Hi Martin,
I think I have solved this problem.
At first I generated a coarse mesh and used it in the simulation. But I found there were two points that gave strange values of free surface elevation. So I deleted these two elements in the BlueKenue and saved the file. Then I made a new boundary conditions file. It didn't work in parallel but worked with one processor like I reported.
I guess the problem was that the action of deleting those two element caused the change of the structure of geometry file. Maybe it left two empty records in the binary file. This empty records might cause the problem during the partitioning process.
What I did to solve this problem is creating a new SLEAFIN object in BlueKenue and then drag the mesh into this new file and save it. So I have a new geometry file but with the same information inside (maybe it has been reorganized).
Thanks for your kind help. Hope this could help someone else.