COSMOCOMP, Running AMUSE on the Durham cluster

AMUSE is installed and ready to run.

After loging in to the cluster as the 'cosmocomp' user, one command is needed to get amuse running. This command will start a "virtualenv" environment capable of running amuse programs.

castor > source amuse/env/bin/activate.csh
[env] castor >

Your promt will change to: [env] castor>

Now, you can run some of the examples interactively

[env] castor > cd amuse/code/examples/simple
[env] castor > mpiexec amuse.sh hrdiagram.py

To run in the queue, use the amuse_script.csh template in the amuse/code/example/simple directory, reproduced below:

#!/bin/tcsh
#
# Batch script for csh users.
# To be submitted with the qsub command provided by the torque module.
#
#PBS -S /bin/tcsh
#PBS -N my_job_name
#PBS -l nodes=2
#PBS -j oe
#PBS -o ./my_job.log
#

# This makes the module command available
source /etc/profile.d/modules.csh

# Make sure we use the right mpirun command - will need to change
# this if you use a different version of openmpi
module load openmpi/intel_11.1/1.4.3

source ${HOME}/amuse/env/bin/activate.csh

# Change to the directory where the job was submitted
cd $PBS_O_WORKDIR

# Run the program
$MPIROOT/bin/mpiexec -n 1 amuse.sh hrdiagram.py

Run this with qsub like so:

> qsub amuse_script.sh