job_gnupar_mpi.pbs

#!/bin/bash
#PBS -q workq
#PBS -l nodes=4:ppn=16
#PBS -l walltime=72:00:00
#PBS -N log_tacocat
#PBS -o $PBS_JOBNAME.out
#PBS -e $PBS_JOBNAME.err
#PBS -A hpc_phyleaux10

## Set working directory

WDIR=$PBS_O_WORKDIR

## Move into working directory

cd $WDIR

## Set number of jobs per node

export JOBS_PER_NODE=1

## Make list of files to pass to your mpi program

ls $WDIR/scripts/emp_analysis_* > files.txt

## Parallel command flags: jobs per node, pbs node file, working directory, and file to write gnu output to
PARALLEL="parallel -j $JOBS_PER_NODE --slf $PBS_NODEFILE --wd $WDIR --joblog log_tacocat.gnu"

## Pass job to run to parallel command. Job here is "mpirun -np 16 rb-mpi"
## The job itself is mpi(on top of gnu parallel), so we pass the number of processors per mpi job to mpirun. 
## files.txt contains the files that you want to pass to your mpi program. 

$PARALLEL -a files.txt mpirun -np 16 rb-mpi {}