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We propose a method to prepare multipartite entangled states such as cluster states and graph states based on the cavity input-output process and single photon measurement.Two quantum gates,a controlled phase gate and a fusion gate between two atoms trapped in respective cavities,are proposed to prepare atomic cluster states and graph states with one and two dimensions.We also introduce a scheme that can generate an arbitrary multipartite photon cluster state which uses two coherent states as a qubit basis.