Re: [Virtuoso-users] Problems with JDBC Connection while performing queries

Thu, 03 Sep 2009 15:51:07 +0000 

Hi Paolo,
Are you making a normal or pooled connection to the database ? As pooled connection would be best if you application/script is making many continuos connects and disconnects during this process as detailed at: 


    	http://docs.openlinksw.com/virtuoso/ 
VirtuosoDriverJDBC.html#jdbc3features


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 2 Sep 2009, at 01:22, Paolo Ciccarese wrote:


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.SimpleGrailsControllerHelp 
er.handleAction(SimpleGrailsControllerHelper.java:368)
    at  
org.codehaus.groovy.grails.web.servlet.mvc.SimpleGrailsControllerHelp 
er.executeAction(SimpleGrailsControllerHelper.java:243)
    at  
org.codehaus.groovy.grails.web.servlet.mvc.SimpleGrailsControllerHelp 
er.handleURI(SimpleGrailsControllerHelper.java:203)
    at  
org.codehaus.groovy.grails.web.servlet.mvc.SimpleGrailsControllerHelp 
er.handleURI(SimpleGrailsControllerHelper.java:138)
    at  
org.codehaus.groovy.grails.web.servlet.mvc.SimpleGrailsController.han 
dleRequest(SimpleGrailsController.java:88)
    at  
org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.ha 
ndle(SimpleControllerHandlerAdapter.java:48)
    at  
org.codehaus.groovy.grails.web.servlet.GrailsDispatcherServlet.doDisp 
atch(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.forwardRequestForUrlMapp 
ingInfo(WebUtils.java:293)
    at  
org.codehaus.groovy.grails.web.util.WebUtils.forwardRequestForUrlMapp 
ingInfo(WebUtils.java:269)
    at  
org.codehaus.groovy.grails.web.util.WebUtils.forwardRequestForUrlMapp 
ingInfo(WebUtils.java:261)
    at  
org.codehaus.groovy.grails.web.mapping.filter.UrlMappingsFilter.doFil 
terInternal(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.obtainConten 
t(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.GrailsReloadServletFilt 
er.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.doF 
ilterInternal(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.doFilterIntern 
al(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$PoolThread.run 
(QueuedThreadPool.java:522)
Caused by:  
org.springframework.jdbc.CannotGetJdbcConnectionException: Could  
not get JDBC Connection; nested exception is  
virtuoso.jdbc3.VirtuosoException: Connection failed: Can't assign  
requested address
    at  
com.commonsemantics.grails.services.utils.QueryService.getSparqlResul 
tRowMaps(QueryService.groovy:23)
    at  
com.commonsemantics.grails.service.indexes.SubclassesIndexingService. 
queryEntity(SubclassesIndexingService.groovy:284)
    at  
com.commonsemantics.grails.service.indexes.SubclassesIndexingService$ 
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.getSparqlResu 
ltRowMaps(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.SubclassesIndexingService 
Tests.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

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