Here you can find a set of containers to help creating a data science core architecture, for example:
- LDAP server
- PostgreSQL server
- File router (NFS and Samba)
- Galaxy server
- Zabbix server
- Software server (i.e. a lot of pre-installed software)
- Interative Compute server (a place for users to login)
- Exploratory Analysis server (JupyterHub with JupyterLab)
- SLURM grid configuration
There is a focus on bioinformatics, but the infrastructure can be used for other applications.
We use Alpine Linux for simple servers (very small footprint) and Ubuntu for larger images. It might happen that some containers are derived from Debian ones.
- Python 2.7 (for ansible) and 3.5+
- docker-py (python-docker on ubuntu)
Check Python version for ansible (conda…)
If you use the setup wizard (strongly recommended for a first install)
- openssl and pyOpenSSL (if you need to generate keys)
(explain with conda)
Virtual Core uses Docker swarm mode. You can check the Swarm mode documentation, though we provide basic instructions:
docker swarm init
Virtual core requires a local Docker registry. Again you can find documentation on the Docker site, but you probably only need to do this:
docker run -d -p 5000:5000 --name registry registry:2
This will install all your servers on the local machine. If you have a very large big-iron machine, this might be what you want. If you have a cluster, this is still a reasonable starting point, though you will have some work to do, especially on the security front.
- Make sure you have a docker with swarm mode installation running.
- Use the wizard to configure the most complicated stuff:
./run_wizard.sh. Typically this will be on http://127.0.0.1:7000/
- Create an overlay virtual network called virtual_core
docker network create --driver overlay --attachable --subnet 172.18.0.0/24 virtual_core. Make sure this is configured everytime you start the system. Also make sure the subnet is OK for you.
- Create a directory that will store all your docker volumes. This might need to be very big. Lets call this your base directory.
cp etc/hosts.sample etc/hosts(you will want to edit this in the future)
- Make sure all variables on
ansible/are correctly defined, especially on the common role
python src/create_directory_structure.py <base_directory>
cd _instance/ansible; ansible-playbook --ask-pass -i ../../etc/hosts main.yml
Installation on a cluster¶
Swarm node joining
The registry shoud be on the head node.