scholarly journals Constraining parameters in state-of-the-art marine pelagic ecosystem models – is it actually feasible with typical observations of standing stocks?

2015 ◽  
Vol 12 (1) ◽  
pp. 227-274
Author(s):  
U. Löptien ◽  
H. Dietze

Abstract. In a changing climate, marine pelagic biogeochemistry may modulate the atmospheric concentrations of climate-relevant species such as CO2 and N2O. To-date, projections rely on earth system models featuring simple pelagic biogeochemical model components, embedded into 3-D-ocean circulation models. Typically, the nucleus of these biogeochemical components are ecosystem models (i.e., a set of partial differential equations) which describe the interaction between nutrients, phytoplankton, zooplankton, and sinking detritus. Most of these models rely on the hyperbolic Michaelis–Menten (MM) formulation which specifies the limiting effect of light and nutrients on carbon assimilation by autotrophic phytoplankton. The respective MM constants, along with other model parameters, are usually tuned by trial-and-error exercises where the parameters are changed until a "reasonable" similarity with observed standing stocks is achieved. Here, we explore with twin experiments (or synthetic "observations") the demands on observations that allow for a more objective estimation of model parameters. We start with parameter retrieval experiments based on "perfect" (synthetic) observations which we, step by step, distort to approach realistic conditions and finally confirm our findings with real-world observations. In summary, we find that MM constants are especially hard to constrain because even modest noise (10%) inherent to observations may hinder the parameter retrieval already. This is of concern since the MM parameters are key to the model's sensitivity to anticipated changes of the external conditions. Further, we illustrate problems associated with parameter estimation based on sparse observations which reveals (additional) parameter dependencies. Somewhat counter to intuition we find, that more observational data can degrade the ability to constrain certain parameters.

Ocean Science ◽  
2015 ◽  
Vol 11 (4) ◽  
pp. 573-590 ◽  
Author(s):  
U. Löptien ◽  
H. Dietze

Abstract. In a changing climate, marine pelagic biogeochemistry may modulate the atmospheric concentrations of climate-relevant species such as CO2 and N2O. To date, projections rely on earth system models, featuring simple pelagic biogeochemical model components, embedded into 3-D ocean circulation models. Most of these biogeochemical model components rely on the hyperbolic Michaelis–Menten (MM) formulation which specifies the limiting effect of light and nutrients on carbon assimilation by autotrophic phytoplankton. The respective MM constants, along with other model parameters, of 3-D coupled biogeochemical ocean-circulation models are usually tuned; the parameters are changed until a "reasonable" similarity to observed standing stocks is achieved. Here, we explore with twin experiments (or synthetic "observations") the demands on observations that allow for a more objective estimation of model parameters. We start with parameter retrieval experiments based on "perfect" (synthetic) observations which we distort, step by step, by low-frequency noise to approach realistic conditions. Finally, we confirm our findings with real-world observations. In summary, we find that MM constants are especially hard to constrain because even modest noise (10 %) inherent to observations may hinder the parameter retrieval already. This is of concern since the MM parameters are key to the model's sensitivity to anticipated changes in the external conditions. Furthermore, we illustrate problems caused by high-order parameter dependencies when parameter estimation is based on sparse observations of standing stocks. Somewhat counter to intuition, we find that more observational data can sometimes degrade the ability to constrain certain parameters.


2014 ◽  
Vol 7 (5) ◽  
pp. 6327-6411
Author(s):  
J. C. P. Hemmings ◽  
P. G. Challenor ◽  
A. Yool

Abstract. Biogeochemical ocean circulation models used to investigate the role of plankton ecosystems in global change rely on adjustable parameters to compensate for missing biological complexity. In principle, optimal parameter values can be estimated by fitting models to observational data, including satellite ocean colour products such as chlorophyll that achieve good spatial and temporal coverage of the surface ocean. However, comprehensive parametric analyses require large ensemble experiments that are computationally infeasible with global 3-D simulations. Site-based simulations provide an efficient alternative but can only be used to make reliable inferences about global model performance if robust quantitative descriptions of their relationships with the corresponding 3-D simulations can be established. The feasibility of establishing such a relationship is investigated for an intermediate complexity biogeochemistry model (MEDUSA) coupled with a widely-used global ocean model (NEMO). A site-based mechanistic emulator is constructed for surface chlorophyll output from this target model as a function of model parameters. The emulator comprises an array of 1-D simulators and a statistical quantification of the uncertainty in their predictions. The unknown parameter-dependent biogeochemical environment, in terms of initial tracer concentrations and lateral flux information required by the simulators, is a significant source of uncertainty. It is approximated by a mean environment derived from a small ensemble of 3-D simulations representing variability of the target model behaviour over the parameter space of interest. The performance of two alternative uncertainty quantification schemes is examined: a direct method based on comparisons between simulator output and a sample of known target model "truths" and an indirect method that is only partially reliant on knowledge of target model output. In general, chlorophyll records at a representative array of oceanic sites are well reproduced. The use of lateral flux information reduces the 1-D simulator error considerably, consistent with a major influence of advection at some sites. Emulator robustness is assessed by comparing actual error distributions with those predicted. With the direct uncertainty quantification scheme, the emulator is reasonably robust over all sites. The indirect uncertainty quantification scheme is less reliable at some sites but scope for improving its performance is identified. The results demonstrate the strong potential of the emulation approach to improve the effectiveness of site-based methods. This represents important progress towards establishing a robust site-based capability that will allow comprehensive parametric analyses to be achieved for improving global models and quantifying uncertainty in their predictions.


2013 ◽  
Vol 6 (1) ◽  
pp. 17-28 ◽  
Author(s):  
E. Siewertsen ◽  
J. Piwonski ◽  
T. Slawig

Abstract. We have ported an implementation of the spin-up for marine ecosystem models based on transport matrices to graphics processing units (GPUs). The original implementation was designed for distributed-memory architectures and uses the Portable, Extensible Toolkit for Scientific Computation (PETSc) library that is based on the Message Passing Interface (MPI) standard. The spin-up computes a steady seasonal cycle of ecosystem tracers with climatological ocean circulation data as forcing. Since the transport is linear with respect to the tracers, the resulting operator is represented by matrices. Each iteration of the spin-up involves two matrix-vector multiplications and the evaluation of the used biogeochemical model. The original code was written in C and Fortran. On the GPU, we use the Compute Unified Device Architecture (CUDA) standard, a customized version of PETSc and a commercial CUDA Fortran compiler. We describe the extensions to PETSc and the modifications of the original C and Fortran codes that had to be done. Here we make use of freely available libraries for the GPU. We analyze the computational effort of the main parts of the spin-up for two exemplar ecosystem models and compare the overall computational time to those necessary on different CPUs. The results show that a consumer GPU can compete with a significant number of cluster CPUs without further code optimization.


2015 ◽  
Vol 8 (3) ◽  
pp. 697-731 ◽  
Author(s):  
J. C. P. Hemmings ◽  
P. G. Challenor ◽  
A. Yool

Abstract. Biogeochemical ocean circulation models used to investigate the role of plankton ecosystems in global change rely on adjustable parameters to capture the dominant biogeochemical dynamics of a complex biological system. In principle, optimal parameter values can be estimated by fitting models to observational data, including satellite ocean colour products such as chlorophyll that achieve good spatial and temporal coverage of the surface ocean. However, comprehensive parametric analyses require large ensemble experiments that are computationally infeasible with global 3-D simulations. Site-based simulations provide an efficient alternative but can only be used to make reliable inferences about global model performance if robust quantitative descriptions of their relationships with the corresponding 3-D simulations can be established. The feasibility of establishing such a relationship is investigated for an intermediate complexity biogeochemistry model (MEDUSA) coupled with a widely used global ocean model (NEMO). A site-based mechanistic emulator is constructed for surface chlorophyll output from this target model as a function of model parameters. The emulator comprises an array of 1-D simulators and a statistical quantification of the uncertainty in their predictions. The unknown parameter-dependent biogeochemical environment, in terms of initial tracer concentrations and lateral flux information required by the simulators, is a significant source of uncertainty. It is approximated by a mean environment derived from a small ensemble of 3-D simulations representing variability of the target model behaviour over the parameter space of interest. The performance of two alternative uncertainty quantification schemes is examined: a direct method based on comparisons between simulator output and a sample of known target model "truths" and an indirect method that is only partially reliant on knowledge of the target model output. In general, chlorophyll records at a representative array of oceanic sites are well reproduced. The use of lateral flux information reduces the 1-D simulator error considerably, consistent with a major influence of advection at some sites. Emulator robustness is assessed by comparing actual error distributions with those predicted. With the direct uncertainty quantification scheme, the emulator is reasonably robust over all sites. The indirect uncertainty quantification scheme is less reliable at some sites but scope for improving its performance is identified. The results demonstrate the strong potential of the emulation approach to improve the effectiveness of site-based methods. This represents important progress towards establishing a robust site-based capability that will allow comprehensive parametric analyses to be achieved for improving global models and quantifying uncertainty in their predictions.


2012 ◽  
Vol 5 (3) ◽  
pp. 2179-2214 ◽  
Author(s):  
E. Siewertsen ◽  
J. Piwonski ◽  
T. Slawig

Abstract. We have ported an implementation of the spin-up for marine ecosystem models based on the "Transport Matrix Method" to graphics processing units (GPUs). The original implementation was designed for distributed-memory architectures and uses the PETSc library that is based on the "Message Passing Interface (MPI)" standard. The spin-up computes a steady seasonal cycle of the ecosystem tracers with climatological ocean circulation data as forcing. Since the transport is linear with respect to the tracers, the resulting operator is represented in so-called "transport matrices". Each iteration of the spin-up involves two matrix-vector multiplications and the evaluation of the used biogeochemical model. The original code was written in C and Fortran. On the GPU, we use the CUDA standard, a specialized version of the PETSc toolkit and a CUDA Fortran compiler. We describe the extensions to PETSc and the modifications of the original C and Fortran codes that had to be done. Here we make use of freely available libraries for the GPU. We analyze the computational effort of the main parts of the spin-up for two exemplary ecosystem models and compare the overall computational time to those necessary on different CPUs. The results show that a consumer GPU can beat a significant number of cluster CPUs without further code optimization.


2015 ◽  
Vol 8 (6) ◽  
pp. 4401-4451
Author(s):  
J. Piwonski ◽  
T. Slawig

Abstract. A general programming interface for parameter identification for marine ecosystem models is introduced. A comprehensive solver software for periodic steady-states is implemented that includes a fixed point iteration (spin-up) and a Newton solver. The software is based on the Portable, Extensible Toolkit for Scientific Computation (PETSc) library and uses transport matrices for efficient off-line simulation in 3-D. In addition to the usage of PETSc's parallel data structures and PETSc's Newton solver, an own load balancing algorithm is implemented. A simple verification is carried out using a well investigated biogeochemical model for phosphate (PO4) and dissolved organic phosphorous (DOP) with 7 parameters. The model is coupled via the interface to transport matrices that correspond to a longitudinal and latitudinal resolution of 2.8125° and 15 vertical layers. Initial tests show that both solvers and the load balancing algorithm work correctly. Further experiments demonstrate the robustness of the Newton solver with respect to parameter variations. Moreover, the numerical tests reveal that, with optimal control settings, the Newton solver converges at least 6 times faster towards a solution than the spin-up. However, additional twin experiments reveal differences between both solvers regarding a derivative-based black-box optimization. Whereas an optimization run with spin-up-based model evaluations is capable to identify model parameters of a reference solution, Newton-based model evaluations result in an inaccurate gradient approximation.


Author(s):  
Christopher J. Arthurs ◽  
Nan Xiao ◽  
Philippe Moireau ◽  
Tobias Schaeffter ◽  
C. Alberto Figueroa

AbstractA major challenge in constructing three dimensional patient specific hemodynamic models is the calibration of model parameters to match patient data on flow, pressure, wall motion, etc. acquired in the clinic. Current workflows are manual and time-consuming. This work presents a flexible computational framework for model parameter estimation in cardiovascular flows that relies on the following fundamental contributions. (i) A Reduced-Order Unscented Kalman Filter (ROUKF) model for data assimilation for wall material and simple lumped parameter network (LPN) boundary condition model parameters. (ii) A constrained least squares augmentation (ROUKF-CLS) for more complex LPNs. (iii) A “Netlist” implementation, supporting easy filtering of parameters in such complex LPNs. The ROUKF algorithm is demonstrated using non-invasive patient-specific data on anatomy, flow and pressure from a healthy volunteer. The ROUKF-CLS algorithm is demonstrated using synthetic data on a coronary LPN. The methods described in this paper have been implemented as part of the CRIMSON hemodynamics software package.


2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
K. S. Sultan ◽  
A. S. Al-Moisheer

We discuss the two-component mixture of the inverse Weibull and lognormal distributions (MIWLND) as a lifetime model. First, we discuss the properties of the proposed model including the reliability and hazard functions. Next, we discuss the estimation of model parameters by using the maximum likelihood method (MLEs). We also derive expressions for the elements of the Fisher information matrix. Next, we demonstrate the usefulness of the proposed model by fitting it to a real data set. Finally, we draw some concluding remarks.


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