Beowulf Cluster Takes Computing to New Heights
by Alex Parker ’04
Dan Stinebring and Manish Mehta are two co-authors of the grant proposal that landed Oberlin's new supercomputer. [Photo by Fuchs/Kasparek Photography.]
A 64-bit supercomputer, coveted for its memory capacity and incredibly fast processing speeds, is the newest high-tech tool to join the College’s mounting collection of complex scientific instruments.
The 64-node “Beowulf Cluster,” acquired last June with a $308,909 grant from the National Science Foundation, is housed in the chemistry department, where faculty say it’s already led to advances in chemistry, astronomy, and physics previously unimagined for Oberlin. Because of its speed and vast amount of memory, the computer can process complex data needed for cutting-edge research, such as understanding the three-dimensional structure of proteins and studying galaxies. Oberlin is believed to be the only undergraduate college nationwide to own such a powerful computer. “An instrument of this magnitude and capability catapults Oberlin’s science division ahead of those at our peer schools,” says Associate Professor of Chemistry Manish Mehta.
Manufactured by the Aspen Systems Corporation in Colorado, the computer is composed of 64 ‘nodes,’ each with two 64-bit processors and 4 gigabytes of memory and a dedicated, system-wide, 8-terabyte file server for permanent data storage. “Each node runs five to ten times faster than a typical desktop computer,” says Mehta. “The processors are linked with a private gigabit Ethernet network technology—overseen by the SuSe Linux operating system—which allows them to work together or divide themselves so several users can work at the same time.” The computer is linked to the outside world by an ultra-high bandwidth fiber-optic connection.
Since its installation last summer, the machine has worked steadily at unraveling massive amounts of data. Ben Sulman, for example, a senior physics major, discovered two pulsars—work stemming from an internship at the National Radio Astronomy Observatory in Charlottesville, Virginia, last summer. Working with astronomer Scott Ransom, Sulman used a radio telescope to study a star cluster known as Terzan 5. Located 28,000 light years from Earth—deep within the center of the Milky Way—the cluster holds a beehive of rapidly spinning millisecond pulsars.
Deciphering the star data was a monumental task. From his laptop in Virginia, Sulman uploaded the data onto Oberlin’s supercomputer and ran a software program designed to sort out pulsars from “false” signals such as radio interference. For a week, the computer searched, suggesting “candidates” worthy of further study. After more tests, Sulman found one—a pulsar the size of Cleveland. “It’s pretty exciting to have that type of computing power at your fingertips,” he says.
It is just that type of student access that encouraged the NSF to fund Oberlin’s proposal. “The proposal did an excellent job of demonstrating a meaningful impact on students and broad, interdisciplinary applications,” says NSF program officer Joan Frye. The grant, which faculty say became the largest single-instrument grant in College history, has paid for the computer’s hardware, several software packages, and a part-time system administrator for three years.
Mehta was the lead author of the grant proposal, joined by Matthew Elrod in chemistry, John Karro in computer science, and Dan Stinebring, the Federighi Professor of Physics and Astronomy. All hope the machine will become a campuswide resource—one eventually, perhaps, that can be shared with the local schools.
The multi-disciplinary nature of its work is already evident. Mehta and his students are using the computer to understand how the presence of water molecules can subtly alter the three-dimensional structure of small proteins and how that variation is manifested in experimentally observable quantities.
Elrod is completing a project in which the chemical reactions in smog formation are explored through computational methods, in hopes of finding the most efficient way to cut down on pollution in big cities. He’s also working to allow students to perform quantum mechanics calculations during sessions of his Quantum Chemistry and Kinetics course this spring.
“Because the supercomputer is actually 64 separate computers wired together, students can now all work at the same time,” he says. “In the past, they had to take turns using a single processor computer. Now, they can compute in real time during the actual lecture.”
In geology, Assistant Professor Laura Moore is modeling the recent geologic evolution of coastal barrier island systems, such as the Outer Banks of North Carolina. She will also run forward simulations allowing her to test hypotheses regarding the future response of coastal systems to rising sea levels. In physics and astronomy, Assistant Professor Chris Martin is modeling the properties of giant molecular clouds in the Milky Way, from which new stars are born, as well as the dynamics of the galaxy as a whole.
And Stinebring, who worked with Ben Sulman on the pulsar search, is using the supercomputer with three Oberlin students to study compact clouds of gas in the Milky Way galaxy.
As for Sulman, just a few weeks into the fall semester, he struck gold again: “I discovered another pulsar,” he says. “This one is actually more exciting because I discovered it using a searching code that I wrote myself.” ATS
Learning and Earning
Landing a summer internship in New York is the stuff of dreams for many undergraduates, but the high cost of city living can make even the most enticing job unattainable. Low-pay or no-pay internships are the norm in a marketplace that brims with college students scrambling for job experience.
But where the marketplace is leaving off, Oberlin is picking up. While interning in Manhattan last summer, seniors Eric Klopfer and Emma Budwig earned $2,500 stipends from the College—monies raised through the Young Alumni Internship Fund and the Class of 1968 Leadership Award.
Budwig, a Latin American studies major, worked at the International Partnership for Service Learning & Leadership, a nonprofit that links students with study abroad and volunteer opportunities. Klopfer, an English and cinema studies major, worked at Marvel Comics, the publishing branch of Marvel Enterprises, while also promoting Shakespeare in the Park for the New York Public Theater part time.
“The internship at Marvel was a great introduction into an aspect of the publishing business that I hadn’t considered before,” says Klopfer, who interacted with comic industry luminaries and marketing personnel to learn what makes for a good script and how to pitch a product.
His was the first stipend awarded from the Young Alumni Internship Fund, a fundraising project created in 2004 for the fifth-year reunion classes of 1999, 2000, and 2001 and expanded into a senior class gift project for the Class of 2005. “It’s a practical way to give liberal arts students a taste of what lies ahead in the professional world,” says 2005 Class President Morgan Shelton.
Budwig, whose stipend came from the Class of 1968 Leadership Award, hopes to put her bilingual skills to work in the Latino community. “The internship was really invaluable, and it helped to shape my career path,” she says.
Wendy Miller, director of career services at Oberlin, says that such success stories affirm the need for internships—and the need for additional funding.
“Internships open students up to a whole new world,” she says. “When I was in college it never crossed my mind to work in New York or DC. But these are the kinds of life-changing opportunities students need to help them figure out what they want to do. And some of them figure out what they don’t want to do, which is just as much of a success.”
Other funded internships are on the way, she says. The Peter Goldsmith Fund, endowed in 2004 in memory of the late former dean of students, will soon award stipends for winter-term projects or summer internships. The 1835 Endowed Fund, established by three alumnae to commemorate Oberlin’s admission of African American students, will support students of color through internships and mentoring in conjunction with the Multicultural Resource Center.
“About half of all Oberlin students will take an internship by the time they graduate,” Miller says. “We’d like to provide more equal access, and we hope funds will grow with additional donations from alumni. It’s a good way to show support and encourage and celebrate good internship experiences.” ATS
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