In this tutorial, it is supposed to use the precompiled version of Quantum-ESPRESSO (6.3) on the smith cluster system, the one operated in the Morikawa group at Osaka University, and you don't have to copy source code or pseudopotential. You are going to use the source in
~ikutaro/QE/src/qe-6.3
and the pseudopotentials placed in
~ikutaro/QE/pseudo/
If you want to use your own version of the code and pseudopotentials, follow the instruction given in the "Installation" page.