It seems like the problem started about 3 to 4 weeks ago after the last update. The strangest thing, is even after I uninstalled All-in-one plugin, the problem continues with thousands of hits on the non-existent /calendar directory, and that is enough to shut down the site. The solution we came up with is to create an empty calendar folder, and then protected the directory with an apache login page. CPU usage dropped immediately from 100% shut down level to 20-50%.