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From Lance Eason <la...@iodinesoftware.com>
Subject Re: LVG component out of memory
Date Fri, 30 Jan 2015 23:38:55 GMT
Depending on the pipeline you're using I'd recommend removing LVG from the
pipeline entirely.  When I did analysis on the pipelines we're using,
AggregatePlaintextUMLSProcessor.xml
/ AggregatePlaintextFastUMLSProcessor.xml, none of the other components in
the pipeline actually made any use of the output from LVG and sure enough
removing it made no difference to the output.  It appears like having it in
the pipeline may be vestigial at this point.  There's a thread on the
developer's list that seemed to come to the same conclusion.

Same for the ConstituencyParser as well.

Of course depending on your pipeline your mileage may vary.

On Fri, Jan 30, 2015 at 3:32 PM, Heather Champion <
imt.heather.champion@gmail.com> wrote:

> 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
>
>
>


-- 
.........................................................
*Lance Eason*
Iodine Software
Vice President of Engineering
lance@iodinesoftware.com
512.785.5195 office | 801.203.8987 fax
.........................................................

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