How can I monitor the load on a VPS with a web server?

Question

Apache HTTP Server

Ubuntu 12.04 system
MySQL 5.5
Apache 2
PHP
On the server test sites on proven (and most importantly always updated) drupal and joomla engines.
From the outside, only 2 are available, with a load of no more than 20 hosts per day.
The other day htop showed that MySQL loads the CPU at 100% (table sizes are not large, the largest is about 10 megabytes and this is for a site on which there are no queries at all)
How can you determine what is causing such a load? If you disable Apache or muscle load immediately returns to normal. As if a large number of requests (the logs do not show this).
If there was adequate attendance of resources, it would be clear what is happening.
And with practically only an admin request of sites, there should not be such a load.
There is also an assumption that on a physical server, neighbors load the processor in this way, but from a virtual machine, as I understand it, you can’t check it.

Answer 1

newrelic.com

Answer 2

Munin. It is easy to install and there are a lot of plugins in the kit, at least for apache and mysql there are definitely.

Answer 3

toster.ru/answer?answer_id=308173#answers_list
There is a wonderful Pinba module for PHP monitoring . You can also configure to log slow MySQL queries.
Take a look at this implementation. There is a mod_performance
module for apache. This whole thing can be perfectly integrated with Zabbix

Answer 4

Munin, Nagios