Difference between revisions of "Job Arrays"

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== Job Array Introduction ==
+
== 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 hundreds, even thousands of jobs for each 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 job in the array.  More details on SLURM job arrays can be found at [https://slurm.schedmd.com/job_array.html https://slurm.schedmd.com/job_array.html]
  
Making a new copy of the script and then submitting each one for every input data file is time consuming. An alternative is to make a job array using the -t option in your '''QSUB''' '''submission''' '''script'''. The -t option allows many copies of the same script to be queued all at once. You can use the '''$PBS_ARRAYID''' environmental variable to differentiate between the different jobs in the array. The amount of resources you specify in the '''QSUB''' '''submission''' '''script''' is the amount of resources the '''job script''' gets each time it is called.
+
== --array parameter ==
 +
*This will create 10 jobs with the $SLURM_ARRAY_TASK_ID iterating 1 through 10 (1,2,3,4,...,8,9.10)
 +
<pre>#SBATCH --array 1-10</pre>
 +
*This will create 10 jobs with the $SLURM_ARRAY_TASK_ID iterating 1 through 19 with step size 2 (1,3,5,7,...,17,19)
 +
<pre>#SBATCH --array 1-20:2</pre>
 +
*This will create 5 jobs with the $SLURM_ARRAY_TASK_ID set to the 5 specified values (1,5,10,15,20)
 +
<pre>#SBATCH --array 1,5,10,15,20</pre>
 +
*This will create 20 jobs with the $SLURM_ARRAY_TASK_ID iterating 1 through 20 (1,2,3,4...,18,19,20) but only run 4 of the jobs at time.
 +
<pre>#SBATCH --array=1-20%4</pre>
  
In this tutorial, we will be using '''three''' files:
+
== Example Script ==
<pre>array.sh
+
This script will submit 10 jobs. Each job will do the following
job.pl
+
*wait for 10 seconds (sleep 10)
job.conf
+
*Output the hostname of the node it ran on (echo "Hostname: `hostname`")
</pre>
+
*Output the $SLURM_ARRAY_TASK_ID
Lets say you want to run '''16 jobs'''. Instead of submitting 16 different jobs, you can submit one job, but use the ''''-t'''' parameter and the '''PBS_ARRAYID''' variable. You can read more about the&nbsp;&nbsp;''''-t''''&nbsp;&nbsp;parameter at&nbsp;[http://docs.adaptivecomputing.com/torque/4-1-4/Content/topics/commands/qsub.htm#T http://docs.adaptivecomputing.com/torque/4-1-4/Content/topics/commands/qsub.htm]
+
*The output file slurm-%A_%a.out will have that information. '''%A''' is the SLURM job number. '''%a''' is value of '''$SLURM_ARRAY_TASK_ID'''
<pre>#PBS -t 0-15</pre>
 
The -t parameter sets the range of the '''PBS_ARRAYID''' variable. So setting it to
 
<pre>#PBS -t 0-4</pre>
 
will cause the qsub script to call the script 5 times, each time updating the '''PBS_ARRAYID''', from 0 to 4 , which results in
 
<pre>( perl job.pl $PBS_ARRAYID )
 
  
perl job.pl 0
+
<pre>#!/bin/bash
perl job.pl 1
+
# ----------------SBATCH Parameters----------------- #
perl job.pl 2
+
#SBATCH -p normal
perl job.pl 3
+
#SBATCH -n 1
perl job.pl 4
+
#SBATCH -N 1
</pre>
+
#SBATCH --mail-user youremail@illinois.edu
== array.sh (Example submission script) ==
+
#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
  
This submission script changes to the current working directory, submits 16 jobs, and reserves 2 processors and 1gb of ram for each job.
 
 
It redirects the stderror and stdout into one file, and emails the job owner on completion or abort.
 
 
For each job , it passes the '-t' parameter to the job.pl script, which in this case is 0 to 15
 
<pre>#!/bin/bash
 
# ----------------QSUB Parameters----------------- #
 
#PBS -q default
 
#PBS -l nodes=1:ppn=2,mem=1000mb
 
#PBS -M youremail@illinois.edu
 
#PBS -m abe
 
#PBS -N array_of_perl_jobs
 
#PBS -t 0-15
 
#PBS -j oe
 
# ----------------Load Modules-------------------- #
 
module load perl/5.16.1
 
 
# ----------------Your Commands------------------- #
 
# ----------------Your Commands------------------- #
cd $PBS_O_WORKDIR
 
perl job.pl $PBS_ARRAYID</pre>
 
== job.pl (Example Perl script ) ==
 
<pre>#!/usr/bin/env perl
 
#This script echos the job array element that has been passed in
 
  
use strict;
+
sleep 10
my $pbs_array_id = shift @ARGV;
+
echo "Hostname: `hostname`"
my $experimentID = $pbs_array_id + 1;
+
echo "Job Array Number: $SLURM_ARRAY_TASK_ID"
my $experimentName = `head -n $pbs_array_id job.conf | tail -n1`;
 
  
print "This is job number $argument \n";
 
print "About to perform experimentID: $argument experimentName:$experimentName\n";
 
 
</pre>
 
</pre>
== job.conf (example configuration file) ==
+
*10 different output files will be created. The output in each one will be like below
<pre>dataset0
+
<pre>
dataset1
+
Hostname: compute-0-16
dataset2
+
Job Array Number: 10
dataset3
 
dataset4
 
dataset5
 
..
 
dataset650
 
 
</pre>
 
</pre>
== Default vs Highthroughput Queue ==
 
  
'''The default queue only allows you to queue up to 150 jobs, but they do not use a walltime limit.'''
+
== Example - Ordered List ==
 +
*Say you have a directory with input data files that are numbered sequentially like below.
 +
*You want to run the program FastQC against these files.
 +
*The input data is located in the directory '''input_data'''
 +
*The results will be placed in the directory '''results'''
 +
<pre>yeast_1_50K.fastq
 +
yeast_2_50K.fastq
 +
yeast_3_50K.fastq
 +
yeast_4_50K.fastq
 +
yeast_5_50K.fastq
 +
yeast_6_50K.fastq
 +
</pre>
 +
*The job array script would be like below.
 +
<pre>#!/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 1-6
 +
# ----------------Load Modules--------------------
 +
module load FastQC/0.11.5-IGB-gcc-4.9.4-Java-1.8.0_152
 +
# ----------------Your Commands------------------- #
  
*This queue is most appropriate for a lot of jobs that may run a long time.
+
echo "Starting FastQC Job"
 +
fastqc -o results/ input_data/yeast_${SLURM_ARRAY_TASK_ID}_50K.fastq
 +
echo "Finishing FastQC Job"
 +
</pre>
  
'''The highthroughput queue allows you to queue up to 550 jobs, but they have a walltime limit.'''
+
== Example - Unordered List ==
 +
*This is for a list of data files that do not have sequential numbers in the filename.
 +
*The input data is located in the directory '''input_data'''
 +
*The results will be located in the directory '''results'''
 +
*This grabs a file from the '''input_data''' directory ('''ls input_data/ | sed -n ${SLURM_ARRAY_TASK_ID}p''') , and then puts that in the variable '''$file'''.
 +
*Then runs fastqc using the '''$file''' variable
  
*This queue is most appropriate for a lot of jobs that you want to run in parallel and finish quickly.
+
<pre>#!/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 1-6
 +
# ----------------Load Modules--------------------
 +
module load FastQC/0.11.5-IGB-gcc-4.9.4-Java-1.8.0_152
 +
# ----------------Your Commands------------------- #
 +
echo "Starting FastQC Job"
 +
file=$(ls input_data/ | sed -n ${SLURM_ARRAY_TASK_ID}p)
 +
fastqc -o results input_data/${file}
 +
echo "Finishing FastQC Job"
 +
</pre>
  
== Effectively Using job_array_index ==
+
== Example - Combining jobs ==
 +
*What if 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 to submit the next batch, submit a single job array job that can handle all of the datasets.
 +
*You need to divide your datasets into groups.  Below is an example bash code that can do it.
 +
*First, all of your input datasets need to be a folder called '''input_data'''
 +
*The variable '''$ITEMS_TO_PROCESS''' specifies the size of each group of jobs should be
 +
*The line '''JOBLIST=$(ls input_data/)''' will store the list of the files in the variable '''$JOB_LIST'''
 +
*Then it will calculate which jobs go into which group using '''$SLURM_ARRAY_TASK_ID''' and '''$ITEMS_TO_PROCESS'' to calculate the '''$START_LINE''' and '''$END_LINE'''
 +
<pre>ITEMS_TO_PROCESS=10
 +
JOBLIST=$(ls input_data/)
 +
START_LINE=$(( ${SLURM_ARRAY_TASK_ID} * ${ITEMS_TO_PROCESS}) +1 )
 +
END_LINE=$(( ${START_LINE] + ${ITEMS_TO_PROCESS} ) -1 )
  
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:
 
<pre> data sets per job = ceiling ( Number of datasets / Number of Job Elements )
 
data sets per Job = ceiling ( 650 / 80 ) = ceiling(8.12500) = 9
 
 
</pre>
 
</pre>
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.
+
*Below is the full script
 +
*In order to use the following script, you will need to properly set
 +
*'--array' (the number of array elements you want)
 +
*ITEMS_TO_PROCESS (the size of each group of jobs)
  
 +
<pre>#!/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 FastQC/0.11.5-IGB-gcc-4.9.4-Java-1.8.0_152
 +
# ----------------Your Commands------------------- #
  
Here is some simple pseudo code for this situation
+
ITEMS_TO_PROCESS=10
<pre>data sets per job = N
+
JOBLIST=$(ls input_data/)
startLineNumber = $PBS_ARRAYID * 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
 
</pre>
 
== Putting it all together (Example Qsub Submission with submissions script, configuration file, and experiment script ==
 
 
 
In order to use the following script, you will need to properly set
 
  
*'-t' (the number of array elements you want)
+
START_LINE=$(( ${SLURM_ARRAY_TASK_ID} * ${ITEMS_TO_PROCESS}) + 1)
 +
END_LINE=$(( ${START_LINE] + ${ITEMS_TO_PROCESS} ) -1)
  
*-itemsToProcess (the number of items in the job.conf list to pass into your script)
 
 
*-Your script , modules and custom settings
 
<pre>#!/bin/bash
 
# ----------------QSUB Parameters----------------- #
 
#PBS -S /bin/bash
 
#PBS -q default
 
#PBS -l nodes=1:ppn=1,mem=1000mb
 
#PBS -M netid@Illinois.edu
 
#PBS -m abe
 
#PBS -N Blast_100_in_chunks_of_10
 
#PBS -d /home/n-z/yournetid/experimentA/
 
# --EDIT HERE
 
#PBS -t 1-10
 
# ----------------Load Modules-------------------- #
 
module load blast/2.2.26
 
# ----------------Your Commands------------------- #
 
# --EDIT HERE
 
itemsToProcess=10
 
jobList="job.conf"
 
  
#No need to edit this
+
#Iteration through START_LINE and END_LINE
taskID=$PBS_ARRAYID
+
for line in `seq ${START_LINE} ${END_LINE}`
startLineNumber=$(($taskID * $itemsToProcess))
 
endLineNumber=$(( $startLineNumber + $itemsToProcess ))
 
startLineNumber=$(( $startLineNumber + 1))
 
#Grab an experiment from the job.conf file
 
for line in `seq $startLineNumber $endLineNumber`
 
 
do
 
do
     experiment=$( head -n $line $jobList | tail -n 1 )
+
     DATA_FILE=$( head -n $line ${JOBLIST} | tail -n 1 )
# --EDIT HERE
+
    fastqc -o results input_data/${DATA_FILE}
echo blastall -i $experiment -o $experiment\.blast
 
 
done
 
done
 
</pre>
 
</pre>
 +
 +
== Resources ==
 +
[https://slurm.schedmd.com/job_array.html https://slurm.schedmd.com/job_array.html]

Latest revision as of 13:00, 2 October 2019

Introduction[edit]

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 hundreds, even thousands of jobs for each 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 job in the array. More details on SLURM job arrays can be found at https://slurm.schedmd.com/job_array.html

--array parameter[edit]

  • This will create 10 jobs with the $SLURM_ARRAY_TASK_ID iterating 1 through 10 (1,2,3,4,...,8,9.10)
#SBATCH --array 1-10
  • This will create 10 jobs with the $SLURM_ARRAY_TASK_ID iterating 1 through 19 with step size 2 (1,3,5,7,...,17,19)
#SBATCH --array 1-20:2
  • This will create 5 jobs with the $SLURM_ARRAY_TASK_ID set to the 5 specified values (1,5,10,15,20)
#SBATCH --array 1,5,10,15,20
  • This will create 20 jobs with the $SLURM_ARRAY_TASK_ID iterating 1 through 20 (1,2,3,4...,18,19,20) but only run 4 of the jobs at time.
#SBATCH --array=1-20%4

Example Script[edit]

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 value of $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"

  • 10 different output files will be created. The output in each one will be like below
Hostname: compute-0-16
Job Array Number: 10

Example - Ordered List[edit]

  • Say you have a directory with input data files that are numbered sequentially like below.
  • You want to run the program FastQC against these files.
  • The input data is located in the directory input_data
  • The results will be placed in the directory results
yeast_1_50K.fastq
yeast_2_50K.fastq
yeast_3_50K.fastq
yeast_4_50K.fastq
yeast_5_50K.fastq
yeast_6_50K.fastq
  • The job array script would be like below.
#!/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 1-6
# ----------------Load Modules--------------------
module load FastQC/0.11.5-IGB-gcc-4.9.4-Java-1.8.0_152
# ----------------Your Commands------------------- #

echo "Starting FastQC Job"
fastqc -o results/ input_data/yeast_${SLURM_ARRAY_TASK_ID}_50K.fastq
echo "Finishing FastQC Job"

Example - Unordered List[edit]

  • This is for a list of data files that do not have sequential numbers in the filename.
  • The input data is located in the directory input_data
  • The results will be located in the directory results
  • This grabs a file from the input_data directory (ls input_data/ | sed -n ${SLURM_ARRAY_TASK_ID}p) , and then puts that in the variable $file.
  • Then runs fastqc using the $file variable
#!/bin/bash
# ----------------SBATCH Parameters----------------- #
#SBATCH -p normal
#SBATCH -n 1
#SBATCH -N 1
#SBATCH --mail-user youremail@illinois.edu
#SBATCH --mail-type BEGIN,END,FAIL 
#SBATCH -J example_array
#SBATCH -D /home/a-m/USERNAME
#SBATCH -o /home/a-m/USERNAME/slurm-%A_%a.out
#SBATCH --array 1-6
# ----------------Load Modules--------------------
module load FastQC/0.11.5-IGB-gcc-4.9.4-Java-1.8.0_152
# ----------------Your Commands------------------- #
echo "Starting FastQC Job"
file=$(ls input_data/ | sed -n ${SLURM_ARRAY_TASK_ID}p)
fastqc -o results input_data/${file}
echo "Finishing FastQC Job"

Example - Combining jobs[edit]

  • What if 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 to submit the next batch, submit a single job array job that can handle all of the datasets.
  • You need to divide your datasets into groups. Below is an example bash code that can do it.
  • First, all of your input datasets need to be a folder called input_data
  • The variable $ITEMS_TO_PROCESS specifies the size of each group of jobs should be
  • The line JOBLIST=$(ls input_data/) will store the list of the files in the variable $JOB_LIST
  • Then it will calculate which jobs go into which group using $SLURM_ARRAY_TASK_ID' and $ITEMS_TO_PROCESS to calculate the $START_LINE and $END_LINE
ITEMS_TO_PROCESS=10
JOBLIST=$(ls input_data/)
START_LINE=$(( ${SLURM_ARRAY_TASK_ID} * ${ITEMS_TO_PROCESS}) +1 )
END_LINE=$(( ${START_LINE] + ${ITEMS_TO_PROCESS} ) -1 )

  • Below is the full script
  • In order to use the following script, you will need to properly set
  • '--array' (the number of array elements you want)
  • ITEMS_TO_PROCESS (the size of each group of jobs)
#!/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 FastQC/0.11.5-IGB-gcc-4.9.4-Java-1.8.0_152
# ----------------Your Commands------------------- #

ITEMS_TO_PROCESS=10
JOBLIST=$(ls input_data/)

START_LINE=$(( ${SLURM_ARRAY_TASK_ID} * ${ITEMS_TO_PROCESS}) + 1)
END_LINE=$(( ${START_LINE] + ${ITEMS_TO_PROCESS} ) -1)


#Iteration through START_LINE and END_LINE
for line in `seq ${START_LINE} ${END_LINE}`
do
    DATA_FILE=$( head -n $line ${JOBLIST} | tail -n 1 )
    fastqc -o results input_data/${DATA_FILE}
done

Resources[edit]

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