This web container has not yet been started @Glassfish 4.0.01 web

I had big trouble resolving this. The problem is that your previous EntityManagerFactory was not closed.

Ensure that you always close the EntityManagerFactory upon undeployment. One way to do it is via a registered ServletContextListener e.g

@Override
public void contextDestroyed(ServletContextEvent sce) {
  EntityManagerFactory emf = getEmf(...);
  emf.close();
}