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 >>>>>>>> >>>>>>> >>>>> >>>> >>> >>
