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.
I think since hdf5 builds both .a and .so it is still necessary when one later wants to do a shared link against the .a. I think this may have only come up because of the way we build netCDF4 later, which may affect the way python-netCDF4 links. The error I was getting in python-netCDF4 is below, which suggests that the .a's aren't relocatable unless you add --with-pic:

2014/09/10 16:10:37 - INFO: [package:run_job] /usr/bin/ld: /lustre/home1/u/cekees/.hashdist/bld/hdf5/vle6ljraatqn/lib/libhdf5_hl.a(H5DS.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used whe
n making a shared object; recompile with -fPIC
2014/09/10 16:10:37 - INFO: [package:run_job] /lustre/home1/u/cekees/.hashdist/bld/hdf5/vle6ljraatqn/lib/libhdf5_hl.a: could not read symbols: Bad value
2014/09/10 16:10:37 - INFO: [package:run_job] collect2: error: ld returned 1 exit status
2014/09/10 16:10:37 - INFO: [package:run_job] /usr/bin/ld: /lustre/home1/u/cekees/.hashdist/bld/hdf5/vle6ljraatqn/lib/libhdf5_hl.a(H5DS.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used whe
n making a shared object; recompile with -fPIC
2014/09/10 16:10:37 - INFO: [package:run_job] /lustre/home1/u/cekees/.hashdist/bld/hdf5/vle6ljraatqn/lib/libhdf5_hl.a: could not read symbols: Bad value
2014/09/10 16:10:37 - INFO: [package:run_job] collect2: error: ld returned 1 exit status