Analysis of scalable data-privatization threading algorithms for hybrid MPI/OpenMP parallelization of molecular dynamics

Kunaseth, Manaschai; Richards, David F.; Glosli, James N.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

doi:10.1007/s11227-013-0915-x

Analysis of scalable data-privatization threading algorithms for hybrid MPI/OpenMP parallelization of molecular dynamics

Journal Article · Fri Apr 05 04:00:00 EDT 2013 · Journal of Supercomputing

DOI:https://doi.org/10.1007/s11227-013-0915-x· OSTI ID:1383808

Kunaseth, Manaschai; Richards, David F.; Glosli, James N.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

Research Organization:: Energy Frontier Research Centers (EFRC) (United States). Center for Energy Nanoscience (CEN)

Sponsoring Organization:: USDOE SC Office of Basic Energy Sciences (SC-22)

DOE Contract Number:: SC0001013

OSTI ID:: 1383808

Journal Information:: Journal of Supercomputing, Journal Name: Journal of Supercomputing Journal Issue: 1 Vol. 66; ISSN 0920-8542

Publisher:: Springer

Country of Publication:: United States

Language:: English

References (14)

GPU accelerated molecular dynamics simulation of thermal conductivities Yang, Juekuan; Wang, Yujuan; Chen, Yunfei Journal of Computational Physics, Vol. 221, Issue 2 https://doi.org/10.1016/j.jcp.2006.06.039	journal	February 2007
Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions Fattebert, J. -L.; Richards, D. F.; Glosli, J. N. Computer Physics Communications, Vol. 183, Issue 12 https://doi.org/10.1016/j.cpc.2012.07.013	journal	December 2012
GPU-accelerated molecular dynamics simulation for study of liquid crystalline flows Sunarso, Alfeus; Tsuji, Tomohiro; Chono, Shigeomi Journal of Computational Physics, Vol. 229, Issue 15 https://doi.org/10.1016/j.jcp.2010.03.047	journal	August 2010
Computing Performance: Game Over or Next Level? Fuller, Samuel H.; Millett, Lynette I. Computer, Vol. 44, Issue 1 https://doi.org/10.1109/MC.2011.15	journal	January 2011
Exploiting hierarchical parallelisms for molecular dynamics simulation on multicore clusters Peng, Liu; Kunaseth, Manaschai; Dursun, Hikmet The Journal of Supercomputing, Vol. 57, Issue 1 https://doi.org/10.1007/s11227-011-0560-1	journal	February 2011
Computing the viscosity of supercooled liquids Kushima, Akihiro; Lin, Xi; Li, Ju The Journal of Chemical Physics, Vol. 130, Issue 22 https://doi.org/10.1063/1.3139006	journal	June 2009
The fast Fourier Poisson method for calculating Ewald sums York, Darrin; Yang, Weitao The Journal of Chemical Physics, Vol. 101, Issue 4 https://doi.org/10.1063/1.467576	journal	August 1994
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation Hess, Berk; Kutzner, Carsten; van der Spoel, David Journal of Chemical Theory and Computation, Vol. 4, Issue 3 https://doi.org/10.1021/ct700301q	journal	February 2008
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems Darden, Tom; York, Darrin; Pedersen, Lee The Journal of Chemical Physics, Vol. 98, Issue 12 https://doi.org/10.1063/1.464397	journal	June 1993
Zonal methods for the parallel execution of range-limited N-body simulations Bowers, Kevin J.; Dror, Ron O.; Shaw, David E. Journal of Computational Physics, Vol. 221, Issue 1 https://doi.org/10.1016/j.jcp.2006.06.014	journal	January 2007
Hybrid Message-Passing and Shared-Memory Programming in a Molecular Dynamics Application On Multicore Clusters Chorley, Martin J.; Walker, David W.; Guest, Martyn F. The International Journal of High Performance Computing Applications, Vol. 23, Issue 3 https://doi.org/10.1177/1094342009106188	journal	June 2009
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 events based algorithm for distributing concurrent tasks on multi-core architectures Holmes, David W.; Williams, John R.; Tilke, Peter Computer Physics Communications, Vol. 181, Issue 2 https://doi.org/10.1016/j.cpc.2009.10.009	journal	February 2010
Simulating solidification in metals at high pressure: The drive to petascale computing Streitz, Frederick H.; Glosli, James N.; Patel, Mehul V. Journal of Physics: Conference Series, Vol. 46 https://doi.org/10.1088/1742-6596/46/1/037	journal	September 2006

Similar Records

Analysis of scalable data-privatization threading algorithms for hybrid MPI/OpenMP parallelization of molecular dynamics

Journal Article · Fri Apr 05 00:00:00 EDT 2013 · Journal of Supercomputing · OSTI ID:1162006

Analysis of Scalable Data-Privatization Threading Algorithms for Hybrid MPI/OpenMP Parallelization of Molecular Dynamics

Journal Article · Tue Feb 07 23:00:00 EST 2012 · Journal of Supercomputing, vol. 66, no. 1, October 1, 2013, pp. 406-430 · OSTI ID:1114737

A Scalable Data-Privatization Threading Algorithm for Hybrid MPI/OpenMP Parallelization of Molecular Dynamics

Conference · Mon Sep 27 00:00:00 EDT 2010 · OSTI ID:1124966

Related Subjects

charge transport
materials and chemistry by design
optics
solar (fuels)
solar (photovoltaic)
solid state lighting
synthesis (novel materials)
synthesis (scalable processing)
synthesis (self-assembly)

Analysis of scalable data-privatization threading algorithms for hybrid MPI/OpenMP parallelization of molecular dynamics

Citation Formats

References (14)

Similar Records

Related Subjects