Paper Citing NAMD - Abstract
Fitch, Blake G.; Rayshubskiy, Aleksandr; Eleftheriou, Maria; Ward, T. J. Christopher; Giampapa, Mark; Pitman, Michael C.; Pitera, Jed; Swope, William C.; Germain, Robert S.
Blue Matter: Scaling of N-body simulations to one atom per node
COMPUTATIONAL MODELING OF MEMBRANE BILAYERS, 60:159-180, 2008
N-body simulations present some of the most interesting challenges in the area of massively parallel computing, especially when the object is to improve the total time to solution for a fixed size problem. The Blue Matter molecular simulation framework has been developed specifically to address these challenges in order to explore programming models for massively parallel machine architectures in a concrete context and to support the scientific goals of the IBM Blue Gene project. This paper reviews the key issues involved in achieving ultra-strong scaling of methodologically correct biomolecular simulations, in particular, the treatment of the long range electrostatic forces present in simulations of proteins in water and membranes. Blue Matter computes these forces using the Particle-Particle-Particle-Mesh Ewald (P3ME) method which breaks the problem up into two pieces, one of which requires the use of three-dimensional Fast Fourier Transforms with global data dependencies and the other which involves computing interactions between pairs of particles within a cut-off distance. We will summarize our exploration of the parallel decompositions used to compute these finite-ranged interactions carried out as part of the Blue Matter development effort, describe some of the implementation details involved in these decompositions, and present the evolution in (strong scaling) performance achieved over the course of this exploration along with evidence for the quality of simulation achieved.
