Job Arrays

Introduction

Job Arrays allow you to run the same job on different datasets without having to create an individual job script for each dataset. Thus you are easily able to submit jobs for hundreds, even thousands of different datasets. This is accomplished by using the #SBATCH --array parameter in the SBATCH script. Then using the $SLURM_ARRAY_TASK_ID environmental variable to specify which dataset to use. The resources (number of processors, memory, etc) you specify in the job script will be identical for each of the job arrays.

--array parameter

Lets say you want to run 10 jobs. Instead of submitting 10 different jobs, you can submit one job, but use the --array parameter and the $SLURM_ARRAY_TASK_ID variable. You can read more about the --array parameter at https://slurm.schedmd.com/job_array.html

#SBATCH --array 1-10

The --array parameter sets the range of the $SLURM_ARRAY_TASK_ID variable. So setting it to

#SBATCH --array 1-4

will cause the qsub script to call the script 4 times, each time updating the $SLURM_ARRAY_TASK_ID, from 1 to 4 , which results in

Example Script

This script will submit 10 jobs. Each job will do the following

• wait for 10 seconds (sleep 10)
• Output the hostname of the node it ran on (echo "Hostname: `hostname`"
• Output the $SLURM_ARRAY_TASK_ID
• The output file slurm-%A_%a.out will have that information. %A is the SLURM job number. %a is the SLURM array task id

#!/bin/bash
# ----------------SBATCH Parameters----------------- #
#SBATCH -p normal
#SBATCH -n 1
#SBATCH -N 1
#SBATCH --mail-user youremail@illinois.edu
#SBATCH --mail-type BEGIN,END,FAIL 
#SBATCH -J example_array
#SBATCH -D /home/a-m/USERNAME
#SBATCH -o /home/a-m/USERNAME/slurm-%A_%a.out
#SBATCH --array 1-10

# ----------------Your Commands------------------- #

sleep 10
echo "Hostname: `hostname`"
echo "Job Array Number: $SLURM_ARRAY_TASK_ID"

• The output will be like below

Hostname: compute-0-16
Job Array Number: 10

job.pl (Example Perl script )

#!/usr/bin/env perl
#This script outputs the job array element that has been passed in

use strict;
my $pbs_array_id = shift @ARGV;
my $experimentID = $pbs_array_id;
my $experimentName = `head -n $pbs_array_id job.conf | tail -n1`;

print "This is job number $pbs_array_id \n";
print "About to perform experimentID: $experimentID experimentName:$experimentName\n";

job.conf (example configuration file)

dataset0
dataset1
dataset2
dataset3
dataset4
dataset5
..
dataset650

Effectively Using job_array_index

You have 650 datasets you want to analyze, but you can only submit 80 jobs at a time. Instead of submitting 80 jobs, and waiting for them to finish, submit a single 80 element array job that can handle all of the datasets.

A simple formula for dividing and sending your datasets to your script is as follows:

 data sets per job = ceiling ( Number of datasets / Number of Job Elements ) 
data sets per Job = ceiling ( 650 / 80 ) = ceiling(8.12500) = 9

So that means that your 80 jobs are each responsible for handling 9 datasets. So each time you call your job script, you need to pass it the position in the list of datasets , which is the $PBS_ARRAYID and the data sets per job ( N ) That way, your job will be able to determine which datasets from the list you need to process.

Here is some simple pseudo code for this situation

data sets per job = N
startLineNumber =  $SLURM_ARRAY_TASK_ID * datasets per job
endLineNumber = startLineNumber + data_sets_per_job

open list of data:
      go to  startLineNumber
                get dataset
                do work with dataset
                if lineNumber <  endLineNumber
                go to next line
 

Putting it all together (Example SBATCH Submission with submissions script, configuration file, and experiment script

In order to use the following script, you will need to properly set

• '--array' (the number of array elements you want)

• -itemsToProcess (the number of items in the job.conf list to pass into your script)

• -Your script , modules and custom settings

#!/bin/bash
# ----------------SBATCH Parameters----------------- #
#SBATCH -p normal
#SBATCH -n 1
SSBATCH -N 1
#SBATCH --mail-user  youremail@illinois.edu
#SBATCH --mail-type BEGIN, END, FAIL 
#SBATCH -J array_of_jobs
#SBATCH --array 1-10
#SBATCH -D /home/a-m/USERNAME

# ----------------Load Modules-------------------- #
module load BLAST+/2.6.0-IGB-gcc-4.9.4
# ----------------Your Commands------------------- #
# --EDIT HERE
itemsToProcess=10
jobList="job.conf"

#No need to edit this
taskID=$SLURM_ARRAY_TASK_ID
startLineNumber=$(($taskID * $itemsToProcess))
endLineNumber=$(( $startLineNumber + $itemsToProcess ))
startLineNumber=$(( $startLineNumber + 1))
#Grab an experiment from the job.conf file
for line in `seq $startLineNumber $endLineNumber`
do
    experiment=$( head -n $line $jobList | tail -n 1 )
# --EDIT HERE
 echo blastall -i $experiment -o $experiment\.blast
done

Resources

https://slurm.schedmd.com/job_array.html