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Congestion Game Scheduling Implementation for High-Throughput Virtual Drug Screening Using BOINC-Based Desktop Grid

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Parallel Computing Technologies (PaCT 2017)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 10421))

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Abstract

Virtual drug screening is one of the most common applications of high-throughput computing. As virtual screening is time consuming, a problem of obtaining a diverse set of hits in a short time is very important. We propose a mathematical model based on game theory. Task scheduling for virtual drug screening in high-performance computational systems is considered as a congestion game between computing nodes to find the equilibrium solutions for best balancing between the number of interim hits and their chemical diversity. We present the developed scheduling algorithm implementation for Desktop Grid and Enterprise Desktop Grid, and perform comprehensive computational experiments to evaluate its performance. We compare the algorithm with two known heuristics used in practice and observe that game-based scheduling outperforms them by the hits discovery rate and chemical diversity at earlier steps.

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Acknowledgments

This work is partially supported by the Russian Fund for Basic Research under grants no. 16-07-00622 and 15-29-07974, and CONACYT (Consejo Nacional de Ciencia y Tecnología, México) under grant no. 178415.

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Authors and Affiliations

  1. Institute of Applied Mathematical Research, Karelian Research Center, Russian Academy of Sciences, Petrozavodsk, Russia

    Natalia Nikitina & Evgeny Ivashko

  2. Computer Science Department, CICESE Research Center, Ensenada, Baja California, Mexico

    Andrei Tchernykh

Authors
  1. Natalia Nikitina
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  2. Evgeny Ivashko
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  3. Andrei Tchernykh
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Corresponding author

Correspondence to Natalia Nikitina .

Editor information

Editors and Affiliations

  1. Russian Academy of Sciences, Novosibirsk, Russia

    Victor Malyshkin

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Nikitina, N., Ivashko, E., Tchernykh, A. (2017). Congestion Game Scheduling Implementation for High-Throughput Virtual Drug Screening Using BOINC-Based Desktop Grid. In: Malyshkin, V. (eds) Parallel Computing Technologies. PaCT 2017. Lecture Notes in Computer Science(), vol 10421. Springer, Cham. https://doi.org/10.1007/978-3-319-62932-2_46

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  • DOI: https://doi.org/10.1007/978-3-319-62932-2_46

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-62931-5

  • Online ISBN: 978-3-319-62932-2

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