When the ERT application is running it creates directories for the ECLIPSE simulations, one for each realization. Here you can choose which of these realization directories to keep and which to delete. 
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Note that if you are using the ERT application to run the EnKF algorithm (i.e. <i>EnKF assimilation</i>), the default behavior is to delete these directories after the simulation results have been internalized. When running the ERT application as a convenient way to start many simulations (i.e. <i>Ensemble experiment</i>), the default behavior is to keep these directories.