New Energy supercomputing program focuses on biology

The Energy Department, which helped map the human genome over the last decade, is launching a new supercomputing program at the interface of biological, physical and computational sciences.

'We're trying, in essence, to make innovative approaches along unconventional paths,' said Aristides Patrinos, Energy's associate director for biological and environmental research, speaking at a recent supercomputer conference.

The Genomes to Life program has four goals:
  • Identify the multiprotein complexes that give cells function and structure

  • Study gene regulatory networks, which govern how cells respond to stimuli from other cells and the environment

  • Understand how microbial communities function, with an eye toward harnessing them

  • Develop the computational infrastructure to study complex biological systems.

An advisory committee to Energy's Office of Science recommended the program get annual funding of $200 million, Patrinos said. See www.doegenomestolife.org for details.

The United States is in good shape in hardware innovations, said Susan Graham, a computer science professor at the University of California at Berkeley. U.S. supercomputer software, however, is in worse shape because of limited investment and a shrinking pool of third-party vendors for high-performance technical applications, Graham said.

Paul A. Gottlieb, the Energy Department's assistant general counsel for technology transfer and intellectual property, said that before he started reviewing Energy's software licensing policies in 2000, the department's researchers had two choices. They could either release code as uncopyrighted scientific data, freely available to all, or they could set restrictive licenses for copyrighted software.

A third option

Now Energy researchers have a third choice: release code as open-source software. Both the BSD and the Gnu general public licenses permit redistribution of source code as well as binary versions. Gnu-style licenses, however, require that modifications to the original code must also be licensed as open source; BSD-type licenses do not have that requirement.

Gottlieb said agency researchers will need to determine whether distribution of government-funded software under the Gnu GPL would lock in the future.

Mainstream Linux distributions are not suited to the specialized needs of high-performance computing, said Jeff Brown, program manager for the Advanced Simulation and Computing Group at Los Alamos National Laboratory.

Los Alamos has a 2,048-processor cluster from Linux Networx Inc. of Bluffdale, Utah, for system software research. Sandia National Laboratories has run a commodity Linux computing project, known as Computational Plant or Cplant, since 1998.

Copyright-style open-source licenses such as the BSD license are best for research because they give the most options for licensing derivative programs, said Todd Needham, manager of Microsoft Corp.'s research programs group.

In other supercomputer news, Platform Computing Inc. has struck a deal with the Defense Department's High-Performance Computing Modernization Program to provide a common job management environment for DOD's largest computing centers.

Standardizing on one scheduling tool for DOD's scientific computers will go a long way toward creating a common user environment for the centers, program director Cray J. Henry said. 'Our customers will not have to suffer through learning five or six different scheduling systems,' he said.

Platform LSF HPC, the Markham, Ontario, company's workload management application for supercomputers and clusters, will handle the scheduling of 10,000 nodes on systems from Cray Inc. of Seattle, IBM Corp., SGI and various Linux vendors, said Rene Copeland, a Platform vice president and federal general manager.

New analysis and reporting features will gather utilization data, which the modernization program staff has largely been doing by hand, Copeland said.

Two of the modernization program's four major shared resource centers, the Naval Oceanographic Office and the Army Engineer R&D Center, are located in Mississippi. The other two centers are at the Army Research Laboratory in Aberdeen, Md., and the Aeronautical Systems Center at Wright-Patterson Air Force Base, Ohio.

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