High Performance Computing - School of Chemistry


University of Glasgow IT services provides a general purpose high-performance computational cluster for researchers within the University. It can be used by staff members and postgraduate students to support their research.

General information about the cluster, such as

  • obtaining the account
  • configuring your account before first use
  • support
  • hardware and software specification

can be found here.

In order to get access to chemistry software, members of the School of Chemistry should add a note on their registration form “add me to compchem group”.

If you have no Linux and High Performance Computing experience, you may find this Linux tutorial and HPC help documents useful. IT services regularly organise training course for people new to HPC.

If you have problems configuring your HPC account before first use, contact our chemistry IT admin, Stuart Mackay, who will be able to help you.

Chemistry software

We have installed a number of software packages on the University cluster that are available only to staff and research students of the School of Chemistry:

  • Gaussian09 rev. D.01
  • Turbomole 6.4
  • Orca and Orca 3.0.3
  • Gromacs 5.0.5
  • NAMD 2.9
  • Autodock

To help our staff with using chemistry software we have prepared a system configuration file and sample scripts for submitting Gaussian, Gromacs, Orca, and Turbomole jobs.

Configuring your account to use chemistry software

After you have set up SSH and email forwarding for your new cluster account (as detailed here), you need to configure your account to allow easy access to chemistry software. You only have to do this once.

  1. Log in to the University cluster with your username and password.
  2. Type the following command:


You are all set now! Again, if you have problems with this contact Stuart Mackay.

Submitting Gaussian / Turbomole / Orca / Gromacs jobs

Sample scripts for submitting jobs with chemistry software are located in: /export/projects/compchem/software/SETTINGS_AND_SCRIPTS/bash

  • gaussian09.C.run is for the previous version of Gaussian09 (rev. C)
  • gaussian09.D.run is for the latest version of Gaussian09 (rev. D)
  • gromacs.run is for Gromacs 5.0.5
  • turbomole.run is for Turbomole 6.4
  • orca3.run is for Orca 3.0.3
  • orca4.run is for Orca

Copy the needed file(s) to your home directory. Each script has a header which explains how to use it and a customizable section that allows to change CPU/memory/time requirements of the job. If you have problems using those scripts you should contact us – Anna Stradomska (if the author of the script is “as”) or Hans Senn (if the author of the script is “hms”).

Disk space for Chemistry

School of Chemistry has a separate disk space on the University cluster at:


This means, that /export/scratch/username is a shortcut to /export/project/compchem/username. Because this is very slow network drive you should not use it as a scratch space for your computations, Instead it is advisable to use local storage available on the computational nodes. If you are using one of the scripts prepared by us, then the script is taking care of that for you.

Be aware that the University cluster has a very limited disk space, and there is no backup policy at all. Therefore, you should not store large amounts of data on the cluster and back up all important data somewhere else.