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 -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]
#SBATCH -p [partition]
#### 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
#SBATCH -J R-Job1
###### Select resources #####
#SBATCH -c 1
#SBATCH --mem=4GB#### Output File #####
#SBATCH -p workq
#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