Dockerfile

# 20220427 modified from headcase Dockerfile by MW to run the V4 HCE model
# Generated by: Neurodocker version 0.7.0+0.gdc97516.dirty
# Latest release: Neurodocker version 0.8.0
# Timestamp: 2022/03/23 15:34:59 UTC
# 
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
# pull request on our GitHub repository:
# 
#     https://github.com/ReproNim/neurodocker
#

FROM nvidia/cuda:9.2-cudnn7-devel-ubuntu16.04

USER root

ENV LANG="en_US.UTF-8" \
    LC_ALL="en_US.UTF-8" \
    ND_ENTRYPOINT="/neurodocker/startup.sh"
RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
    && apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
    apt-utils \
    bzip2 \
    ca-certificates \
    curl \
    locales \
    unzip \
    git \
    vim \
    build-essential \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
    && dpkg-reconfigure --frontend=noninteractive locales \
    && update-locale LANG="en_US.UTF-8" \
    && chmod 777 /opt && chmod a+s /opt \
    && mkdir -p /neurodocker \
    && if [ ! -f "$ND_ENTRYPOINT" ]; then \
    echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
    &&   echo 'set -e' >> "$ND_ENTRYPOINT" \
    &&   echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
    &&   echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
    fi \
    && chmod -R 777 /neurodocker && chmod a+s /neurodocker

ENTRYPOINT ["/neurodocker/startup.sh"]

RUN mkdir /home/hce_user
RUN mkdir /home/hce_user/hce_workdir
RUN mkdir /home/hce_user/hce_outdir


# add nonroot user
RUN groupadd -r hce_user && useradd --no-log-init -r -g hce_user hce_user

WORKDIR /home/hce_user/hce_workdir

# add yaml to my_docker folder and here
COPY ["./hce_gpu.yml", "/home/hce_user/hce_workdir/hce_gpu.yml"]

COPY ["./code/", "/home/hce_user/hce_workdir/code/"]

COPY ["./requirements.txt", "/home/hce_user/hce_workdir/requirements.txt"]

COPY ["./keras.json", "/home/hce_user/.keras/keras.json"]

COPY ["./theanorc", "/home/hce_user/.theanorc"]

COPY ["./bashrc", "/home/hce_user/.bashrc"]

ENV CONDA_DIR="/opt/miniconda-latest" \
    PATH="/opt/miniconda-latest/bin:$PATH"
RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
    && echo "Downloading Miniconda installer ..." \
    && conda_installer="/tmp/miniconda.sh" \
    && curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
    && bash "$conda_installer" -b -p /opt/miniconda-latest \
    && rm -f "$conda_installer" \
    && conda update -yq -nbase conda \
    && conda config --system --prepend channels conda-forge \
    && conda config --system --set auto_update_conda false \
    && conda config --system --set show_channel_urls true \
    && sync && conda clean -y --all && sync \
    # create dcetester from yaml file
    && conda env create -f /home/hce_user/hce_workdir/hce_gpu.yml \
    && sync && conda clean -y --all && sync

# install separate pip packages
RUN bash -c "source activate hce_gpu \
    && conda install https://repo.continuum.io/pkgs/main/linux-64/python-2.7.18-h02575d3_0.tar.bz2 \
    && conda install https://anaconda.org/conda-forge/pip/19.3.1/download/linux-64/pip-19.3.1-py27_0.tar.bz2 \
    &&   pip install --no-cache-dir  \
    "-r" \
    "/home/hce_user/hce_workdir/requirements.txt"" \
    && rm -rf ~/.cache/pip/* \
    && sync \
    && sed -i '$isource activate hce_gpu' $ND_ENTRYPOINT

RUN chown -R hce_user /home/hce_user

# give hce_user access to gpus/cuda via 'video' group
RUN usermod -a -G video hce_user
RUN chown -R hce_user /neurodocker

# Set this env so script can tell if being run in docker container
ENV IN_A_DOCKER_CONTAINER=true