Follow below steps and run the mysql performance tuning script on your cPanel server -
1. cd /usr/local/src
2. wget http://cpanelkb.net/download/cpanel-mysql-tuning.sh
3. chmod 755 cpanel-mysql-tuning.sh
4. ./cpanel-mysql-tuning.sh
1. Make a copy of my.cnf file before you make any changes -
cd /etc
cp my.cnf my.cnf_bk
2. Edit my.cnf with your favorite editor - vi my.cnf
3. Add the variables to my.cnf file as per the mysql script recommendations.
4. Finally, restart mysql service - service mysql restart
You will observe a great performance on the server.