From the documentation, "If you execute the Linux Installer with 'root' user privileges, the installer will create and run JIRA using a dedicated user account."
I would like to set up this system account to also send email from the local smtp service. So I need to set the password for the jira system user. Would this affect the functionality of JIRA? I don't recall already having set the password for this system user, but I don't know if JIRA requires that its system user to have a particular password. Thanks.
No, it doesn't care about the password for the Jira user on a linux box. It runs as that user, but doesn't log-in (you can make it a no-login account). Also, most mail servers allow you to create accounts with username and password totally different from the user you are mailing from.
Here's what my main user's setup (on a Red Hat box):
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