When editing the AXIGPIO in the block design always make sure to the recreate HDL Wrapper and then check the ports according to PMOD JA1.
Heres what they should look like:
PMOD Site Bitt
JA10 Y11 7
JA9 AA11 6
JA8 Y10 5
JA7 AA9 4
JA4 AB11 3
JA3 AB10 2
JA2 AB9 1
JA1 AA8 0
I think these are inverted. I posted a figure with correct mapping.
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