Skip to content

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:

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

CRIB is the ITC Geospatial Computing Platform.

To run the STEMMUS-SCOPE model, you need to have input data either from in-situ measurements or from remote sensing. Plumber2 site data are avialable under project directory on CRIB. This folder includes:

  • Plumber2_data: the forcing/driving data provided by PLUMBER2.
  • SoilProperty: the soil texture data and soil hydraulic parameters.

In addition to site data, the remote sensing data are available on CRIB in global_data folder.

Data required by the model are in a folder named "input". Below the directory explanations are from SCOPE documentation:

  • directional: the observer’s zenith and azimuth angles.(only used for multi-angle simulations (if the option ‘directional’ is switched on in parameters).
  • fluspect_parameters: absorption spectra of different leaf components are provided, according to PROSPECT 3.1, as well as Fluspect input: standard spectra for PSI and PSII.
  • leafangles: example leaf inclination distribution data are provided.
  • radiationdata: RTMo.m calculates spectra based on MODTRAN5 outputs (T-18 system).Note that in the input data (files as well as the spreadsheet), the broadband input radiation may be provided. SCOPE linearly scales the input spectra of the optical and the thermal domain in such a way that the spectrally integrated input shortwave and long-wave radiation matches with the measured values.
  • soil_spectra: the soil spectrum is provided. Note that it is also possible to simulate a soil reflectance spectrum with the BSM model. In that case, the values for the BSM model parameters are taken from the input data, and the archived spectra in this folder are not used.
  • input_data.xlsx: the input to SCOPE model is provided. It provides parameter inputs for PROSPECT, leaf_biochemical, fluorescence, soil, canopy, aerodynamic, angles, photosynthetic temperature dependence functional parameters, etc.
  • input_soilLayThick.csv (optional): A file to change the discretization of the soil layers of the STEMMUS model. An example of this file is in example_data folder. This file (if needed) should be copied into the InputPath folder. If this file is used, it will override the default settings of the soil layers. The file has three columns: 1) layer number, 2) layer thickness, and 3) maximum root depth. The user is free to change the values of the three columns. Also, the number of rows determines the number of the soil layers and the total thickness of the soil column (sum of soil layer thickness).

Snellius is the Dutch National supercomputer hosted at SURF.

To run the STEMMUS-SCOPE model, you need to have input data either from in-situ measurements or from remote sensing. Data required by the model are in a folder named "data" in the project directory einf2480 on Snellius. This directory includes:

  • forcing/plumber2_data: the forcing/driving data provided by PLUMBER2.
  • model_parameters/soil_property: the soil texture data and soil hydraulic parameters.
  • model_parameters/vegetation_property:
  • directional
  • fluspect_parameters
  • leafangles
  • radiationdata
  • soil_spectra
  • input_data.xlsx
  • input_soilThick.csv (optional)

In addition to site data, the remote sensing data are available on Snellius in global_data folder.

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/

See example configuration files below:

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.

Config file: it is a text file that sets the paths required by the model. For example, see config_file_crib.txt or config_file_crib_global.txt in this repository. This file includes:

  • SoilPropertyPath: a path to soil texture data and soil hydraulic parameters.
  • InputPath: this is the working/running directory of the model and should include the data of directional, fluspect_parameters, leafangles, radiationdata, soil_spectra, and input_data.xlsx.
  • OutputPath: this is the base path to store outputs of the model. When the model runs, it creates sitename_timestamped directories under this path.
  • ForcingPath: a path to the forcing/driving data. I.e. the Plumber2 dataset.
  • Location: Location where the model should be run. Currently, the model runs at the site scale. For example, if we put FI-Hyy here, the model runs at the FI-Hyy site.
  • StartTime: The start time of the model, in the ISO 8601 format. For example: 2001-01-01T00:00. Note that the time can only be defined in half hour increments. If you want the start time to be the first available data point of the forcing data, you can set StartTime to NA.
  • EndTime: The end time of the model. Formatted the same way as the StartTime. For example: 2001-12-31T23:30. If you want the end time to be the last available data point of the forcing data, you can set EndTime to NA.

To edit the config file, open the file with a text editor and change the paths. The variable names e.g. SoilPropertyPath should not be changed. Also, note a / is required at the end of each line.

As explained above, the "InputPath" directory of the model is considered as the working/running directory and should include some data required by the model. As seen in the config file, the "InputPath" is now set as same as the "input" folder. This means that the "input" folder is treated as the model's working/running directory. However, it is possible to create a different working/running directory and set the "InputPath" to it. Then, you should copy the required data i.e. directional, fluspect_parameters, leafangles, radiationdata, soil_spectra, and input_data.xlsx to the working/running directory.

Config file: it is a text file that sets the paths required by the model. For example, see config_file_snellius.txt or config_file_snellius_global.txt in this repository. This file includes:

  • SoilPropertyPath: a path to soil texture data and soil hydraulic parameters.
  • InputPath: this is the working/running directory of the model and should include the data of directional, fluspect_parameters, leafangles, radiationdata, soil_spectra, and input_data.xlsx.
  • OutputPath: this is the base path to store outputs of the model. When the model runs, it creates sitename_timestamped directories under this path.
  • ForcingPath: a path to the forcing/driving data. I.e. the Plumber2 dataset.
  • Location: Location where the model should be run. Currently, the model runs at the site scale. For example, if we put FI-Hyy here, the model runs at the FI-Hyy site.
  • StartTime: The start time of the model, in the ISO 8601 format. For example: 2001-01-01T00:00. Note that the time can only be defined in half hour increments. If you want the start time to be the first available data point of the forcing data, you can set StartTime to NA.
  • EndTime: The end time of the model. Formatted the same way as the StartTime. For example: 2001-12-31T23:30. If you want the end time to be the last available data point of the forcing data, you can set EndTime to NA.

To edit the config file, open the file with a text editor and change the paths. The InputPath and OutputPath are user-defined directories, make sure they exist and you have right permissions. The variable name e.g. SoilPropertyPath should not be changed. Also, note a / is required at the end of each line.

As explained above, the "InputPath" directory of the model is considered as the working/running directory and should include some data required by the model. As seen in the config file, the "InputPath" is now set to an "input" folder under "scratch-shared" directory. This means that the "input" folder is treated as the model's working/running directory. However, it is possible to create a different working/running directory and set the "InputPath" to it. Then, you should copy the required data i.e. directional, fluspect_parameters, leafangles, radiationdata, soil_spectra, and input_data.xlsx to the working/running directory. For example: cp -r /projects/0/einf2480/model_parameters/vegetation_property/* /scratch-shared/EcoExtreML/STEMMUS_SCOPE/input/<your_work_dir>