Setting up a GROMACS cluster Philip Fowler, 28th April 2016 0 shares 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:Twitter Related Pages: 1 2 3 4 5 computing molecular dynamics skills
citizen science Automated detection of bacterial growth on 96-well plates (AMyGDA) 11th December 20175th August 2018 I am involved in an international collaboration, the Comprehensive Resistance Prediction for Tuberculosis: an International Consortium… Share this:Twitter Read More
citizen science bashthebug.net alpha launch 3rd October 20166th April 2017 I’m planning to launch a citizen science project, bashthebug.net, in 2017 which has two distinct… Share this:Twitter Read More
antimicrobial resistance Accelerating Oxford Nanopore basecalling 26th January 20175th August 2018 It looks innocuous sitting on the desk, an Oxford Nanopore MinION, but it can produce… Share this:Twitter Read More