The problem of finite element simulation of incompressible fluid flow in porous medium is considered. The porous medium is characterized by the X-ray microtomography technique in three dimensions. The finite calculus-based stabilization technique is reviewed to implement the equal order finite element interpolation functions for both velocity and pressure. A noble preconditioner, the nodal block diagonal preconditioner, is considered whose performance is thoroughly investigated. Combining this preconditioner with a standard iterative solver during the computational homogenization procedure, it is possible to carry out the large-scale fluid flow simulation for estimating permeability of the porous medium with reasonable accuracy and reliability. Copyright © 2013 John Wiley & Sons, Ltd.