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Kick all the tires before you buy the product
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Translating theory to practice is never easy. Morgan gives us the right steps in a play environment to move from dev.mysql.com native MySQL rpm’s to the new MySQL yum repository. I thought I would try it out.

1. Confirming existing packages

A necessary step, however immediately I have more dependencies including Perl DBD (used in several utilities) including MHA.

$ sudo su -
$ rpm -qa | grep -i mysql
MySQL-devel-5.6.13-1.el6.x86_64
MySQL-test-5.6.13-1.el6.x86_64
MySQL-shared-compat-5.6.13-1.el6.x86_64
MySQL-server-5.6.13-1.el6.x86_64
perl-DBD-MySQL-4.013-3.el6.x86_64
MySQL-client-5.6.13-1.el6.x86_64
MySQL-embedded-5.6.13-1.el6.x86_64
MySQL-shared-5.6.13-1.el6.x86_64
mha4mysql-node-0.54-1.el5.noarch

A further trap in the more complex real-world environments, in my case the installation of Percona XtraBackup. This will become apparent in the next step. We need to check for these packages.

$ rpm -qa | grep -i percona
percona-release-0.0-1.x86_64
percona-xtrabackup-2.1.4-656.rhel6.x86_64

1. Update your environment

There is a mixed blessing here. Assuming you keep your machines current (and you should), the impact here should be minimal, but buyer beware. In my case the update wanted to update java-1.7.0-openjdk. Should not be a big deal, but what other products are impacted by updates? Java on this system for example is used by the New Relic MySQL Monitoring. What if there was some important application component that may become unravelled with some update.

Doing a blanket update on a reasonably current CentOS 6.4 system broke.

$ yum update
...
Installing:
 Percona-SQL-shared-compat                      x86_64                5.0.92-b23.89.rhel6                      percona                1.1 M
     replacing  MySQL-shared.x86_64 5.6.13-1.el6
 Percona-Server-shared-compat                   x86_64                5.5.34-rel32.0.591.rhel6                 percona                3.4 M
     replacing  MySQL-shared.x86_64 5.6.13-1.el6
 Percona-Server-shared-compat-51                x86_64                5.1.72-rel14.10.597.rhel6                percona                2.4 M
     replacing  MySQL-shared.x86_64 5.6.13-1.el6
 kernel                                         x86_64                2.6.32-358.23.2.el6                      updates                 26 M
Transaction Summary
============================================================================================================================================
Install       4 Package(s)
Upgrade      26 Package(s)

...
Transaction Check Error:
  file /usr/lib64/libmysqlclient.so.12.0.0 from install of Percona-SQL-shared-compat-5.0.92-b23.89.rhel6.x86_64 conflicts with file from package MySQL-shared-compat-5.6.13-1.el6.x86_64
  file /usr/lib64/libmysqlclient.so.14.0.0 from install of Percona-SQL-shared-compat-5.0.92-b23.89.rhel6.x86_64 conflicts with file from package MySQL-shared-compat-5.6.13-1.el6.x86_64
  file /usr/lib64/libmysqlclient_r.so.12.0.0 from install of Percona-SQL-shared-compat-5.0.92-b23.89.rhel6.x86_64 conflicts with file from package MySQL-shared-compat-5.6.13-1.el6.x86_64
  file /usr/lib64/libmysqlclient_r.so.14.0.0 from install of Percona-SQL-shared-compat-5.0.92-b23.89.rhel6.x86_64 conflicts with file from package MySQL-shared-compat-5.6.13-1.el6.x86_64
  file /usr/lib64/libmysqlclient.so.16.0.0 from install of Percona-Server-shared-compat-5.5.34-rel32.0.591.rhel6.x86_64 conflicts with file from package MySQL-shared-compat-5.6.13-1.el6.x86_64
  file /usr/lib64/libmysqlclient_r.so.16.0.0 from install of Percona-Server-shared-compat-5.5.34-rel32.0.591.rhel6.x86_64 conflicts with file from package MySQL-shared-compat-5.6.13-1.el6.x86_64
  file /usr/lib64/libmysqlclient.so.12.0.0 conflicts between attempted installs of Percona-Server-shared-compat-5.5.34-rel32.0.591.rhel6.x86_64 and Percona-SQL-shared-compat-5.0.92-b23.89.rhel6.x86_64
  file /usr/lib64/libmysqlclient.so.14.0.0 conflicts between attempted installs of Percona-Server-shared-compat-5.5.34-rel32.0.591.rhel6.x86_64 and Percona-SQL-shared-compat-5.0.92-b23.89.rhel6.x86_64
  file /usr/lib64/libmysqlclient_r.so.12.0.0 conflicts between attempted installs of Percona-Server-shared-compat-5.5.34-rel32.0.591.rhel6.x86_64 and Percona-SQL-shared-compat-5.0.92-b23.89.rhel6.x86_64
  file /usr/lib64/libmysqlclient_r.so.14.0.0 conflicts between attempted installs of Percona-Server-shared-compat-5.5.34-rel32.0.591.rhel6.x86_64 and Percona-SQL-shared-compat-5.0.92-b23.89.rhel6.x86_64
...

The problem here is an unhealthy relationship between repositories for Percona Xtrabackup. I don’t know the reason, but this is the curse of dependencies that make real world upgrades more complex.

Updating just MySQL is rather useless as it’s installed by rpm.

$ yum update MySQL-server
Loaded plugins: fastestmirror, presto
Loading mirror speeds from cached hostfile
 * base: mirror.cogentco.com
 * extras: mirror.cogentco.com
 * updates: mirror.trouble-free.net
Setting up Update Process
No Packages marked for Update

Removing existing MySQL

Stopping MySQL is easy. Making a decision about, should I backup important files, like the config file, or the data should be considered here. The reality is for a production system, assume something unexpected will happen, even if you have tested it. Being able to go back in any step of an upgrade is actually more important than the step itself. So the following IS NOT ENOUGH in a production system.

service mysql stop

This old dinosaur learned a new trick in the yum interactive shell. Cool!

Note, I am doing a point release upgrade here, from .13 to .14.

$ yum shell
> remove MySQL-client-5.6.13-1.el6 MySQL-embedded-5.6.13-1.el6 MySQL-server-5.6.13-1.el6 MySQL-shared-5.6.13-1.el6 MySQL-devel-5.6.13-1.el6 MySQL-test-5.6.13-1.el6 MySQL-shared-compat-5.6.13-1.el6
> install mysql-community-server
> run

Now the fun begins, you have to read carefully what is happening, check out the Removing for dependencies section.

============================================================================================================================================
 Package                              Arch                 Version                            Repository                               Size
============================================================================================================================================
Installing:
 mysql-community-server               x86_64               5.6.14-3.el6                       mysql-community                          51 M
Removing:
 MySQL-client                         x86_64               5.6.13-1.el6                       installed                                81 M
 MySQL-devel                          x86_64               5.6.13-1.el6                       installed                                19 M
 MySQL-embedded                       x86_64               5.6.13-1.el6                       installed                               431 M
 MySQL-server                         x86_64               5.6.13-1.el6                       installed                               235 M
 MySQL-shared                         x86_64               5.6.13-1.el6                       installed                               8.4 M
 MySQL-shared-compat                  x86_64               5.6.13-1.el6                       installed                                11 M
 MySQL-test                           x86_64               5.6.13-1.el6                       installed                               318 M
Installing for dependencies:
 mysql-community-client               x86_64               5.6.14-3.el6                       mysql-community                          18 M
 mysql-community-common               x86_64               5.6.14-3.el6                       mysql-community                         296 k
 mysql-community-libs                 x86_64               5.6.14-3.el6                       mysql-community                         1.8 M
Removing for dependencies:
 cronie                               x86_64               1.4.4-7.el6                        @CentOS6-Base/$releasever               166 k
 cronie-anacron                       x86_64               1.4.4-7.el6                        @CentOS6-Base/$releasever                43 k
 crontabs                             noarch               1.10-33.el6                        @CentOS6-Base/$releasever               2.4 k
 mha4mysql-node                       noarch               0.54-1.el5                         installed                                98 k
 percona-xtrabackup                   x86_64               2.1.4-656.rhel6                    @percona                                 24 M
 perl-DBD-MySQL                       x86_64               4.013-3.el6                        @base                                   338 k
 postfix                              x86_64               2:2.6.6-2.2.el6_1                  @CentOS6-Base/$releasever               9.7 M
 sysstat                              x86_64               9.0.4-20.el6                       @base                                   807 k

Transaction Summary
============================================================================================================================================
Install       4 Package(s)
Remove       15 Package(s)

Also, you need to quit the yum shell.

> quit
Leaving Shell

Verification

So, we have now installed MySQL via the new yum repositories, and we can verify this.

$ service mysqld start
Starting mysqld:                                           [  OK  ]
$ mysql -e "SELECT VERSION()"
+------------+
| VERSION()  |
+------------+
| 5.6.14-log |
+------------+
$ chkconfig mysqld on

But, we now have a broken system, because dependencies were removed.

Extra steps needed

Installation of Percona Backup.

$ yum install percona-xtrabackup
Loaded plugins: fastestmirror, presto
Loading mirror speeds from cached hostfile
 * base: mirrors.advancedhosters.com
 * extras: mirror.cogentco.com
 * updates: mirror.trouble-free.net
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package percona-xtrabackup.x86_64 0:2.1.5-680.rhel6 will be installed
--> Processing Dependency: perl(DBD::mysql) for package: percona-xtrabackup-2.1.5-680.rhel6.x86_64
--> Running transaction check
---> Package perl-DBD-MySQL.x86_64 0:4.013-3.el6 will be installed
--> Processing Dependency: libmysqlclient.so.16(libmysqlclient_16)(64bit) for package: perl-DBD-MySQL-4.013-3.el6.x86_64
--> Processing Dependency: libmysqlclient.so.16()(64bit) for package: perl-DBD-MySQL-4.013-3.el6.x86_64
--> Running transaction check
---> Package Percona-Server-shared-51.x86_64 0:5.1.72-rel14.10.597.rhel6 will be installed
--> Finished Dependency Resolution

Dependencies Resolved

============================================================================================================================================
 Package                                  Arch                   Version                                      Repository               Size
============================================================================================================================================
Installing:
 percona-xtrabackup                       x86_64                 2.1.5-680.rhel6                              percona                 6.8 M
Installing for dependencies:
 Percona-Server-shared-51                 x86_64                 5.1.72-rel14.10.597.rhel6                    percona                 2.1 M
 perl-DBD-MySQL                           x86_64                 4.013-3.el6                                  base                    134 k

Transaction Summary
============================================================================================================================================
Install       3 Package(s)

Total size: 9.1 M
Total download size: 2.3 M
Installed size: 30 M
Is this ok [y/N]: y
Downloading Packages:
Setting up and reading Presto delta metadata
Processing delta metadata
Package(s) data still to download: 2.3 M
(1/2): Percona-Server-shared-51-5.1.72-rel14.10.597.rhel6.x86_64.rpm                                                 | 2.1 MB     00:00
(2/2): perl-DBD-MySQL-4.013-3.el6.x86_64.rpm                                                                         | 134 kB     00:00
--------------------------------------------------------------------------------------------------------------------------------------------
Total                                                                                                       9.7 MB/s | 2.3 MB     00:00
Running rpm_check_debug
Running Transaction Test
Transaction Test Succeeded
Running Transaction
  Installing : Percona-Server-shared-51-5.1.72-rel14.10.597.rhel6.x86_64                                                                1/3
  Installing : perl-DBD-MySQL-4.013-3.el6.x86_64                                                                                        2/3
  Installing : percona-xtrabackup-2.1.5-680.rhel6.x86_64                                                                                3/3
  Verifying  : percona-xtrabackup-2.1.5-680.rhel6.x86_64                                                                                1/3
  Verifying  : perl-DBD-MySQL-4.013-3.el6.x86_64                                                                                        2/3
  Verifying  : Percona-Server-shared-51-5.1.72-rel14.10.597.rhel6.x86_64                                                                3/3 

Installed:
  percona-xtrabackup.x86_64 0:2.1.5-680.rhel6                                                                                               

Dependency Installed:
  Percona-Server-shared-51.x86_64 0:5.1.72-rel14.10.597.rhel6                      perl-DBD-MySQL.x86_64 0:4.013-3.el6                     

Complete!

Please explain this one to be batman, removing MySQL removed the sysstat package. Very weird.

$ iostat
-bash: iostat: command not found
$ yum install sysstat
Loaded plugins: fastestmirror, presto
Loading mirror speeds from cached hostfile
 * base: mirrors.advancedhosters.com
 * extras: mirror.cogentco.com
 * updates: centos.someimage.com
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package sysstat.x86_64 0:9.0.4-20.el6 will be installed
--> Processing Dependency: /etc/cron.d for package: sysstat-9.0.4-20.el6.x86_64
--> Running transaction check
---> Package cronie.x86_64 0:1.4.4-7.el6 will be installed
--> Processing Dependency: dailyjobs for package: cronie-1.4.4-7.el6.x86_64
--> Processing Dependency: /usr/sbin/sendmail for package: cronie-1.4.4-7.el6.x86_64
--> Running transaction check
---> Package cronie-anacron.x86_64 0:1.4.4-7.el6 will be installed
--> Processing Dependency: crontabs for package: cronie-anacron-1.4.4-7.el6.x86_64
---> Package postfix.x86_64 2:2.6.6-2.2.el6_1 will be installed
--> Running transaction check
---> Package crontabs.noarch 0:1.10-33.el6 will be installed
--> Finished Dependency Resolution

Dependencies Resolved

============================================================================================================================================
 Package                              Arch                         Version                                 Repository                  Size
============================================================================================================================================
Installing:
 sysstat                              x86_64                       9.0.4-20.el6                            base                       225 k
Installing for dependencies:
 cronie                               x86_64                       1.4.4-7.el6                             base                        70 k
 cronie-anacron                       x86_64                       1.4.4-7.el6                             base                        29 k
 crontabs                             noarch                       1.10-33.el6                             base                        10 k
 postfix                              x86_64                       2:2.6.6-2.2.el6_1                       base                       2.0 M

Transaction Summary
============================================================================================================================================
Install       5 Package(s)

Total download size: 2.4 M
Installed size: 11 M
Is this ok [y/N]: y
Downloading Packages:
Setting up and reading Presto delta metadata
Processing delta metadata
Package(s) data still to download: 2.4 M
(1/5): cronie-1.4.4-7.el6.x86_64.rpm                                                                                 |  70 kB     00:00
(2/5): cronie-anacron-1.4.4-7.el6.x86_64.rpm                                                                         |  29 kB     00:00
(3/5): crontabs-1.10-33.el6.noarch.rpm                                                                               |  10 kB     00:00
(4/5): postfix-2.6.6-2.2.el6_1.x86_64.rpm                                                                            | 2.0 MB     00:00
(5/5): sysstat-9.0.4-20.el6.x86_64.rpm                                                                               | 225 kB     00:00
--------------------------------------------------------------------------------------------------------------------------------------------
Total                                                                                                        21 MB/s | 2.4 MB     00:00
Running rpm_check_debug
Running Transaction Test
Transaction Test Succeeded
Running Transaction
  Installing : 2:postfix-2.6.6-2.2.el6_1.x86_64                                                                                         1/5
  Installing : cronie-1.4.4-7.el6.x86_64                                                                                                2/5
  Installing : crontabs-1.10-33.el6.noarch                                                                                              3/5
  Installing : cronie-anacron-1.4.4-7.el6.x86_64                                                                                        4/5
  Installing : sysstat-9.0.4-20.el6.x86_64                                                                                              5/5
  Verifying  : crontabs-1.10-33.el6.noarch                                                                                              1/5
  Verifying  : cronie-1.4.4-7.el6.x86_64                                                                                                2/5
  Verifying  : 2:postfix-2.6.6-2.2.el6_1.x86_64                                                                                         3/5
  Verifying  : sysstat-9.0.4-20.el6.x86_64                                                                                              4/5
  Verifying  : cronie-anacron-1.4.4-7.el6.x86_64                                                                                        5/5 

Installed:
  sysstat.x86_64 0:9.0.4-20.el6                                                                                                             

Dependency Installed:
  cronie.x86_64 0:1.4.4-7.el6    cronie-anacron.x86_64 0:1.4.4-7.el6    crontabs.noarch 0:1.10-33.el6    postfix.x86_64 2:2.6.6-2.2.el6_1   

Complete!

Re-installing MySQL MHA node.

$ cd /tmp
$ wget http://mysql-master-ha.googlecode.com/files/mha4mysql-node-0.54-0.el6.noarch.rpm
$ sudo rpm -ivh mha4mysql-node-*.noarch.rpm

There is now a lot more work needed to check and recheck the dependencies and verify what did work previously still works.

At this time doing this on 20 DB servers to move to the new yum repository is a fail for this client. It’s simply not worth it.

Conclusion

Theory easy, practice not to easy!

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