Yes, "on the CPU and GPU" is fine. As John says in a comment, it's an instance of conjunction reduction. I disagree with the characterization that it's a matter of omitting the second "the", however, or that there is a process of conjunction reduction, even.
It is a general fact about conjunction that you can conjoin several constituents of the same category to create a constituent of that same category. That is what is going on here. "CPU" and "GPU" are nouns, consequently "CPU and GPU" is a noun. You can make a noun phrase by adding "the" to a noun, so "the CPU and GPU" is a good noun phrase. Then, that serves as the object of the preposition "on".
So the structure is [ on [ the [ CPU and GPU ] ] ], rather than what you get by omitting the second article from [ on [ [ the CPU ] and [ (the) GPU ] ] ].
Although in The Syntactic Phenomena of English, McCawley continues the tradition of treating conjunction reduction as a transformational process (which I do not accept), I am in agreement with him about the structure of the reduced form. The phrase in question does not have a conjunction of two noun phrases, but rather a conjunction of two nouns. (See McCawley's book for supporting evidence.)