| Commit message (Collapse) | Author | Age | Files | Lines |
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H5FD_FLMAP_SINGLE to H5FD_FLMAP_DICHOTOMY.
Also changed H5O_copy_search_comm_dt_check() to use H5O_obj_class() to get object type instead of H5O_get_info(...TRUE...) saving time in traversing metadata.
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STDIO VFD fixes (HDFFV-7917). Mainly Windows correctness issues (propagated from the SEC2 VFD and the old Windows VFD) and issues where large files are accessed.
Tested on:
64-bit Mac OS-X
64-bit Windows 7
jam
koala
ostrich
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Tested: windows (big test using stdio only fails - this will be filed for further investigation)
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H5_HAVE_WIN32_API and H5_HAVE_VISUAL_STUDIO defines only need to be set on windows. Autotools configure is not affected.
Trunk passed for a week and cmake branch has been in place > 3 weeks.
Tested: local linux
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big.c:
Changed the test to run Huge Dataset (tens of GB), Xtra large dataset(4GB big),
Large dataset (2GB big), or merely 1GB big, depending on if the file system
supports sparse file or if it supports larger than 32bigs I/O.
H5FDstdio.c:
Removed an incorrect condition that whether STDIO VFD supports
larger than 32bits I/O depends on the support of fseeko. Windows does not
use that. Instead, it uses _fseeki64 to support larger than 32bits I/O.
Tested: h5committest, jam (serial).
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Fixed a typo in the Windows definitions. Had __ftelli64, should be _ftelli64.
Tested by Allen in Windows platform.
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The STDIO only checked for fseeko and incorrectly assumed it can support file
sizes larger than 32bits. Fixed it by making to use fseeko64 if supported, else
use fseeko. To simplify the code, assume fseeko which is a POSIX function must
be supported. Therefore, fseek is not used at all.
(Note: the above applies to Unix-like system. The Windows platform has
hardcoding using Windows functions which are NOT POSIX compliant.)
Tested: h5committested. Also tested in BP (AIX) 32/64 and enable/disable-largefile.
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failures in the trunk.
H5FD_stdio_truncate() windows code: need to do a rewind
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Bring r18650 from trunk to 1.8 branch:
Bring back various minor tweaks & cleanups from the revise_chunks
branch.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
(h5committested on trunk)
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Bring r18011 from trunk to 1.8 branch:
Bring Coverity changes into the trunk: (also other minor cleanups)
r17991:
Fix Coverity items 175 and 176. Fixed memory leak on error in print_enum in
H5LT.c.
r17993: (r17992 was not a Coverity change)
Close Coverity issue #206: inconsistently checking whether dt->shared was
non-NULL after H5T_alloc() returned a valid 'dt' value (which should guarantee
that dt->shared is valid).
r17994:
Fix Coverity item 149. Fixed file handle leak on error in H5FD_stdio_open.
r17995:
Fixed Coverity issues 154 to 161:
Added H5MP_close routine to error handling in the event *mp has not been
freed before error.
r17996:
Close Coverity issue #126: potentially leaking merged_spans on routine failure.
r17997:
Fix Coverity items 147 and 148. Fixed resource leaks on error in H5FDloc.c.
r17998:
Coverity issue 269-272:
Added integer result variable to functions that could return negative.
Assigned to unsigned after checking.
Added H5E_BEGIN_TRY block around H5Tclose and removed H5E_THROW in the
catch block.
Checked buffer is NULL before free. Changed HGOTO_ERROR outside of the if
block to H5E_THROW.
r17999:
Close Coverity issue #127: release temporary spans in more generic manner.
(Also add error checking to previous fix)
r18000:
Resolved Coverity issues 211 and 212 in H5T.c. Added comments to ignore
Coverity warning regarding not checking pointer for NULL, as we are using
an assert which catches the issue.
r18001:
Fix Coverity item 146. Fixed resource leak on error in H5O_layout_copy.
r18002:
Fix Coverity items 143 and 145. Fixed resource leaks on error in
H5D_compact_copy and H5D_contig_copy.
r18003:
Close Coverity issue #192: close file on error
r18004:
Fix Coverity issue #125: release temporary spans on error
r18005:
Resolved Coverity issues 5, 25, and 83 (in H5T.c):
Separated embedded functions in order to check for NULL on return of
H5I_object before passing into H5T_copy.
Check to see if new_dt is NULL within error handling before
dereferencing it.
Ignore Coverity's dead code warnings as the checks that lead to the code
are machine dependent.
r18006:
Coverity 63,70,73: Checked result of function before assigning to an unsigned
variable.
r18007:
Coverity 78,79: added continue statement if H5Pget_filter2 returns negative.
r18008:
Fixed Coverity issue # 138:
Added support in error handling to free dst pointer (if allocated) on error.
r18009:
Whitespace & coding style cleanup
Tested on:
Mac OS X/32 10.6.2 (amazon) w/debug & production
(h5committested on trunk)
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Bring r17010,17017,17021-17022,17029-17031,17035 back from trunk:
"temporary" file allocation space changes.
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/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 debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.7 (amazon) in debug mode
Mac OS X/32 10.5.7 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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Bring r16560 back from trunk.
Tested on:
Mac OS X/32 10.5.6 (amazon) debug & production
(Following up with tests on more platforms)
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Bring r15861 back from trunk to 1.8 release branch.
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 r15800 back from trunk:
- File free space branch changes through r15794
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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Remove trailing whitespace from C/C++ source files, with the following
script:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Tested on:
Mac OS X/32 10.5.5 (amazon)
No need for h5committest, just whitespace changes...
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Bring back r15510 & r15512 from trunk:
Fix compiler warnings and formatting.
Tested on:
Mac OS X/32 10.5.4 (amazon)
More tests upcoming
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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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Rename new error handling API routines from H5E<foo>_stack() to
H5E<foo>2().
Tested on:
Mac OS X/32 10.4.9 (amazon)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
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Clean up code and reduce compiler warnings...
Tested on:
Mac OS X/32 10.4.9 (amazon)
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will
check if fseeko is available. Using it instead of fseek can support
big files because the offset is of type off_t not long int. Also
added the test for STDIO in big.c.
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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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More progress on creation order for attribbutes - they are now basically
working for "compact" attribute storage.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
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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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Clean up some of the warnings on 64-bit Linux...
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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:
The GASS VFL driver header file was bringing in the <string.h> header file,
which several other source code modules needed also, but weren't including
explicitly themselves.
Solution:
Add includes for <string.h> to files which actually need them.
Platforms tested:
FreeBSD 4.11 (sleipnir) w/C++ as CC
Configuration not tested by h5committest...
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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:
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Description: Restore 6 old error API functions back to the library to be backward
compatible with v1.6. They are H5Epush, H5Eprint, H5Ewalk, H5Eclear, H5Eset_auto,
H5Eget_auto. These functions do not have error stack as parameter.
Solution: Internally, these functions use default error stack.
Platforms tested: h5committest and fuss.
Misc. update: RELEASE.txt
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Code cleanup
Description:
Various minor tweaks to clean code up and bring it into closer
syncronization with the release branch.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
h5committested
IRIX64 6.5 (modi4)
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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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Code cleanup
Description:
De-linted more modules
Platforms tested:
FreeBSD 4.8 (sleipnir) w/ & w/o stream enabled
too minor to require h5committest
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Code refactoring
Description:
Chase new error API usage by adding error class to calls to H5Epush().
Platforms tested:
h5committested
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A bug fix for windows.
Description:
Many tests failed on windows when stdio driver is on.
I suspect it is the compiler bug.
After some investigation, the symptom is:
The signature of HDF5 file cannot be found.
The real problem is the signature was appended at the end of the whole
file instead of inserting at the starting of the file.
It seems when the file pointer(signature) is reset to the starting of the file,
windows mis-placed it to the end of the file after finding the file is close to
the end.
Solution:
Fortuately, ftell and fseek still function well on windows,
so I use ftell and fseek to force the file pointer to go to the position it is supposed
to go.
Platforms tested:
since the only change in this file is within ifdef WIN32 macro; it won't
affect the mainstream platforms, so I don't have to three platforms.
Platforms to confirm(test with basic function): Linux 2.4
Platforms to throughly test: windows 2000 with VS6.0
test on three different
Misc. update:
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A compiling error fixed for windows only
Description:
Use file handler instead of file stream at H5FDstdio.c when using getfileHandle function of windows.
Solution:
see above, however; stdio driver tests failed on windows. I am still investigating the bug.
The current check will not fix the failure of stdio driver test on windows.
The good news is that it won't affect the release since the default driver used for test is sec2 driver and
all tests passed for sec2 driver on windows.
Platforms tested:
windows 2000 and confirmed at Linux.
Since the only change is two-line code inside #ifdef WIN32 #endif macro block,
it is not necessary to test all UNIX platforms. Still confirmed at eirene.
Misc. update:
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Bug fix.
Description:
The stdio filer driver is not reducing the file's size in the manner
that the sec2 driver does.
Solution:
Copy code from the sec2 for handling this properly.
Platforms tested:
h5committested
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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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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
Description:
Clean up compile warnings.
Platforms tested:
FreeBSD 4.6 (sleipnir) w and w/o parallel
Linux 2.2.x (eirene) w/FORTRAN & C++
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN & parallel
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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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New feature.
Description:
Added a "small data" block allocation mechanism to the library, similar to
the mechanism used for allocating metadata currently.
See the RFC for more details:
http://hdf.ncsa.uiuc.edu/RFC/SmallData/SmallData.html
This reduces the number of I/O operations which hit the disk for my test
program from 19 to 15 (i.e. from 393 to 15, overall).
Platforms tested:
Solaris 2.7 (arabica) w/FORTRAN and FreeBSD 4.5 (sleipnir) w/C++
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New feature
Description:
Add 'closing' parameter to H5FDflush and VFL "flush" functions, per
http://hdf.ncsa.uiuc.edu/RFC/VFLFlush/VFLFlush.html
Platforms tested:
IRIX64 6.5 (modi4)
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Purpose:
eliminate warnings on win32
Description:
some conversion warnings were being issued
Solution:
added some type casts
Platforms tested:
w2000, linux
changed the HDmemset to include a cast in win32; this was just to eliminate a compiler
warning. probably the macro can also be used in unix
#ifdef WIN32
#define HDmemset(X,C,Z) memset((void*)(X),C,Z)
#else /* WIN32 */
#define HDmemset(X,C,Z) memset(X,C,Z)
#endif /* WIN32 */
the list of previous warnings was
D:\disk_w\hdf5\src\H5FDstdio.c(659) : warning C4244: 'initializing' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Fcontig.c(435) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Fcontig.c(497) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Fcontig.c(915) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Fcontig.c(982) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(912) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(995) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(1936) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(2019) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(2862) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(2864) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(2948) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(3690) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(3692) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(3776) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Shyper.c(5167) : warning C4244: '+=' : conversion from '__int64 ' to 'unsigned int ', possible loss of data
D:\disk_w\hdf5\src\H5Tvlen.c(371) : warning C4244: '=' : conversion from 'unsigned __int64 ' to 'unsigned int ', possible loss of data
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Back out changes.
Description:
Back out changes to VFL 'flush' API function, pending review.
Platforms tested:
IRIX64 6.5 (modi4)
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New Feature
Description:
The VFL flush function is called immediately before a file is closed.
This can cause duplicate syncronization actions to occur, if the VFL
close function also performs them.
Solution:
Added 'closing' parameter to VFL 'flush' operation. This allows the VFL
flush function to bypass operations that will be duplicated within the VFL
close function.
Additionally, use the 'closing' parameter to bypass calls to MPI_File_sync()
when set. Since MPI_File_close() also syncronizes the file, this avoids
the terrible performance hit taken when calling MPI_File_sync() as the file
is closing.
Platforms tested:
IRIX64 6.5 (modi4)
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