Hi, everyone. First off, I'd like to say "awesome and thank you" for the cTAKES 3.2 release and information. I've been following those pages and it's been really helpful for helping me move along in my own progress. Really cool stuff.
So I'm using the Collection Processing Engine (with ytex and umls) and I'm trying to process ~1 million notes (as opposed to the about 30 in the given demo). I've tried this the past 2 days and when I come back in to check the progress I see that I've received an error about 14000 notes into the process: org.apache.uima.analysis_engine.AnalysisEngineProcessException: Annotator processing failed. CausedBy: org.springframework.transaction.CannotCreateTransactionException: Could not open Hibernate Session for transaction; nested exception is com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: The last packet successfully received from the server was 53,888,249 milliseconds ago. The last packet sent successfully to the server was 53,888,249 milliseconds ago. is longer than the server configured value of 'wait_timeout'. You should consider either expiring and/or testing connection validity before use in your application, increasing the server configured values for client timeouts, or using the Connector/J connection property 'autoReconnect=true' to avoid this problem. So, in my own debugging, I have ensured that autoReconnect true was on (it always has been). I looked at my CPE output in the command prompt and noticed a "PacketTooBigException" so I increased the packet max size to 1G (the max for sql server). I increased the time allowed for timeouts. I'm really unsure of what to do here. Should I find a way to see if there is a problematic note that is giving me issues (though I can't understand how 1 note would make a packet too large)? Should I try to do some horizontal sharding and break the problem into smaller chunks (though I would think this program could handle large datasets since it's using a query language)? I'm just at a loss with this error, especially since it takes so long to actually spit the error out at me. Thanks in advance everyone, Clayton -- -- Clayton Turner email: caturn...@g.cofc.edu phone: (843)-424-3784 web: claytonturner.blogspot.com ------------------------------------------------------------------------------------------------- “When scientifically investigating the natural world, the only thing worse than a blind believer is a seeing denier.” - Neil deGrasse Tyson
