Disk full, du tells different. How to further investigate?

Just stumbled on this page when trying to track down an issue on a local server.

In my case the df -h and du -sh mismatched by about 50% of the hard disk size.

This was caused by apache (httpd) keeping large log files in memory which had been deleted from disk.

This was tracked down by running lsof | grep "/var" | grep deleted where /var was the partition I needed to clean up.

The output showed lines like this:
httpd 32617 nobody 106w REG 9,4 1835222944 688166 /var/log/apache/awstats_log (deleted)

The situation was then resolved by restarting apache (service httpd restart), and cleared up 2gb of disk space, by allowing the locks on deleted files to be cleared.

Check for files on located under mount points. Frequently if you mount a directory (say a sambafs) onto a filesystem that already had a file or directories under it, you lose the ability to see those files, but they're still consuming space on the underlying disk. I've had file copies while in single user mode dump files into directories that I couldn't see except in single usermode (due to other directory systems being mounted on top of them).

I agree with OldTroll's answer as the most probable cause for your "missing" space.

On Linux you can easily remount the whole root partition (or any other partition for that matter) to another place in you filesystem say, /mnt, for example, just issue a

mount -o bind / /mnt

then you can do a

du -h /mnt

and see what is using up your space.

In my case this had to do with large deleted files. It was fairly painful to solve before I found this page, which set me on the correct path.

I finally solved the problem by using lsof | grep deleted, which showed me which program was holding two very large log files (totalling 5GB of my available 8GB root partition).

See what df -i says. It could be that you are out of inodes, which might happen if there are a large number of small files in that filesystem, which uses up all the available inodes without consuming all the available space.

Files that are open by a program do not actually go away (stop consuming disk space) when you delete them, they go away when the program closes them. A program might have a huge temporary file that you (and du) can't see. If it's a zombie program, you might need to reboot to clear those files.

For me, I needed to run sudo du as there were a large amount of docker files under /var/lib/docker that a non-sudo user doesn't have permission to read.

Try this to see if a dead/hung process is locked while still writing to the disk: lsof | grep "/mnt"

Then try killing off any PIDs which are stuck (especially look for lines ending in "(deleted"))

This is the easiest method I have found to date to find large files!

Here is a example if your root mount is full / (mount /root) Example:

cd / (so you are in root)

ls | xargs du -hs

Example Output:

 9.4M   bin
 63M    boot
 4.0K   cgroup
 680K   dev
 31M    etc
 6.3G   home
 313M   lib
 32M    lib64
 16K    lost+found
 61G    media
 4.0K   mnt
 113M   opt
 du: cannot access `proc/6102/task/6102/fd/4': No such file or directory
 0  proc
 19M    root
 840K   run
 19M    sbin
 4.0K   selinux
 4.0K   srv
 25G    store
 26M    tmp

then you would notice that store is large do a cd /store

and run again

ls | xargs du -hs

Example output: 
 109M   backup
 358M   fnb
 4.0G   iso
 8.0K   ks
 16K    lost+found
 47M    root
 11M    scripts
 79M    tmp
 21G    vms

in this case the vms directory is the space hog.

One more possibility to consider - you are almost guaranteed to see a big discrepancy if you are using docker, and you run df/du inside a container that is using volume mounts. In the case of a directory mounted to a volume on the docker host, df will report the HOST's df totals. This is obvious if you think about it, but when you get a report of a "runaway container filling the disk!", make sure you verify the container's filespace consumption with something like du -hs <dir>.