Port to garnet.erdc.hpc.mil (Cray XE6)

- Added XE6 specification in proteus.garnet.gnu example profile
- Fixed issues where packages started actions before PROLOGUE
- Directly provide MPI compilers where needed
- Parmetis version bump / customization
- HDF5 customization for batch environment / dynamic linking
- NumPy compiler support customization
- Customize configuration of PETSc when on an XE6