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Title: Optimizing legacy molecular dynamics software with directive-based offload

Abstract

The directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In our paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We also demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also result in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMAS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel (R) Xeon Phi (TM) coprocessors and NVIDIA GPUs: The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS. (C) 2015 Elsevier B.V. All rights reserved.

Authors:
 [1]; ORCiD logo [2];  [3];  [3];  [4]
+ Show Author Affiliations
  1. Intel Corporation, Portland, OR (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  3. Shell India Markets Private Limited, Bangalore (India)
  4. Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1261448
Alternate Identifier(s):
OSTI ID: 1246679
Grant/Contract Number:  
AC05-00OR22725; AC04-94AL85000
Resource Type:
Accepted Manuscript
Journal Name:
Computer Physics Communications
Additional Journal Information:
Journal Volume: 195; Journal Issue: C; Journal ID: ISSN 0010-4655
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; Molecular dynamics; Xeon Phi; GPU; Coprocessor; Accelerator; Many-core; PERFORMANCE; POTENTIALS; MORPHOLOGY

Citation Formats

Michael Brown, W., Carrillo, Jan-Michael Y., Gavhane, Nitin, Thakkar, Foram M., and Plimpton, Steven J. Optimizing legacy molecular dynamics software with directive-based offload. United States: N. p., 2015. Web. doi:10.1016/j.cpc.2015.05.004.
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Michael Brown, W., Carrillo, Jan-Michael Y., Gavhane, Nitin, Thakkar, Foram M., & Plimpton, Steven J. Optimizing legacy molecular dynamics software with directive-based offload. United States. https://doi.org/10.1016/j.cpc.2015.05.004
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Michael Brown, W., Carrillo, Jan-Michael Y., Gavhane, Nitin, Thakkar, Foram M., and Plimpton, Steven J. Thu . "Optimizing legacy molecular dynamics software with directive-based offload". United States. https://doi.org/10.1016/j.cpc.2015.05.004. https://www.osti.gov/servlets/purl/1261448.
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@article{osti_1261448,
title = {Optimizing legacy molecular dynamics software with directive-based offload},
author = {Michael Brown, W. and Carrillo, Jan-Michael Y. and Gavhane, Nitin and Thakkar, Foram M. and Plimpton, Steven J.},
abstractNote = {The directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In our paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We also demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also result in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMAS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel (R) Xeon Phi (TM) coprocessors and NVIDIA GPUs: The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS. (C) 2015 Elsevier B.V. All rights reserved.},
doi = {10.1016/j.cpc.2015.05.004},
journal = {Computer Physics Communications},
number = C,
volume = 195,
place = {United States},
year = {Thu May 14 00:00:00 EDT 2015},
month = {Thu May 14 00:00:00 EDT 2015}
}
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Publisher's Version of Record
https://doi.org/10.1016/j.cpc.2015.05.004
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