Merge pull request #1887 from shimwell/adding_libmesh_to_docker

Adding libmesh to docker
2026-07-28 06:05:58 -04:00 · 2021-12-16 12:37:00 -05:00 · 2021-12-16 12:37:00 -05:00 · 7f5e9e73d8
commit 7f5e9e73d8
parent c6328d5504 180fb66490
9 changed files with 323 additions and 119 deletions
--- a/.github/workflows/dockerhub-publish-dagmc-libmesh.yml
+++ b/.github/workflows/dockerhub-publish-dagmc-libmesh.yml
@ -0,0 +1,36 @@
+name: dockerhub-publish-latest-dagmc-libmesh
+
+on:
+  push:
+    branches: master
+
+jobs:
+  main:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      -
+        name: Login to DockerHub
+        uses: docker/login-action@v1 
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      -
+        name: Build and push
+        id: docker_build
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          tags: openmc/openmc:latest-libmesh
+          build-args: |
+            build_dagmc=on
+            build_libmesh=on
+            compile_cores=2
+      -
+        name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}
--- a/.github/workflows/dockerhub-publish-dagmc.yml
+++ b/.github/workflows/dockerhub-publish-dagmc.yml
@ -28,7 +28,7 @@ jobs:
          push: true
          tags: openmc/openmc:latest-dagmc
          build-args: |
-            include_dagmc=true
+            build_dagmc=on
            compile_cores=2
      -
        name: Image digest
--- a/.github/workflows/dockerhub-publish-dev.yml
+++ b/.github/workflows/dockerhub-publish-dev.yml
@ -29,6 +29,7 @@ jobs:
          tags: openmc/openmc:develop
          build-args: |
            compile_cores=2
+            openmc_branch=develop
      -
        name: Image digest
        run: echo ${{ steps.docker_build.outputs.digest }}
--- a/.github/workflows/dockerhub-publish-develop-dagmc-libmesh.yml
+++ b/.github/workflows/dockerhub-publish-develop-dagmc-libmesh.yml
@ -0,0 +1,37 @@
+name: dockerhub-publish-develop-dagmc-libmesh
+
+on:
+  push:
+    branches: develop
+
+jobs:
+  main:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      -
+        name: Login to DockerHub
+        uses: docker/login-action@v1 
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      -
+        name: Build and push
+        id: docker_build
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          tags: openmc/openmc:develop-dagmc
+          build-args: |
+            build_dagmc=on
+            build_libmesh=on
+            compile_cores=2
+            openmc_branch=develop
+      -
+        name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}
--- a/.github/workflows/dockerhub-publish-develop-dagmc.yml
+++ b/.github/workflows/dockerhub-publish-develop-dagmc.yml
@ -28,8 +28,9 @@ jobs:
          push: true
          tags: openmc/openmc:develop-dagmc
          build-args: |
-            include_dagmc=true
+            build_dagmc=on
            compile_cores=2
+            openmc_branch=develop
      -
        name: Image digest
        run: echo ${{ steps.docker_build.outputs.digest }}
--- a/.github/workflows/dockerhub-publish-develop-libmesh.yml
+++ b/.github/workflows/dockerhub-publish-develop-libmesh.yml
@ -0,0 +1,36 @@
+name: dockerhub-publish-develop-libmesh
+
+on:
+  push:
+    branches: develop
+
+jobs:
+  main:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      -
+        name: Login to DockerHub
+        uses: docker/login-action@v1 
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      -
+        name: Build and push
+        id: docker_build
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          tags: openmc/openmc:develop-dagmc
+          build-args: |
+            build_libmesh=on
+            compile_cores=2
+            openmc_branch=develop
+      -
+        name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}
--- a/.github/workflows/dockerhub-publish-libmesh.yml
+++ b/.github/workflows/dockerhub-publish-libmesh.yml
@ -0,0 +1,35 @@
+name: dockerhub-publish-latest-libmesh
+
+on:
+  push:
+    branches: master
+
+jobs:
+  main:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      -
+        name: Login to DockerHub
+        uses: docker/login-action@v1 
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      -
+        name: Build and push
+        id: docker_build
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          tags: openmc/openmc:latest-libmesh
+          build-args: |
+            build_libmesh=on
+            compile_cores=2
+      -
+        name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}
--- a/.github/workflows/dockerhub-publish-release-dagmc.yml
+++ b/.github/workflows/dockerhub-publish-release-dagmc.yml
@ -31,7 +31,7 @@ jobs:
          push: true
          tags: openmc/openmc:${{ env.RELEASE_VERSION }}-dagmc
          build-args: |
-            include_dagmc=true
+            build_dagmc=on
            compile_cores=2
      -
        name: Image digest
--- a/290
+++ b/290
@ -1,149 +1,207 @@
-# To build with OpenMC
+# To build with OpenMC and by default this Dockerfile builds the master branch of OpenMC.
 # docker build -t openmc .

+# To build with OpenMC develop branch
+# docker build -t openmc_develop --build-arg openmc_branch=develop .
+
 # To build with OpenMC and DAGMC enabled
-# docker build -t openmc_dagmc --build-arg include_dagmc=true .
+# docker build -t openmc_dagmc --build-arg build_dagmc=on --build-arg compile_cores=4 .

-# To make use of multiple cores during the compile stages of the docker build
-# docker build -t openmc_dagmc --build-arg compile_cores=8 .
+# To build with OpenMC and Libmesh enabled
+# docker build -t openmc_libmesh --build-arg build_libmesh=on --build-arg compile_cores=4 .

-FROM ubuntu:latest
+# To build with both DAGMC and Libmesh enabled
+# docker build -t openmc_dagmc_libmesh --build-arg build_dagmc=on --build-arg build_libmesh=on --build-arg compile_cores=4 .

-# By default this Dockerfile builds OpenMC without dagmc
-ARG include_dagmc=false
+# sudo docker run image_name:tag_name or ID with no tag sudo docker run ID number
+
+FROM debian:bullseye-slim
+
+# By default this Dockerfile builds OpenMC without DAGMC and LIBMESH support
+ARG build_dagmc=off
+ARG build_libmesh=off

 # By default one core is used to compile
 ARG compile_cores=1

+# Set default value of HOME to /root
+ENV HOME=/root
+
+# OpenMC variables
+ARG openmc_branch=master
+ENV OPENMC_REPO='https://github.com/openmc-dev/openmc'
+
+# Embree variables
+ENV EMBREE_TAG='v3.12.2'
+ENV EMBREE_REPO='https://github.com/embree/embree'
+ENV EMBREE_INSTALL_DIR=$HOME/EMBREE/
+
+# MOAB variables
+ENV MOAB_TAG='5.3.0'
+ENV MOAB_REPO='https://bitbucket.org/fathomteam/moab/'
+
+# Double-Down variables
+ENV DD_TAG='v1.0.0'
+ENV DD_REPO='https://github.com/pshriwise/double-down'
+ENV DD_INSTALL_DIR=$HOME/Double_down
+
+# DAGMC variables
+ENV DAGMC_BRANCH='develop'
+ENV DAGMC_REPO='https://github.com/svalinn/DAGMC'
+ENV DAGMC_INSTALL_DIR=$HOME/DAGMC/
+
+# LIBMESH variables
+ENV LIBMESH_TAG='v1.6.0'
+ENV LIBMESH_REPO='https://github.com/libMesh/libmesh'
+ENV LIBMESH_INSTALL_DIR=$HOME/LIBMESH
+
 # Setup environment variables for Docker image
 ENV CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx \
-    PATH=/opt/openmc/bin:/opt/NJOY2016/build:$PATH \
-    LD_LIBRARY_PATH=/opt/openmc/lib:$LD_LIBRARY_PATH \
+    LD_LIBRARY_PATH=${DAGMC_INSTALL_DIR}/lib:$LD_LIBRARY_PATH \
    OPENMC_CROSS_SECTIONS=/root/nndc_hdf5/cross_sections.xml \
    OPENMC_ENDF_DATA=/root/endf-b-vii.1 \
    DEBIAN_FRONTEND=noninteractive

-# Install dependencies from Debian package manager
+# Install and update dependencies from Debian package manager
 RUN apt-get update -y && \
    apt-get upgrade -y && \
    apt-get install -y \
-        python3-pip python-is-python3 wget git gfortran g++ cmake \
+        python3-pip python-is-python3 wget git build-essential cmake \
        mpich libmpich-dev libhdf5-serial-dev libhdf5-mpich-dev \
        libpng-dev && \
    apt-get autoremove

 # Update system-provided pip
-RUN pip3 install --upgrade pip
+RUN pip install --upgrade pip

 # Clone and install NJOY2016
-RUN git clone https://github.com/njoy/NJOY2016.git /opt/NJOY2016 && \
-    cd /opt/NJOY2016 && \
-    mkdir build && cd build && \
-    cmake -Dstatic=on .. && make 2>/dev/null && make install
+RUN cd $HOME && git clone --depth 1 https://github.com/njoy/NJOY2016.git && \
+    cd NJOY2016 && mkdir build && cd build && \
+    cmake -Dstatic=on .. && make 2>/dev/null -j${compile_cores} install && \
+    rm -rf $HOME/NJOY2016

-# Clone and install OpenMC without DAGMC
-RUN if [ "$include_dagmc" = "false" ] ; \
-    then git clone --recurse-submodules https://github.com/openmc-dev/openmc.git /opt/openmc ; \
-    cd /opt/openmc ; \
-    mkdir -p build ; \
-    cd build ; \
-    cmake -Doptimize=on \
-          -DHDF5_PREFER_PARALLEL=on .. ; \
-    make -j"$compile_cores" ; \
-    make -j"$compile_cores" install ; \
-    cd ..  ; \
-    pip install -e .[test] ; \
+
+RUN if [ "$build_dagmc" = "on" ]; then \
+        # Install addition packages required for DAGMC
+        apt-get -y install libeigen3-dev libnetcdf-dev libtbb-dev libglfw3-dev \
+        && pip install --upgrade numpy cython \
+        # Clone and install EMBREE
+        && mkdir -p $HOME/EMBREE && cd $HOME/EMBREE \
+        && git clone --single-branch -b ${EMBREE_TAG} --depth 1 ${EMBREE_REPO} \
+        && mkdir build && cd build \
+        && cmake ../embree \
+                    -DCMAKE_INSTALL_PREFIX=${EMBREE_INSTALL_DIR} \
+                    -DEMBREE_MAX_ISA=NONE \
+                    -DEMBREE_ISA_SSE42=ON \
+                    -DEMBREE_ISPC_SUPPORT=OFF \
+        && make 2>/dev/null -j${compile_cores} install \
+        && rm -rf ${EMBREE_INSTALL_DIR}/build ${EMBREE_INSTALL_DIR}/embree ; \
+        # Clone and install MOAB
+        mkdir -p $HOME/MOAB && cd $HOME/MOAB \
+        && git clone  --single-branch -b ${MOAB_TAG} --depth 1 ${MOAB_REPO} \
+        && mkdir build && cd build \
+        && cmake ../moab -DENABLE_HDF5=ON \
+                      -DENABLE_NETCDF=ON \
+                      -DBUILD_SHARED_LIBS=OFF \
+                      -DENABLE_FORTRAN=OFF \
+                      -DENABLE_BLASLAPACK=OFF \
+        && make 2>/dev/null -j${compile_cores} install \
+        && cmake ../moab \
+                    -DENABLE_PYMOAB=ON \
+                    -DBUILD_SHARED_LIBS=ON \
+        && make 2>/dev/null -j${compile_cores} install \
+        && cd pymoab && bash install.sh \
+        && python setup.py install \
+        && rm -rf $HOME/MOAB ; \
+        # Clone and install Double-Down
+        mkdir -p $HOME/Double_down && cd $HOME/Double_down \
+        && git clone --single-branch -b ${DD_TAG} --depth 1 ${DD_REPO} \
+        && mkdir build && cd build \
+        && cmake ../double-down -DCMAKE_INSTALL_PREFIX=${DD_INSTALL_DIR} \
+                             -DMOAB_DIR=/usr/local \
+                             -DEMBREE_DIR=${EMBREE_INSTALL_DIR} \
+        && make 2>/dev/null -j${compile_cores} install \
+        && rm -rf ${DD_INSTALL_DIR}/build ${DD_INSTALL_DIR}/double-down ; \
+        # Clone and install DAGMC
+        mkdir -p $HOME/DAGMC && cd $HOME/DAGMC \
+        && git clone --single-branch -b ${DAGMC_BRANCH} --depth 1 ${DAGMC_REPO} \
+        && mkdir build && cd build \
+        && cmake ../DAGMC -DBUILD_TALLY=ON \
+                       -DCMAKE_INSTALL_PREFIX=${DAGMC_INSTALL_DIR} \
+                       -DMOAB_DIR=/usr/local \
+                       -DDOUBLE_DOWN=ON \
+                       -DDOUBLE_DOWN_DIR=${DD_INSTALL_DIR} \
+                       -DCMAKE_PREFIX_PATH=${DD_INSTALL_DIR}/lib \
+                       -DBUILD_STATIC_LIBS=OFF \
+        && make 2>/dev/null -j${compile_cores} install \
+        && rm -rf ${DAGMC_INSTALL_DIR}/DAGMC ${DAGMC_INSTALL_DIR}/build ; \
    fi

-# install addition packages required for DAGMC
-RUN if [ "$include_dagmc" = "true" ] ; \
-    then apt-get --yes install libeigen3-dev ; \
-    apt-get --yes install libnetcdf-dev ; \
-    apt-get --yes install libtbb-dev ; \
-    apt-get --yes install libglfw3-dev ; \
+
+RUN if [ "$build_libmesh" = "on" ]; then \
+        # Install addition packages required for LIBMESH
+        apt-get -y install m4 libnetcdf-dev libpnetcdf-dev \
+        # Install LIBMESH
+        && mkdir -p $HOME/LIBMESH && cd $HOME/LIBMESH \
+        && git clone --shallow-submodules --recurse-submodules --single-branch -b ${LIBMESH_TAG} --depth 1 ${LIBMESH_REPO} \
+        && mkdir build && cd build \
+        && ../libmesh/configure \
+                    --prefix=${LIBMESH_INSTALL_DIR} CXX=mpicxx CC=mpicc FC=mpifort F77=mpif77 \
+                    --enable-exodus \
+                    --enable-mpi \
+                    --enable-silent-rules \
+                    --enable-unique-id \
+                    --disable-eigen \
+                    --disable-fortran \
+                    --disable-lapack \
+                    --disable-examples \
+                    --disable-warnings \
+                    --disable-maintainer-mode \
+                    --disable-metaphysicl \
+                    --with-methods="opt" \
+                    --without-gdb-command \
+                    --with-cxx-std-min=2014 \
+        && make 2>/dev/null -j${compile_cores} install \
+        && rm -rf ${LIBMESH_INSTALL_DIR}/build ${LIBMESH_INSTALL_DIR}/libmesh ; \
    fi

-# Clone and install Embree
-RUN if [ "$include_dagmc" = "true" ] ; \
-    then git clone --single-branch --branch v3.12.2 https://github.com/embree/embree.git ; \
-    cd embree ; \
-    mkdir build ; \
-    cd build ; \
-    cmake .. -DCMAKE_INSTALL_PREFIX=.. \
-             -DEMBREE_ISPC_SUPPORT=OFF ; \
-    make -j"$compile_cores" ; \
-    make -j"$compile_cores" install ; \
-    fi
-
-# Clone and install MOAB
-RUN if [ "$include_dagmc" = "true" ] ; \
-    then pip install --upgrade numpy cython ; \
-    mkdir MOAB ; \
-    cd MOAB ; \
-    mkdir build ; \
-    git clone  --single-branch --branch 5.2.1 https://bitbucket.org/fathomteam/moab.git ; \
-    cd build ; \
-    cmake ../moab -DENABLE_HDF5=ON \
-                  -DENABLE_NETCDF=ON \
-                  -DBUILD_SHARED_LIBS=OFF \
-                  -DENABLE_FORTRAN=OFF \
-                  -DENABLE_BLASLAPACK=OFF ; \
-    make -j"$compile_cores" ; \
-    make -j"$compile_cores" install ; \
-    rm -rf * ; \
-    cmake ../moab -DBUILD_SHARED_LIBS=ON \
-                  -DENABLE_HDF5=ON \
-                  -DENABLE_PYMOAB=ON \
-                  -DENABLE_FORTRAN=OFF \
-                  -DENABLE_BLASLAPACK=OFF ; \
-    make -j"$compile_cores" ; \
-    make -j"$compile_cores" install ; \
-    fi
-
-# Clone and install Double-Down
-RUN if [ "$include_dagmc" = "true" ] ; \
-    then git clone --single-branch --branch main https://github.com/pshriwise/double-down.git ; \
-    cd double-down ; \
-    mkdir build ; \
-    cd build ; \
-    cmake .. -DCMAKE_INSTALL_PREFIX=.. \
-             -DMOAB_DIR=/usr/local \
-             -DEMBREE_DIR=/embree ; \
-    make -j"$compile_cores" ; \
-    make -j"$compile_cores" install ; \
-    fi
-
-# Clone and install DAGMC
-RUN if [ "$include_dagmc" = "true" ] ; \
-    then mkdir DAGMC ; \
-    cd DAGMC ; \
-    git clone --single-branch --branch 3.2.0 https://github.com/svalinn/DAGMC.git ; \
-    mkdir build ; \
-    cd build ; \
-    cmake ../DAGMC -DBUILD_TALLY=ON \
-                   -DCMAKE_INSTALL_PREFIX=/DAGMC/ \
-                   -DMOAB_DIR=/usr/local \
-                   -DBUILD_STATIC_LIBS=OFF \
-                   -DBUILD_STATIC_EXE=OFF ; \
-    make -j"$compile_cores" install ; \
-    rm -rf /DAGMC/DAGMC /DAGMC/build ; \
-    fi
-
-# Clone and install OpenMC with DAGMC
-RUN if [ "$include_dagmc" = "true" ] ; \
-    then git clone --recurse-submodules https://github.com/openmc-dev/openmc.git /opt/openmc ; \
-    cd /opt/openmc ; \
-    mkdir build ; \
-    cd build ; \
-    cmake -Doptimize=on \
-          -Ddagmc=ON \
-          -DDAGMC_DIR=/DAGMC/ \
-          -DHDF5_PREFER_PARALLEL=on ..  ; \
-    make -j"$compile_cores" ; \
-    make -j"$compile_cores" install ; \
-    cd ..  ; \
-    pip install -e .[test] ; \
-    fi
+# clone and install openmc
+RUN mkdir -p ${HOME}/OpenMC && cd ${HOME}/OpenMC \
+    && git clone --shallow-submodules --recurse-submodules -b ${openmc_branch} --depth=1 ${OPENMC_REPO} \
+    && mkdir build && cd build ; \
+    if [ ${build_dagmc} = "on" ] && [ ${build_libmesh} = "on" ]; then \
+        cmake ../openmc \
+            -Doptimize=off \
+            -Ddebug=off \
+            -DHDF5_PREFER_PARALLEL=on \
+            -Ddagmc=on \
+            -Dlibmesh=on \
+            -DCMAKE_PREFIX_PATH="${DAGMC_INSTALL_DIR};${LIBMESH_INSTALL_DIR}" ; \
+    fi ; \
+    if [ ${build_dagmc} = "on" ] && [ ${build_libmesh} = "off" ]; then \
+        cmake ../openmc \
+            -Doptimize=off \
+            -Ddebug=off \
+            -DHDF5_PREFER_PARALLEL=on \
+            -Ddagmc=ON \
+            -DCMAKE_PREFIX_PATH=${DAGMC_INSTALL_DIR} ; \
+    fi ; \
+    if [ ${build_dagmc} = "off" ] && [ ${build_libmesh} = "on" ]; then \
+        cmake ../openmc \
+            -Doptimize=off \
+            -Ddebug=off \
+            -DHDF5_PREFER_PARALLEL=on \
+            -Dlibmesh=on \
+            -DCMAKE_PREFIX_PATH=${LIBMESH_INSTALL_DIR} ; \
+    fi ; \
+    if [ ${build_dagmc} = "off" ] && [ ${build_libmesh} = "off" ]; then \
+        cmake ../openmc \
+            -Doptimize=off \
+            -Ddebug=off \
+            -DHDF5_PREFER_PARALLEL=on ; \
+    fi ; \
+    make 2>/dev/null -j${compile_cores} install \
+    && cd ../openmc && pip install -e .[test,depletion-mpi]

 # Download cross sections (NNDC and WMP) and ENDF data needed by test suite
-RUN /opt/openmc/tools/ci/download-xs.sh
+RUN ${HOME}/OpenMC/openmc/tools/ci/download-xs.sh