Budi, You can also try out ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml available in the current 3.2.1-rc. It contains a new dictionary lookup algorithm from Sean that is roughly 1000% faster for each pipeline.
--Pei From: Kim Ebert [mailto:[email protected]] Sent: Monday, November 17, 2014 11:55 AM To: [email protected] Subject: Re: Using Ctakes takes a long time to process text Hi, cTakes currently is single threaded. To increase throughput, we use a patch or two to run several pipelines at once. To Increase your performance, I would recommend splitting up the work into multiple batches. To get cTakes to run multiple threads, you have to patch the LVG. I believe the patch is available in the bug tracker. You also would need to run them as separate pipelines inside of UIMA. You can't just say increase the number of threads for this operation. While we aren't using static variables, state is maintained inside of the object. http://uima.apache.org/downloads/releaseDocs/2.1.0-incubating/docs/html/tutorials_and_users_guides/tutorials_and_users_guides.html#ugr.tug.applications.multi_threaded https://issues.apache.org/jira/browse/CTAKES-151 [IMAT Solutions]<http://imatsolutions.com> Kim Ebert Software Engineer [Office:]801.669.7342 [email protected]<mailto:[email protected]> On 11/16/2014 12:06 AM, Budi Wibowo wrote: Hello, i'm using CTAKES for class project. I'm using CPE to process clinical text notes. I ran the software with -Xmx10g command. I have 16g in my machine. my problem is: running the CPE takes a long long time. I'm processing 175 clinical notes with a total of 40MB for all the notes. CPE has been running close to 4 hours now, and it's only been able to process 104 out of 175. I'm using the "test1.xml" CPE descriptor and "AggregatePlaintextUMLSProcessor.xml" analysis engine(clinical-text-pipeline). it seems like java is only using 2 core out of the 16 I have. RAM usage hover between 5-8gb. is there anyway i can make the software run a bit faster?
