Large-Scale Biomolecular Dynamics Using SMP Clusters

The authors have applied Message Passing Interface (MPI) / OpenMP hybrid parallel programming model to molecular dynamics (MD) method for simulating a protein structure on a symmetric multiprocessor (SMP) cluster architecture. In that architecture, it can be expected that the hybrid parallel programming model, which uses the message passing library such as MPI for inter-SMP node communication and the loop directives such as OpenMP for intra-SMP node parallelization, is the most effective one. In this study, the parallel performance of the hybrid style has been compared with that of conventional flat parallel programming style, which uses only MPI, both in case that the fast multipole method (FMM) is employed for computing long-distance interactions and that is not employed. The computer environments used here are Hitachi SR8000/MPP placed at the University of Tokyo. The results of calculation are as follows: Without using FMM, the parallel efficiency using 16 SMP nodes (128 PEs) is: - 90% with the hybrid style, - 75% with the flat-MPI style, for MD simulation with 33,402 atoms. With FMM, the parallel efficiency using 16 SMP nodes (128 PEs) is: - 60% with the hybrid style, - 48% with the flat-MPI style, for MD simulation with 117,649 atoms.