A system includes an automated place and route tool to generate a layout of an integrated circuit (IC) die based on a gate level circuit description. A machine readable persistent storage medium includes a first portion encoded with a first gate-level description of first and second circuit patterns to be formed on first and second IC dies, respectively, and a second portion encoded with a second gate level description of the plurality of circuit patterns received from the tool. The second gate level description includes power and ground ports, and the first gate level description does not include power and ground ports. A processor-implemented verification module is provided for comparing the first and second gate level descriptions and outputting an error report if the second gate level description has an error. The verification module outputs a verified second gate-level description of the first and second circuit patterns.