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
