This paper presents a parallel implementation and validation of an accurate and efficient three-dimensional computational model (3D numerical wave tank), based on fully nonlinear potential flow (FNPF) theory, and its extension to incorporate the motion of a laboratory snake piston wavemaker, as well as an absorbing beach, to simulate experiments in a large-scale 3D wave basin. This work is part of a long-term effort to develop a “virtual” computational wave basin to facilitate and complement large-scale physical wave-basin experiments. The code is based on a higher-order boundary-element method combined with a fast multipole algorithm (FMA). Particular efforts were devoted to making the code efficient for large-scale simulations using high-performance computing platforms. The numerical simulation capability can be tailored to serve as an optimization tool at the planning and detailed design stages of large-scale experiments at a specific basin by duplicating its exact physical and algorithmic features. To date, waves that can be generated in the numerical wave tank (NWT) include solitary, cnoidal, and airy waves. In this paper we detail the wave-basin model, mathematical formulation, wave generation, and analyze the performance of the parallelized FNPF-BEM-FMA code as a function of numerical parameters. Experimental or analytical comparisons with NWT results are provided for several cases to assess the accuracy and applicability of the numerical model to practical engineering problems.