Hi Hugh, I tried with the last driver but I still have the same problems. I am not sure it is helpful but, if I add dummy code to increase the time elapsed in between the queries, it seems behaving much much better (it often completes the task without triggering connection problems).
Thank you for your help Paolo On Tue, Sep 1, 2009 at 6:36 PM, Hugh Williams <hwilli...@openlinksw.com>wrote: > Hi Paolo, > Can you please try using the latest cut of the Virtuoso JDBC Driver to see > how this fares. It can be downloaded from the following FTP URL: > > ftp://download.openlinksw.com/support/vos/virtjdbc3.jar > > Best Regards > Hugh Williams > Professional Services > OpenLink Software > Web: http://www.openlinksw.com > Support: http://support.openlinksw.com > Forums: http://boards.openlinksw.com/support > > > > On 1 Sep 2009, at 18:42, Paolo Ciccarese wrote: > > Hi Hugh, > I increased the memory of the grails application to 1Gb. But it barely > reaches 240Mb. > > I am attaching the virtuoso.ini that I haven't changed and the log file. > This is the exception as I see it in the console (after about 30000 queries > of the same type): > > 2009-09-01 13:34:49,632 [798417047@qtp0-0] ERROR > errors.GrailsExceptionResolver - > org.springframework.jdbc.CannotGetJdbcConnectionException: Could not get > JDBC Connection; nested exception is virtuoso.jdbc3.VirtuosoException: > Connection failed: Can't assign requested address > org.codehaus.groovy.runtime.InvokerInvocationException: > org.springframework.jdbc.CannotGetJdbcConnectionException: Could not get > JDBC Connection; nested exception is virtuoso.jdbc3.VirtuosoException: > Connection failed: Can't assign requested address > at > org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:92) > at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:234) > at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1062) > at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:926) > at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:893) > at groovy.lang.Closure.call(Closure.java:279) > at groovy.lang.Closure.call(Closure.java:274) > at org.codehaus.groovy.grails. > web.servlet.mvc.SimpleGrailsControllerHelper.handleAction > (SimpleGrailsControllerHelper.java:368) > at org.codehaus.groovy.grails. > web.servlet.mvc.SimpleGrailsControllerHelper.executeAction > (SimpleGrailsControllerHelper.java:243) > at org.codehaus.groovy.grails. > web.servlet.mvc.SimpleGrailsControllerHelper.handleURI > (SimpleGrailsControllerHelper.java:203) > at org.codehaus.groovy.grails. > web.servlet.mvc.SimpleGrailsControllerHelper.handleURI > (SimpleGrailsControllerHelper.java:138) > at org.codehaus.groovy.grails. > web.servlet.mvc.SimpleGrailsController.handleRequest > (SimpleGrailsController.java:88) > at org.springframework. > web.servlet.mvc.SimpleControllerHandlerAdapter.handle > (SimpleControllerHandlerAdapter.java:48) > at org.codehaus.groovy.grails. > web.servlet.GrailsDispatcherServlet.doDispatch > (GrailsDispatcherServlet.java:264) > at org.springframework.web.servlet.DispatcherServlet.doService > (DispatcherServlet.java:807) > at org.springframework.web.servlet.FrameworkServlet.processRequest > (FrameworkServlet.java:571) > at org.springframework.web.servlet.FrameworkServlet.doGet > (FrameworkServlet.java:501) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:689) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) > at > org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:502) > at > org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1124) > at org.springframework.web.filter.OncePerRequestFilter.doFilter > (OncePerRequestFilter.java:70) > at > org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1115) > at org.springframework.web.filter.OncePerRequestFilter.doFilter > (OncePerRequestFilter.java:70) > at > org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1115) > at org.springframework.web.filter.OncePerRequestFilter.doFilter > (OncePerRequestFilter.java:70) > at > org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1115) > at > org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:361) > at > org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216) > at > org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:181) > at > org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:766) > at > org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:417) > at org.mortbay.jetty.servlet.Dispatcher.forward(Dispatcher.java:334) > at org.mortbay.jetty.servlet.Dispatcher.forward(Dispatcher.java:126) > at org.codehaus.groovy.grails. > web.util.WebUtils.forwardRequestForUrlMappingInfo(WebUtils.java:293) > at org.codehaus.groovy.grails. > web.util.WebUtils.forwardRequestForUrlMappingInfo(WebUtils.java:269) > at org.codehaus.groovy.grails. > web.util.WebUtils.forwardRequestForUrlMappingInfo(WebUtils.java:261) > at org.codehaus.groovy.grails. > web.mapping.filter.UrlMappingsFilter.doFilterInternal > (UrlMappingsFilter.java:181) > at org.springframework.web.filter.OncePerRequestFilter.doFilter > (OncePerRequestFilter.java:76) > at > org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1115) > at org.codehaus.groovy.grails. > web.sitemesh.GrailsPageFilter.obtainContent(GrailsPageFilter.java:221) > at org.codehaus.groovy.grails.web.sitemesh.GrailsPageFilter.doFilter > (GrailsPageFilter.java:126) > at > org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1115) > at org.codehaus.groovy.grails. > web.servlet.filter.GrailsReloadServletFilter.doFilterInternal > (GrailsReloadServletFilter.java:101) > at org.springframework.web.filter.OncePerRequestFilter.doFilter > (OncePerRequestFilter.java:76) > at > org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1115) > at org.codehaus.groovy.grails. > web.servlet.mvc.GrailsWebRequestFilter.doFilterInternal > (GrailsWebRequestFilter.java:65) > at org.springframework.web.filter.OncePerRequestFilter.doFilter > (OncePerRequestFilter.java:76) > at > org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1115) > at org.springframework. > web.filter.CharacterEncodingFilter.doFilterInternal > (CharacterEncodingFilter.java:96) > at org.springframework.web.filter.OncePerRequestFilter.doFilter > (OncePerRequestFilter.java:76) > at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate > (DelegatingFilterProxy.java:236) > at org.springframework.web.filter.DelegatingFilterProxy.doFilter > (DelegatingFilterProxy.java:167) > at > org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1115) > at > org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:361) > at > org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216) > at > org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:181) > at > org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:766) > at > org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:417) > at > org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152) > at org.mortbay.jetty.Server.handle(Server.java:324) > at > org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:534) > at > org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:864) > at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:533) > at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:207) > at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:403) > at > org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:409) > at > org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:522) > Caused by: org.springframework.jdbc.CannotGetJdbcConnectionException: Could > not get JDBC Connection; nested exception is > virtuoso.jdbc3.VirtuosoException: Connection failed: Can't assign requested > address > at > com.commonsemantics.grails.services.utils.QueryService.getSparqlResultRowMaps(QueryService.groovy:23) > at > com.commonsemantics.grails.service.indexes.SubclassesIndexingService.queryEntity(SubclassesIndexingService.groovy:284) > at > com.commonsemantics.grails.service.indexes.SubclassesIndexingService$queryEntity.callCurrent(Unknown > Source) > at > com.commonsemantics.grails.service.indexes.SubclassesIndexingService.indexHierarchy(SubclassesIndexingService.groovy:173) > at > com.commonsemantics.grails.service.indexes.SubclassesIndexingService.this$2$indexHierarchy(SubclassesIndexingService.groovy) > at > com.commonsemantics.grails.service.indexes.SubclassesIndexingService$this$2$indexHierarchy.callCurrent(Unknown > Source) > at > com.commonsemantics.grails.service.indexes.SubclassesIndexingService.doSecondTraversal(SubclassesIndexingService.groovy:101) > at > com.commonsemantics.grails.service.indexes.SubclassesIndexingService.this$2$doSecondTraversal(SubclassesIndexingService.groovy) > at > com.commonsemantics.grails.service.indexes.SubclassesIndexingService$this$2$doSecondTraversal.callCurrent(Unknown > Source) > at > com.commonsemantics.grails.service.indexes.SubclassesIndexingService.process(SubclassesIndexingService.groovy:82) > at > com.commonsemantics.grails.service.indexes.SubclassesIndexingService.this$2$process(SubclassesIndexingService.groovy) > at > com.commonsemantics.grails.service.indexes.SubclassesIndexingService$this$2$process.callCurrent(Unknown > Source) > at > com.commonsemantics.grails.service.indexes.SubclassesIndexingService.indexVocabulary(SubclassesIndexingService.groovy:75) > at > com.commonsemantics.grails.service.indexes.SubclassesIndexingService$indexVocabulary.callCurrent(Unknown > Source) > at > com.commonsemantics.grails.service.indexes.SubclassesIndexingService.indexVocabularies(SubclassesIndexingService.groovy:66) > at > com.commonsemantics.grails.service.indexes.SubclassesIndexingService$indexVocabularies.call(Unknown > Source) > at > com.commonsemantics.grails.service.indexes.SubclassesController$_closure2.doCall(SubclassesController.groovy:26) > at > com.commonsemantics.grails.service.indexes.SubclassesController$_closure2.doCall(SubclassesController.groovy) > Caused by: virtuoso.jdbc3.VirtuosoException: Connection failed: Can't > assign requested address > at virtuoso.jdbc3.VirtuosoConnection.connect(Unknown Source) > at virtuoso.jdbc3.VirtuosoConnection.connect(Unknown Source) > at virtuoso.jdbc3.VirtuosoConnection.<init>(Unknown Source) > at virtuoso.jdbc3.Driver.connect(Unknown Source) > at java.sql.DriverManager.getConnection(DriverManager.java:582) > at java.sql.DriverManager.getConnection(DriverManager.java:154) > ... 18 more > > > thank you, > Paolo > > On Tue, Sep 1, 2009 at 1:25 PM, Hugh Williams <hwilli...@openlinksw.com>wrote: > >> Hi Paolo, >> How did you increase the amount of available memory ? >> >> Can you provide a copy of your Virtuoso configuration (virtuoso.ini) and >> log (virtuoso.log) files for analysis ... >> >> Best Regards >> Hugh Williams >> Professional Services >> OpenLink Software >> Web: http://www.openlinksw.com >> Support: http://support.openlinksw.com >> Forums: http://boards.openlinksw.com/support >> >> >> >> On 31 Aug 2009, at 17:46, Paolo Ciccarese wrote: >> >> I am currently working on some algorithms for indexing subclasses in >> ontologies expressed in OWL. I therefore traverse the ontology performing a >> list of queries. Unfortunately, most of the times, the indexing process is >> not completing due to the following error: >> >> Could not get JDBC Connection; nested exception is >> virtuoso.jdbc3.VirtuosoException: Connection failed: Can't assign requested >> address >> >> org.springframework.jdbc.CannotGetJdbcConnectionException: Could not get >> JDBC Connection; nested exception is virtuoso.jdbc3.VirtuosoException: >> Connection failed: Can't assign requested address >> at >> com.commonsemantics.grails.services.utils.QueryService.getSparqlResultRowMaps(QueryService.groovy:23) >> at >> com.commonsemantics.grails.services.utils.QueryService$getSparqlResultRowMaps.call(Unknown >> Source) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService.querySubclasses(SubclassesIndexingService.groovy:224) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService$querySubclasses.callCurrent(Unknown >> Source) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService.recursiveIndexing(SubclassesIndexingService.groovy:154) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService.this$2$recursiveIndexing(SubclassesIndexingService.groovy) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService$this$2$recursiveIndexing.callCurrent(Unknown >> Source) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService.recursiveIndexing(SubclassesIndexingService.groovy:163) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService.this$2$recursiveIndexing(SubclassesIndexingService.groovy) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService$this$2$recursiveIndexing.callCurrent(Unknown >> Source) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService.recursiveIndexing(SubclassesIndexingService.groovy:163) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService.this$2$recursiveIndexing(SubclassesIndexingService.groovy) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService$this$2$recursiveIndexing.callCurrent(Unknown >> Source) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService.recursiveIndexing(SubclassesIndexingService.groovy:163) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService.this$2$recursiveIndexing(SubclassesIndexingService.groovy) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService$this$2$recursiveIndexing.callCurrent(Unknown >> Source) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService.recursiveIndexing(SubclassesIndexingService.groovy:163) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService.this$2$recursiveIndexing(SubclassesIndexingService.groovy) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService$this$2$recursiveIndexing.callCurrent(Unknown >> Source) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService.recursiveIndexing(SubclassesIndexingService.groovy:163) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService.this$2$recursiveIndexing(SubclassesIndexingService.groovy) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService$this$2$recursiveIndexing.callCurrent(Unknown >> Source) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService.indexHierarchy(SubclassesIndexingService.groovy:136) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService.this$2$indexHierarchy(SubclassesIndexingService.groovy) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService$this$2$indexHierarchy.callCurrent(Unknown >> Source) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService.indexVocabulary(SubclassesIndexingService.groovy:86) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService$indexVocabulary.callCurrent(Unknown >> Source) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService.indexVocabularies(SubclassesIndexingService.groovy:69) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingService$indexVocabularies.call(Unknown >> Source) >> at >> com.commonsemantics.grails.service.indexes.SubclassesIndexingServiceTests.testSomething(SubclassesIndexingServiceTests.groovy:35) >> at _GrailsTest_groovy$_run_closure4.doCall(_GrailsTest_groovy:203) >> at _GrailsTest_groovy$_run_closure4.call(_GrailsTest_groovy) >> at _GrailsTest_groovy$_run_closure2.doCall(_GrailsTest_groovy:147) >> at >> _GrailsTest_groovy$_run_closure1_closure19.doCall(_GrailsTest_groovy:113) >> at _GrailsTest_groovy$_run_closure1.doCall(_GrailsTest_groovy:96) >> at TestApp$_run_closure1.doCall(TestApp.groovy:66) >> at gant.Gant$_dispatch_closure4.doCall(Gant.groovy:324) >> at gant.Gant$_dispatch_closure6.doCall(Gant.groovy:334) >> at gant.Gant$_dispatch_closure6.doCall(Gant.groovy) >> at gant.Gant.withBuildListeners(Gant.groovy:344) >> at gant.Gant.this$2$withBuildListeners(Gant.groovy) >> at gant.Gant$this$2$withBuildListeners.callCurrent(Unknown Source) >> at gant.Gant.dispatch(Gant.groovy:334) >> at gant.Gant.this$2$dispatch(Gant.groovy) >> at gant.Gant.invokeMethod(Gant.groovy) >> at gant.Gant.processTargets(Gant.groovy:495) >> at gant.Gant.processTargets(Gant.groovy:480) >> Caused by: virtuoso.jdbc3.VirtuosoException: Connection failed: Can't >> assign requested address >> at virtuoso.jdbc3.VirtuosoConnection.connect(Unknown Source) >> at virtuoso.jdbc3.VirtuosoConnection.connect(Unknown Source) >> at virtuoso.jdbc3.VirtuosoConnection.(Unknown Source) >> at virtuoso.jdbc3.Driver.connect(Unknown Source) >> at java.sql.DriverManager.getConnection(DriverManager.java:525) >> at java.sql.DriverManager.getConnection(DriverManager.java:140) >> >> I am working in a Grails (version 1.1.1) environment, Virtuoso (version >> 5.0.11), Drivers (jdbc3). >> >> I am performing really simple queries of the type: >> sparql $NAMESPACE_PREFIXES SELECT ?subject ?label FROM <$vocabularyUri> >> WHERE {?subject rdfs:subClassOf <$uri>. ?subject rdfs:label ?label} >> >> Again, with the same setup, sometimes (rarely) the process completes >> sometimes not. It blows up in different steps of the indexing (can be after >> 129, 876, 3000, 12000... queries). Increasing the amount of memory available >> delays the blow up, but I still have the problem. >> >> Any idea that could help me? >> >> Thank you >> Paolo >> >> -- >> Paolo Ciccarese >> >> ------------------------------------------------------------------------------ >> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >> 30-Day >> trial. Simplify your report design, integration and deployment - and focus >> on >> what you do best, core application coding. Discover what's new with >> Crystal Reports now. >> http://p.sf.net/sfu/bobj-july_______________________________________________ >> Virtuoso-users mailing list >> Virtuoso-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/virtuoso-users >> >> >> > > > -- Paolo Ciccarese
