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* [svn-r16804] Purpose: Fix bug 1548Neil Fortner2009-04-201-0/+2
| | | | | | | | | 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-r16802] Purpose: Fix bug 1516Neil Fortner2009-04-201-0/+2
| | | | | | | | | | | Description: h5repack previously would not take named datatypes into consideration when copying datasets and attributes. This would cause extra anonymous datatypes in the target file at best, and cause errors halfway through the repacking at worst. h5repack should now always handle named datatypes correctly. Named datatypes are also now converted to the native type when -n is given. Tested: jam, linew, smirom (h5committest)
* [svn-r16798] corrected typos in fortran APIScot Breitenfeld2009-04-201-4/+4
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* [svn-r16793] Description:Mike McGreevy2009-04-201-0/+3
| | | | | | | | | | | | - 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-r16783] Added information about new fortran wrappers added:Scot Breitenfeld2009-04-171-0/+7
| | | | | | | H5D_h5dget_access_plist_f H5I_h5iis_valid_f H5P_h5pset_chunk_cache_f H5P_h5pget_chunk_cache_f
* [svn-r16767] Fix a comment in H5Pdapl.c, update RELEASE.txt with chages to ↵Neil Fortner2009-04-161-0/+4
| | | | | | | | factory free lists. Tested: kate
* [svn-r16750] New feature (Bug ID: 1345):Albert Cheng2009-04-141-0/+2
| | | | | | | | Added a Make target of check-all-install to test the correctness of installing via the prefix= or $DESTDIR options. Platforms tested: h5committested and jam serial mode. Then test check-all-install by hand.
* [svn-r16744] Added fixed bug 1536, about the include for the _getcwd() function.Allen Byrne2009-04-141-0/+2
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* [svn-r16740] Snapshot version 1.8 release 2 (post12)Larry Knox2009-04-121-1/+1
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* [svn-r16732] added 2 new entriesPedro Vicente Nunes2009-04-101-0/+3
| | | | | | - h5diff new flag, -c, --compare, list objects that are not comparable. PVN - 2009/4/2 - 1368 - h5diff new flag, -N, --nan, avoids NaNs detection. PVN - 2009/4/2
* [svn-r16731] Purpose: Fix bug 1539bNeil Fortner2009-04-101-0/+2
| | | | | | | | | | 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 Knox2009-04-101-1/+1
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* [svn-r16712] Purpose: Fix bug 1423Neil Fortner2009-04-081-1/+4
| | | | | | | | | | | | | | 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-r16709] added The scale index return value in H5DSiterate_scales was ↵Pedro Vicente Nunes2009-04-081-6/+11
| | | | | | not always + incremented. (PVN - 2009/4/8 - 1538)
* [svn-r16705] Snapshot version 1.8 release 2 (post10)Larry Knox2009-04-081-1/+1
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* [svn-r16699] Purpose: Fix bug 503Neil Fortner2009-04-081-0/+2
| | | | | | | | | 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 Fortner2009-04-071-0/+2
| | | | | | | | | | | 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-r16668] Corrected the urls for h5dump xml dtd and schemaAllen Byrne2009-04-031-0/+1
| | | | Tested: Fedora 10 gcc
* [svn-r16658] merge from trunk 16656Pedro Vicente Nunes2009-04-021-0/+1
| | | | | | | | #1402 (B1) h5repack does not preserve creation order indexing. ISSUE : h5repack does not handle group creation order flags. ACTION: call H5P(g)(s)et_link_creation_order functions when handling groups, add new groups with these flags to the test generation program, and verify results in the test program. TEST: in the test program, function that compares property lists, added code to verify groups DOCS: Added the note to RELEASE.txt: "h5repack now handles group creation order. PVN - 2009/4/2 - 1402".
* [svn-r16649] Snapshot version 1.8 release 2 (post9)Larry Knox2009-04-011-1/+1
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* [svn-r16647] fix typoPedro Vicente Nunes2009-04-011-1/+1
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* [svn-r16644] add mention to #1501Pedro Vicente Nunes2009-04-011-3/+7
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* [svn-r16616] Purpose: Fix bug 1499Neil Fortner2009-03-261-5/+7
| | | | | | | | | | | 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-r16598] merge 16597 from trunkPedro Vicente Nunes2009-03-231-0/+6
| | | | | | | | | | | | | #1047 (B1) The h5lt info routines are returning data in transposed form. ISSUE : the dimension array of the function h5ltget_dataset_info_f was not transposed (because of C-FORTRAN storage order, the FORTRAN function calls the C function with the same name). SOLUTION: transpose the array. ACTION: add a test case. added the note Fortran High-Level APIs: ------ - Lite: The h5ltget_dataset_info_f function (gets information about a dataset) was not correctly returning the dimension array (PVN - 2009/3/23) tested: linux
* [svn-r16595] Purpose: fix bug 1189Neil Fortner2009-03-231-0/+5
| | | | | | | | | | | 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 Knox2009-03-161-1/+1
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* [svn-r16572] #1462 By selecting a compression type, a big endian byte order ↵Pedro Vicente Nunes2009-03-111-0/+2
| | | | | | | | | | | | | | | | | | | was being selected. When reading the compression parameter keyword, the compression type read flag was incorrectly set to read, removed this line of code in->configOptionVector[COMPRESS] = 1; Modified one configuration file to have the COMPRESSION-TYPE GZIP Keyword. Entered a bug description fix of - h5import: By selecting a compression type, a big endian byte order was being selected (PVN - 2009/11/3) tested: linux
* [svn-r16562] Purpose:Mike McGreevy2009-03-101-0/+4
| | | | | | | | | | | | | | | | | | 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-r16555] Purpose:Mike McGreevy2009-03-091-0/+3
| | | | | | | | | | | | | | | | | Bug Fix Description: Removing the code from configure which strips the '-g' flag from CFLAGS when in production mode. The current default CFLAGS in production mode does not include '-g', as intended, but we should allow users to override this and enable '-g' by setting the CFLAGS environment variable if desired. Note that this applies to FCFLAGS and CXXFLAGS as well. Tested: kagiso, linew, liberty
* [svn-r16546] Moved long_long comment to correct location under bugs fixed ↵Allen Byrne2009-03-051-3/+3
| | | | since section.
* [svn-r16544] Added text that long_long macro was removed. This should have ↵Allen Byrne2009-03-051-0/+3
| | | | been added with r16490.
* [svn-r16526] Snapshot version 1.8 release 2 (post7)HDF Tester2009-03-021-1/+1
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* [svn-r16524] Purpose: Fix bugs related to H5Dset_extent and fill valuesNeil Fortner2009-02-271-0/+2
| | | | | | | | | 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-r16486] Snapshot version 1.8 release 2 (post6)HDF Tester2009-02-151-1/+1
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* [svn-r16481] Purpose: Improve chunk cacheNeil Fortner2009-02-121-0/+2
| | | | | | | | | | | 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 Fortner2009-02-121-0/+2
| | | | | | | | | | | | | | | 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 Fortner2009-02-121-0/+2
| | | | | | | | | | | | 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 Fortner2009-02-121-1/+4
| | | | | | | | | | | | 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-r16398] Snapshot version 1.8 release 2 (post5)HDF Tester2009-02-011-1/+1
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* [svn-r16381] Purpose: Enable copying of dense attributesNeil Fortner2009-01-291-0/+1
| | | | | | | | | 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-r16379] Purpose: Fix a bug encountered when copying shared messagesNeil Fortner2009-01-291-0/+2
| | | | | | | | | | | | | 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-r16361] 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-r16346] Snapshot version 1.8 release 2 (post4)HDF Tester2009-01-251-1/+1
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* [svn-r16341] Description:Frank Baker2009-01-222-3/+3
| | | | | | Changed 'THG' to 'The HDF Group' in various HDF5 source files, most of which are <subdirectory>/COPYING. -- Closes Bugzilla entry 1403.
* [svn-r16331] Snapshot version 1.8 release 2 (post3)HDF Tester2009-01-181-1/+1
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* [svn-r16309] Purpose: Fix problem with H5TpackNeil Fortner2009-01-141-0/+2
| | | | | | | | | 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)
* [svn-r16291] Purpose:Mike McGreevy2009-01-091-0/+2
| | | | | | | | | | | | | | | svn merge Description: merging revision 16290 from trunk to 1.8 (revision 16290 contains the code that maintains a min_clean_fraction of the metadata cache in serial). Tested: smirom, jam
* [svn-r16285] - h5repack: When user doesn't specify a chunk size, h5repack ↵Pedro Vicente Nunes2009-01-081-4/+10
| | | | | | | | | | | | now defines a default chunk size as the same size of the size of the hyperslab used to read the chunks. The size of the hyperslabs are defined as the size of each dimension or a predefined constant, whatever is smaller. This assures that the chunk read fits in the chunk cache. (PVN - 2008/11/21) - H5Dset_extent: when shrinking dimensions, some chunks were not deleted. (PVN - 2009/01/8)
* [svn-r16282] Purpose: Add functions to allow more flexible traversal of ↵Neil Fortner2009-01-081-3/+9
| | | | | | | | | | | external links. Description: Added H5Pset/get_elink_cb to allow the user to specify a callback function to be called whenever an external link is traversed. Added H5Pset/get_elink_acc_flags to allow the user to specify the file access flags to use to open the target file of an external link. All these properties are set on a LAPL. Tested: jam (trunk version tested with h5committest)
* [svn-r16267] Revert RELEASE.txt to the version before it was mostly deleted ↵Neil Fortner2009-01-061-1/+419
| | | | | | | | by hdftest. Update version number listed at the top. Tested: vim
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