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jupyter_env_setup.sh to set up working environment on cloud
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‎ECCO-ACCESS/Cloud_access_to_ECCO_datasets/jupyter_env_setup.sh‎

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#!/bin/bash
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# # Shell script for setting up conda, jupyter, essential Python packages on an AWS EC2 instance.
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# # Assumes that the ECCO-v4-Python-Tutorial Github repository has already been downloaded using:
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# sudo dnf update -y
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# sudo dnf install git -y
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# cd ~
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# git clone https://github.com/ECCO-GROUP/ECCO-v4-Python-Tutorial.git
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# # Then run this script:
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# sudo chmod 755 ~/ECCO-v4-Python-Tutorial/ECCO-ACCESS/Cloud_access_to_ECCO_datasets/jupyter_env_setup.sh
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# ~/ECCO-v4-Python-Tutorial/ECCO-ACCESS/Cloud_access_to_ECCO_datasets/jupyter_env_setup.sh
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# # Start body of script
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# install wget
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sudo dnf install wget -y
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# retrieve and install miniforge in /opt/
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# assuming EBS volume is already attached to instance
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mkdir -p /tmp
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wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh" -O /tmp/Miniforge3.sh
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sudo bash /tmp/Miniforge3.sh -b -p /opt/conda
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sudo chmod -R a+w /opt/conda
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source "/opt/conda/etc/profile.d/conda.sh"
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source "/opt/conda/etc/profile.d/mamba.sh"
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red_start='\033[0;31m'
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nocolor_start='\033[0m+'
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echo -e "${red_start}Completed Miniforge3 installation${nocolor_start}"
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# add conda and mamba to path
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mamba init
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# set paths to environment and package directories
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printf '\n# set conda environment and package directories' >> ~/.bashrc
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printf '\nexport CONDA_ENVS_PATH=/opt/conda/envs' >> ~/.bashrc
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printf '\nexport CONDA_PKGS_DIRS=/opt/conda/pkgs' >> ~/.bashrc
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source ~/.bashrc
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# create jupyter environment under /opt/conda/envs/
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# (in EBS storage to save space in home directory)
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mamba create --name jupyter python=3.8 -y
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echo -e "${red_start}Created jupyter environment${nocolor_start}"
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# install python packages (using mamba) in jupyter environment
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mamba activate jupyter
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mamba install requests tqdm numpy pandas -y
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mamba install xorg-libice libexpat libevent -y
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mamba install nspr alsa-lib libogg libpq -y
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mamba install xorg-renderproto xorg-xf86vidmodeproto graphite2 expat -y
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mamba install libgpg-error dbus -y
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mamba install libflac gettext -y
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mamba install xcb-util-wm xorg-libx11 xcb-util-image -y
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mamba install xkeyboard-config -y
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mamba install libxkbcommon fonts-conda-forge font-ttf-ubuntu gstreamer zlib -y
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mamba install xorg-xextproto libpng attr mpg123 -y
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mamba install pixman libvorbis glib-tools -y
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mamba install libsystemd0 xcb-util-keysyms xorg-libxrender libllvm15 -y
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mamba install font-ttf-dejavu-sans-mono pcre2 font-ttf-inconsolata font-ttf-source-code-pro -y
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mamba install lame nss xorg-xproto pthread-stubs xorg-libxdmcp -y
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mamba install libgcrypt xorg-libsm xorg-libxext fonts-conda-ecosystem xorg-kbproto mysql-libs -y
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mamba install fontconfig libjpeg-turbo xcb-util-renderutil -y
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mamba install glib -y
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mamba install freetype libcap libcups libopus -y
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mamba install gst-plugins-base mysql-common xcb-util -y
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mamba install cairo -y
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mamba install libsndfile harfbuzz xorg-libxau -y
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mamba install libglib libxcb -y
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mamba install qt-main -y
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mamba install pyqt -y
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mamba install matplotlib -y
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mamba install netcdf4 -y
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mamba install scipy -y
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mamba install geos -y
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mamba install proj pyproj -y
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mamba install cartopy -y
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mamba install notebook -y
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mamba install progressbar -y
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mamba install gsw -y
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# install remaining packages using pip
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# (mamba installs tend to get killed on t2.micro)
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pip install dask
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pip install xarray
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pip install jupyterlab
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pip install s3fs
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pip install ecco_v4_py
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echo -e "${red_start}Completed Python package installations${nocolor_start}"
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# NASA Earthdata authentication
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# check if credentials are already archived in ~/.netrc, and if not then prompt the user for them
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earthdata_cred_stored=0
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if [ -f ~/.netrc ]; then
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if grep -q "machine urs.earthdata.nasa.gov" ~/.netrc; then
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earthdata_cred_stored=1
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fi
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fi
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if [ $earthdata_cred_stored -eq 0 ]; then
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if [ -f ~/.netrc ]; then sudo chmod 600 ~/.netrc; fi
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read -p 'NASA Earthdata username: ' uservar
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read -sp 'NASA Earthdata password: ' passvar
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echo -e "machine urs.earthdata.nasa.gov\n login ${uservar}\n password ${passvar}\n" >> ~/.netrc
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fi
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sudo chmod 400 ~/.netrc
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echo -e "${red_start}Set up NASA Earthdata authentication${nocolor_start}"
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# set up Jupyter lab, to be opened in a tmux session using password
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PW="$(python3 -c 'from notebook.auth import passwd; import getpass; print(passwd(getpass.getpass(), algorithm="sha256"))')"
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jlab_start="\'jupyter lab --no-browser --autoreload --port=9889 --ip=\'127.0.0.1\' --NotebookApp.token=\'\' --NotebookApp.password=\"$PW\" --notebook-dir=\"~/ECCO-v4-Python-Tutorial/Tutorials_as_Jupyter_Notebooks\" \'"
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tmux new-session -d -s jupyterlab ${jlab_start}
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blue_start='\033[0;34m'
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echo -e "${red_start}Started Jupyter lab in tmux session jupyterlab"
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echo -e "${red_start}Access from your local machine in a browser window at"
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echo -e "${blue_start}http://127.0.0.1:9889/"
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echo -e "${red_start}tmux session can be accessed with"
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echo -e "${blue_start}tmux -a -t jupyterlab"
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echo -e "${red_start}and terminated with"
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echo -e "${blue_start}tmux kill-ses -t jupyterlab"

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