Dynamic Topology Aware Load Balancing Algorithms for MD Applications
Authors:
Abhinav Bhatele, Laxmikant V. Kale
Parallel Programming Laboratory, Department of Computer Science, University
of Illinois at Urbana-Champaign
submitted to Philosophical Transactions of the Royal Society A, 2008
Molecular Dynamics applications are important for bio-molecular simulations to enhance our understanding of biological phenomena. 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. The focus of the paper is new schemes deployed in the load balancers to make them efficient and analysis of the performance benefits achieved. Specifically, the paper will demonstrate the technique of topology-aware mapping on n-way SMP clusters and 3D torus architectures to improve scalability and performance.