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Table of Contents Table of Contents Introduction Supercomputing Resources Overview Supercomputers Research Laboratories Supercomputing Institute Programs Graduate Programs Collaborative Programs Other Collaborators Research Scholars Undergraduate Interns Researchers and Administration Fellows of the Institute National Advisory Board Administrative Staff Technical Support Staff Committee Members 1999-2001 External Support Conferences Sponsored Symposia Ongoing and Recently Completed Research Projects from January 1, 2000 to March 15, 2001 University of Minnesota-Duluth Campus College of Science and Engineering Department of Chemistry Department of Physics University of Minnesota-Twin Cities Campus College of Agricultural, Food, and Environmental Sciences Department of Biosystems and Agricultural Engineering Department of Soil, Water, and Climate College of Biological Sciences Bioprocess Technology Institute College of Biological Sciences and Medical School Department of Biochemistry, Molecular Biology, and Biophysics College of Liberal Arts Department of Economics Department of Geography Department of Political Science Department of Psychology College of Natural Resources Department of Wood and Paper Science College of Pharmacy Department of Medicinal Chemistry Department of Pharmaceutics Curtis L. Carlson School of ManagementTable of Contents School of Public Health Epidemiology Institute of Technology Department of Aerospace Engineering and Mechanics Alzheimer's Research Center Department of Astronomy Department of Biomedical Engineering Department of Chemical Engineering and Materials Science Department of Chemistry and Chemical Physics Program Department of Civil Engineering St. Anthony Falls Laboratory Department of Computer Science and Engineering Department of Electrical and Computer Engineering Department of Geology and Geophysics Institute for Mathematics and Its Applications School of Mathematics Department of Mechanical Engineering Department of Physics Medical School Cancer Center Department of Cell Biology and Neuroanatomy Center for Computational Genomics and Bioinformatics Department of Laboratory Medicine and Pathology Department of Microbiology Department of Neuroscience Department of Orthopaedic Surgery Department of Pharmacology Department of Physiology Department of Psychiatry Department of Surgery Metropolitan State University Department of Information and Computer Sciences Minnesota State University-Mankato Department of Management Index and Bibliography Index of Principal Investigators Research Reports Bibliography for January 1, 2000-March 15, 2001 Overview Founded in 1984, the Supercomputing Institute is an interdisciplinary research program spanning all colleges of the University of Minnesota. The Supercomputing Institute provides supercomputing resources and user support to faculty and students and is a linchpin program in the University¹s broad- based digital technology effort. The mission of the Supercomputing Institute is supercomputing research. This includes all aspects of high-performance computing and scientific modeling and simulation, as well as graphics, visualization, and high-performance network communications. Supercomputing research is defined broadly to include a variety of research activities from many disciplines. This research involves the use of high-performance computing environments to address problems in science and engineering that could not otherwise be attempted. Such efforts often result in domain-specific algorithms and codes that exploit the available computing environments as well as visualization techniques to enhance insight, make displays more informative, and add multimedia value to communications and work environments. In many cases, these research activities may involve research aimed at the design or evaluation of high-performance computing hardware, operating systems, networking, and general-purpose algorithms and software. The Supercomputing Institute's resources are available to researchers at the University of Minnesota and other post-secondary educational institutions in the State of Minnesota. In addition, the Supercomputing Institute organizes and hosts symposia, workshops, and seminars, and coordinates other educational and collaborative activities to promote supercomputing research, increase university- industry collaboration, and promote technology transfer. Supercomputers In 1981, the University of Minnesota was the first American university to acquire a supercomputer (a Cray-1B). The Supercomputing Institute was created in 1984 to provide leading-edge, high- performance computing resources to the University of Minnesota¹s research community. From its inception through mid-1998, the supercomputing resources offered to the University of Minnesota research community have included a Cray-2, an ETA 10, a Cray X-MP, an IBM 3090, a Cray M90, a Cray T3D, a twelve-processor Cray C90, and a Cray T3E-900. The Supercomputing Institute has continued the strong tradition of providing University of Minnesota researchers with leading-edge, high-performance computing technologies and diversified programs that complement these technologies. In May of 1998, the Institute began offering its researchers access to a 256-processor IBM SP Silvernode supercomputer with 192 GB of memory. This IBM SP supercomputer was a 64-node machine with four 332 MHz 604e processors and 3 GB of memory on each node. In May 1999, the Institute upgraded the IBM SP by acquiring 80 WinterHawk nodes. Each of the WinterHawk nodes contained two 200 MHz Power3 processors sharing 1 GB of memory for a total of 160 WinterHawk processors. In November 1999, 17 NightHawk nodes were added to the WinterHawk nodes. In April 2000, the WinterHawk nodes were upgraded to WinterHawk+ technology. The Institute¹s IBM SP supercomputer currently comprises 390 processors with 663 GB of memory. It consists of 79 four-processor and 3 two-processor WinterHawk+ nodes with 391 GB of memory and 17 four- processor NightHawk nodes with 272 GB of memory. The NightHawk nodes utilize the 222 MHz Power3 processors and WinterHawk+ nodes utilize the 375 MHz Power3+ processor. In addition, the Institute has a 16-processor Silvernode IBM SP with 12 GB of memory. The Silvernode SP utilizes the 332 MHz PowerPC 604e processor. The IBM supercomputer resources are available in coordination with the IBM Shared University Research (SUR) partnership. In May 2001, the Supercomputing Institute installed two 96-processor SGI Origin 3800s. Each SGI Origin 3800 has 144 GB of memory. These supercomputers utilize 500 MHz R14000 processors. The total amount of disk available to users of the IBM SP systems is 3.5 Terabytes. The total amount of disk available to users of the SGI Origin 2000 systems is currently 2.0 Terabytes. The supercomputing resources are currently located at the Supercomputing Institute¹s facilities in the Minnesota Technology Corridor at the edge of the West Bank of the Minneapolis Campus of the University. In Winter 2002, the Institute will be relocating to the newly renovated Walter Library Digital Technology Center on the East Bank Mall of the Minneapolis Campus. These IBM and SGI supercomputers offer the Supercomputing Institute¹s researchers access to state- of-the-art, high-performance computing technology. In addition, the Supercomputing Institute is continuing its commitment to a diversified array of computing laboratories, collaborations, and programs. These include the Basic Sciences Computing Laboratory, the Scientific Development and Visualization Laboratory, the Medicinal Chemistry-Supercomputing Institute Visualization/ Workstation Laboratory, and interdisciplinary Ph.D. programs in Scientific Computing and Computational Neuroscience. Research Laboratories Basic Sciences Computing Laboratory Since 1996, the Supercomputing Institute has provided high-performance work stations and visualization equipment to enhance the research capabilities of the University community through the Nils Hasselmo Hall, which is located on the East Bank campus of the University of Minnesota. The facility occupies approximately 1700 square feet that includes a workstation room, video/graphics room, machine room, and two offices. The laboratory houses state-of-the-art computing platforms and graphics workstations including a variety of SGI workstations and an IBM Intellistation. The Supercomputing Institute provides technical support and user support for these high-performance computing resources, and the laboratory is available to all University of Minnesota researchers. This laboratory was overseen and guided during 200001 by the following committees: Executive Committee Douglas H. Ohlendorf, Biochemistry, Molecular Biology, and Biophysics Donald G. Truhlar, Supercomputing Institute Director, Chemistry, Chemical Physics, and Scientific Computation Steering Committee Kevin Mayo, Biochemistry, Molecular Biology, and Biophysics, chair Leonard J. Banaszak, Biochemistry, Molecular Biology, and Biophysics David Live, Biochemistry, Molecular Biology, and Biophysics Hans G. Othmer, Mathematics and Scientific Computation Renata M. Wentzcovitch, Chemical Engineering and Materials Science George L. Wilcox, Neuroscience and Scientific Computation Scientific Development and Visualization Laboratory The Supercomputing Institute¹s Scientific Development and Visualization Laboratory, which is located in the Supercomputing Institute¹s facilities in the Supercomputer Center Building, provides front-end equipment, including SGI and IBM workstations, Macintosh workstations,
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