Task #8415: Added dynspec Dockerfile

.gitattributes

@@ -2356,6 +2356,9 @@ CMake/variants/variants.node521 -text
 CMake/variants/variants.phi -text
 CMake/variants/variants.sharkbay -text
 Docker/docker-build-all.sh -text
+Docker/dynspec/Dockerfile -text
+Docker/dynspec/bashrc -text
+Docker/dynspec/chuser.sh -text
 Docker/lofar-base/Dockerfile.tmpl -text
 Docker/lofar-base/bashrc -text
 Docker/lofar-base/bashrc.d/00-casacore -text

Docker/CMakeLists.txt

@@ -57,6 +57,7 @@ endforeach()
 
 # Install everything else
 install(DIRECTORY
+  dynspec
   lofar-base
   lofar-pipeline
   lofar-outputproc

Docker/docker-build-all.sh

@@ -12,5 +12,6 @@ cd ${LOFARROOT}/share/docker
 build lofar-base && \
 build lofar-pipeline && \
 build lofar-outputproc && \
-build lofar-tbb
+build lofar-tbb && \
+build dynspec
 

Docker/dynspec/Dockerfile

+#
+# base
+#
+FROM ubuntu:12.04
+
+#
+# common-environment
+#
+ENV USER=lofar
+ENV INSTALLDIR=/opt
+
+#
+# environment
+#
+ENV DEBIAN_FRONTEND=noninteractive \
+    PYTHON_VERSION=2.7
+
+#
+# versions
+# Requires boost 1.48
+# Remove casacore?
+#
+ENV CASACORE_VERSION=2.0.3 \
+    CASAREST_VERSION=1.4.1 \
+    PYTHON_CASACORE_VERSION=2.0.1 \
+    BOOST_VERSION=1.48
+
+#
+# set-uid
+#
+ENV UID=1000
+
+#
+# set-build-options
+#
+ENV J=6
+
+#
+# Base and runtime dependencies
+#
+#RUN sed -i 's/archive.ubuntu.com/osmirror.rug.nl/' /etc/apt/sources.list 
+RUN apt-get update && apt-get upgrade -y
+RUN apt-get install -y sudo 
+#python2.7 libpython2.7 
+#    apt-get install -y libblas3 liblapacke python-numpy libcfitsio3 libwcs4 libfftw3-bin libhdf5-7 libboost-python${BOOST_VERSION}.0 && \
+#    apt-get install -y nano
+
+
+
+#
+# setup-account
+#
+RUN echo 'ALL ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers && \
+    sed -i 's/requiretty/!requiretty/g' /etc/sudoers && \
+    useradd -m -u ${UID} ${USER} && \
+    chmod a+wr /etc/passwd /etc/group
+
+#
+# setup install dir
+#
+RUN mkdir -p ${INSTALLDIR} && chown ${USER}.${USER} ${INSTALLDIR}
+
+
+USER ${USER}
+
+#
+# *******************
+# Lofar User Software
+# *******************
+#
+RUN sudo apt-get update && sudo apt-get upgrade -y && \
+    sudo apt-get install -y g++ gfortran flex swig bison subversion \
+                     zlib1g-dev libatlas-base-dev liblapack-dev \
+                     libncurses5-dev libfreetype6-dev libpng12-dev \
+                     python-dev python-tk python-pyfits tk8.5-dev fftw3-dev \
+                     libbz2-dev libghc-readline-dev \
+                     git git git-core git-doc git-man git-svn \
+                     valgrind 
+
+RUN sudo apt-get install -y libboost${BOOST_VERSION}-all-dev \
+                     wcslib-dev \
+                     cmake cmake-doc cmake-curses-gui make \
+                     libgsl0-dev \
+                     python-matplotlib \
+                     python-sphinx \
+                     libcfitsio3-dev \
+                     python-numpy \
+                     num-utils \
+                     python-scipy \
+                     libblas-dev \
+                     python-sip-dev \
+                     openmpi-bin openmpi-common \
+                     ipython
+
+RUN cd $INSTALLDIR && svn co http://usg.lofar.org/svn/code/trunk lofarsoft && \
+    export LOFARSOFT=${INSTALLDIR}/lofarsoft && . $LOFARSOFT/devel_common/scripts/init.sh && \
+    cd $LOFARSOFT && ./bootstrap && cd build && cmake -DCASACORE_FROM_LATEST_SVN_REVISION=ON . && make rebuild_cache  && \
+    rm -rf $LOFARSOFT/src/Pulsar 
+
+ENV LOFARSOFT=${INSTALLDIR}/lofarsoft
+
+RUN sudo apt-get install -y libhdf5-serial-dev python-h5py
+
+RUN . $LOFARSOFT/devel_common/scripts/init.sh && cd $LOFARSOFT/build && make dal
+
+RUN cd /opt/lofarsoft/src/Dynspec-Toolkit/Dynspec-CEP2/src/ICD3-ICD6-Rebin && \
+    g++ -O3 -s -Wall -o DynspecPart  *cpp -I /opt/lofarsoft/release//include -L /opt/lofarsoft/release//lib -llofardal -lhdf5 && \
+    sudo ln -s /opt/lofarsoft/src/Dynspec-Toolkit/Dynspec-CEP2/Beam2Dynspec-Rebin /usr/local/bin/Beam2Dynspec-Rebin && \
+    sudo ln -s /opt/lofarsoft/src/Dynspec-Toolkit/Dynspec-CEP2/src/ICD3-ICD6-Rebin/DynspecPart /usr/local/bin/DynspecPart && \
+    cd /opt/lofarsoft/src/Dynspec-Toolkit/Dynspec-CEP2/src/ICD3-ICD6-Quicklook && \
+    g++ -O3 -s -Wall -o DynspecQuick  *cpp -I /opt/lofarsoft/release//include -L /opt/lofarsoft/release//lib -llofardal -lhdf5 && \
+    sudo ln -s /opt/lofarsoft/src/Dynspec-Toolkit/Dynspec-CEP2/Beam2Dynspec-Quick /usr/local/bin/Beam2Dynspec-Quick && \
+    sudo ln -s /opt/lofarsoft/src/Dynspec-Toolkit/Dynspec-CEP2/src/ICD3-ICD6-Quicklook/DynspecQuick /usr/local/bin/DynspecQuick && \
+    cd /opt/lofarsoft/src/Dynspec-Toolkit/Dynspec-CEP2/src/ICD3-ICD6-Complete && \
+    g++ -O3 -s -Wall -o DynspecAll  *cpp -I /opt/lofarsoft/release//include -L /opt/lofarsoft/release//lib -llofardal -lhdf5 && \
+    sudo ln -s /opt/lofarsoft/src/Dynspec-Toolkit/Dynspec-CEP2/Beam2Dynspec-Complete /usr/local/bin/Beam2Dynspec-Complete && \
+    sudo ln -s /opt/lofarsoft/src/Dynspec-Toolkit/Dynspec-CEP2/src/ICD3-ICD6-Complete/DynspecAll /usr/local/bin/DynspecAll && \
+    cd /opt/lofarsoft/src/Dynspec-Toolkit/Dynspec-Tool/src/ICD6-Linear-Polar && \
+    g++ -O3 -s -Wall -o Dynspec_Linear_Polar   *cpp -I /opt/lofarsoft/release//include -L /opt/lofarsoft/release//lib -llofardal -lhdf5 && \
+    sudo ln -s /opt/lofarsoft/src/Dynspec-Toolkit/Dynspec-Tool/Dynspec-LinPol /usr/local/bin/Dynspec-LinPol && \
+    sudo ln -s /opt/lofarsoft/src/Dynspec-Toolkit/Dynspec-Tool/src/ICD6-Linear-Polar/Dynspec_Linear_Polar /usr/local/bin/Dynspec_Linear_Polar && \
+    cd /opt/lofarsoft/src/Dynspec-Toolkit/Dynspec-Tool/src/ICD6-Rebin    && \ 
+    g++ -O3 -s -Wall -o Dyn2Dyn  *cpp -I /opt/lofarsoft/release//include -L /opt/lofarsoft/release//lib -llofardal -lhdf5 && \
+    sudo ln -s /opt/lofarsoft/src/Dynspec-Toolkit/Dynspec-Tool/Dynspec-Rebin /usr/local/bin/Dynspec-Rebin && \
+    sudo ln -s /opt/lofarsoft/src/Dynspec-Toolkit/Dynspec-Tool/src/ICD6-Rebin/Dyn2Dyn /usr/local/bin/Dyn2Dyn && \
+    cd /opt/lofarsoft/src/Dynspec-Toolkit/Dynspec-Tool/src/ICD6-Substraction && \
+    g++ -O3 -s -Wall -o Dynspec_Substraction  *cpp -I /opt/lofarsoft/release//include -L /opt/lofarsoft/release//lib -llofardal -lhdf5 && \
+    sudo ln -s /opt/lofarsoft/src/Dynspec-Toolkit/Dynspec-Tool/Dynspec-Substract /usr/local/bin/Dynspec-Substract && \
+    sudo ln -s /opt/lofarsoft/src/Dynspec-Toolkit/Dynspec-Tool/src/ICD6-Substraction/Dynspec_Substraction /usr/local/bin/Dynspec_Substraction 
+
+
+
+
+
+#
+# config
+#
+COPY bashrc /opt/bashrc
+
+#
+# entry
+#
+#COPY ["bashrc", "bashrc.d", "${INSTALLDIR}/"]
+
+COPY chuser.sh /usr/local/bin/chuser.sh
+ENTRYPOINT ["/usr/local/bin/chuser.sh"]
+

Docker/dynspec/bashrc

+#!/bin/bash
+
+# lofar
+[ -r ${INSTALLDIR}/lofar/lofarinit.sh ] && source ${INSTALLDIR}/lofar/lofarinit.sh
+export PATH PYTHONPATH LD_LIBRARY_PATH LOFARROOT
+
+# qpid
+#source ${INSTALLDIR}/qpid/.profile
+
+# lofarsoft
+echo "sourcing init"
+source ${LOFARSOFT}/devel_common/scripts/init.sh
+
+export PYTHONPATH=$PYTHONPATH:${LOFARSOFT}/release/lib/python/dal
+export LD_LIBRARY_PATH=LD_LIBRARY_PATH:${LOFARSOFT}/release/lib

Docker/dynspec/chuser.sh

+#!/usr/bin/env bash
+
+# Correct UID
+export UID=`id -u`
+
+# Configure user
+if [ -z "${USER}" ]; then
+  export USER=${UID}
+fi
+
+# Create home directory
+if [ -z "${HOME}" ]; then
+  export HOME=/home/${USER}
+  mkdir -p $HOME && cd $HOME
+fi
+
+# Add user to system
+fgrep -q ":x:${UID}:" /etc/passwd || echo "${USER}:x:${UID}:${UID}::${HOME}:/bin/bash" >> /etc/passwd
+fgrep -q ":x:${UID}:" /etc/group  || echo "${USER}:x:${UID}:" >> /etc/group
+
+# Set the environment
+[ -e /opt/bashrc ] && source /opt/bashrc
+
+# Run the requested command
+if [ -z "$*" ]; then
+  exec /bin/bash
+else
+  exec "$@"
+fi