Fix nest server-mpi service in Docker compose (#257)

* Add docopt-ng and clean lines * Add more env variables for NEST Server MPI * Add service for nest-server-mpi in docker-compose * Update entrypoint to reduce logging

Author: babsey

docker-compose.yml

@@ -1,5 +1,3 @@
-version: "3"
-
 services:
  nest-server:
  image: nest/nest-simulator:3.8
@@ -9,6 +7,18 @@ services:
  ports:
  - "52425:52425"
 
+ # nest-server-mpi:
+ # image: nest-simulator:master-mpi
+ # environment:
+ # LOCAL_USER_ID: "`id -u $USER`"
+ # NEST_CONTAINER_MODE: "nest-server-mpi"
+ # NEST_SERVER_MPI_NUM: 3
+ # NEST_SERVER_MPI_LOGGER_LEVEL: "INFO"
+ # OMPI_ALLOW_RUN_AS_ROOT: 1
+ # OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
+ # ports:
+ # - "52425:52425"
+
  nest-desktop:
  image: nest/nest-simulator:3.8
  environment:

src/dev/Dockerfile

@@ -14,7 +14,7 @@ ENV TERM=xterm \
  OMPI_ALLOW_RUN_AS_ROOT=1 \
  OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 
- RUN apt-get update && apt-get install -y --no-install-recommends \
+RUN apt-get update && apt-get install -y --no-install-recommends \
  automake \
  autotools-dev \
  build-essential \
@@ -96,16 +96,18 @@ RUN cd ${SRC_PATH} && \
  tar -xzf ${NEST_VERSION}.tar.gz
 
 # Installing the requirements_docs.txt stops at some time with an error
- # Installing every package fix it.
+# Installing every package fix it.
 RUN python3 -m pip install sphinx>=6.2.1 sphinx_rtd_theme sphinx_autobuild sphinx-tabs && \
  python3 -m pip install sphinx_design sphinx-material sphinx-copybutton sphinx-carousel && \
  python3 -m pip install sphinx-notfound-page sphinxcontrib-mermaid sphinxcontrib-plantuml nbsphinx && \
  python3 -m pip install numpydoc example Image breathe csvkit docutils PyYAML>=4.2b1 tqdm yamllint && \
- # RUN python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements_docs.txt
- python3 -m pip install sphinx_gallery==0.13.0 'numpy<=1.26' && \
- chmod +x ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_music.sh && \
- ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_music.sh && \
- mkdir ${SRC_PATH}/nest-build && cd $_ && \
+# RUN python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements_docs.txt
+ python3 -m pip install sphinx_gallery==0.13.0 'numpy<=1.26'
+
+RUN chmod +x ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_music.sh && \
+ ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_music.sh
+
+RUN mkdir ${SRC_PATH}/nest-build && cd $_ && \
  cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/nest \
  -Dwith-optimize="-O2" \
  -Dwith-warning=ON \
@@ -126,15 +128,16 @@ RUN python3 -m pip install sphinx>=6.2.1 sphinx_rtd_theme sphinx_autobuild sphin
  make install
 
 RUN python3 -m pip install --upgrade pip setuptools wheel && \
-python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements.txt && \
-python3 -m pip install --upgrade nest-desktop && \
-python3 -m pip install --upgrade scipy && \
-python3 -m pip install --upgrade gsl wheel setuptools swig
+ python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements.txt && \
+ python3 -m pip install --upgrade nest-desktop && \
+ python3 -m pip install --upgrade scipy && \
+ python3 -m pip install --upgrade gsl wheel setuptools swig && \
+ # Latest update to nestml v8.0.0-rc3
+ python3 -m pip install nestml==8.0.0rc3 && \
+ python3 -m pip install docopt-ng
 
-#Latest update to nestml v8.0.0
-RUN python3 -m pip install nestml==8.0.0 && \
-python3 -m pip install nestml-server@git+https://github.com/babsey/nestml-server@v1.0-b8 && \
-python3 -m pip install --upgrade pygsl@git+https://github.com/pygsl/pygsl@v2.4.0
+RUN python3 -m pip install nestml-server@git+https://github.com/babsey/nestml-server@v1.0-b8
+ # python3 -m pip install --upgrade pygsl@git+https://github.com/pygsl/pygsl@v2.4.0 && \
 
 COPY entrypoint.sh /usr/local/bin/entrypoint.sh
 RUN chmod +x /usr/local/bin/entrypoint.sh

src/dev/entrypoint.sh

@@ -53,7 +53,14 @@ elif [[ "${MODE}" = 'nest-server' ]]; then
 elif [[ "${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 "${NEST_SERVER_MPI_NUM:-1}" nest-server-mpi
+
+ export NEST_SERVER_ACCESS_TOKEN="${NEST_SERVER_ACCESS_TOKEN}"
+ export NEST_SERVER_CORS_ORIGINS="${NEST_SERVER_CORS_ORIGINS:-*}"
+ export NEST_SERVER_DISABLE_AUTH="${NEST_SERVER_DISABLE_AUTH:-1}"
+ export NEST_SERVER_DISABLE_RESTRICTION="${NEST_SERVER_DISABLE_RESTRICTION:-1}"
+ export NEST_SERVER_ENABLE_EXEC_CALL="${NEST_SERVER_ENABLE_EXEC_CALL:-1}"
+ export NEST_SERVER_MODULES="${NEST_SERVER_MODULES:-import nest; import numpy; import numpy as np}"
+ exec mpirun -np "${NEST_SERVER_MPI_NUM:-1}" nest-server-mpi --host "${NEST_SERVER_HOST}" --port "${NEST_SERVER_PORT}"
 
 elif [[ "${MODE}" = 'nestml-server' ]]; then
  export NESTML_SERVER_HOST="${NESTML_SERVER_HOST:-0.0.0.0}"