SLiM

Overview

SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Simulations are configured via the integrated Eidos scripting language that allows interactive control over practically every aspect of the simulated evolutionary scenarios.

Version 4.0.1 is installed on the CSF. The installation includes Eidos.

Restrictions on use

There are no restrictions on accessing SLiM on the CSF. It is release under the GNU GPL v3 license and all user must adhere to that license.

Set up procedure

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.

Load one of the following modulefiles:

module load apps/gcc/slim/4.0.1         # Provides SLiM and Eidos

Running the application

Please do not run SLiM on the login node. Jobs should be submitted to the compute nodes via batch.

Serial batch job submission

Create a batch submission script (which will load the modulefile in the jobscript), for example:

#!/bin/bash --login
#$ -cwd             # Job will run from the current directory
                    # NO -V line - we load modulefiles in the jobscript

# Load the version you require
module load apps/gcc/slim/4.0.1

slim optional_flags scriptfile

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Further info

• SLiM website

Updates

None.