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/5.2 # Provides SLiMgui(v5.2), SLiM(v5.2) and Eidos(v4.2) 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.
If you want to run SLiMgui please user Interactive Job(see below)
Serial batch job submission
Create a batch submission script (which will load the modulefile in the jobscript), for example:
#!/bin/bash --login #SBATCH -p serial #SBATCH -t 1-0 module purge module load apps/gcc/slim/5.2 slim optional_flags sliminput.slim
Submit the jobscript using:
sbatch scriptname
where scriptname is the name of your jobscript.
SLiMgui in interactive job
Start an interactive job and then run SLiMgui:
srun -p interactive -n 4 -t 0-2 --pty bash module purge module load apps/gcc/slim/5.2 SLiMgui
Further info
Updates
None.