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arXiv · 1901.06229

Exploiting OpenMP & OpenACC to Accelerate a Molecular Docking Mini-App in Heterogeneous HPC Nodes

Emanuele Vitali·Davide Gadioli·Gianluca Palermo·Andrea Beccari·Carlo Cavazzoni·Cristina Silvano
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Abstract

In drug discovery, molecular docking is the task in charge of estimating the position of a molecule when interacting with the docking site. This task is usually used to perform screening of a large library of molecules, in the early phase of the process. Given the amount of candidate molecules and the complexity of the application, this task is usually performed using High-Performance Computing (HPC) platforms. In modern HPC systems, heterogeneous platforms provide a better throughput with respect to homogeneous platforms. In this work, we ported and optimized a molecular docking application to a heterogeneous system, with one or more GPU accelerators, leveraging a hybrid OpenMP and OpenACC approach. We prove that our approach has a better exploitation of the node compared to pure CPU/GPU data splitting approaches, reaching a throughput improvement up to 36% while considering the same computing node.

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Emanuele Vitali, Davide Gadioli, Gianluca Palermo, Andrea Beccari, Carlo Cavazzoni, Cristina Silvano. 2019-01-18. Exploiting OpenMP & OpenACC to Accelerate a Molecular Docking Mini-App in Heterogeneous HPC Nodes. https://arxiv.org/abs/1901.06229

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