Summary

Keypoints

• Load and run

  • Use the desired R version from the module system e.g. module load  R/4.1.1

  • Use Rscript to run a script or R to start the interpreter/REPL

• Packages

  • Always check for preinstalled packages e.g. R_packages on UPPMAX

    • use library(<pkg-name>) to see if available

• Isolated environments

  • With a virtual environment you can tailor an environment with specific versions.

  • You can make it for each project you have for reproducibility using renv or conda on UPPMAX.

• Batch mode

  • The SLURM scheduler handles allocations to the calculation nodes

  • Batch jobs runs without interaction with user

  • A batch script consists of a part with SLURM parameters describing the allocation and a second part describing the actual work within the job, for instance one or several R scripts.

  • Remember to include possible input arguments to the R script in the batch script.

• Interactive work on calculation nodes

  • Start an interactive session on a calculation node by a SLURM allocation (similar flags)

    • At HPC2N: salloc …

    • At UPPMAX: interactive …

  • Follow the same procedure as usual by loading the R module and possible prerequisites.

• Using RStudio

  • Rstudio is available both on UPPMAX and HPC2N and works well through a graphical ThinLinc Session.

Not really clear? (5 min)

• Discuss in breakout rooms

• Learn from each other

See also

• Content from NBIS R course from 2021: https://nbisweden.github.io/RaukR-2021/

• CodeRefinery develops and maintains training material on software best practices for researchers that already write code.

  • Their material addresses all academic disciplines and tries to be as programming language-independent as possible. https://coderefinery.org/lessons/

• Learn more about R packages: https://r-pkgs.org/