Example script (hello.R):

sayHello <- function(){
  print("hello")
}
sayHello()

User can execute R scripts from the command line with the following commands:

1. R CMD BATCH script.R
2. Rscript script.R

Note: With the R CMD BATCH command the output of the R script is redirected to file instead of the screen

Next user must embed the script to the SLURM batch job file/control file (submit.sbatch):

#!/bin/bash
#SBATCH --job-name helloworld # Name for your job
#SBATCH --ntasks 1 # Number of task
#SBATCH --time 5 # Runtime in minutes.
#SBATCH --mem=2000 # Reserve 2 GB RAM for the job
#SBATCH --partition serial # Partition to submit
#SBATCH --output hello.out # Standard out goes to this file
#SBATCH --error hello.err # Standard err goes to this file
#SBATCH --mail-user username@uef.fi # this is the email you wish to be notified at
#SBATCH --mail-type ALL # ALL will alert you of job beginning, completion, failure etc

module load r # load modules

Rscript hello.R # Execute the script

User can submit the job to the compute queue with the sbatch command. Note that the batch file (and R script and data) must be located at the /home/ disk.

sbatch submit.sbatch

User can monitor the progress of the job with the squeue command. JOBID is provided by the sbatch commmand when the job is submitted.

squeue -j JOBID

Also while the job is running user can login to executing compute node with the ssh command. When job is over the ssh session is terminated.

ssh sampo1

Interactive session

User can get an interactive sessions for whatever purpose. For this to be effective free node is more or less required. Following command will open bash session to any free node on the serial parallel for the next 5 minutes.

srun -p serial --pty -t 0-00:05 /bin/bash

Slurm job efficiency report (seff) and Accounting

SLURM can provide the user with various job statistics. Like memory usage and CPU time. for example with seff (Slurm job effiency report) it is possible to monitor on how efficiency the job was.

seff JOBID

It is particularly useful to add following line to the end of the sbatch script:

seff $SLURM_JOBID

or if you wish to have more detailed information

# show all own jobs contained in the accounting database
sacct
# show specific job
sacct -j JOBID
# specify fields
sacct -j JOBID -o JobName,MaxRSS,MaxVMSize,CPUTime,ConsumedEnergy
# show all fields
sacct -j JOBID -o ALL