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* [svn-r16300] Added an option to avoid dealing with NaNs Pedro Vicente Nunes2009-01-1317-96/+136
| | | | | | | -N, --nan Avoid NaNs detection Note: there is no shell script run for datasets with NaN because the output is non portable (different results and NaN strings for different systems) Tested: windows, linux
* [svn-r16299] Print a message ofPedro Vicente Nunes2009-01-135-9/+74
| | | | | | | | | Storage: information not available When displaying storage information for VL and dataset region types Added 2 shell runs that display this information #818 Tested: windows, linux
* [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 McGreevy2009-01-096-216/+2347
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r16284] Pedro Vicente Nunes2009-01-081-1/+8
| | | | | | | | | | | - h5repack: When user doesn't specify a chunk size, h5repack now defines a default chunk size as the same size of the size of the hyperslab used to read the chunks. The size of the hyperslabs are defined as the size of each dimension or a predefined constant, whatever is smaller. This assures that the chunk read fits in the chunk cache. (PVN - 2008/11/21) - H5Dset_extent: when shrinking dimensions, some chunks were not deleted. (PVN - 2009/01/8)
* [svn-r16281] Purpose: Add functions to allow more flexible traversal of ↵Neil Fortner2009-01-0815-26/+606
| | | | | | | | | | | 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-r16279] Description:Quincey Koziol2009-01-0831-494/+582
| | | | | | | | | | | | | | Bring revision 16278 back from revise_chunks branch: Update layout information in DCPL to unify all information in one underlying property and switch to using H5O_layout_t for storing it, which simplifies things considerably. Also, fix many compiler warnings. Tested on: FreeBSD/32 6.3 (duty) in debug mode (Original patch tested on many machines)
* [svn-r16273] Added a test for shrinking to 0 dimemsionsPedro Vicente Nunes2009-01-081-226/+351
| | | | Tested: windows, linux
* [svn-r16271] Bug fix.Albert Cheng2009-01-061-37/+12
| | | | | | | | | The Tail command in jam (a newer linux) does not accept the +2l option. It ended up wiping most of the release_doc/RELEASE.txt file contents. Replaced the "tail +2l" by "sed -e 1d". Tested: Tested in Jam to verify it functions properly again.
* [svn-r16266] Revert RELEASE.txt to the version before it was mostly deleted ↵Neil Fortner2009-01-061-1/+617
| | | | | | | | by hdftest. Update version number listed at the top. Tested: vim
* [svn-r16262] Description:Scot Breitenfeld2009-01-051-1/+1
| | | | | | | | added missing reference in h5lget_name_by_idx_f: !DEC$ATTRIBUTES reference :: for character strings being passed in to C to fix bug in VMS.
* [svn-r16235] Description:Scot Breitenfeld2008-12-301-2/+0
| | | | | | | Cosmetic changes, Also tested -r16231 on: Jam (intel 10.1) Smirom (intel 10.1)
* [svn-r16231] Description:Scot Breitenfeld2008-12-301-1/+4
| | | | Added chunk property to the data set because changes in the cC function H5Dset_extent now require/check that the data set is chunked.
* [svn-r16229] merge 16228Pedro Vicente Nunes2008-12-291-20/+20
| | | | | cleaned more linux warnings tested: linux
* [svn-r16227] cleaned some linux warningsPedro Vicente Nunes2008-12-291-3/+1
| | | | tested: linux
* [svn-r16225] removed some debug messagesPedro Vicente Nunes2008-12-291-18/+0
| | | | tested: windows, linux
* [svn-r16223] Modified H5Dset_extent so that it fails when called for compact ↵Pedro Vicente Nunes2008-12-292-159/+1707
| | | | | | | | datasets and contiguous with no external storage new test program: It adds tests for several ranks, use of fill value or not, compression, different fill value allocation times, use of different storage layouts, and external files tested: windows, linux
* [svn-r16220] Snapshot version 1.9 release 26HDF Tester2008-12-289-678/+34
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* [svn-r16217] Bug fixPedro Vicente Nunes2008-12-236-2016/+2106
| | | | | | | PG compiler complains about array out of bounds (a rank of zero was not checked) Adding a scalar dataset to the test generator program. this case is run on a previous existing run, the case was added to 2 existing files Tested: windows, linux
* [svn-r16214] Added HDlseek to the H5FD_core_truncate function in H5FDcore.c ↵Raymond Lu2008-12-222-1/+8
| | | | | | | | | to rewind the file pointer to the beginning of the file. Otherwise, the file might be re-extended later on Open VMS. Also updated the return value for the HDlseek to be more appropriate. Tested 1.8 on Open VMS.
* [svn-r16209] Purpose:Choonghwan Lee2008-12-193-6/+10
| | | | | | | | | | | | | | Bug fix (#1357) Description: Three filters have not assigned correct value to one value-result argument, "buf_size". N-bit, szip, and scale offset filter have had this problem. However, I don't think this problem has been making buffer overrun because those filters were informing the caller that the "buf", another value-result argument, is smaller than it actually is. If there was actual buffer overrun, I believe another problem exists although I don't know. Tested: jam, smirom, linew Although all test were passed, I'm concerned about valgrind memcheck error. There can be another miscommunication between filter and the caller.
* [svn-r16207] Added new file H5Bdbg.c to windows project file. Will test ↵Allen Byrne2008-12-184-44/+195
| | | | using VS2008 Express.
* [svn-r16204] Description:Quincey Koziol2008-12-186-258/+302
| | | | | | | | | | | | | | | | | | | | | Moved v1 B-tree debugging routines into separate module and thinned out header files a bit. Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode 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
* [svn-r16202] Added HDlseek in front of the truncate function in ↵Raymond Lu2008-12-151-1/+7
| | | | | | | | | H5FD_sec2_truncate for VMS only. On Open VMS, if the last read or write put the file pointer beyond the current file size (it happens when an object is deleted), the file can be extended when it's truncated. Tested v1.8 on VMS.
* [svn-r16196] Description:Scot Breitenfeld2008-12-157-6/+32
| | | | | | | | added: !DEC$ATTRIBUTES reference :: for character strings being passed in to C to fix bug in VMS.
* [svn-r16194] Purpose:Mike McGreevy2008-12-154-31/+10
| | | | | | | | | | | | | | | | | | | | | | | Bug Fix Description: Resolved issues with broken sanity checks that were failing when the 'b2' debugging package was enabled (v2 b-tree debugging): - Fixed outdated assertions that would not compile. They now compile and function correctly. - Removed too far outdated assertions that would require too much unnecessary refactoring of code in order to satisfy their initial purpose. - Re-enabled b2 debugging package when "--enable-debug=all" is specified on the configure line. Tested: jam, smirom, linew
* [svn-r16189] Changed references of H5Distore to H5Dbtree in project files. ↵Allen Byrne2008-12-124-4/+4
| | | | (Related to revision 16180)
* [svn-r16187] Description:Quincey Koziol2008-12-113-4/+4
| | | | | | | Change a few more "istore" references in comments to "chunk" or "btree". Tested on: None, just comments
* [svn-r16182] Description:Quincey Koziol2008-12-1115-401/+396
| | | | | | | | | | | | | | | | | | | | | | Rename internal routines, variables, macros, typedefs, etc. for chunked dataset storage from "istore" to some variant of "chunk" or "btree". Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode 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
* [svn-r16180] Description:Quincey Koziol2008-12-114-6/+6
| | | | | | | | | | Rename the current chunk indexing routines module for B-tree indices to better reflect their purpose, and to make the upcoming extensible array index module fit in better. Tested: FreeBSD/32 6.3 Too minor to require h5committest
* [svn-r16179] Description:Quincey Koziol2008-12-111-2/+2
| | | | | | | | Use the H5F_KVALUE macro in a couple more places, to make the code easier to read. Tested on: Mac OS X only (very minor)
* [svn-r16176] Remove terminal whitespace in links.c, H5Lexternal.c, H5Pfapl.cNeil Fortner2008-12-093-29/+29
| | | | Tested: jam
* [svn-r16173] Updated fix of the missing argument of open() in zip_perf.c.Albert Cheng2008-12-091-0/+2
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* [svn-r16170] Code clean up.Albert Cheng2008-12-091-13/+12
| | | | | | | Function get_unique_name() had potential string overflow problem. Fixed. Also removed some unused macros. Tested by h5committest.
* [svn-r16167] Bug fix: 1089Albert Cheng2008-12-091-3/+3
| | | | | | | | | | | | Description: One open() call with O_CREAT flag did not have the third required argument. Solution: Added the right third argument. Also changed all open() calls to HDopen macros for more portable coding. Tested: h5committested.
* [svn-r16166] Description:Frank Baker2008-12-081-6/+6
| | | | Change all occurrences of 'THG' to 'The HDF Group'.
* [svn-r16161] Purpose: Add new source file to WindowsScott Wegner2008-12-052-0/+8
| | | | | | | | | | Description: Recently the new source file H5EAdbkpage.c was added to the main library source code. This checkin also adds it to the Windows project files. Note: Windows builds are still failing on the earray test, although for other reasons. I'm also looking into this. Tested: VS2005 on WinXP
* [svn-r16158] Test the non deletion of a chunk for the case chunk_offset == ↵Pedro Vicente Nunes2008-12-041-2/+240
| | | | | | dimension by shrinking first, then expanding to original size and compare buffers of initialized values Tested: windows, linux
* [svn-r16156] close & re-open the file for the test of non-default B-tree ↵Pedro Vicente Nunes2008-12-041-0/+29
| | | | | | | internal 'K' value (There was a bug where a non-default B-tree internal 'K' value was not being stored in the file) this is a rewrite of the old set_extent.c test program tested: windows, linux
* [svn-r16152] added comments and removed unnecessary codePedro Vicente Nunes2008-12-021-16/+63
| | | | tested: windows, linux
* [svn-r16150] Change a call to H5FL_fac_free to H5FL_FAC_FREE so it works ↵Neil Fortner2008-12-021-1/+1
| | | | | | | | correctly when free lists are disabled. Tested: jam
* [svn-r16148] reorganized the set_extent test to be more modularPedro Vicente Nunes2008-12-021-83/+116
| | | | tested: windows, linux
* [svn-r16144] Removed the check of H5Dset_extent for the space to be ↵Pedro Vicente Nunes2008-12-012-4/+12
| | | | | | chunked, since external datasets can be extended Tested: windows, linux
* [svn-r16143] add a test for recent fixes of H5Dset_extentPedro Vicente Nunes2008-12-011-625/+541
| | | | tested: windows, linux
* [svn-r16142] Added a check to H5Dset_extent for the space to be chunked, ↵Pedro Vicente Nunes2008-12-012-19/+11
| | | | | | | | exit with error otherwise A call to H5Dset_extent in the external test was removed Tested: windows, linux
* [svn-r16138] Snapshot version 1.9 release 25HDF Tester2008-11-309-24/+24
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