Add automated docker builds for Nektar++, a build environment and a Jupyter notebook image.

.dockerignore

+# Exclude the usual build environment stuff.
+.clang-format
+.git
+.gitignore
+.gitlab-ci.yml
+ThirdParty
+build
+builds
+.DS_Store
+
+# Make sure Dockerfiles aren't included in build context to
+# improve caching.
+pkg/docker/nektar/Dockerfile
+pkg/docker/nektar-workbook/Dockerfile
+pkg/docker/nektar-env/Dockerfile
+

.gitignore

 .*
 !.gitignore
+!.gitlab-ci.yml
 !.gitattributes
 !.clang-format
+!.dockerignore
 # Ignore builds and ThirdParty directories
 build
 builds

.gitlab-ci.yml

+stages:
+  - docker-build-env
+  - docker-build-image
+  - docker-test-image
+  - docker-cleanup-image
+
+before_script:
+  - docker login -u "$CI_REGISTRY_USER" -p "$CI_REGISTRY_PASSWORD" $CI_REGISTRY
+
+.docker_build_template: &docker_build_template
+  image: docker:stable
+  stage: docker-build-image
+  only:
+    - master
+    - /^docker\/.*$/
+  script:
+    - docker pull ${image_name} || true
+    - DOCKER_BUILDKIT=1 docker build -t ${image_name} -f ${dockerfile} .
+    - docker tag ${image_name} ${image_name}:$CI_COMMIT_SHORT_SHA
+    - docker push ${image_name}:$CI_COMMIT_SHORT_SHA
+    - if [ ! -z $CI_COMMIT_TAG ]; then docker tag ${image_name} ${image_name}:$CI_COMMIT_TAG; docker push ${image_name}:$CI_COMMIT_TAG; fi
+    - docker push ${image_name}:latest
+
+.docker-test-template: &docker_test_template
+  image: docker:stable
+  stage: docker-test-image
+  only:
+    - master
+    - /^docker\/.*$/
+  script:
+    - docker pull ${image_name} || true
+    - docker create --name ${container_name}-$CI_COMMIT_SHORT_SHA -t ${image_name}:latest
+    - docker cp $(pwd)/${test_dir} ${container_name}-$CI_COMMIT_SHORT_SHA:/docker-entrypoint
+    - docker start ${container_name}-$CI_COMMIT_SHORT_SHA
+    - docker exec ${container_name}-$CI_COMMIT_SHORT_SHA ${test_cmd}
+    - docker rm -f ${container_name}-$CI_COMMIT_SHORT_SHA
+
+docker-build-env:
+  <<: *docker_build_template
+  stage: docker-build-env
+  variables:
+    image_name: nektarpp/nektar-env
+    dockerfile: pkg/docker/nektar-env/Dockerfile
+  only:
+    refs:
+      - master
+      - /^docker\/.*$/
+    changes:
+      - pkg/docker/nektar-env/Dockerfile
+
+docker-build-nektar:
+  <<: *docker_build_template
+  variables:
+    image_name: nektarpp/nektar
+    dockerfile: pkg/docker/nektar/Dockerfile
+
+docker-build-workbook:
+  <<: *docker_build_template
+  variables:
+    image_name: nektarpp/nektar-workbook
+    dockerfile: pkg/docker/nektar-workbook/Dockerfile
+
+docker-test-nektar:
+  <<: *docker_test_template
+  variables:
+    image_name: nektarpp/nektar
+    container_name: nektar
+    test_dir: solvers/IncNavierStokesSolver/Tests
+    test_cmd: mpirun -n 3 IncNavierStokesSolver data/ChanFlow_m3_par.xml
+
+docker-cleanup-nektar:
+  stage: docker-cleanup-image
+  when: on_failure
+  script:
+    - docker rm -f nektar-$CI_COMMIT_SHORT_SHA

CHANGELOG.md

@@ -190,6 +190,9 @@ v5.0.0
 **Tester**
 - Fix build with boost 1.67 (!947)
 
+**Packaging:**
+- Add Dockerfiles and gitlab CI configuration for automatic builds (!1021)
+
 v4.4.2
 ------
 **Library**

pkg/docker/nektar-env/Dockerfile

+FROM debian:buster-slim
+
+LABEL maintainer="David Moxey <d.moxey@exeter.ac.uk>"
+
+RUN DEBIAN_RELEASE=buster && \
+    echo "deb http://deb.debian.org/debian ${DEBIAN_RELEASE} non-free" > \
+        /etc/apt/sources.list.d/debian-non-free.list && \
+    apt-get update && \
+    apt-get install -y build-essential cmake git \
+    libboost-thread-dev libboost-iostreams-dev libboost-filesystem-dev libboost-system-dev \
+    libboost-program-options-dev libboost-python-dev libboost-numpy-dev libboost-regex-dev \
+    libfftw3-dev libhdf5-dev libhdf5-mpi-dev liblapack-dev liboce-foundation-dev \
+    liboce-modeling-dev liboce-ocaf-dev libtet1.5-dev libtriangle-dev \
+    libtinyxml-dev mpi-default-dev petsc-dev zlib1g-dev python-numpy libptscotch-dev \
+    libarpack2-dev
+
+RUN groupadd nektar && useradd -m -g nektar nektar
+USER nektar:nektar
+WORKDIR /home/nektar

pkg/docker/nektar-env/README.md

+# `nektar-env` image
+
+This image is designed to provide a build environment for Nektar++ based on the
+Debian 10 (buster) build image. It installs all libraries to enable Nektar++ to
+be compiled with most/all third-party dependencies turned on. In particular we
+install the following development libraries:
+
+- Boost
+- TinyXML
+- LAPACK/BLAS
+- OpenMPI (enables `NEKTAR_USE_MPI`)
+- FFTW (enables `NEKTAR_USE_FFT`)
+- Python and Boost.Python (enables `NEKTAR_BUILD_PYTHON`)
+- HDF5 (enables `NEKTAR_USE_HDF5`)
+- OCE, Triangle and TetGen (enables `NEKTAR_USE_MESHGEN`)
+- PETSc (enables `NEKTAR_USE_PETSC`)
+- ARPACK (enables `NEKTAR_USE_ARPACK`)
+
+## Building
+
+No particular context is required to build this image. Building using the below
+or similar.
+
+```sh
+docker build -t nektarpp/nektar-env -f Dockerfile .
+```

pkg/docker/nektar-workbook/Dockerfile

+FROM jupyter/scipy-notebook:ae5f7e104dd5 AS build
+
+USER root
+RUN apt-get update && \
+    apt-get install -y libtinyxml-dev && \
+    rm -rf /var/lib/apt/lists/*
+
+USER $NB_UID
+RUN conda install --quiet --yes cmake==3.14.3 boost==1.69 jupyter_contrib_nbextensions && \
+    jupyter contrib nbextension install --sys-prefix && \
+    jupyter nbextension enable --sys-prefix hide_input/main && \
+    jupyter nbextension enable --sys-prefix hide_input_all/main && \
+    jupyter nbextension enable --sys-prefix init_cell/main && \
+    jupyter nbextension enable --sys-prefix equation-numbering/main
+
+USER root
+COPY . /tmp/nektar
+RUN cd /tmp/nektar && mkdir build && cd build && \
+    cmake -DNEKTAR_BUILD_SOLVERS=OFF -DNEKTAR_BUILD_UTILITIES=ON -DNEKTAR_BUILD_PYTHON=ON \
+          -DNEKTAR_USE_PYTHON3=ON -DNEKTAR_BUILD_TESTS=OFF -DNEKTAR_BUILD_UNIT_TESTS=OFF \
+          -DNEKTAR_BUILD_DEMOS=OFF -DNEKTAR_USE_SCOTCH=OFF -DCMAKE_INSTALL_PREFIX=/usr/local .. && \
+    make -j$(nproc) install && \
+    chown -R $NB_UID:$NB_UID /tmp/nektar && \
+    cd /tmp/nektar/build && sudo -u $NB_USER make nekpy-install-system && cd && rm -R /tmp/nektar
+
+USER $NB_UID
\ No newline at end of file

pkg/docker/nektar-workbook/README.md

+# `nektar-workbook` image
+
+This image is based on the `scipy-notebook` image but augments it with the
+`NekPy` Python interface. It also includes the `NekMesh` and `FieldConvert`
+utilities for post-processing.
+
+## Building
+
+The image requires as build context the path to the Nektar++ source tree.  Build
+the image using a command similar to:
+
+```sh
+docker build -t nektarpp/nektar-notebook -f Dockerfile ~/nektar++
+```

pkg/docker/nektar/Dockerfile

+FROM nektarpp/nektar-env:latest AS build
+
+LABEL maintainer="David Moxey <d.moxey@exeter.ac.uk>"
+
+COPY --chown=nektar:nektar . /home/nektar
+
+ARG BUILD_DEMOS=OFF
+ARG BUILD_SOLVERS=ON
+ARG INSTALL_PREFIX=/usr/local
+
+RUN mkdir build && cd build &&                \
+    cmake                                     \
+    -DNEKTAR_BUILD_DEMOS=${BUILD_DEMOS}       \
+    -DNEKTAR_BUILD_TESTS=OFF                  \
+    -DNEKTAR_BUILD_UNIT_TESTS=OFF             \
+    -DNEKTAR_BUILD_SOLVERS=${BUILD_SOLVERS}   \
+    -DNEKTAR_BUILD_PYTHON=ON                  \
+    -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX}  \
+    -DNEKTAR_USE_MESHGEN=ON                   \
+    -DNEKTAR_USE_MPI=ON                       \
+    -DNEKTAR_USE_ARPACK=ON                    \
+    -DNEKTAR_USE_FFTW=ON                      \
+    -DNEKTAR_USE_HDF5=ON                      \
+    -DNEKTAR_USE_CCM=ON                       \
+    .. &&                                     \
+    make -j$(nproc)
+
+USER root
+RUN cd build && make install && make nekpy-install-system && cd ..
+USER nektar
+
+FROM debian:buster-slim
+RUN DEBIAN_RELEASE=buster && \
+    echo "deb http://deb.debian.org/debian ${DEBIAN_RELEASE} non-free" > \
+        /etc/apt/sources.list.d/debian-non-free.list && \
+    apt-get update && \
+    apt-get install -y \
+    openssh-client nano vim binutils \
+    libboost-thread1.67 libboost-iostreams1.67 libboost-filesystem1.67 libboost-system1.67 \
+    libboost-program-options1.67 libboost-python1.67 libboost-regex1.67 libboost-numpy1.67 \
+    libfftw3-3 libhdf5-103 libhdf5-openmpi-103 liblapack3 liboce-foundation11 \
+    liboce-modeling11 liboce-ocaf11 libtet1.5 libtriangle-1.6 python-numpy \
+    openmpi-bin libpetsc3.10 libptscotch-6.0 libarpack2 libtinyxml2.6.2v5 && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+ARG INSTALL_PREFIX=/usr/local
+COPY --from=build ${INSTALL_PREFIX} ${INSTALL_PREFIX}
+
+# Set up entrypoint for copying test files.
+COPY pkg/docker/nektar/docker-entrypoint.sh /usr/local/bin/docker-entrypoint.sh
+RUN chmod +x /usr/local/bin/docker-entrypoint.sh && \
+    ln -s /usr/local/bin/docker-entrypoint.sh /
+ENTRYPOINT ["/usr/local/bin/docker-entrypoint.sh"]
+
+RUN groupadd nektar && useradd -m -g nektar nektar
+USER nektar
+WORKDIR /home/nektar
+CMD ["/bin/bash"]

pkg/docker/nektar/README.md

+# `nektar` image
+
+This image provides a full installation of Nektar++ with the following options
+enabled:
+
+- `NEKTAR_USE_MPI`
+- `NEKTAR_USE_FFT`
+- `NEKTAR_BUILD_PYTHON`
+- `NEKTAR_USE_HDF5`
+- `NEKTAR_USE_MESHGEN`
+- `NEKTAR_USE_PETSC`
+- `NEKTAR_USE_CCM`
+
+## Building
+
+The image is built using `nektarpp/nektar-env` and requires as build context the
+path to the Nektar++ source tree. It supports three additional build arguments:
+
+- `BUILD_DEMOS` can be set to `ON` to build demos, which are disabled by
+  default;
+- `BUILD_SOLVERS` can be set to `OFF` to disable build of solvers, which are
+  enabled by default;
+- `INSTALL_PREFIX` can be set to adjust the install prefix, which is
+  `/usr/local` by default.
+  
+Then build the image using a command similar to:
+
+```sh
+docker build -t nektarpp/nektar -f Dockerfile ~/nektar++
+```
+
+Note that this is a multi-stage build: after the initial build phase is
+completed, the build tree is erased along with development headers, and the
+libraries/executables installed into a fresh Debian 10 container (with
+appropriate packages for runtime libraries). If you want to keep the build
+files, you should instead only build up to the end of the build stage using
+`--target build`:
+
+```sh
+docker build --target build -t nektar-build -f Dockerfile ~/nektar++
+```

pkg/docker/nektar/docker-entrypoint.sh

+#!/bin/bash
+
+set -e
+
+if [ -d /docker-entrypoint ]; then
+    mkdir -p $HOME/data
+    cp -r /docker-entrypoint/* $HOME/data
+fi
+
+exec "$@"