First Commit

Dockerfile.base

+FROM centos:7
+MAINTAINER Giuliano Taffoni <giuliano.taffoni@inaf.it>
+ENV CONTAINER_NAME='ALMAGAL'
+USER root
+
+#
+# Set enviroment
+#
+
+ARG J=2
+ARG INSTALL_DIR=/opt/
+ARG CASARELEASE="casa-pipeline-release-5.6.1-8.el7.tar.gz"
+# Settings relevant to the installed software.
+
+ENV CASAVERSION="5.6.1-8"
+ENV CASABIN="/opt/casa-pipeline-release-5.6.1-8.el7/bin"
+ENV DEBIAN_FRONTEND=noninteractive
+#
+# System installs
+#
+RUN yum -y update  && yum -y upgrade
+# remove automatic updates and warnings
+#
+
+RUN yum  -y install gcc g++ gfortran git make cmake wget sudo
+RUN yum -y install freetype libX11 libXft vim-enhanced libGL libSM libXext libXrandr  libXi libXcursor libXinerama
+RUN cd /tmp/ && wget https://casa.nrao.edu/download/distro/casa-pipeline/release/el7/${CASARELEASE}
+RUN tar zxvf /tmp/${CASARELEASE}  -C /opt/
+RUN rm -f /tmp/${CASARELEASE}
+
+# Add group. We chose GID 65527 to try avoiding conflicts.
+RUN groupadd -g 65527 metagroup
+
+# Add user. We chose UID 65527 to try avoiding conflicts.
+RUN useradd metauser -d /home/metauser -u 65527 -g 65527 -m -s /bin/bash
+
+# Add metuaser user to sudoers
+RUN echo "metauser  ALL=(ALL)NOPASSWD: ALL" >> /etc/sudoers
+
+# update PATH
+RUN echo "PATH=${CASABIN}:\$PATH" >> /home/metauser/.bash_profile
+RUN mkdir /home/metauser/.casa
+COPY files/init.py /home/metauser/.casa
+COPY files/analysis_scripts_sing.tgz /home/metauser/
+RUN  cd /home/metauser && tar zxvf /home/metauser/analysis_scripts_sing.tgz  
+# Prepare to make a clean enviroment to share with SINGULARITY
+RUN mv /home/metauser /metauser_home_vanilla
+RUN chmod 777  /metauser_home_vanilla
+
+# Give write access to anyone to the home folder so the entrypoint will be able
+# to copy over the /home/matauser_vanilla into /home/skauser (for Singularity)
+RUN chmod 777 /home
+RUN for i in  `ls ${CASABIN}/`; do ln -s ${CASABIN}/${i} /usr/local/bin/; done
+#----------------------
+# Entrypoint
+#----------------------
+
+# Copy entrypoint
+COPY entrypoint.sh /
+
+# Give right permissions
+RUN chmod 755 /entrypoint.sh
+
+# Set entrypoint
+ENTRYPOINT ["/entrypoint.sh"]
+
+USER metauser

build-base.sh

+#!/bin/bash
+
+if [ "x$TAG" == "x"]; then
+	TAG=latest
+if
+
+docker build -t morgan1971/almagal:$TAG -f Dockerfile.base .

entrypoint.sh

+#!/bin/bash
+
+# Exit on any error. More complex stuff could be done in future
+# (see https://stackoverflow.com/questions/4381618/exit-a-script-on-error)
+set -e
+
+if [ "x$SAFE_MODE" == "xTrue" ]; then
+
+    echo ""
+    echo "[INFO] Not executing entrypoint as we are in safe mode, just opening a Bash shell."
+    exec /bin/bash
+
+else
+    echo ""
+    echo "[INFO] Executing entrypoint..."
+    #---------------------
+    #   Setup home
+    #---------------------
+     
+    if [ ! -f "/home/metauser/.initialized" ]; then
+        echo "[INFO] Setting up home"
+        [ ! -d "/home/metauser" ] &&  mkdir -p /home/metauser
+        # Copy over vanilla home contents
+        if [ "x$DEBUG" == "xTrue" ] ; then
+          ls -la /home/metauser
+          ls -la /metauser_home_vanilla/
+        fi 
+        for x in /metauser_home_vanilla/* /metauser_home_vanilla/.[!.]* /metauser_home_vanilla/..?*; do
+            if [ -e "$x" ]; then cp -a "$x" /home/metauser/; fi
+        done
+        if [ "x$DEBUG" == "xTrue" ] ; then
+          ls -la /home/metauser
+        fi
+        # Mark as initialized
+        [ ! -f "/home/metauser/.initialized" ] && touch /home/metauser/.initialized
+    fi
+
+    #---------------------
+    #   Save env
+    #---------------------
+    echo "[INFO] Dumping env"
+
+    # Save env vars for later usage (e.g. ssh)
+
+    env | \
+    while read env_var; do
+      if [[ $env_var == HOME\=* ]]; then
+          : # Skip HOME var
+      elif [[ $env_var == PWD\=* ]]; then
+          : # Skip PWD var
+      else
+          echo "export $env_var" >> /tmp/env.sh
+      fi
+    done
+
+
+    echo "[INFO] Moving to /home/metauser and setting as home"
+    cd /home/metauser
+    export HOME=/home/metauser
+
+    echo "[INFO] Setting new prompt @$CONTAINER_NAME container"
+    echo 'export PS1="${debian_chroot:+($debian_chroot)}\u@$CONTAINER_NAME@\h:\w\$ "' >> /home/metauser/.bash_profile
+    source /home/metauser/.bash_profile
+
+    # Set entrypoint command
+     if [ "x$@" == "x" ]; then
+        # Start!
+            echo -n "[INFO] Will execute entrypoint command: "
+            echo ""
+            echo "=============================================================="
+            echo ""
+            echo "      Welcome to the EUROEXA $CONTAINER_NAME container!"
+            echo ""
+            echo "=============================================================="
+            echo ""
+            echo "You are now in /home/skauser with write access as user \"$(whoami)\"."
+            echo ""
+            echo "Remember that contents inside this container, unless stored"
+            echo "on a persistent volume mounted from you host machine, will"
+            echo "be wiped out when exiting the container."
+            echo ""
+            COMMAND="/bin/bash"
+        else
+            COMMAND="$@"
+        fi
+fi
+exec $COMMAND

files/init.py

+import sys
+sys.path.append("/usr/lib/python2.7/site-packages")
+sys.path.append("/usr/lib64/python2.7/site-packages")
+sys.path.append("/home/metauser/analysis_scripts/")
+import analysisUtils as aU

run_singularity.sh

+#!/bin/bash
+#
+# This Script allows to execute the conatiner using singularity
+# in an isolated enviroment
+#
+# author <giuliano.taffoni@inaf.it>
+#
+
+if [ 'XXX'$1 = 'XXX' ]; then
+    COMMAND=/bin/bash
+else
+    COMMAND=$1
+fi
+CONTAINER_NAME="morgan1971/almagal"
+CONTAINER_VERSION="v0.1.0"
+export BASE_PORT=
+export SINGULARITYENV_BASE_PORT=$BASE_PORT
+export CONTAINER_NAME="docker://${CONTAINER_NAME}:${CONTAINER_VERSION}"
+
+HOMEDIR=`mktemp -d -t singularity_XXXXXXX`
+mkdir $HOMEDIR/tmp
+mkdir $HOMEDIR/home
+export FLAGS="--pid --writable-tmpfs --no-home --home=/home/metauser --workdir ${HOMEDIR}/tmp -B${HOMEDIR}:/home/  --containall --cleanenv"
+
+singularity run  $FLAGS  ${CONTAINER_NAME} $COMMAND
+
+rm -fr ${HOMEDIR}