Upgrade failing due to lack of space (on rootfs?)

Hello,

I tried making system updates through

 sudo pacman -Syu garuda-hooks

and I have a failure that looks like it comes from not enough disk space:

:: Synchronising package databases...
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
 chaotic-aur is up to date
warning: garuda-hooks-2.6.2-1 is up to date -- reinstalling
:: Starting full system upgrade...
resolving dependencies...
looking for conflicting packages...
warning: dependency cycle detected:
warning: python-ipykernel will be installed before its python-jupyter_client dependency
warning: dependency cycle detected:
warning: python-jupyterlab_server will be installed before its jupyter-server dependency
warning: dependency cycle detected:
warning: jupyterlab will be installed before its jupyter-server dependency

Packages (211) colord-gtk4-0.3.0-2  garuda-video-linux-config-1:r62.889aefa-6  garuda-welcome-1.1.4-2
               gdm-42.0+r11+g4a52f026-1  gedit-42.0-1  gedit-plugins-42.0-1  gegl-0.4.36-2
               geocode-glib-3.26.2+r9+g6047da3-2  gimp-2.10.30-2  git-2.36.0-1  gjs-2:1.72.0-1
               glslang-11.9.0-1  gnome-autoar-0.4.3-2  gnome-bluetooth-3.34.5-3  gnome-bluetooth-3.0-42.0-1
               gnome-calculator-42.0-1  gnome-color-manager-3.36.0+r25+g4aab8b59-1
               gnome-control-center-42.1-1  gnome-desktop-4-1:42.1-1  gnome-disk-utility-42.0-1
               gnome-firmware-42.1-1  gnome-logs-42.0-1  gnome-screenshot-41.0+r25+g45f08f0-1
               gnome-session-42.0-1  gnome-settings-daemon-42.1-1  gnome-shell-1:42.0-1
               gnome-software-42.1-1  gnome-software-packagekit-plugin-42.1-1  gnome-sound-recorder-42.0-1
               gnome-system-monitor-42.0-1  gnome-terminal-3.44.0-1  gnome-tweaks-42beta+r9+gc66d8c3-1
               gnustep-base-1.28.0-4  gpsd-3.24-1  graphicsmagick-1.3.38-1  groff-1.22.4-7  gsound-1.0.3-2
               gst-plugin-pipewire-1:0.3.51-1  gtk4-1:4.6.3-1  gtksourceview5-5.4.1-1  gvfs-afc-1.50.1-1
               gvfs-goa-1.50.1-1  gvfs-google-1.50.1-1  gvfs-gphoto2-1.50.1-1  gvfs-mtp-1.50.1-1
               gvfs-nfs-1.50.1-1  gvfs-smb-1.50.1-1  gzip-1.12-1  hplip-1:3.22.4-1  hwloc-2.7.1-1
               imath-3.1.5-1  intel-compute-runtime-22.17.23034-1  intel-graphics-compiler-1:1.0.11061-1
               intel-opencl-clang-13.0.0.r5+g1490bd4-1  intel-ucode-20220419-1  inxi-3.3.15.1-1
               ipp-usb-0.9.20-2  iproute2-5.17.0-3  ipython-8.3.0-1  jasper-2.0.33-2  jfsutils-1.1.15-8
               js91-91.8.0-1  jupyter-nbclassic-0.3.7-2  jupyter-nbclient-0.6.0-1  jupyter-nbconvert-6.5.0-3
               jupyter-nbformat-5.3.0-2  jupyter-notebook-6.4.11-1  jupyter-server-1.17.0-1
               jupyter-widgetsnbextension-1:3.6.0-2  jupyterlab-3.3.4-1  jupyterlab_pygments-0.2.0-1
               lapack-3.10.1-1  lib32-libva-mesa-driver-22.0.2-1  lib32-mesa-vdpau-22.0.2-1
               lib32-opencl-mesa-22.0.2-1  lib32-vulkan-mesa-layers-22.0.2-1  lib32-vulkan-radeon-22.0.2-1
               libadwaita-1:1.1.1-1  libbpf-0.7.0-1  libcdr-0.1.7-4  libcgif-0.3.0-1  libe-book-0.1.3-11
               libgdm-42.0+r11+g4a52f026-1  libgee-0.20.5-2  libgnomekbd-1:3.26.1+r5+g54da436-1
               libgweather-40.0+r87+g80e5a652-2  libgweather-4-4.0.0-1  libical-3.0.14-3
               libinput-gestures-2.73-1  libmspub-0.1.4-12  libnautilus-extension-42.1.1-1  libnma-1.8.38-1
               libnma-common-1.8.38-1  libnma-gtk4-1.8.38-1  libnumbertext-1.0.10-1  libopenmpt-0.6.3-1
               libpamac-aur-11.3.0-0  libpgm-5.3.128-2  libpipeline-1.5.6-1  libqxp-0.0.2-8
               libreoffice-still-7.2.6-2  libutf8proc-2.7.0-2  libvisio-0.1.7-7  libxvmc-1.0.13-1
               libzmf-0.0.2-12  linux-firmware-20220411.705f19a-1  linux-firmware-whence-20220411.705f19a-1
               linux-zen-5.17.5.zen1-1  linux-zen-headers-5.17.5.zen1-1  lollypop-1.4.33-1  lrzip-0.641-2
               luajit-2.1.0.beta3.r397.g20aea939-1  lzip-1.23-2  mercurial-6.1.1-1  micro-2.0.10-4
               mobile-broadband-provider-info-20220315-1  modemmanager-1.18.8-1  mpg123-1.29.3-2
               mtools-1:4.0.39-1  mutter-42.0-2  nautilus-42.1.1-1  networkmanager-fortisslvpn-1.4.0-2
               networkmanager-l2tp-1.20.0-3  networkmanager-openconnect-1.2.8-2
               networkmanager-openvpn-1.8.18-2  networkmanager-pptp-1.2.10-2  networkmanager-support-1-3
               networkmanager-vpnc-1.2.8-2  opencl-mesa-22.0.2-1  openexr-3.1.5-1  openfortivpn-1.17.2-1
               os-prober-btrfs-1.79-5  pamac-aur-10.4.0-0  pipewire-alsa-1:0.3.51-1
               pipewire-pulse-1:0.3.51-1  pipewire-v4l2-1:0.3.51-1  pipewire-zeroconf-1:0.3.51-1
               pkcs11-helper-1.29.0-1  plymouth-git-22.02.122.r45.ge960111-1  python-babel-2.10.1-1
               python-click-8.1.3-1  python-dnspython-1:2.2.1-1  python-entrypoints-0.4-2
               python-evdev-1.5.0-1  python-fastjsonschema-2.15.3-1  python-ipykernel-6.13.0-1
               python-ipywidgets-7.7.0-3  python-jinja-1:3.0.3-2  python-jupyter_client-7.3.0-1
               python-jupyter_core-4.10.0-1  python-jupyterlab_server-2.13.0-1  python-nest-asyncio-1.5.5-1
               python-pillow-9.1.0-1  python-prometheus_client-0.14.1-1  python-pygments-2.12.0-1
               python-pynput-1.7.6-2  python-pyqt5-sip-12.10.1-1  python-reportlab-3.6.9-1
               python-setuptools-1:59.5.0-1  python-testpath-0.6.0-1  python-tomlkit-0.10.2-1
               python-zipp-3.8.0-1  qt6-5compat-6.3.0-2  qt6-base-6.3.0-3  qt6-declarative-6.3.0-1
               qt6-imageformats-6.3.0-1  qt6-svg-6.3.0-1  qt6-translations-6.3.0-1  qt6-wayland-6.3.0-1
               raptor-2.0.15-19  samba-4.16.0-6  scrcpy-1.23-2  sdl-1:1.2.15+r406+gf1caf909-1  semver-7.3.7-1
               shaderc-2022.1-3  signal-desktop-5.41.0-1  simple-scan-42.1-1
               skypeforlinux-stable-bin-8.83.0.408-1  slack-desktop-4.25.1-1  snapper-0.10.1-1
               sof-firmware-2.1.1-1  suitesparse-5.12.0-1  sushi-41.2-1  systemd-sysvcompat-250.5-1
               teams-1.5.00.10453-1  telegram-desktop-3.7.3-1  tepl-6.00.0-5  tor-0.4.6.10-1
               tracker3-miners-3.3.0-2  unarchiver-1.10.7-6  vde2-2.3.2-21  vim-8.2.4827-1
               vim-runtime-8.2.4827-1  virtualbox-6.1.34-2  virtualbox-ext-oracle-6.1.34-1
               virtualbox-ext-vnc-6.1.34-2  virtualbox-guest-iso-6.1.34-1  virtualbox-host-dkms-6.1.34-2
               virtualbox-sdk-6.1.34-2  vlc-3.0.17.4-2  vte-common-0.68.0-2  vte3-0.68.0-2
               vulkan-headers-1:1.3.211-1  webkit2gtk-4.1-2.36.1-1  wpa_supplicant-2:2.10-4
               xdg-desktop-portal-gnome-42.1-1  xorg-setxkbmap-1.3.3-1  xorg-xauth-1.1.2-1
               xorg-xwayland-22.1.1-1  zenity-3.42.1-1  garuda-hooks-2.6.2-1

Total Download Size:      0.35 MiB
Total Installed Size:  3889.04 MiB
Net Upgrade Size:        87.85 MiB

:: Proceed with installation? [Y/n] y
:: Retrieving packages...
 sdl-1:1.2.15+r406+gf1caf909-1-x86_64  359.4 KiB  3.19 MiB/s 00:00 [------------------------------------] 100%
(211/211) checking keys in keyring                                 [------------------------------------] 100%
(211/211) checking package integrity                               [------------------------------------] 100%
(211/211) loading package files                                    [------------------------------------] 100%
(211/211) checking for file conflicts                              [------------------------------------] 100%
(211/211) checking available disk space                            [------------------------------------] 100%
error: Partition / too full: 35018 blocks needed, 4 blocks free
error: not enough free disk space
error: failed to commit transaction (not enough free disk space)
Errors occurred, no packages were upgraded.

However my disk is not really full, I can still create files etc. I tried removing libreoffice to make space but then I had a "fail to run transaction hooks" errors. I had something regarding a PGP key which seemed to be fixed by updating archlinux-keyring yet the above issue still stands.

When I run: df -h I get

Filesystem      Size  Used Avail Use% Mounted on
dev             3.7G     0  3.7G   0% /dev
run             3.7G  2.0M  3.7G   1% /run
rootfs          3.7G  3.7G   12K 100% /
tmpfs           3.7G     0  3.7G   0% /dev/shm
/dev/nvme0n1p1  256M   31M  226M  13% /boot/efi
/dev/dm-0       144G   17G  126G  12% /home
/dev/dm-0       144G   17G  126G  12% /root
/dev/dm-0       144G   17G  126G  12% /srv
/dev/dm-0       144G   17G  126G  12% /var/cache
/dev/dm-0       144G   17G  126G  12% /var/log
/dev/dm-0       144G   17G  126G  12% /var/tmp
tmpfs           3.7G  416K  3.7G   1% /home/guest
tmpfs           3.7G  6.6M  3.7G   1% /tmp
tmpfs           754M  108K  754M   1% /run/user/1000
/dev/sda1       239G  162G   77G  68% /run/media/benoitseron/3334-6434

hence it seems that the problem would be with rootfs, right?

The ouput of garuda-inxi:

System:
  Kernel: 5.16.16-zen1-1-zen arch: x86_64 bits: 64 compiler: gcc v: 11.2.0
    parameters: BOOT_IMAGE=/@/.snapshots/18/snapshot/boot/vmlinuz-linux-zen
    root=UUID=075bb302-40dc-4147-96e2-52264d053f21
    cryptdevice=UUID=ebbed3b6-b8d5-43db-99f1-10e395d7d447:luks-ebbed3b6-b8d5-43db-99f1-10e395d7d447
    root=/dev/mapper/luks-ebbed3b6-b8d5-43db-99f1-10e395d7d447 quiet splash
    rd.udev.log_priority=3 vt.global_cursor_default=0 loglevel=3
    rootflags=defaults,noatime,noautodefrag,compress=zstd,[email protected]/.snapshots/18/snapshot
  Desktop: GNOME v: 41.5 tk: GTK v: 3.24.33 wm: gnome-shell dm: GDM v: 41.3
    Distro: Garuda Linux base: Arch Linux
Machine:
  Type: Laptop System: Microsoft product: Surface Pro 7
    v: 124I:00046T:000M:0100000D:0B:07F:0C:05P:48S:1E:0Y:1K:0U:04R:5
    serial: <superuser required> Chassis: type: 9
    serial: <superuser required>
  Mobo: Microsoft model: Surface Pro 7 serial: <superuser required>
    UEFI: Microsoft v: 13.101.140 date: 12/14/2021
Battery:
  ID-1: BAT1 charge: 31.7 Wh (81.7%) condition: 38.8/43.2 Wh (89.8%)
    volts: 8.5 min: 7.6 model: DYN M1109597 type: Li-ion serial: <filter>
    status: charging cycles: 179
CPU:
  Info: model: Intel Core i5-1035G4 bits: 64 type: MT MCP arch: Ice Lake
    family: 6 model-id: 0x7E (126) stepping: 5 microcode: 0xA8
  Topology: cpus: 1x cores: 4 tpc: 2 threads: 8 smt: enabled cache:
    L1: 320 KiB desc: d-4x48 KiB; i-4x32 KiB L2: 2 MiB desc: 4x512 KiB
    L3: 6 MiB desc: 1x6 MiB
  Speed (MHz): avg: 1137 high: 1201 min/max: 400/3700 scaling:
    driver: intel_pstate governor: powersave cores: 1: 1201 2: 1201 3: 1201
    4: 1152 5: 1102 6: 1100 7: 1101 8: 1042 bogomips: 23961
  Flags: avx avx2 ht lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx
  Vulnerabilities:
  Type: itlb_multihit status: KVM: VMX disabled
  Type: l1tf status: Not affected
  Type: mds status: Not affected
  Type: meltdown status: Not affected
  Type: spec_store_bypass
    mitigation: Speculative Store Bypass disabled via prctl
  Type: spectre_v1
    mitigation: usercopy/swapgs barriers and __user pointer sanitization
  Type: spectre_v2
    mitigation: Enhanced IBRS, IBPB: conditional, RSB filling
  Type: srbds status: Not affected
  Type: tsx_async_abort status: Not affected
Can't use string ("edid-sync") as a HASH ref while "strict refs" in use at /usr/bin/inxi line 28619, <$fh> line 1.
System:
  Kernel: 5.16.16-zen1-1-zen arch: x86_64 bits: 64 compiler: gcc v: 11.2.0
    parameters: BOOT_IMAGE=/@/.snapshots/18/snapshot/boot/vmlinuz-linux-zen
    root=UUID=075bb302-40dc-4147-96e2-52264d053f21
    cryptdevice=UUID=ebbed3b6-b8d5-43db-99f1-10e395d7d447:luks-ebbed3b6-b8d5-43db-99f1-10e395d7d447
    root=/dev/mapper/luks-ebbed3b6-b8d5-43db-99f1-10e395d7d447 quiet splash
    rd.udev.log_priority=3 vt.global_cursor_default=0 loglevel=3
    rootflags=defaults,noatime,noautodefrag,compress=zstd,[email protected]/.snapshots/18/snapshot
  Desktop: GNOME v: 41.5 tk: GTK v: 3.24.33 wm: gnome-shell dm: GDM v: 41.3
    Distro: Garuda Linux base: Arch Linux
Machine:
  Type: Laptop System: Microsoft product: Surface Pro 7
    v: 124I:00046T:000M:0100000D:0B:07F:0C:05P:48S:1E:0Y:1K:0U:04R:5
    serial: <superuser required> Chassis: type: 9
    serial: <superuser required>
  Mobo: Microsoft model: Surface Pro 7 serial: <superuser required>
    UEFI: Microsoft v: 13.101.140 date: 12/14/2021
Battery:
  ID-1: BAT1 charge: 31.7 Wh (81.7%) condition: 38.8/43.2 Wh (89.8%)
    volts: 8.5 min: 7.6 model: DYN M1109597 type: Li-ion serial: <filter>
    status: charging cycles: 179
CPU:
  Info: model: Intel Core i5-1035G4 bits: 64 type: MT MCP arch: Ice Lake
    family: 6 model-id: 0x7E (126) stepping: 5 microcode: 0xA8
  Topology: cpus: 1x cores: 4 tpc: 2 threads: 8 smt: enabled cache:
    L1: 320 KiB desc: d-4x48 KiB; i-4x32 KiB L2: 2 MiB desc: 4x512 KiB
    L3: 6 MiB desc: 1x6 MiB
  Speed (MHz): avg: 1205 high: 1284 min/max: 400/3700 scaling:
    driver: intel_pstate governor: powersave cores: 1: 1200 2: 1159 3: 1162
    4: 1236 5: 1201 6: 1201 7: 1200 8: 1284 bogomips: 23961
  Flags: avx avx2 ht lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx
  Vulnerabilities:
  Type: itlb_multihit status: KVM: VMX disabled
  Type: l1tf status: Not affected
  Type: mds status: Not affected
  Type: meltdown status: Not affected
  Type: spec_store_bypass
    mitigation: Speculative Store Bypass disabled via prctl
  Type: spectre_v1
    mitigation: usercopy/swapgs barriers and __user pointer sanitization
  Type: spectre_v2
    mitigation: Enhanced IBRS, IBPB: conditional, RSB filling
  Type: srbds status: Not affected
  Type: tsx_async_abort status: Not affected
Can't use string ("edid-sync") as a HASH ref while "strict refs" in use at /usr/bin/inxi line 28619, <$fh> line 1.
Garuda (2.6.2-1):
  System install date:     2022-03-28
  Last full system update: 2022-03-29
  Is partially upgraded:   Yes
  Relevant software:       NetworkManager
  Windows dual boot:       Probably (Run as root to verify)
  Snapshots:               Snapper
  Failed units:            snapper-cleanup.service 

Any help would be greatly appreciated! Thanks in advance.

Well, the problem is clear and df -h is showing this to you:

Filesystem      Size  Used Avail Use% Mounted on
...
rootfs          3.7G  3.7G   12K 100% /

What you need is to delete some files on your / filesystem (which I can't give advice of because even the /var/cache is on another partition) if you want to upgrade. I don't understand why do you create a root partition with so little space.

Honestly, it would be better to just reinstall and give a lot of more space to / because you will be facing this issue almost everytime you want to update or install something.

2 Likes

I don't think I manually wrote that partition size myself, just did a standard install.

And if I reinstall then I have to reparametrise/reinstall everything on my computer, right? isn't there a way to avoid having to do that?

You're currently booted into a snapshot!
Run garuda-update in terminal and you will see.

You have to restore the snapshot via BTRFS Assistant before you can update your system.

Please always apply system updates with garuda-update

6 Likes

Yes I did this because the previous update failed (I used the snapshot for a week or two)... Now indeed, it works after restoring the snapshot, thanks a lot.

Is there a point in trying to increase the partition size of root with something like gparted to avoid further problems?

Your disk space probably isn't a problem. When you are booted into a snapshot, / is an overlayfs. It was probably the overlay that was running out of space.

We can see for sure if you share df -h now that you are no longer booted into the snapshot.

4 Likes

Here is what I get

Filesystem      Size  Used Avail Use% Mounted on
dev             3.7G     0  3.7G   0% /dev
run             3.7G  1.9M  3.7G   1% /run
/dev/dm-0       144G   26G  117G  18% /
tmpfs           3.7G     0  3.7G   0% /dev/shm
/dev/dm-0       144G   26G  117G  18% /home
/dev/dm-0       144G   26G  117G  18% /root
/dev/dm-0       144G   26G  117G  18% /srv
/dev/dm-0       144G   26G  117G  18% /var/log
/dev/dm-0       144G   26G  117G  18% /var/cache
/dev/dm-0       144G   26G  117G  18% /var/tmp
tmpfs           3.7G  400K  3.7G   1% /home/guest
tmpfs           3.7G  8.0K  3.7G   1% /tmp
/dev/nvme0n1p1  256M   31M  226M  13% /boot/efi
tmpfs           754M  731M   24M  97% /run/user/1000

seems ok no?

1 Like

Yes, you have 117GiB free. That should be plenty :wink:

1 Like

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