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To get the netcdf files working under windows you need the following:
Visual studio >= 7, Visual C++ 6 doesnt support long longs, this will work but you have to manually disable large file support.
An updated cfortran.h, A patch has been sent in 2002 to mr burrow, maintainer of the cfortran bridge http://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg01463.html . I think his whereabouts are not known. The patch is part of default linux distributions.