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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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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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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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New fortran wrappers added.
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Omnibus raw data I/O revisions, with wide-ranging changes and
refactoring, in order to prepare for implementing "fast append" feature.
These changes remove the majority of the code duplication for raw data
I/O which has crept in over the last ten years and introduces a more object-
oriented design for operating on different types of dataset storage.
Chunked storage no longer has it's own I/O routines, it is now handled
as either contiguous (if chunk is not pulled into the cache) or compact (if the
chunk is cached in memory).
No bug or feature changes, at least intentionally... :-)
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (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/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.5.2 (amazon) in debug mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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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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optimization codes:
1. Provide another option for users to do independent IO with MPI file setview(collectively)
2. With the request of collective IO from users, using Independent IO with MPI file setview if we find collective IO is not good for the applications for IO per chunk(multi-chunk IO) case. Previously we used pure independent IO and that actually performed small IO(IO each row) for this case. The recent performance study suggested the independent IO with file setview can acheieve significantly better performance than collective IO when not many processes participate in the IO.
3. For applications that explicitly choose to do collective IO per chunk case, the library won't do any optimization(gather/broadcast) operations. The library simply passes the collective IO request to MPI-IO.
Tested at copper, kagiso, heping, mir and tungsten(cmpi and mpich)
Kagiso is using LAM, t_mpi test was broken even.
The cchunk10 test failed at heping and mir. I suspected it was an MPICH problem. Will investigate later.
Everything passed at copper.
at tungsten: the old cmpi bug(failed at esetw) is still there. Other tests passed.
Some sequential fheap tests failed at kagiso.
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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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Some collective chunk IO macro names are confusing, change them to more meaningful
names.
Description:
H5Pset_dxpl_mpio_chunk_opt will set a flag so that the library can do one linked IO or multi-chunk IO with collective in chunking storage directly. That is, the library won't do analyses to determine this.
The flags for the enum type we used before are:
H5FD_MPIO_OPT_ONE_IO
H5FD_MPIO_OPT_MULTI_IO
They are not good names because of the following two reasons:
1. It doesn't reflect chunking storage
2. OPT is kind of redundant and misleading,
Solution:
We change the names to
H5FD_MPIO_CHUNK_ONE_IO
H5FD_MPIO_CHUNK_MULTI_IO
Platforms tested:
Since only macro names are changed, no need to test with h5committest.
heping(mpich 1.2.6)
Misc. update:
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Code maintenance
Description:
Remove flexible parallel code
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 (heping)
Solaris 2.9 (shanti)
Linux 2.4/64 (mir)
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New APIs to add for collective chunk IO
Description:
Three new APIs
H5Pset_dxpl_mpio_chunk_opt_ratio
H5Pset_dxpl_mpio_chunk_opt_num
H5Pset_dxpl_mpio_chunk_opt
for optional optimization choices from users.
Solution:
Haven't added tests yet, won't affect other parts of the library.
Will add tests after urgent investigations of memory leaking problems from NASA Aura team.
Platforms tested:
heping: both parallel and sequential
shanti
Misc. update:
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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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Bug fix
Description:
Address the failure in the FORTRAN builds by making some more of the
MPI-related typedefs in the library available outside of parallel builds.
Platforms tested:
Linux 2.4 (verbena) w/FORTRAN & C++
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Bug fix
Description:
Fix a couple of bugaboos in the serial build that crept in
Platforms tested:
FreeBSD 4.9 (sleipnir)
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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