Search found 22 matches

by nizar
Wed Sep 15, 2010 11:20 am
Forum: NEURON + Python
Topic: import neuron MPI_Allreduce
Replies: 16
Views: 5716

Re: import neuron MPI_Allreduce

When I looked for _ZN3MPI3Win4FreeEv in your /usr/lib/*mpi*.so and /usr/lib/openmpi/*.so I could not find any mention of it. Also (the few) other people who have launched python and used mpi and neuron have not mentioned this problem to me. I admit I have only worked around the problem by avoiding ...
by nizar
Wed Sep 15, 2010 10:17 am
Forum: NEURON + Python
Topic: import neuron MPI_Allreduce
Replies: 16
Views: 5716

Re: import neuron MPI_Allreduce

http://www.neuron.yale.edu/hg/neuron/nrn/rev/9627af59454a fixes the problem by avoiding the include of mpi.h in the c++ file used to extend python with NEURON. This makes me question whether your mpi is complete in regard to the c++ interface. But no matter. The work around should be quite effectiv...
by nizar
Wed Sep 15, 2010 8:17 am
Forum: NEURON + Python
Topic: import neuron MPI_Allreduce
Replies: 16
Views: 5716

Re: import neuron MPI_Allreduce

It's neuron-7.2 (alpha) nrniv -python -mpi shows no errors: numprocs=1 NEURON -- VERSION 7.2 (458:6f3a69e6667a) 2010-08-19 Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008 See http://www.neuron.yale.edu/credits.html but launching python and extending with NEURON Python 2.6.5 (release26-m...
by nizar
Wed Sep 15, 2010 5:12 am
Forum: NEURON + Python
Topic: import neuron MPI_Allreduce
Replies: 16
Views: 5716

Re: import neuron MPI_Allreduce

Trying to install on other machines, but now getting

Code: Select all

ImportError: /usr/lib64/python2.6/site-packages/neuron/hoc.so: undefined symbol: _ZN3MPI3Win4FreeEv
Any hint?

Thanks,
N.
by nizar
Sun Sep 05, 2010 9:33 am
Forum: NEURON + Python
Topic: import neuron MPI_Allreduce
Replies: 16
Views: 5716

Re: import neuron MPI_Allreduce

Thanks Hines, replacing gcc -shared... with mpicc -shared solved one problem, but then when doing python from mpi4py import MPI from neuron import h I get segmentation fault, I couldn't know why, but replacing mpich2 with open mpi solved all issues!. Now all works together perfectly, python-2.6, neu...
by nizar
Tue Aug 24, 2010 5:12 am
Forum: NEURON + Python
Topic: import neuron MPI_Allreduce
Replies: 16
Views: 5716

Re: import neuron MPI_Allreduce

No difference after updating LD_LIBRARY_PATH echo $LD_LIBRARY_PATH: /usr/local/nrn/x86_64/lib:/opt/mpich2/lib import neuron from python: Python 2.6.5 (release26-maint, Aug 22 2010, 12:25:09) [GCC 4.4.3] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import neuro...
by nizar
Sun Aug 22, 2010 10:29 am
Forum: NEURON + Python
Topic: import neuron MPI_Allreduce
Replies: 16
Views: 5716

Re: import neuron MPI_Allreduce

Looks like you skipped the python setup.py install step--see http://www.neuron.yale.edu/neuron/download/compile_linux I didn't, My original post: installing nrnpython under src/nrnpython: running install running build running build_py creating build creating build/lib.linux-x86_64-2.6 creating buil...
by nizar
Sun Aug 22, 2010 7:30 am
Forum: NEURON + Python
Topic: import neuron MPI_Allreduce
Replies: 16
Views: 5716

import neuron MPI_Allreduce

Hello all, I'm trying to make neuron, python and mpich2 all work together. compiling neuron: ./configure --prefix=`pwd` --with-nrnpython=/usr/bin/python2 --with-paranrn --with-mpi MPICC=/opt/mpich2/bin/mpicc MPICXX=/opt/mpich2/bin/mpicxx && make && make install compiling mpich2: ./configure --prefix...
by nizar
Mon Jul 16, 2007 2:38 pm
Forum: Parallel NEURON
Topic: mpi neuron output
Replies: 7
Views: 7096

The multiple printing of banners signifies that the program is running not as a parallel program but as n independent non-communicating programs. What has been left out when you launch is the -mpi argument after the nrniv. nrn-5.9 was compiled with 'always_call_mpi_init=yes' , hence there was no ne...
by nizar
Mon Jul 16, 2007 1:15 pm
Forum: Parallel NEURON
Topic: mpi neuron output
Replies: 7
Views: 7096

in the previous release we had, nrn-5.9, there was no need to include the -nobanner, more convenient.. the banner is a new behavior(?). it does make sense that only the master process print the banner. running 'mpiexec -n 500 ...', for example, will result in 500 printed banners if the -nobanner was...
by nizar
Mon Jul 16, 2007 11:33 am
Forum: Parallel NEURON
Topic: mpi neuron output
Replies: 7
Views: 7096

You want to get rid of the banner? nrngui -h reveals a list of command line options that include -nobanner do not print startup banner Indeed, the -nobanner disables the banner. Apart from UNIX/Linux solutions like making an alias, Is there a way to tell nrniv to disable the banner when running par...
by nizar
Mon Jul 16, 2007 4:51 am
Forum: Parallel NEURON
Topic: mpi neuron output
Replies: 7
Views: 7096

mpi neuron output

Hi, We had neuron 5-9.9 and just upgraded to 6.0.3, compiled with: ./configure --prefix=`pwd` --without-x --with-paranrn --with-mpi MPICC=/opt/mpich2/bin/mpicc MPICXX=/opt/mpich2/bin/mpicxx I had to edit mpispike.c according to https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=946 the test in $NEUR...
by nizar
Fri Nov 03, 2006 12:19 pm
Forum: UNIX/Linux
Topic: nrn --with-mpi
Replies: 15
Views: 14701

Running parallel, all is fine.

10q
by nizar
Mon Oct 30, 2006 4:57 pm
Forum: UNIX/Linux
Topic: nrn --with-mpi
Replies: 15
Views: 14701

hines wrote:Good. Looks like you are on your way.
wow...
I'll make more tests and let you know.

very many thanks.
by nizar
Mon Oct 30, 2006 4:04 pm
Forum: UNIX/Linux
Topic: nrn --with-mpi
Replies: 15
Views: 14701

The -mpi argument is not implemented unless you are using a 6.0 alpha version. right Are you sure that is all the stdout/stderr information. There should have been a first line printed that gives the number of hosts used. If you used a -mpi arg then any machine that got to the point of execution wh...