When multiple subsystem instances are targeted for transceivers in the same quad, the GTCOMMON and IBUFDS need to be shared. The transceiver outputs of the instance configured to Include Shared Logic in Core need to be connected to inputs of an instance configured to Include Shared Logic in IP Example Design . An example where the RX clock is synchronous between both the instances is shown in the following figure. The connections shown in blue are specific to connections for sharing logic. The rest are regular connections.