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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.

If you are not sure about the I/O Banks Voltage supplies then there are some options to try.

DONE LED

If there is on board LED directly connected to FPGA "DONE" output, then it is also possible to control it as long as it is possible to configure the FPGA (or PL portion of Zynq).

MIO LED

If there is a LED directly connected to lower MIO Bank of the Zynq then this LED is also always controllable, as this Bank has to be powered for the device to boot. This LED can also be controlled if the PL portion of the Zynq is not configured or even un-powered.