umich-biostatistics / HPC-R-Examples

Example R jobs and scripts for HPC use.

HPC R Examples

Note

This branch contains slurm files specific to the Great Lakes.

Check branches for other HPC Clusters or environments

Summary

These are example R and SLURM scripts that can be used to show various methods of running jobs on an HPC cluster.

The examples perform a simple bootstrap analysis on a generated dataset. It's a basic example that doesn't require much computational power but can be time-consuming for large datasets or many bootstrap iterations.

Examples

Job Type	Definition
simple	A simple R and SLURM script that shows how to run your code on the cluster with no frills.
parallel	how to run the same simple job, but use multiple cores to split up the work.
array	Split the simple job into a job array, spreading the work across multiple CPUs running in parallel

Usage

Tip

The Parallel example will used the UMICH CRAN mirror to install the parallelly package if not installed.

1. Connect to terminal session on greatlakes.arc-ts.umich.edu
2. cd into desired directory
3. git clone
4. cd into one of the examples
5. Update .slurm file with the appropraite SLURM account
   • find . -type f -name "*.slurm" -exec sed -i 's/SLURM_ACCOUNT/your_account_here/g' {} +
6. sbatch bs_EXAMPLE.slurm (replace EXAMPLE with proper name)
7. sq to view your job queue
8. Once complete, my_job_statistics JOB_ID (replace JOB_ID with that of your job)