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getting_started.md

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Requiremnets

Computig resource

To run the STEMMUS-SCOPE model, you can use one of the following computing resources:

  • CRIB is the ITC Geospatial Computing Platform.
  • Snellius is the Dutch National supercomputer hosted at SURF.

Otherwise, you can run the model on your local device if you have the correct set of software and data.

Software

To run the STEMMUS-SCOPE model, you need one of the following:

Model source code

The source code of STEMMUS_SCOPE can be found in the GitHub repository https://github.com/EcoExtreML/STEMMUS_SCOPE under the folder src. Download the latest version of the model from the repository or get it using git clone in a terminal:

git clone https://github.com/EcoExtreML/STEMMUS_SCOPE.git

Data

To run the STEMMUS-SCOPE model, you need to have input data either from in-situ measurements or from remote sensing. Before running the model, you need to prepare input data and a configuration file for one site/location. This can be done using setup() function in the python package PyStemmusScope. See example datasets below:

=== "Example dataset on Zenodo" A pre-processed example dataset for one site can be found on Zenodo here.

=== "Data on CRIB" CRIB is the ITC Geospatial Computing Platform.

{% include-markdown "./STEMMUS_SCOPE_on_CRIB.md" start="### Dataflow of STEMMUS_SCOPE on CRIB" end="### Configuration file" heading-offset=2%}

=== "Data on Snellius" Snellius is the Dutch National supercomputer hosted at SURF.

{% include-markdown "./STEMMUS_SCOPE_on_Snellius.md" start="### Dataflow of STEMMUS_SCOPE on Snellius" end="### Configuration file" heading-offset=2%}

Configuration file

The configuration file is a text file that sets the paths required by the model. The configuration file should contain the following information:

WorkDir=/path_to_working_directory/
SoilPropertyPath=/path_to_soil_property_data/
ForcingPath=/path_to_forcing_data/
Location=AU-DaS
directional=/path_to_directional_data/
fluspect_parameters=/path_to_fluspect_parameters_data/
leafangles=/path_to_leafangles_data/
radiationdata=/path_to_radiation_data/
soil_spectrum=/path_to_soil_spectra_data/
InitialConditionPath=/path_to_soil_initial_condition_data/
input_data=/path_to_input_data.xlsx_file/
StartTime=2001-01-01T00:00
EndTime=2001-01-02T00:00
InputPath=/path_to_model_input_folder/
OutputPath=/path_to_model_output_folder/

The configuration file could also contain the optional key FullCSVfiles. If FullCSVfiles=0, the model will not store some large binary files in csv format. The default value is FullCSVfiles=1. To know which files are stored in csv format, see the function bin_to_csv() in src/+io folder.

FullCSVfiles=0

See example configuration files below:

=== "Example configuration file" An example configuration file can be found here. If setup() function in the python package PyStemmusScope is used to prepare data, the model configuration file including InputPath and OutputPath and the data of one site/location will be generated automatically.

=== "Example configuration file on CRIB" {% include-markdown "./STEMMUS_SCOPE_on_CRIB.md" start="### Configuration file" heading-offset=2%}

=== "Example configuration file on Snellius" {% include-markdown "./STEMMUS_SCOPE_on_Snellius.md" start="### Configuration file" heading-offset=2%}