1. Activate the logging of mysql slow queries.

mysqladmin var |grep log_slow_queries
| log_slow_queries | OFF |

If log_slow_queries is ON then we already have it enabled. This setting is by default disabled – meaning that if you don’t have log_slow_queries defined in the mysql server config this will be disabled.
The mysql variable long_query_time (default 1) defines what is considered as a slow query. In the default case, any query that takes more than 1 second will be considered a slow query.

Ok, now for the scope of this article we will enable the mysql slow query log. In order to do to do this in your mysql server config file (/etc/my.cnf RHEL/Centos or /etc/mysql/my.cnf on Debian, etc.) in the mysqld section we will add:

[mysqld]
long_query_time = 1
log-slow-queries = /var/log/mysql/mysql-slow.log


This configuration will log all queries that take more than 1 sec in the file /var/log/mysql/mysql-slow.log. You will probably want to define these based on your particular setup (maybe you will want the logs in a different location and/or you will consider a higher value than 1 sec to be slow query).

Once you have done the proper configurations to enable mysql to log slow queries you will have to reload the mysql service in order to activate the changes.
2. Investigate the mysql slow queries log.

After we enabled slow query logging we can look inside the log file for each slow query that was executed by the server. Various details are logged to help us understand how was the query executed:

Time: how long it took to execute the query
Lock: how long was a lock required
Rows: how many rows were investigated by the query (this can help see quickly queries without indexes)
Host: the actual host that launched the query (this can be localhost, or a different one in multiple servers setup)
The actual mysql query.

This information allows us to see what queries need to be optimized, but on a high traffic server and with lots of slow queries this log can grow up very fast making it very difficult to find any relevant information inside it.
In this case we have two choices:

We increase the long_query_time and we focus on the queries that take the most time to complete, and we gradually decrease this once we solve the queries.
We use some sort of tool to parse the slow query log file and have it show us the most used queries.