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They raise beacons which communicate via laser with satellites, thus avoiding giving away position from radio or audio.

They use audio for short-range underwater communication, but this has side effect of giving away position.

US also built giant ELF (extra low frequency) transmitter to send orders to subs which operated till 2004.

Fun fact: subs have all necessary codes to launch nuclear strike on board since there is no way to transmit these code to them if they are submerged.