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* [svn-r17266] Description:Quincey Koziol2009-07-308-338/+335
| | | | | | | | | Clean up various compiler warnings from IRIX64 build Tested on: Mac OS X/32 (amazon) debug & production (yes, I know it's not an IRIX64 system :-) Too minor to require h5committest
* [svn-r17208] Fixed a small bug in the fractal heap code involving filtered ↵Neil Fortner2009-07-211-0/+61
| | | | | | fractal heaps. Tested: jam, linew, smirom (h5committest)
* [svn-r17179] I added a test of H5Tencode/decode for variable-length string ↵Raymond Lu2009-07-131-13/+131
| | | | | | | | type. This test is for the bug fix of #1585 in last round of checkin. Tested on jam. I used h5committest for the same change in the trunk.
* [svn-r17150] Description:Quincey Koziol2009-07-021-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | Bring r17148:17149 from trunk into 1.8 branch: Refactor how chunked dataset information is computed, moving it earlier and avoiding more recomputation. 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 10.5.7 (amazon) in debug mode Mac OS X/32 10.5.7 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17147] Description:Quincey Koziol2009-07-022-29/+30
| | | | | | | | | | | Bring r17146 from trunk to 1.8 branch: Bring a bunch of misc. improvements & tweaks from the revise_chunks branch back to the trunk, so that future merges won't be so painful. Tested on: FreeBSd/32 6.3 (duty) (h5committested on trunk)
* [svn-r17131] Corrected some typos. No test is needed.Raymond Lu2009-06-301-2/+2
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* [svn-r17127] A revision from last round of checkin (r17124). H5Aopen_name ↵Raymond Lu2009-06-291-4/+4
| | | | | | | | | has been deprecated. I replaced it with H5Aopen in this round. I also updated some hard-coded numbers with some macros. Tested on jam only. I have tested the same change for the trunk.
* [svn-r17124] Bug fix #1513. Reading an empty attribute caused seg fault. ↵Raymond Lu2009-06-261-0/+62
| | | | | | | | | | | | The flag "initialized" in the attribute structure wan't set correctly. It caused some confusion in H5A_read. This flag was actually redundant because the library can alwasy check if the data buffer is present. To fix it, I removed the "initialized" flag in the attribute structure and let H5A_read check the data buffer. I tested it on jam only but have tested the same change for the trunk on jam, smirom, and linew.
* [svn-r17109] Purpose: Fix bug in H5Z_filter_infoNeil Fortner2009-06-251-0/+11
| | | | | | | | | | | Description: Previously, when H5Z_filter_info was called for a filter that was not present, it would succeed and return the information from one position past the end of the pipeline, possibly causing a segfault. This affected at least H5Pget_fitler_by_id1/2, and possibly other API functions. Fixed to properly return failure. Tested: jam, linew, smirom (h5committest)
* [svn-r17083] Description:Quincey Koziol2009-06-181-12/+196
| | | | | | | | | | | | | | | | | | | | | | | Bring r17010,17017,17021-17022,17029-17031,17035 back from trunk: "temporary" file allocation space changes. 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 10.5.7 (amazon) in debug mode Mac OS X/32 10.5.7 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17026] Purpose: fix bug 1593Neil Fortner2009-06-101-0/+204
| | | | | | | | | | | | Description: When using H5T_copy on committed datatypes that are already open, H5T_copy would properly use the already existing shared struct, but would still deep copy all of the fields in that struct. This would cause memory leaks, and in the case of a compound containing a vlen (or reference), the change in size would cause the size of the resulting type to be set to an incorrect value. Changed H5T_copy to properly avoid deep copies when using a reopened shared struct. Tested: jam, linew, smirom (h5committest), purify on jam
* [svn-r16993] Snapshot version 1.8 release 3 (snap0)Larry Knox2009-06-011-18/+18
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* [svn-r16922] Allow an error class to use other class's major or minor ↵Raymond Lu2009-05-052-13/+31
| | | | | | errors. Added a test for it, too. Tested on jam - simple change. I've tested it for the trunk.
* [svn-r16920] Description:Quincey Koziol2009-05-054-26/+374
| | | | | | | | | | | | | | | | | | | | | | | | | | | | Merge these trunk revisions which occurred during the 1.8.3 release code freeze back to the 1.8 branch: From Quincey: 16845 16847 16849 16851 16858 16869 16897 From Ray: 16859 16880 From Allen: 16863 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-r16808] Purpose: Fix bug 1533Neil Fortner2009-04-201-5/+40
| | | | | | | | | | | 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 Fortner2009-04-201-24/+35
| | | | | | | | | 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 McGreevy2009-04-201-10/+10
| | | | | | | | | | | | - 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-r16778] A minor correction of previous checkin. The original files ↵Raymond Lu2009-04-171-8/+6
| | | | | | | | created with v1.6 library could be deleted by cleanup routine. I corrected it in this checkin. Tested on jam - simple change.
* [svn-r16758] The test of family file compatibility with v1.6 used the ↵Raymond Lu2009-04-153-11/+56
| | | | | | | | | | original family files under the library source directory. Since the test opens the files with write mode, it's safer to make copies of the original files. I added the copying step in test_family_compat in vfd.c. I changed the Makefile.am to clean up the copied files. I created a new family_v16_00000.h5 with v1.6 library. Tested on jam - supposed to be simple change.
* [svn-r16740] Snapshot version 1.8 release 2 (post12)Larry Knox2009-04-121-0/+0
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* [svn-r16733] Revert change to family_16_00000.h5 from latest snapshot ↵Neil Fortner2009-04-101-0/+0
| | | | | | release. Raymond is working on fixing this.
* [svn-r16731] Purpose: Fix bug 1539bNeil Fortner2009-04-101-4/+72
| | | | | | | | | | 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 Knox2009-04-102-0/+0
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* [svn-r16712] Purpose: Fix bug 1423Neil Fortner2009-04-082-15/+75
| | | | | | | | | | | | | | 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-r16699] Purpose: Fix bug 503Neil Fortner2009-04-081-23/+69
| | | | | | | | | 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 Fortner2009-04-072-0/+90
| | | | | | | | | | | 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 Lu2009-04-011-1/+42
| | | | | | | | | 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-r16616] Purpose: Fix bug 1499Neil Fortner2009-03-261-0/+120
| | | | | | | | | | | 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 Lu2009-03-251-2/+2
| | | | | | | | 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 Lu2009-03-243-1/+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 Fortner2009-03-234-9/+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-r16577] Description:Quincey Koziol2009-03-121-1/+1
| | | | Actually set the exit value for the test (*sigh*)
* [svn-r16575] Description:Quincey Koziol2009-03-121-228/+200
| | | | | | | | | | | Bring r16574 back from trunk: 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 (other platforms tested on trunk)
* [svn-r16566] Description:Quincey Koziol2009-03-1118-237/+225
| | | | | | | | 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-r16538] 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-r16524] 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-r16519] merge 16518 from trunkPedro Vicente Nunes2009-02-261-13/+15
| | | | | | 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-r16512] merge 16511 from trunkPedro Vicente Nunes2009-02-232-8/+8
| | | | | | | bug fix: TESTING2 macro introduced recently for the test suite (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-r16495] Description:Quincey Koziol2009-02-192-16/+23
| | | | | | | | | | | 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 Koziol2009-02-191-1/+1
| | | | | | | | | | | 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 Byrne2009-02-187-158/+158
| | | | | | | | | replacing all instances with long long. Tested: h5comittest fedora 10 x64 XP32, VNET
* [svn-r16487] Checkin for moving messages forward into continuation message:Vailin Choi2009-02-162-2/+103
| | | | | | src/H5Oalloc.c, test/ohdr.c, toshm.c Fixed couple of problems in src/H5Odbg.c. h5committested.
* [svn-r16481] 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-r16478] 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-r16476] 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-r16474] 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-r16471] 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-r16467] 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-r16440] Description:Quincey Koziol2009-02-052-46/+203
| | | | | | | | | | | Bring r16435 from revise_chunks branch back to 1.8 branch: 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)
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