Supercomputing in Pennsylvania, 2004

With Commonwealth of Pennsylvania support, PSC provides education, consulting, advanced network access and computational resources to scientists and engineers across the state.

Photo of Beverly Clayton

Beverly Clayton, PSC executive director, coordinates PSC’s program for Pennsylvania researchers.

Global Supercomputing Comes to Pittsburgh

From November 6-12 more than 6,000 people from around the world will gather at Pittsburgh’s David Lawrence Convention Center for SC2004. The annual conference of the global supercomputing community brings together equipment and software manufacturers, researchers and others to share ideas and assess new developments in high-performance computing, networking and storage.

SC04 Logo

Through the efforts of PSC executive director Beverly Clayton, who serves on the steering committee, and other PSC staff, the conference is in Pittsburgh for the second time — having been here before in 1996 — with an associated economic boon estimated at $9 million.

Economic Development

Photo of the PSC Biomedical Research Group

Teacher Tech ‘04

Pittsburgh-area science teachers are using a Calculator Based Laboratory, a hand-held, data-collection system that works with various sensor technologies. From August 2-6, PSC sponsored a weeklong workshop for Pittsburgh-area science teachers. Presented in collaboration with Rice University’s Center for Equity and Excellence in Education and the National Science Foundation, the workshop introduced new technologies for helping to teach science and raised awareness about teacher roles in shaping and encouraging the next generation of scientists.

PSC’s high-performance computing and networking help to boost the competitiveness of Pennsylvania business and industry and are among the resources the state can point to in attracting new business. Recognizing this, the Pennsylvania Department of Economic and Community Development features PSC machine time and consulting in incentive packages it offers to select companies.

As a PSC Industrial Affiliate, Pittsburgh-based PPG Industries uses LeMieux, PSC’s terascale system, and the quantum-chemistry program GAUSSIAN for computational modeling in several aspects of its product lines as a global supplier of coatings, glass, fiberglass and chemicals.

This year PSC presented a third annual customized technology-briefing day to staff from the Bechtel Bettis Atomic Power Laboratory in Pittsburgh. PSC consultants provided information on how to develop, manage and use a parallel distributed-computing environment.

Research in Pennsylvania

Photo of Ken Merz

Ken Merz, Pennsylvania State University.

By supporting Pennsylvania university researchers, PSC resources help to attract research funds to the state. During the past year, more than 290 Pennsylvania researchers from 11 institutions used PSC computing. Pennsylvania usage of PSC’s CRAY T3E totaled 1.25 million hours. In addition, Pennsylvania researchers received allocations through NSF of nearly 10 million hours on LeMieux, PSC’s terascale system, along with 450,000 hours on PSC’s HP Marvel systems. The projects represented here (facing page) exemplify how supercomputing plays a role in scientific and engineering research in Pennsylvania.

Biomolecules and the Search for Drugs

Image of urea in active site of urease.

Using LeMieux, PSC’s terascale system, Merz carried out a quantum-mechanical study of urease, a metalloenzyme that plays important roles in the nitrogen metabolism of plants and microbes. Urease in soil can release large quantities of toxic ammonia, affecting crop yields, and it also constitutes a virulence factor in human and animal infections of the urinary tract. This graphic from PSC calculations shows details of the urease active-site structure.

Professor Ken Merz of Penn State’s Department of Chemistry leads a research group that develops and uses computational methods to further understanding of biomolecules. They are especially interested in metalloenzymes, an important class of enzymes that carry out myriad biological functions. These enzymes are involved in diseases ranging from periodontal disease to arthritis and cancer, and drugs that inhibit and regulate these enzymes could be useful in treating these diseases.

Merz, who is also CEO of QuantumBio Inc, a biotechnology company he cofounded, works on developing improved computational techniques that include quantum-mechanical approaches — highly precise and at the same time computationally expensive — together with more conventional classical approaches. Some of his recent work has focused on an approach that will make it feasible to carry out fully quantum calculations on molecules as large as enzymes.

When the Earth Shakes

Photo of Omar Ghattas and Jacobo Bielak

Omar Ghattas (left) and Jacobo Bielak, Carnegie Mellon University, finalists in the 2004 Computerworld award for Science, which recognizes innovation in information technology that benefits society.

One of the main lessons of recent urban earthquakes is the need for better information about where and how much the ground will shake. A multi-disciplinary team led by Jacobo Bielak, Omar Ghattas and David O’Hallaron of Carnegie Mellon University have used LeMieux, PSC’s terascale system, to simulate soil conditions for the Los Angeles earthquake basin with much greater accuracy than has before been possible. For this work, they received the 2003 Gordon Bell Prize, one of high-performance computing’s most prestigious awards, and their work was recognized as a finalist for the 2004 Computerworld award in Science.

Using 3,000 LeMieux processors, they carried out the most detailed simulation yet of the 1994 Northridge earthquake, allowing soil to vibrate at two cycles per second, doubling the previous high frequency for earthquake simulation. Because of LeMieux, this group also made significant progress on the “inverse problem,” a sophisticated approach that makes it possible to recover deep geological features based on seismic recordings at the surface.