This detailed guide is mainly for FreeBSD, however the idea coincides for Linux. Every once a while, when I upgrade my FreeBSD box, the system prefers to shutdown my MySQL web server. Therefore, I need to begin it again after the upgrade is done. Sadly, the update process isn’t smooth every time. Sometimes it will toss me some mistake..

/usr/local/etc/rc.d/mysql.server start

Oh well, I got the following error messages:

Starting MySQL..... ERROR! The server quit without updating PID file.

Sometimes, the message will tell you the exact location of which PID file:

Starting MySQL..... ERROR! The server quit without updating PID file (/var/db/mysql/www.icesquare.com.pid).

There are several solutions to troubleshoot these problems. I will go over each one by one.

Solution 1: Reboot The Computer

Although it sounds simple, but it truly works. Throughout the system update, the OS may disable some of your daemons. Rather than fixing each one at a time, the easiest way is to begin everything over. For example, I skilled this problem today after updating the Apache and Ruby (Yes, MySQL isn’t component of the update), and I obtained this mistake message later. After rebooting the computer system, the mistake message is gone.

Solution 2: Remove Your MySQL Config File

If you have actually customized your MySQL setup submit, MySQL might not like it couple of variations after (MySQL isn’t backward compatibility pleasant). It could be the issue of utilizing an unsupported variable, or something comparable. The simplest method is to eliminate your setup submit, and attempt to begin the MySQL web server once more:

Backup your MySQL configuration first.

mv /etc/my.cnf /etc/my.cnf.backup

And restart the MySQL server again:

/usr/local/share/mysql/mysql.server start

Hopefully you will see the following message:

Starting MySQL. SUCCESS!

Solution 3: Upgrade Your Database File

Sometimes, the newer MySQL doesn’t like the database created in earlier version. I discovered this when I upgrade to MySQL 5.5.7:

Starting MySQL..... ERROR! The server quit without updating PID file (/var/db/mysql/www.icesquare.com.pid).

Since MySQL tells me which PID file causes the problem, I open the file and take a look what’s going on:

sudo tail /var/db/mysql/www.icesquare.com.err

And I saw something interesting: tables: Table ‘mysql.proxies_priv’ doesn’t exist:

101112 10:49:16  InnoDB: Initializing buffer pool, size = 128.0M
101112 10:49:16  InnoDB: Completed initialization of buffer pool
101112 10:49:16  InnoDB: highest supported file format is Barracuda.
101112 10:49:17  InnoDB: 1.1.3 started; log sequence number 1589404
101112 10:49:17 [ERROR] Fatal error: Can't open and lock privilege tables: Table 'mysql.proxies_priv' doesn't exist
101112 10:49:17 mysqld_safe mysqld from pid file /var/db/mysql/www.icesquare.com.pid ended

The reason is very simple. MySQL could not open a table created in the earlier version (< 5.7.7) because it is not compatible with the current version. So, we can try to start the MySQL in safe mode through rc.d. First, you can edit the /etc/rc.conf and put the following into the file:

mysql_enable="YES"
mysql_args="--skip-grant-tables --skip-networking"

Restart MySQL through rc.d:

/usr/local/etc/rc.d/mysql-server start

If you did it right, you should see something like the following:

Starting MySQL.. SUCCESS!

Now, MySQL is already running the safe-mode. We want to perform a MySQL upgrade on all tables:

sudo mysql_upgrade

You should see something like this:

Looking for 'mysql' as: mysql
Looking for 'mysqlcheck' as: mysqlcheck
Running 'mysqlcheck' with connection arguments: '--port=3306' '--socket=/tmp/mysql.sock'
Running 'mysqlcheck' with connection arguments: '--port=3306' '--socket=/tmp/mysql.sock'
mysql.columns_priv                                 OK
mysql.db                                           OK
mysql.event                                        OK
mysql.func                                         OK
mysql.general_log                                  OK
mysql.help_category                                OK
mysql.help_keyword                                 OK
mysql.help_relation                                OK
mysql.help_topic                                   OK
mysql.host                                         OK
mysql.ndb_binlog_index                             OK
mysql.plugin                                       OK
mysql.proc                                         OK
mysql.procs_priv                                   OK
mysql.servers                                      OK
mysql.slow_log                                     OK
mysql.tables_priv                                  OK
mysql.time_zone                                    OK
mysql.time_zone_leap_second                        OK
mysql.time_zone_name                               OK
mysql.time_zone_transition                         OK
mysql.time_zone_transition_type                    OK
mysql.user                                         OK
Running 'mysql_fix_privilege_tables'...
OK

Now, we want to switch the MySQL back to normal mode by commenting the extra options in /etc/rc.conf:

mysql_enable="YES"
#mysql_args="--skip-grant-tables --skip-networking"

And restart MySQL through /etc/rc.d:

/usr/local/etc/rc.d/mysql-server restart

Now the MySQL is up and running again!