Example of SLURM array job for Everlyn

beast-array.sbatch

#!/usr/bin/bash -l
#SBATCH -p batch
#SBATCH -n 8
#SBATCH -J prank

# Start a job array with eight CPUs total where we iterate over 1,000+ FASTA
# files and start a prank command for each one. SLURM ensures that there are
# no more than eight running at the same time within the same allocation.
#
# See: https://support.ceci-hpc.be/doc/_contents/QuickStart/SubmittingJobs/SlurmTutorial.html#packed-jobs-example

# Location of input files
DATA_DIR=/home/aorth/phyml
# Location to write output files in node's scratch space
SCRATCH_DIR=/var/scratch/aorth/2018-02-13-prank

# Create scratch directory and move into it
mkdir -p $SCRATCH_DIR
cd $SCRATCH_DIR

# Load a specific version of prank
module load prank/170427

# Change to directory of input files
cd $DATA_DIR

# Iterate over all FASTA files
for file in Hircus-*.fas; do
    # Run prank with 1 CPU, output to scratch directory
    srun -n1 --exclusive prank -d=$file -o=$SCRATCH_DIR/${file%.fas} -codon -F -f=paml &
done
wait