The most simple variant to run fsck is to force fsck on restart, and then restart your system:

sudo touch /forcefsck

The other option is to swich the system to runlevel 1 (logs-out any userRunning fsck on a mounted filesystem can do SEVERE damage), unmount all partitions. run fsck & repair, remount all drives, increase the runlevel to 3 and continue.

1) Take system down to runlevel one (make sure you run all command as root user):
# init 1

2)Unmount file system, for example if it is /home (/dev/sda3) file system then type command:

# umount /home

OR

# umount /dev/sda3

3) Now run fsck on the partition:

# fsck /dev/sda3

However be sure to specify the file system type using -t option. Recenly one of our sys admin run the command on ext3 file system w/o specifying file system. Result was more corruption as fsck by default assumes ext2 file system.

# fsck -t ext3 /dev/sda3

OR

# fsck.ext3 /dev/sda3

Tip if you don’t know your file system type then typing mount command will display file system type.

fsck will check the file system and ask which problems should be fixed or corrected. If you don’t wanna type y every time then you can use pass -y option to fsck.

# fsck -y /dev/sda3

Please not if any files are recovered then they are placed in /home/lost+found directory by fsck command.

4) Once fsck finished, remount the file system:

# mount /home

5) Go to multiuser mode

# init 3

Read man page of fsck for more information. Make sure you replace /dev/sda3 with your actual device name.