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As explained by Osvaldo Artal, this has to do with the 2GB limit for NetCDF files. To solve this edit

create_climfile (and create_oafile) changing in line 90

nc = netcdf(clmname,clobber);

with

mode = bitor(nc_noclobber_mode,nc_64bit_offset_mode); nc_create_empty(clmname,mode); nc = netcdf(clmname,'write');

If the function nc_create_empty is not found add this to your start.m

addpath([myutilpath,'mexcdf/snctools'])