Upgrade fails due to "No space left on device"

System:

Operating System: Bazzite 41 based on Fedora Atomic
KDE Plasma Version: 6.3.3
KDE Frameworks Version: 6.12.0
Qt Version: 6.8.2
Kernel Version: 6.13.7-108.bazzite.fc41.x86_64 (64-bit)
Graphics Platform: Wayland
Processors: 12 × AMD Ryzen 5 5600X 6-Core Processor
Memory: 15.5 GiB of RAM
Graphics Processor: AMD Radeon RX 6700 XT
Product Name: X570S PG Riptide

I’m stuck with this issue I’m struggling to find a solution for googling about it so I’d like to ask for some help, please.

So apparently the rpm-ostree upgrade fails due to “No space left on device” despite my system still having 62G of free disk space. The problem is temporary fixed when I delete some big files but keeps on coming back eventually - confirmed to immediately cause it when I try another ujust upgrade.
/dev/sda3 465G 401G 62G 87% /sysroot

What’s interesting is that this “No space left on device” issue is also affecting my flatpaks, particularly Chrome and Steam:

Steam Logs

i386-linux-gnu-capsule-capture-libs: warning: cannot create symlink /proc/self/fd/18/lib/i386-linux-gnu/libGL.so.1: No space left on device
i386-linux-gnu-capsule-capture-libs: warning: cannot create symlink /proc/self/fd/18/lib/i386-linux-gnu/libunistring.so.5: No space left on device
i386-linux-gnu-capsule-capture-libs: warning: cannot create symlink /proc/self/fd/18/lib/i386-linux-gnu/libnss_compat.so.2: No space left on device
i386-linux-gnu-capsule-capture-libs: warning: cannot create symlink /proc/self/fd/18/lib/i386-linux-gnu/libnss_compat.so.2: No space left on device
i386-linux-gnu-capsule-capture-libs: warning: cannot create symlink /proc/self/fd/18/lib/i386-linux-gnu/libnss_compat.so.2: No space left on device
i386-linux-gnu-capsule-capture-libs: warning: cannot create symlink /proc/self/fd/18/lib/i386-linux-gnu/libnss_dns.so.2: No space left on device
i386-linux-gnu-capsule-capture-libs: warning: cannot create symlink /proc/self/fd/18/lib/i386-linux-gnu/libnss_dns.so.2: No space left on device
i386-linux-gnu-capsule-capture-libs: warning: cannot create symlink /proc/self/fd/18/lib/i386-linux-gnu/libnss_dns.so.2: No space left on device
i386-linux-gnu-capsule-capture-libs: warning: cannot create symlink /proc/self/fd/18/lib/i386-linux-gnu/libnss_files.so.2: No space left on device
i386-linux-gnu-capsule-capture-libs: warning: cannot create symlink /proc/self/fd/18/lib/i386-linux-gnu/libnss_files.so.2: No space left on device
i386-linux-gnu-capsule-capture-libs: warning: cannot create symlink /proc/self/fd/18/lib/i386-linux-gnu/libnss_files.so.2: No space left on device
pressure-vessel-wrap[23008]: E: Unable to create symlink "/var/home/ll/.local/share/Steam/ubuntu12_64/steam-runtime-sniper/var/tmp-DT4Z52//lib/ld-linux.so.2" -> "/run/host/usr/lib/ld-linux.so.2": No space left on device

Forgot to copy the flatpak Chrome logs but it was definitely complaining about having no space when I tried to run it from the terminal cause it refused to run using the GUI.

A reboot appears to temporarily fix the issue but it comes back shortly after. For now I’ve prevented rpm-ostree from automatically upgrading by adding a 0.0.0.0 hosts file entry for ghcr.io

Below are logs that I encounter when I use the ujust upgrade command:

── 20:55:33 - System update ────────────────────────────────────────────────────
Pulling manifest: ostree-image-signed:docker://ghcr.io/ublue-os/bazzite:stable
error: Preparing import: Fetching manifest: Writing cached pending manifest: Unable to write detached metadata: renameat(7e/tmp.5BVcNL, 7e/cd0af554328210e06aea8f051d4e2c38adb500d25de612125014d28795615e.commitmeta): No space left on device
System update failed: 
   0: Command failed: `/usr/bin/rpm-ostree upgrade`
   1: `/usr/bin/rpm-ostree` failed: exit status: 1

Location:
   src/steps/os/linux.rs:228
Retry? (y)es/(N)o/(s)hell/(q)uit

── 23:13:34 - System update ────────────────────────────────────────────────────
Pulling manifest: ostree-image-signed:docker://ghcr.io/ublue-os/bazzite:stable
Staging deployment... done
error: Staging deployment: Initializing deployment: Checking out deployment tree: Hardlinking bc/c06975f9552319ccf765680a88ca3f53afe40706108bf898b9c5f077a04654.file to QPdfOutputIntent: No space left on device
System update failed: 
   0: Command failed: `/usr/bin/rpm-ostree upgrade`
   1: `/usr/bin/rpm-ostree` failed: exit status: 1

Location:
   src/steps/os/linux.rs:228
Retry? (y)es/(N)o/(s)hell/(q)uit

What is the size of your boot partition?

And what is the output of rpm-ostree status

I too seem to have simliiar problem:
bazzite-gnome-asus-nvidia:stable (Bazzite 42)

df -h

Filesystem      Size  Used Avail Use% Mounted on
/dev/dm-0       930G  902G   22G  98% /sysroot
composefs        43M   43M     0 100% /
devtmpfs        4.0M     0  4.0M   0% /dev
tmpfs            12G   75M   12G   1% /dev/shm
efivarfs        128K   12K  112K  10% /sys/firmware/efi/efivars
tmpfs           4.7G  6.4M  4.7G   1% /run
tmpfs           1.0M     0  1.0M   0% /run/credentials/systemd-cryptsetup@luks\x2d1f645581\x2d1cd9\x2d4899\x2db886\x2d112f7a5c8f49.service
tmpfs           1.0M     0  1.0M   0% /run/credentials/systemd-journald.service
tmpfs            12G  592K   12G   1% /tmp
/dev/dm-0       930G  902G   22G  98% /var
/dev/nvme1n1p2  974M  297M  610M  33% /boot
/dev/dm-0       930G  902G   22G  98% /var/home
/dev/nvme1n1p1  599M   13M  587M   3% /boot/efi
tmpfs           1.0M     0  1.0M   0% /run/credentials/systemd-resolved.service
tmpfs           2.4G  256K  2.4G   1% /run/user/1000
dwarfs          759M  759M     0 100% /tmp/.mount_remp1168361715037699597

update

── 18:34:27 - System update ────────────────────────────────────────────────────
Pulling manifest: ostree-image-signed:docker://ghcr.io/ublue-os/bazzite-gnome-asus-nvidia:stable
Importing: ostree-image-signed:docker://ghcr.io/ublue-os/bazzite-gnome-asus-nvidia:stable (digest: sha256:00351b24d7263782891ed2483d239c80181781a66c91ba041e4bd20f8118273b)
ostree chunk layers already present: 70
ostree chunk layers needed: 2 (279.6 MB)
[0/2] Fetching ostree chunk 814edd17b0d88362243 (271.7 MB)… done
[1/2] Fetching ostree chunk 18b285e7e0ed5f4e004 (7.9 MB)… done
Checking out tree 81f18df… done
Inactive requests:
qemu (already provided by qemu-2:9.2.3-1.fc42.x86_64)
firewall-config (already provided by firewall-config-2.3.0-5.fc42.noarch)
libvirt (already provided by libvirt-11.0.0-1.fc42.x86_64)
libvirt-daemon-config-network (already provided by libvirt-daemon-config-network-11.0.0-1.fc42.x86_64)
Enabled rpm-md repositories: copr:copr.fedorainfracloud.org:bazzite-org:vk_hdr_layer copr:copr.fedorainfracloud.org:ilyaz:LACT copr:copr.fedorainfracloud.org:rodoma92:kde-cdemu-manager copr:copr.fedorainfracloud.org:rodoma92:rmlint copr:copr.fedorainfracloud.org:rok:cdemu copr:copr.fedorainfracloud.org:ublue-os:packages charm fedora-rar fedora-steam updates fedora tailscale-stable terra-extras terra google-chrome rpmfusion-nonfree-nvidia-driver rpmfusion-nonfree-steam copr:copr.fedorainfracloud.org:phracek:PyCharm copr:copr.fedorainfracloud.org:nucleo:gocryptfs copr:copr.fedorainfracloud.org:bazzite-org:vk_hdr_layer:ml updates-archive
Updating metadata for ‘copr:copr.fedorainfracloud.org:bazzite-org:vk_hdr_layer’… done
Updating metadata for ‘copr:copr.fedorainfracloud.org:ilyaz:LACT’… done
Updating metadata for ‘copr:copr.fedorainfracloud.org:rodoma92:kde-cdemu-manager’… done
Updating metadata for ‘copr:copr.fedorainfracloud.org:rodoma92:rmlint’… done
Updating metadata for ‘copr:copr.fedorainfracloud.org:rok:cdemu’… done
Updating metadata for ‘copr:copr.fedorainfracloud.org:ublue-os:packages’… done
Updating metadata for ‘charm’… done
Updating metadata for ‘fedora-rar’… done
Updating metadata for ‘fedora-steam’… done
Updating metadata for ‘updates’… done
Updating metadata for ‘fedora’… done
Updating metadata for ‘tailscale-stable’… done
Updating metadata for ‘terra-extras’… done
Updating metadata for ‘terra’… done
Updating metadata for ‘google-chrome’… done
Updating metadata for ‘rpmfusion-nonfree-nvidia-driver’… done
Updating metadata for ‘rpmfusion-nonfree-steam’… done
Updating metadata for ‘copr:copr.fedorainfracloud.org:phracek:PyCharm’… done
Updating metadata for ‘copr:copr.fedorainfracloud.org:nucleo:gocryptfs’… done
Updating metadata for ‘copr:copr.fedorainfracloud.org:bazzite-org:vk_hdr_layer:ml’… done
Updating metadata for ‘updates-archive’… done
Importing rpm-md… done
rpm-md repo ‘copr:copr.fedorainfracloud.org:bazzite-org:vk_hdr_layer’; generated: 2025-03-24T06:15:22Z solvables: 4
rpm-md repo ‘copr:copr.fedorainfracloud.org:ilyaz:LACT’; generated: 2025-04-20T06:38:32Z solvables: 12
rpm-md repo ‘copr:copr.fedorainfracloud.org:rodoma92:kde-cdemu-manager’; generated: 2025-02-03T18:36:13Z solvables: 8
rpm-md repo ‘copr:copr.fedorainfracloud.org:rodoma92:rmlint’; generated: 2025-02-03T19:26:47Z solvables: 4
rpm-md repo ‘copr:copr.fedorainfracloud.org:rok:cdemu’; generated: 2025-03-30T05:57:52Z solvables: 33
rpm-md repo ‘copr:copr.fedorainfracloud.org:ublue-os:packages’; generated: 2025-04-29T03:45:37Z solvables: 388
rpm-md repo ‘charm’; generated: 2025-04-01T23:42:24Z solvables: 553
rpm-md repo ‘fedora-rar’; generated: 2025-03-11T08:10:23Z solvables: 1
rpm-md repo ‘fedora-steam’; generated: 2025-03-20T08:34:03Z solvables: 9
rpm-md repo ‘updates’; generated: 2025-04-29T01:04:57Z solvables: 8462
rpm-md repo ‘fedora’; generated: 2025-04-11T05:17:07Z solvables: 76879
rpm-md repo ‘tailscale-stable’; generated: 2025-04-24T18:51:35Z solvables: 120
rpm-md repo ‘terra-extras’; generated: 2025-04-29T17:09:48Z solvables: 159
rpm-md repo ‘terra’; generated: 2025-04-29T22:24:56Z solvables: 2134
rpm-md repo ‘google-chrome’; generated: 2025-04-29T18:11:30Z solvables: 4
rpm-md repo ‘rpmfusion-nonfree-nvidia-driver’; generated: 2025-04-25T10:42:21Z solvables: 17
rpm-md repo ‘rpmfusion-nonfree-steam’; generated: 2025-04-18T08:19:16Z solvables: 1
rpm-md repo ‘copr:copr.fedorainfracloud.org:phracek:PyCharm’; generated: 2025-04-24T11:58:20Z solvables: 33
rpm-md repo ‘copr:copr.fedorainfracloud.org:nucleo:gocryptfs’; generated: 2025-04-22T05:19:39Z solvables: 35
rpm-md repo ‘copr:copr.fedorainfracloud.org:bazzite-org:vk_hdr_layer:ml’; generated: 2025-03-24T06:15:23Z solvables: 4
rpm-md repo ‘updates-archive’; generated: 2025-04-29T20:50:10Z solvables: 8040
Resolving dependencies… done
Will download: 9 packages (15.9 MB)
Downloading from ‘updates’… done
Downloading from ‘updates-archive’… done
Importing packages… done
error: importing RPMs: Importing package ‘python3-numpy’: Importing archive: ostree-tar: Failed to handle file: ostree-tar: Failed to import file: Writing content object: min-free-space-percent ‘3%’ would be exceeded, at least 9.1 MB requested
System update failed:
0: Command failed: /usr/sbin/rpm-ostree upgrade
1: /usr/sbin/rpm-ostree failed: exit status: 1

Location:
src/steps/os/linux.rs:228
Retry? (y)es/(N)o/(s)hell/(q)uit

rpm-ostree status:

State: idle
Deployments:
● ostree-image-signed:docker://ghcr.io/ublue-os/bazzite-gnome-asus-nvidia:stable
Digest: sha256:238953190bdbc7a3d1c39e5c174f80358337abcea6e3b4483c8d35cf6683c942
Version: 42.20250417 (2025-04-17T07:39:15Z)
LayeredPackages: adb alsa-lib-devel ansible bridge-utils cmake freerdp gocryptfs helm htop iotop libguestfs-tools mc nmon pandoc patchelf pipx powerline-fonts python3-wheel rclone seabios srm sshuttle strace tesseract-devel
virt-install virt-manager virt-top virt-v2v virt-viewer w3m wipe wol xclip xpra

Your /boot has 297MB free.

Do you have pinned images? Which image are you on?

The size of my boot partition is 465.8G / the whole 512 GB SSD

└─sda3        8:3    0 464.2G  0 part /var/home
                                      /var
                                      /sysroot/ostree/deploy/default/var
                                      /usr
                                      /etc
                                      /
                                      /sysroot

Here’s the output of rpm-ostree status

rpm-ostree status
State: idle
Deployments:
● (error fetching image metadata)
                Timestamp: 2025-03-31T05:06:20Z

  ostree-image-signed:docker://ghcr.io/ublue-os/bazzite:stable
                   Digest: sha256:c1056a20b97e2f74e97c3648026a9c276654643cca57bdd32c5ec34759b1bf12
                  Version: 41.20250301.1 (2025-03-03T05:05:01Z)

  ostree-image-signed:docker://ghcr.io/ublue-os/bazzite:stable
                   Digest: sha256:27a2080fa23ac2152ebaa61bbd3f504fc60e57a7f29f6e7ea1f77f8842a7b969
                  Version: 40.20240921.1 (2024-09-22T12:36:54Z)
                   Pinned: yes

/boot for you would likely be /dev/sda2. /dev/sda3 is your root partition.

Oh wait, yeah I do have pinned images.
Do I move the pin to the new one? iirc I pinned that because I originally did not have an intention to upgrade, and eventually I forgot about the pin.

/boot for you would likely be /dev/sda2. /dev/sda3 is your root partition.

Oh right, here’s my boot:

/dev/sda2       974M  628M  279M  70% /boot

Yepp. Likely the issue is that you have that pinned image. It is over 6 months old and likely doesn’t share anything with your other images at this point.

But you too have less than 30% available on /boot and likely the newest image just doesn’t fit.

1 Like

Any thoughts on my similiar error?

Man, many thanks! I’ve unpinned the image which will hopefully fix the issue. Can’t reboot right now but I’ll see a few hours from now.

iirc I must’ve manually partitioned which caused me to have this size of /boot
What’s the recommended size for the /boot partition to serve as my reference in the future?

That’s a common error I encounter when my / partition is almost out of space - 97% used disk space and above.

Go delete/move some large files until you hit like 94% or lower then try it again.

likely the same issue. You also have less than 300 MB available in /boot

Turns out, recommended size of /boot is 1GB which is the installer’s default according to discussion in this thread:

In my case, looks like /boot has 610M free.

How much free space does your / have?
Do specify the percentage of Use% as shown when using the command:

df -h

df -h:

Filesystem      Size  Used Avail Use% Mounted on
/dev/dm-0       930G  902G   22G  98% /sysroot
composefs        43M   43M     0 100% /
devtmpfs        4.0M     0  4.0M   0% /dev
tmpfs            12G   75M   12G   1% /dev/shm
efivarfs        128K   12K  112K  10% /sys/firmware/efi/efivars
tmpfs           4.7G  6.4M  4.7G   1% /run
tmpfs           1.0M     0  1.0M   0% /run/credentials/systemd-cryptsetup@luks\x2d1f645581\x2d1cd9\x2d4899\x2db886\x2d112f7a5c8f49.service
tmpfs           1.0M     0  1.0M   0% /run/credentials/systemd-journald.service
tmpfs            12G  592K   12G   1% /tmp
/dev/dm-0       930G  902G   22G  98% /var
/dev/nvme1n1p2  974M  297M  610M  33% /boot
/dev/dm-0       930G  902G   22G  98% /var/home
/dev/nvme1n1p1  599M   13M  587M   3% /boot/efi
tmpfs           1.0M     0  1.0M   0% /run/credentials/systemd-resolved.service
tmpfs           2.4G  256K  2.4G   1% /run/user/1000
dwarfs          759M  759M     0 100% /tmp/.mount_remp1168361715037699597

Your /var is 98% full

It has 22G free, How many gigs would be needed for an rpm-ostree upgrade?

Your error message says must have a minimum of 3% free. You have 2% free.

I don’t think this is an amount of free space but a relative check.

Additionally. Btrfs like other CoW filesystems doesn’t behave well when almost completely full.

1 Like

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