In this work we analyze the performance of the Weather Research and Forecasting (WRF) model using both empirical data and an accurate analytic performance model. WRF is a large-scale mesoscale numerical weather prediction system designed for both operational forecasting and atmospheric research. It is in active development at the National Center for Atmospheric Research (NCAR), and can use 1,000 s of processors in parallel. In this work we compare the performance of WRF on a cluster-based system (AMD Opteron processors interconnected with 4x SDR Infiniband) to that on a mesh-based system (IBM Blue Gene/L interconnected with a proprietary 3-D torus). In addition, we develop a performance model of WRF that is validated against these two systems and that exhibits high prediction accuracy. The model is then used to examine the performance of a near-term future generation supercomputer.