I am using Ubuntu 12.04 with the Xubuntu Desktop package installed and am having problems with an internal NTFS hard drive.

Entire directories seem to be emptied without warning or going to the waste basket. This has been happening for at least a couple of months; I first noticed a problem when music files weren't being read into the library by Rhythmbox but assumed it was a Rhythmbox problem.

I've now noticed that a directory with nearly 500GB of files/sub-directories has been emptied. The strange thing, however, is that the drive isn't showing an increase in the amount of free space it has - as though the files are still there.

When doing an ls of the specific folder that seems to be emptied, I receive an input/output error, but can ls the root of the drive fine.

I don't have Windows installed on this machine either, and most of the other related questions seem to be related to dual booting Windows.

Any ideas on the cause of the problem and how to fix it?


Couple weeks ago in my windows OS I had similar problems which sounded like a hard drive failure in your case. I ran a program that checks for these kind of things.

Didn't know what was causing the problem as my windows os would freeze up after 5mins particularly when I would open certain programs. Then I heard massive clicking from it which was a sign of death. After much research I found a program called Hard Drive Regenerator, your friendly pirate should know where to get it; just burn the iso once he gives it to you. Life saver works with all kinds of partitions and takes an hour or so to scan for bad sectors and close to a day if all sectors need to be remapped and deleted.

The bad sectors were spreading like a virus, so the program remapped them into a part of the hard drive where the bad sectors are failed when hard drives are developed. I'd run that to check for any physical problems. Also I did backup my files before running it, you can leave it, but reccomends saving your files. I had 1537 512 byte sectors causing my hard drive to click and pc to freeze. After running that my hard drive passed the SMART test.

  • I should point out the reason why I recommend that tool so much as the member down below recommend others. I ended up using all the m$ tools and even downloaded a top rated windows tool which is made specifically for that stuff. I did a fresh format installation of windows, still had the problem even though kubuntu was running fine. Only after I used that tool did my problems cease and its been a couple of weeks. I recommend a full HD sweep with it. Other programs seem like a waste of time and be sure to run it in on boot if you choose to and not in an OS. – user140393 Mar 30 '13 at 14:35

Sounds like a problem I'm currently coping with myself. I have an external NTFS formatted HDD and I was getting the same symptoms as you. Input/Output errors all over the place and entire folders of files just disappearing. After weeks of diagnosing and attempted repairs I have been forced to recover what data I can and reformat the drive. I suspect the issue lies with Linux's hacked together support for NTFS(since Microsoft won't provide the code for proper support), but I can't check that until I've finished recovering my 1TB of data to my numerous small HDDs and other storages, and then Reformat the drive to see of the drive itself is bad or if it really was the fault of Ubuntu.

In the end my best advice is to assume the worst and start backing up all the data you can. Also switch the drive to Read-Only so you can make sure nothing new gets written to the drive further increasing the problems. After you've finished backing up you can A) attempt repairing the drive using NTFS repair tools, or B) try Reformatting it to something other than NTFS(I'd recommend Ext3 if it's primarily Linux used).

Sorry I can't help more.

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