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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

Abstract

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.

Authors:
 [1];  [2];  [1];  [3]
  1. Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois (United States)
  2. Oak Ridge Leadership Computing Facility, Oak Ridge National Laboratory, Oak Ridge, TN (United States)
  3. Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1567407
DOE Contract Number:  
AC05-00OR22725
Resource Type:
Conference
Journal Name:
HIGH PERFORMANCE COMPUTING, ISC HIGH PERFORMANCE 2016 INTERNATIONAL WORKSHOPS
Additional Journal Information:
Journal Volume: 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
Subject:
Computer Science

Citation Formats

Stone, John E., Hynninen, Antti-Pekka, Phillips, James C., and Schulten, Klaus. 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. United States: N. p., 2016. Web. doi:10.1007/978-3-319-46079-6_14.
Stone, John E., Hynninen, Antti-Pekka, Phillips, James C., & Schulten, Klaus. 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. United States. doi:10.1007/978-3-319-46079-6_14.
Stone, John E., Hynninen, Antti-Pekka, Phillips, James C., and Schulten, Klaus. Fri . "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". United States. doi:10.1007/978-3-319-46079-6_14.
@article{osti_1567407,
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},
author = {Stone, John E. and Hynninen, Antti-Pekka and Phillips, James C. and Schulten, Klaus},
abstractNote = {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.},
doi = {10.1007/978-3-319-46079-6_14},
journal = {HIGH PERFORMANCE COMPUTING, ISC HIGH PERFORMANCE 2016 INTERNATIONAL WORKSHOPS},
number = ,
volume = 9945,
place = {United States},
year = {2016},
month = {1}
}

Conference:
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