Difference between revisions of "SLURM/ArrayJobs"

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Line 15: Line 15:
 
#SBATCH --time=0-00:05:00
 
#SBATCH --time=0-00:05:00
  
# short partition should do it
+
# default partition should do it
#SBATCH --partition short
+
#SBATCH --partition default
  
 
# 500MB memory per core
 
# 500MB memory per core

Revision as of 19:07, 29 June 2017

#!/bin/bash

#####################
# job-array example #
#####################

#SBATCH --job-name=example

# 16 jobs will run in this array at the same time
#SBATCH --array=1-16

# run for five minutes
#              d-hh:mm:ss
#SBATCH --time=0-00:05:00

# default partition should do it
#SBATCH --partition default

# 500MB memory per core
# this is a hard limit 
#SBATCH --mem-per-cpu=500MB

# you may not place bash commands before the last SBATCH directive

# define and create a unique scratch directory
SCRATCH_DIRECTORY=/scratch0/${USER}/job-array-example/${SLURM_JOBID}
mkdir -p ${SCRATCH_DIRECTORY}
cd ${SCRATCH_DIRECTORY}

cp ${SLURM_SUBMIT_DIR}/test.py ${SCRATCH_DIRECTORY}

# each job will see a different ${SLURM_ARRAY_TASK_ID}
echo "now processing task id:: " ${SLURM_ARRAY_TASK_ID}
python test.py > output_${SLURM_ARRAY_TASK_ID}.txt

# after the job is done we copy our output back to $SLURM_SUBMIT_DIR
cp output_${SLURM_ARRAY_TASK_ID}.txt ${SLURM_SUBMIT_DIR}

# we step out of the scratch directory and remove it
cd ${SLURM_SUBMIT_DIR}
rm -rf ${SCRATCH_DIRECTORY}

# happy end
exit 0