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Provisioning and configuration management for an Arvados Cluster to be used for COVID research during the 2020 Biohackathon in Barcelona.

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Build an Arvados Cluster using Salt

Welcome!

For general information and context, please see our Wiki, here

Setup

To use this project to provision an Arvados cluser you will need Docker Compose.

There are two parts to this project. A provisioning mechanism and a configuration management system.

Provisioning

This project uses salt-cloud to provision the infrastructure required by an Arvados Cluster. To encapsulate the technicalities of salt-cloud from your workstation, we have wrapped them in Docker containers that can be run using Docker Compose for convenience.

Before you can use this facility, you will need to configure your cloud provider. Salt-cloud supports a variety of cloud providers natively, for which you should only need to add a config file to the directory linked previously.

Example:

  • Provision a brand new cluster: docker-compose run provision
  • To destroy an Arvados cluster: docker-compose run destroy

When provisioning a new cluster, the provisioning system will preinstall Salt minions to all of the virtual machines configured and configure the salt "master" (we will use the term orchestrator from now on). It will also accept the salt-keys of all the minions. It will then run salt once to configure the entire cluster.

Should nothing go awry, you should have a functioning cluster after running the above command. Because this project is a work in progress, expect things to go awry.

Contributor

Setup

This project depends on the repositories shown in the gitfs_remotes section of the roots.conf file. Feel free to clone those and glance over them to become familiar with the structure of the project.

How these dependencies fit together is described in the formula's top file and the pillar top file.

The structure of the provisioned infrastructure is described in the salt-cloud map file

links

the COVID-19 hackathon

The SURFsara HPC cloud

arvados

Specs

See cloud/map

main server

fast disk for database

compute worker nodes

0+ nodes Depends on workload; scaled dynamically in the cloud

user shell nodes

0+ Depends on workload

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Provisioning and configuration management for an Arvados Cluster to be used for COVID research during the 2020 Biohackathon in Barcelona.

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