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We present a description of the ModelE2 version of the Goddard Institute for Space Studies (GISS) General Circulation Model (GCM) and the configurations used in the simulations performed for the Coupled Model Intercomparison Project Phase 5 (CMIP5). We use six variations related to the treatment of the atmospheric composition, the calculation of aerosol indirect effects, and ocean model component. Specifically, we test the difference between atmospheric models that have noninteractive composition, where radiatively important aerosols and ozone are prescribed from precomputed decadal averages, and interactive versions where atmospheric chemistry and aerosols are calculated given decadally varying emissions. The impact of the first aerosol indirect effect on clouds is either specified using a simple tuning, or parameterized using a cloud microphysics scheme. We also use two dynamic ocean components: the Russell and HYbrid Coordinate Ocean Model (HYCOM) which differ significantly in their basic formulations and grid. Results are presented for the climatological means over the satellite era (1980-2004) taken from transient simulations starting from the preindustrial (1850) driven by estimates of appropriate forcings over the 20th Century. Differences in base climate and variability related to the choice of ocean model are large, indicating an important structural uncertainty. The impact of interactive atmospheric composition on the climatology is relatively small except in regions such as the lower stratosphere, where ozone plays an important role, and the tropics, where aerosol changes affect the hydrological cycle and cloud cover. While key improvements over previous versions of the model are evident, these are not uniform across all metrics. [ABSTRACT FROM AUTHOR]