Merge pull request #395 from eitsupi/refactoring/core-scripts

Refactoring core Rocker scripts
rocker-org · Apr 1, 2022 · 89d36d2 · 89d36d2
2 parents 98738ed + d968d4f
commit 89d36d2
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Showing 20 changed files with 366 additions and 370 deletions.
diff --git a/scripts/default_user.sh b/scripts/default_user.sh
@@ -1,30 +1,31 @@
 #!/bin/bash
 set -e
 
-if id -u "${user}" >/dev/null 2>&1; then
-    echo 'rstudio user already exists'
-else
-  ## Need to configure non-root user for RStudio
-  DEFAULT_USER=${1:-${DEFAULT_USER:-rstudio}}
-  useradd -s /bin/bash -m $DEFAULT_USER
-  echo "${DEFAULT_USER}:${DEFAULT_USER}" | chpasswd
-  addgroup ${DEFAULT_USER} staff
+DEFAULT_USER=${1:-${DEFAULT_USER:-"rstudio"}}
 
-  mkdir -p /home/${DEFAULT_USER}/.rstudio/monitored/user-settings
-  echo "alwaysSaveHistory='0' \
-      \nloadRData='0' \
-      \nsaveAction='0'" \
-      > /home/${DEFAULT_USER}/.rstudio/monitored/user-settings/user-settings
+if id -u "${DEFAULT_USER}" >/dev/null 2>&1; then
+    echo "User ${DEFAULT_USER} already exists"
+else
+    ## Need to configure non-root user for RStudio
+    useradd -s /bin/bash -m "$DEFAULT_USER"
+    echo "${DEFAULT_USER}:${DEFAULT_USER}" | chpasswd
+    addgroup "${DEFAULT_USER}" staff
 
-  chown -R "${DEFAULT_USER}:${DEFAULT_USER}" "/home/${DEFAULT_USER}"
+    ## Rocker's default RStudio settings, for better reproducibility
+    mkdir -p "/home/${DEFAULT_USER}/.rstudio/monitored/user-settings"
+    cat <<EOF >"/home/${DEFAULT_USER}/.rstudio/monitored/user-settings/user-settings"
+alwaysSaveHistory="0"
+loadRData="0"
+saveAction="0"
+EOF
+    chown -R "${DEFAULT_USER}:${DEFAULT_USER}" "/home/${DEFAULT_USER}"
 fi
 
 # If shiny server installed, make the user part of the shiny group
 if [ -x "$(command -v shiny-server)" ]; then
-  adduser ${DEFAULT_USER} shiny
+    adduser "${DEFAULT_USER}" shiny
 fi
 
 ## configure git not to request password each time
 git config --system credential.helper 'cache --timeout=3600'
 git config --system push.default simple
-
diff --git a/scripts/init_set_env.sh b/scripts/init_set_env.sh
@@ -3,11 +3,10 @@
 
 ## Set our dynamic variables in Renviron.site to be reflected by RStudio Server or Shiny Server
 exclude_vars="HOME PASSWORD RSTUDIO_VERSION BATCH_USER_CREATION"
-for file in /var/run/s6/container_environment/*
-do
-  sed -i "/^${file##*/}=/d" ${R_HOME}/etc/Renviron.site
-  regex="(^| )${file##*/}($| )"
-  [[ ! $exclude_vars =~ $regex ]] && echo "${file##*/}=$(cat $file)" >> ${R_HOME}/etc/Renviron.site || echo "skipping $file"
+for file in /var/run/s6/container_environment/*; do
+    sed -i "/^${file##*/}=/d" "${R_HOME}/etc/Renviron.site"
+    regex="(^| )${file##*/}($| )"
+    [[ ! $exclude_vars =~ $regex ]] && echo "${file##*/}=$(cat "${file}")" >>"${R_HOME}/etc/Renviron.site" || echo "skipping ${file}"
 done
 
 ## only file-owner (root) should read container_environment files:

diff --git a/scripts/init_userconf.sh b/scripts/init_userconf.sh
@@ -11,21 +11,14 @@ UMASK=${UMASK:=022}
 LANG=${LANG:=en_US.UTF-8}
 TZ=${TZ:=Etc/UTC}
 
-bold=$(tput bold)
-normal=$(tput sgr0)
-
-if [[ ${DISABLE_AUTH,,} == "true" ]]
-
-then
-	mv /etc/rstudio/disable_auth_rserver.conf /etc/rstudio/rserver.conf
-	echo "USER=$USER" >> /etc/environment
+if [[ ${DISABLE_AUTH,,} == "true" ]]; then
+    mv /etc/rstudio/disable_auth_rserver.conf /etc/rstudio/rserver.conf
+    echo "USER=$USER" >>/etc/environment
 fi
 
-if grep --quiet "auth-none=1" /etc/rstudio/rserver.conf
-then
-	echo "Skipping authentication as requested"
-elif [ -z "$PASSWORD" ]
-then
+if grep --quiet "auth-none=1" /etc/rstudio/rserver.conf; then
+    echo "Skipping authentication as requested"
+elif [ -z "$PASSWORD" ]; then
     PASSWORD=$(pwgen 16 1)
     printf "\n\n"
     tput bold
@@ -36,76 +29,64 @@ then
     printf "\n\n"
 fi
 
-if [ "$USERID" -lt 1000 ]
-# Probably a macOS user, https://github.com/rocker-org/rocker/issues/205
-  then
+if [ "$USERID" -lt 1000 ]; then # Probably a macOS user, https://github.com/rocker-org/rocker/issues/205
     echo "$USERID is less than 1000"
     check_user_id=$(grep -F "auth-minimum-user-id" /etc/rstudio/rserver.conf)
-    if [[ ! -z $check_user_id ]]
-    then
-      echo "minumum authorised user already exists in /etc/rstudio/rserver.conf: $check_user_id"
+    if [[ -n $check_user_id ]]; then
+        echo "minumum authorised user already exists in /etc/rstudio/rserver.conf: $check_user_id"
     else
-      echo "setting minumum authorised user to 499"
-      echo auth-minimum-user-id=499 >> /etc/rstudio/rserver.conf
+        echo "setting minumum authorised user to 499"
+        echo auth-minimum-user-id=499 >>/etc/rstudio/rserver.conf
     fi
 fi
 
-if [ "$USERID" -ne 1000 ]
-## Configure user with a different USERID if requested.
-  then
+if [ "$USERID" -ne 1000 ]; then ## Configure user with a different USERID if requested.
     echo "deleting the default user"
-    userdel $DEFAULT_USER
+    userdel "$DEFAULT_USER"
     echo "creating new $USER with UID $USERID"
-    useradd -m $USER -u $USERID
-    mkdir -p /home/$USER
-    chown -R $USER /home/$USER
-    usermod -a -G staff $USER
-elif [ "$USER" != "$DEFAULT_USER" ]
-  then
+    useradd -m "$USER" -u $USERID
+    mkdir -p /home/"$USER"
+    chown -R "$USER" /home/"$USER"
+    usermod -a -G staff "$USER"
+elif [ "$USER" != "$DEFAULT_USER" ]; then
     ## cannot move home folder when it's a shared volume, have to copy and change permissions instead
-    cp -r /home/$DEFAULT_USER /home/$USER
+    cp -r /home/"$DEFAULT_USER" /home/"$USER"
     ## RENAME the user
-    usermod -l $USER -d /home/$USER $DEFAULT_USER
-    groupmod -n $USER $DEFAULT_USER
-    usermod -a -G staff $USER
-    chown -R $USER:$USER /home/$USER
+    usermod -l "$USER" -d /home/"$USER" "$DEFAULT_USER"
+    groupmod -n "$USER" "$DEFAULT_USER"
+    usermod -a -G staff "$USER"
+    chown -R "$USER":"$USER" /home/"$USER"
     echo "USER is now $USER"
 fi
 
-if [ "$GROUPID" -ne 1000 ]
-## Configure the primary GID (whether rstudio or $USER) with a different GROUPID if requested.
-  then
-    echo "Modifying primary group $(id $USER -g -n)"
-    groupmod -g $GROUPID $(id $USER -g -n)
+if [ "$GROUPID" -ne 1000 ]; then ## Configure the primary GID (whether rstudio or $USER) with a different GROUPID if requested.
+    echo "Modifying primary group $(id "${USER}" -g -n)"
+    groupmod -g $GROUPID "$(id "${USER}" -g -n)"
     echo "Primary group ID is now custom_group $GROUPID"
 fi
 
 ## Add a password to user
 echo "$USER:$PASSWORD" | chpasswd
 
 # Use Env flag to know if user should be added to sudoers
-if [[ ${ROOT,,} == "true" ]]
-  then
-    adduser $USER sudo && echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
+if [[ ${ROOT,,} == "true" ]]; then
+    adduser "$USER" sudo && echo '%sudo ALL=(ALL) NOPASSWD:ALL' >>/etc/sudoers
     echo "$USER added to sudoers"
 fi
 
 ## Change Umask value if desired
-if [ "$UMASK" -ne 022 ]
-  then
-    echo "server-set-umask=false" >> /etc/rstudio/rserver.conf
-    echo "Sys.umask(mode=$UMASK)" >> /home/$USER/.Rprofile
+if [ "$UMASK" -ne 022 ]; then
+    echo "server-set-umask=false" >>/etc/rstudio/rserver.conf
+    echo "Sys.umask(mode=$UMASK)" >>/home/"$USER"/.Rprofile
 fi
 
 ## Next one for timezone setup
-if [ "$TZ" !=  "Etc/UTC" ]
-  then
-    ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+if [ "$TZ" != "Etc/UTC" ]; then
+    ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ >/etc/timezone
 fi
 
 ## Update Locale if needed
-if [ "$LANG" !=  "en_US.UTF-8" ]
-  then
+if [ "$LANG" != "en_US.UTF-8" ]; then
     /usr/sbin/locale-gen --lang $LANG
     /usr/sbin/update-locale --reset LANG=$LANG
 fi
diff --git a/scripts/install_binder.sh b/scripts/install_binder.sh
@@ -10,20 +10,20 @@ DEFAULT_USER=${DEFAULT_USER:-rstudio}
 NB_USER=${NB_USER:-${DEFAULT_USER}}
 NB_UID=${NB_UID:-1000}
 WORKDIR=${WORKDIR:-/home/${NB_USER}}
-usermod -l ${NB_USER} ${DEFAULT_USER}
+usermod -l "${NB_USER}" "${DEFAULT_USER}"
 # Create a venv dir owned by unprivileged user & set up notebook in it
 # This allows non-root to install python libraries if required
-mkdir -p ${PYTHON_VENV_PATH} && chown -R ${NB_USER} ${PYTHON_VENV_PATH}
+mkdir -p "${PYTHON_VENV_PATH}"
+chown -R "${NB_USER}" "${PYTHON_VENV_PATH}"
 
 # And set ENV for R! It doesn't read from the environment...
-echo "PATH=${PATH}" >> ${R_HOME}/etc/Renviron.site
-echo "export PATH=${PATH}" >> ${WORKDIR}/.profile
+echo "PATH=${PATH}" >>"${R_HOME}/etc/Renviron.site"
+echo "export PATH=${PATH}" >>"${WORKDIR}/.profile"
 
+cd "${WORKDIR}"
 ## This gets run as user
-su ${NB_USER}
-cd ${WORKDIR}
-python3 -m venv ${PYTHON_VENV_PATH}
-pip3 install --no-cache-dir jupyter-rsession-proxy>=2.0 notebook jupyterlab
+sudo -u "${NB_USER}" python3 -m venv "${PYTHON_VENV_PATH}"
+pip3 install --no-cache-dir jupyter-rsession-proxy notebook jupyterlab >=2.0
 
 R --quiet -e "devtools::install_github('IRkernel/IRkernel')"
 R --quiet -e "IRkernel::installspec(prefix='${PYTHON_VENV_PATH}')"
diff --git a/scripts/install_cuda-10.1.sh b/scripts/install_cuda-10.1.sh
@@ -1,28 +1,29 @@
 #!/bin/bash
 set -e
 
-apt-get update && apt-get install -y --no-install-recommends \
-gnupg2 curl ca-certificates && \
-    curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub | apt-key add - && \
-    echo "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64 /" > /etc/apt/sources.list.d/cuda.list && \
-    echo "deb https://developer.download.nvidia.com/compute/machine-learning/repos/ubuntu1804/x86_64 /" > /etc/apt/sources.list.d/nvidia-ml.list && \
-    apt-get purge --autoremove -y curl && \
+apt-get update
+apt-get install -y --no-install-recommends \
+    gnupg2 curl ca-certificates
+curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub | apt-key add -
+echo "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64 /" >/etc/apt/sources.list.d/cuda.list
+echo "deb https://developer.download.nvidia.com/compute/machine-learning/repos/ubuntu1804/x86_64 /" >/etc/apt/sources.list.d/nvidia-ml.list
+apt-get purge --autoremove -y curl
 rm -rf /var/lib/apt/lists/*
 
 CUDA_VERSION=${CUDA_VERSION:-10.1.243}
 CUDA_PKG_VERSION=${CUDA_PKG_VERSION:-10-1=$CUDA_VERSION-1}
 
 # For libraries in the cuda-compat-* package: https://docs.nvidia.com/cuda/eula/index.html#attachment-a
-apt-get update && apt-get install -y --no-install-recommends \
-    cuda-cudart-$CUDA_PKG_VERSION \
-    cuda-compat-10-1 && \
-    ln -s cuda-10.1 /usr/local/cuda && \
+apt-get update
+apt-get install -y --no-install-recommends \
+    "cuda-cudart-${CUDA_PKG_VERSION}" \
+    cuda-compat-10-1 &&
+    ln -s cuda-10.1 /usr/local/cuda &&
     rm -rf /var/lib/apt/lists/*
 
 # Required for nvidia-docker v1
-echo "/usr/local/nvidia/lib" >> /etc/ld.so.conf.d/nvidia.conf && \
-    echo "/usr/local/nvidia/lib64" >> /etc/ld.so.conf.d/nvidia.conf
-
+echo "/usr/local/nvidia/lib" >>/etc/ld.so.conf.d/nvidia.conf &&
+    echo "/usr/local/nvidia/lib64" >>/etc/ld.so.conf.d/nvidia.conf
 
 ## PATH & LD_LIBRARY_PATH are wrong?
 PATH=${PATH:-/usr/local/nvidia/bin:/usr/local/cuda/bin:${PATH}}
@@ -36,58 +37,53 @@ NVIDIA_REQUIRE_CUDA=${NVIDIA_REQUIRE_CUDA:-"cuda>=10.1 brand=tesla,driver>=384,d
 ## Tensorflow config for cuda runtime.
 ## Adapted from:
 
-ARCH=
 CUDA=10.1
 CUDNN=7.6.4.38-1
-CUDNN_MAJOR_VERSION=7
-LIB_DIR_PREFIX=x86_64
 LIBNVINFER=6.0.1-1
 LIBNVINFER_MAJOR_VERSION=6
 
 #SHELL ["/bin/bash", "-c"]
 # Pick up some TF dependencies
-        # There appears to be a regression in libcublas10=10.2.2.89-1 which
-        # prevents cublas from initializing in TF. See
-        # https://github.com/tensorflow/tensorflow/issues/9489#issuecomment-562394257
-apt-get update && apt-get install -y --no-install-recommends --allow-downgrades \
-        build-essential \
-        cuda-command-line-tools-10-1 \
-        libcublas10=10.2.1.243-1 \
-        cuda-nvrtc-10-1 \
-        cuda-cufft-10-1 \
-        cuda-curand-10-1 \
-        cuda-cusolver-10-1 \
-        cuda-cusparse-10-1 \
-        curl \
-        libcudnn7=${CUDNN}+cuda10.1 \
-        libfreetype6-dev \
-        libhdf5-serial-dev \
-        libzmq3-dev \
-        pkg-config \
-        software-properties-common \
-        unzip
+# There appears to be a regression in libcublas10=10.2.2.89-1 which
+# prevents cublas from initializing in TF. See
+# https://github.com/tensorflow/tensorflow/issues/9489#issuecomment-562394257
+apt-get update
+apt-get install -y --no-install-recommends --allow-downgrades \
+    build-essential \
+    cuda-command-line-tools-10-1 \
+    libcublas10=10.2.1.243-1 \
+    cuda-nvrtc-10-1 \
+    cuda-cufft-10-1 \
+    cuda-curand-10-1 \
+    cuda-cusolver-10-1 \
+    cuda-cusparse-10-1 \
+    curl \
+    libcudnn7=${CUDNN}+cuda10.1 \
+    libfreetype6-dev \
+    libhdf5-serial-dev \
+    libzmq3-dev \
+    pkg-config \
+    software-properties-common \
+    unzip
 
 # Install TensorRT if not building for PowerPC
-apt-get update && \
-        apt-get install -y --no-install-recommends libnvinfer${LIBNVINFER_MAJOR_VERSION}=${LIBNVINFER}+cuda${CUDA} \
-        libnvinfer-plugin${LIBNVINFER_MAJOR_VERSION}=${LIBNVINFER}+cuda${CUDA} \
-        && apt-get clean \
-        && rm -rf /var/lib/apt/lists/*
+apt-get update
+apt-get install -y --no-install-recommends libnvinfer${LIBNVINFER_MAJOR_VERSION}=${LIBNVINFER}+cuda${CUDA} \
+    libnvinfer-plugin${LIBNVINFER_MAJOR_VERSION}=${LIBNVINFER}+cuda${CUDA}
+apt-get clean
+rm -rf /var/lib/apt/lists/*
 
 # For CUDA profiling, TensorFlow requires CUPTI.
-LD_LIBRARY_PATH==${LD_LIBRARY_PATH:-/usr/local/cuda/extras/CUPTI/lib64:/usr/local/cuda/lib64:$LD_LIBRARY_PATH}
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH:-/usr/local/cuda/extras/CUPTI/lib64:/usr/local/cuda/lib64:$LD_LIBRARY_PATH}
 
 # Link the libcuda stub to the location where tensorflow is searching for it and reconfigure
 # dynamic linker run-time bindings
 ln -s /usr/local/cuda/lib64/stubs/libcuda.so /usr/local/cuda/lib64/stubs/libcuda.so.1
-echo "/usr/local/cuda/lib64/stubs" > /etc/ld.so.conf.d/z-cuda-stubs.conf
+echo "/usr/local/cuda/lib64/stubs" >/etc/ld.so.conf.d/z-cuda-stubs.conf
 ldconfig
 
 ## Add nvtop
 #/rocker_scripts/install_nvtop.sh
 
-
 ## Add tensorflow-gpu==1.15 dependencies on the CUDA 10.0 libraries:
 /rocker_scripts/install_tf1_cuda_10_0.sh
-
-