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• W2963179050 abstract "Different parallel frameworks for implementing data analysis applications have been proposed by the HPC and Big Data communities. In this paper, we investigate three task-parallel frameworks: Spark, Dask and RADICAL-Pilot with respect to their ability to support data analytics on HPC resources and compare them to MPI. 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 a physical system of O(100k) atoms over μsecs 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 leaflet identification. We evaluate Spark, Dask and RADICAL-Pilot with respect to their abstractions and runtime engine capabilities to support these algorithms. We provide a conceptual basis for comparing and understanding different frameworks that enable users to select the optimal system for each application. We also provide a quantitative performance analysis of the different algorithms across the three frameworks." @default.
• W2963179050 created "2019-07-30" @default.
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• W2963179050 date "2018-08-13" @default.
• W2963179050 modified "2023-10-16" @default.
• W2963179050 title "Task-parallel Analysis of Molecular Dynamics Trajectories" @default.
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• W2963179050 doi "https://doi.org/10.1145/3225058.3225128" @default.
• W2963179050 hasPublicationYear "2018" @default.
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