In this study, the multi-relaxation-time lattice Boltzmann method is applied to investigate the oscillatory instability of lid-driven flows in two-dimensional semi-elliptical cavities with different vertical to horizontal aspect ratios K in the range of 1.0--3.0. The program implemented in this study is parallelized using CUDA (compute unified device architecture), a parallel computing platform, and computations are carried out on NVIDIA Tesla K40c GPU. To carry out precise calculations, the CUDA algorithm is extensively investigated, and its parallel efficiency indicates that the maximum speedup is 47.6 times faster. Furthermore, the steady--oscillatory Reynolds numbers are predicted by implementing the CUDA-based programs. The amplitude coefficient is defined to quantify the time-dependent oscillation of the velocity magnitude at the monitoring point. The simulation results indicate that the transition Reynolds numbers correlate negatively with the aspect ratio of the semi-elliptical cavity, and are smaller than those of the rectangular cavity at the same aspect ratio. In addition, the detailed vortex structures of the semi-elliptical cavity within a single period are also investigated when the Reynolds number is larger than the steady--oscillatory value to determine the effects of periodic oscillation of the velocity magnitude.