A method of configuring a programmable integrated circuit device. A channel source within the virtual fabric is configured to receive input data from a first kernel outside of the virtual fabric and on the programmable integrated circuit device, and a channel sink within the virtual fabric is configured to transmit output data to the first kernel. The configuring of the channel source is modified such that the channel source receives input data from a second kernel in response to detecting a change in operation of the programmable integrated circuit device.