Press Archive

SDSC Establishes Collaboration with the Environmental Molecular Sciences Laboratory to Develop Improved Molecular Software

Published 01/15/1996

For more information, contact:
Ann Redelfs
619-534-5113 (FAX)

Greg Koller
Pacific Northwest Laboratory

The San Diego Supercomputer Center (SDSC) is one of three powerful computing centers to establish a strategic partnership with the Environmental Molecular Sciences Laboratory (EMSL), a new facility being created by the Department of Energy (DOE) to support basic research in the environmental molecular sciences. These partnerships will lead to improved software that will be used to help solve some of the world's most complex scientific problems, including environmental restoration, energy efficiency, and biomedical challenges. The resulting research collaborations also will make molecular modeling software developed at the EMSL available to the broader scientific community. The other two agreements are with the National Energy Research Supercomputing Center (NERSC) in northern California and the Maui High Performance Computing Center (MHPCC) in Hawaii.

The EMSL is located at DOE's Pacific Northwest National Laboratory in Richland, WA, and is funded by DOE's Office of Health and Environmental Research. Once finished, the EMSL will contain a molecular science computing facility with state-of-the-art high performance computational and visualization capabilities.

The three supercomputer centers will test, evaluate, and provide access to a new generation of molecular modeling software being developed at the EMSL. Chemistry is a major focus of research activities at SDSC, where the EMSL software will be used and tested in-house and then made available to SDSC's user community.

"The EMSL is a world leader in developing computational chemistry codes for massively parallel computer systems," says Dr. Robert Eades, manager of the EMSL's molecular science computing facility. "The new codes show excellent performance and scalability."

"SDSC's program in developing new computational chemistry methods and our large chemist user community will benefit greatly from this collaboration," adds Peter Taylor, associate director for scientific research and a computational quantum chemist at SDSC. "In addition, we expect that the EMSL will benefit from the feedback provided by our user community. Further, as visualization in computational chemistry is a focus area at both SDSC and EMSL, we expect new collaborations to emerge in this area. Kim Baldridge and Jerry Greenberg, computational chemists at SDSC, have made their quantum mechanical visualization tool QMView available to EMSL researchers. Greenberg has also made his molecular dynamics visualization tool MDMovie available.

Through the partnerships, SDSC and the other centers will gain access to the EMSL-developed molecular modeling software package called NWChem and the molecular modeling environment called the Extensible Computational Chemistry Environment, or ECCE'. NWChem will provide users with 10-100 times more computing capability than is available on conventional supercomputers. NWChem already features many molecular modeling methods including Hartree-Fock, density functional, perturbation theory, and first derivatives. New capabilities are being added in each release.

"NWChem features major design improvements over traditional codes since it was designed to be modular, extensible, and highly efficient," explains Eades. "In particular, NWChem will interface readily with other program suites to retain existing capability while making new functionality accessible to others."

ECCE' integrates NWChem and other codes into a seamless environment so scientists can perform complex molecular modeling and simulation tasks from desktop workstations. ECCE' components include graphical user interfaces, visualization applications, and scientific data management, all tailored for computational chemistry applications. This capability enables easy and accurate creation, visualization, storage, analysis, and retrieval of molecular simulations.

According to EMSL Director Thom Dunning, the collaborations are an important step in advancing computational molecular science to a point where it can help solve the nation's most difficult environmental problems. "The environmental molecular science problems that we encounter at DOE sites, whether they involve modeling the crown ethers used to extract radionuclides from complex waste mixtures or the mechanisms involved in the biodegradation of chlorinated hydrocarbons, simply cannot be solved with existing technology," he says. "NWChem and ECCE' provide the capability needed to accurately model molecules containing hundreds, even thousands, of atoms. The understanding of fundamental molecular processes provided by the simulations will lead not only to solutions to complex environmental remediation, waste processing, health, and ecological problems, but also to better energy use strategies and new biomedical technologies."

Each of the three supercomputing centers is managed by a different federal agency and, according to Eades, the agreements will bring the agencies together, allowing them to pool their findings and draw on a bigger knowledge base to solve computational molecular science problems within their jurisdiction.

SDSC operates three supercomputers -- an eight-processor vector CRAY C90, a 128-processor parallel CRAY T3D, and a 400-node parallel Intel Paragon -- as well as a $6-million Advanced Scientific Visualization Laboratory. SDSC serves more than 5,100 researchers from more than 240 institutions and industrial partners. In operation since 1986, the center is closely affiliated with the University of California, San Diego and is administered by General Atomics for the National Science Foundation.

NERSC is being moved from Livermore, CA, to the Lawrence Berkeley National Laboratory in Berkeley. It is the principal supplier of production high performance computing and networking services to the nation's computational science community supported by DOE's Office of Energy Research. NERSC houses a CRAY Y-MP C90, two CRAY-2 production supercomputers, one CRAY T3D parallel computer, one Y-MP EL, Supercomputing Auxiliary Servers, and extensive facilities for data storage and communications. The center was created in 1974 and has more than 4,000 users.

The MHPCC is managed by a consortium led by the University of New Mexico under a cooperative agreement administered by the U.S. Air Force's Phillips Laboratory in Albuquerque, NM. It houses the world's second largest installation of the IBM RS/6000 Scalable POWERparallel system, with a total of 480 processors, offering a capacity of 125 billion calculations per second (125 gigaflops). The MHPCC also provides state-of-the-art computer graphics and high performance storage system technologies. It provides training and support services to the Department of Defense, other government agencies, and commercial and academic users. The MHPCC was created in September 1993, and more than 1,300 researchers worldwide use the facility. In summer 1995, the EMSL and the Phillips Laboratory signed a Memorandum of Understanding regarding the development of NWChem at the Maui facility.

The Pacific Northwest National Laboratory in Richland and Sequim, WA, is one of nine national, multiprogram laboratories. Battelle Memorial Institute of Columbus, OH, manages the facility for DOE. The $230-million EMSL is a national collaborative user facility nearing completion at the Pacific Northwest National Laboratory.