I am having some issue with php files suddenly running - any idea what this can be?
Its not any one user, it looks like its all your users opening up multiple php and httpd connections all at once. This is a snip of the log for php and httpd processes:
At 5:24pm there were no php processes running.
At 5:25pm there were 131 php processes running.
At 5:26pm there were 167 php processes running.
At 5:27pm there were 171 php processes running.
Same goes for the httpd processes:
At 5:24pm there were 11 httpd processes
At 5:25pm there were 140 httpd proccesses
sudo atop -r -b 17:24 -l 5
As you can see its not a gradual increase of php processes it a sudden change. Which is what leads me to believe its something in your SilverStripe trying to update information or run some processes for the sites at some internal interval, and since its going off all at once for all your users and sites its causing a sudden resource issue with the server.