Numerical scheme, grid generation and parallelization algorithm are presented for numerical simulation of complex process of silicon-based films growth in plasma enhanced chemical vapor deposition reactors. MPI-based computing environment and advanced interactive software with graphic user interface, real-time visualization system and Web access were recently developed to provide distributed parallel multitask calculation and visualization on Linux clusters. Analysis of system performance and cluster load balance showed the bottlenecks of parallel implementation and the ways of algorithms improvement.