Out of kernel tuning and optimizations for portable large-scale docking experiments on GPUs

Gianmarco Accordi, Davide Gadioli, Emanele Vitali, Luigi Crisci, Biagio Cosenza, Andrea Beccari, Gianluca Palermo
Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
The Journal of Supercomputing, 2024


   title={Out of kernel tuning and optimizations for portable large-scale docking experiments on GPUs},

   author={Accordi, Gianmarco and Gadioli, Davide and Vitali, Emanele and Crisci, Luigi and Cosenza, Biagio and Beccari, Andrea and Palermo, Gianluca},

   journal={The Journal of Supercomputing},





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Virtual screening is an early stage in the drug discovery process that selects the most promising candidates. In the urgent computing scenario, finding a solution in the shortest time frame is critical. Any improvement in the performance of a virtual screening application translates into an increase in the number of candidates evaluated, thereby raising the probability of finding a drug. In this paper, we show how we can improve application throughput using Out-of-kernel optimizations. They use input features, kernel requirements, and architectural features to rearrange the kernel inputs, executing them out of order, to improve the computation efficiency. These optimizations’ implementations are designed on an extreme-scale virtual screening application, named LiGen, that can hinge on CUDA and SYCL kernels to carry out the computation on modern supercomputer nodes. Even if they are tailored to a single application, they might also be of interest for applications that share a similar design pattern. The experimental results show how these optimizations can increase kernel performance by 2x, respectively, up to 2.2x in CUDA and up to 1.9x, in SYCL. Moreover, the reported speedup can be achieved with the best-proposed parameterization, as shown by the data we collected and reported in this manuscript.
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