In this paper, a three dimensional numerical wave basin is developed to study the wave interaction with vertical cylinder using the meshless method based on the Meshless Local Petrov Galerkian (MLPG) method. The computation is carried out on the shared type memory allocation, using the OpenMP constructs. The boundary surfaces are treated as the moving particle instead of the fixed particle. The pressure gradients on the tank boundary surface are estimated considering it as 2D. The model is applied to simulate small wave and steep waves and its interaction with the vertical cylinder. The computational results obtained are validated against the experimental data and good agreement is observed. Copyright © 2017 by the International Society of Offshore and Polar Engineers (ISOPE).