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* [svn-r12902] Checkin of Shared Object Header Message work.James Laird2006-11-131-0/+14
| | | | | | | | | | | | 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-r12767] Description:Quincey Koziol2006-10-161-1/+1
| | | | | | | | Code cleanup to improve formatting & reduce compiler warnings. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12708] Description:Quincey Koziol2006-10-031-44/+41
| | | | | | | | | | | | | | | | | | | Add the "use the latest version of the format" support to datatype messages. And a regression test to check that it's working. Also, found that we have been over-allocating space for compound datatype messages (when they have array datatypes or can use the latest version of the format) and trimmed the size back. Clean up datatype & dataspace encode/decode routines by having them allocate & release "fake" file structures, which gets them out of needing to "know" about the internals of file structures. Other minor whitespace/formatting cleanups, etc. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12706] Description:Quincey Koziol2006-10-021-19/+17
| | | | | | | | | Clean up some of the warnings on 64-bit Linux... Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2) Too minor to require h5committest
* [svn-r12700] Alert:Quincey Koziol2006-10-021-61/+52
| | | | | | | | | | | | | | | | | | | | | | | | | | | | File format is not stable, don't keep files produced! Description: First stage of checkins modifying the format of groups to support creation order. Implement "dense" storage for links in groups. Try to clarify some of the symbols for the H5L API. Add the H5Pset_latest_format() flag for FAPLs, to choose to use the newest file format options (including "dense" link storage in groups) Add the H5Pset_track_creation_order() flag for GCPLs, to enable creation order tracking in groups (although no index on creation order yet). Remove --enable-group-revision configure flag, as file format issues are now handled in a backwardly/forwardly compatible way. Clean up lots of compiler warnings and other minor formatting issues. Tested on: FreeBSD/32 4.11 (sleipnir) w/threadsafe Linux/32 2.4 (heping) w/FORTRAN & C++ Linux/64 2.4 (mir) w/enable-v1.6 compa Mac OSX/32 10.4.8 (amazon) AIX 5.3 (copper) w/parallel & FORTRAN
* [svn-r12218] Purpose:Quincey Koziol2006-04-101-19/+0
| | | | | | | | | | | | | Code cleanup Description: Remove remnents of references to unimplemented H5S_COMPLEX dataspace. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 32-bit (heping) Linux 2.4 64-bit (mir) Solaris 2.9 (shanti)
* [svn-r11712] Purpose:Quincey Koziol2005-11-151-36/+35
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | New feature Description: Check in baseline for compact group revisions, which radically revises the source code for managing groups and object headers. WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! This initiates the "unstable" phase of the 1.7.x branch, leading up to the 1.8.0 release. Please test this code, but do _NOT_ keep files created with it - the format will change again before the release and you will not be able to read your old files!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! Solution: There's too many changes to really describe them all, but some of them include: - Stop abusing the H5G_entry_t structure and split it into two separate structures for non-symbol table node use within the library: H5O_loc_t for object locations in a file and H5G_name_t to store the path to an opened object. H5G_entry_t is now only used for storing symbol table entries on disk. - Retire H5G_namei() in favor of a more general mechanism for traversing group paths and issuing callbacks on objects located. This gets us out of the business of hacking H5G_namei() for new features, generally. - Revised H5O* routines to take a H5O_loc_t instead of H5G_entry_t - Lots more... Platforms tested: h5committested and maybe another dozen configurations.... :-)
* [svn-r11686] Purpose:Quincey Koziol2005-11-071-0/+101
| | | | | | | | | | | | | | | | | | | New feature Description: Add in baseline "object copy" code from Peter [in the form of a new API routine: H5Gcopy()]. There's still some work to do (like handling variable- length datatypes and possibly support for references) and it hasn't been tested on mounted files yet, but the core functionality is there and working correctly. I've also got a set of patches to update the 1.6 branch with tweaks to keep the branches mostly in sync, but Elena will kill me if I import them before the 1.6.5 release is out... :-) Platforms tested: FreeBSD 4.11 (sleipnir) h5committested
* [svn-r11245] Purpose:Quincey Koziol2005-08-131-38/+38
| | | | | | | | | | | | | | | | | | | | Code cleanup Description: Trim trailing whitespace, which is making 'diff'ing the two branches difficult. Solution: Ran this script in each directory: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11078] Purpose:Quincey Koziol2005-07-171-1/+1
| | | | | | | | | | | | | | | Bug fix Description: Correct memory leak when a dataset is attempted to be opened, but turns out to be a group or named datatype. Also, clean up code that was leading to the leak and zero out empty group entries to help prevent similar errors in the future. Platforms tested: FreebSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11014] Purpose:Quincey Koziol2005-07-021-3/+3
| | | | | | | | | | | | Code cleanup Description: Refactor metadata cache to merge "dirtied" flag in with other flags for H5AC_unprotect and H5C_unprotect. Platforms tested: FreeBSD 4.11 (sleipnir) h5committest
* [svn-r10978] Purpose:John Mainzer2005-06-241-2/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | Interim checkin of code changes moving management of the is_dirty flag into the cache code. Description: Prior to this checkin, management of the is_dirty flag was handled above the level of the metadata cache. This can no longer be allowed, as it introduces a race condition in the proposed fix for a cache coherency bug in PHDF5. Solution: Move management fo the is_dirty flag to the cache code proper. Entries are now marked as dirty via a flag on the unprotect call. Platforms tested: h5committested Misc. update:
* [svn-r10628] Purpose:Quincey Koziol2005-04-181-2/+4
| | | | | | | | | | | Code cleanup Description: Clean up various warnings reported by the Windows team. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r9857] Purpose: MaintenanceElena Pourmal2005-01-221-3/+0
| | | | | | | | | | | | | | Description: Removed PABLO from the source Solution: Platforms tested: arabica with 64-bit, copper with parallel, heping with GNU C and C++ and PGI fortran (but I disabled hl, there is some weird problem only on heping: F9XMODFLAG is not propagated to the Makefile files Misc. update:
* [svn-r9727] Purpose:Quincey Koziol2004-12-291-8/+32
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-) Description: Generally speaking, this is the "signed->unsigned" change to selections. However, in the process of merging code back, things got stickier and stickier until I ended up doing a big "sync the two branches up" operation. So... I brought back all the "infrastructure" fixes from the development branch to the release branch (which I think were actually making some improvement in performance) as well as fixed several bugs which had been fixed in one branch, but not the other. I've also tagged the repository before making this checkin with the label "before_signed_unsigned_changes". Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel & fphdf5 FreeBSD 4.10 (sleipnir) w/threadsafe FreeBSD 4.10 (sleipnir) w/backward compatibility Solaris 2.7 (arabica) w/"purify options" Solaris 2.8 (sol) w/FORTRAN & C++ AIX 5.x (copper) w/parallel & FORTRAN IRIX64 6.5 (modi4) w/FORTRAN Linux 2.4 (heping) w/FORTRAN & C++ Misc. update:
* [svn-r9354] Purpose:Quincey Koziol2004-10-011-232/+37
| | | | | | | | | | | | | | | | Bug fix & code cleanup Description: More dataset cleanups to get to a point where we can fix the chunked I/O bug. Also fix a couple of errors in the recent file object resurrection changes which should hopefully address the recent daily test failres (H5T.c) Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) h5committest
* [svn-r9273] Purpose:John Mainzer2004-09-181-0/+120
| | | | | | | | | | | | | | | | | | | | | | | | | | | Port fix of parallel I/O mode confusion bug from the 1.6 tree to the 1.7 tree. Description: Collective I/O is not supported for point selections. Thus when some processes attempted I/O with point selections, and others without, some attempted collective I/O while others did independent I/O. Solution: Arranged for all processes to compare notes before starting I/O, and for all to use independent I/O if any one of them can't do collective I/O. Platforms tested: copper h5committested eirene (parallel) Misc. update:
* [svn-r8987] Purpose:Quincey Koziol2004-08-021-12/+12
| | | | | | | | | | | | Code cleanup Description: Fix another batch of minor differences between the development and release branches. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8981] Purpose:Quincey Koziol2004-08-021-3/+7
| | | | | | | | | | | | | Code cleanup Description: Various minor tweaks to clean code up and bring it into closer syncronization with the release branch. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel h5committested IRIX64 6.5 (modi4)
* [svn-r8964] Purpose:Quincey Koziol2004-07-281-4/+24
| | | | | | | | | | | | Revise new feature Description: Add buffer type and version # bytes to the encoded datatype and dataspace buffers (for H5Tencode & H5Sencode) Platforms tested: FreeBSD 4.10 (sleipnir) Too minor to require h5committest
* [svn-r8953] James Laird2004-07-271-0/+32
| | | | | | | | | | | | | | | | Purpose: Bug fix Description: When a simple dataspace is created, its extent should be set before using it, or it will silently function as a NULL dataspace. Solution: Added checks on user-supplied dataspaces. Now dataspaces without extents set will throw errors; users must explicitly set a dataspace to be NULL. Platforms tested: sleipnir, windows
* [svn-r8943] Purpose:Quincey Koziol2004-07-261-0/+2
| | | | | | | | | | | | Bug fix Description: Close memory leak I introduced in H5Sencode() routine. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8932] Purpose:Quincey Koziol2004-07-221-4/+4
| | | | | | | | | | | | | | | | | | | | Code cleanup Description: Clean up collective chunking code a bit. Also, add '--enable-instrument' configure flag to have a mechanism for determining that optimized operations happened correctly in the library (instead of just the "normal" way) by allowing 'flag' properties to be set outside the library and set when the "right" thing happens. This is mainly for debugging and regression checks, so we make certain we don't break optimized I/O by accident. It's enabled by default when --enable-debug is on (which is on by default in the development branch and off by default in the release branch), but can also be independently controlled with its own configure flag. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel IBM p690 (copper) w/parallel
* [svn-r8927] Purpose:Quincey Koziol2004-07-221-49/+39
| | | | | | | | | | | Code cleanup Description: Clean up various recent changes a little. Platforms tested: FreeBSD 4.10 (sleipnir) Too minor to require h5committest
* [svn-r8921] Purpose: new featureRaymond Lu2004-07-211-0/+233
| | | | | | | | | | | | | | Description: This is the second step of checkin for encoding and decoding objects. H5Tencode and H5Tdecode have been committed in the previous step. H5Sencode and H5Sdecode are checked in this time. Solution: Given object ID, these functions encode and decode object information into and from binary buffer and return new object ID. They take advantage of the existing codes of object header message and encode in the same format. Platforms tested: fuss and h5committest. Misc. update: RELEASE.txt
* [svn-r8906] Purpose:MuQun Yang2004-07-201-6/+17
| | | | | | | | | | | | | | | | | | | | | | | Adding the first round of patches about supporting collective chunk IO in HDF5 Description: The current HDF5 library doesn't support collective MPIO with chunk storage. When users set collective option in their data transfer with chunk storage, the library silently converted the option to INDEPENDENT and that caused trememdous performance penalty. Some application like WRF-parallel HDF5 IO module has to use contiguous storage for this reason. However, chunking storage has its own advantage(supporting compression filters and extensible dataset), so to make collective MPIO possible inside HDF5 with chunking storage is a very important task. This check-in make collective chunk IO possible for some special cases. The condition is as follows(either case is fine with using collective chunk IO) 1. for each process, the hyperslab selection of the file data space of each dataset is regular and it is fit in one chunk. 2. for each process, the hyperslab selection of the file data space of each dataset is single and the number of chunks for the hyperslab selection should be equal. Solution: Lift up the contiguous storage requirement for collective IO. Use H5D_isstore_get_addr to get the corresponding chunk address. Then the original library routines will take care of getting the correct address to make sure that MPI FILE TYPE is built correctly for collective IO> Platforms tested: arabica(sol), copper(AIX), eirene(Linux) parallel test is checked at copper. Misc. update:
* [svn-r8899] James Laird2004-07-201-0/+3
| | | | | | | | | | | | | | | | Purpose: Bug Fix Description: Calling H5Sset_extent_simple to change a dataspace's maxdims from nonzero to zero causes errors (infinite loops, seg faults, asserts) because the pointer to the maximum size isn't cleaned up properly Solution: Clean up that pointer. Added a test for this case. Platforms tested: sleipnir (very minor change)
* [svn-r8760] Purpose:Quincey Koziol2004-06-291-1/+1
| | | | | | | | | | | | | Code cleanup & small bug fix Description: Regenerate dependency files Add htri_t as separate type from hbool_t for code tracing purposes. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel too minor to require h5committest
* [svn-r8731] Purpose:Quincey Koziol2004-06-231-8/+9
| | | | | | | | | | | | | | | Code cleanup & minor optimization Description: Re-work the way interface initialization routines are specified in the library to avoid the overhead of checking for them in routines where there is no interface initialization routine. This cleans up warnings with gcc 3.4, reduces the library binary size a bit (about 2-3%) and should speedup the library's execution slightly. Platforms tested: FreeBSD 4.10 (sleipnir) w/gcc34 h5committest
* [svn-r8707] Changed the way HDF5 handles hid_t's and added API functions to ↵James Laird2004-06-181-3/+3
| | | | allow users to register IDs and ID types at runtime.
* [svn-r8696] Purpose:Quincey Koziol2004-06-161-2/+3
| | | | | | | | | | | | | | | | | Code optimizations Description: Eliminate memset() call in H5S_set_extent_simple(). Use malloc() instead of calloc in H5B<mumble>. Change global heap code to track heap objects that are in use in order to allocate new objects more quickly and also to avoid memset() and calloc() calls. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8677] Purpose:Quincey Koziol2004-06-141-117/+66
| | | | | | | | | | | | | | | | | | | Code cleanup & optimization Description: Remove old structures that used a union to store information about the dataspace extent and just store the information directly in the dataspace extent itself. Remove ifdef'd references to permutation ordering in dataspaces. We'll definitely need more than this code if/when we implement this feature. Change allocation of dataspace information from calloc() to malloc(). Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8673] Purpose:Quincey Koziol2004-06-131-29/+29
| | | | | | | | | | | | | | | | | | Code optimization Description: Revised dataspace selections to use a more "object oriented" mechanism to set the function pointers for each selection and selection iterator. This reduces the amount and number of times that dataspace selection info has to be copied. Additionally, change hyperslab selection information to be dynamically allocated instead of an inline struct. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8590] Purpose:Quincey Koziol2004-05-271-1/+5
| | | | | | | | | | | | | | | | | | | | | Code optimization & bug fix Description: When dimension information is being stored in the storage layout message on disk, it is stored as 32-bit quantities, possibly truncating the dimension information, if a dimension is greater than 32-bits in size. Solution: Fix the storage layout message problem by revising file format to not store dimension information, since it is already available in the dataspace. Also revise the storage layout data structures to be more compartmentalized for the information for contiguous, chunked and compact storage. Platforms tested: FreeBSD 4.9 (sleipnir) w/parallel Solaris 2.7 (arabica) h5committest
* [svn-r8544] Purpose:Quincey Koziol2004-05-201-9/+31
| | | | | | | | | | | | | | Code optimization Description: Expand the use of macros to inline trivial function pointer lookup and calls to reduce the overall number of functions invoked during normal operation of the library. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.9 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8520] Purpose:Quincey Koziol2004-05-131-18/+2
| | | | | | | | | | | | Code optimization Description: Don't make a separate allocation for the selection offset - incorporate it into the selection structure as a fixed size array. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.9 (sleipnir) w/parallel
* [svn-r8496] Purpose:Quincey Koziol2004-05-081-4/+8
| | | | | | | | | | | | | Code optimization Description: Further reduce the number of copies we make of a hyperslab selection for chunked I/O, especially when we are only going to throw the old selection away for a new one. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.9 (sleipnir) w/parallel
* [svn-r8448] Purpose:Quincey Koziol2004-05-011-7/+0
| | | | | | | | | | | | Code optimization Description: Remove redundant error checking. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.9 (sleipnir) too minor to require h5committest
* [svn-r8408] Purpose:Quincey Koziol2004-04-221-2/+11
| | | | | | | | | | | | | | Code optimization Description: Instead of dynamicly allocating various arrays for various pieces of information about a selection or selection iterator, just use fixed size array of size H5S_MAX_RANK (as the rest of the library does). Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.9 (sleipnir) h5committest
* [svn-r8376] Purpose:Quincey Koziol2004-04-171-154/+32
| | | | | | | | | | | | | | | | | Code cleanup Description: Update null dataspace changes to try to write older version of dataspace information whenever possible. Refactor common code to only one location. Allow I/O operations to succeed on null dataspaces. Platforms tested: FreeBSD 4.9 (sleipnir) h5committest
* [svn-r8330] Purpose: Last step of check-in for Null dataspaceRaymond Lu2004-04-081-36/+34
| | | | | | | | | | | Description: Mainly are header message changes for dataspace. In last round of check-in, a new header message for dataspace to created, which is not a good way. Now, there will be no new message for dataspace, but just add the type of dataspace in the message while increment its version number. Backward compatibility is addressed. The attribute design is modified accordingly. Platforms tested: h5committest
* [svn-r8314] Purpose: Progressive check-inRaymond Lu2004-04-061-31/+113
| | | | | | | | | | Description: NULL dataspace. This step is mainly for dataspace header message and a test. Solution: The test mainly checks NULL dataspace features. Backward compatibility is tested in the fill value test. Platforms tested: h5committest
* [svn-r8301] Purpose:Quincey Koziol2004-04-061-1/+1
| | | | | | | | | | | | | Code optimization Description: Move handling for free list arrays that have no maximum size to separate set of routines and optimize computations for free list arrays with maximum size to avoid re-computing sizes all the time. Platforms tested: h5committest Solaris 2.7 (arabica)
* [svn-r8276] *** empty log message ***Raymond Lu2004-03-241-9/+39
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* [svn-r7926] Purpose:Quincey Koziol2003-12-101-4/+14
| | | | | | | | | | | | Bug fix Description: Clean up a few allocations of zero-sized blocks that were detected with the new free-list assertions. Platforms tested: FreeBSD 4.9 (sleipnir) w & w/o parallel too minor to require h5committest
* [svn-r7917] Purpose:Quincey Koziol2003-12-061-2/+2
| | | | | | | | | | | | | | | | | | | Code cleanup Description: Clean up compiler warnings, especially the 'FUNC' variable not used which comes out in production mode. Solution: Had to add a new FUNC_ENTER_NOAPI_NOINIT_NOFUNC macro for those non-API functions which don't need the 'FUNC' variable defined. (This will be _so_ much easier when C99 is standard on all our supposed platforms, since it has a __FUNC__ macro... ) Platforms tested: FreeBSD 4.9 (sleipnir) too minor for h5committest (although there were lots of files changed, the change was minor in each one)
* [svn-r7789] Purpose:Quincey Koziol2003-10-291-7/+0
| | | | | | | | | | | | | | | Bug fix & code cleanups Description: Change our use of MPI derived datatypes to not create datatypes with "0-sized" lengths, which causes the LANL Q machine to hang. Also, get rid of "prefer MPI derived datatypes" environment variable since it has no advantage. Platforms tested: FreeBSD 4.9 (sleipnir) w & w/o parallel h5committest
* [svn-r7754] Purpose:Quincey Koziol2003-10-271-1/+19
| | | | | | | | | | | | | Code cleanup Description: Straighten out more goofiness in the MPI code dealing with collective I/O transfers - mostly make certain that a view is set if-and-only-if collective I/O is occurring on raw data (and vice versa for views and independent I/O) Platforms tested: FreeBSD 4.9 (sleipnir) w/parallel & FPHDF5 too minor to repquire h5committest
* [svn-r6942] Purpose:Quincey Koziol2003-05-311-23/+46
| | | | | | | | | | | | | | | | | Performance improment Description: Speed up chunked dataset I/O. This breaks down into several areas: - Compute chunk selections in the file by using hyperslab operations instead of iterating over each element in the selection. - If the file and memory selections are the same shape, use the file chunk selections to compute the memory chunk selections. This required several additional dataspace, dataspace selection and hyperslab routines. Platforms tested: h5committestted (although Fortran tests failed for some reason)
* [svn-r6837] Purpose:Quincey Koziol2003-05-081-79/+9
| | | | | | | | | | | | | | | Code cleanup. Description: Move many package or internal function prototypes and macro definitions into tighter scope according to their current use. Added more comments where appropriate. Eliminate ancient, unused functions. Added a couple "accessor" functions to get parts of data structures which were moved out of scope. Platforms tested: h5committested
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