Parallel simulation of Brownian dynamics on shared memory systems with OpenMP and Unified Parallel C
| Autor: | Guillermo L. Taboada, Carlos Teijeiro, Godehard Sutmann, Juan Touriño |
|---|---|
| Rok vydání: | 2012 |
| Předmět: |
Computer science
PGAS Structure (category theory) Parallel computing 010402 general chemistry 01 natural sciences Theoretical Computer Science Shared memory Brownian dynamics 0103 physical sciences Unified Parallel C Code (cryptography) Partitioned global address space Parallel simulation computer.programming_language 010304 chemical physics OpenMP 0104 chemical sciences Hardware and Architecture UPC computer Software Information Systems |
| Zdroj: | RUC. Repositorio da Universidade da Coruña instname The Journal of Supercomputing |
| ISSN: | 1573-0484 0920-8542 |
| DOI: | 10.1007/s11227-012-0843-1 |
| Popis: | This is a post-peer-review, pre-copyedit version of an article published in The Journal of Supercomputing. The final authenticated version is available online at: https://doi.org/10.1007/s11227-012-0843-1 [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. Ministerio de Ciencia e Innovación; TIN2010-16735 Spanish network CAPAP-H3; TIN2010-12011-E Xunta de Galicia; 2010/6 |
| Databáze: | OpenAIRE |
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