R

R is a programming language that often is used for data analytics, statistical programming, and graphical visualization.

 

On Rivanna, R is available through our module system.  To load R, simply type:

module load gcc R

(Notice that we included gcc in the load command. R has many computationally-intensive packages that are built with C, C++, or Fortran. By including gcc, we ensure that the same environment used for building R and its packages is loaded.)

 

Rstudio,a development environment for R, also is supported through its own module, but you must load a version of R first. For example, to load and run Rstudio, you could type the following:

module load gcc R/3.5.1
module load rstudio
rstudio &

 

After you have developed your R program, you can submit it to the compute nodes by using a SLURM job command script similar to the following: 

#!/bin/bash
#SBATCH -n 1
#SBATCH -t 01:00:00
#SBATCH -o myRprog.out
#SBATCH -p standard
#SBATCH -A mygroup

module load gcc R/3.5.1
Rscript myRprog.R

This script should saved in a file, called (for example) job.slurm.  To run your job, you would submit the script by typing:

sbatch job.slurm

 

R can be run in parallel, either as multicore or with MPI (message passing interface).  To run a parallel R job that uses MPI, the SLURM script would be similar to the following:

#!/bin/bash
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=10
#SBATCH -t 00:30:00
#SBATCH -o myRprog.out
#SBATCH -p parallel
#SBATCH -A mygroup

module load gcc
module load openmpi
module load R

srun Rscript myRprog.R

 

Contact arcs@virginia.edu for consulting in optimizing and parallelizing your scripts.