% $Id: lyttonmpi.txt,v 1.1 2005/08/23 15:47:59 hines Exp $

MPICH must be compiled for every machine type that you want to use in your parallel environment.

NEURON must be built and accessible on every individual cpu (node) on which you wish to run in parallel

  • Make sure that you can readily log into yourself (or other nodes) without a password. I will assume in what follows that you are using ssh to access machines. To test access to your local machine use ‘ssh localhost’. If you require a password to login you may want to use RSA??

  • By default MPICH assumes that you will be using rsh to login to remote nodes. This is unlikelyto be the case on a current machine. Therefore, the environmental variable RSHCOMMAND mush be set BEFORE compile MPICH. This can be done as follows.

    export RSHCOMMAND=”ssh” # sh/bash setenv RSHCOMMAND “ssh” # csh

  • We assume that you are using a machine that utilizes TCP/IP for communication. This being the case you will use the following command to configure and compile:

    ./configure –with-device=ch_p4 –prefix=WHERE_YOU_WANT_IT make make install

  • After apparently successful installation you can test the installation as follows.

    cd examples/basic/ make mpirun -np 2 hello++

    This should return messages from 2 nodes (or from the same CPU if only 1 CPU)

    Hello World! I am 0 of 2 Hello World! I am 1 of 2

  • Before continuing with the NEURON compilation make sure that the paths are set correctly on the machine, ie for bash

    export MPICH= … # eg /home/you/mpich-1.2.7/i686 export MPICH_PATH=”${MPICH}/bin” export MPICH_LIB=”${MPICH}/lib” export PATH=”${MPICH_PATH}:${PATH}” export LD_LIBRARY_PATH=”${MPICH_LIB}:${LD_LIBRARY_PATH}”

  • NEURON compilation is done using the –with-mpi flag to configure ./configure –prefix=WHERE_TO –with-iv=WHERE_IS_IV –with-mpi make make install

  • to test the parallel NEURON

    cd src/parallel mpirun -np 2 /home/billl/nrniv/nrn-5.8.39/x86_64/bin/nrniv test0.hoc

    which should return

    hello from id 0 on YOUR_MACHINE

    hello from id 1 on YOUR_MACHINE