Off-the-shelf NEMO climatological ORCA1

This section summarizes guidelines to deploy and run a climatological 1º global circulation NEMO configuration (ORCA1) in different modelling contexts.

Initial conditions of the configuration are based on the Gouretski, 2019 Argo-WOCE climatology, and the atmospheric forcing are those from COREv2 normal year . More details about the scientific context of the configuration can be found in this paper.

Prerequisites:

  • Operating NEMO environment with XIOS (see NEMO doc for help)

or:

  • Installed Apptainer

  • Morays container (see below)

Apptainer on Linux

# For Ubuntu
sudo apt update && sudo apt install -y software-properties-common
sudo add-apt-repository -y ppa:apptainer/ppa
sudo apt update && sudo apt install -y apptainer

# For amd64 Debian
sudo apt update
sudo apt install -y wget
cd /tmp
wget https://github.com/apptainer/apptainer/releases/download/v1.4.3/apptainer_1.4.3_amd64.deb
sudo apt install -y ./apptainer_1.4.3_amd64.deb

Warning

For other Linux distributions, please refer to this guide.

Apptainer on macOS

# Apptainer is available on macOS via LIMA (LInux virtual MAchines)
brew install qemu lima  # Install with brew
port install qemu lima  # Install with macports

# Create Linux VM with Apptainer
limactl start template://apptainer
limactl shell apptainer
# IMPORTANT: type 'cd' to go in VM home, 'pwd' should return '/home/<your_name>.linux'
cd

# NB1: copy files from VM to host
limactl cp apptainer:/path/to/file  /host/destination

Run Morays container

# Get your hardware architecture
uname -m
#  aarch64 --> arm64
#  x86_64  --> amd64
ARCH=arm64

# Download image
wget https://github.com/morays-community/morays-doc/releases/download/containers/morays_env_${ARCH}.sif

# Run container: should print " >>>> Welcome in Morays environment ! <<<< "
apptainer run --writable-tmpfs --bind $(pwd):/home/jdoe/to_host morays_env_${ARCH}.sif

1. Deploy climatological ORCA1

Get a copy of NEMO. For now, the material described in this documentation is compatible with NEMO version 5.0.1 only:

# Clone NEMO
mkdir -p ~/to_host
cd ~/to_host
git clone --branch 5.0.1 https://forge.nemo-ocean.eu/nemo/nemo.git ~/to_host/nemo_5.0.1

Clone ORCA1 repository in the NEMO config directory:

# Clone ORCA1
git clone https://github.com/alexis-barge/ORCA1.git ~/to_host/nemo_5.0.1/cfgs/ORCA1

Install and build (will download inputs and forcing files):

# Build ORCA1
cd ~/to_host/nemo_5.0.1/cfgs/ORCA1
./deploy.sh

Warning

You might need to adapt the template arch file arch-ORCA1_GCC.fcm if you are not running the Morays container.

2. Run standard ORCA1 configuration

Once installed, the configuration is ready to be executed classically:

cd ~/to_host/nemo_v5.0.1/cfgs/ORCA1/EXP00/RUN_DEFAULT
mpirun -np 4 ./nemo.exe

3. Python-wrapped ORCA1

The configuration is compatible with the NEMO Python wrapper Aronnax to be steered from a Python environment. Install Aronnax:

# Clone Aronnax
cd ~/to_host
git clone --branch v0.5.x https://github.com/alexis-barge/Aronnax.git Aronnax

# Compile Aronnax
cd ~/to_host/Aronnax
NEMO_BLD=~/to_host/nemo_v5.0.1/cfgs/ORCA1   pip install .

Warning

If you are not running the Morays container, XIOS must be compiled with -fPIC flag first (or equivalent depending on your compiler). For instance:

cat XIOS/arch/arch-XIOS.fcm
    %CCOMPILER      mpicc -fPIC
    %FCOMPILER      mpif90 -fPIC

or if you are using XIOS3 or later:

./make_xios --full --prod --arch <YOUR_MACHINE> --dynamic

To simulate one year, run the following commands in a Python script or interpreter:

import Aronnax

solver = Aronnax.NEMO(config="ORCA1_RUN", nproc=4)
solver.start()
solver.advance(years=1)
solver.finish(write_restart=True)

Note

More informations about use of Aronnax can be found in its dedicted documentation.

4. Hybrid ML-ORCA1

To set up a hybrid Python-ORCA1 configuration, follow the steps described in this tutorial, starting from section 2.

Also you can get inspired by using this base to deploy the ORCA1_AirSeaFluxes test case. As a reminder, the procedure to deploy a Morays experiment is described in this section.