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* [svn-r24060] Bring revisions #24002 - 24029 from trunk to revise_chunks.Vailin Choi2013-08-229-1279/+1282
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* [svn-r24034] Bring revisions #23977 - 23984 from trunk to revise_chunks.Vailin Choi2013-08-205-3/+44
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* [svn-r23959] Bring revisions #23745 - 23862 from trunk to revise_chunks.Vailin Choi2013-07-311-58/+58
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* [svn-r23954] Bring revisions #23715 - 23745 from trunk to revise_chunks.Vailin Choi2013-07-311-0/+14
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* [svn-r23948] Bring revisions #23670 - 23713 from trunk to revise_chunks.Vailin Choi2013-07-306-28/+17
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* [svn-r23946] Bring revisions #23597 - #23670 from trunk to revise_chunks.Vailin Choi2013-07-304-10/+542
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* [svn-r23852] Added a user instruction of the atomic test.DLS_20130630Albert Cheng2013-06-301-0/+48
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* [svn-r23851] Bug fix: after printing usage for -h option, it should have ↵Albert Cheng2013-06-301-0/+1
| | | | | | | | | ended the program. Solution: added exit(0) after usage(). This is not a good fix but will work for now. Test: jam.
* [svn-r23848] Bug fix:Albert Cheng2013-06-291-1/+1
| | | | | | | | The script execute the program by just $program which will not work if the user does not have "." in the $PATH. Changed it to "./$program" to avoid this problem. Tested: koala.
* [svn-r23828] Fix 2 bugs for SWMR access:Vailin Choi2013-06-265-27/+418
| | | | | | 1) H5O_load() in H5Ocache.c: when reading a block that is > spec_read siez, read the whole block in again and possibly decode the header. 2) H5F_accum_write() in H5Faccum.c: for a large write that is >= H5F_ACCUM_MAX_SIZE, flush the metadata in the accumulator first before the write. Tests are added to test/ohdr.c and test/accum.c. h5committested.
* [svn-r23802] Added use case 1.9, Appending n-1 dimensional planes.Albert Cheng2013-06-211-0/+37
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* [svn-r23792] Added use case 1.8, use_append_mchunks.Albert Cheng2013-06-181-66/+161
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* [svn-r23777] Implement SWMR-5:Albert Cheng2013-06-151-1/+10
| | | | | | | | Replace H5Fflush in writer with H5Dflush and file close/reopen with H5Drefresh. Use cases seem to run faster. Keeping the old code so that later on, I may test the performance between the two. Tested: koala.
* [svn-r23775] Implement SWMR-5:Albert Cheng2013-06-145-788/+516
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Implemented use case 1.9: Appending n-1 dimensional planes Adding the option "-y" which allows chunks to be thicker (more than 1 plane). This supports use case 1.9 which have chunks of multiple planes but writing is still appending one plane at a time. Using -y with "use_append_chunk", would provide the use case of writing a plane to a partial chunk. Using -y with "use_append_mchunks", would provide the use case of writing a plane to multiple partial chunks. Also added the option -n which specifies how many planes to write instead of the defaults of chunksize number of planes. This allows the final dataset to be other than a cube. test/use_append_mchunks.c: test/use_common.c: test/use.h: test/use_append_chunk.c: I also overhauled code in use_append_mchunks and use_append_chunk: 1. creating a set_parameter() to customize individual use case; 2. combine the create_uc_file(), read_uc_file() and write_uc_file() of both use cases appending one plane per chunks and one plane per multiple chunks. Moved these combined create/read/write functions into use_common.c to make future modification and maintence easier. test/test_usecases.sh.in: Added a simple test to demonstarte how to use -y to run use case 1.9. Tested: h5committest, except cmake, passed. Hand tested in Koala for various options.
* [svn-r23774] The standalone writer & reader tests that check atomic ↵Vailin Choi2013-06-144-21/+616
| | | | read-write operation on the system.
* [svn-r23760] Implement SWMR-5:Albert Cheng2013-06-124-8/+601
| | | | | | | | | | | | | | | | Implemented use case 1.8 program--SWRM read/write multiple chunks at a time. test/use_append_mchunks.c: The program. test/Makefile.am: test/Makefile.in: Added program use_append_mchunks. test/test_usecases.sh.in: Added simple tests for use_append_mchunks. MANIFEST: Updated for new file. Tested: h5committest, except cmake, passed. Hand tested in Koala for various options.
* [svn-r23757] Simple clean up--removed couple old commented line.Albert Cheng2013-06-121-2/+0
| | | | Tested: h5committested.
* [svn-r23750] Bug fix: SWMR-hh1 and SWMR-2Albert Cheng2013-06-101-3/+15
| | | | | | | | | | | | | | | When zlib is not available (use "configure --without-zlib"), some tests failed to not using compression features. Solution: test/dsets.c: Conditional blocked out use of zlib compression code. tools/h5ls/testh5ls.sh.in: Temporary commented out test code that uses datafile that has zlib compressed data. Tested: h5committest (cmake does not work but that is ignored for now.) Also, hand tested in koala using "configure --without-zlib".
* [svn-r23730] Fixed a typo (size should be 256) and some formatting.Albert Cheng2013-06-021-11/+14
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* [svn-r23729] First edition of User Guide of SWMR Use Case programs.Albert Cheng2013-06-021-0/+88
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* [svn-r23728] Updated the comments of create, write, and read process.Albert Cheng2013-06-021-7/+8
| | | | Tested: koala.
* [svn-r23727] Added test/test_usecases.sh for testing use cases.Albert Cheng2013-06-023-3/+125
| | | | Tested: h5committest.
* [svn-r23726] Changed use case programs to more descriptive names.Albert Cheng2013-06-015-21/+25
| | | | | | | | | | usecase1_7.c -> use_append_chunk; usecase_common.c -> use_common.c; usecase.h -> use.h. MANIFEST updated with new names. Tested: h5committest.
* [svn-r23725] Added two new features:Albert Cheng2013-05-313-64/+136
| | | | | | | | | | | 1. "-f filename" can create the test file somewhere other than the current directory or <progname>.h5. This allows running tests in different filesystems, for example. 2. "-l w|r" can launch only the writer or the reader (default does both). This allows launching writer (includes the "create file") in one process and launching the reader somewhere else. (The "-f" helps too.) Tested: h5committested.
* [svn-r23724] Add use case 1.7--SWRM read/write one chunk at a time.Albert Cheng2013-05-315-6/+699
| | | | Tested: h5committest.
* [svn-r23601] Bring revisions #23341 - 23597 from trunk to revise_chunks.Vailin Choi2013-04-1911-100/+1482
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* [svn-r23600] Bring revisions #23085 - #23341 from trunk to revise_chunks.Vailin Choi2013-04-1916-133/+1237
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* [svn-r23599] Bring revisions 22802 : 23085 from trunk to revise_chunks.Vailin Choi2013-04-1834-149/+1331
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* [svn-r23582] Bring revisions 22708:22730 from trunk to revise_chunks.Vailin Choi2013-04-127-29/+155
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* [svn-r23577] Bring revisions 22708:22730 from trunk to revise_chunks.Vailin Choi2013-04-115-30/+25
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* [svn-r23574] Bring revisions 22690 - 22708 from trunk to revise_chunks.Vailin Choi2013-04-111-123/+178
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* [svn-r23568] Bring revision 22634:22690 from trunk to revise_chunks.Vailin Choi2013-04-093-125/+306
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* [svn-r23135] Purpose: Fix bug in SWMR object header codeNeil Fortner2013-01-042-11/+48
| | | | | | | | | | | | | Descriptions: When removing object header messages, it is possible for object header continuation messages to move to a different chunk. When this happens, flush dependencies need to be updated to reflect the new structure. This change adds code to update the flush dependencies, and a test for this. Also fixed a bug where the flush dependency no the object header proxy was not being destroyed when an object header chunk was deleted. Tested: ummon
* [svn-r23104] Purpose: Add object header flush dependenciesNeil Fortner2012-12-141-14/+1
| | | | | | | | | | | Description: Added flush dependencies between object header chunks. Also added a new object header proxy object, which is a child dependency of all object header chunks. All objects which are child dependencies of an object header should set up a flush dependency on the object header proxy, so the dependency applies to all object header chunks. Tested: ummon; jam (fails ph5diff -v, unrelated), koala, ostrich (h5committest)
* [svn-r23095] Purpose: Refactor flush dependency code, add support for ↵Neil Fortner2012-12-124-1050/+1652
| | | | | | | | | | | | | | | multiple parents Description: Reworked how flush dependencies worked internally, allowing multiple flush dependency parents, and removing the notion of flush dependency heights, instead keeping track of the number of dirty descendents to determine if parents can be flushed. Also removed the requirement that cache clients destroy flush dependencies before eviction (this is now handled by the cache) and removed the maximum number of passes (the cache should detect infinite loops elsewhere). Added test cases for this. Tested: durandal
* [svn-r22922] Purpose:Dana Robinson2012-10-186-40/+39
| | | | | | | | | | | Moved the file open/close back inside the loop in the SWMR reader code. Without the open/close, the cache never refreshes so we always see the initial amount. Made a couple of other minor changes to the SWMR code. Tested on: jam
* [svn-r22918] Purpose:Dana Robinson2012-10-1811-1190/+2124
| | | | | | | | | | | | - Added comments to files, functions, etc. - Some readers changed to keep the file open throughout the life of the program instead of closing it before sleeping. This is in the hopes that there will be more opportunities for cache issues without the close. - Other minor changes. Tested on: jam
* [svn-r22898] Purpose:Dana Robinson2012-10-1310-514/+780
| | | | | | | | | | | | | Updates the SWMR testing - All readers/writers now consume and emit their random seeds for debugging. - Output uses unbuffered I/O for more readable output. - The random seeds are now based on a more fine-grained time measurement to ensure each reader has a different random seed. Tested on: jam
* [svn-r22784] Purpose:Dana Robinson2012-09-181-7/+5
| | | | | | | | | | | | | | | Add flush dependencies to the fixed array code. Description: Added basic flush dependency wiring to the fixed array code. Does not include the test code, which will be added soon. NOTE: The Makefile.in change in test/ is not due to any changes made here. It appears to be from a missing bin/reconfigure in a prior checkin. Tested: jam (there is an existing flush/refresh test error)
* [svn-r22761] Purpose: Fix testswmr failuresNeil Fortner2012-09-132-2/+2
| | | | | | | | | | Description: Patched H5B2 shadowed list implementation to remove nodes from the shadowed list when they are evicted, and added some missing initializations. Also removed inadvertent temporary changes to the tests that disabled srandom, added assertions and fixed formatting. Tested: ummon
* [svn-r22669] Description:Quincey Koziol2012-08-1214-58/+74
| | | | | | | | Merge r22634:2266 from trunk to revise_chunks branch Tested on: Mac OSX/64 10.7.4 (amazon) w/debug, gcc-4.7.x, C++, FORTRAN and threadsafe (h5committest not needed on this branch)
* [svn-r22636] Description:Quincey Koziol2012-08-061-0/+99
| | | | | | | | Bring r22599:22634 from trunk to revise_chunks branch Tested on: Mac OSX/64 10.7.4 (amazon) w/gcc 4.7.x, C++ & FORTRAN (No need for h5committest yet on this branch)
* [svn-r22600] Description:Quincey Koziol2012-07-2516-244/+333
| | | | | | | | Bring r22251:22599 from trunk to revise_chunks branch. Tested on: Mac OSX/64 10.7.4 (amazon) w/gcc 4.7.1, C++ & FORTRAN (Not h5committested yet, as this branch doesn't require it)
* [svn-r22520] Made a few changes to error comparisons.Dana Robinson2012-07-051-50/+53
| | | | | Tested on jam. This branch still has h5diff errors. The library tests all pass, though.
* [svn-r22422] Purpose: Add support for SWMR with v2 b-treesNeil Fortner2012-05-3010-73/+84
| | | | | | | | | | | | | Description: Adds SWMR support to the v2 b-trees when used as a chunk index. Because each node keeps track of the total number of records reachable through each of its children, nodes must be shadowed every time a descendent record is inserted or removed. This implementation prevents this from happening, however, if the node has already been shadowed since the last time the v2 b-tree header was flushed. Also modified SWMR test to include v2 b-trees. Tested: jam, koala, ostrich (h5committest), durandal Note: There is a preexisting failure in the ph5diff (-v) test
* [svn-r22421] Misc enhancements for revise_chunks branch noticed while ↵Neil Fortner2012-05-302-8/+1
| | | | | | | | working on v2 b-trees, but not related to v2 b-trees. Tested: durandal
* [svn-r22254] Description:Quincey Koziol2012-04-0615-53/+5405
| | | | | | | | | | | | | | | | | | | | | | | | Bring r22085:22251 from trunk to revise_chunks branch. Also tackle some testing issues in test/objcopy.c test and clean up some warnings. Tested on: FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode FreeBSD/64 8.2 (freedom) w/gcc4.6, w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (koala) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, w/threadsafe, in production mode Linux/PPC 2.6 (ostrich) w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-ia64 2.6 (ember) w/Intel compilers, w/paralle, C++ & FORTRAN, in production mode Mac OS X/32 10.7.3 (amazon) in debug mode Mac OS X/32 10.7.3 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode Mac OS X/32 10.7.3 (amazon) w/parallel, in debug mode
* [svn-r22127] Purpose: Fix earray failureNeil Fortner2012-03-221-4/+114
| | | | | | | | | | | | | Description: In H5Dearray.c, functions would "swizzle" the chunk offset and "down" number of chunks in order to more the unlimited dimension to be the first dimension, but they would not swizzle the chunk dimensions. This could cause two chunks to have the same index, causing problems. Modified code to swizzle the chunk dimensions, and added a test. Note: There is still a problem with h5watch that appears to be unrelated. Tested: durandal
* [svn-r22105] Description:Quincey Koziol2012-03-2140-2814/+5531
| | | | | | | | | | Bring r20557:22085 from trunk to this branch, also fixing some other issues/failures in the branch simultaneously. The h5repack tests are still failing, but Neil will be checking into those, so the branch can be fully functional again. Tested on: Mac OSX/64 10.7.3 (amazon) w/debug
* [svn-r21989] Purpose: Add SWMR capability to v1 b-treeNeil Fortner2012-02-2711-57/+1949
| | | | | | | | | | | | | | | | | | | | | Description: Adds SWMR capability to v1 b-trees, and the chunk index using v1 b-trees. With this implementation, flush dependencies are always on when in the cache. This will allow attritbutes to be used for "checkpointing" data when object header dependencies are fixed - i.e. if a writer writes data before an attribute in that dataset's object header, then if a reader sees the updated attribute the written data is guaranteed to be visible, as long as that dataset's b-tree nodes are evicted from the reader's cache. Also adds support for compression with SWMR. Also fixes earray implementation to not free (reuse) the file space for deleted chunks and outdated versions of compressed chunks when doing SWMR writes. These should eventually be added to a timeout list. Adds testing for these cases. Tested: durandal