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I tried using bidirectional buffers to send/receive data over the pins, but that doesn't work.
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As explained in the DE3 User Manual, the male and female HSTC connectors have crossed LVDS Rx and Tx pins. You can either use fast differential LVDS connections, then you must follow the intended Tx and Rx assignment, or single ended connections with an arbitrary selected data direction. Also bidirectional I/Os are an option. But due to the said Tx/Rx crossing, you don't connect same pin numbers of adjacent boards.