This paper describes a novel decomposition for N-body simulations that has enabled Blue Matter to approach the effective limits of concurrency for molecular dynamics using particle-mesh (FFT-based) methods for handling electrostatic interactions. Using this decomposition, Blue Matter running on Blue Gene/L has achieved simulation rates in excess of 1000 time steps per second and demonstrated significant speed-ups to O(1) atom per node. Blue Matter employs a Communicating Sequential Process (CSP) style model with application communication state machines compiled to hardware interfaces. The scalability achieved has enabled methodologically rigorous biomolecular simulations on biologically interesting systems, such as membrane-bound proteins, whose time scales dwarf previous work on those systems. Further scaling improvements will require exploration of alternative algorithms for treating the long range electrostatics.
By: Blake G. Fitch; Aleksandr Rayshubskiy; Maria Eleftheriou; T. J. Christopher Ward; Mark Giampapa; Michael C. Pitman; Robert S. Germain
Published in: RC23956 in 2006
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