Fix NEST docker v2.20.2 (#214)

* Merge build and deploy to fix deploy problems

* Rework nest build (no boost, music)

* Update workflow and activate in CI build

ci-templates/003_2.20.2.gitlab-ci.yml

@@ -2,49 +2,28 @@
 ###               v2.20.2                   ###
 ###############################################
 
+
 Build_2202:
   stage: build
   needs: ["Build_Base"]
   rules:
-   - when: never
+    - when: always
   script:
-    - docker pull $DOCKER_REGISTRY_IMAGE:2.20.2  || true
-    - docker build 
-        --cache-from $DOCKER_REGISTRY_IMAGE:2.20.2  
-        --tag $DOCKER_REGISTRY_IMAGE:2.20.2.$CI_PIPELINE_ID 
+    # Build
+    - docker pull nest/nest-simulator:2.20.2 || true
+    - docker build
+        --cache-from nest/nest-simulator:2.20.2
+        --tag nest/nest-simulator:2.20.2
         ./src/2.20.2
-    - docker push $DOCKER_REGISTRY_IMAGE:2.20.2.$CI_PIPELINE_ID
-  tags:
-    - shell-runner
-
-Test_2202:
-  stage: test
-  needs: ["Build_2202"]
-  rules:
-   - when: never
-  script:
-    - docker pull $DOCKER_REGISTRY_IMAGE:2.20.2.$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 5000:5000  
-        --name $CI_PIPELINE_ID $DOCKER_REGISTRY_IMAGE:2.20.2.$CI_PIPELINE_ID
-    - docker ps
-  tags:
-    - shell-runner
-
-Deploy_2202:
-  stage: deploy
-  needs: ["Test_2202"]
-  rules:
-   - when: never
-  script:
-    - docker pull $DOCKER_REGISTRY_IMAGE:2.20.2.$CI_PIPELINE_ID
-    - docker tag $DOCKER_REGISTRY_IMAGE:2.20.2.$CI_PIPELINE_ID $DOCKER_REGISTRY_IMAGE:2.20.2
-    - docker push $DOCKER_REGISTRY_IMAGE:2.20.2
+    # Test
+    - docker run -i --rm nest/nest-simulator:2.20.2 bash /opt/test-nest.sh
+    # Deploy
     - echo -n $DOCKERHUB_REGISTRY_TOKEN | docker login -u $DOCKERHUB_REGISTRY_USER --password-stdin
-    - docker tag $DOCKER_REGISTRY_IMAGE:2.20.2 nest/nest-simulator:2.20.2
     - docker push nest/nest-simulator:2.20.2
+    - docker tag nest/nest-simulator:2.20.2 $DOCKER_REGISTRY_IMAGE:2.20.2
+    - docker push $DOCKER_REGISTRY_IMAGE:2.20.2  
     - docker logout $DOCKERHUB_REGISTRY
+    - docker logout $DOCKER_REGISTRY
   tags:
     - shell-runner
+

src/2.20.2/Dockerfile

@@ -1,4 +1,4 @@
-FROM buildpack-deps:focal as builder2202
+FROM ubuntu:focal
 LABEL maintainer="[email protected]"
 
 ENV TERM=xterm \
@@ -8,9 +8,12 @@ ENV TERM=xterm \
 RUN apt-get update && apt-get install -y --no-install-recommends \
     build-essential libtool automake autotools-dev libreadline8 libreadline-dev freeglut3-dev \
     gosu \
+    curl \
     cmake \
     cython3 \
     jq \
+    jupyter-notebook \
+    less \
     libboost-filesystem-dev \
     libboost-regex-dev \
     libboost-wave-dev \
@@ -27,12 +30,17 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     libpcre3-dev \
     libpython3.8 \
     llvm-dev \
+    nano \
     openmpi-bin \
+    openssh-client \
+    openssh-server \
     pandoc \
     pep8 \
     python3-dev \
+    python3-flask \
+    python3-flask-cors \
+    python3-restrictedpython \
     python3-ipython \
-    python3-jupyter-core \
     python3-matplotlib \
     python3-mpi4py \
     python3-nose \
@@ -49,114 +57,47 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     vera++ \
     wget  && \
     apt-get autoremove -y && \
-    rm -rf /var/lib/apt/lists/* && \
-    # update-alternatives --remove-all python && \
-    update-alternatives --install /usr/bin/python python /usr/bin/python3 10 && \
-    update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10 && \
-    python3 -m pip install --upgrade pip setuptools wheel mock
-
-
-# Install music
-RUN wget https://github.com/INCF/MUSIC/archive/master.tar.gz && \
-    tar -zxf master.tar.gz && \
-    mkdir music-build music-install && \
-    cd MUSIC-master && \
-    sh ./autogen.sh && \
-    cd ../music-build && \
-    ../MUSIC-master/configure --prefix=/opt/music-install && \
-    make && \
-    make install && \
-    cd / && \
-    rm master.tar.gz
+    rm -rf /var/lib/apt/lists/* 
 
+# # Install music
+# RUN wget https://github.com/INCF/MUSIC/archive/master.tar.gz && \
+#     tar -zxf master.tar.gz && \
+#     mkdir music-build music-install && \
+#     cd MUSIC-master && \
+#     sh ./autogen.sh && \
+#     cd ../music-build && \
+#     ../MUSIC-master/configure --prefix=/opt/music-install && \
+#     make && \
+#     make install && \
+#     cd / && \
+#     rm master.tar.gz
 
 # Install NEST
 RUN wget https://github.com/nest/nest-simulator/archive/refs/tags/v2.20.2.tar.gz && \
-    mkdir nest-build && \
+    mkdir /nest-build && \
     tar zxf v2.20.2.tar.gz && \
-    cd  nest-build && \
+    cd  /nest-build && \
     cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/nest/ \
-        -Dwith-warning=ON \
-        -Dwith-boost=ON \
-        -Dwith-ltdl=ON \
-        -Dwith-gsl=ON \
-        -Dwith-readline=ON \
-        -Dwith-python=ON \
+        -Dwith-python=3 \
         -Dwith-mpi=ON \
         -Dwith-openmp=ON \
-        -Dwith-libneurosim=OFF \
-        -Dwith-music=/opt/music-install \
-        ../nest-simulator-2.20.2 && \
-    make
-RUN cd  nest-build && make install
-
-
-###############################################################################
-
-FROM ubuntu:focal
-LABEL maintainer="[email protected]"
+        ../nest-simulator-2.20.2 &&\
+    make && make install
 
-ENV TERM=xterm \
-    TZ=Europe/Berlin \
-    DEBIAN_FRONTEND=noninteractive
-
-RUN apt-get update && apt-get install -y --no-install-recommends \
-        build-essential \
-        curl \
-        libpcre3 \
-        libpcre3-dev \
-        gosu \
-        jupyter-notebook \
-        less \
-        libgomp1 \
-        libgsl-dev  \
-        libltdl7 \
-        libopenmpi-dev \
-        libomp-dev \
-        libpython3.8 \
-        nano \
-        openmpi-bin \
-        openssh-client \
-        openssh-server \
-        python3-dev \
-        python3-flask \
-        python3-flask-cors \
-        python3-restrictedpython \
-        python3-matplotlib \
-        python3-mpi4py \
-        python3-numpy \
-        python3-pip \
-        python3-scipy \
-        python3-setuptools \
-        python3-pandas \
-        python3-sympy \
-        python3-tk \
-        wget  && \
-    apt-get autoremove -y && \
-    rm -rf /var/lib/apt/lists/* && \
-    update-alternatives --install /usr/bin/python python /usr/bin/python3 10 && \
-    update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10 && \
-    python3 -m pip install quantities lazyarray neo  && \
-    python3 -m pip install uwsgi &&\
-    # wget https://github.com/NeuralEnsemble/PyNN/archive/nest-dev.tar.gz && \
-    # tar -xzf nest-dev.tar.gz && \
-    # cd PyNN-nest-dev && \
-    # python3 setup.py install && \
-    # cd .. && rm -rf PyNN-nest-dev && rm nest-dev.tar.gz
-    python3 -m pip install --no-binary :all: PyNN && \
-    python3 -m pip install Flask  --user && \
-    python3 -m pip install Flask-cors  --user && \
-    python3 -m pip install RestrictedPython  --user && \
+RUN python3 -m pip install --upgrade pip setuptools wheel mock --user &&\
+    python3 -m pip install quantities lazyarray neo --user && \
+    python3 -m pip install uwsgi --user &&\
+    python3 -m pip install PyNN --user && \
+    python3 -m pip install Flask --user && \
+    python3 -m pip install Flask-cors --user && \
+    python3 -m pip install RestrictedPython --user && \
     python3 -m pip install nest-desktop --user &&\
     python3 -m pip install uwsgi --user &&\
-    python3 -m pip install jupyterlab --user &&\
     python3 -m pip install nestml --user
 
-COPY --from=builder2202 /opt/nest /opt/nest
-COPY --from=builder2202 /opt/music-install /opt/music-install
+RUN python3 -m pip install jupyterlab --user
 
 COPY entrypoint.sh /usr/local/bin/entrypoint.sh
 RUN chmod +x /usr/local/bin/entrypoint.sh
-
 EXPOSE 5000 8000 8080
 ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]

src/2.20.2/entrypoint.sh

@@ -6,7 +6,7 @@ IP_ADDRESS=$(hostname --ip-address)
 source /opt/nest/bin/nest_vars.sh
 
 # Running NEST to test and to copy the .nestrc into /home/nest
-nest --help
+#nest --help
 
 export MUSIC_ROOT_DIR=/opt/music-install
 export MUSIC_ROOT=${MUSIC_ROOT_DIR}
@@ -31,7 +31,7 @@ elif [[ "${MODE}" = 'jupyterlab' ]]; then
 
 elif [[ "${MODE}" = 'notebook' ]]; then
     mkdir -p /opt/data; cd /opt/data
-    exec jupyter-notebook --ip="${IP_ADDRESS}" --port=8080 --no-browser --allow-root
+    exec /root/.local/bin/jupyter-notebook --ip="${IP_ADDRESS}" --port=8080 --no-browser --allow-root
 
 else
     exec "$@"