Refactoring the molecular docking simulation for heterogeneous, manycore processors systems

Junshi Chen, Han Lin, Weihao Liang, Yang Yu, Wenting Han, Hong An, Yong Chen, Xin Liu

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

Abstract

This paper presents a scalable design and implementation of the molecular docking application DOCK for a large-scale high performance computing system, the Sunway TaihuLight supercomputer, which provisions a heterogeneous, manycore processor architecture that consists of management processing elements (MPEs) and clusters of computing processing elements (CPEs). The key innovation is a novel refactoring of DOCK on the CPEs. Optimization techniques for data redundancy minimization to fit data in cache, software-controlled prefetching into scratchpads, memory access coalescing, software caches, vectorization and loop unrolling are employed to improve the exploitation of the computational resources. For a single docking process, the refactored version using both the MPE and CPE cluster achieved 260x to 402x speedup compared against the original ported version using MPE only. To scale the DOCK to the full Sunway Taihulight system with 10,649,600 cores (including all MPE and CPE cores), we present an MPI communication domain partition scheme as well. For docking 9 million small compounds to a Zika virus target protein, we manage to scale to 131,072 MPEs, and 8,388,608 CPEs, with a total of 8,519,680 cores.

Original languageEnglish
Title of host publicationProceedings - 15th IEEE International Symposium on Parallel and Distributed Processing with Applications and 16th IEEE International Conference on Ubiquitous Computing and Communications, ISPA/IUCC 2017
EditorsGregorio Martinez, Richard Hill, Geoffrey Fox, Peter Mueller, Guojun Wang
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1031-1038
Number of pages8
ISBN (Electronic)9781538637906
DOIs
StatePublished - May 25 2018
Event15th IEEE International Symposium on Parallel and Distributed Processing with Applications and 16th IEEE International Conference on Ubiquitous Computing and Communications, ISPA/IUCC 2017 - Guangzhou, China
Duration: Dec 12 2017Dec 15 2017

Publication series

NameProceedings - 15th IEEE International Symposium on Parallel and Distributed Processing with Applications and 16th IEEE International Conference on Ubiquitous Computing and Communications, ISPA/IUCC 2017

Conference

Conference15th IEEE International Symposium on Parallel and Distributed Processing with Applications and 16th IEEE International Conference on Ubiquitous Computing and Communications, ISPA/IUCC 2017
CountryChina
CityGuangzhou
Period12/12/1712/15/17

Keywords

  • Heterogeneous
  • Manycore
  • Molecular docking
  • Optimization
  • Sunway TaihuLight Supercomputer

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  • Cite this

    Chen, J., Lin, H., Liang, W., Yu, Y., Han, W., An, H., Chen, Y., & Liu, X. (2018). Refactoring the molecular docking simulation for heterogeneous, manycore processors systems. In G. Martinez, R. Hill, G. Fox, P. Mueller, & G. Wang (Eds.), Proceedings - 15th IEEE International Symposium on Parallel and Distributed Processing with Applications and 16th IEEE International Conference on Ubiquitous Computing and Communications, ISPA/IUCC 2017 (pp. 1031-1038). (Proceedings - 15th IEEE International Symposium on Parallel and Distributed Processing with Applications and 16th IEEE International Conference on Ubiquitous Computing and Communications, ISPA/IUCC 2017). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISPA/IUCC.2017.00157