I have been having issue with JIRA (500 user license) & msql, server related, running on CentOS and Hyper V virtual machine together with 4 cpus & 4gb ram. As my number of users grew up to 310 and more users, the JIRA application always heard proxy error problems, availability issues and loading issues. I did some reading and moved it to VMWare virtual machine with more cpus and 8gb ram, and ran the application and DB in separate virtual machines.
After the JIRA was moved to a new virtual machine VMware, it became worse. always proxy error, instead of improve. My current JIRA version is 6.3.15. Mostly when this happen in the previous environment and new environment we troubleshoot, look at the logs and most of the time, we do not find any problem. How we fix the issue is by restarting the server and everything gets back to normal.
Did you try to increase JVM Memory settings in setenv.sh ? Default settings are small
JVM_MINIMUM_MEMORY="384m"
JVM_MAXIMUM_MEMORY="768m"
May be try bumping them up to "1024m", "4096m"
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