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For this example we're going to be using the rocker/tidyverse (external site) Docker image. At the time of writing the latest available R version is 4.3.1. It provides an R installation, the RStudio server, the R devtools and the Tidyverse collection for data science. This image ships with a startup script that allows for a number of runtime options to be specified: see the USE menu in the Rocker homepage (external site).

Setting up the job script

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The following script launches an RStudio server on the compute node. The first step in the script creates a working directory before launching Rstudio.

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After reading the instructions provided in the slurm-xxxx.out file, you need to open a separate terminal window in your own computer. In that terminal, execute the command that will perform the ssh tunneling between a port in the local computer and a port on the compute node where the RStudio container is running. In this case:

ssh -N -f -L 8787:z123nid001008:8787 matilda@setonix.pawsey.org.au

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Clean up when you are finished

Once you have finished:

• Cancel In the Pawsey cluster, cancel your job with scancel.

• Kill In your local computer, kill the SSH tunnel, based on the command displayed in the output file. In this case (from your local computer):

kill $( ps x | grep 'ssh.*-L *8787:

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nid001008:8787' | awk '{print $1}' )

External links

• DockerHub
• The Rocker Project ("Docker Containers for the R Environment")
• R devtools ("providing R functions that simplify many common tasks")
• The Tidyverse collection ("R packages for data science")
• Jupyter Docker Stacks ("a set of ready-to-run Docker images containing Jupyter applications and interactive computing tools")

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