Implementation and evaluation of MPI‐based parallel MD program

Abstract

AbstractThe message‐passing interface (MPI)‐based object‐oriented particle–particle interactions (PPI) library is implemented and evaluated. The library can be used in the n‐particle simulation algorithm designed for a ring of p interconnected processors. The parallel simulation is scalable with the number of processors, and has the time requirement proportional to n2/p if n/p is large enough, which guarantees optimal speedup. In a certain range of problem sizes, the speedup becomes superlinear because enough cache memory is available in the system. The library is used in a simple way by any potential user, even with no deep programming knowledge. Different simulations using particles can be implemented on a wide spectrum of different computer platforms. The main purpose of this article is to test the PPI library on well‐known methods, e.g., the parallel molecular dynamics (MD) simulation of the monoatomic system by the second‐order leapfrog Verlet algorithm. The performances of the parallel simulation program implemented with the proposed library are competitive with a custom‐designed simulation code. Also, the implementation of the split integration symplectic method, based on the analytical calculation of the harmonic part of the particle interactions, is shown, and its expected performances are predicted. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 84: 23–31, 2001