Re: Regarding Apached cTakes
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 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 > 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 < > pabramowit...@gmail.com > >> 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 < > 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 > 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. >
Re: Regarding Apached cTakes
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 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 > 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 >> 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 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:
Re: Regarding Apached cTakes
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 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 > 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 > > > 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. > > >
Re: Regarding Apached cTakes
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 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 > > 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
Re: Regarding Apached cTakes
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 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 > 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
Re: Regarding Apached cTakes
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 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
Re: Regarding Apached cTakes
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.(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
Re: Regarding Apached cTakes
Can you send the logged messages in the console(terminal)? Rehan On Thu, May 31, 2018 at 1:59 PM, Ankit Bisht wrote: > Hello, > > Can someone please help me in this? > > Best, > Ankit > > On Tue, May 29, 2018 at 3:24 PM, Ankit Bisht > 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 > > >
Re: Regarding Apached cTakes
That exception is often the sign that it doesn't see your umls username and password. You need to give it through the environment, via a Piper file if you're using it, or directly in the XML descriptor for the dictionary lookup. Check in the user guide for help. Or exclude the lookup altogether. On Tue, May 29, 2018, 11:32 PM Ankit Bisht 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 >
