How to run GENESIS on Lewis

If you use an MS Windows operating system and have not already done so then download and install an xwindows server.  Directions for installing a free xwindowing system may be found here.

Some things need to be done on Lewis before using GENESIS via Xwindows:
a. Copy the .simrc file into your home directory:
cp   /share/apps/Genesis/genesis-2.3/genesis/.simrc   /home/<userid>/
b. Copy the Scripts directory into your data directory:
cp   -r   /share/apps/Genesis/genesis-2.3/genesis/Scripts   /home/<userid>/data/
c. Put /share/apps/Genesis/genesis-2.3/genesis into your path.  In the .bashrc file it would look like this:
export GENESIS_HOME=/share/apps/Genesis/genesis-2.3
export PATH=/opt/mpich/gnu/bin:$PATH:/sbin:/usr/sbin:$GENESIS_HOME/pgenesis/bin:$GENESIS_HOME/genesis
Note that this also includes PGENESIS, a parallelized version of GENESIS.  You need to log off and back in so the newly modified .bashrc file can be read.

If you have installed the Cygwin Xwindowing system correctly the icon should be on your desktop.
  1. Clicking on that will open a window with the Cygwin logo on it.  At the prompt type "startxwin.sh".
  2. Another window appears which has a large "X" at the top-left.  In the command line of that window type "ssh -X lewis.rnet.missouri.edu -l <userid>" and hit return.  Enter your password.  You should see your home directory on Lewis.
  3. IMPORTANT!!! At the command prompt type gocomp.  This will take you to a compute node on Lewis that is designated for interactive sessions using GENESIS.  If you do not execute this command you will remain on the "head" node, where you will be a nuisance to all other users and GENESIS performance less than it could be.
  4. To reach the Purkinje tutorial from your home directory cd to data/Script/purkinje.  Once there type "genesis TUTORIAL.g".  In this case three windows should appear.  Directions for how to use the Tutorial can be found with the "HELP" button.  Other examples in the Scripts directory may be found under "neuron" and "MultiCell", and there may be others.  Once in the directory type "genesis Neuron" or "genesis MultiCell" to start a session.
  5. The most graceful way to exit a GENESIS session is to click the "QUIT" button on the Control window.  Simply clicking on the x to close the windows sometimes causes problems with seeing what you are typing at the command line.

How to run PGENESIS on Lewis

A non-X version of PGENESIS is now installed on lewis, under the directory /share/apps/genesis-2.3/pgenesis. There are some sample scripts that you can copy to your own directory under /share/apps/genesis-2.3/pgenesis/Scripts. Most of the samples assume an X11 environment, but the farm2.g script shows distributing very simple tasks over 10 CPUs. Here is a sample LSF job script to run it:
#BSUB -J farm2job
#BSUB -oo farm2job.o%J
#BSUB -eo farm2job.e%J
#BSUB -n 10
#BSUB -a mvapich
/share/apps/bin/pgenesis -nox -nodes 10 farm2.g
The "-nox" parameter is necessary to run the non-X version. The number of nodes (CPUs) specified by "-nodes" should match the number of CPUs specified by the BSUB "-n" parameter.

For general information about submitting jobs to LSF, please go here.