High CPU usage by mysql process (9 replies)

Hi,
On a dedicated server (Specifications below), Ubuntu 15.04, lighttpd. I have a problem with a high CPU usage of mysql process. In "htop" usage of mysql process is jumping from 0% to 500%.
On the server there are running scripts in node.js and page in PHP.

Even though I turn off all the running scripts high cpu usage for mysql still appears. Could it be fault of configuration or mysql have a problem with multiple cores?

I would highly appreciate any help with solving that problem.

Server Specs:
RAM: 256G
DYSK: SSD 2x480G
Intel(R) Xeon(R) CPU E5-2630 v3 @ 32x 2.40GHz (20480KB cache)

Cheers!