How to install and run OMERO in production

Simon Li
Open Microscopy Environment
University of Dundee

OME 2020 OMERO Systems Installation and Configuration workshop

Overview

Server requirements
Current recommended deployments
Live demo: Ansible from scratch
A little bit of Docker

Short break
Questions, more demos, discussions

Aim

Persuade you not to install OMERO manually...

Who am I?

Software engineer and sysadmin at the OME since 2012

Where do we start?

Get a server
Install an operating system

Server specification?

outreach.openmicroscopy.org: 4 CPU 32 GB RAM
omero.lifesci.dundee.ac.uk: 4 CPU 32 GB RAM
demo.openmicroscopy.org: 8 CPU 48 GB RAM

Operating system?

Does the distribution matter?

We test several OMERO on multiple operating systems but there's no substitute for running in production

Which operating system (1)

Used by all our production systems, which means we've already found most of the bugs

Image Data Resource https://idr.openmicroscopy.org
University of Dundee https://omero.lifesci.dundee.ac.uk
Demo server https://demo.openmicroscopy.org

Which operating system (2)

18.04

Popular amongst the OME community

New: omero-server support

Coming soon ....

20.04

How should you install OMERO?

The hard way:

Good for learning about OMERO
Or if you've got several hours and nothing to do

Configuration management

What is configuration management?

A systematic way to setup and configure your servers
"Infrastructure as code": Apply the software development process to managing servers

"Infrastructure as code"

Self-documenting
Version control
GitHub code reviews

Why should you consider it?

Fully automated installation, configuration and upgrades

Installs all dependencies
Manages OMERO databases including upgrades
Reproducible deployments
You can copy our infrastructure!

Relatively easy to setup
Just requires SSH access to servers
Everything configured with YAML


                  pip install ansible

Still not convinced?

Live demo!

Docker

ome/docker-example-omero


              wget https://raw.githubusercontent.com/ome/\
              docker-example-omero/master/docker-compose.yml

              docker-compose up -d

Even easier than Ansible, if you're happy working with containers.


                apt-get update
                apt-get install docker-compose docker.io

Scaling up OMERO

IDR: Behind the scenes

⇳

server
web

⇳

Infrastructure as code

If we can deploy one server with Ansible, we can deploy 2, or 3 ....
Clear separation between data and applications

⇳

read-only
public web

read-only

read-write

⇳

idr.openmicroscopy.org wss://idr.openmicroscopy.org/omero-ws

68 vCPU 264 GB RAM
Storage: 760 GB ephemeral 1.7 TB block 170+ TB read-only NFS

How do you debug and test a 150+ TB system?

➕

➕ IDR/deployment

⬇

Production

Staging

Test-1

Test-2

Useful links

ome/ansible-example-omero-onenode

ome/ansible-example-omero-addons

ome/omero-deployment-examples

System Administrator Documentation

IDR/deployment

ome/prod-playbooks

Setting up OMERO in a new lab

Time for a short break