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Christopher Bull

Aspiring Oceanographer at the British Antarctic Survey. 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 https://github.com/chrisb13/BUILD_CONFIG_NEMO.git
cd GSW-Fortran/test
vi makefile   #in particular fill the FC and NETCDF_INCDIR variables
make
./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 https://github.com/TEOS-10/GSW-Fortran.git

The gsw_data_v3_0.nc file provided in this repository should be fine, but in case you start again from the original file (i.e. from github.com/TEOS-10/GSW-Fortran.git), you will need to modify it to avoid NaN in some places (otherwise, skip the next 4 lines):

./compile.sh remove_NaN_from_gsw_data_v3_0.f90
./remove_NaN_from_gsw_data_v3_0
ncks -x -v ocean_ref,ndepth_ref,deltaSA_ref,SA_ref,SAAR_ref GSW-Fortran/test/gsw_data_v3_0.nc gsw_data_v3_0.nc
ncks -A gsw_data_v3_0_to_be_ncks-A.nc gsw_data_v3_0.nc

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 compile_ALL.sh, adapt fortran compiler (and maybe netcdf path), then execute it: ./compile_ALL.sh. 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