How do I control my fan speed?

I don't think you need to control fan speed, actually fan should not make much sound even at high speeds.

If you look at the output of sensors command for my dual-core computer and compare it with yours, you'll find that the fan speed your computer is using is keeping your processors cool, which is important.In my case the processor temp are high but fan speed is low.

Adapter: ISA adapter
Core 0:       +74.0°C  (high = +76.0°C, crit = +100.0°C)
Core 1:       +67.0°C  (high = +76.0°C, crit = +100.0°C)

w83627dhg-isa-0a10
Adapter: ISA adapter
Vcore:        +1.10 V  (min =  +0.00 V, max =  +1.74 V)
in1:          +1.26 V  (min =  +0.05 V, max =  +0.23 V)  ALARM
AVCC:         +3.36 V  (min =  +2.98 V, max =  +3.63 V)
+3.3V:        +3.38 V  (min =  +2.98 V, max =  +3.63 V)
in4:          +1.26 V  (min =  +0.02 V, max =  +0.36 V)  ALARM
in5:          +0.78 V  (min =  +1.16 V, max =  +1.86 V)  ALARM
in6:          +0.88 V  (min =  +0.28 V, max =  +0.02 V)  ALARM
3VSB:         +3.39 V  (min =  +2.98 V, max =  +3.63 V)
Vbat:         +3.31 V  (min =  +2.70 V, max =  +3.30 V)  ALARM
fan1:           0 RPM  (min =  405 RPM, div = 128)  ALARM
fan2:        1110 RPM  (min = 6490 RPM, div = 8)  ALARM
fan3:           0 RPM  (min = 1054 RPM, div = 128)  ALARM
fan4:           0 RPM  (min = 10546 RPM, div = 128)  ALARM
fan5:           0 RPM  (min = 10546 RPM, div = 128)  ALARM
temp1:        +38.0°C  (high = +64.0°C, hyst = -43.0°C)  sensor = thermistor
temp2:        +58.0°C  (high = +80.0°C, hyst = +75.0°C)  sensor = diode
temp3:        +42.5°C  (high = +80.0°C, hyst = +75.0°C)  sensor = thermistor
cpu0_vid:    +0.000 V
intrusion0:  ALARM

aditya@aditya-desktop:~$ 

I'll suggest you to check if the hardware installation of fans is correct(either yourself or from some expert). The sound should vanish by little bit tweaking.If it doesn't work then you may consider decreasing the fan speed by using fancontrol

WARNING
Please be careful when using the fan control features of your mainboard, in addition to the risk of burning your CPU, at higher temperatures there will be a higher wearout of your other hardware components, too. So if you plan to use these components in 50 years, maybe you shouldn't use fancontrol at all. Also please keep in mind most fans aren't designed to be powered by a PWMed voltage. In practice it doesn't seem to be a major issue, the fans will get slightly warmer, just be sure to have a temperature alarm and/or shutdown call, in case some fan fails, because you probably won't hear it anymore ;)

How to use Fancontrol

• First install fancontrol

  sudo apt-get install fancontrol
  

• Use pwmconfig, an script to manage fancontrol

  pwmconfig
  

  Now follow the instructions to configure your fan speed.