High Performance Computing with the R programming language

This material was developed for a pilot 2-day workshop at the University of Warwick in March 2022, associated with the Sulis tier 2 HPC service and funded by EPSRC grant EP/W032201/1.

This version is the material used in the pilot and contains instructions/examples tailored to the Sulis HPC service. It is forked from the upstream repository of Dr Michael Schubert to retain the Sulis specific elements.

Day 1

Morning: Intoduction to HPC and the Sulis tier 2 service

• Capabilities of the computing cluster
• How to connect
• Starting a basic job

Afternoon: Quick Start

• Copying and editing files via the command-line
• Interactive jobs, batch jobs
• parallel package, cluster objects, and future

Afternoon: Neovim as IDE

• The Nvim-R plugin to interactively develop in a remote session
• Persistent server sessions using tmux

Day 2

Morning: Breakpoint example

• An MCMC breakpoint detection method as example
• Tasks vs. threads for bigger jobs
• R packages for HPC use: slurmR and clustermq

Afternoon: Workflows

• GNU parallel and GNU make
• Snakemake
• The targets R package

Afternoon:

• Possibility for attendees to work on their own projects with help from the instructors