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You need metrics-based monitoring and logs. Something that will tell you what containers are using what CPU time when. Something like cAdvisor is a good tool. It can monitor the CPU use of docker containers and systemd units. (Set DefaultCPUAccounting=yes in /etc/systemd/system.conf)
You probably also want to monitor the OS, something like the node_exporter or telegraf can be used to gather data about the memory utilization, network traffic, swap activity, etc.
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