Task-parallel analysis of molecular dynamics trajectories

Ioannis Paraskevakos, George Chantzialexiou, Andre Luckow, Thomas E. Cheatham, Mahzad Khoshlessan, Oliver Beckstein, Geoffrey C. Fox, Shantenu Jha

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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 secs 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.

Original languageEnglish (US)
Title of host publicationProceedings of the 47th International Conference on Parallel Processing, ICPP 2018
PublisherAssociation for Computing Machinery
ISBN (Print)9781450365109
DOIs
StatePublished - Aug 13 2018
Event47th International Conference on Parallel Processing, ICPP 2018 - Eugene, United States
Duration: Aug 14 2018Aug 16 2018

Publication series

NameACM International Conference Proceeding Series

Other

Other47th International Conference on Parallel Processing, ICPP 2018
CountryUnited States
CityEugene
Period8/14/188/16/18

Keywords

  • Data analytics
  • MD analysis
  • MD simulations analysis
  • Task-parallel

ASJC Scopus subject areas

  • Software
  • Human-Computer Interaction
  • Computer Vision and Pattern Recognition
  • Computer Networks and Communications

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  • Cite this

    Paraskevakos, I., Chantzialexiou, G., Luckow, A., Cheatham, T. E., Khoshlessan, M., Beckstein, O., Fox, G. C., & Jha, S. (2018). Task-parallel analysis of molecular dynamics trajectories. In Proceedings of the 47th International Conference on Parallel Processing, ICPP 2018 [a49] (ACM International Conference Proceeding Series). Association for Computing Machinery. https://doi.org/10.1145/3225058.3225128