Create Dockerfile

Dockerfile

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+FROM nvidia/cuda:11.3.1-base-ubuntu20.04
+
+ENV DEBIAN_FRONTEND=noninteractive \
+        TZ=Europe/Paris
+
+# Remove any third-party apt sources to avoid issues with expiring keys.
+# Install some basic utilities
+RUN rm -f /etc/apt/sources.list.d/*.list && \
+    apt-get update && apt-get install -y --no-install-recommends \
+    curl \
+    ca-certificates \
+    sudo \
+    git \
+    wget \
+    procps \
+    git-lfs \
+    zip \
+    unzip \
+    htop \
+    vim \
+    nano \
+    bzip2 \
+    libx11-6 \
+    build-essential \
+    libsndfile-dev \
+    software-properties-common \
+ && rm -rf /var/lib/apt/lists/*
+
+RUN add-apt-repository ppa:flexiondotorg/nvtop && \
+    apt-get upgrade -y && \
+    apt-get install -y --no-install-recommends nvtop
+
+RUN curl -sL https://deb.nodesource.com/setup_14.x  | bash - && \
+    apt-get install -y nodejs && \
+    npm install -g configurable-http-proxy
+
+# Create a working directory
+WORKDIR /app
+
+# Create a non-root user and switch to it
+RUN adduser --disabled-password --gecos '' --shell /bin/bash user \
+ && chown -R user:user /app
+RUN echo "user ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/90-user
+USER user
+
+# All users can use /home/user as their home directory
+ENV HOME=/home/user
+RUN mkdir $HOME/.cache $HOME/.config \
+ && chmod -R 777 $HOME
+
+# Set up the Conda environment
+ENV CONDA_AUTO_UPDATE_CONDA=false \
+    PATH=$HOME/miniconda/bin:$PATH
+RUN curl -sLo ~/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-py39_4.10.3-Linux-x86_64.sh \
+ && chmod +x ~/miniconda.sh \
+ && ~/miniconda.sh -b -p ~/miniconda \
+ && rm ~/miniconda.sh \
+ && conda clean -ya
+
+WORKDIR $HOME/app
+
+#######################################
+# Start root user section
+#######################################
+
+USER root
+
+# User Debian packages
+## Security warning : Potential user code executed as root (build time)
+RUN --mount=target=/root/packages.txt,source=packages.txt \
+    apt-get update && \
+    xargs -r -a /root/packages.txt apt-get install -y --no-install-recommends \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN --mount=target=/root/on_startup.sh,source=on_startup.sh,readwrite \
+        bash /root/on_startup.sh
+
+RUN mkdir /data && chown user:user /data
+
+#######################################
+# End root user section
+#######################################
+
+USER user
+
+# Pull chemprop from github
+RUN git clone https://github.com/chemprop/chemprop.git
+RUN cd chemprop
+
+# build an empty conda environment with appropriate Python version
+RUN conda create --name chemprop_env python=3.11*
+
+SHELL ["conda", "run", "--no-capture-output", "-n", "chemprop_env", "/bin/bash", "-c"]
+
+
+
+# Python packages
+RUN --mount=target=requirements.txt,source=requirements.txt \
+    pip install --no-cache-dir --upgrade -r requirements.txt
+
+
+
+# Copy the current directory contents into the container at $HOME/app setting the owner to the user
+COPY --chown=user . $HOME/app
+
+RUN chmod +x start_server.sh
+
+COPY --chown=user login.html /home/user/miniconda/lib/python3.9/site-packages/jupyter_server/templates/login.html
+
+ENV PYTHONUNBUFFERED=1 \
+        GRADIO_ALLOW_FLAGGING=never \
+        GRADIO_NUM_PORTS=1 \
+        GRADIO_SERVER_NAME=0.0.0.0 \
+        GRADIO_THEME=huggingface \
+        SYSTEM=spaces \
+        SHELL=/bin/bash
+
+CMD ["./start_server.sh"]
+####################################################### FROM CHEMPROP DOCKERFILE ##########################################################
+# Dockerfile
+#
+# Builds a Docker image containing Chemprop and its required dependencies.
+#
+# Build this image with:
+#  git clone https://github.com/chemprop/chemprop.git
+#  cd chemprop
+#  docker build --tag=chemprop:latest .
+#
+# Run the built image with:
+#  docker run --name chemprop_container -it chemprop:latest
+#
+# Note:
+# This image only runs on CPU - we do not provide a Dockerfile
+# for GPU use (see installation documentation). 
+
+# Parent Image
+#FROM continuumio/miniconda3:latest
+
+# Install libxrender1 (required by RDKit) and then clean up
+#RUN apt-get update && \
+#    apt-get install -y \
+#    libxrender1 && \
+#    apt-get autoremove -y && \
+#    apt-get clean -y
+
+#WORKDIR /opt/chemprop
+
+# build an empty conda environment with appropriate Python version
+RUN conda create --name chemprop_env python=3.11*
+
+# This runs all subsequent commands inside the chemprop_env conda environment
+#
+# Analogous to just activating the environment, which we can't actually do here
+# since that requires running conda init and restarting the shell (not possible
+# in a Dockerfile build script)
+SHELL ["conda", "run", "--no-capture-output", "-n", "chemprop_env", "/bin/bash", "-c"]
+
+# Follow the installation instructions then clear the cache
+ADD chemprop chemprop
+ENV PYTHONPATH /opt/chemprop
+ADD LICENSE.txt pyproject.toml README.md ./
+RUN conda install pytorch cpuonly -c pytorch && \
+    conda clean --all --yes && \
+    python -m pip install . && \
+    python -m pip cache purge
+
+# when running this image, open an interactive bash terminal inside the conda environment
+RUN echo "conda activate chemprop_env" > ~/.bashrc
+ENTRYPOINT ["/bin/bash", "--login"]