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"S. A. Agulhas II" is powered by four six-cylinder Wärtsilä 6L32 medium-speed diesel generating sets, each producing . To fulfill the International Maritime Organisation’s Safe Return to Port requirement, the main engines are located in two separate engine rooms and the ship is capable of returning to port with one engine room flooded. Designed according to the power plant principle in which the main generators supply electricity for all shipboard consumers, "S. A. Agulhas II" has no separate auxiliary generators. In case of emergency, electricity is provided by a Volvo Penta emergency diesel generator.