Final updates to Dockerfiles

TESTgroup-BNL · Jun 14, 2023 · bcbccfe · bcbccfe
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diff --git a/arm64_docker_builds.txt b/arm64_docker_builds.txt
@@ -33,20 +33,21 @@ docker buildx create --name multibuilder --use
 # Step 2. Change to local simulation_containers git repo directory
 cd /Users/sserbin/Data/GitHub/simulation_containers
 
-# Step 3a. Build an ARM64 compliant version of the ELM docker. This is for local builds only
-#docker buildx build --push -t fasstsimulation/elm-builds:elm_v2-for-ngee_arm64 --no-cache  \
-#--platform linux/arm64 -f docker/elm/elm_v2-for-ngee/Dockerfile_arm64 .
-
-# Step 3b. Build multi-arch ELM
+# Step 3a. Build multi-arch ELM
 docker buildx build --push -t serbinsh/ngeearctic_elm_containers:elm_v2-for-ngee_multiarch --no-cache  \
 --platform linux/amd64,linux/arm64 -f docker/elm/elm_v2-for-ngee/Dockerfile_multiarch .
 
-# Step 3c. Build AMD64 and ARM64 compliant version of the serial lib ELM docker. This is for local builds only
-docker buildx build --push -t fasstsimulation/elm-builds:elm_v2-for-ngee-serial_multiarch --no-cache  \
+# Step 3b. Build AMD64 and ARM64 compliant version of the serial lib ELM docker. This is for local builds only
+docker buildx build --push -t serbinsh/ngeearctic_elm_containers:elm_v2-for-ngee-serial_multiarch --no-cache  \
 --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
 # Step 1. Create a new docker builder  (only needs to be done once)
 docker buildx create --name multibuilder --use

diff --git a/docker/jupyter/Dockerfile_elmlab_3.3.2 b/docker/jupyter/Dockerfile_elmlab_3.3.2
@@ -6,56 +6,50 @@
 # ----------------------------------------------------------------------
 
 # grab the jupyter-lab container
-FROM fasstsimulation/fasst_simulation_tools:fasst_jupyterlab_3.3.2
+FROM serbinsh/ngeearctic_elm_containers:ngeearctic_jupyterlab_3.3.2
 LABEL maintainer.name="Shawn P. Serbin" \
       maintainer.email="[email protected]" \
       author.name="Shawn P. Serbin" \
       author.email="[email protected]" \
       description="ELM Analysis Jupyter-Lab Container"
 
-ENV TOOLS_REPOSITORY_RAW_URL=https://raw.githubusercontent.com/FASSt-simulation/fasst_simulation_tools
+ENV REPOSITORY_RAW_URL=https://raw.githubusercontent.com/TESTgroup-BNL/ngeearctic_elm_containers
 
 # Copy in example plotting scripts for use with model output
 # add Ben Sulman's matplotlib plotting ascetics defaults
 RUN cd "/home/${NB_USER}/scripts" \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/elm_scripts/plotting/plot_KG64_ELM_output.py \
+   && wget $REPOSITORY_RAW_URL/main/scripts/elm_scripts/plotting/plot_KG64_ELM_output.py \
    && chmod 775 plot_KG64_ELM_output.py \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/elm_scripts/plotting/plot_ELM_output.py \
+   && wget $REPOSITORY_RAW_URL/main/scripts/elm_scripts/plotting/plot_ELM_output.py \
    && chmod 775 plot_ELM_output.py \
    && cd "/home/${NB_USER}" \
    && mkdir -p "/home/${NB_USER}/.config/matplotlib" \
    && cd "/home/${NB_USER}/.config/matplotlib" \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/elm_scripts/plotting/matplotlibrc \
+   && wget $REPOSITORY_RAW_URL/main/scripts/elm_scripts/plotting/matplotlibrc \
    && cd "/home/${NB_USER}" \
    && fix-permissions "/home/${NB_USER}"
 
 # Add example jupyter notebook scripts here
 RUN cd "/home/${NB_USER}/scripts" \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_variable.ipynb \
+   && wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_variable.ipynb \
    && chmod 775 plot_ELM_variable.ipynb \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_variable_2D.ipynb \
+   && wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_variable_2D.ipynb \
    && chmod 775 plot_ELM_variable_2D.ipynb \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_output.ipynb \
+   && wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_output.ipynb \
    && chmod 775 plot_ELM_output.ipynb \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_radiation.ipynb \
+   && wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_radiation.ipynb \
    && chmod 775 plot_ELM_radiation.ipynb \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_moisture_temperature.ipynb \
+   && wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_moisture_temperature.ipynb \
    && chmod 775 plot_moisture_temperature.ipynb \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_soil_BGC.ipynb \
+   && wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_soil_BGC.ipynb \
    && chmod 775 plot_soil_BGC.ipynb \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_veg_data.ipynb \
+   && wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_veg_data.ipynb \
    && chmod 775 plot_veg_data.ipynb \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_ensembles.ipynb \
+   && wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_ensembles.ipynb \
    && chmod 775 plot_ELM_ensembles.ipynb \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_compare_cases.ipynb \
+   && wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_compare_cases.ipynb \
    && chmod 775 plot_ELM_compare_cases.ipynb
 
-# add back in if we want examples showing how to run the model from within a notebook
-#   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/run_ELM_KG64_basic.ipynb \
-#   && chmod 775 run_ELM_KG64_basic.ipynb \
-#   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/run_plot_KG64_ELM_output.ipynb \
-#   && chmod 775 run_plot_KG64_ELM_output.ipynb
-
 # Setup default user, when enter docker container
 USER ${NB_UID}
 WORKDIR "${HOME}"

diff --git a/docker/jupyter/Dockerfile_elmlab_gee_3.3.2 b/docker/jupyter/Dockerfile_elmlab_gee_3.3.2
@@ -6,59 +6,53 @@
 # ----------------------------------------------------------------------
 
 # grab the jupyter-lab container
-FROM fasstsimulation/fasst_simulation_tools:fasst_jupyterlab_3.3.2_gee
+FROM serbinsh/ngeearctic_elm_containers:ngeearctic_jupyterlab_3.3.2_gee
 LABEL maintainer.name="Shawn P. Serbin" \
       maintainer.email="[email protected]" \
       author.name="Shawn P. Serbin" \
       author.email="[email protected]" \
       description="ELM Analysis Jupyter-Lab Container"
 
-ENV TOOLS_REPOSITORY_RAW_URL=https://raw.githubusercontent.com/FASSt-simulation/fasst_simulation_tools
+ENV REPOSITORY_RAW_URL=https://raw.githubusercontent.com/TESTgroup-BNL/ngeearctic_elm_containers
 
 # Copy in example plotting scripts for use with model output
 # add Ben Sulman's matplotlib plotting ascetics defaults
 RUN cd "/home/${NB_USER}/scripts" \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/elm_scripts/plotting/plot_KG64_ELM_output.py \
+   && wget $REPOSITORY_RAW_URL/main/scripts/elm_scripts/plotting/plot_KG64_ELM_output.py \
    && chmod 775 plot_KG64_ELM_output.py \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/elm_scripts/plotting/plot_ELM_output.py \
+   && wget $REPOSITORY_RAW_URL/main/scripts/elm_scripts/plotting/plot_ELM_output.py \
    && chmod 775 plot_ELM_output.py \
    && cd "/home/${NB_USER}" \
    && mkdir -p "/home/${NB_USER}/.config/matplotlib" \
    && cd "/home/${NB_USER}/.config/matplotlib" \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/elm_scripts/plotting/matplotlibrc \
+   && wget $REPOSITORY_RAW_URL/main/scripts/elm_scripts/plotting/matplotlibrc \
    && cd "/home/${NB_USER}" \
    && fix-permissions "/home/${NB_USER}"
 
 # Add example jupyter notebook scripts here
 RUN cd "/home/${NB_USER}/scripts" \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_variable.ipynb \
+   && wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_variable.ipynb \
    && chmod 775 plot_ELM_variable.ipynb \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_variable_2D.ipynb \
+   && wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_variable_2D.ipynb \
    && chmod 775 plot_ELM_variable_2D.ipynb \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_output.ipynb \
+   && wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_output.ipynb \
    && chmod 775 plot_ELM_output.ipynb \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_radiation.ipynb \
+   && wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_radiation.ipynb \
    && chmod 775 plot_ELM_radiation.ipynb \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_moisture_temperature.ipynb \
+   && wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_moisture_temperature.ipynb \
    && chmod 775 plot_moisture_temperature.ipynb \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_soil_BGC.ipynb \
+   && wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_soil_BGC.ipynb \
    && chmod 775 plot_soil_BGC.ipynb \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_veg_data.ipynb \
+   && wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_veg_data.ipynb \
    && chmod 775 plot_veg_data.ipynb \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_ensembles.ipynb \
+   && wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_ensembles.ipynb \
    && chmod 775 plot_ELM_ensembles.ipynb \
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_compare_cases.ipynb \
+   && wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_compare_cases.ipynb \
    && chmod 775 plot_ELM_compare_cases.ipynb \
    # GEE notebooks
-   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_vs_GEE_data.ipynb \
+   && wget $REPOSITORY_RAW_URL/main/notebooks/ngeearctic/plot_ELM_vs_GEE_data.ipynb \
    && chmod 775 plot_ELM_vs_GEE_data.ipynb
 
-# add back in if we want examples showing how to run the model from within a notebook
-#   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/run_ELM_KG64_basic.ipynb \
-#   && chmod 775 run_ELM_KG64_basic.ipynb \
-#   && wget $TOOLS_REPOSITORY_RAW_URL/main/notebooks/ngeearctic/run_plot_KG64_ELM_output.ipynb \
-#   && chmod 775 run_plot_KG64_ELM_output.ipynb
-
 # Setup default user, when enter docker container
 USER ${NB_UID}
 WORKDIR "${HOME}"

diff --git a/docker/jupyter/README.txt b/docker/jupyter/README.txt
@@ -2,10 +2,18 @@
 
 Building dual-platform jupyter-lab containers for analyzing ELM output
 
-# 1. First build the main jupyter-lab container, e.g. Jupyter-Lab 3.3.2. Run this within the repo directory
+# 1a. First build the main jupyter-lab container, e.g. Jupyter-Lab 3.3.2. Run this within the repo directory
 docker buildx build --push -t serbinsh/ngeearctic_elm_containers:ngeearctic_jupyterlab_3.3.2 --no-cache  \
 --platform linux/amd64,linux/arm64 -f docker/jupyter/Dockerfile_lab_3.3.2 .
 
-# 2. Second build the elmlab container which includes all of the example notebooks. Run this within the repo directorys
+# 1b. First build the main jupyter-lab container w/ GEE, e.g. Jupyter-Lab 3.3.2. Run this within the repo directory
+docker buildx build --push -t serbinsh/ngeearctic_elm_containers:ngeearctic_jupyterlab_3.3.2_gee --no-cache  \
+--platform linux/amd64,linux/arm64 -f docker/jupyter/Dockerfile_lab_gee_3.3.2 .
+
+# 2a. Second build the elmlab container which includes all of the example notebooks. Run this within the repo directorys
 docker buildx build --push -t serbinsh/ngeearctic_elm_containers:elmlab_3.3.2 --no-cache  \
---platform linux/amd64,linux/arm64 -f docker/jupyter/Dockerfile_elmlab_3.3.2 .
+--platform linux/amd64,linux/arm64 -f docker/jupyter/Dockerfile_elmlab_3.3.2 .
+
+# 2b. Second build the elmlab container w/ GEE which includes all of the example notebooks. Run this within the repo directorys
+docker buildx build --push -t serbinsh/ngeearctic_elm_containers:elmlab_gee_3.3.2 --no-cache  \
+--platform linux/amd64,linux/arm64 -f docker/jupyter/Dockerfile_elmlab_gee_3.3.2 .