Absolutely > On Apr 29, 2016, at 11:42 AM, Kris Kuhlman <[email protected]> > wrote: > > Thanks for figuring this out. Will the patched fipy version be available from > the github repository? > > Kris > > On Wed, Apr 27, 2016 at 3:17 PM, Keller, Trevor (Fed) > <[email protected]> wrote: > Looking into the rest of the FiPy source, we're already calling > allgather(sendobj) in several places, and rarely calling allgather(sendobj, > recvobj). To preserve the existing function calls (all of which are > lower-case) and mess with the code the least, removing the recvobj argument > appears to be the right call after all. > > Working on the PR. > > Trevor > > ________________________________________ > From: [email protected] <[email protected]> on behalf of Guyer, > Jonathan E. Dr. (Fed) <[email protected]> > Sent: Wednesday, April 27, 2016 4:39:05 PM > To: FIPY > Subject: Re: globalValue in parallel > > It sounds like you're volunteering to put together the pull request with > appropriate tests > > > On Apr 27, 2016, at 4:06 PM, Keller, Trevor (Fed) <[email protected]> > > wrote: > > > > The mpi4py commit mentions that the receive object is no longer needed for > > the lower-case form of the commands. Browsing the full source shows that > > the upper-case commands retain both the send and receive objects. To avoid > > deviating too far from the MPI standard, I'd like to suggest changing the > > case (Allgather instead of allgather), rather than dropping buffers, in our > > mpi4pyCommWrapper.py. > > > > Trevor > > > > > > ________________________________________ > > From: [email protected] <[email protected]> on behalf of Guyer, > > Jonathan E. Dr. (Fed) <[email protected]> > > Sent: Wednesday, April 27, 2016 3:53:39 PM > > To: FIPY > > Subject: Re: globalValue in parallel > > > > It looks like 'recvobj' was removed from mpi4py about two years ago: > > > > https://bitbucket.org/mpi4py/mpi4py/commits/3d8503a11d320dd1c3030ec0dbce95f63b0ba602 > > > > but I'm not sure when it made it into the released version. > > > > > > It looks like you can safely edit fipy/tools/comms/mpi4pyCommWrapper.py to > > remove the 'recvobj' argument. > > > > > > We'll do some tests and push a fix as soon as possible. Thanks for alerting > > us to the issue. > > > > Filed as https://github.com/usnistgov/fipy/issues/491 > > > > > >> On Apr 27, 2016, at 2:23 PM, Kris Kuhlman <[email protected]> > >> wrote: > >> > >> I built the trilinos-capable version of fipy. It seems to work for serial > >> (even for a non-trivial case), but I am getting errors with more than one > >> processor with a simple call to globalValue(), which I was trying to use > >> to make a plot by gathering the results to procID==0 > >> > >> I used the latest git version of mpi4py and trilinos. Am I doing something > >> wrong (is there a different preferred way to gather things to a single > >> processor to save or make plots?) or do I need to use a specific version > >> of these packages and rebuild? It seems the function is expecting > >> something with a different interface or call structure. > >> > >> Kris > >> > >> python test.py > >> hello from 0 out of 1 [ 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1.] > >> > >> `--> ~/local/trilinos-fipy/anaconda/bin/mpirun -np 1 python test.py > >> hello from 0 out of 1 [ 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. > >> 1. 1.] > >> > >> --> ~/local/trilinos-fipy/anaconda/bin/mpirun -np 2 python test.py > >> hello from 1 out of 2 > >> Traceback (most recent call last): > >> File "test.py", line 6, in <module> > >> print 'hello from',fp.tools.parallel.procID,'out > >> of',fp.tools.parallel.Nproc,p.globalValue > >> File > >> "/home/klkuhlm/local/trilinos-fipy/anaconda/lib/python2.7/site-packages/fipy/variables/cellVariable.py", > >> line 163, in globalValue > >> self.mesh._globalNonOverlappingCellIDs) > >> File > >> "/home/klkuhlm/local/trilinos-fipy/anaconda/lib/python2.7/site-packages/fipy/variables/meshVariable.py", > >> line 171, in _getGlobalValue > >> globalIDs = > >> numerix.concatenate(self.mesh.communicator.allgather(globalIDs)) > >> File > >> "/home/klkuhlm/local/trilinos-fipy/anaconda/lib/python2.7/site-packages/fipy/tools/comms/mpi4pyCommWrapper.py", > >> line 75, in allgather > >> return self.mpi4py_comm.allgather(sendobj=sendobj, recvobj=recvobj) > >> File "MPI/Comm.pyx", line 1288, in mpi4py.MPI.Comm.allgather > >> (src/mpi4py.MPI.c:109141) > >> TypeError: allgather() got an unexpected keyword argument 'recvobj' > >> hello from 0 out of 2 > >> Traceback (most recent call last): > >> File "test.py", line 6, in <module> > >> print 'hello from',fp.tools.parallel.procID,'out > >> of',fp.tools.parallel.Nproc,p.globalValue > >> File > >> "/home/klkuhlm/local/trilinos-fipy/anaconda/lib/python2.7/site-packages/fipy/variables/cellVariable.py", > >> line 163, in globalValue > >> self.mesh._globalNonOverlappingCellIDs) > >> File > >> "/home/klkuhlm/local/trilinos-fipy/anaconda/lib/python2.7/site-packages/fipy/variables/meshVariable.py", > >> line 171, in _getGlobalValue > >> globalIDs = > >> numerix.concatenate(self.mesh.communicator.allgather(globalIDs)) > >> File > >> "/home/klkuhlm/local/trilinos-fipy/anaconda/lib/python2.7/site-packages/fipy/tools/comms/mpi4pyCommWrapper.py", > >> line 75, in allgather > >> return self.mpi4py_comm.allgather(sendobj=sendobj, recvobj=recvobj) > >> File "MPI/Comm.pyx", line 1288, in mpi4py.MPI.Comm.allgather > >> (src/mpi4py.MPI.c:109141) > >> TypeError: allgather() got an unexpected keyword argument 'recvobj' > >> ------------------------------------------------------- > >> Primary job terminated normally, but 1 process returned > >> a non-zero exit code.. Per user-direction, the job has been aborted. > >> ------------------------------------------------------- > >> -------------------------------------------------------------------------- > >> mpirun detected that one or more processes exited with non-zero status, > >> thus causing > >> the job to be terminated. The first process to do so was: > >> > >> Process name: [[1719,1],1] > >> Exit code: 1 > >> -------------------------------------------------------------------------- > >> > >> <test.py>_______________________________________________ > >> fipy mailing list > >> [email protected] > >> http://www.ctcms.nist.gov/fipy > >> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > > > > > > _______________________________________________ > > fipy mailing list > > [email protected] > > http://www.ctcms.nist.gov/fipy > > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > > > > _______________________________________________ > > fipy mailing list > > [email protected] > > http://www.ctcms.nist.gov/fipy > > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > > > _______________________________________________ > fipy mailing list > [email protected] > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > > _______________________________________________ > fipy mailing list > [email protected] > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > > _______________________________________________ > fipy mailing list > [email protected] > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
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