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hdf5_1_10
* commit '54957d37f5aa73912763dbb6e308555e863c43f4':
Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
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Remove all traces of MPI-POSIX VFD and GPFS detection/code.
Remove remaining traces of stream VFD.
Remove testpar/t_posix_compliant test (it's not actually verifying anything).
Clean up H5D__mpio_opt_possible() further.
Moved environment variable that disables MPI collective operations into
MPI-IO VFD (instead of it being in src/H5S.c).
A few other small code cleanups.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/parallel & serial
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Correct some dynamically sized arrays that fail on Windows.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/parallel
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Check in Mohamad's changes to support collective I/O on point selections,
along with some other minor cleanups.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/parallel & serial
(h5committest forthcoming)
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exclusively.
Part of the preparation for a fix for HDFFV-8551.
Tested on:
32-bit LE linux (jam) w/ parallel and Fortran.
There are no behavior changes, so testing was minimal.
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HDFFV-8146 - Remove "multi-chunk IO without optimization" sub-feature from MPI I/O optimization for chunked dataset feature
Description:
The “multi-chunk IO without optimization” feature is removed and made the related xfer property (H5FD_MPIO_CHUNK_MULTI_IO) go directly to “multi-chunk-io” feature.
Also update/fix/cleanup testings (chunk collective IO and actual chunk opt mode) accordingly.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), fred (mac64-LE), Windows (32-LE cmake), cmake (jam)
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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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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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When enable-debug is turned on, a special macro block H5_HAVE_INSTRUMENTED_LIBRARY inside HDF5 will be executed to check if some collective chunk IO test cases are being run with the correct settings(one link, multiple chunk etc.). However,when complicated derived datatype in some mpi-io packages are not supported, the library has to switch one link IO with/without the optimization to multiple chunk IO with/without the optimization. The current testsuite doesn't know this and generates a false assertion failure message.
This check-in fix this problem by providing a second property to avoid the false faiure message.
Tested at abe(NCSA linux cluster) and kagiso.
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Move H5Pinsert() out of old "compat v1.6" section and into API
versioning, switching internal usage to H5Pinsert2().
Add regression test for H5Pinsert1()
Clean up some other minor warnings.
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 10.4.10 (amazon) in debug mode
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Add H5Dcreate to API versioned routines, replacing internal usage with
H5Dcreate2
Fix thread-safe error stack initialization for API versioned error
stack printing routines.
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 10.4.10 (amazon) in debug mode
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Make H5Dopen versioned and change all internal usage to use H5Dopen2
Add simple regression test for H5Dopen1
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 10.4.10 (amazon) in debug 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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Fix parallel build failure for property list class initialization refactor.
Tested on:
AIX (copper) w/parallel
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independent IO with file setview.
To activite this test,
add the command option -i.
For example, at IBM AIX, type "poe testphdf5 -i" will test the library with independent IO with file setview. It simply replaces all the collective IO tests with independent IO with file setview.
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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 mul
ti-chunk IO with collective in chunking storage directly. That is, the library won't do an
alyses 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.
Misc. update:
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Adding parallel tests for optional collective chunk APIs
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
have been added to the libraries.
This check-in adds six tests to verify the funcationality and correctedness
of these APIs.
These tests need to be verified with 3 or more processors and with MPI-IO driver only.
Solution:
Using H5Pinsert, H5Pget, H5Pset to verify that the library indeed goes into the branch we hope for.
Using H5_HAVE_INSTRUMENT macro to isolate these changes so that it won't affect or be misused by the application.
Platforms tested:
h5committest(shanti still refused to be connected)
Parallel tests on heping somehow are skipped. Manually testing at heping. Have checked
1,2,3,4,5 processes.
Misc. update:
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Add tests for optional APIs to support collective chunk IO
Description:
In order to test whether library picks up the user's options,
The number of chunks need to be varied for different processes,
Selection of the number of processes selected in one chunk also
need to be varied.
Solution:
Create two cases,
1. Each chunk only selected by one unique process, this case
library should use independent for collective call.
2. One-third of the processes occupies the top half of the whole domain,
The rest of the processes occupies the lower half of the domain.
The total number of chunk is a fixed number 8.
Platforms tested:
Linux 2.4 with mpich 1.2.6(only)
Since I only checked in the code that handles the selection, haven't added any new tests yet. So it won't affect any platforms.
Misc. update:
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change the array size of collective chunking features of parallel tests.
Description:
Previously array size for collective optimization tests
including
cchunk1,
cchunk2,
cchunk3,
cchunk4,
ccontw,
ccontr,
cschunkw,
cschunkr,
ccchunkw,
ccchunkr
are fixed,
They are only valid for some good number of processors(1,2,3,4,6,8,12,16,24,32,48 etc).
Recently there are more requests for parallel tests to be valid on some odd number of processes such as 5,7,11,13 etc.
Solution:
I change the array size to be dynamic rather than static. Now the fastest change array size is a function of mpi_size. dim2 = constant *mpi_size. After some tunings, theoretically the above tests should be valid for any number of processors. However, other parallel tests still need to be tuned.
To verify the correctness of these tests, using mpirun -np 5 ./testphdf5 -b cchunk1 at heping.
Platforms tested:
h5committest(shanti is refused to be connected)
at heping, 5 and 7 processes are used to verify the correctness.
Misc. update:
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Add new tests
Description:
Collective IO doesn't work for some platforms/mpio packages when more than
one process has no contributions to IO.
Solution:
1. Add a collective IO test to verify the correctness of the library when
more than one process has no contributions to IO.
2. Add the similar MPI-IO test in t_mpi to help us maintain in more platforms.
Platforms tested:
heping, mir, copper
Misc. update:
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Enhance collective chunk IO supports
Description:
Add a new test to check the correctness of the HDF5 library behavior for collective IO mode when one process doesn't have any contribution for IO.
Solution:
Platforms tested:
IBM AIX 5.2(copper)
Linux (heping) mpich-1.2.6
Misc. update:
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Code clean-up for collective regular chunk IO tests.
Description:
Add descriptions for each tests for future maintenance.
Solution:
Platforms tested:
Mostly comments, No need to use h5committest.
heping(linux 2.4)
Misc. update:
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bug fix
Description:
The previous version always tests with mpi-IO driver even when mpi-posix driver is set.
Solution:
Add the option to test mpi-posix driver for the first round collective chunk IO test.
Platforms tested:
IRIX64, AIX 5.1, Linux 2.4
Misc. update:
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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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Updating phase 2 work of collective IO
Description:
The current collective IO tests cannot test for number of processors bigger than
some values, this change will lift those restriction. However, the test may be slower.
Solution:
Platforms tested:
linux 2.4, AIX 5.1, Linux 2.4 IA64 and IRIX 6.5
(I haven't tested big number of processors with the restriction of the machine)
Misc. update:
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typo fix and small improvement.
Description:
t_coll_chunk.c:
ccdataset_vrfy() was using a wrong routine name to identify itself.
testphdf5.c:
Add a definition of NFILENAME to be the common dimension size of
FILENAME[] and filenames[][] since they must have the same first
dimension size.
Platforms tested:
h5committested.
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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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Bug fix
Description:
Relax restrictions on parallel I/O to allow compressed, chunked datasets
to be read in parallel (collective access will be degraded to independent
access, but will retrieve the information still).
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Solaris 2.7 (arabica)
IRIX64 6.5 (modi4)
h5committest
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Make collective chunk IO test more general
Description:
Previously collective chunk IO test is only fit for processor =4 with
the dimension size to be set small; sometimes people would like to test
with more than 4 processors(5,6 or more), the test therefore failed.
Solution:
To make the test case more general, dimensional size of the data is set to be large(right now 288 for each dimension), the disjoint hyperslab selection is re-calculated. Now the test cases should pass with 5,6 or 12 processors. Note, there is nothing wrong with the implementation of the library, it is the test case that causes the failure with the number of processor greater than 4.
Platforms tested:
Only at eirene, since only the test code is modified a little and it is very slow to test the parallel case.
Misc. update:
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Code cleanup
Description:
Clean up collective chunking code a bit.
Also, add '--enable-instrument' configure flag to have a mechanism for
determining that optimized operations happened correctly in the library (instead
of just the "normal" way) by allowing 'flag' properties to be set outside the
library and set when the "right" thing happens. This is mainly for debugging
and regression checks, so we make certain we don't break optimized I/O by
accident. It's enabled by default when --enable-debug is on (which is on by
default in the development branch and off by default in the release branch),
but can also be independently controlled with its own configure flag.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
IBM p690 (copper) w/parallel
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To test collective chunk IO properly.
Description:
See the previous message.
Solution:
See the previous message.
Platforms tested:
arabica(Sol 2.7), eirene(Linux), copper(AIX)
Misc. update:
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To add collective chunk IO tests.
Description:
three tests are added.
1. Only one hyperslab for each process, and this hyperslab is fit in exactly one chunk.
2. non-contiguous hyperslabs in each process, these hyperslabs are fit in one chunk.
3. Single hyperslab for each process, smaller chunk is assigned. Number of chunks for
every process is equal.
Solution:
the dataset size is set to be very small, will enlarge later.
Platforms tested:
AIX 5.1(copper)
Misc. update:
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