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* [svn-r6549] Purpose:MuQun Yang2003-04-011-4/+452
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This is the first check-in message related to szip support at HDF5 1.6 release Description: szip compression support is required by NASA ESDIS. The compression algorithm is a good compression algorithm for scientific data. In HDF5, we add another filter function to make szip as a default compression package as we did for gzip(or zlib). Solution: In the configure.in and configure, I handled szip exactly the same as what zlib was built into the HDF5. Currently if you don't specify in the configure command line with: ./configure --with-szlib=/..... Unless you put your szip library in your path,you will build the same HDF5 library like before. Also, I only use static szip library to test with HDF5. Platforms tested: Since there are changes of configure.in and configure,I didn't use h5committest. I tested with four platforms. 1) Linux 2.4 (eirene) 2) Solaris 2.7(arabica) 3) windows 2000(VS 6.0) 4) SGI IRIX6.5-64(modi4) For test 1)-3), only basic C tests were done For modi4 test, I tested 64-bit C,parallel and fortran. ALl tests passed, except a warning message from szip library when checksum is used in some order, which doesn't cause any real problems. Misc. update:
* [svn-r6483] Snapshot version 1.5 release 49HDF Admin2003-03-151-9/+9
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* [svn-r6482] Purpose:Bill Wendling2003-03-141-1/+3
| | | | | | Update Description: Added newest ed_* directories in the docs...
* [svn-r6446] Snapshot version 1.5 release 48HDF Admin2003-03-011-9/+9
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* [svn-r6407] Snapshot version 1.5 release 47HDF Admin2003-02-151-9/+9
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* [svn-r6400] Raymond Lu2003-02-121-3/+3
| | | | | | | | | | | Purpose: Change feature Description: Switch to Fletcher32 from Adler32 checksum Platforms tested: arabica, eirene, modi4 Misc. update: MANIFEST and RELEASE.txt updated.
* [svn-r6389] Purpose:Bill Wendling2003-02-101-7/+12
| | | | | | | | | | | | Update Description: Added Flexible Parallel HDF5 support to the ending message that configure spits out. Reordered a few other of the messages so that they're in alphabetical order. Platforms tested: Linux
* [svn-r6386] Purpose:Quincey Koziol2003-02-101-0/+67
| | | | | | | | | | | | | | Bug fix Description: The "system scope" for threads isn't supported on all platforms. Solution: Add detection of this feature to the configure script and check for "H5_HAVE_SYSTEM_SCOPE_THREADS" in the appropriate places. Platforms tested: modi4 w/threadsafe
* [svn-r6383] Purpose:Quincey Koziol2003-02-071-4/+33
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | New feature for developers. Description: Added "function stack" tracing to library. This allows developers (there is no public API) to call H5FS_print within the library and get a listing of the functions traversed to reach that point in the library. Eventually, I may add support for reporting the parameters to each function also... Mainly for debugging parallel I/O programs, but I think it will come in handy in other cases also. The function stack tracking is controlled with a configure switch: --enable-funcstack, which defaults to enabled currently. When we branch for 1.6, we should change the default setting on the branch to be disabled. Also, added a destructor to the thread-specific keys when thread-safety is turned on in the library. Otherwise, they were leaking memory and causing difficult to debug errors in threaded programs (like the test/ttsafe test). Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} FreeBSD 4.7 (sleipnir) w/thread-safety enabled. Misc. update: Updated MANIFEST with new files added (src/H5FS.c & src/H5FDprivate.h) Update release_docs/RELEASE with thread-safety bug fix.
* [svn-r6375] Raymond Lu2003-02-041-1/+8
| | | | | | | | | | | Purpose: New feature Description: Added Adler32 checksum as a filter in pipeline Platforms tested: arabica (fortran), eirene (, C++), modi4 (parallel, fortran) Misc. update: Update release_docs/RELEASE.
* [svn-r6358] Snapshot version 1.5 release 46HDF Admin2003-02-011-9/+9
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* [svn-r6353] Purpose:Bill Wendling2003-01-301-0/+11
| | | | | | | | | | | Update Description: Updated the configure scripts. Fortran and C++ didn't have proper checks for Linux LFS support. Also needed to remove the "-g" flag from the compile line if --enable-production is set. For that, I took how it's being done in HDF5 Lite... Platforms tested: Linux
* [svn-r6317] Purpose:Bill Wendling2003-01-231-3/+47
| | | | | | | | | | | | | | | | | | Bug Fix Description: Some compilers were having problems if we included the -I/usr/include and -L/usr/lib flags which are completely redundant. This could occur if the user configured with something like: ./configure --with-zlib=/usr/include,/usr/lib Solution: Check if the --with-* command is specified with /usr/include and /usr/lib. If so, then don't place them in the compile macros. Platforms tested: Linux, Modi4
* [svn-r6293] Purpose:Albert Cheng2003-01-171-3/+5
| | | | | | | | | | Another patch Description: libtool will fail if pgcc compiler is used. Now apply the patch if gcc is NOT used. Platforms tested: Tested only on eirene because I am sure it is correct and am trying to beat the daily test checkout.
* [svn-r6285] Purpose:Albert Cheng2003-01-151-0/+14
| | | | | | | | | | | | | | | | | | | a patch Description: When intel compilers (icc, ecc) are used in a linux system, the libtool generated has a wrong setting of '$wl" for linking. Put in a "ed ..." command script to edit the generated libtool with the proper setting. The libtool people has fixed this problem. This can ben taken out when that version of libtool is released. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)}? YES. Other platforms/configurations tested? platinum and titan using gcc and intel CC. Misc. update: Update MANIFEST if you add or remove any file. Update release_docs/RELEASE for bug fixes, new features, etc. Update applicable document files too.
* [svn-r6267] Snapshot version 1.5 release 45HDF Admin2003-01-111-9/+10
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* [svn-r6252] Purpose:Quincey Koziol2003-01-091-4/+79
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Lots of performance improvements & a couple new internal API interfaces. Description: Performance Improvements: - Cached file offset & length sizes in shared file struct, to avoid constantly looking them up in the FCPL. - Generic property improvements: - Added "revision" number to generic property classes to speed up comparisons. - Changed method of storing properties from using a hash-table to the TBBT routines in the library. - Share the propery names between classes and the lists derived from them. - Removed redundant 'def_value' buffer from each property. - Switching code to use a "copy on write" strategy for properties in each list, where the properties in each list are shared with the properties in the class, until a property's value is changed in a list. - Fixed error in layout code which was allocating too many buffers. - Redefined public macros of the form (H5open()/H5check, <variable>) internally to only be (<variable>), avoiding innumerable useless calls to H5open() and H5check_version(). - Reuse already zeroed buffers in H5F_contig_fill instead of constantly re-zeroing them. - Don't write fill values if writing entire dataset. - Use gettimeofday() system call instead of time() system when checking the modification time of a dataset. - Added reference counted string API and use it for tracking the names of objects opening in a file (for the ID->name code). - Removed redundant H5P_get() calls in B-tree routines. - Redefine H5T datatype macros internally to the library, to avoid calling H5check redundantly. - Keep dataspace information for dataset locally instead of reading from disk each time. Added new module to track open objects in a file, to allow this (which will be useful eventually for some FPH5 metadata caching issues). - Remove H5AC_find macro which was inlining metadata cache lookups, and call function instead. - Remove redundant memset() calls from H5G_namei() routine. - Remove redundant checking of object type when locating objects in metadata cache and rely on the address only. - Create default dataset object to use when default dataset creation property list is used to create datasets, bypassing querying for all the property list values. - Use default I/O vector size when performing raw data with the default dataset transfer property list, instead of querying for I/O vector size. - Remove H5P_DEFAULT internally to the library, replacing it with more specific default property list based on the type of property list needed. - Remove redundant memset() calls in object header message (H5O*) routines. - Remove redunant memset() calls in data I/O routines. - Split free-list allocation routines into malloc() and calloc()- like routines, instead of one combined routine. - Remove lots of indirection in H5O*() routines. - Simplify metadata cache entry comparison routine (used when flushing entire cache out). - Only enable metadata cache statistics when H5AC_DEBUG is turned on, instead of always tracking them. - Simplify address comparison macro (H5F_addr_eq). - Remove redundant metadata cache entry protections during dataset creation by protecting the object header once and making all the modifications necessary for the dataset creation before unprotecting it. - Reduce # of "number of element in extent" computations performed by computing and storing the value during dataspace creation. - Simplify checking for group location's file information, when file has not been involving in file-mounting operations. - Use binary encoding for modification time, instead of ASCII. - Hoist H5HL_peek calls (to get information in a local heap) out of loops in many group routine. - Use static variable for iterators of selections, instead of dynamically allocation them each time. - Lookup & insert new entries in one step, avoiding traversing group's B-tree twice. - Fixed memory leak in H5Gget_objname_idx() routine (tangential to performance improvements, but fixed along the way). - Use free-list for reference counted strings. - Don't bother copying object names into cached group entries, since they are re-created when an object is opened. The benchmark I used to measure these results created several thousand small (2K) datasets in a file and wrote out the data for them. This is Elena's "regular.c" benchmark. These changes resulted in approximately ~4.3x speedup of the development branch when compared to the previous code in the development branch and ~1.4x speedup compared to the release branch. Additionally, these changes reduce the total memory used (code and data) by the development branch by ~800KB, bringing the development branch back into the same ballpark as the release branch. I'll send out a more detailed description of the benchmark results as a followup note. New internal API routines: Added "reference counted strings" API for tracking strings that get used by multiple owners without duplicating the strings. Added "ternary search tree" API for text->object mappings. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} Other platforms/configurations tested? FreeBSD 4.7 (sleipnir) serial & parallel Solaris 2.6 (baldric) serial
* [svn-r6231] Purpose:Albert Cheng2003-01-031-4/+112
| | | | | | | | | | | | | | | new feature Description: Added MPICH/MPE instrumentation support. All source code are bracketed by the macro H5_HAVE_MPE. Use "--enable-mpe" to configure it in. Currently only worked in Eirene because the MPE library is not installed in all machines yet. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)}? Yep. Other platforms/configurations tested? --enable-mpe feature tested in Eirene.
* [svn-r6221] Snapshot version 1.5 release 44HDF Admin2002-12-211-9/+9
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* [svn-r6193] Snapshot version 1.5 release 43HDF Admin2002-12-071-9/+9
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* [svn-r6134] Purpose:Albert Cheng2002-11-241-78/+0
| | | | | | | | | Cleanup Description: Removed the option (--enable-parallel=mpich). It did not work. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)}? All passed.
* [svn-r6133] Snapshot version 1.5 release 42HDF Admin2002-11-231-9/+9
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* [svn-r6122] Purpose:Quincey Koziol2002-11-201-9/+9
| | | | | | | Bump version number Description: I made a snapshot available for the SAF team, so bump the version number.
* [svn-r6110] Purpose:Quincey Koziol2002-11-201-6/+1
| | | | | | | | | | | | | | | Code cleanup/new feature Description: Removed poorly named H5_HAVE_COMPRESSION flag in favor of H5_HAVE_FILTER_DEFLATE. Added new test files for "missing filter" testing. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} FreeBSD 4.7 (sleipnir)
* [svn-r6070] Purpose:Quincey Koziol2002-11-111-4/+55
| | | | | | | | | | | | | | | | | | | | | | | New feature. Description: Add in '--enable-filters=filter1,filter2' flag to configure script. This can also be used as '--enable-filters=all' or just '--enable-filters' to enable all the internal I/O filters in the library. This flag can also be set to '--disable-filters' to disable all the internal I/O filters. Individual filters can not be disabled due to the limitations of autoconf. Additionally, added "H5_HAVE_FILTER_<foo>" macros to H5pubconf.h header file, so the presence of each filter can be detected. This is in preparation for Kent's shuffling filter to be imported shortly. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} Tested FreeBSD 4.7 (sleipnir) also
* [svn-r6050] Snapshot version 1.5 release 40HDF Admin2002-11-021-9/+9
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* [svn-r6033] Snapshot version 1.5 release 39HDF Admin2002-10-261-9/+9
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* [svn-r6027] Purpose:Bill Wendling2002-10-231-4/+23
| | | | | | | | | Update Description: Added new files to the MANIFEST and added a new configure switch for enabling building of the Flexible parallel HDF5 module. Platforms tested: Modi4 Eirene Arabica
* [svn-r5979] Snapshot version 1.5 release 38HDF Admin2002-10-121-9/+9
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* [svn-r5973] Purpose:Pedro Vicente Nunes2002-10-091-1/+2
| | | | | | | | | added h5fiff to configure and makefiles Platforms tested: linux 2.4.18
* [svn-r5949] Snapshot version 1.5 release 37HDF Admin2002-09-281-9/+9
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* [svn-r5927] Snapshot version 1.5 release 36HDF Admin2002-09-141-9/+9
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* [svn-r5912] Snapshot version 1.5 release 35HDF Admin2002-09-071-9/+9
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* [svn-r5908] Snapshot version 1.5 release 34HDF Admin2002-08-311-9/+9
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* [svn-r5878] Purpose:Albert Cheng2002-08-191-21/+36
| | | | | | | | | | | | fix/feature Description: v1.4's configure had enable-trace default as on. That is not right for production code as it increase the object code and uses up compute time. Changed --enable-trace default to depend on --enable-debug. If debug is on, trace is on. Otherwise it is off. Also added the printing of CFLAGS, CPPFLAGS, and LDFLAGS in the summary. Platforms tested: eirene, arabica (pp).
* [svn-r5869] Snapshot version 1.5 release 33HDF Admin2002-08-101-9/+9
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* [svn-r5844] Purpose:Bill Wendling2002-08-081-0/+1
| | | | | | | | Small Coding Change Description: Zeroed out the MPI_Status structure in one of our tests to determine if MPI_Get_count() works on the machine or not. This is similar to what we do in the library code to the status...
* [svn-r5841] Snapshot version 1.5 release 32HDF Admin2002-08-031-9/+9
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* [svn-r5810] Purpose:Bill Wendling2002-07-171-1/+1
| | | | | | | | | | | Fix Description: Better check for versions of Linux. We didn't support kernels with major version numbers >2 and minor version numbers <4... Solution: Fixed to check just that. Platforms tested: Linux 2.2 && 2.4
* [svn-r5807] Purpose:Bill Wendling2002-07-171-126/+372
| | | | | | | | | | | | | | | | | | | | | | | | | Update, Bug Fix, and Feature Add Description: - Updated how AC_{ENABLE,WITH} help messages were being generated. Autoconf now gives you an AC_HELP_STRING macro to use to create them. - Fixed the problem with Linux LFS on RedHat 7.3 machines. It wasn't finding getdents64(), so we can't rely on that being present anymore... - Added GPFS detection and setting. - Updated how compression is specified. It's no longer necessary to test for HAVE_ZLIB_H, HAVE_LIBZ, and HAVE_COMPRESS2. The one macro {H5_}HAVE_COMPRESSION takes care of all of these. Solution: Changed the check for Linux LFS from looking for getdents() to looking at the version number of the kernel (using the uname -r command). You can still override with the --enable-linux-lfs switch if you really believe that your <2.4 kernel has LFS support. Platforms tested: Linux (2.2 and 2.4)
* [svn-r5795] Purpose:Quincey Koziol2002-07-151-1/+1
| | | | | | | | | | | New feature Description: Changed parallel I/O tests to use test script instead of just running testphdf5 executable. This allows the MPI-posix driver to be tested easily. Platforms tested: FreeBSD 4.6 (sleipnir) w/parallel and IRIX64 6.5 (modi4) w/parallel
* [svn-r5782] Purpose:Quincey Koziol2002-07-121-5/+435
| | | | | | | | | | | New feature Description: Add support in for "dmalloc" debugging malloc library to configure script and library headers. Platforms tested: IRIX64 6.5 (modi4) and FreeBSD 4.6 (sleipnir)
* [svn-r5774] Snapshot version 1.5 release 31HDF Admin2002-07-061-9/+9
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* [svn-r5727] Purpose:Albert Cheng2002-06-291-5/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | Porting to AIX 5.x Description: These have been tested out in v1.4. Folding them in here. aclocal.m4: Snow's names were not included in the special hack. Added its names in. Removed the trailing * in pacific.llnl.gov too. configure.in: fortran/configure.in: Added a case to group all AIX 5.* versions as aix5.x. This allows them to share one common config/*aix5.x file. configure: fortran/configure: Derived from configure.in (done in eirene). config/powerpc-ibm-aix4.x: Added a comment explaining why not to cache sizeof size_t and off_t fortran/config/powerpc-ibm-aix4.x: Turned of cache of sizeof size_t and off_t because they are depedent on compiler options. config/powerpc-ibm-aix5.x: fortran/config/powerpc-ibm-aix5.x: New config file for AIX 5.X Platforms tests: LLNL Blue, Frost, Snow, both serial and parallel.
* [svn-r5726] Snapshot version 1.5 release 30HDF Admin2002-06-291-9/+9
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* [svn-r5506] Snapshot version 1.5 release 29HDF Admin2002-06-021-9/+9
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* [svn-r5465] Snapshot version 1.5 release 28HDF Admin2002-05-281-9/+9
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* [svn-r5275] Snapshot version 1.5 release 27HDF Admin2002-04-271-9/+9
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* [svn-r5266] Purpose:Bill Wendling2002-04-251-9/+9
| | | | | | | | | Update Description: Updated the h5vers script to automatically update the configure.in files so that they reflect the correct version in the AC_INIT line. Platforms tested: Linux
* [svn-r5235] Purpose:Bill Wendling2002-04-231-16/+35
| | | | | | | | | | | | | | | | Update Description: Updated the way we used the AC_INIT macros so that it's current to the new standard way and not deprecated anymore. Also, added a test for some functions during parallel Fortran configure. This required the creation of an H5config_fortran.h file so that we can test for these... Platforms tested: Elena is going to test the changes to the fortran after she checks in her other code. I will test on SDSC machines after getting her code. The other changes were tested on Linux.
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