R Sample Scripts

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

The variable $PBS_O_WORKDIR indicates the directory where the PBS script file is located and launched from. Replace the example email address provided to your 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 PBS Submission Script (/apps/samples/PBS/R.pbs)

###### Select resources #####
#PBS -N [Name of Job]
#PBS -l ncpus=[number of cpu's required, most likely 1]
#PBS -l mem=[amount of memory required]
#PBS -l walltime=[how long the job should run for - you may wish to remove this line]

#### Output File #####
#PBS -o $PBS_O_WORKDIR/[output (standard out) file name]

#### Error File #####
#PBS -e $PBS_O_WORKDIR/[input (standard out) file name]

##### Queue #####
#pbs -q workq

##### Mail Options #####
#PBS -m abe
#PBS -M [your email address]

##### Change to current working directory #####
cd $PBS_O_WORKDIR

##### Execute Program #####
R --vanilla < [Your R file].R > [R output file name]

Real Example

###### Select resources #####
#PBS -N R-Job1
#PBS -l ncpus=1
#PBS -l mem=1g

#### Output File #####
#PBS -o $PBS_O_WORKDIR/R-job1.out

#### Error File #####
#PBS -e $PBS_O_WORKDIR/R-job1.err

##### Queue #####
#pbs -q workq

##### Mail Options #####
#PBS -m abe #PBS -M j.bell@cqu.edu.au

##### Change to current working directory #####
cd $PBS_O_WORKDIR

##### Execute Program #####
R --vanilla < input.R > results

Executing script on the cluster

The Einstein Cluster 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:

qsub [pbs_script_file]

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

qstat -an