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* [svn-r16594] Purpose: fix bug 1189Neil Fortner2009-03-2314-39/+251
| | | | | | | | | | | Description: Some files apparently exist in the wild which have corrupt symbol table messages on the root group. These files can be opened by 1.6 (which uses the cached information in the superblock) but not by 1.8. This patch fixes 1.8 and 1.9 so they can now open these files, and will correct them if necessary. Also fix some potential (rare) problems with array datatype versions. Tested: jam (parallel; h5committest not working on linew or smirom)
* [svn-r16587] Description:Quincey Koziol2009-03-178-51/+408
| | | | | | | | | | | | | | | | | | | | Add infrastructure & tests for "flush dependencies" in metadata cache, which allow relationships that specify which order to flush metadata entries in. 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 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 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-r16579] Snapshot version 1.9 release 35Larry Knox2009-03-152-3/+3
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* [svn-r16561] Purpose:Mike McGreevy2009-03-101-3/+3
| | | | | | | | | | | | | | | | | | Bug Fix Description: Fixing BZ #1381. The --includedir=DIR configure option, which is used to specify the installation location of C header files, did not work correctly as the path was hard-coded in config/commence.am. I'm presuming this is because an older version of automake didn't know where to put c header files. In any case, removing this line now defaults the includedir to the same directory that it is currently hard-coded to, and also fixes the configure flag to allow customization of this value. Tested: jam, liberty
* [svn-r16560] Description:Quincey Koziol2009-03-1026-416/+384
| | | | | | | | | | Remove another call to H5E_clear_stack() from within the library. Clean up lots of compiler warnings. Tested on: Mac OS X/32 10.5.6 (amazon) (followup on other platforms forthcoming)
* [svn-r16553] Snapshot version 1.9 release 34Larry Knox2009-03-082-3/+3
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* [svn-r16540] Move variable declaration to the top of the block in ↵Neil Fortner2009-03-041-1/+2
| | | | | | H5G_dense_iterate Tested: Fedora 10 (too minor for full committest)
* [svn-r16532] Description:Quincey Koziol2009-03-023-9/+11
| | | | | | | | | | Pass the chunk "user data" to H5D_chunk_unlock(), so that chunks with an address already aren't reallocated. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r16525] Snapshot version 1.9 release 33HDF Tester2009-03-012-3/+3
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* [svn-r16523] Purpose: Fix bugs related to H5Dset_extent and fill valuesNeil Fortner2009-02-273-227/+312
| | | | | | | | | Description: In some situations it was possible for the fill value to not be written to parts of a chunked dataset, particularly when extending and/or shrinking. Prior to the fix for the chunk cache (1015) these bugs would have been exceedingly rare. Tested: jam, smirom, linew (h5committest)
* [svn-r16518] have 2 expected outputs for 2 h5ls runs depending if run on a ↵Pedro Vicente Nunes2009-02-261-0/+1
| | | | | | | big or little endian machine. Configure.in was modified to export a variable carrying endianess information to testh5ls.sh. This script then compares the current run with 2 expected outputs, one for a big-endian machine (linew was used to generate the output), other for little endian (jam was used to generate the output) the way h5ls prints types, it starts searching for NATIVE types first. One solution would be h5ls not to detect these native types, using for example the same print datatype function that h5dump does, that would make the output look the same on all platforms ("32-bit little-endian integer" would be printed instead). Drawback, this "native" information would not be available. Other solution is to have not one but 2 expected outputs and make the shell script detect the endianess and compare with one output or other tested: h5committest
* [svn-r16516] To improve the performance of querying the info of a link (bug ↵Raymond Lu2009-02-241-45/+66
| | | | | | | | | | | #1404). When the index was set to creation order in query function but there's no creation order indexed in the file, the library tried to build and sort a table of all links. To optimize it, let the library use the B-tree for names of the links. Tested on jam. I tested the same change for v1.8 with h5committest.
* [svn-r16506] Snapshot version 1.9 release 32HDF Tester2009-02-222-3/+3
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* [svn-r16504] Maintenance: Fixed a typo discovered while compiling on AIX systemElena Pourmal2009-02-201-1/+1
| | | | Platforms tested: Mac OSX and AIX (by Ed) (minor fix)
* [svn-r16499] Description:Quincey Koziol2009-02-191-1/+7
| | | | | | | | Cache chunk info for newly created chunk. Tested on: FreeBSD/32 6.3 (duty) (Tests included in upcoming revise_chunks branch changes)
* [svn-r16489] Fixed bug #1459 by eliminating the macro long_long and ↵Allen Byrne2009-02-1819-230/+212
| | | | | | | | | | | replacing all instances with long long. Tested: h5comittest fedora 10 x64 Vista 32, VS2005, IVF101 XP32, Cygwin
* [svn-r16488] Description:Quincey Koziol2009-02-171-153/+58
| | | | | | | | | Clean up code and eliminate resource leaks. Also avoid "null" I/O when chunk doesn't exist and we can skip it. Tested on: Mac OS X/32 10.5.6 (amazon) (too minor to require h5committest)
* [svn-r16484] Snapshot version 1.9 release 31HDF Tester2009-02-152-3/+3
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* [svn-r16483] Description:Quincey Koziol2009-02-129-146/+182
| | | | | | | | | Clean up (i.e. remove) more internal calls to H5E_clear_stack(), along with some other minor code cleanups. Tested on: Mac OS X/32 10.5.6 (amazon) (too minor to require h5committest)
* [svn-r16480] Purpose: Improve chunk cacheNeil Fortner2009-02-124-16/+64
| | | | | | | | | | | Description: The meaning of the "nbytes" field in H5D_rdcc_t was not clear, and some places assumed it was the maximum size of the chunk cache, while some assumed it was the current size of the chunk cache. The end result was that only 1 chunk could be held in cache at a time. This field has been replaced by "nbytes_max" and "nbytes_used". Performance of cached I/O should improve greatly. Tested: jam, smirom (h5committest)
* [svn-r16477] Purpose: Fix problem with opening an attribute multiple times ↵Neil Fortner2009-02-126-20/+20
| | | | | | | | | | | | | | | through multiple file handles. Description: An attribute's "oloc" field which specifies the file it resides in was located in the attribute's "shared" structure. So when an attribute was opened multiple times all of the handles for that attribute pointed to the same file id, even if different file id's were used to open the different handles for the attribute. The "oloc" has been moved to the top level H5A_t struct. Tested: jam, smirom (h5committest)
* [svn-r16475] Purpose: Fix rare error when adding a new object header messageNeil Fortner2009-02-121-57/+126
| | | | | | | | | | | | Description: Since the new object header format, it has been possible for a situation to be created where none of the messages are large enough to hold a continuation message and there are no null messages to merge with. This makes it impossible to add a new object header chunk. This case will now be handled by moving every message in the last chunk to the newly allocated one, except for null messages which are deleted. Tested: jam, smirom (h5committest)
* [svn-r16473] Purpose: fix problems related to 'self-referential' attributesNeil Fortner2009-02-1235-152/+217
| | | | | | | | | | | | Description: When an attribute was created with a datatype or dataspace that was shared in the same object header that the attribute was in, the attribute could not be deleted. Changes made to ensure that the attribute can be deleted both when the attribute is in the object header and when it is shared in the heap. Object header message decode routines now take an "open_oh" parameter to enable them to avoid opening the same object header twice. Tested: jam, smirom (h5committest)
* [svn-r16465] Performance Improvement(bug #1450). When a chunk is bigger ↵Raymond Lu2009-02-113-18/+174
| | | | | | | | | than the cache size and isn't allocated on disk, the library still loaded it in the cache, which is redundant. I changed it to bypass the cache and added a test in dsets.c. Tested on jam and smirom.
* [svn-r16453] Snapshot version 1.9 release 30HDF Tester2009-02-082-3/+3
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* [svn-r16436] Checkin for moving messages forward into continuation message:Vailin Choi2009-02-052-8/+148
| | | | | src/H5Oalloc.c, test/ohdr.c, toshm.c Fixed couple of problems in src/H5Odbg.c.
* [svn-r16414] Description:Quincey Koziol2009-02-032-15/+29
| | | | | | | | | | Eliminate some more calls to H5E_clear_stack() from within library code. Clean up some warnings & comments also. Tested on: Mac OS X/32 10.5.6 (amazon) (Too minor to require h5committest)
* [svn-r16401] Description:Quincey Koziol2009-02-031-1/+1
| | | | | | | | | Correct error introduced in r16353 with layout version, and add test so it gets caught earlier. Tested on: FreeBSD/32 6.3 (duty) Too minor to require h5committest
* [svn-r16399] Description:Quincey Koziol2009-02-023-24/+21
| | | | | | | | Remove some internal calls to H5E_clear_stack(). Tested on: FreeBSD/32 6.3 (duty) Too minor to require h5committest
* [svn-r16397] Snapshot version 1.9 release 29HDF Tester2009-02-012-3/+3
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* [svn-r16394] Description:Quincey Koziol2009-02-017-14/+14
| | | | | | | | | | | | Rename H5O_msg_read_real -> H5O_msg_read_oh, to be more consistent with other routines in library. Move H5O_msg_read_oh and H5O_msg_exists_oh from package to private header file, so other routines in library can use them. Tested on: FreeBSD/32 6.3 (duty) Too minor to require h5committest
* [svn-r16391] Description:Quincey Koziol2009-01-318-50/+109
| | | | | | | | Add more metadata statistics to extensible array header. Tested on: FreeBSD 6.3 (duty) (too minor to require h5committest)
* [svn-r16386] Fix various warnings (errors in pgcc) associated with ↵Neil Fortner2009-01-303-15/+13
| | | | | | | | yesterday's dense attribute object copy commit. Tested: jam (gcc and pgcc)
* [svn-r16382] Description:Quincey Koziol2009-01-291-18/+18
| | | | | | | Re-insert some whitespace formatting that was accidentally removed. Tested on: None - just eyeballed.
* [svn-r16380] Purpose: Enable copying of dense attributesNeil Fortner2009-01-294-287/+607
| | | | | | | | | Description: Attribute object copy routines have been moved from H5Oattr.c to H5Aint.c. These routines are now shared between compact and densely stored attributes. New routines written to support the copying of dense attributes. This patch wasmostly written by Peter Cao. Tested: jam, smirom (h5committest)
* [svn-r16378] Description:Allen Byrne2009-01-291-23/+25
| | | | | | | | | Changed max macro in earray.c to avoid Windows conflict. Changed if(test) to assert(test) in H5FDcore.c - H5FD_core_open() Tested on: Windows: XP32, XP64, Vista32, Vista64 H5committest.
* [svn-r16376] Purpose: Fix a bug encountered when copying shared messagesNeil Fortner2009-01-296-14/+41
| | | | | | | | | | | | | Description: When attempting to copy an object with a message shared in its own object header, the library attempts to protect the same object header twice. Previously, it was possible for the object header to be protected with write access in one or both of these protects, which would be illegal. The library should now always protect with read only access in this case. The conditions for fixing incorrect datatype versions have been made weaker to support this change. The version will only be corrected if the object header the datatype is in is modified. Tested: jam, smirom (h5committest)
* [svn-r16367] Description:Quincey Koziol2009-01-272-40/+121
| | | | | | | | | | Refactor internal address encode/decode routines slightly, to allow for more flexible use. Tested on: Mac OS X/32 (amazon) FreeBSD/32 (duty) (too minor to require h5committest)
* [svn-r16366] Description:Quincey Koziol2009-01-276-15/+116
| | | | | | | | | Add context pointer for extensible array client callbacks. Tested on: Mac OS X/32 (amazon) FreeBSD/32 (duty) (too minor to require full h5committest)
* [svn-r16364] Description:Quincey Koziol2009-01-271-3/+3
| | | | | | | | Clean up a few compiler warnings Tested on: Mac OS X/32 (amazon) (too minor to require h5committest)
* [svn-r16360] Purpose: Fix potential error with H5Tset_orderNeil Fortner2009-01-271-0/+2
| | | | | | | | Description: H5Tset_order will now properly reject H5T_ORDER_NONE for most datatypes. Previously this could cause major problems as the file could not be flushed. Tested: jam, smirom (h5committest)
* [svn-r16354] Description:Quincey Koziol2009-01-2714-245/+520
| | | | | | | | | | | Bring r16353 back from revise_chunks branch: Refactor internal layout information, making it easier to add another type of chunk index. Tested on: FreeBSD/32 6.3 (duty) (other platforms tested with original patch)
* [svn-r16347] Purpose: enhancements the H5Tinsert, H5TpackNeil Fortner2009-01-262-32/+135
| | | | | | | | | | | | Description: H5Tinsert will now detect when a compound type that was previously not packed becomes packed due to out of offset order insertion of a member. H5Tinsert will now attempt to keep members sorted by offset order. This should improve performance of H5Tinsert in all cases due to the fact that it no longer needs to check every other member for overlapping, and should improve performance of H5Tpack and possibly type conversion when compounds are packed out of order. Tested: jam, smirom (h5committest)
* [svn-r16344] Snapshot version 1.9 release 28HDF Tester2009-01-252-3/+3
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* [svn-r16340] Description:Frank Baker2009-01-221-1/+1
| | | | | | Changed 'THG' to 'The HDF Group' in various HDF5 source files, most of which are <subdirectory>/COPYING. -- Closes Bugzilla entry 1403.
* [svn-r16329] Snapshot version 1.9 release 27HDF Tester2009-01-182-3/+3
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* [svn-r16324] Purpose:Mike McGreevy2009-01-151-102/+77
| | | | | | | | | | | | | | | Code Cleanup Description: - Pulled out repetitive cache stats code into its own new macro. - Converted HDasserts in cache stats macros to if / HGOTO_ERROR statments in order to keep code consistent. Tested: jam, smirom, liberty
* [svn-r16321] Purpose:Albert Cheng2009-01-141-0/+2
| | | | | | | | | | | Improvement Description: Modified the warning messages from the Version mismatch checking to suggest the users to try recompiling or checking the shared lib setting. Platforms tested: Tested in Jam only since it was just a simple text string changes.
* [svn-r16316] Added support for OpenVMS pathname for external links.Raymond Lu2009-01-143-5/+42
| | | | Tested on jam. Tested v1.8 on OpenVMS.
* [svn-r16308] Purpose: Fix problem with H5TpackNeil Fortner2009-01-141-2/+7
| | | | | | | | | Description: If a compound type was packed except for some extra space at the end, H5Tpack would not modify the type and the extra space would remain. Changed H5T_is_packed to fix this behaviour. Tested: jam, smirom (h5committest - linew down)
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