James Phillips, Gengbin Zheng, Sameer Kumar, and Laxmikant Kale.
NAMD: Biomolecular simulation on thousands of processors.
In Proceedings of the IEEE/ACM SC2002 Conference, Technical
Paper 277, pp. 1-18. IEEE Press, Baltimore, Maryland, 2002.
PHIL2002-LK
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.
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