If you know how to use docker, you know how to use NEST.
Currently the following docker images are provided
- nest/nest-simulator:dev
- nest/nest-simulator:2.20.2
- nest/nest-simulator:3.0
- nest/nest-simulator:3.1
- nest/nest-simulator:3.2
- nest/nest-simulator:3.3
- nest/nest-simulator:3.4
- nest/nest-simulator:3.5
- nest/nest-simulator:3.6
- nest/nest-simulator:3.7
- nest/nest-simulator:3.8
You can use the docker images direct out of docker-registry.ebrains.eu like this:
docker pull nest/nest-simulator:TAG
TAG is '2.20.2', '3.2', '3.3', '3.4', '3.5', '3.6', '3.7', '3.8'or 'dev'.
Jupyter notebook with NEST 2.20.2:
docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -v $(pwd):/opt/data -e NEST_CONTAINER_MODE=notebook \
-p 8080:8080 nest/nest-simulator:2.20.2
Jupyter lab with NEST 2.20.2
docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -v $(pwd):/opt/data -e NEST_CONTAINER_MODE=jupyterlab \
-p 8080:8080 nest/nest-simulator:2.20.2
To use 'docker-compose' you need the definition file from the git repository. Download it:
wget https://raw.githubusercontent.com/nest/nest-docker/master/docker-compose.yml
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NEST Server
docker-compose up nest-serveror
docker run -it --rm -e NEST_CONTAINER_MODE=nest-server -p 52425:52425 \ nest/nest-simulator:3.8Starts the NEST API server container and opens the corresponding port 52425. Test it with
curl localhost:52425/api. -
NEST Desktop
docker-compose up nest-desktopor
docker run -it --rm -e NEST_CONTAINER_MODE=nest-server -p 52425:52425 \ nest/nest-simulator:3.8 docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -p 54286:54286 \ -e NEST_CONTAINER_MODE=nest-desktop nest/nest-simulator:3.8Starts the NEST server and the NEST desktop web interface. Port 54286 is also made available. Open in the web browser:
http://localhost:54286 -
Jupyter notebook with NEST
docker-compose up nest-notebookor
docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -v $(pwd):/opt/data -e NEST_CONTAINER_MODE=notebook \ -p 8080:8080 nest/nest-simulator:3.8Starts a notebook server with pre-installed NEST 3.8. The corresponding URL is displayed in the console.
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Jupyter lab with NEST
docker-compose up nest-jupyterlabor
docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -v $(pwd):/opt/data -e NEST_CONTAINER_MODE=jupyterlab \ -p 8080:8080 nest/nest-simulator:3.8Starts a jupyter lab server with pre-installed NEST 3.8. The corresponding URL is displayed in the console.
To stop and delete running containers use docker-compose down.
If you want to use the compose configurtion for the dev NEST version, use the file option, e.g.:
wget https://raw.githubusercontent.com/steffengraber/nest-docker/master/docker-compose.yml
docker-compose -f docker-compose-dev.yml up nest-notebook
e.g.:
docker run -it --rm -v %cd%:/opt/data -p 8080:8080 -e NEST_CONTAINER_MODE=<args> \
nest/nest-simulator:<version>
In Powershell, '%cd%' might not work for the current directory. Then you should explicitly specify a folder with existing write permissions.
In any case, this will download the docker image with the pre-installed NEST master from docker-registry.ebrains.eu and start it. After booting an URL is presented. Click on it or copy it to your browser. Voilá jupyter notebook starts from the docker image.
You can update the image with:
docker pull nest/nest-simulator:<version>
You can clone this repository and use the shell script:
sh run.sh [--help] <command> [<args>] [<version>]
--help print this usage information.
<command> can be either 'provision', 'run' or 'clean'.
[<args>] can be either 'notebook', 'jupyterlab', or 'interactice'.
[<version>] kind of docker image (e.g. 'dev', '2.12.0', '2.14.0',
'2.16.0', '2.18.0', '3.0', '3.1', '3.2', '3.3', '3.4', '3.5',
'3.6', '3.7', '3.8' or 'all').
Example: sh run.sh provision dev
sh run.sh run notebook dev
sh run.sh run jupyterlab dev
In the next steps, VERSION is the kind of docker image you want to use (3.8, dev, ...)
Two little steps to get started
This step is only necessary if you want to build the images directly from the docker files.
sh run.sh provision VERSION
Be careful with the version 'all'. This really takes a long time.
After every build of a NEST docker image, there are two more images - the one with the name of the NEST version (e.g. 'nest/nest-simulator:latest') and another without any name. The last one you can delete. More information about this so called 'multi-stage build' here: https://docs.docker.com/develop/develop-images/multistage-build/
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with Jupyter Notebook (recommended)
sh run.sh run notebook VERSION(For VERSION see above)
Open the displayed URL in your browser and have fun with Jupyter Notebook and NEST.
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in interactive mode
sh run.sh run interactive VERSION(For VERSION see above)
After the prompt 'Your python script:' enter the filename of the script you want to start. Only the filename without any path. The file has to be in the path where you start the script.
sh run.sh clean
Be careful. This stops EVERY container and delete then EVERY NEST Images.
In the folder with your music scripts run:
docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` \
-v $(pwd):/opt/data \
nest/nest-simulator:3.8 /bin/bash
You are now on container's shell.
cd /opt/nest/share/doc/nest/examples/music/
mpirun --allow-run-as-root -np 2 music ./minimalmusicsetup.music
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Delete ALL(!) images (USE WITH CAUTION!)
docker system prune -fa --volumes -
Export a docker image
docker save nest/nest-simulator:3.8 | gzip -c > nest-docker.tar.gz -
Import a docker image
gunzip -c nest-docker.tar.gz | docker load -
Execute an interactive bash shell on a running container.
docker exec -it <nest_container_name> bash -
If there is a standard user, use this to login as root:
docker exec -it --workdir /root --user root <nest_container_name> bash
docker login docker-registry.ebrains.eu
docker build -t nest-simulator:<VERSION> /path/to/recipe --squash
docker tag nest/nest-simulator:<VERSION> nest/nest-simulator:<VERSION>
docker push nest/nest-simulator:<VERSION>