diff --git a/CHANGELOG.md b/CHANGELOG.md index 6b449f222..d2c238a09 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -38,6 +38,7 @@ Code freeze date: YYYY-MM-DD ### Removed - `climada.util.earth_engine.py` Google Earth Engine methods did not facilitate direct use of GEE data in CLIMADA. Code was relocated to [climada-snippets](https://github.com/CLIMADA-project/climada-snippets). [#1109](https://github.com/CLIMADA-project/climada_python/pull/1109) - `doc.climada_util_earth_engine.ipynb` Tutorial about GEE not relevant to CLIMADA Core. Tutorial notebook was relocated to [climada-snippets](https://github.com/CLIMADA-project/climada-snippets). [#1109](https://github.com/CLIMADA-project/climada_python/pull/1109) +- `doc.development.Guide_Euler.ipynb` tutorial is not part of the climada docs anymore. For using climada on the ETHZ HPC Cluster Euler, see https://gitlab.ethz.ch/climada/climada-on-euler/ instead. [#1329](https://github.com/CLIMADA-project/climada_python/pull/1329) ## 6.1.0 diff --git a/doc/development/Guide_Euler.ipynb b/doc/development/Guide_Euler.ipynb deleted file mode 100644 index 7d91f270d..000000000 --- a/doc/development/Guide_Euler.ipynb +++ /dev/null @@ -1,506 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Using Climada on the Euler Cluster (ETH internal)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "\n", - "## Access to Euler\n", - "\n", - "See https://scicomp.ethz.ch/wiki/Getting_started_with_clusters for details on how to register at and get started with Euler.\n", - "\n", - "For all steps below, first enter the Cluster via SSH." - ] - }, - { - "cell_type": "markdown", - "metadata": { - "tags": [] - }, - "source": [ - "\n", - "## Installation directory and working directory\n", - "\n", - "Please, get familiar with the various Euler storage options: https://scicomp.ethz.ch/wiki/Storage_systems.
\n", - "As a general rule: use `/cluster/project` for installation and `/cluster/work` for data processing.\n", - "\n", - "For ETH WCR group members, the suggested installation and working directories are `/cluster/project/climate/$USER` and `/cluster/work/climate/$USER` respectively.
\n", - "You may have to create the installation directory:\n", - "\n", - "```bash\n", - "mkdir -p /cluster/project/climate/$USER \\\n", - " /cluster/work/climate/$USER\n", - "```" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Climada installation in a virtual environment" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "\n", - "### 1. Load dependencies\n", - "\n", - "```bash\n", - "module load \\\n", - " gcc/12.2.0 \\\n", - " stack/2024-06 \\\n", - " python/3.11.6 \\\n", - " hdf5/1.14.3 \\\n", - " geos/3.9.1 \\\n", - " sqlite/3.43.2 \\\n", - " eccodes/2.25.0 \\\n", - " gdal/3.6.3 \\\n", - " eth_proxy\n", - "\n", - "module load proj\n", - "module unload proj\n", - "```\n", - "\n", - "(The last two lines may seem odd but they are working around a conficting dependency version situation.)\n", - "\n", - "You need to execute this every time you login to Euler before Climada can be used.\n", - "To safe yourself from doing it manually, append these lines to the ~/.bashrc script, which is automatically executed upon logging in to Euler." - ] - }, - { - "cell_type": "markdown", - "id": "4dad7c27", - "metadata": {}, - "source": [ - "\n", - "### 2. Create and prepare virtual environment\n", - "\n", - "```bash\n", - "envname=climada_env\n", - "\n", - "# create environment\n", - "python -m venv --system-site-packages /cluster/project/climate/$USER/venv/$envname\n", - "\n", - "# acitvate it\n", - ". /cluster/project/climate/$USER/venv/$envname/bin/activate\n", - "\n", - "# install python kernel (to be used in JupyterHub, s.b.)\n", - "python -m ipykernel install --user --name $envname\n", - "```" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 3. Install dependencies\n", - "\n", - "```bash\n", - "pip install \\\n", - " --no-binary fiona \\\n", - " --no-binary rasterio \\\n", - " pyproj==3.7.1 \\\n", - " fiona \\\n", - " rasterio\n", - "\n", - "pip install \\\n", - " 'numpy<2' \\\n", - " netcdf4 \\\n", - " gdal==3.6.3 \\\n", - " geopandas \\\n", - " xarray \\\n", - " cartopy \\\n", - " sparse \\\n", - " salib \\\n", - " pyarrow \\\n", - " xlrd\n", - "```" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### 4. Install Climada\n", - "\n", - "There are two options. Either install from the downloaded repository (option A), or use a particular released version (option B).\n", - "\n", - "#### option A\n", - "```bash\n", - "cd /cluster/project/climate/$USER # or wherever you plan to download the repository\n", - "git clone https://github.com/CLIMADA-project/climada_python.git # unless this has been done before\n", - "cd climada_python\n", - "pip install -e .\n", - "```\n", - "If you need to work with a specific branch of Climada, you can do so by checking out to the target branch `your_branch` by running `git checkout your_branch` after having cloned the Climada repository and before running `pip install -e .`.\n", - "\n", - "#### option B\n", - "\n", - "```bash\n", - "pip install climada=5.0\n", - "```\n", - "\n", - "or whatever version you prefer" - ] - }, - { - "cell_type": "markdown", - "id": "479e0ac2", - "metadata": {}, - "source": [ - "\n", - "### 5. Adjust the Climada configuration\n", - "\n", - "Edit a configuration file according to your needs (see [Configuration](../development/Guide_Configuration.ipynb)).\n", - "Create a climada.conf file e.g., in /cluster/home/$USER/.config with the following content:\n", - "\n", - "```json\n", - "{\n", - " \"local_data\": {\n", - " \"system\": \"/cluster/work/climate/USERNAME/climada/data\",\n", - " \"demo\": \"/cluster/project/climate/USERNAME/climada/data/demo\",\n", - " \"save_dir\": \"/cluster/work/climate/USERNAME/climada/results\"\n", - " }\n", - "}\n", - "```\n", - "(Replace USERNAME with your nethz-id.)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "\n", - "### 6. Test the installation\n", - "\n", - "Check installation in login node:\n", - "\n", - "```bash\n", - "python -m unittest climada.engine.test.test_impact_calc\n", - "```\n", - "\n", - "This should prompt the usual \"`OK`\" in the end.\n", - "Once that succeeded you may want to test the installation also in a compute node, just for the sake of it:\n", - "\n", - "```bash\n", - "sbatch --wrap=\"python -m unittest climada.engine.test.test_impact_calc\"\n", - "```\n", - "\n", - "Look for the \"`OK`\" in the hereby created `slurm-[XXXXXXX].out` file\n", - "\n", - "Please see the docs at https://slurm.schedmd.com/ on how to use the `slurm` batch system\n", - "and the Wiki https://scicomp.ethz.ch/wiki/Transition_from_LSF_to_Slurm for a mapping of `lsf` commands to their `slurm` equivalents." - ] - }, - { - "cell_type": "markdown", - "id": "e5c90bff", - "metadata": {}, - "source": [ - "### 7. Optional: Install Climada Petals\n", - "\n", - "To install Climada Petals, repeat the steps described in step 4A, but replacing the climada_python with the climada_petals repository:\n", - "```bash\n", - "cd /cluster/project/climate/$USER # or wherever you plan to download the repository\n", - "git clone https://github.com/CLIMADA-project/climada_petals.git # unless this has been done before\n", - "cd climada_petals\n", - "pip install -e .\n", - "```" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "\n", - "## Run a Jupyter Notebook on Euler" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "It is possible to run a Jupyter Notebook on Euler within a JupytherHub instance running as an interactive slurm job.\n", - "See the documentation https://scicomp.ethz.ch/wiki/JupyterHub.\n", - "\n", - "For using climada inside the jupyter notebook, you need to create a customized `jupyterlabrc` file by running the following lines:\n", - "\n", - "```bash\n", - "mkdir -p ~/.config/euler/jupyterhub\n", - "cat > ~/.config/euler/jupyterhub/jupyterlabrc < Using fixtures for writing tests Guide_Review - Guide_Euler Authors <../misc/AUTHORS>