Hello Peter, 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
-Ankit On Sat, Jun 2, 2018 at 1:04 AM, Peter Abramowitsch <[email protected]> wrote: > The best thing would be for you to look at some of the other launch > scripts in the bin directory of a release. There you’ll find examples of > passing both memory and UMLS parameters. > > Sent from my iPad > > > On Jun 1, 2018, at 18:36, Ankit Bisht <[email protected]> > wrote: > > > > 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 > >>>>>>>> > >>>>>>> > >>>>> > >>>> > >>> > >> >
