Paper Citing NAMD - Abstract
Falcon, Ayose; Faraboschi, Paolo; Ortega, Daniel
An adaptive synchronization technique for parallel simulation of networked clusters
ISPASS 2008: IEEE INTERNATIONAL SYMPOSIUM ON PERFORMANCE ANALYSIS OF SYSTEMS AND SOFTWARE, 22-31, 2008
Computer clusters are a very cost-effective approach for High Performance Computing, but simulating a complete cluster is still an open research problem. The obvious approach-to parallelize individual node simulators-is complex and slow. Combining individual parallel simulators implies synchronizing their progress of time. This can be accomplished with a variety of parallel discrete event simulation techniques, but unfortunately any straightforward approach introduces a synchronization overhead causing up two orders of magnitude of slowdown with respect to the simulation speed of an individual node. In this paper we present a novel adaptive technique that automatically adjusts the synchronization boundaries. By dynamically relaxing accuracy over the least interesting computational phases we dramatically increase performance with a marginal loss of precision. For example, in the simulation of an 8-node cluster running NAMD (a parallel molecular dynamics application) we show an acceleration factor of 26x over the deterministic "ground truth " simulation, at less than a 1% accuracy error
