add db-client scripts (#74)

* add db-client scripts

Author: haobibo

docker_atom/work/script-setup-db-clients.sh

@@ -0,0 +1,42 @@
+source /opt/utils/script-utils.sh
+
+
+setup_postgresql_client() {
+  local VER_PG=${VERSION_PG:-"14"}
+  # from: https://www.postgresql.org/download/linux/ubuntu/
+  echo "deb http://apt.postgresql.org/pub/repos/apt $(lsb_release -cs)-pgdg main" > /etc/apt/sources.list.d/pgdg.list
+  curl https://www.postgresql.org/media/keys/ACCC4CF8.asc | sudo apt-key add -
+  sudo apt-get update
+  # will download ~9MB files and use ~55MB disk after installation
+  sudo apt-get -y install "postgresql-client-${VER_PG}"
+  echo "@ Version of psql client: $(psql --version)"
+}
+
+
+setup_mysql_client() {
+  sudo apt-get update
+  # will download ~5MB files and use ~76MB disk after installation
+  sudo apt-get -y install mysql-client
+  echo "@ Version of mysql client: $(mysql --version)"
+}
+
+
+setup_mongosh_client() {
+  # from: https://www.mongodb.com/docs/mongodb-shell/install/
+  echo "deb [ arch=amd64,arm64 ] https://repo.mongodb.org/apt/ubuntu $(lsb_release -cs)/mongodb-org/6.0 multiverse" > /etc/apt/sources.list.d/mongodb-org-6.0.list
+  curl -sL https://www.mongodb.org/static/pgp/server-6.0.asc | sudo apt-key add -
+  sudo apt-get update
+  # will download ~38MB files and use ~218MB disk after installation
+  sudo apt-get -y install mongodb-mongosh
+  echo "@ Version of mongosh client: $(mongosh --version)"
+}
+
+
+setup_redis_client() {
+  # from https://redis.io/docs/getting-started/installation/install-redis-on-linux/
+  curl -fsSL https://packages.redis.io/gpg | sudo gpg --dearmor -o /usr/share/keyrings/redis-archive-keyring.gpg
+  echo "deb [signed-by=/usr/share/keyrings/redis-archive-keyring.gpg] https://packages.redis.io/deb $(lsb_release -cs) main" | sudo tee /etc/apt/sources.list.d/redis.list
+  sudo apt-get update
+  sudo apt-get -y install redis-tools
+  echo "@ Version of redis-cli: $(redis-cli --version)"
+}

docker_atom/work/script-setup.sh

@@ -29,7 +29,7 @@ trusted-host=pypi.python.org pypi.org files.pythonhosted.org
 EOF
   fi
 
-  echo "export PATH=$PATH:${CONDA_PREFIX}/bin"		>> /etc/profile
+  echo 'export PATH=${PATH}:${CONDA_PREFIX:-"/opt/conda"}/bin'		>> /etc/profile
   ln -sf "${CONDA_PREFIX}/bin/conda" /usr/bin/
 
      conda config --system --prepend channels conda-forge \
@@ -53,9 +53,10 @@ EOF
 }
 
 setup_conda_with_mamba() {
-  mkdir -pv "${CONDA_PREFIX}"
+  local PREFIX="${CONDA_PREFIX:-/opt/conda}"
+  mkdir -pv "${PREFIX}"
   VERSION_PYTHON=${1:-"3.10"}; shift 1;
-  mamba install -y --root-prefix="${CONDA_PREFIX}" --prefix="${CONDA_PREFIX}" -c "conda-forge" conda pip python="${VERSION_PYTHON}"
+  mamba install -y --root-prefix="${PREFIX}" --prefix="${PREFIX}" -c "conda-forge" conda pip python="${VERSION_PYTHON}"
   setup_conda_postprocess
 }
 

docker_atom/work/script-utils.sh

@@ -4,7 +4,7 @@ set -x
 install_echo()    { cat $1 | cut -d "%" -f 1 | sed '/^$/d' | xargs -r -n1 printf '%s\n' ; }
 
 # function to install apt-get packages from a text file which lists package names (add comments with % char)
-install_apt()     { apt-get -qq update -yq --fix-missing && apt-get -qq install -yq --no-install-recommends `cat $1 | cut -d '%' -f 1` ; }
+install_apt()     { apt-get -qq update -yq --fix-missing && apt-get -qq install -yq --no-install-recommends $(cat "$1" | cut -d '%' -f 1) ; }
 
 # function to install conda packages from a text file which lists package names (add comments with % char)
 install_conda()   { cat $1 | cut -d "%" -f 1 | sed '/^$/d' | xargs -r -n1 conda install -yq ; }
@@ -44,8 +44,8 @@ install_mvn() { cat $1 | cut -d "%" -f 1 | xargs -r -n1 -I {} mvn dependency:cop
 install__clean(){
   which apt-get && apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/*
   which mamba   && mamba clean -ya && rm -rf ~/micromamba
-  which conda   && conda clean -ya && ( rm -rf /opt/conda/pkgs/* || true )
-  find /opt/conda/lib | grep -E "(__pycache__|\.pyc|\.pyo$)" | xargs rm -rf
+  which conda   && conda clean -ya && ( rm -rf "${CONDA_PREFIX:-/opt/conda}"/pkgs/* || true )
+  find "${CONDA_PREFIX:-/opt/conda}"/lib | grep -E "(__pycache__|\.pyc|\.pyo$)" | xargs rm -rf
   which npm     && npm cache clean --force
   rm -rf /opt/conda/share/jupyter/lab/staging
   ( rm -rf /tmp/.* /tmp/* /var/log/* /var/cache/* /root/.cache /root/.* || true )
@@ -72,21 +72,21 @@ list_installed_packages() {
 }
 
 fix_permission() {
-  DIRECTORY=$1; GROUP_ID=$2; shift 2;
-  for d in "$DIRECTORY"; do
+  GROUP_ID=${1:-0}; shift 1;
+  for d in "$@"; do
       find "${d}" \
           ! \( \
               -group "${GROUP_ID}" \
               -a -perm -g+rwX \
           \) \
-          -exec chgrp "${GROUP_ID}" {} \; \
-          -exec chmod g+rwX {} \;
+          -exec chgrp "${GROUP_ID}" -- {} \+ \
+          -exec chmod g+rwX -- {} \+
       # setuid, setgid *on directories only*
       find "${d}" \
           \( \
               -type d \
               -a ! -perm -6000 \
           \) \
-          -exec chmod +6000 {} \;
+          -exec chmod +6000 -- {} \+;
   done
 }

docker_base/Dockerfile

@@ -15,6 +15,7 @@ RUN source /opt/utils/script-setup.sh \
  && echo "Install tini:" && setup_tini \
  && echo "Install Mamba:" && setup_mamba \
  && echo "Install Python ${PYTHON_VERSION} and conda:" && setup_conda_with_mamba ${PYTHON_VERSION} \
+ && fix_permission 0 ${CONDA_PREFIX} \
  && echo "Replace system Python3 with conda Python - note that /bin and /sbin are symlinks of /usr/bin in docker image ubuntu" \
  && PYTHON_VERSION_DEFAULT=$(py3versions -v -i) \
  && sed -i "s/${PYTHON_VERSION_DEFAULT}/${PYTHON_VERSION}/g" /usr/share/python3/debian_defaults \

docker_cuda/Dockerfile

@@ -6,6 +6,9 @@ FROM ${BASE_NAMESPACE:+$BASE_NAMESPACE/}${BASE_IMG}
 
 LABEL maintainer="haobibo@gmail.com"
 
+# Let NVIDIA docker ignore cuda requirement check
+ENV NVIDIA_DISABLE_REUIRE=1
+
 # For cuda version 10.0, the image is solely serverd for legacy tensorflow 1.15, which requires python 3.7
 # For tensorflow 2.x or torch, python>=3.9 is supported.
 RUN echo ${CUDA_VERSION} && nvcc --version \