TY - GEN
T1 - NAMD
T2 - 2002 IEEE/ACM Conference on Supercomputing, SC 2002
AU - Phillips, James C.
AU - Zheng, Gengbin
AU - Kumar, Sameer
AU - Kalé, Laxmikant V.
N1 - NAMD was developed as a part of biophysics research at the Theoretical Biophysics Group (Beckman Institute, University of Illinois), which operates as an NIH Resource for Macromolecular Modeling and Bioinformatics. This resource is led by principle investigators Professors Klaus Schulten (Director), Robert Skeel, Laxmikant Kaléand Todd Martinez. We are thankful for their support, encouragement, and cooperation. Prof. Skeel and coworkers have designed the specific numerical algorithms used in NAMD. We are grateful for the funding to the resource provided by the National Institutes of Health (NIH PHS 5 P41 RR05969-04).
NAMD was developed as a part of biophysics research at the Theoretical Biophysics Group (Beckman Institute, University of Illinois), which operates as an NIH Resource for Macromolecular Modeling and Bioinformatics. This resource is led by principle investigators Professors Klaus Schulten (Director), Robert Skeel, Laxmikant Kal? and Todd Martinez. We are thankful for their support, encouragement, and cooperation. Prof. Skeel and coworkers have designed the specific numerical algorithms used in NAMD. We are grateful for the funding to the resource provided by the National Institutes of Health (NIH PHS 5 P41 RR05969-04). NAMD itself is a collaborative effort. NAMD 1 was implemented by a team including: Robert Brunner, Andrew Dalke, Attila Gursoy, Bill Humphrey and Mark Nelson. NAMD 2, the current version, was implemented and is being enhanced by by a team consisting of: Milind Bhandarkar, Robert Brunner, Paul Grayson, Justin Gullingsrud, Attila Gursoy, David Hardy, Neal Krawetz, Jim Phillips, Ari Shinozaki, Krishnan Varadarajan, Gengbin Zheng, and Fangqiang Zhu. This research has benefited directly from the Charm++ framework at the Parallel Programming Laboratory (http://charm.cs.uiuc.edu), and especially its load balancing framework and strategies, the work on the performance tracing and visualization tool projections), and its recent extensions for using chip-level performance counters. For help with the results in this papers, as well as for relevant work on Charm++, we thank Orion Lawlor, Ramkumar Vadali, Joshua Unger, Chee-Wai Lee, and Sindhura Bandhakavi. Charm++ framework is also being used and supported by the Center for Simulation of Advanced Rockets (CSAR or simply the Rocket Center) at the University of Illinois at Urbana-Champaign, funded by the Department of Energy (via subcontract B341494 from Univ. of California,), and the NSF NGS grant (NSF EIA 0103645) for developing this programming system for even larger parallel machines extending into PetaFLOPS level performance. The parallel runs were carried out primarily at the Pittsburgh Supercomputing Center (PSC) and also at the National Center for Supercomputing Applications (NCSA). We are thankful to these organizations and their staff for their continued assistance and for the early access and computer time we were provided for this work. In particular we would like to thank David O'Neal, Sergiu Sanielevici, John Kochmar and Chad Vizino from PSC and Richard Foster (Hewlett Packard) for helping us make the runs at PSC Lemieux and providing us with technical support. Computer time at these centers was provided by the National Resource Allocations Committee (NRAC MCA93S028).
Charm++ framework is also being used and supported by the Center for Simulation of Advanced Rockets (CSAR or simply the Rocket Center) at the University of Illinois at Urbana-Champaign, funded by the Department of Energy (via subcontract B341494 from Univ. of California, ), and the NSF NGS grant (NSF EIA 0103645) for developing this programming system for even larger parallel machines extending into PetaFLOPS level performance.
PY - 2002
Y1 - 2002
N2 - NAMD is a fully featured, production molecular dynamics program for high performance simulation of large biomolecular systems. We have previously, at SC2000, presented scaling results for simulations with cutoff electrostatics on up to 2048 processors of the ASCI Red machine, achieved with an object-based hybrid force and spatial decomposition scheme and an aggressive measurement-based predictive load balancing framework. We extend this work by demonstrating similar scaling on the much faster processors of the PSC Lemieux Alpha cluster, and for simulations employing efficient (order N log N) particle mesh Ewald full electrostatics. This unprecedented scalability in a biomolecular simulation code has been attained through latency tolerance, adaptation to multiprocessor nodes, and the direct use of the Quadrics Elan library in place of MPI by the Charm++/Converse parallel runtime system.
AB - NAMD is a fully featured, production molecular dynamics program for high performance simulation of large biomolecular systems. We have previously, at SC2000, presented scaling results for simulations with cutoff electrostatics on up to 2048 processors of the ASCI Red machine, achieved with an object-based hybrid force and spatial decomposition scheme and an aggressive measurement-based predictive load balancing framework. We extend this work by demonstrating similar scaling on the much faster processors of the PSC Lemieux Alpha cluster, and for simulations employing efficient (order N log N) particle mesh Ewald full electrostatics. This unprecedented scalability in a biomolecular simulation code has been attained through latency tolerance, adaptation to multiprocessor nodes, and the direct use of the Quadrics Elan library in place of MPI by the Charm++/Converse parallel runtime system.
UR - https://www.scopus.com/pages/publications/85114705648
UR - https://www.scopus.com/pages/publications/85114705648#tab=citedBy
U2 - 10.1109/SC.2002.10019
DO - 10.1109/SC.2002.10019
M3 - Conference contribution
AN - SCOPUS:85114705648
T3 - Proceedings of the International Conference on Supercomputing
BT - Proceedings of the IEEE/ACM SC 2002 Conference, SC 2002
PB - Association for Computing Machinery
Y2 - 16 November 2002 through 22 November 2002
ER -