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Evaluating the Energy Efficiency of OpenCL-accelerated AutoDock Molecular Docking

Leonardo Solis-Vasquez, Diogo Santos-Martins, Andreas Koch, Stefano Forli
Embedded Systems and Applications Group, Technische Universitat Darmstadt, Darmstadt, Germany
28th EUROMICRO International Conference on Parallel, Distributed and Network-Based Processing (PDP’20), 2020

@inproceedings{solis2020evaluating,

   title={Evaluating the Energy Efficiency of OpenCL-accelerated AutoDock Molecular Docking},

   author={Solis-Vasquez, Leonardo and Santos-Martins, Diogo and Koch, Andreas and Forli, Stefano},

   booktitle={Submitted to the 28th Euromicro International Conference on Parallel, Distributed, and Network-based Processing (PDP). Submitted},

   year={2020}

}

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AUTODOCK is a molecular docking application that consists of a genetic algorithm coupled with the Solis-Wets localsearch method. Despite its wide usage, its power consumption on heterogeneous systems has not been evaluated extensively. In this work, we evaluate the energy efficiency of an OpenCL-accelerated version of AUTODOCK that, along with the traditional SolisWets method, newly incorporates the ADADELTA gradient-based local search. Executions on a Nvidia V100 GPU yielded energy efficiency improvements of up to 297x (Solis-Wets) and 137x (ADADELTA) with respect to the original AUTODOCK baseline.
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