A computer-implemented method generates a plurality of clusters based on components included in a design under test (DUT); classifies a subset of clusters of the plurality of clusters as tangled clusters; modifies at least two tangled clusters of the subset of clusters based on overlap between the at least two tangled clusters; determines, for each tangled cluster in the subset of clusters, a gate count based on the interconnectivity of the tangled cluster; and partitions the DUT among a plurality of field-programmable gate arrays (FPGAs) based on the gate count determined for each tangled cluster from the subset of clusters.