Running neuron with MPI using debian package

Running neuron with MPI using debian package

Postby roybens » Sat Mar 11, 2017 6:38 pm

Hi,
I am trying to use neuron on a cluster without shared libraries we used the debian package as shifter image and NEURON is runnig well.
The problem is when i am trying to use MPI i get only one process. I am trying to use the simple example from the parallelcontext documentation i get nprocs=1
My guess is that the debian package is not built with MPI is there a waythat is built with MPI?
Thanks in advance
Roy

Here is my submitting script:

#!/bin/bash
#SBATCH -N 1
#SBATCH -C haswell
#SBATCH -p debug
#SBATCH -J testMPI
#SBATCH --mail-user=bens.roy@gmail.com
#SBATCH -t 00:01:00

#OpenMP settings:
export OMP_NUM_THREADS=32
export OMP_PLACES=threads
export OMP_PROC_BIND=spread


#run the application:
srun -n 1 -c 32 --cpu_bind=cores shifter --image=docker:lgerhardt/neuron:v1 nrniv -mpi testMPI.hoc

And this is what i get:
numprocs=1
NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
See http://www.neuron.yale.edu/neuron/credits

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