RStudio403MKL.def

BootStrap: docker
From: ubuntu:20.04

%labels
  Maintainer Dror Shvadron
  R_Version 4.0.3
  RStudio_Version 1.3.1093
  MKL_Version intel-mkl-64bit-2020.0-088
  Image_Name singularity-rstudio-mkl
  Image_Version singularity-rstudio-mkl-01

%help
  This will run RStudio Server with tidyverse and support for knitting

%runscript
  exec port_and_password "${@}"

%apprun R
  exec R "${@}"

%apprun Rscript
  exec Rscript "${@}"

%apprun rserver
  exec rserver "${@}"

%apprun rstudio
  exec rserver "${@}"

%apprun default
  exec "${@}"

%apprun pp
  exec port_and_password "${@}"

%environment
  export PATH=/usr/lib/rstudio-server/bin:${PATH}:/usr/lib/rstudio-server/bin/pandoc
  export SHELL=/bin/bash
  export LC_ALL=en_US.UTF-8
  export LANG=en_US.UTF-8
  export LANGUAGE=en_US.UTF-8
  export MKL_THREADING_LAYER=GNU

%setup
  install -Dv \
    rstudio_auth_1_3.sh \
    ${SINGULARITY_ROOTFS}/usr/lib/rstudio-server/bin/rstudio_auth
  install -Dv \
    ldap_auth.py \
    ${SINGULARITY_ROOTFS}/usr/lib/rstudio-server/bin/ldap_auth

  install -Dv \
    port_and_password_1_3.sh \
    ${SINGULARITY_ROOTFS}/usr/lib/rstudio-server/bin/port_and_password

%post
  # Software versions
  export R_VERSION=4.0.3
  export RSTUDIO_VERSION=1.3.1093
  export MKL_VERSION=intel-mkl-64bit-2020.0-088

  export DEBIAN_FRONTEND=noninteractive

  # Get dependencies
  apt-get update
  apt-get install -y --no-install-recommends \
    apt-utils \
    gnupg2 \
    locales \
    ca-certificates \
    wget \
    gdebi-core \
    libssl1.1 \
    libssl-dev \
    dpkg-sig \
    python3-ldap3

  # Configure default locale
  echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
  locale-gen en_US.utf8
  /usr/sbin/update-locale LANG=en_US.UTF-8
  export LC_ALL=en_US.UTF-8
  export LANG=en_US.UTF-8

  # Install MKL (following http://dirk.eddelbuettel.com/blog/2018/04/15/#018_mkl_for_debian_ubuntu)
  cd /tmp
  wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB
  apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB
  sh -c 'echo deb https://apt.repos.intel.com/mkl all main > /etc/apt/sources.list.d/intel-mkl.list'
  apt-get update
  apt-get install -y ${MKL_VERSION}
  # bug (?) fix (see https://github.com/eddelbuettel/mkl4deb)
  echo "MKL_THREADING_LAYER=GNU" >> /etc/environment
  mkdir -p /etc/rstudio
  echo "MKL_THREADING_LAYER=GNU" >> /etc/rstudio/rsession-profile
  echo "MKL_THREADING_LAYER=GNU" >> /etc/profile
  # There is an additional setting that is required (see https://cran.rstudio.com/doc/manuals/r-patched/R-admin.html#MKL)
  # echo "MKL_INTERFACE_LAYER=GNU,LP64" >> /etc/environment

  ## update alternatives
  update-alternatives --install /usr/lib/x86_64-linux-gnu/libblas.so     \
                    libblas.so-x86_64-linux-gnu      /opt/intel/mkl/lib/intel64/libmkl_rt.so 50
  update-alternatives --install /usr/lib/x86_64-linux-gnu/libblas.so.3   \
                    libblas.so.3-x86_64-linux-gnu    /opt/intel/mkl/lib/intel64/libmkl_rt.so 50
  update-alternatives --install /usr/lib/x86_64-linux-gnu/liblapack.so   \
                    liblapack.so-x86_64-linux-gnu    /opt/intel/mkl/lib/intel64/libmkl_rt.so 50
  update-alternatives --install /usr/lib/x86_64-linux-gnu/liblapack.so.3 \
                    liblapack.so.3-x86_64-linux-gnu  /opt/intel/mkl/lib/intel64/libmkl_rt.so 50
  echo "/opt/intel/lib/intel64"     >  /etc/ld.so.conf.d/mkl.conf
  echo "/opt/intel/mkl/lib/intel64" >> /etc/ld.so.conf.d/mkl.conf
  ldconfig


  # Install R
  echo "deb http://cran.r-project.org/bin/linux/ubuntu focal-cran40/" > /etc/apt/sources.list.d/r.list
  apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
  # apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
  apt-get update
  apt-get install -y --no-install-recommends \
    r-base=${R_VERSION}* \
    r-base-core=${R_VERSION}* \
    r-base-dev=${R_VERSION}* \
    r-recommended=${R_VERSION}* \
    r-base-html=${R_VERSION}* \
    r-doc-html=${R_VERSION}* \
    libcurl4-openssl-dev \
    libssl-dev \
    libxml2-dev \
    libcairo2-dev \
    libxt-dev \
    libglpk-dev \
    libgmp3-dev \
    libharfbuzz-dev \
    libfribidi-dev

  # Add a default CRAN mirror.  Using CRAN binary timestamp 2020-12-15
  echo "options(repos = c(CRAN = 'https://packagemanager.rstudio.com/all/__linux__/focal/287740'), download.file.method = 'libcurl')" >> /usr/lib/R/etc/Rprofile.site

  # Add a directory for host R libraries
  mkdir -p /library
  echo "R_LIBS_SITE=/library:\${R_LIBS_SITE}" >> /usr/lib/R/etc/Renviron.site

  # Clean up
  # rm -rf /var/lib/apt/lists/*

  # Install RStudio Server
  # not working
  #   gpg2 --keyserver keys.gnupg.net --recv-keys 3F32EE77E331692F 

  # alternative?
   gpg2 --keyserver hkps://peegeepee.com --recv-keys 3F32EE77E331692F

  wget --no-verbose \
       -O rstudio-server.deb \
       "https://download2.rstudio.org/server/bionic/amd64/rstudio-server-${RSTUDIO_VERSION}-amd64.deb" && \
       dpkg-sig --verify rstudio-server.deb && \
    gdebi -n rstudio-server.deb && \
    rm rstudio-server.deb

  # Install tidyverse, here, and packages necessary for knitting to HTML 
  # Using CRAN binary timestamp 2020-12-15
  Rscript -e "install.packages(pkgs = c('tidyverse','here','caTools','rprojroot','Rcpp', 'base64enc', 'digest', 'evaluate', 'glue', 'highr', 'htmltools', 'jsonlite', 'knitr', 'magrittr', 'markdown', 'mime', 'rmarkdown', 'rprojroot', 'stringi', 'stringr', 'tinytex', 'xfun', 'yaml'), \
     repos='https://packagemanager.rstudio.com/all/__linux__/focal/287740', \
     dependencies=TRUE, \
     clean = TRUE)"

# Install additional packages
  Rscript -e "install.packages(pkgs = c('drake', 'igraph', 'fixest','fst', 'lubridate', 'ggthemes'), \
     repos='https://packagemanager.rstudio.com/all/__linux__/focal/287740', \
     dependencies=TRUE, \
     clean = TRUE)"


  # Install extra stuff
  apt-get install -y --no-install-recommends \
    bsdmainutils \
    iproute2 \
    libxml2-dev \
    curl \
    wget \
    bzip2 \
    ca-certificates \
    sudo \
    locales \
    emacs \
    less \
    make \
    git \
    ssh \
    htop \
    jq \
    vim

  # Clean up
  apt-get clean && rm -rf /var/lib/apt/lists/*

  # Make Mountpoints
  mkdir -p /data
  mkdir -p /workspace