MarMOT 1.1 Software

MarMOT 1.1.1 was released on 23rd January 2015 under the CeCILL Free Software License Agreement. This page distributes a slightly different version from 18 Feb 2015. The only difference is a correction to a filename. The code and release date are identical. The software is designed for use on UNIX-based systems, including LINUX and MacOSX. A tar archive (6MB) containing the MarMOT 1.1.1 open source distribution can be downloaded by clicking on the link below. Download of this archive indicates acceptance of the terms of the licence, available at:

http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html (English version) or

http://www.cecill.info/licences/Licence_CeCILL_V2.1-fr.html (French version)

CLICK HERE TO DOWNLOAD MarMOT 1.1.1 SOFTWARE

The archive unpacks to create a new directory called marmot_2015-02-18 that contains the following 3 sub-directories.

marmot-1.1.1 contains the MarMOT 1.1.1 software distribution released under the

CeCILL licence on 23 Jan 2015

marmot-1.0 contains the MarMOT 1.0 description and user guide (Hemmings, 2009),

freely available for non-commercial use from the NERC Open Research

Archive (NORA) at http://nora.nerc.ac.uk/

well1024a contains source code for the WELL1024a random number generator

developed by Panneton et al. (2006) freely available for non-

commercial use from http://www.iro.umontreal.ca/~panneton/well/

To unpack the archive use the following UNIX commands or equivalent.

gunzip marmot_2015-02-18.tar.gz

tar -xvf marmot_2015-02-18.tar

References:

Hemmings, John C.P., 2009 A marine model optimization test-bed for ecosystem model evaluation: MarMOT version 1.0 description and user guide. Southampton UK, National Oceanography Centre Southampton, 111pp. (National Oceanography Centre Southampton Research and Consultancy Report 67)

Panneton, F., L'Ecuyer, P. & Matsumoto, M., 2006. Improved Long-Period Generators Based on Linear Recurrences Modulo 2, ACM Transactions on Mathematical Software, 32, 1-16.

New Features in MarMOT 1.1

Originally released in 2013, MarMOT 1.1 is a significantly improved product with respect to the MarMOT 1.0 prototype in terms of functionality, usability and numerical accuracy. The new MarMOT Model Evaluator includes the following additional features and modifications.

Time- and depth-dependent perturbation rate forcing, supporting parameterization of horizontal flux divergences of the biogeochemical tracers.
Time- and depth-dependent relaxation rates for the tracers. As an alternative to relaxation towards reference fields, individual tracers can be completely replaced by the reference fields at each time step allowing detailed analysis of process dynamics.
Extra 'ft' (scalar) and 'fkt' (full depth) type forcing items to allow different grids to be used for different input variables.
Output table indicating the options applying to each simulation. All relevant options appear in the table whether user selected or default.
Improved time-stepping numerics.
NEMO-compatible advection & diffusion schemes.
Support for variable sinking/swimming speeds.
New diagnostics.
Generic plankton model code interface supporting models with multiple plankton types. The MEDUSA model is now included (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).
Support for chlorophyll data assimilation using the nitrogen balancing scheme of Hemmings et al. (Hemmings, J. C. P., Barciela, R. M. & Bell, M. J., 2008. Ocean colour data assimilation with material conservation for improving model estimates of air-sea CO2 flux, J. Mar. Res. 66, 87-126).

The MarMOT 1.1 code includes a new version of the host Generic Function Analyzer (GFAn) program providing extended services as follows.

Double precision binary option for output tables (alternative to ASCII).
Output of internal item table data to external files. This allows data extracted from larger files or NetCDF data sets to be saved, avoiding the need for re-extraction.
Partial logging option for large data tables to allow data from such tables to be written safely to the GFAn log file.
Options for controlling the GFAn processing sequence to suppress unnecessary steps.
Detailed GFAn Optimizer reporting is extended to the Powell direction set algorithm.

?If you would like MarMOT 1.1.0 rather than 1.1.1 (recommended only for comparison with old MarMOT 1.1.0 runs) click here