A PCI Express system comprising: a PCI Express adapter; and a PCI Express root complex coupled to the PCI Express adapter, the PCI root complex including: a protocol stack coupled to the PCI express adapter and configured to transmit information to and receive information from the PCI express adapter; an application specific logic module; and a fencing module coupled between the application specific logic module and the protocol stack and configured to, when in operation, block all signals from the application specific logic module from reaching the protocol stack.