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I have started on the design myself..... We are considering using the FT2232H chip probably. Have you any good suggestions of how to implement interrutps ? We were thinking of usinging a dedicated endpoint for this purpose (I found out from FTDI they have 2 IN endpoints and 2 OUT endpoints !)
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You don't need to do anything at the USB end, that is the point of using these devices :)
The FT2232H will show up as two serial ports. Your host code can access them just like it would a USB-to-serial serial port. Under Linux they will show up as /dev/ttyUSBx devices, and under Linux as COM port devices.
At the FPGA end, you just need to implement the FIFO interface to your hardware. The SIWU (send-immediate/wake-up) signal can be used to trigger the data to be sent 'faster', i.e., send-now, rather than waiting for a full USB packet to be buffered.
Did you order an evaluation kit? FTDI have a module FT2232HQ_mini_module for $27
http://www.digikey.com/product-detail/en/ft2232h%20mini%20module/768-1030-nd/2027252 I haven't tried interfacing to this board yet (I have a module I was given at ESC, but have not had time to test it). I have used the UM245R module, and it was easy to work with. I have a couple of the FT232H modules that should show up in a couple of days.
Cheers,
Dave