If you are a relative MySQL newbie like me, and someone tells you to backup your databases, you might make the same mistake that I did and copy the database files (all of those .frm, MYD and .MYT files) to a backup folder instead of using MySQL's built in backup method.
Of course, when you make this kind of mistake, often you are required to restore from backups, so you copy the files back to their original location and MySQL bombs on you when you try to start it.
In my case, I backed up the entire /var/lib/mysql directory to /tmp/mysql-backups. When I copied the /tmp/mysql-backups stuff back to /var/lib/mysql, nothing worked. Doing a 'cat /var/log/mysqld.log' showed a "Can't find file: './mysql/plugin.frm' (errno: 13)" error.
Turns out that you have to reset permissions on those files and do some work with SELinux to get that to allow the mysql account to access the databases.
This help is specific to MySQL using InnoDB on CentOS 6.x. I have no way of knowing if it will work for any other configurations.
Here's how to restore your databases and reset the permissions assuming that you have a backup of the entire /var/lib/mysql directory. I'm going to do a bunch of similar chown/chmod statements below just to be sure. You could do the same thing by doing
'chown -R mysql:mysql <directory>' and you'll want to do the separate commands for chmod since the directories and files should have different allowed operations.
rm -rf /var/lib/mysql
cp -r /tmp/mysql-backups/* /var/lib/mysql
chown mysql:mysql /var/lib/mysql
chown mysql:mysql /var/lib/mysql/*
chmod 660 /var/lib/mysql/*
chown mysql:mysql /var/lib/mysql/mysql
chmod 700 /var/lib/mysql/mysql
chown mysql:mysql /var/lib/mysql/mysql/*
chmod 660 /var/lib/mysql/mysql/*
Do the chown and chmod commands as shown for any other directories that you have under /var/lib/mysql
If you tried to start mysql right now, you'd still get the same error though if you have SELinux turned on, so now we have to fix that.
chcon -v --type=mysqld_db_t /var/lib/mysql
chcon -v --type=mysqld_db_t /var/lib/mysql/*
chcon -v --type=mysqld_db_t /var/lib/mysql/mysql
chcon -v --type=mysqld_db_t /var/lib/mysql/mysql/*
And so forth for any directories that you have under /var/lib/mysql
If you started mysql now, you'd see this error now "[ERROR] Can't start server : Bind on unix socket: Permission denied". SELinux is still blocking access so now you have to do the following:
semanage fcontext -a -t mysqld_db_t "/var/lib/mysql(/.*)?"
restorecon -Rv /var/lib/mysql
It is likely that you will only have to do the 'restorecon' command above, but I'm being thorough here.
You can now start the mysql service ('service mysqld start') and it should work without issues.