Running sedflux with PBS/Torque

If you are running sedflux on a cluster, you will most likely have to submit your sedflux simulation through a queuing system. This page describes how this might be done with PBS/Torque. The first step is to create a submission script that will run sedflux. An example of such a script is:

#! /bin/sh
#PBS -l nodes=1:ppn=1
 
RUN_DIR=$HOME/my_simulation_dir
INIT_FILE=my_init_file.kvf
 
cd $RUN_DIR && \
sedflux -3 --init-file=$INIT_FILE --msg="Brief description of simulation"

This script will run sedflux in 3D mode in $RUNDIR with the initialization file $INIT_FILE. The options to sedflux are the same as if running from the command line. Notice that you must supply a run description message on the command line (the –msg option). This is because the script will not be run interactively; without this option, sedflux will prompt you to provide a description. To submit this job to the queue, use qsub.

> qsub run_sedflux.sh

In this case we’ve named the above script, run_sedflux.sh. The exact details of how this is done will depend on your particular system. There are lots of good resources on the internet that describe queuing systems. For example: