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A few days ago, after login the hard drive didn't make any sound and I could open any program very fast. But now the disk sounds like it's doing some I/O readings (like a crackling noise of some sorts ) and the programs take longer to open up.

What could be the problem?

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Install iotop and see what's using the drive on start up. – Uri Herrera Nov 19 '11 at 6:32

It's dying, get your data off it ASAP. You're lucky that the disk is even giving you an audible warning. Most SATA drives just fail to spin up one day. Whatever you do, don't turn it off until you get your stuff off it. Then we can start running smart tests on it to verify how far gone it is.

Might I suggest a nice backup program called [deja-dup]?1

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