Resolved Update Stuck

[Catia]

I logged into Plesk today and it said there were 37 updates that needed to be installed. So I clicked on update and after an hour it still said it was updating. So I decided something had gone wrong and tried to open Plesk in a new window, but I can't get in and my server seems to be completely down. Help.

Here's the list of things it was updating... I have no idea what to do.

- apparmor 2.10.95-0ubuntu2.7 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 2.10.95-0ubuntu2.6 from Ubuntu for xenial-security by Ubuntu repo)

- apparmor-profiles 2.10.95-0ubuntu2.7 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 2.10.95-0ubuntu2.6 from Ubuntu for xenial-security by Ubuntu repo)

- apparmor-utils 2.10.95-0ubuntu2.7 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 2.10.95-0ubuntu2.6 from Ubuntu for xenial-security by Ubuntu repo)

- dh-apparmor 2.10.95-0ubuntu2.7 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 2.10.95-0ubuntu2.6 from Ubuntu for xenial-security by Ubuntu repo)

- ghostscript 9.18~dfsg~0-0ubuntu2.7 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 9.18~dfsg~0-0ubuntu2.6 from now repo)

- libapparmor-perl 2.10.95-0ubuntu2.7 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 2.10.95-0ubuntu2.6 from Ubuntu for xenial-security by Ubuntu repo)

- libapparmor1 2.10.95-0ubuntu2.7 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 2.10.95-0ubuntu2.6 from Ubuntu for xenial-security by Ubuntu repo)

- libcryptsetup4 2:1.6.6-5ubuntu2.1 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 2:1.6.6-5ubuntu2 from Ubuntu for xenial by Ubuntu repo)

- libcups2 2.1.3-4ubuntu0.3 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 2.1.3-4 from Ubuntu for xenial by Ubuntu repo)

- libcupsimage2 2.1.3-4ubuntu0.3 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 2.1.3-4 from Ubuntu for xenial by Ubuntu repo)

- libgd3 2.1.1-4ubuntu0.16.04.8 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 2.1.1-4ubuntu0.16.04.7 from now repo)

- libgs9 9.18~dfsg~0-0ubuntu2.7 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 9.18~dfsg~0-0ubuntu2.6 from now repo)

- libgs9-common 9.18~dfsg~0-0ubuntu2.7 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 9.18~dfsg~0-0ubuntu2.6 from now repo)

- linux-firmware 1.157.12 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 1.157.11 from Ubuntu for xenial-security by Ubuntu repo)

- python3-apparmor 2.10.95-0ubuntu2.7 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 2.10.95-0ubuntu2.6 from Ubuntu for xenial-security by Ubuntu repo)

- python3-libapparmor 2.10.95-0ubuntu2.7 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 2.10.95-0ubuntu2.6 from Ubuntu for xenial-security by Ubuntu repo)

- bind9 1:9.10.3.dfsg.P4-8ubuntu1.8 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 1:9.10.3.dfsg.P4-8ubuntu1.7 from now repo)

- bind9-host 1:9.10.3.dfsg.P4-8ubuntu1.8 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 1:9.10.3.dfsg.P4-8ubuntu1.7 from now repo)

- bind9utils 1:9.10.3.dfsg.P4-8ubuntu1.8 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 1:9.10.3.dfsg.P4-8ubuntu1.7 from now repo)

- dnsutils 1:9.10.3.dfsg.P4-8ubuntu1.8 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 1:9.10.3.dfsg.P4-8ubuntu1.7 from now repo)

- libbind9-140 1:9.10.3.dfsg.P4-8ubuntu1.8 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 1:9.10.3.dfsg.P4-8ubuntu1.7 from now repo)

- libdns-export162 1:9.10.3.dfsg.P4-8ubuntu1.8 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 1:9.10.3.dfsg.P4-8ubuntu1.7 from now repo)

- libdns162 1:9.10.3.dfsg.P4-8ubuntu1.8 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 1:9.10.3.dfsg.P4-8ubuntu1.7 from now repo)

- libirs141 1:9.10.3.dfsg.P4-8ubuntu1.8 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 1:9.10.3.dfsg.P4-8ubuntu1.7 from now repo)

- libisc-export160 1:9.10.3.dfsg.P4-8ubuntu1.8 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 1:9.10.3.dfsg.P4-8ubuntu1.7 from now repo)

- libisc160 1:9.10.3.dfsg.P4-8ubuntu1.8 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 1:9.10.3.dfsg.P4-8ubuntu1.7 from now repo)

- libisccc140 1:9.10.3.dfsg.P4-8ubuntu1.8 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 1:9.10.3.dfsg.P4-8ubuntu1.7 from now repo)

- libisccfg140 1:9.10.3.dfsg.P4-8ubuntu1.8 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 1:9.10.3.dfsg.P4-8ubuntu1.7 from now repo)

- liblwres141 1:9.10.3.dfsg.P4-8ubuntu1.8 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 1:9.10.3.dfsg.P4-8ubuntu1.7 from now repo)

- libpython3.5-minimal 3.5.2-2ubuntu0~16.04.2 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 3.5.2-2ubuntu0~16.04.1 from Ubuntu for xenial-security by Ubuntu repo)

- libpython3.5-stdlib 3.5.2-2ubuntu0~16.04.2 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 3.5.2-2ubuntu0~16.04.1 from Ubuntu for xenial-security by Ubuntu repo)

- libxml2 2.9.3+dfsg1-1ubuntu0.3 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 2.9.3+dfsg1-1ubuntu0.2 from now repo)

- python-libxml2 2.9.3+dfsg1-1ubuntu0.3 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 2.9.3+dfsg1-1ubuntu0.2 from now repo)

- python3.5 3.5.2-2ubuntu0~16.04.2 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 3.5.2-2ubuntu0~16.04.1 from Ubuntu for xenial-security by Ubuntu repo)

- python3.5-minimal 3.5.2-2ubuntu0~16.04.2 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 3.5.2-2ubuntu0~16.04.1 from Ubuntu for xenial-security by Ubuntu repo)

- apache2 2.4.18-2ubuntu3.5 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 2.4.18-2ubuntu3.4 from now repo)

- apache2-bin 2.4.18-2ubuntu3.5 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 2.4.18-2ubuntu3.4 from now repo)

- apache2-data 2.4.18-2ubuntu3.5 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 2.4.18-2ubuntu3.4 from now repo)

- apache2-utils 2.4.18-2ubuntu3.5 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 2.4.18-2ubuntu3.4 from now repo)

- ntpdate 1:4.2.8p4+dfsg-3ubuntu5.7 from Ubuntu for xenial-updates by Ubuntu repo (currently installed version: 1:4.2.8p4+dfsg-3ubuntu5.6 from now repo)

 

[UFHH01]

Hi Catia,

it's really hard to guess, what might have happened, as you don't provide any decent log - entries, nor do you provide a FQDN or IP, so that we might be able to check and investigate together with you, if your server is actually reachable at all.

Sometimes it is necessary to reboot a server after updates/upgrades ( which is quite rare ) and most server providers offer as well options to do that over their very own control panel, in case that you are not able to login over SSH to correct possible misconfigurations, stuck services, or hanging processes over the command line.

For more ( and better ) suggestion and work-arounds, pls. consider to provide more informations, so that we are to investigate the issues/errors/problems together with you, or consider to contact your server provider to ask for help.

 

[mr-wolf]

Hi Catia,

it's really hard to guess, what might have happened, as you don't provide any decent log - entries, nor do you provide a FQDN or IP, so that we might be able to check and investigate together with you, if your server is actually reachable at all.

Sometimes it is necessary to reboot a server after updates/upgrades ( which is quite rare )
.

I think it's due to a combination of the update of apparmor and the original 4.4 kernel.
Suffered the same on one machine.

Mine is upgraded

uname -r
4.10.0-35-generic

 

[Catia]

I finally gave up and rebooted the sever. Couldn't provide any logs or any more info, because I had no access to the machine. Anyhow, I seem to be back to square one. Plesk gave me this message: Update failed. Task is not responding: id=557, pid=25297, type=pum-update-packages - don't know what "pum" means.

So it still says that there are 37 packages that need to be updated, but I'm scared to try it again. Mr-wolf, how did you get it to update? Only thing I can think of is to try updating one at a time so I can see where the problem is.

 

[UFHH01]

Hi Catia,

pls. consider to use the commands ( logged in as user "root" over SSH ):

apt-get autoremove

apt-get upgrade

Repeat both commands, if you experience issues/errors/problems and post your output from the command line, if you still experience issues/errors/problems after a second try.

 

[Bitpalast]

, type=pum-update-packages - don't know what "pum" means.

pum = Plesk update manager

 

[mr-wolf]

I finally gave up and rebooted the sever. Couldn't provide any logs or any more info, because I had no access to the machine. Anyhow, I seem to be back to square one. Plesk gave me this message: Update failed. Task is not responding: id=557, pid=25297, type=pum-update-packages - don't know what "pum" means.

So it still says that there are 37 packages that need to be updated, but I'm scared to try it again. Mr-wolf, how did you get it to update? Only thing I can think of is to try updating one at a time so I can see where the problem is.

uname -r
apt-get install --install-recommends linux-generic-hwe-16.04
apt-get autoremove
reboot
apt-get autoremove
uname -r
apt-get upgrade

My server continued having the problem after a reboot.
On the net I found something about apparmor having some bug with kernel lower than 4.4.0-38.57

During the upgrade of apparmor it reloads the rules and hangs. After the kernel was upgraded the apparmor upgrade is no problem anymore.

All this was quite new to me, please let me know how you fare with all this.
I normally only reboot a server only a few times during the installation period and then never again.
This problem made an exception.

Please let us know the versions of your kernel before/after reboot and if your problem is solved.

My physical 16.04 servers are now on 4.10.0-35-generic. I have no control over my hired OpenVZ container.
That one is on 4.4.0-042stab124.2, but should be fine too

 

[UFHH01]

Hi Catia,
hi mr-wolf,

pls. consider to DE-activate "apparmor", in case that you experience issues/errors/problems with it on Debian/Ubuntu - based systems, but pls. don't remove the package from your server, as this might conflict mit Plesk Onyx components and extensions!

=> How to disable AppArmor?

( Pls. leave out step 2. and read the warning )​

After a successfull reboot, when you upgraded your kernel ( such a reboot is necessary, to take advantage of the new kernel fetaures ), you may certainly RE-activate "apparmor" with the commands:

systemctl start apparmor.service
update-rc.d apparmor defaults

 

[Catia]

OK. Sorry I vanished from this thread. I had a few homeowner disasters that absorbed all of my attention for a while.

So here's the update. I had my provider submit a ticket to Plesk, because I was really nervous about trying to follow your suggestions - not anything wrong with your suggestions, I'm just not great in the Linux command line environment, and I wanted to be sure that I wasn't going to be causing more problems than I was solving.

Plesk confirmed that the problem was indeed a bug in the kernel causing the Apparmor update to hang. Here is the fix they sent me:

The following error occurs on attempt to execute the following command:

# dpkg --configure -a
dpkg: error processing package apparmor-utils (--configure):
dependency problems - leaving unconfigured Errors were encountered while processing:
bind9
apparmor
apparmor-profiles
apparmor-utils

The reason of this behavior is bug in the Ubuntu kernel - #1579135: AppArmor profile reloading causes an intermittent kernel BUG
In order to resolve the issue, it will be required to perform the following steps:

1. Temporarily remove AppArmor post-install scripts in order to prevent AppArmor from reloading:

# mv /var/lib/dpkg/info/apparmor.postinst ~/
# mv /var/lib/dpkg/info/apparmor-profiles.postinst ~/

2. Disable AppArmor:

# /etc/init.d/apparmor stop
# /etc/init.d/apparmor teardown
# update-rc.d -f apparmor remove

3. Run dpkg --configure -a to fix the initial error:

# dpkg --configure -a

4. Upgrade Ubuntu kernel to version 4.4.0-38.57 or newer and reboot the server. For example, for version 4.4.0-72:

# apt update
# apt install linux-image-4.4.0-72-generic
# sudo reboot

5. Move back AppArmor post-install scripts and reconfigure apparmor-profiles package:

# mv ~/apparmor.postinst /var/lib/dpkg/info/
# mv ~/apparmor-profiles.postinst /var/lib/dpkg/info/
# dpkg-reconfigure apparmor
# dpkg-reconfigure apparmor-profiles

6. Start AppArmor:

/etc/init.d/apparmor start


This resolved the problem.
Thanks to everyone for the help.