SC20 Proceedings

The International Conference for High Performance Computing, Networking, Storage, and Analysis

Parallelizing Irregular Computations for Molecular Docking


Workshop:IA^3 2020: 10th Workshop on Irregular Applications: Architectures and Algorithms

Authors: Leonardo Solis-Vasquez (Technical University Darmstadt), Diogo Santos-Martins and Andreas F. Tillack (Scripps Research Institute), Andreas Koch (Technical University Darmstadt), and Jérôme Eberhardt and Stefano Forli (Scripps Research Institute)


Abstract: AUTODOCK is a molecular docking software widely used in computational drug design. Its time-consuming executions have motivated the development of AUTODOCK-GPU, an OpenCL-accelerated version that can run on GPUs and CPUs. This work discusses the development of AUTODOCK-GPU from a programming perspective, detailing how our design addresses the irregularity of AUTODOCK while pushing towards higher performance. Details on required data transformations, re-structuring of complex functionality, as well as the performance impact of different configurations are also discussed. While AUTODOCK-GPU reaches speedup factors of 373x on a Titan V GPU and 58x on a 48-core Xeon Platinum 8175M CPU, experiments show that performance gains are highly dependent on the molecular complexity under analysis. Finally, we summarize our preliminary experiences when porting AUTODOCK onto FPGAs.


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