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* [svn-r18702] Description:Quincey Koziol2010-05-051-2/+2
| | | | | | | | | | | | | | | | | | | | | | | Bring r18672 from metadata journaling "merging" branch to trunk: Mostly changes to move to only using one 'user data' parameter for calls to H5AC_protect(), along with some minor reformatting code cleanups. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.3 (amazon) in debug mode Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r18616] Description:Quincey Koziol2010-04-221-7/+7
| | | | | | | | Clean up compiler warnings. Tested on: Mac OS X/32 10.6.3 (amazon) w/debug (too minor to require h5committest)
* [svn-r18612] Description:Quincey Koziol2010-04-221-2/+2
| | | | | | | | Clean up compiler warnings & code formatting Tested on: Mac OS X/32 10.6.3 (amazon) w/debug (too minor to require h5committest)
* [svn-r16847] Description:Quincey Koziol2009-04-231-2/+14
| | | | | | | | | | | | | Bring r16846 from revise_chunks branch back to trunk: Fix broken (for how long?) H5_ASSIGN_OVERFLOW macro to actually detect overflows during assignments, along with several errors it [now] detected. Cleaned up a fix minor warnings and/or pieces of code also. Tested on: FreeBSD/32 6.3 (duty) in debug mode (h5committest not needed - multi-platform test performed on branch)
* [svn-r16702] Purpose: Improve performance of factory free lists.Neil Fortner2009-04-081-8/+16
| | | | | | | | | | | Description: Factory free lists were formerly implemented as block free lists. This was inefficient as factories can only be one size, and implementing them as blocks (which can be variable size) wastedd computation and space. They have been rewritten with a separate implementation, which is simlar to regular free lists except they can be dynamically created and destroyed. Tested: jam, linew, smirom (h5committest)
* [svn-r16560] Description:Quincey Koziol2009-03-101-8/+8
| | | | | | | | | | Remove another call to H5E_clear_stack() from within the library. Clean up lots of compiler warnings. Tested on: Mac OS X/32 10.5.6 (amazon) (followup on other platforms forthcoming)
* [svn-r16137] Description:Quincey Koziol2008-11-281-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | Add support for paging large data blocks to extensible arrays Clean up allocation/destroy code for extensible array index, super and data blocks Add a couple of routines to set/get bit values in memory buffers Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15510] Description:Quincey Koziol2008-08-211-1/+1
| | | | | | | | Clean up warnings & formatting Tested on: Mac OS X/32 10.5.4 (amazon) More tests forthcoming
* [svn-r13814] Description:Quincey Koziol2007-05-291-1/+1
| | | | | | | | | | | | | | 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-r13772] Description:Quincey Koziol2007-05-201-5/+5
| | | | | | | Reduce compiler warnings when free list manager is disabled. Tested on: FreeBSD/32 6.2 (duty)
* [svn-r13770] Description:Quincey Koziol2007-05-191-1/+4
| | | | | | | Clean up various memory leaks, etc. Tested on: FreeBSD/32 6.2 (duty)
* [svn-r13751] Description:Quincey Koziol2007-05-141-2/+2
| | | | | | | | | Reduce the number of warnings when free lists are disabled. Tested on: Mac OS X /32 10.4.9 (amazon) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [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-r12739] Added Direct I/O driver to VFD. It's only supported by SGI ↵Raymond Lu2006-10-101-1/+1
| | | | | | | | | | Altix (cobalt). There's a configure option --enable-direct-vfd/--disable-direct-vfd to enable/disable Direct I/O support. The default is enabled. There's a small test in test/vfd.c. Another way to test it is to set environment variable HDF5_DRIVER to "direct" and run "make check" in the test/ directory. There'll be some further improvement in the following checkin including allowing user to provide memory boundary value, file block size, and copying buffer size.
* [svn-r12560] Description:Quincey Koziol2006-08-101-3/+3
| | | | | | | Correct some typos in comments Testing: None needed
* [svn-r12320] Purpose:Quincey Koziol2006-05-021-1/+1
| | | | | | | | | | code cleanup Description: Finish H5FS->H5CS internal API name changes... Platforms tested: FreeBSD 4.11 (sleipnir) w/ & w/o --enable-codestack
* [svn-r11852] Purpose:Quincey Koziol2006-01-021-18/+18
| | | | | | | | | | | 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-r11282] Purpose:Quincey Koziol2005-08-201-23/+61
| | | | | | | | | | | | | | | | | New debugging feature Description: Add some code to track where memory from the internal free list allocator is allocated within the library. It's not quite ready for "prime time" yet, but it's close enough to be useful. This is disabled by default and requires the H5FL_TRACK macro in src/H5FLprivate.h to be uncommented to activate during debugging. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 Too minor to require full h5committest
* [svn-r11245] Purpose:Quincey Koziol2005-08-131-1/+1
| | | | | | | | | | | | | | | | | | | | 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-r10857] Purpose:Quincey Koziol2005-06-031-1/+1
| | | | | | | | | | Code cleanup Description: Re-enable free-list management in the library Platforms tested: None - eyeballed - too minor to require h5committest
* [svn-r10847] Purpose: Bug fixRaymond Lu2005-06-021-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: See details from Bug #213. Family member file size wasn't saved anywhere in file. When family file is opened, the first member size determine the member size. Solution: This is the fourth step of checkin. A test suit is added for h5repart, including a program to generate the test files, a script file to run h5repart, and a program to verify repartitioned files can be opened by the library. There's a change from the first step of checkin. Family name template is no longer saved in the superblock because different pathname can make the name different. In the third step of checkin, h5repart has been modified. If h5repart is used to change the size of family member file, the new size(actual member size) is saved in the superblock. In the second step of checkin, multi driver is checked against the driver name saved in superblock. Wrong driver will result in a failure with an error message indicating multi driver should be used. This change includes split driver because it's a special case for multi driver. In the first step of checkin. Family member size and name template(unused at this stage) are saved in file superblock. When file is reopened,the size passed in thrin superblock. A different size will trigger a failure with an error message indicating the right size. Wrong driver to open family file will cause a failure, too. Platforms tested: h5committest and fuss. Misc. update: MANIFEST
* [svn-r10618] Purpose:Quincey Koziol2005-04-161-1/+1
| | | | | | | | | | | | | Bug fix Description: Correct typo in "base array" free list macro when free list macros are disabled. Platforms tested: FreeBSD 4.11 (sleipnir) Solaris 2.9 (shanti) Too minor to require h5committest
* [svn-r10580] Purpose:Quincey Koziol2005-04-081-12/+21
| | | | | | | | | | | Code optimization Description: Add "base" size to array free list code, to accomodate skip list nodes. Platforms tested: FreeBSD 4.11 (sleipnir) Solaris 2.9 (shanti)
* [svn-r10547] Purpose:Quincey Koziol2005-04-051-1/+1
| | | | | | | | | | | Bug fix (sorta) Description: Re-enable free-lists in library. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r10535] Purpose: Spliting TestRaymond Lu2005-04-041-1/+1
| | | | | | | | | | | | Description: Split test/dtypes.c because it's so big. Moved all integer-integer, floating-floating, integer-floating, floating-integer, derived integer, derived floating conversion tests to a new test program, dt_atomic.c. The test remains the same basically. Platforms tested: fuss and h5committest Misc. update: MANIFEST
* [svn-r9978] Purpose:Xuan Bai2005-02-101-16/+16
| | | | | | | | | | | | | | | | | | | Bug fix. Description: Quincey changed "entern H5_DLL" to "H5_DLLVAR" in hdf5/src/H5FLprivate.h which caused some symbols can not be exported correctly by HDF5 DLL. Solution: Change "H5_DLLVAR" back to "extern H5_DLL". Platforms tested: Visual C++ 6.0 on Windows XP. .NET 2003 on Windows XP. Heping (Linux 2.4). (Note: I talked with Elena and Quincey about this failure. Quincey asked me to check in this fix.) Misc. update:
* [svn-r9939] Purpose:Quincey Koziol2005-02-041-16/+16
| | | | | | | | | | | | | New feature Description: Expand v2 B-tree code to support splitting the root node when enough records are inserted and move metadata cache callbacks into their own source file. Platforms tested: FreeBSD 4.11 (sleipnir) w/parallel Too minor for h5committest
* [svn-r9928] Purpose:Quincey Koziol2005-02-031-0/+35
| | | | | | | | | | | | | New feature Description: Add basic code for new B-tree implementation. They don't do much yet, aren't hooked up to anything yet and the format may change, but I'd like to start getting them into the daily tests. Platforms tested: FreeBSD 4.11 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8946] Purpose:Quincey Koziol2004-07-261-2/+2
| | | | | | | | | | | | | | | | | | Code cleanup, sorta Description: Added ifdef sections for "H5_USING_PURIFY" in various places in the code, which are designed to reduce the spurious "uninitialized memory read" warnings from purify which are actually OK. Note that this macro will have to be turned on by adding it to the CFLAGS for the build - I didn't think it was important enough to add a configure flag for. Also, the changes in H5HG.c optimize the walks through the objects in a heap to only look at the 'used' entries instead of all the 'allocated' entries. Platforms tested: Solaris 2.7 (arabica) w/purify Not tested by h5committest
* [svn-r8922] Purpose: Restore the original codeRaymond Lu2004-07-211-1/+1
| | | | | | | | Description: Line 38, "#define H5_NO_FREE_LISTS" were commented out during debugging Solution: put back in. Platforms tested: No test needed
* [svn-r8921] Purpose: new featureRaymond Lu2004-07-211-1/+1
| | | | | | | | | | | | | | Description: This is the second step of checkin for encoding and decoding objects. H5Tencode and H5Tdecode have been committed in the previous step. H5Sencode and H5Sdecode are checked in this time. Solution: Given object ID, these functions encode and decode object information into and from binary buffer and return new object ID. They take advantage of the existing codes of object header message and encode in the same format. Platforms tested: fuss and h5committest. Misc. update: RELEASE.txt
* [svn-r8301] Purpose:Quincey Koziol2004-04-061-14/+73
| | | | | | | | | | | | | Code optimization Description: Move handling for free list arrays that have no maximum size to separate set of routines and optimize computations for free list arrays with maximum size to avoid re-computing sizes all the time. Platforms tested: h5committest Solaris 2.7 (arabica)
* [svn-r7988] Purpose:Quincey Koziol2003-12-291-1/+1
| | | | | | | | | | | Bug fixes & code cleanup Description: Back out some of the debugging that was inadvertently checked in recently. Platforms tested: FreeBSD 4.9 (sleipnir) too minor to require h5committest
* [svn-r7984] Purpose: bug fixRaymond Lu2003-12-291-1/+1
| | | | | | | Description: VL datatype fails in certain way(hard to describe) Platforms tested: h5committest
* [svn-r6936] Purpose:Quincey Koziol2003-05-311-3/+3
| | | | | | | | | | | | | | | Bug fix Description: When free lists where disabled, the macros for array free list operations could possibly expand in ways that allowed incorrect numbers of objects to be operated on. Solution: Put parentheses around macro arguments when performing operations with them. Platforms tested: h5committestted (although Fortran tests failed for some reason)
* [svn-r6546] Purpose:Bill Wendling2003-03-311-4/+14
| | | | | | | | | | | | Update Description: Updated copyright statement in files which hadn't been updated yet. Platforms tested: Linux (Only comment change) Misc. update:
* [svn-r6278] Purpose:Quincey Koziol2003-01-141-30/+51
| | | | | | | | | | | | Code cleanup Description: Add 'H5_DLL' macro to H5FL macros, in order to allow Windows builds to work. Platforms tested: FreeBSD 4.7 (sleipnir) Visual Studio 6.0
* [svn-r6252] Purpose:Quincey Koziol2003-01-091-9/+29
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Lots of performance improvements & a couple new internal API interfaces. Description: Performance Improvements: - Cached file offset & length sizes in shared file struct, to avoid constantly looking them up in the FCPL. - Generic property improvements: - Added "revision" number to generic property classes to speed up comparisons. - Changed method of storing properties from using a hash-table to the TBBT routines in the library. - Share the propery names between classes and the lists derived from them. - Removed redundant 'def_value' buffer from each property. - Switching code to use a "copy on write" strategy for properties in each list, where the properties in each list are shared with the properties in the class, until a property's value is changed in a list. - Fixed error in layout code which was allocating too many buffers. - Redefined public macros of the form (H5open()/H5check, <variable>) internally to only be (<variable>), avoiding innumerable useless calls to H5open() and H5check_version(). - Reuse already zeroed buffers in H5F_contig_fill instead of constantly re-zeroing them. - Don't write fill values if writing entire dataset. - Use gettimeofday() system call instead of time() system when checking the modification time of a dataset. - Added reference counted string API and use it for tracking the names of objects opening in a file (for the ID->name code). - Removed redundant H5P_get() calls in B-tree routines. - Redefine H5T datatype macros internally to the library, to avoid calling H5check redundantly. - Keep dataspace information for dataset locally instead of reading from disk each time. Added new module to track open objects in a file, to allow this (which will be useful eventually for some FPH5 metadata caching issues). - Remove H5AC_find macro which was inlining metadata cache lookups, and call function instead. - Remove redundant memset() calls from H5G_namei() routine. - Remove redundant checking of object type when locating objects in metadata cache and rely on the address only. - Create default dataset object to use when default dataset creation property list is used to create datasets, bypassing querying for all the property list values. - Use default I/O vector size when performing raw data with the default dataset transfer property list, instead of querying for I/O vector size. - Remove H5P_DEFAULT internally to the library, replacing it with more specific default property list based on the type of property list needed. - Remove redundant memset() calls in object header message (H5O*) routines. - Remove redunant memset() calls in data I/O routines. - Split free-list allocation routines into malloc() and calloc()- like routines, instead of one combined routine. - Remove lots of indirection in H5O*() routines. - Simplify metadata cache entry comparison routine (used when flushing entire cache out). - Only enable metadata cache statistics when H5AC_DEBUG is turned on, instead of always tracking them. - Simplify address comparison macro (H5F_addr_eq). - Remove redundant metadata cache entry protections during dataset creation by protecting the object header once and making all the modifications necessary for the dataset creation before unprotecting it. - Reduce # of "number of element in extent" computations performed by computing and storing the value during dataspace creation. - Simplify checking for group location's file information, when file has not been involving in file-mounting operations. - Use binary encoding for modification time, instead of ASCII. - Hoist H5HL_peek calls (to get information in a local heap) out of loops in many group routine. - Use static variable for iterators of selections, instead of dynamically allocation them each time. - Lookup & insert new entries in one step, avoiding traversing group's B-tree twice. - Fixed memory leak in H5Gget_objname_idx() routine (tangential to performance improvements, but fixed along the way). - Use free-list for reference counted strings. - Don't bother copying object names into cached group entries, since they are re-created when an object is opened. The benchmark I used to measure these results created several thousand small (2K) datasets in a file and wrote out the data for them. This is Elena's "regular.c" benchmark. These changes resulted in approximately ~4.3x speedup of the development branch when compared to the previous code in the development branch and ~1.4x speedup compared to the release branch. Additionally, these changes reduce the total memory used (code and data) by the development branch by ~800KB, bringing the development branch back into the same ballpark as the release branch. I'll send out a more detailed description of the benchmark results as a followup note. New internal API routines: Added "reference counted strings" API for tracking strings that get used by multiple owners without duplicating the strings. Added "ternary search tree" API for text->object mappings. Platforms tested: Tested h5committest {arabica (fortran), eirene (fortran, C++) modi4 (parallel, fortran)} Other platforms/configurations tested? FreeBSD 4.7 (sleipnir) serial & parallel Solaris 2.6 (baldric) serial
* [svn-r5959] Raymond Lu2002-10-041-0/+1
| | | | | | | Purpose: Performance improvement for compact dataset. Platforms tested: Linux 2.2(eirene), Solaris 2.7(arabica), IRIX64 6.5(modi4)
* [svn-r5931] MuQun Yang2002-09-201-11/+11
| | | | | | | | | | | | Purpose: __DLL__ is a keyword in some platforms and __DLL__ is also defined as a macro for windows DLL applications. That causes problems. Description: Solution: Use H5_DLL*** to replace __DLL***__ at all header files. Change the macro defination at H5api_adpt.h. Platforms tested: linux2.2.18smp, irix64, solaris 2.7 and windows 2000
* [svn-r5787] Purpose:Quincey Koziol2002-07-121-1/+1
| | | | | | | | | | Update code Description: Re-enable free-lists, which were accidentally disabled from last checkin. Platforms tested: FreeBSD 4.6 (sleipnir)
* [svn-r5785] Purpose:Quincey Koziol2002-07-121-0/+37
| | | | | | | | | | Code update Description: Re-arrange to disable free-list code in a more transparent way. Platforms tested: FreeBSD 4.6 (sleipnir)
* [svn-r4978] Purpose:Quincey Koziol2002-02-171-1/+1
| | | | | | | | Code cleanup Description: Cleanup compiler warnings found by the SGI compiler and gcc 3.0 Platforms tested: FreeBSD 4.5 w/gcc 3.0 (hack) && IRIX64 (modi4)
* [svn-r4842] Purpose:Quincey Koziol2002-01-171-20/+9
| | | | | | | | | | | | Feature improvement Description: Re-write how the free-list headers were used, to reduce the amount of space added to each malloc request. Reduced header for array and block free list items from 24 bytes to 8 bytes and eliminated the header for fixed-size free list items entirely. This should reduce the amount of memory that the library uses. Platforms tested: FreeBSD 4.5 (sleipnir) & IRIX64 6.5 (modi4)
* [svn-r4355] Purpose:Quincey Koziol2001-08-141-15/+15
| | | | | | | | | | | | | | | | | | | | | | Code cleanup (sorta) Description: When the first versions of the HDF5 library were designed, I remembered vividly the difficulties of porting code from a 32-bit platform to a 16-bit platform and asked that people use intn & uintn instead of int & unsigned int, respectively. However, in hindsight, this was overkill and unnecessary since we weren't going to be porting the HDF5 library to 16-bit architectures. Currently, the extra uintn & intn typedefs are causing problems for users who'd like to include both the HDF5 and HDF4 header files in one source module (like Kent's h4toh5 library). Solution: Changed the uintn & intn's to unsigned and int's respectively. Platforms tested: FreeBSD 4.4 (hawkwind)
* [svn-r4038] Purpose:Quincey Koziol2001-06-211-11/+11
| | | | | | | | | | | | | Code clean/bug fix Description: H5FL (free-list manager) code currently is taking an hsize_t as the size of a memory block to allocate. On many machines, the size of an hsize_t is greater than the size of a size_t, potentially leading to incorrect memory allocations in rare circumstances. Solution: Changed hsize_t parameters and variables to size_t. Platforms tested: FreeBSD 4.3 (hawkwind)
* [svn-r3781] Purpose:Bill Wendling2001-04-051-3/+3
| | | | | | | | | | | | | | | | | | Update Description: Changed #include <hdf_file.h> construct to #include "hdf_file.h" so that the GNU compiler can more easily pick up the dependencies which it places in the .depend and Dependencies files. Also regenerated the Dependencies to go along with this. Platforms tested: Linux
* [svn-r3252] Purpose:Quincey Koziol2001-01-091-7/+7
| | | | | | | | | | | | | Code cleanup. Description: Fixed _lots_ (I mean _tons_) of warnings spit out by the gcc with the extra warnings. Including a few show-stoppers for compression on IRIX machines. Solution: Changed lots of variables' types to more sensible and consistent types, more range-checking, more variable typecasts, etc. Platforms tested: FreeBSD 4.2 (hawkwind), IRIX64-64 (modi4)
* [svn-r3236] Purpose:Quincey Koziol2001-01-041-4/+4
| | | | | | | | Clean up code. Description: Cleaned up various compiler warnings. Platforms tested: FreeBSD 4.2 (hawkwind)
* [svn-r2711] Purpose:Quincey Koziol2000-10-201-1/+1
| | | | | | | | | | | | Bug fix. Description: When the maximum number of elements in a fixed size, free-list managed array was allocated, the free-list code was writing off the end of the array. Solution: Changed definition of free-list managed arrays to allocate correct space for the array. Platforms tested: Solaris 2.5 (baldric) w/Purify
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