| Commit message (Collapse) | Author | Age | Files | Lines |
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* Modify temporary rpath for testing in java example scripts.
* Update URL in source file Copyright headers for web copy of COPYING
file - files not in src or test.
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* Basic alignment with async branch - trivial changes to reduce clutter in overall diff.
* Update minor error code to reflect change within library
* Update the error output to match library
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This reverts commit 8b9338ab57eec0cc8fa5a36c44d7b28e52e9a466.
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collective read of full (HS_ALL), contiguous, atomic datasets by all the processes in the file communicator.
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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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Align w/revise_chunks branch
Tested on:
MacOSX/64 10.11.4 (amazon) w/parallel
(h5committest forthcoming)
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Bring "don't filter partial edge chunks" capability from revise_chunks
to trunk.
Tested on:
MacOSX/64 10.11.4 (amazon) w/debug, production & parallel
(h5committest forthcoming)
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- set default to FALSE
- fix some bugs.
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features/autotools_rework
branch.
Removed the configure option that allows selective disabling of individual
internal filters (fletcher32, shuffle, etc.).
This feature mucked up the code with a lot of #ifdefs, saved very little space,
and was not scalable to a general scheme for library size reduction. We've
decided to remove the feature while we investigate a more general scheme for
decreasing the library size.
Part of: HDFFV-9086
Tested on: h5committest
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proportional to the process count without regard to the 64KB limit for
compact datasets.
tested on jam with parallel.
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HDF5_PARAPREFIX is ignored in parallel dense attribute and performance tests.
tested on Jam w/ parallel.
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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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with 1
or 2 processes.
First bug is in testpar/t_mdset.c, where the test reports an error in
addition to skipping the test if there are less than three procs. Fix
to just skip the test.
Second bug is in testpar/t_dset.c in actual_io_mode tests, where
incorrect expected value for IO mode was set if the number of procs
running the test is 1.
tested with h5committest.
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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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Daily test failed in koala with parallel and v16compat API from the previous
commit r22735.
Descriptoin:
Changed to use H5Dopen2() instead of H5Dopen().
Tested: koala --enable-parallel --with-default-api-version=v16.
No h5committest test since this is limited to parallel test program.
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Correct API version mistake w/H5Acreate -> H5Acreate2
Tested on:
Mac OSX/64 10.8.3 (amazon) w/parallel
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Stop aliasing property to indicate internal collective metadata operations
with property to perform collective raw data operations from the application.
Tested on:
Mac OSX/64 10.8.3 (amazon) w/paralllel
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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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HDFFV-8143 Provide a routine(s) for telling the user why the library broke collective data access
Description:
Fixed Daily test failed from the previous commit r22735. (ember)
Also changed H5Pget_mpio_no_collective_cause() parameter type from
H5D_mpio_no_collective_cause_t to uint32_t due to change to return
combined bitmap value which can be not emun defined value.
Tested:
jam (linux32-LE), koala-pp (linux64-LE), ember, h5committest
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HDFFV-8143 Provide a routine(s) for telling the user why the library broke collective data access
Description:
Daily test failed from the previous commit r22735. (ember)
Skip tests not to disrupt other tests while finding a solution for ember.
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HDFFV-8143 Provide a routine(s) for telling the user why the library broke collective data access
Description:
Daily test failed from the previous commit r22735. (ember)
Follow actual_io function to sync before go futher as this is similar
function.
Tested:
jam (linux32-LE), koala-pp (linux64-LE), ember
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HDFFV-8143 Provide a routine(s) for telling the user why the library broke collective data access
Description:
Daily test failed from the previous commit r22735. (koala , ember)
Fixed failure due to not be able to read external-storage file from external test.
Tested:
jam (linux32-LE), koala-pp (linux64-LE)
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HDFFV-8143 Provide a routine(s) for telling the user why the library broke collective data access
Description:
Added H5Pget_mpio_no_collective_cause() function that retrive reasons why the collective I/O was broken during Read/Write IO access.
Reasons to break collective I/O:
- SET_INDEPENDENT
- DATATYPE_CONVERSION
- DATA_TRANSFORMS
- MPIPOSIX
- NOT_SIMPLE_OR_SCALAR_DATASPACES (NULL Space)
- POINT_SELECTIONS
- NOT_CONTIGUOUS_OR_CHUNKED_DATASET (Compact or External-Storage)
- FILTERS
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
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test with cmd arguments -o or -x
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Clean up more FUNC_ENTER/FUNC_LEAVE macros and move H5D & H5T code toward
the final design (as exemplified by the H5EA & H5FA code).
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug & parallel
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opened with the MPI-IO VFD
Add test cases for these two routines
Jira issue HDFFV-7961
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Check in "actual I/O mode" feature to trunk. Will merge back to 1.8 branch
after it bakes over the weekend.
Tested on:
FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode
FreeBSD/64 8.2 (freedom) w/gcc4.6, 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 (koala) 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, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-ia64 2.6 (ember) 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 10.6.8 (amazon) in debug mode
Mac OS X/32 10.6.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
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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Fix typo from recent changes
Tested on:
None - just eyeballed.
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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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Deprecate H5Dextend in favor of H5Dset_extent (without using API
versioning, due to changed behavior) and switch internal usage to H5Dset_extent
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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Clean up a few remaining API compatibility issues in the H5E API for
parallel configurations
Tested on:
FreeBSD/64 6.2 (liberty) w/parallel
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1. In H5Dwrite and H5Dread, let the data buffer point to a fake address if the application passes
in an empty buffer. This is mainly for MPIO programs that some processes may not have any
data to write or read but still participate the I/O. This solution solves some MPI's problem
like the ChaMPIon on tungsten which doesn't support empty buffer.
2. The ChaMPIon on tungsten doesn't support complex derived MPI data type correctly and collective
I/O when some processes don't have any data to write or read correctly. Detect the compiler
"cmpicc" in the system-specific config file and set the variables for these two cases to false.
The PHDF5 library already has set up a way to switch collective chunked I/O to independent
under these two cases.
3. A bug fix - During the work of the optimization for compound data I/O, the case for switching
collective chunked I/O to independent I/O was leftout. Fixed it by adding I/O caching to it in
H5D_multi_chunk_collective_io in H5Dmpio.c.
Tested on tungsten, cobalt, and kagiso for parallel; on linew and smirom for serial.
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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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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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