Merge pull request #200 from steffengraber/add-v36

Add NEST v3.6 and start rework of CI

ci-templates/000_3.5.gitlab-ci.yml

@@ -6,7 +6,7 @@ Build_35:
   stage: build
   needs: ["Build_Base"]
   rules:
-   - when: always
+   - when: never
   script:
     - docker pull $DOCKER_REGISTRY_IMAGE:3.5 || true
     - docker build
@@ -35,7 +35,6 @@ Test_35:
 Deploy_35:
   stage: deploy
   needs: ["Test_35"]
-  when: always
   script:
     - docker pull $DOCKER_REGISTRY_IMAGE:3.5.$CI_PIPELINE_ID
     - docker tag $DOCKER_REGISTRY_IMAGE:3.5.$CI_PIPELINE_ID $DOCKER_REGISTRY_IMAGE:3.5

ci-templates/000_3.6.gitlab-ci.yml

@@ -0,0 +1,30 @@
+###############################################
+###               v3.6                     ###
+###############################################
+
+Build_36:
+  stage: build
+  needs: ["Build_Base"]
+  script:
+    - docker pull nest/nest-simulator:3.6 || true
+    - docker build
+        --cache-from nest/nest-simulator:3.6
+        --tag $DOCKER_REGISTRY_IMAGE:3.6.$CI_PIPELINE_ID
+        ./src/3.6
+    # Simple test
+    - docker run -i --rm nest/nest-simulator:3.6 bash /opt/test-nest.sh
+  tags:
+    - shell-runner
+
+Deploy_36:
+  stage: deploy
+  needs: ["Build_36"]
+  when: never
+  script:    
+    - echo -n $DOCKERHUB_REGISTRY_TOKEN | docker login -u $DOCKERHUB_REGISTRY_USER --password-stdin
+    - docker push nest/nest-simulator:3.6
+    - docker logout $DOCKERHUB_REGISTRY
+  only:
+    - master
+  tags:
+    - shell-runner

ci-templates/000_dev.gitlab-ci.yml

@@ -8,42 +8,21 @@ Build_Dev:
   rules:
     - when: always
   script:
-    - docker pull $DOCKER_REGISTRY_IMAGE:dev || true
+    - docker pull push nest/nest-simulator:dev || true
     - docker build
-        --cache-from $DOCKER_REGISTRY_IMAGE:dev
-        --tag $DOCKER_REGISTRY_IMAGE:dev.$CI_PIPELINE_ID
+        --cache-from nest/nest-simulator:dev
+        --tag nest/nest-simulator:dev
         ./src/dev
-    - docker push $DOCKER_REGISTRY_IMAGE:dev.$CI_PIPELINE_ID
-  tags:
-    - shell-runner
-
-Test_Dev:
-  stage: test
-  needs: ["Build_Dev"]
-  rules:
-    - when: always
-  script:
-    - docker pull $DOCKER_REGISTRY_IMAGE:dev.$CI_PIPELINE_ID
-    - docker stop $(docker ps -q) 2>/dev/null || true
-    - docker rm -f $(docker ps -aq) 2>/dev/null || true
-    - docker ps
-    - docker run -i -d --rm -e NEST_CONTAINER_MODE=nest-server -p 52425:52425
-        --name $CI_PIPELINE_ID $DOCKER_REGISTRY_IMAGE:dev.$CI_PIPELINE_ID
-    - docker run -i --rm $DOCKER_REGISTRY_IMAGE:dev.$CI_PIPELINE_ID bash /opt/test-nest.sh
-    - docker ps
+    # Simple test
+    - docker run -i --rm nest/nest-simulator:dev bash /opt/test-nest.sh
   tags:
     - shell-runner
 
 Deploy_Dev:
   stage: deploy
-  needs: ["Test_Dev"]
-  when: always
+  needs: ["Build_Dev"]
   script:
-    - docker pull $DOCKER_REGISTRY_IMAGE:dev.$CI_PIPELINE_ID
-    - docker tag $DOCKER_REGISTRY_IMAGE:dev.$CI_PIPELINE_ID $DOCKER_REGISTRY_IMAGE:dev
-    - docker push $DOCKER_REGISTRY_IMAGE:dev
     - echo -n $DOCKERHUB_REGISTRY_TOKEN | docker login -u $DOCKERHUB_REGISTRY_USER --password-stdin
-    - docker tag $DOCKER_REGISTRY_IMAGE:dev nest/nest-simulator:dev
     - docker push nest/nest-simulator:dev
     - docker logout $DOCKERHUB_REGISTRY
   only:

src/3.6/Dockerfile

@@ -0,0 +1,56 @@
+FROM docker-registry.ebrains.eu/nest/nest-simulator:nest-simulator-build-base as builder
+LABEL maintainer="[email protected]"
+
+ARG NEST_VERSION=3.6
+ARG SRC_PATH=/tmp
+
+
+# Install NEST and NESTML
+RUN wget "https://github.com/nest/nest-simulator/archive/refs/tags/v${NEST_VERSION}.tar.gz" -P ${SRC_PATH} && \
+    cd ${SRC_PATH} && tar -xzf ${NEST_VERSION}.tar.gz && ls -l && \
+    python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/doc/requirements.txt && \
+    python3 -m pip install sphinx_gallery==0.10.1
+
+RUN mkdir nest-build && cd nest-build && \
+    cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/nest \
+          -Dwith-warning=ON \
+          -Dwith-userdoc=ON \
+          -Dwith-boost=ON \
+          -Dwith-ltdl=ON \
+          -Dwith-gsl=ON \
+          -Dwith-readline=ON \
+          -Dwith-python=ON \
+          -Dwith-mpi=ON \
+          -Dwith-openmp=ON \
+          -Dwith-libneurosim=OFF \
+          -Dwith-music=/opt/music-install \ 
+          -Dwith-hdf5=ON \
+          ${SRC_PATH}/nest-simulator-${NEST_VERSION} && \
+    make -j $(nproc) && \
+    make docs && \
+    make install
+
+
+
+###############################################################################
+# DEPLOY
+
+FROM docker-registry.ebrains.eu/nest/nest-simulator:nest-simulator-deploy-base
+LABEL maintainer="[email protected]"
+
+COPY --from=builder /opt/nest /opt/nest
+COPY --from=builder /opt/music-install /opt/music-install
+
+RUN python3 -m pip install --upgrade pip && \
+    python3 -m pip install nest-desktop --pre && \
+    python3 -m pip uninstall nestml -y && \
+    python3 -m pip install https://github.com/nest/nestml/archive/refs/heads/master.zip --upgrade
+
+COPY entrypoint.sh /usr/local/bin/entrypoint.sh
+RUN chmod +x /usr/local/bin/entrypoint.sh
+
+COPY test-nest.sh /opt/test-nest.sh
+RUN chmod +x /opt/test-nest.sh
+
+EXPOSE 8080 52425 54286
+ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]

src/3.6/entrypoint.sh

@@ -0,0 +1,55 @@
+#!/bin/bash
+set -e
+IP_ADDRESS=$(hostname --ip-address)
+
+# NEST environment
+source /opt/nest/bin/nest_vars.sh
+
+# Running NEST to test and to copy the .nestrc into /home/nest
+nest --help
+
+export MUSIC_ROOT_DIR=/opt/music-install
+export MUSIC_ROOT=${MUSIC_ROOT_DIR}
+MUSIC_PATH=${MUSIC_ROOT_DIR}
+export LD_LIBRARY_PATH=${MUSIC_PATH}/lib:$LD_LIBRARY_PATH
+export PATH=${MUSIC_PATH}/bin:$PATH
+export CPATH=${MUSIC_PATH}/include:$CPATH
+export PYTHONPATH=${MUSIC_PATH}/lib/python3.8/site-packages:$PYTHONPATH
+
+MODE="${NEST_CONTAINER_MODE:-$1}"
+if [[ "${MODE}" = 'interactive' ]]; then
+    read -p "Your python script: " name
+    echo Starting: $name
+    # Start
+    mkdir -p /opt/data; cd /opt/data
+    exec python3 /opt/data/$name
+
+elif [[ "${MODE}" = 'jupyterlab' ]]; then
+    mkdir -p /opt/data; cd /opt/data
+    exec /usr/local/bin/jupyter-lab --ip="${IP_ADDRESS}" --port=8080 --no-browser --allow-root
+
+elif [[ "${MODE}" = 'nest-desktop' ]]; then
+    export NEST_DESKTOP_HOST="${NEST_DESKTOP_HOST:-0.0.0.0}"
+    export NEST_DESKTOP_PORT="${NEST_DESKTOP_PORT:-54286}"
+    exec nest-desktop start
+
+elif [[ "${MODE}" = 'nest-server' ]]; then
+    export NEST_SERVER_HOST="${NEST_SERVER_HOST:-0.0.0.0}"
+    export NEST_SERVER_MODULES="${NEST_SERVER_MODULES:-nest,numpy}"
+    export NEST_SERVER_PORT="${NEST_SERVER_PORT:-52425}"
+    export NEST_SERVER_RESTRICTION_OFF="${NEST_SERVER_RESTRICTION_OFF:-1}"
+    export NEST_SERVER_STDOUT="${NEST_SERVER_STDOUT:-1}"
+    exec nest-server start
+
+elif [[ "${MODE}" = 'nest-server-mpi' ]]; then
+    export NEST_SERVER_HOST="${NEST_SERVER_HOST:-0.0.0.0}"
+    export NEST_SERVER_PORT="${NEST_SERVER_PORT:-52425}"
+    exec mpirun -np "${NEST_SERVER_MPI_NUM:-1}" nest-server-mpi
+
+elif [[ "${MODE}" = 'notebook' ]]; then
+    mkdir -p /opt/data; cd /opt/data
+    exec jupyter-notebook --ip="${IP_ADDRESS}" --port=8080 --no-browser --allow-root
+
+else
+    exec "$@"
+fi

src/3.6/test-nest.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+# run mpiexec as root
+export OMPI_ALLOW_RUN_AS_ROOT=1
+export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+
+# install what is needed
+pip3 install pytest-xdist pytest-timeout junitparser
+
+HDF5_DISABLE_VERSION_CHECK=1
+
+cd /opt/nest/share/nest/testsuite/
+bash do_tests.sh --prefix=/opt/nest --with-python=/usr/bin/python