Software for applications includes:

• FOAM (Fast Ocean-Atmosphere Model) is a coupled ocean/atmosphere model that incorporates all the physics needed for multicentury simulations. It uses a combination of improved ocean model formulation and reduced-resolution atmosphere model to reduce computational requirements by a factor of ten relative to similar models. It uses parallel processing techniques to allow execution on parallel platforms that are more cost-effective than the vector multiprocessors traditionally used for climate modeling.
• HAAC is a framework of hardware-accelerated cosmology codes for heterogeneous systems, portable across different architectures 
• MCT (Model Coupling Toolkit) is a software library for constructing parallel coupled models from individual parallel models. MCT is designed for high performance and portability and offers a programming model similar to MPI. Core services include component registration, decomposition description, indexible data storage, parallel data transfer, and interpolation.
• MG-RAST is a SEED-based environment that allows users to upload metagenomes for automated analyses.
• Model SEED is a resource for high-throughput reconstruction of metabolic models
• Nek5000 is an open-source computational fluid dynamics solver based on the spectral element method. It is actively used in the Cesar project and has run on the Blue Gene/Q with 1 MPI million ranks — a watershed!
• NekLBM is a spectral-element discontinuous Galerkin Lattice-Boltzmann fluid solver.
• NekCEM is a high-fidelity electromagnetic solver.
• ParVis, designed specifically for analyzing ultra-large climate datasets, includes both parallel tools and visualization techniques.
• RGG (Reactor Geometry and mesh Generator) generates several types of nuclear reactor assembly/core geometry meshes.
• UNIC is an unstructured, deterministic neutron transport code that allows a highly detailed description of a nuclear reactor core in numerical simulations.