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:
- Complete Torque guide
- CSDMS cluster (where I run sedflux mostly)