Beagle Supercomputer to Help Provide Transformational Innovations in Biomedical Research

A new supercomputer has been developed for biomedical simulation and data analysis.

The Computation Institute (CI), a joint initiative between the University of Chicago (UChicago; IL, USA) and Argonne [U.S.] National Laboratory (Argonne, IL, USA), announced the introduction of Beagle, a 150-teraflop, 18,000-core Cray (Seattle, WA, USA) XE6 supercomputer that will support computation, simulation, and data analysis for the biomedical research community.

Made possible by a grant from the U.S. National Institutes of Health (NIH; Bethesda, MD, USA) National Center for Research Resources (NCRR), Beagle will be housed in the new Theory and Computing Sciences (TCS) building at Argonne and will be available for use by UChicago researchers, their collaborators, and other investigators in the United States.

"Innovative research requires access to the latest technologies,” said NCRR director Barbara Alving, M.D. "This high-performance tool will serve as a core resource that will help ensure scientists remain at the forefront of modern biomedical research.”

The system is named after HMS Beagle, the ship that carried Charles Darwin on his famous scientific voyage in 1831. While Darwin's Beagle enabled discoveries that established a unifying theory for all life sciences, the unique capabilities of UChicago's Beagle will enable transformative innovation in basic, translational, and clinical research leading to improved diagnostic strategies and life-sustaining medical treatment.

Beagle is scheduled to dock in the TCS machine room by the end of 2010, with her maiden voyage, for early adopters, set for the 202nd anniversary of Darwin's birthday, February 12, 2011. The system should be placed into full production by the second quarter of the calendar year.

Dr. Ian Foster, director of the CI and principal investigator for the project, with UChicago's team of technical and domain specialists, identified the need for a powerful computational environment that would serve the growing resource-intensive requirements of the biomedical research community. "Computation is fundamentally changing the nature of research in most disciplines, and biomedical researchers with access to advanced computational resources are more likely to make transformative progress,” said Dr. Foster. "We are excited about the opportunity to advance the biomedicine research frontier and greatly appreciate the support of the NIH-NCRR for this initiative.”

Twelve NIH-funded biomedical research teams, with more than 100 faculty, students, staff, and postdoctoral scholars from multiple research institutions, will be among Beagle's early adopters. Teams presented a case for additional and dedicated computing resources in support of research covering multiple arenas, including the prevention and treatment of cancer, improved management of burn victims, better drug design, genetics, and inherited disorders, and the development of patient-specific medicine.

The wide diversity among the teams' research strategies will provide computational scientists, high-performance computing (HPC) consultants and systems administrators with a fertile proving ground so that Beagle can be customized for a range of biomedical research applications before going into full production.

"The convergence of whole-genome experimental data sets and digitalized clinical data from hospital patient records is changing the landscape of biomedical research,” said Conrad Gilliam, dean for research and graduate education in the UChicago biological sciences division. "UChicago is poised to lead this exciting new phase of discovery with nationally recognized leadership in high-end computation, evolutionary genetics and genomics, and translational research, along with a history of interdisciplinary problem-solving. The arrival of Beagle will challenge our best minds as we forge new modes of inquiry to extract meaningful biological and medical information from these massive tomes of data,” he added.

UChicago's Dr. Benoit Roux anticipates that Beagle will be an important resource for furthering scientists' understanding of several membrane proteins that play a key role in human health because their malfunction is often the cause of disease. "To understand and comprehend how membrane proteins work, one must be able to visualize the manner in which these molecular machines move and change their shape, atom by atom, as they go about their business. Beagle will enable us to perform the detailed computations necessary to reach this goal,” said Dr. Roux.

Beagle is anticipated to place among the top 50 fastest supercomputers in the world and will be one of the fastest systems fully devoted to life sciences. Beagle uses a unique combination of AMD multicore processors, Cray's powerful Gemini system interconnect, and three-dimensional (3D) torus topology in an infrastructure designed to scale to more than 1 million processor cores.

Designed for scalability, with future investments, Beagle can be upgraded to achieve sustained petaflops performance. "We are honored to provide UChicago and NIH with one of the world's most powerful life sciences supercomputers,” said Barry Bolding, vice president of Cray's products division. "Cray specifically designs systems to improve scientific productivity, and we look forward to the important health-related research results that these innovative teams will produce with the aid of the Cray XE6 supercomputer.”

The CI is a joint initiative between UChicago and Argonne. It is an intellectual nexus for scientists and scholars pursuing multidisciplinary research, and a resource center for developing and applying innovative computational approaches. The CI is home to over 100 faculty, fellows, and staff researching complex, system-level problems in such areas as bioinformatics, biomedicine, neuroscience, genomics, metagenomics, energy, and climate, astronomy, and astrophysics, computational economics, and molecular engineering. TeraGrid, the world's largest, most comprehensive distributed cyber infrastructure for open scientific research is managed by the CI team.

Cray provides highly advanced supercomputers and services and support to government, industry, and academia. Cray technology is designed to enable scientists and engineers to achieve remarkable breakthroughs by accelerating performance, improving efficiency and extending the capabilities of their most demanding applications.

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