A method of operating an engine having at least one cylinder including an intake valve and an exhaust valve, the method comprising of injecting a first amount of fuel into the cylinder; auto-igniting a first mixture of air and said first amount of fuel by compressing said first mixture; injecting a second amount of fuel into the cylinder after auto-igniting said first mixture; combusting a secondmixture of said second amount of fuel and gasses from auto-ignition of said first mixture; holding an intake valve of the cylinder closed between auto-igniting the first mixture and combusting the second mixture; and exhausting said combusted second mixture.