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The motherboard (Gigabyte Z77-D3H) controls my 3-pin CPU fan just fine. My system fans are a 3-pin fan (plugged into SYS_FAN1), and a 4-pin fan plugged into SYS_FAN3. All 3 of the system fan headers are 4-pin, but the user manual states that SYS_FAN1 is really a 3-pin header (that it can control the speed of a 3-pin fan) and the 4th pin is just a reserve. All my fans have a max RPM of 2000.

Normally, all the fans run around 1000 RPMs when I'm not doing anything intensive. This proves that the motherboard can set the speed. However,when I run Folding@Home and my temperatures increase (around 70C) only the CPU fan increases to around 2000 RPMs. The system fans stay around 1000 RPMs. Through the BIOS I am able to disable the system fan control and the system fans then run at max RPMs (meaning the motherboard was doing something).

I've updated the BIOS to the latest version and tried out Speedfan, but neither helped my situation. What I'd like is for the system fans to ramp up their RPMs as needed. Any thoughts?

Tl;dr: My system (case) fans, but not my CPU fan, are always stuck around 1000 RPMs out of 2000 no matter the temperature. I have both voltage (3-pin) controlled and PWM controlled (4-pin) fans plugged into my motherboard as system fans.

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What's the system temps like? maybe they arn't speeding up cause the system dosen't need it? –  Journeyman Geek Oct 22 '12 at 3:17
    
@journeyman With F@H running I'm hitting around 70C. I believe they should be speeding up because at that temperature my CPU fan is at maximum RPMs. –  Andrew Oct 22 '12 at 4:46
    
PWM requires a 4-pin connector. allpinouts.org/index.php/… –  Aki Oct 22 '12 at 6:47
    
@Aki One of my system fans is a 4-pin plugged into a real 4-pin header. Still doesn't change RPMs. –  Andrew Oct 22 '12 at 11:03

2 Answers 2

The case fans have nothing to do with cooling the CPU. That's a job for the CPU fan. The case fans merely circulate air by introducing fresh outside air, and exhausting stale, hot air. Thus, what you're experiencing seems right. The CPU fan increases speed to keep CPU cool, but the system temperature (not CPU temperature) is not high enough to trigger increase in case fan speed. If you operated your PC in a hot environment, the case fan speed should (assuming your motherboard has a "system" thermal sensor) increase.

This is the general rule of thumb. Of course, different manufacturers may have different cooling control systems implemented into their BIOS. Harrymc's answer is valid too

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The thread Motherboard fan controller only controlling one fan discusses your problem.

The conclusion there is that this is an built-in limitation, so that, as you observed, only the system fans are controllable :

only sysfan1 can be voltage controlled, while 2 and 3 are PWM controlled. As your fans can only be voltage controlled, only fan plugged as sysfan1 can be controlled.

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