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* [svn-r28995] Removed unused packages from list in --enable-debug=<pkgs> ↵Dana Robinson2016-01-273-17/+1
| | | | | | | | | | configure option (also updated CMake). Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial autotools serial CMake (CMake 3.3.2)
* [svn-r28986] Added H5_DLLVAR to H5AC_dxpl_id.Dana Robinson2016-01-271-1/+1
| | | | | Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial and parallel autotools
* [svn-r28982] Fixed H5ST_dump signature problem and added st to the list ofDana Robinson2016-01-271-1/+3
| | | | | | | packages with extra debugging output. Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial autotools
* [svn-r28972] Removed option to clear file buffers from autotools, CMake, and ↵Dana Robinson2016-01-2616-82/+44
| | | | | | | | | | | | library. Buffers that will be written to disk will now always be cleared since not doing this has huge security implications. Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0, x86_64) gcc 5.2.1 serial autotools parallel autotools (MPICH 3.1.4) serial CMake
* [svn-r28957] fix non-parallel bug.Mohamad Chaarawi2016-01-221-1/+2
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* [svn-r28950] - remove META_FLUSH_COLLECTIVELY property for delayed sanity ↵Mohamad Chaarawi2016-01-2148-527/+529
| | | | | | | | | | checks from metadata dxpls - remove H5AC_ind_dxpl_id and use only H5AC_dxpl_id everywhere instead. - remove flush_me_collectively flag from cache entries - add a collective sanity check (MPI_Barrier) for every HDF5 API routine that could possibly touch the file. This is trigerred when the environment variable H5_COLL_API_SANITY_CHECK is set to a non 0 digit. tested on BB-8 with serial and parallel.
* [svn-r28916] Description:Quincey Koziol2016-01-1513-251/+346
| | | | | | | | Normalize against incoming changes from the phdf5_metadata_opt branch. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r28894] Description:Quincey Koziol2016-01-1414-219/+214
| | | | | | | | Normalize against changes on phdf5_metadata_opt branch to trunk Tested on: MacoSX/64 10.11.2 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r28861] Minor warning format string fix (HDFFV-9640).Dana Robinson2016-01-121-1/+1
| | | | | Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 autotools parallel only (MPICH 3.1.4)
* [svn-r28832] Description:Quincey Koziol2016-01-061-1/+3
| | | | | | | | | Reset driver info message when superblock load fails. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel Linux/32 2.6.x (jam) w/serial Linux/64 2.6.x (mayll) w/serial
* [svn-r28824] Description:Quincey Koziol2016-01-061-3/+0
| | | | | | | Reduce asserts on buffer alignment. Tested on: Linux/32 & Linux/64 2.6.x (jam & myall) w/serial
* [svn-r28819] Description:Quincey Koziol2016-01-061-14/+22
| | | | | | | | | Align internal memory sanity checking buffer, to avoid problems when optimization is enabled. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel Linux/32 2.6.x (jam) w/serial
* [svn-r28815] Description:Quincey Koziol2016-01-062-0/+26
| | | | | | | | | | Add internal routine to sanity check all blocks allocated through H5MM interface. Tested on: Linux/32 2.6.x (jam) w/serial Linux/64 2.6.x (mayll) w/serial MacOSX/64 10.11.2 (amazon) w/serial & parallel
* [svn-r28811] Description:Quincey Koziol2016-01-063-10/+10
| | | | | | | | | Switch v2 B-tree min & max records to be void*'s to be cleaner and generate less warnings. Tested on: Linux/32 2.6.x (jam) w/serial MacOSX/64 10.11.2 (amazon) w/serial & parallel
* [svn-r28802] Description:Quincey Koziol2016-01-051-3/+3
| | | | | | | Correct another H5MM_free => H5MM_xfree Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel
* [svn-r28800] Description:Quincey Koziol2016-01-052-6/+6
| | | | | | | Correct H5MM_free => H5MM_xfree Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel
* [svn-r28798] Description:Quincey Koziol2016-01-053-2/+5
| | | | | | | | Add missing H5MMprivate.h header file Tested on: Linux/32 2.6.x (jam) w/serial MacOSX/64 10.11.2 (amazon) w/serial & parallel
* [svn-r28797] Description:Quincey Koziol2016-01-059-64/+54
| | | | | | | | Clean up another round of memory allocation mis-matches. Tested on: Linux/32 2.6.x (jam) w/serial MacOSX/64 10.11.2 (amazon) w/serial & parallel
* [svn-r28795] Description:Quincey Koziol2016-01-052-3/+8
| | | | | | | | Clean up more memory allocation mis-matches. Tested on: Linux/32 2.6.x (jam) w/serial MacOSX/64 10.11.2 (amazon) w/serial & parallel
* [svn-r28790] Description:Quincey Koziol2016-01-041-2/+2
| | | | | | | | Correct non-portable 'SIZE_T_MAX' to 'SIZET_MAX'. Tested on: Linux/32 2.6.x (jam) w/default compilers (h5committest forthcoming)
* [svn-r28777] Description:Quincey Koziol2016-01-036-48/+351
| | | | | | | | | | Add --enable-memory-alloc-sanity-check option to configure, to track and sanity check memory allocations within the library. This is orthogonal to the --enable-using-memchecker option and can be used with/without it. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r28773] Description:Quincey Koziol2016-01-031-1/+13
| | | | | | | | | Clear memory for shared message info when "deferring" and using memory checker, so valgrind doesn't whine. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r28769] Description:Quincey Koziol2016-01-032-4/+6
| | | | | | | | More memory cleanups and leak elimination. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r28761] Description:Quincey Koziol2016-01-017-54/+192
| | | | | | | | | | | | Clean up many mismatches between malloc/free and H5MM_malloc/H5MM_xfree in the library and tests (and use of H5free_memory and H5Dvlen_reclaim). Also make H5Ocopy use a private version of H5Lexists, which doesn't internally throw (and suppress) errors when an object (or the path to it) isn't found in the destination. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r28756] Description:Quincey Koziol2015-12-302-21/+29
| | | | | | | | Minor code neatening and cleanups (same as r28755) on revise_chunks branch. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (Too minor for h5committest)
* [svn-r28742] Description:Quincey Koziol2015-12-2910-190/+646
| | | | | | | | | Add 'update' operation to v2 B-trees, which will insert a new record, or modify an existing one, depending on if the record exists or not. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r28730] Snapshot version 1.9 release 233HDF Tester2015-12-281-2/+2
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* [svn-r28723] Description:Quincey Koziol2015-12-226-59/+187
| | | | | | | | | Bring over rest of performance improvements for extending chunked datasets and normalize against revise_chunks branch. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel) (h5committest forthcoming)
* [svn-r28717] Description:Quincey Koziol2015-12-211-9/+6
| | | | | | | | Minor change to align w/revise_chunks branch Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (too minor for h5committest)
* [svn-r28710] Description:Quincey Koziol2015-12-197-145/+162
| | | | | | | | | | | | Bring r28708 from revise_chunks branch: Fix earray, farray and btree2 use of incorrect file pointer when two files are opened and used to access the data structure. Misc. minor code cleanups as well. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel h5committest forthcoming
* [svn-r28702] Description:Quincey Koziol2015-12-171-1/+1
| | | | | | | Fix typo in comment. Tested on: (Unneeded)
* [svn-r28696] Minor normalization with revise_chunks.Dana Robinson2015-12-171-0/+1
| | | | | Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial only
* [svn-r28663] Merge of r28662 from revise_chunks.Dana Robinson2015-12-151-1/+2
| | | | Whitespace only.
* [svn-r28646] Minor normalization with revise_chunks.Dana Robinson2015-12-1420-57/+11
| | | | | | | | | Also purged obsolete /*ARGSUSED*/ from the library. Tested on: Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial only (these changes have been in revise_chunks for a long time)
* [svn-r28643] Add H5D_t pointer to chunk callback.Dana Robinson2015-12-143-8/+9
| | | | | | | | | Normalization for future single chunk indexing. Tested on: Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial only (these changes have been in revise_chunks for a long time)
* [svn-r28629] Minor normalization with revise_chunks.Dana Robinson2015-12-143-24/+18
| | | | | | | Tested on: Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial only (these changes have been in revise_chunks for a long time)
* [svn-r28626] Brought VFD-level file locking code over from revise_chunks.Dana Robinson2015-12-1411-45/+720
| | | | | | | Tested on: Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial only (these changes have been in revise_chunks for a long time)
* [svn-r28624] Minor normalization of H5FA package with revise_chunks.Dana Robinson2015-12-1410-427/+417
| | | | | | | Tested on: Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial only (these changes have been in revise_chunks for a long time)
* [svn-r28620] Minor normalization of H5HL package with revise_chunks.Dana Robinson2015-12-142-6/+7
| | | | | | | Tested on: Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial only (these changes have been in revise_chunks for a long time)
* [svn-r28616] Normalization of H5HL package with revise_chunks.Dana Robinson2015-12-1411-924/+1028
| | | | | | | | | NOTE: Flush dependency code was not moved. Tested on: Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 w/ CMake 3.3.2 serial only (Autotools and CMake since new files were added) (these changes have been in revise_chunks for a long time)
* [svn-r28614] Normalization of H5FS package with revise_chunks.Dana Robinson2015-12-149-477/+395
| | | | | | | | | Mostly minor fixes like warnings, etc. Tested on: Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial only (these changes have been in revise_chunks for a long time)
* [svn-r28612] Normalization of H5G package with revise_chunks.Dana Robinson2015-12-148-23/+25
| | | | | | | | | Mostly minor fixes like warnings, etc. Tested on: Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial only (these changes have been in revise_chunks for a long time)
* [svn-r28606] Description:Quincey Koziol2015-12-1324-273/+267
| | | | | | | | | | Revisions to normalize revise chunks vs. trunk, plus push dataset metadata changes into the cache immediately (instead of holding them within the dataset data structures). Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest not required on this branch)
* [svn-r28581] Brought flock changes over from revise_chunks as well as a fewDana Robinson2015-12-113-2/+186
| | | | | | | minor tweaks from H5private.h. Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial only, autotools and CMake (3.3.2)
* [svn-r28533] Fix loops in H5Dvirtual.c to only loop over used entries in VDS ↵Neil Fortner2015-12-071-3/+3
| | | | | | | | mapping list, instead of all allocated entries. Tested: ummon (too minor for full h5committest)
* [svn-r28499] Correct working dirAllen Byrne2015-12-031-1/+1
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* [svn-r28497] Avoid race condition on creating same source file.Allen Byrne2015-12-031-4/+21
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* [svn-r28452] Description:Quincey Koziol2015-11-2315-65/+60
| | | | | | | | Normalization changes against revise_chunks branch. Tested on: MacOSX/64 10.11.1 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r28422] Description:Quincey Koziol2015-11-2024-419/+584
| | | | | | | | | | Revert most of r27549, since revise_chunks code requires debugging contexts for v2 B-trees. Also, misc. warning cleanups and alignments w/changes on revise_chunks branch. Tested on: MacOSX/64 10.11.1 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r28416] Description:Quincey Koziol2015-11-203-67/+76
| | | | | | | | | Refactor time conversion code to put all the system-specific changes into one routine, H5_make_time, in H5system.c. Tested on: MacOSX/64 10.11.1 (amazon) w/serial & parallel (h5committest forthcoming)
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