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I'm running Debian (Raspbmc). I have a number of external hard drives connected via USB. These HDD are powered by an external power supply.

Since I often fall asleep while watching movies, I want to automatically shut down my machine after 2 hours. This is not a problem with the machine (Debian) itself , but my external HDD are still running and are extremely loud. Is there any way I can't stop these HDD from spinning via the OS? And is this safe (since there is still a running power source)?

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I am not sure how well this works via USB, but you might be able to use hdparm -S 241 /dev/sdX to let external SATA drives spin down if they are idle. (Replace the X with your drive letter). –  Hennes Aug 5 '12 at 14:52
    
On my system I successfully use sdparm --command=stop /dev/disk/by-label/mydisk to spin down the drive immediately. –  Marco Aug 5 '12 at 14:57
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When your machine shutdown the data reading also stopped. So the reading head is not working anymore. I'm not sure about your device but some devices stop the disk rotation even at the idle states (even with powered machine). So probably your device have same option too. But it is wiser to take a look at the manual instructions of device.

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