1) Select "Window->Open perspective->Other...->Prolog".
2) Open the preferences dialog from menu "Window->Preferences"
3) Go to the SWI compiler preferences in "Prolog->Compilers->Swi Compiler" and select the swi prolog console executable. ie: c:\prolog\SWI-Prolog\bin\plcon.exe or /usr/lib/pl-5.X.X/bin/i686-linux-gnu-pl
4) Go to "Prolog->Compilers" and make sure the default compiler is "Swi Compiler"