Universities switch on high-power computing projects

After doing research for years using computer clusters, Iowa State University has a high-performance supercomputer running to decipher the corn genome. Meanwhile, Georgia Institute of Technology deepened its high-performance computing relationship with the Oak Ridge National Laboratory (ORNL).

At Iowa State, the delivery of its new IBM Blue Gene/L hardware on Jan. 20 marked the first-ever supercomputer on the school's Ames campus, according to Srinivas Aluru, professor of electrical and computer engineering at the university. The machine, which offers peak performance of 5.7 trillion floating-point operations per second (TFLOPS) from its 2,048 IBM PowerPC 440 CPUs, will allow university researchers to work on the corn genome project, study proteins in organisms and perform other research, Aluru said.

The new machine is more than 10 times as powerful as any high-performance computer currently on campus, he said.

The machine ranks 73rd on the Top 500 list of supercomputers around the world. Four other universities, including Boston University, MIT, Princeton University and the University of California, San Diego, also have Blue Gene machines, Aluru said. The new machine ranks in the top 10 at U.S. colleges and universities, and among the top 15 around the world, he said. The machine was bought with a US$600,000 award from the National Science Foundation and another $650,000 from the university.

Meanwhile, at Georgia Tech, the College of Computing yesterday announced the expansion of a collaboration between the university and the ORNL, including joint appointments of staff members and the creation of a Georgia Tech minicampus at the laboratory in Oak Ridge, Tenn. The partnership expansion is being done with ORNL and UT-Battelle, a nonprofit company that manages and operates the ORNL for the U.S. Department of Energy.

Richard A. DeMillo, dean of Georgia Tech's College of Computing, said the relationship with the ORNL will broaden to provide more research opportunities for the school's faculty and students.

As part of the expanded agreement, the school will be opening a small facility of up to 5,000 square feet at the lab where students and faculty members can do their research, he said. "It's going to be a platform for lots of interesting programs," DeMillo said.

One project involves resource-sharing among high-performance computing centers around the world, he said. For researchers, it's often difficult to transfer their work and custom applications to various machines because hardware configurations can be so varied. Some high-performance computing facilities use large clusters, while some use stand-alone supercomputers. Added to that is a mix of operating systems from Linux to AIX to proprietary Cray software, he said.

"Right now, the high-performance computing world is a patchwork quilt," DeMillo said. The problem for researchers is that often when they put their applications on larger hardware, the applications no longer work as designed. The expanded partnership will work to find answers to solve these problems, he said.

The first joint faculty appointment between the two institutions is that of Thomas Zacharia, the associate lab director for the ORNL's Computing and Computational Sciences Directorate, who was also named a professor at Georgia Tech's College of Computing.

At Iowa State, the corn genome research is intended to help find new ways to engineer sturdier, healthier corn, which is becoming an increasingly important alternative fuel source, said Patrick Schnable, a professor at the school's Center for Plant Genomics. The corn genome is a genetic blueprint for how corn is assembled and how it develops.

The three-year, US$29.5 million project to sequence the corn genome began last November and involves Iowa State and three other universities.

Sequencing a genome reveals an organism's genetic blueprint and opens the door for researchers to discover the role each gene plays in the life of the organism.

The sequence data will be generated at the Genome Sequencing Center at Washington University School of Medicine in St. Louis, Mo., while other work is performed at the University of Arizona, Tucson, and the Cold Spring Harbor Laboratory in New York. The project is funded by the National Science Foundation, the U.S. Departments of Agriculture and the U.S. Department of Energy.

The genome work is expected to help scientists find better ways to produce corn with traits such as enhanced nutrient composition for better food and feed, higher energy content for renewable fuel production, or improved characteristics for use in industrial raw materials, according to the university.

The new Blue Gene/L supercomputer will drastically help with the work, because the research can be done faster, enabling repeated testing, Schnable said. The data will begin pouring out in the next month, he said. "Plant scientists will be making use of this data right away," he said. "The supercomputer is a new step here."

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