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High Performance Computing with the R programming language

Below is a brief overview of the course content.

Day 1

Morning: Technical Introduction by HPC admins

  • 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

  • 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