/
How-to run R

How-to run R

Owned by Mark Allen
Last updated: Oct 27, 2020
2 min read

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

Note: packages within each version of R are not the same! There may be different packages or different package versions.

Intel R

Intel is the default. To run an Intel compiled version of R, e.g 4.0.2, 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. E.g. 4.0.2, run:

$ 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

The output above shows the executable to R version 4.0.2 built with gcc7.

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" ...

Running R 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

Running R in Batch

For longer running non-interactive use cases call R in batch.

First, create your file, e.g. demo.r, which contains R syntax.

Next, create your batch job file, e.g. r-job.srun, and add desired slurm declarations, module(s), and call to the application.

#!/bin/bash #SBATCH --account=<pirg-name> #SBATCH --job-name=r-job #SBATCH --output=r-job.out #SBATCH --error=r-job.err module load R/4.0.2 R --save < /gpfs/projects/<pirg-name>/<user-name>/demo.r

‘Save current workspace’ with --save

The example above preserves R session output. Also include the save.image function in your demo.r file, e.g. save.image("/gpfs/projects/<pirg-name>/<user-name>/demo.RData")

Submit the job

Use the sbatch command to submit the job.

$ sbatch r-job.srun



Related content