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I think this might be what you are looking for... I changed the critical thresholds down and now fan noise is much lower.
https://twiki.cern.ch/twiki/bin/view/FIOgroup/IpmiWinThresholdTune
Sorry to necro this thread, but I found this via a somewhat-related google search, and thought I'd point out that this is backwards. Per Supermicro:The 5 fan headers on the X9SCM-F all have independent RPM feedback, but only two PWMs are actually used to control them. FANA (for the CPU) is on PWM1 and FAN1 to FAN4 is on PWM2.
FANA is for add-on card and controlled by system temperature. FAN1~4 is controlled by CPU temperature. CPU Heatsink fan should not be connected to FAN-A. CPU Heatsink fan can be connected to FAN-1. Chassis fans can be connected to FAN-2~4 or FAN-A.