I run piwik on one of my high traffic websites, and it uses a lot of server resources specially CPU. We did a lot of server optimizations. But all of our server engineers concluded that the file piwik.php in the root of Piwik, is the major script putting pressure on resources and needs to be optimized.
How many pageviews are you tracking?
What is the server configuration?
Enable mysql slow query log and see which requests are slow?
I have about 500k pageviews
we have 2 servers, 1 for files and 1 for DB, the one for files is having the high load which has this specs: Intel Core i3-540 3.06GHz H/T RAM 8GB Storage 2 1000GB RAID: SW Traffic: 20TB
Shall I enable mysql slow query log on my DB server, or files server?
This is not a bug. Please get in touch with Piwik professionnal support. http://piwik.org/support