Question Confused by fan hub - help!

Mar 27, 2025
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Greetings. I'm preparing for a new build, and I am completely confused by how to setup my case fans with the fan hub that came with my case. I have three 3-pin DC fans, and of course I have my CPU cooler. The fan hub that came with my case has six 3-pin headers, and three 4-pin PWM headers; one of the 4-pin headers is indicated as the Main/CPU 4-pin PWM fan with the RPM reported to the motherboard.

I would like my fan speeds to vary based on the case temperature, but I really have no idea how to set these up properly to achieve this result. Should I plug my CPU cooler into the motherboard's CPU_FAN header or the fan hub? Since the 3-pin fans are DC, does it matter whether they are plugged into the fan hub or the fan headers on my motherboard? Last but not least, how do I know which fan mode to set in my BIOS?

As you can see, I'm totally confused when it comes to proper fan setup with a fan hub. :) Thanks for any assistance!
 
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Thanks for the reply! Case is a Fractal Design Refine 7 and the motherboard is an MSI Tomahawk X870E.

EDIT: I just noticed a typo in my original post - the fan hub came with my CASE, not with the motherboard. Sorry about that. I will edit it to correct it.
 
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You should not make connections based solely on the labels of that fan hub in the case, and I'll explain why and how.

The fan headers on your mobo can be divided into two similar groups that differ in one important detail. Every header does its job of controlling its fan's speed according to an actual temperature measurement by a sensor. The CPU_FAN header uses ONLY the sensor called CPU Core actually built into the CPU chip, so of course you want to use THAT header to connect your real CPU cooler fan. All of the SYS_FAN headers will give you an option in their respective configuration screens to use EITHER that same sensor inside the CPU chip, OR a different sensor on the MOBO that is a much better measure of cooling needs of all the mobo components. Normally each of these will be set to that Mobo sensor, but you can check to be sure. (The header labelled PUMP_SYS1 CAN be used as a SYS_FAN header OR as a PUMP header for AIO cooler systems. Unless you have a liquid-loop AIO system with a radiator, you do not need to use this header for a pump.)

So your Case Ventilation fans (the three included with that case) should be controlled by a SYS_FAN header. To do that you should connect the cable from the Hub unit (see case manual p. 20, item on the far right) to one of the mobo SYS_FAN headers. Then plug in the three 3-pin case fans to 3-pin outputs of the Hub. Do NOT connect your CPU cooler fan to this Hub. Connect that, instead, directly to the CPU_FAN header. This will ensure that the CPU cooler is guided by the real internal CPU temperture, and the case ventialtion fans are all guided by the temp sensor on the mobo.

There is one small "glitch" that this might cause. Doing as above sends NO fan speed signal to the Hub's Main / CPU Fan output, so the hub will report to its SYS_FAN host header NO fan speed. That header monitors the speed signal for possible fan failure, and may show you an alarm that your case fan has failed. This is a false warning. In fact, becasue all your case fans are connected via that Hub, the mobo can NOT monitor the speeds of ANY of those three for you. So, from time to time YOU should merely look to verify they all still are working.

If yo do not have it yet, download the manual for BIOS Setup adjustment from here

https://download-2.msi.com/archive/mnu_exe/mb/AMDAM5800BIOS_English.pdf?utm_source=msi&utm_medium=qr-code&utm_campaign=MB_UserGuide&utm_term=BIOS&utm_content=Manual Link

See p. 5 for how to enter BIOS Setup. Basically when you start up, immediately press and hold down the "Del" key until the Setup opening menu appears (p6). Use the F5 key to reach the Hardware Monitor section (p. 18). See p. 19 for the details of the fan header configuration screen. At upper left you select which header you are working on. For each one you work on, start at bottom centre and click on All Set Default. For the CPU_FAN header and most CPU cooler fans, the default settings as shown in the manual should be correct. For the one SYS_FAN header you use to connect the Hub you need to make some changes.
1. At upper centre-left UNset the marker for Fan Type Auto Detect amd then below that set to PWM. This is becsue the "Auto Detect" system relies on what fan speed readings the header receives, and in your case that will be NO speed signal, so it will get its setting wrong! Then you set to the correct PWM setting for what that Hub needs as input. (The hub, presumbaly, "translates" the PWM speed signal it gets from the header into the correct Voltages output to its 3-pin fans for speed control.)
2. To right of centre, second from top, set the Temperture Source Select to Motherboard or System, NOT to CPU Core. When done, use the "X" at top right corner to return the the Main Menu (p.6). There on the top right corner click on the tiny box with the "-" sign to get to the Exit Menu (p. 66). There choose Save Changes and Reboot.

When this all is done, the CPU cooler fan will be automatically controlled according to the temperture inside the CPU chip, and that fan's speed signal will be shown in BIOS Setup (and in the MSI Centre software tool) and montoired for possible fan failure. The three case ventilatioon fans will be controlled together through the Hub by the SYS_FAN header in use guided by the other temp sensor on the mobo. But you will not "see" any case fan speed anywhere, nor can they be monitored for failure.

IF you actuallly want to see case fan speeds and have them monitored for failure, that CAN be done by connecting each fan to its own individual SYS_FAN header and configuring all of them to the same cooling strategy, BUT setting the fan Type to DC rather than PWM. You have six SYS_FAN header available for this. This way does not use the Hub at all. If you need more details on this way, post back here.
 
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You should not make connections based solely on the labels of that fan hub in the case, and I'll explain why and how.

The fan headers on your mobo can be divided into two similar groups that differ in one important detail. Every header does its job of controlling its fan's speed according to an actual temperature measurement by a sensor. The CPU_FAN header uses ONLY the sensor called CPU Core actually built into the CPU chip, so of course you want to use THAT header to connect your real CPU cooler fan. All of the SYS_FAN headers will give you an option in their respective configuration screens to use EITHER that same sensor inside the CPU chip, OR a different sensor on the MOBO that is a much better measure of cooling needs of all the mobo components. Normally each of these will be set to that Mobo sensor, but you can check to be sure. (The header labelled PUMP_SYS1 CAN be used as a SYS_FAN header OR as a PUMP header for AIO cooler systems. Unless you have a liquid-loop AIO system with a radiator, you do not need to use this header for a pump.)

So your Case Ventilation fans (the three included with that case) should be controlled by a SYS_FAN header. To do that you should connect the cable from the Hub unit (see case manual p. 20, item on the far right) to one of the mobo SYS_FAN headers. Then plug in the three 3-pin case fans to 3-pin outputs of the Hub. Do NOT connect your CPU cooler fan to this Hub. Connect that, instead, directly to the CPU_FAN header. This will ensure that the CPU cooler is guided by the real internal CPU temperture, and the case ventialtion fans are all guided by the temp sensor on the mobo.

There is one small "glitch" that this might cause. Doing as above sends NO fan speed signal to the Hub's Main / CPU Fan output, so the hub will report to its SYS_FAN host header NO fan speed. That header monitors the speed signal for possible fan failure, and may show you an alarm that your case fan has failed. This is a false warning. In fact, becasue all your case fans are connected via that Hub, the mobo can NOT monitor the speeds of ANY of those three for you. So, from time to time YOU should merely look to verify they all still are working.

If yo do not have it yet, download the manual for BIOS Setup adjustment from here

https://download-2.msi.com/archive/mnu_exe/mb/AMDAM5800BIOS_English.pdf?utm_source=msi&utm_medium=qr-code&utm_campaign=MB_UserGuide&utm_term=BIOS&utm_content=Manual Link

See p. 5 for how to enter BIOS Setup. Basically when you start up, immediately press and hold down the "Del" key until the Setup opening menu appears (p6). Use the F5 key to reach the Hardware Monitor section (p. 18). See p. 19 for the details of the fan header configuration screen. At upper left you select which header you are working on. For each one you work on, start at bottom centre and click on All Set Default. For the CPU_FAN header and most CPU cooler fans, the default settings as shown in the manual should be correct. For the one SYS_FAN header you use to connect the Hub you need to make some changes.
1. At upper centre-left UNset the marker for Fan Type Auto Detect amd then below that set to PWM. This is becsue the "Auto Detect" system relies on what fan speed readings the header receives, and in your case that will be NO speed signal, so it will get its setting wrong! Then you set to the correct PWM setting for what that Hub needs as input. (The hub, presumbaly, "translates" the PWM speed signal it gets from the header into the correct Voltages output to its 3-pin fans for speed control.)
2. To right of centre, second from top, set the Temperture Source Select to Motherboard or System, NOT to CPU Core. When done, use the "X" at top right corner to return the the Main Menu (p.6). There on the top right corner click on the tiny box with the "-" sign to get to the Exit Menu (p. 66). There choose Save Changes and Reboot.

When this all is done, the CPU cooler fan will be automatically controlled according to the temperture inside the CPU chip, and that fan's speed signal will be shown in BIOS Setup (and in the MSI Centre software tool) and montoired for possible fan failure. The three case ventilatioon fans will be controlled together through the Hub by the SYS_FAN header in use guided by the other temp sensor on the mobo. But you will not "see" any case fan speed anywhere, nor can they be monitored for failure.

IF you actuallly want to see case fan speeds and have them monitored for failure, that CAN be done by connecting each fan to its own individual SYS_FAN header and configuring all of them to the same cooling strategy, BUT setting the fan Type to DC rather than PWM. You have six SYS_FAN header available for this. This way does not use the Hub at all. If you need more details on this way, post back here.
Thank you for the incredibly detailed and helpful response. So, even though my case fans are DC fans and not PWM fans, I should still select the PWM setting in my BIOS? And the fans will still adjust their speed based on the case temperature?
 
Yes, set the header that feeds signals to the Hub to PWM. This goes back to the details of the differences of design for 3- and 4-pin fans, which each need DIFFERENT signals for control. That Hub is designed to send the correct signals to each type, and hence has separate groups of outputs. What it does for the 4-pin outputs is merely forward to those fans the PWM signal it receives from the host header. But for the 3-pin fan outputs it "translates" that PWM signal in the proper variable Voltage signals such fans require.

Any mobo fan header can accept from its fan the speed signal (a series of pulses to be counted) from only one fan. So any Splitter or Hub will send back to its host header only the speed of ONE of its fans and ignore all the rest. On your particular Hub the only output that can feed back its fan's speed signal is No. 1 which is for a 4-pin PWM-type fan. You will not be plugging any fan into that. You have only 3-pin case fans to plug into other Hub outputs. That is why I noted the "glitch" that MAY give you a false warning that the fan(s) connected to that header (via the hub) are not working.
 
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I have three 3-pin DC fans, and of course I have my CPU cooler.
Case is a Fractal Design Refine 7 and the motherboard is an MSI Tomahawk X870E.
Your motherboard has cpu, pump fan headers and 6 system fan headers.
You have plenty of fan headers to connect all fans without use of a fan hub.

3pin fans have to be regulated in DC mode.
4pin fans have to be regulated in PWM mode.