Title :
Blue Matter: Approaching the Limits of Concurrency for Classical Molecular Dynamics
Author :
Fitch, Blake G ; Rayshubskiy, Aleksandr ; Eleftheriou, Maria ; Ward, T. J Christopher ; Giampapa, Mark ; Pitman, Michael C ; Germain, Robert S.
Author_Institution :
IBM Res. Div., IBM Thomas J. Watson Res. Center, Yorktown Heights, NY
Abstract :
This paper describes a novel spatial-force decomposition for N-body simulations for which we observe O(sqrt(p)) communication scaling. This 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. Major scaling improvements require exploration of alternative algorithms for treating the long range electrostatics
Keywords :
biology computing; biomembranes; communicating sequential processes; fast Fourier transforms; mesh generation; molecular biophysics; parallel programming; proteins; Blue Gene/L; Blue Matter; FFT; N-body simulation; biologically interesting system; biomolecular simulation; communicating sequential process; communication state machine; electrostatic interactions; hardware interface; molecular dynamics; particle-mesh method; spatial-force decomposition; Biological system modeling; Biomembranes; Computational modeling; Concurrent computing; Electrostatics; Hardware; Nanobioscience; Parallel programming; Permission; Scalability;
Conference_Titel :
SC 2006 Conference, Proceedings of the ACM/IEEE
Conference_Location :
Tampa, FL
Print_ISBN :
0-7695-2700-0
Electronic_ISBN :
0-7695-2700-0