: added support for -p option for unsigned long_long data. PVN - - 2007/02/26 - - h5diff: added support for comparing dataset regions. PVN - 2007/02/20 - - h5diff: added support for reading and comparing by hyperslabs for large files. - PVN - 2007/02/20 - - h5diff: printing of dataset dimensions along with dataset name. PVN -2007/02/19 - - h5dump now uses the new API function H5Rget_name to display the name - of the dataset referenced instead of its ID. PVN - 2007/02/19 - - Added new tool, h5mkgrp. QAK - 2007/02/14 - - Added new tool, h5copy. PVN - 2006/7/15 - - Removed obsolete pdb2hdf5 tool from tools/misc -JML 2005/10/24 - - Added build_h5perf_alone.sh that builds h5perf by standalone mode. - AKC - 2005/09/18. - - Sped up h5dump on files with large numbers of objects. - QAK - 2005/08/25 - - Added a standalone mode for building h5perf. AKC - 2005/08/12 - - new tool, h5jam. See reference manual. 2004/10/08 - - h5repack.sh did not report errors encountered during tests. It does - now. AKC - 2004/04/02 - - Added the MPI-I/O and MPI-POSIX drivers to the list of VFL drivers - available for h5dump and h5ls. RPM & QAK - 2004/02/01 - - Added option --vfd= to h5ls to allow a VFL driver to be selected - by a user. RPM & QAK - 2004/02/01 - - Added option -showconfig to compiler tools (h5cc,h5fc,h5c++). - AKC - 2004/01/08 - - Install the "h5cc" and "h5fc" tools as "h5pcc" and "h5pfc" - respectively if library is built in parallel mode. - WCW - 2003/11/04 - - Added metadata benchmark (perform/perf_meta). SLU - 2003/10/03 - - Changed output of "OID"s from h5dump from "<number>-<number>" to - "<number". This affects both the "regular" and XML output. - QAK - 2003/08/08 - - Changed output of file IDs and "OID"s from h5ls from - "<number>:<number>:<number>:<number>" to "<number>:<number>" - QAK - 2003/08/08 - - High-Level APIs: - ------ - - Fortran interfaces for the Image, Table and Lite APIs. PVN - 2007/5/1 - - New HDF5 Dimension Scale API (H5DS) allows dimension scales to be - created in an HDF5 file and associated with specific datasets. PVN - 2007/5/1 - - There are two new functions in the Lite library, H5LTtext_to_dtype - and H5LTdtype_to_text. H5LTtext_to_dtype creates a HDF5 data type - given a text description; H5LTdtype_to_text converts a data type - to text description. Only DDL definition is supported as text - desciption now. SLU - 2006/05/17 - - Added Packet Table API for creating tables with less overhead than - H5TB API. Added C++ wrapper for Packet Tables. See documentation. - JML - 2004/03/28 - - Documentation - ------------- - - The documentation for this release is largely complete, but - trails the source code. A few of the newer functions are - not yet documented. FMB - 2007/04/18 - - The user documents for this release can be accessed directly at - this location: - http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/doc/ - The most recent document versions (updated daily) in the - 1.8 development branch can be accessed at this location: - http://www.hdfgroup.uiuc.edu/HDF5/doc_dev_snapshot/H5_dev/ - FMB - 2007/04/18 - - -Support for new platforms, languages and compilers. -======================================= - - Added support for Free-BSD on amd64 with GNU C and Fortran compilers - 4.2.1 - EIP - 2007/06/25 - - Added support for sequential and parallel libraries for Intel 64 Linux - cluster (abe.ncsa.uiuc.edu). Among three MPICH packages available on - this machine, only Open MPI works. The VMI has seg fault in hyperslab.c - and bittests.c tests. The MVAPICH2 complained about mpd not running - the parallel test. (see Known Problems section for more info) - EIP - 2007/06/25 - - Added support for HPUX11.23 for both 32 and 64-bit; HDF5 C++ - - Added support for 64-bit Windows with Visual Studio .NET and 2005. - SJW - 2007/06/25 - - Added suport for HPUX11.23 for both 32 and 64-bit; HDF5 C++ - shared library is not supported with +DD64 flag. - EIP - 2006/06/22 - - Added support for VAX floating numbers for Alpha Open VMS 7.3.2 - EIP - 2006/05/05 - - Fixed broken make.com files in tools directories - EIP - 2006/05/05 - - Added support for Alpha Open VMS 7.3.2 EIP - 2006/04/15 - - Added support for Cray X1. JML - 2005/10/03 - - PGI Fortran compiler is supported on Linux64 systems (x86_64) - EIP - 2004/08/19 - - Absoft compiler f95 v9.0 supported on Linux 2.4 - EIP - 2004/07/29 - - HDF5 Fortran APIs are supported on Mac OSX with IBM XL Fortran - compiler version 8.1. This is a default compiler. - - HDF5 Fortran APIs are supported on MAC OSX with Absoft F95 compiler - version 8.2; set F9X environment varibale to f95, for example - setenv F9X f95 - Use --disable-shared --enable-static configure flags when Absoft - compiler is used. - EIP - 2004/07/27 - - HDF5 Fortran APIs are supported on MAC OSX with IBM XL Fortran - Compiler version 8.1 Use "--disable-shared --enable-static" - configure flags along with the "--enable-fortran" flag to build - Fortran library. EIP - 2004/01/07 - -Bug Fixes since HDF5-1.6.0 release -================================== - - Library - ------- - - Changed library's behavior for reading files that might have - corrupted object header information from a previous (buggy) - version of the library. By default, the library now rebuilds the - correct object header information instead of issuing an error. - Previous "strict" file format interpretation can be enabled with - the "--enable-strict-format-checks" configure option. - QAK - 2008/01/13 - - Fixed several bugs with writing fill values for datasets that have - a variable-length datatype or component datatype. QAK - 2007/06/19 - - STDIO driver didn't support files bigger than 2GB because the OFFSET - parameter of fseek is of type LONG INT, not big enough for big files. - Use fseeko instead for big files if it's available on the system. - SLU - 2007/4/5 - - Fixed a bug in H5Sselect_valid() that caused an incorrect value to - be returned (0) instead of FAIL on error conditions such as the - selection or extent not being defined. CMC - 2007/01/17 - - Fixed the MULTI driver problem (Bug #731) that corruptted the data. - SLU - 2007/1/12 - - Fixed file corruption bug which could write an incorrect number of - messages to an object's header under certain circumstances. - Generally, the sequence of actions to generate this bug looks - like this: - - Create an object - - Close the file - - Re-open the file - - Add 2 (or more) attributes to the object - - Close the file - - Re-open the file - - Delete one of the attributes on the object - - Add a smaller attribute to the object - - Delete the smaller atttribute on the object - - Add a larger attribute on the object - - After this, the number of header messages stored for the object - will be off by one. Other sequences of modifying attributes on an - object could also trigger this bug. If you are opening an - object and the bottom few messages of the HDF5 error stack - resembles this, the object has been affected by this bug: - - #007: ../../hdf5_v1.6/src/H5C.c line 3887 in H5C_load_entry(): unable to load entry - major(08): Meta data cache layer - minor(40): Unable to load metadata into cache - #008: ../../hdf5_v1.6/src/H5Ocache.c line 332 in H5O_load(): corrupt object header - too few messages - major(12): Object header layer - minor(40): Unable to load metadata into cache - - Specifically, "corrupt object header" is the best string to search - for in the HDF5 error stack output. - - If your files have been affected by this bug, or you are concerned - that your files might have been, please contact the HDF Helpdesk - at help@hdfgroup.org for a tool to detect and repair files - affected by this problem. QAK - 2006/6/16 - - Fixed various problems with retrieving names of objects, especially - with mounted files. QAK - 2005/12/25 - - Fixed core dump when closing root groups opened through two different - file handles that operate on the same actual file. QAK - 2005/10/02 - - Corrected errors when performing various operations on a group opened - by dereferencing an object reference. QAK - 2005/07/30 - - Fixed a bug with named datatypes where a copy of a named datatype - used to create a dataset would accidentally use the original - named datatype for the dataset's datatype. QAK - 2005/07/23 - - Made H5Fget_name() be consistent and always return name of actual - file the ID is in. (Instead of the name of the top file in a - file mounting hierarchy). QAK - 2005/07/19 - - Reworked internal file mounting semantics to hopefully eliminate - mounting problems. We now require that files that are mounting - together all have the same "file close degree". QAK - 2005/07/19 - - More bug fixes on holding open files that are mounted and have - IDs open. QAK - 2005/07/14 - - Don't unmount child files until the parent file actually closes. - (Previously, if an object is holding open a file, the child files - would get unmounted too early). QAK - 2005/07/05 - - Fixed bug where unmounted files could cause the library to go into - an infinite loop when shutting down. QAK - 2005/06/30 - - The library didn't save the information of family driver in file. - The original file member size was lost after file was closed (see - bug #213). This has been fixed by saving driver name and member - file size in the superblock. SLU - 2005/6/24 - - Fixed bug with hyperslab selections that use selection offsets and - operate on chunked datasets going into infinite loop or dumping - core. QAK - 2005/06/17 - - Corrected memory leak and possible corruption when opening a group. - QAK - 2005/06/17 - - Added check for opaque datatype tags being too long (check against - H5T_OPAQUE_TAG_MAX, currently set to 256). QAK - 2005/06/14 - - Fixed various errors in maintaining names for open objects in the - face of unusual mount & unmount operations. QAK - 2005/06/08 - - "SEMI" and "STRONG" file close degree settings now apply only to the - particular file ID being closed, instead of operating on all open - file IDs for a given file. QAK - 2005/06/01 - - For family driver, the library didn't save member size in file. - When file is reopened, the size of 1st member file determine the - member size. Now member size is saved in file and is used to - define member file size. Wrong file access property of member size - will result in a failure. Using any other driver except family - will cause library to return error. So is multi driver. SLU - - 2005/05/24 - - Fixed error in opening object in group that was opened in mounted - file which has been unmounted. QAK - 2005/03/17 - - Fixed a racing condition in MPIPOSIX virtual file drive close - function. Now all processes must completed the close before any - of them is returned. This prevents some "faster" processes start - accessing the file for another purpose (e.g., open with truncate) - while other "slower" processes have not closed the same file with - the previous purpose. AKC - 2005/03/01 - - H5Tget_member_value calls for enum datatype didn't return correct - value if H5Tenum_valueof was called first. It's fixed. SLU - - 2005/02/08 - - For variable-length string, H5Tget_class returned H5T_STRING as its - class. But H5Tdetect_class and H5Tget_member_class considered it - as H5T_VLEN. This is fixed to let all these 3 functions treat it - as H5T_STRING. SLU - 2005/02/08 - - The byte order of 1-byte integer types was fixed as little endian - even on a big-endian machine. This has been corrected. SLU - - 2005/02/07 - - Fix segmentation fault when calling H5Fflush with an attribute that - hasn't had a value written to it open. QAK - 2004/10/18 - - Back up supporting bitfield and time types in H5Tget_native_type. - Leave it to future support. The function simply returns error - message of "not support" for bitfield and time types. - SLU - 2004/10/5 - - Fixed address check in Core VFL driver to avoid spurious address/size - overflows for odd valued addresses and/or sizes. QAK - 2004/09/27 - - Fixed parallel bug in which some processes attempted collective - I/O while others did independent I/O. Bug appeared when some - processes used point selections, and others didn't. JRM - 2004/9/15 - - Corrected error where dataset region references were written in an - incorrect way on Cray machines. PVN & QAK - 2004/09/13 - - The H5Tget_native_type now determines the native type for integers - based on the precision. This is to avoid cases of wrongly converting - an int to a short in machines that have a short of 8 bytes but with - 32bit precision (e.g Cray SV1). PVN - 2004/09/07 - - Changed H5Dread() to not overwrite data in an application's buffer - with garbage when accessing a chunked dataset with an undefined - fill value and an unwritten chunk is uncountered. QAK - 2004/08/25 - - Fixed error which could cause a core dump when a type conversion - routine was registered after a compound datatype had been - converted and then an equivalment compound datatype was converted - again. QAK - 2004/08/07 - - Fixed memory overwrite when encoding "multi" file driver information - for file's superblock. QAK - 2004/08/05 - - Fixed obscure bug where a filter which failed during chunk allocation - could allow library to write uncompressed data to disk but think - the data was compressed. QAK - 2004/07/29 - - Fixed bug where I/O to an extendible chunked dataset with zero-sized - dimensions would cause library to fail an assertion. - QAK - 2004/07/27 - - Fixed bug where chunked datasets which have filters defined, - allocation time set to "late" and whose chunks don't align with - the dataspace bounds could have incorrect data stored when - overwriting the entire dataset on the first write. QAK - 2004/07/27 - - Added check to ensure that dataspaces have extents set. JML-2004/07/26 - - Fixed bug on some Solaris systems where HDF5 would try to use - gettimeofday() when that function didn't work properly. - JML - 2004/07/23 - - Fixed bug in H5Sset_extent_simple where setting maximum size to - non-zero, then to zero would cause an error. JML - 2004/07/20 - - Allow NULL pointer for buffer parameter to H5Dread & H5Dwrite - when not writing data ("none" selection or hyperslab or point - selection with no elements defined). QAK - 2004/07/20 - - Calling H5Gcreate() on "/" or "." throws an error instead of - failing quietly. JML - 2004/07/19 - - Fixed bug where setting file address size to be very small could - trigger an assert if the file grew to more than 64 KB. Now throws - an error and data can be recovered. JL/NF - 2004/07/14 - - Fixed bug where "resurrecting" a dataset was failing. - QAK - 2004/07/14 - - Fixed bug where incorrect data could be read from a chunked dataset - after it was extended. QAK - 2004/07/12 - - Fixed failure to read data back from file of compound type with - variable-length string as field. SLU - 2004/06/10 - - Fixed potential file corruption bug when a block of metadata could - overlap the end of the internal metadata accumulator buffer and - the buffer would be extended correctly, but would incorrectly - change it's starting address. QAK - 2004/06/09 - - Opaque datatype with no tag failed for some operations. Fixed. - SLU - 2004/6/3 - - Fixed potential file corruption bug where dimensions that were - too large (a value greater than could be represented in 32-bits) - could cause the incorrect amount of space to be allocated in a - file for the raw data for the dataset. QAK - 2004/06/01 - - Fixed dtypes "sw long double -> double" failure in QSC class - machines. AKC - 2004/4/16 - - Fixed problem with fletcher32 filter when converting data of different - endianess. PVN - 2004/03/10 - - Fixed problem with H5Tget_native_type() not handling opaque fields - correctly. QAK - 2004/01/31 - - Fixed several errors in B-tree deletion code which could cause a - B-tree (used with groups and chunked datasets) to become corrupt - with the right sequence of deleted objects. QAK - 2004/01/19 - - Fixed small internal memory leaks of fill-value information. - QAK - 2004/01/13 - - Fixed bug that caused variable-length datatypes (strings or sequences) - used for datasets in files with objects that were unlinked to - fail to be read/written to a file. QAK - 2004/01/13 - - Detect situation where szip 'pixels per block' is larger than the - fastest changing dimension of a dataset's chunk size and disallow - this (due to limits in szip library). QAK - 2003/12/31 - - Fixed bug with flattened hyperslab selections that would generate - incorrect hyperslab information with certain high-dimensionality - combinations of start/stride/count/block information. - QAK - 2003/12/31 - - Fixed bug with variable-length datatypes used in compound datatypes. - SLU - 2003/12/29 - - Fixed bug in parallel I/O routines that would cause reads from - "short datasets" (datasets which were only partially written out) - to return invalid data. QAK & AKC - 2003/12/19 - - Fixed bug where scalar dataspaces for attributes were reporting as - simple dataspaces. QAK - 2003/12/13 - - Fixed problem with selection offsets of hyperslab selections in - chunked datasets causing the library to go into an infinite loop. - QAK - 2003/12/13 - - Fixed H5Giterate to avoid re-using index parameter after iteration - callback has been called (allows iteration callback to modify the - index parameter itself). QAK - 2003/12/06 - - Fixed various floating-point conversion problems, including a - change which could corrupt data when converting from double->float. - QAK - 2003/11/24 - - Changed "single process" metadata writing in library to collective - I/O by all processes, in order to guarantee correct data being - written with MPI-I/O. QAK - 2003/11/20 - - Fixed problems with fill values and variable-length types and also - I/O on VL values that were set to NULL. QAK - 2003/11/08 - - Fixed problems with MPI datatypes that caused ASCI Q machine to - hang. QAK - 2003/10/28 - - Removed HDF5_MPI_PREFER_DERIVED_TYPES environment variable support, - since it had no benefit. QAK - 2003/10/28 - - Single hyperslab selections (which were set with only one call to - H5Sselect_hyperslab) that had dimensions that could be "flattened" - but were interspersed with dimensions that could not be flattened - were not correctly handled, causing core dumps. QAK - 2003/10/25 - - Fixed incorrect datatype of the third parameter to the Fortran90 - h5pset(get)_cache_f subroutine (INTEGER to INTEGER(SIZE_T)) - EIP - 2003/10/13 - - Fixed problems with accessing variable-length data datatypes on - Crays. QAK - 2003/10/10 - - Fixed potential file corruption bug when too many object header - messages (probably attributes, from a user perspective) were - inserted into an object header and certain other conditions were - met. QAK - 2003/10/08 - - Changed implementation of internal ID searching algorithm to avoid - O(n) behavior for many common cases. QAK - 2003/10/06 - - Allow partial parallel writing to compact datasets. QAK - 2003/10/06 - - Correctly create reference to shared datatype in attribute, instead - of making a copy of the shared datatype in the attribute. - QAK - 2003/10/01 - - Revert changes which caused files >2GB to fail when created with - MPI-I/O file driver on certain platforms. QAK - 2003/09/16 - - Allow compound datatypes to grow in size. SLU - 2003/09/10 - - Detect if a type is already packed before attempting to pack it - again or check if it is locked. SLU - 2003/09/10 - - Corrected bug when opening a file twice with read-only permission - for one open and then closing the read-only access file ID would - generate an error. QAK - 2003/09/10 - - Corrected bug in repeated calls to H5Pget_access_plist() which would - incorrectly manage reference counts of internal information and - eventually blow up. QAK - 2003/09/02 - - Return rank of the array datatype on successful call to - H5Tget_array_dims(). QAK - 2003/08/30 - - Corrected bug in H5Tdetect_class which was not correctly detecting - datatype classes of fields in nested compound datatypes in some - circumstances. QAK - 2003/08/30 - - Corrected bug in sieve buffer code which could cause loss of data - when a small dataset was created and deleted in quick succession. - QAK - 2003/08/27 - - Corrected bug in H5Gget_objname_by_idx which was not allowing NULL - for the name when just querying for the object name's length. - QAK - 2003/08/25 - - Corrected bug in variable-length string handling which could - generate a core dump on writing variable-length strings as part - of a compound datatype on certain architectures. QAK - 2003/08/25 - - Corrected bug in H5Tget_native_type which would incorrectly compute - the size of certain compound datatypes and also incorrectly - compute the offset of the last field for those compound datatypes. - QAK - 2003/08/25 - - Corrected bug in H5Tget_native_type which would drop string datatype - metadata (padding, etc.) QAK - 2003/08/25 - - Corrected bugs in H5Gget_num_objs, H5Gget_objname_by_idx and - H5Gget_objtype_by_idx to allow them to accept location IDs, not just - group IDs. QAK - 2003/08/21 - - Corrected bug when using scalar dataspace for memory selection and - operating on chunked dataset. QAK - 2003/08/18 - - Corrected bugs with multiple '/' characters in names for H5Glink - and H5Gunlink. QAK - 2003/08/16 - - Corrected bug with user blocks that didn't allow a user block to - be inserted in front of a file after the file was created. - QAK - 2003/08/13 - - Corrected errors with using point selections to access data in - chunked datasets. QAK - 2003/07/23 - - Corrected error with variable-length datatypes and chunked datasets - caused H5Dwrite to fail sometimes. QAK - 2003/07/19 - - Modified library and file format to support storing indexed storage - (chunked dataset) B-tree's with non-default internal 'K' values. - QAK - 2003/07/15 - - Returned H5T_BKG_TEMP support to library after it was accidentally - removed. QAK - 2003/07/14 - - Configuration - ------------- - - Configure can now use any tr command. No more need for - defining variable TR nor is it supported. -AKC 2006/05/19 - - Parallel I/O with the MPI-I/O driver will no longer work if the - filesystem is not POSIX compliant. The "HDF5_MPI_1_METAWRITE" - environment variable has been removed. QAK - 2004/01/30 - - Fixed the error that cause "make install" to fail because of the - macro definition syntax of "prefix?=..." AKC - 2003/07/22 - - Performance - ------------- - - Optimized I/O for enumerated datatypes that are a superset of source - enumerated datatype. QAK - 2005/03/19 - - More optimizations to inner loops of datatype conversions for - integers and floats which give a 10-50% speedup. QAK - 2003/11/07 - - Hoisted invariant 'if/else's out of inner datatype conversion loop for - integer and floating-point values, giving about a 20% speedup. - QAK - 2003/10/20 - - Tools - ----- - - Fixed h5dump regarding the display of blocks in hyperslab - selections. PVN 2008/01/16 - - Fixed h5diff regarding the display of NaN (Not a Number) - values. PVN 2008/01/16 - - Fixed h5dump regarding the parsing of binary output parameters. - PVN 2008/01/16 - - Fixed memory problems in h52gif and gif2h5. PVN 2008/01/16 - - Fixed h5repack dealing with NULL references. PVN 2008/01/16 - - Fixed h5dump & h5ls to display attributes in "name" order, rather - than the order they are encountered in the object header. - QAK - 2007/10/04 - - Fixed h5dump regarding the display of named datatypes - attributes. PVN 2007/03/13 - - Fixed h5dump regarding the display of group comments. PVN - 2007/03/13 - - Fixed h5dump regarding the display of hardlinks pointing - to the root group. PVN 2007/03/13 - - Fixed h5diff percentage option -p. PVN 2007/03/05 - - Fixed h5dump that caused array indices greater than 2 ^32-1 - not to be printed correctly - PVN 2007/2/19 - - Fixed h5dump to print attributes data in ASCII if -r option is used. - AKC - 2004/11/18 - - Fixed space utilization reported in h5ls to correct error in formula - used. QAK - 2004/10/22 - - Fixed h5redeploy which sometimes complain too many argument for the - test command. (The complain did not hinder the h5redploy to - proceed correctly.) AKC - 2003/11/03 - - Fixed a segmentation fault of h5diff when percentage option is used. - AKC - 2003/08/27 - - Switched away from tools using internal "fixtype" function(s) to use - H5Tget_native_type() internally. QAK - 2003/08/25 - - - Documentation - ------------- - - - F90 APIs - -------- - - h5pget_driver_f was returning information that could not be - interpreted by fortran application program; fixed. EIP - 2005/04/10 - - -Platforms Tested -================ -Platforms marked with * were not tested for hdf5-1.8.0-rc* release -(This information is somewhat out of date and may be inaccurate. It will be - updated for a later 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 -* AIX 5.3 (32/64 bit) xlc 7.0.0.8 - xlC 7.0.0.8 - xlf 09.01.0000.0007 -* Cray X1 water 3.0.35 Cray Standard C Version 5.4.0.7.4 - Cray Fortran 5.4.0.7.3 - Cray C++ 5.4.0.7.4 - 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 - -* HP-UX B.11.23 HP aC++/ANSI C B3910B A.06.00 - HP F90 v2.9.2 - HP aC++/ANSI C B3910B A.06.00 - 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, g95 (GCC 4.0.3) - (smirom) PGI 6.2-5 (pgcc, pgf90, pgCC) - Intel 9.1 (icc, iort, icpc) - Linux 2.6.5-7.252.1-rtgfx #1 - SMP ia64 Intel(R) C++ Version 9.0 - (cobalt) Intel(R) Fortran Itanium(R) Version 9.0 - 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 i86pc Sun C 5.7 - Sun Fortran 95 8.1 - Sun C++ 5.7 - 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 - - -Supported Configuration Features Summary -(This table was not modified for 1.8.0-rc* release; for information contact help@hdfgroup.org) -======================================== - - 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 - <blank> = 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 -Cray XT3 (16) n n n n n n -AIX-5.2 & 5.3 32-bit y y y y y y -AIX-5.2 & 5.3 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 -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 -HPUX11.00 y n y x n -HPUX11.23-32bit y n n y n -HPUX11.23-64bit y dna n y n -Cray XT3 (16) n n n n n -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 -Mac OS X 10.4 PowerPC -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 discovered two problems when running collective IO parallel HDF5 tests - with chunking storage on 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 wrong derived data type and corrupt data - may be generated. - This only happens when turning on collective IO with chunking storage - with some complex selections. We haven't found these problems on other - MPI-IO compilers. If you encounter these problems, you may use Independent IO - instead. - - 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. Higher level of optimization - causes failures in several HDF5 library tests. -* For HPUX 11.23 many tools tests failed for 64-bit version when linked to the - shared libraries (tested for 1.8.0-beta2) -* For SNL, Red Storm: only paralle HDF5 is supported. The serial tests pass - and the parallel tests also pass with lots of non-fatal error messages. -* For LLNL, uP: both serial and parallel pass. Zeus: serial passes but - parallel fails with a known proglem in MPI. ubgl: serial passes but - parallel fails. -* on SUN 5.10 C++ test 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, Scaleoffset filter isn't supported. The filter cannot be applied to - HDF5 data generated on VAX. Scaleoffset filter only supports 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, we found that if more than two processes - contribute no IO and the application asks to do IO with collective, we found - that when using 4 processors, a simple collective write will be hung - sometimes. This can be verified with t_mpi test under testpar. -* On IRIX6.5, when C compiler version >7.4, the complicate MPI derived data type - code will work. However, the user should be aware to enlarge MPI_TYPE_MAX environment - variable to some certian value in order to use collective irregular selection code. - For example, the current parallel HDF5 test needs to enlarge MPI_TYPE_MAX to - 200,000 to make the test pass. -* The dataset created or rewritten with the v1.6.3 library or after can't - be read with the v1.6.2 library or before when 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 wasn't 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 is no - longer the same as before on little-endian system. The library release - after 1.6.4 can still read the dataset created or rewritten with the library - of v1.6.2 or before. SLU - 2005/6/30 -* For the version 6(6.02 and 6.04) of Portland Group compiler on AMD Opteron - processor, there's a bug in the compiler for optimization(-O2). The library - failed in several tests but all related to 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". HDF5 does not use sockets (except for stream-VFD). This is - due to problems of the poe command trying to set up the debug socket. - Check if there are many old /tmp/s.pedb.* staying around. These are - sockets used by the poe command and left behind due to failed commands. - Ask your system administrator to clean them out. Lastly, request IBM - to provide a mean to run poe without the debug socket. - -* The C++ library's tests fails when compiling with PGI C++ compiler. The - workaround until the problem is correctly handled is to use the - flag "--instantiate=local" prior to the configure and build steps, as: - setenv CXX "pgCC --instantiate=local" for pgCC 5.02 and higher - - -* The stream-vfd test uses ip port 10007 for testing. If another - application is already using that port address, the test will hang - indefinitely and has to be terminated by the kill command. To try the - test again, change the port address in test/stream_test.c to one not - being used in the host. - -* The --enable-static-exec configure flag fails to compile for Solaris - platforms. This is due to the fact that not all of the system - libraries on Solaris are available in a static format. - - The --enable-static-exec configure flag also fails to correctly compile - on IBM SP2 platform for the serial mode. The parallel mode works fine - with this option. - - It is suggested that you don't use this option on these platforms - during configuration. - -* With the gcc 2.95.2 compiler, HDF 5 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 Stream VFD was not tested yet under Windows. It is not supported - in the TFLOPS machine. - - -* The ./dsets tests failed in the TFLOPS machine if the test program, - dsets.c, is compiled with the -O option. The hdf5 library still works - correctly with the -O option. The test program works fine if it is - compiled with -O1 or -O0. Only -O (same as -O2) causes the test - program to fail. - -* Certain platforms give false negatives when testing h5ls: - - Cray J90 and Cray T90IEEE give errors during testing when displaying - some floating-point values. These are benign differences due to - the different precision in the values displayed and h5ls appears to - be dumping floating-point numbers correctly. - -* Before building HDF5 F90 Library from source on Crays - replace H5Aff.f90, H5Dff.f90 and H5Pff.f90 files in the fortran/src - subdirectory in the top level directory with the Cray-specific files - from this site: - ftp://www.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.0-pre/PATCH/ - -* 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 HDF5 fortran library, - compilation may fail for fortranlib_test.f90, fflush1.f90 and fflush2.f90 - complaining about exit subroutine. Comment out the line - IF (total_error .ne. 0) CALL exit (total_error) - -* On IA32 and IA64 systems, if you use a compiler other than GCC (such as - Intel's ecc or icc compilers), you will need to modify the generated - "libtool" program after configuration is finished. On or around line 104 of - the libtool file, there are lines which look like: - - # How to pass a linker flag through the compiler. - wl="" - - change these lines to this: - - # How to pass a linker flag through the compiler. - wl="-Wl," - - UPDATE: This is now done automatically by the configure script. However, if - you still experience a problem, you may want to check this line in the - libtool file and make sure that it has the correct value. - -* Information about building with PGI and Intel compilers is available in - INSTALL file sections 5.7 and 5.8 - -* 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 HDF 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 h5copy tool - -%%%%1.6.7%%%% Release Information for hdf5-1.6.7 (31/January/08) - -HDF5 version 1.6.7 released on Thu Jan 31 21:09:10 CST 2008 -================================================================================ - -INTRODUCTION -============ -This document describes the differences between HDF5-1.6.6 and HDF5-1.6.7 -It contains information on the platforms tested and known problems in -HDF5-1.6.7. For more details, check the HISTORY.txt file in the HDF5 source. - -HDF5 documentation can be found in the distributed release source code -in the subdirectory doc/html/ or on the THG (The HDF Group) FTP server: - - ftp://ftp.hdfgroup.org/HDF5/docs/ - -Documentation for the current release in the HDF5 Release 1.6.x series is -also on the HDF web site: - - http://hdfgroup.org/HDF5/doc1.6/ - -For more information, see the HDF5 home page: - - http://hdfgroup.org/products/hdf5/ - -If you have any questions or comments, please see the HDF Support page -for a list of available resources: - - http://hdfgroup.org/services/support.html - - -CONTENTS -======== -- New Features -- Support for New Platforms, Languages and Compilers -- Bug Fixes since HDF5-1.6.6 -- Documentation -- Platforms Tested -- Supported Configuration Features Summary -- Known Problems - - -New Features -============ - Configuration: - ------------------------- - '--enable-stream-vfd' and '--disable-stream-vfd' are no longer valid - configure options because the stream I/O driver has ben removed from - the distribution. - - Source code distribution - ======================== - Library: - -------- - The stream I/O driver is not included with the HDF5 Library in this - release. The source code files hdf5/src/H5FDstream.c and - hdf5/src/H5FDstream.h and the driver ENUM value H5FD_STREAM have been - removed. - - Parallel Library: - ----------------- - None - - Tools: - ------ - None - - F90 API: - -------- - None - - C++ API: - -------- - None - - -Support for New Platforms, Languages and Compilers -================================================== - -No new platorms, languages, or compilers are supported in this release. - - -Bug Fixes since HDF5-1.6.6 Release -================================== - - Library - ------- - - H5Iget_name could not be used with an object identifier returned - by H5Rdereference; the function would not be able to determine - a valid object name. It has been fixed. SLU - 2008/1/30 - - Changed library's behavior for reading files that might have - corrupted object header information from a previous (buggy) - version of the library. By default, the library now rebuilds the - correct object header information instead of issuing an error. - Previous "strict" file format interpretation can be enabled with - the "--enable-strict-format-checks" configure option. - QAK - 2008/01/13 - - Fixed bug in H5Epush() which was clearing the error stack before - pushing new error value. QAK - 2007/08/23 - - Fixed bug in H5Ewalk() which was not passing back the return value - from error stack walking callback. QAK - 2007/08/23 - - - Configuration - ------------- - None - - - Performance - ------------- - None - - - Tools - ----- - None - - - Documentation - ------------- - None - - - F90 API - ------- - None - - - C++ API - ------- - None - - -Documentation -============= - HDF5 documentation can be found in the distributed release source - code in the subdirectory doc/html/ (start with index.html) or on the - THG (The HDF Group) FTP server: - - ftp://ftp.hdfgroup.org/HDF5/docs/ - - Online documentation for the current release in the HDF5 Release 1.6.x - series can be found on the THG web site: - - http://hdfgroup.org/HDF5/doc1.6/ - - A listing of interface changes from release to release can be found - in the document "HDF5 Software Changes from Release to Release": - - http://hdfgroup.org/HDF5/doc1.6/ADGuide/Changes.html - - Since the stream I/O driver is not included in this release, the - functions H5Pset_fapl_stream and H5Pget_fapl_stream and the stream - ENUM value H5FD_STREAM have been removed from the documentation. - - -Platforms Tested -================ - - AIX 5.2 (32/64 bit) xlc 8.0.0.11 - (datastar) xlC 8.0 - xlf 10.01.0000.0002 - - FreeBSD 6.2 (32- and 64-bit) gcc and g++3.4.6 - (duty and liberty) gcc and g++ 4.2.1 - - IRIX64 6.5 MIPSpro cc 7.4.4m - (ucar mop1 64 & n32) F90 MIPSpro 7.4.4m (64 only) - C++ MIPSpro cc 7.4.4m - - Linux 2.4.21-47.ELsmp #1 SMP gcc 3.2.3 - i686 i386 GNU/Linux - (osage) - - Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6 - SMP i686 i386 G95 (GCC 4.0.3 (g95 0.91!) April 18 2007) - (kagiso) PGI C, Fortran, C++ 7.0-7 32-bit - Intel(R) C Compiler for 32-bit - applications, Version 9.1 - Intel(R) C++ Compiler for 32-bit - applications, Version 9.1 - Intel(R) Fortran Compiler for 32-bit - applications, Version 9.1 - Absoft 32-bit Fortran 95 10.0.4 - MPICH mpich2-1.0.6p1 compiled with - gcc 4.2.1 and G95 (GCC 4.0.3 (g95 0.91!) - - Linux 2.6.16.46-0.12-debug #1 Intel(R) C++ Version 10.0.025 - SMP ia64 GNU/Linux Intel(R) Fortran Itanium(R) Version 10.0.025 - (ucar hir1) - - Linux 2.6.16.46-0.14-smp #1 Intel(R) C++ for Intel(R) EM64T Ver. 9.1.037 - SMP x86_64 GNU/Linux Intel(R) Fortran Intel(R) EM64T Ver. 9.1.031 - (smirom) PGI C, Fortran, C++ Version 7.0-7 - for 64-bit target on x86-64 - tested for both 32- and 64-bit binaries - - Linux 2.6.5-7.287.3-sn2 #1 Intel(R) C++ Version 9.0 - Altix SMP ia64 Intel(R) Fortran Itanium(R) Version 9.0 - (cobalt) SGI MPI - - SunOS 5.8 32- and 64-bit Sun WorkShop 6 update 2 C 5.3 - (sol) Sun WorkShop 6 update 2 Fortran 95 6.2 - Sun WorkShop 6 update 2 C++ 5.3 - - 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 2.4.21-32.0.1.ELsmp-perfctr-lustre - (tungsten) Intel(R) C++ Version 9.0 - Intel(R) Fortran Compiler Version 9.0 - PGI C Version 6.0-5 - PGI C++ Version 6.0-5 - PGI Fortran Version 6.0-5 - gcc (GCC) 3.2.2 (Red Hat Linux 3.2.2-5) - - Xeon Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp - (abe) Intel(R) C++ Version 10.0 - Intel(R) Fortran Compiler Version 10.0 - Open MPI 1.2.2 - - 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 - Intel(R) Fortran Compiler Version 8.1 - mpich-gm-1.2.6..14-intel-r2 - - Windows XP Visual Studio 6.0 - Visual Studio .NET (with Intel Fortran 9.1) - Visual Studio 2005 (with Intel Fortran 9.1) - cygwin (gcc 3.4.4) - - Windows Vista Visual studio 2005 - MAC OS X Intel Darwin 8.10.1 - i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 - g95 0.91 - - -Supported Configuration Features Summary -======================================== - -Key: y = Tested and supported - n = Not supported or not tested in this release - C = Cluster - W = Workstation - ( ) = Footnote appears below second table - -Platform C F90 F90 C++ zlib SZIP - parallel parallel -Solaris2.8 32-bit n y n y n y -Solaris2.8 64-bit n y n n y y -Solaris2.10 32-bit n y n y y y -Solaris2.10 64-bit n y n n y y -IRIX64_6.5 32-bit n n n n y y -IRIX64_6.5 64-bit n y n n y y -WinXP Visual Studio 6.0 n n n y y y -WinXP CYGWIN n n n y y y -WinXP 2005 n y n y y y -WinXP .Net n y n y y y -WinVista 2005 n n n y y y -Mac OS X 10.4.10 n y n y y y -AIX-5.2 & 5.3 32- and 64-bit y y y y y y -FreeBSD 6.2 32- and 64-bit n n n y y y -RedHat Linux 2.4.21 W n n n n y n -RedHat Linux 2.6.9-42 i686 GNU (1) W y y y y y y -RedHat Linux 2.6.9-42 i686 Intel W n y n y y n -RedHat Linux 2.6.9-42 i686 PGI W n y n y y n -SuSE Linux 2.6.16 x86_64 GNU (1) W y y n y y y -SuSE Linux 2.6.16 x86_64 Intel W n y n y y n -SuSE Linux 2.6.16 x86_64 PGI W n y n y y n -RHEL 4 Linux 2.6.9 Xeon Lustre C n y n y y y -RedHat Linux 2.4 Xeon Lustre C n y n y y n -SuSE Linux 2.4 ia64 C y y y y y y -SuSe Linux 2.6.5 SGI Altix ia64 n y n y y y - - -Platform Shared static- Thread- - libraries(4) exec safe -Solaris2.8 32- and 64-bit y n y -Solaris2.10 32- and 64-bit y n y -IRIX64_6.5 32-bit y n y -IRIX64_6.5 64-bit y n y -WinXP Visual Studio 6.0 y n n -WinXP CYGWIN y n n -WinXP 2005 y n n -WinXP .Net y n n -WinVista 2005 y n n -Mac OS X 10.4.10 y n n -AIX-5.2 & 5.3 32- and 64-bit n n n -FreeBSD 6.2 32- and 64-bit y n n -RedHat Linux 2.4.21 W y n n -SuSE Linux 2.6.9-42 i686 GNU (1) W y n y -SuSE Linux 2.6.9-42 i686 Intel W y n n -SuSE Linux 2.6.9-42 i686 PGI W n n n -SuSE Linux 2.6.16 x86_64 GNU (1) W y n y -SuSE Linux 2.6.16 x86_64 Intel W y n n -SuSE Linux 2.6.16 x86_64 PGI W n n n -RHEL 4 Linux 2.6.9 Xeon Lustre C y n n -RedHat Linux 2.4 Xeon Lustre C y n n -SuSE Linux 2.4 ia64 C y n n -SuSe Linux 2.6.5 SGI Altix ia64 n n n - -Compiler versions for each platform are listed in the "Platforms Tested" -table found elsewhere in this file (RELEASE.txt). Unless otherwise noted, -compilers used are the system compilers. - -Footnotes: -(1) Fortran compiled with g95. - - -Known Problems -============== -* We discovered two problems when running collective IO parallel HDF5 tests - with chunking storage with 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. - This only happens when turning on collective IO with chunking storage - with some complex selections. We haven't found these problems on other - MPI-IO compilers. If you encounter these problems, you may use Independent - IO instead. - - To avoid this problem, 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 - -* QSC (an HP alpha-based OSF1 cluster) does not create h5pfc correctly. It - does not include the -lmpi properly. This will be fixed in the next - release. AKC - 2007/08/07. - -* On IRIX64 6.5 (UCAR SGI mop1), when testing HDF5 tools with an HDF5 shared - library, especially for h5repacktst and h52gifgentst, the following (or a - similar) error message may appear: - "523648:lt-h5repacktst: rld: Fatal Error: Cannot Successfully map soname - 'libh5test.so.1' under any of the filenames .......(bunch of directories) - " - And the testing will fail. - - We believe this is a libtool problem. One way to get rid of this is to - add the paths of libh5test.so.1 and libh5.so.1 to the shared library path. - - For 32-bit: - You may do this, under csh: - setenv LD_LIBRARYN32_PATH .......(existing paths):[full path of HDF5 - directory/test/.libs]:[full path of HDF5 directory/src/.libs] - - For 64-bit: - setenv LD_LIBRARY64_PATH ......(existing paths):[full path of HDF5 - directory/test/.libs]:[full path of HDF5 directory/src/.libs] - - NOTE: This problem ONLY affects the testing of the HDF5 library when you - build from source. It won't affect any applications that would like to link - with the HDF5 shared library since the shared library path needs to be set - anyway. KY - 2007/8/2 - -* QSC (an HP alpha-based OSF1 cluster) failed the testpar/testphdf5 sub-test - "calloc". All other tests passed. This indicates that a dataset using - chunked storage created by serial HDF5 may not work properly with parallel - HDF5. The calloc test can be skipped by running "prun ... testphdf5 -x - calloc". AKC - 2007/7/12. - -* The Intel C Compiler for the Linux x86_64 platform (EM64T-based, v8.1) has - an optimization error in the datatypes conversion code. Before running - configure, edit the file config/intel-flags by changing the setting of - PROD_CFLAGS from -O3 to -O0. Then run configure. AKC - 2005/11/10. - -* When testing parallel HDF5 with the C compiler version MIPSpro 7.4.3 on IRIX - 6.5, set the environment variable MPI_TYPE_MAX to be a bigger number, for - example 120000, in order to pass the complicated collective IO tests inside - the parallel HDF5 library. This is not a problem inside the parallel HDF5 - library. You can always set a bigger number on your system. KY - 2005/10/6 - -* A contiguous or chunked dataset created by a sequential version of HDF5 - might not be able to be modified with a parallel version of the library. - Use the H5Pset_alloc_time function with H5D_ALLOC_TIME_EARLY to set up the - dataset creation property list to avoid the problem. EIP - 2005/09/09 - -* A dataset created or rewritten with the v1.6.3 library or after can't - be read with the v1.6.2 library or before when Fletcher32 EDC (a 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 wasn't 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 is no - longer the same as before on little-endian system. HDF5 library releases - after 1.6.4 can still read datasets created or rewritten with an HDF5 - library of v1.6.2 or before. SLU - 2005/7/8 - -* For version 6 (6.02 and 6.04) of the Portland Group compiler on AMD Opteron - processor, there's 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. - -* test/big fails sometimes with the message "Possible overlap with another - region." The test selects regions randomly, and this error occurs when - two regions overlap each other; it is a bug in the test and not in - HDF5. Since the error is triggered by a random situation, it will - usually disappear if the test is re-run. - -* Newer SGI MIPSpro compilers (version 7.4.x) support C99 features but - have a "guard" statement in stdint.h that will #error and skip the rest - of the header file if the C99 option is not used explicitly. Hardsetting - $CC to c99 will resolve the problem. AKC - 2004/12/13 - -* 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 also fail with messages like "The socket name is already - in use". HDF5 does not use sockets. This is due to problems of the - poe command trying to set up the debug socket. Check 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. Ask your system - administrator to clean them out. Lastly, request IBM to provide a means - to run poe without the debug socket. - -* The h5dump tests may fail to match the expected output on some platforms - (e.g. parallel jobs, Windows) where the error messages directed to - "stderr" do not appear in the "right order" with output from stdout. - This is not an error. - -* The --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 the IBM SP2 platform for the serial mode. The parallel mode works fine - with this option. - - The --enable-static-exec configure flag also fails to correctly compile - on the HPUX 11.00. - - It is suggested that you don't use this option on these platforms - during configuration. - -* Use the --disable-shared configure flag if building with an Absoft Fortran - compiler. - -* Information about building with PGI and Intel compilers is available in - INSTALL file sections 5.7 and 5.8. - -* In LANL QSC, the new cc compiler has problems converting small values of - long long (absolute values less than 1**-308) to double. This triggers - the test/dtypes to report failure in the following test: - Testing random sw long double -> double conversions - If -ieee is used, the converted doubles spread over the range 0.0 to - 10**-308. If -ieee is not used, the converted double values are mostly - 0.0, but occasionally appear as 10**-308. This has been reported to the - system staff. - - All other tests have passed. - -* On at least one system, SDSC DataStar, the scheduler (in this case - LoadLeveler) sends job status updates to standard error when you run - any executable that was compiled with the parallel compilers. - - This causes problems when running "make check" on parallel builds, as - many of the tool tests function by saving the output from test runs, - and comparing it to an exemplar. - - The best solution is to reconfigure the target system so it no longer - inserts the extra text. However, this may not be practical. - - In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to - the configure and build. This will cause "make check" to continue after - detecting errors in the tool tests. However, in the case of SDSC DataStar, - it also leaves you with some 150 "failed" tests to examine by hand. - - A second solution is to write a script to run serial tests and filter - out the text added by the scheduler. A sample script used on SDSC - DataStar is given below, but you will probably have to customize it - for your installation. - - Observe that the basic idea is to insert the script as the first item - on the command line which executes the test. The script then - executes the test and filters out the offending text before passing - it on. - - #!/bin/csh - - set STDOUT_FILE=~/bin/serial_filter.stdout - set STDERR_FILE=~/bin/serial_filter.stderr - - rm -f $STDOUT_FILE $STDERR_FILE - - ($* > $STDOUT_FILE) >& $STDERR_FILE - - set RETURN_VALUE=$status - - cat $STDOUT_FILE - - tail +3 $STDERR_FILE - - exit $RETURN_VALUE - - You get the HDF5 make files and test scripts to execute your filter script - by setting the environment variable "RUNSERIAL" to the full path of the - script prior to running configure for parallel builds. Remember to - "unsetenv RUNSERIAL" before running configure for a serial build. - - Note that the RUNSERIAL environment variable exists so that we can - 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. JM - 2004/9/15 - -%%%%1.6.6%%%% Release Information for hdf5-1.6.6 (16/August/08) - -HDF5 version 1.6.6 released on Thu Aug 16 11:17:10 CDT 2007 -================================================================================ - -INTRODUCTION -============ -This document describes the differences between HDF5-1.6.5 and -HDF5-1.6.6 It contains information on the platforms tested and -known problems in HDF5-1.6.6. For more details, check the HISTORY.txt -file in the HDF5 source. - -HDF5 documentation can be found in the distributed release source -code in the subdirectory doc/html/ or on the THG (The HDF Group) -ftp server (ftp.hdfgroup.org) in the directory: - - /HDF5/docs/ - -Documentation for the current release is also on the HDF web site: - - http://hdfgroup.org/HDF5/doc/ - -For more information, see the HDF5 home page at: - - http://hdfgroup.org/HDF5/ - -If you have any questions or comments, please send them to: - - help@hdfgroup.org - - -CONTENTS -======== -- New Features -- Support for New Platforms, Languages and Compilers -- Bug Fixes since HDF5-1.6.5 -- Documentation -- Platforms Tested -- Supported Configuration Features Summary -- Known Problems - - -New Features -============ - Configuration: - ------------------------- - - HDF5 now uses autoconf 2.61 to generate configure. MAM - 2007/7/25. - - Source code distribution - ======================== - Library: - -------- - - None - - Parallel Library: - ----------------- - - None - - Tools: - ------ - - h52gif and gif2h5: Both these tools were revised to include High - Level Image API support. Tests were added to /hl/tools/gif2h5. - PVN - 2007/04/13 - - h5dump: Added support for double long type H5T_NATIVE_LDOUBLE. - PVN - 2007/03/13 - - h5dump: Added support for binary output; see usage. PVN 2007/03/13 - - h5repack: Added support for reading and writing by hyperslabs for - large files. PVN - 2007/03/01 - - h5repack: A new option allows the copy to use the source file type - (default) instead of the previous conversion to native type. - PVN - 2007/03/01 - - h5repack: Added output of the percentage of compression achieved. - PVN - 2007/03/01 - - h5diff: Added support for comparing dataset regions. PVN - - 2007/02/20 - - h5diff: Added support for reading and comparing by hyperslabs for - large files. PVN - 2007/02/20 - - h5diff: Added printing of dataset dimensions along with dataset - name. - PVN - 2007/02/19 - - F90 API: - -------- - - None - - C++ API: - -------- - - Added support for Szip: DSetCreatPropList::setSzip - BMR 2007/01/24 - - -Support for New Platforms, Languages and Compilers -================================================== - - Added support for MAC Intel (Darwin 8.8.2) (gcc 4.0.1 and g95 0.91) - EIP - 2007/02/13 - - Added support for GNU C compiler version 4.2.1 for FreeBSD 6.2 - (32- and 64-bit) - - -Bug Fixes since HDF5-1.6.5 Release -================================== - - Library - ------- - - Fixed several bugs with writing fill values for datasets that have - a variable-length datatype or component datatype. QAK - -2007/06/19 - - STDIO driver didn't support files bigger than 2GB because the OFFSET - parameter of fseek is of type LONG INT, not big enough for big - files. Use fseeko instead for big files if it's available on the - system. SLU - 2007/4/5 - - Relaxed restrictions on attribute operations to allow a file ID to - be used as the "location ID". If a file ID is used, the attribute - operation will occur on the root group of the file. - QAK - 2007/02/09 - - Fixed a bug in H5Sselect_valid() that caused an incorrect value to - be returned (0) instead of FAIL on error conditions such as the - selection or extent not being defined. CMC - 2007/01/05 - - Fixed potential file corruption bug which could overwrite a portion - of an object's header when an attribute was renamed. If the new - name for the attribute was longer than the old name, it was -possible - that the attribute would grow enough to overwrite another message - in the object's header. QAK - 2007/01/02 - - Fixed file corruption bug which could write an incorrect number of - messages to an object's header under certain circumstances. - Generally, the sequence of actions to generate this bug looks - like this: - - Create an object. - - Close the file. - - Re-open the file. - - Add 2 (or more) attributes to the object. - - Close the file. - - Re-open the file. - - Delete one of the attributes on the object. - - Add a smaller attribute to the object. - - Delete the smaller atttribute on the object. - - Add a larger attribute on the object. - - After this, the number of header messages stored for the object - will be off by one. Other sequences of modifying attributes on an - object could also trigger this bug. If you are opening an - object and the bottom few messages of the HDF5 error stack - resembles the following, the object has been affected by this bug: - - #007: ../../hdf5_v1.6/src/H5C.c line 3887 in H5C_load_entry(): -unable to load entry - major(08): Meta data cache layer - minor(40): Unable to load metadata into cache - #008: ../../hdf5_v1.6/src/H5Ocache.c line 332 in H5O_load(): -corrupt object header - too few messages - major(12): Object header layer - minor(40): Unable to load metadata into cache - - Specifically, "corrupt object header" is the best string to search - for in the HDF5 error stack output. - - If your files have been affected by this bug, or you are concerned - that your files might have been, please contact the HDF Helpdesk - at help@hdfgroup.org for a tool to detect and repair files - affected by this problem. QAK - 2006/6/16 - - - Fixed various problems with retrieving names of objects, especially - with mounted files. QAK - 2005/12/25 - - Configuration - ------------- - - Changed to default to --disable-shared if parallel is enabled. - AKC - 2007/5/12 - - Corrected a coding error in configure when it tries to locate the - needed MPI and MPI-IO library for the fortran interface. - AKC - 007/5/9. - - Changed default fortran compiler to g95 when gcc is used. - AKC - 007/2/17. - - Configure can now use any tr command. No more need for - defining the variable TR, nor is it supported. AKC - 2006/05/20 - - Performance - ------------- - - None - - Tools - ----- - - Fixed a bug in h5dump regarding the display of named datatypes - attributes. PVN - 2007/03/13 - - Fixed a bug in h5dump regarding the display of group comments. - PVN - 2007/03/13 - - Fixed a bug in h5dump regarding the display of hardlinks pointing - to the root group. PVN - 2007/03/13 - - Fixed a bug in the h5diff percentage option -p. PVN - 2007/03/05 - - Fixed a bug in h5dump that caused array indices greater than 2^32-1 - not to be printed correctly. PVN - 2007/2/19 - - Documentation - ------------- - - Corrected errors and extended the descriptions in Reference Manual - entries for several functions. - - F90 API - ------- - - None - - C++ API - ------- - - Changed - StrType::StrType(const size_t& size); - to - StrType::StrType(const int dummy, const size_t& size); - because the first one clashed with - StrType::StrType(const hid_t existing_id); - BMR 2007/05/03 - - Wrappers of H5Rcreate had incorrect prototypes. Added these - overloaded functions: - IdComponent::reference(void* ref, const char* name, -DataSpace& - dataspace, H5R_type_t ref_type = H5R_DATASET_REGION) - IdComponent::void reference(void* ref, const char* name) - IdComponent::reference(void* ref, const H5std_string& name) - and will remove these incorrect member functions: - DataSet::Reference - DataType::Reference - Group::Reference - H5File::Reference - - Added wrappers for H5Rdereference as constructors: - DataSet(IdComponent& obj, void* ref); - Group(IdComponent& obj, void* ref); - DataType(IdComponent& obj, void* ref); - - -Documentation -============= - - HDF5 documentation can be found in the distributed release source - code in the subdirectory doc/html/ (start with index.html) or on the - THG (The HDF Group) ftp server (ftp.hdfgroup.org) in the directory: - - /HDF5/docs/ - - Online documentation for the current release can be found on the THG - web site: - - http://hdfgroup.org/HDF5/doc/ - - -Platforms Tested -================ - - AIX 5.2 (32/64 bit) xlc 6.0.0.8 - (datastar) xlC 6.0.0.9 - xlf 8.1.1.7 - mpcc_r 6.0.0.8 - mpxlf_r 8.1.1.7 - - AIX 5.3 (32/64 bit) xlc 7.0.0.0 - (copper) xlC 7.0. - xlf 9.1.0.3 - - FreeBSD 6.2 (32- and 64-bit) gcc and g++3.4.6 - (duty and liberty) gcc and g++ 4.2.1 - - HP-UX B.11.23 HP aC++/ANSI C B3910B A.06.02 - (sirius) HP F90 v3.1 (32-bit only) - HP aC++/ANSI C B3910B A.06.02 - - IRIX64 6.5 MIPSpro cc 7.4.4m - (ucar mop1 64 & n32) F90 MIPSpro 7.4.4m (64 only) - C++ MIPSpro cc 7.4.4m - - Linux 2.4.21-47.ELsmp #1 SMP gcc 3.2.3 - i686 i386 GNU/Linux - (osage) - - Linux 2.6.9-42.0.10.ELsmp #1 gcc (GCC) 3.4.6 - SMP i686 i386 G95 (GCC 4.0.3 (g95 0.91!) Nov 21 2006) - (kagiso) PGI C, Fortran, C++ 6.2-5 32-bit - icc (ICC) 9.1 - Intel(R) C++ Compiler for 32-bit - applications, Version 9.1 - Intel(R) Fortran Compiler for 32-bit - applications, Version 9.1 - Absoft 32-bit Fortran 95 10.0.4 - MPICH mpich2-1.0.4p1 compiled with - gcc 3.4.6 and G95 (GCC 4.0.3 (g95 0.91!) - - Linux 2.6.16.46-0.12-debug #1 - SMP ia64 GNU/Linux Intel(R) C++ Version 10.0.025 - (ucar hir1) Intel(R) Fortran Itanium(R) Version 10.0.025 - - Linux 2.6.16.46-0.14-smp #1 Intel(R) C++ for Intel(R) EM64T Ver. 9.1.037 - SMP x86_64 GNU/Linux Intel(R) Fortran Intel(R) EM64T Ver. 9.1.031 - (smirom) PGI C, Fortran, C++ Version 6.2-5 - for 64-bit target on x86-64 - tested for both 32- and 64-bit binaries - - Linux 2.6.5-7.283-rtgfx Altix - SMP ia64 Intel(R) C++ Version 9.0 - (cobalt) Intel(R) Fortran Itanium(R) Version 9.0 - SGI MPI - - OSF1 V5.1 (QSC) Compaq C V6.5-011 - (See "Known Problems.") HP Fortran V5.5A-3548 - Compaq C++ V6.5-036 - MPIX200_64_r13.4 - - SunOS 5.8 32- and 64-bit Sun WorkShop 6 update 2 C 5.3 - (sol) Sun WorkShop 6 update 2 Fortran 95 6.2 - Sun WorkShop 6 update 2 C++ 5.3 - - 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 2.4.21-32.0.1.ELsmp-perfctr-lustre - (tungsten) Intel(R) C++ Version 9.0 - Intel(R) Fortran Compiler Version 9.0 - PGI C Version 6.0 - PGI C++ Version 6.0 - PGI Fortran Version 6.0 - gcc (GCC) 3.2.2 (Red Hat Linux 3.2.2-5) - - Xeon Linux 2.6.9-42.0.10.EL_lustre-1.4.10.1smp - (abe) Intel(R) C++ Version 10.0 - Intel(R) Fortran Compiler Version 10.0 - Open MPI 1.2.2 - - IA-64 Linux 2.4.21.SuSE_292.til1 - ia64 gcc (GCC) 3.2.2 - (NCSA tg-login) Intel(R) C++ Version 8.0 - Intel(R) Fortran Compiler Version 8.0 - mpich-gm-1.2.5..10-intel-r2 - - Windows XP Visual Studio 6.0 - Visual Studio .NET (with Intel Fortran 9.0) - Visual Studio 2005 (with Intel Fortran 9.0) - cygwin (gcc 3.4.4) - - MAC OS X Intel Darwin 8.10.1 - i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 - g95 0.91 - - -Supported Configuration Features Summary -======================================== - -Key: y = Tested and supported - n = Not supported or not tested in this release - C = Cluster - W = Workstation - ( ) = Footnote appears below second table - -Platform C F90 F90 C++ zlib SZIP - parallel parallel -Solaris2.8 32- and 64-bit n y n y y y -Solaris2.10 32- and 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 n n y y -HPUX11.23-32bit n y n y y y -HPUX11.23-64bit n n n y y y -WinXP Visual Studio 6.0 n n n y y y -WinXP CYGWIN n n n y y y -WinXP 2005 n y n y y y -WinXP .Net n y n y y y -Mac OS X 10.4.10 n y n y y y -AIX-5.2 & 5.3 32- and 64-bit y y y y y y -FreeBSD 6.2 32- and 64-bit n n n y y y -RedHat Linux 2.4.21 W n n n y y y -SuSE Linux 2.6.9-42 i686 GNU (1) W y y y y y y -SuSE Linux 2.6.9-42 i686 Intel W n y n y y y -SuSE Linux 2.6.9-42 i686 PGI W n y n y y y -SuSE Linux 2.6.16 x86_64 GNU (1) W y y y y y y -SuSE Linux 2.6.16 x86_64 Intel W n y n y y y -SuSE Linux 2.6.16 x86_64 PGI W n y n y y y -RHEL 4 Linux 2.6.9 Xeon Lustre C y y y y y y -RedHat Linux 2.4 Xeon Lustre C n y n y y y -SuSE Linux 2.4 ia64 C y y y y y y -SuSe Linux 2.6.16 SGI Altix ia64 n y n y y y -SuSe Linux 2.6.5 SGI Altix ia64 n y n y y y -OSF1 v5.1 y y y y y n - - -Platform Shared static- Thread- STREAM- - libraries(4) exec safe VFD -Solaris2.8 32- and 64-bit y n y y -Solaris2.10 32- and 64-bit y n y y -IRIX64_6.5 32-bit y n y y -IRIX64_6.5 64-bit y n y y -HPUX11.23-32bit y (3) n n y -HPUX11.23-64bit y (3) n n y -WinXP Visual Studio 6.0 y n n n -WinXP CYGWIN y n n n -WinXP 2005 y n n n -WinXP .Net y n n n -Mac OS X 10.4.10 y n n y -AIX-5.2 & 5.3 32- and 64-bit n n n y -FreeBSD 6.2 32- and 64-bit y n n y -RedHat Linux 2.4.21 W y n n y -SuSE Linux 2.6.9-42 i686 GNU (1) W y n y y -SuSE Linux 2.6.9-42 i686 Intel W y n n y -SuSE Linux 2.6.9-42 i686 PGI W n n n y -SuSE Linux 2.6.16 x86_64 GNU (1) W y n n y -SuSE Linux 2.6.16 x86_64 Intel W y n n y -SuSE Linux 2.6.16 x86_64 PGI W n n n y -RHEL 4 Linux 2.6.9 Xeon Lustre C y n n y -RedHat Linux 2.4 Xeon Lustre C y n n y -SuSE Linux 2.4 ia64 C y n n y -SuSe Linux 2.6.16 SGI Altix ia64 n n n y -SuSe Linux 2.6.5 SGI Altix ia64 n n n y -OSF1 v5.1 n n n y - -Compiler versions for each platform are listed in the "Platforms Tested" -table found elsewhere in this file (RELEASE.txt). Unless otherwise noted, -compilers used are the system compilers. - -Footnotes: -(1) Fortran compiled with g95. -(2) In most cases, shared libraries are provided only for the C library, - except on Windows where they are provided for C, C++, and Fortran. -(3) C++ works only with static libraries. - - -Known Problems -============== -* QSC (an HP alpha-based OSF1 cluster) does not create h5pfc correctly. It - does not include the -lmpi properly. This will be fixed in the next - release. AKC - 2007/08/07. - -* On IRIX64 6.5 (UCAR SGI mop1), when testing HDF5 tools with an HDF5 shared - library, especially for h5repacktst and h52gifgentst, the following (or - similar) error message may appear: - "523648:lt-h5repacktst: rld: Fatal Error: Cannot Successfully map soname - 'libh5test.so.1' under any of the filenames .......(bunch of directories) - " - And the testing will fail. - We believe this is a libtool problem. One way to get rid of this is to - add the paths of libh5test.so.1 and libh5.so.1 to the shared library path. - - For 32-bit: - You may do this, under csh: - setenv LD_LIBRARYN32_PATH .......(existing pathes):[full path of HDF5 - directory/test/.libs]:[full path of HDF5 directory/src/.libs] - - For 64-bit: - setenv LD_LIBRARY64_PATH ......(existing pathes):[full path of HDF5 - directory/test/.libs]:[full path of HDF5 directory/src/.libs] - - NOTE: This problem ONLY affects the testing of the HDF5 library when you - build from source. It won't affect any applications that would like to link - with the HDF5 shared library since the shared library path needs to be set - anyway. KY - 2007/8/2 - -* QSC (an HP alpha-based OSF1 cluster) failed the testpar/testphdf5 sub-test - "calloc". All other tests passed. This indicates that a dataset using - chunked storage created by serial HDF5 may not work properly with parallel - HDF5. The calloc test can be skipped by running "prun ... testphdf5 -x - calloc". AKC - 2007/7/12. - -* The Intel C Compiler for the Linux x86_64 platform (EM64T-based, v8.1) has - an optimization error in the datax types conversion code. Before running - configure, edit the file config/intel-flags by changing the setting of - PROD_CFLAGS from -O3 to -O0. Then run configure. AKC - 2005/11/10. - -* When testing parallel HDF5 with the C compiler version MIPSpro 7.4.3 on IRIX - 6.5, set the environment variable MPI_TYPE_MAX to be a bigger number, for - example 120000, in order to pass the complicated collective IO tests inside - the parallel HDF5 library. This is not a problem inside the parallel HDF5 - library. You can always set a bigger number on your system. KY - 2005/10/6 - -* A contiguous or chunked dataset created by a sequential version of HDF5 - might not be able to be modified with a parallel version of the library. - Use the H5Pset_alloc_time function with H5D_ALLOC_TIME_EARLY to set up the - dataset creation property list to avoid the problem. EIP - 2005/09/09 - -* The dataset created or rewritten with the v1.6.3 library or after can't - be read with the v1.6.2 library or before when Fletcher32 EDC (a 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 wasn't 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 is no - longer the same as before on little-endian system. The library release - after 1.6.4 can still read the dataset created or rewritten with the library - of v1.6.2 or before. SLU - 2005/7/8 - -* For version 6 (6.02 and 6.04) of the Portland Group compiler on AMD Opteron - processor, there's 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. - -* test/big fails sometimes with the message "Possible overlap with another - region." The test selects regions randomly, and this error occurs when - two regions overlap each other; it is a bug in the test and not in - HDF5. Since the error is triggered by a random situation, it will - usually disappear if the test is re-run. - -* Newer SGI MIPSpro compilers (version 7.4.x) support C99 features but - have a "guard" statement in stdint.h that will #error and skip the rest - of the header file if the C99 option is not used explicitly. Hardsetting - $CC to c99 will resolve the problem. AKC - 2004/12/13 - -* 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 also fail with messages like "The socket name is already - in use". HDF5 does not use sockets (except for stream-VFD). This is - due to problems of the poe command trying to set up the debug socket. - Check 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. - Ask your system administrator to clean them out. Lastly, request IBM - to provide a means to run poe without the debug socket. - -* The h5dump tests may fail to match the expected output on some platforms - (e.g. parallel jobs, Windows) where the error messages directed to - "stderr" do not appear in the "right order" with output from stdout. - This is not an error. - -* The stream-vfd test uses ip port 10007 for testing. If another - application is already using that port address, the test will hang - indefinitely and has to be terminated by the kill command. To try the - test again, change the port address in test/stream_test.c to one not - being used in the host. - -* The --enable-static-exec configure flag fails to compile for Solaris - platforms. This is due to the fact that not all of the system - libraries on Solaris are available in a static format. - - The --enable-static-exec configure flag also fails to correctly compile - on the IBM SP2 platform for the serial mode. The parallel mode works fine - with this option. - - The --enable-static-exec configure flag also fails to correctly compile - on the HPUX 11.00. - - It is suggested that you don't use this option on these platforms - during configuration. - -* The Stream VFD is not supported under Windows. - -* Use the --disable-shared configure flag if building with Absoft Fortran - compiler. - -* Information about building with PGI and Intel compilers is available in - INSTALL file sections 5.7 and 5.8. - -* In LANL QSC, the new cc compiler has problems converting small values of - long long (absolute values less than 1**-308) to double. This triggers - the test/dtypes to report failure in the following test: - Testing random sw long double -> double conversions - If -ieee is used, the converted doubles spread over the range 0.0 to - 10**-308. If -ieee is not used, the converted double values are mostly - 0.0, but occasionally appear as 10**-308. This has been reported to the - system staff. - - All other tests have passed. - -* On at least one system, SDSC DataStar, the scheduler (in this case - LoadLeveler) sends job status updates to standard error when you run - any executable that was compiled with the parallel compilers. - - This causes problems when running "make check" on parallel builds, as - many of the tool tests function by saving the output from test runs, - and comparing it to an exemplar. - - The best solution is to reconfigure the target system so it no longer - inserts the extra text. However, this may not be practical. - - In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to - the configure and build. This will cause "make check" to continue after - detecting errors in the tool tests. However, in the case of SDSC DataStar, - it also leaves you with some 150 "failed" tests to examine by hand. - - A second solution is to write a script to run serial tests and filter - out the text added by the scheduler. A sample script used on SDSC - DataStar is given below, but you will probably have to customize it - for your installation. - - Observe that the basic idea is to insert the script as the first item - on the command line which executes the test. The script then - executes the test and filters out the offending text before passing - it on. - - #!/bin/csh - - set STDOUT_FILE=~/bin/serial_filter.stdout - set STDERR_FILE=~/bin/serial_filter.stderr - - rm -f $STDOUT_FILE $STDERR_FILE - - ($* > $STDOUT_FILE) >& $STDERR_FILE - - set RETURN_VALUE=$status - - cat $STDOUT_FILE - - tail +3 $STDERR_FILE - - exit $RETURN_VALUE - - You get the HDF5 make files and test scripts to execute your filter script - by setting the environment variable "RUNSERIAL" to the full path of the - script prior to running configure for parallel builds. Remember to - "unsetenv RUNSERIAL" before running configure for a serial build. - - Note that the RUNSERIAL environment variable exists so that we can - 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. JM - 2004/9/15 - - %%%%1.6.5%%%% Release Information for hdf5-1.6.5 (10/November/05) diff --git a/release_docs/INSTALL b/release_docs/INSTALL index 4a9a567..1444bf2 100644 --- a/release_docs/INSTALL +++ b/release_docs/INSTALL @@ -1,733 +1,674 @@ -Instructions for the Installation of HDF5 Software -================================================== - -This file provides instructions for installing the HDF5 software. -If you have any problems with the installation, please see The HDF Group's -support page at the following location: - - http://www.hdfgroup.org/services/support.html - -CONTENTS --------- - 1. Obtaining HDF5 - - 2. Quick installation - 2.1. Windows - 2.2. RedStorm (Cray XT3) - - 3. HDF5 dependencies - 3.1. Zlib - 3.2 Szip (optional) - 3.3. MPI and MPI-IO - - 4. Full installation instructions for source distributions - 4.1. Unpacking the distribution - 4.1.1. Non-compressed tar archive (*.tar) - 4.1.2. Compressed tar archive (*.tar.Z) - 4.1.3. Gzip'd tar archive (*.tar.gz) - 4.1.4. Bzip'd tar archive (*.tar.bz2) - 4.2. Source versus build directories - 4.3. Configuring - 4.3.1. Specifying the installation directories - 4.3.2. Using an alternate C compiler - 4.3.3. Configuring for 64-bit support - 4.3.4. Additional compilation flags - 4.3.5. Compiling HDF5 wrapper libraries - 4.3.6. Specifying other programs - 4.3.7. Specifying other libraries and headers - 4.3.8. Static versus shared linking - 4.3.9. Optimization versus symbolic debugging - 4.3.10. Parallel versus serial library - 4.3.11. Threadsafe capability - 4.3.12. Backward compatibility - 4.4. Building - 4.5. Testing - 4.6. Installing HDF5 - - 5. Using the Library - - 6. Support - - A. Warnings about compilers - A.1. GNU (Intel platforms) - A.2. DEC - A.3. SGI (Irix64 6.2) - A.4. Windows/NT - - B. Large (>2GB) versus small (<2GB) file capability - - C. Building and testing with other compilers - C.1. Building and testing with Intel compilers - C.2. Building and testing with PGI compilers + Instructions for the Installation of HDF5 Software + ================================================== + +WARNING: This file was not updated for the 1.8.0-beta* releases. If you have any problems with the HDF5 + installation please contact help@hdfgroup.org + + CONTENTS + -------- + 1. Obtaining HDF5 + + 2. Warnings about compilers + 2.1. GNU (Intel platforms) + 2.2. DEC + 2.3. SGI (Irix64 6.2) + 2.4. Windows/NT + + 3. Quick installation + 3.1. Windows + 3.2. RedStorm (Cray XT3) + + 4. HDF5 dependencies + 4.1. Zlib + 4.2 Szip + 4.3. MPI and MPI-IO + + 5. Full installation instructions for source distributions + 5.1. Unpacking the distribution + 5.1.1. Non-compressed tar archive (*.tar) + 5.1.2. Compressed tar archive (*.tar.Z) + 5.1.3. Gzip'd tar archive (*.tar.gz) + 5.1.4. Bzip'd tar archive (*.tar.bz2) + 5.2. Source vs. Build Directories + 5.3. Configuring + 5.3.1. Specifying the installation directories + 5.3.2. Using an alternate C compiler + 5.3.3. Configuring for 64-bit support + 5.3.4. Additional compilation flags + 5.3.5. Compiling HDF5 wrapper libraries + 5.3.6. Specifying other programs + 5.3.7. Specifying other libraries and headers + 5.3.8. Static versus shared linking + 5.3.9. Optimization versus symbolic debugging + 5.3.10. Large (>2GB) vs. small (<2GB) file capability + 5.3.11. Parallel vs. serial library + 5.3.12. Threadsafe capability + 5.3.13. Backward compatibility + 5.3.14. Network stream capability + 5.4. Building + 5.5. Testing + 5.6. Installing + 5.7 Building and testing with Intel compilers + 5.8 Building and testing with PGI compilers + + 6. Using the Library + + 7. Support ***************************************************************************** 1. Obtaining HDF5 - The latest supported public release of HDF5 is available from - ftp://ftp.hdfgroup.org/HDF5/current/src. For Unix and UNIX-like - platforms, it is available in tar format compressed with gzip. - For Microsoft Windows, it is in ZIP format. - - The HDF team also makes snapshots of the source code available on - a regular basis. These snapshots are unsupported (that is, the - HDF team will not release a bug-fix on a particular snapshot; - rather any bug fixes will be rolled into the next snapshot). - Furthermore, the snapshots have only been tested on a few - machines and may not test correctly for parallel applications. - Snapshots, in a limited number of formats, can be found on THG's - development FTP server: - - ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/snapshots - - -2. Quick installation - For those who don't like to read ;-) the following steps can be used - to configure, build, test, and install the HDF5 Library, header files, - and support programs. For example, to install HDF5 version X.Y.Z at - location /usr/local/hdf5, use the following steps. - - $ gunzip < hdf5-X.Y.Z.tar.gz | tar xf - - $ cd hdf5-X.Y.Z - $ ./configure --prefix=/usr/local/hdf5 <more configure_flags> - $ make - $ make check # run test suite. - $ make install - $ make check-install # verify installation. - - Some versions of the tar command support the -z option. In such cases, - the first step above can be simplified to the following: - - $ tar zxf hdf5-X.Y.Z.tar.gz - - <configure_flags> above refers to the configure flags appropriate - to your installation. For example, to install HDF5 with the - Fortran and C++ interfaces and with SZIP compression, the - configure line might read as follows: - - $ ./configure --prefix=/usr/local/hdf5 --enable-fortran \ - --enable-cxx --with-szlib=PATH_TO_SZIP - - In this case, PATH_TO_SZIP would be replaced with the path to the - installed location of the SZIP library. - -2.1. Windows - Users of Microsoft Windows should see the INSTALL_Windows files for - detailed instructions. - -2.2. RedStorm (Cray XT3) - Users of the Red Storm machine, after reading this file, should read - the Red Storm section in the INSTALL_parallel file for specific - instructions for the Red Storm machine. The same instructions would - probably work for other Cray XT3 systems, but they have not been - verified. - - -3. HDF5 dependencies -3.1. Zlib - The HDF5 Library includes a predefined compression filter that - uses the "deflate" method for chunked datasets. If zlib-1.1.2 or - later is found, HDF5 will use it. Otherwise, HDF5's predefined - compression method will degenerate to a no-op; the compression - filter will succeed but the data will not be compressed. - -3.2. Szip (optional) - The HDF5 Library includes a predefined compression filter that - uses the extended-Rice lossless compression algorithm for chunked - datasets. For more information about Szip compression and license - terms, see http://hdfgroup.org/doc_resource/SZIP/. - - Precompiled Szip binaries for each supported platform and a source - tar file can be found at ftp://ftp.hdfgroup.org/lib-external/szip/. - - To configure the HDF5 Library with the Szip compression filter, use - the '--enable-szlib=/PATH_TO_SZIP' flag. For more information, see - section 4.3.7, "Specifying other libraries and headers." - - Starting with release 1.6.3, Szip library binaries are distributed - with the encoder enabled (a license may be required to use this binary) - and with the encoder disabled (freely usable without a license). - If the encoder enabled binary is used, Szip compression encoding is - available for an HDF5 application; if the encoder disabled binary is - used, Szip compression is not available. Szip decoding is always - available for applications (i.e., an HDF5 application can always read - Szip-compressed data) if the Szip filter is present, regardless of the - binary used. - -3.3. MPI and MPI-IO - The parallel version of the library is built upon the foundation - provided by MPI and MPI-IO. If these libraries are not available - when HDF5 is configured, only a serial version of HDF5 can be built. - - -4. Full installation instructions for source distributions - -4.1. Unpacking the distribution - The HDF5 source code is distributed in a variety of formats which - can be unpacked with the following commands, each of which creates an - 'hdf5-X.Y.Z' directory, where X.Y.Z is the HDF5 version numbers. - -4.1.1. Non-compressed tar archive (*.tar) - - $ tar xf hdf5-X.Y.Z.tar - -4.1.2. Compressed tar archive (*.tar.Z) - - $ uncompress -c < hdf5-X.Y.Z.tar.Z | tar xf - - Or - $ tar Zxf hdf5-X.Y.Z.tar.Z - -4.1.3. Gzip'd tar archive (*.tar.gz) - - $ gunzip < hdf5-X.Y.Z.tar.gz | tar xf - - Or - $ tar zxf hdf5-X.Y.Z.tar.gz - -4.1.4. Bzip'd tar archive (*.tar.bz2) - - $ bunzip2 < hdf5-X.Y.Z.tar.bz2 | tar xf - - Or - $ tar jxf hdf5-X.Y.Z.tar.bz2 - -4.2. Source versus build directories - On most systems the build can occur in a directory other than the - source directory, allowing multiple concurrent builds and/or - read-only source code. In order to accomplish this, one should - create a build directory, cd into that directory, and run the - `configure' script found in the source directory (configure - details are below). For example, - $ mkdir built-fortran - $ cd build-fortran - $ ../hdf5-X.Y.Z/configure --enable-fortran ... - - Unfortunately, this does not work on recent Irix platforms (6.5? - and later) because that `make' does not understand the VPATH variable. - However, HDF5 also supports Irix `pmake' which has a .PATH target - which serves a similar purpose. Here's what the Irix man pages say - about VPATH, the facility used by HDF5 makefiles for this feature: - - The VPATH facility is a derivation of the undocumented - VPATH feature in the System V Release 3 version of make. - System V Release 4 has a new VPATH implementation, much - like the pmake(1) .PATH feature. This new feature is also - undocumented in the standard System V Release 4 manual - pages. For this reason it is not available in the IRIX - version of make. The VPATH facility should not be used - with the new parallel make option. - -4.3. Configuring - HDF5 uses the GNU autoconf system for configuration, which - detects various features of the host system and creates the - Makefiles. On most systems it should be sufficient to say: - - $ ./configure - Or - $ sh configure - - The configuration process can be controlled through environment - variables, command-line switches, and host configuration files. - For a complete list of switches type: - - $ ./configure --help - - The host configuration files are located in the `config' - directory and are based on architecture name, vendor name, and/or - operating system which are displayed near the beginning of the - `configure' output. The host config file influences the behavior - of configure by setting or augmenting shell variables. - -4.3.1. Specifying the installation directories - The default installation location is the HDF5 directory created in - the build directory. Typing `make install' will install the HDF5 - Library, header files, examples, and support programs in hdf5/lib, - hdf5/include, hdf5/doc/hdf5/examples, and hdf5/bin. To use a path - other than hdf5, specify the path with the `--prefix=PATH' switch: - - $ ./configure --prefix=/usr/local - - If shared libraries are being built (the default), the final - home of the shared library must be specified with this switch - before the library and executables are built. - - HDF5 can be installed into a different location than the prefix - specified at configure time; see section 4.6, "Installing HDF5," - for more details. - -4.3.2. Using an alternate C compiler - By default, configure will look for the C compiler by trying - `gcc' and `cc'. However, if the environment variable "CC" is set - then its value is used as the C compiler. For instance, one would - use the following line to specify the native C compiler on a system - that also has the GNU gcc compiler (users of csh and derivatives - will need to prefix the commands below with `env'): - - $ CC=cc ./configure - - A parallel version of HDF5 can be built by specifying `mpicc' - as the C compiler. (The `--enable-parallel' flag documented - below is optional in this case.) Using the `mpicc' compiler - will insure that the correct MPI and MPI-IO header files and - libraries are used. - - $ CC=/usr/local/mpi/bin/mpicc ./configure - -4.3.3. Configuring for 64-bit support - Several machine architectures support 32-bit or 64-bit binaries. - The options below describe how to enable support for different options. - - On Irix64, the default compiler is `cc'. To use an alternate compiler, - specify it with the CC variable: - - $ CC='cc -n32' ./configure - - Similarly, users compiling on a Solaris machine and desiring to - build the distribution with 64-bit support should specify the - correct flags with the CC variable: - - $ CC='cc -xarch=v9' ./configure - - To configure AIX 64-bit support including the Fortran and C++ APIs, - (Note: need to set $AR to 'ar -X 64'.) - Serial: - $ CFLAGS=-q64 FFLAGS=-q64 CXXFLAGS=-q64 AR='ar -X 64'\ - ./configure --enable-fortran - Parallel: (C++ not supported with parallel) - $ CFLAGS=-q64 FFLAGS=-q64 AR='ar -X 64'\ - ./configure --enable-fortran - -4.3.4. Additional compilation flags - If addtional flags must be passed to the compilation commands, - specify those flags with the CFLAGS variable. For instance, - to enable symbolic debugging of a production version of HDF5, one - might say: - - $ CFLAGS=-g ./configure --enable-production - -4.3.5. Compiling HDF5 wrapper libraries - One can optionally build the Fortran and/or C++ interfaces to the - HDF5 C library. By default, both options are disabled. To build - them, specify `--enable-fortran' and `--enable-cxx', respectively. - - $ ./configure --enable-fortran - $ ./configure --enable-cxx - - Configuration will halt if a working Fortran 90 or 95 compiler or - C++ compiler is not found. Currently, the Fortran configure tests - for these compilers in order: f90, pgf90, f95. To use an - alternate compiler specify it with the FC variable: - - $ FC=/usr/local/bin/g95 ./configure --enable-fortran - - Note: The Fortran and C++ interfaces are not supported on all the - platforms the main HDF5 Library supports. Also, the Fortran - interface supports parallel HDF5 while the C++ interface does - not. - - Note: See sections 4.7 and 4.8 for building the Fortran library with - Intel or PGI compilers. - -4.3.6. Specifying other programs - The build system has been tuned for use with GNU make but also - works with other versions of make. If the `make' command runs a - non-GNU version but a GNU version is available under a different - name (perhaps `gmake'), then HDF5 can be configured to use it by - setting the MAKE variable. Note that whatever value is used for - MAKE must also be used as the make command when building the - library: - - $ MAKE=gmake ./configure - $ gmake - - The `AR' and `RANLIB' variables can also be set to the names of - the `ar' and `ranlib' (or `:') commands to override values - detected by configure. - - The HDF5 Library, include files, and utilities are installed - during `make install' (described below) with a BSD-compatible - install program detected automatically by configure. If none is - found, the shell script bin/install-sh is used. Configure does not - check that the install script actually works; if a bad install is - detected on your system (e.g., on the ASCI blue machine as of - March 2, 1999) you have two choices: - - 1. Copy the bin/install-sh program to your $HOME/bin - directory, name it `install', and make sure that $HOME/bin - is searched before the system bin directories. - - 2. Specify the full path name of the `install-sh' program - as the value of the INSTALL environment variable. Note: do - not use `cp' or some other program in place of install - because the HDF5 makefiles also use the install program to - change file ownership and/or access permissions. - -4.3.7. Specifying other libraries and headers - Configure searches the standard places (those places known by the - systems compiler) for include files and header files. However, - additional directories can be specified by using the CPPFLAGS - and/or LDFLAGS variables: - - $ CPPFLAGS=-I/home/robb/include \ + The latest supported public release of HDF5 is available from + ftp://hdf.ncsa.uiuc.edu/HDF5/current/src. For Unix platforms, it is + available in tar format compressed with gzip. For Microsoft Windows, + it is in ZIP format. + + The HDF team also makes snapshots of the source code available on + a regular basis. These snapshots are unsupported (that is, the + HDF team will not release a bug-fix on a particular snapshot; + rather any bug fixes will be rolled into the next snapshot). + Furthermore, the snapshots have only been tested on a few + machines and may not test correctly for parallel applications. + Snapshots can be found at + ftp://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/snapshots in a limited + number of formats. + + +2. Warnings about compilers + OUTPUT FROM THE FOLLOWING COMPILERS SHOULD BE EXTREMELY SUSPECT + WHEN USED TO COMPILE THE HDF5 LIBRARY, ESPECIALLY IF + OPTIMIZATIONS ARE ENABLED. IN ALL CASES, HDF5 ATTEMPTS TO WORK + AROUND THE COMPILER BUGS BUT THE HDF5 DEVELOPMENT TEAM MAKES NO + GUARANTEES THAT THERE ARE OTHER CODE GENERATION PROBLEMS. + +2.1. GNU (Intel platforms) + Versions before 2.8.1 have serious problems allocating registers + when functions contain operations on `long long' data types. + Supplying the `--disable-hsizet' switch to configure (documented + below) will prevent hdf5 from using `long long' data types in + situations that are known not to work, but it limits the hdf5 + address space to 2GB. + +2.2. COMPAQ/DEC + The V5.2-038 compiler (and possibly others) occasionally + generates incorrect code for memcpy() calls when optimizations + are enabled, resulting in unaligned access faults. HDF5 works + around the problem by casting the second argument to `char *'. + The fortran module (5.4.1a) fails in compiling some fortran + programs. Need to use 5.5.0 or more. + +2.3. SGI (Irix64 6.2) + The Mongoose 7.00 compiler has serious optimization bugs and + should be upgraded to MIPSpro 7.2.1.2m. Patches are available + from SGI. + +2.4. Windows/NT + The MicroSoft Win32 5.0 compiler is unable to cast unsigned long + long values to doubles. HDF5 works around this bug by first + casting to signed long long and then to double. + + A link warning: defaultlib "LIBC" conflicts with use of other libs + appears for debug version of VC++ 6.0. This warning will not affect + building and testing hdf5 libraries. + + +3. Quick installation + For those that don't like to read ;-) the following steps can be + used to configure, build, test, and install the HDF5 library, + header files, and support programs. + + $ gunzip < hdf5-1.6.0.tar.gz | tar xf - + $ cd hdf5-1.6.0 + $ make check + $ make install + +3.1. Windows + Users of Microsoft Windows should see the INSTALL_Windows for + detailed instructions. + +3.2. RedStorm (Cray Xt3) + Users of the Red Storm machine, after reading this file, should read + the Red Storm section in the INSTALL_parallel file for specific + instructions for the Red Storm machine. The same instructions would + probably work for other Cray XT3 systems but they have not been + verified. + + +4. HDF5 dependencies +4.1. Zlib + The HDF5 library has a predefined compression filter that uses + the "deflate" method for chunked datatsets. If zlib-1.1.2 or + later is found then HDF5 will use it, otherwise HDF5's predefined + compression method will degenerate to a no-op (the compression + filter will succeed but the data will not be compressed). + +4.2. Szip + The HDF5 library has a predefined compression filter that uses + the extended-Rice lossless compression algorithm for chunked + datatsets. For more information about Szip compression and license terms + see http://hdf.ncsa.uiuc.edu/HDF5/doc_resource/SZIP/index.html. + Precompiled szip binaries for each supported platform and source tar ball + file can be found at ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/ + +4.3. MPI and MPI-IO + The parallel version of the library is built upon the foundation + provided by MPI and MPI-IO. If these libraries are not available + when HDF5 is configured then only a serial version of HDF5 can be + built. + + +5. Full installation instructions for source distributions +5.1. Unpacking the distribution + The HDF5 source code is distributed in a variety of formats which + can be unpacked with the following commands, each of which + creates an `hdf5-1.6.0' directory. + +5.1.1. Non-compressed tar archive (*.tar) + + $ tar xf hdf5-1.6.0.tar + +5.1.2. Compressed tar archive (*.tar.Z) + + $ uncompress -c < hdf5-1.6.0.tar.Z | tar xf - + +5.1.3. Gzip'd tar archive (*.tar.gz) + + $ gunzip < hdf5-1.6.0.tar.gz | tar xf - + +5.1.4. Bzip'd tar archive (*.tar.bz2) + + $ bunzip2 < hdf5-1.6.0.tar.bz2 | tar xf - + +5.2. Source vs. Build Directories + On most systems the build can occur in a directory other than the + source directory, allowing multiple concurrent builds and/or + read-only source code. In order to accomplish this, one should + create a build directory, cd into that directory, and run the + `configure' script found in the source directory (configure + details are below). + + Unfortunately, this does not work on recent Irix platforms (6.5? + and later) because that `make' doesn't understand the VPATH + variable. However, hdf5 also supports Irix `pmake' which has a + .PATH target which serves a similar purpose. Here's what the man + pages say about VPATH, which is the facility used by HDF5 + makefiles for this feature: + + The VPATH facility is a derivation of the undocumented + VPATH feature in the System V Release 3 version of make. + System V Release 4 has a new VPATH implementation, much + like the pmake(1) .PATH feature. This new feature is also + undocumented in the standard System V Release 4 manual + pages. For this reason it is not available in the IRIX + version of make. The VPATH facility should not be used + with the new parallel make option. + +5.3. Configuring + HDF5 uses the GNU autoconf system for configuration, which + detects various features of the host system and creates the + Makefiles. On most systems it should be sufficient to say: + + $ ./configure OR + $ sh configure + + The configuration process can be controlled through environment + variables, command-line switches, and host configuration files. + For a complete list of switches type: + + $ ./configure --help + + The host configuration files are located in the `config' + directory and are based on architecture name, vendor name, and/or + operating system which are displayed near the beginning of the + `configure' output. The host config file influences the behavior + of configure by setting or augmenting shell variables. + +5.3.1. Specifying the installation directories + Typing `make install' will install the HDF5 library, header + files, examples, and support programs in /usr/local/lib, + /usr/local/include, /usr/local/doc/hdf5/examples, and + /usr/local/bin. To use a path other than + /usr/local specify the path with the `--prefix=PATH' switch: + + $ ./configure --prefix=$HOME + + If shared libraries are being built (the default) then the final + home of the shared library must be specified with this switch + before the library and executables are built. + + HDF5 can be installed into a different location than the prefix + specified at configure time; see the section on Installing HDF5 + for more details. + +5.3.2. Using an alternate C compiler + By default, configure will look for the C compiler by trying + `gcc' and `cc'. However, if the environment variable "CC" is set + then its value is used as the C compiler (users of csh and + derivatives will need to prefix the commands below with `env'). + For instance, to use the native C compiler on a system which also + has the GNU gcc compiler: + + $ CC=cc ./configure + + A parallel version of hdf5 can be built by specifying `mpicc' + as the C compiler (the `--enable-parallel' flag documented + below is optional in this case). Using the `mpicc' compiler + will insure that the correct MPI and MPI-IO header files and + libraries are used. + + $ CC=/usr/local/mpi/bin/mpicc ./configure + +5.3.3. Configuring for 64-bit support + Several machine architectures support 32-bit or 64-bit binaries. + The options below describe how to enable support for different options. + + On Irix64 the default compiler is `cc'. To use an alternate + compiler specify it with the CC variable: + + $ CC='cc -n32' ./configure + + Similarly, users compiling on a Solaris machine and desiring to + build the distribution with 64-bit support should specify the + correct flags with the CC variable: + + $ CC='cc -xarch=v9' ./configure + + To configure AIX 64-bit support including fortran API and C++, + (Note: need to set $AR to 'ar -X 64'.) + Serial: + $ CFLAGS=-q64 FFLAGS=-q64 CXXFLAGS=-q64 AR='ar -X 64'\ + $ ./configure --enable-fortran + Parallel: (C++ not supported with parallel) + $ CFLAGS=-q64 FFLAGS=-q64 AR='ar -X 64'\ + $ ./configure --enable-fortran + +5.3.4. Additional compilation flags + If addtional flags must be passed to the compilation commands + then specify those flags with the CFLAGS variable. For instance, + to enable symbolic debugging of a production version of HDF5 one + might say: + + $ CFLAGS=-g ./configure --enable-production + +5.3.5. Compiling HDF5 wrapper libraries + One can optionally build the Fortran and/or C++ interface to the + HDF5 C library. By default, both options are disabled. To build + them, specify `--enable-fortran' and `--enable-cxx' respectively. + + $ ./configure --enable-fortran + $ ./configure --enable-cxx + + Configuration will halt if a working Fortran 90 or 95 compiler or + C++ compiler is not found. Currently, the Fortran configure tests + for these compilers in order: f90, pgf90, f95. To use an + alternative compiler specify it with the F9X variable: + + $ F9X=/usr/local/bin/g95 ./configure --enable-fortran + + Note: The Fortran and C++ interfaces are not supported on all the + platforms the main HDF5 library supports. Also, the Fortran + interface supports parallel HDF5 while the C++ interface does + not. + + Note: On Cray T3Es the following files should be modified before + building the Fortran Library: + fortran/src/H5Dff.f90 + fortran/src/H5Aff.f90 + fortran/src/H5Pff.f90 + Check for "Comment if on T3E ..." comment and comment out + specified lines or use a patch from HDF FTP server + ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/ + + Note: See sections 5.7 and 5.8 for how to build Fortran Library with + PGI or Intel compilers. + +5.3.6. Specifying other programs + The build system has been tuned for use with GNU make but works + also with other versions of make. If the `make' command runs a + non-GNU version but a GNU version is available under a different + name (perhaps `gmake') then HDF5 can be configured to use it by + setting the MAKE variable. Note that whatever value is used for + MAKE must also be used as the make command when building the + library: + + $ MAKE=gmake ./configure + $ gmake + + The `AR' and `RANLIB' variables can also be set to the names of + the `ar' and `ranlib' (or `:') commands to override values + detected by configure. + + The HDF5 library, include files, and utilities are installed + during `make install' (described below) with a BSD-compatible + install program detected automatically by configure. If none is + found then the shell script bin/install-sh is used. Configure + doesn't check that the install script actually works, but if a + bad install is detected on your system (e.g., on the ASCI blue + machine as of March 2, 1999) you have two choices: + + 1. Copy the bin/install-sh program to your $HOME/bin + directory, name it `install', and make sure that $HOME/bin + is searched before the system bin directories. + + 2. Specify the full path name of the `install-sh' program + as the value of the INSTALL environment variable. Note: do + not use `cp' or some other program in place of install + because the HDF5 makefiles also use the install program to + also change file ownership and/or access permissions. + +5.3.7. Specifying other libraries and headers + Configure searches the standard places (those places known by the + systems compiler) for include files and header files. However, + additional directories can be specified by using the CPPFLAGS + and/or LDFLAGS variables: + + $ CPPFLAGS=-I/home/robb/include \ LDFLAGS=-L/home/robb/lib \ - ./configure - - HDF5 uses the zlib library for two purposes: it provides support - for the HDF5 deflate data compression filter, and it is used by - the h5toh4 converter and the h4toh5 converter in support of - HDF4. Configure searches the standard places (plus those specified - above with the CPPFLAGS and LDFLAGS variables) for the zlib - headers and library. The search can be disabled by specifying - `--without-zlib' or alternate directories can be specified with - `--with-zlib=INCDIR,LIBDIR' or through the CPPFLAGS and LDFLAGS - variables: - - $ ./configure --with-zlib=/usr/unsup/include,/usr/unsup/lib - - $ CPPFLAGS=-I/usr/unsup/include \ - LDFLAGS=-L/usr/unsup/lib \ - ./configure - - The HDF5-to-HDF4 and HDF4-to-HDF5 conversion tool requires the - HDF4 library and header files, which are detected the same way as - zlib. The switch to give to configure is `--with-hdf4'. Note - that HDF5 requires a newer version of zlib than the one shipped - with some versions of HDF4. Also, unless you have the "correct" - version of HDF4, the confidence testing will fail in the tools - directory. - - HDF5 includes Szip as a predefined compression method (see 3.2). - To enable Szip compression, the HDF5 Library must be configured - and built using the Szip Library: - - $ ./configure --with-szlib=/Szip_Install_Directory - -4.3.8. Static versus shared linking - The build process will create static libraries on all systems and - shared libraries on systems that support dynamic linking to a - sufficient degree. Either form of the library may be suppressed by - saying `--disable-static' or `--disable-shared'. - - $ ./configure --disable-shared - - Shared C++ and Fortran libraries will be built if shared libraries - are enabled. - - To build only statically linked executables on platforms which - support shared libraries, use the `--enable-static-exec' flag. - - $ ./configure --enable-static-exec - -4.3.9. Optimization versus symbolic debugging - The library can be compiled to provide symbolic debugging support - so it can be debugged with gdb, dbx, ddd, etc., or it can be - compiled with various optimizations. To compile for symbolic - debugging (the default for snapshots), say `--disable-production'; - to compile with optimizations (the default for supported public - releases), say `--enable-production'. On some systems the library - can also be compiled for profiling with gprof by saying - `--enable-production=profile'. - - $ ./configure --disable-production #symbolic debugging - $ ./configure --enable-production #optimized code - $ ./configure --enable-production=profile #for use with gprof - - Regardless of whether support for symbolic debugging is enabled, - the library can also perform runtime debugging of certain packages - (such as type conversion execution times and extensive invariant - condition checking). To enable this debugging, supply a - comma-separated list of package names to to the `--enable-debug' - switch. See "Debugging HDF5 Applications" for a list of package - names: - - http://www.hdfgroup.org/HDF5/doc/H5.user/Debugging.html - - Debugging can be disabled by saying `--disable-debug'. - The default debugging level for snapshots is a subset of the - available packages; the default for supported releases is no - debugging (debugging can incur a significant runtime penalty). - - $ ./configure --enable-debug=s,t #debug only H5S and H5T - $ ./configure --enable-debug #debug normal packages - $ ./configure --enable-debug=all #debug all packages - $ ./configure --disable-debug #no debugging - - HDF5 can also print a trace of all API function calls, their - arguments, and the return values. To enable or disable the - ability to trace the API say `--enable-trace' (the default for - snapthots) or `--disable-trace' (the default for public releases). - The tracing must also be enabled at runtime to see any output - (see "Debugging HDF5 Applications," reference above). - -4.3.10. Parallel versus serial library - The HDF5 Library can be configured to use MPI and MPI-IO for - parallelism on a distributed multi-processor system. Read the - file INSTALL_parallel for detailed explanations. - -4.3.11. Threadsafe capability - The HDF5 Library can be configured to be thread-safe (on a very - large scale) with the `--enable-threadsafe' flag to the configure - script. Some platforms may also require the '-with-pthread=INC,LIB' - (or '--with-pthread=DIR') flag to the configure script. - For further details, see "HDF5 Thread Safe Library": - - http://www.hdfgroup.org/HDF5/doc/TechNotes/ThreadSafeLibrary.html - -4.3.12. Backward compatibility - The 1.8 version of the HDF5 Library can be configured to operate - identically to the v1.6 library with the - --with-default-api-version=v16 - configure flag. This allows existing code to be compiled with the - v1.8 library without requiring immediate changes to the application - source code. For addtional configuration options and other details, - see "API Compatibility Macros in HDF5": - - http://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html - -4.4. Building - The library, confidence tests, and programs can be built by - saying just: - - $ make - - Note that if you have supplied some other make command via the MAKE - variable during the configuration step, that same command must be - used here. - - When using GNU make, you can add `-j -l6' to the make command to - compile in parallel on SMP machines. Do not give a number after - the `-j' since GNU make will turn it off for recursive invocations - of make. - - $ make -j -l6 - -4.5. Testing - HDF5 comes with various test suites, all of which can be run by - saying - - $ make check - - To run only the tests for the library, change to the `test' - directory before issuing the command. Similarly, tests for the - parallel aspects of the library are in `testpar' and tests for - the support programs are in `tools'. - - The `check' consists of two sub-tests, check-s and check-p, which - are for serial and parallel tests, respectively. Since serial tests - and parallel tests must be run with single and multiple processes - respectively, the two sub-tests work nicely for batch systems in - which the number of processes is fixed per batch job. One may submit - one batch job, requesting 1 process, to run all the serial tests by - "make check-s"; and submit another batch job, requesting multiple - processes, to run all the parallel tests by "make check-p". - - Temporary files will be deleted by each test when it completes, - but may continue to exist in an incomplete state if the test - fails. To prevent deletion of the files, define the HDF5_NOCLEANUP - environment variable. - - The HDF5 tests can take a long time to run on some systems. To perform - a faster (but less thorough) test, set the HDF5TestExpress environment - variable to 2 or 3 (with 3 being the shortest run). To perform a - longer test, set HDF5TestExpress to 0. 1 is the default. - -4.6. Installing HDF5 - The HDF5 Library, include files, and support programs can be - installed in a (semi-)public place by saying `make install'. The - files are installed under the directory specified with - `--prefix=DIR' (default is 'hdf5') in directories named `lib', - `include', and `bin'. The directories, if not existing, will be - created automatically, provided the mkdir command supports the -p - option. - - If `make install' fails because the install command at your site - somehow fails, you may use the install-sh that comes with the - source. You will need to run ./configure again. + ./configure + + HDF5 uses the zlib library for two purposes: it provides support + for the HDF5 deflate data compression filter, and it is used by + the h5toh4 converter and the h4toh5 converter in support of + HDF4. Configure searches the standard places (plus those + specified above with CPPFLAGS and LDFLAGS variables) for the zlib + headers and library. The search can be disabled by specifying + `--without-zlib' or alternate directories can be specified with + `--with-zlib=INCDIR,LIBDIR' or through the CPPFLAGS and LDFLAGS + variables: + + $ ./configure --with-zlib=/usr/unsup/include,/usr/unsup/lib + + $ CPPFLAGS=-I/usr/unsup/include \ + LDFLAGS=-L/usr/unsup/lib \ + ./configure + + The HDF5-to-HDF4 and HDF4-to-HDF5 conversion tool requires the + HDF4 library and header files which are detected the same way as + zlib. The switch to give to configure is `--with-hdf4'. Note + that HDF5 requires a newer version of zlib than the one shipped + with some versions of HDF4. Also, unless you have the "correct" + version of hdf4 the confidence testing will fail in the tools + directory. + + HDF5 has Szip predefined compression method (see 4.2). To enable + Szip compression, HDF5 library has to be configured and build using + Szip Library + + $ ./configure --with-szlib=/Szip_Install_Directory + +5.3.8. Static versus shared linking + The build process will create static libraries on all systems and + shared libraries on systems that support dynamic linking to a + sufficient degree. Either form of library may be suppressed by + saying `--disable-static' or `--disable-shared'. + + $ ./configure --disable-shared + + Shared C++ and Fortran libraries will be built if shared libraries + are enabled. + + To build only statically linked executables on platforms which + support shared libraries, use the `--enable-static-exec' flag. + + $ ./configure --enable-static-exec + +5.3.9. Optimization versus symbolic debugging + The library can be compiled to provide symbolic debugging support + so it can be debugged with gdb, dbx, ddd, etc or it can be + compiled with various optimizations. To compile for symbolic + debugging (the default for snapshots) say `--disable-production'; + to compile with optimizations (the default for supported public + releases) say `--enable-production'. On some systems the library + can also be compiled for profiling with gprof by saying + `--enable-production=profile'. + + $ ./configure --disable-production #symbolic debugging + $ ./configure --enable-production #optimized code + $ ./configure --enable-production=profile #for use with gprof + + Regardless of whether support for symbolic debugging is enabled, + the library also is able to perform runtime debugging of certain + packages (such as type conversion execution times, and extensive + invariant condition checking). To enable this debugging supply a + comma-separated list of package names to to the `--enable-debug' + switch (see Debugging.html for a list of package names). + Debugging can be disabled by saying `--disable-debug'. The + default debugging level for snapshots is a subset of the + available packages; the default for supported releases is no + debugging (debugging can incur a significant runtime penalty). + + $ ./configure --enable-debug=s,t #debug only H5S and H5T + $ ./configure --enable-debug #debug normal packages + $ ./configure --enable-debug=all #debug all packages + $ ./configure --disable-debug #no debugging + + HDF5 is also able to print a trace of all API function calls, + their arguments, and the return values. To enable or disable the + ability to trace the API say `--enable-trace' (the default for + snapthots) or `--disable-trace' (the default for public + releases). The tracing must also be enabled at runtime to see any + output (see Debugging.html). + +5.3.10. Large (>2GB) vs. small (<2GB) file capability + In order to read or write files that could potentially be larger + than 2GB it is necessary to use the non-ANSI `long long' data + type on some platforms. However, some compilers (e.g., GNU gcc + versions before 2.8.1 on Intel platforms) are unable to produce + correct machine code for this data type. To disable use of the + `long long' type on these machines say: + + $ ./configure --disable-hsizet + +5.3.11. Parallel vs. serial library + The HDF5 library can be configured to use MPI and MPI-IO for + parallelizm on a distributed multi-processor system. Read the + file INSTALL_parallel for detailed explanations. + +5.3.12. Threadsafe capability + The HDF5 library can be configured to be thread-safe (on a very + large scale) with the with the `--enable-threadsafe' flag to + the configure script. Some platforms may also require the + '-with-pthread=INC,LIB' (or '--with-pthread=DIR') flag to the configure + script as well. Read the file doc/TechNotes/ThreadSafeLibrary.html + for further details. + +5.3.13. Backward compatibility + The 1.8 version of the HDF5 library can be configured to operate + identically to the v1.6 library with the `--enable-hdf5v1_6' + configure flag. This allows existing code to be compiled with the + v1.8 library without requiring immediate changes to the + application source code. This flag will only be supported in the + v1.8 branch of the library, it will not be available in v1.9+. + +5.3.14. Network stream capability + The HDF5 library can be configured with a network stream file + driver with the `--enable-stream-vfd' configure flag. This option + compiles the "stream" Virtual File Driver into the main library. + See the documentation on the Virtual File Layer for more details + about the use of this driver. The network stream capability is + enabled by default, except for use in parallel or with a parallel + compiler, where it is disabled. Explicitly enabling Stream-VFD + will allow for its use in parallel. + +5.4. Building + The library, confidence tests, and programs can be build by + saying just: + + $ make + + Note that if you supplied some other make command via the MAKE + variable during the configuration step then that same command + must be used here. + + When using GNU make you can add `-j -l6' to the make command to + compile in parallel on SMP machines. Do not give a number after + th `-j' since GNU make will turn it off for recursive invocations + of make. + + $ make -j -l6 + +5.5. Testing + HDF5 comes with various test suites, all of which can be run by + saying + + $ make check + + To run only the tests for the library change to the `test' + directory before issuing the command. Similarly, tests for the + parallel aspects of the library are in `testpar' and tests for + the support programs are in `tools'. + + Temporary files will be deleted by each test when it complets, + but may continue to exist in an incomplete state if the test + fails. To prevent deletion of the files define the HDF5_NOCLEANUP + environment variable. + + The HDF5 tests can take a long time to run on some systems. To + perform a faster (but less thorough) test, set the HDF5TestExpress + environment variable to 2 or 3 (with 3 being the shortest run). + To perform a longer test, set HDF5TestExpress to 0. 1 is the default. + +5.6. Installing + The HDF5 library, include files, and support programs can be + installed in a (semi-)public place by saying `make install'. The + files are installed under the directory specified with + `--prefix=DIR' (or '/usr/local') in directories named `lib', + `include', and `bin'. The prefix directory must exist prior to + `make install', but its subdirectories are created automatically. + + If `make install' fails because the install command at your site + somehow fails, you may use the install-sh that comes with the + source. You need to run ./configure again. $ INSTALL="$PWD/bin/install-sh -c" ./configure ... $ make install - If you want to install HDF5 in a location other than the location - specified by the `--prefix=DIR' flag during configuration (or - instead of the default location, `hdf5'), you can do that - by running the deploy script: + If you want to install HDF5 in a location other than the location + specified by the `--prefix=DIR' flag during configuration (or + instead of the default location, `/usr/local'), you can do that + by running the deploy script: $ bin/deploy NEW_DIR - This will install HDF5 in NEW_DIR. Alternately, you can do this - manually by issuing the command: + This will install hdf5 in NEW_DIR. Alternately, you can do this + manually by issuing the command: - $ make install prefix=NEW_DIR + $ make install prefix=NEW_DIR - where NEW_DIR is the new directory where you wish to install HDF5. - If you do not use the deploy script, you should run h5redeploy in - NEW_DIR/bin directory. This utility will fix the h5cc, h5fc and - h5c++ scripts to reflect the new NEW_DIR location. + where NEW_DIR is the new directory you wish to install HDF5. If + you do not use the deploy script, you should run h5redeploy in + NEW_DIR/bin directory. This utility will fix h5cc, h5fc and + h5c++ scripts to reflect the new NEW_DIR location. - The library can be used without installing it by pointing the - compiler at the `src' and 'src/.libs' directory for include files and - libraries. However, the minimum which must be installed to make - the library publicly available is: + The library can be used without installing it by pointing the + compiler at the `src' and 'src/.libs' directory for include files and + libraries. However, the minimum which must be installed to make + the library publically available is: - The library: - ./src/.libs/libhdf5.a + The library: + ./src/.libs/libhdf5.a - The public header files: - ./src/H5*public.h, ./src/H5public.h + The public header files: + ./src/H5*public.h, ./src/H5public.h ./src/H5FD*.h except ./src/H5FDprivate.h, ./src/H5api_adpt.h - The main header file: - ./src/hdf5.h - - The configuration information: - ./src/H5pubconf.h - - The support programs that are useful are: - ./tools/h5ls/h5ls (list file contents) - ./tools/h5dump/h5dump (dump file contents) - ./tools/misc/h5repart (repartition file families) - ./tools/misc/h5debug (low-level file debugging) - ./tools/h5import/h5import (imports data to HDF5 file) - ./tools/h5diff/h5diff (compares two HDF5 files) - ./tools/gifconv/h52gif (HDF5 to GIF converter) - ./tools/gifconv/gif2h5 (GIF to HDF5 converter) + The main header file: + ./src/hdf5.h + The configuration information: + ./src/H5pubconf.h + + The support programs that are useful are: + ./tools/h5ls/h5ls (list file contents) + ./tools/h5dump/h5dump (dump file contents) + ./tools/misc/h5repart (repartition file families) + ./tools/misc/h5debug (low-level file debugging) + ./tools/h5import/h5import (imports data to HDF5 file) + ./tools/h5diff/h5diff (compares two HDF5 files) + ./tools/gifconv/h52gif (HDF5 to GIF converter) + ./tools/gifconv/gif2h5 (GIF to HDF5 converter) -5. Using the Library - Please see the "HDF5 User's Guide" and the "HDF5 Reference Manual": +5.7 Building and testing with Intel compilers - http://www.hdfgroup.org/HDF5/doc/ - Most programs will include <hdf5.h> and link with -lhdf5. - Additional libraries may also be necessary depending on whether - support for compression, etc., was compiled into the HDF5 Library. + When Intel compilers are used (icc or ecc), you will need to + modify the generated "libtool" program after configuration is finished. + On or around line 104 of the libtool file, there are lines which + look like: - A summary of the HDF5 installation can be found in the - libhdf5.settings file in the same directory as the static and/or - shared HDF5 Libraries. + # How to pass a linker flag through the compiler. + wl="" + Change these lines to this: -6. Support - Support is described in the README file. + # How to pass a linker flag through the compiler. + wl="-Wl," + UPDATE: This is now done automatically by the configure script. However, + if you still experience a problem, you may want to check this line in + the libtool file and make sure that it has the correct value. -***************************************************************************** - APPENDIX -***************************************************************************** + * To build the Fortran library using Intel compiler on Linux 2.4, one has to + x Use -fpp -DDEC$=DEC_ -DMS$=MS_ compiler flags to disable + DEC and MS compiler directives in source files in fortran/src, fortran/test + and fortran/examples directories. + e.g., setenv F9X 'ifc -fpp -DDEC$=DEC_ -DMS$=MS_' + (do not use double quotes since $ is interpreted in them.) -A. Warnings about compilers - Output from the following compilers should be extremely suspected - when used to compile the HDF5 Library, especially if optimizations are - enabled. In all cases, HDF5 attempts to work around the compiler bugs. - -A.1. GNU (Intel platforms) - Versions before 2.8.1 have serious problems allocating registers - when functions contain operations on `long long' datatypes. - Supplying the `--disable-hsizet' switch to configure (documented - in Appendix B, "Large (>2GB) versus small (<2GB) file capability,") - will prevent HDF5 from using `long long' datatypes in - situations that are known not to work, but it limits the HDF5 - address space to 2GB. - -A.2. COMPAQ/DEC - The V5.2-038 compiler (and possibly others) occasionally - generates incorrect code for memcpy() calls when optimizations - are enabled, resulting in unaligned access faults. HDF5 works - around the problem by casting the second argument to `char *'. - The Fortran module (5.4.1a) fails in compiling some Fortran - programs. Use 5.5.0 or higher. - -A.3. SGI (Irix64 6.2) - The Mongoose 7.00 compiler has serious optimization bugs and - should be upgraded to MIPSpro 7.2.1.2m. Patches are available - from SGI. - -A.4. Windows/NT - The Microsoft Win32 5.0 compiler is unable to cast unsigned long - long values to doubles. HDF5 works around this bug by first - casting to signed long long and then to double. - - A link warning: defaultlib "LIBC" conflicts with use of other libs - appears for debug version of VC++ 6.0. This warning will not affect - building and testing HDF5 Libraries. - - -B. Large (>2GB) versus small (<2GB) file capability - In order to read or write files that could potentially be larger - than 2GB, it is necessary to use the non-ANSI `long long' data - type on some platforms. However, some compilers (e.g., GNU gcc - versions before 2.8.1 on Intel platforms) are unable to produce - correct machine code for this datatype. To disable use of the - `long long' type on these machines, say: - - $ ./configure --disable-hsizet - -C. Building and testing with other compilers -C.1. Building and testing with Intel compilers - When Intel compilers are used (icc or ecc), you will need to modify - the generated "libtool" program after configuration is finished. - On or around line 104 of the libtool file, there are lines which - look like: - - # How to pass a linker flag through the compiler. - wl="" - - Change these lines to this: - - # How to pass a linker flag through the compiler. - wl="-Wl," - - UPDATE: This is now done automatically by the configure script. - However, if you still experience a problem, you may want to check this - line in the libtool file and make sure that it has the correct value. - - * To build the Fortran library using Intel compiler on Linux 2.4, - one has to perform the following steps: - x Use the -fpp -DDEC$=DEC_ -DMS$=MS_ compiler flags to disable - DEC and MS compiler directives in source files in the fortran/src, - fortran/test, and fortran/examples directories. - E.g., setenv F9X 'ifc -fpp -DDEC$=DEC_ -DMS$=MS_' - Do not use double quotes since $ is interpreted in them. - - x If Version 6.0 of Fortran compiler is used, the build fails in - the fortran/test directory and then in the fortran/examples - directory. To proceed, edit the work.pcl files in those - directories to contain two lines: + x If Version 6.0 of Fortran compiler is used, build fails in + the fortran/test directory and then in the + fortran/examples directory; to proceed, edit the work.pcl files in + those directories to contain two lines work.pc ../src/work.pc - x Do the same in the fortran/examples directory. + x Do the same in fortran/examples directory + x Problem with work.pc files was resolved for newest version of the compiler (7.0) + + * To build the Fortran Library on IA32 follow step described above, except + that DEC and MS compiler directives should be removed manually or + use a patch from HDF FTP server ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/ + + +5.8 Building and testing with PGI compilers + + When PGI C and C++ compilers are used (pgcc or pgCC), you will need to + modify the generated "libtool" program after configuration is finished. + On or around line 104 of the libtool file, there are lines which + look like: - x A problem with work.pc files was resolved for the newest version - of the compiler (7.0). + # How to pass a linker flag through the compiler. + wl="" - * To build the Fortran library on IA32, follow the steps described - above, except that the DEC and MS compiler directives should be - removed manually or use a patch from HDF FTP server: + Change these lines to this: - ftp://ftp.hdfgroup.org/HDF5/current/ + # How to pass a linker flag through the compiler. + wl="-Wl," + UPDATE: This is now done automatically by the configure script. However, + if you still experience a problem, you may want to check this line in + the libtool file and make sure that it has the correct value. -C.2. Building and testing with PGI compilers - When PGI C and C++ compilers are used (pgcc or pgCC), you will need to - modify the generated "libtool" program after configuration is finished. - On or around line 104 of the libtool file, there are lines which - look like this: + To build HDF5 C++ Library with pgCC (version 4.0 and later), set + environment variable CXX to "pgCC -tlocal" + setenv CXX "pgCC -tlocal" + before running the configure script. - # How to pass a linker flag through the compiler. - wl="" - Change these lines to this: +6. Using the Library + Please see the User Manual in the doc/html directory. - # How to pass a linker flag through the compiler. - wl="-Wl," + Most programs will include <hdf5.h> and link with -lhdf5. + Additional libraries may also be necessary depending on whether + support for compression, etc. was compiled into the hdf5 library. - UPDATE: This is now done automatically by the configure script. However, - if you still experience a problem, you may want to check this line in - the libtool file and make sure that it has the correct value. + A summary of the hdf5 installation can be found in the + libhdf5.settings file in the same directory as the static and/or + shared hdf5 libraries. - To build the HDF5 C++ Library with pgCC (version 4.0 and later), set - the environment variable CXX to "pgCC -tlocal" - setenv CXX "pgCC -tlocal" - before running the configure script. +7. Support + Support is described in the README file. diff --git a/release_docs/INSTALL_Cygwin.txt b/release_docs/INSTALL_Cygwin.txt index b63d294..0cb0968 100644 --- a/release_docs/INSTALL_Cygwin.txt +++ b/release_docs/INSTALL_Cygwin.txt @@ -98,7 +98,29 @@ Install HDF5 on Cygwin $ bunzip2 < hdf5-1.8.0.tar.bz2 | tar xf - -3. Configuring +3. Setup environment + + In the latest version of the Cygwin DLL, a bug was introduced + relating to the 'timezone' global variable and C99 support. As + work-around, we must use a special compiler flag. + + 3.1. In the command prompt you plan to build from, run the + command: + + export CFLAGS="-ansi ${CFLAGS}" + + 3.2 (Optional) If you plan to build C++ libraries, also + run the command: + + export CXXFLAGS="-ansi ${CXXFLAGS}" + + 3.3 (Optional) If you plan to build Fortran libraries, also + run the command: + + export FCFLAGS="-ansi ${FCFLAGS}" + + +4. Configuring Notes: See detailed information in hdf5/release_docs/INSTALL, part 5. Full installation instructions for source @@ -112,19 +134,19 @@ Install HDF5 on Cygwin In short, - 3.1 To configure HDF5 C Library, using + 4.1 To configure HDF5 C Library, using $ ./configure - 3.2 To configure HDF5 C/C++ Library, using + 4.2 To configure HDF5 C/C++ Library, using $ ./configure --enable-cxx - 3.3 To configure HDF5 C/Fortran Library, using + 4.3 To configure HDF5 C/Fortran Library, using $ ./configure --enable-fortran - 3.4 To configure HDF5 C with Szip library, using + 4.4 To configure HDF5 C with Szip library, using $ ./configure --with-szlib="path to szlib" @@ -135,15 +157,15 @@ Install HDF5 on Cygwin $ ./configure --with-szlib=/cygdrive/c/szip - 3.5 To configure HDF5 C without Zlib, + 4.5 To configure HDF5 C without Zlib, To disable zlib, using $ ./configure --without-zlib - 3.6 Two ways to configure HDF5 C with specified Zlib + 4.6 Two ways to configure HDF5 C with specified Zlib - 3.6.1 Using + 4.6.1 Using $ ./configure --with-zlib=INCDIR,LIBDIR @@ -153,7 +175,7 @@ Install HDF5 on Cygwin $ ./configure --with-zlib=/cygdrive/c/usr/include,/cygdrive/c/usr/lib - 3.6.2 Through the CPPFLAGS and LDFLAGS Variables + 4.6.2 Through the CPPFLAGS and LDFLAGS Variables For example, if zlib was installed in the directory /cygdrive/c/usr then using the following command to configure @@ -163,7 +185,7 @@ Install HDF5 on Cygwin $ LDFLAGS=-L/cygdrive/c/usr/lib \ $ ./configure - 3.7 To specify the installation directories, using + 4.7 To specify the installation directories, using $ ./configure --prefix="path for installation" @@ -174,7 +196,7 @@ Install HDF5 on Cygwin the path with the `--prefix=PATH' switch as in the above command. - 3.8 Combination of Switches + 4.8 Combination of Switches All of the above switches can be combined together. For example, if users want to configure HDF5 C/C++/Fortran @@ -209,7 +231,7 @@ Install HDF5 on Cygwin --enable-fortran <"If no more switches, then hit Enter"> -4. Make and Make Check +5. Make and Make Check After configuration is done successfully, run the following series of commands to build, test and install HDF5 @@ -220,20 +242,23 @@ Install HDF5 on Cygwin Before run "make install", check output file for "make check", there should be no failures at all. -5. Make Install +6. Make Install $ make install > "output file name" -6. Check installed HDF5 library +7. Check installed HDF5 library After step 4, go to your installation directory, there should be three subdirectories: "bin" "include" and "lib". -7. Known Problems +8. Known Problems Shared libraries can not be built on Cygwin In release 1.8.0. + There are issues linking with the latest Cygwin DLL. As a work-around, + make sure to follow the steps described in step 3 above. + ----------------------------------------------------------------------- Need Further assistance, email help@hdfgroup.org diff --git a/release_docs/INSTALL_VMS.txt b/release_docs/INSTALL_VMS.txt index 0245024..fd997c5 100644 --- a/release_docs/INSTALL_VMS.txt +++ b/release_docs/INSTALL_VMS.txt @@ -1,6 +1,6 @@ Building and installation instructions for Alpha Open VMS HDF5 1.8.0 release - February 12, 2008 + January 2008 diff --git a/release_docs/INSTALL_Windows.txt b/release_docs/INSTALL_Windows.txt index 1facd81..daedadd 100644 --- a/release_docs/INSTALL_Windows.txt +++ b/release_docs/INSTALL_Windows.txt @@ -829,14 +829,20 @@ To build and test HDF5 High Level C examples: Select "Build" -> "Build Solution" or "Rebuild Solution" to build release version of project "allhlcexamples". - When the debug and release build is done, binaries will be built in the - following subdirectories of c:\MyHDFstuff\hdf5\examples\ - - ex_image[1-2](dll) - ex_lite1(dll) - ex_table[01-12](dll) - ex_ds1(dll) - ptExample[FL+VL](dll) + When the debug and release build is done, there should be the following + subdirectories in c:\MyHDFstuff\hdf5\examples\ + + allhlcexamples + ex_images + ex_imagesdll + ex_lite + ex_litedll + ex_table + ex_tabledll + ex_ds + ex_dsdll + ex_packet + ex_packetdll 3. Invoke a command prompt and run the batch file Install_hlcexamples.bat which resides in the top level directory (c:\MyHDFstuff\hdf5). This file diff --git a/release_docs/INSTALL_parallel b/release_docs/INSTALL_parallel index e8f8bad..b0e0a86 100644 --- a/release_docs/INSTALL_parallel +++ b/release_docs/INSTALL_parallel @@ -61,7 +61,7 @@ The "--enable-parallel" is optional in this case. Make sure your environment variables are set correctly to compile and execute a single process mpi applications for the SP machine. Unfortunately, the setting varies from machine to machine. E.g., the following works for the -IBM SP machine at LLNL. +Blue machine of LLNL. setenv MP_PROCS 1 setenv MP_NODES 1 @@ -102,7 +102,7 @@ This allows for >2GB sized files on Linux systems and is only available with Linux kernels 2.4 and greater. -2.4. Red Storm (Cray XT3) (for v1.8 and later) +2.4. Red Storm (Cray XT3) (for v1.8 only) ------------------------- The following steps are for building the Parallel HDF5 for the Red Storm compute nodes. They would probably work for other Cray XT3 systems but have @@ -180,28 +180,15 @@ environment variable at the time `make check' is run (or the value 3). 4. Parallel test suite ---------------------- -The testpar/ directory contains tests for Parallel HDF5 and MPI-IO. Here are -some notes about some of the tests. - -The t_mpi tests the basic functionalities of some MPI-IO features used by -Parallel HDF5. It usually exits with non-zero code if a required MPI-IO -feature does not succeed as expected. One exception is the testing of -accessing files larger than 2GB. If the underlying filesystem or if the -MPI-IO library fails to handle file sizes larger than 2GB, the test will -print informational messages stating the failure but will not exit with -non-zero code. Failure to support file size greater than 2GB is not a fatal -error for HDF5 because HDF5 can use other file-drivers such as families of -files to bypass the file size limit. - -The t_posix_compliant tests if the file system is POSIX compliant when POSIX -and MPI IO APIs are used. This is for information only and it always exits -with 0 even when non-compliance errors have occurred. This is to prevent -the test from aborting the remaining parallel HDF5 tests unnecessarily. - -The t_cache does many small sized I/O requests and may not run well in a -slow file system such as NFS disk. If it takes a long time to run it, try -set the environment variable $HDF5_PARAPREFIX to a file system more suitable -for MPI-IO requests before running t_cache. +The testpar/ directory contains tests for Parallel HDF5 and MPI-IO. The t_mpi +tests the basic functionalities of some MPI-IO features used by Parallel HDF5. +It usually exits with non-zero code if a required MPI-IO feature does not +succeed as expected. One exception is the testing of accessing files larger +than 2GB. If the underlying filesystem or if the MPI-IO library fails to +handle file sizes larger than 2GB, the test will print informational messages +stating the failure but will not exit with non-zero code. Failure to support +file size greater than 2GB is not a fatal error for HDF5 because HDF5 can +use other file-drivers such as families of files to bypass the file size limit. By default, the parallel tests use the current directory as the test directory. This can be changed by the environment variable $HDF5_PARAPREFIX. For example, diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 881865b..f1f58b6 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -1,20 +1,32 @@ -HDF5 version 1.9.5 currently under development +HDF5 version 1.8.0 currently under development ================================================================================ INTRODUCTION -This document describes the differences between HDF5-1.9.0 and -HDF5 1.9.x snapshot, and contains information on the platforms -tested and known problems in HDF5-1.9.x. -For more details check the HISTORY*.txt files in the HDF5 source. +This document describes the differences between HDF5-1.6.* and +Hdf5 1.8.0 release candidate "HDF5-1.8.0-rc*", and contains information +on the platforms tested and known problems in HDF5-1.8.0-rc*. +For more details check the HISTORY.txt file in the HDF5 source. + + +Links to HDF5 1.8.0-rc* source code, documentation, and additional materials +can be found on THG's development server (www.hdfgroup.uiuc.edu) at the +following location: + http://www.hdfgroup.uiuc.edu/HDF5/release/beta/obtain518.html +User documentation for the beta can be accessed directly at this location: + http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/doc/ + +New features of the upcoming 1.8.0 release are described in +the "What's New in 1.8.0?" document: + http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/WhatsNew180.html + +New and modified APIs are described briefly in + http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/WhatsNew180.html +and will be listed in the "HDF5 Software Changes" document: + http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/doc/ADGuide/Changes.html -Links to HDF5 1.9.x source code can be found on THG's development -FTP server at the following location: - ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/snapshots -User documentation for the snapshot can be accessed directly at this location: - http://www.hdfgroup.uiuc.edu/HDF5/doc_dev_snapshot/H5_dev/ For more information, see the HDF5 home page: @@ -29,7 +41,7 @@ CONTENTS - New Features - Support for new platforms and languages -- Bug Fixes since HDF5-1.8.0 +- Bug Fixes since HDF5-1.6.0 - Platforms Tested - Known Problems @@ -38,71 +50,940 @@ New Features ============ Configuration: - ------------- + -------------- + - Removed stream-vfd from the HDF5 library. - AKC 2007/11/19. + - Updated versions of autotools. HDF5 now uses automake 1.10.0, + autoconf 2.61, and libtool 1.5.22. MAM - 2007/7/25. + - Changed default fortran compiler to g95 when gcc is used. - AKC + 2007/2/17. + - 'make check-vfd' can now be run from the top level directory. Not all + tests that 'make check' invokes work with certain Virtual File Drivers, + so those tests have been skipped. - MAM 2006/7/17 + - Added the variable HDF5TestExpress to control how long tests run. + Setting it to a value between 0 and 3 controls how thoroughly the + library is tested, with 0 being an "exhaustive run" and 3 being a + very quick "smoke test." 1 (a "full run") is the default. + -JML 2006/6/21 + - If both shared and static libraries are installed, now both will be + tested during 'make install'. -MAM 2006/06/21 + - Added support to explicity enable stream_vfd or shared libraries + when using parallel via the '--enable-stream_vfd' and + '--enable-shared' options, respectively. If not explicity defined, + These settings default to enabled when parallel is not used, + and disabled when parallel is used. -MAM 2006/06/17 + - Remove the flexible parallel code and the --enable-fphdf5 + configure option, it was never up to production standards + anyway. -QAK 2006/4/20 + - Added a macro hdf5_mpi_special_collective_io_works to filter out + some mpi-io packages that don't support collective IO for no IO + contributions in some processes. -KY 2006/2/16 + - Added -shlib option to link against installed shared libraries to + h5c++ and h5fc. -JML 2005/11/1 + - Added --enable-build-all option to configure, which only developers + should need to use. -JML 2005/10/24 + - Configure uses the 'TR' variable to let the user override the path + to the 'tr' utility. -JML 2005/10/17 + - Configure can recognize -lmpich as a form of MPI library. -AKC- + 2005/9/28. + - MD5 checksumming has been added to snapshot releases. Release + tarballs will be accompanied by .md5 checksum files, which can + be verified using the md5sum utility. -JML 2005/9/6 + - Some configure flags are incompatible (e.g., the C++ APIs cannot + be built using the parallel version of HDF5). configure will now + output errors when some common incompatible features are used + together. -JML 2005/9/6 + - A new API function, H5Tis_hard(), was added to the library. It + checks if a conversion function is a compiler (hard) conversion. + SLU - 2005/9/6 + - t_mpi will run the test_mpio_derived_dtype by default unless it is + known not working (indicated by macro H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS + not defined.) -AKC- 2005/8/23. + - Test execution has changed in a number of ways: + When make is invoked in parallel (using -j), sequential tests + are now executed as parallel make targets. This should make them + finish more quickly on machines with multiple processors. + Since test output is garbled when they are executed by parallel make, + tests now dump their output to foo.log files and foo.logsh files + (for test scripts). These logs are printed to the screen only + when a test fails or when all tests in the current directory have + completed successfully. + When tests pass, they will create a foo.chkexe file. + This prevents the test from executing again until the test or + main library changes. + All files generated by tests (*.chkexe, *.log, and any *.h5 files + created) can be removed by invoking 'make check-clean'. + Sequential and parallel library tests can now be invoked separately. + 'make check-s' will execute only sequential tests, and 'make check-p' + will execute only parallel tests. 'make check' will still execute + all tests. + -JML 2005/08/03 + - On windows, all.zip is deprecated. users should + read INSTALL_Windows.txt to know the details. + Reasons to deprecate all.zip: + 1. Avoid confliction for windows programmers + 2. Decrease size of CVS tree by adding all.zip + 3. Avoid using winzip as the intermediate step + --KY 2005/04/22 + - When HDF5 is created as a shared library, it now uses libtool's + shared library versioning scheme. -JML 2005/04/18 + - HDF5 now uses automake 1.9.5 to generate Makefiles.in. + This has a number of effects on users: + The Fortran compiler should be set using the environment + variable $FC, not $F9X. F9X still works, but is depreciated. + The output of make may be different. This should be only a + cosmetic effect. + make depened (or make dep) is no longer recognized, since automake + handles dependency tracking. + Some new configure options exist. --enable-dependency-tracking + and --disable-dependency-tracking are used to control automake's + dependency tracking. Dependencies are on by default *on most + platforms and compilers*. If --enable-dependency-tracking is + used, they will be enabled on any platform. However, this can + slow down builds or even cause build errors in some cases. + Likewise, --disable-dependency-tracking can speed up builds and + avoid some build errors. + Some make targets have alternate names. make check-install and + make installcheck do the same thing, for instance. + pmake on IRIX can be invoked from the root directory, but the + -V flag must be used to invoke it in any subdirectory or it + will give an error about undefined variables. + JML 2005/01 - 2005/03 + - Hardware conversion between long double and integers is also added. + SLU 2005/02/10 + - Started to support software conversion between long double and + integers. Hardware conversion will come very soon. SLU - 2005/1/6 + - Intel v8.0 compiler would infinite loop when compiling some test + code with -O3 option. Changed enable-production default compiler + option to -O2. AKC - 2004/12/06 + - Long double is assumed to be a supported C data type. It is a + stanadard C89 type. AKC - 2004/10/22 + - The IA64 will use ecc as the C++ compiler by default. + - Added some initial support for making valgrind/Purify (or similar + memory checking products) happier by initializing buffers to zero + and disabling the internal free list code. To take advantage of + this, use the "--enable-using-memchecker" configure option when + building the library. QAK - 2004/07/23 + - Fixed the long compile time of H5detect.c when v7.x Intel Compiler + is used with optimization NOT off. AKC - 2004/05/20 + - Fixed configure setting of C++ for OSF1 platform. AKC - 2004/01/06 + - Prefix default is changed from /usr/local to `pwd`/hdf5. + AKC - 2003/07/09 Library: -------- + - Removed size restrictions on attributes, when using the "latest" + version of the file format. - QAK - 2007/02/21 + - Relaxed restrictions on attribute operations to allow a file ID to + be used as the "location ID". If a file ID is used, the attribute + operation will occur on the root group of the file. + - QAK - 2007/02/09 + - Enabled the CORE driver to read an existing file depending on + the setting of the backing_store for H5Pset_fapl_core and file + open flags. - SLU - 2006/11/30 + - Added new H5Gget_info_by_idx() routine to query the information about + a group according to the order within an index. + - QAK - 2006/11/27 + - Added new H5Gget_info() routine to query the information about a + group by name. + - QAK - 2006/11/27 + - Added new H5Oget_info_by_idx() routine to query the information about + an object in a group according to the order within an index. + - QAK - 2006/11/26 + - Added new H5Oget_info() routine to query the information about an + object in a group by name. + - QAK - 2006/11/26 + - Added new H5Oopen_by_idx() routine to open an object in a group + according to the order within an index. + - QAK - 2006/11/20 + - Added new H5Literate() routine to iterate over links in a group + according to the order within an index. + - QAK - 2006/11/20 + - Added new H5Ldelete_by_idx() routine to delete a link according to + the order within an index. + - QAK - 2006/11/13 + - Added new H5Lget_val_by_idx() routine to query the value of a soft link + according to the order within an index. + - QAK - 2006/11/13 + - Added new H5Lget_name_by_idx() routine to query the name of a link + according to the order within an index. + - QAK - 2006/11/12 + - Added new H5Rget_name() routine to determine the name of the object + that a reference points to, as long as the object is still + reachable in the group hierarchy. + - QAK - 2006/11/10 + - Added new H5Lget_info_by_idx() routine to query the link information + according to the order within an index. + - QAK - 2006/11/10 + - Added feature to H5Iget_name to allow retrieving the name of any + object's ID, as long as the object is still reachable in the + group hierarchy. + - LA - 2006/11/01 + - Added External and User-defined links. + External links are links from one HDF5 file to another; they + require both the name of the file and a path within that file. + User-defined links allow users to supply callback functions + for link traversals, allowing links to exhibit essentially + any behavior. + External links are a kind of user-defined link, so their default + behavior can be overridden by the user. + -JML 2006/8/23 + - Added H5Oopen and H5Oclose for opening objects of unknown type + (as link callback functions do). + -JML 2006/8/23 + - Added H5Oopen_by_addr, H5Oincr_refcount, and H5Odecr_refcount for + opening objects by address. Be very careful with these! + -JML 2006/8/23 + - Added H5Fget_intent to get the "intent" of a file (whether it + was opened with read-write access or read-only. + -JML 2006/8/23 + - Added Link Access Property Lists. They currently contain two + properties, nlinks (H5Pget/set_nlinks) and elink_prefix + (H5Pget/set_elink_prefix). nlinks controls how many soft and + user-defined traversals are allowed before HDF5 assumes it has + found a cycle (previously this defaulted to 16). + The elink_prefix is a filesystem path that is prefixed to the + names of any external link files opened using this LAPL. + -JML 2006/8/23 + - Add H5L link APIs. Old APIs (H5Glink, H5Gmove, etc.) are still + supported but deprecated. + New APIs are: + H5Llink - create a link to an object given its ID + H5Lmove - just like H5Gmove2 + H5Lcopy - copy a link without copying the underlying object + H5Lcreate_hard - like H5Glink2 for hard links + H5Lcreate_soft - like H5Glink2 for soft links + H5Ldelete - just like H5Gunlink + H5Lget_val - just like H5Gget_linkval + H5Lget_info - gets link-specific info (like H5Gget_objinfo) + + In addition, H5Gcreate_anon, H5Tcommit_anon, and H5Dcreate_anon + no longer create links to objects; objects must be manually linked + using H5Llink or they will be deleted when the ID is closed. + + Link Creation Property Lists can be used to pass character + encoding (ASCII or UTF-8) for link names and to set the Intermediate + Group Creation Flag: + H5Pset_char_encoding, H5Pget_char_encoding + H5Pset_copy_object, H5Pget_copy_object + -JML 2006/7/5 + - Added managements of collective IO supports for chunking storage + inside parallel HDF5 + 1) Implemented One IO with collective mode for all chunks in the + application by building one MPI derived datatype accross all + chunks. + 2) Implemented the decision-making support to do collective IO inside + MPI-IO per chunk. + 3) Added the decision-making support to do one IO accross all chunks + or to do multiple IOs with each IO per chunk. + 4) Added the support to handle the case some processes won't do any IOs in + collectively. + 5) Some MPI-IO package(mpich 1.2.6 or lower, e.g.) cannot handle + collective IO correctly for the case when some processes have no + contributions to IOs, a special macro is added to change + collective IO mode to independent IO mode inside HDF5 library. + + Currently we find that MPICH at Linux and vender MPI-IO package at NCSA + Altix cannot handle this case. + + "hdf5_mpi_special_collective_io_works=${hdf5_mpi_special_collective_io_works='no'}" + has been added at the end of file <ia64-linux-gnui> and + <linux-gnulibc1>. + + If MPI-IO packages at your Linux and Altix support this case, + please comment out the last line and report to us at + help@hdfgroup.org. We can tune in our configuration to + support this. + + KY - 2006/02/16 + - Added character encoding to attribute creation property lists. + JML - 2006/01/02 + - Added H5Gcopy() routine to copy objects between while keeping + data in compressed form. QAK - 2005/11/06 + - Added H5Sextent_equal() routine. QAK - 2005/11/06 + - Added HSYS_ERROR which retrieves the system error message and pushes + it to the error stack. This gives more information of the failed + system call. AKC - 2005/08/04 + - Added H5F_OBJ_LOCAL flag to H5Fget_obj_count() & H5Fget_obj_ids(), to + allow querying for objects in file that were opened with a particular + file ID, instead of all objects opened in file with any file ID. + QAK - 2005/06/01 + - Added H5T_CSET_UTF8 character set to mark datatypes that use the + UTF-8 Unicode character encoding. Added tests to ensure that + library handles UTF-8 object names, attributes, etc. -JL 2005/05/13 + - HDF5 supports collective MPI-IO for irregular selection with HDF5 + dataset. Irregular selection is when users use H5Sselect_hyperslab + more than once for the same dataset. + Currently, not all MPI-IO packages support complicated MPI derived + datatype used in the implementation of irregular + selection INSIDE HDF5. + 1) DEC 5.x is not supporting complicated derived datatype. + 2) For AIX 5.1, + if your poe version number is 3.2.0.19 or lower, + please edit powerpc-ibm-aix5.x under hdf5/config, + Find the line with + << hdf5_mpi_complex_derived_datatype_works>> + and UNCOMMENT this line before the configure. + check poe version with the following command: + lpp -l all | grep ppe.poe + 3) For Linux cluster, + if mpich version is 1.2.5 or lower, collective irregular selection + IO is not supported, internally independent IO is used. + 4) For IRIX 6.5, + if C compiler version is 7.3 or lower, collective irregular selection + IO is not supported, internally independent IO is used. + 5) For platforms which internally used mpich, if the + mpich version is 1.2.5 or lower, please find the + corresponding config file and add + hdf5_mpi_complex_derived_datatype_works='no' at the + end of the configuration file. For example, at NCSA + SGI Altix, the internal mpich library is 1.2.5. So + hdf5_mpi_complex_derived_datatype_works='no' should be + added at the end of the config file ia64-linux-gnu. + KY - 2005/09/12 + We also found not all MPI-IO packages support collective IO with one + or more processes to have no contributions to IO. + For mpich version 1.2.6 or lower and all IRIX machine, + if the library checks that there are no IO contributions for some + processes, collective IO request is replaced with + independent inside HDF5. + KY - 2006/05/04 + + - HDF5 N-bit filter + HDF5 support N-bit filter from this version, + The N-Bit filter is used effectively for compressing data of N-Bit + datatype as well as compound and array datatype with N-Bit fields. + KY - 2005/04/15 + - HDF5 scaleoffset filter + HDF5 supports scaleoffset filter for users to do data + compression through HDF5 library. + Scale-Offset compression performs a scale and/or offset operation + on each data value and truncates the resulting value to a minimum + number of bits and then stores the data. + Scaleoffset filter supports floating-point and integer datatype. + Please check the HDF5 reference manual for this. + KY - 2005/06/06 + - Retired SRB vfd (--with-srb). Functions H5Pset_fapl_srb and + H5Pget_fapl_srb were removed. EIP - 2005/04/07 + - Retired GASS vfd (--with-gass). Functions H5Pset_fapl_gass and + H5Pget_fapl_gass are removed too. AKC - 2005/3/3 + - Pablo was removed from the source code EIP - 2005/01/21 + - Modified registration of SZIP to dynamically detect the presence + or absence of the encoder. Changed configure and Makefiles, + and tests to dynamically detect encoder. BEM - 2004/11/02 + - Added function H5Pget_data_transform, together with the previously + added H5Pset_data_transform, to support the data transform + feature. AKC - 2004/10/26 + - Compound datatype has been enhanced with a new feature of size + adjustment. The size can be increased and decreased(without + cutting the last member) as long as it doesn't go down to zero. + No API change is involved. SLU - 2004/10/1 + - Put back 6 old error API functions to be backward compatible with + version 1.6. They are H5Epush, H5Eprint, H5Ewalk, H5Eclear, + H5Eset_auto, H5Eget_auto. Their new equivalent functions are + called H5Epush_stack, H5Eprint_stack, H5Ewalk_stack, + H5Eclear_stack, H5Eset_auto_stack, H5Eget_auto_stack. SLU - + 2004/9/2 + - 4 new API functions, H5Tencode, H5Tdecode, H5Sencode, H5Sdecode were + added to the library. Given object ID, these functions encode and + decode HDF5 objects(data type and space) information into and from + binary buffer. SLU - 2004/07/21 + - Modified the way how HDF5 calculates 'pixels_per_scanline' parameter for + SZIP compression. Now there is no restriction on the size and shape of the + chunk except that the total number of elements in the chunk cannot be + bigger than 'pixels_per_block' parameter provided by the user. + EIP - 2004/07/21 + - Added support for SZIP without encoder. Added H5Zget_filter_info + and changed H5Pget_filter and H5Pget_filter_by_id to support this + change. JL/NF - 2004/06/30 + - SZIP always uses K13 compression. This flag no longer needs to + be set when calling H5Pset_szip. If the flag for CHIP + compression is set, it will be ignored (since the two are mutually + exclusive). JL/NF - 2004/6/30 + - A new API function H5Fget_name was added. It returns the name + of the file by object(file, group, data set, named data type, + attribute) ID. SLU - 2004/06/29 + - Added support for user defined identifier types. NF/JL - 2004/06/29 + - A new API function H5Fget_filesize was added. It returns the + actual file size of the opened file. SLU - 2004/06/24 + - New Feature of Data transformation is added. AKC - 2004/05/03. + - New exception handler for datatype conversion is put in to + replace the old overflow callback function. This exception + handler is set through H5Pset_type_conv_cb function. + SLU - 2004/4/27 + - Added option that if $HDF5_DISABLE_VERSION_CHECK is set to 2, + will suppress all library version mismatch warning messages. + AKC - 2004/4/14 + - A new type of dataspace, null dataspace(dataspace without any + element) was added. SLU - 2004/3/24 + - Data type conversion(software) from integer to float was added. + SLU - 2004/3/13 + - Data type conversion(software) from float to integer was added. + Conversion from integer to float will be added later. + SLU -2004/2/4 + - Added new H5Premove_filter routine to remove I/O pipeline filters + from dataset creation property lists. PVN - 2004/01/26 + - Added new 'compare' callback parameter to H5Pregister & H5Pinsert + routines. QAK - 2004/01/07 + - Data type conversion(hardware) between integers and floats was added. + SLU 2003/11/21 + - New function H5Iget_file_id() was added. It returns file ID given + an object(dataset, group, or attribute) ID. SLU 2003/10/29 + - Added new fields to the H5G_stat_t for more information about an + object's object header. QAK 2003/10/06 + - Added new H5Fget_freespace() routine to query the free space in a + given file. QAK 2003/10/06 + - Added backward compatability with v1.6 for new Error API. SLU - + 2003/09/24 + - Changed 'objno' field in H5G_stat_t structure from 'unsigned long[2]' + to 'haddr_t'. QAK - 2003/08/08 + - Changed 'fileno' field in H5G_stat_t structure from 'unsigned long[2]' + to 'unsigned long'. QAK - 2003/08/08 + - Changed 'hobj_ref_t' type from structure with array field to 'haddr_t'. + QAK - 2003/08/08 + - Object references (hobj_ref_t) can now be compared with the 'objno' + field in the H5G_stat_t struct for testing if two objects are the + same within a file. QAK - 2003/08/08 + - Switched over to new error API. SLU - 2003/07/25 Parallel Library: ----------------- + - Added mpich2 as a testing "platform" informally. AKC - 2005/9/28. + - A dataset created in serial mode with H5D_ALLOC_TIME_INCR allocation + setting was not extendible, either explicitly by H5Dextend or + implicitly by writing to unallocated chunks. Library now allocates + more space when needed or directed if the file is opened by parallel + mode, independent of what the dataset allocation mode is. + CC/AKC - 2005/08/29. + - Allow compressed, chunked datasets to be read in parallel. + QAK - 2004/10/04 + - Add options of using atomicity and file-sync to test_mpio_1wMr. + AKC - 2003/11/13 + - Added parallel test, test_mpio_1wMr, which tests if the + underlaying parallel I/O system is conforming to the POSIX + write/read requirement. AKC - 2003/11/12 Fortran Library: ---------------- + - added support for shared Fortran libraries. -JML 2005/09/20 + - added missing h5tget_member_class_f function + EIP 2005/04/06 + - added new functions h5fget_name_f and h5fget_filesize_f + EIP 2004/07/08 + - h5dwrite/read_f and h5awrite/read_f functions only accept dims parameter + of the type INTEGER(HSIZE_T). + - added support for native integers of 8 bytes (i.e. when special + compiler flag is specified to set native fortran integers to 8 bytes, + for example, -i8 flag for PGI and Absoft Fortran compilers, + -qintsize=8 flag for IBM xlf compiler). + EIP 2005/06/20 + - added support for "big" REAL and DOUBLE PRECISION types + (usually the size is specified by compilers flags like + -r8, -r16, etc.) + Known problem: multi file test fails when REAL is 16 bytes. + EIP 2005/09/8 C++ Library: ---------------- + - added support for shared C++ libraries. -JML 2005/09/20 + - Added missing member functions + H5::CompType::getMemberArrayType + H5::CompType::getMemberVarLenType + H5::AbstractDs::getArrayType + H5::AbstractDs::getVarLenType + H5::CommonFG::openArrayType + H5::CommonFG::openVarLenType + H5::PropList::copyProp -- this will replace the current + H5::PropList::copyProp in later releases due + to incorrect prototype. + H5::IdComponent::getHDFObjType + BMR - 2005/08/08 Tools: ------ + - h5repack and h5diff changed command line parameter syntax to be + similar to h5dump, adding also long switch names. PVN - 2008/1/16 + - h5repack now supports adding multiple filters to all objects. + PVN - 2008/1/16 + - h5dump lists groups and attributes in requested orders (by name and + creation order, both ascending and descending). PVN - 2007/10/5 + - h5import imports string (text) data. PVN - 2007/10/5 + - h52gif and gif2h5: Both these tools were revised to include the High + Level Image API support, and tests were added to /hl/tools/gif2h5. + PVN - 2007/04/13 + - h5dump: added support for double long type H5T_NATIVE_LDOUBLE. PVN + 2007/03/13 + - h5dump: added support for binary output, see usage. PVN 2007/03/13 + - h5repack: added support for the new nbit and scaleoffset filters. + PVN - 2007/05/07 + - h5repack: now uses the API function H5Ocopy (of the tool h5copy) to + recreate objects if there is not a user input for changes. PVN - + 2007/05/07 + - h5repack: added support for reading and repacking by hyperslabs for + large files. PVN - 2007/03/01 + - h5repack: a new option allows the copy using the file type (default) + instead of the previous conversion to native type. PVN - 2007/03/01 + - h5repack: output the percentage of compression used. PVN - 2007/03/01 + - h5diff: added support for -p option for unsigned long_long data. PVN + - 2007/02/26 + - h5diff: added support for comparing dataset regions. PVN - 2007/02/20 + - h5diff: added support for reading and comparing by hyperslabs for large files. + PVN - 2007/02/20 + - h5diff: printing of dataset dimensions along with dataset name. PVN -2007/02/19 + - h5dump now uses the new API function H5Rget_name to display the name + of the dataset referenced instead of its ID. PVN - 2007/02/19 + - Added new tool, h5mkgrp. QAK - 2007/02/14 + - Added new tool, h5copy. PVN - 2006/7/15 + - Removed obsolete pdb2hdf5 tool from tools/misc -JML 2005/10/24 + - Added build_h5perf_alone.sh that builds h5perf by standalone mode. + AKC - 2005/09/18. + - Sped up h5dump on files with large numbers of objects. + QAK - 2005/08/25 + - Added a standalone mode for building h5perf. AKC - 2005/08/12 + - new tool, h5jam. See reference manual. 2004/10/08 + - h5repack.sh did not report errors encountered during tests. It does + now. AKC - 2004/04/02 + - Added the MPI-I/O and MPI-POSIX drivers to the list of VFL drivers + available for h5dump and h5ls. RPM & QAK - 2004/02/01 + - Added option --vfd= to h5ls to allow a VFL driver to be selected + by a user. RPM & QAK - 2004/02/01 + - Added option -showconfig to compiler tools (h5cc,h5fc,h5c++). + AKC - 2004/01/08 + - Install the "h5cc" and "h5fc" tools as "h5pcc" and "h5pfc" + respectively if library is built in parallel mode. + WCW - 2003/11/04 + - Added metadata benchmark (perform/perf_meta). SLU - 2003/10/03 + - Changed output of "OID"s from h5dump from "<number>-<number>" to + "<number". This affects both the "regular" and XML output. + QAK - 2003/08/08 + - Changed output of file IDs and "OID"s from h5ls from + "<number>:<number>:<number>:<number>" to "<number>:<number>" + QAK - 2003/08/08 High-Level APIs: ------ + - Fortran interfaces for the Image, Table and Lite APIs. PVN - 2007/5/1 + - New HDF5 Dimension Scale API (H5DS) allows dimension scales to be + created in an HDF5 file and associated with specific datasets. PVN - 2007/5/1 + - There are two new functions in the Lite library, H5LTtext_to_dtype + and H5LTdtype_to_text. H5LTtext_to_dtype creates a HDF5 data type + given a text description; H5LTdtype_to_text converts a data type + to text description. Only DDL definition is supported as text + desciption now. SLU - 2006/05/17 + - Added Packet Table API for creating tables with less overhead than + H5TB API. Added C++ wrapper for Packet Tables. See documentation. + JML - 2004/03/28 Documentation ------------- + - The documentation for this release is largely complete, but + trails the source code. A few of the newer functions are + not yet documented. FMB - 2007/04/18 + - The user documents for this release can be accessed directly at + this location: + http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/doc/ + The most recent document versions (updated daily) in the + 1.8 development branch can be accessed at this location: + http://www.hdfgroup.uiuc.edu/HDF5/doc_dev_snapshot/H5_dev/ + FMB - 2007/04/18 + Support for new platforms, languages and compilers. ======================================= - -Bug Fixes since HDF5-1.8.0 release + - Added support for Free-BSD on amd64 with GNU C and Fortran compilers + 4.2.1 + EIP - 2007/06/25 + - Added support for sequential and parallel libraries for Intel 64 Linux + cluster (abe.ncsa.uiuc.edu). Among three MPICH packages available on + this machine, only Open MPI works. The VMI has seg fault in hyperslab.c + and bittests.c tests. The MVAPICH2 complained about mpd not running + the parallel test. (see Known Problems section for more info) + EIP - 2007/06/25 + - Added support for HPUX11.23 for both 32 and 64-bit; HDF5 C++ + - Added support for 64-bit Windows with Visual Studio .NET and 2005. + SJW - 2007/06/25 + - Added suport for HPUX11.23 for both 32 and 64-bit; HDF5 C++ + shared library is not supported with +DD64 flag. + EIP - 2006/06/22 + - Added support for VAX floating numbers for Alpha Open VMS 7.3.2 + EIP - 2006/05/05 + - Fixed broken make.com files in tools directories + EIP - 2006/05/05 + - Added support for Alpha Open VMS 7.3.2 EIP - 2006/04/15 + - Added support for Cray X1. JML - 2005/10/03 + - PGI Fortran compiler is supported on Linux64 systems (x86_64) + EIP - 2004/08/19 + - Absoft compiler f95 v9.0 supported on Linux 2.4 + EIP - 2004/07/29 + - HDF5 Fortran APIs are supported on Mac OSX with IBM XL Fortran + compiler version 8.1. This is a default compiler. + - HDF5 Fortran APIs are supported on MAC OSX with Absoft F95 compiler + version 8.2; set F9X environment varibale to f95, for example + setenv F9X f95 + Use --disable-shared --enable-static configure flags when Absoft + compiler is used. + EIP - 2004/07/27 + - HDF5 Fortran APIs are supported on MAC OSX with IBM XL Fortran + Compiler version 8.1 Use "--disable-shared --enable-static" + configure flags along with the "--enable-fortran" flag to build + Fortran library. EIP - 2004/01/07 + +Bug Fixes since HDF5-1.6.0 release ================================== Library ------- - - Fixed the problem with the searching of target file for H5Lcreate_external(). - The searching pattern will depend on whether the target file's - pathname is an absolute or a relative path. Please see the description - in the RM for H5Lcreate_external(). (VC - 4/8/08) - - Fixed possible file corruption bug when encoding datatype - descriptions for compound datatypes whose size was between - 256 & 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 handle invalid location - ID correctly. (QAK - 2008/03/11) - + - Changed library's behavior for reading files that might have + corrupted object header information from a previous (buggy) + version of the library. By default, the library now rebuilds the + correct object header information instead of issuing an error. + Previous "strict" file format interpretation can be enabled with + the "--enable-strict-format-checks" configure option. + QAK - 2008/01/13 + - Fixed several bugs with writing fill values for datasets that have + a variable-length datatype or component datatype. QAK - 2007/06/19 + - STDIO driver didn't support files bigger than 2GB because the OFFSET + parameter of fseek is of type LONG INT, not big enough for big files. + Use fseeko instead for big files if it's available on the system. + SLU - 2007/4/5 + - Fixed a bug in H5Sselect_valid() that caused an incorrect value to + be returned (0) instead of FAIL on error conditions such as the + selection or extent not being defined. CMC - 2007/01/17 + - Fixed the MULTI driver problem (Bug #731) that corruptted the data. + SLU - 2007/1/12 + - Fixed file corruption bug which could write an incorrect number of + messages to an object's header under certain circumstances. + Generally, the sequence of actions to generate this bug looks + like this: + - Create an object + - Close the file + - Re-open the file + - Add 2 (or more) attributes to the object + - Close the file + - Re-open the file + - Delete one of the attributes on the object + - Add a smaller attribute to the object + - Delete the smaller atttribute on the object + - Add a larger attribute on the object + + After this, the number of header messages stored for the object + will be off by one. Other sequences of modifying attributes on an + object could also trigger this bug. If you are opening an + object and the bottom few messages of the HDF5 error stack + resembles this, the object has been affected by this bug: + + #007: ../../hdf5_v1.6/src/H5C.c line 3887 in H5C_load_entry(): unable to load entry + major(08): Meta data cache layer + minor(40): Unable to load metadata into cache + #008: ../../hdf5_v1.6/src/H5Ocache.c line 332 in H5O_load(): corrupt object header - too few messages + major(12): Object header layer + minor(40): Unable to load metadata into cache + + Specifically, "corrupt object header" is the best string to search + for in the HDF5 error stack output. + + If your files have been affected by this bug, or you are concerned + that your files might have been, please contact the HDF Helpdesk + at help@hdfgroup.org for a tool to detect and repair files + affected by this problem. QAK - 2006/6/16 + - Fixed various problems with retrieving names of objects, especially + with mounted files. QAK - 2005/12/25 + - Fixed core dump when closing root groups opened through two different + file handles that operate on the same actual file. QAK - 2005/10/02 + - Corrected errors when performing various operations on a group opened + by dereferencing an object reference. QAK - 2005/07/30 + - Fixed a bug with named datatypes where a copy of a named datatype + used to create a dataset would accidentally use the original + named datatype for the dataset's datatype. QAK - 2005/07/23 + - Made H5Fget_name() be consistent and always return name of actual + file the ID is in. (Instead of the name of the top file in a + file mounting hierarchy). QAK - 2005/07/19 + - Reworked internal file mounting semantics to hopefully eliminate + mounting problems. We now require that files that are mounting + together all have the same "file close degree". QAK - 2005/07/19 + - More bug fixes on holding open files that are mounted and have + IDs open. QAK - 2005/07/14 + - Don't unmount child files until the parent file actually closes. + (Previously, if an object is holding open a file, the child files + would get unmounted too early). QAK - 2005/07/05 + - Fixed bug where unmounted files could cause the library to go into + an infinite loop when shutting down. QAK - 2005/06/30 + - The library didn't save the information of family driver in file. + The original file member size was lost after file was closed (see + bug #213). This has been fixed by saving driver name and member + file size in the superblock. SLU - 2005/6/24 + - Fixed bug with hyperslab selections that use selection offsets and + operate on chunked datasets going into infinite loop or dumping + core. QAK - 2005/06/17 + - Corrected memory leak and possible corruption when opening a group. + QAK - 2005/06/17 + - Added check for opaque datatype tags being too long (check against + H5T_OPAQUE_TAG_MAX, currently set to 256). QAK - 2005/06/14 + - Fixed various errors in maintaining names for open objects in the + face of unusual mount & unmount operations. QAK - 2005/06/08 + - "SEMI" and "STRONG" file close degree settings now apply only to the + particular file ID being closed, instead of operating on all open + file IDs for a given file. QAK - 2005/06/01 + - For family driver, the library didn't save member size in file. + When file is reopened, the size of 1st member file determine the + member size. Now member size is saved in file and is used to + define member file size. Wrong file access property of member size + will result in a failure. Using any other driver except family + will cause library to return error. So is multi driver. SLU - + 2005/05/24 + - Fixed error in opening object in group that was opened in mounted + file which has been unmounted. QAK - 2005/03/17 + - Fixed a racing condition in MPIPOSIX virtual file drive close + function. Now all processes must completed the close before any + of them is returned. This prevents some "faster" processes start + accessing the file for another purpose (e.g., open with truncate) + while other "slower" processes have not closed the same file with + the previous purpose. AKC - 2005/03/01 + - H5Tget_member_value calls for enum datatype didn't return correct + value if H5Tenum_valueof was called first. It's fixed. SLU - + 2005/02/08 + - For variable-length string, H5Tget_class returned H5T_STRING as its + class. But H5Tdetect_class and H5Tget_member_class considered it + as H5T_VLEN. This is fixed to let all these 3 functions treat it + as H5T_STRING. SLU - 2005/02/08 + - The byte order of 1-byte integer types was fixed as little endian + even on a big-endian machine. This has been corrected. SLU - + 2005/02/07 + - Fix segmentation fault when calling H5Fflush with an attribute that + hasn't had a value written to it open. QAK - 2004/10/18 + - Back up supporting bitfield and time types in H5Tget_native_type. + Leave it to future support. The function simply returns error + message of "not support" for bitfield and time types. + SLU - 2004/10/5 + - Fixed address check in Core VFL driver to avoid spurious address/size + overflows for odd valued addresses and/or sizes. QAK - 2004/09/27 + - Fixed parallel bug in which some processes attempted collective + I/O while others did independent I/O. Bug appeared when some + processes used point selections, and others didn't. JRM - 2004/9/15 + - Corrected error where dataset region references were written in an + incorrect way on Cray machines. PVN & QAK - 2004/09/13 + - The H5Tget_native_type now determines the native type for integers + based on the precision. This is to avoid cases of wrongly converting + an int to a short in machines that have a short of 8 bytes but with + 32bit precision (e.g Cray SV1). PVN - 2004/09/07 + - Changed H5Dread() to not overwrite data in an application's buffer + with garbage when accessing a chunked dataset with an undefined + fill value and an unwritten chunk is uncountered. QAK - 2004/08/25 + - Fixed error which could cause a core dump when a type conversion + routine was registered after a compound datatype had been + converted and then an equivalment compound datatype was converted + again. QAK - 2004/08/07 + - Fixed memory overwrite when encoding "multi" file driver information + for file's superblock. QAK - 2004/08/05 + - Fixed obscure bug where a filter which failed during chunk allocation + could allow library to write uncompressed data to disk but think + the data was compressed. QAK - 2004/07/29 + - Fixed bug where I/O to an extendible chunked dataset with zero-sized + dimensions would cause library to fail an assertion. + QAK - 2004/07/27 + - Fixed bug where chunked datasets which have filters defined, + allocation time set to "late" and whose chunks don't align with + the dataspace bounds could have incorrect data stored when + overwriting the entire dataset on the first write. QAK - 2004/07/27 + - Added check to ensure that dataspaces have extents set. JML-2004/07/26 + - Fixed bug on some Solaris systems where HDF5 would try to use + gettimeofday() when that function didn't work properly. + JML - 2004/07/23 + - Fixed bug in H5Sset_extent_simple where setting maximum size to + non-zero, then to zero would cause an error. JML - 2004/07/20 + - Allow NULL pointer for buffer parameter to H5Dread & H5Dwrite + when not writing data ("none" selection or hyperslab or point + selection with no elements defined). QAK - 2004/07/20 + - Calling H5Gcreate() on "/" or "." throws an error instead of + failing quietly. JML - 2004/07/19 + - Fixed bug where setting file address size to be very small could + trigger an assert if the file grew to more than 64 KB. Now throws + an error and data can be recovered. JL/NF - 2004/07/14 + - Fixed bug where "resurrecting" a dataset was failing. + QAK - 2004/07/14 + - Fixed bug where incorrect data could be read from a chunked dataset + after it was extended. QAK - 2004/07/12 + - Fixed failure to read data back from file of compound type with + variable-length string as field. SLU - 2004/06/10 + - Fixed potential file corruption bug when a block of metadata could + overlap the end of the internal metadata accumulator buffer and + the buffer would be extended correctly, but would incorrectly + change it's starting address. QAK - 2004/06/09 + - Opaque datatype with no tag failed for some operations. Fixed. + SLU - 2004/6/3 + - Fixed potential file corruption bug where dimensions that were + too large (a value greater than could be represented in 32-bits) + could cause the incorrect amount of space to be allocated in a + file for the raw data for the dataset. QAK - 2004/06/01 + - Fixed dtypes "sw long double -> double" failure in QSC class + machines. AKC - 2004/4/16 + - Fixed problem with fletcher32 filter when converting data of different + endianess. PVN - 2004/03/10 + - Fixed problem with H5Tget_native_type() not handling opaque fields + correctly. QAK - 2004/01/31 + - Fixed several errors in B-tree deletion code which could cause a + B-tree (used with groups and chunked datasets) to become corrupt + with the right sequence of deleted objects. QAK - 2004/01/19 + - Fixed small internal memory leaks of fill-value information. + QAK - 2004/01/13 + - Fixed bug that caused variable-length datatypes (strings or sequences) + used for datasets in files with objects that were unlinked to + fail to be read/written to a file. QAK - 2004/01/13 + - Detect situation where szip 'pixels per block' is larger than the + fastest changing dimension of a dataset's chunk size and disallow + this (due to limits in szip library). QAK - 2003/12/31 + - Fixed bug with flattened hyperslab selections that would generate + incorrect hyperslab information with certain high-dimensionality + combinations of start/stride/count/block information. + QAK - 2003/12/31 + - Fixed bug with variable-length datatypes used in compound datatypes. + SLU - 2003/12/29 + - Fixed bug in parallel I/O routines that would cause reads from + "short datasets" (datasets which were only partially written out) + to return invalid data. QAK & AKC - 2003/12/19 + - Fixed bug where scalar dataspaces for attributes were reporting as + simple dataspaces. QAK - 2003/12/13 + - Fixed problem with selection offsets of hyperslab selections in + chunked datasets causing the library to go into an infinite loop. + QAK - 2003/12/13 + - Fixed H5Giterate to avoid re-using index parameter after iteration + callback has been called (allows iteration callback to modify the + index parameter itself). QAK - 2003/12/06 + - Fixed various floating-point conversion problems, including a + change which could corrupt data when converting from double->float. + QAK - 2003/11/24 + - Changed "single process" metadata writing in library to collective + I/O by all processes, in order to guarantee correct data being + written with MPI-I/O. QAK - 2003/11/20 + - Fixed problems with fill values and variable-length types and also + I/O on VL values that were set to NULL. QAK - 2003/11/08 + - Fixed problems with MPI datatypes that caused ASCI Q machine to + hang. QAK - 2003/10/28 + - Removed HDF5_MPI_PREFER_DERIVED_TYPES environment variable support, + since it had no benefit. QAK - 2003/10/28 + - Single hyperslab selections (which were set with only one call to + H5Sselect_hyperslab) that had dimensions that could be "flattened" + but were interspersed with dimensions that could not be flattened + were not correctly handled, causing core dumps. QAK - 2003/10/25 + - Fixed incorrect datatype of the third parameter to the Fortran90 + h5pset(get)_cache_f subroutine (INTEGER to INTEGER(SIZE_T)) + EIP - 2003/10/13 + - Fixed problems with accessing variable-length data datatypes on + Crays. QAK - 2003/10/10 + - Fixed potential file corruption bug when too many object header + messages (probably attributes, from a user perspective) were + inserted into an object header and certain other conditions were + met. QAK - 2003/10/08 + - Changed implementation of internal ID searching algorithm to avoid + O(n) behavior for many common cases. QAK - 2003/10/06 + - Allow partial parallel writing to compact datasets. QAK - 2003/10/06 + - Correctly create reference to shared datatype in attribute, instead + of making a copy of the shared datatype in the attribute. + QAK - 2003/10/01 + - Revert changes which caused files >2GB to fail when created with + MPI-I/O file driver on certain platforms. QAK - 2003/09/16 + - Allow compound datatypes to grow in size. SLU - 2003/09/10 + - Detect if a type is already packed before attempting to pack it + again or check if it is locked. SLU - 2003/09/10 + - Corrected bug when opening a file twice with read-only permission + for one open and then closing the read-only access file ID would + generate an error. QAK - 2003/09/10 + - Corrected bug in repeated calls to H5Pget_access_plist() which would + incorrectly manage reference counts of internal information and + eventually blow up. QAK - 2003/09/02 + - Return rank of the array datatype on successful call to + H5Tget_array_dims(). QAK - 2003/08/30 + - Corrected bug in H5Tdetect_class which was not correctly detecting + datatype classes of fields in nested compound datatypes in some + circumstances. QAK - 2003/08/30 + - Corrected bug in sieve buffer code which could cause loss of data + when a small dataset was created and deleted in quick succession. + QAK - 2003/08/27 + - Corrected bug in H5Gget_objname_by_idx which was not allowing NULL + for the name when just querying for the object name's length. + QAK - 2003/08/25 + - Corrected bug in variable-length string handling which could + generate a core dump on writing variable-length strings as part + of a compound datatype on certain architectures. QAK - 2003/08/25 + - Corrected bug in H5Tget_native_type which would incorrectly compute + the size of certain compound datatypes and also incorrectly + compute the offset of the last field for those compound datatypes. + QAK - 2003/08/25 + - Corrected bug in H5Tget_native_type which would drop string datatype + metadata (padding, etc.) QAK - 2003/08/25 + - Corrected bugs in H5Gget_num_objs, H5Gget_objname_by_idx and + H5Gget_objtype_by_idx to allow them to accept location IDs, not just + group IDs. QAK - 2003/08/21 + - Corrected bug when using scalar dataspace for memory selection and + operating on chunked dataset. QAK - 2003/08/18 + - Corrected bugs with multiple '/' characters in names for H5Glink + and H5Gunlink. QAK - 2003/08/16 + - Corrected bug with user blocks that didn't allow a user block to + be inserted in front of a file after the file was created. + QAK - 2003/08/13 + - Corrected errors with using point selections to access data in + chunked datasets. QAK - 2003/07/23 + - Corrected error with variable-length datatypes and chunked datasets + caused H5Dwrite to fail sometimes. QAK - 2003/07/19 + - Modified library and file format to support storing indexed storage + (chunked dataset) B-tree's with non-default internal 'K' values. + QAK - 2003/07/15 + - Returned H5T_BKG_TEMP support to library after it was accidentally + removed. QAK - 2003/07/14 Configuration ------------- + - Configure can now use any tr command. No more need for + defining variable TR nor is it supported. -AKC 2006/05/19 + - Parallel I/O with the MPI-I/O driver will no longer work if the + filesystem is not POSIX compliant. The "HDF5_MPI_1_METAWRITE" + environment variable has been removed. QAK - 2004/01/30 + - Fixed the error that cause "make install" to fail because of the + macro definition syntax of "prefix?=..." AKC - 2003/07/22 Performance ------------- + - Optimized I/O for enumerated datatypes that are a superset of source + enumerated datatype. QAK - 2005/03/19 + - More optimizations to inner loops of datatype conversions for + integers and floats which give a 10-50% speedup. QAK - 2003/11/07 + - Hoisted invariant 'if/else's out of inner datatype conversion loop for + integer and floating-point values, giving about a 20% speedup. + QAK - 2003/10/20 Tools ----- - - Fixed bug in h5diff that prevented datasets & attributes with - variable-length string elements from comparing correctly. - (QAK - 2008/02/28) - - h5import bug on Windows w/binary datasets. fread in windows needs a - binary file to be open with 'rb' instead of 'r' otherwise it - terminates execution if an end of file character is found on the - input file. Besides that the binary file generated needs to be open - with 'wb' , otherwise an end of line character is read twice. - (PVN - 2008/02/19) - - 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) - + - Fixed h5dump regarding the display of blocks in hyperslab + selections. PVN 2008/01/16 + - Fixed h5diff regarding the display of NaN (Not a Number) + values. PVN 2008/01/16 + - Fixed h5dump regarding the parsing of binary output parameters. + PVN 2008/01/16 + - Fixed memory problems in h52gif and gif2h5. PVN 2008/01/16 + - Fixed h5repack dealing with NULL references. PVN 2008/01/16 + - Fixed h5dump & h5ls to display attributes in "name" order, rather + than the order they are encountered in the object header. + QAK - 2007/10/04 + - Fixed h5dump regarding the display of named datatypes + attributes. PVN 2007/03/13 + - Fixed h5dump regarding the display of group comments. PVN + 2007/03/13 + - Fixed h5dump regarding the display of hardlinks pointing + to the root group. PVN 2007/03/13 + - Fixed h5diff percentage option -p. PVN 2007/03/05 + - Fixed h5dump that caused array indices greater than 2 ^32-1 + not to be printed correctly - PVN 2007/2/19 + - Fixed h5dump to print attributes data in ASCII if -r option is used. + AKC - 2004/11/18 + - Fixed space utilization reported in h5ls to correct error in formula + used. QAK - 2004/10/22 + - Fixed h5redeploy which sometimes complain too many argument for the + test command. (The complain did not hinder the h5redploy to + proceed correctly.) AKC - 2003/11/03 + - Fixed a segmentation fault of h5diff when percentage option is used. + AKC - 2003/08/27 + - Switched away from tools using internal "fixtype" function(s) to use + H5Tget_native_type() internally. QAK - 2003/08/25 Documentation @@ -111,23 +992,27 @@ Bug Fixes since HDF5-1.8.0 release F90 APIs -------- - - - C++ APIs - -------- - - Fixed bug that caused segfaults in Attribute::read. (BMR - 2008/04/20) - - Fixed bug in PropList::getClassName to use portable HDfree instead - of free. (BMR - 2008/04/20) + - h5pget_driver_f was returning information that could not be + interpreted by fortran application program; fixed. EIP - 2005/04/10 Platforms Tested ================ +Platforms marked with * were not tested for hdf5-1.8.0-rc* release +(This information is somewhat out of date and may be inaccurate. It will be + updated for a later release) - AIX 5.2 (32/64 bit) xlc 8.0.0.11 +* 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 +* AIX 5.3 (32/64 bit) xlc 7.0.0.8 + xlC 7.0.0.8 + xlf 09.01.0000.0007 +* Cray X1 water 3.0.35 Cray Standard C Version 5.4.0.7.4 + Cray Fortran 5.4.0.7.3 + Cray C++ 5.4.0.7.4 FreeBSD 6.2-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305 (duty) g++ 3.4.6 [FreeBSD] 20060305 gcc 4.2.1 20080123 @@ -139,11 +1024,14 @@ Platforms Tested g++ 4.2.1 20080123 gfortran 4.2.1 20080123 +* HP-UX B.11.23 HP aC++/ANSI C B3910B A.06.00 + HP F90 v2.9.2 + HP aC++/ANSI C B3910B A.06.00 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 +* Linux 2.6.9 (RHEL4) Intel 10.0 compilers (abe.ncsa.uiuc.edu) Linux 2.4.21-47 gcc 3.2.3 20030502 (osage) @@ -160,6 +1048,9 @@ Platforms Tested 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 i86pc Sun C 5.7 + Sun Fortran 95 8.1 + Sun C++ 5.7 SunOS 5.10 cc: Sun C 5.8 (linew) f90: Sun Fortran 95 8.2 CC: Sun C++ 5.8 @@ -184,91 +1075,105 @@ Platforms Tested 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 +* Alpha Open VMS 7.3 Supported Configuration Features Summary +(This table was not modified for 1.8.0-rc* release; for information contact help@hdfgroup.org) ======================================== 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 - <blank> = testing incomplete on this feature or platform - W or C indicates workstation or cluster, respectively. - -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 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 -AIX-5.2 32-bit y y y y y y -AIX-5.2 64-bit y y y y y y -Cray XT3 (not tested - for this release) n n n n n n -Windows XP n y(3) n(3) y y y -Windows XP x64 n y(3) n(3) 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 6.2 32-bit n n n y y y -FreeBSD 6.2 64-bit -RedHat EL4 2.6.9 i686 GNU W y(2) y(4) y(2) y y y -RedHat EL4 2.6.9 i686 Intel W n y n y y n -RedHat EL4 2.6.9 i686 PGI W n y n y y n -SuSe Linux 2.6.16 x86_64 GNU (5) W y(2) y n y y y -SuSe Linux 2.6.16 x86_64 Int (5) W n y n y n n -SuSe Linux 2.6.16 x86_64 PGI (5) W n y n y n n -RHL9 Linux 2.4 Xeon Lustre Intel C n y n y y n -RHEL3 Linux 2.4 Xeon Intel W n y n n y n -RHEL4 Linux 2.6 Xeon Lustre Int C n y n y y n -SuSE Linux 2.4 ia64 Intel C y(1) y y y y y -SuSe Linux 2.6.5 - SGI Altix ia64 Intel C n y n y n 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 -SunOS 5.8 32-bit y y y x y -SunOS 5.8 64-bit y y y x y -SunOS 5.10 32-bit y y y x y -SunOS 5.10 64-bit y y y x y -IRIX64_6.5 32-bit y n y x y -IRIX64_6.5 64-bit y y n x y -AIX-5.2 32-bit n n n x n -AIX-5.2 64-bit n n n x n -Cray XT3 (not tested - for this release) n n n x n -Windows XP y y(3) y y y -Windows XP x64 y y(3) y y y -Windows Vista y n n y y -Mac OS X 10.4 Intel Duo y y y x n -FreeBSD 6.2 32-bit y y y x n -FreeBSD 6.2 64-bit y y y x n -RHEL4 2.6.9 i686 GNU W y y(4) y x y -RHEL4 2.6.9 i686 Intel W y y y x n -RHEL4 2.6.9 i686 PGI W y y y x n -SuSE Linux 2.6.16 x86_64 GNU (5) W y y y x y -SuSE Linux 2.6.16 x86_64 Intel(5) W y y y x n -SuSE Linux 2.6.16 x86_64 PGI(5) W y y y x n -RHL9 Linux 2.4 Xeon Lustre Intel C y y y x n -RHEL3 Linux 2.4 Xeon Intel W y n n x n -RHEL4 Linux 2.6 Xeon Lustre Intel C y y y x n -SuSE Linux 2.4 ia64 Intel C y y y x n -SuSe Linux 2.6.5 - SGI Altix ia64 Intel C n n n x n + <blank> = 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 +Cray XT3 (16) n n n n n n +AIX-5.2 & 5.3 32-bit y y y y y y +AIX-5.2 & 5.3 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 +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 +HPUX11.00 y n y x n +HPUX11.23-32bit y n n y n +HPUX11.23-64bit y dna n y n +Cray XT3 (16) n n n n n +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 +Mac OS X 10.4 PowerPC +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. - (2) Using mpich2 1.0.6. - (3) Using Visual Studio 2005 or Cygwin - (4) With PGI and Absoft compilers. - (5) AMD Opteron x86_64 + (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. @@ -405,6 +1310,12 @@ Known Problems the different precision in the values displayed and h5ls appears to be dumping floating-point numbers correctly. +* Before building HDF5 F90 Library from source on Crays + replace H5Aff.f90, H5Dff.f90 and H5Pff.f90 files in the fortran/src + subdirectory in the top level directory with the Cray-specific files + from this site: + ftp://www.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.0-pre/PATCH/ + * 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 @@ -417,6 +1328,23 @@ Known Problems complaining about exit subroutine. Comment out the line IF (total_error .ne. 0) CALL exit (total_error) +* On IA32 and IA64 systems, if you use a compiler other than GCC (such as + Intel's ecc or icc compilers), you will need to modify the generated + "libtool" program after configuration is finished. On or around line 104 of + the libtool file, there are lines which look like: + + # How to pass a linker flag through the compiler. + wl="" + + change these lines to this: + + # How to pass a linker flag through the compiler. + wl="-Wl," + + UPDATE: This is now done automatically by the configure script. However, if + you still experience a problem, you may want to check this line in the + libtool file and make sure that it has the correct value. + * Information about building with PGI and Intel compilers is available in INSTALL file sections 5.7 and 5.8 |