How to run R

Versions

As of this article update, we have the following versions of R installed on Talapas,

3.3.3
3.3.3_intel-17
3.4.1
3.4.2
3.4.3
3.4.4
3.5.1
3.5.3
3.6.1
3.6.1_gcc7
3.6.2
4.0.2
4.0.2_gcc7

Intel R

Intel is the default. To run an Intel compiled version of R, run,

$ module load R/4.0.2
$ R

gcc R

We have 2 versions of R compiled with gcc7 (3.6.1_gcc7 and 4.0.2_gcc7) built specifically to support RStan. To use these versions you must first load gcc,

$ module load gcc

Lmod is automatically replacing "intel/17" with "gcc/7.3".

$ module load R/4.0.2
$ R

Verify the path of the R executable that is loaded use the bash command which

$ which R
/packages/R/4.0.2_gcc7/bin/R

Packages

To list installed packages and version information, run

$ module load R/4.0.2
$ R
> installed.packages()[,c("Package","Version")]
                     Package                Version
abind                "abind"                "1.4-5"
...

Interactive

1. ssh onto a talapas login node, How-to Log Into Talapas

2. Start an interactive job, How-to Start an Interactive Job

3. Once on the allocated node enter,

$ module load R/4.0.2
$ R

Batch

For longer running non-interactive use cases call Mathematica in batch. Create the file math-job.srun. In the file, add the desired slurm declarations, load the module, call the application.

#!/bin/bash

#SBATCH --account=<pirg-name>
#SBATCH --job-name=mat-job
#SBATCH --output=mat-job.out
#SBATCH --error=mat-job.err

module load Mathematica

math -run < math-file.m

Submit the job

Use the sbatch command to submit the job.

$ sbatch mat-job.srun