Sure you can. Since a single compiler can already output different code for different parts (K10 vs. C2D, say), you are not comparing the identical code across processors.
So, you're looking to see which processor can "get the job done", i.e. PERFORM, best. So you might as well compare the performance of the best code you can get for each part, and that may mean using different compilers for your source code (i.e. the job).
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