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Christopher Bull

Aspiring Oceanographer at Northumbria University. Big data python enthusiast. Outdoor adventurer.

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Building the pre-processing tools

Suggested reading:

Prepare the pre-processing tools (GSW TOOLBOX and Nico’s regional tools):

First you may need the TEOS10 toolbox to convert from EOS80 to TEOS10. To avoid issues with updates on the GSW-Fortran tools, Nico has cloned the 2016 GSW-Fortran in this repository:

git clone
cd GSW-Fortran/test
vi makefile   #in particular fill the FC and NETCDF_INCDIR variables
./gsw_check   # to check (some have to work, maybe not all of them)
cd ../..

NB: In case you want to check for updates (not recommended), you can still do: git clone

The file provided in this repository should be fine, but in case you start again from the original file (i.e. from, you will need to modify it to avoid NaN in some places (otherwise, skip the next 4 lines):

./ remove_NaN_from_gsw_data_v3_0.f90
ncks -x -v ocean_ref,ndepth_ref,deltaSA_ref,SA_ref,SAAR_ref GSW-Fortran/test/
ncks -A

Back in root of BUILD_CONFIG_NEMO.git. Edit your own namelist, e.g. namelist_WED12, and link namelist_pre to it:

vi namelist_${CONFIG}
ln -s -v namelist_${CONFIG} namelist_pre  # in BUILD_CONFIG_NEMO dir

Edit, adapt fortran compiler (and maybe netcdf path), then execute it: ./ Create a directory where you will store all the netcdf files created along the following steps, e.g.:

mkdir $WORKDIR/input/nemo_${CONFIG}  # WARNING: this must correspond to the namelist entry "config_dir"
In category: nemo