Supercomputing cluster aids systems biology researchers

One of the most powerful supercomputing clusters in the world is being used by the Center for the Study of Systems Biology, where it aids Georgia Research Alliance Eminent Scholar and systems biologist Jeffrey Skolnick in ground-breaking research in the fields of computational biology, bioinformatics and systems biology.

“One of the goals of the center is to apply fundamental ideas to practical applications,” Skolnick said. “We want to look at the whole.”

This method of problem-solving can be targeted at a wide variety of issues such as the minimization of side-effects of various drugs and treatments (such as chemotherapy, which has the undesired side effect of hair loss) or the prediction of protein shapes.

“We want to understand how living components interact and work so that we can try and reduce side effects,” Skolnick said.

The center is currently involved in protein research as well as in analysis of interactions between DNA and RNA. These analyses, according to Skolnick, are CPU-intensive and involve considerable calculations that must be computed with a high degree of accuracy.

“I just completed a calculation,” Skolnick said. “On one computer it would have taken two hundred years, but on four thousand computers, [it took] just three weeks. Now the calculation becomes very practical.”

Another example involves the analysis of gene expression of different cancers in order to modify possible treatments. According to Skolnick, a normal computer would take approximately 150,000 days to compute the required calculations whereas the supercomputer cluster takes a little over two months.

“We need this computer power, and I could not do my research without it,” Skolnick said.

That power is considerable: a 35 ton Cluster 1350 system by IBM consisting of 1,000 nodes, each with two dual-core AMD processors. Each node has a four-gigabyte RAM and a 150-gigabyte hard drive. It is connected by Gigabit Ethernet that has wiring stretched over five miles. The cluster releases a million BTUs of heat and has a power density of 200 watts per square foot, which is four times the power density that a normal room can handle.

The heat radiated by the cluster means that it requires special storage courtesy of BellSouth.

“You can’t put it in any room,” Skolnick said. “You have to keep it cool.”

Accordingly, BellSouth has employed the use of IBM Cool Blue Door air conditioning technology which uses the existing chilled water supply in air conditioning systems common to most data centers. As a result, server heat emissions are decreased by as much as 55 percent.

The center is primarily associated with the School of Biology but will utilize the services of various professionals in connection with the cluster.

“We’ll be hiring a whole bunch of people to flush out efforts of biomedical engineers [and] computer scientists….This is a very multidisciplinary problem. You want to use nanodevices and also apply the principles of chemical engineering,” Skolnick said.

While Skolnick was recruited by Tech, the Center is funded by many different sources, such as the Georgia Research Alliance and the National Institutes of Health. IBM was chosen from a list of vendors. “IBM provided the most cost-effective value in terms of price performance and densities,” Skolnick said.

Not your standard IBM...

• 35-ton Cluster 1350 system consisting of 1,000 nodes
• Each node has two dual-core AMD processors, four gigabytes of RAM, 150-gigabyte hard drive
• Gigabit Ethernet connection with wiring spanning over five miles
• Power density of 200 watts per square foot