In a general aspect, a quantum computing method is described. In some aspects, a control system in a quantum computing system assigns subsets of qubit devices in a quantum processor to respective cores. The control system identifies boundary qubit devices residing between the cores in the quantum processor and generates control sequences for each respective core. A signal delivery system in communication with the control system and the quantum processor receives control signals to execute the control sequences, and the control signals are applied to the respective cores in the quantum processor.