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* [svn-r22901] Purpose:Dana Robinson2012-10-161-1/+1
| | | | | | | | Fixes a bug in H5Fsuper_cache.c where a logical AND was used instead of a bitwise AND. Tested on: miette (Mac OS-X 10.8 / clang) (very minor change)
* [svn-r22900] Purpose:Dana Robinson2012-10-151-0/+7
| | | | | | | | Create/destroy flush dependency between the fractal heap header and the 'huge' v2 B-tree. Tested on: jam (still has flush refresh test error)
* [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-r22894] Purpose:Dana Robinson2012-10-121-1/+1
| | | | | | | | Very minor change to an error reporting routine in the extensible array code. Tested on: jam (very minor change)
* [svn-r22887] Purpose:Dana Robinson2012-10-1216-142/+130
| | | | | | | | Fixes a variety of compile warnings and issues in the B-tree and heap code. Tested on: jam
* [svn-r22885] Purpose:Dana Robinson2012-10-119-125/+288
| | | | | | | | Adds some additional flush dependency plumbing and fixes some minor issues with the v2 B-tree code. Tested on: local Ubuntu VM
* [svn-r22833] Purpose:Dana Robinson2012-09-279-64/+309
| | | | | | | | | Basic SWMR and flush dependency plumbing for fractal heaps. Does not include flush dependency creation code. Changes to the H5EA* code were just some indenting issues. Tested on jam
* [svn-r22813] Purpose:Dana Robinson2012-09-262-2/+148
| | | | | | Add H5FSint.c file missing from last check-in. Tested on: jam
* [svn-r22812] Purpose:Dana Robinson2012-09-2529-1364/+1297
| | | | | | | | Mainly to add SWMR flush dependencies to the free space manager (H5FS) code. Also fixes a few issues with the local heap and the fixed array code, and brings the MANIFEST up to date. Tested on: jam
* [svn-r22794] Purpose:Dana Robinson2012-09-204-98/+118
| | | | | | | | Merge r22694 and r22700 from the trunk. These are minor fractal heap edits. Tested: jam (minor change, has baked in trunk)
* [svn-r22792] Purpose:Dana Robinson2012-09-201-0/+1
| | | | | | | | | | Add flush dependencies to the fixed array code. Description: Updated MANIFEST. Tested: jam (there is an existing flush/refresh test error)
* [svn-r22790] Purpose:Dana Robinson2012-09-191-0/+1
| | | | | | | | | | Add flush dependencies to the fixed array code. Description: Updated CMakeLists.txt for new H5FAint.c file. Tested: jam (there is an existing flush/refresh test error)
* [svn-r22789] Purpose:Dana Robinson2012-09-191-0/+141
| | | | | | | | | | Add flush dependencies to the fixed array code. Description: Forgot to add new file. Tested: jam (there is an existing flush/refresh test error)
* [svn-r22784] Purpose:Dana Robinson2012-09-188-164/+308
| | | | | | | | | | | | | | | 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 Fortner2012-09-136-14/+82
| | | | | | | | | | 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-r22680] Description:Quincey Koziol2012-08-151-2/+2
| | | | | | | | Correct H5P_init_def_layout() to H5P__init_def_layout(), per Windows daily test failure Tested on: Windows daily test
* [svn-r22678] Replace regex char deleted from last checkinAllen Byrne2012-08-141-1/+1
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* [svn-r22672] Remove extraneous textAllen Byrne2012-08-131-15/+1
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* [svn-r22669] Description:Quincey Koziol2012-08-1251-363/+778
| | | | | | | | 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 Koziol2012-08-06115-1969/+2352
| | | | | | | | 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 Koziol2012-07-25229-7165/+12045
| | | | | | | | 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-r22530] The changes in these files added dangling links.Allen Byrne2012-07-092-0/+0
| | | | Tested: local cmake
* [svn-r22529] Change parameter to use options->follow_links instead of TRUEAllen Byrne2012-07-091-4/+4
| | | | Tested: local cmake - h5diff_472 and _475 now pass
* [svn-r22522] Merge trunk revision 22520 cmake files and h5dump/h5diff and ↵Allen Byrne2012-07-0675-1034/+4315
| | | | configure to branch
* [svn-r22521] Forgot to check in new source files.Dana Robinson2012-07-063-0/+458
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* [svn-r22520] Made a few changes to error comparisons.Dana Robinson2012-07-055-64/+67
| | | | | Tested on jam. This branch still has h5diff errors. The library tests all pass, though.
* [svn-r22518] Added flush dependencies for SWMR to the local heap code.Dana Robinson2012-07-055-39/+259
| | | | | Tested on jam. This branch still has h5diff errors. The library tests all pass, though.
* [svn-r22515] Converted local heap (H5HL) code to use the new ↵Dana Robinson2012-07-0512-1253/+919
| | | | | | | | | | enter/leave/error macro scheme. Also created separate prefix and data block files so that the local heap code more closely resembles the rest of the data structures. Tested on jam. This branch still has h5diff errors. The library tests all pass, though.
* [svn-r22512] Added BEGIN_FUNC_VOID and END_FUNC_VOID macros to support void ↵Dana Robinson2012-07-031-145/+169
| | | | | | | | | | | functions under the new error handling macro scheme. Also added some helpful comments and cleaned up some formatting. Tested on jam, which has h5diff errors at this time. The library tests all pass so I'm going to check this in.
* [svn-r22508] Minor comment edit to correct return type.Dana Robinson2012-07-021-2/+1
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* [svn-r22422] Purpose: Add support for SWMR with v2 b-treesNeil Fortner2012-05-3039-432/+2898
| | | | | | | | | | | | | 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 Fortner2012-05-305-18/+9
| | | | | | | | working on v2 b-trees, but not related to v2 b-trees. Tested: durandal
* [svn-r22255] Fix windows compile errors: Allen Byrne2012-04-065-98/+99
| | | | | | | vs2008 needed H5private.h in H5Oflush.c VS needs windows export decoration (H5DLLVAR) in header used by source file of origin Tested: windows
* [svn-r22254] Description:Quincey Koziol2012-04-06284-2328/+13472
| | | | | | | | | | | | | | | | | | | | | | | | 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-r22251] Added missing files to CMake configuration file.Dana Robinson2012-04-041-0/+2
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* [svn-r22241] Fix the failures for h5watch due to format indentation.Vailin Choi2012-04-023-3/+9
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* [svn-r22187] Purpose: Fix dsets failure on ostrichNeil Fortner2012-03-294-20/+23
| | | | | | | | | | | | | | | Description: The "support" and "unsupport" chunk index callbacks took H5D_chunk_common_ud_t udata pointers, which seems reasonable because the udata is only needed to locate the chunk, and does not need to return anything to the callers. However, for v1 b-trees, H5D_btree_found must be called in order to locate the chunk, and this function assumes that the udata is an H5D_chunk_ud_t and writes to fields that are not in H5D_chunk_common_ud_t. Modified the support and unsupport callbacks to take H5D_chunk_ud_t. Note: h5watch still fails Tested: durandal, ostrich
* [svn-r22172] Fix uninitialized return values.Neil Fortner2012-03-282-3/+3
| | | | Tested: jam
* [svn-r22132] Description:Quincey Koziol2012-03-231-0/+1
| | | | | | | Add missing testfile. (Branch still not passing all tests) Tested on: Mac OSX/64 10.7.3 (amazon) w/debug)
* [svn-r22127] Purpose: Fix earray failureNeil Fortner2012-03-225-87/+168
| | | | | | | | | | | | | 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 Koziol2012-03-211153-66248/+132522
| | | | | | | | | | 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-r22062] Purpose: Fix bugs in chunk cache's SWMR implementationNeil Fortner2012-03-136-49/+159
| | | | | | | | | | | | | | | | | | | | | Description: Two issues were found with the chunk cache's SWMR implementation: 1. Some places were not properly setting the rdcc field in the index udata struct. Fixed. May eventually need to add an rdcc field to the idx_info struct. 2. While recalculating the indices for chunks in a dataset being resized, it was possible for the chunk cache to attempt to flush a chunk before all the indices were updated, which caused problems when a node split and flush dependencies needed to be updated, because the child nodes could not be found in the chunk cache due to the index being out of date. Modified algorithm in H5D_chunk_update_cache to keep a temporary list of entries that got "bumped", and only evict them after all chunks have updated indices. Also modified H5D_chunk_update_flush_dep and H5D_chunk_update_flush_dep to search this temporary list when looking for the child chunk entry. As a side effect, chunks are now more likely to remain in cache after a call to H5Dset_extent (even without SWMR), so performance should improve slightly.
* [svn-r21989] Purpose: Add SWMR capability to v1 b-treeNeil Fortner2012-02-2724-315/+3208
| | | | | | | | | | | | | | | | | | | | | 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
* [svn-r21938] Fix for bad makefile clean code that removes hl/test/test_ld ↵Dana Robinson2012-02-135-5/+4
| | | | and hl/tools/h5watch .h5 files. These files are never regenerated and subsequent make checks after a clean will fail. This is just a temporary fix as the generator code and autotools files need a revisit.
* [svn-r20559] Description:Quincey Koziol2011-04-19180-1649/+6880
| | | | | | | | | | | | | | | | | | Bring r20407:20557 from trunk to revise_chunks branch Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) 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 (amani) 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 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-ia64 2.6 (ember) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
* [svn-r20555] Purpose: Improve performance when edge chunk filters are ↵Neil Fortner2011-04-191-12/+37
| | | | | | | | | | | | | | | | disabled with no chunk cache. Description: When edge chunk filters and the chunk cache are disabled, the library would previously go through the lock/unlock routines then immediately evict the chunk as is done for filtered datasets, even for the unfiltered edge chunks. This forced the entire chunk to be read/written, even if only part of the chunk was selected. Modified the chunk cache to detect this case, and read/write only the selected portion directly from/to the unfiltered chunk. Tested: jam, amani (h5committest, heiwa down), fedora
* [svn-r20408] Description:Quincey Koziol2011-04-0449-330/+352
| | | | | | | Bring r20382:20407 from trunk to revise_chunks branch. Tested on: Linux/32 2.6 (chicago) w/C++
* [svn-r20383] Description:Quincey Koziol2011-03-31130-7786/+22833
| | | | | | | Bring r19714:20382 from trunk to revise_chunks branch Tested: Linux 2.6/64 (chicago)
* [svn-r20236] Add new files to MANIFEST.Vailin Choi2011-03-141-1/+69
| | | | h5committested.
* [svn-r20196] This checkin consists of the following:Vailin Choi2011-03-0781-82/+7285
| | | | | | | | | | | | | | | A) - Changes to add the new tool "h5watch" to High Level - Changes to add three new High Level public routines for retrieving elements appended to a dataset B) A patch from Mike M. to fix the H5Dflush/refresh problem: src/H5Dpkg.h src/H5Dint.c src/H5D.c C) Fix for an assertion failure in H5FS_sect_link_size() in H5FSsection.c src/H5Dbtree2.c h5committested; tested also on linew, duty, fred.
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