The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. In molecular dynamics the fast multipole method (FMM) is an attractive alternative to Ewald summation for calculating
electrostatic interactions due to the operation counts. However when applied to small particle systems and
taken to many processors it has a high demand for interprocessor communication. In a distributed memory environment
this demand severely limits applicability of the FMM to systems with O(10 K atoms). We present an algorithm
that allows for fine grained overlap of communication and computation, while not sacrificing synchronization and
determinism in the equations of motion. The method avoids contention in the communication subsystem making it feasible
to use the FMM for smaller systems on larger numbers of processors. Our algorithm also facilitates application of
multiple time stepping techniques within the FMM. We present scaling at a reasonably high level of accuracy compared
with optimized Ewald methods.
Revised: April 7, 2011 |
Published: March 1, 2005
Citation
Kurzak J., and B.M. Pettitt. 2005. "Communications Overlapping in Fast Multipole
Particle Dynamics Methods." Journal of Computational Physics 203, no. 2:731-743. doi:10.1016/j.jcp.2004.09.012