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Physical Chemistry

Built in a Day, Temporary Supercomputer Solves Tough Problem

by Amanda Yarnell
September 27, 2004 | A version of this story appeared in Volume 82, Issue 39

ACS meeting attendees saw just how easy it is to set up your own temporary supercomputer.
ACS meeting attendees saw just how easy it is to set up your own temporary supercomputer.


Built In A Day, Temporary Supercomputer Solves Tough Problem

At last month's American Chemical Society national meeting in Philadelphia, a small band of computational chemists built a supercomputer in a single morning and used it to interrogate a protein-protein interaction important for anthrax infection. Unlike traditional supercomputers--permanent installations that are normally too expensive for anyone but government labs and big universities or corporations to build--this one was gone by mid-afternoon and cost next to nothing to put together.

"Most chemists can't get time at a big, traditional supercomputer" to tackle computationally demanding chemical problems, said Michelle Francl, a chemistry professor at Bryn Mawr College. "But this kind of supercomputer is far more accessible," she added, pointing out that primarily undergraduate institutions, community colleges, and even high schools could get in on the act. In addition to a few loaned computers, all that's needed are plenty of cables, an Ethernet switch, and the right software. She estimated that it would cost about $2,500 to put together a supercomputer from 48 laptops. But nearly everything on that list probably can be borrowed, she added.

The demonstration at the ACS meeting, sponsored by software company Semichem, was the result of collaboration between the Division of Computers in Chemistry and the organizers of FlashMob I, an instant supercomputer built in the University of San Francisco's gym one day last spring. FlashMob computing is the brainchild of Patrick Miller, a professor of computer science at USF who also happens to be Francl's younger brother. His graduate supercomputing class hatched the idea of asking volunteers to loan their laptops to build a temporary supercomputer. Using software that Miller designed, the students successfully linked more than 100 loaner computers in the proof-of-concept run in April.

But the ACS event was the first time a FlashMob supercomputer has been put to use to solve a scientific problem. Francl and Miller used the instant supercomputer--a few dozen loaned laptops sitting in a sea of cables--to tackle a problem suggested by Jeffrey D. Evanseck, a chemistry professor at Duquesne University, Pittsburgh. Evanseck had been trying to use molecular dynamics to calculate the structural motions required for a human protein known as calmodulin to bind and activate anthrax's toxic EF protein in water. He'd been unable to run this simulation in his own lab, but the instant supercomputer conquered it in just 40 minutes. "That's pretty darn impressive," he said.

Other people have linked out-of-the-box PCs together to make permanent (but less costly) supercomputers. "But a FlashMob supercomputer is temporary and organized on the fly to solve a single problem," Miller said. No need to dedicate permanent space or equipment or personnel to the project; it can be built when you need it, where you need it. "It can bring supercomputing to the masses," he enthused.



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