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Newer version of the Quartus(12.0) is installed now and I am able to build the PCIe system.
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OK. I think that 13.x has better support for PCIe now ... but I have not looked at that version yet.
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But I am not able to communicate with the board. I am working on a linux machine, and lspci command shows no track of the altera board being connected. I noticed in your pdf that sometimes wthout the reconfiguration reset logic, the device would never negotiate with a X4 width. The design currently under test is without reconfiguration reset logic and withX4 width. Would this be a problem?
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Download one of the original example designs that comes with the kit. If that design shows up ok, then you know that your problem is related to your current design.
Cheers,
Dave