Tutorial on Building a PFLOTRAN Docker Image

# Base image and setup
FROM ubuntu:22.04 AS base
LABEL org.opencontainers.image.ref.name="ubuntu"
LABEL org.opencontainers.image.version="22.04"
LABEL org.opencontainers.image.authors="Pin Shuai"
LABEL org.opencontainers.image.description="Docker image for running PFLOTRAN v6.0 with JupyterLab"

ARG NB_USER=aggie
ARG NB_UID=1000
ARG NB_GID=100
ARG PETSC_VERSION=v3.21.4  # Replace with the desired PETSc version so it works with the pflotran branch
ARG pflotran_branch=v6.0  # Replace with the desired PFLOTRAN branch
ENV DEBIAN_FRONTEND=noninteractive
ENV NB_USER=$NB_USER NB_UID=$NB_UID NB_GID=$NB_GID
ENV SHELL=/bin/bash
ENV PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

ENV PETSC_DIR=/scratch/petsc \
    PETSC_ARCH=petsc-arch 

# Add fix-permissions script
COPY fix-permissions /usr/local/bin/fix-permissions
RUN chmod +x /usr/local/bin/fix-permissions

# Install prerequisites
RUN apt update -qq && \
    apt install -y --no-install-recommends \
        git make cmake gcc gfortran g++ wget nano vim python3 python3-pip lcov ca-certificates && \
    apt clean && \
    rm -rf /var/lib/apt/lists/*


# Create user and set permissions. -m creates the home directory, -s sets the shell, -N does not create a group
RUN useradd -m -s /bin/bash -N -u $NB_UID $NB_USER && \
    fix-permissions /home/$NB_USER

# Conda and Python setup
USER $NB_USER
WORKDIR /home/$NB_USER

# install jupyter and Install Python packages
RUN pip3 install -U virtualenv
RUN pip3 install -U jupyterlab h5py matplotlib hydroeval numpy scipy pandas && pip3 cache purge
ENV PATH=/home/${NB_USER}/.local/bin:$PATH

# Add JupyterLab configuration
USER root
COPY jupyter_server_config.py /etc/jupyter/
COPY jupyter_notebook_config.py /etc/jupyter/
RUN chmod +x /etc/jupyter/jupyter_server_config.py 
RUN chmod +x /etc/jupyter/jupyter_notebook_config.py
RUN mkdir /home/${NB_USER}/.jupyter
COPY jupyter_notebook_config.py /home/${NB_USER}/.jupyter
RUN chmod +x /home/${NB_USER}/.jupyter/jupyter_notebook_config.py
RUN chown -R $NB_USER /home/${NB_USER}/.jupyter
COPY start.sh start-notebook.sh start-singleuser.sh /usr/local/bin/
RUN chmod +x /usr/local/bin/start*.sh

# Set up the build environment
WORKDIR /scratch

# Expose ports and final configuration
ENV JUPYTER_ENABLE_LAB=yes
EXPOSE 8888

# Build MPICH
RUN wget https://www.mpich.org/static/downloads/4.1/mpich-4.1.tar.gz --no-check-certificate

# Copy and build PETSc
COPY ./build-petsc.sh /scratch/build-petsc.sh
RUN chmod +x /scratch/build-petsc.sh && /scratch/build-petsc.sh
ENV PATH=/scratch/mpich-4.1/install/bin:$PATH

# Verify PETSc environment
RUN echo "PETSC version = ${PETSC_VERSION}" && \
    echo "PETSC directory = ${PETSC_DIR}" && \
    echo "PETSC arch = ${PETSC_ARCH}"

# Build PFLOTRAN
RUN git clone https://bitbucket.org/pflotran/pflotran.git /scratch/pflotran && \
    cd /scratch/pflotran && \
    git checkout ${pflotran_branch} 
RUN echo "PFLOTRAN branch = ${pflotran_branch}"
WORKDIR /scratch/pflotran/src/pflotran
RUN make clean && \
    make -j4 \
        gnu_code_coverage=1 \
        gnu_runtime_checks=1 \
        catch_warnings_as_errors=1 \
        pflotran 

WORKDIR /scratch/pflotran/src/pflotran/bin
RUN cp ../pflotran .

RUN chown $NB_UID:$NB_GID --from=root:root -R  /scratch/pflotran/src 

# Set PFLOTRAN environment variables
ENV PFLOTRAN_DIR=/scratch/pflotran \
    PFLOTRAN_EXE=/scratch/pflotran/src/pflotran/pflotran

# Set work directory back to user home
USER $NB_USER
WORKDIR /home/${NB_USER}
# RUN echo "Current user is: $(whoami) in working directory: $(pwd)"
# add pflotran to PATH 
ENV PATH=/scratch/pflotran/src/pflotran/bin:$PATH

# append the PATH and additional commands to the bashrc
RUN echo $PATH && \
    echo "export PATH=${PATH}" >> ~/.bashrc

# Copy the local .bashrc file into the image
COPY ./local_bashrc /scratch/local_bashrc
# Append the local .bashrc to the user's .bashrc in the image
RUN cat /scratch/local_bashrc >> ~/.bashrc

# Copy the local .vimrc file into the image
COPY ./local_vimrc /scratch/local_vimrc
# Append the local .vimrc to the user's .vimrc in the image
RUN touch ~/.vimrc && cat /scratch/local_vimrc >> ~/.vimrc

# Copy the local gitconfig file into the image
COPY ./gitconfig /scratch/gitconfig
# Append the local gitconfig to the user's gitconfig in the image
RUN touch ~/.gitconfig && cat /scratch/gitconfig >> ~/.gitconfig

# Final stage: Add metadata and expose ports
# LABEL maintainer="Your Name <your.email@example.com>"
EXPOSE 8888

# create a work directory
WORKDIR /home/${NB_USER}/work

# This will use the existing multiplatform image as the base image. Choose the platform that you want to use.
FROM pshuai/jupyter-pflotran-multiplatform:base_v6 AS base

USER root
# Install packages: tree
RUN apt update -qq && \
    apt install -y --no-install-recommends \
        tree && \
    apt clean && \
    rm -rf /var/lib/apt/lists/*

ARG NB_USER=aggie

EXPOSE 8888

USER ${NB_USER}
# cd to work directory
WORKDIR /home/${NB_USER}/work