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 ]
