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* [svn-r16614] 3. #1501 (B1) tools bug if dataset is larger than ↵Pedro Vicente Nunes2009-03-2516-21/+191
| | | | | | | | | | | | 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). tested: linux (h5commitest failed , apparently it did not detect the code changes in /tools/lib that fix the bug: the error in an assertion in the hyperslab of 0. I am sure that making h5ccomitest --distclean will detect the new code , but don't want to wait more 3 hours :-) )
* [svn-r16612] I changed the API function H5Dopen to H5Dopen2, which I ↵Raymond Lu2009-03-251-2/+2
| | | | | | introduced in recent checkin. Tested on jam - simple change.
* [svn-r16611] In previous checkin (r16609), the flag "write_driver" wasn't ↵Raymond Lu2009-03-253-13/+9
| | | | | | | | necessary as Quincey pointed out. I took it out and used the driver address instead. Tested on jam - simple change.
* [svn-r16609] 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-r16606] Description:Quincey Koziol2009-03-242-0/+109
| | | | | | | | | Add H5AC_create_flush_dependency() and H5AC_destroy_flush_dependency() wrappers for similarly named routines in H5C layer. Tested on: FreeBSD/32 6.3 (duty) Too minor to require h5committest
* [svn-r16600] Description:Quincey Koziol2009-03-245-1434/+3571
| | | | | | | | | | | | | | | | | | Ensure that metadata cache entries with flush dependencies are written to the file in the correct order (for serial I/O, at least). 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-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-r16599] added the notePedro Vicente Nunes2009-03-231-0/+6
| | | | | | | 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)
* [svn-r16597] #1047 (B1) The h5lt info routines are returning data in ↵Pedro Vicente Nunes2009-03-232-21/+86
| | | | | | 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. tested: h5committest
* [svn-r16596] Update RELEASE.txt with changes committed in revision 16594.Neil Fortner2009-03-231-0/+6
| | | | Tested: kate
* [svn-r16594] Purpose: fix bug 1189Neil Fortner2009-03-2319-48/+384
| | | | | | | | | | | 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-r16588] Pedro 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-r16587] Description:Quincey Koziol2009-03-1711-463/+3232
| | | | | | | | | | | | | | | | | | | | 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-r16584] added the OUTPUT-ARCHITECTURE STD that was previously removed Pedro Vicente Nunes2009-03-161-0/+1
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* [svn-r16579] Snapshot version 1.9 release 35Larry Knox2009-03-159-23/+23
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* [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-r16571] corrected the date on the release.txt entry and a comment on ↵Pedro Vicente Nunes2009-03-112-2/+2
| | | | the script
* [svn-r16570] modified the last entry to be on top , not lastPedro Vicente Nunes2009-03-111-2/+3
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* [svn-r16569] the conf file needs a byte order entry because of the way the ↵Pedro Vicente Nunes2009-03-111-0/+1
| | | | | | | | tool validates the output with h5dump (comparing the h5dump current output with a h5dump output from a pre-existent h5 file). added the byte order keyword that was removed on the last check in tested: linux, solaris
* [svn-r16568] #1462 By selecting a compression type, a big endian byte order ↵Pedro Vicente Nunes2009-03-114-5/+8
| | | | | | | | | | | | | | | | 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-r16563] removed commnented code Pedro Vicente Nunes2009-03-101-13/+0
| | | | tested: linux
* [svn-r16561] Purpose:Mike McGreevy2009-03-1043-122/+125
| | | | | | | | | | | | | | | | | | 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 Koziol2009-03-1072-1356/+1203
| | | | | | | | | | 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-r16554] 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-r16553] Snapshot version 1.9 release 34Larry Knox2009-03-089-24/+24
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* [svn-r16552] Correct typo.Larry Knox2009-03-061-1/+1
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* [svn-r16549] 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-r16548] Updated MANIFEST for new files in vms/tools.Larry Knox2009-03-051-0/+2
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* [svn-r16545] Added text that long_long macro was removed. This should have ↵Allen Byrne2009-03-051-0/+3
| | | | been added with r16489.
* [svn-r16542] Add h5stat and misc to the tools directory.Raymond Lu2009-03-042-0/+93
| | | | Not tested yet.
* [svn-r16540] 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-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-r16532] Description:Quincey Koziol2009-03-023-9/+11
| | | | | | | | | | 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 FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r16525] Snapshot version 1.9 release 33HDF Tester2009-03-019-24/+24
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* [svn-r16523] 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-r16521] Changed windows batch file due r16518. As all windows OS are ↵Allen Byrne2009-02-261-2/+2
| | | | | | | always LE on all platforms, simply added le to the two locations where these files are used. Tested: Vista 32 VS2008
* [svn-r16518] have 2 expected outputs for 2 h5ls runs depending if run on a ↵Pedro Vicente Nunes2009-02-2649-38/+150
| | | | | | | 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-r16516] To improve the performance of querying the info of a link (bug ↵Raymond Lu2009-02-241-45/+66
| | | | | | | | | | | #1404). When the index was set to creation order in query 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 the links. Tested on jam. I tested the same change for v1.8 with 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 Tester2009-02-2210-29/+30
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* [svn-r16504] 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-r16502] bug fix: a comma accidently left on a conditional typedef was ↵Pedro Vicente Nunes2009-02-201-4/+13
| | | | | | causing compilition error on AIX tested: h5commitest
* [svn-r16501] remove a strange character from a commentPedro Vicente Nunes2009-02-201-2/+2
| | | | tested: h5committest
* [svn-r16499] Description:Quincey Koziol2009-02-191-1/+7
| | | | | | | | Cache chunk info for newly created chunk. Tested on: FreeBSD/32 6.3 (duty) (Tests included in upcoming revise_chunks branch changes)
* [svn-r16492] revert gcc PROD_CFLAGS to "-O", which was incorrectly changed ↵Allen Byrne2009-02-191-1/+1
| | | | by rev 16489.
* [svn-r16489] Fixed bug #1459 by eliminating the macro long_long and ↵Allen Byrne2009-02-1852-615/+560
| | | | | | | | | | | replacing all instances with long long. Tested: h5comittest fedora 10 x64 Vista 32, VS2005, IVF101 XP32, Cygwin
* [svn-r16488] Description:Quincey Koziol2009-02-173-169/+81
| | | | | | | | | 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-r16484] Snapshot version 1.9 release 31HDF Tester2009-02-159-24/+24
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* [svn-r16483] Description:Quincey Koziol2009-02-1210-147/+183
| | | | | | | | | 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 Fortner2009-02-126-16/+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)
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