Nemo

Welcome to the Bristol Nemo Page!
Here are a few tips and comments based on Bristol's experiences compiling and running NEMO. Hopefully, you will find some useful.

Please take a look the official NEMO webpage before continuing with this page.

Model Compilation
In the steps below, I'm assuming that you are interested in the ORCA2_LIM version of the model.

If you follow the steps described on the official NEMO webpage, you will be able to download and compile the model, with one caveat. When using newer versions of the NetCDF libraries--such as v3.6.2 installed on the Quest cluster--you will need to change line 210 of modipsl/util/AA_make.gdef to "NCDF_INC = /usr/local/netcdf/3.6.2/pgi-251/include" and line 211 to "NCDF_LIB = -L/usr/local/netcdf/3.6.2/pgi-251/lib -lnetcdf -lnetcdff".

Running the Model
Nemo provides a test case, ORCA2_LIM, for a global ocean run coupled with the sea-ice model. The run simulates one year. The configuration for ORCA2_LIM is downloaded through CVS when getting Nemo and the necessary forcing files are provided through a link on the Nemo website or can be copied from ~ggdaqw/NEMO_forcing as detailed below.

The instructions for running the model are not so clear. You will need two things to run the model; (i) some forcing files; and (ii) a run script. Assuming you are running on the Quest cluster, you can obtain forcing files for an example job by copying the directory ~ggdagw/NEMO_forcing and it's contents to you home directory. If you adopt the same directory name, you will be able to use this runscript. Place the runscript into the directory modipsl/config/ORCA2_LIM/EXP00. I named it Job_EXP.new. You will need to create the directory "$DUMP2HOLD/NEMO" in your home directory to collect the output. You can submit the job by typing "qsub Job_EXP.new", check whether it is running using "showq", and obviously look in the output directory.

Mediterranean Sea
Sediment cores recovered from the Mediterranean Sea reveal distinct layers of organic rich material thought to be associated with deep water anoxia, caused by either a shut down in deep water circulation, an increase in productivity, or both. One of the ways this could have happened is by a large increase in fresh water runoff into the basin. We intend to use a Mediterranean configuration of NEMO to study how point sources of freshwater, represented by low delta-18-O, are circulated around the Mediterranean, and compare the modeled distribution with records of delta-18-O during these "Mediterranean Anoxic Events".

Amundsen Sea
Thinning of the Pine Island Glacier, West Antarctica, has been observed during the 1990s. It has been suggested that relatively warm water at the base of the ice shelf has triggered the thinning. The source of and mechanism driving this warm water is unknown.

We are constructing a regional model of the Amunsden Sea using Nemo to investigate ocean circulation close to Pine Island Bay. Input data at the sea surface and at the open boundaries are constructed using output data from the OCCAM global ocean model.

Regional model
How to set up a regional model starting from the ORCA2_LIM test case:


 * 1) Create a new configuration for the regional model.
 * 2) * In directory modipsl/config/ create a new directory AMUNDSEN, for example, and copy the contents of the ORCA2_LIM directory into AMUNDSEN.
 * 3) * Edit file fait_config in modipsl/modeles/UTIL/. Add  to   and add the line.
 * 4) Change CPP keys by editing BB_make.ldef in modipsl/config/AMUNDSEN/scripts/. Remove   since you're not running a global model and add   to invoke open boundary conditions instead.
 * 5) TIP: modify tradmp.F90 in modipsl/modeles/NEMO/OPA_SRC/TRA/. Replace the line   with  . If you don't make the change you'll get the error message  . With this change you can apply tracer damping as in the ORCA configurations (i.e. global models for various resolutions) without special treatment for particular areas such as the Mediterranean or the Red Sea that are grid dependent.
 * 6) Set the new domain resolution in par_oce.F90 in modipsl/modeles/NEMO/OPA_SRC/. Parameters for the resolution are   and.
 * 7) Set parameters in obc_oce.F90 and obc_par.F90 in modipsl/modeles/NEMO/OPA_SRC/OBC/.
 * 8) * obc_oce.F90:  is the number of open boundaries, i.e. set to 1, 2, 3 or 4.
 * 9) * obc_par.F90: set logical parameter  to   if open boundary conditions are to be applied to part or all of the eastern face of the domain. Alter   and/or   if the open boundary covers only part of the eastern face. Similarly for ,  ,  ,  ,  ,   and  ,  ,.
 * 10) In the input file namelist set   to 0. Assuming you have no closed seas, i.e. Mediterranean and Red Sea in  ORCA2.
 * 11) Generate input data from the ORCA2_LIM test case files using the AGRIF package.

Bathymetry
There are some pre-processing packages available on the NEMO website. I don't recommend using the bathymetry package OPABAT. It uses idl and fortran routines contained in IDL_OPABAT3.tar. The instructions are in French and some of the files are missing. Instead, use the AGRIF nesting tools. The instructions are clear and the package also interpolates the input files from the ORCA2_LIM test case.

AGRIF package
AGRIF is designed to create fine regional grids (child grids) in a form that NEMO can read in from a coarse NEMO global grid. The idea is to run the fine grid with the global grid to provide local increased resolution where the model needs it. It is possible to genrate the child bathymetry by interpolating from the global bathymetry and high resolution topography. It blends the coarse and fine resolutions over a few cells at the edges of the child grid. It also creates input files for the child grid from the global input files.

You can download the source code (Nesting_tools_NEMO.tar) and the user's manual (doc_nesting_tools.pdf) from the NEMO website. The manual tells you how to untar and make the executable files, run the executables and gives some theory about the interpolation schemes. The executables are
 * generates the longitude, latitude and metrics for the child grid,
 * generates the bathymetry,
 * generates the necessary input files (nav_lon and nav_lat in the child files aren't correct but NEMO doesn't use them) and
 * interpolates the global restart file to the child grid.

These executables use one namelist. AGRIF provides an example namelist, pacifique_tropical, in Nesting_tools/bin. To run the example copy coordinates.nc, bathy_level.nc, bathy_meter.nc, taux_1m.nc, tauy_1m.nc, data_1m_potential_temperature_nomask.nc, data_1m_potential_temperature_nomask.nc, flx.nc, runoff_1m_nomask.nc and geothermal_heating.nc from ORCA2_LIM test case to Nesting_tools/bin. You will also need to acquire bathymetry_meter_ORCA_R05.nc, which I found it by typing the filename into google. Alternatively, try setting. Run the executables in Nesting_tools/bin in order using

where * is coordinates, bathy and then data (you don't need to do restart).

Wiki example
This text is very imprtant. This is less so.

Listen very carefully, I shall say this only once:


 * 1) put kettle on
 * 2) find mug
 * 3) add water to tea bag--in mug!


 * slurp
 * read
 * slurp

can be done in any order

An external link is a search engine

A link to another wiki page is the genie project