High-Performance Computing for Agent-Based Modellers

We are offering a free two full-day training course (29 February and 1 March 2024) in using HPC with agent-based models (with a particular focus on NetLogo). This is a 'draft' course (manage your expectations accordingly) based on a presentation used at Hutton to teach post-docs and Ph. D. students how to use our cluster with their agent-based models.

In-person and on-line options are available. There are places for approximately 10 in-person attendees in total, who will need to make their own travel and accommodation arrangements, and pay for these themselves.

Course timetable:

All times are in GMT (UTC+0)

Thursday 29 February 2024

09:00-09:30 Arrival/testing AV/VC and coffee for those present

09:30-10:30 Preparing a NetLogo model to run on HPC. Read ahead.

10:30-11:00 Break

11:00-12:00 Understanding your HPC admin and how to help them help you. Read ahead / tool.

12:00-13:00 Lunch

13:00-14:00 Guest lecture -- Diana Suleimenova, Brunel University: "Bringing agent-based simulation applications to the exascale using the SEAVEA toolkit"

14:00-15:00 Everything you didn't want to know about the Java Virtual Machine but now have to, Secure Shell, and running NetLogo from the command line

15:00-15:30 Break

15:30-17:00 Unix shell scripting

18:30-20:30 Complementary dinner for those attending in person (venue to be decided)

Friday 1 March 2024

09:00-09:30 Arrival, AV/VC check and coffee

09:30-11:00 Unix shell scripting and writing SLURM scripts

11:00-11:30 Break

11:30-12:30 Some (possibly) helpful tools. Read ahead.

12:30-13:30 Lunch

13:30-14:30 Guest lecture -- Diana Suleimenova, Brunel University: "Hands-on tutorial: Executing agent-based forced displacement simulations on ARCHER2"

14:30-15:15 Running and monitoring your experiment

15:15-15:45 Coffee

15:45-16:45 Working with sensitive data. Read ahead.

16:45-17:00 Feedback and close

What you will need:

You will need a laptop, on which you have at least the following installed (negotiate with your IT department accordingly if you have institutional constraints):

  • Windows laptops:
    • Up-to-date (version 6.3 or later) NetLogo. Ideally, you would have permission to modify files in the installation folder.
    • One of the Windows Subsystems for Linux (e.g. Ubuntu)
    • A text editor suitable for coding -- e.g. Notepad++, Visual Studio Code, or VSCodium. NOT Notepad or Wordpad -- these are unsuitable.
    • May not be necessary to install separately, but make sure you have ssh and/or PuTTY installed.
  • Mac laptops:
  • Linux laptops:
    • Up-to-date (version 6.3 or later) NetLogo. Ideally you would have permission to modify files in the installation folder.
    • A text editor suitable for editing code. These usually come with distributions, but you could try Brackets if not.

Apply to attend:

To apply to attend, please send an email to gary.polhill@hutton.ac.uk with the following information:

  1. Who you are and where you work
  2. Brief motivation for attending and what you hope to get out of it
  3. Whether you want to attend in person (we are hoping that you'd actually get to run an ABM on a cluster) or remotely (you probably wouldn't)
    • If in person, details of any dietary restrictions or accessibility adjustments you need.


This course is being done as part of the ExAMPLER project, funded by the EPSRC, with support from the Scottish Government's Strategic Research Programme Topic on Large-Scale Modelling.

Event Date