Difference between revisions of "SLURM/ArrayJobs"

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(Created page with "<pre> #!/bin/bash ##################### # job-array example # ##################### #SBATCH --job-name=example # 16 jobs will run in this array at the same time #SBATCH --a...")
 
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# define and create a unique scratch directory
 
# define and create a unique scratch directory
SCRATCH_DIRECTORY=/global/work/${USER}/job-array-example/${SLURM_JOBID}
+
SCRATCH_DIRECTORY=/scratch0/${USER}/job-array-example/${SLURM_JOBID}
 
mkdir -p ${SCRATCH_DIRECTORY}
 
mkdir -p ${SCRATCH_DIRECTORY}
 
cd ${SCRATCH_DIRECTORY}
 
cd ${SCRATCH_DIRECTORY}

Revision as of 19:06, 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

# short partition should do it
#SBATCH --partition short

# 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