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the Stratix IV is the RootPort and so was modified to provide the 100Mhz clock and the NIOS II SW needs to do enumeration.
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OK, this clarifies your setup, thanks.
Since your Stratix IV GX is the root-complex, it is responsible for performing the tasks that a BIOS would in a PC. This same issue occurs when you design a system with a PowerPC as the root-complex, and the solution there is to use U-Boot to configure the PCIe. So your solution would also be to get U-Boot built with PCIe support for NIOS II. I've no idea if that has been done before. Check out the latest U-Boot source and try to built it. If it fails, then post a message to the U-Boot mailing list. Don't just email asking for help, email what you are trying to do, and what fails when you try to build U-Boot.
Cheers,
Dave
Honored Contributor
