| Commit message (Collapse) | Author | Age | Files | Lines |
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defines H5_HAVE_WIN32_API and H5_HAVE_VISUAL_STUDIO defines to use. These can be properly set during configurration.
Tested: windows and local linux - reviewed internally
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Correct spelling error in macro. (FUNC_ENTER_NOAPI_NOFUNC_NOINIT ->
FUNC_ENTER_NOAPI_NOINIT_NOFUNC)
Tested on:
Eyeballed only.
(h5committest not required for this branch)
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Clean up code a bit, move new "terminate" VFD callback to new position
in H5FD_class_t struct.
Tested on:
Mac OS X/32 10.6.7 (amazon) w/debug & production
(h5committest not required on this branch)
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Initial commit of John Biddescomb's VFD & MPI tweaks.
Tested on:
None (yet)
(h5committest not required for this branch)
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__MWERKS__.
Metraowerks compiler is no more. Make the code cleaner.
Tested: H5committest plus jam serial.
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Bring "round robin" metadata write strategy code from 'round_robin'
branch to the trunk.
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 debug 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
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Bring back various minor tweaks & cleanups from the revise_chunks
branch.
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-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
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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)
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Various bug fixes & cleanups with VFDs and file free space changes,
along with cleaning up compiler warnings.
Enable more VFDs (for 'make check-vfd' testing) for many tests.
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 (kagiso) 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
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Bring file free space branch changes through r15795 into trunk, which
includes a fair bit of code cleanup & rearrangement along with a couple of
bug fixes also.
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 (kagiso) 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
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reference count
> 1.
Description: Added a new field 'app_count' to H5I_id_info_t struct, to track
the reference count on an id due to the application. the old 'count' field
tracks the total. Generally any id visible to the application gets placed
in app_count. Added app_ref boolean parameter to H5I_inc_ref, H5I_dec_ref,
H5I_register, H5I_clear_type, and a few other functions, to specify whether
the operation(s) being performed on the id(s) are due to the application
(TRUE) or not (FALSE). Test added for this case.
Tested: kagiso, smirom, linew (h5committest)
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WIN32, so I've standardized all #ifdef's to use _WIN32. This should not affect any other platform.
Tested:
Visual Studio (32- and 64-bit) on Win XP
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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.
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The problem
came from the EOA for the whole MULTI file. It's taken out because it's
meaningless for MULTI file. Instead, each individual file has its EOA.
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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.
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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
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Repair synchronization bug in the metadata cache in PHDF5
Also repair numerous other bugs that surfaced in testing the
bug fix.
Description:
While operations modifying metadata must be collective, we allow
independant reads. This allows metadata caches on different processes
to adjust to different sizes, and to place the entries on their dirty
lists in different orders. Since only process 0 actually writes
metadata to disk (all other processes thought they did, but the writes
were discarded on the theory that they had to be collective), this made
it possible for another process to modify metadata, flush it, and then
read it back in in its original form (pre-modification) form. The
possibilities for file corruption should be obvious.
Solution:
Make the policy that only process 0 can write to file explicit, and
visible to the metadata caches. Thus only process 0 may flush dirty
entries -- all other caches must retain dirty entries until they are
informed by process 0 that the entries are clean.
Synchronization is handled by counting the bytes of dirty cache entries
created, and then synching up between the caches whenever the sum
exceeds an (eventually user specified) limit. Dirty metadata creation
is consistent across all processes because all operations modifying
metadata must be collective.
This change uncovered may bugs which are repaired in this checkin.
It also required modification of H5HL and H5O to allocate file space
on insertion rather than on flush from cache.
Platforms tested:
H5committest, heping(parallel & serial)
Misc. update:
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Code cleanup
Description:
#ifdef out blksize field in file structure for non-GPFS builds.
Platforms tested:
None - just eyeballed - very minor.
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new features
Description:
add support for compiling the library and testphdf5 in Windows
Solution:
Platforms tested:
Linux
AIX
Solaris
Windows VC6
Misc. update:
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Code cleanup
Description:
Clean up unused variables & use portability macros better
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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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
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Code cleanup
Description:
Clean up various warnings reported by the Windows team.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Bug fix.
Description:
"testphdf -p" would with data verification errors. The reasons were
that the MPIPOSIX driver file open and close, especially the close
routine provide no "coordination" between processes. The testphdf5
tests reuse the same file for test data file by opening using H5Fcreate
with the HDF5_FCC_TRUNC option. The test routines do not provide any
code to ensure that all processes have finished one test before moving
to the next test. Some "faster" process would have finished verifying
its portion of data as correct and move to the next test which opens
the same file with TRUNCATOIN which truncates the previous data file.
But some "slower" processes are still verifying the "previous" data
file which all of a sudden got truncated by the "faster" process.
Solution:
Technically, the test program should be fixed to ensure all processes
have finished one test before any is allowed to move to the next test.
OTOH, the MPIO VFD has no problem with this test because MPI-IO requires
File open and close be called collectively correct and ensure it is
returned properly.
I choose to fix the MPIPOSIX close routine to provide some sort of
coordination between processes by requiring all processes to have
completed the close of a file before it is returned to user space.
This makes the MPIPOSIX close routine behaves more like the MPIO
close routine, thus provide more protection for user applications
that fail to code in the coordination. But having the barrier
in the MPIPOSIX close routine would penalize applications where
it is "okay" for some processes to close its file handle and race
ahead to do other things since it is not going to access this file,
therefore whether other processes are still using the file is immaterial.
Maybe this protective coordination should be optional and can be turned
off by confident users who need not this sort of protection.
Platforms tested:
"h5committested" and tested in modi4 and tesla.
Misc. update:
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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:
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Code cleanup & minor optimization
Description:
Re-work the way interface initialization routines are specified in the
library to avoid the overhead of checking for them in routines where there is
no interface initialization routine. This cleans up warnings with gcc 3.4,
reduces the library binary size a bit (about 2-3%) and should speedup the
library's execution slightly.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/gcc34
h5committest
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Code cleanup
Description:
Add destructor to match constructor fr VFLs when they are shut down by the
library.
Solution:
Added H5FD_*_term() routines to "undo" changes made in H5FD_*_init()
routines.
Platforms tested:
IBM p690 (copper)
too minor to require h5committest
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Bug fix/optimization
Description:
Address slowdown in MPI-I/O file metadata operations that was introduced
mid-stream. We now _require_ a POSIX compliant parallel file system for the
MPI-I/O file driver (as well as for the MPI-POSIX file driver).
Also optimized file open operation when the file is being created by
reducing the number of collective & syncronizing calls.
Additionally, refactor the MPI routines into a common place, eliminating
duplicated code.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/parallel
h5committest
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Code cleanup, bug fixes
Description:
Wrap up rest of changes necessary for fixing the "short" MPI-I/O read
problem that Robb reported.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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Bug fix
Description:
Our previous "optimization" of metadata writing which only wrote metadata
from one process was abusing MPI-I/O and after some consultation with Rob Ross
and Rajeev Thakur, Albert & I have come up with a solution...
Solution:
Instead of only writing from one process, issue a collective write
operation with all processes, for metadata writes.
Platforms tested:
FreeBSD 4.9 (sleipnir)
h5committest
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Code cleanup
Description:
More collective/independent cleanups to straighten out code contortions.
Platforms tested:
FreeBSD 4.9 (sleipnir)
FreeBSD 4.9 (sleipnir) w/parallel
Linux 2.4 (verbena) w/fortran & C++
Solaris 2.7 (arabica) w/64-bit extensions enabled
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Code cleanup
Description:
De-linted more code
Platforms tested:
FreeBSD 4.8 (sleipnir) w/parallel
too minor to require h5committest
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Version update
Description:
Removed 1.4 compatibility code in the library.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Code cleanup/Feature removal
Description:
Remove "round robin" writing of metadata in MPI VFDs (and a couple of other
places). This never really worked the way I hoped it would and it causes
problems on certain machines.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/parallel
Too small for triple check.
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Compatibility fix
Description:
The H5P[set|get]_fapl_mpiposix calls changed between v1.4.x and v1.5.x.
Solution:
Wrap them in the v1.4 backward compatibility #ifdefs and update tests, etc.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/paralle & v1.4 compatibility
h5committest pointless
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Update
Description:
Some of the TRACE macros were updated to reflect a new parameter.
Platforms tested:
Linux
Solaris w/ zlib
Irix w/ zlib
Misc. update:
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Change
Description:
Instead of using the "USE_GPFS" macro, use the "H5_HAVE_GPFS" macro
which is defined during configuration and then use the new parameter
to the H5P{get,set}_fapl_mpiposix functions to control if GPFS is
enabled or not.
Platforms tested:
Modi4 (only affects the parallel stuff, so no need for full testing).
Misc. update:
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Code cleanup.
Description:
Cleaned up a few debugging printfs.
Platforms tested:
FreeBSD 4.8 (sleipnir)
Triple check not needed.
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Feature Add
Description:
Added knob so that the programmer can enable or disable GPFS
hints during runtime instead of having it only enabled at
configure/compile time. Some of the public APIs were changed
to add an extra parameter for this option...
Platforms tested:
Blue (LLNL). It only affects the MPI/POSIX driver, so no need
to test it on non-GPFS platforms.
Misc. update:
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Purpose:
Code cleanup
Description:
Removed debug statement bracketed by H5FDmpiposix_DEBUG or alike.
They were added in by mistakes.
Platforms tested:
Did not h5committested but tested in Copper since there changes are
limited in parallel codes.
Misc. update:
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Feature
Description:
Added the feature to store and return a duplicate of Communicator in
the access of property list and file operations. (no duplicate for
INFO object because MPIPOSIX driver does not process INFO object.
Platforms tested:
Did not h5committested because these are all MPI code and well protected
by HAVE_PARALLEL.
Tested in eirene and modi4, both parallel mode.
Misc. update:
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New Feature
Description:
Added support for the lock and unlock function calls for file
drivers. Only FPHDF5 uses this feature. All of these drivers don't
define lock or unlock methods.
Platforms tested:
Linux, Modi4, Sol
Misc. update:
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Potential bug fix.
Description:
The code to rotate the metadata writing process may not be compiled
correctly in all cases.
Solution:
Change from using "++mpi_round" to "mpi_round+1"
Platforms tested:
Eyeballed...
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Code cleanup
Description:
Clean up some compiler warnings
Platforms tested:
FreeBSD 4.7 (sleipnir)
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Bug Fix
Description:
Metadata cache in parallel I/O can cause hangs in applications which
perform independent I/O on chunked datasets, because the metadata cache
can attempt to flush out dirty metadata from only a single process, instead
of collectively from all processes.
Solution:
Pass a dataset transfer property list down from every API function which
could possibly trigger metadata I/O.
Then, split the metadata cache into two sets of entries to allow dirty
metadata to be set aside when a hash table collision occurs during
independent I/O.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) serial & parallel
Misc. update:
Updated release_docs/RELEASE
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Code cleanup/new feature.
Description:
Split FUNC_LEAVE into API and non-API specific versions. This allows a
solution to compiling this branch with C++, as well as reducing the size
of the binaries produced.
Platforms tested:
FreeBSD 4.7 (sleipnir) w/serial, parallel (including MPE) & thread-safe
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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
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Bug fix
Description:
Correct another missing field I overlooked earlier.
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Bug fix
Description:
Add missing 'naccess' field required for GPFS token management code.
Platforms tested:
FreeBSD 4.7 (sleipnir)
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Purpose:
Feature; Optimization
Description:
Clients pass `-1' or make their own #define for HDF5 functions
that take an optional object ID.
Blue's GPFS is slow for typical SAF restart dumps.
Solution:
Added a #define for H5I_INVALID_HID
Added GPFS-specific code to H5FDmpiposix.c that tells mmfsd to
forego byte range token prefetching. This code can be compiled
into the library by defining USE_GPFS_HINTS. The plan is to either
generalize this so it's detected during configure and turned
on/off at runtime, or to move it up into DSL/SAF with the new HDF5
functions to that return the low-level file handle.
Platforms tested:
SuSE Linux (arborea), gcc and mpich-1.2.4
SunOS (baldric), gcc
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Purpose:
New API functions
Description:
Added API functions to return pointer to low-level file handle
(H5Fget_vfd_handle and H5FDget_vfd_handle) and related property list
setting functions(H5Pset_family_offset and H5Pset_multi_type).
Platforms tested:
Linux 2.2(eirene), Solaris 2.7(arabica), IRIX64 6.5(modi4)
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