I was bit by atop a few years back and swore it off. I would get perfectly periodic 10m hangs on MySQL. Apparently they changed the default runtime options such that it used an expensive metric gathering technique with a 10m cron job that would hang any large memory process on the system. It was one of those “no freaking way” revelations after 3 days troubleshooting everything.

Interesting reading through the related submission comments and seeing other hard to troubleshoot bugs. I don’t think atop devs are to blame, my guess is that what you have to do to make a tool like atop work means you are hooking into lots of places that have potential to have unintended consequences.