Performance analysis of parallel scientific codes is becoming increasingly difficult due to the rapidly growing complexity of applications and architectures. Existing tools fall short in providing intuitive views that facilitate the process of performance debugging and tuning. In this paper, we exploit a recent idea of projecting and visualizing performance data on the communication and hardware domain for faster, more intuitive analysis of applications. We leverage several performance analysis and visualization tools to showcase the discovery of scalability bottlenecks in a structured AMR library. Using novel techniques to project per-phase timing data, application data, and communication data on a communication graph, we identify a previously elusive scaling bottleneck in the library. We present solutions that mitigate this problem, resulting in 22% improvement in the performance for a 65,536-core run on an IBM Blue Gene/P system.
A new parallel algorithm, based on the Berger-Rigoutsos algorithm for clustering grid points into logically rectangular regions, is presented. The clustering operation is frequently performed in the dynamic gridding steps of structured adaptive mesh refinement (SAMR) calculations. A previous study revealed that although the cost of clustering is generally insignificant for smaller problems run on relatively few processors, the algorithm scaled inefficiently in parallel and its cost grows with problem size. Hence, it can become significant for large scale problems run on very large parallel machines, such as the new BlueGene system (which has O(10 4) processors). We propose a new task-parallel algorithm designed to reduce communication wait times. Performance was assessed using dynamic SAMR re-gridding operations on up to 16K processors of currently available computers at Lawrence Livermore National Laboratory. The new algorithm was shown to be up to an order of magnitude faster than the baseline algorithm and had better scaling trends.
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