Setting up a GROMACS cluster Philip Fowler, 28th April 2016 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. Fingerless gloves and a woolly hat can be useful in a cold, noisy machine room 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 Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Related Pages: 1 2 3 4 5 computing molecular dynamics skills
computing GROMACS on AWS: Performance and Cost 17th January 20163rd March 2019 So we have created an Amazon Machine Image (AMI) with GROMACS installed. In this post… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More
computing How to setup a Gramble 14th April 2016 This is a Gramble, which of course is short for a GROMACS Bramble, or, in… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More
molecular dynamics A simple tutorial on analysing membrane protein simulations. 3rd September 2014 I’m teaching a short tutorial on how to analyse membrane protein simulations next week at… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More