A GPU enabled Tidyverse Dockerfile

tidyverse-gpu-dockerfile

FROM rocker/tidyverse:latest

MAINTAINER "Sam Abbott" contact@samabbott.co.uk


 
## Shell tools
RUN apt-get update && apt-get install -y --force-yes --allow-unauthenticated --no-install-recommends --no-upgrade \
     curl \
## R package dependencies
      python-pip python-setuptools python-dev build-essential \
      libopenmpi-dev libcurl4-openssl-dev \
      gnupg \
      cmake libncurses5-dev
 
## CUDA Version
ENV CUDA_MAJOR_VERSION=9.2
ENV CUDA_MAJOR_VERSION_HYP=9.2
ENV CUDA_MINOR_VERSION=9.2.148-1
ENV NVIDIA_REQUIRE_CUDA="cuda>=9.2"

## CUDA Install
RUN wget -nv -P /root/manual http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1604/x86_64/7fa2af80.pub \
 && echo "47217c49dcb9e47a8728b354450f694c9898cd4a126173044a69b1e9ac0fba96  /root/manual/7fa2af80.pub" | sha256sum -c --strict - \
 && apt-key add /root/manual/7fa2af80.pub \
 && wget -nv -P /root/manual http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1604/x86_64/cuda-repo-ubuntu1604_${CUDA_MINOR_VERSION}_amd64.deb \
 && dpkg -i /root/manual/cuda-repo-ubuntu1604_${CUDA_MINOR_VERSION}_amd64.deb \
 && echo 'deb http://developer.download.nvidia.com/compute/machine-learning/repos/ubuntu1604/x86_64 /' > /etc/apt/sources.list.d/nvidia-ml.list \
 && rm -rf /root/manual \
 && apt-get update  && apt-get install --no-install-recommends -y \
      cuda-toolkit-${CUDA_MAJOR_VERSION_HYP} \
      libcudnn7 \
      libcudnn7-dev \
 && ls /usr/local/cuda-${CUDA_MAJOR_VERSION}/targets/x86_64-linux/lib/stubs/* | xargs -I{} ln -s {} /usr/lib/x86_64-linux-gnu/ \
 && ln -s libcuda.so /usr/lib/x86_64-linux-gnu/libcuda.so.1 \
 && ln -s libnvidia-ml.so /usr/lib/x86_64-linux-gnu/libnvidia-ml.so.1

ENV CUDA_HOME=/usr/local/cuda
ENV PATH=$CUDA_HOME/bin:$PATH
ENV LD_LIBRARY_PATH=$CUDA_HOME/lib64:$CUDA_HOME/extras/CUPTI/lib64:$LD_LIBRARY_PATH
ENV NVIDIA_VISIBLE_DEVICES=all
ENV NVIDIA_DRIVER_CAPABILITIES=compute,utility 


## Get JAVA
RUN apt-get update -qq \
  && apt-get -y --no-install-recommends install \
    default-jdk \
    default-jre \
  && R CMD javareconf


# Set up env variables in R
RUN echo "rsession-ld-library-path=$LD_LIBRARY_PATH" | tee -a /etc/rstudio/rserver.conf \
  && echo "Sys.setenv(CUDA_HOME=\"$CUDA_HOME\"); Sys.setenv(CUDA_PATH=\"$CUDA_HOME\"); Sys.setenv(PATH=\"$PATH\")" | tee -a /usr/local/lib/R/etc/Rprofile.site

# Tensorflow, Keras, Xgboost for GPU
RUN pip install wheel setuptools scipy --upgrade \
  && pip install h5py pyyaml requests Pillow tensorflow-gpu keras dvc xgboost
  
### R Xgboost
RUN git clone --recursive https://github.com/dmlc/xgboost \
  && mkdir -p xgboost/build && cd xgboost/build \
  && cmake .. -DUSE_CUDA=ON -DR_LIB=ON \
  && make install -j$(nproc) 

## Get latest release of h2o
RUN Rscript -e 'install.packages("h2o", type="source", repos="http://h2o-release.s3.amazonaws.com/h2o/latest_stable_R")'