OceanVar2 Test case

This repository provides all the needed files and a step-by-step guide on how to use OceanVar2 in the Mediterranean Sea, using the NEMO model.

To run the test case, you need

• 

• 

  • (or similar to manage python packages)
  • A fortran Compiler and the required modules on a cluster (see below)

The Python packages required to run the Test Case are:

• sys
• netCDF4
• numpy
• glob
• cftime
• datetime
• copy
• scipy
• cartopy
• matplotlib
• ssl
• urllib
• dateutil
• warnings
• os
• xarray
• shutil
• csv
• subprocess
• re
• ttide_py
• gsw-Python

The System libraries required to run the Test Case are:

• HDF5
• NetCDF-C
• NetCDF-fortran
• parallel NetCDF
• curl
• perl
• nco
• cdo
• fortran compiler

Installation

First step, is to load the needed modules in a cluster or the PC you are using

LOAD ENVIRONMENT

The following is an example on modules needed on our cluster

module load anaconda/3-2022.10

module load impi-2021.6.0/2021.6.0

module load intel-2021.6.0/libszip/2.1.1-tvhyi

module load oneapi-2022.1.0/2022.1.0

module load oneapi-2022.1.0/mkl/2022.1.0

module load intel-2021.6.0/impi-2021.6.0/hdf5-threadsafe/1.13.3-zbgha

module load intel-2021.6.0/impi-2021.6.0/netcdf-c-threadsafe/4.9.0-wpe4t

module load intel-2021.6.0/impi-2021.6.0/netcdf-fortran-threadsafe/4.6.0-75oow

module load intel-2021.6.0/impi-2021.6.0/parallel-netcdf/1.12.3-eshb5

module load intel-2021.6.0/curl/7.85.0-djjip

module load intel-2021.6.0/perl/5.36.0-jj4hw

module load intel-2021.6.0/perl-uri/1.72-6at2i

module load intel-2021.6.0/nco/5.0.6-jp6y4

module load intel-2021.6.0/cdo-threadsafe

USAGE STEPS

Download locally the test case input files in "MedFS831"

git clone -b main git@github.com:CMCC-Foundation/MedFS831.git MedFS831

move the the new directory

cd MedFS831

Download the NEMO model

git clone --branch 4.2.0 https://forge.nemo-ocean.eu/nemo/nemo.git  medsea-nemo42

Copy the architecture file to compile NEMO

cp MyNEMO/MY_ARCH/arch-X64_JUNO.fcm medsea-nemo42/arch/.

EDIT: possibly modify arch-X64_JUNO.fcm according to computer architecture

Copy the bash script provided with the test case to compile NEMO in the proper directory

 cp MyNEMO/MY_INSTALL/run_makenemo.bsh medsea-nemo42/.

-- EDIT: XIOS path in medsea-nemo42/run_makenemo.bsh

vi medsea-nemo42/run_makenemo.bsh

Move to the proper directory and compile NEMO

cd medsea-nemo42
sh run_makenemo.bsh

Copy the bash script provided with the test case to compile NEMO tools in the proper directory

cp ../MyNEMO/MY_INSTALL/run_maketools.bsh tools/.

-- EDIT: XIOS path in tools/run_maketools.bsh

vi tools/run_maketools.bsh

Move in the proper directory and compile

cd tools
sh run_maketools.bsh

Now create the NEMO Mediterranean Configuration

    cd DOMAINcfg
    cp  ../../../MyNEMO/MY_NAMELIST/namelist_cfg_MedFS831_dom namelist_cfg
    ln -fs ../../../DATA/STATIC/bathy_meter.nc .
    ./make_domain_cfg.exe
    cd ../../../MyTOOLS/BDY_NEMO
    python mk_bdycoords.py

Execute the first NEMO run (1 day) needed for some static files

cd ../../SCRIPT/

Edit the submission script

 vi submit_MedFS831.bsh
    date_end=20210101
    OCEANVAR=false
    ln_obsmisfits=false

and submit (or execute in you PC)

 bsub < submit_MedFS831.bsh

Create OceanVar2 static geometric files

cd  ../MyTOOLS/COAST_DIST
./compile.bsh
./cstdst.x
cd ../GRD_OCEANVAR
python mk_oceanvar_grd.py

Prepare the observations

cd ../OBS_NEMO
bsub < run_prep.bsh

Download locally the OceanVar2 code

 cd ../../
 git clone -b main git@github.com:CMCC-Foundation/OceanVar2 oceanvar2

Compile OceanVar2

cd  oceanvar2/src
./link_in_work
cd ../work/
make all

Execute the NEMO analysis (1 month)

cd ../../SCRIPT/

Edit the submission script for the analysis (OCEANVAR=true)

vi submit_MedFS831.bsh
  date_end=20210131
  OCEANVAR=true
  ln_obsmisfits=true

and submit (or execute in you PC)

bsub < submit_MedFS831.bsh

Edit the submission script for the simulation (OCEANVAR=false)

vi submit_MedFS831.bsh
  date_end=20210131
  OCEANVAR=false
  ln_obsmisfits=true

and submit (or execute in you PC)

bsub < submit_MedFS831.bsh

Group the misfit files into daily files

cd ../MyTOOLS/POST

Edit the Python script to processing simulation misfits

vi submit_aggregate_NemoMisfits.bsh
  analysis=false

and submit (or execute in you PC)

bsub < submit_aggregate_NemoMisfits.bsh

Edit the Python script to processing analysis misfits

vi submit_aggregate_NemoMisfits.bsh
analysis=true

and submit (or execute in you PC)

bsub < submit_aggregate_NemoMisfits.bsh

Compute the misfits

python cmp_misfits_ins.py
python cmp_misfits_sla.py

Create the figures

python  mk_figure01.py
python  mk_figure04.py
python  mk_figure06.py

If everything works fine you will obtain these figures.