Running FOCI-OpenIFS

[toc]

Further info

• Running OpenIFS atmosphere only
• FOCI-OpenIFS 4.0
• FOCI-OpenIFS-AGRIF 4.0
• OpenIFS
• NEMO

You will need

• Patience
• Access to an HPC
• Miniconda / Miniforge
• ESM-Tools (GitHub account is recommended, but not required)
• Access to gitlab.dkrz.de, git.geomar.de

Prerequisites

Get ESM-Tools (https://github.com/esm-tools/esm_tools/)

You'll need to load a module with git LFS support. Typically (glogin, levante etc) you can do

module load git

On nesh you will need

module load oneapi2023-env
module load git-lfs

On olaf you will need

module load git-lfs

Then get ESM-Tools

mkdir esm
cd esm

git clone https://github.com/esm-tools/esm_tools

Install Perl (util in ESM-Tools)

cd esm_tools/utils/
./install_perl.sh

Install ESM-Tools

First load an anaconda environment (on most machines):

module load anaconda3

or similar. Run python --version to check that python is not newer than 3.10.

NESH does not have an anaconda environment, so you'll need to install your own (see Miniconda further down).

Then install ESM-Tools

cd ../
./install.sh

If you get an issue with LC_ALL being unset, then just set it in your .bashrc file. See also "INSTALLING" on the ESM-Tools git page.

If it complains about the python version, then you can install your own Miniconda environment and build ESM-Tools that way. First install Miniconda:

curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o Miniconda3.sh 
bash Miniconda3.sh -b -p ${HOME}/miniconda3
${HOME}/miniconda3/bin/conda init bash

Log out and log in again for the changes to take effect.

Make sure you have an older Python

conda install python=3.10

Then install ESM-Tools

cd esm/esm
./install.sh

Switch to GEOMAR branch

cd
cd esm/esm_tools/
git checkout geomar_dev

Set up access tokens for git servers

Github:

• Log into github.com.
• Profile picture upper right corner -> Settings -> Developer settings -> Personal access tokens -> Generate new token (classic)
• Click "repo" box. Name it after the machine, e.g. olaf or nesh. Click Generate token.
• Copy code

Gitlab (DKRZ, GEOMAR, etc)

• Log into gitlab e.g. gitlab.dkrz.de or git.geomar.de
• Click your profile logo near the + sign in the top left.
• Choose "Preferences" -> "Access Tokens" -> "Add new token".
• Name it after the machine, e.g. olaf or nesh, empty the "expiration date" box, click "read_repository" and "write_repository", "Create personal access token".
• Copy code

Make a ${HOME}/.netrc file on the HPC (glogin, levante, olaf etc) with contents

machine github.com login <github_username> password <token_code_from_github> 
machine gitlab.dkrz.de login <dkrz_username> password <token_code_from_dkrz> 
machine git.geomar.de login <geomar_email> password <token_code_from_geomar> 

Save and close the file.

Set up the environment

Your experiments should run and be stored on the WORK, PROJ, or SCRATCH directory, depending on the machine used. So we need to create that directory.

To make life easier, we will make a link in our HOME directory to that directory.

On olaf:

ESM_DIR=/proj/internal_group/iccp/$USER/esm-experiments/

On glogin or blogin:

ESM_DIR=/scratch/usr/$USER/esm-experiments/

On nesh:

ESM_DIR=$WORK/esm-experiments/

Then do

cd 
cd esm
mkdir -vp $ESM_DIR
ln -sfv $ESM_DIR esm-experiments

Install model

Get the code

cd esm
mkdir models
cd models
esm_master get-focioifs-4.0 

Compile

esm_master comp-focioifs-4.0

Run an experiment

Here we make a new experiment my_first_exp. You can set the experiment name with the -e flag.

cd 
cd esm/esm_tools/runscripts/focioifs/
esm_runscripts focioifs4-piCtrl-initial-olaf.yaml -e my_first_exp 

Changing model parameters (scenario, configuration etc)

The runscript for FOCI-OpenIFS 4.0 on NESH (Kiel University machine) explains the parameters set for a coupled experiment: runscripts/focioifs/focioifs4-piCtl-initial-nesh.yaml.

For examples on how to change namelist parameters for OpenIFS, see runscript for OpenIFS on NESH: runscripts/oifs/oifs-43r3-climMEMODEL-nesh.yaml.

These examples should be enough to get an idea on how to change scenario (piControl, historical, 4xCO2 etc), model resolution, time step.

Join the communities

Documentation for the model components are here:

• OpenIFS
• NEMO

User forums you should join:

• OpenIFS
• NEMO

The model does not run. Why?!