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* [svn-r15485] Purpose: Allow library to shut down properly when objects have ↵Neil Fortner2008-08-191-8/+8
| | | | | | | | | | | | | | | | reference count > 1. Description: Added a new field 'app_count' to H5I_id_info_t struct, to track the reference count on an id due to the application. the old 'count' field tracks the total. Generally any id visible to the application gets placed in app_count. Added app_ref boolean parameter to H5I_inc_ref, H5I_dec_ref, H5I_register, H5I_clear_type, and a few other functions, to specify whether the operation(s) being performed on the id(s) are due to the application (TRUE) or not (FALSE). Test added for this case. Tested: kagiso, smirom, linew (h5committest)
* [svn-r15131] Description:Quincey Koziol2008-06-031-5/+65
| | | | | | | | | | | | | | | | | | | | | | Finish omnibus chunked dataset I/O refactoring, to separate general actions on chunked datasets from actions that are specific to using the v1 B-tree index. Cleaned up a few bugs and added some additional tests also. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.5.2 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14903] Undoing change committed in r14902.Scot Breitenfeld2008-04-301-151/+283
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* [svn-r14902] Merged fortran_1_8 branch changes r14505:14901 into the trunk. ↵Scot Breitenfeld2008-04-301-283/+151
| | | | New fortran wrappers added.
* [svn-r14860] Description:Quincey Koziol2008-04-241-151/+283
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Omnibus raw data I/O revisions, with wide-ranging changes and refactoring, in order to prepare for implementing "fast append" feature. These changes remove the majority of the code duplication for raw data I/O which has crept in over the last ten years and introduces a more object- oriented design for operating on different types of dataset storage. Chunked storage no longer has it's own I/O routines, it is now handled as either contiguous (if chunk is not pulled into the cache) or compact (if the chunk is cached in memory). No bug or feature changes, at least intentionally... :-) Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.5.2 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14306] Description:Quincey Koziol2007-11-291-4/+4
| | | | | | | | Add call to reset cached chunk info after initialization of chunk data storage. Tested on: Linux/64 2.4(smirom) w/parallel
* [svn-r13997] Moved H5D_istore_lock and H5D_istore_unlock from ↵Raymond Lu2007-07-211-4/+4
| | | | | | | | | H5D_istore_writevv and H5D_istore_readvv to H5D_chunk_write and H5D_chunk_read to avoid frequent lock and unlock and to improve some performance. Tested with h5committest on THG machines.
* [svn-r13942] Description:Quincey Koziol2007-07-051-3/+2
| | | | | | | | | Minor code & comment cleanups Tested on: Mac OS X/32 10.4.10 (amazon) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13918] Description:Quincey Koziol2007-06-261-163/+30
| | | | | | | | | | Refactor fill value buffer code into one location, for better long-term maintenance. Tested on: Mac OS X/32 10.4.10 (amazon) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13878] Description:Quincey Koziol2007-06-191-11/+16
| | | | | | | | | Improve efficiency of writing VL-datatype fill values. Tested on: Mac OS X/32 10.4.9 (amazon) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13870] Description:Quincey Koziol2007-06-151-37/+134
| | | | | | | | | | Fix writing variable-length datatype fill values for contiguous dataset storage Tested on: Mac OS X/32 10.4.9 (amazon) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13814] Description:Quincey Koziol2007-05-291-2/+2
| | | | | | | | | | | | | | Change back to clearing memory buffers by default, but give users option to disable this, for performance reasons (--disable-clear-file-buffers). Also, add configure option (--enable-using-memchecker) to conveniently control making the library "play nice" with memory checking tools like valgrind and purify. Tested on: Mac OS X/32 10.4.9 (amazon) FreeBSD/32 6.2 (duty) Linux/32 2.6 (kagiso)
* [svn-r13253] Updated all C and C++ style source code files with the THG ↵Albert Cheng2007-02-071-2/+3
| | | | | | | | | copyright notice. Tested platform: Kagiso only since it is only a comment block change. If it works in one machine, it should work in all, I hope. Still need to check the parallel build on copper.
* [svn-r13167] Description:Quincey Koziol2007-01-221-44/+43
| | | | | | | | | | | Get rid of two different types of fill value struct (merge H5O_fill_t and H5O_fill_new_t) and clean up & simplify dataset initialization code. (In preparation for shared object header message method call refactoring). Tested on: FreeBSD/32 6.2 (duty) Mac OS X/32 10.4.8 (amazon)
* [svn-r13063] Cleaned up some memory issues when copying, in preparation for ↵James Laird2006-12-141-8/+6
| | | | | | | | | checking in code to copy shared messages. Should be fewer memory leaks and fewer "uninitialized memory reads." Tested on kagiso, smirom, and Windows.
* [svn-r13002] Description:Quincey Koziol2006-11-301-82/+75
| | | | | | | | | | | | Fix problem with copying objects when the dataset to copy has an "older" version of the layout message and needs to compute the size of the dataset's storage after the dataspace information is available. Minor random cleanups also... Tested on: FreeBSD/32 4.11 (sleipnir) Too minor/weird to test w/h5committest...
* [svn-r12842] Description:Quincey Koziol2006-11-021-2/+2
| | | | | | | | | | | | | | | | Refactor generic property list initialization code to put property list specific routines in property list modules, instead of scattered to the four winds. Also, introduce property list class initialization objects, to make adding new property list classes in the library easier. Fix daily test failure by using H5Pget_elink_prefix() API routine instead of looking at the "raw" generic property list information. Tested on: Mac OS X/32 10.4.8 (amazon) FreeBSD/32 4.11 (sleipnir) w/threadsafe Linux/32 2.4 (heping) w/C++ & FORTRAN Linux/64 2.4 (mir) w/build-all & 1.6 compat
* [svn-r12803] Description:Quincey Koziol2006-10-231-3/+8
| | | | | | | | | | | | | | Finish new version of the I/O pipeline message, which is much smaller than the previous version. This version is used with the "use the latest version of the format" flag. Closed several memory leaks/overruns (found with valgrind). Also, lots of compiler & formatting cleanups. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12706] Description:Quincey Koziol2006-10-021-2/+2
| | | | | | | | | 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-r12680] Description:Quincey Koziol2006-09-251-75/+109
| | | | | | | | | Review, revise & checkin in Peter's latest round of object copy changes, which add basic support for datasets & attributes with reference datatypes. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12474] Quincey Koziol2006-07-151-4/+4
| | | | | | | | Clean up some compiler warnings. Tested on: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r12440] Purpose:Quincey Koziol2006-06-271-2/+2
| | | | | | | | | | | 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 Koziol2006-06-261-0/+3
| | | | | | | | | | | | | 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-r12189] Purpose:Quincey Koziol2006-04-011-1/+8
| | | | | | | | | | | | | | New/expanded features Description: Check in Peter's changed for the object copy code: - Allow/fix copying datasets using named variable-length datatypes - Start adding framework for property list to control how object copying occurs. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11899] Purpose:Quincey Koziol2006-01-281-36/+52
| | | | | | | | | | | | | | | | Bug fix & new feature Description: Support variable-length datatypes in compact data storage and chunked data storage, along with attributes. Bug fix on the H5T_vlen_set_loc to allow for changing the file on a variable-length datatype on disk. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 Can't h5committest right now, due to missing cache files.
* [svn-r11771] Purpose:Quincey Koziol2005-12-081-1/+2
| | | | | | | | | | | | Code cleanup Description: Fix a bunch of warnings flagged by Windows compilers. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11758] Purpose:Quincey Koziol2005-12-041-1/+212
| | | | | | | | | | | | | New feature Description: Add in a combination of Peter's & my code to support copying variable-length data from one file to another, although currently only supported with contiguous data storage. Platforms tested: FreeBSD 4.11 (sleipnir) h5committest
* [svn-r11712] Purpose:Quincey Koziol2005-11-151-5/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r11593] Purpose:Quincey Koziol2005-10-211-19/+26
| | | | | | | | | | | | Code cleanup Description: Clean up & standardize a bit in preparation for coding standards discussion. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11245] Purpose:Quincey Koziol2005-08-131-8/+8
| | | | | | | | | | | | | | | | | | | | 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-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 Koziol2004-12-291-57/+62
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r9342] Purpose:Quincey Koziol2004-09-301-122/+149
| | | | | | | | | | | | | | | | 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-r9329] James Laird2004-09-281-84/+84
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Purpose: Feature Description: 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-r9101] Purpose:Quincey Koziol2004-08-171-284/+246
| | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r8981] Purpose:Quincey Koziol2004-08-021-1/+1
| | | | | | | | | | | | | 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-r8731] Purpose:Quincey Koziol2004-06-231-12/+2
| | | | | | | | | | | | | | | 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-r8673] Purpose:Quincey Koziol2004-06-131-1/+1
| | | | | | | | | | | | | | | | | | 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-r8613] Purpose:Quincey Koziol2004-06-051-148/+185
| | | | | | | | | | | | | | | | | 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 Misc. update:
* [svn-r8590] Purpose:Quincey Koziol2004-05-271-22/+7
| | | | | | | | | | | | | | | | | | | | | 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-r8287] Purpose:Quincey Koziol2004-03-301-2/+2
| | | | | | | | | | | | | | Bug fix/code cleanup Description: Copy Robb's feature in SSlib that checks that the name of the function used in the FUNC_ENTER macro is actually the name of function. Fixed a bunch of typos & copy-n-pasto's for functions with incorrect names. Platforms tested: FreeBSD 4.9 (sleipnir) w/parallel too minor to require h5committest
* [svn-r8126] Purpose:Quincey Koziol2004-01-311-29/+3
| | | | | | | | | | | | | | | | | Bug fix/optimization Description: Address slowdown in MPI-I/O file metadata operations that was introduced mid-stream. We now _require_ a POSIX compliant parallel file system for the MPI-I/O file driver (as well as for the MPI-POSIX file driver). Also optimized file open operation when the file is being created by reducing the number of collective & syncronizing calls. Additionally, refactor the MPI routines into a common place, eliminating duplicated code. Platforms tested: FreeBSD 4.9 (sleipnir) w/parallel h5committest
* [svn-r7917] Purpose:Quincey Koziol2003-12-061-2/+1
| | | | | | | | | | | | | | | | | | | 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-r7763] Purpose:Quincey Koziol2003-10-281-1/+2
| | | | | | | | | | | | | | | | | Bug fix Description: Code was using an internal DXPL with collective I/O turned on during independent I/O operations to fill dataset on disk. Solution: Switched to internal DXPL with independent I/O Platforms tested: FreeBSD 4.9 (sleipnir) FreeBSD 4.9 (sleipnir) w/parallel Linux 2.4 (verbena) w/fortran & C++ Solaris 2.7 (arabica) w/64-bit extensions enabled
* [svn-r7426] Purpose:Quincey Koziol2003-08-281-1/+1
| | | | | | | | | | | | | | | | | Bug fix Description: When datasets are deleted from a file, they are removed from the sieve buffer, but instead of invalidating only the part of the sieve buffer affected, the sieve buffer code would throw away the entire sieve buffer, potentially including other raw data in the buffer that hadn't been written to disk yet. Solution: Improve the sieve buffer clearing code to handle partial invalidations. Platforms tested: FreeBSD 4.8 (sleipnir) h5committest
* [svn-r7210] Purpose:Quincey Koziol2003-07-111-13/+7
| | | | | | | | | | | | | Refactoring code Description: Refactored "IS_H5FD_MPIO || IS_H5FD_MPIPOSIX || IS_H5FD_FPHDF5" combination of macros in many places into single IS_H5FD_MPI macro, which has the same definition, but should be easier to maintain. Platforms tested: FreeBSD 4.8 (sleipnir) h5committest
* [svn-r7192] Purpose:Quincey Koziol2003-07-091-8/+0
| | | | | | | | | | | Code cleanup Description: Clean up various minor warnings in the library. Platforms tested: FreeBSD 4.8 (sleipnir) too small to need h5committest
* [svn-r7122] Purpose:Quincey Koziol2003-06-301-4/+1
| | | | | | | | | | | | | Code cleanup/Feature removal Description: Remove "round robin" writing of metadata in MPI VFDs (and a couple of other places). This never really worked the way I hoped it would and it causes problems on certain machines. Platforms tested: FreeBSD 4.8 (sleipnir) w/parallel Too small for triple check.
* [svn-r7116] Purpose:Quincey Koziol2003-06-271-1/+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-r6961] Purpose:Quincey Koziol2003-06-041-1/+1
| | | | | | | | | | | | | | | | Bug fix Description: An earlier checkin changed some of the assumptions about single block hyperslabs, causing them to fail in odd ways. Solution: Fix errors with single block hyperslabs by keying off of count==1 instead of stride==1. Platforms tested: FreeBSD 4.8 (sleipnir) w/parallel h5committested
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