A parallel particle cluster algorithm using nearest neighbour graphs and passive target communication

Abstract

We present a parallel cluster algorithm for $N$-body simulations which uses a nearest neighbour search algorithm and one-sided messaging passing interface (MPI) communication. The nearest neighbour is defined by the Euclidean distance in three-dimensional space. The resulting directed nearest neighbour graphs that are used to define the clusters are split up in an iterative procedure with MPI remote memory access (RMA) communication. The method has been implemented as part of the elliptical parcel-in-cell (EPIC) method targeting geophysical fluid flows. The parallel scalability of the algorithm is discussed by means of an artificial and a standard fluid dynamics test case. The cluster algorithm shows good weak and strong scalability up to 16,384 cores with a parallel weak scaling efficiency of about 80% for balanced workloads. In poorly balanced problems, MPI synchronisation dominates execution of the cluster algorithm and thus drastically worsens its parallel scalability.