Plesk update failed: There is a MySQL server running, but we failed in our attempts to stop it

Symptoms

• Plesk update failed with following error:

  # cat /var/log/plesk/panel.log
  [...]
  Preparing to unpack .../mariadb-server-10.0_10.0.32-0+deb8u1_amd64.deb ...
  47146
  There is a MySQL server running, but we failed in our attempts to stop it.
  Stop it yourself and try again!
  dpkg: warning: subprocess old pre-removal script returned error exit status 1
  dpkg: trying script from the new package instead ...
  47146
  There is a MySQL server running, but we failed in our attempts to stop it.
  Stop it yourself and try again!
  dpkg: error processing archive /var/cache/apt/archives/mariadb-server-10.0_10.0.32-0+deb8u1_amd64.deb (--unpack):
  subprocess new pre-removal script returned error exit status 1
  insserv: warning: script 'apf' missing LSB tags and overrides
  Errors were encountered while processing:
  /var/cache/apt/archives/mariadb-server-10.0_10.0.32-0+deb8u1_amd64.deb
  E: Sub-process /usr/bin/dpkg returned an error code (1)
  [...]

• Same issue happens trying to install MariaDB-Server-10.0 from apt-get install CLI utility.

Cause

MariaDB Server pre-removal script fails to stop the current MySQL process. For more information about this issue, check Official Debian bug notes.

Resolution

1. Connect to the server using SSH.

2. Perform a full database backup:

   # mysqldump -uadmin -p`cat /etc/psa/.psa.shadow` -f --all-databases > /root/all_databases_backup`date +%F-%s`.sql

3. Stop MySQL service manually:

   # service mysql stop

4. Check if mysql still is running:

   # pidof -c /usr/sbin/mysqld
   7327

   # ps awufx | grep mysql | grep -v grep
   root 7187 0.0 0.0 21820 3504 ? S 21:32 0:00 /bin/bash /usr/bin/mysqld_safe
   mysql 7327 0.1 2.0 624472 81944 ? Sl 21:32 0:00 \_ /usr/sbin/mysqld --basedir=/usr --datadir=/var/lib/mysql --plugin-dir=/usr/lib/mysql/plugin --user=mysql --skip-log-error --pid-file=/var/run/mysqld/mysqld.pid --socket=/var/run/mysqld/mysqld.sock --port=3306
   root 7328 0.0 0.0 23684 2476 ? S 21:32 0:00 \_ logger -t mysqld -p daemon.error

5. Kill mysql processes manually (PIDs coming from the above example):

   # kill -9 7187 7327 7328

6. Check that there aren't mysql processes running:

   # pidof -c /usr/sbin/mysqld
   (Empty Output)

7. Install/update MariaDB-Server manually:

   # apt-get install mariadb-server-10.0
   [...]
   Preparing to unpack .../mariadb-server-10.0_10.0.32-0+deb8u1_amd64.deb ...
   Unpacking mariadb-server-10.0 (10.0.32-0+deb8u1) over (10.0.30-0+deb8u2) ...
   Processing triggers for systemd (215-17+deb8u7) ...
   Processing triggers for man-db (2.7.0.2-5) ...
   Setting up mariadb-server-10.0 (10.0.32-0+deb8u1) ...
   insserv: warning: script 'apf' missing LSB tags and overrides