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SW4STM32 and SW4Linux fully supports the STM32MP1 asymmetric multicore Cortex/A7+M4 MPUs

   With System Workbench for Linux, Embedded Linux on the STM32MP1 family of MPUs from ST was never as simple to build and maintain, even for newcomers in the Linux world. And, if you install System Workbench for Linux in System Workbench for STM32 you can seamlessly develop and debug asymmetric applications running partly on Linux, partly on the Cortex-M4.
You can get more information from the ac6-tools website and download (registration required) various documents highlighting:

System Workbench for STM32


empty project using HAL and USB device middleware

when I run CubeMX and select the Nucleo-64 STM32F446RE I get an unresolvable error in the clock configuration. Seems as if the chip expects an HSE input. but why that?
I checked CubeMX for your board. Seems like HSE is not possible to use. Probably some peripheral use XTAL pins on this board.

isn’t it possible to create a project with HAL without using CubeMX?
It is possible, but CubeMX makes life easy with building all initialization and creating a starting point project.

a good starting point to evaluate the module step by step
Download CubeF4 from the ST side. It provides a lot of good demos.