The problem
If you're using a PWM controlled fan with a low minimal speed together with a Supermicro motherboard there's a good chance that the fan speed will be go up and down the whole time, while the system generates lots of critical fan alerts.
The reason for this is that these boards are build for servers in a datacenter, and these machines would overheat fast if their often small but very fast turning fans would stop working.
The solution
You can use IPMI software to change the lower fan speed limit to a lower value.
with ipmitool:
# Find the right fan
ipmitool -U <USERNAME> -H <KVM-IP> sensor
# Set a lower minimal speed limit for FAN1
ipmitool -U <USERNAME> -H <KVM-IP> sensor thresh FAN1 lower 150 225 300
With impi-sensors-config (part of FreeIPMI):
ipmi-sensors-config --filename=ipmi.config --checkout
vi impi.conf # change fan thresholds
ipmi-sensors-config --filename=ipmi.config --commit