As you may know, Bitmain is switching over to an auto-benchmarking/calibration model without any fan speed controls.  I just received a 14 TH/s S9 with auto-freq firmware installed (previously this speed model was fixed frequency).  I added the following to bmminer.conf:

"bitmain-fan-ctrl" : true,
"bitmain-fan-pwm" : "40",

Kernel log shows:
Set fixed fan speed=40
FAN PWM: 40

However it appears to only have affected the speed of the secondary fan (Fan6) while the primary fan (Fan3) is still on auto-speed.

Thoughts?