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I had a more obvious problem there which i didnt identify when posting this. The problem is that the system needs to be rebooted for the PCI system to be enumerated and when its done, the the FPGA is also restarted, which makes it lose its bit stream, hence not detected. Could you suggest any solution which would not require a separate power supply to the board. I am currently trying to keep the program in its CFI flash and configure it upon restart.
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The procedure depends on whether you use one machine or two.
A.) Using one machine, boot and use Quartus to configure the board, then restart the machine.
A restart causes the machine to reboot and re-enumerate the PCIe bus, and hopefully causes it to find the DE4.
B.) Using two machines, power-on the machine with the DE4 board plugged in and hit ESC or DEL to enter the BIOS. Use your other machine running Quartus to configure the DE4. Then allow the machine with the DE4 to boot.
Personally I prefer method B.
Cheers,
Dave