Aiida FLEXPART plugin

An AiiDA plugin for the Flexpart cosmo and ifs simulations.

This plugin contains 4 types of calculations:

• flexpart.cosmo
• flexpart.ifs
• flexpart.post
• collect.sens

The workflow:

• flexpart.multi_dates: A workflow that can be used to submit flexpart calculations for multiple days.

• AiiDA FLEXPART plugin

  • Installation
    • Computers setup
    • Codes Setup
    • Enable caching
  • Workflow
    • Structure
    • Running the workflow launcher
    • Monitoring the workflow
  • Flexpart Aiidalab app
    • Running the workflow
    • Quering
  • Development guide

Installation

Install the plugins with:

pip install -e .

Install Aiida shell:

pip install aiida-shell

Additional packages for Aiidalab:

pip install aiidalab-widgets-base

(it can also be installed through Aiidalab web)

Computers setup

It is necessary to setup two different configurations of Daint. The configuration files are in /config by the names of computer-daint.yaml and computer-daint-direct.yaml. To set up the computers:

verdi computer setup --config NAME.yaml

followed by:

verdi computer configure core.ssh COMPUTER-NAME

refer to the daint-configure.yaml for answering the questions asked by Aiida after runnign the above line.

Finally, test the computer with:

verdi computer test COMPUTER-NAME

After the setup of both computers, daint and daint-direct, you can check the configuration of each by:

verdi computer list

Should display:

Report: List of configured computers
Report: Use 'verdi computer show COMPUTERLABEL' to display more detailed information
* daint
* daint-direct-106
* localhost

Codes setup

Use the following line with all the .yaml files in /config that start with code_

verdi code create core.code.installed --config NAME.yaml

Similarly as with the computers, one can check the list of all the installed codes by:

verdi code list

Should display:

Full label                           Pk  Entry point
---------------------------------  ----  -------------------
flexpart_cosmo@daint                  1  core.code.installed
flexpart_ifs@daint                    2  core.code.installed
post-processing@daint                 3  core.code.installed
check-cosmo-data@daint-direct-106     4  core.code.installed
check-ifs-data@daint-direct-106       5  core.code.installed

Note that the pk numbers may differ.

Enable caching

Make sure caching is enabled by typing:

verdi config list caching

if False, enable it with:

verdi config set caching.default_enabled True

Workflow

Structure

The following is the workflow structure. It will loop over all the given dates. If model offline is not none, integration_time_offline should be greater than zero. The available models for cosmo are: cosmo7, cosmo1 and kenda1. And the ECMWF models: IFS_GL_05, IFS_GL_1, IFS_EU_02 and IFS_EU_01. Both, model and model offline can be set as a list of the previous.

   graph TD;
      id1{MODEL}--cosmo models-->PREPARE_COSMO_METEO_FILES;
      id1{MODEL}--ecmwf models-->PREPARE_IFS_METEO_FILES;

      subgraph  -
      PREPARE_COSMO_METEO_FILES-->RUN_FLEXPART_COSMO;
      end
      subgraph IFS
      PREPARE_IFS_METEO_FILES-->RUN_FLEXPART_IFS;
      end

      RUN_FLEXPART_COSMO-->id2{MODEL_OFFLINE};
      id2{MODEL_OFFLINE}--ecmwf models-->PREPARE_IFS_METEO_FILES;
      id2{MODEL_OFFLINE}--none -->POST-PROCESSING;
      RUN_FLEXPART_IFS-->POST-PROCESSING;

The second step deals withthe various results of the post-processings produced previously.

   graph TD;

      POST-PROCESSING_1 -->COLLECT_SENSITIVITIES;
      POST-PROCESSING_2 -->COLLECT_SENSITIVITIES;
      POST-PROCESSING_3 -->COLLECT_SENSITIVITIES;
      POST-PROCESSING_4 -->COLLECT_SENSITIVITIES;

      COLLECT_SENSITIVITIES --> RESULTS(NetCFD);

Next:

   graph TD;

      NetCFD_1-- external --> INVERSION;
      NetCFD_2-- observations --> INVERSION;
      NetCFD_3-- FLEXPART --> INVERSION;

      INVERSION --> RESULTS;

Storage

Results will be stashed in /store/empa/em05/{username}/aiida_stash directory, and will include the following:

• header*
• partposit_inst*
• grid_time_*.nc
• aiida.out
• boundary_sensitivity_*.nc (post-processsing only)

And from the collect sensitivities calcjob:

• <LOCATION>_<DOMAIN>_<YYYYMM>.nc
• aiida.out

Running the workflow with the launcher

The workflow can be triggered directly through a verdi command that launchs the script example_workflow_combi.py. The calculation inputs are in several yaml files in /example/inputs/. The script reads directly from the yaml files. Some parameters, however, need to be settled from the launcher script, e.g., simulation_dates, model, model_offline, etc.

cd aiida-flexpart/examples
verdi run example_workflow_combi.py --code flexpart-cosmo@daint

Monitoring the workflow

The worflow can be monitored using

verdi process list

or

verdi process status PK

To check the status of terminated jobs use:

verdi process list -a

Flexpart Aiidalab app

Check Aiidalab user guide for details on how to use and configure Aiida lab.

docker run -p 8888:8888 aiidalab/full-stack

Note

NOTE

Development guide