Issue Upgrading from MySQL 5.5 to 5.7 on CentOS 6

[Shawnosaurus]

I own a Plesk (reseller) license as part of major web company's hosting services, so the Plesk support system doesn't allow me to file tickets. I'm hoping to get an official response and resolution on this issue.

Upgrade history: I previously upgraded MySQL from 5.0 to 5.5 using Plesk 12.5's control panel. Now on CentOS 6.10, with Plesk 17.8.11, I'm trying to upgrade MySQL 5.5 to 5.7 through the command line as described in the help support article.

Problem: Running yum update mysql (from step 8), I get the following errors...

Resolving Dependencies
--> Running transaction check
---> Package mysql.x86_64 0:5.5.30-1.el6.remi will be obsoleted
--> Processing Dependency: mysql(x86-64) = 5.5.30-1.el6.remi for package: mysql-bench-5.5.30-1.el6.remi.x86_64
--> Processing Dependency: mysql(x86-64) = 5.5.30-1.el6.remi for package: mysql-server-5.5.30-1.el6.remi.x86_64
--> Processing Dependency: mysql(x86-64) = 5.5.30-1.el6.remi for package: mysql-devel-5.5.30-1.el6.remi.x86_64
---> Package mysql-community-client.x86_64 0:5.7.30-1.el6 will be obsoleting
--> Processing Dependency: mysql-community-libs(x86-64) >= 5.7.9 for package: mysql-community-client-5.7.30-1.el6.x86_64
--> Running transaction check
---> Package mysql-bench.x86_64 0:5.5.30-1.el6.remi will be obsoleted
---> Package mysql-community-devel.x86_64 0:5.7.30-1.el6 will be obsoleting
---> Package mysql-community-libs.x86_64 0:5.7.30-1.el6 will be obsoleting
--> Processing Dependency: mysql-community-common(x86-64) >= 5.7.9 for package: mysql-community-libs-5.7.30-1.el6.x86_64
---> Package mysql-community-server.x86_64 0:5.7.30-1.el6 will be obsoleting
--> Processing Dependency: libnuma.so.1(libnuma_1.2)(64bit) for package: mysql-community-server-5.7.30-1.el6.x86_64
--> Processing Dependency: libnuma.so.1(libnuma_1.1)(64bit) for package: mysql-community-server-5.7.30-1.el6.x86_64
--> Processing Dependency: libnuma.so.1()(64bit) for package: mysql-community-server-5.7.30-1.el6.x86_64
---> Package mysql-devel.x86_64 0:5.5.30-1.el6.remi will be obsoleted
---> Package mysql-libs.x86_64 0:5.5.30-1.el6.remi will be obsoleted
--> Processing Dependency: libmysqlclient.so.18()(64bit) for package: php-mysql-5.4.13-1.el6.remi.x86_64
--> Processing Dependency: libmysqlclient.so.18(libmysqlclient_16)(64bit) for package: php-mysql-5.4.13-1.el6.remi.x86_64
--> Processing Dependency: libmysqlclient.so.18(libmysqlclient_18)(64bit) for package: php-mysql-5.4.13-1.el6.remi.x86_64
---> Package mysql-server.x86_64 0:5.5.30-1.el6.remi will be obsoleted
--> Running transaction check
---> Package mysql-community-common.x86_64 0:5.7.30-1.el6 will be installed
---> Package mysql-libs.x86_64 0:5.5.30-1.el6.remi will be obsoleted
--> Processing Dependency: libmysqlclient.so.18()(64bit) for package: php-mysql-5.4.13-1.el6.remi.x86_64
--> Processing Dependency: libmysqlclient.so.18(libmysqlclient_16)(64bit) for package: php-mysql-5.4.13-1.el6.remi.x86_64
--> Processing Dependency: libmysqlclient.so.18(libmysqlclient_18)(64bit) for package: php-mysql-5.4.13-1.el6.remi.x86_64
---> Package numactl.x86_64 0:2.0.9-2.el6 will be installed
--> Finished Dependency Resolution
Error: Package: php-mysql-5.4.13-1.el6.remi.x86_64 (installed)
           Requires: libmysqlclient.so.18(libmysqlclient_16)(64bit)
           Removing: mysql-libs-5.5.30-1.el6.remi.x86_64 (installed)
               libmysqlclient.so.18(libmysqlclient_16)(64bit)
           Obsoleted By: mysql-community-libs-5.7.30-1.el6.x86_64 (mysql57-community)
               Not found
           Available: mysql-libs-5.5.28-3.el6.remi.x86_64 (mt_dv_extras)
               libmysqlclient.so.18(libmysqlclient_16)(64bit)
           Available: mysql-libs-5.5.29-1.el6.remi.x86_64 (mt_dv_extras)
               libmysqlclient.so.18(libmysqlclient_16)(64bit)
           Available: mysql-libs-5.1.73-8.el6_8.i686 (base)
               Not found
Error: Package: php-mysql-5.4.13-1.el6.remi.x86_64 (installed)
           Requires: libmysqlclient.so.18(libmysqlclient_18)(64bit)
           Removing: mysql-libs-5.5.30-1.el6.remi.x86_64 (installed)
               libmysqlclient.so.18(libmysqlclient_18)(64bit)
           Obsoleted By: mysql-community-libs-5.7.30-1.el6.x86_64 (mysql57-community)
               Not found
           Available: mysql-libs-5.5.28-3.el6.remi.x86_64 (mt_dv_extras)
               libmysqlclient.so.18(libmysqlclient_18)(64bit)
           Available: mysql-libs-5.5.29-1.el6.remi.x86_64 (mt_dv_extras)
               libmysqlclient.so.18(libmysqlclient_18)(64bit)
           Available: mysql-libs-5.1.73-8.el6_8.i686 (base)
               Not found
Error: Package: php-mysql-5.4.13-1.el6.remi.x86_64 (installed)
           Requires: libmysqlclient.so.18()(64bit)
           Removing: mysql-libs-5.5.30-1.el6.remi.x86_64 (installed)
               libmysqlclient.so.18()(64bit)
           Obsoleted By: mysql-community-libs-5.7.30-1.el6.x86_64 (mysql57-community)
               Not found
           Available: mysql-libs-5.5.28-3.el6.remi.x86_64 (mt_dv_extras)
               libmysqlclient.so.18()(64bit)
           Available: mysql-libs-5.5.29-1.el6.remi.x86_64 (mt_dv_extras)
               libmysqlclient.so.18()(64bit)
           Available: mysql-libs-5.1.73-8.el6_8.i686 (base)
               Not found
You could try using --skip-broken to work around the problem
You could try running: rpm -Va --nofiles --nodigest

I've already tried the yum clean all suggestion from the article comment. And I've found a similar issue without a resolution.

Can the Plesk team or someone who may have resolved this chime in on what to do?

 

[IgorG]

I can only assume that this is due to the use of the third-party remi repository. You could try to disable it at least.
Or contact Plesk Support Team How to get support directly from Plesk? because detailed investigation directly on your server is required.

 

[Shawnosaurus]

Hey @IgorG, thanks for the reply. I'd purchase support directly, but I can't submit the form to start the process due to the licensing issue I previously mentioned.

I did try your disable suggestion as well. I think what was tripping me up was the remi package wasn't coming from a remi repo name, but rather the "mt_dv_extras" repo. I found this by through repoquery -i mysql:

Name        : mysql
Version     : 5.5.30
Release     : 1.el6.remi
Architecture: x86_64
Size        : 29846535
Packager    : http://blog.famillecollet.com/
Group       : Applications/Databases
URL         : http://www.mysql.com
Repository  : mt_dv_extras
Summary     : MySQL client programs and shared libraries
Source      : mysql-5.5.30-1.el6.remi.src.rpm

I disabled, ran through some article steps again and got the same errors from my original post. Let me know if you have other suggestions.

I'm getting in touch with Plesk licensing and purchase support team to see what other options there are for support help with a reseller license. In the meantime, I figure I could add details and refer to this thread if I'm able to open a ticket.

 

[Shawnosaurus]

I have a resolution, thanks to Remi Collet.

... switch from php-mysql (which use libmysqlclient) to php-mysqlnd which provides the same set of extensionx using the PHP native driver.

yum shell
> remove php-mysql
> install php-mysqlnd
> run

After that, yum update mysql will run properly.

But then service mysqld start gets "MySQL Daemon failed to start".

Saw a comment which tipped me off, and then verified what's causing this by looking at the log: tail -f /var/log/mysqld.log.

I had a couple instances of deprecated MySQL configuration variable "innodb_additional_mem_pool_size" in "/etc/my.cnf" I opened the file with vi editor to remove the lines: vi /etc/my.cnf.

Then I could upgrade the database: MYSQL_PWD=`cat /etc/psa/.psa.shadow` mysql_upgrade -uadmin.

But I couldn't restart MySQL after, and essentially saw a bunch of errors about "Wrapper /var/www/cgi-bin/cgi_wrapper/cgi_wrapper cannot be accessed: (2)No such file or directory". The "psa-php5-configurator" package was missing, according to a Plesk support article. So I ran the following:

rpm -Uvh --force --nodeps http://autoinstall.plesk.com/PSA_17.8.11/dist-rpm-CentOS-6-x86_64/opt/php5/psa-php5-configurator-1.7.0-cos6.build1708180212.17.x86_64.rpm
/usr/local/psa/admin/bin/httpdmng --reconfigure-all

After which, I could start MySQL again, then finish the upgrade steps by updating package versions inside Plesk.

On a side note, I did hear back from Plesk Customer Success team about support for my license, and apparently my only option is to ask for help from my hosting company. They have no articles on how to do this upgrade, and when I asked for assistance I found they have an unpublished MySQL upgrade service for a one-time $79 fee. This is on top of the monthly premium I'm already paying them for "managed" VPS hosting. So my feedback point is, this type of licensing and business model isn't conducive to retaining customers for either Plesk or the hosting company. I'm going to be migrating hosts to a company that offers the same specs at a much lower cost, and also setting up a platform architecture and control panel that has a more active and accessible community behind it.