Parallel Molecular Dynamics Simulations of Alkane/Hydroxylated α-Aluminium Oxide Interfaces

In this paper we describe a practical implementation of parallel computation for the molecular dynamics (MD) simulation of an alkane/aluminum oxide interface. A serial MD program was converted into a parallel code utilizing the message passing interface (MPI). This code was evaluated on a twelve processor symmetrical multiprocessor as well as on a cluster of four processor SMPs. A maximum speedup of 5.25 was achieved with twelve processors on the large shared memory machine. The cluster performance saturated at a speedup of 4.5 with two nodes. High communication costs and considerable load imbalance in the system were identified as areas that need further investigation for obtaining better performance. Key words: Molecular dynamics, message passing, SMP cluster. 1 Introduction Molecular dynamics (MD) studies are widely used to investigate the structural and dynamical properties of a wide range of materials. The popularity of MD is mainly due to its ability to provide a detailed desc..