On the parallelization of molecular dynamics codes
GP Trabado and O Plata and EL Zapata, COMPUTER PHYSICS COMMUNICATIONS, 147, 711-715 (2002).
Molecular dynamics (MD) codes present a high degree of spatial data locality and a significant amount of independent computations. However, most of the parallelization strategies are usually based on the manual transformation of sequential programs either by completely rewriting the code with message passing routines or using specific libraries intended for writing new MID programs. In this paper we propose a new library- based approach (DDLY) which supports parallelization of existing short- range MID sequential codes. The novelty of this approach is that it can directly handle the distribution of common data structures used in MD codes to represent data (arrays, Verlet lists, link cells), using domain decomposition. Thus, the insertion of run-time support for distribution and communication in a MID program does not imply significant changes to its structure. The method is simple, efficient and portable. It may be also used to extend existing parallel programming languages, such as HPF. (C) 2002 Elsevier Science B.V. All rights reserved.
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