The presented study is motivated by the development of parallel numerical methods, algorithms, and software tools for micro finite element simulation of human bones. The voxel representation of the bone micro structure is obtained from a high resolution computer tomography image.The reference volume element has a strongly heterogeneous micro structure composed of solid and fluid phases. Cruzeix-Raviart and Rannacher-Turek nonconforming finite elements are used to discretize the arising strongly heterogeneous elasticity problems. The efficiency of codes incorporating BoomerAMG and parallel MIC(0) will be discussed. The size of the considered large scale problems goes beyond a billion of degrees of freedom. The presented parallel numerical tests include results on IBM Blue Gene/P machine of the Bulgarian Supercomputing Center. The ongoing Bulgarian NSF project Center of Excellence on Supercomputing Applications will be introduced.