I don't think you quite understand Macs Fan Control. Each fan is controlled separately.

IMac HDD Fan Control is an HDD fan control for the Mac operating systems by using which the Mac users can control the speed and noise of the fan of the Mac. IMac HDD Fan Control basically provides a full control to the users over the fan of their Mac operating systems.

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A MBP only has two fans. If you want them to both work the same, then you should select the same sensor - The CPU sensor that typically runs hotter.

You will see that in the configuration window. Then set the 'kick in' temperature to around 40º C. Do this for each fan. Configuring SMC Fan Control is just as easy but is done based only on setting the base fan speed. SMC Fan Control is only capable of setting the idle fan speed. That may be a better choice for a laptop than Macs Fan Control, but you should try them out before deciding which you prefer. As for iStat Menues you do not have to switch profiles.

Create your desired profile as the 'Default' profile or the 'Medium' profile, select that profile as the default, then Save your settings. There is no need to switch them to anything. I use iStat to set the fans on my iMac and I never need to change them. Both cores are contained in a single chip, so the object is to cool the chip. Tying to the hotter of the two cores assures that core won't overheat because the other core is cooler. On the computer I have that uses Macs Fan Control that is how I set it up.

I don't know if Mac Fan Control acknowledges one fan for the CPU and one for the GPU, but if so, then, yes, I would set it up separately. SMC Fan Control is essentially the same as iStat Menues. Personally, the internal fan control contained in the SMC chip in your computer is adequate to assure that the CPU and GPU do not overheat. I wouldn't recommend using any such software and trust that the Apple engineers know what they are doing. Laptops run hot because they are small, thin, and light. There isn't much room inside to provide huge cooling devices.

Apple's manuals tell you not to use them on your lap because of the possibility of burning your thighs or causing overheating damage to the computer. Apple does not even refer to them as 'laptops.' They are called 'Notebook' computers. They also are not gaming machines. Although you can play some games on them any game that makes heavy demands on the processors will cause them to become uncomfortably hot unless you take external cooling precautions. Personally, the internal fan control contained in the SMC chip in your computer is adequate to assure that the CPU and GPU do not overheat. 😁😁😁😢😢😢 Personally I LOL about 'protection from Apple'.

I have an iMac 27' 2010 late and GPU breaked for overheat. The iMac is Out of warranty, so, I send my iMac for a 'Reballing' GPU and now it is working again. I process every day 2 video and GPU Goes to 79ºC during converting video tu mp4.

Apple engineers not put fans to max rpm for break hardware! If i Use iStat and put to MAX fan rpm the GPU goes down to 52ºC, a very safe temperature for work and i don't think about noise, simply is better for my iMac work with less temperature. Apple Suck one more time. And better not speak about Apple Care and putting refurbished components like Panels. I don't want an iMac for gaming. Apple have the best publicity in Media, Video and Photo, but his hardware work at too high temperature and the life of components shorted at high temperatures.

Another way software for control fans is the better solution to work with low temperatures. Sorry my bad english but I am from Europe, Spain. I bought a used 2011 iMac, and the HD fan was running all-out all the time. (Typical problem with this vintage, whenever a non-Apple HD was installed without a special temp sensor cable.) SMC Fan Control didn't solve the problem, but Macs Fan Control did it nicely - and it let me link the fan speed to the HD temperature, the way it should be. The two cores are in the same chip, so there won't be more than a degree of difference between them - it won't matter which you choose.