You need to configure RCW to enable GPIO.
For example, if you want to use GPIO3_DAT12, you need to configure RCW[EC1_SAI4_5_PMUX] as 1.

In dts arch/arm64/boot/dts/freescale/fsl-ls1028a.dtsi, make sure the following GPIO device nodes are defined.
gpio1: gpio@2300000 {
compatible = "fsl,ls1028a-gpio","fsl,qoriq-gpio";
reg = <0x0 0x2300000 0x0 0x10000>;
interrupts = <GIC_SPI 36 IRQ_TYPE_LEVEL_HIGH>;
gpio-controller;
#gpio-cells = <2>;
interrupt-controller;
#interrupt-cells = <2>;
little-endian;
};
gpio2: gpio@2310000 {
compatible = "fsl,ls1028a-gpio","fsl,qoriq-gpio";
reg = <0x0 0x2310000 0x0 0x10000>;
interrupts = <GIC_SPI 36 IRQ_TYPE_LEVEL_HIGH>;
gpio-controller;
#gpio-cells = <2>;
interrupt-controller;
#interrupt-cells = <2>;
little-endian;
};
gpio3: gpio@2320000 {
compatible = "fsl,ls1028a-gpio","fsl,qoriq-gpio";
reg = <0x0 0x2320000 0x0 0x10000>;
interrupts = <GIC_SPI 37 IRQ_TYPE_LEVEL_HIGH>;
gpio-controller;
#gpio-cells = <2>;
interrupt-controller;
#interrupt-cells = <2>;
little-endian;
};
Linux Kernel configuration is as the following.
