Performance modeling and composition: a case study in cell simulation

Presents a case study in the use of performance modeling for parallel application development, with a biological cell simulation as our target application. We show that a simple performance model is adequate for determining data layout for arrays and linked structures, and validate our model against experimental results for some application kernels. We quantify the importance of optimizing across program components using information about the machine performance and input characteristics. The cell simulation application has two phases, one regular and one irregular. The model closely predicts actual performance within the regular phase and allows for qualitative design comparisons in the irregular one. The resulting application is written in Split-C and runs on multiple platforms.