www.neuron.yale.edu

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 ...

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...

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...

Trying to install on other machines, but now getting
Any hint?

Thanks,
N.

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...

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"...

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...

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: ./co...

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...

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...

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...

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...

Running parallel, all is fine.

10q

hines wrote:Good. Looks like you are on your way.

wow...
I'll make more tests and let you know.

very many thanks.

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...