Optimal Execution of Co-analysis for Large-scale Molecular Dynamics Simulations

P Malakar and V Vishwanath and C Knight and T Munson and ME Papka, SC '16: PROCEEDINGS OF THE INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS, 702-713 (2016).

The analysis of scientific simulation data enables scientists to derive insights from their simulations. This analysis of the simulation output can be performed at the same execution site as the simulation using the same resources or can be done at a different site. The optimal output frequency is challenging to decide and is often chosen empirically. We propose a mathematical formulation for choosing the optimal frequency of data transfer for analysis and the feasibility of performing the analysis, under the given resource constraints such as network bandwidth, disk space, available memory, and computation time. We propose formulations for two cases of co-analysis - local and remote. We consider various analyses features such as computation time, input data and memory requirement, importance of the analysis and minimum frequency required for performing the analysis. We demonstrate the effectiveness of our approach using molecular dynamics applications on the Mira and Edison supercomputers.

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