DEODE Scripting System

About

The DEODE Scripting System provides a deode python package that runs the Destination Earth on Demand Extremes system.

See the project’s documentation page for more information.

Set up environment

Make sure you have python>=3.10

Start by adding the $HOME/.local/bin directory in your PATH:

export PATH="$HOME/.local/bin:$PATH"

We highly recommend you to also put the statement listed above in your shell configuration file, so you don’t need to do this the next time you log in. Then, run:

On Atos (hpc-login)

module load python3/3.10.10-01
module load ecflow

On LUMI

ml use /scratch/project_465000527/jasinskas/scl/modules/
ml pyeccodes_23
ml scl-ecflow_23

On Macs (local install only)
```
brew install pyenv
pyenv install 3.10.10
# (or which ever version you want to universalise)
pyenv global 3.10.10
```
Add eval “$(pyenv init –path)” to ~/.zprofile (or ~/.bash_profile or ~/.zshrc, whichever you need). Relaunch the shell and check that Python works, or run $ source ~/.zprofile

Installation

First checkout the deode source code from github:

git clone git@github.com:destination-earth-digital-twins/Deode-Workflow.git
cd Deode-Workflow

For development, use forks as specified in the Development guidelines. To clone the forked repository, use the following command, replacing <username> with your GitHub username:

git clone git@github.com:<username>/Deode-Workflow.git
cd Deode-Workflow

Then install/reinstall poetry by runnning the following commands in your shell:

# Clean eventual previous install
curl -sSL https://install.python-poetry.org | python3 - --uninstall
rm -rf ${HOME}/.cache/pypoetry/ ${HOME}/.local/bin/poetry ${HOME}/.local/share/pypoetry
# Download and install poetry
curl -sSL https://install.python-poetry.org | python3 -
poetry install
# Add the poetry shell command as a plugin (for poetry >= v2.0.0)
poetry self add poetry-plugin-shell

Finally, install pygdal, which is required for climate generation. pygdal depends on gdal, which is notoriously troublesome as dependency when targeting many systems. The versions of pygdal and the system’s gdalshould match.

To install gdal and pygdal run the follow in commands in your shell:

On Atos (hpc-login)

module load gdal/3.6.2
poetry shell
pip install pygdal==3.6.2.11

If installation is not succesful, please contact the IT support in your organisation or HPC facility.

Important

Deode-Workflow should be installed in a folder accessible by ecflow server.

On Atos, it should be installed in your $HOME or $PERM directory.

Usage

Initially set up the environment by repeating the steps in Set up environment, navigate to the root level of the Deode-Workflow install directory and activate python virtual environment:

poetry shell

Alternatively, to activate a deode installation located in an arbitrary directory MY_DEODE_SOURCE_DIRECTORY, please run:

poetry shell --directory=MY_DEODE_SOURCE_DIRECTORY

Test that deode works by running:

deode -h

The Configuration File

Before you can use deode (apart from the -h option), you will need a configuration file written in the TOML format. Please take a look at the default config.toml file, as well as the project’s Doc Page, for more information about this.

To see all configs currently in place in your deode setup, please run

deode show config

Command line options

After completing the setup, you should be able to run

deode [opts] SUBCOMMAND [subcommand_opts]

where [opts] and [subcommand_opts] denote optional command line arguments that apply, respectively, to deode in general and to SUBCOMMAND specifically.

Please run deode -h for information about the supported subcommands and general deode options. For info about specific subcommands and the options that apply to them only, please run deode SUBCOMMAND -h (note that the -h goes after the subcommand in this case).

Examples

These examples assume that you have successfully Set up environment installed Deode-Workflow, navigated to the root level of your deode install directory and loaded the python environment. The examples also assume that the binaries and input data for the ACCORD CSCs is in place. Please contact your local ACCORD members for advice if this is not the case.

Running ecflow suite on ATOS or LUMI

The following command will run the full suite using the default experiment:

deode case ?deode/data/config_files/configurations/cy48t3_arome -o cy48t3_arome.toml --start-suite

Running the `"Forecast"` task from the `hpc-login`’s command line

The command below runs deode’s task "Forecast" using the batch system rules defined in your config.toml:

deode run --task Forecast --config-file cy48t3_arome.toml

Note that this requires a previous run of the ecflow suite for the given config file to have finished succesfully.

This way, the stand alone forecast will pick the input data from the existing run and output the result in the same directories (as defined by the config file).

For other platforms a new config file would have to be created first. Please consult the configure cases section in the documentation for more information.