• Supercomputers are a natural place for people to want netCDF.
• Supercomputers can be difficult to build on, because the user interface node is not always the same as the target platform.
• Cross-compilation is the correct answer for many supercomputers, but this does not play well with the way the netCDF configure script learns about your fortran compiler. Use the --disable-fortran-compiler-check and the --disable-fortran-type-check.
• Expect better from the 4.0.1 release, but supercomputers will probably always be more difficult to deal with.
• Use --enable-parallel-tests if you are building with MPI and your platform supports mpiexec.
• You must build HDF5 with --enable-parallel (and with MPI compilers or options) or parallel netCDF I/O will not be built.

2008 Unidata NetCDF Workshop for Developers and Data Providers > Porting and Testing the NetCDF C/Fortran/C++ Libraries