sbatch_hcp.sh

#!/bin/bash

#SBATCH --mail-type=ALL
#SBATCH --mail-user=yi.wei@uconn.edu
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=16gb
#SBATCH --time=30:00:00
#SBATCH -e error_%A_%a.log                        
#SBATCH -o output_%A_%a.log                       
#SBATCH --job-name=HCP
#SBATCH --partition=serial

export OMP_NUM_THREADS=8
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=8

module load singularity

singularity run --cleanenv \
--bind /scratch/psyc5171/exercises/mbdata/bids:/data \
--bind /scratch/psyc5171/yiw15105/hw6/hcp:/output \
/scratch/psyc5171/containers/hcpbids_4.0.sif \
/run.py \
 --participant_label 01 \
 --license_key /data/code/license.txt \
 --gdcoeffs /data/code/coeff.grad \
 --anat_unwarpdir z \
/data /output participant