Merge pull request #26 from rocker-org/ubuntu

Ubuntu-based image

Author: cboettig

ubuntu/10.0/Dockerfile

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+FROM nvidia/cuda:10.0-cudnn7-devel
+
+LABEL org.label-schema.license="GPL-2.0" \
+      org.label-schema.vcs-url="https://github.com/rocker-org/rocker-versioned" \
+      org.label-schema.vendor="Rocker Project" \
+      maintainer="Carl Boettiger <[email protected]>"
+
+ENV TERM=xterm
+
+## cuda:9.0 is xenial, cuda:10.0 is bionic
+ARG UBUNTU_VERSION=bionic
+ARG R_HOME=/usr/lib/R
+ARG DEBIAN_FRONTEND=noninteractive
+
+
+#ENV R_VERSION=${R_VERSION:-3.6.0}
+ENV LC_ALL=en_US.UTF-8
+ENV LANG=en_US.UTF-8
+COPY install_R.sh /tmp/install_R.sh
+RUN  . /tmp/install_R.sh
+
+
+
+COPY install_rstudio.sh /tmp/install_rstudio.sh
+#RUN . /tmp/install_rstudio.sh
+COPY userconf.sh /etc/cont-init.d/userconf
+EXPOSE 8787
+#CMD ["/init"]
+
+
+
+COPY install_tidyverse.sh /tmp/install_tidyverse.sh
+#RUN . /tmp/install_tidyverse.sh
+
+
+
+COPY install_verse.sh /tmp/install_verse.sh
+#RUN . /tmp/install_verse.sh
+
+
+
+## Use Configure CUDA for R, use NVidia libs for BLAS
+ENV CUDA_HOME=/usr/local/cuda
+ENV PATH=$PATH:$CUDA_HOME/bin
+ENV LD_LIBRARY_PATH=$CUDA_HOME/lib64/libnvblas.so:$LD_LIBRARY_PATH:$CUDA_HOME/lib64:$CUDA_HOME/extras/CUPTI/lib64
+ENV NVBLAS_CONFIG_FILE=/etc/nvblas.conf
+COPY config_R_cuda.sh /tmp/config_R_cuda.sh
+RUN . /tmp/config_R_cuda.sh
+
+
+ENV PYTHON_VENV_PATH=/opt/venv 
+ENV RETICULATE_PYTHON_ENV=$PYTHON_VENV_PATH
+ENV PATH=${PYTHON_VENV_PATH}/bin:${PATH}
+COPY install_python.sh /tmp/install_python.sh
+RUN . /tmp/install_python.sh
+
+
+
+COPY install_tensorflow-gpu.sh /tmp/install_tensorflow-gpu.sh
+#RUN . /tmp/install_tensorflow-gpu.sh
+

ubuntu/10.0/config_R_cuda.sh

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+#!/bin/sh
+
+set -e
+
+## CUDA environmental variables configuration for RStudio
+
+## cli R inherits these, but RStudio needs to have these set in as follows:
+## (From https://tensorflow.rstudio.com/tools/local_gpu.html#environment-variables)
+echo "\n\
+      \nCUDA_HOME=$CUDA_HOME\
+      \nPATH=$PATH" >> ${R_HOME}/etc/Renviron 
+ 
+if test -f /etc/rstudio/rserver.conf; then 
+  echo "rsession-ld-library-path=$LD_LIBRARY_PATH" >> /etc/rstudio/rserver.conf
+fi
+
+touch /var/log/nvblas.log && chown :staff /var/log/nvblas.log
+
+## Configure R & RStudio to use drop-in CUDA blas
+## Allow R to use CUDA for BLAS, with fallback on openblas
+echo "\nNVBLAS_LOGFILE /var/log/nvblas.log \
+      \nNVBLAS_CPU_BLAS_LIB /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 \
+      \nNVBLAS_GPU_LIST ALL" > /etc/nvblas.conf
+
+echo "NVBLAS_CONFIG_FILE=$NVBLAS_CONFIG_FILE" >> ${R_HOME}/etc/Renviron
+
+
+## We don't want to set LD_PRELOAD globally
+##ENV LD_PRELOAD=/usr/local/cuda/lib64/libnvblas.so
+#
+### Instead, we will set it before calling R, Rscript, or RStudio:
+#mv /usr/bin/R /usr/bin/R_
+#mv /usr/bin/Rscript /usr/bin/Rscript_
+#
+#echo '\#!/bin/sh \
+#      \n LD_PRELOAD=/usr/local/cuda/lib64/libnvblas.so /usr/bin/R_ "$@"' \
+#      > /usr/bin/R && \
+#    chmod +x /usr/bin/R && \
+#    echo '#!/bin/sh \
+#          \n LD_PRELOAD=/usr/local/cuda/lib64/libnvblas.so /usr/bin/Rscript_ "$@"' \
+#      > /usr/bin/Rscript && \
+#    chmod +x /usr/bin/Rscript
+#
+#echo '#!/usr/bin/with-contenv bash \
+#      \n## load /etc/environment vars first: \
+#      \n for line in \$( cat /etc/environment ) ; do export $line ; done \
+#      \n export LD_PRELOAD=/usr/local/cuda/lib64/libnvblas.so \
+#      \n exec /usr/lib/rstudio-server/bin/rserver --server-daemonize 0' \
+#      > /etc/services.d/rstudio/run
+#

ubuntu/10.0/install_R.sh

@@ -0,0 +1,29 @@
+#!/bin/sh
+set -e
+
+echo "deb https://cloud.r-project.org/bin/linux/ubuntu ${UBUNTU_VERSION}-cran35/" >> /etc/apt/sources.list && \
+    gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 && \
+    gpg -a --export E298A3A825C0D65DFD57CBB651716619E084DAB9 | apt-key add - && \
+    apt-get update && \
+    apt-get -y install --no-install-recommends \
+      ca-certificates \
+      less \
+      littler \
+      libopenblas-base \
+      locales \
+      r-base-dev \
+      vim-tiny \
+      wget && \
+    rm -rf /var/lib/apt/lists/*
+
+echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen && \
+  locale-gen en_US.utf8 && \
+  /usr/sbin/update-locale LANG=${LANG}
+
+Rscript -e "install.packages(c('littler', 'docopt'))"
+ln -s /usr/lib/R/site-library/littler/examples/install.r /usr/local/bin/install.r \
+  && ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r \
+  && ln -s /usr/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
+  && ln -s /usr/local/lib/R/site-library/littler/bin/r /usr/local/bin/r
+
+

ubuntu/10.0/install_nvtop.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+set -e
+
+apt-get update && apt-get -y install cmake libncurses5-dev libncursesw5-dev git
+git clone https://github.com/Syllo/nvtop.git
+mkdir -p nvtop/build && cd nvtop/build
+cmake .. -DNVML_RETRIEVE_HEADER_ONLINE=True
+make
+make install
+

ubuntu/10.0/install_python.sh

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+#/bin/sh
+set -e
+
+apt-get update && apt-get install -y --no-install-recommends \
+        libpython3-dev \
+        python3-pip \
+        python3-venv && \
+    rm -rf /var/lib/apt/lists/*
+python3 -m venv ${PYTHON_VENV_PATH}
+pip3 install --no-cache-dir virtualenv
+
+## Ensure RStudio inherits this env var
+echo "\nRETICULATE_PYTHON_ENV=${RETICULATE_PYTHON_ENV}" >> ${R_HOME}/etc/Renviron
+
+## symlink these because reticulate hardwires these PATHs...
+ln -s ${PYTHON_VENV_PATH}/bin/pip /usr/local/bin/pip
+ln -s ${PYTHON_VENV_PATH}/bin/virtualenv /usr/local/bin/virtualenv
+
+chown :staff ${PYTHON_VENV_PATH}
+

ubuntu/10.0/install_rstudio.sh

@@ -0,0 +1,104 @@
+#!/bin/sh
+
+S6_VERSION=${S6_VERSION:-v1.21.7.0}
+S6_BEHAVIOUR_IF_STAGE2_FAILS=2
+export PATH=/usr/lib/rstudio-server/bin:$PATH
+PANDOC_TEMPLATES_VERSION=${PANDOC_TEMPLATES_VERSION:-2.6}
+
+## Download and install RStudio server & dependencies
+## Attempts to get detect latest version, otherwise falls back to version given in $VER
+## Symlink pandoc, pandoc-citeproc so they are available system-wide
+apt-get update \
+  && apt-get install -y --no-install-recommends \
+    file \
+    git \
+    libapparmor1 \
+    libcurl4-openssl-dev \
+    libedit2 \
+    libssl-dev \
+    lsb-release \
+    psmisc \
+    procps \
+    python-setuptools \
+    sudo \
+    wget \
+    libclang-dev \
+    libobjc-6-dev \
+    libobjc4 \
+    libgc1c2 \
+  && rm -rf /var/lib/apt/lists/*
+
+
+if [ -z "$RSTUDIO_VERSION" ]; 
+  then RSTUDIO_URL="https://www.rstudio.org/download/latest/stable/server/${UBUNTU_VERSION}/rstudio-server-latest-amd64.deb"; 
+  else RSTUDIO_URL="http://download2.rstudio.org/server/${UBUNTU_VERSION}/amd64/rstudio-server-${RSTUDIO_VERSION}-amd64.deb"; 
+fi
+wget -q $RSTUDIO_URL \
+  && dpkg -i rstudio-server-*-amd64.deb \
+  && rm rstudio-server-*-amd64.deb
+
+## Symlink pandoc & standard pandoc templates for use system-wide
+ln -s /usr/lib/rstudio-server/bin/pandoc/pandoc /usr/local/bin \
+  && ln -s /usr/lib/rstudio-server/bin/pandoc/pandoc-citeproc /usr/local/bin \
+  && git clone --recursive --branch ${PANDOC_TEMPLATES_VERSION} https://github.com/jgm/pandoc-templates \
+  && mkdir -p /opt/pandoc/templates \
+  && cp -r pandoc-templates*/* /opt/pandoc/templates && rm -rf pandoc-templates* \
+  && mkdir /root/.pandoc && ln -s /opt/pandoc/templates /root/.pandoc/templates
+
+
+## RStudio wants an /etc/R, will populate from $R_HOME/etc
+mkdir -p /etc/R \
+  && echo "\n\
+    \n# Configure httr to perform out-of-band authentication if HTTR_LOCALHOST \
+    \n# is not set since a redirect to localhost may not work depending upon \
+    \n# where this Docker container is running. \
+    \nif(is.na(Sys.getenv('HTTR_LOCALHOST', unset=NA))) { \
+    \n  options(httr_oob_default = TRUE) \
+    \n}" >> ${R_HOME}/etc/Rprofile.site \
+  && echo "PATH=${PATH}" >> ${R_HOME}/etc/Renviron
+
+
+## Need to configure non-root user for RStudio
+useradd rstudio \
+  && echo "rstudio:rstudio" | chpasswd \
+  && mkdir /home/rstudio \
+  && chown rstudio:rstudio /home/rstudio \
+  && addgroup rstudio staff 
+  ## Prevent rstudio from deciding to use /usr/bin/R if a user apt-get installs a package
+
+R_BIN=`which R`
+echo "rsession-which-r=${R_BIN}" >> /etc/rstudio/rserver.conf
+## use more robust file locking to avoid errors when using shared volumes:
+echo "lock-type=advisory" >> /etc/rstudio/file-locks
+
+## Optional configuration file to disable authentication
+cp /etc/rstudio/rserver.conf /etc/rstudio/disable_auth_rserver.conf
+echo "auth-none=1" >> /etc/rstudio/disable_auth_rserver.conf
+
+## configure git not to request password each time
+git config --system credential.helper 'cache --timeout=3600' \
+  && git config --system push.default simple
+
+## Set up S6 init system
+wget -P /tmp/ https://github.com/just-containers/s6-overlay/releases/download/${S6_VERSION}/s6-overlay-amd64.tar.gz \
+  && tar xzf /tmp/s6-overlay-amd64.tar.gz -C / \
+  && mkdir -p /etc/services.d/rstudio \
+  && echo "#!/usr/bin/with-contenv bash \
+          \n## load /etc/environment vars first: \
+          \n for line in $( cat /etc/environment ) ; do export $line > /dev/null; done \
+          \n exec /usr/lib/rstudio-server/bin/rserver --server-daemonize 0" \
+          > /etc/services.d/rstudio/run \
+  && echo "#!/bin/bash \
+          \n rstudio-server stop" \
+          > /etc/services.d/rstudio/finish \
+  && mkdir -p /home/rstudio/.rstudio/monitored/user-settings \
+  && echo "alwaysSaveHistory='0' \
+          \nloadRData='0' \
+          \nsaveAction='0'" \
+          > /home/rstudio/.rstudio/monitored/user-settings/user-settings \
+  && chown -R rstudio:rstudio /home/rstudio/.rstudio
+
+
+#COPY userconf.sh /etc/cont-init.d/userconf
+# EXPOSE 8787
+# CMD ["/init"]

ubuntu/10.0/install_tensorflow-gpu.sh

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+#!/bin/sh
+set -e
+
+apt-get update && apt-get install -y --no-install-recommends \
+        build-essential \
+        curl \
+        libfreetype6-dev \
+        libhdf5-serial-dev \
+        libzmq3-dev \
+        pkg-config \
+        software-properties-common \
+        unzip
+
+## FIXME set versions Consider renv
+#R -e "renv::restore()"
+pip3 install --no-cache-dir tensorflow-gpu tensorflow-probability keras h5py pyyaml requests Pillow 
+chown -R rstudio:rstudio ${PYTHON_VENV_PATH}
+
+R -e "install.packages('keras')"
+R -e "install.packages('remotes'); remotes::install_github('greta-dev/greta')"
+

ubuntu/10.0/install_tidyverse.sh

@@ -0,0 +1,26 @@
+#!/bin/sh
+set -e
+
+apt-get update -qq && apt-get -y --no-install-recommends install \
+    libxml2-dev \
+    libcairo2-dev \
+    libsqlite3-dev \
+    libmariadbd-dev \
+    libmariadb-client-lgpl-dev \
+    libpq-dev \
+    libssh2-1-dev \
+    unixodbc-dev \
+    libsasl2-dev && \
+  rm -rf /var/lib/apt/lists/*
+
+install2.r --error \
+    --deps TRUE \
+    tidyverse \
+    dplyr \
+    devtools \
+    formatR \
+    remotes \
+    selectr \
+    caTools \
+    BiocManager
+

ubuntu/10.0/install_verse.sh

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+#!/bin/sh
+
+set -e
+
+export PATH=$PATH:/opt/TinyTeX/bin/x86_64-linux/
+
+## Add LaTeX, rticles and bookdown support
+wget "https://travis-bin.yihui.name/texlive-local.deb" \
+  && dpkg -i texlive-local.deb \
+  && rm texlive-local.deb \
+  && apt-get update \
+  && apt-get install -y --no-install-recommends \
+    cmake \
+    default-jdk \
+    fonts-roboto \
+    ghostscript \
+    libbz2-dev \
+    libicu-dev \
+    liblzma-dev \
+    libhunspell-dev \
+    libmagick++-dev \
+    librdf0-dev \
+    libv8-dev \
+    qpdf \
+    texinfo \
+    ssh \
+    less \
+    vim \
+    libzmq3-dev \
+    libopenmpi-dev \
+  && rm -rf /var/lib/apt/lists/* 
+
+install2.r --error tinytex
+
+## Admin-based install of TinyTeX:
+wget -qO- \
+    "https://github.com/yihui/tinytex/raw/master/tools/install-unx.sh" | \
+    sh -s - --admin --no-path \
+  && mv ~/.TinyTeX /opt/TinyTeX \
+  && /opt/TinyTeX/bin/*/tlmgr path add \
+  && tlmgr install metafont mfware inconsolata tex ae parskip listings \
+  && tlmgr path add \
+  && Rscript -e "tinytex::r_texmf()" \
+  && chown -R root:staff /opt/TinyTeX \
+  && chown -R root:staff ${R_HOME}/site-library \
+  && chmod -R g+w /opt/TinyTeX \
+  && chmod -R g+wx /opt/TinyTeX/bin \
+  && echo "PATH=${PATH}" >> ${R_HOME}/etc/Renviron
+ 
+
+install2.r --error --deps TRUE \
+    bookdown rticles rmdshower rJava
+
+