Task/dsapp 1 - ADCIRC Interactive VM

applications/adcirc-interactive/Dockerfile

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+FROM jupyter/minimal-notebook:latest AS base
+
+USER root
+WORKDIR /
+LABEL maintainer="TACC-Carlos D. <[email protected]>"
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && \
+    apt-get install -y \
+        git \
+        wget \
+        mpich \
+        ghostscript \
+        graphicsmagick \
+        gdal-bin \
+        ffmpeg \
+        libxt-dev \
+        libxaw7-dev \
+        libhdf5-dev \
+        libnetcdff-dev \
+        cmake \
+        ca-certificates \
+        gpg \
+        git-lfs \
+        ssh \
+        libboost-dev \
+        libxml2-dev \
+        libjpeg-dev \
+        python3 \
+        sshfs \
+        netcdf-bin \
+        libopenmpi-dev \
+        bc \
+        gfortran \
+        perl \
+        gcc \
+        g++ \
+        tar \
+        gzip \
+        zlib1g-dev \
+        libcurl4-openssl-dev \
+        software-properties-common \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+FROM base AS figuregen_data
+
+WORKDIR /
+LABEL maintainer="TACC-Carlos D. <[email protected]>"
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN mkdir -p /data
+RUN wget https://fossies.org/linux/misc/GMT/gmt-4.5.18-src.tar.bz2 \
+    && tar -xf gmt-4.5.18-src.tar.bz2 \
+    && cd gmt-4.5.18/ \
+    && ./configure --enable-netcdf \
+    && make \
+    && make install-gmt \
+    && make install-data \
+    && make clean \
+    && wget https://fossies.org/linux/misc/GMT/gshhg-gmt-2.3.7.tar.gz \
+    && tar -zxvf gshhg-gmt-2.3.7.tar.gz \
+    && cd share \
+    && mkdir coast \
+    && cd coast \
+    && mv /gmt-4.5.18/gshhg-gmt-2.3.7/* .
+
+FROM figuregen_data AS figuregen_build
+
+COPY --from=figuregen_data /gmt-4.5.18 /usr/local/gmt-4.5.18
+RUN git clone https://github.com/cdelcastillo21/FigureGen.git /figuregen 
+
+RUN cd figuregen \
+    && ls \
+    && mkdir build \
+    && cd build \
+    && cmake .. -DCMAKE_Fortran_COMPILER=gfortran -DUSE_MPI=OFF -DUSE_NETCDF=ON -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch" \
+    && make \
+    && cp figuregen /usr/local/bin/figuregen-serial \
+    && cd .. && rm -rf build \
+    && mkdir build \
+    && cd build \
+    && cmake .. -DCMAKE_Fortran_COMPILER=mpif90 -DUSE_MPI=ON -DUSE_NETCDF=ON -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch" \
+    && make \
+    && cp figuregen /usr/local/bin/figuregen \
+    && cp -r /figuregen/autotest /usr/local/share/figuregen-tests
+
+ENV PATH="/figuregen/build:/gmt-4.5.18/bin:${PATH}"
+
+FROM base AS adcirc_build
+
+COPY adcirc_compile.sh /usr/local/bin/adcirc_compile
+RUN chmod +x /usr/local/bin/adcirc_compile && \
+    adcirc_compile v56.0.2 https://github.com/adcirc/adcirc 1 /usr/local/src/adcirc-v56.0.2
+
+FROM base AS jupyter_lab_base
+
+RUN mamba install -c conda-forge -y \
+        jupyterlab=4.1.8 \
+		ipykernel \
+		nodejs \
+		flake8 \
+		black \
+		isort \
+		autopep8 \
+		ipympl \
+		yapf \
+		jupyter_bokeh \
+		jupyterlab-lsp \
+		python-lsp-server  \
+		jupyterlab-git \
+		jupyterlab-spellchecker \
+		jlab-enhanced-cell-toolbar \
+		curl && \
+	mamba clean --all -f -y && \
+    pip install \
+		ipympl \
+		jupyterlab_code_formatter \
+        jupyterlab_favorites \
+		jupyterlab-link-share  \
+		jupyterlab_recents \
+        jupyter-collaboration \
+		jupyterlab_theme_solarized_dark 
+		# jupyterlab-vim \
+		# jupyterlab-topbar  \
+		# jupyterlab-topbar-text \
+
+RUN jupyter lab build
+
+
+FROM jupyter_lab_base AS python_kernels
+
+RUN rm -rf /home/jovyan/.cache 
+USER jovyan
+WORKDIR /home/jovyan
+
+# Python wants to build from 
+SHELL ["/bin/bash", "-o", "pipefail", "-c", "-i"]
+RUN mamba create --name kalpana -y -c conda-forge \
+        python=3.11 \
+        ipykernel \
+        fiona \
+        cmocean \
+        matplotlib \
+        numpy \
+        geopandas \
+        pandas \
+        shapely \
+        tqdm \
+        netCDF4 \
+        simplekml \
+        scipy \
+        pathlib \
+        rioxarray \
+        loguru \
+        pyproj \
+        cartopy && \
+	mamba clean --all -f -y && \
+    conda activate kalpana && \
+    ipython kernel install --user --name=kalpana && \
+    git clone https://github.com/cdelcastillo21/TACC-Kalpana Kalpana && \
+    cd Kalpana && \
+    pip install -e .
+
+# ML Kernel - Useful? 
+# RUN mamba create --name ml -y -c conda-forge \
+#         python=3.11 \
+#         jax \
+#         jaxlib \
+#         pytorch \
+#         torchvision \
+#         tensorflow \
+#         tensorflow-probability \
+#         scikit-learn \
+#         scikit-image \
+#         pandas \
+#         numpy \
+#         matplotlib \
+#         seaborn \
+#         xarray \
+#         dask \
+#         mlflow && \
+# 	mamba clean --all -f -y && \
+#     conda activate ml && \
+#     ipython kernel install --user --name=ml
+
+FROM python_kernels AS final
+
+USER root
+
+COPY --from=figuregen_build /usr/local/bin/figuregen /usr/local/bin/figuregen
+COPY --from=figuregen_build /usr/local/bin/figuregen-serial /usr/local/bin/figuregen-serial
+COPY --from=figuregen_data /gmt-4.5.18 /gmt-4.5.18
+COPY --from=adcirc_build /usr/local/bin/adcprep /usr/local/bin/adcprep
+COPY --from=adcirc_build /usr/local/bin/adcirc /usr/local/bin/adcirc
+COPY --from=adcirc_build /usr/local/bin/padcirc /usr/local/bin/padcirc
+COPY --from=adcirc_build /usr/local/bin/adcswan /usr/local/bin/adcswan
+COPY --from=adcirc_build /usr/local/bin/padcswan /usr/local/bin/padcswan
+COPY --from=adcirc_build /usr/local/bin/adcirc_compile /usr/local/bin/adcirc_compile
+
+COPY run.sh /tapis/run.sh
+RUN chmod +x /tapis/run.sh
+
+RUN groupadd --gid 816877 G-816877
+RUN usermod -u 458981 -G G-816877 jovyan
+USER 458981
+
+WORKDIR /home/jovyan
+ENTRYPOINT [ "/tapis/run.sh" ]
+SHELL ["/bin/bash", "-c"]

applications/adcirc-interactive/README.md

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+# ADCIRC Interactive App
+
+JupyterLab Instance with ADCIRC and supporting applications (FigureGen and Kalpana) installed natively.
+
+## Building Docker Image
+
+The Dockerfile to build the ADCIRC Interactive App Image uses a multi-stage build. You must use [docker buildx](https://docs.docker.com/reference/cli/docker/buildx/) to build the container. You can build it in stages, such as:
+
+```bash
+docker buildx build --platform linux/amd64,linux/arm64 -t clos21/ds-adcirc-interactive:latest --target final --load --push .
+```
+
+This command:
+- Builds for both AMD64 and ARM64 architectures. Note the current vm where the adcirc interactive app is deployed requires linux/amd64
+- Tags the image as `clos21/ds-adcirc-interactive:base`
+- Uses the `base` stage in a multi-stage Dockerfile. Will build only up to this stage, and give it the above tag name
+- Loads the image into Docker's local image store
+- Pushes the image to the configured registry (only do this when ready to push the image out)
+
+Ensure you're in the directory containing your Dockerfile when running this command.
+
+## Multi-stage Build Structure
+
+This Dockerfile uses a multi-stage build to create an interactive ADCIRC environment. Here's an overview of the different stages and what each adds:
+
+1. **base**: 
+   - Starting point based on jupyter/minimal-notebook
+   - Installs system dependencies and tools
+
+2. **figuregen_data**: 
+   - Builds on `base`
+   - Downloads and installs GMT (Generic Mapping Tools)
+
+3. **figuregen_build**: 
+   - Builds on `figuregen_data`
+   - Clones and compiles FigureGen
+
+4. **adcirc_build**: 
+   - Builds on `base`
+   - Compiles ADCIRC
+
+5. **jupyter_lab_base**: 
+   - Builds on `base`
+   - Installs JupyterLab and related extensions
+
+6. **python_kernels**: 
+   - Builds on `jupyter_lab_base`
+   - Sets up Python environments and installs scientific packages
+
+7. **final**: 
+   - Builds on `python_kernels`
+   - Copies built artifacts from previous stages
+   - Sets up final environment configurations
+
+
+The container build tree can thus be visualized as:
+
+```
+base
+├── figuregen_data
+│   └── figuregen_build
+├── adcirc_build
+└── jupyter_lab_base
+    └── python_kernels
+        └── final
+```
+
+**Warning**: Sometimes the python kernel build fails (specifically mamba) due to weird bugs with parallelization issues. Try building the images in stages if this happpens.