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The simulations are taking the best part of an hour to complete on my Dell Latitude D620 laptop with Intel Core2duo T7200. I know not much about the circuit can be told from what I'm describing but is this normal performance? I've noticed that the simulator seems to be single threaded, so only making use of one CPU core.
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Yes, this is normal in the sense that QuartusII doesn't make use of multi-threading. I have used QII on quad-core machines and it still operates as a single-thread. If you are using WindowsXP minimize all other windows that you are not using and you can check in the task manager, it drastically reduces cpu usage.