Terminal inside bc_desktop app throwing error

sarat · December 1, 2025, 7:44pm

Hi Support,

We are seeing following error when I start desktop with gnome and open terminal inside -

Failed to start transient scope unit: Process org.freedesktop.systemd1 exited with status 1

We are using AL2023 AMI for the compute nodes. Did anyone encountered similar issue? Can you please help to resolve this issue?

Thanks
Sarat

jeff.ohrstrom · December 1, 2025, 8:58pm

Not really sure about this one. We see issues with desktops a lot, but not this specific error.

Are there other log lines in output.log that may indicate something more?

sarat · December 1, 2025, 9:11pm

output.log has no specific error related to this, but when I check journalctl –user -f, I see these entries -
Dec 01 20:20:02 comp-4xl-103 gnome-shell[44032]: Registering session with GDM
Dec 01 20:20:02 comp-4xl-103 gnome-shell[44032]: Error registering session with GDM: GDBus.Error:org.freedesktop.DBus.Error.ServiceUnknown: The name is not activatable
Dec 01 20:20:19 comp-4xl-103 tracker-miner-fs-3.desktop[44592]: (tracker-extract-3:44592): GLib-WARNING **: 20:20:19.270: getpwuid_r(): failed due to unknown user id (2016508)
Dec 01 20:20:58 comp-4xl-103 dbus-daemon[43888]: [session uid=2016508 pid=43886] Activating service name=‘org.gtk.vfs.Metadata’ requested by ‘:1.11’ (uid=2016508 pid=44032 comm=“/usr/bin/gnome-shel>
Dec 01 20:20:58 comp-4xl-103 dbus-daemon[43888]: [session uid=2016508 pid=43886] Successfully activated service ‘org.gtk.vfs.Metadata’
Dec 01 20:24:56 comp-4xl-103 gnome-session[43890]: gnome-session-binary[43890]: WARNING: Could not get session path for session. Check that logind is properly installed and pam_systemd is getting u>
Dec 01 20:24:56 comp-4xl-103 gnome-session-binary[43890]: WARNING: Could not get session path for session. Check that logind is properly installed and pam_systemd is getting used at login.
Dec 01 20:26:13 comp-4xl-103 org.gnome.Shell.desktop[44032]: Xlib: extension “DPMS” missing on display “:1”.
Dec 01 20:26:14 comp-4xl-103 gnome-session[43890]: gnome-session-binary[43890]: WARNING: Could not get session path for session. Check that logind is properly installed and pam_systemd is getting u>
Dec 01 20:26:14 comp-4xl-103 gnome-session-binary[43890]: WARNING: Could not get session path for session. Check that logind is properly installed and pam_systemd is getting used at login.
Dec 01 20:30:11 comp-4xl-103 dbus-daemon[43888]: [session uid=2016508 pid=43886] Activating service name=‘org.gnome.Settings.SearchProvider’ requested by ‘:1.11’ (uid=2016508 pid=44032 comm=”/usr/b>
Dec 01 20:30:11 comp-4xl-103 dbus-daemon[43888]: [session uid=2016508 pid=43886] Activating service name=‘org.gnome.Nautilus’ requested by ‘:1.11’ (uid=2016508 pid=44032 comm=“/usr/bin/gnome-shell >
Dec 01 20:30:11 comp-4xl-103 dbus-daemon[43888]: [session uid=2016508 pid=43886] Activating service name=‘org.gnome.Calculator.SearchProvider’ requested by ‘:1.11’ (uid=2016508 pid=44032 comm=”/usr>
Dec 01 20:30:11 comp-4xl-103 dbus-daemon[43888]: [session uid=2016508 pid=43886] Activating service name=‘org.gnome.seahorse.Application’ requested by ‘:1.11’ (uid=2016508 pid=44032 comm=“/usr/bin/>
Dec 01 20:30:11 comp-4xl-103 gnome-shell[44032]: Received error from D-Bus search provider firefox.desktop: Gio.DBusError: GDBus.Error:org.freedesktop.DBus.Error.ServiceUnknown: The name org.mozill>
Dec 01 20:30:11 comp-4xl-103 dbus-daemon[43888]: [session uid=2016508 pid=43886] Successfully activated service ‘org.gnome.Settings.SearchProvider’
Dec 01 20:30:12 comp-4xl-103 dbus-daemon[43888]: [session uid=2016508 pid=43886] Successfully activated service ‘org.gnome.seahorse.Application’
Dec 01 20:30:12 comp-4xl-103 dbus-daemon[43888]: [session uid=2016508 pid=43886] Successfully activated service ‘org.gnome.Calculator.SearchProvider’
Dec 01 20:30:12 comp-4xl-103 gnome-shell[44032]: Received error from D-Bus search provider firefox.desktop: Gio.DBusError: GDBus.Error:org.freedesktop.DBus.Error.ServiceUnknown: The name org.mozill>
Dec 01 20:30:12 comp-4xl-103 org.gnome.Settings.SearchProvider[45971]: libEGL warning: DRI3: Screen seems not DRI3 capable
Dec 01 20:30:12 comp-4xl-103 org.gnome.Settings.SearchProvider[45971]: libEGL warning: DRI3: Screen seems not DRI3 capable
Dec 01 20:30:12 comp-4xl-103 org.gnome.Settings.SearchProvider[45971]: MESA: error: ZINK: failed to choose pdev
Dec 01 20:30:12 comp-4xl-103 org.gnome.Settings.SearchProvider[45971]: libEGL warning: egl: failed to create dri2 screen
Dec 01 20:30:12 comp-4xl-103 nautilus[45969]: Connecting to org.freedesktop.Tracker3.Miner.Files
Dec 01 20:30:12 comp-4xl-103 dbus-daemon[43888]: [session uid=2016508 pid=43886] Successfully activated service ‘org.gnome.Nautilus’
Dec 01 20:30:12 comp-4xl-103 org.gnome.Nautilus[45969]: libEGL warning: DRI3: Screen seems not DRI3 capable
Dec 01 20:30:12 comp-4xl-103 org.gnome.Nautilus[45969]: libEGL warning: DRI3: Screen seems not DRI3 capable
Dec 01 20:30:12 comp-4xl-103 org.gnome.Nautilus[45969]: error: XDG_RUNTIME_DIR is invalid or not set in the environment.
Dec 01 20:30:12 comp-4xl-103 org.gnome.Nautilus[45969]: MESA: error: ZINK: failed to choose pdev
Dec 01 20:30:12 comp-4xl-103 org.gnome.Nautilus[45969]: libEGL warning: egl: failed to create dri2 screen
Dec 01 20:30:18 comp-4xl-103 dbus-daemon[43888]: [session uid=2016508 pid=43886] Activating service name=‘org.gnome.Ptyxis’ requested by ‘:1.11’ (uid=2016508 pid=44032 comm=”/usr/bin/gnome-shell " >
Dec 01 20:30:18 comp-4xl-103 org.gnome.Ptyxis[46049]: libEGL warning: DRI3: Screen seems not DRI3 capable
Dec 01 20:30:18 comp-4xl-103 org.gnome.Ptyxis[46049]: libEGL warning: DRI3: Screen seems not DRI3 capable
Dec 01 20:30:18 comp-4xl-103 org.gnome.Ptyxis[46049]: MESA: error: ZINK: failed to choose pdev
Dec 01 20:30:18 comp-4xl-103 org.gnome.Ptyxis[46049]: libEGL warning: egl: failed to create dri2 screen
Dec 01 20:30:18 comp-4xl-103 dbus-daemon[43888]: [session uid=2016508 pid=43886] Successfully activated service ‘org.gnome.Ptyxis’
Dec 01 20:30:18 comp-4xl-103 ptyxis-agent[46057]: Failed to process podman containers: Failed to execute child process “podman” (No such file or directory)
Dec 01 20:30:19 comp-4xl-103 dbus-daemon[43888]: [session uid=2016508 pid=43886] Activating service name=‘org.freedesktop.systemd1’ requested by ‘:1.71’ (uid=2016508 pid=46078 comm="systemd-run --u>
Dec 01 20:30:19 comp-4xl-103 dbus-daemon[43888]: [session uid=2016508 pid=43886] Activated service ‘org.freedesktop.systemd1’ failed: Process org.freedesktop.systemd1 exited with status 1

jeff.ohrstrom · December 1, 2025, 9:56pm

Sorry didn’t welcome you before - Hi and welcome!

I don’t like this error. We have to set this explicitly for our desktops. Specifically for MATE, but that could also apply to Gnome.

github.com/OSC/osc-ood-config

apps.awesim.org/apps/bc_desktop/submit/slurm.yml.erb

0e47f2b61


      
          
            image = '/apps/project/ondemand/singularity/mate-rhel8/mate-rhel8.sif'
          -%>
          ---
          batch_connect:
            before_script: |
              # Export the module function if it exists
              [[ $(type -t module) == "function"  ]] && export -f module
          
              # MATE acts strange in pitzer-exp and doesn't like /var/run/$(id -u)
              export XDG_RUNTIME_DIR="$TMPDIR/xdg_runtime"
          
              # reset SLURM_EXPORT_ENV so that things like srun & sbatch work out of the box
              export SLURM_EXPORT_ENV=ALL
          script:
            accounting_id: "<%= account %>"
            native:
              <%- slurm_args.each do |arg| %>
                - "<%= arg %>"
              <%- end %>

sarat · December 1, 2025, 11:26pm

I was able to workaround this issue my wrapping systemd-run and saving it in user’s home -


cat > ~/bin/systemd-run << ‘EOF’


#!/bin/bash

while [[ $# -gt 0 ]]; do
case “$1” in
–user|–scope|–collect|–quiet|–property=|–service-type=)
shift
;;
–same-dir)
shift
;;
–)
shift
break
;;
*)
break
;;
esac
done


if [[ $# -gt 0 ]]; then
exec “$@”
else
exec “${SHELL:-/bin/bash}”
fi
EOF

and updating PATH as SAFE_PATH=$(echo -n “$PATH” | tr : ‘\0’ | grep -zvE ^“$HOME”‘($|/)’ | tr ‘\0’ : | head -c -1) and export PATH=“~/bin:$SAFE_PATH”

sarat · December 1, 2025, 11:28pm

Updating export XDG_RUNTIME_DIR="$TMPDIR/xdg_runtime" made no difference, but above workaround patched the issue.

jeff.ohrstrom · December 2, 2025, 2:05pm

Oh, this was for one single user? Not all across your system?

sarat · December 2, 2025, 2:22pm

This is the case for all users. Just added a wrapper for systemd-run and save it in user’s home and use it instead of system’s one fixed the issue.

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Terminal inside bc_desktop app throwing error

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