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I run Windows Vista and Ubuntu 9.10 dual boot. Today while booting windows, it informed me that there was something wrong with my hard disk and it would perform a check, and made some fixes.

Only when I wanted to boot into ubuntu again did I realise that the disk check had corrupted my linux partition. Ubuntu's load screen shows up, but just before the login screen it says that the filesystem could not be mounted.

Is there a way I can fix this? And how do I prevent windows from doing the same in the future?

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did you use Wubi to install Ubuntu? or did you install it to its own partition on the hard drive? Windows disk checking should not corrupt a separate Ubuntu partition (or a Wubi install, for that matter). you may have a hardware problem with the harddrive. – quack quixote Feb 26 '10 at 6:02
it's installed on its own partition. Now that you mention it, Ubuntu did say that my disk had "bad sectors", but after reading around, many posts said that was harmless. Also, windows wanted to check my drive for some time now, but I've always skipped it. The problem only occured after allowing the check to run, though this could be coincidence. – box9 Feb 26 '10 at 6:31
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Use the Ubuntu livecd.
1. Start up the live system from the liveCD
2. Open up a terminal
3. You can check the partition by typing: sudo fdisk -l OR cfdisk

Here you can see your partitions. Check for Linux or ext4/ext3 and such words (anything what is not SWAP or ntfs).

After you identified your partition (it'll be like: /dev/sda1) type: e2fsck.
You'll see the options which you can use to fix the partition.(or type man fsck)

For example use this: e2fsck -a /dev/sda1

From the man page:
-a Automatically repair the file system without any questions (use this option with caution). Note that e2fsck(8) supports -a for backwards compatibility only. This option is mapped to e2fsck's -p option which is safe to use, unlike the -a option that some file system checkers support.

Be careful, and read the manual page thoroughly.

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Thanks, I tried this and discovered I didn't need to go so far as fixing the disk, the live CD could read the partition perfectly. I did use Linux Mint instead of Ubuntu for the Live CD though – box9 Feb 27 '10 at 1:00
Any livecd does the job which got the utilities. Thought you had the simple Ubuntu disc. :) (By the way this would only repair your partition so you'd be able to boot up your sys.) – Shiki Feb 27 '10 at 5:08
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