NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
Object-oriented framework and product lines
Proceedings of the first conference on Software product lines : experience and research directions: experience and research directions
A parallel java grande benchmark suite
Proceedings of the 2001 ACM/IEEE conference on Supercomputing
ECOOP '01 Proceedings of the 15th European Conference on Object-Oriented Programming
A domain-specific language for parallel and grid computing
Proceedings of the 2008 AOSD workshop on Domain-specific aspect languages
Proceedings of the 18th ACM international symposium on High performance distributed computing
Feature models, grammars, and propositional formulas
SPLC'05 Proceedings of the 9th international conference on Software Product Lines
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This paper presents a case study of using product-lines to address the variability of optimization methods and target platform mappings in high-performance molecular dynamics simulations. We use Feature Oriented Programming to incrementally extend the base algorithm by composing performance enhancement features with the core functionality. Developed features encapsulate common optimization methods in molecular dynamics simulations and target platform mappings. The main benefits of the approach are: 1) it promotes an incremental development, where optimizations and mappings are developed incrementally and simultaneously with the core functionality; 2) complex optimizations and mappings can be obtained by composing basic features. The performance of synthesized products is comparable to the performance of products developed with traditional parallel programming techniques. In this approach complex optimizations become easier to develop, by composing basic features, providing a performance advantage over traditional programming techniques.