We analyse the concurrency and performance of the various types of force calculations involved in the molecular dynamics simulation of large protein or polyelectrolyte molecules. Although this analysis can in principle be used to write a meta-program to optimize load-balancing of this application on an MPP system, we argue that it is an enormous undertaking not appropriate for the computational scientist. Instead we argue that it is better to exploit research in parallel execution environments which provide automatic load-balancing for concurrent Object-Oriented applications. We also argue that use of Object-Oriented technology in the design of simulation software encapsulates the natural concurrency of the system. We illustrate this point with a discussion of the constraint force calculation for a polymeric molecule.
|Number of pages||12|
|Journal||Computer Physics Communications|
|Publication status||Published - Aug 2 1996|
ASJC Scopus subject areas
- Hardware and Architecture
- Physics and Astronomy(all)