Progress in Scaling Biomolecular Simulations to Petaflop Scale Platforms

This paper describes some of the issues involved with scaling biomolecular simulations onto massively parallel machines drawing on the Blue Matter application team’s experiences with Blue Gene/L. Our experiences in scaling biomolecular simulation to one atom/node on BG/L should be relevant to scaling biomolecular simulations onto larger peta-scale platforms because the path to increased performance is through the exploitation of increased concurrency so that even larger systems will have to operate in the extreme strong scaling regime. Petascale platforms also present challenges with regard to the correctnessm of biomolecular simulations since longer time-scale simulations are more likely to encounter significant energy drift. Total energy drift data for a microsecondscale simulation is presented along with the measured scalability of various components of a molecular dynamics time-step

By: Blake G. Fitch; Aleksandr Rayshubskiy; Maria Eleftheriou; T. J. Christopher Ward; Mark Giampapa; Michael C. Pitman; Robert S. Germain

Published in: Progress in Scaling Biomolecular Simulaltions to Petaflop Scale Platforms Lecture Notes in Computer ScienceBerlin, Germany, vol.4375, p.279-88 in 2006

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