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Dockerfile.wholebrain
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Dockerfile.wholebrain
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# Built with arch: amd64 flavor: lxde image: nvidia/cudagl:11.1.1-devel-ubuntu20.04
#
################################################################################
# base system
################################################################################
FROM nvidia/cudagl:11.1.1-devel-ubuntu20.04 as system
RUN sed -i 's#http://archive.ubuntu.com/ubuntu/#mirror://mirrors.ubuntu.com/mirrors.txt#' /etc/apt/sources.list;
# built-in packages
ENV DEBIAN_FRONTEND noninteractive
RUN apt update \
&& apt install -y --no-install-recommends software-properties-common curl apache2-utils \
&& apt update \
&& apt install -y --no-install-recommends --allow-unauthenticated \
supervisor nginx sudo net-tools zenity xz-utils \
dbus-x11 x11-utils alsa-utils \
mesa-utils libgl1-mesa-dri \
&& apt autoclean -y \
&& apt autoremove -y \
&& rm -rf /var/lib/apt/lists/*
# install debs error if combine together
RUN apt update \
&& apt install -y --no-install-recommends --allow-unauthenticated \
xvfb x11vnc \
vim-tiny \
&& apt autoclean -y \
&& apt autoremove -y \
&& rm -rf /var/lib/apt/lists/*
RUN apt update \
&& apt install -y gpg-agent \
&& rm -rf /var/lib/apt/lists/*
# Install libraries and tools used for c++ compilation
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
clinfo \
cmake \
git \
libboost-all-dev \
libfftw3-dev \
libfontconfig1-dev \
libfreeimage-dev \
liblapack-dev \
liblapacke-dev \
libopenblas-dev \
libhdf5-serial-dev \
libxmu-dev \
libxi-dev \
libgl-dev \
ocl-icd-opencl-dev \
opencl-headers \
wget \
xorg-dev && \
rm -rf /var/lib/apt/lists/*
RUN apt update \
&& apt install -y --no-install-recommends --allow-unauthenticated \
lxde gtk2-engines-murrine gnome-themes-standard gtk2-engines-pixbuf gtk2-engines-murrine arc-theme \
&& apt autoclean -y \
&& apt autoremove -y \
&& rm -rf /var/lib/apt/lists/*
# Additional packages require ~600MB
# libreoffice pinta language-pack-zh-hant language-pack-gnome-zh-hant firefox-locale-zh-hant libreoffice-l10n-zh-tw
# tini to fix subreap
ARG TINI_VERSION=v0.18.0
ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /bin/tini
RUN chmod +x /bin/tini
# ffmpeg
RUN apt update \
&& apt install -y --no-install-recommends --allow-unauthenticated \
ffmpeg \
&& rm -rf /var/lib/apt/lists/* \
&& mkdir /usr/local/ffmpeg \
&& ln -s /usr/bin/ffmpeg /usr/local/ffmpeg/ffmpeg
# python library
COPY rootfs/usr/local/lib/web/backend/requirements.txt /tmp/
RUN apt-get update \
&& dpkg-query -W -f='${Package}\n' > /tmp/a.txt \
&& apt-get install -y python3-pip python3-dev build-essential \
&& pip3 install setuptools wheel && pip3 install -r /tmp/requirements.txt \
&& ln -s /usr/bin/python3 /usr/local/bin/python \
&& dpkg-query -W -f='${Package}\n' > /tmp/b.txt \
&& apt-get remove -y `diff --changed-group-format='%>' --unchanged-group-format='' /tmp/a.txt /tmp/b.txt | xargs` \
&& apt-get autoclean -y \
&& apt-get autoremove -y \
&& rm -rf /var/lib/apt/lists/* \
&& rm -rf /var/cache/apt/* /tmp/a.txt /tmp/b.txt
# Install OpenGL related libraries from source (requires python to build)
# Build GLFW from source
RUN git clone --depth 1 --branch 3.3.4 https://github.com/glfw/glfw.git && \
cd glfw && \
mkdir build && \
cd build && \
cmake -DCMAKE_INSTALL_PREFIX=/usr .. && \
make -j4 && \
make install
#Add GLFW update: GLU
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
libgl1-mesa-dev \
libglu1-mesa-dev
# Build GLEW from source
RUN git clone --depth 1 https://github.com/nigels-com/glew.git && \
cd glew && \
cd auto && \
make && \
cd .. && \
make && \
make install && \
make clean
#Clone GLM. Build not needed as the library is header-only
RUN git clone --depth 1 https://github.com/g-truc/glm.git
#Build ann using Cmake:
COPY ann /ann
RUN cd /ann \
&& cmake -DCMAKE_BUILD_TYPE=Release . \
&& make ANN
# Setting up symlinks for libcuda and OpenCL ICD
RUN ln -s /usr/local/cuda/lib64/stubs/libcuda.so /usr/lib/libcuda.so.1 && \
ln -s /usr/lib/libcuda.so.1 /usr/lib/libcuda.so && \
mkdir -p /etc/OpenCL/vendors && \
echo "libnvidia-opencl.so.1" > /etc/OpenCL/vendors/nvidia.icd && \
echo "/usr/local/nvidia/lib" >> /etc/ld.so.conf.d/nvidia.conf && \
echo "/usr/local/nvidia/lib64" >> /etc/ld.so.conf.d/nvidia.conf
ENV PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:${PATH}
WORKDIR /root
RUN cd /tmp && \
wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB && \
apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB && \
rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB && \
echo "deb https://apt.repos.intel.com/oneapi all main" | tee /etc/apt/sources.list.d/oneAPI.list && \
add-apt-repository "deb https://apt.repos.intel.com/oneapi all main" && \
apt update -y && apt install -y intel-basekit
SHELL ["/bin/bash", "-c"]
#
################################################################################
# builder
################################################################################
FROM nvidia/cudagl:11.1.1-devel-ubuntu20.04 as builder
RUN apt-get update \
&& apt-get install -y --no-install-recommends curl ca-certificates gnupg patch
# nodejs
RUN curl -sL https://deb.nodesource.com/setup_12.x | bash - \
&& apt-get install -y nodejs
# yarn
RUN curl -sS https://dl.yarnpkg.com/debian/pubkey.gpg | apt-key add - \
&& echo "deb https://dl.yarnpkg.com/debian/ stable main" | tee /etc/apt/sources.list.d/yarn.list \
&& apt-get update \
&& apt-get install -y yarn
# build frontend
COPY web /src/web
RUN cd /src/web \
&& yarn \
&& yarn build
RUN sed -i 's#app/locale/#novnc/app/locale/#' /src/web/dist/static/novnc/app/ui.js
################################################################################
# merge
################################################################################
FROM system
LABEL maintainer="wang.ningyuan.mail2@gmail.com"
COPY src_wholebrain /src/neuronephys
#Build neuronephys:
RUN cd /src/neuronephys \
&& cmake -B build \
-DCMAKE_BUILD_TYPE=Release \
-DANN_ROOT=/ann \
-DGLM_ROOT=/glm \
&& cd build \
&& make \
&& mv neuronephys ../neuronephys
COPY cortex_connectivity_1m_1k_exc.h5 /src/neuronephys/cortex_connectivity_1m_1k_exc.h5
COPY cortex_connectivity_1m_1k_inh.h5 /src/neuronephys/cortex_connectivity_1m_1k_inh.h5
COPY CUBIC_regionID_lookup_no_comma.json /src/neuronephys/CUBIC_regionID_lookup_no_comma.json
COPY 2d_brain_region.bmp /src/neuronephys/2d_brain_region.bmp
COPY --from=builder /src/web/dist/ /usr/local/lib/web/frontend/
COPY rootfs /
RUN ln -sf /usr/local/lib/web/frontend/static/websockify /usr/local/lib/web/frontend/static/novnc/utils/websockify && \
chmod +x /usr/local/lib/web/frontend/static/websockify/run
EXPOSE 80
WORKDIR /src/neuronephys
ENV HOME=/home/ubuntu \
SHELL=/bin/bash
HEALTHCHECK --interval=30s --timeout=5s CMD curl --fail http://127.0.0.1:6079/api/health
ENTRYPOINT ["/startup.sh"]