Thanks Peter. I have not done that before. How could it be done? Would it be done like this: java -Xms512M -Xmx3g ClassName?
-Ankit On Fri, Jun 1, 2018 at 12:05 PM, Peter Abramowitsch <[email protected] > wrote: > 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 <[email protected]> > 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 < > > [email protected]> > > 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 <[email protected]> > > > 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 < > > > [email protected]> wrote: > > > >> Can you send the logged messages in the console(terminal)? > > > >> > > > >> Rehan > > > >> > > > >> On Thu, May 31, 2018 at 1:59 PM, Ankit Bisht < > > > [email protected]> > > > >> wrote: > > > >> > > > >> > Hello, > > > >> > > > > >> > Can someone please help me in this? > > > >> > > > > >> > Best, > > > >> > Ankit > > > >> > > > > >> > On Tue, May 29, 2018 at 3:24 PM, Ankit Bisht < > > > [email protected]> > > > >> > 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 > > > >> > > > > > >> > > > > > > > > > > >
