A method controlling combustion modes of an engine with at least a first and second cylinder, the engine having a first actuator configured to control at least intake valves of the first and second cylinder and a second actuator configured to control at least exhaust valves of the first and second cylinders, the method comprising of sending a first signal to the first actuator which adjusts operation of at least intake valves of the first and second cylinder and a second signal to the second actuator which adjusts operation of at least exhaust valves of the first and second cylinder, said first and second signals sent at different crank angles, and transitioning combustion modes of said first and second cylinders, said combustion modes including spark ignition and homogeneous compression ignition.