My roommate and I entered into a one year lease and we have another 5 months left on the lease. His dog, which is on the lease, had a litter of 9 puppies and he has not cared for them properly and leaves them for hours on end, and all night, and when I arrive home, there is dog feces, urine all over the carpets and walls of every room in our 3 bedroom. I have spoken with the leasing agency and they have documented the damage and served him with a 10 notice to remove the animals or be evicted. The problem is that not only is the puppy problem probably going to be solved, but what about the smell I have to now live with? I didn't dig holes in the carpet, or in the walls, nor did I chew up the wood trim. Who in their right mind can live like this? What can I do? I need out.

You/landlord are going to have to get him evicted first. Then go after him for damages.
You are going to have to talk it over with your landlord about cleaning and new carpeting.
Bleach and pet stain remover like Odo Ban should get the smell out.