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I have only one disk in my computer, a 80 GB SSD. It is formatted as a single ext4 partition (no swap), and all the usual folders are installed on it (I keep lots of data on external media, but /home and all the rest is on the SSD).

Today I booted it and I got a message that the drive is full. I opened Disk Usage Analyzer to look at what takes up space. It insists that 67.8 GB of the disk are used, and that / is taking up 36.4 GB. Which leads to the question, where are the missing 30 GB, if not on the file system?!

Just to have a comparison, I added up all the sizes of all readable folders listed in Nautilus as subfolders of / (including the hidden ones). I got 20.9 GB. Trash was unreadable, but I know it has 16.2 GB, so the sum is 36.1 GB, around the same as what Disk Usage Analyzer is reporting. There were some system folders which were unreadable, like proc, but I doubt that they add up to 30 GB - else it wouldn't be possible to install Ubuntu on small disks, and I've seen it run on 2.5 GB. I think they must be the 0.3 GB difference between my calculation and the Disk Usage Analyzer's report.

So I'd like to know, what is eating up these 30 GB and how do I get it to free them?

alt text

Edit with answers to CYREX's questions

  1. Booted from Ubuntu 10.10 64-bit live CD (same as my system).

    fsck result: 

    root@ubuntu:~# fsck /dev/sda1
fsck from util-linux-ng 2.17.2
e2fsck 1.41.12 (17-May-2010)
/dev/sda1: clean, 265956/4890624 files, 18073343/19537408 blocks

  2. Booted from the SSD. Emptied the trash, and the 16 GB from there are now free. The 30 GB are still missing.

    alt text

  3. I'm not experienced enough to know what counts as weird in a log. Here are my messages log and my syslog since last boot. Maybe you can find something in them:

  4. Here it got really strange. I plugged in an external 500 GB HDD. Disk Usage Analyzer overreported the available space, then showed space missing (76 GB used, but only 24 in folders).

    alt text

Booted again from the LiveCD, started the Disk Usage Analyzer from it and got the same results as from the installed Ubuntu, within 1-2 GB.

Edit with answer to CodeMonk:

That would have been a nice solution, but the partition is really 80 GB - I mean 74 GB + marketing "error", anyway the whole disk is formatted. It also shows that over 50 GB are used, so where are the 30 GB if not in files and folders?

alt text

GParted also reports the correct size of the external HDD.

alt text

karel
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rumtscho
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  • Sometimes is best to not trust on GUI tools, open a terminal and run, get a summarized report of used space per dir on the root: sudo du -sm /* – João Pinto Dec 15 '10 at 10:42
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    By not expanding the Disk Usage Analyzer entry for / in your first and second screenshots, you've blinded yourself (and us) to the sizes of all the subordinate directories which the ring chart clearly shows as being occupied by something. It could be something as simple as /var/log/syslog being filled with some hugely complaining hardware, but we need that data. – msw Dec 15 '10 at 13:00
  • Have you tried looking for the logfiles? I remember I had my KVM switch and wireless keyboard not playing nice together after a reboot which caused a logfile to grow and filling up all the space (after two days). Replugging the device helped. May be different for your server, but hopefully gives you a hint. – LiveWireBT Oct 08 '12 at 21:01

8 Answers8

35

If you use Disk Analyzer as a normal user there can be some files that you can't access or see. You can try to start it with superuser privileges. Open a terminal, or press ALT+F2 and type:

gksudo baobab

Baobab is the geeky name of the Disk Analyzer if you are wondering. Maybe it can now show you where those missing megabytes are.

pLumo
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Javier Rivera
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18

I solved it - thanks to all your advice, especially that of Javier Riveira, who suggested running Disk Analyzer with sudo rights (I didn't know this can have influence on the results).

I have Crashplan, and it is making backups to some of the external drives. So there is a backup set which goes to Milly, and another one which goes to Sto_Lat, once every 15 minutes (these are the names of the external drives). When I have at some point started the computer without these drives, Crashplan has found no folders under /media/Milly and /media/Sto_Lat, so it has just created them and has written backups to them.

For some reason, Disk Analyzer does not show these folders when started without sudo. Nautilus shows them, but lists the size of /media at 16 KB, when it is actually 30 GB.

I only noticed this when I dismounted all external drives, including Milly and Sto_Lat, and started gksudo baobab. Then I saw my external drives where there should be none - but not all of them but only the backup targets - and realised that these are not mounted drives, but eponymous folders created by Crashplan. There must be something weird going on when I mount the drive at the same name as the existing folder, I wonder why I don't get an error message or something...

BTW, this also solves why Disk Analyzer shows the sizes of Milly at 530 GB instead of 500 GB - these are the "missing" 30 GB, it counts the folder and the real drive together.

Now I only need a way to delete the folders without breaking Crashplan or remaining without backups.

Community
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rumtscho
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  • You should mark this as the accepted answer, I've added a link to Javier's answer so he can get upvotes for the tip. – Jorge Castro Dec 15 '10 at 21:17
  • This is exactly the same problem I had. One of my backup disks had died but my backup script still attempted to backup to the /mnt/Backup-Drive folder, filling up my root disk. – Michael Robinson Aug 31 '13 at 16:51
  • The reason you need sudo is that parts of the file system, are not readable to the user you're running as. This makes total sense, imagine if any user could read your full backups for example. – arielf Sep 07 '15 at 01:36
  • @arielf I guess I had never given it much thought. But I sure expect a disk space counting utility to give me an accurate picture of the disk space used and free, maybe displaying a grey blob saying "this part is full, but you don't have the rights to see what's in there". I am quite surprised as a user when the files I have no right to read are counted towards free disk space. – rumtscho Sep 07 '15 at 08:06
  • Well, you could simply run df which doesn't do a full directory scan and just gives the total vs free space of a partition. But if you want a full directory scan, with the detail given by baobab or filelight (at the individual file level), then full read permissions to the directories are needed. – arielf Sep 07 '15 at 21:23
  • Mounting a folder under an existing path will "shadow" this path. Meaning that while the folder is mounted you will see the contents of the mounted folder and you cannot access the original folder contents. Once you unmount the folder, the original contents will be visible again. This is the expected behavior of mount on Linux and there is nothing wired about it. Example: /media/data contains some files, you mount your external hard disk as data under /media, then it will shadow your original data folder. – lanoxx Jan 18 '17 at 17:24
6

You can use the Disk Usage Analyzer to scan your directories and see where your space is going on the filesystem.

alt text

As for not being able to see 30GB of your disk, open up GParted and see how the space is allocated on the disk. It may be that your partition scheme isn't what you thought it was.

GParted

Nick Pascucci
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5

You can use du to show this:

cd /
sudo du -hcsx -- .[!.]* * | sort -rh | head

or

sudo du -hcsx -- * | sort -rh | head

This will show what is using the most space.

mchid
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4

As default there are 10% of your disk space reserved for the root user. You can change that using sudo tune2fs -m %percentage %device. In your case that would be sudo tune2fs -m 1 /dev/cciss/c0d0p1 for reducing the reservation to 1%. You can set it to any other number you like but I would not recommend 0%.

André Stannek
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1

Do the following at let me know how it went:

  1. Insert a LiveCd and fsck your /dev/sda1
  2. Clean your Trash Can.
  3. See the Log File Viewer for weird stuff that is happening.
  4. Test (If you can) with a normal HDD (Not SSD). Just to remove that option.

Let me know how it went.

Luis Alvarado
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1

I really don't know if this helps you, but in my case I also experienced that, my HDD was loosing free space over time without a reason. It turned out that the default settings in synaptic package manager was also a contributor to that. The default settings in the preferences, under the file tab will instruct synaptic to keep all downloaded packages in the cache. Over the time that can accumulate a nice mountain of files. I changed the settings to delete downloaded packages after installation. That helped to recover quite a nice amount of free space.

Again I'm really not sure if that helps in your case, but you might check the synaptic cache, maybe that's full with files that are obsolete.

AndyB
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0

This answer is same as Javier Rivera's answer in this very question, but for Ubuntu 18.04+ as gksudo command is no longer available.

If you use Disk Analyzer as a normal user there can be some files that you can't access or see. You can try to start it with superuser privileges.

To run Disk Analyzer with superuser privileges:

sudo -H baobab
sazzad
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