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* [svn-r16594] Purpose: fix bug 1189Neil Fortner2009-03-234-9/+132
| | | | | | | | | | | 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 Koziol2009-03-173-412/+2824
| | | | | | | | | | | | | | | | | | | | 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-r16576] Description:Quincey Koziol2009-03-121-1/+1
| | | | Actually set the exit value for the test (*sigh*)
* [svn-r16574] Description:Quincey Koziol2009-03-121-228/+200
| | | | | | | | | | | | | | | | | | | | | | Clean up many compiler warnings and make test return non-zero exit code when a failure is detected. 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 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-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 Koziol2009-03-1018-237/+225
| | | | | | | | | | 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-r16539] Added more test case for bypassing the cache. In ↵Raymond Lu2009-03-031-17/+49
| | | | | | | | | | | test_big_chunks_bypass_cache, test the correctness of the data when the fill value is defined or not. The library should let the chunks bypass the cache depending on the size of the chunks and whether to write fill value to the chunks. Tested on jam - simple change.
* [svn-r16523] Purpose: Fix bugs related to H5Dset_extent and fill valuesNeil Fortner2009-02-271-19/+48
| | | | | | | | | 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-r16511] bug fix: TESTING2 macro introduced recently for the test suite ↵Pedro Vicente Nunes2009-02-232-8/+8
| | | | | | (it adds an extra space at the beginning of output, for indentation) was already available for HL and caused compilation problems on AIX. Replaced the name with TESTING_2 tested: h5committest
* [svn-r16506] Snapshot version 1.9 release 32HDF Tester2009-02-221-5/+6
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* [svn-r16489] Fixed bug #1459 by eliminating the macro long_long and ↵Allen Byrne2009-02-188-160/+160
| | | | | | | | | | | replacing all instances with long long. Tested: h5comittest fedora 10 x64 Vista 32, VS2005, IVF101 XP32, Cygwin
* [svn-r16488] Description:Quincey Koziol2009-02-172-16/+23
| | | | | | | | | 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-r16483] Description:Quincey Koziol2009-02-121-1/+1
| | | | | | | | | 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 Fortner2009-02-121-0/+184
| | | | | | | | | | | 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 Fortner2009-02-121-1/+164
| | | | | | | | | | | | | | | 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 Fortner2009-02-121-0/+84
| | | | | | | | | | | | 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 Fortner2009-02-121-0/+131
| | | | | | | | | | | | 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-r16472] Change H5Dopen to H5Dopen2 - fixes compile error - too many ↵Larry Knox2009-02-121-1/+1
| | | | arguments for H5Dopen1 when using v1.6 compatible flag. Trivial change, tested on smirom and jam.
* [svn-r16466] Performance Improvement(bug #1450). When a chunk is bigger ↵Raymond Lu2009-02-111-0/+135
| | | | | | | | | | 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-r16439] Description:Quincey Koziol2009-02-052-46/+203
| | | | | | | | | | | Bring r16435 from revise_chunks branch back to trunk: Expand object copy tests for chunked datasets to include 1-D datasets with an unlimited dimension. (Fix typo in comment for test/links.c) Tested on: FreeBSD/32 6.3 (duty) in debug mode (more thoroughly tested already on revise_chunks branch)
* [svn-r16436] Checkin for moving messages forward into continuation message:Vailin Choi2009-02-052-2/+103
| | | | | src/H5Oalloc.c, test/ohdr.c, toshm.c Fixed couple of problems in src/H5Odbg.c.
* [svn-r16431] Uncomment a h5cleanup() call previously accidently left commented Pedro Vicente Nunes2009-02-051-1/+1
| | | | Tested: linux
* [svn-r16423] bug fix: a open call was not made the expected FAPLPedro Vicente Nunes2009-02-041-9/+11
| | | | tested: windows, linux (split, sec2)
* [svn-r16419] #1449 Change set_extent test to use standard standalone test ↵Pedro Vicente Nunes2009-02-042-28/+41
| | | | | | | | | | | | | | | | | | framework Call h5_fixname (with an array of test filenames) for generating the filename to create and then call h5_cleanup() when the tests pass, to delete the files created and close the FAPL from h5_fileaccess(). Defined a macro #define TESTING2(WHAT) {printf(" Testing %-62s",WHAT); fflush(stdout);} Similar to TESTING, except that it has a initial indentation space. The effect is for nested loop tests Testing with old file format: Testing with fill value, no compression PASSED tested: windows, linux
* [svn-r16417] Description:Quincey Koziol2009-02-041-83/+69
| | | | | | | | | | | Bring r16416 from revise_chunks branch to trunk: Bring closer to standard standalone test format, add checks for using the latest file format and close dataset ID leaked. Tested on: FreeBSD/32 6.3 (duty) (too minor to require h5committest)
* [svn-r16405] #1449 Change set_extent test to use standard standalone test ↵Pedro Vicente Nunes2009-02-031-61/+66
| | | | | | | | | | | | | | | | framework use a fapl obtained by h5_fileaccess to the call of H5Fcreate and redo the test calls with h5_reset(); fapl = h5_fileaccess(); nerrors += do_ranks( fapl ) < 0 ? 1 : 0; nerrors += test_external( fapl ) < 0 ? 1 : 0; nerrors += do_layouts( fapl ) < 0 ? 1 : 0; tested: windows, linux
* [svn-r16397] Snapshot version 1.9 release 29HDF Tester2009-02-011-2/+2
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* [svn-r16391] Description:Quincey Koziol2009-01-311-1/+51
| | | | | | | | Add more metadata statistics to extensible array header. Tested on: FreeBSD 6.3 (duty) (too minor to require h5committest)
* [svn-r16382] Description:Quincey Koziol2009-01-291-34/+34
| | | | | | | Re-insert some whitespace formatting that was accidentally removed. Tested on: None - just eyeballed.
* [svn-r16380] Purpose: Enable copying of dense attributesNeil Fortner2009-01-291-28/+161
| | | | | | | | | 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 Byrne2009-01-291-44/+44
| | | | | | | | | 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-r16372] Description:Quincey Koziol2009-01-293-8/+15
| | | | | | | | Clean up files produced from set_extent testing. Tested on: FreeBSD/32 6.3 (duty) (too minor to require h5committest)
* [svn-r16370] Modify test_pack_ooo to always output the state of randomly ↵Neil Fortner2009-01-281-45/+37
| | | | | | | | generated variables when it fails, even in the sections that do not use the random variables. Tested: jam
* [svn-r16360] Purpose: Fix potential error with H5Tset_orderNeil Fortner2009-01-271-0/+167
| | | | | | | | 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-r16347] Purpose: enhancements the H5Tinsert, H5TpackNeil Fortner2009-01-261-2/+249
| | | | | | | | | | | | 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-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-r16338] Purpose: Mike McGreevy2009-01-221-5/+0
| | | | | | | | | | | | | | Bug Fix Description: Removing some unnecessary system headers from test/cache.c which snuck their way into one of my previous check-ins ... thanks to Allen for catching this while testing on Windows. Tested: Windows, Linux
* [svn-r16327] Added some missing file names for OpenVMS. Tested on OpenVMS ↵Raymond Lu2009-01-161-0/+4
| | | | for 1.8.
* [svn-r16316] Added support for OpenVMS pathname for external links.Raymond Lu2009-01-142-25/+93
| | | | Tested on jam. Tested v1.8 on OpenVMS.
* [svn-r16308] Purpose: Fix problem with H5TpackNeil Fortner2009-01-141-2/+124
| | | | | | | | | 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-r16296] Neil Fortner2009-01-111-2/+7
| | | | | | Disable more file drivers incompatible with family file driver in external_set_elink_cb in links.c. Tested: jam check-vfd
* [svn-r16294] Changes to links.c to prevent the core file driver from being ↵Neil Fortner2009-01-101-8/+9
| | | | | | | | used as the member file driver for a family file. This was causing problems with check-vfd. Tested: jam
* [svn-r16292] Purpose: Mike McGreevy2009-01-101-2/+1
| | | | | | | | | | | | | Bug Fix Descriotion: Removing problematic debugging code, and switching a leftover TRUE verbose statement to FALSE in cache_common.c Tested: jam, liberty
* [svn-r16290] Purpose: Mike McGreevy2009-01-092-29/+1643
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Adding code to maintain a min_clean_fraction in the cache in serial mode. Description: The metadata cache now has the ability to maintain a min_clean_fraction when in serial mode. The default initial cache size has been changed from 1MB to 2MB, and the default min_clean_fraction has been set at 30%. This check-in includes modifications to H5C.c to support maintaining a min_clean_size, including the addition of clean_index_size and dirty_index_size trackers, modifications to the H5C_make_space_in_cache algorithm, as well as associated test code and additional statistics tracking variables. Maintaining the min_clean_fraction addresses the possibility of experiencing a "metadata blizzard" when the cache gets completely full with dirty entries. Upon having to make space, the cache would previously need to flush every single entry in the cache before coming across a clean entry which could be evicted. This resulted in unnecessary flushing of oftentimes hot entries in the cache. Maintaining the min_clean_fraction ensures that, when space is needed, clean entries are more readily available to evict. Tested: jam, smirom, linew (h5committest)
* [svn-r16289] Minor change to links.c to clear a warning.Neil Fortner2009-01-091-2/+0
| | | | Tested: jam
* [svn-r16287] Fix one of the new tests in links.c. external_set_elink_cb no ↵Neil Fortner2009-01-091-18/+22
| | | | | | | | longer copies the driver information from property list to property list. Tested: jam
* [svn-r16281] Purpose: Add functions to allow more flexible traversal of ↵Neil Fortner2009-01-081-0/+278
| | | | | | | | | | | 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, linew, smirom (h5committest)
* [svn-r16273] Added a test for shrinking to 0 dimemsionsPedro Vicente Nunes2009-01-081-226/+351
| | | | Tested: windows, linux
* [svn-r16229] merge 16228Pedro Vicente Nunes2008-12-291-20/+20
| | | | | cleaned more linux warnings tested: linux
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