Issue Cannot restart MySql after attempting to upgrade from version 5.5.55 to 5.6

[Craig1986]

Earlier, I attempting to upgrade my MySQL, from version 5.5.55 to 5.6, using the SSH Client 'PuTTY'.

This being my first time, I decided to strictly follow this Plesk Article. I managed to reach step 10 within the 'Plesk on CentOS 6' drop down menu.

As per the step, I then tried to start the MySQL. Unfortunately, this did not work; where I received the following message:

MySQL Daemon failed to start
Starting mysqld: [FAILED]​

I have checked a variety of questions, on this forum, as well as other online resources. Unfortunately, nothin seems to be helping me. Maybe I am overlooking something.

Where would I begin, in terms of starting to figure out where the problem is and how to resolve such an issue? Maybe there is some kind of MySQL Log I could retrieve from the web files that would help indicate where the problem resides?


MySQL Log

[System] [MY-011012] [Server] Starting upgrade of data directory.
[ERROR] [MY-013090] [InnoDB] Unsupported redo log format (0). The redo log was created before MySQL 5.7.9
[ERROR] [MY-012930] [InnoDB] Plugin initialization aborted with error Generic error.
[ERROR] [MY-011013] [Server] Failed to initialize DD Storage Engine.
[ERROR] [MY-010020] [Server] Data Dictionary initialization failed.
[ERROR] [MY-010119] [Server] Aborting
[System] [MY-010910] [Server] /usr/sbin/mysqld: Shutdown complete (mysqld 8.0.16) MySQL Community Server - GPL.
[Warning] [MY-011070] [Server] 'Disabling symbolic links using --skip-symbolic-links (or equivalent) is the default. Consider not using this option as it' is deprecated and will be removed in a future release.
[System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.16) starting as process 4283
[System] [MY-011012] [Server] Starting upgrade of data directory.
[ERROR] [MY-013090] [InnoDB] Unsupported redo log format (0). The redo log was created before MySQL 5.7.9
[ERROR] [MY-012930] [InnoDB] Plugin initialization aborted with error Generic error.
[ERROR] [MY-011013] [Server] Failed to initialize DD Storage Engine.
[ERROR] [MY-010020] [Server] Data Dictionary initialization failed.
[ERROR] [MY-010119] [Server] Aborting
[System] [MY-010910] [Server] /usr/sbin/mysqld: Shutdown complete (mysqld 8.0.16) MySQL Community Server - GPL.
[Warning] [MY-011070] [Server] 'Disabling symbolic links using --skip-symbolic-links (or equivalent) is the default. Consider not using this option as it' is deprecated and will be removed in a future release.
[System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.16) starting as process 4608
[System] [MY-011012] [Server] Starting upgrade of data directory.
[ERROR] [MY-013090] [InnoDB] Unsupported redo log format (0). The redo log was created before MySQL 5.7.9
[ERROR] [MY-012930] [InnoDB] Plugin initialization aborted with error Generic error.
[ERROR] [MY-011013] [Server] Failed to initialize DD Storage Engine.
[ERROR] [MY-010020] [Server] Data Dictionary initialization failed.
[ERROR] [MY-010119] [Server] Aborting
[System] [MY-010910] [Server] /usr/sbin/mysqld: Shutdown complete (mysqld 8.0.16) MySQL Community Server - GPL.
[Warning] [MY-011070] [Server] 'Disabling symbolic links using --skip-symbolic-links (or equivalent) is the default. Consider not using this option as it' is deprecated and will be removed in a future release.
[System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.16) starting as process 4939
[System] [MY-011012] [Server] Starting upgrade of data directory.
[ERROR] [MY-013090] [InnoDB] Unsupported redo log format (0). The redo log was created before MySQL 5.7.9
[ERROR] [MY-012930] [InnoDB] Plugin initialization aborted with error Generic error.
[ERROR] [MY-011013] [Server] Failed to initialize DD Storage Engine.
[ERROR] [MY-010020] [Server] Data Dictionary initialization failed.
[ERROR] [MY-010119] [Server] Aborting
[System] [MY-010910] [Server] /usr/sbin/mysqld: Shutdown complete (mysqld 8.0.16) MySQL Community Server - GPL.

 

[Ales]

... I decided to strictly follow this Plesk Article. I managed to reach step 10 within the 'Plesk on CentOS 6' drop down menu.

The log you've posted indicates that you have installed MySQL 8 and not 5.6. There is an explicit warning in the instructions not to install MySQL 8 as Plesk isn't compatible with it.

Make sure that you've followed step 7.2 and enabled only the desired MySQL version. Downgrade the packages if necessary.

The information returned by these commands could help establish what's the current situation:

cat /etc/redhat-release
ls -als /etc/yum.repos.d
cat /etc/yum.repos.d/mysql-community.repo
rpm -q mysql-server

 

[Craig1986]

The log you've posted indicates that you have installed MySQL 8 and not 5.6. There is an explicit warning in the instructions not to install MySQL 8 as Plesk isn't compatible with it.

Make sure that you've followed step 7.2 and enabled only the desired MySQL version. Downgrade the packages if necessary.

The information returned by these commands could help establish what's the current situation:

cat /etc/redhat-release
ls -als /etc/yum.repos.d
cat /etc/yum.repos.d/mysql-community.repo
rpm -q mysql-server

Thank you for your reply.

How would I go about downgrading? Are you saying by simply following step 7.2 and then selecting version 5.6 below, would be enough to downgrade?

[mysql56-community]
enabled=1

If that is the case, I receive the following screen message when entering the commands in step 7.2:

E325: ATTENTION
Found a swap file by the name "/etc/yum.repos.d/.mysql-community.repo.swp"
owned by: root dated: Thu Jun 13 00:08:02 2019
file name: /etc/yum.repos.d/mysql-community.repo
modified: YES
user name: root host name: mail.example.com
process ID: 7360
While opening file "/etc/yum.repos.d/mysql-community.repo"
dated: Thu Feb 22 08:36:47 2018

(1) Another program may be editing the same file. If this is the case,
be careful not to end up with two different instances of the same
file when making changes. Quit, or continue with caution.
(2) An edit session for this file crashed.
If this is the case, use ":recover" or "vim -r /etc/yum.repos.d/mysql-community.repo"
to recover the changes (see ":help recovery").
If you did this already, delete the swap file "/etc/yum.repos.d/.mysql-community.repo.swp"
to avoid this message.
"/etc/yum.repos.d/mysql-community.repo" 65L, 1862C
Press ENTER or type command to continue

What would I need to do, in order to solve this issue; so that I can continue with step 7.2?

UPDATE
I have managed to remove the Swap file by removing it directly within the Web Files, via the FTP approach. I am now presented with the following options:

# Enable to use MySQL 5.5
[mysql55-community]
name=MySQL 5.5 Community Server
baseurl=http://repo.mysql.com/yum/mysql-5.5-community/el/6/$basearch/
enabled=0
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-mysql

# Enable to use MySQL 5.6
[mysql56-community]
name=MySQL 5.6 Community Server
baseurl=http://repo.mysql.com/yum/mysql-5.6-community/el/6/$basearch/
enabled=0
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-mysql

# Enable to use MySQL 5.7
[mysql57-community]
name=MySQL 5.7 Community Server
baseurl=http://repo.mysql.com/yum/mysql-5.7-community/el/6/$basearch/
enabled=0
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-mysql

[mysql80-community]
name=MySQL 8.0 Community Server
baseurl=http://repo.mysql.com/yum/mysql-8.0-community/el/6/$basearch/
enabled=1
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-mysql

[mysql-connectors-community]
name=MySQL Connectors Community
baseurl=http://repo.mysql.com/yum/mysql-connectors-community/el/6/$basearch/
enabled=1
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-mysql

[mysql-tools-community]
name=MySQL Tools Community
baseurl=http://repo.mysql.com/yum/mysql-tools-community/el/6/$basearch/
enabled=1
gpgcheck=1​

Am I right in thinking that I simply enable version 5.6 by replace the relevant '0' with a '1' and then disable the 5.8 version by exchanging the relevant '1' with a '0'? With that being done, how would I then go about to proceed with the installation?

 

[Ales]

Let me say this first and get it out of the way, I strongly advise setting up a test server (a local virtual machine will do) in order to test various procedures there. System administration should not be learned on a live server, as this can lead to a catastrophic results...

That being said, the current situation needs resolving! Yes, replace the relevant 'enabled=0' with a 'enabled=1' and vice versa, for [mysql56-community] and [mysql80-community] respectively. Make sure that the file is saved afterwards.

After you've done this and preferably before going any further, please post the output of these commands:

cat /etc/redhat-release
ls -als /etc/yum.repos.d
cat /etc/yum.repos.d/mysql-community.repo
rpm -q mysql-server

This will just tell us a bit more about the current state of your OS. One thing I'm wondering about is where MySQL 5.5.55 came from in the first place, as this isn't the default RHEL/CentOS 6 MySQL version.

 

[Craig1986]

Let me say this first and get it out of the way, I strongly advise setting up a test server (a local virtual machine will do) in order to test various procedures there. System administration should not be learned on a live server, as this can lead to a catastrophic results...

That being said, the current situation needs resolving! Yes, replace the relevant 'enabled=0' with a 'enabled=1' and vice versa, for [mysql56-community] and [mysql80-community] respectively. Make sure that the file is saved afterwards.

After you've done this and preferably before going any further, please post the output of these commands:

cat /etc/redhat-release
ls -als /etc/yum.repos.d
cat /etc/yum.repos.d/mysql-community.repo
rpm -q mysql-server

This will just tell us a bit more about the current state of your OS. One thing I'm wondering about is where MySQL 5.5.55 came from in the first place, as this isn't the default RHEL/CentOS 6 MySQL version.

Thank you for your advice regarding testing on a local server. Am I right in assuming you are referring to software such as XAMPP? Whilst I have performed a full backup of the Web Files and MySQL Database, I guess I am still learning the System Administration the hard way.

cat /etc/redhat-release:
CentOS release

ls -als /etc/yum.repos.d:
total 188
 4 drwxr-xr-x.   2 root root  4096 Jun 14 03:04 .
12 drwxr-xr-x. 107 root root 12288 Jun 14 03:47 ..
 4 -rw-r--r--.   1 root root   827 Jun 14 02:59 atomic.repo
12 -rw-r--r--.   1 root root 12288 Jun 13 23:40 .atomic.repo.swp
 4 -rw-r--r--.   1 root root   647 Jun 26  2018 CentOS-Debuginfo.repo
 4 -rw-r--r--.   1 root root   289 Jun 26  2018 CentOS-fasttrack.repo
 4 -rw-r--r--.   1 root root   630 Jun 26  2018 CentOS-Media.repo
12 -rw-r--r--.   1 root root  8854 Jun 26  2018 CentOS-Vault.repo
 4 -rw-r--r--.   1 root root   957 Nov  5  2012 epel.repo
 4 -rw-r--r--.   1 root root  1056 Nov  5  2012 epel-testing.repo
 4 -rw-r--r--.   1 root root  1862 Jun 14 03:06 mysql-community.repo
12 -rw-r--r--.   1 root root 12288 Jun 13 22:30 .mysql-community.repo.swm
12 -rw-r--r--.   1 root root 12288 Jun 13 18:21 .mysql-community.repo.swn
12 -rw-r--r--.   1 root root 12288 Jun 13 18:12 .mysql-community.repo.swo
 4 -rw-r--r--.   1 root root  1885 Feb 22  2018 mysql-community-source.repo
 4 -rw-r--r--.   1 root root   353 Jan  2 08:38 plesk-migrator.repo
 4 -rw-r--r--.   1 root root   546 Jun 12 15:37 plesk.repo
 4 -rw-r--r--.   1 root root   446 Dec 21 17:50 remi-glpi91.repo
 4 -rw-r--r--.   1 root root   446 Dec 21 17:50 remi-glpi92.repo
 4 -rw-r--r--.   1 root root   446 Dec 21 17:50 remi-glpi93.repo
 4 -rw-r--r--.   1 root root   446 Dec 21 17:50 remi-glpi94.repo
 4 -rw-r--r--.   1 root root   456 Dec 21 17:50 remi-php54.repo
 4 -rw-r--r--.   1 root root  1314 Dec 21 17:50 remi-php70.repo
 4 -rw-r--r--.   1 root root  1314 Dec 21 17:50 remi-php71.repo
 4 -rw-r--r--.   1 root root  1314 Dec 21 17:50 remi-php72.repo
 4 -rw-r--r--.   1 root root  1314 Dec 21 17:50 remi-php73.repo
 4 -rw-r--r--.   1 root root  2605 Dec 21 17:50 remi.repo
12 -rw-r--r--.   1 root root 12288 Jun 13 11:48 .remi.repo.swn
12 -rw-r--r--.   1 root root 12288 Jun 13 11:40 .remi.repo.swo
 4 -rw-r--r--.   1 root root   750 Dec 21 17:50 remi-safe.repo
 4 -rw-r--r--.   1 root root   636 Aug 20  2018 tortix-common.repo

cat /etc/yum.repos.d/mysql-community.repo:
# Enable to use MySQL 5.5
[mysql55-community]
name=MySQL 5.5 Community Server
baseurl=http://repo.mysql.com/yum/mysql-5.5-community/el/6/$basearch/
enabled=0
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-mysql

# Enable to use MySQL 5.6
[mysql56-community]
name=MySQL 5.6 Community Server
baseurl=http://repo.mysql.com/yum/mysql-5.6-community/el/6/$basearch/
enabled=1
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-mysql

# Enable to use MySQL 5.7
[mysql57-community]
name=MySQL 5.7 Community Server
baseurl=http://repo.mysql.com/yum/mysql-5.7-community/el/6/$basearch/
enabled=0
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-mysql

[mysql80-community]
name=MySQL 8.0 Community Server
baseurl=http://repo.mysql.com/yum/mysql-8.0-community/el/6/$basearch/
enabled=0
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-mysql

[mysql-connectors-community]
name=MySQL Connectors Community
baseurl=http://repo.mysql.com/yum/mysql-connectors-community/el/6/$basearch/
enabled=1
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-mysql

[mysql-tools-community]
name=MySQL Tools Community
baseurl=http://repo.mysql.com/yum/mysql-tools-community/el/6/$basearch/
enabled=1
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-mysql

[mysql-tools-preview]
name=MySQL Tools Preview
baseurl=http://repo.mysql.com/yum/mysql-tools-preview/el/6/$basearch/
enabled=0
gpgcheck=1
gpgkey=file:/etc/pki/rpm-gpg/RPM-GPG-KEY-mysql

[mysql-cluster-7.5-community]
name=MySQL Cluster 7.5 Community
baseurl=http://repo.mysql.com/yum/mysql-cluster-7.5-community/el/6/$basearch/
enabled=0
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-mysql

[mysql-cluster-7.6-community]
name=MySQL Cluster 7.6 Community
baseurl=http://repo.mysql.com/yum/mysql-cluster-7.6-community/el/6/$basearch/
enabled=0
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-mysql

rpm -q mysql-server:
package mysql-server is not installed

Since posting this query, I have managed to be able to get the MySQL to start. That said, the '500 Internal Server Error' message is now appearing when I head to the Domain associated with this server. Additionally, the Apache Test page is being triggered when I try to access the Mail Server/Webmail.

Would I be right in believing that whilst I have managed to install the MySQL 5.6, I now need to resolve the outstanding issues by dealing with the 'package mysql-server is not installed' message?

Also, I have run the 'mysql --version' command, which has outputted:

# mysql --version
mysql  Ver 14.14 Distrib 5.6.44, for Linux (x86_64) using  EditLine wrapper

I thought this acted as confirmation that MySQL was installed successfully but obviously that is not what the other output is suggesting.

Adding to the confusion is the fact that when I run the command 'yum install mysql-server', I generate the following output, despite the above command indicating MySQL Server has not been installed.

Package mysql-community-server-5.6.44-2.el6.x86_64 already installed and latest version
Nothing to do