Hi Debdipto and Gundolf, I checked all the launch scripts and in all of them JVM memory related args are set to -Xms512M -Xmx3g as: -Dlog4j.configuration=file:\%CTAKES_HOME%\config\log4j.xml -Xms512M -Xmx3g .
The system has 32 GB RAM and good hard disk space. -Ankit On Fri, Jun 8, 2018 at 1:22 PM, Debdipto Misra <[email protected]> wrote: > Try running it after increasing the Java Heap Space size.You are running > into GC Overhead error because your hsql db fails to initialize. > > > > On Fri, Jun 8, 2018 at 12:32 PM Schenk, Gundolf <[email protected]> > wrote: > >> Hi Ankit, >> >> >> >> Thanks for the screenshot and the log output. I can only guess: >> >> 1) I can see out-of-memory errors. So perhaps you are running low on >> memory. >> >> >> >> 2) The other message that caught my attention is the UMLS dictionary. >> Perhaps something went wrong with the installation fo the metathesaurus. >> Are you using it? >> >> >> >> Cheers, >> >> Gundolf. >> >> >> >> >> >> *From: *Ankit Bisht <[email protected]> >> *Date: *Friday, June 8, 2018 at 09:20 >> *To: *"Schenk, Gundolf" <[email protected]> >> *Cc: *"[email protected]" <[email protected]> >> *Subject: *Re: Regardng Apache cTakes >> >> >> >> 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 >> <https://protect2.fireeye.com/url?k=d2cb505296f21a07.d2cb774f-3da4a1b0ae9ebae2&u=http://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 >> <https://protect2.fireeye.com/url?k=d2cb505296f21a07.d2cb774f-3da4a1b0ae9ebae2&u=http://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.produceResource( >> AnalysisEngineFactory_impl.java:94) >> >> at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource( >> CompositeResourceFactory_impl.java:62) >> >> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279) >> >> at org.apache.uima.UIMAFramework.produceAnalysisEngine( >> UIMAFramework.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(AggregateAnalysisEngine_impl.java:373) >> >> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl. >> initialize(AggregateAnalysisEngine_impl.java:186) >> >> at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource( >> AnalysisEngineFactory_impl.java:94) >> >> at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource( >> CompositeResourceFactory_impl.java:62) >> >> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279) >> >> at org.apache.uima.UIMAFramework.produceAnalysisEngine( >> UIMAFramework.java:371) >> >> at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484) >> >> at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor( >> MainFrame.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. >> UmlsJdbcRareWordDictionary >> >> at org.apache.ctakes.dictionary.lookup2.ae >> <https://protect2.fireeye.com/url?k=d2cb505296f21a07.d2cb774f-3da4a1b0ae9ebae2&u=http://lookup2.ae> >> .AbstractJCasTermAnnotator.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. >> UmlsJdbcRareWordDictionary >> >> at org.apache.ctakes.dictionary.lookup2.dictionary. >> DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser. >> java:199) >> >> at org.apache.ctakes.dictionary.lookup2.dictionary. >> DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser. >> java:156) >> >> at org.apache.ctakes.dictionary.lookup2.dictionary. >> DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser. >> java:128) >> >> at org.apache.ctakes.dictionary.lookup2.ae >> <https://protect2.fireeye.com/url?k=d2cb505296f21a07.d2cb774f-3da4a1b0ae9ebae2&u=http://lookup2.ae> >> .AbstractJCasTermAnnotator.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. >> DictionaryDescriptorParser.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.JdbcConnectionFactory. >> getConnection(JdbcConnectionFactory.java:84) >> >> at org.apache.ctakes.dictionary.lookup2.dictionary. >> JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91) >> >> at org.apache.ctakes.dictionary.lookup2.dictionary. >> JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72) >> >> at org.apache.ctakes.dictionary.lookup2.dictionary. >> UmlsJdbcRareWordDictionary.<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.JdbcConnectionFactory. >> getConnection(JdbcConnectionFactory.java:84) >> >> at org.apache.ctakes.dictionary.lookup2.dictionary. >> JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91) >> >> at org.apache.ctakes.dictionary.lookup2.dictionary. >> JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72) >> >> at org.apache.ctakes.dictionary.lookup2.dictionary. >> UmlsJdbcRareWordDictionary.<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. >> DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser. >> java:196) >> >> at org.apache.ctakes.dictionary.lookup2.dictionary. >> DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser. >> java:156) >> >> at org.apache.ctakes.dictionary.lookup2.dictionary. >> DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser. >> java:128) >> >> at org.apache.ctakes.dictionary.lookup2.ae >> <https://protect2.fireeye.com/url?k=d2cb505296f21a07.d2cb774f-3da4a1b0ae9ebae2&u=http://lookup2.ae> >> .AbstractJCasTermAnnotator.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 >> >> >> >> >> > > > -- > Thanks and regards > Deb >
