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Performance Portability of Molecular Docking Miniapp On Leadership Computing Platforms...

by Mathialakan Thavappiragasam, Aaron Scheinberg, Wael R Elwasif, Oscar R Hernandez Mendoza, Ada A Sedova
Publication Type
Conference Paper
Book Title
2020 IEEE/ACM International Workshop on Performance, Portability and Productivity in HPC (P3HPC)
Publication Date
Page Numbers
36 to 44
Publisher Location
Georgia, United States of America
Conference Name
SC20 P3HPC: 2020 International Workshop on Performance, Portability, and Productivity in HPC
Conference Location
Virtual, Tennessee, United States of America
Conference Sponsor
IEEE Computer Society
Conference Date

Rapidly changing computer architectures, such as those found at high-performance computing (HPC) facilities, present the need for mini-applications (miniapps) that capture essential algorithms used in large applications to test program performance and portability, aiding transitions to new systems. The COVID-19 pandemic has fueled a flurry of activity in computational drug discovery, including the use of supercomputers and GPU acceleration for massive virtual screens for therapeutics. Recent work targeting COVID-19 at the Oak Ridge Leadership Computing Facility (OLCF) used the GPU-accelerated program AutoDock-GPU to screen billions of compounds on the Summit supercomputer. In this paper we present the development of a new miniapp, miniAutoDock-GPU, that can be used to evaluate the performance and portability of GPU-accelerated protein-ligand docking programs on different computer architectures. These tests are especially relevant as facilities transition from petascale systems and prepare for upcoming exascale systems that will use a variety of GPU vendors. The key calculations, namely, the Lamarckian genetic algorithm combined with a local search using a Solis-Wets based random optimization algorithm, are implemented. We developed versions of the miniapp using several different programming models for GPU acceleration, including a version using the CUDA runtime API for NVIDIA GPUs, and the Kokkos middle-ware API which is facilitated by C++ template libraries. A third version, currently in progress, uses the HIP programming model. These efforts will help facilitate the transition to exascale systems for this important emerging HPC application, as well as its use on a wide range of heterogeneous platforms.