That's good. But the fact that the stack trace shows you're out of memory, probably indicates that the JVM memory related args are not successfully being passed. They should be set to -Xms512M -Xmx3g or greater.
Peter On Fri, Jun 1, 2018 at 5:03 PM, Ankit Bisht <ankitsinghbish...@gmail.com> wrote: > Hello Peter, > > Thanks for showing your concern on this issue. The machine on which I am > running cTakes has 32 GB of Ram and 100 GB of Memory left. > > -Ankit > > On Fri, Jun 1, 2018 at 2:31 AM, Peter Abramowitsch < > pabramowit...@gmail.com> > wrote: > > > Hi Ankit > > > > It looks like your answer is near the bottom of the stacktrace you sent. > > The machine is out of memory. In general with these traces the root > cause > > of an error will be near the bottom, but as it is propagated up the many > > layers of the application, the messages become more generic. > > > > So in your case the root cause is: > > > Caused by: org.hsqldb.HsqlException: error in script file line: 1141005 > > java.lang.OutOfMemoryError: GC overhead limit exceeded > > > > In general Ctakes scripts launch the app with parameters that specify the > > memory needed, but if either these are left out, or the machine itself > > doesn’t have the available resources, you will get this error. > > > > - Peter > > > > Sent from my iPad > > > > > On Jun 1, 2018, at 02:51, Ankit Bisht <ankitsinghbish...@gmail.com> > > wrote: > > > > > > Hello Rehan, > > > > > > Are you talking about the below messages? I took them from CAS visual > > debugger tool = > Tools => View log file . I have also attached the > > snapshot of exception that I am getting. Please let me know if you need > > anything else. > > > > > > 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. > > 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.initializeAggregateAnalysisEng > > ine(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. > > 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. > > 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.DelegatingConstructorAccessorI > mpl.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.DelegatingConstructorAccessorI > mpl.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. > > AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:129) > > > at org.apache.uima.analysis_engine.impl. > > PrimitiveAnalysisEngine_impl.initializeAnalysisComponent( > > PrimitiveAnalysisEngine_impl.java:266) > > > > > > -Ankit > > > > > >> On Thu, May 31, 2018 at 8:42 PM, Shafiuddin Rehan Ahmed < > > shafiuddin.ah...@colorado.edu> wrote: > > >> Can you send the logged messages in the console(terminal)? > > >> > > >> Rehan > > >> > > >> On Thu, May 31, 2018 at 1:59 PM, Ankit Bisht < > > ankitsinghbish...@gmail.com> > > >> wrote: > > >> > > >> > Hello, > > >> > > > >> > Can someone please help me in this? > > >> > > > >> > Best, > > >> > Ankit > > >> > > > >> > On Tue, May 29, 2018 at 3:24 PM, Ankit Bisht < > > ankitsinghbish...@gmail.com> > > >> > wrote: > > >> > > > >> > > 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. > DefaultJCastermAnnotaor" > > >> > failed > > >> > > > > >> > > I am following the cTAKES 4.0 User Install Guide but still facing > > some > > >> > > problems. > > >> > > > > >> > > Regards > > >> > > Ankit > > >> > > > > >> > > > > > > >
