in Cortex-M4 project, you should see SPI1 clock init in HAL_SPI_MspInit(), only used in Development Mode (i.e. without Linux).
In Linux DT, you should see CLK_SPI2S1_PLL3Q line in stm32mp157f-yourproject-mx-u-boot.dtsi
please check you have :
&m4_spi1{
...
status = "okay";
}
in stm32mp157f-yourproject-mx.dts
but also that you don't have any &spi1 node status = "okay" (as SPI1 must not be enabled for Linux if assigned to M4)
Check also that pll3 is correctly defined in DT.
Usually, this work out of the box with CubeMx generated DT.
Regards.
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