BOTH 3-pin and 4-pin fans CAN be controlled by a motherboard (mobo) OR by a separate fan controller. The differences are in the hows and whys, so let's review.
First, you should recognize that "Control" can have several meanings, although there are only two of particular interest here. The simplest form of control allows you to manually set a fixed fan speed, and it will stay there until you change it. This could be done either by controlling the voltage of the power supplied to the fan (the 3-pin design, see below), or by altering the PWM signal for a 4-pin fan. This is the type of control available from most separate fan controllers, and MAY also be an option for a fan connected to a mobo port.
The other main type is automatic control, more properly a negative feedback automatic control loop, which is what almost all motherboard fan ports offer. In this system there is a temperature sensor that actually measures the temperature of some important point and feeds the information into a fan controller (actually, a software loop contained in the BIOS chip). In addition the controller loop has a Setpoint (the target temperature to reach at the sensor), a Gain setting, and a Zero Offset setting. (These last two may be apparent to the user as something more useful, however. For example, on my machine I get to specify the low temperature below which the fan will shut off, and the high temperature at which the fan will be running full speed.) This feedback controller system constantly compares the actual measured temperature from the sensor to the Setpoint. As the temperature changes, the fan speed is changed to bring the temperature back to Setpoint. It's called a "negative feedback" control loop because the result of the controller's action (the actual measured temperature) is fed BACK to the controller, and its response is to generate an action in the OPPOSITE direction from the changes in the measured variable (higher temperature generates more cooling).
So, the automatic controllers built into mobos constantly change the fan's speed according to what is required by actual measurement. Manual controllers do not do this. Of course, IF you have temperature sensors and readout devices available, you yourself can monitor the temperature you have chosen to watch, and reach down and turn the fan speed control knob. But you probably won't do this every second!
The particular fan controller you linked to has six separate fan control channels, each for one fan and using one manual speed knob. It also has several temperature sensors included that you can mount on your mobo or inside your case, and it will show you those temps. But as far as I can see, it does not provide any automatic control loops - it just shows you the temps, and allows you to adjust fan speeds. NOTE that this system can NOT show you the temperature INSIDE the CPU, which is what most mobos CAN give you. The mobo does this by monitoring a temperature sensor already built into the CPU case by the chip's manufacturer.
So, given that we want to control a fan's speed, how is that done? 3-pin and 4-pin fans accomplish this differently. Hence, the controller system needs to know what kind of fan is being used, so it can send the proper signals.
A 3-pin fan has 3 wires running to it. Pin 1 (Black wire) is Ground of the power supply. Pin 2 (Red) is the + side of the DC supply, and it varies from 0 to +12 VDC. Pin 3 (Yellow) actually takes a signal generated inside the fan motor and carries it back to the controller (mobo or separate controller unit) to be monitored. This signal is a series of pulses - 2 pulses per motor revolution - so just counting the pulses in a fixed time tells you the rotational speed (rpm) of the fan. To control the fan's speed, the controller just changes the voltage supplied to Pin 2, somewhere within the range 0 to +12VDC. Actually, it rarely goes down to 0VDC unless the controller really wants to shut the fan off. You see, a small DC motor like this that is running will probably stall if the supply voltage drops below about 3 VDC. And then, to get it started up again, it will probably require at least 5 VDC. NOTE that, even though the controller has access to the actual fan speed signal, it does NOT use this in any automatic speed control strategy. Fan speed is based on the measured TEMPERATURE of the device being cooled, and not on the actual fan speed. For example, the CPU cooling fan's speed, when controlled by the automatic controller in the mobo, is adjusted according to the actual temperature inside the CPU case, as measured by the sensor inside there.
A 4-pin fan works differently, and it has 4 wires running to it - surprise! Again, Pin 1 is Ground, Pin 2 is +12 VDC, Pin 3 is the speed pulse signal being returned, and the extra Pin 4 is the PWM signal from the mobo to the fan motor. For these fans, Pin 2 is ALWAYS at +12 VDC - it does not vary the way a 3-pin fan's Pin 2 does. (BUT, see later for the exception). Inside the fan motor housing there is a small controller chip that regulates the flow of current available from the Ground and +12 VDC supply lines to the actual motor according to the PWM signal. PWM stands for Pulse Width Modulation. The signal is a bit like a square wave - it is either fully on or fully off - but is different in that the time on / time off ratio changes, and that's what changes the fan speed. This PWM signal is used like an inhibitor - when it is on, the tiny in-motor chip cuts off the current to the motor. When the PWM signal is off, the tiny chip sends the full +12VDC supply to the motor. As the PWM signal switches rapidly on and off, the motor gets a current supply turned off and on, and the result is a speed less than the motor's maximum speed. The big advantage of a 4-pin fan is that it can be controlled to slower speeds than a 3-pin can. Why? because for very low speeds the PWM signal just restricts the current supply to the fan to very short pulses, BUT they are pulses of a full +12 VDC, so the fan keeps getting a strong "kick" every pulse and does not stall so easily. Likewise, a 4-pin fan can be started up at a low signal.
So, a 3-pin fan's speed is changed by altering the voltage of its Pin 2 supply line. A 4-pin fan gets +12VDC all the time on that Pin 2, but the little chip inside the motor case then regulates that according to the % time off of the PWM signal from Pin 4.
Now, the designers of these fans went to some trouble to build in backwards compatibility. 3-pin fans came first. (Actually, 2-pin fans came before that - they just had no Pin 3 Yellow wire to send back a speed pulse signal.) When 4-pin fans were introduced, two things were done. First, the connector on the end of the fan wires is designed so that it will plug into a standard 3-pin fan's port on a mobo, and the first 3 pins on the fan connector are exactly the same signals as the 3-pin system's outlet on the mobo. In this case, the second feature kicks in. The 4-pin fan just gets NO signal on its PWM line, and the Pin 2 signal is not a constant +12VDC - it varies the way a 3-pin fan expects. So the 4-pin fan operates exactly like a 3-pin fan, with no PWM "on" signal to inhibit current flow through the tiny chip inside the fan's case.
Now, how about the other way around? Plug a 3-pin fan into a 4-pin mobo outlet. Now we have that fan supplied with the same signals on the first 3 pins it always expected, EXCEPT for one thing. The supply on Pin 2 is always +12VDC, and the 3-pin fan does not ever receive the PWM signal on Pin 4 (because it could not use it, anyway!), so this fan will run at full speed all the time. Well, at least we get cooling this way, even if it's too much at times.
And here's where we get to the "it depends ..." stuff. A mobo with automatic feedback control supplying a 3-pin fan port will always do its job by varying the voltage on Pin 2, and both 3-pin and 4-pin fans can work with that. But consider the mobos with 4-pin fan ports. SOME of them do as I said above - they operate solely as 4-pin controller systems, and any 3-pin fan plugged into them will always run full speed. SOME mobo makers, however, offer you an option in BIOS Setup for that 4-pin fan port. You can set the controller for this port to use either 3-pin or 4-pin mode, thus making the controller send out the exactly right kind of signal for the fan you have plugged in. And a few mobo makers actually have this adjustment automated - the mobo controller itself figures out which type of fan is plugged in, and adjusts its control mode accordingly. Now that's smart!
For the user, figuring out which way a mobo maker set up a 4-pin fan port is not easy - I often find the mobo manual is unclear on this feature. Sometimes it becomes clear when you actually go into BIOS Setup and examine the port options. Sometimes the mobo maker's Tech Support people can tell you. Sometimes you gotta figure it out yourself.
So, what to do? If you want automatic fan speed control to keep certain parts to a particular temperature, you almost always do this via the fan ports on the mobo. That can become difficult if you have a lot of fans, and not enough mobo ports, but that's a different discussion. On the other hand, if you prefer to do your own fan speed settings and not have them change by themselves, then you probably want a separate fan controller module, and that may allow you more fan control channels.
Which mobo ports to use? First, the one marked CPU_FAN should ONLY be used for the fan cooling the CPU chip. Its control loop is using the sensor built into the CPU case, and it will always adjust the fan speed according to that internal temp. Moreover, SOME mobos add an extra precaution on this control loop. They check the CPU_FAN speed and, if it ever drops to zero (or if there is no fan connected here), they send out an alarm and may shut down the entire machine in a very few seconds! This is to prevent severe overheating of the CPU with no cooling fan running, and the system does not wait for the measured CPU temp to rise suddenly. On systems like this, if you do NOT run your CPU fan from this port, you should go into BIOS Setup for the CPU fan and tell it NOT to monitor that fan and activate alarms based on it.
You will find one or two (occasionally more) mobo ports called SYS_FANx. These are intended for case fans, and they usually are linked to a separate temperature sensor built into the mobo. However, I have seen mobos in which ONE of these was set up with feedback control based on the mobo temp, and the other had no fan speed control - it just ran full speed.
You may find a port called PSU_FAN. The original design here was NOT to control a fan. SOME (not all) PSU's have a set of wires coming out just like the 3 leads from a 3-pin fan, and these should connect to the mobo PSU_FAN port. All this really does is allow the fan inside the PSU to send its speed signal (on the Pin 3 Yellow wire) to the mobo for monitoring. The port does not control the speed of the PSU's fan. IF that fan's speed is under some control, that is done entirely within the PSU itself. However, on many mobos it appears that this PSU_FAN port on the mobo actually has the Ground and +12 VDC lines connected. So, if you do NOT plug into it the leads from the PSU, you can plug in instead a standard 3-pin (or even a 4-pin) fan and it will simply run at full speed all the time.
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