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Merge pull request #93 from EcoExtreML/add_doc_nb
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Add an example notebook to run the model with global data
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SarahAlidoost authored Feb 8, 2024
2 parents e97a9f6 + 2309bb7 commit 9202ad4
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4 changes: 2 additions & 2 deletions docs/installation_instructions.md
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Expand Up @@ -23,7 +23,7 @@ installed there. See [Install PyStemmusScope](#install-pystemmusscope).

## On your own machine

Choose how do you want to run the model, see [Run the model](notebooks/run_model_in_notebook.ipynb).
Choose how do you want to run the model, see [Run the model](notebooks/run_model_on_different_infra.ipynb).

## Install PyStemmusScope

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JupyterLab will open automatically in your browser. Now, you can run the
notebook
[run_model_in_notebook.ipynb](https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing/blob/main/docs/notebooks/run_model_in_notebook.ipynb).
[run_model_on_different_infra.ipynb](https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing/blob/main/docs/notebooks/run_model_on_different_infra.ipynb).

## Install MATLAB Runtime

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"cell_type": "markdown",
"metadata": {},
"source": [
"# Running the STEMMUS_SCOPE model\n",
"## Which options are available?\n",
"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",
"# Running the STEMMUS_SCOPE model on a system\n",
"\n",
"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`. Depending on your system (OS, Matlab availability, etc.), there are a few ways you can run the model. Choose how do you want to run the model:\n",
"\n",
"\n",
"[**Executable file**](#1-using-executable-file)\n",
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"cell_type": "markdown",
"metadata": {},
"source": [
"Perform <echo $DISPLAY> in a terminal in the Remote Desktop (of Crib Platform), and check the output (should be similar to :1.0 ). Then execute the following line accordingly."
"&emsp; If you are on CRIB, to use Jupyter interface and MATLAB license manager at the same time, first perform <echo $DISPLAY> in a terminal in the Remote Desktop of Crib Platform, and check the output which should be similar to :1.0 . Then execute the following line accordingly."
]
},
{
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"metadata": {},
"outputs": [],
"source": [
"# For CRIB users\n",
"%env DISPLAY=:1.0"
]
},
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],
"metadata": {
"kernelspec": {
"display_name": "pyss_octave",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:50:36) [MSC v.1929 64 bit (AMD64)]"
"version": "3.10.13"
},
"vscode": {
"interpreter": {
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