GCOMS1k Domains

Grid Generation

produces: Bathy domain.cfg list of domains, lat and lon limits = e.g. BLZE12 Name convention is 4 letters then LME number

Replace all in this doc for cut-and-paste

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On livljobs7

export DOMNAM=MOMZ30
export CONFIG=GCOMS1k
export WDIR=/projectsa/accord/$CONFIG
export INPUTS=$WDIR/INPUTS
export  OUTPUTS=$WDIR/OUTPUTS
export INPUTS_ARCH=/work/n01/n01/$USER/$CONFIG/INPUTS/
export CDIR_ARCH=/work/n01/n01/$USER/$CONFIG/nemo/cfgs/$CONFIG
mkdir -p $INPUTS/$DOMNAM

exec ssh-agent $SHELL 
ssh-add ~/.ssh/id_rsa_archer

module load  matlab/2016b ; matlab &

In matlab:

cd /work/jholt/Git/GCOMS1k/STARTFILES/Generate_Domains/Mfiles
environment
edit extract_LMEs_guide.m : define iwant_LMEs

run in MATLAB

extract_LMEs_guide
``
Indentifier = MOMZ30  
Extracts gebco bathymetry if needed 

Run GridBuilder for : MOMZ30

load bathy from /projectsa/accord/GCOMS1k/LME/LME_Bathy/LME_12_GEBCO_bathy.nc 
mask setting Use GSHHG
Adjust area, rotation and number of cells to target resolution
Start box at bottom left
load/save grid file to /projectsa/accord/GCOMS1k/Grid_files/MOMZ30_Grid.mat

exit grid builder

Back in Matlab:

DOMNAM='MOMZ30' `` run GridBuilder_to_NEMO

Produces: MOMZ30_bathy_meter.nc MOMZ30_coordinates.nc

On Livljobs6

ssh [email protected] mkdir $INPUTS_ARCH/$DOMNAM
cd $INPUTS/$DOMNAM
scp $DOMNAM\_bathy_meter.nc $DOMNAM\_coordinates.nc [email protected]:$INPUTS_ARCH/$DOMNAM

Generate domain_cfg on ARCHER (below)

rsync  -uvt   login.archer.ac.uk:$INPUTS_ARCH/$DOMNAM/*.nc $INPUTS/$DOMNAM/

Generate DOMCFG

On archer2

export CONFIG=GCOMS1k
export WORK=/work/n01/n01
export WDIR=$WORK/$USER/$CONFIG
export REPO_DIR=$WORK/$USER/Git/GCOMS1k

export INPUTS=$WDIR/INPUTS
export TEMPLATES=$REPO_DIR/STARTFILES/TEMPLATES
export CDIR=$WDIR/nemo/CONFIG
export TDIR=$WDIR/nemo/tools
export DOMNAM=GTHI35_2

export HPC_TARG=archer2
export COMPILER=cray
export MPI_TARG=mpich
. $REPO_DIR/scripts/env/${HPC_TARG}/${COMPILER}-${MPI_TARG}-ucx

cd $INPUTS/$DOMNAM

ln -s $TDIR/DOMAINcfg/*.xml .
ln  -s $TDIR/DOMAINcfg/namelist_ref .
ln -s $DOMNAM\_coordinates.nc coordinates.nc 
ln -s $DOMNAM\_bathy_meter.nc bathy_meter.nc
ln  -s  $TDIR/DOMAINcfg/rs .
ln -s $TDIR/DOMAINcfg/make_domain_cfg.exe .

cp $TEMPLATES/domain_namelist_cfg namelist_cfg
cp $REPO_DIR/scripts/make_domain.slurm .

To find domain size

ncdump -h bathy_meter.nc 

edit namelist_cfg for domain size

vi namelist_cfg

run domain_cfg tool

sbatch make_domain.slurm

tidy when done

mv domain_cfg.nc $DOMNAM\_domain_cfg.nc
rm domain_cfg.[oe]* *.xml rs namelist_ref coordinates.nc bathy_meter.nc make_domain_cfg.exe layout.dat output.namelist.dyn stdouterr_cfg ocean.output

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Use LME's to number domains