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running a simulink desktop real-time model as .m file

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Hello everyone,
So i have made a controller as a simulink model and im trying to run it from matlab editor. The simulink model runs in simulink desktop real-time, and it's output is connected to a hardware and the input is connected back to the software.
The problem is that when i run the simulation from simulink, the controller works fine and it does it's job, but when i run it from matlab editor, it goes crazy. The controlled variable keeps rising and the controller does not work.
Im using the following code to run the simulation:-
clear all
simout = sim('PI_Controller.slx');
Im guessing the problem is with sim command. Maybe there is a different command for running a simulation that runs in ream-time?
Im attachment is a Photo of my Model.
What am i missing here?

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