Many ways!

A power supply with a switch on so you can power down the unit after you've done your safe shutdown.

Power the fan from the USB port so that it goes of with the Pi.

One of these circuits that will shut off the power to the whole device a couple of minutes after the shutdown is initiated (although you might need a new case):

https://www.msldigital.com (they have a riser cable to get it away from your fan too)

http://mausberry-circuits.myshopify.com/collections/frontpage

https://lowpowerlab.com/shop/product/91

@TheComicCondor can you tell me why you cant do both

Sounds good, exactly the answer I was looking for.

Well, I've solved it myself.
I put it here in case someone serves.

What it does when starting the emulator N64 is to restart the GPIO of the Raspberry Pi and the pins that are configured as output PWM are put to full power.

What I have done to solve it is to insert the following command:

Gpio -g mode 18 pwm

I put it inside the infinite loop that checks the temperature.

I hope that it would be useful to someone.

@flop I'll attempt to wire the pi with a fan and a transistor going to pin 12 (GPIO 18) and I'll report back with findings.

@Wizardling I can't speak to the general design choice for an outward blowing fan in most consumer electronics blow outward. This won't prevent dust accumulation because what goes out must come in somewhere else. This is usually remedied with air filters of some kind.

I use an inward blower and it seems to be working great. My Pi3 generally runs about 20 degrees cooler with the fan. I also use a heatsink applied with arctic silver thermal adhesive so the cooling is quite efficient. I'm not concerned about dust buildup because I just use it for gaming sessions that last no more than a couple hours once or twice a week so I imagine to get enough dust buildup to cause a problem will take years.

Ya, it's nice and keeps things cool... but again, if have a cable (game controller) with a metal end on it, one small touch at the wrong time and ZAP! there goes your board, possible MicroSD Card as well.

Not so much a worry on mine, but I know for sure that the 2 kids will have stuff getting into it, and one of them has a cat. Enough said on that one. :)

@flop said in Fan GPIO and code control:

If your fan makes much noise, you could change the GPIO voltage pin of 5v to 3.3v!.

i dont think thats a good idea....fan draws too much current....