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SLURM Submit script example
More information about the submit script can be found using the Job Script Generator [old].
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#!/bin/bash #SBATCH -J namd_example #SBATCH -e namd_example.%j.err #SBATCH -o namd_example.%j.out #SBATCH -p std #SBATCH -n 4 #SBATCH -t 02-00:00 module load apps/namd/2.13 ## # Modify the input and output files! INPUT_FILE=namd_example.com OUTPUT_FILE=namd_example.log cp -r ${SLURM_SUBMIT_DIR}/${INPUT_FILE} ${SCRATCH} cd ${SCRATCH} srun `which namd2` ${INPUT_FILE} > ${OUTPUT_FILE} cp ./${OUTPUT_FILE} ${SLURM_SUBMIT_DIR} |
Sbatch options:
The options shown in the example are detailed below. For more information and a more comprehensive list of available options, see the sbatch command page.
- -J: Name for the job's allocation.
- -e: Name of the stderr redirection filename.
- -o: Name of the stdout redirection filename.
- -p: Name of the partition (queue) where the job will be submitted.
-n: Number of tasks.
- -t: Set the job's time limit. If the job don't finish before the time runs out, it will be killed.
Benchmarks
Fig: Comparison between jobs with and without GPGPUs.