A run is a single model simulation. It starts at time zero and continues until its defined endpoint is reached. A run is defined by its parameter file. This tells the model how long to run, and what to do during the run.
The basic time unit in the run is the timestep. You set the length and number of the timesteps. Each timestep, the model asks each behavior to do its work, whatever that work may be. The behaviors are run in the order in which they are listed in the parameter file. The model counts off the timesteps until it has finished the specified number, then cleans up its memory and shuts down.