Why all the pins on a chip are not GPIOs?

All the pins in SOC are not GPIO. A specific group of pins mapped as GPIO. Other pins are configured for specific protocols like DDR, SPI, I2C... etc. GPIO is generic pins can be used for any purpose based on user requirement. It can be used for handling IRQs, trigger Resets, Glow LEDs..etc.

for example, Consider a FPGA is connected to SOC via GPIOs. User need to program the FPGA via these GPIO pins. In SOC side user need to write a specific program with mentioned sequence to drive those GPIO to program the FPGA config file

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