Computational fluid dynamics (CFD) is one of the branches of fluid mechanics that uses numerical methods and algorithms to solve and analyze problems that involve fluid flows. Annual hourly fast flow simulations are needed for some applications in building industry, such as the conceptual design of indoor environment, or coupled with energy simulation to provide deep analysis on the performance of the buildings. Year round simulation, which consists of 8760 (365×24) independent hourly simulations, is needed to help the designer investigate the problem clearly. However, CFD computation is time consuming, and usually only two or three extreme cases can be simulated in practice. Annual hourly simulation using the traditional method can be considered as a computational intractable problem. Based on previous researches, even though the fast fluid dynamics (FFD) algorithm combined with the General Purposed Graphics Processing Unit (GPGPU) hardware acceleration can make CFD simulation much faster (400x), annual hourly simulation still requires CFD performance to be further improved by 10-20x to make it practical. In this study, a minimal spanning tree based scheduling algorithm is developed, which always gives the best CFD simulation strategy that reuses previous calculated results to generate new results, thus making iteration convergence much faster. It is shown in the paper that the annual hourly simulation by GPGPU accelerated FFD by using this new algorithm requires a similar simulation time to the one used to perform two or three extreme cases of simulation using the traditional method.