Dynamic topology aware load balancing algorithms for molecular dynamics applications

Abstract

Molecular Dynamics applications enhance our understanding of biological phenomena through bio-molecular simulations. Large-scale parallelization of MD simulations is challenging because of the small number of atoms and small time scales involved. Load balancing in parallel MD programs is crucial for good performance on large parallel machines. This paper discusses load balancing algorithms deployed in a MD code called Namd. It focuses on new schemes deployed in the load balancers and provides an analysis of the performance benefits achieved. Specifically, the paper presents the technique of topology-aware mapping on 3D mesh and torus architectures, used to improve scalability and performance. These techniques have a wide applicability for latency intolerant applications. Copyright 2009 ACM.