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Its a debug tool. Read the documentation. Try and use it. Once you understand how to use it, you will be able to determine if its useful to you.
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I used it some time ago and I know basically what it can do. I don't know it very well and I can be wrong but I don't think it could be very useful for the matter.
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Sure, if you can define what a "waiting command" is in your hardware design.
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I was thinking of a flag that would only make the sdram writing enable when it's '1'.
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Have you created a simulation of your system? If not, you should. It will help you understand your design much better, since it gives you full visibility into what is going on. The simulation waveform view will also help you see why SignalTap II is useful.
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You're right, I haven't done so and I'm starting to think it's a big error. I'll do it first thing tomorrow (if my work let me enough time)...