Optimizing legacy molecular dynamics software with directive-based offload

Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.

doi:10.1016/j.cpc.2015.05.004

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

Journal Article · Thu May 14 00:00:00 EDT 2015 · Computer Physics Communications

DOI:https://doi.org/10.1016/j.cpc.2015.05.004· OSTI ID:1261448

Michael Brown, W. ^[1];

^[2]; Gavhane, Nitin ^[3]; Thakkar, Foram M. ^[3]; Plimpton, Steven J. ^[4]

Intel Corporation, Portland, OR (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Shell India Markets Private Limited, Bangalore (India)
Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

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.

View Accepted Manuscript (DOE)

View Accepted Manuscript (Publisher)

Cite

Export

Save

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)

Grant/Contract Number:: AC05-00OR22725; AC04-94AL85000

OSTI ID:: 1261448

Alternate ID(s):: OSTI ID: 1246679

Journal Information:: Computer Physics Communications, Vol. 195, Issue C; ISSN 0010-4655

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 26 works

Citation information provided by
Web of Science

References (17)

Implementing molecular dynamics on hybrid high performance computers – short range forces Brown, W. Michael; Wang, Peng; Plimpton, Steven J. Computer Physics Communications, Vol. 182, Issue 4 https://doi.org/10.1016/j.cpc.2010.12.021	journal	April 2011
Implementing molecular dynamics on hybrid high performance computers – Particle–particle particle-mesh Brown, W. Michael; Kohlmeyer, Axel; Plimpton, Steven J. Computer Physics Communications, Vol. 183, Issue 3 https://doi.org/10.1016/j.cpc.2011.10.012	journal	March 2012
An Evaluation of Molecular Dynamics Performance on the Hybrid Cray XK6 Supercomputer Michael Brown, W.; Nguyen, Trung D.; Fuentes-Cabrera, Miguel Procedia Computer Science, Vol. 9 https://doi.org/10.1016/j.procs.2012.04.020	journal	January 2012
Implementing molecular dynamics on hybrid high performance computers—Three-body potentials Brown, W. Michael; Yamada, Masako Computer Physics Communications, Vol. 184, Issue 12 https://doi.org/10.1016/j.cpc.2013.08.002	journal	December 2013
Fast Parallel Algorithms for Short-Range Molecular Dynamics Plimpton, Steve Journal of Computational Physics, Vol. 117, Issue 1 https://doi.org/10.1006/jcph.1995.1039	journal	March 1995
A flexible algorithm for calculating pair interactions on SIMD architectures Páll, Szilárd; Hess, Berk Computer Physics Communications, Vol. 184, Issue 12 https://doi.org/10.1016/j.cpc.2013.06.003	journal	December 2013
A generalized Gay-Berne intermolecular potential for biaxial particles Berardi, R.; Fava, C.; Zannoni, C. Chemical Physics Letters, Vol. 236, Issue 4-5 https://doi.org/10.1016/0009-2614(95)00212-M	journal	April 1995
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins ^† MacKerell, A. D.; Bashford, D.; Bellott, M. The Journal of Physical Chemistry B, Vol. 102, Issue 18 https://doi.org/10.1021/jp973084f	journal	April 1998
Quiet high-resolution computer models of a plasma Hockney, R. W.; Goel, S. P.; Eastwood, J. W. Journal of Computational Physics, Vol. 14, Issue 2 https://doi.org/10.1016/0021-9991(74)90010-2	journal	February 1974
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes Ryckaert, Jean-Paul; Ciccotti, Giovanni; Berendsen, Herman J. C. Journal of Computational Physics, Vol. 23, Issue 3 https://doi.org/10.1016/0021-9991(77)90098-5	journal	March 1977
Molecular Dynamics Simulation of Dark-adapted Rhodopsin in an Explicit Membrane Bilayer: Coupling between Local Retinal and Larger Scale Conformational Change Crozier, Paul S.; Stevens, Mark J.; Forrest, Lucy R. Journal of Molecular Biology, Vol. 333, Issue 3 https://doi.org/10.1016/j.jmb.2003.08.045	journal	October 2003
On the morphology of polymer-based photovoltaics Liu, Feng; Gu, Yu; Jung, Jae Woong Journal of Polymer Science Part B: Polymer Physics, Vol. 50, Issue 15 https://doi.org/10.1002/polb.23063	journal	March 2012
Development and testing of a general amber force field Wang, Junmei; Wolf, Romain M.; Caldwell, James W. Journal of Computational Chemistry, Vol. 25, Issue 9 https://doi.org/10.1002/jcc.20035	journal	January 2004
Modelling of P3HT:PCBM interface using coarse-grained forcefield derived from accurate atomistic forcefield To, T. T.; Adams, S. Physical Chemistry Chemical Physics, Vol. 16, Issue 10 https://doi.org/10.1039/c3cp54308k	journal	January 2014
Liquid crystal nanodroplets in solution Brown, W. Michael; Petersen, Matt K.; Plimpton, Steven J. The Journal of Chemical Physics, Vol. 130, Issue 4 https://doi.org/10.1063/1.3058435	journal	January 2009
Rupture mechanism of liquid crystal thin films realized by large-scale molecular simulations Nguyen, Trung Dac; Carrillo, Jan-Michael Y.; Matheson, Michael A. Nanoscale, Vol. 6, Issue 6 https://doi.org/10.1039/C3NR05413F	journal	January 2014
Computational aspects of many-body potentials Plimpton, Steven J.; Thompson, Aidan P. MRS Bulletin, Vol. 37, Issue 5 https://doi.org/10.1557/mrs.2012.96	journal	May 2012

Cited By (6)

Design considerations for GPU-aware collective communications in MPI: Design considerations for GPU-Aware collective communications in MPI Faraji, Iman; Afsahi, Ahmad Concurrency and Computation: Practice and Experience, Vol. 30, Issue 17 https://doi.org/10.1002/cpe.4667	journal	May 2018
Accelerating AIREBO: Navigating the Journey from Legacy to High‐Performance Code Höhnerbach, Markus; Bientinesi, Paolo Journal of Computational Chemistry, Vol. 40, Issue 14 https://doi.org/10.1002/jcc.25796	journal	February 2019
Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations Jung, Jaewoon; Nishima, Wataru; Daniels, Marcus Journal of Computational Chemistry, Vol. 40, Issue 21 https://doi.org/10.1002/jcc.25840	journal	April 2019
An Efficient Optimization of Hll Method for the Second Generation of Intel Xeon Phi Processor Kulikov, I. M.; Chernykh, I. G.; Glinskiy, B. M. Lobachevskii Journal of Mathematics, Vol. 39, Issue 4 https://doi.org/10.1134/s1995080218040091	journal	May 2018
Numerical Modeling of Hydrodynamic Turbulence with Self-gravity on Intel Xeon Phi KNL Kulikov, Igor; Chernykh, Igor; Berendeev, Evgeny Parallel Computational Technologies: 13th International Conference, PCT 2019, Kaliningrad, Russia, April 2–4, 2019, Revised Selected Papers, p. 309-322 https://doi.org/10.1007/978-3-030-28163-2_22	book	August 2019
Using Compiler Directives for Performance Portability in Scientific Computing: Kernels from Molecular Simulation Sedova, Ada; Tillack, Andreas F.; Tharrington, Arnold Accelerator Programming Using Directives https://doi.org/10.1007/978-3-030-12274-4_2	book	January 2019

Similar Records

Investigation of Portable Event-Based Monte Carlo Transport Using the NVIDIA Thrust Library

Journal Article · Wed Jun 15 00:00:00 EDT 2016 · Transactions of the American Nuclear Society · OSTI ID:1261448

Bleile, Ryan C.; Brantley, Patrick S.; Dawson, Shawn A.; +2 more

Storage-Intensive Supercomputing Benchmark Study

Technical Report · Tue Oct 30 00:00:00 EDT 2007 · OSTI ID:1261448

Cohen, J; Dossa, D; Gokhale, M; +4 more

Towards Achieving Performance Portability Using Directives for Accelerators

Conference · Tue Nov 01 00:00:00 EDT 2016 · OSTI ID:1261448

Lopez, M. Graham; Larrea, Veronica Vergara; Joubert, Wayne; +4 more

Related Subjects

97 MATHEMATICS AND COMPUTING
Molecular dynamics
Xeon Phi
GPU
Coprocessor
Accelerator
Many-core
PERFORMANCE
POTENTIALS
MORPHOLOGY

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

Citation Formats

References (17)

Cited By (6)

Similar Records

Related Subjects