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Shawn P. Serbin
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Final updates to Dockerfiles
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‎arm64_docker_builds.txt‎

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@@ -33,20 +33,21 @@ docker buildx create --name multibuilder --use
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# Step 2. Change to local simulation_containers git repo directory
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cd /Users/sserbin/Data/GitHub/simulation_containers
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# Step 3a. Build an ARM64 compliant version of the ELM docker. This is for local builds only
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#docker buildx build --push -t fasstsimulation/elm-builds:elm_v2-for-ngee_arm64 --no-cache \
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#--platform linux/arm64 -f docker/elm/elm_v2-for-ngee/Dockerfile_arm64 .
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# Step 3b. Build multi-arch ELM
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# Step 3a. Build multi-arch ELM
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docker buildx build --push -t serbinsh/ngeearctic_elm_containers:elm_v2-for-ngee_multiarch --no-cache \
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--platform linux/amd64,linux/arm64 -f docker/elm/elm_v2-for-ngee/Dockerfile_multiarch .
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# Step 3c. Build AMD64 and ARM64 compliant version of the serial lib ELM docker. This is for local builds only
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docker buildx build --push -t fasstsimulation/elm-builds:elm_v2-for-ngee-serial_multiarch --no-cache \
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# Step 3b. Build AMD64 and ARM64 compliant version of the serial lib ELM docker. This is for local builds only
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docker buildx build --push -t serbinsh/ngeearctic_elm_containers:elm_v2-for-ngee-serial_multiarch --no-cache \
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--platform linux/amd64,linux/arm64 -f docker/elm/elm_v2-for-ngee/Dockerfile_serial_multiarch .
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#### Build a multi-platform version of the jupyter-lab simulation_container
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# Step 1. Create a new docker builder (only needs to be done once)
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docker buildx create --name multibuilder --use

‎docker/jupyter/Dockerfile_elmlab_3.3.2‎

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# ----------------------------------------------------------------------
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# grab the jupyter-lab container
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FROM fasstsimulation/fasst_simulation_tools:fasst_jupyterlab_3.3.2
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FROM serbinsh/ngeearctic_elm_containers:ngeearctic_jupyterlab_3.3.2
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LABEL maintainer.name="Shawn P. Serbin" \
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maintainer.email="[email protected]" \
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author.name="Shawn P. Serbin" \
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author.email="[email protected]" \
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description="ELM Analysis Jupyter-Lab Container"
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ENV TOOLS_REPOSITORY_RAW_URL=https://raw.githubusercontent.com/FASSt-simulation/fasst_simulation_tools
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ENV REPOSITORY_RAW_URL=https://raw.githubusercontent.com/TESTgroup-BNL/ngeearctic_elm_containers
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# Copy in example plotting scripts for use with model output
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# add Ben Sulman's matplotlib plotting ascetics defaults
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RUN cd "/home/${NB_USER}/scripts" \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/elm_scripts/plotting/plot_KG64_ELM_output.py \
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&& wget $REPOSITORY_RAW_URL/main/scripts/elm_scripts/plotting/plot_KG64_ELM_output.py \
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&& chmod 775 plot_KG64_ELM_output.py \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/elm_scripts/plotting/plot_ELM_output.py \
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&& wget $REPOSITORY_RAW_URL/main/scripts/elm_scripts/plotting/plot_ELM_output.py \
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&& chmod 775 plot_ELM_output.py \
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&& cd "/home/${NB_USER}" \
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&& mkdir -p "/home/${NB_USER}/.config/matplotlib" \
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&& cd "/home/${NB_USER}/.config/matplotlib" \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/elm_scripts/plotting/matplotlibrc \
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&& wget $REPOSITORY_RAW_URL/main/scripts/elm_scripts/plotting/matplotlibrc \
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&& cd "/home/${NB_USER}" \
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&& fix-permissions "/home/${NB_USER}"
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# Add example jupyter notebook scripts here
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RUN cd "/home/${NB_USER}/scripts" \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_variable.ipynb \
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&& wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_variable.ipynb \
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&& chmod 775 plot_ELM_variable.ipynb \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_variable_2D.ipynb \
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&& wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_variable_2D.ipynb \
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&& chmod 775 plot_ELM_variable_2D.ipynb \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_output.ipynb \
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&& wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_output.ipynb \
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&& chmod 775 plot_ELM_output.ipynb \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_radiation.ipynb \
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&& wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_radiation.ipynb \
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&& chmod 775 plot_ELM_radiation.ipynb \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_moisture_temperature.ipynb \
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&& wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_moisture_temperature.ipynb \
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&& chmod 775 plot_moisture_temperature.ipynb \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_soil_BGC.ipynb \
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&& wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_soil_BGC.ipynb \
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&& chmod 775 plot_soil_BGC.ipynb \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_veg_data.ipynb \
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&& wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_veg_data.ipynb \
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&& chmod 775 plot_veg_data.ipynb \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_ensembles.ipynb \
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&& wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_ensembles.ipynb \
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&& chmod 775 plot_ELM_ensembles.ipynb \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_compare_cases.ipynb \
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&& wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_compare_cases.ipynb \
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&& chmod 775 plot_ELM_compare_cases.ipynb
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# add back in if we want examples showing how to run the model from within a notebook
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# && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/run_ELM_KG64_basic.ipynb \
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# && chmod 775 run_ELM_KG64_basic.ipynb \
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# && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/run_plot_KG64_ELM_output.ipynb \
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# && chmod 775 run_plot_KG64_ELM_output.ipynb
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# Setup default user, when enter docker container
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USER ${NB_UID}
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WORKDIR "${HOME}"

‎docker/jupyter/Dockerfile_elmlab_gee_3.3.2‎

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# ----------------------------------------------------------------------
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# grab the jupyter-lab container
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FROM fasstsimulation/fasst_simulation_tools:fasst_jupyterlab_3.3.2_gee
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FROM serbinsh/ngeearctic_elm_containers:ngeearctic_jupyterlab_3.3.2_gee
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LABEL maintainer.name="Shawn P. Serbin" \
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maintainer.email="[email protected]" \
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author.name="Shawn P. Serbin" \
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author.email="[email protected]" \
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description="ELM Analysis Jupyter-Lab Container"
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ENV TOOLS_REPOSITORY_RAW_URL=https://raw.githubusercontent.com/FASSt-simulation/fasst_simulation_tools
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ENV REPOSITORY_RAW_URL=https://raw.githubusercontent.com/TESTgroup-BNL/ngeearctic_elm_containers
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# Copy in example plotting scripts for use with model output
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# add Ben Sulman's matplotlib plotting ascetics defaults
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RUN cd "/home/${NB_USER}/scripts" \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/elm_scripts/plotting/plot_KG64_ELM_output.py \
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&& wget $REPOSITORY_RAW_URL/main/scripts/elm_scripts/plotting/plot_KG64_ELM_output.py \
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&& chmod 775 plot_KG64_ELM_output.py \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/elm_scripts/plotting/plot_ELM_output.py \
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&& wget $REPOSITORY_RAW_URL/main/scripts/elm_scripts/plotting/plot_ELM_output.py \
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&& chmod 775 plot_ELM_output.py \
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&& cd "/home/${NB_USER}" \
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&& mkdir -p "/home/${NB_USER}/.config/matplotlib" \
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&& cd "/home/${NB_USER}/.config/matplotlib" \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/elm_scripts/plotting/matplotlibrc \
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&& wget $REPOSITORY_RAW_URL/main/scripts/elm_scripts/plotting/matplotlibrc \
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&& cd "/home/${NB_USER}" \
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&& fix-permissions "/home/${NB_USER}"
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# Add example jupyter notebook scripts here
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RUN cd "/home/${NB_USER}/scripts" \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_variable.ipynb \
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&& wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_variable.ipynb \
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&& chmod 775 plot_ELM_variable.ipynb \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_variable_2D.ipynb \
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&& wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_variable_2D.ipynb \
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&& chmod 775 plot_ELM_variable_2D.ipynb \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_output.ipynb \
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&& wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_output.ipynb \
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&& chmod 775 plot_ELM_output.ipynb \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_radiation.ipynb \
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&& wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_radiation.ipynb \
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&& chmod 775 plot_ELM_radiation.ipynb \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_moisture_temperature.ipynb \
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&& wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_moisture_temperature.ipynb \
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&& chmod 775 plot_moisture_temperature.ipynb \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_soil_BGC.ipynb \
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&& wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_soil_BGC.ipynb \
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&& chmod 775 plot_soil_BGC.ipynb \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_veg_data.ipynb \
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&& wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_veg_data.ipynb \
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&& chmod 775 plot_veg_data.ipynb \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_ensembles.ipynb \
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&& wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_ensembles.ipynb \
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&& chmod 775 plot_ELM_ensembles.ipynb \
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_compare_cases.ipynb \
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&& wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_compare_cases.ipynb \
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&& chmod 775 plot_ELM_compare_cases.ipynb \
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# GEE notebooks
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&& wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_vs_GEE_data.ipynb \
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&& wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_vs_GEE_data.ipynb \
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&& chmod 775 plot_ELM_vs_GEE_data.ipynb
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# add back in if we want examples showing how to run the model from within a notebook
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# && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/run_ELM_KG64_basic.ipynb \
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# && chmod 775 run_ELM_KG64_basic.ipynb \
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# && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/run_plot_KG64_ELM_output.ipynb \
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# && chmod 775 run_plot_KG64_ELM_output.ipynb
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# Setup default user, when enter docker container
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USER ${NB_UID}
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WORKDIR "${HOME}"

‎docker/jupyter/README.txt‎

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Building dual-platform jupyter-lab containers for analyzing ELM output
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# 1. First build the main jupyter-lab container, e.g. Jupyter-Lab 3.3.2. Run this within the repo directory
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# 1a. First build the main jupyter-lab container, e.g. Jupyter-Lab 3.3.2. Run this within the repo directory
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docker buildx build --push -t serbinsh/ngeearctic_elm_containers:ngeearctic_jupyterlab_3.3.2 --no-cache \
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--platform linux/amd64,linux/arm64 -f docker/jupyter/Dockerfile_lab_3.3.2 .
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# 2. Second build the elmlab container which includes all of the example notebooks. Run this within the repo directorys
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# 1b. First build the main jupyter-lab container w/ GEE, e.g. Jupyter-Lab 3.3.2. Run this within the repo directory
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docker buildx build --push -t serbinsh/ngeearctic_elm_containers:ngeearctic_jupyterlab_3.3.2_gee --no-cache \
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--platform linux/amd64,linux/arm64 -f docker/jupyter/Dockerfile_lab_gee_3.3.2 .
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# 2a. Second build the elmlab container which includes all of the example notebooks. Run this within the repo directorys
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docker buildx build --push -t serbinsh/ngeearctic_elm_containers:elmlab_3.3.2 --no-cache \
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--platform linux/amd64,linux/arm64 -f docker/jupyter/Dockerfile_elmlab_3.3.2 .
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--platform linux/amd64,linux/arm64 -f docker/jupyter/Dockerfile_elmlab_3.3.2 .
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# 2b. Second build the elmlab container w/ GEE which includes all of the example notebooks. Run this within the repo directorys
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docker buildx build --push -t serbinsh/ngeearctic_elm_containers:elmlab_gee_3.3.2 --no-cache \
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--platform linux/amd64,linux/arm64 -f docker/jupyter/Dockerfile_elmlab_gee_3.3.2 .

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