Performance characterization of molecular dynamics techniques for biomolecular simulations

Large-scale simulations and computational modeling using molecular dynamics (MD) continues to make significant impacts in the field of biology. It is well known that simulations of biological events at native time and length scales requires computing power several orders of magnitude beyond today’s commonly available systems. Supercomputers, such as IBM Blue Gene/L and Cray XT3, will soon make tens to hundreds of teraFLOP/s of computing power available by utilizing thousands of processors. The popular algorithms and MD applications, however, were not initially designed to run on thousands of processors. In this paper, we present detailed investigations of the performance issues, which are crucial for improving the scalability of the MD-related algorithms and applications on massively parallel processing (MPP) architectures. Due to the varying characteristics of biological input problems, we study two prototypical biological complexes that use the MD algorithm: an explicit solvent ...

• Type: Conference
• Year: 2006
• Where: PPOPP
• Authors: Sadaf R. Alam, Jeffrey S. Vetter, Pratul K. Agarwal, Al Geist
• Keywords: Blue Gene/L, Distributed And Parallel Computing, Implicit Solvent, Input Problem, PPOPP 2006