What fan mode are you using? It appears that all fans are running full-speed so you either have the fan mode set to "Full" or the thresholds are wonky and the BMC has panicked and is running all fans at full.
Looks like your running in a Fractal node 804. This case is a "Dual-Zone" case with a zone for the system (main) board and another zone for the hard disks.
One issue is that, if the X11SSL has two zone cooling, it is likely setup like similar boards in that FAN1-FAN4 are controlled by CPU temperature as is FAN-A except in "Optimal" and "Heavy-IO" modes where the FAN-A header is separately controlled by an additional thermal sensor usually located on the system-board close to the PCIe slots. This seems to be designed so that you can have a separate cooling zone to accommodate expansion cards that get hot such as GPUs or HBAs/RAID controllers. So the dual-zone controller on the motherboard is unlikely to work well in the dual zone case you have.
4-wire fans have 4 leads; 12V, Ground, TAC & PWM. The first two and the last are outputs and provide power and the speed signal to the fans and so can have multiple fans connected to them. The third line, TAC, is the tachometer signal, and is input from a connected fan that tells the motherboard at what speed the fan is rotating. This can only be extended from a single fan. That is why one of the fan connector on your "Y" connector has three wires and the other four. The one with the four wires is the one which will provide the connected fans speed to the motherboard.
Yes, you need to adjust the FAN thresholds more. I would use 1800, 1900 and 2000 for your upper thresholds as you already have one fan running at 1500 rpm so that may be causing the BMC to panic (see the alerts in the IPMI management) and force the fans to full speed.
Your lower thresholds should likely be fine but I'm not certain if zero is a valid value.
Have you tried rebooting your BMC from IPMI? - this will sometimes fix things.
The
Noctua NF-F12 PWM fans as well as the
Noctua NF-A14 PWM fan are both rated for:
300rpm +/- 20% so 240-360rpm minimal speed
1500 +/- 10% so 1350-1650rpm maximum speed OR 1200 +/-10%, so 1080-1320rpm maximum speed with the Low Noise Adapters (LNA)
Take these values with a healthy dose of salt and look at how they actually perform.
If I was using that case I would likely:
1. Put your "FAN-A" in the lower left position and not in the top of the case. Why? Because you have an LSI HBA chip on that board, at the bottom front, and it WILL get hot and is, aside from the CPU, the only thing in the hot zone you need to worry about keeping cool. Yes there is the PCH, VRM, DIMMs etc. but they will all survive most ambient temperatures and can, in normal circumstances, just be ignored. Try to visualize the airflow through the case as if you pass smoke through it so you could see it (don't do this please, I've looked inside cases of smokers and it's nasty) The best airflow is a direct path, in the front and out the back and this is the assumption most cases are built with. Top fans positions are usually meant for water coolers for gaming rigs and bottom fan positions for providing airflow for hot GPUs and I/O Cards.
The exception may be for the hard drive area where the fans might work better pulling hot air out from above the hard drives. Again - test while your system is under load.
2. Connect all the fans in the hot zone to FAN-1 through FAN-4 and run them using "Optimal" then they will be controlled by the CPU temp and should run slowly. If they are too loud then use the speed limiters provided with the Noctuas to drop them down a notch.
3. Connect the fans in the HDD zone to the FAN-A connector and use a script to monitor the HDD temperature from the SMART info to control the fans and tweak as necessary
OR just use a Y connector and connect them to the case's voltage-controlled fan speed controller. Start at the lowest setting and run a scrub or other utility that makes the disks run hard for at least 20 to 30 minutes for the heat to soak in and check the SMART data and see how hot the disks are. If there mostly at or below about 40C (season to taste here) then your good. If there still a little too hot then try the next higher speed setting and repeat until satisfied.
My Define R4 case is so silent under load that you can't tell that it is running especially since I disconnected the annoyingly bright blue power LED from the power lead and connected it to the FAN Fail/Pwr Problem LED. This works for me but I'm not certain what your design goals are. My NAS is buried in my basement and serves media to the house so it doesn't have to be pretty or quite. I assume that most people who buy the smallish cases are space-constrained and need to have to NAS situated in a livable space in the house and thus are willing to trade-off function to get form.