We are running our instances of JIRA and Confluence in separate VMs, with another separate VM acting as the DB server. We have nightly disc backups of the VMs taking place, however I want to ensure that we are definitely employing the best backup method that we can. In your opinion, what is the best backup method that we can employ, in our situation, to ensure the speediest, and reasonably complete, restoration possible.
You can automate the JIRA backup service as described at http://confluence.atlassian.com/display/JIRA/Automating+JIRA+Backups
However, when the data is huge, backing up the XML isn't always the best solution. If you have too much of data, I would recommend backing up the DB at regular intervals. You can always restore DB and re-index JIRA if something goes wrong!
To add to Jobin's answer, one thing to check is export time - do a manual xml backup from the UI and time it - that will tell you how long the regular backup will take and you can then balance that against the option of doing a database backup.
In my experience, which is mostly with larger corporate Jira installs, if it takes more than a few seconds, you've got enough volume to start looking at database backups. With corporates, there's always some form of standard database backup you can use, most places I've worked never even thought there might be another way to do it! You will have to think about re-indexing vs import of xml. And yes, attachments need to be regularly and frequently backed up (if you have a lot, look at incremental backups, as they do tend to be quite static). The application server area is less important - in fact, most of my clients don't need it at all. We've got Jira (and the rest) packaged up so they can be deployed on any of our standard servers with a couple of lines of script. Mods, tweaks and plugins are in source control too.
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