Improving computation efficiency using input and architecture features for a virtual screening application

Virtual screening is an early stage of the drug discovery process that selects the most promising candidates. In the urgent computing scenario it is critical to find a solution in a short time frame. In this paper, we focus on a real-world virtual screening application to evaluate out-of-kernel opti...

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Bibliographic Details
Published in:arXiv.org 2023-03
Main Authors: Accordi, Gianmarco, Vitali, Emanuele, Gadioli, Davide, Crisci, Luigi, Cosenza, Biagio, Bisson, Mauro, Fatica, Massimiliano, Beccari, Andrea, Palermo, Gianluca
Format: Article
Language:English
Subjects:
Computational efficiency
Computing time
Optimization
Screening
Online Access:Get full text
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Summary:Virtual screening is an early stage of the drug discovery process that selects the most promising candidates. In the urgent computing scenario it is critical to find a solution in a short time frame. In this paper, we focus on a real-world virtual screening application to evaluate out-of-kernel optimizations, that consider input and architecture features to improve the computation efficiency on GPU. Experiment results on a modern supercomputer node show that we can almost double the performance. Moreover, we implemented the optimization using SYCL and it provides a consistent benefit with the CUDA optimization. A virtual screening campaign can use this gain in performance to increase the number of evaluated candidates, improving the probability of finding a drug.
ISSN:2331-8422