System partition full (45Gb)

I have a problem with Fedora 38 Workstation Gnome
Since a few days ago, I have the system partition (/) full and it has 45Gb.
I have been investigating and I think it is the flatpak. Let me explain.
I have 13 applications installed. I have downloaded Warehouse to manage them.
But doing a Flatpak List, I have 4 versions of Mesa, as many versions of Adwaita theme, QGnomePlataform, KDE Plataform… Many, not all, appear in the dostware manager to uninstall, but I don’t know if I should…
These 2 folders in particular occupy:
var/lib/flatpak/repo - 9Gb
var/lib/flatpak/runtime - 8Gb

Any ideas?

Please share the output of du -sh /var/lib/flatpak/{repo,app,runtime}

sometimes flatpak uninstall --unusedmakes you get rid of runtimes that are not in use anymore.

Obviously, I try --unused… without results (see the image)
The “runtime” folder mark 97M, but the gnome marks 7Gb
I hacve only 12 apps, 1,7Gb

Captura desde 2023-10-30 18-52-57

I’d suggest to remove flatpak cache folder contents manually. I had to do that multiple times, finally upgraded storage.

So that means the real disk usage of flatpak is ~9GB total. As I mentioned elsewhere, app and runtime are hardlink farms into repo, so they don’t take up a significant amount of additional space. With hardlinks (unlike symbolic links), each link is equivalent; they’re both directory entries pointing at the same inode. Thus it’s technically not incorrect to say that runtime is using 7GB in isolation, but the total usage is still 9GB, not not 9GB+7GB+1.7GB.

When you have a small number of apps installed, it’s normal for the runtimes to take up relatively more space, especially if the apps use different runtimes or if some are IDEs that use SDKs which are larger.

My previous suggestion was to consider using the user flatpak installation if you have plenty of free space in /home.

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Excuse me. Is the first post. Thanks

I don’t see this option/folder.
I have searched and did not find it. (on spanish)
Any instruction??
sorry for the inconvenience

Hello @zicoxy3 ,
Could you please type inxi -P in a terminal and paste the output here so we can see your partition setup? It should give something like this …

[jakfrost ~]$ inxi -P 
  ID-1: / size: 221.98 GiB used: 10.32 GiB (4.6%) fs: btrfs dev: /dev/sda3
  ID-2: /home size: 931.51 GiB used: 269.95 GiB (29.0%) fs: btrfs
    dev: /dev/sdc1
  ID-3: /var size: 207.57 GiB used: 198.03 GiB (95.4%) fs: btrfs
    dev: /dev/sdb2
  ID-4: swap-2 size: 16 GiB used: 0 KiB (0.0%) fs: swap dev: /dev/sdb1

Check temporary directories & files with this command - ls /var/tmp/flatpak-cache-*. You can verify disk usage with the Disk Usage Analyzer (a GNOME app, normally included to Fedora install), you will find directories taking most of storage space using that app.

ID-1: / size: 40.95 GiB used: 32.56 GiB (79.5%) fs: ext4 dev: /dev/nvme1n1p2
ID-2: /boot/efi size: 951.1 MiB used: 42.7 MiB (4.5%) fs: vfat
dev: /dev/nvme1n1p1
ID-3: /home size: 415.21 GiB used: 209.53 GiB (50.5%) fs: ext4
dev: /dev/nvme1n1p3

I deleted some applications in flatpak, so there is more space. Previously it reached 3Gb free.
On Flatpak list

  • 4 Mesa versions
  • 4 Gnome plataform…

Yeah, /var is the hog. It was what I was sort of pointing out above, I have my / as a separate partition and you can see my /var is consuming 192Gb while the root partition is only using just over 10Gb. So the 45Gb is fine for / if you have another partition for /var, I personally have had poor experiences with making a root partition less than 120Gb in recent years (if that partition holds /var as well).

To keep root partition size from growing with flatpak installs, you can always install all of the software into your user space. (It’ll take up space on your home partition, instead.)

I’m not sure if there’s a way to set that as the default for graphical installs, but on the command line it’s just a matter of adding --user to each command, e.g.:

flatpak install --user org.blender.Blender
flatpak update --user


It’s unfortunate you’re not using lvm volumes on that system. If you were, it’d be relatively painless to bleed off a little of your home partition’s space and reallocate it to the root partition instead. (You’d still have to boot to recovery in order to shrink the home partition while it was offline, but then you could grow the root partition into the freed space despite it being non-contiguous. LVM is really kind of the bee’s knees, once you get familiar with it.)

After adding the flathub remote to the user installation, you can remove it from the system installation:

flatpak --user remote-add --if-not-exists flathub
flatpak --user install $(flatpak --system list --app --columns=application)
flatpak --system remote-delete flathub

Any Fedora flatpaks will remain installed in the system installation, but they’ll be ‘shadowed’ by Flathub versions in the user installation. You can remove the fedora remote to remove those as well:

flatpak --system remote-delete fedora

And you can add it back to the user installation if desired:

flatpak --user remote-add fedora oci+