No Speed Limits
With support from the McDiarmid Institute, Victoria University and AUT University, the University of Canterbury is driving New Zealand research with the recent installation of Australasias’s fastest computer.
Next to the bus schedules posted at University of Canterbury’s College of Engineering is a recruitment poster asking, “What is Electrical Engineering?” Anyone taking time to read the answers: “electric power, electronics, computer engineering, nanotechnology” and then the bottom line, “the 21st century is calling” will notice a hum emanating from the white doors with a yellow Do Not Enter sticker about 25 centimetres to the left.
Behind those doors stands Victoria University’s, AUT University’s and the McDiarmid Institute’s commitment to engineering and bringing New Zealand into the 21st century in the form of the Southern hemisphere’s fastest, most powerful computer. Called Blue Gene and manufactured by IBM, it’s the Lamborghini of supercomputers. Two black refrigerator-sized boxes with purple racing stripes and aerodynamic angles support 2,048 dual processors (the latest Mac laptop has two), which can reach speeds up to ten trillion calculations per second.
Blue Gene features 500 gigabytes of memory (the Mac has two), more than 1,000 fiber optic cables labeled “SAO352” or “EIP2C10” or “SWB9” and countless blinking green lights. Compared to the massive Cray computers, which burn about 650kW per year, Blue Gene is incredibly fuel-efficient, burning only 50kW per year. The $5 million dream machine, of which the McDiarmid Institute contributed about $700,000, is parked in a secure, video-monitored, temperature (20oC) and humidity (44%) controlled space.
Computing hot-rods are standard issue at Harvard, Princeton and the Massachusetts Institute of Technology. With Blue Gene now up and running at Canterbury University and available to anyone who wants to use it, New Zealand researchers are now on the same computing level as these American heavyweights. “There’s always been some guy with a bigger computer,” says MacDiarmid Institute principal investigator Shaun Hendy. “Blue Gene has pushed us to a new plane in that we can compete internationally.”
Hendy and his research team use Blue Gene for more than a dozen nanotechnology-related projects. They are using computer models to create energy-efficient, low-cost fuel cells. Today’s fuel cells use catalysts made out of platinum, one of the world’s rarest and most expensive metals. Hendy hopes to replace them with cheaper tungsten-carbide structures, but there are a large variety of reactions that influence the catalyst’s performance. Running thousands of tungsten-carbide simulations through Blue Gene’s 2,048 parallel processors is quicker and cheaper than building individual structures and extensively testing each one. With Blue Gene, Hendy says he can study potential catalytic reactions without the need for expensive materials and time-consuming experiments. “It’s my virtual experimental tool kit,” he says.
Hendy uses the same took kit to study circuits made from nanoclusters–clumps of 10 to 100,000 atoms with electrical properties. Their conductivity depends on how each atom behaves individually and in concert with others. Hendy says that an ordinary laptop can simulate the behaviour of 1,000 atoms. But with Blue Gene, the activity of 100,000 atoms can be divided among the dual processors, which communicate with each other through fiber optic cables for efficient modeling and data analysis. Two thousand computers from Dick Smiths couldn’t do the job because they lack a fast connection between them, Hendy says.
One of the first people to use Blue Gene is Dmitri Schebarchov, Hendy’s MSc student. He’s filling virtual nanotubes with nanoparticles–like stacking tennis balls in tubes–to create nanowires. Nanowires have the potential to revolutionize the electronics industry because they are smaller than commercial transistors. The smaller the wires, the greater number engineers can incorporate in circuits to increase electronics’ performance. Hendy says the project looks promising, but he can’t give too much away. “Our nanowires are now in the lab phase. We’re going to patent them.”
Back at Canterbury University, mechanical engineering professor Tim David’s office sits a few floors above Blue Gene in a rather less tidy environment of used coffee cups and bike gear. David uses the supercomputer to understand the pathological process of atherosclerosis, the number one killer of both men and women in Western countries.
Endothelial cells line arteries and are constantly exposed to blood flow. Their molecular malfunctions and altered enzyme pathways, either from changes in blood composition or their own self-destruction, but probably a combination of both, create cholesterol-laden arterial plaques.
Plaques weaken arteries and change endothelial cell function, which reduces arteries’ ability to dilate and contract. In turn, arterial dysfunction changes the blood’s oxygen and carbon dioxide concentrations. “It’s all horribly complicated,” David says.
He uses Blue Gene to model everything from blood composition changes to endothelial cell damage, enzyme pathways that lead to plaque formation, all the way to blood flow dynamics and arterial malfunction. “Understanding arterial topology is important in resolving the question, ‘why do people get cardiovascular disease?’”
David says that Canterbury University, like Lamborghini owners, is in an exclusive club. “You can’t just say, ‘I’d like to buy a Blue Gene’ and take one from the shelf.” Without the McDiarmid’s and other academic institution’s support of Blue Gene, New Zealand would remain outside the circle of academic powerhouses and outside the 21st century.
Below: Dr Shaun Hendy and Dmitri Schebarchov