Applying Multi-cell MD Method to Shared-Memory Multi-core Systems

Abstract

For decades, the main parallelization systems have been message passing ones, in which there are many parallel methods whose efficiencies are very high. The multi-cell MD (Molecular Dynamics) method is also a parallel one that is widely used for molecular dynamics simulation on the message passing systems. Cluster is still the main environment for parallel computing and every node in the cluster is generally the shared-memory multi-core computer. In this paper, we propose a data structure and a method so that the multi-cell MD method can be also used on the shared-memory multi-core systems. The proposed data structure and method are designed on the basis of the Torus network structure, the characteristic of the multi-cell MD method and a work sharing structure of OpenMP. Experimental results show that our method allows the multi-cell MD method to be used on the shared-memory multi-core systems and the parallel efficiency per a time step of that is increased about 10% than the HS (Half-Shell) method.