Early experiences porting the NAMD and VMD molecular simulation and analysis software to GPU-accelerated openPOWER platforms

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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.

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9945 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

OtherInternational Workshops on High Performance Computing, ISC High Performance 2016 and Workshop on 2nd International Workshop on Communication Architectures at Extreme Scale, ExaComm 2016, Workshop on Exascale Multi/Many Core Computing Systems, E-MuCoCoS 2016, HPC I/O in the Data Center, HPC-IODC 2016, Application Performance on Intel Xeon Phi – Being Prepared for KNL and Beyond, IXPUG 2016, International Workshop on OpenPOWER for HPC, IWOPH 2016, International Workshop on Performance Portable Programming Models for Accelerators, P^3MA 2016, Workshop on Virtualization in High-Performance Cloud Computing, VHPC 2016, Workshop on Performance and Scalability of Storage Systems, WOPSSS 2016
CountryGermany
CityFrankfurt
Period6/19/166/23/16

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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