Paper Citing NAMD - Abstract
Fitch, Blake G.; Rayshubskiy, Aleksandr; Eleftheriou, Maria; Ward, T. J. Christopher; Giampapa, Mark; Zhestkov, Yuri; Pitman, Michael C.; Suits, Frank; Grossfield, Alan; Pitera, Jed; Swope, William; Zhou, Ruhong; Feller, Scott; Germain, Robert S.
Blue matter: Strong scaling of molecular dynamics on blue Gene/L
COMPUTATIONAL SCIENCE - ICCS 2006, PT 2, PROCEEDINGS, 3992:846-854, 2006
This paper presents strong scaling performance data for the Blue Matter molecular dynamics framework using 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 under 2.3 milliseconds for a 43,222 atom protein/lipid system. This is equivalent to a simulation rate of over 76 nanoseconds per day and represents an unprecedented time-to-solution for biomolecular simulation as well as continued speed-up to fewer than three atoms per node. On a smaller, solvated lipid system with 13,758 atoms, we have achieved continued speedups through fewer than one atom per node and less than 2 milliseconds/time-step. On a 92,224 atom system, we have achieved floating point performance of over 1.8 TeraFlops/second on 16,384 nodes. Strong scaling of fixed-size classical molecular dynamics of biological systems 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.
