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My Ubuntu server is EST, but all times in Jira are UTC.

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You need to add a JVM parameter:

-Duser.timezone=EST

Add this to the JAVA_OPTS variable in setenv.sh (or setenv.bat if you're on Windows) in the bin subdirectory of your installation and restart JIRA.

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Fabulous, thanks. I played with the setting further and used -Duser.timezone=America/New_York to get Jira to pick up EDT properly. – ed209 Mar 27 '11 at 23:14
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To elaborate on setting JVM parameters on startup: confluence.atlassian.com/display/JIRA/… – Jess Telford Jun 21 '11 at 7:01
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