Your EnergyPlus simulation is completing, as evidenced by this line: EnergyPlus Run Time=00hr 00min 3.05sec. The repeating warning that Could not resolve matched surface construction conflicts between surfaces '1', and '1', area calculation may be incorrect is a known issue pertaining to non-symmetrical unsymmetrical constructions of matched surfaces. It appears that the issue is being resolved, and the message should not have any impact on your simulation results.