The first method I pointed you to (varying pertlim in the CAM namelist) is a very common an recognized method to create ensemble runs.For instance, it what was used to create the Large ensemble done at NCAR.See: http://www2.cesm.ucar.edu/models/experiments/LENSIt is an ensemble of 30 runs created using round off error introduced through the CAM namelist (i.e. varying pertlim)http://www2.cesm.ucar.edu/models/experiments/LENS/instructionsThey varied pertlim from pertlim = 1.d-14, 2.d-14, ..., 30.d-14to create their 30 ensemble members. I am not very familiar with the multi instance. To my knowledge, it is used for data assimilation but not really to create traditionnal ensemble.See: http://www.cesm.ucar.edu/models/cesm1.2/cesm/doc/usersguide/x834.html