sbatch_hcp.sh

#!/bin/bash

# Add your SLURM options here
#SBATCH --mail-type=ALL 			# Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=oliver.mcneil@uconn.edu	# Your email address
#SBATCH --nodes=1					# OpenMP requires a single node
#SBATCH --ntasks=1					# Run a single serial task
#SBATCH --cpus-per-task=8
#SBATCH --mem=16gb
#SBATCH --time=48:00:00				# Time limit hh:mm:ss
#SBATCH -e error_%A_%a.log			# Standard error
#SBATCH -o output_%A_%a.log			# Standard output
#SBATCH --job-name=HCP_hw6			# Descriptive job name
#SBATCH --partition=serial            # Use a serial partition 24 cores/7days

# Add commands needed to run HCP
export OMP_NUM_THREADS=8			#<= cpus-per-task
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=8	#<= cpus-per-task

module load singularity

singularity run --cleanenv \
--bind /scratch/psyc5171/exercises/mbdata/bids:/data \
--bind /scratch/ham19006/hw6/results:/out \
/scratch/psyc5171/containers/hcpbids_4.0.sif \
/run.py \
--license_key "31749" \
--gdcoeffs /data/code/coeff.grad \
--anat_unwarpdir z \
/data /out participant