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Pyiron

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Description

pyiron is an integrated development environment (IDE) for computational materials science. It integrates several computational/analysis tools in a common platform and provides various functionalities for creation, management and sharing of your workflows.

Setup

Requirements

In order to run pyiron, prepare for the following hardware-requirements:

  • for running jupyterhub: > 2 GB of RAM, 2 VCPU
  • overall resources on the server should be proportional to the number of users: ~2 GB of RAM, 2 VCPU, 10 GB of storage per user

Morever, we assume the following:

  • This setup uses Keycloak as identity provider. Therefore, a client id and secret are needed.
  • For simplicity, we assume that all jobs are run on the same server as the jupyterhub container.
  • The configuration of the hostnames is assumed to be done separately by the admin, e.g. creating the A-record, etc

1. Clone the Repository

Clone this GitHub repository into your pmd-server’s root directory:

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git clone https://github.com/materialdigital/pyiron_workflow_environment_deployment pyiron

Just to give you a brief overview what’s in there:

File Description
config.json a json file containing the configurable environment variables: keycloak client details, name of pyiron docker images, users’ resources, and Postgres database Password
static.json a json file containing the non-configurable environment variables
nginx/pyiron.conf A template of the configuration file for the Nginx reverse proxy
docker-compose.yml the compose file, which runs jupyterhub and its Postgres database services.

2. Configure Nginx

For the Nginx reverse proxy, you need to provide a configuration file. A template is provided in the repository under repo_path/nginx/pyiron.conf
After adding the domain, and the path to the SSL certificates and key (as described here), you should copy it to the nginx directory:

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cp nginx/pyiron.conf ../data/nginx/

Of course, here it is assumed that the PMD-S core repo is the parent directory of the pyiron deployment directory.

3. Obtaining SSO credentials

You can obtain SSO credentials to connect to the MaterialDigital SSO (A) or use your own Keycloak instance (B) as identity provider (IDP)

Submit a request for pyiron SSO credentials via the Material Digital contact form. In the form provide the URL you have reserved for your pyiron instance.

(B) local SSO

If you choose to use a local Keycloak instance, you can create a keycloak-client via the following steps:

1) Sign in as the admin of the keycloak instance
2) Select your desirable realm
3) Select clients from the left panel
4) On the top right-hand side, select create
5) Enter a client ID, and a root URL. For the URL, you should provide the url of pyiron

6) click save
7) In the setting tab, change the access type to confidential, and save
8) From the credential tab, you can obtain the client secret

4. Select Pyiron Docker Images

In the next step, You need to customize the central configuration file config.json. There, you will need to provide tag-names for a set of pyiron docker images you can choose from when starting a session. Pyiron offers various docker images corresponding to its modules: atomistics, continuum, md, etc.

The docker images are available on docker hub: https://hub.docker.com/u/pyiron, and the corresponding dockerfiles can also be found via https://github.com/pyiron/docker-stacks.

5. Adapt config.json and Generate Files for Docker-Compose.

Edit config.json to reflect your environment: be sure to replace the placeholders <keycloak_domain> and <pyiron_domain> in the URLs with the correct destination for the keycloak-instace (either local or shared across PMD-participants) and for the pyiron-service at hand.

Moreover, you need the keycloak-realm (placeholder <realm>, the client id, and the client secret (see Step 3. if you chose to configure keycloak by yourself).

Also, do not forget to choose eligible image-tags for base, atomistic, continuum and experimental (see Step 4).

The details of the keys in config.json can be found in the table below.

key definition
OAUTH2_TOKEN_URL Keycloak Token URL; here you need only to change the domain and the realm”
OAUTH2_AUTHORIZE_URL Keycloak authorize URL; here you need only to change the domain and the realm
OAUTH2_USERDATA_URL Keycloak userdate URL; here you need only to change the domain and the realm
OAUTH_CALLBACK_URL Keycloak call back URL; here you need only to change the domain
CLIENT_ID The client ID defined in Keycloak
CLIENT_SECRET The secret for the client, provided from the Keycloak instance
PYIRON_BASE The relevant information of pyiron_base image in the form of image_name:tag, e.g. pyiron/base:2021-06-04
PYIRON_ATOMISTIC The relevant information of pyiron_atomistics image in the form of image_name:tag, e.g. pyiron/pyiron:2021-06-04
PYIRON_CONTINUUM The relevant information of pyiron_continuum image in the form of image_name:tag, e.g. pyiron/continuum:2021-06-04
PYIRON_EXPERIMENTAL The relevant information of pyiron_experimental image in the form of image_name:tag, e.g. pyiron/experimental:2021-06-04
MEM_LIMIT The limiting amount of RAM per user
CPU_LIMIT The limiting amount of VCPU per user
ADMIN_USER The username of jupyterhub admin, this username should be consistent with the username in the keycloak instance
POSTGRES_PASSWORD A password for the postgres database

6. Generate the env-files

To generate the environment files, run the configure.py script from the parent directory. The script can also be found here

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cd pyiron
# run `configure.py` script from the pmd-server parent directory
# in the case that python3 is installed on the host OS:
python3 ../scripts/configure.py
# otherwise you can use a docker container to run the script via: 
docker run --rm -v $PWD/:/tmp/ -v $PWD/../scripts/configure.py:/tmp/configure.py-w /tmp  python:3-alpine  python configure.py   

7. Run docker-compose

Run the compose-script to start the containers via:

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docker-compose up -d 

HPC connection (will be added soon)

In principal, the pyiron docker containers can submit jobs to the cluster according to pyiron documentation in here. This feature will be added to pyiron docker images in the next release.

Room for modification

Here we assumed a semi-automated deployment with minimal changes needed from the side of IT administrators. However, many things can be changed, such as:

  • building a customized jupyterhub; this gives the possibility to change the jupyterhub configuration
  • In the current setup, we assumed to have four jupyter environments based on: pyiron_base, pyiron_atomistics, and pyiron_continuum, pyiron_experimental. This list can be extended in the case of a customized jupyterhub build.
tags: PMD Deployment guide

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