On the Migration of the Scientific Code Dyana from SMPs to Clusters of PCs and on to the Grid

Dyana is a molecular biology code used in the study of infectious prion proteins. Like many other scientific codes, Dyana was migrated successfully from vector supercomputers to some more cost-effective cluster of commodity PCs. A further migration to a widely distributed grid computing platform looks very tempting because many of these platforms promise the use of nearly free compute-cycles on the Internet. Not all codes are equally suited for all platforms. Even embarrassingly parallel codes might require a significant re-engineering effort for a migration from one platform to another. A better understanding of the performance characteristics of a code is required before a migration is attempted. To address this problem, we present a systematic method to study the viability of a code migration from one platform to another, before it is actually undertaken. We construct an analytic performance model of the application. We use the previous migration from SMPs to commodity clusters of PCs to validate and calibrate the model. Finally, we extrapolate the performance of Dyana widely distributed computing on the grid and we suggest optimizations in the process of migration. Our general model predicts that Dyana can efficiently use up to 42000 processors with its current workload and is therefore well suited for grid computing on the Internet.