chenejac
commented
9 years ago Jim Blake said:
Thank you Louis. I will have a look and let you know what I find.
Open chenejac opened 9 years ago
chenejac
commented
9 years ago Jim Blake said:
Thank you Louis. I will have a look and let you know what I find.
chenejac
commented
9 years ago Jim Blake said:
Louis: I am not able to reproduce this problem. Perhaps you can tell me in more detail how to do so?
I started with the distributed release, running in Tomcat 7.0.53 on a MacBook Pro with OS X 10.9.5, and java version "1.7.0_51" Java(TM) SE Runtime Environment (build 1.7.0_51-b13) Java HotSpot(TM) 64-Bit Server VM (build 24.51-b03, mixed mode)
I allocated 1 gigabyte of memory to Tomcat (see attached setenv.sh).
I created an empty database for the test.
I started Tomcat and quickly attached jvisualvm to it, so I could monitor memory usage. When the startup was complete, I shut it down (see attached log and images).
I started Tomcat again, and again monitored with jvisualvm. The startup completed successfully, and again I shut down Tomcat (see attached log and images).
chenejac
commented
9 years ago Truc Muche said:
Thank you for you work.
I don't know what can i can give you in addition of my message... What do you want exactly ? Have you any idea of what can cause that kind of bug so i can look somewhere ? I don't have access to server until next monday, but i know it runs on :
I will try with your setenv.sh file next monday.
Regards, Louis C.
Truc Muche (Migrated from VIVO-1028) said:
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)