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Regarding Stratix IV GX dev kit, problem is that the reference manual quotes 12 channels with 8.5 Gbps + 6 with 3.5 Gpbs (I don't know why).
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Let me look at the schematic ... p8 has the transceiver connections on the FPGA. The transceivers are all connected to true transceiver channels, not the 6.5Gbps CMU channels, so they are all capable of 8.5Gbps. Its possible that they don't want to 'quote' that due to the layout. I've been using the HSMC connections at 5Gbps without issues.
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I am also not sure about the PCI: can I just use that physical interface but custom configure the transceivers?
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Yep, you can configure it to do what you like. The only caveat is that the transmitters have AC-coupling caps on them. If you needed a DC connection, you could replace them easily enough.
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The DE4 is a little bit of the same: it quotes only 12 transceivers available.
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I don't have one of these, so you'd just have to look at the schematic and see what they've routed. Chances are they are not quoting the PCIe interface transceivers in that list, since they assume you'll want to use the board in a PCIe slot. However, both boards work fine standalone on the bench.
Cheers,
Dave