Bilge Acun, David J. Hardy, Laxmikant Kale, Ke Li, James C. Phillips, and
John E. Stone.
Scalable molecular dynamics with NAMD on the Summit system.
IBM Journal of Research and Development, 62:4:1-4:9, 2018.
ACUN2019-JS
NAMD is a parallel molecular dynamics application that has been used to
make breakthroughs in understanding the structure and dynamics of large
biomolecular complexes, such as viruses like HIV and various types of
influenza. State-of-the-art biomolecular simulations often require integration
of billions of timesteps, computing all interatomic forces for each
femtosecond timestep. Molecular dynamics simulation of large biomolecular
systems and long-timescale biological phenomena requires tremendous
computing power. NAMD harnesses the power of thousands of
heterogeneous processors to meet this demand. In this paper, we present
algorithm improvements and performance optimizations that enable NAMD
to achieve high performance on the IBM Newell platform (with POWER9
processors and NVIDIA Volta V100 GPUs) which underpins the Oak Ridge
National Laboratory's Summit and Lawrence Livermore National Laboratory's
Sierra supercomputers. The Top-500 supercomputers June 2018 list shows
Summit at the number one spot with 187 Petaflop/s peak performance and
Sierra third with 119 Petaflop/s. Optimizations for NAMD on Summit include:
data layout changes for GPU acceleration and CPU vectorization, improving
GPU offload efficiency, increasing performance with PAMI support in
Charm++, improving efficiency of FFT calculations, improving load balancing,
enabling better CPU vectorization and cache performance, and providing an
alternative thermostat through stochastic velocity rescaling. We also present
performance scaling results on early Newell systems.
Download Full Text
The manuscripts available on our site are provided for your personal
use only and may not be retransmitted or redistributed without written
permissions from the paper's publisher and author. You may not upload any
of this site's material to any public server, on-line service, network, or
bulletin board without prior written permission from the publisher and
author. You may not make copies for any commercial purpose. Reproduction
or storage of materials retrieved from this web site is subject to the
U.S. Copyright Act of 1976, Title 17 U.S.C.
