The open multi-processing parallelism was implemented into a serial code to compute a high-order boundary integral equation based on the second Green's identity. on symmetric multiprocessing computer platforms. The parallel code is augmented to a three-dimensional potential numerical wave tank for fully nonlinear wave-body interaction problems in the time domain. The non-uniform rational B-Spline surface was manipulated to define the geometry of the computational boundaries and the distribution of boundary values either as a high-order iso-geometric formulation. The material node approach and fourth-order Runge-Kutta time integration method were compounded for time marching the fully nonlinear free surface boundary. The propagation of a fifth-order Stokes wave was simulated to examine the scalability of the parallel constructs implementation. Afterwards, the second-order Stokes wave interaction with a cylindrical pile was modeled as a practical case study to show the benefits of the parallel code. The results were compared with former experiments and numerical studies.