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.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.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.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.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 >> > > >> > >
