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.

While different use cases require different setups, this documentation describes the simplest setup of a NOMAD OASIS. It would allow a group to use NOMAD for local research data management, while using NOMAD’s central user-management and its users. There are several environment in which you can run a NOMAD OASIS: base-metal linux, docker with docker-compose, and in a kubernetes cluster. We recommend using docker/docker-compose.

Before you start

We need to register some information about your OASIS in the central user management:

• The hostname for the machine you run NOMAD on. This is important for redirects between your OASIS and the central NOMAD user-management and to allow your users to upload files (via GUI or API). Your machine needs to be accessible under this hostname from the public internet. The host name needs to be registered with the central NOMAD in order to configure the central user- management correctly.

• Your NOMAD account that should act as an admin account for your OASIS. This account must be declared to the central NOMAD as an OASIS admin in order to give it the necessary rights in the central user- management.

• You will need to know your NOMAD user-id. This information has to be provided by us.

Please write us to register your NOMAD account as an OASIS admin and to register your hostname. Please replace the indicated configuration items with the right information.

In principle, you can also run your own user management. This is not yet documented.

docker and docker compose

Pre-requisites

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

You will need a single computer, with docker and docker-compose installed.

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

Configuration overview

All docker container are configured via docker-compose an 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

• nomad.yaml

• nginx.conf

In this example, we have all files in the same directory (the directory we also work from). You can download examples files from here.

Docker compose

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

version: '3.4'

x-common-variables: &nomad_backend_env
    NOMAD_RABBITMQ_HOST: rabbitmq
    NOMAD_ELASTIC_HOST: elastic
    NOMAD_MONGO_HOST: mongo

services:
    # broker for celery
    rabbitmq:
        restart: always
        image: rabbitmq:3.7.17
        container_name: nomad_oasis_rabbitmq
        environment:
            - RABBITMQ_ERLANG_COOKIE=SWQOKODSQALRPCLNMEQG
            - RABBITMQ_DEFAULT_USER=rabbitmq
            - RABBITMQ_DEFAULT_PASS=rabbitmq
            - RABBITMQ_DEFAULT_VHOST=/
        volumes:
            - nomad_oasis_rabbitmq:/var/lib/rabbitmq

    # the search engine
    elastic:
        restart: always
        image: docker.elastic.co/elasticsearch/elasticsearch:6.3.2
        container_name: nomad_oasis_elastic
        environment:
            - discovery.type=single-node
        volumes:
            - nomad_oasis_elastic:/usr/share/elasticsearch/data

    # the user data db
    mongo:
        restart: always
        image: mongo:4
        container_name: nomad_oasis_mongo
        environment:
            - MONGO_DATA_DIR=/data/db
            - MONGO_LOG_DIR=/dev/null
        volumes:
            - nomad_oasis_mongo:/data/db
        command: mongod --logpath=/dev/null # --quiet

    # nomad worker (processing)
    worker:
        restart: always
        image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:stable
        container_name: nomad_oasis_worker
        environment:
            <<: *nomad_backend_env
            NOMAD_SERVICE: nomad_oasis_worker
        links:
            - rabbitmq
            - elastic
            - mongo
        volumes:
            - ./nomad.yaml:/app/nomad.yaml
            - nomad_oasis_files:/app/.volumes/fs
        command: python -m celery worker -l info -A nomad.processing -Q celery,calcs,uploads

    # nomad app (api + gui)
    app:
        restart: always
        image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:stable
        container_name: nomad_oasis_app
        environment:
            <<: *nomad_backend_env
            NOMAD_SERVICE: nomad_oasis_app
        links:
            - rabbitmq
            - elastic
            - mongo
        volumes:
            - ./nomad.yaml:/app/nomad.yaml
            - nomad_oasis_files:/app/.volumes/fs
        command: ./run.sh

    # nomad gui (a reverse proxy for nomad)
    gui:
        restart: always
        image: nginx:1.13.9-alpine
        container_name: nomad_oasis_gui
        command: nginx -g 'daemon off;'
        volumes:
            - ./nginx.conf:/etc/nginx/conf.d/default.conf
        links:
            - app
        ports:
            - 80:80

volumes:
    nomad_oasis_mongo:
    nomad_oasis_elastic:
    nomad_oasis_rabbitmq:
    nomad_oasis_files:

There are no mandatory changes necessary.

A few things to notice:

• All services use docker volumes for storage. This could be changed to host mounts.

• It mounts three configuration files that need to be provided (see below): nomad.yaml, nginx.conf, env.js.

• The only exposed port is 80. This could be changed to a desired port if necessary.

• The NOMAD images are pulled from our gitlab in Garching, the other services use images from a public registry (dockerhub).

• All container will be named nomad_oasis_*. These names can be used to later reference the container with the docker cmd.

• The NOMAD images we use are tagged stable. This could be replaced with concrete version tags.

• The services are setup to restart always, you might want to change this to no while debugging errors to prevent indefinite restarts.

nomad.yaml

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

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

services:
  api_host: '<your-host>'
  api_prefix: '/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

meta:
  release: 'oasis'
  deployment_id: '<your-host>'
  maintainer_email: '<oasis admin email>'

mongo:
    db_name: nomad_v0_8

elastic:
    index_name: nomad_v0_8

You need to change:

• Replace your-host and admin credentials respectively.

• api_base_path defines the path under with the app is run. It needs to be changed, if you use a different base path.

• The admin user credentials (id, username, password, email).

A few things to notice:

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

• We will use your hostname as deployment_id. When you publish uploads from your Oasis to the central NOMAD, this will be added as upload metadata and allow to see where the upload came from.

nginx.conf

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

server {
    listen        80;
    server_name   www.example.com;
    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\/uploads\/?$ {
        client_max_body_size 35g;
        proxy_request_buffering off;
        proxy_pass http://app:8000;
    }

    location ~ \/api\/(raw|archive) {
        proxy_buffering off;
        proxy_pass http://app:8000;
    }

    location ~ \/api\/mirror {
        proxy_buffering off;
        proxy_read_timeout 600;
        proxy_pass http://app:8000;
    }

    location ~ \/encyclopedia\/ {
        proxy_intercept_errors on;
        error_page 404 = @redirect_to_encyclopedia_index;
        proxy_pass http://app:8000;
    }

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

You need to change:

• Replace <your-host>

A few things to notice:

• It configures the base path (nomad-oasis) at multiple places. It needs to be changed, if you use a different base path.

• You can use the server to server additional content if you like.

• client_max_body_size sets a limit to the possible upload size.

• 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/uploads and ../api/raw.

gunicorn

Gunicorn is the WSGI-server that runs the nomad app. Consult the gunicorn documentation for configuration options.

Starting and stopping 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 for debugging problems, it is recommended to start services separately:

docker-compose up -d mongodb 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

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

If everything works, the gui should be available under:

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

If you run into troubles, use the dev-tools of you 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

base linux (without docker)

Pre-requisites

We will run NOMAD from the nomad-lab Python package. This package contains all the necessary code for running 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 3.7, preferable a Python virtual environment

• elasticsearch 6.x, running without users and authentication, preferable on the default settings

• mongodb 4.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/rae/beta/dist/nomad-lab.tar.gz" -o nomad-lab.tar.gz
pip install nomad-lab.tar.gz[all]

Configure NOMAD - 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:

• Replace your-host and admin credentials respectively.

• api_base_path defines the path under with 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.

Configure NOMAD - 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:

gunicorn "${params[@]}" -b 0.0.0.0:8000 nomad.app:app

And the NOMAD worker, that runs the NOMAD processing.

celery worker -l info -A nomad.processing -Q celery,calcs,uploads

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 (0.7.x to 0.8.x)

This documentation is outdated and will be removed in future releases.

Between versions 0.7.x and 0.8.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.

First, shutdown the OASIS and remove all old container.

docker-compose stop
docker-compose rm -f

Update you config files (docker-compose.yaml, nomad.yaml, nginx.conf) according to the latest documentation (see above). Especially make sure to select a new name for databases and search index in your nomad.yaml (e.g. nomad_v0_8). This will allow us to create new data while retaining the old, i.e. to copy the old data over.

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 argument, it will copy all data over and then reprocess the data to create data in the new archive format and populate the search index. The default database name in version 0.7.x installations was nomad_fairdi. Be patient.

docker exec -ti nomad_oasis_app bash -c 'nomad admin migrate --mongo-db nomad_fairdi'

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 your 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 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 resources that the worker might consume:

• limit the number of worker processes and thereby lower the number of used cores

• disable or limit multi-threading

• 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 just a single core, you can alter the worker service command in the docker-compose.yml and add a --concurrency argument:

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

See also the celery documentation.

Limiting the use of threads

You can also reduce the usable threads that Python packages based on OpenMP might use to reduce the threads that might be spawn 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?

Current, NOMAD supports the following mechanism to organize data: data always belongs to one upload, one uploading user, and is assigned an upload datetime; uploads can have a custom name data can be assigned to multiple independent datasets data can hold a proprietary id called “external_id” data can be assigned multiple authors in addition to the uploading user The next NOMAD release (0.8.x) will contain more features to filter data based on uploader and upload time. It will also include a revised search bar that makes it easier to filter for external_id or upload_name.

Is there some rights-based visibility?

No. Currently, NOMAD only supports uploader controlled visibility. The uploader decides when to make an upload public (with or without embargo). The embargo can be used to limit the visibility of an upload to users that the uploader want to share his upload with.

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. we, you can use a dedicated dataset for publishable data.

How to upload?

Will will probably provide functionality in the API of the central NOMAD to upload data from an Oasis to the central NOMAD. We will 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/rae/docs/ops.html#operating-a-nomad-oasis

How do version numbers work?

There are still a lot of thing 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?

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

How to backup my Oasis?

To backup your Oasis at least the file data and mongodb data needs to be backed up. You determined the path to your file data (your uploads) during the installation. 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: https://docs.mongodb.com/manual/core/backups/. We suggest a simple mongodump export that is backed up alongside your files. The elasticsearch contents can be reproduced with the information in files and mongodb.