Supercomputing for everyone

Mario Antonioletti and Iain Bethune of EPCC write here about EPCC's participation in two science festivals.

We demonstrated the power and utility of supercomputers at the British Science Festival in Aberdeen and Bang Goes The Borders in Melrose. At both events the audience showed a high level of interest in finding out what supercomputing is all about. 

Our goal was to encourage the general public to interact directly with a supercomputer. We already had the supercomputer – HECToR, the UK's national supercomputing service – but we needed an application.

Visual Molecular Dynamics (VMD) is an application that allows systems to be visualized while being simulated by an underlying code. We chose NAMD2 to run the simulation as it is a supported application on HECToR and is well integrated with VMD. Not only does VMD let you visualize a system as it runs – including zooming, rotating and panning - but it also allows external forces to be applied to an atom or molecule. These are fed back into the simulation in real time.

Scientific simulation

Now we required an interesting simulation to tell a compelling story.

Professor Charles Laughton (University of Nottingham) has studied the thermodynamics of ligand binding using the mouse major urinary protein3. The simulation itself is simply a protein embedded in a water molecule. Inside the protein is a pheromone molecule – the protein acts as a slow release for any of the more volatile pheromone particles that may be trapped inside.

Using NAMD to model the system and VMD to visualise it, we created a demo where the audience could apply external forces to try to pull the pheromone out of the protein.

Thanks to Cray, we had a Cray XT4 blade to show alongside the demo. This is the type used in HECToR and it was a big crowd pleaser!

Demonstrating parallel algorithms

We also wanted to convey how a task could be performed faster by following a parallel algorithm (this is the set of steps required to solve a specific problem using several computer processors or cores working at the same time).

We printed cards numbered 1–60, shuffled a subset of them and asked a willing volunteer to sort them. Invariably this took too long, so we stopped this early having demonstrated the point. We then got several members of the audience to act as computer cores. They were each given a subset of cards which they sorted by swapping highest and lowest numbers, until all the highest cards were at one end of the line and all the lowest were at the other.

Having played the part of a supercomputer, the audience moved on to trying to pull the pheromone out of the mouse protein, with the demo running on 256 cores remotely on HECToR while being displayed locally using VMD at Aberdeen. So not only did our audience get to play the part of a supercomputer, they also got to play with the real thing!

We also took our demo to Melrose’s “Bang Goes The Borders” festival, which offers children a chance to experience science from laser physics to zombies – and now supercomputers too.