An engineering subroutine was a type of subroutine related to warp engines.
In 2154, the Klingons entered a subroutine into the warp matrix of Enterprise, which altered the engineering subroutines to make the warp reactor explode once the ship went below warp five. Trip Tucker was able to repair them by shutting down the reactor, reset the algorithms and then restart the engine. (ENT: "Divergence")
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