Boosting research with high-performance collaboration

Developing software to support the new Square Kilometre Array (SKA) and probing the structure of conjugate vaccines are two of the diverse fields that drive the work of the Department of Computer Science’s Associate Professor Michelle Kuttel. Kuttel’s research in computational science involves high-performance computing (HPC), which uses simulations and intensive calculations to answer scientific questions.

Image by Stephen Williams

“I need to use high-performance computers for my collaborative research – whether it be to help astronomers develop more efficient searches for astronomical bodies in SKA data, or to explain cinical results by building virtual models of vaccine components, and then investigating their structure and dynamics,” explains Kuttel.

The key is HPC

Together with innovative algorithms and analytical methods, Kuttel relies on the exceptional speed of HPC to power her work. In particular, the specialised ‘mini-supercomputer’, incorporating graphical processing cards, enables Kuttel to get results more quickly, and to solve problems that are simply not tractable on an average personal computer.

“These computers work so much faster than normal computers. I’m doing in a year what would normally take 10 years to do,” says Kuttel.

Kuttel was one of the first researchers at UCT to build and use parallel computer processors, but she concedes it was a challenge.

“Years ago, a donation of around R250 000-worth of machinery landed in my office. It sounded wonderful at first; but I had to house the machines, organise power, and install and maintain them. As an academic working in scientific computing, being the systems administrator as well as the researcher is a bit of a nightmare,” says Kuttel.

Centralising HPC capacity in eResearch

But UCT has found a way to free up time for researchers like Kuttel; they can now focus completely on their research, while UCT eResearch’s dedicated HPC team takes care of the systems administration.

“It’s been fantastic,” says Kuttel. “They are extremely helpful. eResearch supports the scientists in many ways – from assistance with the purchasing process, to installation and maintenance of the machines and software. They solve technical problems very rapidly.”

HPC specialist Andrew Lewis says the team members are on hand to set up systems and follow up with help.

“A large part of our job is administering the cluster – checking on security loopholes, new versions of software, installation of software packages, and maintaining the system.”

He says ICTS had been considering HPC facilities since about 2010. It also needed to get the researchers on board.

“The idea was to get a central unit, staffed by professionals and trained specifically in HPC – and then convince sceptical researchers that we could support their research.”

The initiative took off. ICTS received seed money to buy hardware, and then worked with researchers to expand on this. The unit needed buy-in from researchers generally, as the infrastructure is expensive; it’s also unlikely that a single research group would able to use it all the time, and to its full capacity. Today the HPC team are located under the eResearch umbrella.

Sharing the resources

Kuttel spotted the opportunity, and channelled research funding into helping to buy a shared resource. While it’s configured to give the lion’s share to Kuttel’s research, other researchers are also able to use it.

Kuttel’s collaboration with eResearch HPC has worked very well, and is the sort of cross-pollination that the university is keen to encourage further.

For Lewis, working in partnership with researchers has been very rewarding. “It’s good to be at the forefront of research, and to know that we are able to give researchers a stable, well-maintained computing facility.”

HPC facilities widely used across disciplines

It’s also good to know how research such as Kuttel’s can be boosted through HPC. In fact, the HPC is used across faculties and research fields at UCT.

In humanities, people can visualise ancient ruins and monuments. In oceanography, researchers can do ocean-temperature modelling. The mathematics department has a project monitoring sardine stocks. Civil engineering is modelling heart valves, and using HPC to design landmine-proof vehicles. HPC is also being used to develop vaccines, and to investigate cancer.

Lewis and his team offer training to researchers as well as back-up; and with interest growing in HPC, it looks set for an exciting future.

“We could easily double the size of the cluster, and we’d use it. We just need to ensure that the output is commensurate with the investment. But we’re tracking citations carefully, and so far we’re doing very well,” he says.