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* [svn-r16818] Fix problem in H5Z.c with --disable-deprecated-symbolsNeil Fortner2009-04-211-0/+6
| | | | Tested: jam (--disable-deprecated-symbols)
* [svn-r16813] New feature(Bug 230):Albert Cheng2009-04-202-0/+67
| | | | | | | | | | | | | | | | | | | | | | | | Embed the content of libhdf5.settings into the hdf5 executables so that an "orphaned" executables can display (via the Unix strings command, for example) the library settings used to build the executables. This is a prototype implementation. Much improvement is needed. configure.in: Added the --disable-embedded-libinfo option to disable this feature. configure: src/H5config.h.in: Generated by autotools like automake. src/H5detect.c: Implement insert_libhdf5_settings() to insert the contents of libhdf5.settings into the library as an extern string variable so that it is included in all HDF5 executable. Much improvement is needed. fortran/src/Makefile.in: Auto-generated by bin/reconfigure. (i.e., I did make any changes to cause its direct regeneration). Tested: Jam serial, using default and --disable-embedded-libinfo, configure options.
* [svn-r16808] Purpose: Fix bug 1533Neil Fortner2009-04-2015-43/+105
| | | | | | | | | | | Description: Previously, there was no versioning for H5Z_class_t. This prevented applications written for 1.6 using custom filters from being able to use the 1.8 library. There is now an H5Z_class1_t and H5Z_class2_t to enable compatibility. H5Zregister is *not* versioned, it determines which version of the struct has been passed in by the value of the first field (id or version, both are ints). Tested: jam, linew, smirom (h5committest), jam (--with-default-api-version=v16)
* [svn-r16804] Purpose: Fix bug 1548Neil Fortner2009-04-202-32/+33
| | | | | | | | | Description: When writing data to a dataset, the data transform was performed after type conversion. This caused an error if the file type was non-native. This has been changed so data transforms are always performed on the memory type. Tested: jam, linew. smirom (h5committest)
* [svn-r16793] Description:Mike McGreevy2009-04-201-4/+4
| | | | | | | | | | | | - Updated bin/reconfigure to use latest version of automake (1.10.2). Regenerated Makefile.in's by running bin/reconfigure. - Added libtool version numbers to c++, fortran, hl, hl c++, and hl fortran libraries. Tested: jam, liberty, smirom
* [svn-r16767] Fix a comment in H5Pdapl.c, update RELEASE.txt with chages to ↵Neil Fortner2009-04-161-1/+1
| | | | | | | | factory free lists. Tested: kate
* [svn-r16743] Added #include <direct.h> to windows section. As discussed in ↵Allen Byrne2009-04-141-0/+1
| | | | | | Bug 1536, this include is needed to supply the _getcwd() function. Tested: XP 32 VS2005
* [svn-r16740] Snapshot version 1.8 release 2 (post12)Larry Knox2009-04-121-2/+2
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* [svn-r16731] Purpose: Fix bug 1539bNeil Fortner2009-04-101-0/+3
| | | | | | | | | | Description: The H5L interface was not marked as uninitialized when H5L_term_interface was called. This caused the interface to not initialize itself later on. This prevented external links from working after calling H5close, because they were never re-registered. Tested: jam, smirom, linew (h5committest)
* [svn-r16725] Snapshot version 1.8 release 2 (post11)Larry Knox2009-04-101-2/+2
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* [svn-r16722] Purpose: Fix problems with "no strict format checks"Neil Fortner2009-04-092-21/+46
| | | | | | | | | | Description: Changed H5G_mkroot to be tolerant of files with symbol table information cached but no symbol table in the root group. Also changed H5G_mkroot to properly clean up in case of an error, and changed H5G_stab_is_valid to properly detect errors in H5O_msg_read. Tested: jam, linew, smirom (h5committest), jam (--disable-strict-format-checks)
* [svn-r16712] Purpose: Fix bug 1423Neil Fortner2009-04-0814-314/+474
| | | | | | | | | | | | | | Description: Versions of the library between 1.3.0 and 1.6.3 have a bug which prevents them from opening any file that does not have the root group's symbol table information cached in the root group's entry in the superblock. Prior to 1.8 this was not an issue as this information was always cached. However, 1.8.0 stopped writing this information (which is not required by the file format specification), and these older versions can therefore not read files created or last written by versions 1.8.0 to 1.8.2. This fix modifies the library to once again add this information to the superblock (when using the old file format). Tested: jam, linew, smirom (h5committest)
* [svn-r16705] Snapshot version 1.8 release 2 (post10)Larry Knox2009-04-081-2/+2
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* [svn-r16703] Purpose: Improve performance of factory free lists.Neil Fortner2009-04-083-166/+459
| | | | | | | | | | | Description: Factory free lists were formerly implemented as block free lists. This was inefficient as factories can only be one size, and implementing them as blocks (which can be variable size) wasted computation and space. They have been rewritten with a separate implementation, which is simlar to regular free lists except they can be dynamically created and destroyed. Tested: jam, linew, smirom (h5committest)
* [svn-r16699] Purpose: Fix bug 503Neil Fortner2009-04-0813-309/+613
| | | | | | | | | Description: Changed Skip list package to use a deterministic skip list. This allows the skip list package to avoid calling rand() and srand(), even on machines without rand_r(). There is no longer a p-value or maximum level for skip lists. Tested: jam, smirom, linew (h5committest)
* [svn-r16695] Purpose: Fix bug 1526Neil Fortner2009-04-071-4/+11
| | | | | | | | | | | Description: Previously, H5Lcopy and H5Lmove would (through H5L_move) improperly apply the "create intermediate groups" property to the source path traversal, and not the destination. Fixed it to apply the property to the destination and not the source. Also fixed H5Lcreate_ud to reject internal link classes without throwing an assertion. Tested: linew, jam, smirom (h5committtest)
* [svn-r16652] Bug fix #1503 - H5Iget_type failed unexpected when an invalid ↵Raymond Lu2009-04-011-19/+19
| | | | | | | | | ID was passed in. I put some argument check in the internal function H5I_find_id and took out the assertion check. I also removed the argument check in H5Iis_valid because it's in H5I_find_id now. Tested on jam and linew - simple change.
* [svn-r16649] Snapshot version 1.8 release 2 (post9)Larry Knox2009-04-011-2/+2
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* [svn-r16616] Purpose: Fix bug 1499Neil Fortner2009-03-262-4/+20
| | | | | | | | | | | Description: Due to a bug in H5F_super_read, every time a file with a user block was opened it would grow by the size of the user block. The bug has been fixed, and comments have been added to clarify when an eoa address should be relative and when it should be absolute. Tested: jam, linew (h5committest)
* [svn-r16613] In previous checkin (r16609), the flag "write_driver" wasn't ↵Raymond Lu2009-03-253-13/+9
| | | | | | | | necessary as Quincey pointed out. I took it out and used the driver address instead. Tested on jam - simple change.
* [svn-r16608] Bug fix (#1161): When a family file created with v1.6 library ↵Raymond Lu2009-03-244-6/+25
| | | | | | | | | | | | is opened and closed with v1.8 library, v1.8 library writes the driver info block in the superblock. But v1.6 doesn't write it. This caused the data after the superblock to be overwritten. The solution is to use a flag to indicate when the original file doesn't have the driver info, v1.8 library doesn't write it either. Tested on jam. I have some trouble to access smirom and linew using h5committest.
* [svn-r16595] 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-r16582] Snapshot version 1.8 release 2 (post8)Larry Knox2009-03-161-2/+2
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* [svn-r16566] Description:Quincey Koziol2009-03-1126-416/+384
| | | | | | | | Bring r16560 back from trunk. Tested on: Mac OS X/32 10.5.6 (amazon) debug & production (Following up with tests on more platforms)
* [svn-r16562] Purpose:Mike McGreevy2009-03-101-3/+3
| | | | | | | | | | | | | | | | | | Bug Fix Description: Fixing BZ #1381. The --includedir=DIR configure option, which is used to spceify installation location of C header files, did not work correctly as the path was hard-coded into 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 which allows for customization of this value. Tested: jam, liberty
* [svn-r16541] 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-r16536] Description:Quincey Koziol2009-03-023-9/+11
| | | | | | | | | | | Bring v16532 back from trunk to v1.8 branch: 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 (h5committest not needed here, performed on trunk)
* [svn-r16526] Snapshot version 1.8 release 2 (post7)HDF Tester2009-03-021-2/+2
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* [svn-r16524] 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-r16519] merge 16518 from trunkPedro Vicente Nunes2009-02-261-0/+1
| | | | | | have 2 expected outputs for 2 h5ls runs depending if run on a 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: jam, linew
* [svn-r16515] To improve the performance of querrying the info of a link(bug ↵Raymond Lu2009-02-241-45/+66
| | | | | | | | | | | #1404). When the index was set to creation order in querry 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 links. Tested with h5committest.
* [svn-r16505] 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-r16500] Description:Quincey Koziol2009-02-191-1/+7
| | | | | | | | | | Bring r16499 back from trunk: Cache chunk info for newly created chunk. Tested on: FreeBSD/32 6.3 (duty) (Tests included in upcoming revise_chunks branch changes)
* [svn-r16495] Description:Quincey Koziol2009-02-191-153/+58
| | | | | | | | | | | Bring r16488 back from trunk: 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-r16494] Description:Quincey Koziol2009-02-199-146/+182
| | | | | | | | | | | Bring r16483 back from trunk: 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-r16490] Fixed bug #1459 by eliminating the macro long_long and ↵Allen Byrne2009-02-1812-202/+184
| | | | | | | | | replacing all instances with long long. Tested: h5comittest fedora 10 x64 XP32, VNET
* [svn-r16487] Checkin for moving messages forward into continuation message:Vailin Choi2009-02-162-8/+148
| | | | | | src/H5Oalloc.c, test/ohdr.c, toshm.c Fixed couple of problems in src/H5Odbg.c. h5committested.
* [svn-r16486] Snapshot version 1.8 release 2 (post6)HDF Tester2009-02-151-2/+2
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* [svn-r16481] 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-r16478] 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-r16476] 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-r16474] 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-r16467] 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-r16415] Description:Quincey Koziol2009-02-032-15/+29
| | | | | | | | | | | | Bring r16414 from trunk into 1.8 branch: 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-r16402] Description:Quincey Koziol2009-02-031-1/+1
| | | | | | | | | | | Bring r16401 back from trunk: 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-r16400] Description:Quincey Koziol2009-02-023-24/+21
| | | | | | | | | | Bring r16399 back from trunk: Remove some internal calls to H5E_clear_stack(). Tested on: FreeBSD/32 6.3 (duty) Too minor to require h5committest
* [svn-r16398] Snapshot version 1.8 release 2 (post5)HDF Tester2009-02-011-2/+2
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* [svn-r16395] Description:Quincey Koziol2009-02-017-14/+14
| | | | | | | | | | | | | | Bring r16394 back from trunk: 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-r16387] 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-r16381] 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)
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