[InterMine Dev] runtime error
vKrishna at jcvi.org
Tue Jul 15 17:21:09 BST 2014
We actually encountered this exact same issue when we were initially getting ThaleMine (our InterMine interface to Arabidopsis thaliana genome data, https://apps.araport.org/thalemine/) up and running on our production systems.
Similar to your observation, we also did notice that this issue resolved itself temporarily after a Tomcat restart.
After spending a lot of time troubleshooting the issue with the help of the InterMine developers and our in-house IT staff, we arrived at the following conclusion:
We believe the cause of the error (red rectangles of death or RROD) was JCVI software that closed connections between servers sitting on different subnets.
We were able to demonstrate days of uptime without any RROD, merely by using a web server and database server that were on the same subnet (though there were other variables that still need to be ruled out).
We still have the outstanding issue that InterMine software, in particular its connection pool, never recovers from a lost connection.
Hope this provides you with a fresh perspective into this particular issue.
On Behalf of the Araport Team
Sr. Bioinformatics Engineer
J. Craig Venter Institute
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