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Guys, I can't figure this out. I recently built a new rig, one that's going to be a starting point for a future proof one. I ended up going with an Enthoo Pro, and a MSI Gaming Z97-G45 Motherboard, just as a reference for later. 

Anyways, my trouble comes in controlling the case fans. I have my CPU fan plugged into CPUFAN1on my motherboard, and my case fans plugged into the fanhub included with my case, which is then plugged into my CPUFAN2 slot on my motherboard. I was hoping to control them, maybe slow them down and grab a couple extra fans so I could keep my system cold while keeping it quiet, but that hasn't been the case. MSI's included Smart fan controller in the Bios doesn't seem to do anything to change the speeds, giving me a constant readout of around 1300 rpm, and every utility I've tried thus far hasn't seemed to make a difference. 

Just a note, I do not have the fanhub connected with the Sata port, just plugged directly into the Fan header in my motherboard. I also recently tried moving the fanhub to my SysFan port, but that resulted in the fans not even turning on (And it was quiet! but not the point)

All I'm asking is some advice on what I might be doing wrong. I see only two options, one, to someone realize what I've been doing wrong and fix this, or two, to takeout the fan hub and just connect the fans to the sys fan ports on my MB. Which would take time to rewire everything but in the long run might be worth the effort. The only problem I have with that is that I'm currently running 5 fans including my CPU fan, and one of the SysFan ports is near the center of my MB. Not exactly ideal placement for looks, but if I have to I'll live with it. 

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Have you tried speed fan?

The BBQ: i7-4770 / 212x / Tri-X R9 290x 1075/1400 / MSI H87-G43 GAMING / EVGA G2 850W / Corsair Spec 03 / Samsung 840 EVO 250gb SSD / Toshiba 2TB HDD / 8gb Kingston DDR3 1600mhz

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Did you check your bios settings? Might need to enable some of the sys fan ports.

i7 4790k @4.7 | GTX 1070 Strix | Z97 Sabertooth | 32GB  DDR3 2400 mhz | Intel 750 SSD | Define R5 | Corsair K70 | Steel Series Rival | XB271, 1440p, IPS, 165hz | 5.1 Surround
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It's an MSI Gaming ... so it has Clickbios and Control Center. If you don't have those installed yet, by all means do so.

Open Control Center

Go to the Green Power tab

There should be options for CPU and one or more System fans

(that is of course assuming that the Z97-G45 has the same Control Center layout as my Z77A-GD65)

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No, mine isn't set like that, but I did easily find the fan control. I also looked up something interesting with the Phanteks PWM hum that came with the case. Apparently Fan1 on the hub is the fan that outputs i'ts rpm to the PWM signal on the CpuFan header on your motherboard. Truth be told I don't know if I have a fan plugged in there or not. Guess I'll have to open my case to find out. It might explain why the RPM reading in Command Center, and my Bios fan control both read 1300~ RPM (it's currently reading between 1340-1370)

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