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Posted to dev@ctakes.apache.org by Ankit Bisht <an...@gmail.com> on 2018/05/29 19:24:35 UTC
Regarding Apached cTakes
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
Posted by Ankit Bisht <an...@gmail.com>.
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 <pa...@gmail.com>
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 <an...@gmail.com>
> 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 <
> pabramowitsch@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 <
> ankitsinghbisht90@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 <
> >>> pabramowitsch@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 <an...@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.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 <
> >>>> Shafiuddin.Ahmed@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 <
> >>>> ankitsinghbisht90@gmail.com>
> >>>>>> wrote:
> >>>>>>
> >>>>>>> Hello,
> >>>>>>>
> >>>>>>> Can someone please help me in this?
> >>>>>>>
> >>>>>>> Best,
> >>>>>>> Ankit
> >>>>>>>
> >>>>>>> On Tue, May 29, 2018 at 3:24 PM, Ankit Bisht <
> >>>> ankitsinghbisht90@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
> >>>>>>>>
> >>>>>>>
> >>>>>
> >>>>
> >>>
> >>
>
Re: Regarding Apached cTakes
Posted by Peter Abramowitsch <pa...@gmail.com>.
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 <an...@gmail.com> 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 <pabramowitsch@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 <an...@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 <
>>> pabramowitsch@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 <an...@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.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 <
>>>> Shafiuddin.Ahmed@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 <
>>>> ankitsinghbisht90@gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> Can someone please help me in this?
>>>>>>>
>>>>>>> Best,
>>>>>>> Ankit
>>>>>>>
>>>>>>> On Tue, May 29, 2018 at 3:24 PM, Ankit Bisht <
>>>> ankitsinghbisht90@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
>>>>>>>>
>>>>>>>
>>>>>
>>>>
>>>
>>
Re: Regarding Apached cTakes
Posted by Ankit Bisht <an...@gmail.com>.
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 <pabramowitsch@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 <an...@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 <
> > pabramowitsch@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 <an...@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.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 <
> > > Shafiuddin.Ahmed@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 <
> > > ankitsinghbisht90@gmail.com>
> > > >> wrote:
> > > >>
> > > >> > Hello,
> > > >> >
> > > >> > Can someone please help me in this?
> > > >> >
> > > >> > Best,
> > > >> > Ankit
> > > >> >
> > > >> > On Tue, May 29, 2018 at 3:24 PM, Ankit Bisht <
> > > ankitsinghbisht90@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
> > > >> > >
> > > >> >
> > > >
> > >
> >
>
Re: Regarding Apached cTakes
Posted by Peter Abramowitsch <pa...@gmail.com>.
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 <an...@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 <
> pabramowitsch@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 <an...@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.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 <
> > Shafiuddin.Ahmed@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 <
> > ankitsinghbisht90@gmail.com>
> > >> wrote:
> > >>
> > >> > Hello,
> > >> >
> > >> > Can someone please help me in this?
> > >> >
> > >> > Best,
> > >> > Ankit
> > >> >
> > >> > On Tue, May 29, 2018 at 3:24 PM, Ankit Bisht <
> > ankitsinghbisht90@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
> > >> > >
> > >> >
> > >
> >
>
Re: Regarding Apached cTakes
Posted by Ankit Bisht <an...@gmail.com>.
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 <pa...@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 <an...@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.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.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.Ahmed@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 <
> ankitsinghbisht90@gmail.com>
> >> wrote:
> >>
> >> > Hello,
> >> >
> >> > Can someone please help me in this?
> >> >
> >> > Best,
> >> > Ankit
> >> >
> >> > On Tue, May 29, 2018 at 3:24 PM, Ankit Bisht <
> ankitsinghbisht90@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
> >> > >
> >> >
> >
>
Re: Regarding Apached cTakes
Posted by Peter Abramowitsch <pa...@gmail.com>.
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 <an...@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 <Sh...@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 <an...@gmail.com>
>> wrote:
>>
>> > Hello,
>> >
>> > Can someone please help me in this?
>> >
>> > Best,
>> > Ankit
>> >
>> > On Tue, May 29, 2018 at 3:24 PM, Ankit Bisht <an...@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
>> > >
>> >
>
Re: Regarding Apached cTakes
Posted by Ankit Bisht <an...@gmail.com>.
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.Ahmed@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 <an...@gmail.com>
> wrote:
>
> > Hello,
> >
> > Can someone please help me in this?
> >
> > Best,
> > Ankit
> >
> > On Tue, May 29, 2018 at 3:24 PM, Ankit Bisht <
> ankitsinghbisht90@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
> > >
> >
>
Re: Regarding Apached cTakes
Posted by Shafiuddin Rehan Ahmed <Sh...@colorado.edu>.
Can you send the logged messages in the console(terminal)?
Rehan
On Thu, May 31, 2018 at 1:59 PM, Ankit Bisht <an...@gmail.com>
wrote:
> Hello,
>
> Can someone please help me in this?
>
> Best,
> Ankit
>
> On Tue, May 29, 2018 at 3:24 PM, Ankit Bisht <an...@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
> >
>
Re: Regarding Apached cTakes
Posted by Ankit Bisht <an...@gmail.com>.
Hello,
Can someone please help me in this?
Best,
Ankit
On Tue, May 29, 2018 at 3:24 PM, Ankit Bisht <an...@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
>
Re: Regarding Apached cTakes
Posted by Peter Abramowitsch <pa...@gmail.com>.
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 <an...@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
>