A quantum computing method for performing a quantum computation, the method comprising: assigning, by operation of a control system in a quantum computing system, subsets of qubit devices (305A-R) in a quantum processor to respective cores (310A-D), wherein neighboring pairs of qubit devices included in the quantum processor are connected and interact through respective connections and each subset of qubit devices comprises multiple qubit devices; identifying, by operation of the control system, boundary qubit devices (305 C, 3051, 305O, 305D, 305J, 305P) that are not assigned to a respective core and reside between the cores in the quantum processor, wherein boundary qubit devices that reside between two or more cores in the quantum processor share non-negligible interactions with qubit devices included in the two or more cores; generating, by operation of the control system, multiple control sequences required to execute the quantum computation, comprising generating a control sequence for each respective core, wherein each control sequence of the multiple control sequences is configured to i) apply a respective sequence of operations to qubit devices assigned to its respective core and ii) apply an identity operation to each boundary qubit device of the respective core; translating the multiple control sequences to respective control signals and delivering, by operation of a signal delivery system in communication with the control system and the quantum processor, the control signals to the quantum processor to execute the multiple control sequences; and applying the control signals to the respective cores in the quantum processor to execute the quantum computation. assigning, by operation of a control system in a quantum computing system, subsets of qubit devices (305A-R) in a quantum processor to respective cores (310A-D), wherein neighboring pairs of qubit devices included in the quantum processor are connected and interact through respective connections and each subset of qubit devices comprises multiple qubit devices; identifying, by operation of the control system, boundary qubit devices (305 C, 3051, 305O, 305D, 305J, 305P) that are not assigned to a respective core and reside between the cores in the quantum processor, wherein boundary qubit devices that reside between two or more cores in the quantum processor share non-negligible interactions with qubit devices included in the two or more cores; generating, by operation of the control system, multiple control sequences required to execute the quantum computation, comprising generating a control sequence for each respective core, wherein each control sequence of the multiple control sequences is configured to i) apply a respective sequence of operations to qubit devices assigned to its respective core and ii) apply an identity operation to each boundary qubit device of the respective core; i) apply a respective sequence of operations to qubit devices assigned to its respective core and ii) apply an identity operation to each boundary qubit device of the respective core; translating the multiple control sequences to respective control signals and delivering, by operation of a signal delivery system in communication with the control system and the quantum processor, the control signals to the quantum processor to execute the multiple control sequences; and applying the control signals to the respective cores in the quantum processor to execute the quantum computation.