Heuristic static load-balancing algorithm applied to the fragment molecular orbital method

Yuri Alexeev, Ashutosh Mahajan, Sven Leyffer, Graham Fletcher, Dmitri G. Fedorov
2012 2012 International Conference for High Performance Computing, Networking, Storage and Analysis  
In the era of petascale supercomputing, the importance of load balancing is crucial. Although dynamic load balancing is widespread, it is increasingly difficult to implement effectively with thousands of processors or more, prompting a second look at static load-balancing techniques even though the optimal allocation of tasks to processors is an NP-hard problem. We propose a heuristic static load-balancing algorithm, employing fitted benchmarking data, as an alternative to dynamic load
more » ... . The problem of allocating CPU cores to tasks is formulated as a mixed-integer nonlinear optimization problem, which is solved by using an optimization solver. On 163,840 cores of Blue Gene/P, we achieved a parallel efficiency of 80% for an execution of the fragment molecular orbital method applied to model protein-ligand complexes quantummechanically. The obtained allocation is shown to outperform dynamic load balancing by at least a factor of 2, thus motivating the use of this approach on other coarse-grained applications.
doi:10.1109/sc.2012.62 dblp:conf/sc/AlexeevMLFF12 fatcat:ed4cztal7nhp7ddqnti4ypsvuq