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If our goal is to make a LED to blink (from PL in Zynq Device), then the safest way is to use FPGA Configuration Master Clock this clock is always available and accessible in the same way, we do not need to know any specifics to the board we have and we do not depend on PS init done by FSBL.

ZYNQ MPSoC Devices

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This design blinks a LED connected to DONE pin and also a VIO Pin, on any Zynq MPSoC device, without using any clocks provided by the externally, and without the use of PS supplied clocks. LED Toggle rate is about 2 Hz.

Valid I/O Voltage

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.

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This is Arduino IDE screenshot after downloading LED Blinky sketch to F32C inside FPGA, selected generic FPGA board with 128K RAM and 100MHz Clock. After download the on-board LED on the FPGA/SoC SoM will blink.

Troubleshooting Tips

If you are not sure to what pins the LED(s) are connected it is possible to create a "dummy" FPGA design with "UNUSED PIN PULLUP" option. If FPGA is loaded with bitfile then any LED that is connected in active high configuration will be on, if the I/O Bank is powered. The internal pullup current is sufficient to make most modern LED to be lit (not very bright).

If you know that there are LED's connected to FPGA and they do not get lit with "unused pin pullup" FPGA design, then most likely the I/O Bank with the LED's has no power.