Partial reconfiguration on heterogeneous field-programmable gate arrays with millions of gates yields better utilization of its different types of resources by swapping in and out the appropriate modules of one or more applications at any instant of time. Given a schedule of sub-task instances where each instance is specified as a netlist of active modules, reconfiguration overhead can be reduced by fixing the position and shapes of modules common across all instances. We propose a global floorplan generation method PartialHeteroFP to obtain same positions for the common modules across all instances such that the heterogeneous resource requirements of all modules in each instance are satisfied, and the total half-perimeter wirelength over all instances is minimal. Experimental results establish that the proposed PartialHeteroFP produces floorplans very fast, with 100% match of common modules and thereby minimizing the partial reconfiguration overhead.