One approach (short version):
Add an annotation to your model, and write the command invoking your program in the annotation's properties' ClickFcn.
For more details, type
doc simulink.annotation
and look at the ClickFcn property.
(long version) Open your model, and double click anywhere on the background. This will add a annoation and a blinking cursor. Type in your annotation and hit escape to stop entering text. Right-click on the annotation and select Properties from the context menu. There is a text area (ClickFcn) to specify the commands to be executed when the annotation is clicked by a user.
