FLASH is a modular, extensible software system that consists of inter-operable modules that can be combined to generate different applications. It has solvers for hydrodynamics, magnetohydrodynamics, equations of state, radiation transfer, diffusion, conduction, opacity, laser energy deposition, particles, nuclear burning, gravity, cosmology, magnetic resistivity, and primordial chemistry.
GMT is Generic Mapping Tools
HDF is the Heirarchical Data Format library.
jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.
The Linpack benchmark is a matrix algebra benchmark that has been around quite a few years.
Loci-Chem is a complex multiphysics simulation package.
Relion is a program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).
The Soil-Plant-Atmosphere model (SPA, Williams et. al 1996) is a process-based model that simulates ecosystem photosynthesis and water balance at fine temporal and spatial scales (30 minute time-step, multiple canopy and soil layers).