systemd upgrade to 229-4ubuntu19 fails

[Sebastian Nohn]

systemd upgrade to 229-4ubuntu19 fails:

Calculating upgrade... Done
The following packages will be upgraded:
  libmysqlclient20 libnss-myhostname libpam-systemd libsystemd0 libudev1
  mysql-client-5.7 mysql-client-core-5.7 mysql-common mysql-server
  mysql-server-5.7 mysql-server-core-5.7 systemd systemd-sysv udev
14 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 23.8 MB of archives.
After this operation, 106 kB of additional disk space will be used.
Do you want to continue? [Y/n]
Get:1 http://mirrors.digitalocean.com/ubuntu xenial-updates/main amd64 systemd-sysv amd64 229-4ubuntu19 [12.4 kB]
Get:2 http://mirrors.digitalocean.com/ubuntu xenial-updates/main amd64 libpam-systemd amd64 229-4ubuntu19 [115 kB]
Get:3 http://mirrors.digitalocean.com/ubuntu xenial-updates/main amd64 libsystemd0 amd64 229-4ubuntu19 [205 kB]
Get:4 http://mirrors.digitalocean.com/ubuntu xenial-updates/main amd64 libnss-myhostname amd64 229-4ubuntu19 [36.4 kB]
Get:5 http://mirrors.digitalocean.com/ubuntu xenial-updates/main amd64 systemd amd64 229-4ubuntu19 [3,811 kB]
Get:6 http://mirrors.digitalocean.com/ubuntu xenial-updates/main amd64 udev amd64 229-4ubuntu19 [992 kB]
Get:7 http://mirrors.digitalocean.com/ubuntu xenial-updates/main amd64 libudev1 amd64 229-4ubuntu19 [55.0 kB]
Get:8 http://mirrors.digitalocean.com/ubuntu xenial-updates/main amd64 mysql-client-core-5.7 amd64 5.7.19-0ubuntu0.16.04.1 [6,020 kB]
Get:9 http://mirrors.digitalocean.com/ubuntu xenial-updates/main amd64 mysql-common all 5.7.19-0ubuntu0.16.04.1 [15.7 kB]
Get:10 http://mirrors.digitalocean.com/ubuntu xenial-updates/main amd64 mysql-client-5.7 amd64 5.7.19-0ubuntu0.16.04.1 [1,654 kB]
Get:11 http://mirrors.digitalocean.com/ubuntu xenial-updates/main amd64 mysql-server-5.7 amd64 5.7.19-0ubuntu0.16.04.1 [2,463 kB]
Get:12 http://mirrors.digitalocean.com/ubuntu xenial-updates/main amd64 mysql-server-core-5.7 amd64 5.7.19-0ubuntu0.16.04.1 [7,588 kB]
Get:13 http://mirrors.digitalocean.com/ubuntu xenial-updates/main amd64 libmysqlclient20 amd64 5.7.19-0ubuntu0.16.04.1 [809 kB]
Get:14 http://mirrors.digitalocean.com/ubuntu xenial-updates/main amd64 mysql-server all 5.7.19-0ubuntu0.16.04.1 [10.8 kB]
Fetched 23.8 MB in 0s (32.4 MB/s)
Preconfiguring packages ...
(Reading database ... 112119 files and directories currently installed.)
Preparing to unpack .../systemd-sysv_229-4ubuntu19_amd64.deb ...
Unpacking systemd-sysv (229-4ubuntu19) over (229-4ubuntu17) ...
Processing triggers for man-db (2.7.5-1) ...
Setting up systemd-sysv (229-4ubuntu19) ...
(Reading database ... 112119 files and directories currently installed.)
Preparing to unpack .../libpam-systemd_229-4ubuntu19_amd64.deb ...
Unpacking libpam-systemd:amd64 (229-4ubuntu19) over (229-4ubuntu17) ...
Preparing to unpack .../libsystemd0_229-4ubuntu19_amd64.deb ...
Unpacking libsystemd0:amd64 (229-4ubuntu19) over (229-4ubuntu17) ...
Processing triggers for man-db (2.7.5-1) ...
Processing triggers for libc-bin (2.23-0ubuntu9) ...
Setting up libsystemd0:amd64 (229-4ubuntu19) ...
Processing triggers for libc-bin (2.23-0ubuntu9) ...
(Reading database ... 112119 files and directories currently installed.)
Preparing to unpack .../libnss-myhostname_229-4ubuntu19_amd64.deb ...
Unpacking libnss-myhostname:amd64 (229-4ubuntu19) over (229-4ubuntu17) ...
Preparing to unpack .../systemd_229-4ubuntu19_amd64.deb ...
Unpacking systemd (229-4ubuntu19) over (229-4ubuntu17) ...
Processing triggers for libc-bin (2.23-0ubuntu9) ...
Processing triggers for man-db (2.7.5-1) ...
Processing triggers for dbus (1.10.6-1ubuntu3.3) ...
Processing triggers for ureadahead (0.100.0-19) ...
Setting up systemd (229-4ubuntu19) ...
addgroup: The group `systemd-journal' already exists as a system group. Exiting.

Broadcast message from <email address hidden> (Sat 2017-07-22 09:07:52 UTC):

systemd[1]: Freezing execution.

Failed to try-restart systemd-networkd.service: Failed to activate service 'org.freedesktop.systemd1': timed out
See system logs and 'systemctl status systemd-networkd.service' for details.

Failed to try-restart systemd-resolved.service: Failed to activate service 'org.freedesktop.systemd1': timed out
See system logs and 'systemctl status systemd-resolved.service' for details.
Failed to try-restart systemd-timesyncd.service: Failed to activate service 'org.freedesktop.systemd1': timed out
See system logs and 'systemctl status systemd-timesyncd.service' for details.
Failed to retrieve unit: Failed to activate service 'org.freedesktop.systemd1': timed out
(Reading database ... 112121 files and directories currently installed.)
Preparing to unpack .../udev_229-4ubuntu19_amd64.deb ...
Unpacking udev (229-4ubuntu19) over (229-4ubuntu17) ...
Failed to execute operation: Failed to activate service 'org.freedesktop.systemd1': timed out
Preparing to unpack .../libudev1_229-4ubuntu19_amd64.deb ...
Unpacking libudev1:amd64 (229-4ubuntu19) over (229-4ubuntu17) ...
Processing triggers for ureadahead (0.100.0-19) ...
Processing triggers for systemd (229-4ubuntu19) ...
Failed to execute operation: Failed to activate service 'org.freedesktop.systemd1': timed out
Processing triggers for man-db (2.7.5-1) ...
Processing triggers for libc-bin (2.23-0ubuntu9) ...
Setting up libudev1:amd64 (229-4ubuntu19) ...
Processing triggers for libc-bin (2.23-0ubuntu9) ...
(Reading database ... 112121 files and directories currently installed.)
Preparing to unpack .../mysql-client-core-5.7_5.7.19-0ubuntu0.16.04.1_amd64.deb ...
Unpacking mysql-client-core-5.7 (5.7.19-0ubuntu0.16.04.1) over (5.7.18-0ubuntu0.16.04.1) ...
Preparing to unpack .../mysql-common_5.7.19-0ubuntu0.16.04.1_all.deb ...
Unpacking mysql-common (5.7.19-0ubuntu0.16.04.1) over (5.7.18-0ubuntu0.16.04.1) ...
Preparing to unpack .../mysql-client-5.7_5.7.19-0ubuntu0.16.04.1_amd64.deb ...
Unpacking mysql-client-5.7 (5.7.19-0ubuntu0.16.04.1) over (5.7.18-0ubuntu0.16.04.1) ...
Processing triggers for man-db (2.7.5-1) ...
Setting up mysql-common (5.7.19-0ubuntu0.16.04.1) ...
(Reading database ... 112121 files and directories currently installed.)
Preparing to unpack .../mysql-server-5.7_5.7.19-0ubuntu0.16.04.1_amd64.deb ...
Failed to execute operation: Failed to activate service 'org.freedesktop.systemd1': timed out
Failed to retrieve unit: Connection timed out
Failed to stop mysql.service: Failed to activate service 'org.freedesktop.systemd1': timed out
See system logs and 'systemctl status mysql.service' for details.
Failed to get load state of mysql.service: Failed to activate service 'org.freedesktop.systemd1': timed out
invoke-rc.d: initscript mysql, action "stop" failed.
dpkg: warning: subprocess old pre-removal script returned error exit status 1
dpkg: trying script from the new package instead ...
Failed to execute operation: Failed to activate service 'org.freedesktop.systemd1': timed out
Failed to retrieve unit: Connection timed out
Failed to stop mysql.service: Failed to activate service 'org.freedesktop.systemd1': timed out
See system logs and 'systemctl status mysql.service' for details.
Failed to get load state of mysql.service: Failed to activate service 'org.freedesktop.systemd1': timed out
invoke-rc.d: initscript mysql, action "stop" failed.
dpkg: error processing archive /var/cache/apt/archives/mysql-server-5.7_5.7.19-0ubuntu0.16.04.1_amd64.deb (--unpack):
 subprocess new pre-removal script returned error exit status 1
Failed to execute operation: Failed to activate service 'org.freedesktop.systemd1': timed out
Failed to retrieve unit: Failed to activate service 'org.freedesktop.systemd1': timed out
Failed to stop mysql.service: Failed to activate service 'org.freedesktop.systemd1': timed out
See system logs and 'systemctl status mysql.service' for details.
Failed to get load state of mysql.service: Failed to activate service 'org.freedesktop.systemd1': timed out
invoke-rc.d: initscript mysql, action "stop" failed.
Failed to execute operation: Failed to activate service 'org.freedesktop.systemd1': timed out
Failed to execute operation: Failed to activate service 'org.freedesktop.systemd1': timed out

ProblemType: Bug
DistroRelease: Ubuntu 16.04
Package: systemd 229-4ubuntu19
ProcVersionSignature: Ubuntu 4.4.0-83.106-generic 4.4.70
Uname: Linux 4.4.0-83-generic x86_64
ApportVersion: 2.20.1-0ubuntu2.10
Architecture: amd64
Date: Sat Jul 22 09:16:11 2017
JournalErrors:
 Hint: You are currently not seeing messages from other users and the system.
       Users in groups 'adm', 'systemd-journal' can see all messages.
       Pass -q to turn off this notice.
 -- No entries --
Lsusb: Bus 001 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
MachineType: DigitalOcean Droplet
ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-4.4.0-83-generic root=UUID=ba2c2685-36b4-44ab-a6bd-13e52580b218 ro console=tty1 root=LABEL=DOROOT notsc clocksource=kvm-clock net.ifnames=0
SourcePackage: systemd
SystemdDelta:
 [EXTENDED] /lib/systemd/system/systemd-resolved.service → /lib/systemd/system/systemd-resolved.service.d/resolvconf.conf
 [EXTENDED] /lib/systemd/system/rc-local.service → /lib/systemd/system/rc-local.service.d/debian.conf
 [EXTENDED] /lib/systemd/system/systemd-timesyncd.service → /lib/systemd/system/systemd-timesyncd.service.d/disable-with-time-daemon.conf

 3 overridden configuration files found.
SystemdFailedUnits: Error: command ['systemctl', 'status', '--full', 'Error:'] failed with exit code 1: Failed to get properties: Failed to activate service 'org.freedesktop.systemd1': timed out
UpgradeStatus: No upgrade log present (probably fresh install)
dmi.bios.date: 04/25/2016
dmi.bios.vendor: DigitalOcean
dmi.bios.version: 20160425
dmi.chassis.type: 1
dmi.chassis.vendor: Bochs
dmi.modalias: dmi:bvnDigitalOcean:bvr20160425:bd04/25/2016:svnDigitalOcean:pnDroplet:pvr20160415:cvnBochs:ct1:cvr:
dmi.product.name: Droplet
dmi.product.version: 20160415
dmi.sys.vendor: DigitalOcean
mtime.conffile..etc.systemd.journald.conf: 2016-09-03T09:56:50.880087

[Sebastian Nohn (sebastian-nohn)]

I even can't reboot the system:

$ sudo reboot
[sudo] password for sebastian:
Failed to start reboot.target: Failed to activate service 'org.freedesktop.systemd1': timed out
See system logs and 'systemctl status reboot.target' for details.
Failed to open /dev/initctl: No such device or address
Failed to talk to init daemon.

[Launchpad Janitor (janitor)]

Status changed to 'Confirmed' because the bug affects multiple users.

[Aleksander Vassdal (avassdal)]

root@Ubuntu-1604-xenial-64-minimal ~ # apt update && apt upgrade
Hit:1 http://mirror.hetzner.de/ubuntu/packages xenial InRelease
Hit:2 http://mirror.hetzner.de/ubuntu/packages xenial-backports InRelease
Hit:3 http://mirror.hetzner.de/ubuntu/packages xenial-updates InRelease
Hit:4 http://mirror.hetzner.de/ubuntu/security xenial-security InRelease
Hit:5 http://security.ubuntu.com/ubuntu xenial-security InRelease
Hit:6 http://de.archive.ubuntu.com/ubuntu xenial InRelease
Hit:7 http://de.archive.ubuntu.com/ubuntu xenial-updates InRelease
Hit:8 http://de.archive.ubuntu.com/ubuntu xenial-backports InRelease
Ign:9 http://download.webmin.com/download/repository sarge InRelease
Hit:10 http://download.webmin.com/download/repository sarge Release
Hit:11 http://dl.ubnt.com/unifi/debian testing InRelease
Hit:13 https://deb.nodesource.com/node_7.x xenial InRelease
Reading package lists... Done
Building dependency tree
Reading state information... Done
34 packages can be upgraded. Run 'apt list --upgradable' to see them.
Reading package lists... Done
Building dependency tree
Reading state information... Done
You might want to run 'apt-get -f install' to correct these.
The following packages have unmet dependencies:
 libpam-systemd : Depends: systemd (= 229-4ubuntu19)
 systemd : Depends: libsystemd0 (= 229-4ubuntu17) but 229-4ubuntu19 is installed
E: Unmet dependencies. Try using -f.
root@Ubuntu-1604-xenial-64-minimal ~ # apt-get -f install
Reading package lists... Done
Building dependency tree
Reading state information... Done
Correcting dependencies... Done
The following packages were automatically installed and are no longer required:
  linux-headers-4.4.0-78 linux-headers-4.4.0-78-generic linux-image-4.4.0-78-generic
  linux-image-extra-4.4.0-78-generic
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  systemd
Suggested packages:
  systemd-ui systemd-container
The following packages will be upgraded:
  systemd
1 upgraded, 0 newly installed, 0 to remove and 33 not upgraded.
3 not fully installed or removed.
Need to get 0 B/3,811 kB of archives.
After this operation, 12.3 kB of additional disk space will be used.
Do you want to continue? [Y/n] Y
(Reading database ... 157791 files and directories currently installed.)
Preparing to unpack .../systemd_229-4ubuntu19_amd64.deb ...
Unpacking systemd (229-4ubuntu19) over (229-4ubuntu17) ...
Processing triggers for dbus (1.10.6-1ubuntu3.3) ...
Processing triggers for ureadahead (0.100.0-19) ...
Processing triggers for man-db (2.7.5-1) ...
Setting up systemd (229-4ubuntu19) ...
addgroup: The group `systemd-journal' already exists as a system group. Exiting.
Failed to try-restart sys...

[Brian Murray (brian-murray)]

There seem to be a few other issues going on, from CurrentDmesg.txt:

[1365111.063806] Out of memory: Kill process 32370 (mysqld) score 270 or sacrifice child
[1365111.066733] Killed process 32370 (mysqld) total-vm:1045444kB, anon-rss:134896kB, file-rss:0kB
[1365111.413214] systemd-journald[631]: Failed to save stream data /run/systemd/journal/streams/8:28796586: No space left on device

Maybe try stopping mysqld and then freeing some disk space.