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* [svn-r9564] Purpose:Quincey Koziol2004-11-231-23/+18
| | | | | | | | | | | | | Code optimization Description: Change how default allocation time is handled internally to the library, to avoid some performance issues with property lists. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) Too minor to require h5committest
* [svn-r9557] Purpose:Quincey Koziol2004-11-221-2/+2
| | | | | | | | | | | | | | | | | | | | | Code cleanup & optimization Description: Improve ADF/CGNS benchmark by reducing the number of internal attribute copies made during creations, opens and writes. Added new H5O_iterate() routine for iterating through messages of a certain type in the object header (attributes are the only message currently that can have multiple instances in the object header). Cross-pollinated various minor code cleanups to reduce diffs between branches. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) Too minor to require h5committest
* [svn-r9359] Purpose:Quincey Koziol2004-10-041-4/+0
| | | | | | | | | | | | | | | Bug fix Description: Relax restrictions on parallel I/O to allow compressed, chunked datasets to be read in parallel (collective access will be degraded to independent access, but will retrieve the information still). Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) IRIX64 6.5 (modi4) h5committest
* [svn-r9356] Purpose:Quincey Koziol2004-10-011-37/+36
| | | | | | | | | | | | | | | | 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-r9343] Purpose:Quincey Koziol2004-09-301-20/+58
| | | | | | | | | | | | | | | | Bug fix/code cleanup Description: Clean up raw data I/O code to bundle the I/O parameters (dataset, DXPL ID, etc) into a single struct to pass around through the dataset I/O routines, since they are always passed together, until very near the bottom of the I/O stack. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) IRIX64 6.5 (modi4) h5committest
* [svn-r9334] James Laird2004-09-281-282/+321
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Purpose: Feature Description: (Same change to release branch) Datatypes and groups now use H5FO "file object" code that was previously only used by datasets. These objects will hold a file open if the file is closed but they have not yet been closed. If these objects are unlinked then relinked, they will not be destroyed. If they are opened twice (even by two different names), both IDs will "see" changes made to the object using the other ID. When an object is opened using two different names (e.g., if a dataset was opened under one name, then mounted and opened under its new name), calling H5Iget_name() on a given hid_t will return the name used to open that hid_t, not the current name of the object (this is a feature, and a change from the previous behavior of datasets). Solution: Used H5FO code that was already in place for datasets. Broke H5D_t's, H5T_t's, and H5G_t's into a "shared" struct and a private struct. The shared structs (H5D_shared_t, etc.) hold the object's information and are used by all IDs that point to a given object in the file. The private structs are pointed to by the hid_t and contain the object's group entry information (including its name) and a pointer to the shared struct for that object. This changed the naming of structs throughout the library (e.g., datatype->size is now datatype->shared->size). I added an updated H5Tinit.c to windows.zip. Platforms tested: Visual Studio 7, sleipnir, arabica, verbena Misc. update:
* [svn-r9102] Purpose:Quincey Koziol2004-08-171-15/+20
| | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug fix Description: 1 - Dataset contiguous storage cache information had a bug where it was possible to try to access invalid cache information if the cache wasn't filled the first time it attempted to loop through the list of offset/length vectors. 2 - Additionally, the contiguous storage cache information was being used in certain circumstances from the chunked dataset I/O code path, which was generally fatal since the chunk storage and contiguous storage information were stored together in a union. Solution: 1 - Avoid special case of first trip through loop over offset/length I/O vectors and always check for the contiguous storage sieve buffer buffer being NULL. 2 - Change the union containing the chunk and contiguous storage cache information into a struct, allowing both to be used at the same time. Platforms tested: FreeBSD 4.10 (sleipnir) h5committested
* [svn-r8985] Purpose:Quincey Koziol2004-08-021-12/+6
| | | | | | | | | | | | | | | | | | | | | Bug fixes & code cleanups Description: Backport MPI-I/O changes from the development branch to the release branch in preparation for bringing Kent's collective chunk I/O changes back. Removed last vestiges of FPHDF5 from this branch, as it was never working here. Various code cleanups & syncrontizations to better align with development branch code and reduce diffs. Regenerate dependencies. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel IRIX64 6.5 (modi4) h5committested
* [svn-r8954] James Laird2004-07-271-0/+6
| | | | | | | | | | | | | | | | 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-r8802] Purpose:Quincey Koziol2004-07-031-36/+89
| | | | | | | | | | | | | | | Code optimization Description: Set up datatype ID for dataset's datatype on disk. This allows us to avoid repeatedly copying the datatype when an ID is needed. Also, clean up a few warnings in various other places. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8753] Nat Furrer2004-06-281-0/+53
| | | | | | | | | | | | | | | | | | | Purpose: Handled SZIP without the encoder present. Description: It is now an error for a user to try to create, extend, or write to a dataset without the encoder present in their SZIP library. Added H5Zget_filter_info to provide users with a way to query HDF5 about the presence (or lack thereof) of the SZIP encoder. Platforms tested: Windows Verbena Arabica Copper Misc. update:
* [svn-r8733] Purpose:Quincey Koziol2004-06-231-3/+3
| | | | | | | | | | | | Code cleanup Description: Reduce compiler warnings on SGI IRIX Platforms tested: FreeBSD 4.10 (sleipnir) SGI IRIX6 (Cheryl's machine) Too minor to require full h5committest
* [svn-r8693] Purpose:Quincey Koziol2004-06-151-4/+4
| | | | | | | | | | | | | Code optimization Description: Avoid making copy of default vlen allocation info when default DXPL is used. Just retarget pointer to point to default info directly. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8687] Purpose:Quincey Koziol2004-06-141-3/+4
| | | | | | | | | | | | | Code optimization Description: Eliminate memcpy() when using default DXPL by pointing at existing default object, instead of copying it. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8674] Purpose:Quincey Koziol2004-06-131-7/+7
| | | | | | | | | | | | | | | | | | 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-r8667] Purpose:Quincey Koziol2004-06-131-1/+6
| | | | | | | | | | | | | | | | Code optimization Description: Restructure conversion loop of variable-length objects to avoid walking through memory backwards and allocating as many temporary buffers. (This uses the optimized method used in the atomic type conversions). Also bring back another optimization for variable-length datatypes that avoids querying the DXPL so many times. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8619] Purpose:Quincey Koziol2004-06-051-1/+1
| | | | Fix makefiles, dependencies & manifest after source file rename.
* [svn-r8614] Purpose:Quincey Koziol2004-06-051-84/+144
| | | | | | | | | | | | | | | Refactor code Description: Move chunk and contiguous cached raw data from file information to dataset information. This simplifies a number of internal interfaces, aligns the code with it's purpose better and should allow more optimizations to the chunked data I/O performance. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) h5committest
* [svn-r8601] Purpose:Quincey Koziol2004-05-311-406/+456
| | | | | | | | | | | | | | | | Code optimization & cleanup Description: Don't recompute the internal index value for looking up the chunk in the hash table, just use the value already computed from iterating through the chunks. Also, back-port some of the various cleanups to the source code from the development branch, to make diffing the code easier. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.9 (sleipnir) w/parallel
* [svn-r8592] Purpose:Quincey Koziol2004-05-271-137/+165
| | | | | | | | | | | | | | | | | | | | | 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-r8543] Purpose:Quincey Koziol2004-05-201-2/+2
| | | | | | | | | | | | | | 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-r8497] Purpose:Quincey Koziol2004-05-081-2/+2
| | | | | | | | | | | | | 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-r8455] Purpose:Quincey Koziol2004-05-011-1/+5
| | | | | | | | | | | | | Code optimization Description: Eliminate more 64-bit multiplies by remebering the size of contiguous datasets as well as chunked datasets. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.9 (sleipnir) too minor to require h5committest
* [svn-r8384] Purpose:Quincey Koziol2004-04-181-21/+21
| | | | | | | | | | | | | Code cleanup Description: Clean up lots of warnings based on those reported from the SGI compilers as well as gcc. Platforms tested: SGI O3900, IRIX64 6.5 (Cheryl's SGI machine) FreeBSD 4.9 (sleipnir) w/ & w/o parallel h5committest
* [svn-r8317] Purpose:Quincey Koziol2004-04-071-12/+93
| | | | | | | | | | | | Code optimization Description: Query the dataset creation and transfer properties less often. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.9 (sleipnir) w/parallel h5committested
* [svn-r8304] Purpose:Quincey Koziol2004-04-061-4/+6
| | | | | | | | | | | | Code optimization Description: Compute the size of a chunk once, when the layout information is set, instead of each time I/O is performed on the chunk. Platforms tested: h5committest Solaris 2.7 (arabica)
* [svn-r8083] Purpose:Quincey Koziol2004-01-191-2/+6
| | | | | | | | | | | | | Bug fix Description: Tweak address comparison of external file list's heap address a bit to pacify Windows. Platforms tested: FreeBSD 4.9 (sleipnir) Asking Pedro to test on Windows Too minor to require h5committest
* [svn-r8058] Purpose:Quincey Koziol2004-01-131-0/+4
| | | | | | | | | | | Bug fix Description: Plug another small memory leak for fill-values. Platforms tested: FreeBSD 4.9 (sleipnir) too minor to require h5committest
* [svn-r8039] Purpose:Quincey Koziol2004-01-081-25/+250
| | | | | | | | | | | | | | | | | | | | Bug fix Description: When two property lists are compared, the H5Pequal routine was just comparing the raw information for the property values. This causes problems when the raw information contains pointers to other information. Solution: Allow a 'compare' callback to be registered for properties, so that a user application get perform the comparison itself, allowing for "deep" compares of the property value. This was exported to the H5Pregister & H5Pinsert routines in the development branch, but not the release branch. Platforms tested: FreeBSD 4.9 (sleipnir) h5committest
* [svn-r8027] Purpose:Quincey Koziol2004-01-061-0/+4
| | | | | | | | | | | | | | | Bug fix Description: Fix small memory leak of fill-value information inside the library. Solution: "reset" the fill-value object header message, so that the internal buffer gets freed. Platforms tested: FreeBSD 4.9 (sleipnir) too minor to require h5committest
* [svn-r7918] Purpose:Quincey Koziol2003-12-061-18/+14
| | | | | | | | | | | | | | | | | | | 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-r7837] Purpose:Quincey Koziol2003-11-121-12/+15
| | | | | | | | | | | Bug fix. Description: Skip over situation where malloc(0) might occur. Platforms tested: IBM p690 (copper) too minor to require h5committest
* [svn-r7726] Purpose:Quincey Koziol2003-10-241-21/+29
| | | | | | | | | | | | Code cleanup Description: Refactored handlier of VFL drivers in file access and data transfer property lists in order to simplify and unify the code dealing with them. Platforms tested: FreeBSD 4.9 (sleipnir) too minor to require h5committest
* [svn-r7543] Purpose:Quincey Koziol2003-10-051-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug fixes and code cleanup Description: Lots of changes here: - Fixed bug #691 - when shared datatypes are used in attributes they are incorrectly copied into the attribute instead of referring the the named datatype in the file. This required bumping the version of the attribute message. The new version of the attribute message is only written out when a shared datatype is used in the attribute. [Also, this format change made the size of the attribute smaller.] - Added information to attribute debugging routine so that shared datatypes are displayed correctly with the h5debug tool. - Refactored the H5O* routines to extract code that was common to several routines into subroutines to call. - Added 'link' method for H5O message sub-classes, which increments the link count on shared objects when a message is created which shares them. - Corrected [unreported] bug where the link count was not being decremented on the shared object when a object header message with a reference to that object was deleted from the file. - Reduced size of shared message from 49 bytes (which was incorrect anyway and should have been 48 bytes) to 10 bytes, which required bumping the version of "shared" messages. - Refactored some of the shared datatype routines to allow for easier queries of "committedness" internally to the library and also added routine to easily increment/decrement the reference count of a shared datatype. Platforms tested: FreeBSD 4.9 (sleipnir) h5committest
* [svn-r7242] Purpose:Quincey Koziol2003-07-211-6/+19
| | | | | | | | | | | | Bug fix Description: Fix bug with combination of fill-values, chunked datasets and variable-length strings. Platforms tested: FreeBSD 4.8 (sleipnir) h5committest
* [svn-r7116] Purpose:Quincey Koziol2003-06-271-3/+4
| | | | | | | | | | | | Update code Description: Move "PABLO_MASK" definition above header file inclusion to avoid problems with inline functions in header files. Platforms tested: FreeBSD 4.8 (sleipnir) h5committest
* [svn-r7058] Purpose:Quincey Koziol2003-06-181-22/+25
| | | | | | | | | | | | | | Bug fix and refactored code Description: Return the file space we have allocated already when a dataset creation fails. Also track the change to the H5Fget_obj_<foo> APIs Platforms tested: FreeBSD 4.8 (sleipnir) h5committest
* [svn-r7037] Purpose:Quincey Koziol2003-06-131-1/+4
| | | | | | | | | | | | | | | | | | Bug fix Description: The fill time in a dataset with no fill value information created with an older version of the library was getting set to H5D_FILL_TIME_ALLOC instead of the new default H5D_FILL_TIME_IFSET and was causing H5Dcreate() calls with that dataset creation property list to fail now. Solution: Set the new default in the fill time initialization for missing fill value information. Platforms tested: FreeBSD 4.8 (sleipnir) h5committest
* [svn-r7029] Purpose:Quincey Koziol2003-06-121-20/+52
| | | | | | | | | | | | | New feature/Bug fix Description: Add new fill time value - H5D_FILL_TIME_IFSET which writes the fill value to a dataset if the user has defined one, otherwise not writing the fill value to the dataset. Platforms tested: FreeBSD 4.8 (sleipnir) serial & parallel h5committest
* [svn-r7016] Purpose:Quincey Koziol2003-06-101-17/+30
| | | | | | | | | | | | | | | | Bug fix Description: Chunked datasets with early space allocation and unlimited dimensions were running into problems where the dataset's "layout" message was marked as constant too early, preventing the dataset's dimensions from being extended. Solution: Change logic for marking the layout message constant to wait a bit longer. Platforms tested: FreeBSD 4.8 (sleipnir) w/parallel h5committest
* [svn-r6878] Purpose:Quincey Koziol2003-05-151-3/+3
| | | | | | | | | | | Code cleanup Description: Limit the scope on more function prototypes/macros/typedefs. Platforms tested: FreeBSD 4.8 (sleipnir) h5committest not necessary.
* [svn-r6869] Purpose:Quincey Koziol2003-05-131-1/+23
| | | | | | | | | | | | | | | | | Bug fix. Description: When the same dataset is opened more than once and those references to the object are left dangling, the library would not correctly shut down the dataset API, potentially allowing the file to be truncated. Solution: "force" the dataset IDs to be released when the dataset API is being shut down by the library. Platforms tested: FreeBSD 4.8 (sleipnir) h5committested
* [svn-r6837] Purpose:Quincey Koziol2003-05-081-4/+15
| | | | | | | | | | | | | | | 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
* [svn-r6825] Purpose:Quincey Koziol2003-05-071-1208/+7
| | | | | | | | | | | | | | | | | | | | | | | | | New feature/enhancement Description: Chunked datasets are handled poorly in several circumstances involving certain selections and chunks that are too large for the chunk cache and/or chunks with filters, causing the chunk to be read from disk multiple times. Solution: Rearrange raw data I/O infrastructure to handle chunked datasets in a much more friendly way by creating a selection in memory and on disk for each chunk in a chunked dataset and performing all of the I/O on that chunk at one time. There are still some scalability (the current code attempts to create a selection for all the chunks in the dataset, instead of just the chunks that are accessed, requiring portions of the istore.c and fillval.c tests to be commented out) and performance issues, but checking this in will allow the changes to be tested by a much wider audience while I address the remaining issues. Platforms tested: h5committested, FreeBSD 4.8 (sleipnir) serial & parallel, Linux 2.4 (eirene)
* [svn-r6738] Purpose:Quincey Koziol2003-04-231-1/+2
| | | | | | | | | | | | Code cleanup Description: Add & improve assertion that was removed in last commit, to check for compact dataset storage. Platforms tested: FreeBSD 4.8 (sleipnir) triple check not necessary.
* [svn-r6729] Raymond Lu2003-04-221-3/+2
| | | | | | | | | | | Purpose: bug fix Description: VL datatype in compact dataset fails because a wrong type size is used. Platforms tested: h5committested Misc. update:
* [svn-r6659] Purpose:Quincey Koziol2003-04-141-3/+4
| | | | | | | | | | | | | | | | New feature, sorta Description: Track changes to various internal APIs Platforms tested: FreeBSD 4.8 (sleipnir) w/C++ Linux 2.4 (burrwhite) w/FORTRAN Solaris 2.7 (arabica) w/FORTRAN IRIX64 6.5 (modi4) w/parallel & FORTRAN (h5committest not run due to my ongoing difficulties with C++ on burrwhite).
* [svn-r6604] Purpose:Quincey Koziol2003-04-091-30/+45
| | | | | | | | | | | | | | | | | | New feature Description: Hooked up internal dataset creation call (H5D_create) to the new "can apply" and "set local" callbacks for filters. Solution: Platforms tested: FreeBSD 4.8 (sleipnir) w/szip Linux 2.4 (sleipnir) w/szip Solaris 2.7 (arabica) w/FORTRAN IRIX64 6.5 (modi4) w/szip, FORTRAN & parallel Misc. update:
* [svn-r6499] Purpose:Bill Wendling2003-03-191-17/+18
| | | | | | | | | | | | | Update Description: Added support for FPHDF5 wherever there was support for MPI/IO and/or MPIPOSIX. Platforms tested: Linux, Modi4, Sol Misc. update:
* [svn-r6411] Purpose:Quincey Koziol2003-02-171-42/+42
| | | | | | | | | | | | | | | | | | | | | | Code cleanup Description: Clean up miscellaneous warnings which have crept into the code. Fix "_POSIX_C_SOURCE not defined" warning on FreeBSD. Adjust gcc compiler flags to be more concise for production mode. Refactor the H5O code so that there is a stronger boundary between code in the H5O package and code in the library which just calls H5O routines. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} FreeBSD 4.7 (sleipnir) serial & parallel and gcc 2.95.4 & gcc 3.2.2 Misc. update: Update MANIFEST if you add or remove any file.
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