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In this paper, the high-order spectral/boundary-element method is developed to calculate the 3-dimensional water waves generated by a submerged body. This method is one of the most efficient numerical methods by which the nonlinear gravity waves can be simulated in time-domain. Three-dimensional free-surface flows generated by a submerged sphere which is moving under the free-surface are calculated. Through example calculations, nonlinear effects on free-surface profiles and hydrodynamic forces are shown. Comparisons with others' results show good agreements.