Knowing that Atlassian supports only single instance of JIRA on self host, that is, you can only have one JIRA instance running in one Tomcat container, how does Atlassian run its own OnDemand? Does Atlassian have a "special" build of JIRA that's multitenant? Or does Atlassian spin up a seperate "instance" everytime a new client signs up as <companyname>.atlassian.net?
Atlassian OnDemand has an architechture which is partially multi-tennant, but mainly instance based.
You can also check out this summit 2012 presentation 'Inside the Atlassian OnDemand Private Cloud' which gives a good run down of the architechture used. If you skip to about 22minutes in it gives a run down of the container.
I hope that helps
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