JHU Computing Club: Parallelism and GPUs

This repository includes material for the 2024/03/05 talk at the JHU Computing Club. In particular, it includes the material on parallelism using R or SLURM at JHPCE. See the Google Slides for the remaining material on using and understanding GPU resources at JHPCE.

All Talk Materials

• Slides on GPUs
• Parallelism Vignette
• JHPCE GPU Documentation

Parallelism in R

First, I cover the BiocParallel R package for making use of multiple CPUs cores on Linux-like machines, including those at JHPCE. The raw R markdown file is available, but I encourage you to follow along with the rendered HMTL. I also conceptually introduce array jobs.

Parallelism by Array Job

Next, the nnSVG array job shell script and R script show a practical case where parallelism can be achieved by dividing the data into units and assigning each unit an array task with one CPU. I'll interactively walk through these scripts.