Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L

Strong scaling of fixed-size classical molecular dynamics to large numbers of nodes is necessary to extend the simulation time to the scale required to make contact with experimental data and derive biologically relevant insights. This paper describes a novel n-body spatial decomposition and a collective communications technique implemented on both MPI and low level hardware interfaces. Using Blue Matter on Blue Gene/L, we have measured scalability through 16,384 nodes with measured time per time-step of just over 3 milliseconds for a 43,222 atom protein/lipid system. This is equivalent to a simulation rate of 50 nanoseconds per day and represents an unprecedented time-to-solution for biomolecular simulation as well as scaling to fewer than three atoms per node. On a larger 92,224 atom system, we have achieved floating point performance of over 1.5 TeraFlops/second on 16,384 nodes. Scientific results using Blue Matter on prototype BG/L hardware have been published and additional scientific studies are underway which will grow in scale as hardware resources become available.

By: Blake G. Fitch; Aleksandr Rayshubskiy; Maria Eleftheriou; T.J. Christopher Ward; Mark Giampapa; Yuri Zhestkov; Michael C. Pitman; Frank Suits; Alan Grossfield; Jed Pitera; William Swope; Ruhong Zhou; Robert S. Germain, Scott Feller

Published in: RC23688 in 2005


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