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The CFSR data are on pressure levels and not on hybrid pressure-sigma levels which is used as default by INT2LM for interpolation. Therefore the data are interpolated to hybrid-pressure first (see subroutine src_pressure_to_hybrid.f90). The interpolation is triggered by the namelist parameter ke_hybrid. ke_hybrid can only take two values 31 and 38 presently. In the case of CFSR you need to set ke_hybrid=38 in the GRID _IN part of the namelist (see example below).
Please also set the following in the CONTRL of the namelist lprog_qi = .FALSE., luse_t_skin = .TRUE.,