Wired Science

One supercomputer at Warwick University is connecting the work of hundreds of science researchers around the world

Science advancement and research and development needs computing power. At the University of Warwick’s Centre for Scientific Computing (CSC), scientists are working with what they can get. Although this might sound precarious, the reality couldn’t be further from the truth. The University’s new server and storage cluster or “supercomputer”, installed in July 2011, has a clever model of supplying all its users with exactly the processing power they need. Across nine University departments and several European and Global projects, academics are allocated space in the computer’s processing capability, which flexes in size according to the size of their need, and the depth of their overall share of the facility. This innovative model is helping Warwick’s scientific research teams stay ahead of the game.

The server and storage cluster supports around 130 registered researchers from the Chemistry, Physics, Engineering, Mathematics, Statistics, Computer Science, Life Sciences, Warwick Manufacturing Group and Systems Biology departments.

Minerva – as the cluster was named in a competition last year – is housed within the physical sciences building and is managed by Matthew Ismail, Computer Manager. Its use for research purposes is overseen by the director, Professor Mark Rodger.

“To put Minerva’s size and power into perspective is important,” says Mark. “The average desktop PC a researcher might access has just a few core processors. The cluster has approximately 3,100 cores, giving it 1,000 times that processing power.”

The cluster can make calculations as fast as 35 trillion per second. It’s the size of eight filing cabinets and requires constant cooling to ensure it can function at the highest possible speed. Minerva is managed at the CSC by a small team in conjunction with OCF plc, the data processing, data management and data storage provider. OCF worked with CSC to design, integrate and configure the cluster.

Scientific computing is a rapidly growing field with development advances meaning that even the latest technology quickly becomes outdated. Francesca – the predecessor of Minerva ­­– was only three years old when it was supplanted by the new machine, and was in the World’s Top 500 clusters when new. To get a sense of the huge demand for scientific computing capabilities across the campus, it’s worth noting that Warwick’s new cluster is three times the size of Francesca.

“Essentially, all that CSC researchers, scientists and academics need to do is access its processing power and start using the cluster, as they would any other facility,” says Mark. “They interact with it using what we call a ‘fair share’ system. When the computer was purchased, each department involved with it bought a share in its capabilities. Processing power is allocated according to the figures generated from each team’s average usage – how and how much they have been using the computer determines their place in the queue for processing power. In general, the biggest shared owners – such as the Physics department, which has around half of the machine’s capability – is the biggest user.”

“When a project needs to make use of its processing power, a user can log-in to a secure web page and submit their job remotely. There is no need for the user to be present. Access to Minerva is instant and the user simply puts the computer to work. The teams tend to access the data, the modelling and any results from their own PC terminals, although we do also have collaboration suites where they can work together.”

The projects benefitting from the use of the cluster are far ranging, both in terms of subject matter, and geographical reach. The nine different departments all have several projects running simultaneously, some of which they are working on in conjunction with other academic establishments across the UK, Europe, America and Australia.

The largest user of Minerva is the University’s Physics MHD (Magneto-Hydro Dynamics) team. It is part of a UK-wide consortium that actually has three facilities: one in Warwick and two in other UK locations. The group at Warwick has around five academics who are producing upwards of 40 papers per year containing research, analysis and modelling executed using Minerva. MHD is the study of fluids in which magnetic interactions are crucial, and is a major component in our understanding of stars, solar corona, space weather, and the impact these have on Earth and its environment. Amongst other things, the team at Warwick is using Minerva to develop better models of the Sun’s atmosphere, and of how radiation is transmitted through it.

Scientific computing is a rapidly growing field with development advances meaning that even the latest technology quickly becomes outdated

The Computational Fluid Dynamics (CFD) team has a long-running project in place on understanding and characterising types of turbulence. Much of the team’s research involves developing models and equations that are computed using Minerva. One such project is modelling the turbulence found around jet engines with a view to reducing their noise. The team means to determine how turbulence arises in such situations using simulated testing, which will lead to better understanding for the aviation industry of how turbulence can be avoided. The team is also working on a study of the behaviour of lungs, and the flow of air and other particles through the lungs during breathing. The projects are connected by the air and fluid dynamics factors, and Minerva’s power is able to help the teams simulate two totally different environments – the hard surface of an engine or car, and the soft, elastic surface of the inside of a human lung. Both experiments involve simulation and testing down to the flow of nanoparticles to discover how performance and safety can be improved, in areas such as passenger comfort and vehicle suspension from one extreme, to how inhaled drugs can be delivered and ingested quicker by the lungs on the other.

Minerva’s power is also being used by the molecular simulation team to understand biomineral formulation – simulating the way in which nature exerts remarkable control to integrate mineral particles of different size, shape and structure into extremely functional hard materials. Mollusc shells, for example, incorporate two different forms of calcium carbonate in a way that confers incredible strength and durability. The team is mapping and simulating the conditions required to create such complex combinations, with the hope of being able to adapt the processes to make new materials that could be used in applications as diverse as medical implants, building or clothing. The same team is also using simulation to test and validate processes which design additives which stop solids forming, for example to stop wax forming in diesel fuel and clogging engines during cold weather.

The systems biology department uses Minerva to look at proteins – the flexibility, structure, and rigidity of proteins and how this helps them to biologically function. Mark says: “The team is also studying mutations of proteins, this could be benign or could be a change of function (if the latter, i.e. a broken function of a protein, we want to know if this could be harmful). We’re interested in understanding how proteins recognise other compounds. We also want to understand how whole cells work, whole networks of cells. All of this work can be a good way of detecting disease.”

Collaboration across multiple geographies using Minerva is happening more and more. An EU-wide project on nanotoxicity involving six institutions is currently in progress. Work is being undertaken on a materials simulation project dealing with gold nanoparticles and their properties, as part of wider research into the development of organic semiconductors, which will be invaluable to the future of the electronics industry.

Minerva’s power is able to help the teams simulate two totally different environments – the hard surface of an engine or car, and the soft, elastic surface of the inside of a human lung

“Minerva is connecting our faculties in ways we haven’t experienced before, and is bringing a more collaborative approach to scientific computing, particularly in the area of shared costs and responsibilities,” concludes Mark. “The advent of Minerva should help our academics, students and associates to function within their projects without worrying about the performance and availability of computing power to back up their research and complete their work.”

The supercomputer at The University of Warwick will continue to serve its science community’s needs as they make extraordinary progress in fields such as robotics, pollution monitoring and aerodynamics. Plans are already in place to grow Minerva’s footprint and capacity to compute even further when the time is right.