eResearch

R Sample Scripts for Slurm:

In order to submit an R job to the cluster, it is suggested to write a script file similar to the one below. Lines beginning with “##” represent comments.

The variable $SLURM_SUBMIT_DIR indicates the directory where the Slurm script file is located and launched from. Replace the example email address provided with your own email address. Change the R Script File name to the name of the R file that you want to be executed on the cluster.

Note all “[…]” are variables that require defining.

Example R Slurm Submission Script (R.slurm)

#!/bin/bash
###### Select resources ######SBATCH -J [Name of Job] 
#SBATCH -c [number of cpu's required, most likely 1] # CPUs per task 
#SBATCH --mem=[amount of memory required(e.g., 4G)] 
#SBATCH -p [partition]#SBATCH -t [how long the job should run for - e.g., 01:00:00 - you may wish to remove this line if the length of time required is unknown]
#### Output File ##### 
#SBATCH -o [output_file].out ## if left blank will default to slurm-[Job Number].out
#### Error File ##### 
#SBATCH -e [error_file].err ## if left blank will default to slurm-[Job Number].err
##### Queue ##### 
#SBATCH -p workq
##### Mail Options ##### 
#SBATCH --mail-type=ALL # Email notifications for job events (begin, end, fail) 
#SBATCH --mail-user=[email address]
##### Change to current working directory ##### 
cd $SLURM_SUBMIT_DIR 
##### Execute Program ##### 
R --vanilla < [Your R file].R > [R output file name]
 

Real Example

#!/bin/bash
###### Select resources ######SBATCH -J R-Job1 
#SBATCH -c 1
#SBATCH --mem=4GB
#SBATCH -p workq#### Output File ##### 
#SBATCH -o R-job1.out
#### Error File ##### 
#SBATCH -e R-job1.err
##### Queue ##### 
#SBATCH -p workq
##### Mail Options ##### 
#SBATCH --mail-type=ALL 
#SBATCH --mail-user=l.decosta@cqu.edu.au
##### Change to current working directory ##### 
cd $SLURM_SUBMIT_DIR 
##### Execute Program ##### 
R --vanilla < input.R > results

Executing script on the cluster

The Ada Lovelace HPC uses a job scheduler that allows you to schedule and run jobs on the various compute nodes. To submit a job, simply execute the command:

sbatch [slurm_script_file]

A handy command, to check if your job is running, queued or completed is by using the command:

squeue -u