Paper Citing NAMD - Abstract
Dixon, M.F.
A runtime adaptive load balancing algorithm for particle simulations
APPLIED PARALLEL COMPUTING: STATE OF THE ART IN SCIENTIFIC COMPUTING, 3732:709-718, 2006
Anew dynamic load balancing algorithm is proposed for particle simulations on clusters of workstations which operates at two levels; it both dynamically defines groups of particles in which the force calculations are localised and at the same time adaptively assigns groups to processors based on the group sizes and runtime CPU usages. It therefore adaptively balances using both the dynamics of the simulation and the load usage of the cluster at runtime. The algorithm is implemented in the POOMA framework and applied to a particle in-cell approximation of a three dimensional elastic particle collision model. Load balancing metrics and parallel scalability is determined on an 8 quad-processor 833MHZ Compaq Alpha cluster connected by a gigabit ethernet.
