MarMOT System Overview

System Overview
21 November 2013
Download PDF version (230 KB)

The MarMOT testbed, introduced by Hemmings & Challenor (2012), provides a common physical and computational environment in which different plankton ecosystem models can be calibrated and compared with each other and with biogeochemical data. It is designed especially for computationally intensive experiments in which models are run in a 1-D framework many times with different input data. Features are provided to support multi-site ensemble water column simulations in a realistic 3-D context, using external environmental data from analyses of 3-D simulations and/or real-world observations.

A particular simulation case is defined by a combination of instances of each input item, selected via a simple case configuration record. Multi-record case tables can be used to set up ensemble runs for sensitivity and uncertainty analyses. Individual cases are identified by site and ensemble member labels. Adjustable model parameters can be optimized over all cases in a given case table to set up multi-site and/or multi-member calibration experiments.

The core of the MarMOT system is a model evaluator that returns a misfit-based cost function value for one or more simulation cases. It is implemented as a specific application within a system referred to as the Generic Function Analyzer (GFAn). GFAn provides a generic data management framework that adapts to the requirements of the application, together with an optimizer for function minimization and a flexible experiment control interface. Input and output files use a standard table format with ASCII and binary versions. A separate set of programs called Table Toolbox is available for working with tables in this format. GFAn and Table Toolbox are written in C. The MarMOT Model Evaluator is written in C (user interface and I/O management) and FORTRAN (simulator procedures and plankton model interface). The software is designed for a UNIX/LINUX system environment.

Ref: Hemmings, J. C. P. and Challenor, P. G., 2012. Addressing the impact of environmental uncertainty in plankton model calibration with a dedicated software system: the Marine Model Optimization Testbed (MarMOT 1.1 alpha). Geosci. Model Dev. 5, 471-498.

MarMOT 1.1 Software Features

Ecosystem Models in MarMOT 1.1

  • NPZD model of Oschlies and Garçon - Ref: Oschlies, A. & Garçon, V., 1999, An eddy-permitting coupled physical-biological model of the North Atlantic. 1. Sensitivity to advection numerics and mixed layer physics, Global Biogeochem. Cy. 13, 135-160
  • HadOCC (UK Met Office code; restricted availability) - Ref: Palmer, J.R. & Totterdell, I.J., 2001, Production and export in a global ocean ecosystem model, Deep-sea Research I 48, 1169-1198; current version includes a variable C:Chl ratio (Geider, R.J., MacIntyre, H.L. & Kana, T.M., 1997, Mar. Ecol. Prog. Ser., 148, 187-200) and modified pathways for products of grazing and mortality; chlorophyll data assimilation is implemented
  • MEDUSA 1.0 - Ref: Yool, A., Popova, E. E., Anderson, T. R., 2011. MEDUSA-1.0: a new intermediate complexity plankton ecosystem model for the global domain. Geosci. Model Dev. 4, 381-417

Supporting Software Tools: Table Toolbox

  • Suite of command line tools for creating, viewing, processing, joining and splitting GFAn compatible data files in ASCII or Table Toolbox Binary formats
  • Programs support standard input and output streams, allowing complex operations combining functions of different tools to be performed by concatenating commands via UNIX/LINUX pipes