How to set QSFP to normal operation (allowing the device to come out of reset)?

Make GPIO pin 118 available for user-space control:
echo 118 > /sys/class/gpio/export
Configure the GPIO pin as an output pin:
echo out > /sys/class/gpio/gpio118/direction
Deassert Reset (bring the QSFP module out of the reset state):
echo 1 > /sys/class/gpio/gpio118/value
Release the control of GPIO pin 118:
echo 118 > /sys/class/gpio/unexport

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Please find the detailed product information here:
Agilex™ 7 (R31A/R31B/R31C) SoC FPGA System on Module