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DTSTAMP:20210402T160558Z
LOCATION:Track 2
DTSTART;TZID=America/New_York:20201113T114000
DTEND;TZID=America/New_York:20201113T121000
UID:submissions.supercomputing.org_SC20_sess221_ws_p3hpc108@linklings.com
SUMMARY:Performance Portability of Molecular Docking Miniapp on Leadership
  Computing Platforms
DESCRIPTION:Workshop\n\nPerformance Portability of Molecular Docking Minia
 pp on Leadership Computing Platforms\n\nThavappiragasam, Scheinberg, Elwas
 if, Hernandez, Sedova\n\nRapidly changing computer architectures, such as 
 those found at high-performance computing (HPC) facilities, present the ne
 ed 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 supercomput
 ers and GPU acceleration for massive virtual screens for therapeutics. Rec
 ent work targeting COVID-19 at the Oak Ridge Leadership Computing Facility
  (OLCF) used the GPU-accelerated program AutoDock-GPU to screen billions o
 f compounds on the Summit supercomputer. Here we present the development o
 f a new miniapp, miniAutoDock-GPU, that can be used to evaluate the perfor
 mance and portability of GPU-accelerated protein-ligand docking programs o
 n different computer architectures. These tests are especially relevant as
  facilities transition from petascale systems and prepare for upcoming exa
 scale systems that will use a variety of GPU vendors. The key calculations
 , namely, the Lamarckian genetic algorithm combined with a local search us
 ing a Solis-Wets based random optimization algorithm, are implemented. We 
 developed versions of the miniapp using several different programming mode
 ls for GPU acceleration, including a version using the CUDA runtime API fo
 r NVIDIA GPUs, and the Kokkos middle-ware API which is facilitated by C++ 
 template libraries. A third version, currently in progress, uses the HIP p
 rogramming model. These efforts will help facilitate the transition to exa
 scale systems for this important emerging HPC application, as well as its 
 use on a wide range of heterogeneous platforms.\n\nRegistration Category: 
 Workshop Reg Pass
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