HECToR: The next stage of super computing

Supplementary content information

A facility for UK researchers managed by the EPSRC, on behalf of Research Councils' UK.

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Professor Arthur Trew – Director, HECToR Facility, University of Edinburgh [AT]

HECToR is a parallel supercomputer. It is capable of doing some 800 million, million calculations per second which, if you struggle with these large numbers, an easier way to think of it may be to say that it is 100,000 calculations per second for every man, woman and child on the planet.

HECToR stands for the High End Computing Terra Scale Resource. It consists of about 30 cabinets, each of them the size of a large wardrobe, that contain the computer and we have another ten cabinets or thereabouts for the disks and the tapes - so it’s very big. It’s got a petabyte of disk space, that’s 1,000 million, million, million, million bytes. If you had this much on your iPod and started listening today you would finish in the year 3153.

We wanted to see if we could portray what HECToR does, given that we had all of these wardrobe - like cabinets. We held a competition – it was won by a girl called Lily Johnson from Heverset Old School in Norwich and it shows the different types of research that we do on HECToR.

Ninety-five per cent of the knowledge that we have about the world around us, comes from two different techniques - we have theory or it comes from experiment. There are however a whole class of problems where the situation is so complex that even if you know the equations, you can’t solve them in a meaningful fashion. The climate is an obvious example of this. So what we do with a computer is we take those equations that we know, to do what the scientist with the pencil cannot. We solve the climate or the weather for a little bit of Edinburgh, a little bit of London and then stitch them all together to produce a picture of the entire globe. There are some 50 different research groups from around the UK that are using the facility, from biology and drug design at one end through engineering, chemistry and all the way to the environment. We’ve recently finished a project in understanding how dinosaurs walk. What two chaps from Manchester did was to discover that although Hadrosaurs actually could hop faster than they could run, safety considerations probably meant that the two legged running gate, similar to the one that we have today, was a more likely form of locomotion. Turbulence is something that bumps you up and down. We also understand that in air craft it is something that creates a lot of noise pollution so we want to understand turbulence to minimise the discomfort to passengers and also to reduce air craft pollution. But on the other hand, in the chemical industry turbulence is used to mix compounds so there has been a lot of work in many different scientific fields on areas such as turbulence and turbulent mixing.

Dr Carole Morrison - Senior Lecturer in Chemistry, University of Edinburgh

My area of research is in molecular simulations. So we run simulations on large computers that allows us to understand the structures of molecules, but more than that to understand the dynamics of molecules as well. This piece of equipment I’m sitting beside just now is an electron diffraction machine, what it allows us to do is to take photographs if you like of molecules using a beam of electrons. Understanding the data that we get off of this machine is really quite complicated so we rely heavily on the use of simulation to be able to guide us to understanding exactly what the data is trying to tell us. This is a model, a very basic model, of a pore of a cell so if you look down the length of this model, these represent alpha helices and down the middle of that you see we’ve got a pore and all sorts of things pass through these pores in your cells every second of every day so things like chlorine ions, sodium ions, potassium ions and hydrogen ions.

Now hydrogen ions are so small we are never ever going to see them experimentally and so the idea is that we can use simulation to be able to model how these hydrogen ions pass in and out of your cells. Why is that important, well it’s how your cells maintain ph neutrality, why your cells don’t get too acidic or too basic and it’s also the mechanism that your cells are able to generate energy, energy to make you think, to make you grow, to be able to fight diseases and so on.

Quantum mechanics is a very, very computational intensive way to model matter, but it was the only way that we could get to the answers we needed in this problem, so Phase 3 HECToR will allow us to be able to expand on our model. We want to adapt it, we want to modify it to make it even more realistic. Work that is only possible having access to very high computational resources.

[AT]

We’re just about to move on to Phase 3 of HECToR which is going to be roughly ten times the performance of HECToR when it started in 2008. This opens up a whole series of new problems that we can start to deal with. We want to look at a whole range of new so called emergent phenomena. These are phenomena that you wouldn’t have predicted just from the appearance of the equations themselves and we believe that these emergent phenomena will appear in chemistry, engineering and in biology as well.

There are these challenges for which HECToR is a stepping stone for other grand challenges for the century we have just entered.