The Japan Hadron Facility (JHF) synchrotrons are expected to store and accelerate ten times larger number of protons than that of the machines under operation (2x10(14) protons in the 50GeV main ring and 5x10(13) protons in the 3GeV booster). A stable operation with a very small beam loss is essential. Beam dynamics not only of the beam core but of the tail and halo should be considered. More specifically, transverse space charge effects have to be taken into account from the design stage of the lattice. In that sense, a conventional way of the lattice optimization, such as maximizing dynamic aperture and minimizing smear, may not be applicable, We have started to simulate commissioning of a high intensity machine. As a first attempt, the tune survey with space charge effects is simulated. Beam loss and emittance growth are examined in the wide range of tune space. Those results are compared with dynamic aperture without space charge effects.