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* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | 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.
* Final merge of page buffering branch to developQuincey Koziol2017-03-141-3/+3
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* [svn-r30270] Fix an issue that could occur when allocating a chunked dataset ↵Neil Fortner2016-08-081-0/+86
| | | | | | | | | in parallel, with an alignment threshold set to be larger than the chunk size but smaller than the size of the small data aggregator. Tested: koala, ostrich (h5committest); jelly, ummon
* [svn-r29079] rename the coll read requirement function.Mohamad Chaarawi2016-02-101-1/+2
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* [svn-r29077] Description:Quincey Koziol2016-02-101-1/+1
| | | | | | | | Normalize against the trunk, in preparation for final merge. Tested on: MacOSX/64 10.11.3 (amazon) w/serial & parallel (h5committest not required on this branch)
* [svn-r27261] apply metadata enhancement patch that was based on the mdc 3 ↵Mohamad Chaarawi2015-06-211-0/+1
| | | | branch.
* [svn-r25401] add serial and parallel regression tests for zero dset ↵Mohamad Chaarawi2014-07-091-0/+57
| | | | read/write bug.
* [svn-r24864] Description:Quincey Koziol2014-03-211-22/+12
| | | | | | | | | | | | | | | | | | 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
* [svn-r24612] fix bugs in parallel tests exposed in corner cases when running ↵Mohamad Chaarawi2014-01-061-6/+3
| | | | | | | | | | | | | | | | 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.
* [svn-r19722] Bug fix for failure in the round robin metadata write ojbect headerJohn Mainzer2010-11-031-0/+3
| | | | | | | metadata confusion test that appeared after Albert modified the test. Cursory commit test. No test on Abe as that system is down, the fix is very minor, and it seems to work in the 1.8.6 branch
* [svn-r19682] Bug 2054: Round Robin code caused H5FFlush to corrupt a file.Albert Cheng2010-10-281-113/+491
| | | | | | | | | John Mainzer fixed the bug and added a test which wrote file and flush a few time; close the file then open it by serial and read simple structure. I changed the test to two parallel running parts of ..._writer and ..._reader and have the reader verify the file after every flush by the writer. Tested: parallel in Jam and Amani.
* [svn-r19646] John Mainzer2010-10-191-6/+6
| | | | | | | | | | Replaced calls to H5Dcreate() and H5Acreate() with calls to H5Dcreate2() and H5Acreate2() respectively in t_mdset.c. This was done to repair a compile failure that occured on a build with the --with-default-api-version=v16 config option Cursory commit test
* [svn-r19632] John Mainzer2010-10-181-1/+1
| | | | | | | Modified test code in t_mdset to use H5Dopen2() instead of H5Dopen1(). This should fix the compile failure when we used --disable-deprecated-symbols Cursory commit test
* [svn-r19622] Port of fix for the round robin parallel flush bug caused by ↵John Mainzer2010-10-171-0/+512
| | | | | | | | | | | | | | | | | | | | | | | | | | the failure of the H5Ocache.c code to update its image of the on disk representation of the object header on a call to the clear callback. This wasn't an issue as long as all flushes of the object header were made from the same process, but if an object header is modified, and then flushed on one process and cleared on the rest, the changes were not be reflected in the images of the on disk representation on all processes where the object header was cleared rather than flushed. If one of these processes did the next flush, the changes were lost in the on disk representation. Fixed this by causing all dirty messages and to be written to the copy of the on disk image maintained by the object header code on both flush and clear. Also added associated test code in t_mdset.c. Also checking in some cache debug code developed while chasing this bug. Commit tested and tested (parallel) on phoenix.
* [svn-r17376] Description:Quincey Koziol2009-08-181-3/+3
| | | | | | | | | | | Make similar change to windows VFD as sec2 VFD, when converting from a family file to a single file. Tweak file sizes expected for parallel tests. Tested on: tg-login3, w/parallel Windows (post facto)
* [svn-r16560] Description:Quincey Koziol2009-03-101-37/+32
| | | | | | | | | | 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)
* [svn-r15825] Description:Quincey Koziol2008-10-091-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | Fix various problems with a the core & sec2 VFDs. Improve the h5_get_file_size() routine to handle files created with VFDs that use multiple files. 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
* [svn-r15628] Description:Quincey Koziol2008-09-161-1/+1
| | | | | | | | | | | | | 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...
* [svn-r15183] Purpose: _WIN32 macro cleanupScott Wegner2008-06-091-6/+0
| | | | | | | | | | Description: As part of our Windows cleanup, we try to remove windows-specific tweaks in the source code. There are many instances where Windows code is introduces via ifdef's. We re-evaluate whether they are still required, and found that many of them are not. Others we change to "feature"-specific code, rather than Windows-specific. Tested: VS2005 on WinXP VS.NET on WinXP h5committest (kagisopp, smirom, linew)
* [svn-r14420] Description:Quincey Koziol2008-01-151-1/+1
| | | | | | | | 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)
* [svn-r14218] Description:Quincey Koziol2007-10-301-3/+3
| | | | | | | | | | | | | | | | | | | | | Changed H5Acreate2 -> H5Acreate_by_name, to be more consistent with other new API routines. Re-added simpler form of H5Acreate2, which creates attributes directly on an object. 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
* [svn-r14217] Description:Quincey Koziol2007-10-301-3/+3
| | | | | | | | | | | | | | | | | | | | | Change H5Aopen -> H5Aopen_by_name, in order to be more consistent with other new API routines. Re-add H5Aopen as a simpler routine, to open attributes on a particular object. (Much like the old H5Aopen_name routine). 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
* [svn-r14199] Description:Quincey Koziol2007-10-111-248/+216
| | | | | | | | | | | | | | | | | | | | | 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
* [svn-r14193] Description:Quincey Koziol2007-10-081-6/+6
| | | | | | | | | | | | | | | | | | | 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
* [svn-r14187] Description:Quincey Koziol2007-10-041-8/+8
| | | | | | | | | | | | | | | | | | | | Put H5Acreate() under API versioning, with all internal usage shifted to H5Acreate2(). Add regression tests for H5Acreate1(). 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
* [svn-r14185] Description:Quincey Koziol2007-10-041-8/+6
| | | | | | | | | | | | | | | | | | | | | Move H5Aopen_name() routine to deprecated symbol section and replace internal usage with H5Aopen(). Add simple regression test for H5Aopen_name() to deprecated routine test. 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
* [svn-r14115] Description:Quincey Koziol2007-08-281-5/+5
| | | | | | | | | | | | | | | | | Remove all plain calls to H5Gopen() from source, replacing them with either H5Gopen2(). Add test for H5Gopen1(). Reformatted several pieces of code, to clean them up. Tested on: FreeBSD/32 6.2 (duty) FreeBSD/64 6.2 (liberty) Linux/32 2.6 (kagiso) Linux/64 2.6 (smirom) Solaris/32 5.10 (linew) Mac OS X/32 10.4.10 (amazon)
* [svn-r14104] Description:Quincey Koziol2007-08-231-3/+3
| | | | | | | | | | | | | Pursue calls to H5Gcreate() relentlessly and ruthlessly exterminate them, leaving only a few tame specimens in text files and comments. ;-) Tested on: Mac OS X/32 10.4.10 (amazon) FreeBSD/32 6.2 (duty) FreeBSD/64 6.2 (liberty) Linux/32 2.6 (kagiso) Linux/64 2.6 (smirom) Solaris/32 5.10 (linew)
* [svn-r13766] In Visual Studio 2005 for 64-bit, _WIN32 is defined, but not ↵Scott Wegner2007-05-181-3/+3
| | | | | | | 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
* [svn-r13253] Updated all C and C++ style source code files with the THG ↵Albert Cheng2007-02-071-2/+3
| | | | | | | | | 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.
* [svn-r12966] Fixed an missing parameter in a printf call in io_mode_confusion.Albert Cheng2006-11-221-1/+1
| | | | Tested in heping pp.
* [svn-r12750] Purpose:Albert Cheng2006-10-121-3/+3
| | | | | | | | | | | Bug Fix (Bug 544) Description: SGI Altix's MPI_File_get_size overflowed at 2GB and more. Replaced h5_mpi_get_file_size calls by h5_get_file_size. Tested: Cobalt.
* [svn-r12554] New tests have been added to test the correctness of ↵MuQun Yang2006-08-091-1/+31
| | | | | | | | 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.
* [svn-r11470] Purpose:John Mainzer2005-09-271-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Repair synchronization bug in the metadata cache in PHDF5 Also repair numerous other bugs that surfaced in testing the bug fix. Description: While operations modifying metadata must be collective, we allow independant reads. This allows metadata caches on different processes to adjust to different sizes, and to place the entries on their dirty lists in different orders. Since only process 0 actually writes metadata to disk (all other processes thought they did, but the writes were discarded on the theory that they had to be collective), this made it possible for another process to modify metadata, flush it, and then read it back in in its original form (pre-modification) form. The possibilities for file corruption should be obvious. Solution: Make the policy that only process 0 can write to file explicit, and visible to the metadata caches. Thus only process 0 may flush dirty entries -- all other caches must retain dirty entries until they are informed by process 0 that the entries are clean. Synchronization is handled by counting the bytes of dirty cache entries created, and then synching up between the caches whenever the sum exceeds an (eventually user specified) limit. Dirty metadata creation is consistent across all processes because all operations modifying metadata must be collective. This change uncovered may bugs which are repaired in this checkin. It also required modification of H5HL and H5O to allocate file space on insertion rather than on flush from cache. Platforms tested: H5committest, heping(parallel & serial) Misc. update:
* [svn-r11450] Purpose:Pedro Vicente Nunes2005-09-211-3/+9
| | | | | | | | | | | | | | | | | | bug fix Description: the MPI_File_get_size returns a different value in one of the tests in Windows comment the code and not run the test in windows a ULL suffix on the harcoded return VRY return number is needed on AIX Solution: Platforms tested: Windows AIX Misc. update:
* [svn-r11448] Purpose:Pedro Vicente Nunes2005-09-211-3/+3
| | | | | | | | | | | | | | | | | | | new features Description: add support for compiling the library and testphdf5 in Windows Solution: Platforms tested: Linux AIX Solaris Windows VC6 Misc. update:
* [svn-r11245] Purpose:Quincey Koziol2005-08-131-149/+149
| | | | | | | | | | | | | | | | | | | | 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
* [svn-r9727] Purpose:Quincey Koziol2004-12-291-37/+36
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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:
* [svn-r9358] Purpose:Quincey Koziol2004-10-041-2/+0
| | | | | | | | | | | | | | | 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
* [svn-r9274] Purpose:John Mainzer2004-09-181-0/+289
| | | | | | | | | | | | | | | | | | | | | | | | | Add test to verify the fix of the parallel I/O mode confusion bug. Description: While the parallel I/O mode confusion bug is fixed, an automated regression test for this bug would be useful. Solution: Added a modified version of the original bug demonstration program to testphdf5. Platforms tested: copper h5committested eirene (parallel) Misc. update:
* [svn-r9149] Purpose:John Mainzer2004-08-241-90/+282
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Fix of bug/feature which caused testphdf5 to fail when run with more than 32 processes. This fix was originally applied to the 1.6 branch, and is now ported to the 1.7 branch. Description: 32 process limit was a hard coded constant. Solution: Modified most of the routines in t_mdset.c to adapt dynamically to the current number of processes. In passing, I also tidied up a few memory leaks. Note that one new routine had been added to the 1.7 version of t_mdset.c since the 1.6/1.7 split. I applied changes to this routine as well. Platforms tested: h5committested Tested on eirene with 4 and 8 processes. Couldn't go higher. I would have like to repeat my 32 - 64 process tests on copper, but was unable to do so as I don't have access to cu12t at present. Perhaps I will be able to manage this in the next few days. However, Albert wanted these changes checked in to the 1.7 branch so he could work with them. Misc. update:
* [svn-r9141] Purpose:Albert Cheng2004-08-241-0/+3
| | | | | | | | | | | Code cleanup. Removed bunch of old options (r,w,v,i,b,e) that are no longer valid or useful after adopting the general test interface. Moved the test of sizeof MPI_Offset into the test routine itself. Platforms tested: Eirene and Sol using pp mode.
* [svn-r8533] Purpose: New test.Raymond Lu2004-05-171-1/+97
| | | | | | | Description: Test dataset and attribute of null dataspace for parallel. Platforms tested: copper and verbena(only parallel is concerned)
* [svn-r8294] Purpose:Albert Cheng2004-04-011-8/+49
| | | | | | | | | | | | | feature Description: Change testphdf5 to use the common test program syntax. Needed to change the protocols of all test programs to fit the requirement of the common test syntax. Platforms tested: "h5committested". Also tested in sol with PP mode.
* [svn-r8096] Purpose:Albert Cheng2004-01-221-8/+8
| | | | | | | | | | | | | | | | Improvement. Description: Complete change of the verbose control to use the routines provided by the test/libh5test.a. Also put in a temporary fix for the H5Eset_auto() and H5Eget_auto() so that the Compat code are isolated in one place rather than all over the source file. Platforms tested: Tested in Eirene (parallel). Misc. update:
* [svn-r8013] Description:Albert Cheng2004-01-031-30/+71
| | | | | | | | | | | | Added a test of fill value before any data is written to a dataset. Rename short_dataset() as dataset_fillvalue() as it reflects better the tests. Also removed the option of -S since the fill value test will be tested always. Platforms tested: "h5committested" Misc. update:
* [svn-r7979] Purpose:Albert Cheng2003-12-251-0/+134
| | | | | | | | | | | | Feature. Description: Added the short_dataset test (was in v1.6 first.) Platforms tested: Tested in eirene (pp) only since these have been tested in v1.6 already. Misc. update:
* [svn-r7615] Purpose:Quincey Koziol2003-10-131-1/+0
| | | | | | | | | | | Code cleanup Description: Clean up various compiler warnings. Platforms tested: FreeBSD 4.9 (sleipnir) w/parallel too minor to require h5committest
* [svn-r7551] Purpose:Quincey Koziol2003-10-061-24/+2
| | | | | | | | | | | | | | | Bug/feature fix. Description: Relax restriction on parallel writing to compact datasets to allow partial I/O. Updates to reference manual mentioning the issues involved are delayed until reference manual 'lock' is removed later this week. Platforms tested: FreeBSD 4.9 (sleipnir) too minor to require h5committest
* [svn-r7480] Purpose:Quincey Koziol2003-09-161-0/+118
| | | | | | | | | | | | | | | | | Bug fix Description: The MPI_File_set_size() routine on ASCI Red is not able to extend files so that they are larger than 2GB. Solution: Add an extra macro which controls whether MPI_File_set_size() can handle >2GB offsets or if our "older" way of reading a byte, then writing a byte at the appropriate offset should be used. Platforms tested: FreeBSD 4.9 (sleipnir) h5committest
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