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Distributing MCell Simulations on the Grid

CSE Department, University of California, San Diego

Thomas M. Bartol, Jr.

Computational Neurobiology Laboratory, Salk Institute

Joel Stiles

Biomedical Applications Group, Pittsburgh Supercomputing Center

Francine Berman

San Diego Supercomputer Center

The computational Grid is a promising platform for the deployment of large-scale scientific and engineering applications. Parameter sweep applications (PSAs) arise in many fields of science and engineering and are structured as sets of "experiments," each of which is executed with a distinct set of parameters. Given that structure, PSAs are particularly well suited to the Grid infrastructure and can be deployed on very large scales. However, deployment is not easy to achieve for the domain scientist given the complexity and multiplicity of the Grid software infrastructure, the heterogeneity of the resources, and the dynamic resource availabilities. It is therefore necessary to provide user-level middleware that acts as an intermediate layer between the application and the Grid. That middleware must address all deployment, data movements, and scheduling issues to provide the user with a transparent way of running his or her simulation on the Grid. In this paper, the authors focus on such middleware specifically targeted to a biology application: MCell. After describing the application and its structure, they describe desired usage scenarios on the Grid and identify user requirements, discuss relevant computer science issues, and propose suitable solutions given currently available Grid technologies. The authors then describe a general-purpose user-level middleware project for PSAs—AppLes Parameter Sweep Template—explain how it can be extended to accommodate MCell’s specific requirements, and introduce current work in that direction.

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