summaryrefslogtreecommitdiffstats
path: root/src
Commit message (Collapse)AuthorAgeFilesLines
* [svn-r12575] Description:Quincey Koziol2006-08-146-22/+126
| | | | | | | | | | | | | Allow the heap ID length to be chosen at heap creation time, to allow for making heap IDs long enough to directly embed the file offset & length of 'huge' objects in the heap ID (which allows them to be retrieved directly from disk, instead of requiring them to be looked up in the B-tree that tracks 'huge' objects) Tested on: FreeBSD/32 4.11 (sleipnir) Linux/64 2.4 (mir) Solaris/64 9 (shanti)
* [svn-r12573] Description:Quincey Koziol2006-08-131-2/+2
| | | | | | | | | | | | Clean up a couple of compiler warnings in the 'huge' object code in the library. Add a bunch of 'huge' object regression tests Tested on: FreeBSD 4.11 (sleipnir) Linux/64 2.4 (mir) Solaris/64 2.9 (shanti)
* [svn-r12572] Description:Quincey Koziol2006-08-133-47/+54
| | | | | | | | | | Refactor new heap's header creation code to be all in the H5HFhdr.c module. Tested on: FreeBSD 4.11 (sleipnir) Linux/64 2.4 (mir) Solaris/64 2.9 (shanti)
* [svn-r12571] Description:Quincey Koziol2006-08-132-3/+32
| | | | | | | | | | | Fix failure in "remove bogus ID" test which turned up randomly (due to random "bogus" IDs being used in test :-) by adding some more defensive checks on object IDs to the object removal code. Tested on: FreeBSD 4.11 (sleipnir) Linux/64 2.4 (mir) Solaris/64 (shanti)
* [svn-r12570] Description:Quincey Koziol2006-08-131-17/+15
| | | | | | | | | | Refactor file memory allocation code slightly, to make it clearer, along with adding/correcting some comments. Tested on: FreeBSD 4.11 (sleipnir) Linux/64 2.4 (mir) Solaris/64 2.9 (shanti)
* [svn-r12568] Description:Quincey Koziol2006-08-123-4/+4
| | | | | | | | | Rename some files, to better align with the names of the functions within them. Tested on: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r12567] Description:Quincey Koziol2006-08-123-25/+25
| | | | | | | | | Correct remaining compilation errors when debugging asserts are turned on in free space manager. Tested in: FreeBSD 4.11 (sleipnir) Too minor for h5committest
* [svn-r12565] Description:Quincey Koziol2006-08-111-12/+12
| | | | | | | | | | | | | | Move metadata cache address rename for fractal heap indirect block immediately after reallocing the storage on disk - to prevent another routine in the library from confusing the cache by allocating more storage and attempting to insert it in metadata cache at the old block's location. Gotta like those monte carlo/random insert & delete tests, which exposed this... :-) Tested: Solaris 2.9 (shanti) Not failing on other machines
* [svn-r12562] Description:Quincey Koziol2006-08-1014-153/+1108
| | | | | | | | | | | | Initial revision to add support for "huge" objects in the heap (which are actually stored directly in the file, but are tracked with v2 B-tree that is accessed through heap header). Testing: FreeBSD 4.11 (sleipnir) Linux/64 2.4 (mir) Linux/32 2.4 (heping) Mac OS X.4 (amazon)
* [svn-r12561] Description:Quincey Koziol2006-08-107-107/+146
| | | | | | | | | | | | Update code formatting a little and refactor to add a better mechanism for performing callbacks when removing records from the B-tree or deleting entire B-tree. Testing: FreeBSD 4.11 (sleipnir) Linux/64 2.4 (mir) Linux/32 2.4 (heping) Mac OS 10.4 (amazon)
* [svn-r12560] Description:Quincey Koziol2006-08-101-3/+3
| | | | | | | Correct some typos in comments Testing: None needed
* [svn-r12555] 1. Erased a strange character added to this codeMuQun Yang2006-08-091-8/+35
| | | | | | | 2. Used to workaround solution to fix the cchunk10 failure caused by the MPICH bug Machine test: heping, mir
* [svn-r12553] This check-in includes the following part of parallel ↵MuQun Yang2006-08-098-226/+544
| | | | | | | | | | | | | | | optimization codes: 1. Provide another option for users to do independent IO with MPI file setview(collectively) 2. With the request of collective IO from users, using Independent IO with MPI file setview if we find collective IO is not good for the applications for IO per chunk(multi-chunk IO) case. Previously we used pure independent IO and that actually performed small IO(IO each row) for this case. The recent performance study suggested the independent IO with file setview can acheieve significantly better performance than collective IO when not many processes participate in the IO. 3. For applications that explicitly choose to do collective IO per chunk case, the library won't do any optimization(gather/broadcast) operations. The library simply passes the collective IO request to MPI-IO. Tested at copper, kagiso, heping, mir and tungsten(cmpi and mpich) Kagiso is using LAM, t_mpi test was broken even. The cchunk10 test failed at heping and mir. I suspected it was an MPICH problem. Will investigate later. Everything passed at copper. at tungsten: the old cmpi bug(failed at esetw) is still there. Other tests passed. Some sequential fheap tests failed at kagiso.
* [svn-r12552] Description:Quincey Koziol2006-08-0711-91/+112
| | | | | | | | | | | More tweaks on fractal heap statistics, to better separate information about managed objects from information about "huge" objects. Also, clean up some compiler warnings, etc. on 64-bit platforms & Windows. Platforms tested: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago)
* [svn-r12551] Description:Quincey Koziol2006-08-078-95/+86
| | | | | | | | | | | Refactor fields in heap header to clean out information from dropped features and also group related fields together more nicely. Add fields to heap header for storing information about "huge" objects. Platforms tested: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago)
* [svn-r12550] Description:Quincey Koziol2006-08-074-39/+95
| | | | | | | | | | | Refactor fractal heap IDs to include "flag byte" as part of the ID. This byte will be used for the heap ID format version as well as flags to indicate whether the heap object is a "tiny"/normal/"huge" object (with storage mechanisms optimized for each type of object). Platforms tested: Linux/32 2.4 (chicago) Too minor to require h5committest
* [svn-r12549] Description:Quincey Koziol2006-08-0714-792/+1125
| | | | | | | | | | Add support for entire heap deletion. Platforms tested: FreeBSD 4.11 (sleipnir) Linux/32 2.4 (chicago) Linux/64 2.4 (mir) Mac OS X (amazon)
* [svn-r12544] Description:Quincey Koziol2006-08-041-0/+2
| | | | | | | | | | | | | | Clean up compiler warnings/failures in test/links.c, especially when --disable-production flag used with --enable-group-revision Modify binary dumping in h5dump to clean up files created [a band-aid solution to not actually creating the files in the srcdir, but better than just leaving the files around... :-/ ] Tested: FreeBSD 4.11 (sleipnir) (w/ configure flags above) Too minor to require h5committest
* [svn-r12543] Description:Quincey Koziol2006-08-041-2/+2
| | | | | | | | | Re-run 'make trace' on this file, so API tracing doesn't issue compiler errors in development builds Tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r12533] Standardized the way path prefixes are passed to external links ↵James Laird2006-08-034-9/+94
| | | | | | using a LAPL. Now there are H5Pget and H5Pset functions for "elink_prefixes".
* [svn-r12531] Fixed a bug that occurred with 64-bit compilers. Types were ↵James Laird2006-08-032-9/+9
| | | | | | | used inconsistently (the nlinks property was an int in some places and a size_t elsewhere--it is now a size_t everywhere).
* [svn-r12528] Added User-Defined links to the library.James Laird2006-08-0245-1302/+3747
| | | | | | | | | | | | | | Users can create external links using H5L_create_external(). These links point to an object in another HDF5 file. Users can alter the behavior of external links or create new kinds of links by registering callbacks using the H5L interface. Added tests, tools support, etc. Also a number of other, minor changes have been made (some restructuring of the H5L interface, for instance). Additional documentation and examples are forthcoming.
* [svn-r12525] Description:Quincey Koziol2006-08-0221-3145/+3003
| | | | | | | | | | | Refactored free space manager to use metadata cache for serialized free space sections. This speeds up the fractal heap test considerably... Tested: FreeBSD 4.11 (sleipnir) Linux 2.4/32 (chicago) Linux 2.4/64 (mir) Mac OS X (amazon)
* [svn-r12519] Fixed "make check-vfd"James Laird2006-07-311-2/+3
| | | | | | | | | | "make check-vfd" will now run all tests in the test directory with different file drivers (at least, all of those tests that use the testing framework's FAPL). Tests that fail will be skipped. This is not a perfect fix, but is better than nothing. Along with this change, check-vfd should be added to the Daily Tests.
* [svn-r12517] Description:Quincey Koziol2006-07-3111-351/+760
| | | | | | | | | | | | | | | Fix the last scattered bunch of problems with the object deletion code, which appears to be completely working now (for objects that are stored within heap blocks - standalone objects aren't implemented yet). Also, re-work the regression test to speed up some of the existing tests and add in 100-200 more combinations of tests - overall, its probably even slower than it was... :-/ Tested: FreeBSD 4.11 (sleipnir) Linux 2.4 (chicago) Mac OS X (amazon)
* [svn-r12504] Pedro Vicente Nunes2006-07-271-0/+4
| | | | | | | | | | | | bug fix calling h5tools_get_fapl running the mpio driver caused H5FD_pl_copy to fail silently in some conditions. a MPI call was made before MPI_Init. solution: corrected the MPI call to be made after MPI_Init and added error return conditions to H5FD_pl_copy and h5tools_get_fapl tested on copper parallel, mir, shanti
* [svn-r12495] Description:Quincey Koziol2006-07-256-564/+765
| | | | | | | | | | Checkpoint further work on object deletion code for fractal heaps. I believe everything is finally working for this sub-task. More regression tests soon, but I don't foresee any problems. Machines: FreeBSD 4.11 (sleipnir) Linux 2.4 (chicago)
* [svn-r12492] Fix compile error for non-debug buildsQuincey Koziol2006-07-231-2/+0
|
* [svn-r12491] Description:Quincey Koziol2006-07-2216-1262/+3871
| | | | | | | | | | Refactored object deletion code for fractal heap to fix scaling problems. Passing all previous tests again now. Tested: FreeBSD 4.11 (sleipnir) Linux 2.4 (chicago) Mac OS X (amazon)
* [svn-r12478] Changed version number to 1.8.0-alpha5 after tagging ↵Elena Pourmal2006-07-171-2/+2
| | | | | | hdf5-1.8.0-alpha4 release with "hdf5_1_8_0_alpha4" tag.
* [svn-r12474] Quincey Koziol2006-07-1514-117/+87
| | | | | | | | Clean up some compiler warnings. Tested on: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r12462] Committed a variety of metadata cache related changes:John Mainzer2006-07-1312-182/+1534
| | | | | | | | | | | | | | | | | | | | | | 1) Added trace file support to the metadata cache. This allows capture of all metadata cache calls in trace files for purposes of optimization and debuging. 2) Added an expunge entry function. This allows an entry to be deleteded from the cache without writing it to disk even if it is dirty. 3) Added a function call to resize pinned entries. 4) Added code to deal with entries that are dirty on load. This is needed in support of a bug fix which can alter object headers on load to repair files. 5) Added progress reporting code to the "MDC API smoke check" test in cache_api.c. To enable the progress reporting, set report_progress to TRUE in mdc_api_call_smoke_check(). Tested with h5committest, and a parallel test on phoenix (dual athelon linux box).
* [svn-r12461] Cleaned up the names of some internal API functions, cleaned up ↵starfire2006-07-105-23/+23
| | | | | | | | | comments, fixed a few tests that used incorrect names for H5L APIs (formerly hidden behind H5_GROUP_REVISION ifdefs Mostly cosmetic changes, tested on mir.
* [svn-r12452] Purpose:James Laird2006-07-0543-1346/+2556
| | | | | | | | | | | | | | | | | | | | | | Feature Description: Revised Link APIs. Solution: New link APIs use H5L* H5*create_expand do not create links to the objects created; this must be done manually with H5Llink. Added APIs to link an object given its ID (H5Llink), to copy links (H5Lcopy), and changed creation APIs (H5Lcreate_hard and H5Lcreate_soft) and query API (H5Lget_linkinfo instead of H5Gget_objinfo). All old APIs are still supported in H5Gdeprec.c . Platforms tested: sol, mir, copper Misc. update: Forgot to update MANIFEST and release docs. Will do after checkin.
* [svn-r12449] Purpose:Quincey Koziol2006-07-019-111/+258
| | | | | | | | | | | | | Code checkpoint Description: Revise fractal heap code to support deletions in up to 2nd level deep indirect blocks. Needs some revisions to support deeper indirect blocks... Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 (chicago) h5committest
* [svn-r12445] Purpose:Albert Cheng2006-06-291-7/+5
| | | | | | | | | | | | Bug #281 Description: The previous fix for bug #281 was not safe. Files got corrupted in some cases. Needs a more comprehensive fix for it. Undo the unsafe fix for now. Platforms tested: h5committested.
* [svn-r12440] Purpose:Quincey Koziol2006-06-2761-1022/+1022
| | | | | | | | | | | Code cleanup Description: Trim trailing whitespace in Makefile.am and C/C++ source files to make diffing changes easier. Platforms tested: None necessary, whitespace only change
* [svn-r12439] Purpose:Quincey Koziol2006-06-2619-126/+412
| | | | | | | | | | | | | New feature Description: Check in Peter's code to add support for "shallow copy", "create intermediate groups", "no attributes" and "expand soft links" support. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 (chicago) w/ & w/o group-revision enabled h5committest
* [svn-r12435] Purpose: Bug fixRaymond Lu2006-06-234-6/+19
| | | | | | | | | | | | Description: Mac OS 10.4 on PowerPC chip has some errors to convert (unsigned) long long to long double. When the bit sequences are 0x003ff..., 0x007fff..., 0x00ffff..., 0x01ffff..., 0x7fffff..., the converted values are twice as big as they should be. Solution: Detect the error in configure and disable the compiler conversion and test case. Platforms tested: h5committest, Mac OS 10.4, and fuss.
* [svn-r12431] Purpose:James Laird2006-06-211-15/+5
| | | | | | | | | | | | | | Configuration feature Description: 'make install' now tests both static and shared libraries if both are installed. Solution: Previously, shared libraries were only tested when static libraries were not installed. Also cleaned up line in commence.am that was including HL library in all Makefiles. Platforms tested: mir (Makefile change only)
* [svn-r12425] Purpose: Bug fixRaymond Lu2006-06-202-6/+11
| | | | | | | | | | | | | | | Description: Data conversion from long double to (unsigned) long long returns some incorrect values on Mac OS 10.4 and SGI IRIX64 6.5. The conversions start to go wrong when the long double is 20041683600089727.779961 (0x4351ccf385ebc8a0bfcc2a...). If adjusting the values higher by assigning 0x...c8a0cf... or 0x...c8a0df..., the converted values go wild. Solution: Detect this error in configure.in and disable compiler conversions from long double to (unsigned) long long for Mac OS 10.4 and IRIX64 6.5. Platforms tested: h5committest, Mac OS 10.4, and IRIX64 6.5.
* [svn-r12424] Purpose:Quincey Koziol2006-06-1924-1390/+2918
| | | | | | | | | | | | | | | | | Code checkpoint Description: Add in more new features for the fractal heap code, mostly bringing in more ability for deleting objects (which isn't completely working yet). Also, checkpoint free space manager code, which is essentially complete (although it needs some more work after the metadata cache has some additional features) Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 (chicago) h5committest
* [svn-r12423] Purpose:Quincey Koziol2006-06-191-0/+9
| | | | | | | | | | | | New feature Description: Add '%t' format for HDfprintf() to print htri_t (and hbool_t) values. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 (chicago) h5committest
* [svn-r12422] Purpose:Quincey Koziol2006-06-191-1/+6
| | | | | | | | | | | | | | | Bug fix Description: Don't attempt to merge object header messages when a file is opened read-only. Mark the object header dirty when messages are merged, as well as the particular message affected. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r12414] Purpose:Quincey Koziol2006-06-171-0/+1
| | | | | | | | | | | | | | | | | Bug fix Description: Fix bug which could lead to files with incorrect count of messages in the header for an object. The exact sequence of operations is complicated and is described in the release notes. Solution: Mark merged null header messages as dirty. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 (chicago) Mac OS/X (amazon)
* [svn-r12411] Purpose:James Laird2006-06-131-0/+1
| | | | | | | | | | | | | | Bug fix - bugzilla #552 Description: On Cray X1, trying to use : as an argument confused the system. Solution: Added a test in configure to see if : as an argument is bad. If so, skipped the test. Platforms tested: mir, Cray X1 (change to configure only)
* [svn-r12400] Purpose:MuQun Yang2006-06-033-7/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Some collective chunk IO macro names are confusing, change them to more meaningful names. Description: H5Pset_dxpl_mpio_chunk_opt will set a flag so that the library can do one linked IO or multi-chunk IO with collective in chunking storage directly. That is, the library won't do analyses to determine this. The flags for the enum type we used before are: H5FD_MPIO_OPT_ONE_IO H5FD_MPIO_OPT_MULTI_IO They are not good names because of the following two reasons: 1. It doesn't reflect chunking storage 2. OPT is kind of redundant and misleading, Solution: We change the names to H5FD_MPIO_CHUNK_ONE_IO H5FD_MPIO_CHUNK_MULTI_IO Platforms tested: Since only macro names are changed, no need to test with h5committest. heping(mpich 1.2.6) Misc. update:
* [svn-r12394] Purpose: MaintenanceElena Pourmal2006-06-011-2/+2
| | | | | | | | | | | Description: Ran /bin/h5vers to change suffix to alpha4 after creating hdf5-1.8.0-alpha3 tar ball and tagging the release with hdf5_1_8_0_alpha3 tag Solution: Platforms tested: Misc. update:
* [svn-r12374] Purpose:John Mainzer2006-05-245-5/+289
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 1) Check in potential fix to unreproduceable bug in t_cache observed on Cobalt 2) Check in code supporting added pinned entry features in the metadata cache. Description: 1) Elena encountered a bug in t_cache when running on Cobalt. On investigation I found a potential race condition in t_cache that could explain her observation. 2) Quincey requested additions to the metadata cache allowing renaming of pinned entryies, and marking of pinned or protected entries as dirty. Solution: 1) Modified t_cache.c to prevent the potential race condition. Elena was unable to reproduce the bug on Cobalt, so we don't know if my fix actually addressed the problem. 2) Added code supporting the requested functions. The changes were relatively trivial, but required substantial new test code. Platforms tested: h5committest, serial test on heping, parallel test on phoenix. Misc. update:
* [svn-r12372] Purpose:James Laird2006-05-232-0/+5
| | | | | | | | | | | Makefile cleanup Description: Cleaned up where files were distcleaned Platforms tested: mir (change only affects distclean)