This model configuration has been developed through the Commonwealth Marine Economies Programme
"Enabling safe and sustainable marine economies across Commonwealth Small Island Developing States".
The Commonwealth Marine Economies (CME) Programme was announced by the British Prime Minister in 2015 to help Commonwealth Small Island Developing States (SIDS) make the most of their natural maritime advantages, to enable sustainable economic growth and alleviate poverty.
The model grid has 1/12° lat-lon resolution and 75 hybrid sigma-z-partial-step vertical levels. The domain covers -4.91°N to -31.56°N, 100.17°E to 54.92°E. For more details on the model parameters, bathymetry and external forcing, see Wilson, Harle and Wakelin (2019). "Development of a regional ocean model for the Caribbean", NOC Research and Consultancy Report No. 65, available from the NERC Open Research Archive.
The following code was used in this configuration:
svn co http://forge.ipsl.jussieu.fr/nemo/svn/NEMO/trunk -r 8395
The initial conditions and boundary data can be downloaded from JASMIN:
http://gws-access.ceda.ac.uk/public/recicle/Caribbean/
NB This recipe has be written with the ARCHER HPC INTEL environment in mind.
# Change to some working directory of choice
export WORK_DIR='path_to_working_directory'
if [ ! -d "$WORK_DIR" ]; then
mkdir $WORK_DIR
fi
cd $WORK_DIR
# Checkout the NEMO code from the SVN Paris repository
svn co http://forge.ipsl.jussieu.fr/nemo/svn/NEMO/trunk -r 8395 nemo
cd nemo/NEMOGCM/CONFIG
# Checkout configuration directory structure
git init .
git clone [email protected]:NOC-MSM/Caribbean.git
# Add it to the configuration list
echo "Caribbean OPA_SRC" >> cfg.txt
You can fold the make_xios command into a serial job. NB $NETCDF_DIR and $HDF5_DIR must be part of your environment. This should be the case if you've used modules to setup the netcdf and hdf5 e.g.
module swap PrgEnv-cray PrgEnv-intel
module load cray-hdf5-parallel
module load cray-netcdf-hdf5parallel
At this point you can checkout and compile XIOS or use a version you already have. If you're starting from scratch:
# Choose an appropriate directory for your XIOS installation
export XIOS_DIR='path_to_checkout_xios'
if [ ! -d "$XIOS_DIR" ]; then
mkdir $XIOS_DIR
fi
cd $XIOS_DIR
svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk@1242 xios
cd xios
cp $WORK_DIR/nemo/NEMOGCM/CONFIG/Caribbean/arch_xios/* ./arch
./make_xios --full --prod --arch XC30_ARCHER --netcdf_lib netcdf4_par --job 4
# Let's update the path to xios
export XIOS_DIR=$XIOS_DIR/xios
Next, compile the NEMO code itself. First we copy the arch files into the appropriate directory.
cd $WORK_DIR/nemo/NEMOGCM/CONFIG/Caribbean
cp ARCH/* ../../ARCH
NB while $XIOS_DIR is in the current environment if you ever compile in a new session $XIOS_DIR will have to be redefined as ../ARCH/arch-XC_ARCHER_Intel.fcm use this environment variable.
cd ../
./makenemo -n Caribbean -m XC_ARCHER_Intel -j 4
That should be enough to produce a valid executable. Now to copy the forcing data from JASMIN.
cd Caribbean/EXP00
wget -r -np -nH --cut-dirs=3 -erobots=off --reject="index.html*" http://gws-access.ceda.ac.uk/public/recicle/Caribbean/
And finally link the XIOS binary to the configuration directory and create a restarts directory.
ln -s $XIOS_DIR/bin/xios_server.exe xios_server.exe
mkdir restarts
Edit and run the run_script.pbs script in ../EXP00 accordingly (namely enter a valid project code) and submit to the queue: qsub run_script.pbs