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

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