| Commit message (Collapse) | Author | Age | Files | Lines |
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cache. Fix issues involving datasets being "not allocated" when they
contain cached raw data.
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removed and replace it with new url for COPYING file.
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1) Integrate the patch
2) Fix bugs when debugging the patch
3) Add test to hl/test/test_dset_opt.c
Tested on moohan, ostrich, platypus, emu, osx1010test, quail, kituo, mayll.
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for revise_chunks (#28908).
Tested on jam, platypus, emu, kite, moohan, ostrich, osx1010test, quail.
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Bring r26213 from trunk to 1.8 branch:
Minor code cleanups, to align with revise_chunks branch.
Tested on:
Mac OSX/64 10.10.2 (amazon) w/serial & parallel
(h5committested on trunk for 2+ weeks)
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Renamed H5_ASSIGN_OVERFLOW() to H5_CHECKED_ASSIGN() and re-ordered
the arguments to be in a more logical order.
Fixes HDFFV-9322
Tested on: h5committest
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- add 2 missing feature flags for VFDs: H5FD_FEAT_HAS_MPI & H5FD_FEAT_ALLOCATE_EARLY and use them as appropriate.
tested with h5commitest
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Aligning code with changes made in VOL branch. This will make porting
non VOL related changes from trunkto the 1.8 branch much easier.
tested h5commitest.
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Bring r24995 and r24998 from the trunk to the 1.8 branch:
r24995:
Improve checks for NULL buffer from user during H5Dread/H5Dwrite calls.
r24998:
Check in Neil's changes for correctly handling case where library is
reinitialized through a deprecated routine.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/serial & paralle
(change has baked on trunk for >7 days)
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Bring r24769 & r24772 from trunk to 1.8 branch:
Check in Mohamad's changes to support collective I/O on point selections,
along with some other minor cleanups.
Correct some dynamically sized arrays that fail on Windows.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/parallel
(And has been through the daily test regime on the trunk)
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Bring r23713 and r23717 from trunk to 1.8 branch:
Clean up warnings, switch library code to use Standard C/POSIX wrapper
macros, remove internal calls to API routines, update checkapi and checkposix
scripts.
Tested on:
Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN
Big-Endian Linux/64 (ostrich)
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header file H5Iprivate.h is included but not H5Pprivate.h.
Tested on koala, jam, ostrich.
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(r23162).
Tested on koala, jam, ostrich.
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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
Merged from HDF5 trunk r22735, r22741 , 22743, 22744, 22763.
Tested:
jam-pp (linux32-LE), koala-pp (linux64-LE), wallaby-pp
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Bring r22287 from trunk to 1.8 branch:
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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memory and caused seg fault. I added checks in two places to make sure the library returns error stack
when it fails to allocate memory. I didn't add any test to the test suite since there is no good way to test it. But I tested and verified the error stack by hand.
Tested on jam - this is a merge from the trunk.
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Bring r21919-21924 from trunk to 1.8 branch: cleanup FUNC_ENTER macros,
etc.
Also removed Subversion mergeinfo tags from a few directories and files.
These are artifacts from non-root merges using pre-1.6 Subversion clients. (This
should fix the problem of unchanged directories looking "changed" during
checkins.)
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug & production
(daily tested on trunk)
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Bring r21442 and r21529 from trunk to 1.8 branch: Add new API routines
for querying if collective raw data I/O was actually performed collectively.
Tested:
Linux/32 2.6 (jam)
(h5committested on trunk)
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Bring r19092 from trunk to 1.8 branch:
Bring "shape same" changes from LBL branch to trunk. These changes
allow shapes that are the same, but projected into dataspaces with different
ranks to be detected correctly, and also contains code to project a dataspace
into greater/lesser number of dimensions, so the I/O can proceed in a faster
way.
These changes also contain several bug fixes and _lots_ of code
cleanups to the MPI datatype creation code.
Many other misc. code cleanup are included as well...
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
(h5committested on trunk)
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Description:
Modified algorithm for extending a dataset with early allocation so it only
deals with the new chunks. Formerly, it would loop over all chunks, checking
to see if each existed in cache and on disk, causing major performance issues
with large numbers of chunks.
Tested: jam, linew, amani (h5committest)
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Bring r18031 from trunk to 1.8 branch:
Bring r18030 from merge_metadata_journaling branch to trunk:
Bring "brush clearing" changes (whitespace & style issues, mostly) from
metadata_journaling branch to the "merging" branch, to converge the trunk and
the metadata_journaling branch.
Also, some other minor cleanups along the way.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
(h5committested on trunk)
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type. But when it's in a
compound type, it says it's a VL type. We want to tell user a VL string is a string. But
internally we treat it as a VL type. I added a flag as a parameter of H5T_detect_class. It
tells whether the caller is the public function H5Tdetect_class. I also added a detection for
VL string in the private function for the compound case (or array or nested VL type).
Tested with h5committest.
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Correct 'src' to 'dst' in error message for H5D_read. (Bz#1683)
Tested on:
Eyeballed only - too minor to require h5committest
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Bring r17778 from trunk to 1.8 branch:
Make check for NULL dataspace a bit safer.
Tested on:
FreeBSD/32 6.3 (duty)
(too minor for h5committest)
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Bring r17281 from trunk to 1.8 branch:
Further refactoring of the dataset layout information, to separate the
storage information from the layout info.
Tested on:
Mac OS X/32 10.5.7 (amazon) debug & production
h5committested on trunk
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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 r16354 back from trunk:
Refactor internal layout information, making it easier to add another
type of chunk index.
Tested on:
FreeBSD/32 (duty)
(other configurations tested with original change)
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Bring revision 16278 back from revise_chunks branch:
Update layout information in DCPL to unify all information in one
underlying property and switch to using H5O_layout_t for storing it, which
simplifies things considerably.
Also, fix many compiler warnings.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(Original patch tested on many machines)
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Description: The optimized "subset" compound conversion function would
improperly copy the "blank" space at the end of compound types. Modified
H5T_conv_struct_init to detect when the subset type has extra space at the end,
and calculate the size of the data that should be copied into the conversion
buffer for each element. Changes to the functions that implement these
conversions.
Tested: kagiso, linew, smirom (h5committest)
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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 r15609 back from trunk:
Omnibus compiler warning cleanup & some formatting happiness.
Tested on:
Mac OS X/32 10.5.4 (amazon)
Too minor to require h5committest
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Bring back revision 15131 from trunk:
Finish omnibus chunked dataset I/O refactoring, to separate general
actions on chunked datasets from actions that are specific to using the v1
B-tree index.
Cleaned up a few bugs and added some additional tests also.
Tested on:
Mac OS X/32 10.5.3 (amazon)
Linux/32 2.4 (chicago)
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Bring revision 15037 from trunk:
Better cleanup of internal structures when no szip encoder.
Tested on:
Linux/32 2.6 (kagiso) w/szip-no encoder
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Bring revision 14860 back to 1.8 branch, change log for rev 14860 is:
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.
Description:
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:
Mac OS X/32 10.5.2 (amazon) w/production
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Correct the prototype for H5Sselect_elements() to take an 'hsize_t *' for
the coordinates, instead of 'hsize_t **'.
Tested on:
Mac OS X/32 10.5.1 (amazon)
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- Avoid trying to update 1-D dataset's chunk indices (they can't change)
- Cache a copy of a dataspace describing a chunk, when doing single
element I/O
- Keep a 'chunk info' struct around, for single element I/O
- Avoid creating a skip list for chunk infos when performing I/O on single
element
Also, minor formatting cleanups to testing code
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
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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- Keep skip list for tracking chunks with dataset (instead of creating/
destroying it for each I/O operation) and just delete the skip list
nodes.
- Avoid computations for normalizing selection offset when offset not set.
- Avoid updating object modification time twice during dataset creation.
- Avoid updating dataset layout message (and object modification time)
until dataset is closed.
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
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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Add call to reset cached chunk info after initialization of chunk data
storage.
Tested on:
Linux/64 2.4(smirom) w/parallel
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- Eliminate some redundant calls to retrieve datatype sizes in chunk read/
write routines.
- Change indexed storage "common" B-tree callback user data to avoid
copying chunk offset and separate "downward" info from "upward" info.
- Cache chunk info (nbytes/filter_mask/address) for last chunk accessed
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
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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- Remember # of elements in file selection, instead of querying more than
once
- Handle building chunk map for single element as special case
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
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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Avoid copying maximum dimensions for temporary dataspaces used for
describing chunks during raw data I/O.
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
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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- Changed name of chunk mapping structure from "fm_map" to "H5D_chunk_map_t"
- Pushed parallel I/O specific fields into ifdef'ed sections, when building
chunk map
- Took out most calls to IS_H5FD_MPI macro
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
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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- Changed H5S_select_shape_same routine to handle scalar dataspace
comparisons correctly. (Added regression tests to verify)
- Simplified chunk map creation, now that scalar dataspaces are handled
in same way as "simple" dataspaces.
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
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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Break up H5D source file into H5D/H5Dint/H5Ddeprec
Attempt fix for "szip noencoder" build failure.
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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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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in H5D_chunk_read and H5D_chunk_write. Tested only on liberty because it's a simple change.
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H5D_istore_writevv and H5D_istore_readvv to
H5D_chunk_write and H5D_chunk_read to avoid frequent lock and unlock and to improve some
performance.
Tested with h5committest on THG machines.
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Refactor fill value buffer code into one location, for better long-term
maintenance.
Tested on:
Mac OS X/32 10.4.10 (amazon)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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No test is needed.
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company. The I/O is optimized when the source and destination
members are a subset of each other one way or another, and
the order is the same, and no conversion is needed. For example:
struct source { struct destination {
TYPE1 A; --> TYPE1 A;
TYPE2 B; --> TYPE2 B;
TYPE3 C; --> TYPE3 C;
}; TYPE4 D;
TYPE5 E;
};
or
struct destination { struct source {
TYPE1 A; --> TYPE1 A;
TYPE2 B; --> TYPE2 B;
TYPE3 C; --> TYPE3 C;
}; TYPE4 D;
TYPE5 E;
};
The optimization is simply moving data from the source to the
appropriate places in the buffer and bypass the reading of
the background data and data conversion.
Tested on smirom, liberty, sol, and copper.
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