SMPクラスタ上のMPI/OpenMPハイブリッド並列分子動力学計算

概要

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The authors applied MPI/OpenMP hybrid parallel programming model to molecular dynamics (MD) for simulating a protein structure. In a symmetric multiprocessor (SMP) cluster 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 was compared with that of conventional flat parallel programming style, which uses only MPI. The computer environments used here are Hitachi SR8000/MPP placed at the University of Tokyo. When using 16 SMP nodes (128 PEs), it was observed that the parallel efficiency with the hybrid style was 90%, which was 15% higher than that of the flat-MPI for MD simulation of a protein with 33 402 atoms.
一般社団法人日本機械学会の論文
2004-04-25