Fan control with external boot

mjf

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I wanted to boot linux on an external HDD and am concerned about the effect on PC cooling.
My PC has a small enclosure with one fan over the CPU & one in the power supply.
The BIOS has Smart Fan enabled. Does anyone know if the BIOS would be controlling the fan regardless of Windows running or not?
 

My Computer

Computer type
PC/Desktop
Computer Manufacturer/Model Number
Own build
OS
Windows 7x64 Home Premium SP1
CPU
Intel i7 2600k
Motherboard
ASUS P8Z68 Deluxe
Memory
G.Skill Ripjaws (DDR3-1600) 2x4GB
Graphics Card(s)
Nvidia GeForce GTS 450; Intel HD Graphics 3000(GT2+)
Monitor(s) Displays
Dell Ultrasharp IPS panel U2311H, Samsung SyncMaster P2350
Screen Resolution
1920x1080
Hard Drives
Samsung 850 Pro SSD 256GB, Samsung SSD 840 120GB, Seagates 1TB Barracuda ST31000528AS x2
PSU
Seasonic M12II 520W
Case
Lian Li Lancool PC-K60
Cooling
Case: 1x120mm, 3x140mm CPU: Hyper 212+
Keyboard
Logitech MK520 (wireless)
Mouse
Logitech MK520
Internet Speed
6-7 Mbps
Antivirus
Norton Security Premium, Malwarebytes on 2 (MSE on 3rd PC)
Browser
FireFox
Other Info
Audio: Logitech Z523 2.1
The Bios normally controls the fan speed. There are programs that you can boost the fan speed with but the Bios itself usually controls the speeds.
 

My Computer

Computer Manufacturer/Model Number
SMN-Productions
OS
Windows 7 x86/x64, Server 2008r2, Web Server 2008
CPU
i7 v2 3930K Steping stone 2
Motherboard
ASUS Rampage IV Extreme
Memory
G.SKILL Ripjaws Z Series 32GB
Graphics Card(s)
AMD HD 5770
Monitor(s) Displays
Acer 21" and Samsung 20"
Hard Drives
Patriot Pyro 80GB
PSU
1000 Watt
Case
HAF-X
Cooling
4 Fans
Keyboard
Black Widow Ultimate
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