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* [svn-r12937] Deleted H5SMpublic.h file, since information in it has been ↵James Laird2006-11-173-28/+2
| | | | | | | | | | moved to H5Opublic.h. Updated Makefile.am, reconfigured. Tested on kagiso.
* [svn-r12935] Added list-to-btree conversion, changed SOHM apis, and pushed ↵James Laird2006-11-1719-285/+491
| | | | | | | | | | | SOHM table version and size information into the superblock to eliminate a read when loading it. This is a file format change, and hopefully the last one (knock on wood). Tested on kagiso and Windows (mostly just a SOHM change).
* [svn-r12933] Description:Quincey Koziol2006-11-175-669/+608
| | | | | | | | | | | Finish migrating "object copy" supporting routines into src/H5Ocopy. Clean up a few minor errors _en passant_ Tested on: FreeBSD/32 4.11 (sleipnir) Linux/32 2.4 (heping) Linux/64 2.4 (mir)
* [svn-r12932] Description:Quincey Koziol2006-11-1716-230/+450
| | | | | | | | | | | | Basic support for H5Literate() routine. Still needs to be fleshed out and refactored to simplify. Also, needs tests. :-) Tested on: FreeBSD/32 4.11 (sleipnir) Linux/32 2.4 (heping) Linux/64 2.4 (mir) AIX/32 5.? (copper) Mac OS X/32 10.4.8 (amazon)
* [svn-r12931] H5L_link is called inside H5O.c but the header file that ↵MuQun Yang2006-11-171-0/+1
| | | | | | | | | | | | | | | | | | declared this function is not included in this file. Windows compiler issued a bad warning that"H5L_link" is not defined but is called. So add header file "H5Lprivate.h" in H5O.c. Hopefully this is the right way. Tested on windows and tested the compiling on Linux. H5L_link is called inside H5O.c but the header file that declared this function is not included in this file. Windows compiler issued a bad warning that"H5L_link" is not defined but is called. So add header file "H5Lprivate.h" in H5O.c. Hopefully this is the right way. Tested on windows and tested the compiling on Linux. H5L_link is called inside H5O.c but the header file that declared this function is not included in this file. Windows compiler issued a bad warning that"H5L_link" is not defined but is called. So add header file "H5Lprivate.h" in H5O.c. Hopefully this is the right way. Tested on windows and tested the compiling on Linux.
* [svn-r12929] Hopefully this really is a fix for the tg-login errors.James Laird2006-11-165-56/+54
| | | | | | | | | | | The version of libtool used by HDF5 isn't directly affected by the reconfigure script; instead, libtoolize --force must be used by hand. Libtool was the source of the problem, so rolling its version back to 1.5.14 should solve the issue (at least temporarily). Reconfigure should still work on both heping and kagiso. Tested on heping, kagiso, and tg-login3.
* [svn-r12922] Description:Quincey Koziol2006-11-163-5/+57
| | | | | | | | | | | Add support for "delete by index" to "old-style" groups, finishing implmentation of H5Ldelete_by_idx() routine. Tested on: FreeBSD/32 4.11 (sleipnir) Linux/32 2.4 (heping) Linux/64 2.4 (mir) Aix/32 5.? (copper)
* [svn-r12921] Description:Quincey Koziol2006-11-161-2/+2
| | | | | | | | Finish adding more tests to "delete by index" for compact/dense groups. Tested on: Mac OS X/32 10.4.8 (amazon) FreeBSD/32 4.11 (sleipnir)
* [svn-r12919] Description:Quincey Koziol2006-11-151-101/+239
| | | | | | | | | More progress toward getting H5Ldelete_by_idx() working - removals on densely stored links should work now (still needs some more tests). Still need to write code for removals on "old-style" groups. Tested on: FreeBSD/32 4.11 (sleipnir)
* [svn-r12917] Pedro Vicente Nunes2006-11-154-53/+53
| | | | | | | | h5repack revision: 1. added a new test due to the introduction of H5Ocopy in the copy of objects (compressed dataset with references, that still must go a second sweep of the file to be regenerated). 2. Moved all the source files from the h5repack test program to a new file h5repacktst.c and removed the old ones (testh5repack*.c). 3. Renamed the binary files from test*.h5 to h5repack*.h5 for easy reference. 4. Modified the shell script to use variables for file names instead of hard coded names
* [svn-r12915] Description:Quincey Koziol2006-11-151-15/+31
| | | | | | | | | | Finish adding "delete by index" feature to v2 B-trees. Tested on: FreeBSD/32 4.11 (sleipnir) Linux/32 2.4 (heping) Linux/64 2.4 (mir) AIX/32 5.? (copper)
* [svn-r12914] Description:Quincey Koziol2006-11-144-23/+468
| | | | | | | | Checkpoint partially working v2 B-tree delete by index code (ifdef'ed out) for further work. Tested on: Linux/32 2.6 (chicago)
* [svn-r12911] Backed up to previous versions of automake and libtool. ↵James Laird2006-11-141-27/+31
| | | | | | | | Hopefully this will fix issues on tg-login3. bin/reconfigure should still work on both heping/mir and kagiso.
* [svn-r12910] Description:Quincey Koziol2006-11-145-84/+377
| | | | | | | | | | | More progress toward getting H5Ldelete_by_idx to work fully - can now delete by index in compact group (but not dense groups or "old-style" groups yet). Need to go write a v2 B-tree routine to delete from the B-tree by index before the dense storage will work properly... Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12908] Description:Quincey Koziol2006-11-141-1/+1
| | | | | | | | | | Replace "//" style comment with "/* */" style comment to fix build on FreeBSD 4.11 (sleipnir) Tested on: FreeBSD/32 4.11 (sleipnir) Linux/32 2.4 (heping) Linux/64 2.4 (mir)
* [svn-r12907] Description:Quincey Koziol2006-11-1417-472/+379
| | | | | | | | | Finish refactoring internal link deletion code, to make it possible to wrap up the H5Ldelete_by_idx() coding. Tested on: Linxu/32 2.6 (chicago) Linxu/64 2.6 (chicago2)
* [svn-r12906] Description:Quincey Koziol2006-11-1311-181/+170
| | | | | | | | | | | | | | | | Straighten out some convoluted code when links were being deleted, which could cause the "delete" callback for user-defined links to not get called when the group they were in was deleted. Had to compromise on the "delete" callback though - only calls the callback with the ID for the file the link is in, instead of the group, since the group is being held open upstream in the calling sequence during a group deletion and this prevents a group and its ID from being created. (This could possibly be worked around, but would cause a fair bit of havoc in the code and I'm not entirely certain it's worth it...) Tested on: Linux/32 2.6 (chicago)
* [svn-r12904] Description:Quincey Koziol2006-11-131-5/+5
| | | | | | | Clean up warnings from undefined macros... Tested on: Linux/64 2.6 (chicago2)
* [svn-r12902] Checkin of Shared Object Header Message work.James Laird2006-11-1359-506/+4611
| | | | | | | | | | | | This feature is still in progress; Shared Object Header Messages are not complete as a feature and are not thoroughly tested. There are still "TODO" comments in the code (comments with the word "JAMES" in them, so as not to be confused with other TODO comments). Hopefully this checkin will reduce the liklihood of conflicts as I finish implementing this feature. All current tests pass on juniper, copper (parallel), heping, kagiso, and mir.
* [svn-r12896] Description:Quincey Koziol2006-11-139-801/+878
| | | | | | | | Move compact storage routines into separate file, to make room for internal routines that operate on links within group operations. Tested on: Linux/32 2.6 (chicago)
* [svn-r12895] Description:Quincey Koziol2006-11-136-165/+544
| | | | | | | | | | | | | Add new H5Lget_val_by_idx() routine & tests. Also includes most of changes for H5Ldelete_by_idx() routine. Tested on: Mac OS X/32 10.4.8 (amazon) FreeBSD/32 4.11 (sleipnir) Linux/32 2.4 (heping) Linux/64 2.4 (mir) AIX/32 5.? (copper)
* [svn-r12894] Description:Quincey Koziol2006-11-1211-460/+656
| | | | | | | | | | | | Add H5Lget_name_by_idx routine & tests Move more H5G routines to deprecated API file Tested on: FreeBSD/32 4.11 (sleipnir) w/threadsafe Linux/32 2.4 (heping) C++ & FORTRAN Linux/64 2.4 (mir) w/build-all & enable_compat1.6 AIX/32 5.? (copper) w/parallel & FORTRAN
* [svn-r12893] Description:Quincey Koziol2006-11-111-3/+4
| | | | | | | | Fix error with retrieving names of object references on big-endian platforms. Tested on: AIX/32 5.? (copper)
* [svn-r12892] Description:Quincey Koziol2006-11-114-6/+160
| | | | | | | | | Add H5Rget_name routine and tests... Tested on: FreeBSD/32 4.11 (sleipnir) Linux/32 2.4 (heping) Linux/64 2.4 (mir)
* [svn-r12891] Description:Quincey Koziol2006-11-111-2/+2
| | | | | | | Correct typo in a few function name macros. Tested on: FreeBSD/32 4.11 (sleipnir)
* [svn-r12890] Description:Quincey Koziol2006-11-118-254/+411
| | | | | | | | | | | | | | | | | Finished implementation of H5Lget_info_by_idx for all cases: old vs. new group formats, compact vs. dense new link storage, increasing vs. decreasing vs. native iteration order. Also, refactor symbol table "foo by index" routines to be more generic and share more code by using a single B-tree iteration callback which makes callbacks to a specific "get <foo>" callback. Tested on: Mac OS X/32 10.4.8 (amazon) FreeBSD/32 4.11 (sleipnir) Linux/32 2.4 (heping) Linux/64 2.4 (mir) AIX/32 5.? (copper)
* [svn-r12888] Pedro Vicente Nunes2006-11-104-53/+53
| | | | | Introduced the second sweep of the file for a case a reference is present and H5Ocopy was not used. Moved the code from file h5repack_refs.c to h5repack_copy.c and removed the first file
* [svn-r12887] A fix for linking issues.James Laird2006-11-105-53/+54
| | | | | | | | | | | | Should disable linking against shared libraries in Fortran for compilers that don't support shared libraries. Should also fix problem when the wrong Fortran file extension was specified. If these changes don't solve the Daily Test issues, I'll look at backing out the autotool version change until I have time to fix them. Tested on heping, kagiso, juniper.
* [svn-r12885] Refactored the H5FD_direct_open and H5FD_direct_write. The ↵Raymond Lu2006-11-091-79/+23
| | | | | | | condition for H5_HAVE_DIRECT_ALIGN not defined simply repeated the code above. Merged this part into the code above. No other significant change.
* [svn-r12882] Changed bin/reconfigure to work on kagiso as well as on AFS ↵James Laird2006-11-088-106/+113
| | | | | | | | Linux machines. Updated to the latest versions of autotools. Tested on kagiso, heping, and juniper. Let me know if you have any problems.
* [svn-r12879] Purpose: Bug fixLeon Arber2006-11-082-13/+22
| | | | | | | Description: Fix a few memory-related bugs in the data transform code. Tested: kagiso (for real this time) w/ valgrind 3.2.1
* [svn-r12878] Description:Quincey Koziol2006-11-078-118/+301
| | | | | | | | Flesh out support for looking up link info by index, some cases for using dense storage are working now. Tested on: Linux/32 2.6 (chicago)
* [svn-r12877] Description:Quincey Koziol2006-11-077-12/+13
| | | | | | | Clean up more compiler warnings. Tested on: Linux/64 2.6 (chicago2)
* [svn-r12876] Description:Quincey Koziol2006-11-071-4/+17
| | | | | | | | Make code that retrieves names for references thrash memory less by keeping track of the current buffer size and only re-allocating it when necessary. Tested on: Linux/64 2.6 (chicago2)
* [svn-r12875] Description:Quincey Koziol2006-11-071-5/+12
| | | | | | | | | | Fix retrieving name for references to root group. Also, move 'ref' test earlier in testing, right after 'getname' test Tested on: Linux/64 2.6 (chicago2)
* [svn-r12873] Decription:Quincey Koziol2006-11-073-9/+14
| | | | | | | | Add support for reverse index lookup to v2 B-trees (needed for reverse index lookup of links in groups) Tested on: Linux/64 2.6 (chicago2)
* [svn-r12872] Description:Quincey Koziol2006-11-0710-148/+609
| | | | | | | | | | | | Implement basic framework for H5Lget_info_by_idx and get it working for creation order indices on compact groups. Clean up code a bit. Close resource link in user-defined link traversal. Tested on: Linux/32 2.6 (chicago)
* [svn-r12871] Description:Quincey Koziol2006-11-071-0/+4
| | | | | | | Clean up a couple of warnings... Tested on: Linux/64 2.6 (chicago2)
* [svn-r12870] Add a new macro H5_HAVE_DIRECT_ALIGN in configure.in. Some ↵Raymond Lu2006-11-062-5/+84
| | | | | | | systems like copper and sleipnir doesn't require alignment for Direct I/O. If this's true, write or read data just like sec2 does.
* [svn-r12869] Description:Quincey Koziol2006-11-0614-614/+925
| | | | | | | | Rename new H5Gcopy() routine to H5Ocopy() as discussed in last Friday's design discussion. Tested on: Linux/32 2.6 (chicago)
* [svn-r12868] Description:Quincey Koziol2006-11-062-5/+5
| | | | | | | | Make API routines that don't initialize the library more consistent, to help with future internal library changes. Tested on: Linux/64 2.6 (chicago2)
* [svn-r12867] Description:Quincey Koziol2006-11-063-217/+401
| | | | | | | Get rid of H5L API calls from within deprecated H5G API calls. Tested on: Linux/32 2.6 (chicago)
* [svn-r12866] Description:Quincey Koziol2006-11-0610-224/+101
| | | | | | | Clean up initialization of H5F & H5L APIs. Tested on: Linux/64 2.6 (chicago2)
* [svn-r12865] Description:Quincey Koziol2006-11-067-39/+47
| | | | | | | Change name of H5Lunlink to H5Ldelete, per our design meeting last Friday. Tested on: Linux/32 2.6 (chicago)
* [svn-r12864] Description:Quincey Koziol2006-11-065-34/+40
| | | | | | | | Changed H5Lget_linkval() to H5Lget_val(), per our design discussion last Friday afternoon. Tested on: Linux/32 2.6 (chicago)
* [svn-r12859] Description:Quincey Koziol2006-11-041-10/+14
| | | | | | | | Fix to handle finding the correct path to an object in a mounted file hierarchy. Tested on: FreeBSD/32 4.11 (sleipnir)
* [svn-r12858] Description:Quincey Koziol2006-11-044-275/+131
| | | | | | | | Clean up code to build name for ID with no name tracked - get rid of global variable, unused routines, etc. Tested on: FreeBSD/32 4.11 (sleipnir)
* [svn-r12855] Description:Quincey Koziol2006-11-031-67/+75
| | | | | | | Further code cleanups to bring into better alignement w/rest of library. Tested on: FreeBSD/32 4.11 (sleipnir)
* [svn-r12854] Description:Quincey Koziol2006-11-031-16/+19
| | | | | | | Clean up some more function name problems and other compiler warnings. Tested on: FreeBSD/32 4.11 (sleipnir)
* [svn-r12853] Description:Quincey Koziol2006-11-031-11/+12
| | | | | | | Correct name of routine in FUNC_ENTER... macro. Tested on: None - just eyeballed, very trivial..
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