A compression ignition engine (10) has a control system (24) for processing data, one or more cylinders (16), a fueling system (18), and a variable valve actuation mechanism (20). Control system (24) develops both fueling data for fueling the engine and timing data representing time during the engine cycle for intake valve closure to a cylinder that will endow the cylinder with an effective compression ratio (ECR) appropriate to current engine operation for causing auto-ignition to occur near or at top dead center in the engine cycle. During a compression upstroke, the cylinder is fueled according to the fueling data and intake valve closure for the cylinder is performed according to the timing data. This creates an air-fuel mixture that is increasingly compressed to the point of auto-ignition near or at top dead center.