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* [svn-r9857] Purpose: MaintenanceElena Pourmal2005-01-22112-342/+2
| | | | | | | | | | | | | | 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-r9854] Purpose:Xiaowen Wu2005-01-211-243/+866
| | | | | | | | | | | | | | | | | | For N-bit filter, Adding parameter mappings from HDF5 compound datatype, array datatype and atomic datatype to cd_values inside HDF5 library. N-bit filter should work with these datatypes(string and variable length datatype haven't been considered) in the near future. Description: This is for debugging purpose, N-bit filter won't be tested in the daily test. Solution: Platforms tested: AIX 5.1 and Linux 2.4. Arabica is too slow. Hopefully shanti can be used soon. Misc. update:
* [svn-r9850] Purpose:John Mainzer2005-01-2010-135/+384
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 1) Provide facilities in cache to allow us to avoid a potential cache consistency bug in the parallel case. 2) Clean up a off by one sanity checking bug. 3) Turn off execution of long running tests in debug mode. Description: 1) In the parallel case, all writes to metadata must be collective, but reads may not be. In pricipal, this allows us to different contents in different caches. This isn't a problem as long as the correct data is always on disk, but unless we can force certain writes immediately, that need not be the case. 2) & 3) should need no further explanation. Solution: 1) Add code allowing us to mark cache entries, and then force these entries to be flushed at a later time. Note that to actually avoid the bug, we will have to modify existing code to use these new features. 2) & 3) should need no further explanation. Platforms tested: heping (serial debug and production) committest (copper, sol, and heping). test failed on heping in the c++ portion of the build, but at Quincey's siggestion, I am proceeding with the checkin. Misc. update:
* [svn-r9849] Purpose: New test and a few bug fixRaymond Lu2005-01-201-2/+2
| | | | | | | | | Description: Test conversion from native integer to derived floating-point type and convert back; test conversion from derived floating-point to derived floating-point types and convert back. Fixed a few minor bugs related to type conversion in the library. Platforms tested: h5committest and fuss
* [svn-r9840] Purpose: Bug fix and new testRaymond Lu2005-01-202-6/+6
| | | | | | | | | | | | | Description: The functions for user-define floating-point type, like H5Tset_fields, H5Tset_offset, H5Tset_precision, H5Tset_size, have some minor bugs. For error checking, the library didn't include offset value somehow. Solution: Corrected those bugs. Platforms tested: h5committest and fuss Misc. update:
* [svn-r9838] Purpose:Quincey Koziol2005-01-191-3/+0
| | | | | | | | | | | | | | | | | | Bug fix Description: Correctly retire the H5E_LEN setting, now that the FORTRAN and C++ APIs have been corrected to not use it either. Solution: Pass in the string buffer length for FORTRAN In the C++ API, call H5Eget_msg() in a manner similar to the way H5Fget_name() is called. Platforms tested: Linux 2.4 (heping) w/FORTRAN & C++ Solaris 2.7 (arabica) w/FORTRAN & C++
* [svn-r9837] Purpose:Quincey Koziol2005-01-191-0/+7
| | | | | | | | | | | | | | | Bug fix Description: Calling HDvsnprintf() several times (should be twice) is incorrect without calling va_end() and va_start() again. Solution: Call va_end() and va_start() before calling HDvsnprintf() again. Platforms tested: Linux 2.4/x86_64 (mir) Too minor to require h5committest
* [svn-r9830] Purpose:Albert Cheng2005-01-171-0/+3
| | | | | | | | | | | | | | | | | | Bug fix Description: Fortran and C++ API failed to compile because they need to use H5E_LEN which was removed. Solution: Restored the H5E_LEN definition. A permenant solution is still needed. Platforms tested: H5committested. (heping, sol, and copper all compiled fine again but sol had an error in testerror.sh which seemed to be a different problem. Also tested in tg-NSCA.
* [svn-r9826] Purpose: Bug fixRaymond Lu2005-01-141-0/+4
| | | | | | | | | | Description: Intel compiler on Linux has some problem to convert long double to unsigned int correctly. Solution: Detect the problem in configure and define a macro to skip this test if it happens. Platforms tested: eirene and fuss. Simple change.
* [svn-r9825] Purpose:Quincey Koziol2005-01-142-6/+21
| | | | | | | | | | | | Bug fix Description: Fix possible overrun in error description string by allocating large enough string on the fly. Platforms tested: FreeBSD 4.10 (sleipnir) Too minor to require h5committest
* [svn-r9816] Purpose:Albert Cheng2005-01-121-48/+48
| | | | | | | | | | | | | | | | | | | | | | | | | | | cleanup warning messages. Description: Compilers complained about local variable shadowed global variables. The global variables d[], m[], nd, na were having the same names as local function arguments. This was a left over when I broke the original one big chunk of code into separated functions to go around the Intel Compiler optimization error. Solution: Appended the global variables with suffix _g, thus d[] => d_g[] m[] => m_g[] nd => nd_g na => na_g This is only an intermediate step. After the changes tested out fine by all machines, need to rename the variables to more meaningful names like dtype_array. Platforms tested: Tested in heping by saving the previous generated H5Tinit.c, regenerated a new H5Tinit.c with the changed code, finally compared the new and old versions were identical.
* [svn-r9807] Purpose: bug fixRaymond Lu2005-01-111-0/+4
| | | | | | | | | | | Description: For FreeBSD (sleipnir), when GNU compilers do conversion from unsigned long long to long double, the last 2 bytes of mantissa are lost. The impact of precision loss isn't significant. Solution: Detect this case on FreeBSD in configure, ignore it in dtypes.c test instead of return failure. Platforms tested: sleipnir, fuss, modi4. These systems are mainly concerned.
* [svn-r9805] Purpose:Quincey Koziol2005-01-111-4/+0
| | | | | | | | | | Code cleanup Description: Remove obsolete support for Watcom C compiler. Platforms tested: None - too minor to require any.
* [svn-r9783] Purpose: Bug fixRaymond Lu2005-01-081-3/+7
| | | | | | | | | | Description: For HP-UX 11.00, the compiler generates 'floating exception' when converting 'long double' to most of integer types. Solution: Define a macro for all other systems except HP-UX 11.00. Hard set this macro to 'no' in config/hpux11.00 to skip this test for HP-UX 11.00. Platforms tested: modi4, kelgia, fuss
* [svn-r9782] Purpose:Xiaowen Wu2005-01-081-22/+22
| | | | | | | | | | Description: Solution: Platforms tested: Misc. update:
* [svn-r9780] Purpose:Quincey Koziol2005-01-081-1/+1
| | | | | | | | | | | | Bug fix Description: Print the thread ID in a little more portable of a fashion, disallowing negative thread IDs. Platforms tested: Linux 2.4 (heping) w/threadsafe Too Minor to require h5committest
* [svn-r9778] Purpose:Quincey Koziol2005-01-085-1968/+221
| | | | | | | | | | | | | | | Remove feature Description: Retire threaded, balanced binary tree code from HDF5 use. Requiescat in pace... Also, regenerate dependencies files. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Too minor to require full h5committesting (the code is already disconnected from everything except its tests)
* [svn-r9767] Purpose: Bug fixRaymond Lu2005-01-061-0/+4
| | | | | | | | | Description: 2 small things to correct: 1. the change in H5config.h.in was wept out by a later change. 2. long long isn't supported on Windows. It's long_long instead. Platforms tested: fuss(linux 2.4)
* [svn-r9766] Purpose:Quincey Koziol2005-01-063-510/+330
| | | | | | | | | | | | | | Code cleanup Description: Transition FPHDF5 to use skip lists for various internal data structures, instead of threaded, balanced binary trees. Also, simplify some of FPHDF5 code some, etc. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel & fphdf5 Too minor to require h5committest
* [svn-r9764] Purpose:Quincey Koziol2005-01-063-161/+709
| | | | | | | | | | | | | | | | New feature Description: Add some additional features to the skip list code that was needed to fully support all the features that the threaded, balanced binary tree code has. Also, updated the property list code to take advantage of a few of the new features. Platforms tested: FreeBSD 4.10 (sleipnir) Too minor to require h5committest
* [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-r9761] Purpose:Albert Cheng2005-01-062-0/+2
| | | | | | | | | | | | | | | | Bug fix. Description: threadsafe test (ttsafe) would seg-fault if --disable-production --enable-debug mode is used. Reason was that the fstack.nused field was not initialized when created. Solution: Init new fstack.nused with 0. Platforms tested: Tested in mir, using development/debug mode. Did not "h5committested" as change is trivial and limited to threadsafe mode.
* [svn-r9759] Purpose:MuQun Yang2005-01-061-0/+545
| | | | | | | | | | | | | | | To add n-bit implementation inside HDF5. Description: This check-in for implementation is for debugging purpose. N-bit filter should be used for the time being. Solution: Platforms tested: sol 2.7, Linux 2.4, Aix 5.1 Misc. update:
* [svn-r9758] Purpose:MuQun Yang2005-01-069-9/+73
| | | | | | | | | | | | | | | | | Adding framework of N-bit filter Description: N-bit filter is required for NetCDF project. To add N-bit filter, configure.in configure, Makefile.in under src and other filter-related source code needs to be updated. Currently, N-bit tests are turned off from the library. So the change will affect daily test. Solution: Platforms tested: sol 2.7, linux 2.4, aix 5.1 Misc. update:
* [svn-r9755] Purpose: New featureRaymond Lu2005-01-062-29/+29
| | | | | | | | | | | | | Description: Start to support software conversion between long double and all integers. Solution: No major changes to the algorithm. Changes to configure is to exclude SGI for long double to integers test because there're too many problems in their compiler. Platforms tested: h5committest, modi4, fuss, Teragrid, arabica Misc. update: RELEASE.txt
* [svn-r9745] Purpose:Xuan Bai2005-01-051-0/+4
| | | | | | | | | | | | | | | | | | | | | | | | | Bug fix. Description: When building H5Z.c with Visual C++ 6.0, I got the following warning message: H5Z.c(1241) : warning C4013: 'SZ_encoder_enabled' undefined; assuming extern returning int Solution: The header file szlib.h should be included in H5Z.c in order to use SZ_encoder_enabled() function. Add the following script into H5Z.c: #ifdef H5_HAVE_SZLIB_H # include "szlib.h" #endif Platforms tested: Heping (Linux) Visual C++ 6.0 on Windows XP/2000. .NET on Windows XP. (Tested with SZIP-with-encoder and SZIP-without-encoder). Misc. update:
* [svn-r9734] Purpose:Quincey Koziol2004-12-304-119/+126
| | | | | | | | | | | | 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-r9730] Purpose:Quincey Koziol2004-12-304-338/+332
| | | | | | | | | | | | | Code cleanup (sorta) Description: Transition the generic property list code from using the threaded, balanced binary tree code (H5TB<foo>() routines) to use skip lists (H5SL<foo>() routines) for internal management of properties, etc. Platforms tested: FreeBSD 4.10 (sleipnir) Too minor to require h5committest
* [svn-r9727] Purpose:Quincey Koziol2004-12-29100-2310/+2158
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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-r9723] Purpose:before_signed_unsigned_changesQuincey Koziol2004-12-292-0/+63
| | | | | | | Add new file Description: Add new PC-Lint/Flexelint configuration files
* [svn-r9700] Purpose:John Mainzer2004-12-221-1/+25
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Fix a bug in the cache caused by a slightly over active sanity check. Description: When the #define H5C_DO_SANITY_CHECKS is TRUE, the macro H5C__DLL_PRE_INSERT_SC is executed prior to inserting an entry in the LRU list. The macro performs a variety of sanity checks, and flags an error if any of the checks fail. Prior to this update, the macro used to check to see if the target list had length 1 and size <= 0. The new epoch marker entries used in the age out cache size reduction algorithm have size zero -- making it possible for this sanity check to fail incorrectly. Note that cache sanity checks are disabled in the CVS version of the code, so this bug and bug fix should be invisible unless you are working with the cache, and turn the sanity checks on. Solution: Removed the offending clause in H5C__DLL_PRE_INSERT_SC. Since the size used in the macro is typically a size_t and thus cannot have negative value, there was no point in changing it to "size < 0". Platforms tested: Ran a serial test on heping. Under the circumstances, I didn't feel the need for further testing. Misc. update:
* [svn-r9687] Purpose:John Mainzer2004-12-185-750/+3525
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Modify the cache code (H5C) to support automatic cache resizing to adapt to the work load at run time. Description: Different applications require different sized caches to maintain an acceptable hit rate. This set of changes attempts to provide the ability to adjust to circumstances automatically. Solution: Added highly configurable code to allow the user to either set a fixed cache size, or allow the cache to grow and shrink according to conditions. If enabled, cache size increases are triggered when the hit rate drops below a user specified threshold in a user specified interval. Cache size reductions (if enabled) are triggered when either the hit rate exceeds some user specified threshold over a user specified interval, when the cache contains "enough" entries that haven't been accessed for a user specified interval, or some mix of the above. See the header comments on the H5C_auto_size_ctl_t structure in H5Cprivate.h for further details. At present, the cache resize configuration options are not accessible via the user API. Must add this. Platforms tested: h5committested, heping (serial), and copper (parallel) 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-r9655] Snapshot version 1.7 release 44HDF Admin2004-12-125-625/+625
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* [svn-r9654] Purpose:Raymond Lu2004-12-103-3/+6
| | | | | | | | | | | | | Description: In file H5FDsec2.c and H5FDlog.c, there's statements like H5_ASSIGN_OVERFLOW(file->eof,sb.st_size,off_t,haddr_t); It assumes sb.st_size from h5_stat_t is of type off_t. But on Windows, it has type __int64. So the H5_ASSIGN_OVERFLOW statement may cause problem. Instead of trying to do switch between Windows and other systems in H5FDsec2.c and H5FDlog.c, define a substituting type in H5private.h to fix the problem. On Windows, this type is __int64; on other systems, it is off_t. Platforms tested: fuss. Simple fix. Already did h5committest for v1.6.
* [svn-r9648] Purpose:MuQun Yang2004-12-081-0/+3
| | | | | | | | | | | | | | | | | | | bug fix Description: The irregular hyperslab span_tree implementation inside H5S_hyper_add_span_element_helper updating the high bound of the span, but forget updating the number of element of the span. New routine obtain_derived_datatype catches the bug. Solution: Updating the number of element of the span as well. Platforms tested: Linux 2.4 and AIX 5.1, both with parallel enabled. Misc. update:
* [svn-r9617] Snapshot version 1.7 release 43HDF Admin2004-12-051-2/+2
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* [svn-r9615] Purpose:Quincey Koziol2004-12-042-1/+67
| | | | | | | | | | | New feature Description: Add callback iteration routine to skip lists. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r9601] Purpose:Quincey Koziol2004-11-302-17/+46
| | | | | | | | | | | New feature Description: Allow skip list keys to be strings (needed for property list support) Platforms tested: FreeBSD 4.10 (sleipnir) Too minor to require h5committest
* [svn-r9598] Purpose:Quincey Koziol2004-11-293-16/+60
| | | | | | | | | | | | | New internal feature Description: Add a "release" routine to the skip lists, which releases all the nodes in the skip list, but keeps the skip list active. Platforms tested: FreeBSD 4.10 (sleipnir) Linux 2.4 (verbena) Too minor to require h5committest
* [svn-r9596] Purpose:Quincey Koziol2004-11-294-218/+165
| | | | | | | | | | | | | Code optimization Description: Retarget metadata cache code from using TBBT routines to using new skiplist routines, for a reasonable speedup (when dealing with dirty metadata) Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) Too minor to require h5committest
* [svn-r9592] Purpose:Quincey Koziol2004-11-291-2/+3
| | | | | | | | | | | | | | | | | Bug fix Description: Re-work array of 'forward' pointers in a way that makes the PGI compiler more happy. Solution: Change from 'H5SL_node_t *forward[1]' to 'H5SL_node_t **forward' and change how array of forward pointers is dealt with. Platforms tested: Linux 2.4 (verbena) w/PGI FreeBSD 4.10 (sleipnir) Configuration not tested w/h5committest
* [svn-r9587] Purpose:Quincey Koziol2004-11-281-8/+13
| | | | | | | | | | | | | | | | | | | | Bug fix Description: Correct off-by-on error which could cause invalid # of levels to be used for a skip list node, in rare circumstances. Change from srandom()/random() to more portable srand()/rand() routines for random # generation. Pre-compute the probability factor for computing the level of new nodes, for a minor speedup. Platforms tested: FreeBSD 4.10 (sleipnir) IRIX64 6.5 (modi4) Solaris 2.8 (sol) AIX 5.1(?) (copper)
* [svn-r9585] Purpose:Quincey Koziol2004-11-272-39/+25
| | | | | | | | | | | | | | Code optimization Description: Begin de-orbital burn of threaded, balanced binary tree code use by switching file open object code over to using them. Initial benchmarks show that skip lists are 5-10x faster than our TBBT code... Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) Too minor to require h5committest
* [svn-r9584] Purpose:Quincey Koziol2004-11-272-5/+6
| | | | | | | | | | | | | | | Code optimization Description: Revise mechanism for calling H5open/H5check to better avoid calling them from internal libray code. Only copy a datatype's group entry information if it has some. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) Too minor to require h5committest
* [svn-r9580] Purpose:Quincey Koziol2004-11-279-20/+845
| | | | | | | | | | | | | | | | | | | | Add new internal data structure Description: Add an implementation of skip lists to the library (see comment in src/H5SL.c for references to the papers describing them) as a potential replacement for our current threaded, balanced binary tree container. Skip lists are much simpler to implement and should be faster to use. Also, added new error codes to release branch, so bump the minor version number to indicate that the library is no longer perfectly compatible with the 1.6.3 release. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) Too minor to require further testing (the skip lists aren't actually used by any library code yet)
* [svn-r9574] Purpose:MuQun Yang2004-11-242-13/+37
| | | | | | | | | | | | | | | 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:
* [svn-r9563] Purpose:Quincey Koziol2004-11-233-39/+134
| | | | | | | | | | | | | 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-r9559] Purpose:Quincey Koziol2004-11-224-26/+34
| | | | | | | | | | | | | Code optimization Description: Switch a few more malloc/free pairs over to using internal free list code, to avoid abusing system memory allocator as badly. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) Too minor to require h5committest
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