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I'm debugging a normal Java application, no GUI, just a lot of computations and ~5 calls in the stack for the main thread when the problem occurs. Basically it keeps saying "Collecting data" in the local variable watch.
So instead of going step-by-step I've tried to add a breakpoint immediately after an press "Resume". Now it says "Waiting until last debugger command completes". 
Have anyone had this problem before? Is changing the debugger the only way to figure this out?
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Remove breakpoints off your method and use them inside the method as that can cause your debug to take a very long time. Try running IntelliJ as admin. I had this issue at work where debugging was extremely slow and running as admin actually made it a lot faster.
To solve this, simply remove the jar of the debugged module from all modules' dependencies in the Project Structure. If you do not know which modules have the debugged module jar as dependencies, you can use some tools (Eg. Sublime Text, bash, ...) to search for the module name which is stored in Intellij *.
The only way to do that is to set a break point outside the loop, or position the cursor outside the loop and do "run until cursor".
Increase memory for IntelliJ IDEA By default, the IDE requests a maximum of 2048 MB. You can change this option in Help → Change memory settings. According to the feedback from some of our users and colleagues with big projects, changing the option to 8GB significantly improves IDE performance.
On IntelliJ (2017.1.4 Community Edition), the following fixed the problem for me:
Re-run the debugger.
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The following fixed it for me on IntelliJ 2018.2.4:
This won't be helpful if you actually need to suspend all the threads for debugging, but it got rid of the "Collecting data..." and "Waiting until last debugger command completes" messages for me. The setting also persists for subsequent breakpoints, so you only need to change it once.
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