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* [svn-r6603] Purpose:Quincey Koziol2003-04-091-3/+4
| | | | | | | | | | | | | | | | | Code cleanup Description: Update dependencies. Solution: Platforms tested: FreeBSD 4.8 (sleipnir) w/szip Linux 2.4 (sleipnir) w/szip Solaris 2.7 (arabica) w/FORTRAN IRIX64 6.5 (modi4) w/szip, FORTRAN & parallel Misc. update:
* [svn-r6601] Elena Pourmal2003-04-081-0/+17
| | | | | | | | | | | | | | | | | | Purpose: This a fix for bug #921 Description: On platforms where big test runs, it creates a set of "solid" 1GB files. Test will take forever (modi4) or will fail if quotas are exceeded. Solution: Default library behavior is to allocate dataset space earlier and to write fill values. I changed the test to use late space allocation and never write fill values. Platforms tested: True64 (PSC), modi4 (sequential and parallel), arabica with 64-bit option(test was skipped there). I also enabled szip and it passed :-) Misc. update:
* [svn-r6597] Purpose:Quincey Koziol2003-04-081-3/+1
| | | | | | | | | | | | | | | Code cleanup Description: Corrected a few comments. Solution: Platforms tested: FreeBSD 4.8 (sleipnir) Linux 2.4 (eirene) Misc. update:
* [svn-r6582] Purpose:Quincey Koziol2003-04-031-351/+46
| | | | | | | | | | | | | | | | | | | | | Code cleanup Description: Updated copyright. Removed szip-specific testing in favor of standard testing, now that bugs in the szip filter are fixed. Updated to latest version of H5Pset_szip API Solution: Platforms tested: FreeBSD 4.8 (sleipnir) IRIX64 6.5 (modi4) w/parallel Misc. update:
* [svn-r6576] Purpose:Quincey Koziol2003-04-031-63/+113
| | | | | | | | | | | | | | Cleanup Description: Update dependencies. Solution: Platforms tested: Linux 2.4 (eirene) Misc. update:
* [svn-r6553] Purpose:MuQun Yang2003-04-011-26/+406
| | | | | | | | | | | | | | | | | | | | | | | | | | | To add tests for szip compression in HDF5 Description: Three tests were added: 1) szip filter itself 3) szip + shuffle + fletch32 2) fletch32 + shuffle + szip Solution: Since H5Dget_storagesize returns 0(Quincey can fix it or it may be gone), I create another function called test_internal_filter_szip, which is the almost the same as test_internal_filter but comments out H5Dget_storage_size function. 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(arabic 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-r6538] Purpose:Bill Wendling2003-03-3161-321/+836
| | | | | | | | | | | | | Update Description: Updated the Copyright statement Platforms tested: Linux (This change is only in the comments, so I just check that the modules still compile) Misc. update:
* [svn-r6525] Purpose:Albert Cheng2003-03-271-0/+2
| | | | | | | | | | | | | | | | New test feature Description: Added the VFD_LIST definition to support the "make check-vfd" tests. Platforms tested: h5committested. Since check-vfd is not invoked by default, I went to each machine to invoke them by hand. The target worked fine but there were errors reported from those driver tests. (Those errors were beyond the scope of this make target test.) Misc. update:
* [svn-r6436] Purpose:Quincey Koziol2003-02-244-11/+1090
| | | | | | | | | | | | | New internal feature Description: Add internal API for building and working with heaps (H5HP). This will be used for the LRU algorithm in the new metadata cache code. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} FreeBSD 4.7 (sleipnir)
* [svn-r6435] Purpose:Quincey Koziol2003-02-241-2/+3
| | | | | | | | | | | | Code cleanup Description: Added more information to information printed for test failure. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)}
* [svn-r6434] Purpose:Quincey Koziol2003-02-241-9/+15
| | | | | | | | | | | | | | Code cleanup Description: Removed extraneous __FUNCTION__ declaration that was causing warnings on Windows. Updated copyright information. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)}
* [svn-r6433] Purpose:Quincey Koziol2003-02-241-37/+37
| | | | | | | | | | | | | | | Code/comment cleanup Description: Made more information about reference-counted strings private to the H5RS package by trimming the typedef used in H5RSprivate.h and switching from using macros for a couple of operations to using functions. Updated copyright information for a few of these files. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)}
* [svn-r6412] Purpose:Quincey Koziol2003-02-172-51/+107
| | | | | | | | | | Code cleanup Description: Update dependencies and clean up a few warnings. Platforms tested: Linux 2.2 (eirene) w/parallel
* [svn-r6411] Purpose:Quincey Koziol2003-02-173-30/+55
| | | | | | | | | | | | | | | | | | | | | | Code cleanup Description: Clean up miscellaneous warnings which have crept into the code. Fix "_POSIX_C_SOURCE not defined" warning on FreeBSD. Adjust gcc compiler flags to be more concise for production mode. Refactor the H5O code so that there is a stronger boundary between code in the H5O package and code in the library which just calls H5O routines. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} FreeBSD 4.7 (sleipnir) serial & parallel and gcc 2.95.4 & gcc 3.2.2 Misc. update: Update MANIFEST if you add or remove any file.
* [svn-r6400] Raymond Lu2003-02-121-47/+47
| | | | | | | | | | | Purpose: Change feature Description: Switch to Fletcher32 from Adler32 checksum Platforms tested: arabica, eirene, modi4 Misc. update: MANIFEST and RELEASE.txt updated.
* [svn-r6398] Purpose:Quincey Koziol2003-02-121-9/+11
| | | | | | | | | | Code cleanup Description: Clean up some compiler warnings Platforms tested: FreeBSD 4.7 (sleipnir)
* [svn-r6387] Purpose:Quincey Koziol2003-02-104-36/+36
| | | | | | | | | | | | | | | | | | | | | | | | | | | Bug Fix Description: Metadata cache in parallel I/O can cause hangs in applications which perform independent I/O on chunked datasets, because the metadata cache can attempt to flush out dirty metadata from only a single process, instead of collectively from all processes. Solution: Pass a dataset transfer property list down from every API function which could possibly trigger metadata I/O. Then, split the metadata cache into two sets of entries to allow dirty metadata to be set aside when a hash table collision occurs during independent I/O. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} FreeBSD 4.7 (sleipnir) serial & parallel Misc. update: Updated release_docs/RELEASE
* [svn-r6386] Purpose:Quincey Koziol2003-02-103-5/+6
| | | | | | | | | | | | | | 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 Koziol2003-02-075-110/+147
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 Lu2003-02-041-113/+395
| | | | | | | | | | | 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-r6330] Purpose:Quincey Koziol2003-01-242-2/+35
| | | | | | | | | | | | | | | Bug Fix Description: When calling H5Fopen with the core VFL driver, but without the H5F_ACC_CREAT flag goes ahead and creates a memory file. Solution: Check for the H5F_ACC_CREAT flag before allowing the memory file to be created. Platforms tested: FreeBSD 4.7 (sleipnir)
* [svn-r6308] Purpose:Quincey Koziol2003-01-212-0/+31
| | | | | | | | | | | | | | | | | Bug fix Description: Currently, when the library encounters an object header message that isn't know, it fails to open that object in the file. Solution: Allow the library to skip over the unknown object header message and continue to process the remaining messages, in the hope that the skipped message isn't important later. If it is important, it will be caught at a higher level of the library. Platforms tested: FreeBSD 4.7 (sleipnir)
* [svn-r6296] Purpose:Quincey Koziol2003-01-172-7/+7
| | | | | | | | | | Code cleanup Description: Reduce warnings on Windows Platforms tested: FreeBSD 4.7 (sleipnir)
* [svn-r6269] Purpose:Quincey Koziol2003-01-131-3/+3
| | | | | | | | | | | | | Code cleanup Description: Various code cleanups to allow the development branch to be compiled with a C++ compiler (i.e. CC=g++ ) Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} FreeBSD 4.7 (sleipnir) C++
* [svn-r6263] Purpose:Quincey Koziol2003-01-101-2/+7
| | | | | | | | | | | | | | | Update test Description: Some of the performance improvements changed the errors that are reported for creating a duplicated dataset in a file, causing this test's hard-coded errors to check for to fail. Solution: Updated error stack reported for dataset creation failure. Platforms tested: FreeBSD 4.7 (sleipnir) w/threads
* [svn-r6255] Purpose:Quincey Koziol2003-01-092-34/+198
| | | | | | | | | | Code cleanup Description: Clean up a few more warnings and update dependencies. Platforms tested: Linux 2.2.18smp (eirene) serial & parallel
* [svn-r6252] Purpose:Quincey Koziol2003-01-0919-72/+1044
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r6213] Raymond Lu2002-12-161-29/+54
| | | | | | | | | | | Purpose: bug fix Description: some arrays were too big, running out of memory limit for some machines. Solution: change to dynamic memory allocation. Platforms tested: arabica, sleipnir
* [svn-r6207] Raymond Lu2002-12-161-0/+100
| | | | | | | | | Purpose: Add more test Description: More tests on nil and zero-sized VL strings. Platforms tested: arabica, eirene
* [svn-r6203] MuQun Yang2002-12-131-5/+6
| | | | | | | | | | | | | | | | Purpose: bug fixed for windows Description: windows fopen functions by default opens a text mode file. It will fail for HDF5 file. So to use HDopen HDread HDclose for test. Solution: Change from fopen, fread, fclose to HDopen, HDread, HDclose. Platforms tested: linux2.2.18smp, windows 2000 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-r6201] Raymond Lu2002-12-121-6/+6
| | | | | | | | | | | Purpose: Bug fix(kinda) Description: Windows handle "fopen, fseek, fread, fclose" C functions slightly different. Solution: change to HDopen, HDlseek, HDread, HDclose to cover both Unix and Windows. Platforms tested: arabica
* [svn-r6196] Raymond Lu2002-12-111-7/+477
| | | | | | | | | Purpose: more tests. Description: a few more test cases. Platforms tested: modi4, eirene, arabica
* [svn-r6171] Purpose:Quincey Koziol2002-12-041-19/+57
| | | | | | | | | | | | | Bug fix Description: Much of the VL-string testing code was recently disabled accidentally. Solution: Re-enable it and add test for writing/reading large string attributes. Platforms tested: FreeBSD 4.7 (sleipnir) - small enough to not need triple-check
* [svn-r6145] Raymond Lu2002-12-023-15/+156
| | | | | | | | | | Purpose: New feature to H5Dget_offset Description: If user block is set, H5Dget_offset should be able to return the absolute offset from the beginning of file. Platforms tested: eirene, arabica
* [svn-r6143] *** empty log message ***Quincey Koziol2002-12-022-12/+10
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* [svn-r6136] Raymond Lu2002-11-251-11/+197
| | | | | | | | | | | Purpose: new functions Description: H5Gget_num_objs, H5Gget_objname_by_idx and H5Gget_objtype_by_idx. Platforms tested: modi4, arabica, eirene Misc. update: RELEASE.txt updated.
* [svn-r6131] Purpose:Quincey Koziol2002-11-213-10/+3
| | | | | | | | | | Code cleanup Description: Clean up compiler warnings from IRIX64 builds. Platforms tested: IRIX64 6.5 (modi4)
* [svn-r6130] Purpose:Quincey Koziol2002-11-211-234/+255
| | | | | | | | | | | | Bug fix. Description: Accomodate 64-bit machines when using 'long' types. Clean up a few more warnings. Platforms tested: IRIX64 6.5 (modi4)
* [svn-r6129] Purpose:Quincey Koziol2002-11-201-20/+46
| | | | | | | | Enhance test. Description: Expanded the nested compound datatype testing slightly. Platforms tested: FreeBSD 4.7 (sleipnir) - too minor for triple check.
* [svn-r6121] Purpose:Quincey Koziol2002-11-201-122/+60
| | | | | | | | | | | | | | | | | Bug fix Description: Array testing routine is creatint huge arrays on the function stack which causes a segmentation fault on Linux & FreeBSD when threadsafe support is enabled. Solution: Allocate data for test dynamically instead of automatically. In general, this should be the preferred method for all data arrays. Platforms tested: FreeBSD 4.7 (sleipnir) w/threadsafe enabled.
* [svn-r6117] Purpose:Quincey Koziol2002-11-202-0/+101
| | | | | | | | | | | | | | New files Description: Add test file for "missing filter" test in dsets.c Add test file generator code. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} FreeBSD 4.7 (sleipnir)
* [svn-r6115] Purpose:Quincey Koziol2002-11-202-127/+408
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Code Cleanup & New Tests Description: tmisc.c: Switched from using H5_HAVE_COMPRESSION flag in favor of H5_HAVE_FILTER_DEFLATE. dsets.c: Switched from using H5_HAVE_COMPRESSION flag in favor of H5_HAVE_FILTER_DEFLATE. Refactored I/O filter tests to allow new filters to be [more] easily added. Added tests for shuffle & deflate+shuffle I/O filters (if the filter(s) are enabled). Added test for creating a new dataset with a filter that is not available. Added test for attempting to read a dataset created with a filter that is not available. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} FreeBSD 4.7 (sleipnir)
* [svn-r6109] *** empty log message ***Quincey Koziol2002-11-202-9/+9
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* [svn-r6099] Raymond Lu2002-11-181-5/+27
| | | | | | | | | | | Purpose: bug fix. Description: h5dump cannot dump data and datatype for VL string. Platforms tested: eirene, arabica Misc. update: MANIFEST, RELEASE.txt
* [svn-r6089] MuQun Yang2002-11-131-0/+127
| | | | | | | | | | | | | | | | | Purpose: Add a testing case for shuffling algorithm. Description: A control test: Since shuffling 8-bit array should not change the original result; so we use a 8-bit array to test whether after shuffling the array keeps the same values. Solution: Platforms tested: eirene,arabica,modi4 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-r6062] Raymond Lu2002-11-072-0/+20
| | | | | | | | | | | | Purpose: New function. Description: H5Dget_offset returns the offset of a dataset's data relative to the beginning of a file. Platforms tested: arabica(simple function, one test should be enough.) Misc. update: RELEASE.txt
* [svn-r6060] Raymond Lu2002-11-063-3/+1404
| | | | | | | | | | | Purpose: Add new functions Description: add H5Tget_native_type and H5Tis_variable_str. Platforms tested: arabica, eirene, modi4 Misc. update: MANIFEST and release_docs/RELEASE updated.
* [svn-r6055] Purpose:Quincey Koziol2002-11-051-4/+165
| | | | | | | | | | | | | | New feature Description: Add support for scalar dataspaces in parallel I/O. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} Also, FreeBSD 4.7 (sleipnir) serial & parallel Misc. update: Update release_docs/RELEASE for bug fixes, new features, etc.
* [svn-r6054] Raymond Lu2002-11-051-5/+5
| | | | | | | | | Purpose: Makefile update Description: Update Makefile.in to handle more output file for cleanup Platforms tested: arabica
* [svn-r6046] Purpose:Albert Cheng2002-10-311-1/+5
| | | | | | | | | | | | | Improvement Description: fillval will fail to find the pre-exist data file if it is run in --srcdir mode without setting $srcdir properly. This is setup properly in the Makefile but unsuspecting users trying just ./fillval were puzzled by the failure. Solution: put in a more descriptive error message with a possible remedy. Platforms tested: Modi4 only since this is just adding a printf statment.
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