  The simulation and parameter optimization of coupled ocean circulation and
ecosystem models in three space dimensions is one of the most challenging tasks
in numerical climate research. Here we present a scientific toolkit that aims
at supporting researchers by defining clear coupling interfaces, providing
state-of-the-art numerical methods for simulation, parallelization and
optimization while using only freely available and (to a great extend)
platform-independent software. Besides defining a user-friendly coupling
interface (API) for marine ecosystem or biogeochemical models, we heavily rely
on the Portable, Extensible Toolkit for Scientific computation (PETSc)
developed at Argonne Nat. Lab. for a wide variety of parallel linear and
non-linear solvers and optimizers. We specifically focus on the usage of
matrix-free Newton-Krylov methods for the fast computation of steady periodic
solutions, and make use of the Transport Matrix Method (TMM) introduced by
Khatiwala et al.
