How do I simulate low lovel entities?

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You can compile any entity at any time provided you set them as top level entity. I do not know which simulation tool you use. But in general you can simulate any low level entity. If you are simulating top level the low level entity must be precompiled before you do the top level. Check your simulation tool user guide.

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good point, if you simulate in ModelSim-AE directly you can just vcom the appropriate files and vsim the correct top.

i usually edit the Quartus/Nativelink ModelSim .do to taste, out of laziness. ;)