Putting install scripts into dockerfile

CI/Dockerfile

@@ -1,9 +1,33 @@
+# Svalinn DAGMC Dockerfile
+
+# Global ARGS set before the first build stage are accessable by all build stages
 ARG UBUNTU_VERSION=18.04
+
+ARG ci_jobs=8
+ARG MOAB_BRANCH=5.4.1
+ARG EMBREE_BRANCH='v3.6.1'
+ARG geant4_version=10.5.1
+
+ARG HDF5_VERSION=1.10.4
+# currently major version must be manually set to match HDF5 version
+ARG HDF5_VERSION_major=1.10
+
+ARG build_dir=/root/build_dir
+ARG install_dir=/root/opt
+
+# clang and gcc are options for the compiler but to use them CC and CXX must be set
+# if clang then change cc to clang and cxx to clang++
+# if gcc then change cc to gcc and cxx to g++
+ARG CC=gcc
+ARG CXX=g++
+
+
 FROM ubuntu:${UBUNTU_VERSION} AS base
 
 # Use bash as the default shell
 SHELL ["/bin/bash", "-c"]
-# Ubuntu Setup
+
+# timezone setup
 ENV TZ=America/Chicago
 RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
 
@@ -33,64 +57,139 @@ RUN apt-get -y update; \
     update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10; \
     pip install cython;
 
+ARG build_dir
+ARG install_dir
 
-# Copy scripts to docker image
-RUN mkdir -p /root/etc/
-COPY CI/ /root/etc/CI
-#TODO move sh file contents into this Dockerfile
-ENV docker_env=/root/etc/CI/env.sh
-
-ENV build_dir=/root/build_dir
-ENV install_dir=/root/opt
-
+ENV build_dir=${build_dir}
+ENV install_dir=${install_dir}
 
 FROM base as external_deps
 
-#setting the COMPILER variable
-ARG COMPILER=gcc
-ENV COMPILER=${COMPILER}
-
-# Set Geant4 env variable
+# accessing gloabl ARGs in build stage
+ARG geant4_version
+ARG EMBREE_BRANCH
+ARG install_dir 
+ARG build_dir
+ARG ci_jobs
+ARG CXX
+ARG CC
+
+ENV geant4_basename=geant4-v${geant4_version}
+ENV geant4_tarball=${geant4_basename}.tar.gz
+ENV geant4_shasum=2397eb859dc4de095ff66059d8bda9f060fdc42e10469dd7890946293eeb0e39
 ENV geant4_build_dir=${build_dir}/geant4
 ENV geant4_install_dir=${install_dir}/geant4
 
-# Build Geant4
-#TODO move sh file contents into this Dockerfile
-RUN /root/etc/CI/docker/build_geant4.sh
-
+RUN mkdir -p ${geant4_build_dir}/build && \
+    cd ${geant4_build_dir} && \
+    wget https://gitlab.cern.ch/geant4/geant4/-/archive/v${geant4_version}/${geant4_tarball} --no-check-certificate && \
+    tar -xzf ${geant4_tarball} && \
+    cd build && \
+    cmake ../${geant4_basename} -DCMAKE_INSTALL_RPATH=${geant4_install_dir}/lib \
+                                -DCMAKE_INSTALL_PREFIX=${geant4_install_dir} \
+                                -DGEANT4_USE_SYSTEM_EXPAT=OFF \
+                                -DCMAKE_BUILD_TYPE=Release \
+                                -DCMAKE_CXX_COMPILER=${CXX} \
+                                -DCMAKE_C_COMPILER=${CC} \
+                                -DBUILD_STATIC_LIBS=ON && \
+    make -j${ci_jobs} && \
+    make install && \
+    cd && \
+    rm -rf ${geant4_build_dir}
+
+# these two double down ENVs don't appear to be used yet
+# However they were in orginal dockerfile, so they have been kept
+# TODO add double down to the dockerfile
 ENV double_down_build_dir=${build_dir}/double-down/
 ENV double_down_install_dir=${install_dir}/double-down/
 
-# Build Embree
-#TODO move sh file contents into this Dockerfile
-RUN /root/etc/CI/docker/build_embree.sh
+ENV embree_install_dir=${install_dir}/embree
+ENV embree_build_dir=${build_dir}/embree
+
+RUN mkdir -p ${embree_build_dir}/build && \
+    cd ${embree_build_dir} && \
+    git clone -b ${EMBREE_BRANCH} https://github.com/embree/embree && \
+    cd build && \
+    cmake ../embree -DCMAKE_INSTALL_PREFIX=${embree_install_dir} \
+                    -DEMBREE_TASKING_SYSTEM=INTERNAL \
+                    -DEMBREE_ISPC_SUPPORT=OFF \
+                    -DEMBREE_TUTORIALS=OFF \
+                    -DEMBREE_TBB_ROOT=/usr && \
+    make -j${ci_jobs} && \
+    make -j${ci_jobs} install && \
+    cd && \
+    rm -rf ${embree_build_dir}
+
 
 FROM external_deps AS hdf5
 
-# Set HDF5 env variable
+# accessing gloabl ARGs in build stage
+ARG HDF5_VERSION_major
+ARG HDF5_VERSION
+ARG install_dir
+ARG build_dir
+ARG ci_jobs
+ARG CXX
+ARG CC
+
 ENV hdf5_build_dir=${build_dir}/hdf5
 ENV hdf5_install_dir=${install_dir}/hdf5
 
-# Build HDF5
-# HDF5 argument possible value: 1.10.4 or system
-ARG HDF5=1.10.4
-ENV HDF5_VERSION=${HDF5}
-#TODO move sh file contents into this Dockerfile
-RUN /root/etc/CI/docker/build_hdf5.sh
+RUN mkdir -p ${hdf5_build_dir}/build && \
+    cd ${hdf5_build_dir} && \
+    wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_VERSION_major}/hdf5-${HDF5_VERSION}/src/hdf5-${HDF5_VERSION}.tar.gz && \
+    tar -xzf hdf5-${HDF5_VERSION}.tar.gz && \
+    cd build && \
+    ../hdf5-${HDF5_VERSION}/configure --enable-shared \
+        --prefix=${hdf5_install_dir} \
+        CXX=${CXX} \
+        CC=${CC} && \
+    make -j${ci_jobs} && \
+    make install && \
+    cd && \
+    rm -rf ${hdf5_build_dir}
+
 
 FROM hdf5 AS moab
 
-ENV PYTHONPATH=/root/build_dir/moab/bld/pymoab/lib/python3.6/site-packages
+# accessing gloabl ARGs in build stage
+ARG install_dir
+ARG MOAB_BRANCH
+ARG build_dir
+ARG ci_jobs
+ARG CXX
+ARG CC
 
 # Set MOAB env variable
 ENV moab_build_dir=${build_dir}/moab
 ENV moab_install_dir=${install_dir}/moab
 
-ARG MOAB=5.3.0
-ENV MOAB_VERSION ${MOAB}
-#TODO move sh file contents into this Dockerfile
-RUN if [ "${MOAB_VERSION}" != "master" ] && [ "${MOAB_VERSION}" != "develop" ]; then \
-        /root/etc/CI/docker/build_moab.sh; \
-    fi;
-
-RUN python -c "import pymoab"
+RUN mkdir -p ${moab_build_dir}/build && \
+    cd ${moab_build_dir} && \
+    git clone -b ${MOAB_BRANCH} --depth 1 https://bitbucket.org/fathomteam/moab && \
+    cd build && \
+    # static building of moab is also an option and was required for older versions
+    # cmake ../moab -DENABLE_HDF5=ON -DHDF5_ROOT=${hdf5_install_dir} \
+    #               -DCMAKE_INSTALL_PREFIX=${moab_install_dir} \
+    #               -DCMAKE_CXX_COMPILER=${CXX} \
+    #               -DCMAKE_C_COMPILER=${CC} \
+    #               -DENABLE_BLASLAPACK=OFF \
+    #               -DBUILD_SHARED_LIBS=OFF \
+    #               -DENABLE_FORTRAN=OFF && \
+    # make -j${ci_jobs} && \
+    # make install && \
+    # rm -rf * && \
+    cmake ../moab -DCMAKE_INSTALL_RPATH=${hdf5_install_dir}/lib:${moab_install_dir}/lib \
+                  -DENABLE_HDF5=ON -DHDF5_ROOT=${hdf5_install_dir} \
+                  -DCMAKE_INSTALL_PREFIX=${moab_install_dir} \
+                  -DCMAKE_CXX_COMPILER=${CXX} \
+                  -DCMAKE_C_COMPILER=${CC} \
+                  -DENABLE_BLASLAPACK=OFF \
+                  -DBUILD_SHARED_LIBS=ON \
+                  -DENABLE_FORTRAN=OFF \
+                  -DENABLE_PYMOAB=ON && \
+    mkdir -p ${moab_build_dir}/build/pymoab/lib/python3.6/site-packages && \
+    PYTHONPATH=${moab_build_dir}/build/pymoab/lib/python3.6/site-packages:${PYTHONPATH} make -j${ci_jobs} && \
+    PYTHONPATH=${moab_build_dir}/build/pymoab/lib/python3.6/site-packages:${PYTHONPATH} make install && \
+    cd && \
+    rm -rf ${moab_build_dir}

CI/scripts/housekeeping.sh

@@ -2,10 +2,6 @@
 
 set -ex
 
-source ${docker_env}
-
-cd ${dagmc_build_dir}
-
 # Ensure clang-format is there
 if ! command -v clang-format &> /dev/null
 then

doc/CHANGELOG.rst

@@ -12,6 +12,7 @@ Next version
    * Using multi stage Dockerfile to reduce the number of Dockerfile (#813)
    * Adding safe folder to allow CI to compile DAGMC (#814)
    * Correction to CMake variable name in OpenMC install instructions (#817)
+   * Move install scripts into Dockerfile  (#822)
    * Updating documentation publishing URL (#823)