PP_sbatch_fs_6.sh

#!/bin/bash

# written by Nathan Muncy on 8/11/17

#SBATCH --time=20:00:00   # walltime
#SBATCH --ntasks=1   # number of processor cores (i.e. tasks)
#SBATCH --nodes=1   # number of nodes
#SBATCH --mem-per-cpu=16gb   # memory per CPU core
#SBATCH -J "PPfs"   # job name

# Compatibility variables for PBS. Delete if not needed.
export PBS_NODEFILE=`/fslapps/fslutils/generate_pbs_nodefile`
export PBS_JOBID=$SLURM_JOB_ID
export PBS_O_WORKDIR="$SLURM_SUBMIT_DIR"
export PBS_QUEUE=batch

# Set the max number of threads to use for programs using OpenMP. Should be <= ppn. Does nothing if the program doesn't use OpenMP.
export OMP_NUM_THREADS=$SLURM_CPUS_ON_NODE



subjDir=$1
subj=$2

FS.Function () {

    recon-all \
    -subjid $1 \
    -all \
    -sd $2 \
    -notal-check \
    -cw256

}


FS.Function $subj $subjDir