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Synthesizing 99K LEs should take an hour or two. If something was difficult, maybe double that. There is no way it should take a day. If it's due to reductions, you want it to do that because the design would most likely be many times larger(if that's the problem). As recommended, start making sub-projects of smaller hierarchies and benchmark those(synthesis times, how large they are, etc.) and see if there is a problem area. If you can send the design, might be worth a Service Request with Altera.
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I have discovered that there is one part of the design that took up a very long synthesizing time. It involved 6 * 1681 amount of small submodules. any advice on this?
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