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Any time you run a diesel out of fuel, you'll get air in the fuel system. Restarting will require that you bleed the air out of the system. The easiest way is usually to remove the fuel filter and fill it with clean fuel (I would recommend replacing the filter now with a new one). Fill it clear up with fuel. Sometimes on the injector pump, there is a primer pump that you can actuate to fill the pump/lines/nozzles. Otherwise after filling the fuel filter, it'll probably start with lots of cranking. Expect lots of smoke and rough running until all of the air is expelled. Good Luck, and be careful to not run out of fuel again!