Shipsims are extremely powerful, specialized processing arrays. As you might expect, virtually everything on a ship is managed by a shipsim, each of which has a different capacity for computing capacity, measured in 'cycles'.
Along with the superstructure requiring X number of cycles just to keep the lights on, most, but not all, modules on your ship use cycles. If your shipsim doesn't have enough cycles available, you won't be able to activate whatever it is you're trying to activate without turning something else off first.
For instance, while firing lasers requires virtually no shipshim cycles, firing homing missiles uses quite a few.