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* [svn-r12081] Purpose:Quincey Koziol2006-03-112-12/+80
| | | | | | | | | | | New feature Description: Update "power of two" macro and add "general" log2() routine. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r12080] Purpose:Quincey Koziol2006-03-111-0/+30
| | | | | | | | | | | | New feature Description: Add "variable-length" 32-bit encode/decode macros, matching the other 64-bit ones, for later use in the fractal heap code. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor for full h5committest
* [svn-r12079] Purpose:Quincey Koziol2006-03-115-1/+11
| | | | | | | | | | | Update code Description: Add a new error value, for later use. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor for full committest
* [svn-r12078] Purpose:Quincey Koziol2006-03-112-41/+222
| | | | | | | | | | | | New features Description: Add "find node greater than or equal to key" and "remove first" operations to skip lists. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r12077] Purpose:Quincey Koziol2006-03-114-11/+17
| | | | | | | | | | | Code cleanup Description: Fix/update formatting, clean up typos, etc. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r12054] Purpose: VMS portElena Pourmal2006-03-092-0/+21
| | | | | | | | | | | | Description: Made small changes to sec2 driver to reflect that VMS systems ino_t is 1dim array of size 3; all changes are marked with H5_VMS variable. Defined HDremove macro for VMS to remove multiple versions of the files. Solution: Platforms tested: heping, VMS server Misc. update:
* [svn-r12035] Purpose:Fang Guo2006-03-071-2/+2
| | | | | | | | | | | | | | Description: Two functions (HDsrand and HDrand) are not declared. They caused compiling errors on Windows. Declare these two functions: H5_DLL int HDrand(); H5_DLL void HDsrand(unsigned int seed); Solution: Platforms tested: Windows XP and heping Misc. update:
* [svn-r12021] Purpose:Leon Arber2006-03-071-2/+2
| | | | | | | | | | | | | | | Bug fix. Description: Fix typo. srand/srandom don't return anything, so don't attempt to return their value. Solution: Platforms tested: heping Misc. update:
* [svn-r12019] Purpose:Leon Arber2006-03-074-17/+57
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug fix/Feature Description: Modify the library to use rand_r, when available, instead of srand. If rand_r is not available, it will try to use srandom/random, and then finally fall back to srand/rand. Solution: A couple places in the library use the srand() function to seed the random number generator. This can cause problems on certain platforms and could theoretically cause problems for users who expect a certain sequence of random numbers following their own call to srand(). Most platforms have an implementation of rand_r, which is identical to rand, except that it allows for explicit storage of the seed value. The configure script will now check for the existence of rand_r to facilitate its use in the library. Two new functions are added, to replace the macros HDsrand/HDrand. These functions are HDrand and HDsrand. HDrand will call rand_r, if available, or random(), if available, and fall back to rand() if neither of those is available. HDsrand will store the seed value locally, if rand_r is available. Otherwise, it will call srandom if available, and fall back to srand otherwise. Platforms tested: heping, mir. Really need to test on Red Storm, since that platform motivated this fix, but the machine is currently not available. Misc. update:
* [svn-r12017] Purpose:Quincey Koziol2006-03-072-3/+3
| | | | | | | | | | | | | | Bug fix Description: Correct problem with new log2(n) routine on 64-bit machines. Solution: Put some casts in to make certain that the values are computed as 32-bit integers. Platforms tested: Linux 2.4 (mir) - 64-bit
* [svn-r12007] Purpose:Quincey Koziol2006-03-051-1/+1
| | | | | | | | | | Bug fix Description: Fix typo in H5HF_dblock_debug() prototype Platforms tested: FreeBSD 4.11 (sleipnir)
* [svn-r12004] Purpose:Quincey Koziol2006-03-0419-169/+1697
| | | | | | | | | | | | | | | | | New feature & code cleanup Description: Update fractal heap to be able to insert objects into a direct block hanging off the header. Extract "octal dump" code into separate routine so that both the local heaps & fractal heaps can use it. Other code cleanups & support to get this far. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4
* [svn-r12003] Purpose:Quincey Koziol2006-03-042-32/+39
| | | | | | | | | | | Code cleanup Description: Fix some warnings & formatting issues Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4
* [svn-r11993] Purpose:James Laird2006-03-011-22/+22
| | | | | | | | | | | | | | Added HL examples Description: Examples existed for the HL lite, image, and table interfaces, but were never included in the distro... until now! Solution: Added source files to CVS, updated Makefile and MANIFEST. Platforms tested: mir, heping, shanti
* [svn-r11991] Purpose:Albert Cheng2006-03-012-15/+7
| | | | | | | | | | | | | | | | | Porting. Description: Red Storm's lustre used srand and rand to initialize their user mode of lustre. HDF5 also uses srand and that messes up Lustre. Solution: Use -DRED_STORM to block out the HDF5 code that calls srand. This is a temporary fix since Lustre has fixed its code from calling srand and rand but the fix is not deployed at Red_storm yet. Platforms tested: Tested at Red-Storm.
* [svn-r11968] Purpose:Quincey Koziol2006-02-2713-3506/+3769
| | | | | | | | | | | | | | Incrementtal checkin Description: Revise & update v2 B-tree code to separate the internal package-specific routines from the library-callable "private" routines. Similar updates for the fractal heap code. Platforms tested: FreeBSD 4.11 (sleipnir) Mac OSX (amazon)
* [svn-r11967] Purpose:Quincey Koziol2006-02-2718-60/+1190
| | | | | | | | | | | | | | | New feature Description: Check in initial "fractal heap" code, for supporting the group redesign. Also, remove some remnants of the segmented heap/block tracker/B+tree code which I didn't find during the last pass. Platforms tested: FreeBSD 4.11 (sleipnir) Mac OSX (amazon) Linux 2.4
* [svn-r11966] Purpose:Quincey Koziol2006-02-279-458/+296
| | | | | | | | | | | | Code cleanup Description: Style fixes for consistency & other minor cleanups Platforms tested: FreeBSD 4.11 (sleipnir) Mac OSX (amazon) Linux 2.4
* [svn-r11965] Purpose:Quincey Koziol2006-02-2428-5011/+35
| | | | | | | | | | | | Maintenance Description: Remove half-built (half-baked? :-) implementation of B+tree, block tracker and segmented heaps. (In preparation for starting the new heap coding) Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 (heping)
* [svn-r11964] Purpose:MuQun Yang2006-02-231-6/+37
| | | | | | | | | | | | | | | | | | | | | | | | | | | bug fix Description: ret_value is not set to SUCCEED in H5D_mpio_select_write That causes the 64-bit intel compiler unhappy. It will give a non-zero number and cause the testing fake failure. Another one is picked up by cmpi again. For one optimization case, another variable is not initialized properly and compiler set an unhappy number, cause the test failed. Solution: Properly initialize those variables. Platforms tested: teragrid:parallel mir:parallel heping: parallel and sequential tungsten:parallel Misc. update: h5committest doesn't finish due to no space left on device. parallel tests still failed at tungsten with cmpi. It looks like it was a bug from cmpi.
* [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 Yang2006-02-213-20/+18
| | | | | | | | | | | | | | 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-r11955] MuQun Yang2006-02-171-1/+1
| | | | | | | | | | | | | | Purpose: Erase one printf line accidently inserted in the code. Description: Solution: Platforms tested: No need to test. Misc. update:
* [svn-r11952] Purpose:MuQun Yang2006-02-161-0/+3
| | | | | | | | | | | | Enhance the collective chunk IO support Description: Solution: Platforms tested: Misc. update:
* [svn-r11950] Purpose:MuQun Yang2006-02-164-468/+1701
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r11899] Purpose:Quincey Koziol2006-01-2816-72/+683
| | | | | | | | | | | | | | | | 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-r11897] Purpose:John Mainzer2006-01-276-165/+873
| | | | | | | | | | | | | | | | | | | | | | | | | | | | 1) Add parallel test for metadata cache 2) Split serial test for metadata cache into two parts 3) Fix bug in which cache was flushed needlessly when the cache wasn't full. 4) Performance improvements 5) Update API for parallel cache coherency bug fix. Description: See above. Solution: See above. Platforms tested: h5committest Misc. update:
* [svn-r11886] Purpose:Quincey Koziol2006-01-237-21/+14
| | | | | | | | | | | | | Code cleanup Description: Check in some of the code cleanups from working on the external link support. (This doesn't include any of the external link features) Platforms tested: FreeBSD 4.11 (sleipnir) Mac OSX.4 (amazon) Linux 2.4
* [svn-r11884] Snapshot version 1.7 release 57HDF Admin2006-01-222-3/+3
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* [svn-r11880] Snapshot version 1.7 release 56HDF Admin2006-01-152-3/+3
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* [svn-r11864] Purpose:James Laird2006-01-051-3/+3
| | | | | | | | | | | | | | | | Cleaned up reconfigure output Description: Added two lines to separate output from trace script from autotools output in reconfigure. Solution: Running reconfigure updated src/Makefile.in as a side effect, since I changed config/lt_vers.am in my last checkin but forgot to run reconfigure then. Platforms tested: mir (cosmetic change to reconfigure script only)
* [svn-r11854] Purpose:James Laird2006-01-021-0/+100
| | | | | | | Bug fix Description: Forgot to 'cvs add' H5Pacpl.c!
* [svn-r11852] Purpose:Quincey Koziol2006-01-022-35/+35
| | | | | | | | | | | Code cleanup/update Description: Update compiler flags for gcc 4.1.x & start cleaning up some of the C++ compatibility Platforms tested: FreeBSD 4.11 (sleipnir) w/gcc 4.1 and/or g++
* [svn-r11850] Purpose:James Laird2006-01-0210-45/+222
| | | | | | | | | | | | | | Feature Description: Added character encoding and attribute creation property lists. Solution: Attributes' character encoding is set via the ACPL. The default is ASCII, with UTF-8 being the other option currently. Platforms tested: heping, mir, sleipnir, copper
* [svn-r11848] Snapshot version 1.7 release 55HDF Admin2006-01-012-3/+3
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* [svn-r11838] Purpose:Quincey Koziol2005-12-2623-690/+852
| | | | | | | | | | | | | | | | Bug fix Description: Retrieving an object's name could fail (in various ways) under certain circumstances (mostly having to do with mounted files). Solution: Re-write & simplify "get object name" code to fix error in a better way than adding yet another hack to the previous pile of hacks... :-) Platforms tested: FreeBSD 4.11 (sleipnir) h5committest
* [svn-r11836] Snapshot version 1.7 release 54HDF Admin2005-12-252-3/+3
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* [svn-r11795] Snapshot version 1.7 release 54HDF Admin2005-12-142-3/+3
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* [svn-r11785] Purpose:Albert Cheng2005-12-111-0/+15
| | | | | | | | | | | | Patch for red-storm. Description: A temporary patch for redstorm, must open a file in the same parallel data filesystem before H5_init_library. Otherwise, it hangs with error: (client.c:568:ptlrpc_check_status()) @@@ type == PTL_RPC_MSG_ERR, err == -114 req@0x57a9660 x1/t0 o38->mds_l2@MDS_PEER_UUID:12 lens 240/272 ref 1 fl Rpc:R/100000/0 rc 0/-114 Platforms tested: Red-storm.
* [svn-r11771] Purpose:Quincey Koziol2005-12-087-20/+24
| | | | | | | | | | | | Code cleanup Description: Fix a bunch of warnings flagged by Windows compilers. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11761] Purpose:Albert Cheng2005-12-052-3/+3
| | | | | | | | | | | | | Unstable format version marker. Description: This marks the Check in baseline for compact group revisions, which radically revises the source code for managing groups and object headers. Earlier versions (1.7.52 or earlier) have the original format. This version and later have the unstable format until further notice. Platforms tested: h5committested.
* [svn-r11758] Purpose:Quincey Koziol2005-12-0438-991/+1549
| | | | | | | | | | | | | 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-r11742] Purpose: Minor correction.Raymond Lu2005-11-181-2/+4
| | | | | | | | | Description: H5Eset_auto_stack() and H5Eset_auto() used FUNC_ENTER_API. It would clear the error stack from the previous API call. It's better to use FUNC_ENTER_API_NOCLEAR to avoid clearing the stack. Platforms tested: fuss - simple change.
* [svn-r11741] Purpose:James Laird2005-11-181-6/+16
| | | | | | | | | | | | | | | | | Bug fix Description: Fortran type generation was broken in two ways. Fixed both. Solution: Firstly, there were a couple of path problems. Fixed a typo and specified the full path of a file. Secondly, the dependencies weren't right when building with HDF5-specific commands (make lib, make check-s, etc.). Tweaked dependencies to fix the problem. Platforms tested: mir, modi4, sleipnir
* [svn-r11739] Purpose:MuQun Yang2005-11-182-30/+5
| | | | | | | | | | | | | | slight code change for efficiency of iteration of chunk address Description: Quincey picked this up because of my inexperience of C. A pair of redundant malloc and free calls will be removed. Solution: Platforms tested: heping(Linux 2.4) too little to be tested. Misc. update:
* [svn-r11738] Purpose:James Laird2005-11-1810-3/+85
| | | | | | | | | | | | | | | | | | | Configure feature Description: Added 'make trace' target. Solution: Added tracing to 1.7. This was done automatically in 1.6, but left out of 1.7 until now (oops!). Tracing in 1.7 only happens manually, when the user types 'make trace.' Tracing automatically requires more framework than it's worth. I also fixed a couple of tracing bugs and ran trace. Platforms tested: mir, sleipnir, modi4 Misc. update:
* [svn-r11737] Purpose:James Laird2005-11-171-0/+8
| | | | | | | | | | | | | | | | | | | | | | | | Bug fix Description: Before this checkin, 'gmake check-s' would fail if there was a file in the current directory named 'check-s'. This is fixed under gmake (not sure how to fix for other makes). Solution: check, progs, install, etc. are what gmake calls "phony" targets, which means that no file should be created. These targets can be specified by a line of the form .PHONY: check progs install ... Automake adds this line for targets it knows about, but HDF5 has a lot of custom rules. This checkin adds a .PHONY line for those rules. I believe that only gmake recognizes the .PHONY line (at least, pmake doesn't seem to), but a partial solution is better than none. This error should occur very rarely anyway (the user has to manually create files with names like 'build-check-s' or '_test'). Platforms tested: mir, sleipnir, modi4
* [svn-r11735] Purpose:Albert Cheng2005-11-162-118/+2
| | | | | | | | | | | | | | | | | | Cleanup. Description: Removed the home-made version of snprintf and vsnprintf since they do not actually enforce the size parameter correctly and could corrupt memory or as a security hole. This block of code has been turned off since Aug 11, 2005 for all platforms except Tflops. No one has reported any problem since--sort of empirical evidence that all platforms except Tflops support both functions. Tflops has retired in September. So, no need to keep this block of code. Also, fixed the HDxxx macro to call the corresponding xxx function. Platforms tested: Tested in heping, both serial and parallel.
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