Usually, when you open PDF files in Okular, it opens in the same okular window all the time. However there are times when you want to refer to more than one pdf file at the same time and would need multiple instances of the software to run. The way to get Okular to run unique instances is by firing it with the
You could also put this in your .bashrc or .bash_aliases if you want it as a permanent fix.
alias okular="okular --unique"