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* [svn-r12374] Purpose:John Mainzer2006-05-245-5/+289
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 1) Check in potential fix to unreproduceable bug in t_cache observed on Cobalt 2) Check in code supporting added pinned entry features in the metadata cache. Description: 1) Elena encountered a bug in t_cache when running on Cobalt. On investigation I found a potential race condition in t_cache that could explain her observation. 2) Quincey requested additions to the metadata cache allowing renaming of pinned entryies, and marking of pinned or protected entries as dirty. Solution: 1) Modified t_cache.c to prevent the potential race condition. Elena was unable to reproduce the bug on Cobalt, so we don't know if my fix actually addressed the problem. 2) Added code supporting the requested functions. The changes were relatively trivial, but required substantial new test code. Platforms tested: h5committest, serial test on heping, parallel test on phoenix. Misc. update:
* [svn-r12372] Purpose:James Laird2006-05-232-0/+5
| | | | | | | | | | | Makefile cleanup Description: Cleaned up where files were distcleaned Platforms tested: mir (change only affects distclean)
* [svn-r12365] Purpose:Quincey Koziol2006-05-234-9/+9
| | | | | | | | | | | Code checkpoint Description: Add a few minor tweaks & corrections to the fractal heap code. Platforms tested: Linux 2.4 (chicago) Too minor to require h5committest
* [svn-r12364] Purpose:Quincey Koziol2006-05-231-2/+2
| | | | | | | | | | | Portability fix Description: Try again to placate the VS 6.0 compiler Platforms tested: Linux 2.4 (chicago) Too minor to require h5committest
* [svn-r12363] Purpose:Quincey Koziol2006-05-231-2/+2
| | | | | | | | | | | | | Bug fix Description: When destroying the cache for a file, don't disconnect the cache from the file structure until after the cache is shut dow, to allow pinned entries to be unpinned. Platforms tested: Linux 2.4 (chicago) Too minor to require h5committest
* [svn-r12362] Purpose:Quincey Koziol2006-05-2221-525/+2036
| | | | | | | | | | | | | | | | | | | | | Code checkpoint Description: Update fractal heap code to allow objects to be deleted Fix bugs in fractal heap object insertion Improve free space manager code to allow sections to be merged and shrink the container Another try at making the Windows compilers happy... Platforms tested: FreeBSD 4.11 (sleipnir) Mac OS X.4/PPC (amazon) Linux 2.4 (chicago & heping) Solaris 2.9 (shanti) AIX 5.? (copper) w/parallel
* [svn-r12358] Purpose:Albert Cheng2006-05-191-24/+23
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug fix. Description: The ${TR}, though avoid the error, is inconvenient. It is needed because configure.in use the char range in the style of 'a-z'. The other style of '[a-z]' is more commonly accepted by all tr but autoconf tends to strip away [], making the syntax rather clumsy. Solution: Learned from autoconf that it avoids the use of character range by just spell all the letters out. Changed our tr commands to use those variables defined by autoconf. Also removed the definition of ${TR} since it will cause inconsistancy when autoconf also use plain 'tr' in its generated code. The Makefile.in are changed because the elimination of ${TR} from configure triggered its removal from all Makefil.in. That is okay because ${TR} is not used at all in Makefile. Platforms tested: h5committested. (sol failed to connected). also tested in shanti using both /usr/ucb/tr and /bin/tr (the bad one before.) Misc. update: Updated both INSTALL and RELEASE files.
* [svn-r12355] Purpose:Quincey Koziol2006-05-181-3/+3
| | | | | | | | | | Bug fix Description: Avoid using double -> hsize_t conversion, to placate VS 6.0 Platforms tested: None, just eyeballed...
* [svn-r12349] Purpose:Quincey Koziol2006-05-1535-2118/+4773
| | | | | | | | | | | | | | | Code checkpoint Description: Checkpoint fractal heap improvements, as well as move the free space manager code that it's using into a separate package. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4/64 (mir) w/C++ & FORTRAN Linux 2.4/32 (heping) Solaris 2.9 (shanti) AIX 5.? (copper) w/FORTRAN & parallel
* [svn-r12348] Purpose:Albert Cheng2006-05-142-13/+11
| | | | | | | | | | | | | | | | | | Bug fix. Description: Some machines (e.g., HPUX) will have off64_t defined but no support for stat64 unless certain LargeFile macro is turned on. This caused the last fix on H5private not quite right which caused compiling failures. Solution: Added stat64 and fstat64 tests and then will use them only if they are supported. Platforms tested: Tested on kelgia, copper and heping (pll). (Compiling alright but tests for kelgia and heping are not done. expect no problems.)
* [svn-r12345] Purpose: Codes for backward compatibility.Raymond Lu2006-05-124-32/+216
| | | | | | | | | | Description: Function prototype H5E_walk_t and structure H5E_error_t wasn't backward compatible. Solution: Make them compatible with v1.6 and provide new definitions of H5E_walk_stack_t and H5E_error_stack_t. Platforms tested: fuss and h5committest.
* [svn-r12343] Purpose:MuQun Yang2006-05-111-16/+48
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug fix for collective chunk IO Description: Several options have been provided inside HDF5 library for obtaining chunk addresses when doing collective chunk IO. One option is to obtain chunk addresses for one process and broadcast to other processes. This option needs all processes to participate. If using link-chunked IO without any optimizations, sometimes this is not true due to the random initialization for one variable at mpich 1.2.7. This is a bug inside the collective chunk IO code. Solution: 1.Initalize all the variables to some safe numbers, 2. Avoid using MPI broadcast to obtain the chunk address if possible until more performance studies have been done. 3. Seems okay to obtain chunk addresses individually for each processor. This option may cover most cases. Platforms tested: h5committest(copper is not usable) NCSA teragrid (mpich 1.2.5) mir 64-bit linux (mpich 1.2.6) Misc. update:
* [svn-r12342] Purpose:Albert Cheng2006-05-102-29/+32
| | | | | | | | | | | | | | | | | | | | | | | | | | | bug fix. Description: Previous H5private.h would attempt to use the off64_t/stat64/etc by checking just sizeof __INT64 being 8. This caused errors in some machines like alpha cluster which is a 64bit machine. Its compiler supports the type __int64 but it does not support off64_t since its off_t is already 64bits big. The above code casued the compiler to complain about the unknown off64_t and such. Solution: H5private.h: Changed the code to use the pseudo standard of off64_t/stat64/etc only if sizeof(off_t) is not 64 bits AND sizeof(off64_t) exists and is 64 bits. This assumes if off64_t is defined, all those stat64, fstat64, etc are supported too. configure.in: configure: Added the testing of sizeof(off64_t) to support the above solution. Platforms tested: h5committested. Also tested at LANL QSC.
* [svn-r12339] Purpose: Maintenance after hdf5-1.8.0-alpha2 releaseElena Pourmal2006-05-061-2/+2
| | | | | | | | | | Description: Changed version suffix to alpha3 Solution: ran bin/h5vers script Platforms tested: Misc. update:
* [svn-r12320] Purpose:Quincey Koziol2006-05-0210-110/+114
| | | | | | | | | | code cleanup Description: Finish H5FS->H5CS internal API name changes... Platforms tested: FreeBSD 4.11 (sleipnir) w/ & w/o --enable-codestack
* [svn-r12319] Quincey Koziol2006-05-022-364/+0
| | | | | | | | | | | | Purpose: Rename feature Description: Rename the "function stack" debugging feature to "call stack", so the H5FS* prefix can be used for free space management code. Platforms tested: Not yet, but soon..
* [svn-r12317] Purpose:Quincey Koziol2006-04-3016-1118/+2684
| | | | | | | | | | | | | | | | Code checkpoint Description: More progress on fractal heap, can now re-open an existing heap, although the free space algorithm still needs work. Also, use the new "pinned entry" metadata cache code. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 (heping) Solaris 9 (shanti) Linux 2.4/64 (mir)
* [svn-r12316] Purpose:Quincey Koziol2006-04-292-13/+17
| | | | | | | | | | | | | | | Code cleanup/feature twist Description: Adjust recent H5AC routines to take H5F_t pointers instead of H5C_t pointers, to match the rest of the H5AC routines. This change propagated into a few of the tests, which also had some compiler warnings cleaned up... Platforms tested: FreeBSD 4.11 (sleipnir) w/parallel Linux 2.4/64 (mir) w/C++ & FORTRAN
* [svn-r12313] Purpose:Quincey Koziol2006-04-292-2/+3
| | | | | | | | | | | Code cleanup Description: Clean up a few minor compiler warnings Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4/64 (mir)
* [svn-r12311] Purpose:John Mainzer2006-04-2811-642/+2060
| | | | | | | | | | | | | | | | | | | | | | | | | Add pinned entry capability to cache. Description: For frequently accessed cache entries, the protect/unprotect overhead is sometimes a bottleneck. Solution: Allow entries to be pinned in the cache. Pinned entries can't be evicted, but can be flushed or modified. Platforms tested: h5committested -- minus one small typo in test/cache.c whose fix was tested on copper and heping only. Misc. update:
* [svn-r12295] Purpose:James Laird2006-04-211-3/+3
| | | | | | | | | | | | | | | | | | | Several bug fixes Description: Added config file for Cray X1 (previous file was misnamed) Simplified some code in hyperslab.c test that seemed to have been confusing compiler on Cray X1. Fixed typo in config/commence.am Cleaned up hl/src/Makefile.am Solution: All four fixes should be straightforward. The failure on Cray was very difficult to debug, but involved arithmetic errors. This change seems to fix it. Platforms tested: heping, copper, sol, some Cray X1 (more testing when system comes back up)
* [svn-r12293] Purpose:Quincey Koziol2006-04-215-1/+11
| | | | | | | | | | Bug fix Description: Fix missing error code from flexible parallel removal Platforms tested: IBM AIX (copper) w/parallel
* [svn-r12292] Purpose:Quincey Koziol2006-04-2027-6515/+87
| | | | | | | | | | | | | Code maintenance Description: Remove flexible parallel code Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 (heping) Solaris 2.9 (shanti) Linux 2.4/64 (mir)
* [svn-r12289] updated version to 1.8.0-alpha2before_removing_fphdf5Albert Cheng2006-04-201-2/+2
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* [svn-r12286] Purpose: Fix bugBinh-Minh Ribler2006-04-201-3/+13
| | | | | | | | | | | | | | | | | Description: The file size test in C++ library failed on Copper because the value returned by h5_get_file_size was intepreted incorrectly due to different interger sizes. Solution: H5private.h: Added check to use stat64 and off64_t where appropriate. h5test.c and h5test.h: used h5_stat_size_t in place of off_t. tattr.cpp: used h5_stat_size_t in place of off_t. Platforms tested: Linux 2.4 (heping) AIX 5.1 (copper) SunOS 5.8 64-bit (sol) - still on going
* [svn-r12283] Purpose:Albert Cheng2006-04-201-8/+0
| | | | | | | | | | Rearragement. Description: Created general HL library header file and moved HL public headers to it. Platforms tested: h5committested.
* [svn-r12278] Purpose: Maintenance after alpha0 releaseElena Pourmal2006-04-181-2/+2
| | | | | | | | | | Description: Ran bin/h5vers script to change version number to 1.8.0-alpha1 Solution: Platforms tested: heping Misc. update:
* [svn-r12276] Purpose: Maintenance/typo fix/1.8.0-alpha0 releaseElena Pourmal2006-04-183-37/+30
| | | | | | | | | | | | | | | | | | | | | | Description: Here is what I did: modified MANIFEST according Quincey's instructions to fix the problem exposed by bin/release (compilation fails because some header files were not included in the distribution) fixed small typo and modified include_HEADERS line in src/Makefile.am to address the problem exposed by bin/release ran bin/h5vers to change version number to 1.8.0-alpha0 ran bin/release to release tar ball to the ftp server Solution: Platforms tested: mir MANY,MANY,MANY times Misc. update:
* [svn-r12261] Purpose:Albert Cheng2006-04-161-15/+16
| | | | | | | | | | | | Improvement Description: Modified the warning messages from the Version mismatch checking to suggest the users to try recompiling or checking the shared lib setting. Platforms tested: Tested in heping only since it was just a simple text string changes. (I did moved the strings around a bit.)
* [svn-r12259] Purpose:Quincey Koziol2006-04-151-0/+2
| | | | | | | | | | | | | Code checkpoint Description: Add more regression tests for odd insertion patterns Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 (heping) Linux 2.4/64 (mir) Solaris 2.9 (shanti)
* [svn-r12258] Purpose:Quincey Koziol2006-04-1516-2070/+2968
| | | | | | | | | | | | | | | | | | | Code checkpoint Description: Add in more fractal heap support for odd allocation patterns (entries that are too large for various block sizes, etc.) Broke out fractal heap code into more source code modules. Refactored fractal heap test to make it more understandable and maintainable for the long term. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 (heping) Linux 2.4/64 (mir) Solaris 2.9 (shanti)
* [svn-r12254] Purpose:Quincey Koziol2006-04-143-27/+44
| | | | | | | | | | | | | | Anti-feature Description: Revert changes to H5G_stat_t struct, to make it compatible with the 1.6.x branch again. The information that was added to the H5G_stat_t struct will be reported through other API routines. Platforms tested: FreeBSD 4.11 (sleipnir) w/C++ Linux 2.4/64 (mir) w/C++ & Fortran Solaris 2.9 (shanti)
* [svn-r12229] Purpose:Pedro Vicente Nunes2006-04-124-0/+15
| | | | | | | | | | | | | | | | | | | | | new feature Description: 1) separated the HL library into "public" and "private" header files, with the same caracteristics as the basic library 2) added the public headers to hdf5.h (with a conditional include macro, defined in configure.in) 3) added the path to HL in all Makefile.am 's , because of the inclusion in hdf5.h Solution: Platforms tested: linux 32, 64 AIX solaris with fortran and c++ (one packet table example fails) Misc. update:
* [svn-r12221] Purpose:Quincey Koziol2006-04-1024-16/+237
| | | | | | | | | | | | | | | "Hide" file format changes (for now) Description: Add ifdef's (controlled by the --enable-group-revision configure flag) to disable group revision changes to the file format, in order to allow alpha release to go ahead without releasing an unsupported version into the wild. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 32-bit (heping) Linux 2.4 64-bit (mir) Solaris 2.9 (shanti)
* [svn-r12219] Purpose:Quincey Koziol2006-04-101-3/+0
| | | | | | | | | | | | | Code cleanup Description: Don't include empty public header files. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 32-bit (heping) Linux 2.4 64-bit (mir) Solaris 2.9 (shanti)
* [svn-r12218] Purpose:Quincey Koziol2006-04-104-28/+1
| | | | | | | | | | | | | 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-r12191] Purpose:Quincey Koziol2006-04-023-8/+10
| | | | | | | | | | | | | Bug fix Description: Correct the handling of the group creation property list when copying objects with the "create intermediate groups" flag. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest (once I pay attention to the compiler warnings... :-)
* [svn-r12190] Purpose:Quincey Koziol2006-04-011-8/+19
| | | | | | | | | | | | Code checkpoint Description: Update fractal heap code to allow skipping direct blocks (that are too small to hold object) when the root indirect block is created. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r12189] Purpose:Quincey Koziol2006-04-0124-135/+478
| | | | | | | | | | | | | | 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-r12184] Purpose:Quincey Koziol2006-03-312-31/+378
| | | | | | | | | | | | | | | Code checkpoint Description: Checkpoint recent additions to fractal heap code, which allow for better support of objects that don't fit into current direct block, requiring skipped direct blocks to be tracked in free section list. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 (chicago & heping) Linux 2.4 (mir) w/64-bit & FORTRAN & C++ Mac OSX (amazon)
* [svn-r12173] Purpose:MuQun Yang2006-03-292-1/+101
| | | | | | | | | | | | | | | | | | | | | | | | | | | Adding parallel tests for optional collective chunk APIs Description: Three new APIs "H5Pset_dxpl_mpio_chunk_opt_ratio H5Pset_dxpl_mpio_chunk_opt_num H5Pset_dxpl_mpio_chunk_opt" for optional optimization choices from users have been added to the libraries. This check-in adds six tests to verify the funcationality and correctedness of these APIs. These tests need to be verified with 3 or more processors and with MPI-IO driver only. Solution: Using H5Pinsert, H5Pget, H5Pset to verify that the library indeed goes into the branch we hope for. Using H5_HAVE_INSTRUMENT macro to isolate these changes so that it won't affect or be misused by the application. Platforms tested: h5committest(shanti still refused to be connected) Parallel tests on heping somehow are skipped. Manually testing at heping. Have checked 1,2,3,4,5 processes. Misc. update:
* [svn-r12162] Purpose:Quincey Koziol2006-03-286-93/+206
| | | | | | | | | | | | Code checkpoint Description: Check in fractal heap code to add basic support for skipping direct blocks when an object is too large to fit in one. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 (chicago)
* [svn-r12161] Purpose:Quincey Koziol2006-03-278-790/+1020
| | | | | | | | | | | | | | | | Code checkpoint Description: Checkpoint fractal heap code at a stable point in development. It appears that adding objects to heaps and reading them back out is now working properly (as long as there are no gaps in the heap and no standalone objects are created). Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 (chicago) Linux 2.4 (mir) w/64-bit & FORTRAN & C++ Solaris 9 (shanti) w/64-bit
* [svn-r12155] Purpose:Quincey Koziol2006-03-261-58/+63
| | | | | | | | | | | Code optimization Description: Tweak file free space allocation routines to optimize them a bit. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r12149] Purpose:James Laird2006-03-231-7/+1
| | | | | | | | | | | | | | | | Bug fix Description: Previous checkin did a bad thing; 'make clean' failed in example directories. Solution: Fixed commence.am so that examples no longer break, and fixed a mistake in conclude.am. Platforms tested: heping (minor makefile change) Misc. update:
* [svn-r12143] Purpose:James Laird2006-03-231-0/+4
| | | | | | | | | | | | | | Bug fix Description: make check-clean didn't clean results of example tests Solution: Fixed Makefiles so that check-clean recurses into example directories. Also a little Makefile cleanup. Platforms tested: mir, modi4, heping, copper
* [svn-r12139] Purpose:MuQun Yang2006-03-231-0/+2
| | | | | | | | | | | | | | | | | | | | | | | | | portibility issue to windows Description: setvbuf on visual studio 2005 needs the size to be greater or equal to 2. <description of setvbuf from msdn library> Buffer size in bytes. Allowable range: 2 <= size <= INT_MAX (2147483647). Internally, the value supplied for size is rounded down to the nearest multiple of 2. h5import used linebuffer option of setvbuf for stderr and stdout and the size is 0 by default. This causes core dump with visual 2005 on windows 64-bit. Solution: 1. Use HDsetvbuf inside h5import.c, 2. Define HDsetvbuf inside windows H5pubconf.h for windows to work around the core dump of h5import test. This is probably a bug inside visual studio 2005. Platforms tested: h5committest windows 6.0 at XP visual 2005 at XP-64bit Misc. update:
* [svn-r12138] Purpose: VMS portElena Pourmal2006-03-222-1/+38
| | | | | | | | | | | | | | Description: Unix remove function removes only the latest version of a file on VMS. Some of our tests create multiple versions of the testfiles and as a result, test programs may be confused, give false negative result, etc. Solution: Created HDremove_all function for VMS that removes all versions of the files. HDremove on VMS is an alias to HDremove_all. Platforms tested: VMS server and heping (to check that nothing is borken on UNIX side) Misc. update:
* [svn-r12133] Purpose:Quincey Koziol2006-03-222-13/+14
| | | | | | | | | | | Code cleanup Description: Update a couple of files that bin/reconfigure rearranged for me... :-) Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r12132] Purpose:Quincey Koziol2006-03-221-1/+3
| | | | | | | | | | | | | Code cleanup Description: Add H5E header to this header, to make certain that the errors in the "inline" routines are handled correctly. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 (chicago) Mac OSX (amazon)
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