Operating an OASIS

Originally, NOMAD Central Repository is a service run at Max-Planck's computing facility in Garching, Germany. However, the NOMAD software is Open-Source, and everybody can run it. Any service that uses NOMAD software independently is called a NOMAD OASIS. A NOMAD OASIS does not need to be fully isolated. For example, you can publish uploads from your OASIS to the central NOMAD installation.

Quick-start

• Find a linux computer.
• Make sure you have docker installed. Docker nowadays comes with docker compose build in. Prior, you needed to install the stand alone docker-compose.
• Download our basic configuration files nomad-oasis.zip
• Run the following commands (skip chown on MacOS and Windows computers)

unzip nomad-oasis.zip
cd nomad-oasis
sudo chown -R 1000 .volumes
docker compose pull
docker compose up -d
curl localhost/nomad-oasis/alive

• Open http://localhost/nomad-oasis in your browser.

To run NORTH (the NOMAD Remote Tools Hub), the hub container needs to run docker and the container has to be run under the docker group. You need to replace the default group id 991 in the docker-compose.yaml's hub section with your systems docker group id. Run id if you are a docker user, or getent group | grep docker to find our your systems docker gid. The user id 1000 is used as the nomad user inside all containers.

This is good as a quick test. We strongly recommend to read the following instructions carefully and adapt the configuration files accordingly. The following might also include meaningful help, if you run into problems.

Before you start

Hardware considerations

Of course this depends on how much data you need to manage and process. Data storage is the obvious aspect here. NOMAD keeps all files that it manages as they are. The files that NOMAD processes in addition (e.g. through parsing) are typically smaller than the original raw files. Therefore, you can base your storage requirements based on the size of the data files that you expect to manage. The additional mongo database and elasticsearch index is comparatively small.

Storage speed is another consideration. You can work with NAS systems. All that NOMAD needs is a "regular" POSIX filesystem as an interface. So everything you can (e.g. docker host) mount should be fine. For processing data obviously relies on read/write speed, but this is just a matter of convenience. The processing is designed to run as managed asynchronous tasks. Local storage might be favorable for mongodb and elasticsearch operation, but it is not a must.

The amount of compute resource (e.g. processor cores) is also a matter of convenience (and amount of expected users). Four cpu-cores are typically enough to support a research group and run application, processing, and databases in parallel. Smaller systems still work, e.g. for testing.

There should be enough RAM to run databases, application, and processing at the same time. The minimum requirements here can be quite low, but for processing the metadata for individual files is kept in memory. For large DFT geometry-optimizations this can add up quickly, especially if many CPU cores are available for processing entries in parallel. We recommend at least 2GB per core and a minimum of 8GB. You also need to consider RAM and CPU for running tools like jupyter, if you opt to use NOMAD NORTH.

Using the central user management

Our recommendation is to use the central user management provided by nomad-lab.eu. We simplified its use and you can use it out-of-the-box. You can even run your system from localhost (e.g. for initial testing). The central user management system is not communicating with your OASIS directly. Therefore, you can run your OASIS without exposing it to the public internet.

There are two requirements. First, your users must be able to reach the OASIS. If a user is logging in, she/he is redirected to the central user management server and after login, she/he is redirected back to the OASIS. These redirects are executed by your user's browser and do not require direct communication.

Second, your OASIS must be able to request (via HTTP) the central user management and central NOMAD installation. This is necessary for non JWT-based authentication methods and to retrieve existing users for data-sharing features.

The central user management will make future synchronizing data between NOMAD installations easier and generally recommend to use the central system. But in principle, you can also run your own user management. See the section on your own user management.

Docker and docker compose

We recommend the installation via docker and docker-compose. It is the most documented, simplest, easiest to update, and generally the most frequently chosen option.

Pre-requisites

NOMAD software is distributed as a set of docker containers and there are also other services required that can be run with docker. Further, we use docker-compose to setup all necessary containers in the simplest way possible.

You will need a single computer, with docker and docker-compose installed. Refer to the official docker (and docker-compose) documentation for installation instructions. Newer version of docker have a re-implementation of docker-compose integrated as the docker compose sub-command. This should be fully compatible and you might chose to can replace docker compose with docker-compose in this tutorial.

The following will run all necessary services with docker. These comprise: a mongo database, an elasticsearch, a rabbitmq distributed task queue, the NOMAD app, NOMAD worker, and NOMAD gui. In this introduction, you will learn what each service does and why it is necessary.

Configuration

All docker containers are configured via docker-compose and the respective docker-compose.yaml file. Further, we will need to mount some configuration files to configure the NOMAD services within their respective containers.

There are three files to configure:

• docker-compose.yaml
• configs/nomad.yaml
• configs/nginx.conf

In this example, we have all files in the same directory (the directory we are also working in). You can download minimal example files here.

docker-compose.yaml

The most basic docker-compose.yaml to run an OASIS looks like this:

version: "3"

services:
  # broker for celery
  rabbitmq:
    restart: unless-stopped
    image: rabbitmq:3.11.5
    container_name: nomad_oasis_rabbitmq
    environment:
      - RABBITMQ_ERLANG_COOKIE=SWQOKODSQALRPCLNMEQG
      - RABBITMQ_DEFAULT_USER=rabbitmq
      - RABBITMQ_DEFAULT_PASS=rabbitmq
      - RABBITMQ_DEFAULT_VHOST=/
    volumes:
      - rabbitmq:/var/lib/rabbitmq
    healthcheck:
      test: ["CMD", "rabbitmq-diagnostics", "--silent", "--quiet", "ping"]
      interval: 10s
      timeout: 10s
      retries: 30
      start_period: 10s

  # the search engine
  elastic:
    restart: unless-stopped
    image: docker.elastic.co/elasticsearch/elasticsearch:7.17.1
    container_name: nomad_oasis_elastic
    environment:
      - ES_JAVA_OPTS=-Xms512m -Xmx512m
      - discovery.type=single-node
    volumes:
      - elastic:/usr/share/elasticsearch/data
    healthcheck:
      test:
        - "CMD"
        - "curl"
        - "--fail"
        - "--silent"
        - "http://elastic:9200/_cat/health"
      interval: 10s
      timeout: 10s
      retries: 30
      start_period: 60s

  # the user data db
  mongo:
    restart: unless-stopped
    image: mongo:5.0.6
    container_name: nomad_oasis_mongo
    environment:
      - MONGO_DATA_DIR=/data/db
      - MONGO_LOG_DIR=/dev/null
    volumes:
      - mongo:/data/db
      - ./.volumes/mongo:/backup
    command: mongod --logpath=/dev/null # --quiet
    healthcheck:
      test:
        - "CMD"
        - "mongo"
        - "mongo:27017/test"
        - "--quiet"
        - "--eval"
        - "'db.runCommand({ping:1}).ok'"
      interval: 10s
      timeout: 10s
      retries: 30
      start_period: 10s

  # nomad worker (processing)
  worker:
    restart: unless-stopped
    image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:latest
    container_name: nomad_oasis_worker
    environment:
      NOMAD_SERVICE: nomad_oasis_worker
      NOMAD_RABBITMQ_HOST: rabbitmq
      NOMAD_ELASTIC_HOST: elastic
      NOMAD_MONGO_HOST: mongo
    depends_on:
      rabbitmq:
        condition: service_healthy
      elastic:
        condition: service_healthy
      mongo:
        condition: service_healthy
    volumes:
      - ./configs/nomad.yaml:/app/nomad.yaml
      - ./.volumes/fs:/app/.volumes/fs
    command: python -m celery -A nomad.processing worker -l info -Q celery

  # nomad app (api + proxy)
  app:
    restart: unless-stopped
    image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:latest
    container_name: nomad_oasis_app
    environment:
      NOMAD_SERVICE: nomad_oasis_app
      NOMAD_SERVICES_API_PORT: 80
      NOMAD_FS_EXTERNAL_WORKING_DIRECTORY: "$PWD"
      NOMAD_RABBITMQ_HOST: rabbitmq
      NOMAD_ELASTIC_HOST: elastic
      NOMAD_MONGO_HOST: mongo
      NOMAD_NORTH_HUB_HOST: north
    depends_on:
      rabbitmq:
        condition: service_healthy
      elastic:
        condition: service_healthy
      mongo:
        condition: service_healthy
      north:
        condition: service_started
    volumes:
      - ./configs/nomad.yaml:/app/nomad.yaml
      - ./.volumes/fs:/app/.volumes/fs
    command: ./run.sh
    healthcheck:
      test:
        - "CMD"
        - "curl"
        - "--fail"
        - "--silent"
        - "http://localhost:8000/-/health"
      interval: 10s
      timeout: 10s
      retries: 30
      start_period: 10s

  # nomad remote tools hub (JupyterHUB, e.g. for AI Toolkit)
  north:
    restart: unless-stopped
    image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:latest
    container_name: nomad_oasis_north
    environment:
      NOMAD_SERVICE: nomad_oasis_north
      NOMAD_NORTH_DOCKER_NETWORK: nomad_oasis_network
      NOMAD_NORTH_HUB_CONNECT_IP: north
      NOMAD_NORTH_HUB_IP: "0.0.0.0"
      NOMAD_NORTH_HUB_HOST: north
      NOMAD_SERVICES_API_HOST: app
      NOMAD_FS_EXTERNAL_WORKING_DIRECTORY: "$PWD"
      NOMAD_RABBITMQ_HOST: rabbitmq
      NOMAD_ELASTIC_HOST: elastic
      NOMAD_MONGO_HOST: mongo
    volumes:
      - ./configs/nomad.yaml:/app/nomad.yaml
      - ./.volumes/fs:/app/.volumes/fs
      - /var/run/docker.sock:/var/run/docker.sock
    user: '1000:991'
    command: python -m nomad.cli admin run hub
    healthcheck:
      test:
        - "CMD"
        - "curl"
        - "--fail"
        - "--silent"
        - "http://localhost:8081/nomad-oasis/north/hub/health"
      interval: 10s
      timeout: 10s
      retries: 30
      start_period: 10s

  # nomad proxy (a reverse proxy for nomad)
  proxy:
    restart: unless-stopped
    image: nginx:1.13.9-alpine
    container_name: nomad_oasis_proxy
    command: nginx -g 'daemon off;'
    volumes:
      - ./configs/nginx.conf:/etc/nginx/conf.d/default.conf
    depends_on:
      app:
        condition: service_healthy
      worker:
        condition: service_started # TODO: service_healthy
      north:
        condition: service_healthy
    ports:
      - 80:80

volumes:
  mongo:
    name: "nomad_oasis_mongo"
  elastic:
    name: "nomad_oasis_elastic"
  rabbitmq:
    name: "nomad_oasis_rabbitmq"
  keycloak:
    name: "nomad_oasis_keycloak"

networks:
  default:
    name: nomad_oasis_network

Changes necessary:

• The group in the value of the hub's user parameter needs to match the docker group on the host. This should ensure that the user which runs the hub, has the rights to access the host's docker.

• On Windows or MacOS computers you have to run the app and worker container without user: '1000:1000' and the north container with user: root.

A few things to notice:

• The app, worker, and north service use the NOMAD docker image. Here we use the latest tag, which gives you the latest beta version of NOMAD. You might want to change this to stable, a version tag (format is vX.X.X, you find all releases here), or a specific branch tag.
• All services use docker volumes for storage. This could be changed to host mounts.
• It mounts two configuration files that need to be provided (see below): nomad.yaml, nginx.conf.
• The only exposed port is 80 (proxy service). This could be changed to a desired port if necessary.
• The NOMAD images are pulled from our gitlab at MPCDF, the other services use images from a public registry (dockerhub).
• All containers will be named nomad_oasis_*. These names can be used later to reference the container with the docker cmd.
• The services are setup to restart always, you might want to change this to no while debugging errors to prevent indefinite restarts.
• Make sure that the PWD environment variable is set. NORTH needs to create bind mounts that require absolute paths and we need to pass the current working directory to the configuration from the PWD variable (see hub service in the docker-compose.yaml).
• The hub service needs to run docker containers. We have to use the systems docker group as a group. You might need to replace 991 with your systems docker group id.

nomad.yaml

NOMAD app and worker read a nomad.yaml for configuration.

services:
  api_host: 'localhost'
  api_base_path: '/nomad-oasis'

oasis:
  is_oasis: true
  uses_central_user_management: true

north:
  jupyterhub_crypt_key: '978bfb2e13a8448a253c629d8dd84ff89587f30e635b753153960930cad9d36d'

meta:
  deployment: 'oasis'
  deployment_url: 'https://my-oasis.org/api'
  maintainer_email: 'me@my-oasis.org'

mongo:
    db_name: nomad_oasis_v1

elastic:
    entries_index: nomad_oasis_entries_v1
    materials_index: nomad_oasis_materials_v1

You should change the following:

• Replace localhost with the hostname of your server. I user-management will redirect your users back to this host. Make sure this is the hostname, your users can use.
• Replace deployment, deployment_url, and maintainer_email with representative values. The deployment_url should be the url to the deployment's api (should end with /api).
• You can change api_base_path to run NOMAD under a different path prefix.
• You should generate your own north.jupyterhub_crypt_key. You can generate one with openssl rand -hex 32.
• On Windows or MacOS, you have to add hub_connect_ip: 'host.docker.internal' to the north section.

A few things to notice:

• Under mongo and elastic you can configure database and index names. This might be useful, if you need to run multiple NOMADs with the same databases.
• All managed files are stored under .volumes of the current directory.

nginx.conf

The GUI container serves as a proxy that forwards requests to the app container. The proxy is an nginx server and needs a configuration similar to this:

map $http_upgrade $connection_upgrade {
    default upgrade;
    ''      close;
}

server {
    listen        80;
    server_name   localhost;
    proxy_set_header Host $host;

    location / {
        proxy_pass http://app:8000;
    }

    location ~ /nomad-oasis\/?(gui)?$ {
        rewrite ^ /nomad-oasis/gui/ permanent;
    }

    location /nomad-oasis/gui/ {
        proxy_intercept_errors on;
        error_page 404 = @redirect_to_index;
        proxy_pass http://app:8000;
    }

    location @redirect_to_index {
        rewrite ^ /nomad-oasis/gui/index.html break;
        proxy_pass http://app:8000;
    }

    location ~ \/gui\/(service-worker\.js|meta\.json)$ {
        add_header Last-Modified $date_gmt;
        add_header Cache-Control 'no-store, no-cache, must-revalidate, proxy-revalidate, max-age=0';
        if_modified_since off;
        expires off;
        etag off;
        proxy_pass http://app:8000;
    }

    location ~ /api/v1/uploads(/?$|.*/raw|.*/bundle?$)  {
        client_max_body_size 35g;
        proxy_request_buffering off;
        proxy_pass http://app:8000;
    }

    location ~ /api/v1/.*/download {
        proxy_buffering off;
        proxy_pass http://app:8000;
    }

    location /nomad-oasis/north/ {
        client_max_body_size 500m;
        proxy_pass http://north:9000;

        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header Host $host;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;

        # websocket headers
        proxy_http_version 1.1;
        proxy_set_header Upgrade $http_upgrade;
        proxy_set_header Connection $connection_upgrade;
        proxy_set_header X-Scheme $scheme;

        proxy_buffering off;
    }
}

A few things to notice:

• It configures the base path (nomad-oasis). It needs to be changed, if you use a different base path.
• You can use the server for additional content if you like.
• client_max_body_size sets a limit to the possible upload size.

You can add an additional reverse proxy in front or modify the nginx in the docker-compose.yaml to support https. If you operate the GUI container behind another proxy, keep in mind that your proxy should not buffer requests/responses to allow streaming of large requests/responses for api/v1/uploads and api/v1/.*/download. An nginx reverse proxy location on an additional reverse proxy, could have these directives to ensure the correct http headers and allows the download and upload of large files:

client_max_body_size 35g;
proxy_set_header Host $host;
proxy_pass_request_headers on;
proxy_buffering off;
proxy_request_buffering off;
proxy_set_header X-Real-IP $remote_addr;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
proxy_pass http://<your-oasis-host>/nomad-oasis;

Running NOMAD

If you prepared the above files, simply use the usual docker compose commands to start everything.

To make sure you have the latest docker images for everything, run this first:

docker compose pull

In the beginning and to simplify debugging, it is recommended to start the services separately:

docker compose up -d mongo elastic rabbitmq
docker compose up app worker gui

The -d option runs container in the background as daemons. Later you can run all at once:

docker compose up -d

Running all services also contains NORTH. When you use a tool in NORTH for the first time, your docker needs to pull the image that contains this tool. Be aware that this might take longer than timeouts allow and starting a tool for the very first time might fail.

You can also use docker to stop and remove faulty containers that run as daemons:

docker stop nomad_oasis_app
docker rm nomad_oasis_app

You can wait for the start-up with curl using the apps alive "endpoint":

curl http://<your host>/nomad-oasis/alive

If everything works, the gui should be available under:

http://<your host>/nomad-oasis/gui/

If you run into problems, use the dev-tools of your browser to check the javascript logs or monitor the network traffic for HTTP 500/400/404/401 responses.

To see if at least the api works, check

http://<your host>/nomad-oasis/alive
http://<your host>/nomad-oasis/api/info

To see logs or 'go into' a running container, you can access the individual containers with their names and the usual docker commands:

docker logs nomad_oasis_app

docker exec -ti nomad_oasis_app /bin/bash

If you want to report problems with your OASIS. Please provide the logs for

• nomad_oasis_app
• nomad_oasis_worker
• nomad_oasis_gui

Provide and connect your own user management

NOMAD uses keycloak for its user management. NOMAD uses keycloak in two ways. First, the user authentication uses the OpenID Connect/OAuth interfaces provided by keycloak. Second, NOMD uses the keycloak realm-management API to get a list of existing users. Keycloak is highly customizable and numerous options to connect keycloak to existing identity providers exist.

This tutorial assumes that you have some understanding of what keycloak is and how it works.

Start with the regular docker-compose installation above. Now you need to modify the docker-compose.yaml to add a keycloak service. You need to modify the nginx.conf to add another location for keycloak. You need to modify the nomad.yaml to tell nomad to use your and not the official NOMAD keycloak.

version: "3"

services:
  # keycloak user management
  keycloak:
    restart: unless-stopped
    image: jboss/keycloak:16.1.1
    container_name: nomad_oasis_keycloak
    environment:
      - PROXY_ADDRESS_FORWARDING=true
      - KEYCLOAK_USER=admin
      - KEYCLOAK_PASSWORD=password
      - KEYCLOAK_FRONTEND_URL=http://localhost/keycloak/auth
      - KEYCLOAK_IMPORT="/tmp/nomad-realm.json"
    command:
      - "-Dkeycloak.import=/tmp/nomad-realm.json -Dkeycloak.migration.strategy=IGNORE_EXISTING"
    volumes:
      - keycloak:/opt/jboss/keycloak/standalone/data
      - ./configs/nomad-realm.json:/tmp/nomad-realm.json
    healthcheck:
      test:
        - "CMD"
        - "curl"
        - "--fail"
        - "--silent"
        - "http://127.0.0.1:9990/health/live"
      interval: 10s
      timeout: 10s
      retries: 30
      start_period: 30s

  # broker for celery
  rabbitmq:
    restart: unless-stopped
    image: rabbitmq:3.11.5
    container_name: nomad_oasis_rabbitmq
    environment:
      - RABBITMQ_ERLANG_COOKIE=SWQOKODSQALRPCLNMEQG
      - RABBITMQ_DEFAULT_USER=rabbitmq
      - RABBITMQ_DEFAULT_PASS=rabbitmq
      - RABBITMQ_DEFAULT_VHOST=/
    volumes:
      - rabbitmq:/var/lib/rabbitmq
    healthcheck:
      test: ["CMD", "rabbitmq-diagnostics", "--silent", "--quiet", "ping"]
      interval: 10s
      timeout: 10s
      retries: 30
      start_period: 10s

  # the search engine
  elastic:
    restart: unless-stopped
    image: docker.elastic.co/elasticsearch/elasticsearch:7.17.1
    container_name: nomad_oasis_elastic
    environment:
      - ES_JAVA_OPTS=-Xms512m -Xmx512m
      - discovery.type=single-node
    volumes:
      - elastic:/usr/share/elasticsearch/data
    healthcheck:
      test:
        - "CMD"
        - "curl"
        - "--fail"
        - "--silent"
        - "http://elastic:9200/_cat/health"
      interval: 10s
      timeout: 10s
      retries: 30
      start_period: 60s

  # the user data db
  mongo:
    restart: unless-stopped
    image: mongo:5.0.6
    container_name: nomad_oasis_mongo
    environment:
      - MONGO_DATA_DIR=/data/db
      - MONGO_LOG_DIR=/dev/null
    volumes:
      - mongo:/data/db
      - ./.volumes/mongo:/backup
    command: mongod --logpath=/dev/null # --quiet
    healthcheck:
      test:
        - "CMD"
        - "mongo"
        - "mongo:27017/test"
        - "--quiet"
        - "--eval"
        - "'db.runCommand({ping:1}).ok'"
      interval: 10s
      timeout: 10s
      retries: 30
      start_period: 10s

  # nomad worker (processing)
  worker:
    restart: unless-stopped
    image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:latest
    container_name: nomad_oasis_worker
    environment:
      NOMAD_SERVICE: nomad_oasis_worker
      NOMAD_RABBITMQ_HOST: rabbitmq
      NOMAD_ELASTIC_HOST: elastic
      NOMAD_MONGO_HOST: mongo
    depends_on:
      rabbitmq:
        condition: service_healthy
      elastic:
        condition: service_healthy
      mongo:
        condition: service_healthy
    volumes:
      - ./configs/nomad.yaml:/app/nomad.yaml
      - ./.volumes/fs:/app/.volumes/fs
    command: python -m celery -A nomad.processing worker -l info -Q celery

  # nomad app (api + proxy)
  app:
    restart: unless-stopped
    image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:latest
    container_name: nomad_oasis_app
    environment:
      NOMAD_SERVICE: nomad_oasis_app
      NOMAD_SERVICES_API_PORT: 80
      NOMAD_FS_EXTERNAL_WORKING_DIRECTORY: "$PWD"
      NOMAD_RABBITMQ_HOST: rabbitmq
      NOMAD_ELASTIC_HOST: elastic
      NOMAD_MONGO_HOST: mongo
    depends_on:
      rabbitmq:
        condition: service_healthy
      elastic:
        condition: service_healthy
      mongo:
        condition: service_healthy
      keycloak:
        condition: service_started
    volumes:
      - ./configs/nomad.yaml:/app/nomad.yaml
      - ./.volumes/fs:/app/.volumes/fs
    command: ./run.sh
    healthcheck:
      test:
        - "CMD"
        - "curl"
        - "--fail"
        - "--silent"
        - "http://localhost:8000/-/health"
      interval: 10s
      timeout: 10s
      retries: 30
      start_period: 10s

  # nomad remote tools hub (JupyterHUB, e.g. for AI Toolkit)
  north:
    restart: unless-stopped
    image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:latest
    container_name: nomad_oasis_north
    environment:
      NOMAD_SERVICE: nomad_oasis_north
      NOMAD_NORTH_DOCKER_NETWORK: nomad_oasis_network
      NOMAD_NORTH_HUB_CONNECT_IP: north
      NOMAD_NORTH_HUB_IP: "0.0.0.0"
      NOMAD_NORTH_HUB_HOST: north
      NOMAD_SERVICES_API_HOST: app
      NOMAD_FS_EXTERNAL_WORKING_DIRECTORY: "$PWD"
      NOMAD_RABBITMQ_HOST: rabbitmq
      NOMAD_ELASTIC_HOST: elastic
      NOMAD_MONGO_HOST: mongo
    depends_on:
      keycloak:
        condition: service_started
      app:
        condition: service_started
    volumes:
      - ./configs/nomad.yaml:/app/nomad.yaml
      - ./.volumes/fs:/app/.volumes/fs
      - /var/run/docker.sock:/var/run/docker.sock
    user: '1000:991'
    command: python -m nomad.cli admin run hub
    healthcheck:
      test:
        - "CMD"
        - "curl"
        - "--fail"
        - "--silent"
        - "http://localhost:8081/nomad-oasis/north/hub/health"
      interval: 10s
      timeout: 10s
      retries: 30
      start_period: 10s

  # nomad proxy (a reverse proxy for nomad)
  proxy:
    restart: unless-stopped
    image: nginx:1.13.9-alpine
    container_name: nomad_oasis_proxy
    command: nginx -g 'daemon off;'
    volumes:
      - ./configs/nginx.conf:/etc/nginx/conf.d/default.conf
    depends_on:
      keycloak:
        condition: service_healthy
      app:
        condition: service_healthy
      worker:
        condition: service_started # TODO: service_healthy
      north:
        condition: service_healthy
    ports:
      - 80:80

volumes:
  mongo:
    name: "nomad_oasis_mongo"
  elastic:
    name: "nomad_oasis_elastic"
  rabbitmq:
    name: "nomad_oasis_rabbitmq"
  keycloak:
    name: "nomad_oasis_keycloak"

networks:
  default:
    name: nomad_oasis_network

A few notes:

• You have to change the KEYCLOAK_FRONTEND_URL variable to match your host and set a path prefix.
• The environment variables on the keycloak service allow to use keycloak behind the nginx proxy with a path prefix, e.g. keycloak.
• By default, keycloak will use a simple H2 file database stored in the given volume. Keycloak offers many other options to connect SQL databases.
• We will use keycloak with our nginx proxy here, but you can also host-bind the port 8080 to access keycloak directly.

Second, we add a keycloak location to the nginx config:

map $http_upgrade $connection_upgrade {
    default upgrade;
    ''      close;
}

server {
    listen        80;
    server_name   localhost;
    proxy_set_header Host $host;

    location /keycloak {
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_set_header X-Forwarded-Proto $scheme;

        rewrite /keycloak/(.*) /$1 break;
        proxy_pass http://keycloak:8080;
    }

    location / {
        proxy_pass http://app:8000;
    }

    location ~ /nomad-oasis\/?(gui)?$ {
        rewrite ^ /nomad-oasis/gui/ permanent;
    }

    location /nomad-oasis/gui/ {
        proxy_intercept_errors on;
        error_page 404 = @redirect_to_index;
        proxy_pass http://app:8000;
    }

    location @redirect_to_index {
        rewrite ^ /nomad-oasis/gui/index.html break;
        proxy_pass http://app:8000;
    }

    location ~ \/gui\/(service-worker\.js|meta\.json)$ {
        add_header Last-Modified $date_gmt;
        add_header Cache-Control 'no-store, no-cache, must-revalidate, proxy-revalidate, max-age=0';
        if_modified_since off;
        expires off;
        etag off;
        proxy_pass http://app:8000;
    }

    location ~ /api/v1/uploads(/?$|.*/raw|.*/bundle?$)  {
        client_max_body_size 35g;
        proxy_request_buffering off;
        proxy_pass http://app:8000;
    }

    location ~ /api/v1/.*/download {
        proxy_buffering off;
        proxy_pass http://app:8000;
    }

    location /nomad-oasis/north/ {
        client_max_body_size 500m;
        proxy_pass http://north:9000;

        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header Host $host;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;

        # websocket headers
        proxy_http_version 1.1;
        proxy_set_header Upgrade $http_upgrade;
        proxy_set_header Connection $connection_upgrade;
        proxy_set_header X-Scheme $scheme;

        proxy_buffering off;
    }
}

A few notes:

• Again, we are using keycloak as a path prefix. We configure the headers to allow keycloak to pick up the rewritten url.

Third, we modify the keycloak configuration in the nomad.yaml:

services:
  api_host: 'localhost'
  api_base_path: '/nomad-oasis'

oasis:
  is_oasis: true
  uses_central_user_management: false

north:
  jupyterhub_crypt_key: '978bfb2e13a8448a253c629d8dd84ff89587f30e635b753153960930cad9d36d'

keycloak:
  server_url: 'http://keycloak:8080/auth/'
  public_server_url: 'http://localhost/keycloak/auth/'
  realm_name: nomad
  username: 'admin'
  password: 'password'

meta:
  deployment: 'oasis'
  deployment_url: 'https://my-oasis.org/api'
  maintainer_email: 'me@my-oasis.org'

mongo:
    db_name: nomad_oasis_v1

elastic:
    entries_index: nomad_oasis_entries_v1
    materials_index: nomad_oasis_materials_v1

You should change the following:

• There are two urls to configure for keycloak. The server_url is used by the nomad services to directly communicate with keycloak within the docker network. The public_server_url is used by the UI to perform the authentication flow. You need to replace localhost in public_server_url with <yourhost>.

A few notes:

• The particular admin_user_id is the Oasis admin user in the provided example realm configuration. See below.

If you open http://<yourhost>/keycloak/auth in a browser, you can access the admin console. The default user and password are admin and password.

Keycloak uses realms to manage users and clients. A default NOMAD compatible realm is imported by default. The realm comes with a test user and password test and password.

A few notes on the realm configuration:

• Realm and client settings are almost all default keycloak settings.
• You should change the password of the admin user in the nomad realm.
• The admin user in the nomad realm has the additional view-users client role for realm-management assigned. This is important, because NOMAD will use this user to retrieve the list of possible users for managing co-authors and reviewers on NOMAD uploads.
• The realm has one client nomad_public. This has a basic configuration. You might want to adapt this to your own policies. In particular you can alter the valid redirect URIs to your own host.
• We disabled the https requirement on the default realm for simplicity. You should change this for a production system.

Backups

To backup your Oasis at least the file data and mongodb data needs to be saved. You determined the path to your file data (your uploads) during the installation. By default all data is stored in a directory called .volumes that is created in the current working directory of your installation/docker-compose. This directory can be backed up like any other file backup (e.g. rsync).

To backup the mongodb, please refer to the official mongodb documentation. We suggest a simple mongodump export that is backed up alongside your files. The default configuration mounts .volumes/mongo into the mongodb container (as /backup) for this purpose. You can use this to export the NOMAD mongo database. Combine this with rsync on the .volumes directory and everything should be set. To create a new mongodump run:

docker exec nomad_oasis_mongo mongodump -d nomad_oasis_v1 -o /backup

The elasticsearch contents can be reproduced with the information in the files and the mongodb.

To create a new oasis with the backup data, create the .volumes directory from your backup. Start the new oasis. Use mongorestore:

docker exec nomad_oasis_mongo mongorestore /backup

Now you still have to recreate the elasticsearch index:

docker exec nomad_oasis_app python -m nomad.cli admin uploads index

A few useful NOMAD commands

The NOMAD command line interface (CLI) provides a few useful administrative functions. To use the NOMAD CLI, open a shell into the app container and run it from there:

docker exec -ti nomad_oasis_app bash

For example you can ls or remove uploads:

nomad admin uploads ls
nomad admin uploads rm -- <upload_id> <upload_id>

You can also reset the processing (of "stuck") uploads and reprocess:

nomad admin uploads reset -- <upload_id>
nomad admin uploads process -- <upload_id>

You can also use the CLI to wipe the whole installation:

nomad admin reset --i-am-really-sure

Base Linux (without docker)

Pre-requisites

We will run NOMAD from the nomad-lab Python package. This package contains all the necessary code to run the processing, api, and gui. But, it is missing the necessary databases. You might be able to run NOMAD in user space.

You will need:

• preferably a linux computer, which Python 3.9, preferable a Python virtual environment
• elasticsearch 7.x, running without users and authentication, preferable on the default settings
• mongodb 5.x, running without users and authentication, preferable on the default settings
• rabbitmq 3.x, running without users and authentication, preferable on the default settings
• nginx
• an empty directory to work in

Install the NOMAD Python package

You should install everything in a virtual environment. For example like this:

virtualenv -p `which python3` nomadpyenv
source nomadpyenv/bin/activate

You can simply install the Python package from pypi:

pip install nomad-lab[all]

If you need the latest version, you can also download the latest package from our "beta" installation.

curl "https://nomad-lab.eu/prod/v1/staging/dist/nomad-lab.tar.gz" -o nomad-lab.tar.gz
pip install nomad-lab.tar.gz[all]

nomad.yaml

The nomad.yaml is our central config file. You should write a nomad.yaml like this:

client:
  url: 'http://<your-host>/nomad-oasis/api'

services:
  api_base_path: '/nomad-oasis'
  admin_user_id: '<your admin user id>'

keycloak:
  realm_name: fairdi_nomad_prod
  username: '<your admin username>'
  password: '<your admin user password>'
  oasis: true

mongo:
    db_name: nomad_v0_8

elastic:
    index_name: nomad_v0_8

You need to change the following:

• Replace your-host and admin credentials respectively.
• api_base_path defines the path under which the app is run. It needs to be changed, if you use a different base path.

A few things to notice:

• Be secretive about your admin credentials; make sure this file is not publicly readable.

nginx

You can generate a suitable nginx.conf with the nomad command line command that comes with the nomad-lab Python package. If you server other content but NOMAD with your nginx, you need to incorporate the config accordingly.

If you have a standard installation of nginx, this might work. Adapt to your set-up:

nomad admin ops nginx-conf > /etc/nginx/conf.d/default.conf
nginx -t
nginx -s reload

If you want to run nginx in docker, this might work. Adapt to your set-up:

nomad admin ops nginx-conf --host host.docker.internal > nginx.conf
docker run --rm -v `pwd`/nginx.conf:/etc/nginx/conf.d/default.conf -p 80:80 nginx:stable nginx -g 'daemon off;' &

Running NOMAD

Before you start, we need to transfer your nomad.yaml config values to the GUI's javascript. You need to repeat this, if you change your nomad.yaml. You can do this by running:

nomad admin ops gui-config

To run NOMAD, you must run two services. One is the NOMAD app, it serves the API and GUI:

the second is the NOMAD worker, that runs the NOMAD processing.

celery -A nomad.processing worker -l info -Q celery

This should give you a working OASIS at http://<your-host>/<your-path-prefix>.

Kubernetes

This is not yet documented.

Migrating from an older version (0.8.x to 1.x)

Between versions 0.10.x and 1.x we needed to change how archive and metadata data is stored internally in files and databases. This means you cannot simply start a new version of NOMAD on top of the old data. But there is a strategy to adapt the data. This should work for data based on NOMAD >0.8.0 and <= 0.10.x.

The overall strategy is to create a new mongo database, copy all information, and then reprocess all data for the new version.

First, shutdown the OASIS and remove all old containers.

docker compose stop
docker compose rm -f

Update your config files (docker-compose.yaml, nomad.yaml, nginx.conf) according to the latest documentation (see above). Make sure to use index and database names that are different. The default values contain a version number in those names, if you don't overwrite those defaults, you should be safe.

Make sure you get the latest images and start the OASIS with the new version of NOMAD:

docker compose pull
docker compose up -d

If you go to the GUI of your OASIS, it should now show the new version and appear empty, because we are using a different database and search index now.

To migrate the data, we created a command that you can run within your OASIS' NOMAD application container. This command takes the old database name as an argument, it will copy all data from the old mongodb to the current one. The default v8.x database name was nomad_fairdi, but you might have changed this to nomad_v0_8 as recommended by our old Oasis documentation.

docker exec -ti nomad_oasis_app bash -c 'nomad admin upgrade migrate-mongo --src-db-name nomad_v0_8'
docker exec -ti nomad_oasis_app bash -c 'nomad admin uploads reprocess'

Now all your data should appear in your OASIS again. If you like, you can remove the old index and database:

docker exec nomad_oasis_elastic bash -c 'curl -X DELETE http://elastic:9200/nomad_fairdi'
docker exec nomad_oasis_mongo bash -c 'mongo nomad_fairdi --eval "printjson(db.dropDatabase())"'

Restricting access to your Oasis

An Oasis works exactly the same way the official NOMAD works. It is open and everybody can access published data. Everybody with an account can upload data. This might not be what you want.

Currently there are two ways to restrict access to your Oasis. First, you do not expose the Oasis to the public internet, e.g. you only make it available on an intra-net or through a VPN.

Second, we offer a simple white-list mechanism. As the Oasis administrator you provide a list of accounts as part of your Oasis configuration. To use the Oasis, all users have to be logged in and be on your white list of allowed users. To enable white-listing, you can provide a list of NOMAD account email addresses in your nomad.yaml like this:

oasis:
    allowed_users:
        - user1@gmail.com
        - user2@gmail.com

Performance considerations

If you run the OASIS on a single computer, like described here (either with docker or bare linux), you might run into problems with processing large uploads. If the NOMAD worker and app are run on the same computer, the app might become unresponsive, when the worker consumes all system resources.

By default, the worker container might have as many worker processes as the system as CPU cores. In addition, each worker process might spawn additional threads and consume more than one CPU core.

There are multiple ways to restrict the worker's resource consumption:

• limit the number of worker processes and thereby lower the number of used cores
• disable or restrict multithreading
• limit available CPU utilization of the worker's docker container with docker

Limit the number of worker processes

The worker uses the Python package celery. Celery can be configured to use less than the default number of worker processes (which equals the number of available cores). To use only a single core only, you can alter the worker service command in the docker-compose.yml and add a --concurrency argument:

command: python -m celery -A nomad.processing worker -l info --concurrency=1 -Q celery

See also the celery documentation.

Limiting the use of threads

You can also reduce the usable threads that Python packages based on OpenMP could use to reduce the threads that might be spawned by a single worker process. Simply set the OMP_NUM_THREADS environment variable in the worker container in your docker-compose.yml:

services:
    worker:
        ...
        environment:
            ...
            OMP_NUM_THREADS: 1

Limit CPU with docker

You can add a deploy.resources.limits section to the worker service in the docker-compose.yml:

services:
    worker:
        ...
        deploy:
            resources:
                limits:
                    cpus: '0.50'

The number refers to the percentage use of a single CPU core. See also the docker-compose documentation.

NOMAD Oasis FAQ

Why use an Oasis?

There are three reasons:

• You want to manage data in private,
• you want local availability of public NOMAD data without network restrictions,
• or you want to manage large amounts of low quality and preliminary data that is not intended for publication.

How to organize data in NOMAD Oasis?

How can I categorize or label my data?

Currently, NOMAD supports the following mechanism to organize data:

• Data always belongs to one upload, which has a main author, and is assigned various metadata, like the time the upload was created, a custom human friendly upload name, etc.
• Data can be assigned to multiple independent datasets.
• Data can hold a proprietary id called “external_id”.
• Data can be assigned to multiple coauthors in addition to the main author.
• Data can be filtered and searched in various ways.

Is there some rights-based visibility?

An upload can be viewed at any time by the main author, the upload coauthors, and the upload reviewers. Other users will not be able to see the upload until it is published and the embargo (if requested) has been lifted. The main author decides which users to register as coauthors and reviewers, when to publish and if it should be published with an embargo. The main author and upload coauthors are the only users who can edit the upload while it is in staging.

How to share data with the central NOMAD?

Keep in mind, it is not entirely clear, how we will do this.

How to designate Oasis data for publishing to NOMAD?

Currently, you should use one of the organizational mechanism to designate data for being published to NOMAD. You can use a dedicated dataset for publishable data.

How to upload?

We will probably provide functionality in the API of the central NOMAD to upload data from an Oasis to the central NOMAD and provide the necessary scripts and detailed instructions. Most likely the data that is uploaded to the central NOMAD can be selected via a search query. Therefore, using a dedicated dataset, would be an easy to select criteria.

How to maintain an Oasis installation?

How to install a NOMAD Oasis?

Follow our guide: https://nomad-lab.eu/prod/v1/docs/ops.html#operating-a-nomad-oasis

How do version numbers work?

There are still a lot of things in NOMAD that are subject to change. Currently, changes in the minor version number (0.x.0) designate major changes that require data migration. Changes in the patch version number (0.7.x) just contain minor changes and fixes and do not require data migration. Once we reach 1.0.0, NOMAD will use the regular semantic versioning conventions.

How to upgrade a NOMAD Oasis?

When we release a new version of the NOMAD software, it will be available as a new Docker image with an increased version number. You simply change the version number in your docker-compose.yaml and restart.

What about major releases?

Going from NOMAD 0.7.x to 0.8.x will require data migration. This means the layout of the data has changed and the new version cannot be used on top of the old data. This requires a separate installation of the new version and mirroring the data from the old version via NOMAD’s API. Detailed instructions will be made available with the new version.

How to move data between installations?

With the release of 0.8.x, we will clarify how to move data between installations. (See last question)