This example runs PAUP on the input file input.nex that resides in the current working directory. A file (here we'll name it pbsjob) is created with the contents:
#!/bin/bash #PBS -c s #PBS -j oe #PBS -m ae #PBS -N jobname #PBS -M jc123456@jcu.edu.au #PBS -l walltime=2000:00:00 echo "------------------------------------------------------" echo " This job is allocated 1 cpu on " cat $PBS_NODEFILE echo "------------------------------------------------------" echo "PBS: Submitted to $PBS_QUEUE@$PBS_O_HOST" echo "PBS: Working directory is $PBS_O_WORKDIR" echo "PBS: Job identifier is $PBS_JOBID" echo "PBS: Job name is $PBS_JOBNAME" echo "------------------------------------------------------" cd $PBS_O_WORKDIR source /etc/profile.d/modules.sh module load paup paup -n input.nex
To submit the job for execution on a HPRC compute node simply enter the command:
qsub pbsjob
If you know this job will require more than 4GB but less than 8GB of RAM, you could use the command:
qsub -l nodes=1:ppn=2 pbsjob