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- Title
Parallel simulation of Brownian dynamics on shared memory systems with OpenMP and Unified Parallel C.
- Authors
Teijeiro, Carlos; Sutmann, Godehard; Taboada, Guillermo; Touriño, Juan
- 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.
- Subjects
PARALLEL processing; SIMULATION methods &; models; WIENER processes; HYDRODYNAMICS; UPC (Computer program language); SEQUENTIAL codes
- Publication
Journal of Supercomputing, 2013, Vol 65, Issue 3, p1050
- ISSN
0920-8542
- Publication type
Article
- DOI
10.1007/s11227-012-0843-1