For real-time you have to create a specific startup.exe and place it on the RT system.
Once you boot the RT system, it will automatically start this exe. The exe shall contain code to communicate with the host application and wait for commands.
Refer to 'reference architectures' (e.g. like this) in case you require more detailed information on how to implement a communication layer.
Norbert
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CEO: What exactly is stopping us from doing this?
Expert: Geometry
Marketing Manager: Just ignore it.