Which version of yEd are you using (see "Help" -> "About")?
On which operating system are you using yEd?
Which version of Java is yEd running on (see "Help" -> "About")?
What is yEd's "Memory Usage" prior to running Hierarchical layout?
How many nodes and edges has your diagram? (When no elements are selected, the number of nodes and edges is displayed in the properties view in the lower right corner.)