singr

A Singularity image for running R, including geospatial system dependencies gdal, geos, proj, and udunits2 (from ppa:ubuntugis/ubuntugis-unstable).

using

After installing or (module load-ing) Singularity, pull the image (~420MB) as a Singularity Image File (.sif) to the working directory:

singularity pull library://cole-brokamp/default/singr:4.3.0

Call the downloaded .sif to run the image, which here presents a bash shell where you can run R:

./singr_4.3.0.sif

releases

The Singularity image tags correspond to version of R and latest refers to the most recently pushed image. Note that different versions may use different base images (e.g. 3.6 uses Ubuntu 18.04, 4.0 uses Ubuntu 20.04, 4.3 uses Ubuntu 22.04).

CCHMC HPC

Optionally, start a tmux or screen session from the HPC login node to keep your session persistently alive

Change to the project directory and run:

bsub -Is -W 10:00 -n 16 -M 250000 -R "span[ptile=16]" "module load singularity; singularity run ~/singr_latest.sif"

This works by supplying the commands needed to run the singularity container. Once the job is running, you will be presented with an interactive shell where you can run R

Double check resources available to R with:

parallel::detectCores()
benchmarkme::get_ram()
benchmarkme::get_cpu()

notes

• use lshosts to see an overview of available compute nodes and their specs
• tmux works from login node to attach to session started on a compute node (leave your job and come back later without having to find the ip address of the compute node)
• singularity imports all system environment variables (github/aws keys, etc)
• singularity automatically mounts $HOME, $PWD, and /tmp