System runs out of space, space returns after restart

This is not an answer, but some tips on how to identify the source of the problem. Exactly which location use your hard drive space.
To find what is taking the space, you can do the following:
  • First, get a listing of the occupied space of the root folders with sudo du -h -d 1 --exclude=/proc --exclude=/run /. This will give you some output like the following:
    309M    /opt
3,8G    /var
512K    /root
(...)
3,5M    /lib32

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