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polish texts in docs
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‎docs/notebooks/run_model_with_different_dataset.ipynb‎

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Running the STEMMUS_SCOPE model\n",
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"# Running the STEMMUS_SCOPE model with different dataset\n",
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"\n",
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"This notebook shows how to run the STEMMUS_SCOPE model uisng the Executable file, including preprocessing and postprocessing. \n",
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"This notebook shows how to run the STEMMUS_SCOPE model uisng the Executable file, including preprocessing and postprocessing. For postprocesisng, the file required_netcdf_variables.csv can be found at https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/utils/csv_to_nc/required_netcdf_variables.csv.\n",
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"\n",
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"## Which options are available?\n",
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"\n",
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"See the [run_model_with_different_options.ipynb](./run_model_with_different_options.ipynb) for avialbale options e.g. Executable file, Matlab, Octave.\n",
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"See the [Run the model with different options](./run_model_with_different_options.ipynb) for avialbale options e.g. Executable file, Matlab, Octave.\n",
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"The STEMMUS_SCOPE executable file is located in a repository https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/run_model_on_snellius/exe/STEMMUS_SCOPE.\n",
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"\n",
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"## Which datasets are available?\n",
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"The config file shows how to set the paths to different data needed by the model. Check the data source on Snelius and CRIB and modify the config file accordingly:\n",
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"\n",
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"#### On CRIB:\n",
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"- Site data: /data/shared/EcoExtreML/STEMMUS_SCOPEv1.0.0/input, config file template https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/config_file_crib.txt\n",
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"- Global data: /data/shared/EcoExtreML/STEMMUS_SCOPEv1.0.0/global_data, config file template https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/run_model_on_snellius/config_file_snellius_global.txt\n",
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"#### On CRIB\n",
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"- Site data:\n",
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" - path to data: `/data/shared/EcoExtreML/STEMMUS_SCOPEv1.0.0/input`,\n",
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" - config file template: https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/config_file_crib.txt\n",
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"- Global data:\n",
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" - path to data `/data/shared/EcoExtreML/STEMMUS_SCOPEv1.0.0/global_data`,\n",
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" - config file template: https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/run_model_on_snellius/config_file_snellius_global.txt\n",
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"\n",
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"#### On SNellius:\n",
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"- Site data: /projects/0/ttse0619/, config file template https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/run_model_on_snellius/config_file_snellius.txt\n",
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"- Global data: /projects/0/ttse0619/global_data, config file template https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/run_model_on_snellius/config_file_snellius_global.txt\n",
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"#### On Snellius\n",
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"- Site data:\n",
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" - path to data: `/projects/0/ttse0619/`,\n",
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" - config file template: https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/run_model_on_snellius/config_file_snellius.txt\n",
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"- Global data:\n",
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" - path to data: `/projects/0/ttse0619/global_data`,\n",
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" - config file template: https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/run_model_on_snellius/config_file_snellius_global.txt\n",
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"\n",
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"Choose how do you want to run the model:\n",
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"\n",
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"path_to_model_src = \"./STEMMUS_SCOPE\""
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"If you run the model on your own machine, make sure `LD_LIBRARY_PATH` is set correctly. To do this, uncomment the cell below and run it:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# # Set LD_LIBRARY_PATH\n",
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"matlab_path = !whereis MATLAB\n",
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"matlab_path = matlab_path.s.split(\": \")[1]\n",
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"os.environ['LD_LIBRARY_PATH'] = (\n",
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" f\"{matlab_path}/MATLAB_Runtime/R2023a/runtime/glnxa64:\"\n",
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" f\"{matlab_path}/MATLAB_Runtime/R2023a/bin/glnxa64:\"\n",
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" f\"{matlab_path}/MATLAB_Runtime/R2023a/sys/os/glnxa64:\"\n",
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" f\"{matlab_path}/MATLAB_Runtime/R2023a/extern/bin/glnxa64:\"\n",
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" f\"{matlab_path}/MATLAB_Runtime/R2023a/sys/opengl/lib/glnxa64\")\n",
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"print(os.environ['LD_LIBRARY_PATH'])"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,

‎docs/notebooks/run_model_with_different_options.ipynb‎

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Running the STEMMUS_SCOPE model\n",
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"# Running the STEMMUS_SCOPE model with different options\n",
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"## Which options are available?\n",
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"This notebook shows steps to run the STEMMUS_SCOPE model, including preprocessing and postprocessing. STEMMUS_SCOPE files are located in a **private** repository https://github.com/EcoExtreML/STEMMUS_SCOPE. To clone the repository locally and access the files, make sure you have right access to the repository. Then specify the path to a config file e.g.`config_file_template.txt`, executable file `STEMMUS_SCOPE` or source code `STEMMUS_SCOPE/src` in the cells below. There are already config files for users on Snellius and CRIB, see `config_file_snellius.txt`, `config_file_crib.txt`. Choose how do you want to run the model:\n",
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"This notebook shows steps to run the STEMMUS_SCOPE model, including preprocessing and postprocessing. STEMMUS_SCOPE files are located in a repository https://github.com/EcoExtreML/STEMMUS_SCOPE. Then specify the path to a config file e.g.`config_file_template.txt`, executable file `STEMMUS_SCOPE` or source code `STEMMUS_SCOPE/src` in the cells below. There are already config files for users on Snellius and CRIB, see `config_file_snellius.txt`, `config_file_crib.txt`. Choose how do you want to run the model:\n",
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"\n",
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"\n",
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"[**Executable file**](#1-using-executable-file)\n",
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],
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"metadata": {
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"kernelspec": {
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"display_name": "pyss_octave",
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:50:36) [MSC v.1929 64 bit (AMD64)]"
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"version": "3.10.13"
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},
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"vscode": {
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"interpreter": {

‎mkdocs.yml‎

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nav:
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- Getting started: index.md
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- Installation: installation_instructions.md
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- Notebook page:
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- Run the model with different options: notebooks/run_model_with_different_options.ipynb
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- Run the model with different dataset: notebooks/run_model_with_different_dataset.ipynb
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- Run the model:
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- Run the model with different options: notebooks/run_model_with_different_options.ipynb
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- Run the model with different dataset: notebooks/run_model_with_different_dataset.ipynb
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- Contributing guide: CONTRIBUTING.md
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- API reference: reference.md
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