Difference between revisions of "SLURM/ArrayJobs"

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Here is an example to get you started using array jobs in [[SLURM]].
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==Array computation example job==
 
==Array computation example job==
 
Save this code to a file called <code>test.py</code>.
 
Save this code to a file called <code>test.py</code>.
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#SBATCH --time=0-00:05:00
 
#SBATCH --time=0-00:05:00
  
# default partition should do it
+
# default qos should do it
#SBATCH --partition default
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#SBATCH --qos=dpart
  
 
# 500MB memory per core
 
# 500MB memory per core

Latest revision as of 19:37, 15 December 2020

Here is an example to get you started using array jobs in SLURM.

Array computation example job

Save this code to a file called test.py.

import time

print('start at ' + time.strftime('%H:%M:%S'))

print('sleep for 10 seconds ...')
time.sleep(10)

print('stop at ' + time.strftime('%H:%M:%S'))

Sbatch submission script

Save this to a file called array.sh and you should be able to submit the job as sbatch array.sh.

#!/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 qos should do it
#SBATCH --qos=dpart

# 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