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STEMMUS_SCOPE on Snellius

Snellius is the Dutch National supercomputer hosted at SURF.

Dataflow of STEMMUS_SCOPE on Snellius:

  1. 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

    For the explanation of the directories see Dataflow of STEMMUS_SCOPE on CRIB.

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

Workflow of STEMMUS_SCOPE on Snellius:

This is the same as the workflow of STEMMUS_SCOPE on crib, see section Workflow of STEMMUS_SCOPE on CRIB.

How to run STEMMUS_SCOPE on Snellius:

  1. Log in to Snellius.

  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.

  3. Check config_file_snellius.txt and change the paths if needed, specifically "InputPath" and "OutputPath".

  4. Follow one of the instructions below:

Run using MATLAB that requires a license

In order to use MATLAB, you need to send a request to add you to the user pool on Snellius. Then, open the file config_file_snellius.txt and set the paths. Then, run the main script STEMMUS_SCOPE_exe.m using MATLAB command line in a terminal on a compute node:

module load 2021
module load MATLAB/2021a-upd3
matlab -nodisplay -nosplash -nodesktop -r "STEMMUS_SCOPE_exe('config_file_snellius.txt');exit;"

To run the codes above on a compute node, you can create a bash script as:

#!/bin/bash
# SLURM settings
#SBATCH -J stemmus_scope
#SBATCH -t 01:00:00
#SBATCH -N 1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH -p thin
#SBATCH --output=./slurm_%j.out
#SBATCH --error=./slurm_%j.out

module load 2021
module load MATLAB/2021a-upd3
matlab -nodisplay -nosplash -nodesktop -r "STEMMUS_SCOPE_exe('config_file_snellius.txt');exit;"

Run using MATLAB Compiler that does not require a license

If you want to run the model as a standalone application, you need MATLAB Runtime version 2023a. This is available on Snellius. You can run the model by passing the path of the config file in a terminal on a compute node:

module load 2021
module load MCR/R2021a.3
./STEMMUS_SCOPE/exe/STEMMUS_SCOPE config_file_snellius.txt

The bash script run_stemmus_scope_snellius.sh in this repository, runs the model at 170 sites (default) on a compute node. The scripts loops over forcing files in the "ForcingPath", creates sitename_timestamped working directories under "InputPath" directory and copies required data to those working dirs. To change the number of sites, open the script and on the last line change the parameter {1..170}. For example env_parallel -n1 -j32 --joblog $log_file loop_func ::: {1..170} will run the model at 32 sites simultaneously. For testing purposes, the time of the bash script is set to 00:10:00. Note that the model run can take long for some of the sites. As the maxium time wall is 5 days on a partition thin, time can be set to5-00:00:00 for a complete run of the model.

You can run the script in a terminal:

cd STEMMUS_SCOPE
mkdir -p slurm
sbatch run_stemmus_scope_snellius.sh

This creates a log file per each forcing file in the folder slurm.