Quartz crystal resonators are typical piezoelectric acoustic wave devices for frequency control applications with mechanical vibration frequency at the radio-frequency (RF) range. Precise analyses of the vibration and deformation are generally required in the resonator design and improvement process. The considerations include the presence of electrodes, mountings, bias fields such as temperature, initial stresses, and acceleration. Naturally, the finite element method is the only effective tool for such a coupled problem with multi-physics nature. The main challenge is the extremely large size of resulted linear equations. For this reason, we have been employing the Mindlin plate equations to reduce the computational difficulty. In addition, we have to utilize the parallel computing techniques on Linux clusters, which are widely available for academic and industrial applications nowadays, to improve the computing efficiency. The general principle of our research is to use open source software components and public domain technology to reduce cost for developers and users on a Linux cluster. We start with a mesh generator specifically for quartz crystal resonators of rectangular and circular types, and the Mindlin plate equations are implemented for the finite element analysis. Computing techniques like parallel processing, sparse matrix handling, and the latest eigenvalue extraction package are integrated into the program. It is clear from our computation that the combination of these algorithms and methods on a cluster can meet the memory requirement and reduce computing time significantly.