It's not clear exactly what you want. As Ralston18 said, full details of your system and intentions would help greatly. You should recognize that any fan that has LIGHTS in its frame is really TWO devices in one unit. There is a MOTOR that spins the fan, and separately there are LIGHTS in the frame. On most current fans there are separate cables with different connectors for these two devices and they go to different mobo headers. SOME non-standard fan systems combine the two cables into one and thus require their own matching connections to proprietary controller ports.
To start, understand how fan MOTORS are controlled.
First, there generally are two different "groups" of fan headers on mobos. ONE is strictly for the CPU and associated devices. It is always guided by the temperature sensor built into your CPU chip. (For some CPU's, there is another related sensor in the chip socket.) This "group" will include CPU_FAN and possibly CPU_OPT and AIO_PUMP. SOME mobos have a header that can be set at your choice to be a PUMP header or a general SYS_FAN header. Generally, a PUMP header does NOT attempt to control its unit's speed because most pumps are designed to operate at full speed all the time. The other "group" is all the others, called SYS_FAN or CHA_FAN, used for CASE ventilation. All of them are guided by a temperature sensor on the motherboard, but very often include an option on each such header to select instead the CPU chip's internal sensor in case you need to use this header for CPU cooling needs. SOME mobos also include other temp sensors on specific mobo components like the Voltage Regulator and North Bridge, etc. and these can be used IF you are dedicating one fan to that particular component.
On some older mobos you might encounter a header called PWR_FAN. These were used only for a feature now obsolete. Some PSU's came with a set of wires coming out that ended in a common 3-pin fan female connector. These carried the speed signal from the cooling fan inside the PSU and the intent simply was to allow the mobo to read that speed and show it to you when you asked for it. This header did no control that PSU fan - the PSU itself did its own cooling control. Further, this header did not normally provide power to anything, BUT some mobo makers did wire it to provide a fixed 12 VDC supply line with no variability so it could power a fan at constant full speed. Unless you have a PSU with those wires, do not use this mobo header.
For each header in general the default PROFILE is to automatically adjust the fan speed according to the current reading of the temperature sensor for that header. Normally there is a default "fan curve" specifying what speed to run for what measured temp, and very often there is another option called "Custom" or "Manual" in which you can specify your own "fan curve". NOTE that this system does NOT aim for a fan SPEED, although it is the speed it manipulates. Its aim is the TEMPERATURE and speed is changed to whatever it takes to get there. In fact, although the speed is measured and displayed for you, that info is not even used for this control process.
The speed signal IS used, however, for an important secondary function. The header monitors that speed signal for NO signal (or, in some cases, a speed below some specified minimum) that indicates the fan has FAILED. When that happens you get a prominent error message on screen so you know it needs fixing. In the particular case of the CPU_FAN header (and maybe others in its group) many mobos are much more aggressive on failure detection. They may actually shut down your entire system in a short time to prevent overheating and damage to your valuable CPU chip without even waiting for the temp sensor to show high readings. They may also refuse to allow a start-up if there is no speed reading signal at that header immediately on start-up.
In each fan header among the PROFILE options often you have other choices like a fixed low speed for quiet, a fixed full speed for max cooling, and sometimes a fixed speed you select manually.
Header options also include items for MODE and Temperature Sensor Source. PROFILE (above) is how the system decides what speed the fans should run. MODE is the type of signals sent to the fan to achieve that speed. This is because fans today come in two different types. An older 3-pin fan's speed can be controlled ONLY by varying the VOLTAGE supplied to it - option is called Voltage or DC. A newer 4-pin fan or PWM fan is supplied with a constant 12 VDC power supply, rather than varying its voltage. Then it also receives a PWM control signal from Pin #4 of the header. Inside that fan there is a small chip that uses the PWM signal to modify the flow of current from that fixed 12 VDC source through the motor windings to achieve speed control. This fan type also CAN be controlled by the older Voltage Control Mode signal system, but using the newer PWM Mode is much preferable.
An older fan header has THREE pins. Pin #1 is Ground, Pin #2 is the +DC Voltage supply that can vary from 12 VDC for full speed down to about 5 VDC minimum for lowest speed without stalling. Pin#3 is the speed signal sent from the fan back to the header. It is a series of 5 VDC pulses (2 pulses per revolution) and the header simply counts them to display speed. The header has a plastic "tongue" sticking up beside the pins and the female connector on the fan motor wires has two ridges down one side that fit around that tongue. So there's only one way to plug in. This header type can function ONLY in the older Voltage Control Mode.
For the newer 4-pin system, those first three pins are almost the same - Pin #2 here is constantly +12 VDC instead of being variable. Then there is the added Pin #4 (outside the range of those ridges on the side of the connector) with the PWM signal.
The mechanical and electrical characteristics of these two systems are VERY similar so you CAN plug either female connector into either mobo male header type. In almost all mobos now you will find only 4-pin male headers. But in the configuration options for each header you can choose whether it behaves as an older 3-pin Voltage Control Mode header, or a newer 4-pin PWM Mode header. If you MISmatch them this is what happens. Plug a 3-pin fan into a 4-pin header set to PWM Mode and it gets a constant 12 VDC power supply from Pin #2 but does NOT receive the PWM control signal. (It has no chip for that, so it could not use it anyway!) So that fan runs full speed all the time - you get lots of cooling with no reduction. Plug a newer 4-pin fan into a header using older Voltage Control Mode and it gets no PWM signal so its chip cannot modify power flow. But the VOLTAGE it gets from Pin #2 IS varying from 12 down to 5 VDC, so its speed IS controlled that way.
There are ways to connect more than one fan to a single mobo header (below). But a header is designed for one fan, so it has limits. First, it normally can supply power up to 1.0 A max current. MANY modern fan MOTORS can operate on 0.10 to 0.25 A max current, so it is OK to connect a few such fans to a single header. (NOTE that for most LIGHTED fans now the lights are fed and controlled from separate headers, so the current limit of the MOTOR header applies only to the MOTOR load of the fan unit.) Secondly, the speed pulse counting system for Pin #3 can deal with the pulse signal coming from only ONE fan. So any system to connect more that one fan means that system MUST send to the header only one fan's signal, and ignore the speeds of all others.
There are three ways to connect multiple fans to a single header. SOME fans are built for a DAISY CHAIN system. EACH has both a female connector for input from the mobo header, and a male output to be used to plug in the next fan in the chain. Most fans are not built this way.
A simple device is a SPLITTER. It just connects all its fans together in parallel for the Ground and +VDC power supply lines, and connects the Pin #3 (speed signal) line of only ONE output to the host header. ALL power for the fans comes from the header with its current limit. All of the fans receive exactly the same power. IF they are identical they all will operate at nearly the same speed; if they are different their speeds may not match, but that really does not matter. Remember, the control is based on a measured temperature, not on the actual fan speed.
The third method is a different device called a FAN HUB. It is similar to a Splitter BUT it gets all power for its fans directly from the PSU via a separate cable connection to a SATA or 4-pin Molex power output connector. So at its output male connectors, it feeds Ground and 12 VDC power lines to all its fans from the PSU and draws NO power from the mobo header. Thus it is NOT subject to the header current limit. (There is a much larger limit from the PSU source, but it is hard to reach that limit with many fans.) The Hub connects all its fans' PWM lines to the host header's signal from Pin #4, but this does NOT overload the ability of that header line. Again, it feeds back to the host header on Pin #3 the speed signal of only ONE of its fans - the one plugged into the marked output connector. So all the fans on the Hub get the SAME PWM signal and will do the same thing, just as a Splitter will do. HOWEVER, note that the HUB is designed to control fan speeds ONLY by distributing the PWM signal from the host header. So it can be used ONLY when the host header is operating in PWM Mode, and it can be used ONLY with 4-pin PWM fans that CAN use that control signal. I will note that there is on the market one unique "Universal" Hub design that can be used with BOTH 3-pin adn 4-pin fans and headers.
Both Splitters and Hubs may appear to be a collection of cable "arms", a small printed circuit board (may need mounting to be sure it does not short out a contact), or a closed box with ports recessed in holes. You cannot tell the difference from those appearances. You also cannot tell the difference from the NAME the seller applies - the all tend to use the two names interchangeably even though they are very different devices! What IS different is that a SPLITTER has only TWO types of connections - one cable to the host header, and several outputs for fans to plug in. A HUB has those PLUS a THIRD connection to a PSU output for POWER to the fans.
As I said initially, LIGHTED fans these days are two devices in one unit. Power and control of the LIGHTS is another topic with its own quirks I have not dealt with here. Suffice to say the lights normally must connect to a mobo header OR to a separate third-part Controller box that matches the light design, and there are Splitters and Hubs for LIGHTS also (different from the fan motor devices). Further, there now are many combo units on the market that combine BOTH a MOTOR Splitter or Hub with a LIGHTING Splitter or Hub in the same box or circuit board.
So, OP, you want control of many FANS - motors only, not interested in lights. Given how those are powered and controlled basically by mobo headers with some limits, you need to define what you want to achieve more clearly. One header can control only ONE fan uniquely - if you connect more than one fan to it, all those fans get the SAME control signals. And in such a connection, you can "see" the speed of only one of them. If you use a simple SPLITTER or a DAISY CHAIN system, the header has a limit of max 1.0 A current to the total load. If you choose a HUB you can avoid that current limit, but then it works only with more modern 4-pin fans.
You want "software control". Virtually all mobo header systems can be configured (each header individually) within BIOS Setup, but that can be done only in that utility and settings are fixed until you re-do them. There are third-party software tools available that run under Windows (or sometimes other OS) that allow you to examine and configure all these header details when running in the real world. But in fact, virtually all of those actually do their jobs by changing the options of each mobo header, and leaving the actual control work to that header. They simply make it easy to access those header settings at any time. Further, almost every mobo comes with such a utility supplied free on its CD full of accessory tools and device drivers. Look for that first and try it out before looking for third-party tools.
IF you want individual control of many fans, you MAY be able to do that for a few if your mobo has enough headers to allow one fan per header. Or maybe a few SMALL groups. BUT IF you need totally separate control of each fan and do not have enough headers, then you can look for third-party Fan Controllers. These are separate modules you can install. Most use their own control panel and manual knobs or buttons to set fan speeds but do NOT have a means to do automatic control according to temperatures measured by the mobo sensors. Access to those sensor readings is tricky. A FEW of these may supply their own sensors that YOU mount, but then you need to know WHERE to mount, and WHAT is the right target temperature for that spot. There may be some such units that can be used with a proprietary software utility rather than front-panel buttons - I don't remember seeing such.
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