Weather Research and Forecasting Model (WRF), http://www.wrf-model.org/index.php, is an HPC software package commonly used in atmospheric science research.

Finite Volume Coastal Ocean Model (FVCOM), http://fvcom.smast.umassd.edu/FVCOM/index.html is an HPC software package used to predict ocean currents in a near-shore environment.

Finite element software packages are too numerous to list here. For a current listing, see the Wikipedia article on finite element analysis software http://en.wikipedia.org/wiki/List_of_finite_element_software_packages.