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* [svn-r29331] Merge of r29150 from trunkDana Robinson2016-03-081-23/+47
| | | | | | | segfault on corrupted file fix Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1 autotools serial
* [svn-r29282] Merge of r29081 from trunk (phdf5_metadata_opt branch merge)Dana Robinson2016-03-061-2/+2
| | | | | | Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1 autotools serial w/ Fortran & C++ autotools parallel (MPICH 3.1.4) w/ Fortran
* [svn-r29253] Merge of r29057 from trunk (dxpl checks in debug builds)Dana Robinson2016-03-031-2/+2
| | | | | | | Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1 autotools serial w/ Fortran and C++ autotools parallel (MPICH 3.1.4) w/ Fortran bin/cmakehdf5 (CMake 3.3.2)
* [svn-r29028] Description:Quincey Koziol2016-02-021-36/+83
| | | | | | | | | | | | | When SWMR writes are enabled, correct record update algorithm to indicate to parent node when a child node that was "only" modified was also "shadowed", so that parent node can update itself (since the address of its child node will move when it is shadowed). Re-enable v2 B-tree SWMR testing. Tested on: MacOSX/64 10.11.3 (amazon) w/serial & parallel (h5committest not required on this branch)
* [svn-r29016] Merge of r28936, 28949, 28960-29009 from trunk.Dana Robinson2016-01-291-14/+8
| | | | | | | Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 autotools serial w/ Fortran and C++ autotools parallel (MPICH 3.1.4) w/ Fortran CMake serial (3.3.2, via cmakehdf5)
* [svn-r28812] Description:Quincey Koziol2016-01-061-4/+4
| | | | | | | | | | | Bring r28811 from trunk to revise_chunks branch: 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-r28803] Description:Quincey Koziol2016-01-051-21/+14
| | | | | | | | | | Bring r28797, r28798, r28800, and r28802 from trunk to revise_chunks branch: Misc. memory allocation cleanups Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest not required on this branch)
* [svn-r28746] Description:Quincey Koziol2015-12-291-4/+0
| | | | | | | | | | Now that v2 B-trees can perform 'update' operations, remove 'need_modify' flag from chunk information and switch v2 B-tree chunk index to use update operation. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest not required on this branch)
* [svn-r28744] Description:Quincey Koziol2015-12-291-13/+432
| | | | | | | | | | | Bring r28742 from trunk, adjusting to shadow B-tree nodes for SWMR: 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 not required on this branch)
* [svn-r28712] Description:Quincey Koziol2015-12-191-2/+2
| | | | | | | | | Switch v2 B-trees to use the same mechanism for setting up flush dependencies as extensible and fixed arrays. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest not required on this branch)
* [svn-r28423] Description:Quincey Koziol2015-11-201-12/+7
| | | | | | | | Normalize against trunk. Tested on: MacOSX/64 10.11.1 (amazon) w/serial & parallel (h5committest not required on this branch)
* [svn-r28348] Description:Quincey Koziol2015-11-151-49/+49
| | | | | | | | Checkpoint warning and coding style cleanups. Tested on: MacOSX/64 10.11.1 (amazon) w/serial & parallel (h5committest not required on this branch)
* [svn-r28093] Merge of r27768 and r27774 from trunkDana Robinson2015-10-161-3/+4
| | | | | | | | | | | | | | | | | | | | | Description: Complete revamp of package initialization/shutdown mechanism in the library. Each package now has a single init/term routine. This new way should avoid packages being re-initialized during library shutdown and is also be _much_ more proactive about giving feedback for resource leaks internal to the library. Introduces a new "module" header file for packages in the library (e.g src/H5Fmodule.h) which sets up some necessary package configuration macros for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly modified version of this header, src/H5FDdrvr_module.h) Also cleaned up a bunch of resources leaks all across the library and tests, along with addressing many warnings, as I encountered them. Tested on: Ubuntu 15.04 (Linux 3.19 x86_64) gcc 4.9.2 serial and parallel (MPICH 3.1.4)
* [svn-r27688] Bring version 3 metadata cache from trunk + adding retries.Vailin Choi2015-09-061-71/+77
| | | | Tested on jam, kite, platypus, quail, moohan, ostrich, osx1010test, emu.
* [svn-r27257] Bring revisions #27084 - #27142 from trunk to revise_chunks. ↵Vailin Choi2015-06-201-1/+1
| | | | Tested on jam, koala, ostrich.
* [svn-r27241] Bring revisions #27058 - #27072 from trunk to revise_chunks. ↵Vailin Choi2015-06-181-290/+290
| | | | h5committested.
* [svn-r27156] Bring revisions #27003 - #27058 from trunk to revise_chunks. ↵Vailin Choi2015-06-061-7/+7
| | | | h5committested.
* [svn-r25941] Fix uninitialized memory error with v2 b-tree shadow pointersNeil Fortner2015-01-021-2/+4
| | | | | Fix swmr_writer and swmr_remove_writer to handle user-supplied seed values greater than 2^31-1
* [svn-r25828] Description:Quincey Koziol2014-11-201-15/+123
| | | | | | | | | | | | | Check in Vailin's performance improvements: - Track min+max for v2 B-trees, so we can more quickly answer queries - Refactor chunk index/hash value computation so that it doesn't have to be updated on cached chunks every time the dataset's dimension sizes change. Tested on: Mac OSX/64 10.10.0 (amazon) w/gcc 4.9, FORTRAN, C++ & parallel (h5committest not required on this branch)
* [svn-r25812] Description:Quincey Koziol2014-11-121-2/+2
| | | | Add a few missing comments.
* [svn-r25810] Description:Quincey Koziol2014-11-121-51/+41
| | | | | | | | Clean up some unused parameters to v2 B-tree internal routines. Tested on: Mac OSX/64 10.10.0 (amazon) w/serial & parallel (h5committest not required on this branch)
* [svn-r25588] Bring revisions #25383, #25388 from revise_chksum_retry to ↵Vailin Choi2014-09-111-151/+0
| | | | | | revise_chunks. h5committested.
* [svn-r25307] Bring revisions #24698 - #24783 from trunk to revise_chunks.Vailin Choi2014-06-171-2/+2
| | | | Tested on jam, koala, ostrich, platypus.
* [svn-r23104] Purpose: Add object header flush dependenciesNeil Fortner2012-12-141-2/+10
| | | | | | | | | | | 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-r22887] Purpose:Dana Robinson2012-10-121-2/+2
| | | | | | | | Fixes a variety of compile warnings and issues in the B-tree and heap code. Tested on: jam
* [svn-r22885] Purpose:Dana Robinson2012-10-111-24/+88
| | | | | | | | Adds some additional flush dependency plumbing and fixes some minor issues with the v2 B-tree code. Tested on: local Ubuntu VM
* [svn-r22761] Purpose: Fix testswmr failuresNeil Fortner2012-09-131-2/+8
| | | | | | | | | | 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-r22636] Description:Quincey Koziol2012-08-061-1/+1
| | | | | | | | 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-r22422] Purpose: Add support for SWMR with v2 b-treesNeil Fortner2012-05-301-147/+1448
| | | | | | | | | | | | | 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-r22105] Description:Quincey Koziol2012-03-211-25/+25
| | | | | | | | | | 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-r19330] Description:Quincey Koziol2010-09-011-47/+47
| | | | | | | | | | | | | | | | | | | | | | Bring r19109:19328 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 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode Mac OS X/32 10.6.4 (amazon) in debug mode Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
* [svn-r18708] Description:Quincey Koziol2010-05-051-126/+214
| | | | | | | | Bring r18638:18704 from trunk to revise_chunks branch. Tested on: Mac OS X/32 10.6.3 (amazon) w/debug & production (h5committest not required on this branch)
* [svn-r18639] Description:Quincey Koziol2010-04-271-55/+55
| | | | | | | | Bring r18619:18638 from trunk to revise_chunks branch. Tested on: FreeBSD/32 6.3 (duty) w/debug (h5committest not required on this branch)
* [svn-r18534] Description:Quincey Koziol2010-04-081-2/+90
| | | | | | | | | | | | | | | | | | Bring r18446:18533 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, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r17896] Description:Quincey Koziol2009-11-161-844/+541
| | | | | | | | | | | | | | | | | | | | | | | | Bring r17546:17895 from trunk to revise_chunks branch. Changes to fixed and extensible array dataset chunk indexing code to accommodate changes to private APIs in those interfaces. Also, other adjustments to source code and expected output in response to changes on the trunk. 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 (smirom) 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, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.2 (amazon) in debug mode Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17270] Description:Quincey Koziol2009-07-301-4/+0
| | | | | | | | Bring r17265:17269 from trunk to revise_chunks branch Tested on FreeBSD/32 6.3 (duty) (h5committest not required on this branch)
* [svn-r16846] Description:Quincey Koziol2009-04-231-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | Fix broken (for how long?) H5_ASSIGN_OVERFLOW macro to actually detect overflows during assignments, along with several errors it [now] detected. Cleaned up a fix minor warnings and/or pieces of code also. 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/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) 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, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.5.6 (amazon) in debug mode Mac OS X/32 10.5.6 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r16369] Description:Quincey Koziol2009-01-281-3/+3
| | | | | | | | Bring r16347:16367 from trunk into revise_chunks branch. Tested on: FreeBSD/32 6.3 (duty) (h5committest not required on this branch)
* [svn-r16194] Purpose:Mike McGreevy2008-12-151-26/+4
| | | | | | | | | | | | | | | | | | | | | | | Bug Fix Description: Resolved issues with broken sanity checks that were failing when the 'b2' debugging package was enabled (v2 b-tree debugging): - Fixed outdated assertions that would not compile. They now compile and function correctly. - Removed too far outdated assertions that would require too much unnecessary refactoring of code in order to satisfy their initial purpose. - Re-enabled b2 debugging package when "--enable-debug=all" is specified on the configure line. Tested: jam, smirom, linew
* [svn-r15800] Description:Quincey Koziol2008-10-071-33/+8
| | | | | | | | | | | | | | | | | | | | | | | Bring file free space branch changes through r15795 into trunk, which includes a fair bit of code cleanup & rearrangement along with a couple of bug fixes also. Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) 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, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15628] Description:Quincey Koziol2008-09-161-7/+7
| | | | | | | | | | | | | Remove trailing whitespace from C/C++ source files, with the following script: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Tested on: Mac OS X/32 10.5.5 (amazon) No need for h5committest, just whitespace changes...
* [svn-r15609] Description:Quincey Koziol2008-09-101-1/+1
| | | | | | | | Omnibus compiler warning cleanup & some reformatting also. Tested on: Mac OS X/32 10.5.4 (amazon) Too minor to require h5committest
* [svn-r15224] Description:Quincey Koziol2008-06-171-14/+24
| | | | | | | Clean up a few more compiler warnings. Tested on: FreeBSD/64 6.2 (liberty)
* [svn-r14903] Undoing change committed in r14902.Scot Breitenfeld2008-04-301-3/+3
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* [svn-r14902] Merged fortran_1_8 branch changes r14505:14901 into the trunk. ↵Scot Breitenfeld2008-04-301-3/+3
| | | | New fortran wrappers added.
* [svn-r14738] Description:Quincey Koziol2008-03-131-3/+3
| | | | | | | | | | Bring r14737 back from the 1.8 branch: Fix bug which would incorrectly encode the member offsets for compound datatypes whose size was between 256 & 511 bytes, when the "use the latest format" feature was enabled. Tested on: Mac OS X/32 10.5.2 (amazon) w/debug FreeBSD/32 6.2 (duty) w/production
* [svn-r13984] Description:Quincey Koziol2007-07-171-59/+61
| | | | | | | | | | | Various code cleanups and refactor recent changes for h5stat to fit into the existing library data structures better. Tested on: Mac OS X/32 10.4.10 (amazon) FreeBSD/32 6.2 (duty) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13978] purpose:Vailin Choi2007-07-131-0/+59
| | | | | | | | | | | | | | New feature. Description: Added routines to report on the amount of storage for: 1) 1.6 btree and heap storage info for groups 2) 1.8 btree, fractal heap storage info for groups, attributes and SOHM table 3) btree storage for chunked datasets 4) 1.8 superblock extension size. Platform tested: h5committested.
* [svn-r13814] Description:Quincey Koziol2007-05-291-9/+9
| | | | | | | | | | | | | | Change back to clearing memory buffers by default, but give users option to disable this, for performance reasons (--disable-clear-file-buffers). Also, add configure option (--enable-using-memchecker) to conveniently control making the library "play nice" with memory checking tools like valgrind and purify. Tested on: Mac OS X/32 10.4.9 (amazon) FreeBSD/32 6.2 (duty) Linux/32 2.6 (kagiso)
* [svn-r13773] Description:Quincey Koziol2007-05-201-45/+45
| | | | | | | Reduce compiler warnings w/gcc 4.2 Tested on: FreeBSD/32 6.2 (duty) w/gcc 4.2
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