Update stack on garnet

@ahmadia, I know this is pretty far from our scheme for updating stable/garnet, but I'm up against some deadlines and need to get this stack installed as a shared  resource.  I  don't need to merge it into master, but I think that, except for the update to numpy 1.8.2, most of these changes can go into master without effecting anyone else. 

The numpy and scipy config changes seem a little redundant--not sure we need to both write site.cfg  and set paths and environment variables. But the stack takes  so long to re-compile on garnet I haven't had time to test without setting BLAS/LAPACK/ATLAS.

The changes to the hdf5, netCDF4,  and python-netCDF4 are all linked together because otherwise python-netCDF tries to link against non-relocatable code.
This sounds like an error in the build for python-netcdf4, which we would like to link dynamically to hdf5.  Thanks for the explanation.