How to submit a batch job to Slurm

What is a batch job?  

A batch job is a task that, once submitted to the scheduler, can run without further interaction from the user. A user writes a script containing both the command(s) to be run and directives for the scheduler as to how the job should be run. The batch system then selects the resources required by the job and decides when and where to run the job. Note: the term “job” is used throughout this documentation to mean a “batch job”.

There are two ways of submitting a job to Slurm:

1. Submit via a Slurm job script - create a bash script that includes directives to the Slurm scheduler
2. Submit via command-line options - provide directives to Slurm via command-line arguments

Both options are described below.

Which servers can you submit jobs from?  

Jobs can be submitted to Slurm from any of the sci servers. Check the current list of servers on that page.

Method 1: Submit via a Slurm job script  

The Slurm job submission command is:

sbatch myjobscript

The job script is a Bash script of user’s application and includes a list of Slurm directives, prefixed with #SBATCH as shown in this example:

#!/bin/bash
#SBATCH --job-name="My test job"
#SBATCH --time=00:01:00
#SBATCH --mem=1M
#SBATCH --account=mygws
#SBATCH --partition=debug
#SBATCH --qos=debug
#SBATCH -o %j.out
#SBATCH -e %j.err

# executable
sleep 5s

Explanation:

Submitting the above script (if you had access to the mygws account) creates a job named My test job with an estimated run time of 00:01:00 (1 minute), memory requirement of 1M (1 Megabyte), run against the account mygws on the partition debug using QoS debug, and writing its STDOUT (standard output) to file %j.out and its STDERR to file %j.err (where %j represents the job ID that the scheduler assigns to the job).

The task itself is the command sleep 5s which just pauses for 5 seconds before exiting. This is what you would replace with your actual processing command(s), so you need to have an idea of how long it will take to run (TIP: run it manually first with time <cmd> to find out!)

• For details about how to pick the right partition, QoS, and account, please read about the Slurm queues on LOTUS.
• For further submission parameters, see the quick reference about job specification.

Method 2: Submit via command-line options  

If you have an existing script, written in any language, that you wish to submit to LOTUS then you can do so by providing Slurm directives as command-line arguments. For example, if you have a script my-script.py that takes a single argument -f <filepath>, you can submit it using sbatch as follows:

sbatch -A mygws -p debug -q debug -t 03:00 -o job01.out -e job01.err my-script.py -f myfile.txt

This approach allows you to submit jobs without writing additional job scripts to wrap your existing code.

Check the official documentation for sbatch, its arguments and their syntax here  .

Method 3: Submit an interactive session via salloc  

Testing a job on LOTUS can be carried out in an interactive manner by obtaining a Slurm job allocation or resources (a set of nodes) via the Slurm command salloc. The code/application is executed and the allocation is released after a specific time - default 30 mins - when the testing is finished.

Interactive execution with pseudo-shell terminal on the compute LOTUS node  

The job is executed on the LOTUS compute node by allocating resources with salloc. See the example below:

salloc -p standard -q high -A mygws --ntasks-per-node=2
salloc: Pending job allocation 23506
salloc: job 23506 queued and waiting for resources
salloc: job 23506 has been allocated resources
salloc: Granted job allocation 23506
salloc: Nodes host580 are ready for job

Official documentation for the salloc command is available here  .

At this point, your shell prompt will change to the LOTUS compute node. You will have the allocated compute that you requested at this shell. For example the command hostname is executed twice as there are 2 CPUs and each outputs the name of the node:

srun hostname
host580.jc.rl.ac.uk
host580.jc.rl.ac.uk

Official documentation for the srun command is available here  .

The job allocation ID 23506 has 2 CPUs on the compute node host580 and can be checked from another terminal as shown below:

squeue -u fred -o"%.18i %.9P %.11j %.8u %.2t %.10M %.6D %.6C %R"
JOBID PARTITION           NAME       USER  ST       TIME  NODES   CPUS NODELIST(REASON)
23506 standard      interactive   fred   R       1:32      1      2 host580

Official documentation for the squeue command is available here  .

Once you’re finished, type exit to relinquish the allocation. This will happen automatically once the time limit on the job runs out.

Job array submission  

Job arrays are groups of jobs with the same executable and resource requirements, but different input files. Job arrays can be submitted, controlled, and monitored as a single unit or as individual jobs or groups of jobs. Each job submitted from a job array shares the same job ID as the job array and is uniquely referenced using an array index. This approach is useful for ‘high throughput’ tasks, for example where you want to run your simulation with different driving data or run the same processing task on multiple data files.

Important note: The maximum job array size that Slurm is configured for is MaxArraySize = 10000. If a Job array of size is greater than 10000 is submitted, Slurm will reject the job submission with the following error message: “Job array index too large. Job not submitted.”

Taking a simple R submission script as an example:

#!/bin/bash 
#SBATCH --job-name=myRtest
#SBATCH --time=30:00
#SBATCH --account=mygws  
#SBATCH --partition=debug
#SBATCH --qos=debug      
#SBATCH -o %j.out 
#SBATCH -e %j.err 

module add jasr
Rscript TestRFile.R dataset1.csv

If you want to run the same script TestRFile.R with input file dataset2.csv through to dataset10.csv, you could create and submit a job script for each dataset. However, by setting up an array job, you could create and submit a single job script.

The corresponding job array script to process 10 input files in a single job submission would look something like this:

#!/bin/bash 
#SBATCH --job-name=myRarray
#SBATCH --time=30:00
#SBATCH --account=mygws  
#SBATCH --partition=debug
#SBATCH --qos=debug
#SBATCH -o %A_%a.out
#SBATCH -e %A_%a.err
#SBATCH --array=1-10

module add jasr
Rscript TestRFile.R datset${SLURM_ARRAY_TASK_ID}.csv

Here the important differences are :

• The array is created by Slurm directive --array=1-10 by including elements numbered [1-10] to represent our 10 variations
• The error and output file have the array index %a included in the name and %A is the job ID.
• The environment variable $SLURM_ARRAY_TASK_ID in the Rscript command is expanded to give the job index

When the job is submitted, Slurm will create 10 tasks under the single job ID. The job array script is submitted in the usual way:

sbatch myRarray.sbatch

If you use the squeue -u <username> command to list your active jobs, you will see 10 tasks with the same Job ID. The tasks can be distinguished by the [index] e.g. jobID_index. Note that individual tasks may be allocated to a range of different hosts on LOTUS.

Troubleshooting  

If you have only recently requested access to JASMIN login services and had this approved, there can sometimes be a delay (typically up to a day, but in rare cases can be longer) before the necessary configuration is created for you on LOTUS. You will not be able to submit jobs to LOTUS until this has been completed. Typically, you would see an error message such as this, after an unsuccessful attempt to submit a job:

sbatch: error: Batch job submission failed: Invalid account or account/partition combination specified

If this occurs, please try again in 24 hours before contacting the JASMIN helpdesk.