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It is very common that modern Integrated Circuits have separate power supply pins for I/O Voltage. That voltage if applied control the output levels from the device, if the Voltage is too low or missing then it is not possible to have enough current from the device I/O Pin to make a LED Lit.

FPGA and SoC SoM's can have fixed and user controlled Voltages for the I/O Banks. It is important to assure that the I/O Bank that controls the LED has a valid Supply Voltage applied.