Looking at all of the facts that we learned about this system so far, it seems that our next best course of action would be to recommend contacting the vagrant user to identify whether the lookbusy and bonnie++ applications should be running with such high resource utilization.
While the previous observations show a high resource utilization, this level of utilization may be expected for this environment. Before we start contacting users, we should first review the historical performance metrics of this server. In most environments, there is some sort of server performance monitoring software such as Munin, Cacti, or one of the many cloud SaaS providers in place that collects and stores system statistics.
If your environment utilizes one of these services, you can use the collected performance data to compare previous performance statistics with the information that we just gathered. If for instance over the past 30 days, the CPU performance was never higher than...