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Diagnose potential DB timeout (no replies)

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Hi,

I am running an instance of Jira which uses MySQL as it's DB. I am trying to diagnose an ongoing issue with the vendor without much luck. Basically every day around what seems to be the same time the application hangs to the point where users receive an Apache page cannot be displayed error. This lasts for upwards of 5 minutes. I have conformed several times when this happens that server resources are not the issue. I have sent thread dumps to the vendor and they have suggested a DB connection timeout but only provided a basic connection test which doesn't even work. Rather than wait on them any longer I have decided to reach out and see if there are any recommended tools, tests, etc I can leverage to test the database, find any routine tasks, etc to determine if it is teh cause or at least rule it out.

I am currently running:
MYSQL version - 5.6.25 MySQL Community Server
Connector - mysql-connector-java-5.1.17-6.el6.noarch
Java version - 1.8.0_45

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