yEd is not designed to handle that many elements. I am afraid the only way to speed up yEd is to reduce the number of elements in your diagram significantly.
Regarding the error dialog, I guess you are running out of memory when trying to arrange diagrams with 100K nodes and edges. You can try to increase the amount of memory available to yEd by following the guidelines in How can I prevent 'Out of Memory' errors in yEd?, however, not all layout algorithms can cope with so many elements - and if they can, they will run for a looong time.