GPIO stands for General Purpose Input Output. Lets assume you want to generate a pulse at pin 39 as in the below image. So you wire the pulse to pin 39. The underline code will create necessary code to configure the pin 39 to be output pin enabling the pin to output pulse. 

[![enter image description here][1]][1]

Below is the code stack between Simulink and Microcontroller. So when you create a Digital Output block the software will essentially convert and configure your Digital Output block into a Digital output pin. The code will convert into binary code to be able to loaded into the micro controller. Below is a high level diagram that explains the process.

[![enter image description here][2]][2]

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**References:**

 - [C2000 Digital Signal Controllers][3]
 - [Embedded Coder Target for Energia][4]


  [1]: https://i.sstatic.net/aU0rS.jpg
  [2]: https://i.sstatic.net/lJOWo.jpg
  [3]: http://focus.ti.com/download/tidc/pdfs/asia/2008/tw_T2_2_Joey_Chen_resized.pdf
  [4]: http://www.mathworks.com/matlabcentral/fileexchange/54929-embedded-coder-target-for-energia/content/html/TIVAgettingstarted.html