Design and performance analysis of a distributed HPC molecular dynamics code on distributed resources
Promita Chakraborty, Shantenu Jha · 2008
Molecular Dynamics (MD) is an important step towards understanding the behavior of biological systems. Even though, the state-of-the-art computational resource and techniques have made it feasible to do large-scale MD simulations, MD remains a very compute-intensive job, especially for large realistic systems. Thus there exists interest in developing and understanding the performance of MD code on multiple distributed HPC resources. To realize this goal, we have developed a preliminary parallel and distributed MD code and benchmarked it on the LONI (Louisiana Optical Network Interface) grid, which uses dedicated light-path networks to connect supercomputers across Louisiana.