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It sounds like the HDD is put into a power saving/sleep mode, spun down, but immediately started up again, and then this repeated 3-4 times, very quickly.
How could I find out what this exactly is, and what causes it?

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If the drive has S.M.A.R.T then you could check what it reports with smartmontools

sudo apt-get install smartmontools
sudo smartctl

or

sudo gsmartcontrol

UPDATE:

To narrow the problem down I would recommend to boot up from LIVE CD/USB and see if to happens or not. It it doesn't happen in LIVE CD/USB that means that the issue is related to a software, i.e. your installed OS. Otherwise I tend to think it is may be related to a hardware.

  • The tests reported no error, however it happens while booted up from LIVE USB. – user Jul 17 '14 at 15:14
  • Did you try to update BIOS to the latest version? – Ruslan Gerasimov Jul 18 '14 at 0:41

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