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* [svn-r13918] Description:Quincey Koziol2007-06-261-248/+4
| | | | | | | | | | 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-r13885] Modify the comment from the checkin last round.Raymond Lu2007-06-191-6/+6
| | | | No test is needed.
* [svn-r13884] The second step of optimization for compound data for the ChicagoRaymond Lu2007-06-191-42/+321
| | | | | | | | | | | | | | | | | | | | | | | | | | company. The I/O is optimized when the source and destination members are a subset of each other one way or another, and the order is the same, and no conversion is needed. For example: struct source { struct destination { TYPE1 A; --> TYPE1 A; TYPE2 B; --> TYPE2 B; TYPE3 C; --> TYPE3 C; }; TYPE4 D; TYPE5 E; }; or struct destination { struct source { TYPE1 A; --> TYPE1 A; TYPE2 B; --> TYPE2 B; TYPE3 C; --> TYPE3 C; }; TYPE4 D; TYPE5 E; }; The optimization is simply moving data from the source to the appropriate places in the buffer and bypass the reading of the background data and data conversion. Tested on smirom, liberty, sol, and copper.
* [svn-r13870] Description:Quincey Koziol2007-06-151-43/+66
| | | | | | | | | | 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-r13842] Description:Quincey Koziol2007-06-081-2/+3
| | | | | | | | | | | | Fix compact dataset storage to initialize VL datatype fill values correctly. Also, fix bug in global heap code when the fix action on a global heap is to delete an object in a heap with no free space. Tested on: Mac OS X/32 10.4.9 (amazon) FreeBSD/32 6.2 (duty)
* [svn-r13825] Description:Quincey Koziol2007-05-311-7/+15
| | | | | | | | | Incremental step forward in fixing problems with fill values that have a variable-length daattype. This set of changes fixes problems with the copying the property list values. tested Tn: Mac OS X/32 10.4.9 (amazon)
* [svn-r13816] Description:Quincey Koziol2007-05-291-29/+33
| | | | | | | | Fix a few typos and a small memory leak. Tested on: FreeBSD/32 6.2 (duty) Linux/64 2.6 (chicago2)
* [svn-r13534] Description:Quincey Koziol2007-03-211-101/+66
| | | | | | | | Minor code cleanups... Tested on: FreeBSD/32 6.2 (duty) Too minor to require h5committest
* [svn-r13531] When a dataset is created and no data is written, but fill ↵Raymond Lu2007-03-201-21/+77
| | | | | | | | | | | | value is defined, if there's VL type of data in the dataset, the address of the data is copied multiple times into the buffer, causing some trouble when the data is released. Instead, this checkin makes multiple copies of fill value first, then does conversion on each element so that each of them has a copy of the VL data. A test is added, too. Tested it on kagiso, sol, and copper.
* [svn-r13475] There's a configure issue linking szip's shared libraries when ↵Mike McGreevy2007-03-081-2/+2
| | | | | | | | | | | | running on kagiso. The static szip libraries are working as intended, but when shared szip libraries are present and intended for use they cannot be opened. A check has been implemented to test if shared szip libraries are functional on current platform. If they are not, and the user is trying to use them, szip is now disbaled and the user is informed. This issue occurs on kagiso, and the resolution was tested on 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 Koziol2007-01-221-93/+88
| | | | | | | | | | | 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-r13068] Ran bin/reconfigure. Some of the scripts have been changed or ↵James Laird2006-12-181-5/+5
| | | | | | | | | haven't been run in a while, so many of the source files were updated with tracing macros, etc. No code changes by me. Tested on kagiso and smirom.
* [svn-r13016] Description:Quincey Koziol2006-12-041-1/+1
| | | | | | | | | | | Finish moving object header message routines into their own source code module, along with renaming them to have "H5O_msg_" prefix... Tested on: Mac OS X/32 10.4.8 (amazon) FreeBSD/32 4.11 (sleipnir) Linux/32 2.4 (heping) AIX/32 5.? (copper)
* [svn-r12844] Description:Quincey Koziol2006-11-021-21/+0
| | | | | | | Fix parallel build failure for property list class initialization refactor. Tested on: AIX (copper) w/parallel
* [svn-r12842] Description:Quincey Koziol2006-11-021-4/+4
| | | | | | | | | | | | | | | | 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-r12700] Alert:Quincey Koziol2006-10-021-240/+237
| | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r12593] Description:Quincey Koziol2006-08-171-10/+14
| | | | | | | | | Clean up some of the parallel chunk I/O compiler warnings and other minor code rearrangement. Tested on: FreeBSD 4.11 (sleipnir) w/paralllel h5committest
* [svn-r12553] This check-in includes the following part of parallel ↵MuQun Yang2006-08-091-1/+3
| | | | | | | | | | | | | | | 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-r12474] Quincey Koziol2006-07-151-53/+43
| | | | | | | | Clean up some compiler warnings. Tested on: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r12440] Purpose:Quincey Koziol2006-06-271-10/+10
| | | | | | | | | | | 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-r12128] Purpose:Quincey Koziol2006-03-221-2/+2
| | | | | | | | | | | Code cleanup Description: Clean up some compiler warnings (esp. those flagged on Windows builds) Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11963] Purpose:MuQun Yang2006-02-221-0/+1
| | | | | | | | | | | | | | | | | | | | bug fix for daily test Description: if (fm->select_chunk) is not NULL at sequential mode and not set by the library, it shouldn't be free. Otherwise, it will cause failures in the daily test. Solution: Explicitly set (fm->select_chunk) to NULL for non-parallel case. Platforms tested: copper with parallel heping with both sequential and parallel shanti with sequential Misc. update: Hopefully only mir failed at daily test.
* [svn-r11961] Purpose:MuQun Yang2006-02-211-5/+6
| | | | | | | | | | | | | | | | | | | | Bug fix in collective IO code Description: When select none occurs in one process, fm->select_chunk hasn't been allocated the memory(not allocated until create_file_hyper); however, this needs to be checked; it was caught with cmpi at NCSA linux cluster. Solution: Relocate the place to allocate the memory space for fm->select_chunk. Platforms tested: cmpi at tungsten mpich at heping kind of minor and let daily test catch other errors. Misc. update: This won't fix the failure at mir.
* [svn-r11960] Purpose:MuQun Yang2006-02-211-1/+1
| | | | | | | | | | | | | | code clean up Description: Clean up some warnings in collective chunk IO code Solution: Platforms tested: heping Misc. update:
* [svn-r11959] Purpose:MuQun Yang2006-02-201-18/+12
| | | | | | | | | | | | | | | | | | | | bug fix Description: During the process of the combination of collective chunk IO code and the original IO code, The return value of a function call hasn't been initialized. On 32-bit mode at modi4, that value isn't set to 0 by default. So a fake error value returns. Solution: Re-arrange the code so that the return value will be set properly. Platforms tested: parallel: modi4 - 32bit heping seq: heping Misc. update:
* [svn-r11950] Purpose:MuQun Yang2006-02-161-309/+127
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Enhanced collective chunk IO supports Description: 1. When using collective IO with chunking storage without any tuning, performance may become worse under some circumstances. 2. Current HDF5 handles raw-data IO per chunk. So for many small chunks, many small IOs will be passed into MPI-IO. That may cause bad performance. 3. For one IO per chunk case, sometimes performance with collective is worse than performance with independent. An obvious case is when only one process is doing IO and all other process are not doing IO, the collective IO will only add overheads for communication. We want to avoid this case. Some management inside our library needs to be done. Solution: - Added managements of collective IO supports for chunking storage inside parallel HDF5 1) Implemented One IO with collective mode for all chunks in the application by building one MPI derived datatype accross all chunks. 2) Implemented the decision-making support to do collective IO inside MPI-IO per chunk. 3) Added the decision-making support to do one IO accross all chunks or to do multiple IOs with each IO per chunk. 4) Added the support to handle the case some processes won't do any IOs in collectively. 5) Some MPI-IO package(mpich 1.2.6 or lower, e.g.) cannot handle collective IO correctly for the case when some processes have no contributions to IOs, a special macro is added to change collective IO mode to independent IO mode inside HDF5 library. Platforms tested: Parallel: IBM AIX 5.2(copper) Linux (heping) mpich-1.2.6 SDSC Teragrid mpich-1.2.5 Linux(Tungsten) mpich-1.2.6 Altix(NCSA cobalt) Seq: Linux(heping) Misc. update:
* [svn-r11712] Purpose:Quincey Koziol2005-11-151-42/+49
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 Koziol2005-10-211-146/+30
| | | | | | | | | | | | 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-r11415] Purpose: Internal design change.Raymond Lu2005-09-141-3/+3
| | | | | | | | | | | | | | | | | Description: H5T_register() replaces any existing data conversion path with a new path. Solution: Added a parameter to H5T_register() and H5T_path_find() to signal the library whether the new conversion path is from API function H5Tregister() or from private function like H5T_init_interface(). If it is from H5Tregister(), replace existing path. If it's from H5T_init_interface() and the library is trying to register default hard conversion functions, don't replace existing path because the path is registered by the library. For example, the library registered H5T_conv_int_float() and is trying to register H5T_conv_long_float(). The size of long is equal to int. There's no need to replace the path H5T_conv_int_float(). Platforms tested: h5committest and fuss.
* [svn-r11402] Purpose: MaintenanceElena Pourmal2005-09-131-2/+2
| | | | | | | | | | | | Description: Compiler complained about const type * variables that were used in the functions that require "non const" parameters. Compilation failed. Solution: Use casting to avoid compilation errors. Platforms tested: SX-6, heping and mir with new g95 Misc. update:
* [svn-r11245] Purpose:Quincey Koziol2005-08-131-7/+7
| | | | | | | | | | | | | | | | | | | | 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-r11241] Purpose:Quincey Koziol2005-08-131-334/+113
| | | | | | | | | | | | | Code cleanup Description: Fix logic error in previous checkin and also finish refactoring I/O initialization, including simplifying all the collective & parallel cases into a more unified mechanism. Platforms tested: FreeBSD 4.11 (sleipnir) w/ & w/o parallel Linux 2.4 (mir)
* [svn-r11240] Purpose:Quincey Koziol2005-08-131-66/+82
| | | | | | | | | | | Bug fix Description: Fix logic error for non-parallel file I/O with library built for parallel I/O capability. Platforms tested: Linux 2.4 (mir) w/parallel
* [svn-r11236] Purpose:Quincey Koziol2005-08-131-421/+298
| | | | | | | | | | | | | | Code cleanup & bug fix Description: Refactor recent collective chunk changes to simplify them. Also, compute the number of chunks by checking the number of objects in the chunk skip list instead of getting the boundaries of the selection and counting the chunks that it overlaps, which is faster and computes correct number for certain selections. Platforms tested: FreeBSD 4.11 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r11235] Purpose:Quincey Koziol2005-08-121-464/+377
| | | | | | | | | | | | | Code cleanup Description: Refactor, simplify and cleanup Kent's recent checking for collective chunk I/O. There's a bug that I need to talk to Kent about and some more cleanups still, but this is reasonable for an interim point. Platforms tested: FreeBSD 4.11 (sleipnir) w/parallel Too minor for h5committest
* [svn-r11231] Purpose:MuQun Yang2005-08-111-38/+492
| | | | | | | | | | | | | | | | | | | | | | | bug fix for collective chunk IO, phase 1 Optimization hasn't been done yet, the collective chunk IO bug should be fixed. Description: In chunking storage, memory space and file space will be remapped, So to check whether file space and memory space are regular in order to use optimized MPI derived datatype for collective call one has to check per-chunk wise instead of per hyperslab wise. Even a regular memory space will be stored in span-tree and will be irregular before chunk IO. Solution: 1. Check file space and memory space per chunk wise instead of per hyperslab wise. 2. For collective IO mode, number of chunks covered by hyperslab may be different. Since we are handing per chunk per IO, for the extra chunk IO for some(not all) processors, collective mode will cause program hanged. So for the extra chunk Io mode independent IO has to be used. 3. On some platforms, Complex MPI derived datatype is not working, so we have to use independent IO for collective IO mode if the selection is irregular. However, when the selection is regular, we do want to use collective IO since that will improve performance. Special cares have to be added for this case. Platforms tested: copper(AIX 5.1) Linux(heping mpich 1.2.6), Teragrid machine, Cobalt(altix), modi4 Misc. update:
* [svn-r10951] Purpose:Quincey Koziol2005-06-181-6/+16
| | | | | | | | | | | | | | | | | Bug fix Description: Hyperslab selections that had a selection offset and were applied to a chunked dataset could get into an infinite loop or core dump if the same selection was used multiple times, with different selection offsets. Solution: "Normalize" the selection with the selection offset, generate the selections for the chunks overlapped and then "denormalize" the selection. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r10705] Purpose:Quincey Koziol2005-04-301-1/+1
| | | | | | | | | | | Code cleanup Description: Clean up a few compiler warnings of various sorts... Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r10574] Purpose:Quincey Koziol2005-04-081-2/+2
| | | | | | | | | | | Code cleanup Description: Clarify error string. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r10545] Purpose:MuQun Yang2005-04-051-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | Activating collective IO supports for irregular selction inside HDF5 dataset. This support doesn't include to build the final complicated MPI derived datatype support for chunking storage. Description: Support collective chunk IO for both contiguous and chunking storage for irregular selection( using H5S_SELECT_OR for multiple hyperslab selection) Solution: Using MPI derived datatype to realize this feature. Problems still need to be investigated: Big size irregular hyperslab selection test may cause MPI hang or abnormalexit with MPICH family on various platforms. This is really hard to debug since sometimes it can work and sometimes it cannot work. We will continue investigating those cases. This may not be parallel HDF5 bugs since with the recent version of poe at IBM platforms, all tests passed. Platforms tested: 1. Linux heping 2.4.21-27.0.1 with mpich 2. AIX 5.1 copper with mpcc_r 3. Altix cobalt SGI linux 2.4.21-sgi304rp05031014_10149 with icc -lmpi 4. Linux Cluster SDSC TG, intel 8-r2 with mpich 1.2.5 5. NCSA Linux Cluster Tungsten, MPICH-TCP-1.2.5.2, Intel 8.0 under lustre 6. NCSA Linux Cluster Tungsten, MPICH-LAM-INTEL711, sometimes not working 7. NCSA Linux CLuster Tungsten, champion-pro-1.2.0-3, not working for other collective IO tests, but work for irregular selection collective IO test. Misc. update:
* [svn-r10187] Purpose:Quincey Koziol2005-03-111-1/+1
| | | | | | | | | | | | | Code cleanup, mostly Description: Remove remaining TBBT error info Add new error code for block tracker Platforms tested: FreeBSD 4.11 (sleipnir) Solaris 2.9 (shanti)
* [svn-r9959] Purpose: Bug fixRaymond Lu2005-02-081-1/+1
| | | | | | | | | | | | Description: For variable-length string, H5Tget_class returned H5T_STRING as its class. But H5Tdetect_class and H5Tget_member_class considered it as H5T_VLEN. This is fixed to let all these 3 functions treat it as H5T_STRING. Some test cases have been added to dtypes.c Platforms tested: heping - already tested for v1.6 with h5committest Misc. update: RELEASE.txt
* [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-r9762] Purpose:Quincey Koziol2005-01-061-1/+1
| | | | | | | | | | Code cleanup Description: Change pablo mask to conform to the style used by the rest of the library Platforms tested: None needed - very, very minor
* [svn-r9734] Purpose:Quincey Koziol2004-12-301-105/+98
| | | | | | | | | | | | Code cleanup Description: Convert chunk iteration code to use skip lists instead of threaded, balanced binary trees. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel & szip Too minor to require h5committest
* [svn-r9727] Purpose:Quincey Koziol2004-12-291-55/+81
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r9665] Purpose:Quincey Koziol2004-12-141-0/+1
| | | | | | | | | | Fix whitespace Description: Clean up whitespace a bit Platforms tested: None, just eyeballed, very minor
* [svn-r9657] Purpose:MuQun Yang2004-12-131-2/+2
| | | | | | | | | | | | | | | | | | small bug fix Description: When checking whether the current chunk covers the irregular hyperslab, the ending point of the chunk is not updated. This will cause the wrong checking output and fail for some irregular hyperslab selection. Solution: Updating the ending point of the chunk. Platforms tested: Linux 2.4 + parallel (too small to use h5committest) Misc. update:
* [svn-r9574] Purpose:MuQun Yang2004-11-241-9/+10
| | | | | | | | | | | | | | | Adding code for using MPI derived datatype to handle collective IO Description: No testing yet, won't affect the library. Solution: Platforms tested: linux 2.4 + mpich 1.2.6 Aix 5.1 + mpcc_r Misc. update:
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