Reenable dockerhub builds and deployment

.gitlab-ci.yml

@@ -3,6 +3,11 @@ stages:
   - build-env-full
   - build-and-test
   - compiler-warnings
+  - package-env
+  - package-build
+  - package-build-dev
+  - package-test
+  - package-deploy
 
 .execution-conditions: &execution-conditions
   only:
@@ -103,8 +108,7 @@ stages:
 
 .build-env-debian-template-default: &build-env-debian-template-default
   <<: *build-env-template
-  stage:
-    build-env-default
+  stage: build-env-default
   variables:
     OS_DISTRO: debian
   script:
@@ -119,8 +123,7 @@ stages:
 
 .build-env-debian-template-full: &build-env-debian-template-full
   <<: *build-env-debian-template-default
-  stage:
-    build-env-full
+  stage: build-env-full
 
 buster-default-build-env:
   <<: *build-env-debian-template-default
@@ -177,8 +180,7 @@ stretch-full-warnings:
 buster-documentation-build-env:
   <<: *execution-conditions
   image: docker:19.03.6
-  stage:
-    build-env-full
+  stage: build-env-full
   script:
     - export IMAGE=$CI_REGISTRY_IMAGE:env-documentation
     - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
@@ -241,8 +243,7 @@ tutorials-build:
 
 .build-env-ubuntu-template-full: &build-env-ubuntu-template-full
   <<: *build-env-ubuntu-template-default
-  stage:
-    build-env-full
+  stage: build-env-full
 
 focal-default-build-env:
   <<: *build-env-ubuntu-template-default
@@ -328,8 +329,7 @@ xenial-full-warnings:
 
 .build-env-centos-template-full: &build-env-centos-template-full
   <<: *build-env-centos-template-default
-  stage:
-    build-env-full
+  stage: build-env-full
 
 centos7-default-build-env:
   <<: *build-env-centos-template-default
@@ -399,21 +399,6 @@ osx-full-warnings:
 # #################  WINDOWS  ####################
 # ################################################
 
-#win7-default-build-and-test:
-#  <<: *build-and-test-template
-#  tags:
-#    - win7
-#  script:
-#    - $Env:path = "$CI_PROJECT_DIR\build\dist\bin;$CI_PROJECT_DIR\ThirdParty;" + $Env:path
-#    - echo $Env:path
-#    - mkdir build
-#    - cd build
-#    - cmake.exe -G "Visual Studio 12 2013 Win64" --config Debug ..
-#    - cmake.exe --build . --target ALL_BUILD --config Debug
-#    - cmake.exe --build . --target INSTALL --config Debug
-#    - ctest --output-on-failure -C Debug -j3
-
-
 win10-default-build-and-test:
   <<: *build-and-test-template
   tags:
@@ -447,3 +432,141 @@ win10-mpi-default-build-and-test:
   after_script:
     - Remove-Item -Recurse -Force build
   needs: []
+
+# ##################################################
+# #################  DOCKERHUB  ####################
+# ##################################################
+
+# Docker Hub build template. We build images and push them into the gitlab
+# container registry first; this way, we can test the images before they are
+# deployed, modify images or test adjustments to the CI by using docker/*
+# branches on gitlab, and test the images before they are deployed.
+#
+# Images are tagged with both :latest and the short SHA commit, so that the
+# correct image version can be grabbed from the container registry.
+.dockerhub_build_template: &dockerhub_build_template
+  image: docker:stable
+  only:
+    - master@nektar/nektar
+    - /^docker\/.*$/@nektar/nektar
+    - tags@nektar/nektar
+  script:
+    - docker login -u "$CI_REGISTRY_USER" -p "$CI_REGISTRY_PASSWORD" $CI_REGISTRY
+    - IMAGE=$CI_REGISTRY_IMAGE/${image_name}
+    - docker pull $IMAGE || true
+    - docker build ${args} --pull -t $IMAGE -f ${dockerfile} .
+    - docker tag $IMAGE $IMAGE:$CI_COMMIT_SHORT_SHA
+    - docker tag $IMAGE $IMAGE:latest
+    - docker push $IMAGE:$CI_COMMIT_SHORT_SHA
+    - docker push $IMAGE:latest
+
+# Docker Hub test template, which runs an image from the gitlab container
+# registry on a particular SHA commit.
+.dockerhub-test-template: &dockerhub_test_template
+  image: ${CI_REGISTRY_IMAGE}/${image_name}:$CI_COMMIT_SHORT_SHA
+  stage: package-test
+  only:
+    - master@nektar/nektar
+    - /^docker\/.*$/@nektar/nektar
+    - tags@nektar/nektar
+
+# Docker Hub deployment template. Only builds for master or tags on the main
+# Nektar repository. The strategy is to login to the container registry and pull
+# an image onto the runner; we then tag the image as appropriate (with :latest
+# and SHA commit, as well as the git tag if this happens to be a tagged commit),
+# then push the image up to Docker Hub. Note that cleanup of images on the
+# runners can be difficult if they are tagged multiple times, so we also perform
+# a quick rmi to make sure we only keep the images from the registry.
+.dockerhub-deploy-template: &dockerhub_deploy_template
+  image: docker:stable
+  stage: package-deploy
+  only:
+    - master@nektar/nektar
+    - tags@nektar/nektar
+  script:
+    - docker login -u "$CI_REGISTRY_USER" -p "$CI_REGISTRY_PASSWORD" $CI_REGISTRY
+    - CI_IMAGE=$CI_REGISTRY_IMAGE/${image_name}:$CI_COMMIT_SHORT_SHA
+    - DH_IMAGE=${DOCKERIO_REGISTRY}/nektarpp/${image_name}
+    - docker pull $CI_IMAGE
+    - docker logout
+    - docker login -u "$DOCKERIO_REGISTRY_USER" -p "$DOCKERIO_REGISTRY_PASSWORD" $DOCKERIO_REGISTRY
+    - if [ ! -z $CI_COMMIT_TAG ]; then docker tag $CI_IMAGE $DH_IMAGE:$CI_COMMIT_TAG; docker push $DH_IMAGE:$CI_COMMIT_TAG; docker rmi $DH_IMAGE:$CI_COMMIT_TAG; fi
+    - docker tag $CI_IMAGE $DH_IMAGE:$CI_COMMIT_SHORT_SHA
+    - docker tag $CI_IMAGE $DH_IMAGE:latest
+    - docker push $DH_IMAGE:$CI_COMMIT_SHORT_SHA
+    - docker push $DH_IMAGE:latest
+    - docker rmi $DH_IMAGE:$CI_COMMIT_SHORT_SHA $DH_IMAGE:latest
+
+# nektarpp/nektar-env image
+dockerhub-build-env:
+  <<: *dockerhub_build_template
+  stage: package-env
+  variables:
+    image_name: nektar-env
+    dockerfile: docker/nektar-env/Dockerfile
+
+# nektarpp/nektar image
+dockerhub-build-nektar:
+  <<: *dockerhub_build_template
+  stage: package-build
+  needs: [ "dockerhub-build-env" ]
+  variables:
+    image_name: nektar
+    dockerfile: docker/nektar/Dockerfile
+    args: --build-arg ENV_IMAGE=$CI_REGISTRY_IMAGE/nektar-env:$CI_COMMIT_SHORT_SHA
+    GIT_SUBMODULE_STRATEGY: normal
+
+# nektarpp/nektar image
+dockerhub-build-workbook:
+  <<: *dockerhub_build_template
+  stage: package-build
+  needs: []
+  variables:
+    image_name: nektar-workbook
+    dockerfile: docker/nektar-workbook/Dockerfile
+
+# nektarpp/nektar-dev image
+dockerhub-build-dev:
+  <<: *dockerhub_build_template
+  stage: package-build-dev
+  needs: [ "dockerhub-build-nektar" ]
+  variables:
+    image_name: nektar-dev
+    args: --build-arg ENV_IMAGE=$CI_REGISTRY_IMAGE/nektar-env:$CI_COMMIT_SHORT_SHA --build-arg NEKTAR_IMAGE=$CI_REGISTRY_IMAGE/nektar:$CI_COMMIT_SHORT_SHA
+    dockerfile: docker/nektar-dev/Dockerfile
+
+# Test the dockerhub images
+dockerhub-test-nektar:
+  <<: *dockerhub_test_template
+  needs: [ "dockerhub-build-nektar" ]
+  variables:
+    image_name: nektar
+  script:
+    - mpirun -n 3 IncNavierStokesSolver $CI_PROJECT_DIR/solvers/IncNavierStokesSolver/Tests/ChanFlow_m3_par.xml
+
+dockerhub-test-nektar-dev:
+  <<: *dockerhub_test_template
+  needs: [ "dockerhub-build-dev" ]
+  variables:
+    image_name: nektar-dev
+  script:
+    - cd $CI_PROJECT_DIR/templates/executable
+    - ./test.sh /usr/local/lib64/nektar++/cmake 3
+
+# Deployment
+dockerhub-deploy-nektar:
+  <<: *dockerhub_deploy_template
+  variables:
+    image_name: nektar
+dockerhub-deploy-nektar-env:
+  <<: *dockerhub_deploy_template
+  variables:
+    image_name: nektar-env
+dockerhub-deploy-nektar-dev:
+  <<: *dockerhub_deploy_template
+  variables:
+    image_name: nektar-dev
+dockerhub-deploy-nektar-workbook:
+  <<: *dockerhub_deploy_template
+  variables:
+    image_name: nektar-workbook

CMakeLists.txt

@@ -101,6 +101,9 @@ SET(LIB_DIR "lib")
 IF( CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64" AND NOT APPLE )
     SET(LIB_DIR "lib64")
 ENDIF()
+IF (DEFINED NEKTAR_LIB_DIR)
+    SET(LIB_DIR ${NEKTAR_LIB_DIR})
+ENDIF()
 SET(CMAKE_INCLUDE_SYSTEM_FLAG_CXX "-isystem ")
 
 SET(NEKTAR_BIN_DIR bin)
@@ -110,11 +113,19 @@ SET(NEKTAR_SHARE_DIR share/nektar++)
 SET(NEKTAR_DOC_DIR share/doc/nektar++)
 SET(NEKTAR_CMAKE_DIR ${LIB_DIR}/nektar++/cmake)
 
+# Allow for overriding final include header directory (for Fedora/CentOS
+# packaging)
+IF (DEFINED NEKTAR_INCLUDE_ROOT)
+    SET(NEKTAR_INCLUDE_DIST_DIR ${NEKTAR_INCLUDE_ROOT}/nektar++)
+ELSE()
+    SET(NEKTAR_INCLUDE_DIST_DIR ${CMAKE_INSTALL_PREFIX}/${NEKTAR_INCLUDE_DIR})
+ENDIF()
+
 # Set ThirdParty locations.
 SET(TPSRC   ${CMAKE_SOURCE_DIR}/ThirdParty)
 SET(TPBUILD ${CMAKE_BINARY_DIR}/ThirdParty)
 SET(TPDIST  ${CMAKE_BINARY_DIR}/ThirdParty/dist)
-SET(TPINC   ${CMAKE_INSTALL_PREFIX}/include/ThirdParty)
+SET(TPINC   ${NEKTAR_INCLUDE_DIST_DIR}/ThirdParty)
 SET(TPLIB   ${CMAKE_INSTALL_PREFIX}/${NEKTAR_LIB_DIR}/nektar++/thirdparty)
 
 # Create ThirdParty source directory if it doesn't exist already.

cmake/Nektar++Config.cmake.in

@@ -30,13 +30,12 @@
 SET(NEKTAR++_FOUND "ON")
 SET(NEKTAR++_VERSION "@NEKTAR_VERSION@")
 SET(NEKTAR++_ROOT_DIR "@CMAKE_INSTALL_PREFIX@")
-SET(NEKTAR++_INCLUDE_DIRS "${NEKTAR++_ROOT_DIR}/@NEKTAR_INCLUDE_DIR@")
+SET(NEKTAR++_INCLUDE_DIRS "@NEKTAR_INCLUDE_DIST_DIR@")
 SET(NEKTAR++_LIBRARY_DIRS "${NEKTAR++_ROOT_DIR}/@NEKTAR_LIB_DIR@")
 SET(NEKTAR++_DEFINITIONS @NEKTAR_DEFINITIONS@)
 SET(NEKTAR++_LIBRARIES @NEKTAR++_LIBRARIES@)
 
-SET(NEKTAR++_TP_INCLUDE_DIRS
-    "${NEKTAR++_ROOT_DIR}/@NEKTAR_INCLUDE_DIR@/ThirdParty")
+SET(NEKTAR++_TP_INCLUDE_DIRS "@NEKTAR_INCLUDE_DIST_DIR@/ThirdParty")
 SET(NEKTAR++_TP_LIBRARIES "")
 SET(NEKTAR++_TP_LIBRARY_DIRS "")
 

docker/nektar-dev/Dockerfile

-FROM nektarpp/nektar-env:latest AS build
+ARG NEKTAR_IMAGE=nektarpp/nektar:latest
+ARG ENV_IMAGE=nektarpp/nektar-env:latest
+FROM $NEKTAR_IMAGE as nektar
+FROM $ENV_IMAGE AS build
 
-LABEL maintainer="David Moxey <d.moxey@exeter.ac.uk>"
+LABEL maintainer="Nektar++ Development Team <nektar-users@imperial.ac.uk>"
 
 ARG INSTALL_PREFIX=/usr/local
 
 USER root
-COPY --from=nektarpp/nektar:latest ${INSTALL_PREFIX} ${INSTALL_PREFIX}
+COPY --from=nektar ${INSTALL_PREFIX} ${INSTALL_PREFIX}
 
 # Set up entrypoint for copying test files.
 COPY docker/nektar/docker-entrypoint.sh /usr/local/bin/docker-entrypoint.sh

docker/nektar-dev/README.md

@@ -6,14 +6,24 @@ image for code development purposes.
 
 ## Building
 
-The image is built using `nektarpp/nektar-env` and requires as build context the
-path to the Nektar++ source tree. It supports the build environment variable:
+The image is built using `nektarpp/nektar-env` or similar and requires as build
+context the path to the Nektar++ source tree. It supports the build environment
+variables:
 
+- `ENV_IMAGE` and `NEKTAR_IMAGE`, which are used to select the environment image
+  and Nektar image to build against. This is used by the CI to e.g. consistently
+  build against the correct commits. By default these are set to
+  `nektarpp/nektar-env:latest` and `nektarpp/nektar:latest`.
 - `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-dev -f ~/nektar++/docker/nektar-dev/Dockerfile ~/nektar++
+docker build \
+    -t nektarpp/nektar-dev \
+    -f ~/nektar++/docker/nektar-dev/Dockerfile \
+    --build-arg ENV_IMAGE=nektarpp/nektar-env:latest \
+    --build-arg NEKTAR_IMAGE=nektarpp/nektar:latest \
+    ~/nektar++
 ```

docker/nektar-env/Dockerfile

 FROM debian:buster-slim
 
-LABEL maintainer="David Moxey <d.moxey@exeter.ac.uk>"
+LABEL maintainer="Nektar++ Development Team <nektar-users@imperial.ac.uk>"
 
 RUN DEBIAN_RELEASE=buster && \
     echo "deb http://deb.debian.org/debian ${DEBIAN_RELEASE} non-free" > \

docker/nektar-workbook/Dockerfile

 FROM jupyter/scipy-notebook:ae5f7e104dd5 AS build
 
+LABEL maintainer="Nektar++ Development Team <nektar-users@imperial.ac.uk>"
+
 USER root
 RUN apt-get update && \
     apt-get install -y libtinyxml-dev && \
@@ -23,4 +25,4 @@ RUN cd /tmp/nektar && mkdir build && cd build && \
     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
+USER $NB_UID

docker/nektar/Dockerfile

-FROM nektarpp/nektar-env:latest AS build
+ARG ENV_IMAGE=nektarpp/nektar-env:latest
+FROM $ENV_IMAGE AS build
 
-LABEL maintainer="David Moxey <d.moxey@exeter.ac.uk>"
+LABEL maintainer="Nektar++ Development Team <nektar-users@imperial.ac.uk>"
 
 COPY --chown=nektar:nektar . /home/nektar
 

docker/nektar/README.md

@@ -13,9 +13,13 @@ enabled:
 
 ## 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:
+The image is built using `nektarpp/nektar-env` or similar and requires as build
+context the path to the Nektar++ source tree. It supports several additional
+build arguments:
 
+- `ENV_IMAGE` is used to select the environment to build against. This is used
+  by the CI to e.g. consistently build against the correct commits. By default
+  this is set to `nektarpp/nektar-env:default`.
 - `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

solvers/ADRSolver/EquationSystems/MMFAdvection.cpp

@@ -868,8 +868,8 @@ NekDouble MMFAdvection::ComputeCirculatingArclength(const NekDouble zlevel,
                                                     const NekDouble Rhs)
 {
 
-    NekDouble Tol = 0.0001, Maxiter = 1000, N = 100, F = 0.0, dF = 0.0;
-    NekDouble newy, y0, tmp;
+    NekDouble Tol = 0.0001, Maxiter = 1000, N = 100;
+    NekDouble newy, F = 0.0, dF = 1.0, y0, tmp;
 
     Array<OneD, NekDouble> xp(N + 1);
     Array<OneD, NekDouble> yp(N + 1);

templates/executable/CMakeLists.txt

@@ -7,7 +7,7 @@
 CMAKE_MINIMUM_REQUIRED(VERSION 3.5.1)
 
 # TODO - Put the name of your project here.
-PROJECT(ExampleSolver)
+PROJECT(ExampleSolver C CXX)
 
 # Finds Nektar++. This may introduce other dependencies, such as Boost.
 FIND_PACKAGE(Nektar++ REQUIRED)

templates/executable/test.sh

@@ -10,7 +10,13 @@ make install
 # Run test case in parallel.
 cd ..
 export OMPI_MCA_btl_vader_single_copy_mechanism=none
-test_output=`mpirun -n $2 ./build/dist/ExampleSolver sample-laplace.xml | grep "L 2 error" | awk '{print ($7 < 1e-10)}'`
+if [[ $EUID -eq 0 ]]; then
+    mpiargs="-n $2 --allow-run-as-root"
+else
+    mpiargs="-n $2"
+fi
+
+test_output=`mpirun $mpiargs ./build/dist/ExampleSolver sample-laplace.xml | grep "L 2 error" | awk '{print ($7 < 1e-10)}'`
 if [ "$test_output" -eq 1 ]; then
     echo "Test passed tolerance"
     exit 0