We ran an agent and server/master on the same system. It is possible that the dual use to /tmp was the problem. At Armen's suggestion we added the following to our wrapper.conf
-Djava.io.tmpdir=SOMEPATH
I can see that the two instances are using different directories
Are you running cleanup cron jobs on the temp directory? If so, they've probably deleted the zip file sent to the agent. This issue will be fixed in Bamboo 5.0 - the jar file will be regenerated if deleted.
Until then you the only workaround is either to restart the server or reconfigure the /tmp cleanup.
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I believe I did add a cleanup step on my plan because the build stores items in tmp. I'll modify the plans to use a subdir of temp.
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I checked our plans and we only clear specific files (xauth and xvfb files) from /tmp. I have no cronjobs running that could do this either and looked through all users and the cron log. So, I don't think there's an automated process running that would clear this file.
Also, if I copy the file to the agent's tmp all is good
scp build@vmbamboo-01:/opt/atlassian/bamboo-agent-home/atlassian-bamboo-agent-installer-4.4.2.jar /tmp/jarClassPath6603717285566365500.jar
and see zero impact when I copy the file to server/master's tmp dir.
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