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From Heather Champion <imt.heather.champ...@gmail.com>
Subject LVG component out of memory
Date Fri, 30 Jan 2015 21:32:57 GMT
Hello,

I have installed cTAKES-3.2.1-bin on linux.  When I try to load an AE that
uses the LVG component, I get a java out of memory error.  I have tried
increasing the Xmx... I've tried values like 1500M, 2500M, 3g, 4g.

Here is the console debug output from doing runctakesCVD.sh

Thanks,
Heather

log4j: reset attribute= "false".
log4j: Threshold ="null".
log4j: Level value for root is  [DEBUG].
log4j: root level set to DEBUG
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss}
%5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
30 Jan 2015 15:18:32 DEBUG OverlapAnnotator - Overlap bitset: {3}
30 Jan 2015 15:18:32 DEBUG DataBinder - DataBinder requires binding of
required fields [srcClassName,destClassName,methodMapArray]
30 Jan 2015 15:18:32  INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg
with config file =
/home/heather/TextAnalytics/cTAKES/apache-ctakes-3.2.1-bin/apache-ctakes-3.2.1/resources/org/apache/ctakes/lvg/data/config/lvg.properties
30 Jan 2015 15:18:32  INFO LvgCmdApiResourceImpl -   config file absolute
path =
/home/heather/TextAnalytics/cTAKES/apache-ctakes-3.2.1-bin/apache-ctakes-3.2.1/resources/org/apache/ctakes/lvg/data/config/lvg.properties
30 Jan 2015 15:18:32  INFO LvgCmdApiResourceImpl - cwd =
/home/heather/TextAnalytics/cTAKES/apache-ctakes-3.2.1-bin/apache-ctakes-3.2.1
30 Jan 2015 15:18:32  INFO LvgCmdApiResourceImpl - cd
/home/heather/TextAnalytics/cTAKES/apache-ctakes-3.2.1-bin/apache-ctakes-3.2.1/resources/org/apache/ctakes/lvg/
java.sql.SQLException: error in script file line: 14 out of memory
at org.hsqldb.jdbc.Util.sqlException(Unknown Source)
at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source)
at org.hsqldb.jdbcDriver.getConnection(Unknown Source)
at org.hsqldb.jdbcDriver.connect(Unknown Source)
at java.sql.DriverManager.getConnection(DriverManager.java:664)
at java.sql.DriverManager.getConnection(DriverManager.java:247)
at gov.nih.nlm.nls.lvg.Db.DbBase.OpenConnection(DbBase.java:40)
at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.InitDbAndTrie(LvgCmdApi.java:1479)
at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.Init(LvgCmdApi.java:1432)
at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.<init>(LvgCmdApi.java:86)
at
org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiResourceImpl.java:89)
at
org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603)
at
org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
at
org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123)
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:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
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:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
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.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346)
at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
at
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)
at java.awt.Component.processMouseEvent(Component.java:6525)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3322)
at java.awt.Component.processEvent(Component.java:6290)
at java.awt.Container.processEvent(Container.java:2234)
at java.awt.Component.dispatchEventImpl(Component.java:4881)
at java.awt.Container.dispatchEventImpl(Container.java:2292)
at java.awt.Component.dispatchEvent(Component.java:4703)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462)
at java.awt.Container.dispatchEventImpl(Container.java:2278)
at java.awt.Window.dispatchEventImpl(Window.java:2739)
at java.awt.Component.dispatchEvent(Component.java:4703)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:751)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:702)
at java.awt.EventQueue$3.run(EventQueue.java:696)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
at
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.awt.EventQueue$4.run(EventQueue.java:724)
at java.awt.EventQueue$4.run(EventQueue.java:722)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:721)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
java.sql.SQLException: error in script file line: 14 out of memory
at org.hsqldb.jdbc.Util.sqlException(Unknown Source)
at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source)
at org.hsqldb.jdbcDriver.getConnection(Unknown Source)
at org.hsqldb.jdbcDriver.connect(Unknown Source)
at java.sql.DriverManager.getConnection(DriverManager.java:664)
at java.sql.DriverManager.getConnection(DriverManager.java:247)
at gov.nih.nlm.nls.lvg.Db.DbBase.OpenConnection(DbBase.java:40)
at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.InitDbAndTrie(LvgCmdApi.java:1479)
at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.Init(LvgCmdApi.java:1432)
at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.<init>(LvgCmdApi.java:86)
at gov.nih.nlm.nls.lvg.Api.LvgLexItemApi.<init>(LvgLexItemApi.java:80)
at
org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiResourceImpl.java:94)
at
org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603)
at
org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
at
org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123)
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:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
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:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
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.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346)
at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
at
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)
at java.awt.Component.processMouseEvent(Component.java:6525)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3322)
at java.awt.Component.processEvent(Component.java:6290)
at java.awt.Container.processEvent(Container.java:2234)
at java.awt.Component.dispatchEventImpl(Component.java:4881)
at java.awt.Container.dispatchEventImpl(Container.java:2292)
at java.awt.Component.dispatchEvent(Component.java:4703)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462)
at java.awt.Container.dispatchEventImpl(Container.java:2278)
at java.awt.Window.dispatchEventImpl(Window.java:2739)
at java.awt.Component.dispatchEvent(Component.java:4703)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:751)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:702)
at java.awt.EventQueue$3.run(EventQueue.java:696)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
at
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.awt.EventQueue$4.run(EventQueue.java:724)
at java.awt.EventQueue$4.run(EventQueue.java:722)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:721)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
30 Jan 2015 15:18:41  INFO LvgCmdApiResourceImpl - cd
/home/heather/TextAnalytics/cTAKES/apache-ctakes-3.2.1-bin/apache-ctakes-3.2.1
30 Jan 2015 15:18:41 DEBUG DataBinder - DataBinder requires binding of
required fields []
30 Jan 2015 15:18:41 DEBUG DataBinder - DataBinder requires binding of
required fields []
30 Jan 2015 15:18:41  INFO LuceneIndexReaderResourceImpl -
indexDir=org/apache/ctakes/dictionary/lookup/rxnorm_index  exists.
30 Jan 2015 15:18:41  INFO LuceneIndexReaderResourceImpl - Loading Lucene
Index into memory:
/home/heather/TextAnalytics/cTAKES/apache-ctakes-3.2.1-bin/apache-ctakes-3.2.1/resources/org/apache/ctakes/dictionary/lookup/rxnorm_index
30 Jan 2015 15:18:41  INFO LuceneIndexReaderResourceImpl - Loaded Lucene
Index, # docs=162563
30 Jan 2015 15:18:41  INFO UmlsDictionaryLookupAnnotator - Parsing
descriptor:
/home/heather/TextAnalytics/cTAKES/apache-ctakes-3.2.1-bin/apache-ctakes-3.2.1/resources/org/apache/ctakes/drugner/lookup/LookupDesc_DrugNER.xml
Adding exclude value[alcohol]
Adding exclude value[air]
Adding exclude value[allergies]
Adding exclude value[allergy]
Adding exclude value[aerosol]
Adding exclude value[bottle]
Adding exclude value[bottles]
Adding exclude value[film]
Adding exclude value[spray]
Adding exclude value[sprays]
Adding exclude value[freez]
Adding exclude value[freeze]
Adding exclude value[frozen]
Adding exclude value[froze]
Adding exclude value[factor xiii]
Adding exclude value[factor]
Adding exclude value[gas]
Adding exclude value[oxygen]
Adding exclude value[paste]
Adding exclude value[powder]
Adding exclude value[oil]
Adding exclude value[oils]
Adding exclude value[solution]
Adding exclude value[solutions]
Adding exclude value[sodium]
Adding exclude value[syrup]
Adding exclude value[inhaler]
Adding exclude value[unit]
Adding exclude value[units]
Adding exclude value[cholesterol]
Adding exclude value[completed]
Adding exclude value[caplet]
Adding exclude value[caplets]
Adding exclude value[cain]
Adding exclude value[dos]
Adding exclude value[dose]
Adding exclude value[doses]
Adding exclude value[transdermal patch]
Adding exclude value[tablet]
Adding exclude value[tablets]
Adding exclude value[patch]
Adding exclude value[patches]
Adding exclude value[pill]
Adding exclude value[pills]
Adding exclude value[program]
Adding exclude value[ointment]
Adding exclude value[oral]
Adding exclude value[diuresed]
Adding exclude value[diurese]
Adding exclude value[capsule]
Adding exclude value[capsules]
Adding exclude value[cane]
Adding exclude value[chewable]
Adding exclude value[cream]
Adding exclude value[topical]
Adding exclude value[lead]
Adding exclude value[led]
Adding exclude value[load]
Adding exclude value[leads]
Adding exclude value[leading]
Adding exclude value[loads]
Adding exclude value[liver]
Adding exclude value[liquid]
Adding exclude value[lozenge]
Adding exclude value[lozenges]
Adding exclude value[nebulizer]
Adding exclude value[nebulize]
Adding exclude value[gel]
Adding exclude value[prostate]
Adding exclude value[be]
Adding exclude value[being]
Adding exclude value[cm]
Adding exclude value[dr]
Adding exclude value[drs]
Adding exclude value[is]
Adding exclude value[hearing]
Adding exclude value[prompting]
Adding exclude value[sutures]
Adding exclude value[tomorrow]
Adding exclude value[water]
Adding exclude value[walker]
Adding exclude value[suspension]
Adding exclude value[sustained]
Adding exclude value[air]
Adding exclude value[md]
Adding exclude value[pm]
Adding exclude value[mg]
Adding exclude value[a]
Adding exclude value[b]
Adding exclude value[c]
Adding exclude value[d]
Adding exclude value[e]
Adding exclude value[f]
Adding exclude value[g]
Adding exclude value[h]
Adding exclude value[i]
Adding exclude value[j]
Adding exclude value[k]
Adding exclude value[l]
Adding exclude value[m]
Adding exclude value[n]
Adding exclude value[o]
Adding exclude value[p]
Adding exclude value[q]
Adding exclude value[r]
Adding exclude value[s]
Adding exclude value[t]
Adding exclude value[q]
Adding exclude value[v]
Adding exclude value[w]
Adding exclude value[x]
Adding exclude value[y]
Adding exclude value[z]
30 Jan 2015 15:18:42  INFO FirstTokenPermLookupInitializerImpl - Exclusion
tagset loaded: [cc, pp, cd, pdt, prp$, pp$, wdt, wrb, ls, prp, dt, ex, pos,
md, wp, to, wps, rp]
30 Jan 2015 15:18:42  INFO UmlsDictionaryLookupAnnotator - Using
ctakes.umlsaddr: https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser:
30 Jan 2015 15:18:43 DEBUG DataBinder - DataBinder requires binding of
required fields []
30 Jan 2015 15:18:43  INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip
30 Jan 2015 15:18:45 DEBUG DataBinder - DataBinder requires binding of
required fields []
30 Jan 2015 15:18:45  INFO ContextDependentTokenizerAnnotator - Finite
state machines loaded.
30 Jan 2015 15:18:45  INFO DrugMentionAnnotator - Finite state machines
loaded.
30 Jan 2015 15:18:45  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
30 Jan 2015 15:18:45  INFO NegationContextAnalyzer - initBoundaryData()
called for ContextInitializer
30 Jan 2015 15:18:45 DEBUG DataBinder - DataBinder requires binding of
required fields []
30 Jan 2015 15:18:45  INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
30 Jan 2015 15:18:46 DEBUG DataBinder - DataBinder requires binding of
required fields []
30 Jan 2015 15:18:46  INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
30 Jan 2015 15:18:46  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
30 Jan 2015 15:18:46  INFO StatusContextAnalyzer - initBoundaryData()
called for ContextInitializer
30 Jan 2015 15:18:46 DEBUG DataBinder - DataBinder requires binding of
required fields [sdModelPath]
30 Jan 2015 15:18:46  INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip

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