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

Title: 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

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

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

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

DOE Contract Number:: SC0001013

OSTI ID:: 1383808

Journal Information:: Journal of Supercomputing, Vol. 66, Issue 1; Related Information: CEN partners with University of Southern California (lead); University of Illinois, Urbana-Champaign; University of Michigan; University of Virginia; ISSN 0920-8542

Publisher:: Springer

Country of Publication:: United States

Language:: English

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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
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
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
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
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
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
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
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
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
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
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

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