Some issues during / after upgrading to 4.2.0

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Ulrich Windl

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Jan 4, 2024, 6:20:34 PMJan 4
to qubes...@googlegroups.com
Hi!


As I had some time, I performed the upgrade to Qubes OS 4.2.0.

Unfortunately there were a few unexpected findings:

* fedora-38 is obsolete already? I thought fedora-37 is???

* my debian-12-dvm template no longer offers Firefox: Qubes settings
say: "Application missing in template (firefox-esr.desktop)", However
the template is the same as before upgrading Qubes-OS

* The post-reboot phase talked about upgrading to 4.1 once;
unfortunately the messages scrolled away.

* Booting after "pre-reboot" showed no UEFI boot entry being present.

* "qmemman.daemon.xswatcher[103730]: do_balance() failed" (see details
at end of message)

* Jan 04 22:52:15 dom0 (o-bridge)[111387]: PAM unable to
dlopen(/usr/lib64/security/pam_sss.so): /usr/lib64/security/pam_sss.so:
cannot open shared object file: No such file or directory
  Jan 04 22:52:15 dom0 (o-bridge)[111387]: PAM adding faulty module:
/usr/lib64/security/pam_sss.so

* In 4.1 there was a shutdown issue: the LUKS device could not be
deactivated as the journal was still writing to the filesystem (see at
end, also)

*** After reboot

* "Jan 04 23:56:34 dom0 systemd-escape[381]: Input
'luks-ef8d52d9-a96f-43de-97b4-d73c63443262' is not an absolute file
system path, escaping is likely not going to be reversible."

* "Jan 04 23:56:35 dom0 systemd-udevd[437]:
/usr/lib/udev/rules.d/50-udev-default.rules:46 Unknown group 'sgx',
ignoring"

* "Jan 04 23:56:35 dom0 kernel: firewire_ohci 0000:05:02.0: DMA context
ARReq has stopped, error code: evt_unknown
    Jan 04 23:56:35 dom0 kernel: firewire_ohci 0000:05:02.0: added OHCI
v1.10 device as card 0, 4 IR + 8 IT contexts, quirks 0x41
    Jan 04 23:56:35 dom0 kernel: firewire_ohci 0000:05:02.0: bad self
ID 0/1 (00000000 != ~00000000)"

* "an 04 22:57:01 dom0 systemd-journald[1013]: File
/run/log/journal/dd4105a4171541cf81528207ed3decb6/system.journal
corrupted or uncleanly shut down, renaming and replacing."

* "Jan 04 22:57:01 dom0 udevadm[1030]: systemd-udev-settle.service is
deprecated. Please fix dmraid-activation.service not to pull it in.
    Jan 04 22:57:01 dom0 kernel: block device autoloading is deprecated
and will be removed."

* "Jan 04 22:57:16 dom0 (systemd)[7250]: PAM unable to
dlopen(/usr/lib64/security/pam_sss.so): /usr/lib64/security/pam_sss.so:
cannot open shared object file: No such file or directory
    Jan 04 22:57:16 dom0 (systemd)[7250]: PAM adding faulty module:
/usr/lib64/security/pam_sss.so
    Jan 04 22:57:16 dom0 (systemd)[7250]:
pam_systemd_home(systemd-user:account): systemd-homed is not available:
Could not activate remote peer: activation request failed: unknown unit."

* "Jan 04 22:57:17 dom0 systemd[7250]: Starting dbus-broker.service -
D-Bus User Message Bus...
    Jan 04 22:57:17 dom0 audit[7188]: USER_START pid=7188 uid=0
auid=1000 ses=2 msg='op=PAM:session_open
grantors=pam_selinux,pam_loginuid,pam_selinux,pam_keyinit,pam_namespace,pam_keyinit,pam_limits,pam_systemd,pam_unix,pam_lastlog,pam_umask,pam_lastlog
acct="master" exe="/usr/sbin/lightdm" hostname=? addr=? termina>
    Jan 04 22:57:17 dom0 dbus-broker-launch[7261]: Service file
'/usr/share/dbus-1/services/org.xfce.Thunar.FileManager1.service' is not
named after the D-Bus name 'org.freedesktop.FileManager1'.
    Jan 04 22:57:17 dom0 dbus-broker-launch[7261]: Policy to allow
eavesdropping in /usr/share/dbus-1/session.conf +31: Eavesdropping is
deprecated and ignored
    Jan 04 22:57:17 dom0 dbus-broker-launch[7261]: Policy to allow
eavesdropping in /usr/share/dbus-1/session.conf +33: Eavesdropping is
deprecated and ignored
    Jan 04 22:57:17 dom0 dbus-broker-launch[7261]: Service file
'/usr/share/dbus-1/services/dbus-qubes-app-menu.service' is not named
after the D-Bus name 'org.qubesos.appmenu'.
    Jan 04 22:57:17 dom0 systemd[7250]: Started dbus-broker.service -
D-Bus User Message Bus."

* "Jan 04 23:01:40 dom0 qubes.SyncAppMenus+-debian-12[9218]: Warning:
ignoring key 'Name' of display-im6.q16

    Jan 04 23:01:41 dom0 qubes.SyncAppMenus+-debian-12[9218]: Warning:
not creating/updating
'/home/master/.local/share/qubes-appmenus/debian-12/apps.templates/display-im6.q16.desktop'
because of missing 'Name' key" ???

* "Jan 05 00:04:25 dom0 qmemman.systemstate[4900]: Xen free = 137217483
too small for satisfy assignments! assigned_but_unused=121323564,
domdict={'0': {'memory_current': 4278190080, 'memory_actual':
4294967296, 'memory_maximum': 4294967296, 'mem_used': 1505382400, 'id':
'0', 'last_target': 4294967296, 'use_hoplug': False, 'no_progress':
False, 'slow_memset_react': False, 'use_hotplug': False}, '1':
{'memory_current': 402698240, 'memory_actual': 402698240,
'memory_maximum': 419430400, 'mem_used': None, 'id': '1', 'last_target':
402653184, 'use_hoplug': False, 'no_progress': False,
'slow_memset_react': False, 'use_hotplug': False}, '2':
{'memory_current': 150994944, 'memory_actual': 150994944,
'memory_maximum': 150994944, 'mem_used': None, 'id': '2', 'last_target':
150994944, 'use_hoplug': False, 'no_progress': False,
'slow_memset_react': False, 'use_hotplug': False}, '3':
{'memory_current': 1503051776, 'memory_actual': 1519765398,
'memory_maximum': 4194304000, 'mem_used': 454008832, 'id': '3',
'last_target': 1537672796, 'use_hoplug': False, 'no_progress': False,
'slow_memset_react': False, 'use_hotplug': True}, '4':
{'memory_current': 1752047616, 'memory_actual': 1768759535,
'memory_maximum': 4194304000, 'mem_used': 541683712, 'id': '4',
'last_target': 1788542049, 'use_hoplug': False, 'no_progress': False,
'slow_memset_react': False, 'use_hotplug': True}, '16':
{'memory_current': 3663560704, 'memory_actual': 3680273744,
'memory_maximum': 4294967296, 'mem_used': 1172312064, 'id': '16',
'last_target': 3592995773, 'use_hoplug': False, 'no_progress': False,
'slow_memset_react': False, 'use_hotplug': True}, '17':
{'memory_current': 2759909376, 'memory_actual': 2776624523,
'memory_maximum': 4194304000, 'mem_used': 896569344, 'id': '17',
'last_target': 2776624523, 'use_hoplug': False, 'no_progress': False,
'slow_memset_react': False, 'use_hotplug': True}, '18':
{'memory_current': 2069704704, 'memory_actual': 2086420452,
'memory_maximum': 4194304000, 'mem_used': 653537280, 'id': '18',
'last_target': 2086420452, 'use_hoplug': False, 'no_progress': False,
'slow_memset_react': False, 'use_hotplug': True}}"

---

Jan 04 22:50:37 dom0 qmemman.daemon.xswatcher[103730]: do_balance() failed
                                                       Traceback (most
recent call last):
                                                         File
"/usr/lib/python3.11/site-packages/qubes/tools/qmemmand.py", line 140,
in domain_list_changed
system_state.do_balance()
                                                         File
"/usr/lib/python3.11/site-packages/qubes/qmemman/systemstate.py", line
301, in do_balance
self.refresh_memactual()
                                                         File
"/usr/lib/python3.11/site-packages/qubes/qmemman/systemstate.py", line
102, in refresh_memactual
                                                           for domain
in self.xc.domain_getinfo():
^^^^^^^^^^^^^^^^^^^^^^^^
xen.lowlevel.xc.Error: (13, 'Permission denied')
Jan 04 22:50:37 dom0 qmemmand[103730]: --- Logging error ---
Jan 04 22:50:37 dom0 qmemmand[103730]: Traceback (most recent call last):
Jan 04 22:50:37 dom0 qmemmand[103730]:   File
"/usr/lib/python3.11/site-packages/qubes/tools/qmemmand.py", line 164,
in meminfo_changed
Jan 04 22:50:37 dom0 qmemmand[103730]:
system_state.refresh_meminfo(domain_id, untrusted_meminfo_key)
Jan 04 22:50:37 dom0 qmemmand[103730]:   File
"/usr/lib/python3.11/site-packages/qubes/qmemman/systemstate.py", line
244, in refresh_meminfo
Jan 04 22:50:37 dom0 qmemmand[103730]:     self.do_balance()
Jan 04 22:50:37 dom0 qmemmand[103730]:   File
"/usr/lib/python3.11/site-packages/qubes/qmemman/systemstate.py", line
301, in do_balance
Jan 04 22:50:37 dom0 qmemmand[103730]: self.refresh_memactual()
Jan 04 22:50:37 dom0 qmemmand[103730]:   File
"/usr/lib/python3.11/site-packages/qubes/qmemman/systemstate.py", line
102, in refresh_memactual
Jan 04 22:50:37 dom0 qmemmand[103730]:     for domain in
self.xc.domain_getinfo():
Jan 04 22:50:37 dom0 qmemmand[103730]: ^^^^^^^^^^^^^^^^^^^^^^^^
Jan 04 22:50:37 dom0 qmemmand[103730]: xen.lowlevel.xc.Error: (13,
'Permission denied')
Jan 04 22:50:37 dom0 qmemmand[103730]: During handling of the above
exception, another exception occurred:
Jan 04 22:50:37 dom0 qmemmand[103730]: Traceback (most recent call last):
Jan 04 22:50:37 dom0 qmemmand[103730]:   File
"/usr/lib64/python3.11/logging/handlers.py", line 987, in emit
Jan 04 22:50:37 dom0 qmemmand[103730]:     msg = self.format(record)
Jan 04 22:50:37 dom0 qmemmand[103730]: ^^^^^^^^^^^^^^^^^^^
Jan 04 22:50:37 dom0 qmemmand[103730]:   File
"/usr/lib64/python3.11/logging/__init__.py", line 953, in format
Jan 04 22:50:37 dom0 qmemmand[103730]:     return fmt.format(record)
Jan 04 22:50:37 dom0 qmemmand[103730]: ^^^^^^^^^^^^^^^^^^
Jan 04 22:50:37 dom0 qmemmand[103730]:   File
"/usr/lib64/python3.11/logging/__init__.py", line 687, in format
Jan 04 22:50:37 dom0 qmemmand[103730]:     record.message =
record.getMessage()
Jan 04 22:50:37 dom0 qmemmand[103730]: ^^^^^^^^^^^^^^^^^^^
Jan 04 22:50:37 dom0 qmemmand[103730]:   File
"/usr/lib64/python3.11/logging/__init__.py", line 377, in getMessage
Jan 04 22:50:37 dom0 qmemmand[103730]:     msg = msg % self.args
Jan 04 22:50:37 dom0 qmemmand[103730]:           ~~~~^~~~~~~~~~~
Jan 04 22:50:37 dom0 qmemmand[103730]: TypeError: %d format: a real
number is required, not str
Jan 04 22:50:37 dom0 qmemmand[103730]: Call stack:
Jan 04 22:50:37 dom0 qmemmand[103730]:   File "/usr/bin/qmemmand", line
5, in <module>
Jan 04 22:50:37 dom0 qmemmand[103730]:     sys.exit(main())
Jan 04 22:50:37 dom0 qmemmand[103730]:   File
"/usr/lib/python3.11/site-packages/qubes/tools/qmemmand.py", line 308,
in main
Jan 04 22:50:37 dom0 qmemmand[103730]: XSWatcher().watch_loop()
Jan 04 22:50:37 dom0 qmemmand[103730]:   File
"/usr/lib/python3.11/site-packages/qubes/tools/qmemmand.py", line 175,
in watch_loop
Jan 04 22:50:37 dom0 qmemmand[103730]:     token.func(self, token.param)
Jan 04 22:50:37 dom0 qmemmand[103730]:   File
"/usr/lib/python3.11/site-packages/qubes/tools/qmemmand.py", line 166,
in meminfo_changed
Jan 04 22:50:37 dom0 qmemmand[103730]: self.log.exception('Updating
meminfo for %d failed', domain_id)
Jan 04 22:50:37 dom0 qmemmand[103730]: Message: 'Updating meminfo for %d
failed'
Jan 04 22:50:37 dom0 qmemmand[103730]: Arguments: ('0',)
---

an 04 22:52:18 dom0 systemd[1]: Queuing reload/restart jobs for marked
units…
Jan 04 22:52:18 dom0 qubesd[103735]: unhandled exception while calling
src=b'dom0' meth=b'admin.vm.Stats' dest=b'dom0' arg=b''
len(untrusted_payload)=0
Jan 04 22:52:18 dom0 qubesd[103735]: Traceback (most recent call last):
Jan 04 22:52:18 dom0 qubesd[103735]:   File
"/usr/lib/python3.11/site-packages/qubes/api/__init__.py", line 297, in
respond
Jan 04 22:52:18 dom0 qubesd[103735]:     response = await self.mgmt.execute(
Jan 04 22:52:18 dom0 qubesd[103735]: ^^^^^^^^^^^^^^^^^^^^^^^^
Jan 04 22:52:18 dom0 qubesd[103735]:   File
"/usr/lib/python3.11/site-packages/qubes/api/admin.py", line 1621, in
vm_stats
Jan 04 22:52:18 dom0 qubesd[103735]:     info_time, info =
self._send_stats_single(info_time, info,
Jan 04 22:52:18 dom0 qubesd[103735]:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Jan 04 22:52:18 dom0 qubesd[103735]:   File
"/usr/lib/python3.11/site-packages/qubes/api/admin.py", line 1567, in
_send_stats_single
Jan 04 22:52:18 dom0 qubesd[103735]:     (info_time, info) =
self.app.host.get_vm_stats(info_time, info,
Jan 04 22:52:18 dom0 qubesd[103735]:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Jan 04 22:52:18 dom0 qubesd[103735]:   File
"/usr/lib/python3.11/site-packages/qubes/app.py", line 392, in get_vm_stats
Jan 04 22:52:18 dom0 qubesd[103735]:     info =
self.app.vmm.xc.domain_getinfo(0, 1024)
Jan 04 22:52:18 dom0 qubesd[103735]: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Jan 04 22:52:18 dom0 qubesd[103735]: xen.lowlevel.xc.Error: (13,
'Permission denied')
Jan 04 22:52:18 dom0 widget-wrapper[8271]: Connection to qubesd
terminated, reconnecting in 1.0 seconds
---

Jan 04 22:52:44 dom0 kernel: audit: type=1130
audit(1704405164.078:1139): pid=1 uid=0 auid=4294967295 ses=4294967295
msg='unit=libvirtd comm="systemd" exe="/usr/lib/systemd/systemd"
hostname=? addr=? terminal=? res=success'
Jan 04 22:52:44 dom0 libvirtd[111833]: libvirt version: 8.9.0, package:
6.fc37 (Unknown, 2023-08-17-23:38:43, )
Jan 04 22:52:44 dom0 libvirtd[111833]: hostname: dom0
Jan 04 22:52:44 dom0 libvirtd[111833]: Unable to configure libxl's
memory management parameters
Jan 04 22:52:44 dom0 libvirtd[111833]: Initialization of Xen state
driver failed: no error
Jan 04 22:52:44 dom0 libvirtd[111833]: Driver state initialization failed
Jan 04 22:52:44 dom0 systemd[1]: libvirtd.service: Deactivated successfully.

...

Jan 04 22:52:44 dom0 systemd[1]: libvirtd.service: Start request
repeated too quickly.
Jan 04 22:52:44 dom0 systemd[1]: libvirtd.service: Failed with result
'start-limit-hit'.
Jan 04 22:52:44 dom0 systemd[1]: Failed to start libvirtd.service -
Virtualization daemon.
---

Jan 04 22:52:44 dom0 qubesd[103735]:   File
"/usr/lib64/python3.11/site-packages/libvirt.py", line 335, in open
Jan 04 22:52:44 dom0 qubesd[103735]:     raise
libvirtError('virConnectOpen() failed')
Jan 04 22:52:44 dom0 qubesd[103735]: libvirt.libvirtError: Failed to
connect socket to '/var/run/libvirt/virtxend-sock': No such file or
directory
Jan 04 22:52:44 dom0 qubesd[103735]: unhandled exception while calling
src=b'dom0' meth=b'admin.vm.CurrentState' dest=b'debian-12' arg=b''
len(untrusted_payload)=0
Jan 04 22:52:44 dom0 qubesd[103735]: Traceback (most recent call last):
Jan 04 22:52:44 dom0 qubesd[103735]:   File
"/usr/lib/python3.11/site-packages/qubes/app.py", line 103, in wrapper
Jan 04 22:52:44 dom0 qubesd[103735]:     return attr(*args, **kwargs)
Jan 04 22:52:44 dom0 qubesd[103735]: ^^^^^^^^^^^^^^^^^^^^^
Jan 04 22:52:44 dom0 qubesd[103735]:   File
"/usr/lib64/python3.11/site-packages/libvirt.py", line 1739, in isActive
Jan 04 22:52:44 dom0 qubesd[103735]:     raise
libvirtError('virDomainIsActive() failed')
Jan 04 22:52:44 dom0 qubesd[103735]: libvirt.libvirtError: internal
error: client socket is closed
Jan 04 22:52:44 dom0 qubesd[103735]: During handling of the above
exception, another exception occurred:
Jan 04 22:52:44 dom0 qubesd[103735]: Traceback (most recent call last):
Jan 04 22:52:44 dom0 qubesd[103735]:   File
"/usr/lib/python3.11/site-packages/qubes/api/__init__.py", line 297, in
respond
Jan 04 22:52:44 dom0 qubesd[103735]:     response = await self.mgmt.execute(
Jan 04 22:52:44 dom0 qubesd[103735]: ^^^^^^^^^^^^^^^^^^^^^^^^
Jan 04 22:52:44 dom0 qubesd[103735]:   File
"/usr/lib/python3.11/site-packages/qubes/api/admin.py", line 1635, in
vm_current_state
Jan 04 22:52:44 dom0 qubesd[103735]:     'mem': self.dest.get_mem(),
Jan 04 22:52:44 dom0 qubesd[103735]: ^^^^^^^^^^^^^^^^^^^
---

Jan 04 22:53:23 dom0 systemd[1]: Stopping systemd-update-utmp.service -
Record System Boot/Shutdown in UTMP...
Jan 04 22:53:23 dom0 audit[111952]: SYSTEM_SHUTDOWN pid=111952 uid=0
auid=4294967295 ses=4294967295 msg=' comm="systemd-update-utmp"
exe="/usr/lib/systemd/systemd-update-utmp" hostname=? addr=? terminal=?
res=success'
Jan 04 22:53:23 dom0 systemd-cryptsetup[111951]: Device
luks-ef8d52d9-a96f-43de-97b4-d73c63443262 is still in use.
Jan 04 22:53:23 dom0 systemd-cryptsetup[111951]: Failed to deactivate:
Device or resource busy
Jan 04 22:53:23 dom0 systemd[1]:
systemd-cryptsetup@luks\x2def8d52d9\x2da96f\x2d43de\x2d97b4\x2dd73c63443262.service:
Control process exited, code=exited, status=1/FAILURE
Jan 04 22:53:23 dom0 systemd[1]:
systemd-cryptsetup@luks\x2def8d52d9\x2da96f\x2d43de\x2d97b4\x2dd73c63443262.service:
Failed with result 'exit-code'.
Jan 04 22:53:23 dom0 systemd[1]: Stopped
systemd-cryptsetup@luks\x2def8d52d9\x2da96f\x2d43de\x2d97b4\x2dd73c63443262.service
- Cryptography Setup for luks-ef8d52d9-a96f-43de-97b4-d73c63443262.
Jan 04 22:53:23 dom0 audit[1]: SERVICE_STOP pid=1 uid=0 auid=4294967295
ses=4294967295
msg='unit=systemd-cryptsetup@luks\x2def8d52d9\x2da96f\x2d43de\x2d97b4\x2dd73c63443262
comm="systemd" exe="/usr/lib/systemd/systemd" hostname=? addr=?
terminal=? res=failed'
Jan 04 22:53:23 dom0 systemd[1]: systemd-update-utmp.service:
Deactivated successfully.
Jan 04 22:53:23 dom0 systemd[1]: Stopped systemd-update-utmp.service -
Record System Boot/Shutdown in UTMP.
...

Jan 04 22:54:53 dom0 systemd[1]: Using hardware watchdog 'iTCO_wdt',
version 0, device /dev/watchdog0
Jan 04 22:54:53 dom0 systemd[1]: Watchdog running with a timeout of 10min.
Jan 04 22:54:53 dom0 kernel: watchdog: watchdog0: watchdog did not stop!
Jan 04 22:54:53 dom0 systemd-shutdown[1]: Using hardware watchdog
'iTCO_wdt', version 0, device /dev/watchdog0
Jan 04 22:54:53 dom0 systemd-shutdown[1]: Watchdog running with a
timeout of 10min.
Jan 04 22:54:53 dom0 systemd-shutdown[1]: Syncing filesystems and block
devices.
Jan 04 22:54:53 dom0 systemd-shutdown[1]: Sending SIGTERM to remaining
processes...
Jan 04 22:54:53 dom0 systemd-journald[942]: Journal stopped
-- Boot 82fbf99c44bb4c9ab5f3db985101cce1 --

Andrew David Wong

unread,
Jan 5, 2024, 10:10:40 PMJan 5
to Ulrich Windl, qubes...@googlegroups.com
On 1/4/24 3:20 PM, Ulrich Windl wrote:
> * fedora-38 is obsolete already? I thought fedora-37 is???
>

No, Fedora 38 has not reached EOL:

https://docs.fedoraproject.org/en-US/releases/eol/

Ulrich Windl (Google)

unread,
Jan 9, 2024, 5:11:10 PMJan 9
to Andrew David Wong, qubes...@googlegroups.com
Hi!

Sorry for the delay, but attached is what I see.

Kind regards,
Ulrich

06.01.2024 04:10:29 Andrew David Wong <a...@qubes-os.org>:
img1.jpg

Andrew David Wong

unread,
Jan 10, 2024, 6:08:56 AMJan 10
to Ulrich Windl (Google), qubes...@googlegroups.com
On 1/9/24 2:11 PM, Ulrich Windl (Google) wrote:
> Hi!
>
> Sorry for the delay, but attached is what I see.
>
> Kind regards,
> Ulrich
>

Thank you for your report. This is a known bug:

https://github.com/QubesOS/qubes-issues/issues/8725

Ulrich Windl

unread,
Jan 19, 2024, 5:42:15 PMJan 19
to qubes...@googlegroups.com
On 1/5/24 00:20, Ulrich Windl wrote:
> Hi!
>
>
> As I had some time, I performed the upgrade to Qubes OS 4.2.0.
>
> Unfortunately there were a few unexpected findings:
>
> * my debian-12-dvm template no longer offers Firefox: Qubes settings
> say: "Application missing in template (firefox-esr.desktop)", However
> the template is the same as before upgrading Qubes-OS


I was able to fix this by clicking "App Shortcuts" and then "Reefresh
applications". So far I thought that is done automatically after each
update of the template...
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