GNOME Display Manager problem after update

[mbkuz]

I completed today (formally successfully) yum update of big set of CentOS 7 RPMs, including a number of components working in GNOME Display manager. After reboot Linux, GNOME Display manager don't work successfully: when I enter a user password in GNOME window, I see messages about restart of some services via systemd, and then again appears GNOME password entry window, so I may only work via command line after Ctrl_Alt_F2 etc. I see nothing wrong in boot.log and Xorg.0.log files, but in /var/log/messages there are many error messages (attached), and I don’t understand the real cause of the problem.

I am not familiar with the settings of X11 and GNOME - my job is in the command line, but here is my home computer where I prefer to work w/CentOS GUI, but now I forced to reboot with Windows.
Tail of /var/log/messages (username used is guest) :

Jan 4 18:40:00 myhome1 systemd-logind: New session 2 of user guest.
Jan 4 18:40:00 myhome1 systemd: Started Session 2 of user guest.
Jan 4 18:40:01 myhome1 systemd: Created slice User Slice of root.
Jan 4 18:40:01 myhome1 systemd: Started Session 3 of user root.
Jan 4 18:40:01 myhome1 systemd: Removed slice User Slice of root.
Jan 4 18:40:02 myhome1 gnome-session-binary[3242]: WARNING: Application 'org.gnome.SettingsDaemon.MediaKeys.desktop' killed by signal 15
Jan 4 18:40:02 myhome1 gnome-session: gnome-session-binary[3242]: WARNING: Application 'org.gnome.SettingsDaemon.MediaKeys.desktop' killed by signal 15
Jan 4 18:40:02 myhome1 gnome-session: gnome-session-binary[3242]: WARNING: Application 'org.gnome.SettingsDaemon.Mouse.desktop' killed by signal 15
Jan 4 18:40:02 myhome1 gnome-session: gnome-session-binary[3242]: WARNING: Application 'org.gnome.SettingsDaemon.Power.desktop' killed by signal 15
Jan 4 18:40:02 myhome1 gnome-session-binary[3242]: WARNING: Application 'org.gnome.SettingsDaemon.Rfkill.desktop' killed by signal 15
Jan 4 18:40:02 myhome1 gnome-session-binary[3242]: WARNING: Application 'org.gnome.SettingsDaemon.ScreensaverProxy.desktop' killed by signal 15
Jan 4 18:40:02 myhome1 gnome-session-binary[3242]: WARNING: Application 'org.gnome.SettingsDaemon.Sharing.desktop' killed by signal 15
... etc
Jan 4 18:40:02 myhome1 journal: Cannot open display:
Jan 4 18:40:02 myhome1 gnome-session-binary[3242]: WARNING: Application 'org.gnome.SettingsDaemon.Color.desktop' killed by signal 15
Jan 4 18:40:02 myhome1 gnome-session-binary[3242]: WARNING: Lost name on bus: org.gnome.SessionManager
...
etc
Jan 4 18:40:02 myhome1 com.redhat.imsettings: [ 1546616402.832809]: IMSettings-Daemon[3566]: INFO: Starting imsettings-daemon...
Jan 4 18:40:02 myhome1 com.redhat.imsettings: [ 1546616402.832914]: IMSettings-Daemon[3566]: INFO: [HOME=/home/guest/.config/imsettings]
Jan 4 18:40:02 myhome1 com.redhat.imsettings: [ 1546616402.832944]: IMSettings-Daemon[3566]: INFO: [XINPUTRCDIR=/etc/X11/xinit/]
Jan 4 18:40:02 myhome1 com.redhat.imsettings: [ 1546616402.832969]: IMSettings-Daemon[3566]: INFO: [XINPUTDIR=/etc/X11/xinit/xinput.d/]
Jan 4 18:40:02 myhome1 com.redhat.imsettings: [ 1546616402.832993]: IMSettings-Daemon[3566]: INFO: [MODULEDIR=/usr/lib64/imsettings]
Jan 4 18:40:02 myhome1 com.redhat.imsettings: [ 1546616402.833017]: IMSettings-Daemon[3566]: INFO: [MODULES=gsettings, qt]
Jan 4 18:40:03 myhome1 org.a11y.Bus: Activating service name='org.a11y.atspi.Registry'
Jan 4 18:40:03 myhome1 org.a11y.Bus: Successfully activated service 'org.a11y.atspi.Registry'
Jan 4 18:40:03 myhome1 org.a11y.atspi.Registry: SpiRegistry daemon is running with well-known name - org.a11y.atspi.Registry
Jan 4 18:40:03 myhome1 gnome-session: generating cookie with syscall
Jan 4 18:40:03 myhome1 gnome-session: generating cookie with syscall
Jan 4 18:40:03 myhome1 gnome-session: generating cookie with syscall
Jan 4 18:40:03 myhome1 gnome-session: generating cookie with syscall
Jan 4 18:40:03 myhome1 gnome-session: gnome-session-binary[3491]: WARNING: Unable to find required component 'org.gnome.SettingsDaemon.A11yKeyboard'
Jan 4 18:40:03 myhome1 gnome-session-binary[3491]: WARNING: Unable to find required component 'org.gnome.SettingsDaemon.A11yKeyboard'
Jan 4 18:40:03 myhome1 gnome-session-binary: Entering running state
Jan 4 18:40:03 myhome1 journal: Cannot open display:
Jan 4 18:40:03 myhome1 com.redhat.imsettings: [ 1546616403.091345]: IMSettings-Daemon[3566]: INFO: Release the ownership of com.redhat.imsettings
Jan 4 18:40:03 myhome1 com.redhat.imsettings: Exiting...
Jan 4 18:40:03 myhome1 com.redhat.imsettings: [ 1546616403.091519]: GLib-GIO[3566]: CRITICAL **: Error while sending AddMatch() message: The connection is closed
Jan 4 18:40:03 myhome1 com.redhat.imsettings: [ 1546616403.091572]: GLib-GIO[3566]: CRITICAL **: Error while sending AddMatch() message: The connection is closed
Jan 4 18:40:03 myhome1 org.gtk.vfs.Daemon: A connection to the bus can't be made
Jan 4 18:40:03 myhome1 com.redhat.imsettings: [ 1546616403.091654]: IMSettings-Daemon[3566]: INFO: Unloading imesttings module: qt
Jan 4 18:40:03 myhome1 com.redhat.imsettings: [ 1546616403.091713]: IMSettings-Daemon[3566]: INFO: Unloading imesttings module: gsettings
Jan 4 18:40:03 myhome1 com.redhat.imsettings: [ 1546616403.091756]: IMSettings-Daemon[3566]: INFO: imsettings-daemon is shut down.
Jan 4 18:40:03 myhome1 systemd-logind: Removed session c2.
Jan 4 18:40:03 myhome1 systemd: Started Session c3 of user gdm.
Jan 4 18:40:03 myhome1 systemd-logind: New session c3 of user gdm.
Jan 4 18:40:03 myhome1 org.a11y.Bus: Activating service name='org.a11y.atspi.Registry'
Jan 4 18:40:03 myhome1 org.a11y.Bus: Successfully activated service 'org.a11y.atspi.Registry'
Jan 4 18:40:03 myhome1 org.a11y.atspi.Registry: SpiRegistry daemon is running with well-known name - org.a11y.atspi.Registry
Jan 4 18:40:03 myhome1 gnome-session: generating cookie with syscall
Jan 4 18:40:03 myhome1 gnome-session: generating cookie with syscall
Jan 4 18:40:03 myhome1 gnome-session: generating cookie with syscall
Jan 4 18:40:03 myhome1 gnome-session: generating cookie with syscall
Jan 4 18:40:04 myhome1 dbus[2299]: [system] Activating via systemd: service name='org.freedesktop.GeoClue2' unit='geoclue.service'
Jan 4 18:40:04 myhome1 systemd: Starting Location Lookup Service...
Jan 4 18:40:04 myhome1 dbus[2299]: [system] Activating via systemd: service name='org.freedesktop.Avahi' unit='dbus-org.freedesktop.Avahi.service'
Jan 4 18:40:04 myhome1 dbus[2299]: [system] Activation via systemd failed for unit 'dbus-org.freedesktop.Avahi.service': Unit not found.
Jan 4 18:40:04 myhome1 journal: Failed to connect to avahi service: Daemon not running
Jan 4 18:40:04 myhome1 dbus[2299]: [system] Successfully activated service 'org.freedesktop.GeoClue2'
Jan 4 18:40:04 myhome1 systemd: Started Location Lookup Service.
Jan 4 18:40:04 myhome1 dbus[2299]: [system] Activating via systemd: service name='org.freedesktop.ModemManager1' unit='dbus-org.freedesktop.ModemManager1.service'
Jan 4 18:40:04 myhome1 dbus[2299]: [system] Activation via systemd failed for unit 'dbus-org.freedesktop.ModemManager1.service': Unit not found.
Jan 4 18:40:04 myhome1 journal: Failed to connect to ModemManager: Error calling StartServiceByName for org.freedesktop.ModemManager1: GDBus.Error:org.freedesktop.systemd1.NoSuchUnit: Unit not found.
Jan 4 18:40:04 myhome1 spice-vdagent[3839]: Cannot access vdagent virtio channel /dev/virtio-ports/com.redhat.spice.0
Jan 4 18:40:04 myhome1 gnome-session: gnome-session-binary[3747]: WARNING: App 'spice-vdagent.desktop' exited with code 1
Jan 4 18:40:04 myhome1 gnome-session-binary[3747]: WARNING: App 'spice-vdagent.desktop' exited with code 1
Jan 4 18:40:04 myhome1 journal: Failed to get current display configuration state: GDBus.Error:org.freedesktop.DBus.Error.NameHasNoOwner: Name "org.gnome.Mutter.DisplayConfig" does not exist
Jan 4 18:40:05 myhome1 gsd-smartcard: ObjectStore.cpp(59): Failed to enumerate object store in /var/lib/softhsm/tokens/
Jan 4 18:40:05 myhome1 gsd-smartcard: SoftHSM.cpp(476): Could not load the object store
Jan 4 18:40:05 myhome1 gsd-smartcard: ObjectStore.cpp(59): Failed to enumerate object store in /var/lib/softhsm/tokens/
Jan 4 18:40:05 myhome1 gsd-smartcard: SoftHSM.cpp(476): Could not load the object store
Jan 4 18:40:05 myhome1 gnome-session-binary: Entering running state
Jan 4 18:40:05 myhome1 journal: Some code accessed the property 'AuthList' on the module 'authList'. That property was defined with 'let' or 'const' inside the module. This was previously supported, but is not correct according to the ES6 standard. Any symbols to be exported from a module must be defined with 'var'. The property access will work as previously for the time being, but please fix your code anyway.
Jan 4 18:40:05 myhome1 org.gnome.Shell.desktop: Window manager warning: "XF86RFKill" is not a valid accelerator
Jan 4 18:40:05 myhome1 journal: Error looking up permission: GDBus.Error:org.freedesktop.portal.Error.NotFound: No entry for geolocation
Jan 4 18:40:05 myhome1 journal: JS WARNING: [resource:///org/gnome/shell/ui/layout.js 29]: reference to undefined property "MetaWindowX11"
Jan 4 18:40:09 myhome1 systemd: Started Getty on tty2.
Jan 4 18:40:21 myhome1 systemd: Created slice User Slice of root.
Jan 4 18:40:21 myhome1 systemd-logind: New session 4 of user root.
Jan 4 18:40:21 myhome1 systemd: Started Session 4 of user root.
Jan 4 18:40:21 myhome1 dbus[2299]: [system] Activating service name='org.freedesktop.problems' (using servicehelper)
Jan 4 18:40:22 myhome1 dbus[2299]: [system] Successfully activated service 'org.freedesktop.problems'
Jan 4 18:41:44 myhome1 systemd-logind: Removed session 1.
Jan 4 18:42:00 myhome1 systemd-logind: Removed session 2.
Jan 4 18:42:00 myhome1 systemd: Removed slice User Slice of guest.


What should I try to change to restore the normal GNOME work (taking into account my full absence of knowledge of X11/GNOME setup) ?

Mikhail

[desertcat]

I completed today (formally successfully) yum update of big set of CentOS 7 RPMs, including a number of components working in GNOME Display manager. After reboot Linux, GNOME Display manager don't work successfully: when I enter a user password in GNOME window, I see messages about restart of some services via systemd, and then again appears GNOME password entry window, so I may only work via command line after Ctrl_Alt_F2 etc. I see nothing wrong in boot.log and Xorg.0.log files, but in /var/log/messages there are many error messages (attached), and I don’t understand the real cause of the problem.

[snip]
What should I try to change to restore the normal GNOME work (taking into account my full absence of knowledge of X11/GNOME setup) ?

Mikhail

Do yourself a BIG favour: DUMP GDM!!!I have had nothing but problems with it. I am currently using lightdm. To install lightdm see this:

viewtopic.php?f=47&t=67166

Unless you have a really specific reason to be using GDM, lightdm will *probably* solve your problems.

[mbkuz]

Thanks !
I performed today yum downgrade of gdm from 3.28.2-10 to 3.28.2.9 (3.26.2.1-5 worked OK), and the problem persists, but I received some clarifications.

If I do not enter the user password in gdm-window, then in /var/log/messages there are strings

Jan 7 20:02:07 myhome1 dbus[2307]: [system] Activating service name='org.freedesktop.problems' (using servicehelper)
Jan 7 20:02:07 myhome1 dbus[2307]: [system] Successfully activated service 'org.freedesktop.problems'

If I then do
#systemctl stop gdm.service
then in /var/log/messages appear a set of messages, including error information, that seems to be related to my problem (for example, about IO error):

Jan 7 20:05:14 myhome1 systemd: Stopping GNOME Display Manager...
Jan 7 20:05:14 myhome1 gnome-session-binary[2692]: WARNING: Application 'org.gnome.SettingsDaemon.A11ySettings.desktop' killed by signal 15
... (a set of this mrssages)
Jan 7 20:05:14 myhome1 gnome-session: gnome-session-binary[2692]: WARNING: Application 'org.gnome.SettingsDaemon.Color.desktop' killed by signal 15
Jan 7 20:05:14 myhome1 journal: Failed to send session response The connection is closed
Jan 7 20:05:14 myhome1 gnome-session: gnome-session-binary[2692]: WARNING: Lost name on bus: org.gnome.SessionManager
Jan 7 20:05:14 myhome1 gnome-session-binary[2692]: WARNING: Application 'org.gnome.SettingsDaemon.Power.desktop' killed by signal 15
Jan 7 20:05:14 myhome1 journal: Error releasing name org.freedesktop.portal.IBus: The connection is closed
Jan 7 20:05:14 myhome1 gnome-session-binary[2692]: WARNING: Application 'org.gnome.SettingsDaemon.PrintNotifications.desktop' killed by signal 15
... (then messages for a set of other SettingsDaemon.SERVICE.desktop)...
Jan 7 20:05:14 myhome1 gnome-session-binary[2692]: WARNING: Application 'org.gnome.SettingsDaemon.Color.desktop' killed by signal 15
Jan 7 20:05:14 myhome1 gnome-session-binary[2692]: WARNING: Lost name on bus: org.gnome.SessionManager
Jan 7 20:05:14 myhome1 journal: Cannot open display:
Jan 7 20:05:14 myhome1 journal: gnome-shell: Fatal IO error 4 (Interrupted system call) on X server :0.
Jan 7 20:05:14 myhome1 gdm: GLib: g_hash_table_find: assertion 'version == hash_table->version' failed
Jan 7 20:05:14 myhome1 systemd: Stopped GNOME Display Manager.
Jan 7 20:05:34 myhome1 systemd-logind: Removed session c1.
Jan 7 20:05:34 myhome1 systemd: Removed slice User Slice of gdm.


Do these messages give a possible way to clarify /correct the problem?
Mikhail

[TrevorH]

When you ran your initial update, did you update _everything_ or just bits of the system? This is most likely 7.6 and there will be a lot of interdependent updates that will need to go on at the same time. We do not test partial updates.

[mbkuz]

Yes, it was 7.5, and I performed a very large set of useful for me (by my opinion) yum updates, but not complete update to 7.6. I now have to work most of the time with GUI (booting Windows instead of CentOS). What is now a practically simple solution for me?

Mikhail

[TrevorH]

Make sure you update everything. The symptoms you show are similar to those we saw during the QA period for 7.6 when not everything had been updated from, 7.5 versions.

[dbport]

I'm having the same issues -- TrevorH, how do I make sure everything is updated?

[TrevorH]

Same way as always: run yum update