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
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> 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, PhD
Biomedical Informatics Research & Development
Instructor of Neurology at Harvard Medical School
Assistant in Neuroscience at Mass General Hospital
Mobile +1-857-366-1524
virtuoso.ini
Description: Binary data
virtuoso.log
Description: Binary data
