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  1. VIVO
  2. VIVO-1028

Ontology loading error

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    Details

    • Type: Bug
    • Status: Open (View Workflow)
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: v1.8, v1.9.0
    • Fix Version/s: None
    • Component/s: Ontology support
    • Labels:
      None
    • Institution:
      University of Toulouse
    • Attachments:
      7
    • Comments:
      3

      Description

      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)

        Attachments

        1. 1st_startup_heap.png
          1st_startup_heap.png
          76 kB
        2. 1st_startup_permgen.png
          1st_startup_permgen.png
          44 kB
        3. 1st_startup.vivo.all.log
          22 kB
        4. 2nd_startup_heap.png
          2nd_startup_heap.png
          52 kB
        5. 2nd_startup_permgen.png
          2nd_startup_permgen.png
          46 kB
        6. 2nd_startup.vivo.all.log
          6 kB
        7. setenv.sh
          0.2 kB

          Activity

            People

            Assignee:
            j2blake Jim Blake
            Reporter:
            louis.c Truc Muche
            Votes:
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            Watchers:
            2 Start watching this issue

              Dates

              Created:
              Updated: