I see a java.lang.OutOfMemoryError: GC overhead limit exceeded error. You could try changing
-Xms512M -Xmx3g to -Xms3g -Xmx6g On Sat, Jun 9, 2018 at 4:45 PM, Ankit Bisht <[email protected]> wrote: > Hello Parth, > > I have already done that. After adding the UMLS credentials also, I am > getting the error > > -Ankit > > On Fri, Jun 8, 2018 at 11:00 PM, Parth Natu <[email protected]> wrote: > >> >> Hi Ankit, >> >> Please add the following parameters before the "-cp" in the Java command >> in the .sh file. >> >> >> -Dctakes.umlsuser=[username] -Dctakes.umlspw=[password] >> >> Try executing the same and let me know the results >> >> Parth >> >> On Jun 9, 2018 at 7:29 AM, <Ankit Bisht <[email protected]>> >> wrote: >> >> Hello Parth, >> >> Please find attached the .sh file. The command is: >> bin/runctakesCVD.sh -desc desc/ctakes-clinical-pipeline/ >> desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml >> I am following this guide: >> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4. >> 0+User+Install+Guide >> -Ankit >> >> On Fri, Jun 8, 2018 at 12:29 PM, Parth Natu <[email protected]> wrote: >> >>> >>> Hello Ankit, >>> Can you attach there edited .sh files and the command that you use to >>> run it? >>> >>> Parth >>> >>> On Jun 8, 2018 at 9:50 PM, <Ankit Bisht <[email protected]>> >>> wrote: >>> >>> Hello Gundolf, >>> >>> I have attached the snapshot of the error which I am getting. >>> Also check my log files, this might help: >>> >>> 10:58:42.492 - 1: org.apache.uima.tools.cvd.MainFrame.handleException(526): >>> SEVERE: Initialization of annotator class "org.apache.ctakes.dictionary. >>> lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: >>> file:/C:/Users/ankit/Desktop/apache-ctakes-4.0.0/desc/ctakes >>> -dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml) >>> org.apache.uima.resource.ResourceInitializationException: >>> Initialization of annotator class "org.apache.ctakes.dictionary. >>> lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: >>> file:/C:/Users/ankit/Desktop/apache-ctakes-4.0.0/desc/ctakes >>> -dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml) >>> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine >>> _impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271) >>> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine >>> _impl.initialize(PrimitiveAnalysisEngine_impl.java:170) >>> at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResou >>> rce(AnalysisEngineFactory_impl.java:94) >>> at org.apache.uima.impl.CompositeResourceFactory_impl.produceRe >>> source(CompositeResourceFactory_impl.java:62) >>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279) >>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram >>> ework.java:407) >>> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_ >>> impl.java:256) >>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine >>> _impl.initASB(AggregateAnalysisEngine_impl.java:429) >>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine >>> _impl.initializeAggregateAnalysisEngine(AggregateAnalysisEng >>> ine_impl.java:373) >>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine >>> _impl.initialize(AggregateAnalysisEngine_impl.java:186) >>> at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResou >>> rce(AnalysisEngineFactory_impl.java:94) >>> at org.apache.uima.impl.CompositeResourceFactory_impl.produceRe >>> source(CompositeResourceFactory_impl.java:62) >>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279) >>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram >>> ework.java:371) >>> at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484) >>> at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFra >>> me.java:476) >>> at org.apache.uima.tools.cvd.CVD.main(CVD.java:164) >>> Caused by: org.apache.uima.resource.ResourceInitializationException: >>> MESSAGE LOCALIZATION FAILED: Can't find resource for bundle >>> java.util.PropertyResourceBundle, key Could not construct >>> org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRare >>> WordDictionary >>> at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnno >>> tator.initialize(AbstractJCasTermAnnotator.java:131) >>> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine >>> _impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266) >>> ... 16 more >>> Caused by: >>> org.apache.uima.analysis_engine.annotator.AnnotatorContextException: >>> MESSAGE LOCALIZATION FAILED: Can't find resource for bundle >>> java.util.PropertyResourceBundle, key Could not construct >>> org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRare >>> WordDictionary >>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >>> scriptorParser.parseDictionary(DictionaryDescriptorParser.java:199) >>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >>> scriptorParser.parseDictionaries(DictionaryDescriptorParser.java:156) >>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >>> scriptorParser.parseDescriptor(DictionaryDescriptorParser.java:128) >>> at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnno >>> tator.initialize(AbstractJCasTermAnnotator.java:129) >>> ... 17 more >>> Caused by: java.lang.reflect.InvocationTargetException >>> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) >>> at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) >>> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown >>> Source) >>> at java.lang.reflect.Constructor.newInstance(Unknown Source) >>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >>> scriptorParser.parseDictionary(DictionaryDescriptorParser.java:196) >>> ... 20 more >>> Caused by: java.sql.SQLException: error in script file line: 1141005 >>> java.lang.OutOfMemoryError: GC overhead limit exceeded >>> at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source) >>> at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source) >>> at org.hsqldb.jdbc.JDBCConnection.<init>(Unknown Source) >>> at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source) >>> at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source) >>> at java.sql.DriverManager.getConnection(Unknown Source) >>> at java.sql.DriverManager.getConnection(Unknown Source) >>> at org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFact >>> ory.getConnection(JdbcConnectionFactory.java:84) >>> at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWord >>> Dictionary.<init>(JdbcRareWordDictionary.java:91) >>> at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWord >>> Dictionary.<init>(JdbcRareWordDictionary.java:72) >>> at org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRare >>> WordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31) >>> ... 25 more >>> Caused by: org.hsqldb.HsqlException: error in script file line: 1141005 >>> java.lang.OutOfMemoryError: GC overhead limit exceeded >>> at org.hsqldb.error.Error.error(Unknown Source) >>> at org.hsqldb.scriptio.ScriptReaderText.readExistingData(Unknown Source) >>> at org.hsqldb.scriptio.ScriptReaderBase.readAll(Unknown Source) >>> at org.hsqldb.persist.Log.processScript(Unknown Source) >>> at org.hsqldb.persist.Log.open(Unknown Source) >>> at org.hsqldb.persist.Logger.open(Unknown Source) >>> at org.hsqldb.Database.reopen(Unknown Source) >>> at org.hsqldb.Database.open(Unknown Source) >>> at org.hsqldb.DatabaseManager.getDatabase(Unknown Source) >>> at org.hsqldb.DatabaseManager.newSession(Unknown Source) >>> ... 34 more >>> Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded >>> at java.util.Arrays.copyOfRange(Unknown Source) >>> at java.lang.String.<init>(Unknown Source) >>> at java.lang.String.substring(Unknown Source) >>> at org.hsqldb.persist.HsqlDatabaseProperties.isVersion18(Unknown Source) >>> at org.hsqldb.Table.insertFromScript(Unknown Source) >>> at org.hsqldb.scriptio.ScriptReaderText.readExistingData(Unknown Source) >>> at org.hsqldb.scriptio.ScriptReaderBase.readAll(Unknown Source) >>> at org.hsqldb.persist.Log.processScript(Unknown Source) >>> at org.hsqldb.persist.Log.open(Unknown Source) >>> at org.hsqldb.persist.Logger.open(Unknown Source) >>> at org.hsqldb.Database.reopen(Unknown Source) >>> at org.hsqldb.Database.open(Unknown Source) >>> at org.hsqldb.DatabaseManager.getDatabase(Unknown Source) >>> at org.hsqldb.DatabaseManager.newSession(Unknown Source) >>> at org.hsqldb.jdbc.JDBCConnection.<init>(Unknown Source) >>> at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source) >>> at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source) >>> at java.sql.DriverManager.getConnection(Unknown Source) >>> at java.sql.DriverManager.getConnection(Unknown Source) >>> at org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFact >>> ory.getConnection(JdbcConnectionFactory.java:84) >>> at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWord >>> Dictionary.<init>(JdbcRareWordDictionary.java:91) >>> at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWord >>> Dictionary.<init>(JdbcRareWordDictionary.java:72) >>> at org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRare >>> WordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31) >>> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) >>> at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) >>> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown >>> Source) >>> at java.lang.reflect.Constructor.newInstance(Unknown Source) >>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >>> scriptorParser.parseDictionary(DictionaryDescriptorParser.java:196) >>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >>> scriptorParser.parseDictionaries(DictionaryDescriptorParser.java:156) >>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >>> scriptorParser.parseDescriptor(DictionaryDescriptorParser.java:128) >>> at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnno >>> tator.initialize(AbstractJCasTermAnnotator.java:129) >>> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine >>> _impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266) >>> >>> >>> -Ankit >>> >>> On Fri, Jun 8, 2018 at 11:24 AM, Schenk, Gundolf < >>> [email protected]> wrote: >>> >>>> Hi Ankit, >>>> >>>> >>>> >>>> I am not sure what is happening. The error message that you posted >>>> either indicates that your pipeline is corrupted and then you need to fix >>>> that, or the error message contains typos and you have an actual problem >>>> with initialization which might be due to missing resources. Please double >>>> check and post the exact error message you are getting. >>>> >>>> >>>> >>>> Cheers, >>>> >>>> Gundolf. >>>> >>>> >>>> >>>> >>>> >>>> *From: *Ankit Bisht <[email protected]> >>>> *Date: *Friday, June 8, 2018 at 08:12 >>>> *To: *"[email protected]" <[email protected]>, "Schenk, >>>> Gundolf" <[email protected]> >>>> *Subject: *Re: Regardng Apache cTakes >>>> >>>> >>>> >>>> Hello Gundolf, >>>> >>>> >>>> >>>> Thanks for replying back. Yes, I follow the cTakes user installation >>>> guide. >>>> >>>> I mean I get the error when I run this command to start ctakes CAS >>>> visual debugger : >>>> >>>> bin\runctakesCVD.bat desc\ctakes-clinical-pipeline\ >>>> desc\analysis_engine\AggregatePlaintextFastUMLSProcessor.xml >>>> >>>> >>>> >>>> -Ankit >>>> >>>> >>>> >>>> On Thu, Jun 7, 2018 at 12:01 PM, Schenk, Gundolf < >>>> [email protected]> wrote: >>>> >>>> Hi Ankit, >>>> >>>> >>>> >>>> Have you followed this guide? >>>> >>>> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4. >>>> 0+User+Install+Guide >>>> >>>> >>>> >>>> What exactly do you mean by “open it”? >>>> >>>> >>>> >>>> Cheers, >>>> >>>> Gundolf. >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> *From: *Ankit Bisht <[email protected]> >>>> *Reply-To: *"[email protected]" <[email protected]> >>>> *Date: *Wednesday, June 6, 2018 at 20:22 >>>> *To: *"[email protected]" <[email protected]> >>>> *Subject: *Regardng Apache cTakes >>>> >>>> >>>> >>>> Hello, >>>> >>>> >>>> >>>> I am trying to use Apache Ctakes. I have installed it but when I am >>>> trying to open it, I am getting an error that >>>> org.apache.uima.resource.resourceinitializationexception: >>>> Initialization of annotator class "org.apached.ctakes.dictionary >>>> .lookup2.ae >>>> <https://protect2.fireeye.com/url?k=b97dad412ab8c249.b97d8a5c-3a2f789363131c1e&u=http://dictionary.lookup2.ae> >>>> .DefaultJCastermAnnotaor" failed >>>> >>>> >>>> >>>> >>>> >>>> Regards >>>> >>>> Ankit Bisht >>>> >>>> >>>> >>> >>> >> >
