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We are trying to interface a Raspberry Pi with an Virtex 5 dev. board to read the configuration memory. We have decided to use the selectmap protocol and we understand the signals involved and sequence of commands.

But where are these pins on the board, is it hardwired or should we set the pins in ucf file? Or is there any other to access these pins at all?

We can't find the answer in any of Xilinx's resource documents. The board in general is Virtex-5 development board, in particular XUPV5-LX110t

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The programming pins are hard wired to the flash chips (SystemACE and Platform Flash: U2, U4, U5). This is documented in the ML50x Schematic file.

You could use the JTAG interface (J1) like a regular programmer does. If so, you need the Raspberry Pi to talk the JTAG protocol.

An alternative solution is to upload a flash programmer design to the FPGA that interfaces the flash chip to a common link like UART. This is used by iMPACT to upload bit files into the flash for permanent storage. First it uploads a design into the FPGA and then it uses this design to move the data from JTAG through the FPGA to the flash.

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