Issue Mysql 5.7.23 upgrade problem

[Lorenzo Ansaloni]

I have a problem upgrading mysql-server-5.7 (5.7.23-0ubuntu0.16.04.1), Plesk version is 17.8.11 Update #15, this is the content of file "parallels-installation-log.txt:

[2018-08-01 13:46:24.492251] Installation started in background
[2018-08-01 13:46:24.492343]
Getting bootstrapper packages to installation list:
[2018-08-01 13:46:24.492415] Following bootstrapper packages will be installed: (empty)
[2018-08-01 13:46:24.492453] ----------------
[2018-08-01 13:46:24.492477] Getting packages to installation list:
[2018-08-01 13:46:24.492520] Following packages will be installed: dummy_obsoleter_ext-docker-0.0
[2018-08-01 13:46:24.492562] ----------------
[2018-08-01 13:46:24.492640] Checking whether the package dependencies are resolved.
[2018-08-01 13:46:24.492688] autoinstaller: read output of DEBIAN_FRONTEND=noninteractive LANG=C apt-get --assume-yes --show-upgraded --purge --no-reinstall -o APT::Get::List-Cleanup=true -o Dpkg::options::=--force-confdef -o Dpkg::options::=--force-confold -o APT::Get::AllowUnauthenticated=false -o Acquire::Retries=3 -t 'xenial*' --just-print install
[2018-08-01 13:46:25.509966] add to install list mysql-server-5.7-5.7.23-0ubuntu0.16.04.1
[2018-08-01 13:46:25.510052] add to install list mysql-server-5.7.23-0ubuntu0.16.04.1
[2018-08-01 13:46:25.536434] Check package set before installation
[2018-08-01 13:46:25.536983] The following packages from not selected components will be installed because they are required by other components' packages you selected for installation:
[2018-08-01 13:46:25.550358] Installing packages
[2018-08-01 13:46:28.799347] Bootstrapper has finished action (exec time: 0 sec.): parent_name='PLESK_17_8_11', sequence='prep', stage='execute', sequence_order='-1', operation='install', exec_cmd='touch /tmp/pp-bootstrapper-mode.flag; touch /var/lock/parallels-panel-maintenance-mode.flag; rm -f /var/lock/parallels-panel-upgrade-failure.flag; :'', m_arch='', output: ~empty
[2018-08-01 13:46:28.808844] Reading package lists...
Building dependency tree...
Reading state information...
mysql-server is already the newest version (5.7.23-0ubuntu0.16.04.1).
mysql-server-5.7 is already the newest version (5.7.23-0ubuntu0.16.04.1).
0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
2 not fully installed or removed.
After this operation, 0 B of additional disk space will be used.
Setting up mysql-server-5.7 (5.7.23-0ubuntu0.16.04.1) ...
update-alternatives: warning: forcing reinstallation of alternative /etc/mysql/mysql.cnf because link group my.cnf is broken
update-alternatives: warning: not replacing /etc/mysql/my.cnf with a link
Checking if update is needed.
Checking server version.
Running queries to upgrade MySQL server.
mysql_upgrade: [ERROR] 3193: Cannot complete the operation because table is referenced by another connection.
mysql_upgrade failed with exit status 5
dpkg: error processing package mysql-server-5.7 (--configure):
 subprocess installed post-installation script returned error exit status 1
dpkg: dependency problems prevent configuration of mysql-server:
 mysql-server depends on mysql-server-5.7; however:
 Package mysql-server-5.7 is not configured yet.

dpkg: error processing package mysql-server (--configure):
 dependency problems - leaving unconfigured
No apport report written because the error message indicates its a followup error from a previous failure.
Errors were encountered while processing:
 mysql-server-5.7
 mysql-server
E: Sub-process /usr/bin/dpkg returned an error code (1)
Bootstrapper has finished action (exec time: 7 sec.): parent_name='PLESK_17_8_11', sequence='pkgs', stage='rollback', sequence_order='1', operation='install', exec_cmd='rm -f /tmp/pp-bootstrapper-mode.flag; rm -f /var/lock/parallels-panel-maintenance-mode.flag; touch /var/lock/parallels-panel-upgrade-failure.flag; /etc/init.d/psa restart; :'', m_arch='', output: ~empty
[2018-08-01 13:47:39.474456] Execute command /opt/psa/admin/bin/send-error-report install --version 17.8.11
[2018-08-01 13:47:39.475435] Warning: Failed to attach to cgroup /sys/fs/cgroup/systemd/user/root/tasks, installer might be unexpectedly killed later by the system
[2018-08-01 13:47:39.477333] Error: An error occurred on attempt to install packages.
Attention! Your software might be inoperable.
Please contact product technical support.

I try resolve the issue via command line:

# apt -f install
Lettura elenco dei pacchetti... Fatto
Generazione albero delle dipendenze
Lettura informazioni sullo stato... Fatto
0 aggiornati, 0 installati, 0 da rimuovere e 2 non aggiornati.
2 non completamente installati o rimossi.
Dopo quest'operazione, verranno occupati 0 B di spazio su disco.
Configurazione di mysql-server-5.7 (5.7.23-0ubuntu0.16.04.1)...
update-alternatives: attenzione: viene forzata l'installazione dell'alternativa /etc/mysql/mysql.cnf poiché il gruppo my.cnf è danneggiato
update-alternatives: attenzione: /etc/mysql/my.cnf non viene sostituito con un collegamento
Checking if update is needed.
This installation of MySQL is already upgraded to 5.7.23, use --force if you still need to run mysql_upgrade
/var/lib/dpkg/info/mysql-server-5.7.postinst: riga 16:  2786 Ucciso                  mysqld --user=mysql --init-file="$1" --socket="$tmpdir/mysqld.sock" --pid-file="$tmpdir/mysqld.pid" > /dev/null 2>&1
dpkg: errore nell'elaborare il pacchetto mysql-server-5.7 (--configure):
 il sottoprocesso installato script di post-installation ha restituito lo stato di errore 137
dpkg: problemi con le dipendenze impediscono la configurazione di mysql-server:
 mysql-server dipende da mysql-server-5.7; comunque:
  Il pacchetto mysql-server-5.7 non è ancora configurato.

dpkg: errore nell'elaborare il pacchetto mysql-server (--configure):
 problemi con le dipendenze - lasciato non configurato
Segnalazione apport non scritta poiché il messaggio di errore indica la presenza di un fallimento precedente.
                                                                                                             Si sono verificati degli errori nell'elaborazione:
 mysql-server-5.7
 mysql-server
N: Viene ignorato il file "plesk.list.ai_back" nella directory "/etc/apt/sources.list.d/" poiché ha un'estensione non valida
E: Sub-process /usr/bin/dpkg returned an error code (1)

During the upgrade process if I make a ps:

root@xxxx:~# ps afx | grep mysql
 1495 pts/3    Ss+    0:00  |           \_ /usr/bin/dpkg --status-fd 70 --configure mysql-server-5.7:amd64 mysql-server:all
 1505 pts/3    S+     0:00  |               \_ /usr/bin/perl -w /usr/share/debconf/frontend /var/lib/dpkg/info/mysql-server-5.7.postinst configure 5.7.22-0ubuntu0.16.04.1
 1521 pts/3    S+     0:00  |                   \_ /bin/bash /var/lib/dpkg/info/mysql-server-5.7.postinst configure 5.7.22-0ubuntu0.16.04.1
 2786 pts/3    Sl+    0:01  |                       \_ mysqld --user=mysql --init-file=/var/lib/mysql-files/tmp.tR5lOb5b1F --socket=/tmp/tmp.np5dYcIhd0/mysqld.sock --pid-file=/tmp/tmp.np5dYcIhd0

 

[Lorenzo Ansaloni]

I have the server with the updates blocked, someone can tell me how to fix?

 

[Lorenzo Ansaloni]

The content of file /var/lib/mysql-files/tmp.tR5lOb5b1F is:

USE mysql;
ALTER USER 'root'@'localhost' IDENTIFIED WITH 'auth_socket';
UPDATE user SET password_expired='N', account_locked='N' WHERE user='root';
FLUSH PRIVILEGES;
SHUTDOWN;

but if I watch into DB mysql ther is no usera named "root", maybe this is the problem?

 

[Bonsai78]

Just an idea .... is there a mix of mariadb and mysql? I read somewhere else, the table structures are different starting from mysql 5.7

 

[Bonsai78]

Question - change mysql version (to 5.7)

 

[Lorenzo Ansaloni]

I have no mariadb installed on the system:

# dpkg -l | grep maria
ii  plesk-libmariadbclient-1.0          1.0.0-ubuntu.16.04.171006.1040             amd64        Mariadb client library.
ii  sw-mariadb-client                   1.0.0-ubuntu16.04.17031416                 amd64        Mariadb client library

and the mysqld version was already the 5.7:

# mysqld --version
mysqld  Ver 5.7.23-0ubuntu0.16.04.1 for Linux on x86_64 ((Ubuntu))

 

[trialotto]

@Lorenzo Ansaloni

Check if you have

1 - /etc/alternatives/my.cnf (a symlink to /etc/mysql/mysql.cnf): if it does not exist, create one,
2 - /etc/mysql/my.cnf.fallback: if it does not exist, just copy my.cnf to my.cnf.fallback

and also check how the fallback config file is written: no underscores, just a point! (read: not my.cnf_fallback or similar).

Afterwards, you can retry to upgrade the MySQL server.

Note that the above is essentially a work-around to some of the known bugs in Ubuntu MySQL packages.

However, I am not sure what exactly is causing your issue, so I am not able to do more than to give you two small work-arounds.

Hope the above helps a bit.......kind regards and keep us posted!