Skip to content
Fowler Lab
Fowler Lab

Predicting antibiotic resistance de novo

  • News
  • Research
    • Overview
    • Manifesto
    • Software
    • Reproducibility
    • Publications
  • Members
  • Teaching
  • Contact
    • PhDs
  • Wiki
Fowler Lab
Fowler Lab

Predicting antibiotic resistance de novo

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
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

Post navigation

Previous post
Next post

Related Posts

computing

GROMACS 4.6

18th October 201323rd September 2018

GROMACS is a scientific code designed to simulate the dynamics of small boxes of stuff, that…

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
antimicrobial resistance

New preprint: rapid prediction of AMR by free energy methods

15th January 202015th January 2020

The story behind this preprint goes back to the workshop on free energy methods run…

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

Improving Software Carpentry workshops

1st November 201223rd September 2018

Aron Ahmadia who helped run the Software Carpentry course has written a nice blog where…

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

Leave a Reply Cancel reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Privacy & Cookies: This site uses cookies. By continuing to use this website, you agree to their use.
To find out more, including how to control cookies, see here: Cookie Policy
    ©2025 Fowler Lab | WordPress Theme by SuperbThemes
     

    Loading Comments...