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AM2434: Custom board GPIO does not toggle

Part Number: AM2434
Other Parts Discussed in Thread: SYSCONFIG

We try the led blink program on Launchpad and it works. On our custom board we use pin  PRG0_PRU0_GPO4/AA2 with same program but this pin does not toggle. The power input to our board increases when program is loaded, so the CPU is doing something. I suspect the sysconfig does not update the pinmux. Please advise anything to try out.