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Specs:

Ryzen 5600X

CM EVO 212

Radeon 5600XT

32GB Corsair Vengence 3200

Corsair RM650

MSI B550 A-Pro

Rosewill Tyrfing

 

Situation:

This morning I was moving some fans around in my case and decided to strip the fan out of the stock Wraith Stealth cooler and use it as a case fan. I removed the heatsink and shroud and plugged it in to a SYS_FAN header on the mobo. When I rebooted the fan spun but the EZ debug light was stuck on the CPU and the system wouldn't post. I unplugged the fan, tried again same issue. I cleared CMOS, tried again, EZ debug stuck on DRAM. I reseated all the RAM, and this time the system booted.

 

Before I try this again, I just want to make sure that it's safe to plug in a CPU cooler fan into a regular system fan header long term. I know the CPU fans spin faster but I'm not sure if that's something the mobo regulates based on which fan is plugged into what header, or if the fans themselves use different voltages.

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https://linustechtips.com/topic/1269164-plugging-cpu-fan-into-sys_fan-header/
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It's safe. 

All fan headers do the same thing, and have the same amount of current capability. Some fan headers that say pump so for water cooler pump may have a slightly higher current rating.

 

Some motherboards have some differences in the sense that they treat some fan headers in a special way.

The header called CPU_FAN may be monitored by the BIOS and the BIOS may give you a warning message if it doesn't detect a fan spinning.  It may also be controlled directly by the bios, adjusting fan speed as the cpu temperature changes.

 

Headers like CHASSIS / CHA_FAN are usually 'dumber', in the sense that they may be only 3 pin headers, or the bios can't control fan speed or you can't set fan speed from Windows. They're made to be for fans you put on case, which spin always at same rpm, silent etc...

 

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