A host system receives a description of a design under test (DUT) that includes multiple IP units and is to be emulated by an emulator. The host system compiles the description of the DUT, which includes synthesizing the description, partitioning the DUT, and mapping the partitions to FPGAs included in the emulator that will emulate the DUT. Each IP unit is part of a single partition or partitioned into multiple partitions and mapped to a different set of FPGAs. The host system identifies connections in the DUT between IP units. The host system designates one or more FPGAs of the emulator that have not been allocated to emulate IP units as interface FPGAs. The host system determines a route for each of the identified connections through one of the interface FPGAs. The connections are routed so that there are no direct connections between the sets of FPGAs of two IP units.