7 replies

Excessive storage usage in /var/lib/containers/storage/overlay

✅ Solved

Hi there, something seems to be wrong with my installation, but I am not sure where to go from here on finding out how to fix it.

I have my installation on an SSD showing 812GB on this partition (in gparted). I have a couple games installed. Some flatpaks. The storage on all these looks normal. Overall, my home folder shows as 230-250 GB (230 by

du

du

, 245 in FileLight).

The rest of my system usage is weird.

`bash
sudo df -h /var
Filesystem      Size  Used Avail Use% Mounted on
/dev/sda4       813G  681G  128G  85% /var

`bash
sudo df -h /var
Filesystem      Size  Used Avail Use% Mounted on
/dev/sda4       813G  681G  128G  85% /var

681G-245G is 436, so the rest of my system is taking... 400G+ of space?

I found the tool btdu to help scan what's taking space.

So far it has scanned that

/var00/lib/containers/storage/overlay

/var00/lib/containers/storage/overlay

is 366GB. It looks like maybe there is some duplication/remnants sticking around in here. There are 11 sub-folders in here that are around 9GB in size, and all contain installations for the same applications.

I do my builds with

bluebuild build

bluebuild build

locally and push the images to ghcr.

rpm-ostree status
State: idle
AutomaticUpdates: stage; rpm-ostreed-automatic.timer: last run 53min ago
Deployments:
● ostree-unverified-registry:ghcr.io/xxx/uxxx:latest
                   Digest: 
                  Version: 42.251228 (2025-12-28T22:11:13Z)

  ostree-unverified-registry:ghcr.io/xxx/uxxx:latest
                   Digest: 
                  Version: 42.251207 (2025-12-07T00:56:36Z)

rpm-ostree status
State: idle
AutomaticUpdates: stage; rpm-ostreed-automatic.timer: last run 53min ago
Deployments:
● ostree-unverified-registry:ghcr.io/xxx/uxxx:latest
                   Digest: 
                  Version: 42.251228 (2025-12-28T22:11:13Z)

  ostree-unverified-registry:ghcr.io/xxx/uxxx:latest
                   Digest: 
                  Version: 42.251207 (2025-12-07T00:56:36Z)

No pinned images sticking around.

I've also tried all the subcommands/options of

rpm-ostree cleanup

rpm-ostree cleanup

and

bluebuild prune

bluebuild prune

.

Is there something obviously wrong in all of this? Hoping to understand what on earth is going on here. Thanks.

GitHub

GitHub - CyberShadow/btdu: sampling disk usage profiler for btrfs

sampling disk usage profiler for btrfs. Contribute to CyberShadow/btdu development by creating an account on GitHub.

Solution

That might be the root container storage so I would suggest running

sudo podman system prune

sudo podman system prune

to clean that up

Jump to solution

BlueBuild•3w ago•

7 replies

KaCii

Excessive storage usage in /var/lib/containers/storage/overlay

✅ Solved

du

du

, 245 in FileLight).

The rest of my system usage is weird.

`bash
sudo df -h /var
Filesystem      Size  Used Avail Use% Mounted on
/dev/sda4       813G  681G  128G  85% /var

`bash
sudo df -h /var
Filesystem      Size  Used Avail Use% Mounted on
/dev/sda4       813G  681G  128G  85% /var

681G-245G is 436, so the rest of my system is taking... 400G+ of space?

I found the tool btdu to help scan what's taking space.

So far it has scanned that

/var00/lib/containers/storage/overlay

/var00/lib/containers/storage/overlay

bluebuild build

bluebuild build

locally and push the images to ghcr.

rpm-ostree status
State: idle
AutomaticUpdates: stage; rpm-ostreed-automatic.timer: last run 53min ago
Deployments:
● ostree-unverified-registry:ghcr.io/xxx/uxxx:latest
                   Digest: 
                  Version: 42.251228 (2025-12-28T22:11:13Z)

  ostree-unverified-registry:ghcr.io/xxx/uxxx:latest
                   Digest: 
                  Version: 42.251207 (2025-12-07T00:56:36Z)

rpm-ostree status
State: idle
AutomaticUpdates: stage; rpm-ostreed-automatic.timer: last run 53min ago
Deployments:
● ostree-unverified-registry:ghcr.io/xxx/uxxx:latest
                   Digest: 
                  Version: 42.251228 (2025-12-28T22:11:13Z)

  ostree-unverified-registry:ghcr.io/xxx/uxxx:latest
                   Digest: 
                  Version: 42.251207 (2025-12-07T00:56:36Z)

No pinned images sticking around.

I've also tried all the subcommands/options of

rpm-ostree cleanup

rpm-ostree cleanup

and

bluebuild prune

bluebuild prune

.

Is there something obviously wrong in all of this? Hoping to understand what on earth is going on here. Thanks.

GitHub

GitHub - CyberShadow/btdu: sampling disk usage profiler for btrfs

sampling disk usage profiler for btrfs. Contribute to CyberShadow/btdu development by creating an account on GitHub.

Solution

That might be the root container storage so I would suggest running

sudo podman system prune

sudo podman system prune

to clean that up

Jump to solution

Excessive storage usage in /var/lib/containers/storage/overlay

Excessive storage usage in /var/lib/containers/storage/overlay

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