TORQUE template script example

The environment setup

Because the TORQUE queue at the CNB-CSIC requires a maximum wall-clock-time, one needs to define the XXXextra1XXX variable. In their environment (.bashrc) one includes:

export RELION_QSUB_EXTRA1="Max number of hours in queue"
export RELION_QSUB_EXTRA1_DEFAULT="72"
export RELION_QSUB_TEMPLATE="/gpfs/fs1/home/bioinfo/scheres/relion-0.9/bin/qsub.bash"

The command used for job submission (to be given in the GUI) is qsub.

The template script

The following script is saved as /gpfs/fs1/home/bioinfo/scheres/relion-0.9/bin/qsub.bash:

#!/bin/bash
### Inherit all current environment variables
#PBS -V
### Job name
#PBS -N XXXnameXXX
### Keep Output and Error
#PBS -k eo
### Queue name
#PBS -q XXXqueueXXX
### Specify the number of nodes and thread (ppn) for your job.
#PBS -l nodes=XXXmpinodesXXX:ppn=XXXthreadsXXX
### Tell PBS the anticipated run-time for your job, where walltime=HH:MM:SS
###PBS -l walltime=XXXextra1XXX:00:00
#################################
### Switch to the working directory;
cd $PBS_O_WORKDIR
### Run:
mpirun --bynode -np XXXmpinodesXXX XXXcommandXXX
echo "done"