Task-parallel Analysis of Molecular Dynamics Trajectories
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Different frameworks for implementing parallel data analytics applications have been proposed by the HPC and Big Data communities. In this paper, we investigate three frameworks: Spark, Dask and RADICAL-Pilot with respect to their ability to support data analytics requirements on HPC resources. We investigate the data analysis requirements of Molecular Dynamics (MD) simulations which are significant consumers of supercomputing cycles, producing immense amounts of data: a typical large-scale MD simulation of physical systems of O(100,000) atoms can produce from O(10) GB to O(1000) GBs of data. We propose and evaluate different approaches for parallelization of a representative set of MD trajectory analysis algorithms, in particular the computation of path similarity and the identification of connected atom. We evaluate Spark, Dask and with respect to the provided abstractions and runtime engine capabilities to support these algorithms. We provide a conceptual basis for comparing and understanding the different frameworks that enable users to select the optimal system for its application. Further, we provide a quantitative performance analysis of the different algorithms across the three frameworks using different high-performance computing resources.
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