Enable slow PHP logging, it can in most cases narrow down the problematic scripts.
Modify: /opt/cpanel/ea-php*/root/etc/php-fpm.d/domain.conf
You can leave the asterisk next to php if you don't know the PHP version and just replace domain.com example if you use nano:
Code:
nano /opt/cpanel/ea-php*/root/etc/php-fpm.d/bob.com.conf
then at the bottom of the config, add:
Code:
request_slowlog_timeout = 10
slowlog = /home/bobcom/logs/bob.com.php.slow.log
replace bobcom with the cpanel user and bob.com with your actual domain.
then restart php-fpm
Code:
/scripts/restartsrv_apache_php_fpm
Now once a script has been serving a single request for more than 10 seconds, it will trace the process and output a bunch of hopefully useful info for you into that log file.
Secondly, you can tail the access log file to see your traffic:
Code:
tail -f /home/bobcom/access-logs/bob.com*
See anything suspicious? Example if running a WordPress site you might see lots of hits to xmlrpc.php and/or wp-login.php
Otherwise, it might just be your site's dynamic usage, again if its WordPress this can in most cases be resolved by simply installing a caching plugin.
Let us know what you find