Setting up a GROMACS cluster

Recently I’ve moved to the John Radcliffe hospital and my old lab kindly let me have some old servers that were switched off. This pushed me to learn how to setup them up as a compute cluster with a scheduler for running GROMACS jobs. I’ve wanted to learn this for years, having used many clusters myself, but haven’t plucked up the courage until now.

This post is a detailed walk-through on how I chose to do this. During the process I did a lot of Googling and have written the post I would have liked to have found; long, comprehensive and a bit verbose.

Since it is long so let’s break it down into four tasks.

1. Install Ubuntu on each machine

2. Setup networking, including sharing directories on the headnode via NFS

3. Using environment modules, compile GROMACS into one of the shared directories so all the machines in the cluster can run lmx

4. Install SLURM