java.lang.OutOfMemoryError: GC overhead limit exceeded

Sakai JIRA | Truc Muche | 2 years ago
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  1. 0

    i have an FC overhead limit on the default installation (after the second start, on the first, all is OK). It happens on Vivo start while loading RDF files. I don't have any content or custom ontology, and i hadn't this error on the 1.7 release. I test to increase the max heap size to 3g, so i think there is something that eats all memory. All others features are working properly, but without any ontology. Erreur log : 2015-05-11 15:32:53,580 INFO [RDFFilesLoader] Loading rdf/display/everytime/dataGetterLabels.n3 2015-05-11 15:32:53,584 INFO [RDFFilesLoader] Loading rdf/display/everytime/displayModelListViews.rdf 2015-05-11 15:32:53,590 INFO [RDFFilesLoader] Loading rdf/display/everytime/homePageDataGetters.n3 2015-05-11 15:32:53,595 INFO [RDFFilesLoader] Loading rdf/display/everytime/localeSelectionGUI.n3 2015-05-11 15:32:53,598 INFO [RDFFilesLoader] Loading rdf/display/everytime/n3ModelChangePreprocessors.n3 2015-05-11 15:32:53,601 INFO [RDFFilesLoader] Loading rdf/display/everytime/orcidInterfaceDataGetters.n3 2015-05-11 15:32:53,603 INFO [RDFFilesLoader] Loading rdf/display/everytime/pageList.n3 2015-05-11 15:32:53,607 INFO [RDFFilesLoader] Loading rdf/display/everytime/permissions.n3 2015-05-11 15:32:53,627 INFO [RDFFilesLoader] Loading rdf/display/everytime/searchIndexerConfigurationVitro.n3 2015-05-11 15:32:53,642 INFO [RDFFilesLoader] Loading rdf/display/everytime/searchIndexerConfigurationVivo.n3 2015-05-11 15:32:53,658 INFO [RDFFilesLoader] Loading rdf/display/everytime/vitroSearchProhibited.n3 2015-05-11 15:32:53,659 INFO [RDFFilesLoader] Loading rdf/display/everytime/vivoConceptDataGetters.n3 2015-05-11 15:32:53,667 INFO [RDFFilesLoader] Loading rdf/display/everytime/vivoListViewConfig.rdf 2015-05-11 15:32:53,697 INFO [RDFFilesLoader] Loading rdf/display/everytime/vivoOrganizationDataGetters.n3 2015-05-11 15:32:53,728 INFO [RDFFilesLoader] Loading rdf/display/everytime/vivoQrCodeDataGetter.n3 2015-05-11 15:32:53,734 INFO [RDFFilesLoader] Loading rdf/display/everytime/vivoSearchProhibited.n3 2015-05-11 15:32:53,807 INFO [RDFFilesLoader] Loading rdf/displayTbox/everytime/displayTBOX.n3 2015-05-11 15:32:53,847 INFO [RDFFilesLoader] Loading rdf/displayDisplay/everytime/displayDisplay.n3 2015-05-11 15:32:53,862 INFO [RDFFilesLoader] Loading rdf/auth/everytime/permission_config.n3 2015-05-11 15:33:06,828 ERROR [FileGraphSetup] java.lang.OutOfMemoryError: GC overhead limit exceeded java.lang.OutOfMemoryError: GC overhead limit exceeded at org.apache.jena.atlas.json.io.parser.TokenizerJSON.parseToken(TokenizerJSON.java:107) at org.apache.jena.atlas.json.io.parser.TokenizerJSON.hasNext(TokenizerJSON.java:63) at org.apache.jena.atlas.iterator.PeekIterator.fill(PeekIterator.java:50) at org.apache.jena.atlas.iterator.PeekIterator.next(PeekIterator.java:92) at org.apache.jena.atlas.json.io.parser.ParserBase.nextToken(ParserBase.java:107) at org.apache.jena.atlas.json.io.parser.JSONP.parseObject(JSONP.java:56) at org.apache.jena.atlas.json.io.parser.JSONP.parseAny(JSONP.java:97) at org.apache.jena.atlas.json.io.parser.JSONP.parseObject(JSONP.java:79) at org.apache.jena.atlas.json.io.parser.JSONP.parseAny(JSONP.java:97) at org.apache.jena.atlas.json.io.parser.JSONP.parseArray(JSONP.java:146) at org.apache.jena.atlas.json.io.parser.JSONP.parseAny(JSONP.java:98) at org.apache.jena.atlas.json.io.parser.JSONP.parseObject(JSONP.java:79) at org.apache.jena.atlas.json.io.parser.JSONP.parseAny(JSONP.java:97) at org.apache.jena.atlas.json.io.parser.JSONP.parseObject(JSONP.java:79) at org.apache.jena.atlas.json.io.parser.JSONP.parse(JSONP.java:50) at org.apache.jena.atlas.json.io.parser.JSONParser.parse(JSONParser.java:58) at org.apache.jena.atlas.json.io.parser.JSONParser.parse(JSONParser.java:40) at org.apache.jena.atlas.json.JSON._parse(JSON.java:147) at org.apache.jena.atlas.json.JSON.parse(JSON.java:43) at com.hp.hpl.jena.sparql.resultset.JSONInput.parse(JSONInput.java:124) at com.hp.hpl.jena.sparql.resultset.JSONInput.process(JSONInput.java:108) at com.hp.hpl.jena.sparql.resultset.JSONInput.fromJSON(JSONInput.java:65) at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.execSelect(RDFServiceGraph.java:402) at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.find(RDFServiceGraph.java:259) at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.find(RDFServiceGraph.java:191) at com.hp.hpl.jena.graph.GraphUtil.findAll(GraphUtil.java:128) at com.hp.hpl.jena.graph.GraphUtil.addInto(GraphUtil.java:183) at com.hp.hpl.jena.rdf.model.impl.ModelCom.add(ModelCom.java:208) at com.hp.hpl.jena.rdf.model.impl.ModelCom.add(ModelCom.java:202) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.RDFServiceJena.isEquivalentGraph(RDFServiceJena.java:567) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.logging.LoggingRDFService.isEquivalentGraph(LoggingRDFService.java:92) at edu.cornell.mannlib.vitro.webapp.servlet.setup.FileGraphSetup.updateGraphInDB(FileGraphSetup.java:218)

    Sakai JIRA | 2 years ago | Truc Muche
    java.lang.OutOfMemoryError: GC overhead limit exceeded
  2. 0

    i have an FC overhead limit on the default installation (after the second start, on the first, all is OK). It happens on Vivo start while loading RDF files. I don't have any content or custom ontology, and i hadn't this error on the 1.7 release. I test to increase the max heap size to 3g, so i think there is something that eats all memory. All others features are working properly, but without any ontology. Erreur log : 2015-05-11 15:32:53,580 INFO [RDFFilesLoader] Loading rdf/display/everytime/dataGetterLabels.n3 2015-05-11 15:32:53,584 INFO [RDFFilesLoader] Loading rdf/display/everytime/displayModelListViews.rdf 2015-05-11 15:32:53,590 INFO [RDFFilesLoader] Loading rdf/display/everytime/homePageDataGetters.n3 2015-05-11 15:32:53,595 INFO [RDFFilesLoader] Loading rdf/display/everytime/localeSelectionGUI.n3 2015-05-11 15:32:53,598 INFO [RDFFilesLoader] Loading rdf/display/everytime/n3ModelChangePreprocessors.n3 2015-05-11 15:32:53,601 INFO [RDFFilesLoader] Loading rdf/display/everytime/orcidInterfaceDataGetters.n3 2015-05-11 15:32:53,603 INFO [RDFFilesLoader] Loading rdf/display/everytime/pageList.n3 2015-05-11 15:32:53,607 INFO [RDFFilesLoader] Loading rdf/display/everytime/permissions.n3 2015-05-11 15:32:53,627 INFO [RDFFilesLoader] Loading rdf/display/everytime/searchIndexerConfigurationVitro.n3 2015-05-11 15:32:53,642 INFO [RDFFilesLoader] Loading rdf/display/everytime/searchIndexerConfigurationVivo.n3 2015-05-11 15:32:53,658 INFO [RDFFilesLoader] Loading rdf/display/everytime/vitroSearchProhibited.n3 2015-05-11 15:32:53,659 INFO [RDFFilesLoader] Loading rdf/display/everytime/vivoConceptDataGetters.n3 2015-05-11 15:32:53,667 INFO [RDFFilesLoader] Loading rdf/display/everytime/vivoListViewConfig.rdf 2015-05-11 15:32:53,697 INFO [RDFFilesLoader] Loading rdf/display/everytime/vivoOrganizationDataGetters.n3 2015-05-11 15:32:53,728 INFO [RDFFilesLoader] Loading rdf/display/everytime/vivoQrCodeDataGetter.n3 2015-05-11 15:32:53,734 INFO [RDFFilesLoader] Loading rdf/display/everytime/vivoSearchProhibited.n3 2015-05-11 15:32:53,807 INFO [RDFFilesLoader] Loading rdf/displayTbox/everytime/displayTBOX.n3 2015-05-11 15:32:53,847 INFO [RDFFilesLoader] Loading rdf/displayDisplay/everytime/displayDisplay.n3 2015-05-11 15:32:53,862 INFO [RDFFilesLoader] Loading rdf/auth/everytime/permission_config.n3 2015-05-11 15:33:06,828 ERROR [FileGraphSetup] java.lang.OutOfMemoryError: GC overhead limit exceeded java.lang.OutOfMemoryError: GC overhead limit exceeded at org.apache.jena.atlas.json.io.parser.TokenizerJSON.parseToken(TokenizerJSON.java:107) at org.apache.jena.atlas.json.io.parser.TokenizerJSON.hasNext(TokenizerJSON.java:63) at org.apache.jena.atlas.iterator.PeekIterator.fill(PeekIterator.java:50) at org.apache.jena.atlas.iterator.PeekIterator.next(PeekIterator.java:92) at org.apache.jena.atlas.json.io.parser.ParserBase.nextToken(ParserBase.java:107) at org.apache.jena.atlas.json.io.parser.JSONP.parseObject(JSONP.java:56) at org.apache.jena.atlas.json.io.parser.JSONP.parseAny(JSONP.java:97) at org.apache.jena.atlas.json.io.parser.JSONP.parseObject(JSONP.java:79) at org.apache.jena.atlas.json.io.parser.JSONP.parseAny(JSONP.java:97) at org.apache.jena.atlas.json.io.parser.JSONP.parseArray(JSONP.java:146) at org.apache.jena.atlas.json.io.parser.JSONP.parseAny(JSONP.java:98) at org.apache.jena.atlas.json.io.parser.JSONP.parseObject(JSONP.java:79) at org.apache.jena.atlas.json.io.parser.JSONP.parseAny(JSONP.java:97) at org.apache.jena.atlas.json.io.parser.JSONP.parseObject(JSONP.java:79) at org.apache.jena.atlas.json.io.parser.JSONP.parse(JSONP.java:50) at org.apache.jena.atlas.json.io.parser.JSONParser.parse(JSONParser.java:58) at org.apache.jena.atlas.json.io.parser.JSONParser.parse(JSONParser.java:40) at org.apache.jena.atlas.json.JSON._parse(JSON.java:147) at org.apache.jena.atlas.json.JSON.parse(JSON.java:43) at com.hp.hpl.jena.sparql.resultset.JSONInput.parse(JSONInput.java:124) at com.hp.hpl.jena.sparql.resultset.JSONInput.process(JSONInput.java:108) at com.hp.hpl.jena.sparql.resultset.JSONInput.fromJSON(JSONInput.java:65) at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.execSelect(RDFServiceGraph.java:402) at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.find(RDFServiceGraph.java:259) at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.find(RDFServiceGraph.java:191) at com.hp.hpl.jena.graph.GraphUtil.findAll(GraphUtil.java:128) at com.hp.hpl.jena.graph.GraphUtil.addInto(GraphUtil.java:183) at com.hp.hpl.jena.rdf.model.impl.ModelCom.add(ModelCom.java:208) at com.hp.hpl.jena.rdf.model.impl.ModelCom.add(ModelCom.java:202) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.RDFServiceJena.isEquivalentGraph(RDFServiceJena.java:567) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.logging.LoggingRDFService.isEquivalentGraph(LoggingRDFService.java:92) at edu.cornell.mannlib.vitro.webapp.servlet.setup.FileGraphSetup.updateGraphInDB(FileGraphSetup.java:218)

    Sakai JIRA | 2 years ago | Truc Muche
    java.lang.OutOfMemoryError: GC overhead limit exceeded

    Root Cause Analysis

    1. java.lang.OutOfMemoryError

      GC overhead limit exceeded

      at org.apache.jena.atlas.json.io.parser.TokenizerJSON.parseToken()
    2. Apache Jena - ARQ (SPARQL 1.1 Query Engine)
      JSONInput.fromJSON
      1. org.apache.jena.atlas.json.io.parser.TokenizerJSON.parseToken(TokenizerJSON.java:107)
      2. org.apache.jena.atlas.json.io.parser.TokenizerJSON.hasNext(TokenizerJSON.java:63)
      3. org.apache.jena.atlas.iterator.PeekIterator.fill(PeekIterator.java:50)
      4. org.apache.jena.atlas.iterator.PeekIterator.next(PeekIterator.java:92)
      5. org.apache.jena.atlas.json.io.parser.ParserBase.nextToken(ParserBase.java:107)
      6. org.apache.jena.atlas.json.io.parser.JSONP.parseObject(JSONP.java:56)
      7. org.apache.jena.atlas.json.io.parser.JSONP.parseAny(JSONP.java:97)
      8. org.apache.jena.atlas.json.io.parser.JSONP.parseObject(JSONP.java:79)
      9. org.apache.jena.atlas.json.io.parser.JSONP.parseAny(JSONP.java:97)
      10. org.apache.jena.atlas.json.io.parser.JSONP.parseArray(JSONP.java:146)
      11. org.apache.jena.atlas.json.io.parser.JSONP.parseAny(JSONP.java:98)
      12. org.apache.jena.atlas.json.io.parser.JSONP.parseObject(JSONP.java:79)
      13. org.apache.jena.atlas.json.io.parser.JSONP.parseAny(JSONP.java:97)
      14. org.apache.jena.atlas.json.io.parser.JSONP.parseObject(JSONP.java:79)
      15. org.apache.jena.atlas.json.io.parser.JSONP.parse(JSONP.java:50)
      16. org.apache.jena.atlas.json.io.parser.JSONParser.parse(JSONParser.java:58)
      17. org.apache.jena.atlas.json.io.parser.JSONParser.parse(JSONParser.java:40)
      18. org.apache.jena.atlas.json.JSON._parse(JSON.java:147)
      19. org.apache.jena.atlas.json.JSON.parse(JSON.java:43)
      20. com.hp.hpl.jena.sparql.resultset.JSONInput.parse(JSONInput.java:124)
      21. com.hp.hpl.jena.sparql.resultset.JSONInput.process(JSONInput.java:108)
      22. com.hp.hpl.jena.sparql.resultset.JSONInput.fromJSON(JSONInput.java:65)
      22 frames
    3. edu.cornell.mannlib
      RDFServiceGraph.find
      1. edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.execSelect(RDFServiceGraph.java:402)
      2. edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.find(RDFServiceGraph.java:259)
      3. edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.find(RDFServiceGraph.java:191)
      3 frames
    4. Apache Jena - Core
      ModelCom.add
      1. com.hp.hpl.jena.graph.GraphUtil.findAll(GraphUtil.java:128)
      2. com.hp.hpl.jena.graph.GraphUtil.addInto(GraphUtil.java:183)
      3. com.hp.hpl.jena.rdf.model.impl.ModelCom.add(ModelCom.java:208)
      4. com.hp.hpl.jena.rdf.model.impl.ModelCom.add(ModelCom.java:202)
      4 frames
    5. edu.cornell.mannlib
      FileGraphSetup.updateGraphInDB
      1. edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.RDFServiceJena.isEquivalentGraph(RDFServiceJena.java:567)
      2. edu.cornell.mannlib.vitro.webapp.rdfservice.impl.logging.LoggingRDFService.isEquivalentGraph(LoggingRDFService.java:92)
      3. edu.cornell.mannlib.vitro.webapp.servlet.setup.FileGraphSetup.updateGraphInDB(FileGraphSetup.java:218)
      3 frames