Update to work better

Author: rowleya

SpiNNaker-nmpiserv/Dockerfile

@@ -15,7 +15,17 @@
 # Use Ubuntu
 FROM ubuntu:noble
 
-RUN apt update && apt install -y openjdk-21-jdk-headless maven git libltdl7
+ARG DOCKER_GROUP_ID
+ARG USER_ID
+ENV DOCKER_GROUP_ID $DOCKER_GROUP_ID
+ENV USER_ID $USER_ID
+
+RUN apt update && apt install -y openjdk-21-jdk-headless maven git libltdl7 nginx
+
+COPY --chown=www-data nginx.conf /etc/nginx/nginx.conf
+
+RUN groupadd -g $DOCKER_GROUP_ID docker
+RUN usermod -a -G docker www-data
 
 # Set the working directory in the container
 WORKDIR /app
@@ -29,5 +39,7 @@ RUN mvn -f JavaSpiNNaker -DskipTests=true -pl SpiNNaker-nmpiserv -am package
 # Get the binary into place
 RUN cp JavaSpiNNaker/SpiNNaker-nmpiserv/target/SpiNNakerNMPI.war .
 
+COPY --chmod=0755 startup.sh /app/startup.sh
+
 # Specify the command to start things
-CMD [ "java", "-Djava.net.preferIPv4Stack=true", "-Djava.awt.headless=true", "-jar", "SpiNNakerNMPI.war", "--spring.config.location=/app/nmpi.properties", "-" , "--server.port=9090" ]
+CMD [ "/app/startup.sh" ]

SpiNNaker-nmpiserv/README.md

@@ -7,16 +7,15 @@ This is a [Spring Boot](https://spring.io/projects/spring-boot) web application.
 ## Usage
 This folder contains configuration which can be used to set up a docker compose instance of the service.  To use this, do the following:
 
- 1. Copy files ``application.properties.example``, ``Dockerfile``, ``docker-compose.yml``. ``nginx.conf`` and ``execute_pynn.bash`` to your deployment folder.
- 2. Rename ``application.properties.example`` to ``application.properties``
- 3. Update ``application.properties`` with valid values for your environment, particularly replacing items in angle brackets.
- 4. Update ``docker-compose.yml`` with valid values for your environment,
- particularly replacing items in angle brackets.
- 4. Run ``docker compose build`` to build the docker environment
- 5. Run ``docker compose start -d`` to start the services
+ 1. Copy files ``nmpi.properties.example``, ``Dockerfile``, ``docker-compose.yml``, ``nginx.conf``, ``startup.sh``, ``env.example`` and ``execute_pynn.bash`` to your deployment folder.
+ 2. Rename ``nmpi.properties.example`` to ``nmpi.properties``
+ 3. Rename ``env.example`` to ``.env``
+ 4. Update ``.env`` with valid values for your environment
+ 5. Run ``docker compose build`` to build the docker environment
+ 6. Run ``docker compose start -d`` to start the services
 
 ### Viewing logs
 You can view the logs of the spalloc server with:
 ```
-docker logs -f nmpi-host
+docker compose logs -f nmpi
 ```

SpiNNaker-nmpiserv/docker-compose.yml

@@ -17,25 +17,21 @@ services:
     build:
       context: .
       dockerfile: Dockerfile
+      args:
+        DOCKER_GROUP_ID: ${DOCKER_GROUP_ID}
+        USER_ID: ${USER_ID}
     container_name: nmpi-host
+    env_file: .env
     ports:
       - "9090:9090"
     networks:
       - nmpi-network
     volumes:
       - ./nmpi.properties:/app/nmpi.properties
       - ./execute_pynn.bash:/app/execute_pynn.bash
-      - <DATA_PATH>:/mnt/data/
-
-  nginx:
-    image: nginx
-    container_name: nmpi-nginx
-    networks:
-      - nmpi-network
-    volumes:
-      - <DOCKER_SOCK_PATH>/docker.sock:/docker.sock
-      - ./nginx.conf:/etc/nginx/nginx.conf
+      - /var/run/docker.sock:/var/run/docker.sock
+      - $DATA_PATH:/mnt/data/
 
 networks:
   nmpi-network:
-    name: nmpi-network
+    name: nmpi-network

SpiNNaker-nmpiserv/docker_image/Dockerfile

@@ -34,7 +34,7 @@ RUN apt-get update --yes && \
     gcc \
     lsof \
     gcc-arm-none-eabi \
-    openjdk-17-jdk \
+    openjdk-21-jdk \
     maven \
     ffmpeg \
     curl \

SpiNNaker-nmpiserv/env.example

@@ -0,0 +1,38 @@
+# Copyright (c) 2025 The University of Manchester
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+# OpenID client id from EBRAINS
+EBRAINS_OPENID_CLIENT_ID=spalloc
+
+# OpenID client secret from EBRAINS
+EBRAINS_OPENID_CLIENT_SECRET=
+
+# The host that people will use to access the NMPI server
+# This is the host name of this machine as seen from outside
+NMPI_SERVER_HOST=
+
+# The API Key to access NMPI services
+NMPI_API_KEY=
+
+# The IP address or URL that should use to speak to the spalloc server
+SPALLOC_SERVER_URL=
+
+# The path to where complete data files should be stored
+DATA_PATH=
+
+# The Group ID of the docker user (found from "getent group docker")
+DOCKER_GROUP_ID=
+
+# The User ID of the current user (found from "id" as the current user)
+USER_ID=

SpiNNaker-nmpiserv/nginx.conf

@@ -70,7 +70,7 @@ http {
         # Virtual Host Configs
         ##
         upstream docker {
-            server unix:/docker.sock;
+            server unix:/var/run/docker.sock;
         }
 
         server {
@@ -81,4 +81,4 @@ http {
                 proxy_pass http://docker/;
             }
         }
-}
+}

…-nmpiserv/application.properties.example …iNNaker-nmpiserv/nmpi.properties.exampleSpiNNaker-nmpiserv/application.properties.example renamed to SpiNNaker-nmpiserv/nmpi.properties.example SpiNNaker-nmpiserv/application.properties.example renamed to SpiNNaker-nmpiserv/nmpi.properties.example

@@ -15,33 +15,40 @@
 spalloc.enabled = True
 spalloc.use_java = False
 spalloc.port = 22244
-spalloc.server = <SPALLOC_SERVER_HOST>
+spalloc.server = ${SPALLOC_SERVER_URL}
 spalloc.user.name = NMPI
 nmpi.compat = False
 nmpi.url = https://nmpi-v3.hbpneuromorphic.eu/
-nmpi.apiKey =
+nmpi.apiKey = ${NMPI_API_KEY}
 nmpi.hardware = SpiNNaker
 results.directory = /mnt/data/nmpi-outputs
-baseserver.url = https://<SPALLOC_SERVER_HOST>
+baseserver.url = https://${NMPI_SERVER_HOST}
 localbaseserver.url = http://nmpi:9090
 cxf.path = /services
 cxf.rest.path = /rest
 callback.path = /callback
 deleteJobsOnExit = true
 liveUploadOutput = true
 requestSpiNNakerMachine = false
-oidc.clientId = <EBRAINS_OPENID_CLIENT_ID>
-oidc.secret = <EBRAINS_OPENID_CLIENT_SECRET>
+oidc.clientId = ${EBRAINS_OPENID_CLIENT_ID}
+oidc.secret = ${EBRAINS_OPENID_CLIENT_SECRET}
 oidc.discovery.uri = https://services.humanbrainproject.eu/oidc/.well-known/openid-configuration
 collab.service.uri = https://services.humanbrainproject.eu/
 document.service.uri = https://services.humanbrainproject.eu/
 results.purge.days = 100
 docker.enabled = true
 docker.image = nmpiexec
-docker.uri = http://nginx/
+docker.uri = http://localhost/
 docker.networkName = nmpi-network
 docker.maxVms = 10
 xen.server.enabled = false
 restartJobExecutorOnFailure = false
 setupScript = file:/app/execute_pynn.bash
 status.update = false
+status.update.type = STATUS_CAKE
+icinga2.url = https://hbpmonitor.bsc.es:5665/
+icinga2.service = UMAN-NMC-spinnaker!NMC-RemoteSpiNNaker-Push
+icinga2.username = uman
+icinga2.password = 
+statusCake.primaryKey =
+statusCake.testID =

SpiNNaker-nmpiserv/startup.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+service nginx start
+java -Djava.net.preferIPv4Stack=true -Djava.awt.headless=true -jar /app/SpiNNakerNMPI.war --spring.config.location=/app/nmpi.properties - --server.port=9090
+service nginx stop