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hw6/sbatch_hcp.sh
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| #!/bin/bash | |
| #SBATCH --mail-type=ALL | |
| #SBATCH --mail-user=aliyar.ozercan@uconn.edu | |
| #SBATCH --nodes=1 | |
| #SBATCH --ntasks=1 | |
| #SBATCH --cpus-per-task=8 | |
| #SBATCH --mem=24gb | |
| #SBATCH --time=48:00:00 | |
| #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 | |
| ##### END OF JOB DEFINITION ##### | |
| # Add your SLURM options here | |
| module load singularity | |
| singularity run --cleanenv \ | |
| --bind /scratch/psyc5171/alo18003/hw6/bids:/data \ | |
| --bind /scratch/psyc5171/alo18003/hw6/hcp:/output \ | |
| /scratch/psyc5171/containers/hcpbids_4.0.sif \ | |
| /run.py \ | |
| --license_key "31749" \ | |
| --gdcoeffs /data/code/coeff.grad \ | |
| --anat_unwarpdir z \ | |
| /data /output participant | |
| # Add commands needed to run HCP | |