Hi Samir, [including the public dev list] Thanks for opening up a new thread on this issue. Would you be able to help narrow down the sentence that you believe is causing the NP2LookupWindow to take 3h to process? I can’t seem to reproduce it on my end. I vaguely remember someone running into something where it could go into a loop, so hopefully maybe they can also chime in…
--Pei From: samir chabou [mailto:[email protected]] Sent: Wednesday, August 14, 2013 7:30 PM To: Chen, Pei Subject: Re: umls lookup issue specifically the NP2LookupWindow that causes de delay ________________________________ From: samir chabou <[email protected]> To: "Chen, Pei" <[email protected]> Sent: Wednesday, August 14, 2013 7:21:18 PM Subject: Re: umls lookup issue Hi Pei I removed the LookupWindowAnnotator went very fast less than 1 min but there was no annotations for EntityMention and EventMention, it looks there is some thinh wrong with the LookupWindowAnnotator Samir ________________________________ From: samir chabou <[email protected]> To: "Chen, Pei" <[email protected]> Sent: Wednesday, August 14, 2013 7:11:57 PM Subject: Re: umls lookup issue Hi Pei I removed the lookupwindowannotation went very fast less than 1 min but there was no annotations for EntityMention and EventMention, it looks there is some thinh wrong with the lookupwindowannotation Samir ________________________________ From: "Chen, Pei" <[email protected]> To: samir chabou <[email protected]> Sent: Wednesday, August 14, 2013 3:40:46 PM Subject: RE: umls lookup issue That is strange- it shouldn’t take that long. I wonder if it’s going into an infinite loop. Have you tried debugging it? Perhaps removing some of the lines in the note or removing the dictionary lookup component itself? --Pei From: samir chabou [mailto:[email protected]] Sent: Wednesday, August 14, 2013 1:14 PM To: Chen, Pei Subject: Re: umls lookup issue Hi Pei, Unfortunately, the removal of the DependencyParsser and Assertion did not make difference (it has been running now for 1h so i stopped). Pei I think the bottle neck was the LookupWindowAnnotator, yesterday when it was running the console showed the LookupWindowAnnotator annotations it took quit time to go from one LookupWindow to an other, also these annotations of lookupwindows was done twice. Memory: Xms500M and Xmx1500 The jdk : JavaSE-1.6 (jre7) below screen capture showing from where i got the memory and jdk info + the structure of AggregatePlaintextUMLSProcessor.xml without the DependencyParsser and Assertion Thanks a lot Samir ________________________________ From: "Chen, Pei" <[email protected]> To: samir chabou <[email protected]> Sent: Wednesday, August 14, 2013 10:08:00 AM Subject: RE: umls lookup issue Hi Samir, It shouldn’t take 3h… it’s a bit strange. cTAKES is much more constrained to memory rather than cpu. Do you know which JDK and what the java memory settings were used? Could you also try removing the new annotators that were added in 3.0? DependencyParser, Assertion Module. See attached as an example. --Pei From: samir chabou [mailto:[email protected]] Sent: Tuesday, August 13, 2013 10:48 PM To: Chen, Pei Subject: Re: umls lookup issue Hi Pei I tried the clinical pipeline as is with no modification except for umls username and password, it took more than 5h on my laptop to process the text sample that i send to you. Then I thought may be my laptop was not performing enough so I tried it in on an other laptop i7, 16M, 2.4Mhz but again it took 3h and plus. I was wondering if you run it within 5minutes what was the environment. Next step as you suggested I will try to create a local db on mysql for the db umls2011ab and proceed the text. But again it strange that in version cTakes 2.5 this same test took less than one minute. Thanks a lot for your cooperation your was appreciated
