Mount Allison enlists supercomputer for cancer research

Researchers at Mount Allison University in New Brunswick are using IBM supercomputing technology to help them discover drugs to repair damaged human DNA in diseases like cancer

and Alzheimer’s.

Their work is part of the Mount Allison Cluster for Advanced Research, financed by the Canada Foundation for Innovation and the New Brunswick Innovation Foundaton, which was founded last May.

The motive behind setting up a virtual lab with IBM rather than maintaining a four-processor system is to study chemical systems on computers instead of mixing together substances in traditional lab experiments, said Stacey Wetmore, a chemistry professor and the project’s lead researcher in Sackville, N.B.

Because labs are used by undergraduate students during the year, the researchers said they need a powerful system like IBM’s to undertake their work during the short summer months.

Another big benefit of using the new lab is Mount Allison’s researchers don’t have to worry about chemical waste disposal or using many expensive chemicals, said Wetmore, who’s been doing DNA research at the university for two and a half years.

The dual processor cluster of IBM eServer xSeries running a Linux operating system can “”look at a lot of different chemical systems a lot more quickly than actually making the molecules in the lab,”” she added.

Mount Allison researchers sought IBM’s help in solving their chemistry problems by using a distributed memory approach in which one processor is directly associated with one memory bank, as opposed to a more expensive shared-memory machine, said Dominic Lam, national high-performance computing manager at IBM Canada in Markham, Ont.

Neither Wetmore nor IBM can pinpoint the amount of money that will be saved by undertaking research projects using a IBM Linux supercomputing cluster. Lam, however, does says the potential cost savings is significant.

“”We now have an opportunity to do research that we simply couldn’t do before, so you can’t even put a dollar price on it,”” added Laurie Ricker, assistant professor of mathematics and computer science, who along with physics professor Mohammad Ahmady is also using the virtual lab.

Ricker said she studies the control of distributed software and is using the cluster to create computational tools as opposed to tapping existing software. Ahmady is performing numerical computations that aim to answer fundamental questions about the universe’s creation.

Implementing IBM’s technology has not come without hitches, Wetmore explained. She said it was challenging to run the software over 168 computers and to make the computers communicate with one another. “”I have commercial chemistry software, but even though different people have it running over multiple computers, it’s still really hard to get it to work on your system.””

IBM ended up dispatching an expert in Wetmore’s computational chemistry software to Mount Allison for a couple of months. “”From my perspective as a chemist, it was a blessing that they had somebody who knew about my software and could spend the time helping us install it.””

She said the other problem was matching Linux’s “”constantly changing”” versions to the software package the researchers were using.

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