what to use to fill the gap of toilet drain pipe
 

My second floor toilet drain pipe has a wide, about half inch gap between the pipe and the floor. What should I use to fill the gap? cement, grout or other material?

Attached picture is view of first floor ceiling, after opened it up.

Always best to replace the rotten floor wood.
However if the toilet flange is securely mounted to the rest of the floor, I would use some expanding foam just to seal up that area.