TCB Publications - Abstract

John E. Stone, Antti-Pekka Hynninen, James C. Phillips, and Klaus Schulten. Early experiences porting the NAMD and VMD molecular simulation and analysis software to GPU-accelerated OpenPOWER platforms. International Workshop on OpenPOWER for HPC (IWOPH'16), pp. 188-206, 2016.

STON2016D All-atom molecular dynamics simulations of biomolecules provide a powerful tool for exploring the structure and dynamics of large protein complexes within realistic cellular environments. Unfortunately, such simulations are extremely demanding in terms of their computational requirements, and they present many challenges in terms of preparation, simulation methodology, and analysis and visualization of results. We describe our early experiences porting the popular molecular dynamics simulation program NAMD and the simulation preparation, analysis, and visualization tool VMD to GPU-accelerated OpenPOWER hardware platforms. We report our experiences with compiler-provided autovectorization and compare with hand-coded vector intrinsics for the POWER8 CPU. We explore the performance benefits obtained from unique POWER8 architectural features such as 8-way SMT and its value for particular molecular modeling tasks. Finally, we evaluate the performance of several GPU-accelerated molecular modeling kernels and relate them to other hardware platforms.

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