Parallel simulation of Brownian dynamics on shared memory systems with OpenMP and Unified Parallel C

Authors:
Carlos Teijeiro;Godehard Sutmann;Guillermo L. Taboada;Juan Touriño
Affiliations:
Computer Architecture Group, University of A Coruña, A Coruña, Spain 15071;Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation, Forschungszentrum Jülich GmbH, Jülich, Germany 52425 and ICAMS, Ruhr-University Bochum, Bochum, Germany 44801;Computer Architecture Group, University of A Coruña, A Coruña, Spain 15071;Computer Architecture Group, University of A Coruña, A Coruña, Spain 15071
Venue:
The Journal of Supercomputing
Year:
2013

Citing 4
Cited 0

New Itô--Taylor expansions

Journal of Computational and Applied Mathematics - Special issue: Selected papers from the conference on computational and mathematical methods for science and engineering (CMMSE-2002) Alicante University, Spain, 20-25 september 2002
Performance Evaluation of MPI, UPC and OpenMP on Multicore Architectures

Proceedings of the 16th European PVM/MPI Users' Group Meeting on Recent Advances in Parallel Virtual Machine and Message Passing Interface
ScaleUPC: a UPC compiler for multi-core systems

Proceedings of the Third Conference on Partitioned Global Address Space Programing Models
Development and performance analysis of a UPC Particle-in-Cell code

Proceedings of the Fourth Conference on Partitioned Global Address Space Programming Model

Quantified Score

Hi-index	0.00

Visualization

Abstract

The simulation of particle dynamics is an essential method to analyze and predict the behavior of molecules in a given medium. This work presents the design and implementation of a parallel simulation of Brownian dynamics with hydrodynamic interactions for shared memory systems using two approaches: (1) OpenMP directives and (2) the Partitioned Global Address Space (PGAS) paradigm with the Unified Parallel C (UPC) language. The structure of the code is described, and different techniques for work distribution are analyzed in terms of efficiency, in order to select the most suitable strategy for each part of the simulation. Additionally, performance results have been collected from two representative NUMA systems, and they are studied and compared against the original sequential code.