Tornadoes remain an active subject of observational and numerical research due to the damage and fatalities they cause worldwide as well as poor understanding of their behavior, such as what processes result in their genesis and what determines their longevity and morphology. A numerical model executed on a supercomputer run at high resolution can serve as a powerful tool for exploring the rapidly evolving tornado-scale features within a simulated storm, but saving large amounts data for meaningful analysis can result in unacceptably slow model performance, an unwieldy amount of saved data, and saved data spread across millions of files. In this paper, a system for efficiently saving and managing hundreds of terabytes of compressed model output is described in order to support a supercomputer simulation of a tornadic supercell thunderstorm. The challenges of managing a simulation spanning over a quarter trillion grid volumes across the Blue Waters supercomputer are also described. The simulated supercell produces a long-track EF5 tornado, and the near-tornado environment is described during tornadogenesis, where single upward-growing vortex undergoes several vortex mergers before transitioning into a multiple vortex tornado.