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Studying Protein Folding on the Grid: Experiences Using CHARMM on NPACI Resources under Legion
San Francisco, California August 07-August 09
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/HPDC.2001.94517210th IEEE International Symposium on ...
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Anand Natrajan, University of Virginia
Anthony D. Fox, University of Virginia
Marty A. Humphrey, University of Virginia
Andrew S. Grimshaw, University of Virginia
Nancy Wilkins-Diehr, University of California at San Diego
Michael Crowley, The Scripps Research Institute
Charles L. Brooks Iii, The Scripps Research Institute
Abstract: One benefit of a computational grid is the ability to run high-performance applications over distributed resources simply and securely. We demonstrated this benefit with an experiment in which we studied the protein-folding process with the CHARMM molecular simulation package over a grid managed by Legion, a grid operating system. High-performance applications can take advantage of grid resources if the grid operating system provides both low-level functionality as well as high-level services. We describe the nature of services provided by Legion for high-performance applications. Our experiences indicate that human factors continue to play a crucial role in the configuration of grid resources, underlying resources can be problematic, grid services must tolerate underlying problems or inform the user, and high-level services must continue to evolve to meet user requirements. Our experiment not only helped a scientist perform an important study, but also showed the viability of an integrated approach such as Legion's for managing a grid.
Citation:
Anand Natrajan, Anthony D. Fox, Marty A. Humphrey, Andrew S. Grimshaw, Nancy Wilkins-Diehr, Michael Crowley, Charles L. Brooks Iii, "Studying Protein Folding on the Grid: Experiences Using CHARMM on NPACI Resources under Legion," hpdc, pp.0014, 10th IEEE International Symposium on High Performance Distributed Computing (HPDC-10 '01), 2001
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