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* [svn-r16740] Snapshot version 1.8 release 2 (post12)Larry Knox2009-04-128-22/+22
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* [svn-r16735] Added H5Groot.c. Not tested yet.Raymond Lu2009-04-101-1/+1
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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-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 Fortner2009-04-103-4/+77
| | | | | | | | | | 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-r16728] merge 16727Pedro Vicente Nunes2009-04-101-15/+15
| | | | | clean linux warnings tested linux
* [svn-r16725] Snapshot version 1.8 release 2 (post11)Larry Knox2009-04-109-21/+21
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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-r16720] merge 16719Pedro Vicente Nunes2009-04-098-5056/+5052
| | | | | clean warnings linux tested linux
* [svn-r16718] merge 16717Pedro Vicente Nunes2009-04-091-28/+43
| | | | | added some print messages tested: linux
* [svn-r16712] Purpose: Fix bug 1423Neil Fortner2009-04-0819-331/+555
| | | | | | | | | | | | | | 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-r16707] merge 16706 from trunkPedro Vicente Nunes2009-04-082-30/+80
| | | | | | | | #1538 (B2) Problems with Dim Scale APIs reported by Mathworks ISSUE2: the scale index input/output parameter value passed to H5DSiterate_scales was not always incremented (it returns the scale index current iteration). SOLUTION FOR ISSUE2: modified the cycle in H5DSiterate_scales so that the scale index is always incremented TEST: added some test cases with calls to invalid indices and H5DSiterate_scales with return scale indices and visitor data tested: linux
* [svn-r16705] Snapshot version 1.8 release 2 (post10)Larry Knox2009-04-087-22/+22
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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 Fortner2009-04-0816-333/+685
| | | | | | | | | 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-r16697] merge 16696 from trunkPedro Vicente Nunes2009-04-082-91/+330
| | | | | | | | | | #1538 (B2) Problems with Dim Scale APIs reported by Mathworks ISSUE: When some functions are called with an invalid dimension index (for example, greater than the rank of the dataset) the function does not immediately fail, rather asserts down the code. SOLUTION: added this check for H5DSdetach_scale, H5DSset_label, H5DSget_label (the other functions have this check) . H5DSiterate_scales also added a check for an invalid dimension scale index TEST: added some test cases with calls to invalid indices DOCS: Nothing added STATUS: done for 1.9, 1.8. closed bug tested: windows, linux
* [svn-r16695] Purpose: Fix bug 1526Neil Fortner2009-04-074-4/+103
| | | | | | | | | | | 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-r16680] Description:Scot Breitenfeld2009-04-0716-1501/+1501
| | | | | | | | | Fixed warnings from absoft's compiler for !DEC$ statements. Solution: There should not be a space after !DEC$ statements, removed the spaces. Platforms tested: Jam with gcc and f95
* [svn-r16677] merge 16676 from trunkPedro Vicente Nunes2009-04-071-3/+11
| | | | | | | | #1521 (B2) H5DSdetach_scale memory leak ISSUE: Purify (Windows Visual Studio 6) complains of a memory leak in H5DSdetach_scale call regarding a H5Aread call (stack is H5A_read, H5T_convert, H5T_conv_vlen, H5T_vlen_seq_mem_write, H5MM_malloc). SOLUTION: When a scale is detached from a dataset, the variable length structure length field is decreased in one entry. The associated pointer must be reallocated with the new length. DOCS AND TEST: Nothing added tested: linux
* [svn-r16672] merge 16671 from trunkPedro Vicente Nunes2009-04-061-1/+1
| | | | fix compiler error on a missing "static" declaration
* [svn-r16668] Corrected the urls for h5dump xml dtd and schemaAllen Byrne2009-04-0362-64/+65
| | | | Tested: Fedora 10 gcc
* [svn-r16665] Added h5tools.h to h5difftst.vcproj.Allen Byrne2009-04-032-4/+11
| | | | | | Added new test to h5repack.bat. Tested on XP64-VS2005--IVF91
* [svn-r16664] merge 16663 from trunkPedro Vicente Nunes2009-04-035-212/+274
| | | | | | | | note : lots of weird warnings of the type ../../../../hdf5/tools/h5repack/h5repacktst.c:3919: warning: will never be executed appear on the same code as 1.9 for the 1.8 branch tested: linux
* [svn-r16662] Remove command to copy h5Tinit.c in copy batch file. H5Tinit.c ↵Allen Byrne2009-04-031-1/+0
| | | | | | is generated during build and no longer exists in the windows/src folder. Tested: XP64 VS2005
* [svn-r16658] merge from trunk 16656Pedro Vicente Nunes2009-04-025-2124/+2541
| | | | | | | | #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-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.
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