Silent running is a stealth mode of operation for naval submarines. The aim is to evade discovery by passive sonar by eliminating superfluous noise: nonessential systems are shut down, the crew is urged to rest and refrain from making any unnecessary sound, and speed is greatly reduced to minimize propeller noise.
https://en.wikipedia.org/wiki/Silent_running_(submarine)
Rig for red on the other hand is prepping for nighttime ops on surface ships and on submarines its prepping to surface and/or come to periscope depth during night ops. Periscope depth is when they start emptying the tubes :)