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I have a fileserver where df reports 94% of / full. But according to du, much less is used:

# df -h /
Filesystem            Size  Used Avail Use% Mounted on
/dev/sda3             270G  240G   17G  94% /
# du -hxs /
124G    /

I read that open but deleted files could be responsible for it but a reboot did not fix this.

This is Linux, ext3.

regards

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5
  • Combine @TCampbell and @Kyle Brandt's answers - reboot and if that doesn't fix it, boot from a rescue CD and run fsck on the unmounted partition.
    – Paul Tomblin
    Commented Aug 21, 2009 at 11:49
  • I already rebooted before. Extensive fsck running right now.
    – Andreas Kuntzagk
    Commented Aug 21, 2009 at 12:08
  • 1
    Ok, after an hour of counting, multiplying allocated blocks with block sizes, counting inodes, the pure truth came out - in my case the huge difference was caused not by a mount, but a hidden .trash folder! It was right under my nose.
    – user176156
    Commented Jun 1, 2013 at 14:21
  • This apparently unwelcome "duplicate question" has MUCH better answers as the "original" it points to :)
    – Chris
    Commented Oct 26, 2018 at 14:31
  • 2 scenarios:[1] df shows more than du: say your block size is 1Kb, and you have three files: 100B, 200B, 500B. They will occupy 3 blocks. DF will report 3K used, du will report 800Bytes used. -----second-case [2]: you have 100 1KB blocks in total and all have 300B files written on them. Then DF will report 100% used, but du will report 30KB used. ------There is third scenario where DU reports much higher then DF. This will be either "deleted but open" files //OR// it will be a hidden mount which has all those files !!!
    – Rajeev
    Commented Jul 10, 2019 at 16:51

7 Answers 7

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37

Ok, found it.

I had a old backup on /mnt/Backup in the same filesystem and then an external drive mounted in that place. So du didn't see the files. So cleaning up this gave me back my disk space.

It probably happened this way: the external drive once was unmounted while the daily backup script run.

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6
  • Interesting, didn't think of that. Mounting a fs on a non-empty directory can do funny things...
    – sleske
    Commented Aug 21, 2009 at 14:20
  • 1
    Ya, that was one of the ones in the link I gave you. That is called an 'overlay mount'.
    – Kyle Brandt
    Commented Aug 21, 2009 at 15:13
  • Youre right Kyle. I totally missed that in this long page.
    – Andreas Kuntzagk
    Commented Aug 21, 2009 at 15:35
  • Andreas, it also doesn't make it that clear, I didn't think of it either.
    – Kyle Brandt
    Commented Aug 21, 2009 at 17:08
  • 7
    chmod mountpoints to 000, so you get errors from scripts instead of them silently filling your root partition
    – user1686
    Commented Aug 23, 2009 at 0:07
18

I don't think you will find a more thorough explanation that then this link for all the reasons it could be off. Some highlights that might help:

  • What is your inode usage, if it is almost at 100% that can mess things up:

    df -i

  • What is your block size? Lots of small files and a large block size could skew it quite a bit.

    sudo tune2fs -l /dev/sda1 | grep 'Block size'

  • Deleted files, you said you investigated this, but to get the total space you could use the following pipeline (I like find instead of lsof just because lsof is a pain to parse):

    sudo find /proc/*/fd -printf "%l\t%s\n" | grep deleted | cut -f2 | (tr '\n' +; echo 0) | bc

However, that is almost 2x off. Run fsck on the partition while it is unmounted to be safe.

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6
  • df -i does not report anything unusual, will go the fsck way now.
    – Andreas Kuntzagk
    Commented Aug 21, 2009 at 11:58
  • 2
    quite many ~blocksize/2 size files can make this problem by filling up entire blocks, creating enormously big unavailable space (in the unavailable part of remaining space in the blocks) so do you store lots of small files there?
    – asdmin
    Commented Aug 21, 2009 at 12:36
  • How would I find out the number of files with such a size?
    – Andreas Kuntzagk
    Commented Aug 21, 2009 at 13:51
  • 2
    First you need to find you block size, so if it 4096, You want a file less then 4KB, so find / -size -4k | wc -l
    – Kyle Brandt
    Commented Aug 21, 2009 at 14:26
  • 1
    Used to fill up volumes with several 100 thousand 3k files... changing filesystem from xfs (on sgi) to reiserfs helped make diskspace more efficient. Not an option for many, but worked for us.
    – ericslaw
    Commented Aug 21, 2009 at 21:55
16

It looks like a case of files being removed while processes still have them open. This disconnect happens because the du command totals up space of files that exist in the file system, while df shows blocks available in the file system. The blocks of an open and deleted file are not freed until that file is closed.

You can find what processes have open but deleted files by examining /proc

find /proc/*/fd -ls | grep deleted
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1
  • 3
    I already investigated this problem (see original post) btw. you can also get that by lsof| grep deleted
    – Andreas Kuntzagk
    Commented Aug 21, 2009 at 11:56
7

The most likely reason in your case is that you have lots of files that are very small (smaller than your block size on the drive). In that case df will report the sum of all used blocks, whereas du will report the actual sum of file sizes.

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2
  • df can show you the status of inodes for the disk or partition too which may shed some more light as to whether or not this is your situation - df -i /
    – DisabledLeopard
    Commented Aug 21, 2009 at 14:41
  • @wolfgangsz Not exactly, unless you use du --apparent.
    – sourcejedi
    Commented Jun 1, 2013 at 15:19
7

I agree that 

lsof +L 1 /home | grep -i deleted

is a good place to start, in my case I notice that I had lots of perl scripts that was running, and keeping a lot of files alive, even though they was supposed to be deleted.

I killed the perl functions, and this made du and df almost identical, case closed.

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2

By default, when you format a filesystem with EXT3, 5% of the drive is reserved for root. df accounts for this reserve when it reports what is available, while du shows what is actually in use.

You can view the reserved blocks by running:

tune2fs -l /dev/sda|grep -i reserve

and you will get something like:

Reserved block count:     412825
Reserved GDT blocks:      1022
Reserved blocks uid:      0 (user root)
Reserved blocks gid:      0 (group root)

If you would like to adjust that to a lower percent, you can do so with something like

tune2fs -m 1 /dev/sda

You can reduce it to 0, however since this is your root filesystem I would be wary of doing that. If the filesystem actually filled it may make maintenance tasks required to clean it up difficult.

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5
  • 1
    That is true, but seems beside the point. The "in use" size reported by du and df differs, and that is independent of reserved blocks.
    – sleske
    Commented Aug 21, 2009 at 12:52
  • The size of disappeared space is not comparable to 5%
    – drAlberT
    Commented Aug 21, 2009 at 12:54
  • Yeah, it still doesn't add up, but I figured that was adding to the discrepancies.
    – Alex
    Commented Aug 21, 2009 at 13:46
  • In my case the size of used space shown by du and df was comparable and there was a lack of 23-24GB. Setting reserved blocks number to 1% freed those 23GB. Thanks!
    – mkll
    Commented Sep 21, 2016 at 12:12
  • work perfectly for my case, but I dunno why my disk is 20 gb, and for reserved blocks is 100mb.
    – vrie
    Commented Nov 22, 2022 at 3:56
-1

Is it possible that perhaps du doesn't add in the size of the directories as well? Still, seems like a HUGE difference though, that can't be responsible for all of it.

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