Minecraft Server CPU Usage

The CPU usage feature of Pterodactyl Panel is useful in determining if something in your server is causing it to overload. In general, the most common cases of high CPU are from things built in the world (usually a 'machine' of some sort) or a plugin (or a few plugins). In some cases, it is normal for a server to display high CPU usage, but may not impact performance at all. In the cases where you do feel a noticeable drop in performance with high CPU (and even in some cases, low CPU), then you will need to troubleshoot the server to find out what the cause is.
Usually the first step is to restart the server to see if the load/performance returns to normal. This will let you know if it is caused by a specific issue in your server or if it is just constant high load no matter what. After that point, you will want to disable all of your plugins (easily done by renaming the "plugins" folder with the server off) and start up your server and monitor the load/performance. If that fixes the problem, then you know that the issue stems from a plugin. At that pint, put all your plugins back in and start to eliminate them one by one, restarting your server each time you remove a plugin to narrow down the plugins to find out which one(s) is causing the high load.
If removing all plugins does not fix the load issue, then your world is the next test. You'll want to create a new empty folder in your server directory then move all your world folders into it (with the server off) so that the server creates new worlds with the same name when you start it up. You can change the level-name as well to generate a new world, but that could affect some plugins that rely on the world name to save data. If changing the world fixes the load/performance issue, then you know it is an issue with something built in the world. Some plugins like "NoLagg" (found on dev.bukkit.org) will help with world issues, but some issues are too deep rooted to fix via a plugin and require using software like MCEdit (http://www.mcedit.net/) to repair the world, which is a complex undertaking in itself.

If you're using Spigot - you can try using the timings feature to determine the cause of lag as well: Troubleshooting Lag Problems with Spigot Minecraft Servers
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