Paper Citing NAMD - Abstract
Lee, Chee Wai; Mendes, Celso; Kale, Laxmikant V.
Towards scalable performance analysis and visualization through data reduction
2008 IEEE INTERNATIONAL SYMPOSIUM ON PARALLEL & DISTRIBUTED PROCESSING, VOLS 1-8, 590-597, 2008
Performance analysis tools based on event tracing are important for understanding the complex computational activities and communication patterns in high performance applications. The purpose of these tools is to help applications scale well to large numbers of processors. However the tools themselves have to be scalable. As application problem sizes grow larger to exploit larger machines, the volume of performance trace data generated becomes unmanagable especially as we scale to tens of thousands of processors. Simultaneously, at analysis time, the amount of information that has to be presented to a human analyst can also become overwhelming. This paper investigates the effectiveness of employing heuristics and clustering techniques in a scalability framework to determine a subset of processors whose detailed event traces should be retained. It is a form of compression where we retain information from processors with high signal content. We quantify the reduction in the volume of performance trace data generated by NAMD, a molecular dynamics simulation application implemented using CHARM++. We show that, for the known performance problem of poor application grainsize, the quality of the trace data preserved by this approach is sufficient to highlight the problem.
