Stop Eclipse/Java running multiple instances

In Eclipse Neon go to Window -> Preferences -> Run/Debug -> Launching and in the Launch Operation section check:

[X] Terminate and Relaunch while launching

In eclipse when you Run/Debug an application a new instance is created.
There are two options:

1. When you run an application it opens up the UI/result in the console. Hence you have to stop the existing application by click on one of these:

2. In debug mode you have to do the same.

Or else you have to handle this in the code. Check this thread: How to restrict Eclipse-RCP application to a single instance?

Hope this is helpful.