Load and run R

Learning objectivesFor teachers

• Practice using the documentation of your HPC cluster

• Load an R module

• Start the R interpreter

• Run an R script

• Download and extract the exercise files

• (optional) Find the different R modules

• (optional) See the list of installed R packages

Introduction

You want to run R on an HPC cluster. For this, you’ll need to read the documentation of your HPC cluster.

In this session, we will use the documentation of your HPC cluster to start R.

Warning

Only do lightweight things!

We are still on the login node, which is shared with many other users. This means, that if we do heavy calculations, all the other users are affected.

How to do heavy calculations will be shown in this course later.

Exercises

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HPC cluster	Login method	Location
COSMOS	Local ThinLinc client	Here
Dardel	Local ThinLinc client	Here
Kebnekaise	Local ThinLinc client	Here
Rackham	Local ThinLinc client	Here
Tetralith	Local ThinLinc client	Here

HPC cluster name	Main breakout room
COSMOS	Room 1
Dardel	Room 2
Kebnekaise	Room 3
Rackham	Room 4
Tetralith	Room 5

Exercise 1: start the R interpreter

• Find the documentation of your HPC cluster

Answer

• Within the documentation of your HPC cluster, search for the documentation about R

Answer

HPC cluster	Page name and location
COSMOS	R Software environment
Dardel	R
Kebnekaise	R
Rackham	R
Tetralith	R

• From the terminal, load the module(s) for R, of the recommend version as shown below

HPC center	R version
COSMOS	4.2.1
Dardel	4.1.1
Kebnekaise	4.1.2
Rackham	4.1.1
Tetralith	4.2.2

Answer

HPC cluster	How to load the module(s) for R
COSMOS	module load GCC/11.3.0 OpenMPI/4.1.4 R/4.2.1
Dardel	module load PDC/23.12 R/4.1.1
Kebnekaise	module load GCC/11.2.0 OpenMPI/4.1.1 R/4.1.2
Rackham	module load R/4.1.1
Tetralith	module load R/4.2.2-hpc1-gcc-11.3.0-bare

• From the terminal, start the R interpreter

Answer

HPC cluster	How to start the R interpreter
COSMOS	R
Dardel	R
Kebnekaise	R
Rackham	R
Tetralith	R

• From the R interpreter, run the R code message("Hello") to verify if this makes the R interpreter show the text ‘Hello’

• From the R interpreter, run the R code quit() to quit the R interpreter and go back to the terminal

Exercise 2: run an R script

To run an R script, we’ll download one, after which we’ll run it:

• From the terminal, run wget https://raw.githubusercontent.com/UPPMAX/R-python-julia-HPC/main/exercises/r/hello.R

• From the terminal, run Rscript hello.R

Exercise 3: download and extract the tarball with exercises

See here how to download and extract the tarball with exercises.

Exercise X1: find and use installed R packages

• From the R interpreter, check which packages are installed, using installed.packages()

Answer

HPC cluster	Answe
COSMOS	installed.packages()
Dardel	installed.packages()
Kebnekaise	installed.packages()
Rackham	installed.packages()
Tetralith	installed.packages()

• From the R interpreter, load the parallel package, using library(parallel)

Answer

HPC cluster	Answe
COSMOS	library(parallel)
Dardel	library(parallel)
Kebnekaise	library(parallel)
Rackham	library(parallel)
Tetralith	library(parallel)

Exercise X2: search for other R versions

Use the module system to find which versions of R are provided by your cluster’s module system.

Answer

HPC cluster	How to search for the R modules
COSMOS	module spider R
Dardel	module spider R
Kebnekaise	module spider R
Rackham	module spider R
Tetralith	module spider R