The last time we checked, stones don't actually cry (or, rather, they cry on the inside). But the wind is making them cry out in a metaphorical way: " Hearing the stones cry out under the horizons" (24). It's like the wind is this strange, invisible power bending the physical world to its own will, almost torturing it in a way. This is what forces the cry out from the stones—even the inanimate world is responding to the wind, as illustrated by this moment of personification.
As for the "roots" of the house, those are being shaken to their foundation by the wind: "We watch the fire blazing,/ And feel the roots of the house move" (21-22). Of course, the house doesn't have literal roots—but that description reminds us how all things are a part of Nature, and so therefore are subject to the laws and (uncaring) powers of the natural world.