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* [svn-r16652] Bug fix #1503 - H5Iget_type failed unexpected when an invalid ↵Raymond Lu2009-04-012-20/+61
| | | | | | | | | 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 Knox2009-04-017-22/+22
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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-r16641] merge from trunk revs 16614, 16629Pedro Vicente Nunes2009-04-0113-25/+182
| | | | | | | | | | | 1. #1501 (B1) tools bug if dataset is larger than H5TOOLS_BUFSIZE limit. ISSUE : the tools use the following formula to read by hyperslabs: hyperslab_size[i] = MIN( dim_size[i], H5TOOLS_BUFSIZE / datum_size) where H5TOOLS_BUFSIZE is a constant defined of 1024K. This is OK as long as the datum_size does not exceed 1024K, otherwise we have a hyperslab size of 0 (since 1024K/(greater than 1024K) = 0). This affects h5dump. h5repack, h5diff SOLUTION: add a check for a 0 size and define as 1 if so. TEST FOR H5DUMP: Defined a case in the h5dump test generator program of such a type (an array type of doubles with a large array dimension, that was the case the user reported). Since the written file commited in svn would be around 1024K, opted for not writing the data (the part of the code where the hyperslab is defined is executed, since h5dump always reads the files). Defined a macro WRITE_ARRAY to enable such writing if needed. Added a run on the h5dump shell script. Added 2 new files to svn: tools/testfiles/tarray8.ddl, tools/testfiles/tarray8.h5. NOTE: while doing this I thought of adding this dataset case to an existing file, but that would add the large array output to those files (the ddls). The issue is that the file list is increasing. TEST FOR H5DIFF: for h5diff the check for reading by hyperslabs is H5TOOLS_MALLOCSIZE (128 * H5TOOLS_BUFSIZE) or 128 Mb. This makes it not possible to add such a file to svn, so used the same method as h5dump (only write the dataset if WRITE_ARRAY is defined). As opposed to h5dump, the hyperslab code is NOT executed when the dataset is empty (dataset is not read). Added the new dataset to existing files and shell run (tools/h5diff/testfiles/h5diff_dset1.h5 and tools/h5diff/testfiles/h5diff_dset2.h5 and output in tools/h5diff/testfiles/h5diff_80.txt). TEST FOR H5REPACK: similar issue as h5diff with the difference that the hyperslab code is run. Added a run to the shell script (with a filter, otherwise the code uses H5Ocopy). FURTHER ISSUES: the type in question ("double") has a different output cross platforms (e.g on liberty some garbage number is printed at some array locations) SOLUTION: defined an "int" type for this test. However the printing of such an array has a bogus output at least in one platform (FreeBsd), so eliminated the test run altogether and filed a bug report on this
* [svn-r16616] Purpose: Fix bug 1499Neil Fortner2009-03-264-9/+147
| | | | | | | | | | | 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 Lu2009-03-254-15/+11
| | | | | | | | 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 Lu2009-03-247-7/+50
| | | | | | | | | | | | 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-r16598] merge 16597 from trunkPedro Vicente Nunes2009-03-233-21/+92
| | | | | | | | | | | | | #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 Fortner2009-03-2320-48/+389
| | | | | | | | | | | 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-r16589] merged from trunk: 16588Pedro Vicente Nunes2009-03-192-4036/+4151
| | | | | | 1. #1487 (B1) DS memory leaks ISSUE 1: On a "go to" error condition, previously allocated buffers were not freed. NOTE: these are "potential" memory leaks because typically the error conditions do not occur, so the potential memory leaks also do NOT occur. ISSUE 2: A function used to read dimension scales realistic data (topography of the North Atlantic, latitude and longitude) was being called without the data buffer being freed. SOLUTION FOR ISSUE 1: added "free" calls for the allocated buffers on the error sections. SOLUTION FOR ISSUE 2: added a "free" call after the read_data function, after using the buffer (on a H5Dwrite and H5Screate_simple). The read_data function reads both data and dimensions from the ASCII data files. DOCS: no docs added. Done for 1.9 and 1.8 STATUS: Closed bug tested: h5committest
* [svn-r16585] added the OUTPUT-ARCHITECTURE STD that was previously removed, ↵Pedro Vicente Nunes2009-03-161-0/+1
| | | | regarding a AIX failure
* [svn-r16582] Snapshot version 1.8 release 2 (post8)Larry Knox2009-03-167-21/+21
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* [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-r16572] #1462 By selecting a compression type, a big endian byte order ↵Pedro Vicente Nunes2009-03-114-4/+6
| | | | | | | | | | | | | | | | | | | 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-r16566] Description:Quincey Koziol2009-03-1172-1356/+1203
| | | | | | | | 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 McGreevy2009-03-1043-122/+125
| | | | | | | | | | | | | | | | | | 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 McGreevy2009-03-093-65/+4
| | | | | | | | | | | | | | | | | 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-r16551] Bug #608: Memory leak in H5DSset_label. Added code to free sub ↵Allen Byrne2009-03-051-225/+258
| | | | | | | | | string ptr's belonging to buffer in H5DSset_label and H5DSget_label. Also added free of buffers in error section of both functions. Potential memory leaks may exist elsewhere, and this will not close the bug. Tested: h5committest vista 32 VS2008
* [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-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-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-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 Tester2009-03-027-22/+22
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* [svn-r16524] Purpose: Fix bugs related to H5Dset_extent and fill valuesNeil Fortner2009-02-275-246/+362
| | | | | | | | | 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-r16522] Changed windows batch file due r16519 and r16520. As all ↵Allen Byrne2009-02-261-2/+2
| | | | | | | windows OS are always LE on all platforms, simply added le to the two locations where these files are used. Tested: Vista 32 VS2008
* [svn-r16520] one file escape deletion from previous check inPedro Vicente Nunes2009-02-261-22/+0
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* [svn-r16519] merge 16518 from trunkPedro Vicente Nunes2009-02-2649-51/+186
| | | | | | 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-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-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-r16503] merge 16502 from trunkPedro Vicente Nunes2009-02-201-4/+13
| | | | | bug fix: a comma accidently left on a conditional typedef was causing compilition error on AIX tested: linux
* [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 Koziol2009-02-193-169/+81
| | | | | | | | | | | 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 Koziol2009-02-1910-147/+183
| | | | | | | | | | | 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-r16493] revert gcc PROD_CFLAGS to "-O", which was incorrectly changed ↵Allen Byrne2009-02-191-1/+1
| | | | by rev 16490.
* [svn-r16490] Fixed bug #1459 by eliminating the macro long_long and ↵Allen Byrne2009-02-1844-585/+530
| | | | | | | | | replacing all instances with long long. Tested: h5comittest fedora 10 x64 XP32, VNET
* [svn-r16487] Checkin for moving messages forward into continuation message:Vailin Choi2009-02-164-10/+251
| | | | | | 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 Tester2009-02-157-22/+22
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* [svn-r16481] Purpose: Improve chunk cacheNeil Fortner2009-02-126-16/+250
| | | | | | | | | | | 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 Fortner2009-02-128-21/+186
| | | | | | | | | | | | | | | 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 Fortner2009-02-123-57/+212
| | | | | | | | | | | | 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 Fortner2009-02-1237-153/+352
| | | | | | | | | | | | 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-r16470] Added two new test cases for compound types to batch file per ↵Allen Byrne2009-02-111-0/+7
| | | | | | | script file changes in rev #16463. Tested: XP32, XP64 - VNET, VS2005
* [svn-r16467] Performance Improvement(bug #1450). When a chunk is bigger ↵Raymond Lu2009-02-114-18/+309
| | | | | | | | | | 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-r16463] merge from trunkPedro Vicente Nunes2009-02-1111-9/+175
| | | | | | | | | | | | | | | | | | | | Bug fix: for compound types, the not comparable test for members was not done Solution: for compound types, recursively apply that check Two new cases are added 1) the compound type has a different number of members. Message printed is <obj1> has X members <obj2> has Y members Where X and Y are the number of members of each compound type being compared 2) the compound type has not comparable types (for example a double and an int at the same index) In this case the message Comparison not possible: object1 is of class1 and object2 is of class2 Is replaced with Comparison not possible: object1 has a class1 and object2 has a class2 Modified the test generator program to have these 2 cases Added a shell run for these 2 cases Tested: h5committest
* [svn-r16460] Maintenance: Brought VMS test script for h5copy up-to-date. Elena Pourmal2009-02-102-9/+50
| | | | | | | Added h5copy testing to the build script. Platforms tested: New script on ALPHA Open VMS server; build script will be tested tonight.
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