Model Based Load Indices (MBLI) for Scientific Simulation Stefan Muszala Ph.D. Dissertation, Department of Electrical and Computer Engineering, University of Colorado. January, 2007. This research presents the data relationships necessary to discover and im- plement a model based load index (MBLI) for load balancing scientific applications on distributed parallel systems. An MBLI is an alternative quantity to run-time measurement-based load indices (RLIs) such as processing time. This newly char- acterized index must be a quantity produced by or required of the scientific model being simulated. An MBLI correlates with a measured process performance parameter that directly represents heterogeneous computational loads and can be used to resolve load imbalances that reduce an applicationâ™s time to completion. The method of obtaining an MBLI occurs during a pre-processing step and does not incur a run-time cost after implementation. Atomic mass, temperature tendency and surface flux are examples of MBLIs found in Molecular Dynamics (MD) models, Atmospheric General Circulation Models (AGCM) and Ocean Circulation Models (OCM) respectively. This research presents the discovery processes for MBLIs in AGCMs, MD models and OCMs. MBLI implementations and performance of an AGCM and MD model (NAMD2) are discussed while executing on Pentium4 Xeon, IBM Power5-p575 and IBM BlueGene/L systems. The AGCM implementation in- cludes results from both a production model, the Community Climate System Model/Community Atmosphere Model (CCSM/CAM3), and from a Load Bal- ancing and Scheduling Framework (LBSF). A particular LBSF implementation includes the first use of Very Fast Simulated Annealing to make load balancing decisions using an MBLI. Finally, a detailed analysis is presented that compares an RLI to an MBLI and clearly shows the overhead and error associated with a run-time measured quantity. [ PDF ]