More update...
It seems that persistance.xml present in gwt-console-server is not read as even if I make any error in it there are error from tomcat. The persistance.xml is in gwt-console-server\WEB-INF\classes .
I still dont understand on what basis it is searching for jdbc/jbpm-ds as my persistance.xml contains java:comp/env/jdbc/jbpm-ds.