A method is presented for partitioning a simulation model into a plurality of subdomains that may each be assigned to one of a plurality of processors. The method includes creating a representation of a topology graph of a simulation model in a tangible, computer readable medium. The topology graph includes a plurality of computational elements and a plurality of connections between those elements. Each of the plurality of connections is weighted to create a plurality of weights, and each of the plurality of weights is scaled. Optionally, the weights can be mapped to different interval of values. Based on the weights information the topology graph is partitioned into two or more subdomains, wherein a partition boundary follows a local topographical minimum in the topology graph. A subdomain is assigned to each of the plurality of processors.