5 Using R

R is available on both Knot and Pod, including different versions of R.

5.1 Loading R

To load R on Knot for interactive use, enter the command

$ R

To load R on Pod for interactive use, enter the commands

$ load module R
$ R

To exit R, use the command q().

Note that the RStudio IDE is not available for use on the clusters.

Remember: Most analyses should be performed on compute nodes by submitting batch jobs. The login node should only be used for simple analyses, testing, or debugging.

5.2 Versions

On Knot, the available version of R is 3.2.2.

On Pod, the available versions of R include

R/3.2.2
R/3.4.4
R/3.5.1-multith
R/3.5.1

The default is the latest version. To load a specific version, for example, use the command load module R/3.4.4.

A different version of R can be installed inside your home directory. For more info see http://csc.cnsi.ucsb.edu/docs/using-r-knot-braid-and-pod.

5.3 Packages

Packages can be installed using the R command install.packages("<package>") and should be stored inside your home folder. When using this command you may be prompted to select a CRAN mirror from which to download; select a USA (CA) mirror with an HTTPS connection for a fast and secure download. R should automatically add the home-based package library to .libPaths() (enter this command to confirm) and set it as default.

5.4 Example job files

5.4.1 Knot

#!/bin/bash
#PBS -l nodes=1:ppn=1
#PBS -l walltime=2:00:00
#PBS -m abe
#PBS -M user@ucsb.edu

cd $PBS_O_WORKDIR

Rscript --vanilla script.R

5.4.2 Pod

#!/bin/bash -l
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --time=2:00:00
#SBATCH --mail-type=ALL
#SBATCH --mail-user=user@ucsb.edu

cd $SLURM_SUBMIT_DIR

module load R
Rscript --vanilla script.R