I have made a 26Go partition for the root of the filesystem and the rest of my hard drive is dedicated to my /home as another partition (excepting boot and swap).

My aim was to be able to install new OS without touching to the /home partition, which is quite convenient but now I face a problem as the root partition is getting full quite fast and cannot exceed 26Go.

I have already optimised the log storage consumption by rotating and setting a small vacuum size.

Nevertheless, I notice that /var/lib/flatpack is quite storage consumming as well as /var/cache/packagekit. Is there a way to clean up these directories in a smart manner?

Last try I did was to boot my computer on a bootable usb stick and try to reshape partitions but it was not possible due to the relative positions they had on the disk.

Any clue to solve this issue?

UPDATE: output of du -x / | sort -n | tail -40

697476  /var/lib/docker/overlay2/cd3b560f48d6382b0fa744d048437ff96649c3a2f24285af6f9fb3ab611d7076/diff/usr
707332  /var/lib/docker/overlay2/721fc618b2deb89956c511d2b0b77ae67dd9d53a067a91ed784a4629c0b449de/diff
707348  /var/lib/docker/overlay2/721fc618b2deb89956c511d2b0b77ae67dd9d53a067a91ed784a4629c0b449de
707764  /var/lib/docker/overlay2/cc614d827df9106c5f62bb3bb521d063dc8dab974af99844d6e9e64d3ee5d8a0/diff
707780  /var/lib/docker/overlay2/cc614d827df9106c5f62bb3bb521d063dc8dab974af99844d6e9e64d3ee5d8a0
707980  /var/lib/docker/overlay2/cd3b560f48d6382b0fa744d048437ff96649c3a2f24285af6f9fb3ab611d7076/diff
707996  /var/lib/docker/overlay2/cd3b560f48d6382b0fa744d048437ff96649c3a2f24285af6f9fb3ab611d7076
711012  /var/lib/docker/overlay2/e72086355691cebebac4ef32fffe6ed389baf132edb1f80dd4e8030629f1db2e/diff/usr
721640  /var/lib/docker/overlay2/e72086355691cebebac4ef32fffe6ed389baf132edb1f80dd4e8030629f1db2e/diff
721656  /var/lib/docker/overlay2/e72086355691cebebac4ef32fffe6ed389baf132edb1f80dd4e8030629f1db2e
724552  /var/lib/flatpak/runtime/org.fedoraproject.Platform/x86_64/f31/7a6986b9f7dded5de860d686ebd9ae83e92aacf87e206f2c82aeb3d50a8db6e8/files/lib64
769152  /usr/bin
782384  /var/lib/flatpak/runtime/org.fedoraproject.Platform/x86_64/f32/e75fe16a369aab408b5830f7f28acf587a566f97393882a4049159edf823f847/files/lib64
868784  /var/spool/abrt
874668  /var/spool
1195084 /usr/lib
1256008 /var/lib/flatpak/runtime/org.fedoraproject.Platform/x86_64/f32/e75fe16a369aab408b5830f7f28acf587a566f97393882a4049159edf823f847/files
1256020 /var/lib/flatpak/runtime/org.fedoraproject.Platform/x86_64/f32/e75fe16a369aab408b5830f7f28acf587a566f97393882a4049159edf823f847
1256028 /var/lib/flatpak/runtime/org.fedoraproject.Platform/x86_64/f32
1277320 /var/lib/flatpak/runtime/org.fedoraproject.Platform/x86_64/f31/7a6986b9f7dded5de860d686ebd9ae83e92aacf87e206f2c82aeb3d50a8db6e8/files
1277332 /var/lib/flatpak/runtime/org.fedoraproject.Platform/x86_64/f31/7a6986b9f7dded5de860d686ebd9ae83e92aacf87e206f2c82aeb3d50a8db6e8
1277340 /var/lib/flatpak/runtime/org.fedoraproject.Platform/x86_64/f31
1380912 /var/cache/PackageKit/31/metadata/updates-31-x86_64/packages
1408084 /var/cache/PackageKit/31/metadata/updates-31-x86_64
1821752 /var/cache/PackageKit/31/metadata
1945008 /var/cache/PackageKit/31
2155512 /var/cache/PackageKit
2457524 /var/cache
2461504 /usr/share
2523868 /usr/lib64
2533372 /var/lib/flatpak/runtime/org.fedoraproject.Platform/x86_64
2533376 /var/lib/flatpak/runtime/org.fedoraproject.Platform
2533380 /var/lib/flatpak/runtime
2847904 /var/lib/flatpak
7444976 /usr
7456240 /var/lib/docker/overlay2
7471132 /var/lib/docker
10733320    /var/lib
14568308    /var
22923848    /
  • 1
    Depending on what you are using the system for, 26GB may not be enough for /. How is the space set up? Is it via LVM? Standard partitioning? Aug 19, 2020 at 18:33
  • du -x / | sort -n | tail -40 will give you an idea where the space has gone. You may add it to the answer. Aug 19, 2020 at 18:44
  • @NasirRiley, / and /home are mounted on standard partitions
    – blondelg
    Aug 19, 2020 at 20:39
  • @ArtemS.Tashkinov, see my update and thanks for this command
    – blondelg
    Aug 19, 2020 at 20:44
  • I did not ask you to use the -h option for du. Please run exactly what I asked for. Aug 19, 2020 at 20:55

1 Answer 1


You could try removing and then reinstalling your flatpack applications with the --user flag. For example:

flatpak --user install flathub org.application.name

Making use of the --user flag will install the applications under your user's home directory which resides under /home.

There are some other great options outlined in this resource.

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .