SIAM Entry Awarded Best Poster

March, 2004
Earlham College Public Affairs Office

Earlham’s poster entry at the Society of Industrial and Applied Mathematics (SIAM) Parallel Processing conference last week in San Francisco had two distinctions.

It was the only entry from an undergraduate school, and it won.

Assistant Professor of Computer Science Charlie Peck '84, Josh Hursey '03, and senior Josh McCoy won the best poster award for their entry, "Benchmarking and Tuning the GROMACS Molecular Dynamics Package on Beowulf Clusters."

This project is the first in a series of collaborations between Earlham's Cluster Computing Group and the Folding@Home project at Stanford University.

The cluster group works with software that simulates protein folding in computers. Proteins are the basis of how biology works, and an important step in the process is studying how proteins fold or self-assemble to carry out their work.

"Rather than performing protein folding experiments in vitro, chemists and other scientists can simulate the process in silica," Peck said. "Some advantages of simulation over wet bench experiments are speed and the ability to observe each step of the process in some detail."

Peck explained that through the Folding@Home project, which is a large-scale distributed computing system, a new way to simulate protein folding was developed that breaks the microsecond barrier by dividing the work between multiple processors with a near linear speed up as processors are added. Thus, with thousands of processors, researchers can break the microsecond barrier and better explore the mysteries of protein folding.

The group's poster examined the performance of GROMACS, a popular open source molecular dynamics package, running on Beowulf clusters. Molecular dynamics is one way to simulate the folding of amino acids into proteins.  Beowulf clusters are parallel computing platforms assembled from commodity-off-the-shelf (COTS) components.  Beowulf clusters enable relatively small research groups to cost-effectively pursue computationally based research.

"I think this award highlights the quality of research that can be achieved in a small, intensive environment such as Earlham," Hursey said. "The close relationship between faculty and students and the interdisciplinary nature of Earlham support a research environment where computer scientists, chemists, mathematicians, and others can easily collaborate on interesting research projects."

McCoy agreed.

"The simple fact that the faculty are willing to spend their time working so closely with undergraduates says a lot for their dedication to education," McCoy said. "Being a part of the Cluster Computing Group, doing research, and going to conferences has helped me to develop the skills needed to perform well at the next level of education."

Mic Jackson, professor of mathematics, said SIAM membership rolls include many of the best and brightest mathematicians in the world.

"The work on protein folding done at Earlham was impressive to the other mathematicians and computer scientists at the meeting," Jackson said. "Their award was a surprise and a significant honor earned in a highly competitive and intellectually rich setting."

"It was a very close atmosphere, and at times a bit intimidating discussing our research goals and future plans with major researchers from national laboratories and research universities around the world," Hursey said.

Along with the poster award, the group brought back another project to work on, Folding@Clusters. As exciting as the initial protein folding work has been, the group is even more excited to begin this new project.

"Instead of being run on many individual computers, the protein folding simulation will be setup to run on a variety of parallel computing platforms," Peck said.  "This will enable researchers to consider different molecular forms and return results more quickly."

Hursey said in many ways the work thus far has been in preparation for the cluster project.

The work of Earlham’s Cluster Computing group has been funded by various grants and donations including Howard Hughes Medical Institute, Arthur Vining Davis Foundation, Apple Computers, Safe Passage Communications and Ray Ontko ‘84.