6533b852fe1ef96bd12ab833

RESEARCH PRODUCT

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

Gianmarco AccordiEmanuele VitaliDavide GadioliLuigi CrisciBiagio CosenzaMauro BissonMassimiliano FaticaAndrea BeccariGianluca Palermo

subject

Computational Engineering Finance and Science (cs.CE)FOS: Computer and information sciencesComputer Science - Distributed Parallel and Cluster ComputingHardware Architecture (cs.AR)Distributed Parallel and Cluster Computing (cs.DC)Computer Science - Computational Engineering Finance and ScienceComputer Science - Hardware Architecture

description

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.

yearjournalcountryeditionlanguage
2023-03-09
http://arxiv.org/abs/2303.06150