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STEMMUS_SCOPE_on_CRIB.md

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STEMMUS_SCOPE on CRIB

CRIB is the ITC Geospatial Computing Platform.

Dataflow of STEMMUS_SCOPE on CRIB:

  1. Data required by the model are in a folder named "input" 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.

    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.

  2. Config file: it is a text file that sets the paths required by the model. For example, see config_file_crib.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.

Workflow of STEMMUS_SCOPE on CRIB:

  1. The model reads the forcing file associated with the specified location, e.g., FI-Hyy_1996-2014_FLUXNET2015_Met.nc from "ForcingPath" and extracts forcing variables in .dat format using filesread.m. The .dat files are stored in the "InputPath" directory. In addition, the model reads the site information i.e. the location and vegetation parameters.
  2. The model reads the soil parameters from "SoilPropertyPath" using soilpropertyread.m.
  3. Some constants are loaded using Constant.m.
  4. The model runs step by step until the whole simulation period is completed i.e till the last time step of the forcing data.
  5. The results are saved as binary files temporarily. Then, the binary files are converted to .csv files and stored in a sitename_timestamped output directory under "OutputPath".

How to run STEMMUS_SCOPE on CRIB:

  1. Log in CRIB with your username and password and select a proper compute unit.
  2. Download the source code from this repository or get it using git clone in a terminal:

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

All the codes can be found in the folder src whereas the executable file in the folder exe.

  1. Check config_file_crib.txt and change the paths if needed, specifically "InputPath" and "OutputPath".
  2. Follow the instructions below:

Run using MATLAB that requires a license

If you want to use MATLAB desktop,

  1. click on the Remote Desktop in the Launcher. Click on the Applications. You will find the 'MATLAB' software under the Research.
  2. After clicking on 'MATLAB', it asks for your account information that is connected to a MATLAB license.
  3. Open the file filesread.m and set the variable CFG to the path of the config file e.g. CFG = '/data/shared/EcoExtreML/STEMMUS_SCOPEv1.0.0/STEMMUS_SCOPE/config_file_crib.txt';.
  4. Then, run the main script STEMMUS_SCOPE.m.

As an alternative, you can run the main script using MATLAB command line in a terminal:

matlab -nodisplay -nosplash -nodesktop -r "run('STEMMUS_SCOPE.m');exit;"