Abstract
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.
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callMore From: TRANSACTIONS OF THE JAPAN SOCIETY OF MECHANICAL ENGINEERS Series A
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
