Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms, In: ISC High Performance 2016: High Performance Computing

Stone, John E.; Hynninen, Antti-Pekka; Phillips, James C.; Schulten, Klaus

doi:10.1007/978-3-319-46079-6_14

Title: Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms, In: ISC High Performance 2016: High Performance Computing

Conference · Fri Jan 01 00:00:00 EST 2016 · HIGH PERFORMANCE COMPUTING, ISC HIGH PERFORMANCE 2016 INTERNATIONAL WORKSHOPS

DOI:https://doi.org/10.1007/978-3-319-46079-6_14· OSTI ID:1567407

Stone, John E. ^[1]; Hynninen, Antti-Pekka ^[2]; Phillips, James C. ^[1]; Schulten, Klaus ^[3]

Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois (United States)
Oak Ridge Leadership Computing Facility, Oak Ridge National Laboratory, Oak Ridge, TN (United States)
Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois (United States)

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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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)

Sponsoring Organization:: USDOE Office of Science (SC)

DOE Contract Number:: AC05-00OR22725

OSTI ID:: 1567407

Journal Information:: HIGH PERFORMANCE COMPUTING, ISC HIGH PERFORMANCE 2016 INTERNATIONAL WORKSHOPS, Vol. 9945; Conference: International Conference on High Performance Computing, Frankfurt, Germany, June 19-23, 2016

Publisher:: Springer International Publishing AG 2016

Country of Publication:: United States

Language:: English

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