title: Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations.
abstract: We have developed a new hybrid (MPI+OpenMP) parallelization scheme for molecular dynamics (MD) simulations by combining a cell-wise version of the midpoint method with pair-wise Verlet lists. In this scheme, which we call the midpoint cell method, simulation space is divided into subdomains, each of which is assigned to a MPI processor. Each subdomain is further divided into small cells. The interaction between two particles existing in different cells is computed in the subdomain containing the midpoint cell of the two cells where the particles reside. In each MPI processor, cell pairs are distributed over OpenMP threads for shared memory parallelization. The midpoint cell method keeps the advantages of the original midpoint method, while filtering out unnecessary calculations of midpoint checking for all the particle pairs by single midpoint cell determination prior to MD simulations. Distributing cell pairs over OpenMP threads allows for more efficient shared memory parallelization compared with distributing atom indices over threads. Furthermore, cell grouping of particle data makes better memory access, reducing the number of cache misses. The parallel performance of the midpoint cell method on the K computer showed scalability up to 512 and 32,768 cores for systems of 20,000 and 1 million atoms, respectively. One MD time step for long-range interactions could be calculated within 4.5 ms even for a 1 million atoms system with particle-mesh Ewald electrostatics.
authors.affiliation: Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo Kobe, 640-0047, Japan, Fax: +81 48 467 4532.
authors.forename: Jaewoon
authors.initials: J
authors.lastname: Jung
authors.forename: Takaharu
authors.initials: T
authors.lastname: Mori
authors.forename: Yuji
authors.initials: Y
authors.lastname: Sugita
mesh_terms: D003201:Computers; D003205:Computing Methodologies; D056004:Molecular Dynamics Simulation; D055672:Static Electricity
keywords: domain decomposition; hybrid parallelization; midpoint cell method; molecular dynamics