I've been running GraphDB SE for a few months now, with automated scripts querying and inserting into a single repository using the SPARQL API. A week or so ago, I noticed the Sesame Workbench stopped working:

When I visit the repository summary page, I see:

Repository Location
ID  d1lod
Title   d1lod
Location    http://lod.dataone.org:8080/openrdf-sesame/repositories/d1lod
Sesame server   http://lod.dataone.org:8080/openrdf-sesame
Repository Size
Number of Statements    Timed out while requesting repository size.
Number of Labeled Contexts  Timed out while requesting labeled contexts.

Last I checked, my repository is about 34 million triples in size, with no contexts.

When I tail -f my main logfile while I refresh the page, I see:

[ERROR] 2016-03-01 19:48:41,755 [repositories/d1lod | o.o.h.s.ProtocolExceptionResolver] Error while handling request
java.lang.NegativeArraySizeException: null
    at com.ontotext.trree.owlim_ext.d.a(Unknown Source)
    at com.ontotext.trree.owlim_ext.d.a(Unknown Source)
    at com.ontotext.trree.owlim_ext.d.a(Unknown Source)
    at com.ontotext.trree.owlim_ext.d.a(Unknown Source)
    at com.ontotext.trree.owlim_ext.d.a(Unknown Source)
    at com.ontotext.trree.owlim_ext.d.a(Unknown Source)
    at com.ontotext.trree.owlim_ext.d.a(Unknown Source)
    at com.ontotext.trree.owlim_ext.d.a(Unknown Source)
    at com.ontotext.trree.owlim_ext.d.a(Unknown Source)
    at com.ontotext.trree.owlim_ext.d.a(Unknown Source)
    at com.ontotext.trree.owlim_ext.d.a(Unknown Source)
    at com.ontotext.trree.owlim_ext.d.a(Unknown Source)
    at com.ontotext.trree.owlim_ext.d.a(Unknown Source)
    at com.ontotext.trree.owlim_ext.d.a(Unknown Source)
    at com.ontotext.trree.owlim_ext.d.a(Unknown Source)
    at com.ontotext.trree.owlim_ext.d.a(Unknown Source)
    at com.ontotext.trree.owlim_ext.d.a(Unknown Source)
    at com.ontotext.trree.owlim_ext.d.a(Unknown Source)
    at com.ontotext.trree.owlim_ext.d.<init>(Unknown Source)
    at com.ontotext.trree.owlim_ext.Repository.initialize(Unknown Source)
    at com.ontotext.trree.owlim_ext.g.initialize(Unknown Source)
    at com.ontotext.trree.owlim_ext.SailImpl.initialize(Unknown Source)
    at org.openrdf.repository.sail.SailRepository.initializeInternal(SailRepository.java:97)
    at org.openrdf.repository.base.RepositoryBase.initialize(RepositoryBase.java:37)
    at org.openrdf.repository.manager.LocalRepositoryManager.createRepository(LocalRepositoryManager.java:167)
    at org.openrdf.repository.manager.RepositoryManager.getRepository(RepositoryManager.java:376)
    at org.openrdf.http.server.repository.RepositoryInterceptor.setRequestAttributes(RepositoryInterceptor.java:118)
    at org.openrdf.http.server.ServerInterceptor.preHandle(ServerInterceptor.java:45)
    at org.openrdf.http.server.repository.RepositoryInterceptor.preHandle(RepositoryInterceptor.java:98)
    at org.openrdf.http.server.repository.RepositoryInterceptor$$FastClassByCGLIB$$d92044ea.invoke(<generated>)
    at net.sf.cglib.proxy.MethodProxy.invoke(MethodProxy.java:191)
    at org.springframework.aop.framework.Cglib2AopProxy$CglibMethodInvocation.invokeJoinpoint(Cglib2AopProxy.java:700)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149)
    at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:131)
    at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:119)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
    at org.springframework.aop.framework.Cglib2AopProxy$DynamicAdvisedInterceptor.intercept(Cglib2AopProxy.java:635)
    at org.openrdf.http.server.repository.RepositoryInterceptor$$EnhancerByCGLIB$$ec518cda.preHandle(<generated>)
    at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:865)
    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:618)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:725)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:504)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
    at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:534)
    at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1081)
    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:658)
    at org.apache.coyote.http11.Http11NioProtocol$Http11ConnectionHandler.process(Http11NioProtocol.java:222)
    at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1566)
    at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1523)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
    at java.lang.Thread.run(Thread.java:745)

The above error is pretty cryptic (at least to me).

No other aduna log files are generating errors at the same time as this request. I've restarted the entire machine and the problem persists. The java process I have (which runs Apache -> Tomcat -> GraphDB) is steady at around 12% CPU usage and 1.85GB of RAM used. I think I've correctly set the max memory size on the java process to 8GB and the VM has 16GB of RAM.

Any help would be greatly appreciated. Thanks in advance.

asked 01 Mar '16, 15:01

amoeba's gravatar image

amoeba
16112
accept rate: 0%


Hi,

Can you try to refresh the summary page of your repository two times? Does the number of statements and contexts show up after that? Stats are extracted from your reposotory using system queries, which if take too long than the timeout defined internally (1s) would return such results that you observe.

I would encorage you to send the full log file to GraphDB Support (graphdb-support@ontotext.com) with the version of GraphDB that you're using, so that we can further help you with your issue.

Best Regards

link

answered 02 Mar '16, 08:38

Venelin%20Kotsev's gravatar image

Venelin Kotsev
4212
accept rate: 20%

Thanks for the response. Refreshing multiple times makes no difference, though it does take a few seconds to load each time. Each time, I am greeted with the "Timed out.." error messages I included above. I can create new repositories and view their summaries, however.

I'll send along an email as you suggest. Thanks!

link

answered 02 Mar '16, 13:16

amoeba's gravatar image

amoeba
16112
accept rate: 0%

I get the "Timed out while requesting repository size" in the summary page (http://localhost:8080/openrdf-workbench/repositories/iserve/summary) when creating a new repository

Repository Size

Number of Statements Timed out while requesting repository size.

Number of Labeled Contexts Timed out while requesting labeled contexts.

any idea to solve it?

link

answered 28 Mar '16, 10:28

hajar's gravatar image

hajar
1111
accept rate: 0%

Hi Hajar,

do you have access to the created repository, e.g. can you perform updates and selects?

link

answered 28 Mar '16, 10:39

Venelin%20Kotsev's gravatar image

Venelin Kotsev
4212
accept rate: 20%

Hi Venelin, Thanks for the response.

in the summary page, under the SPARQL update, I try the execute the query

INSERT DATA {
    <http://exampleSub> <http://examplePred> <http://exampleObj> .
}

but the application crashes

link

answered 28 Mar '16, 10:57

hajar's gravatar image

hajar
1111
accept rate: 0%

That is strange, it seems that you were not able to create the repository.

Can you please zip-up all graphd logs and send them to us at: graphdb-support@ontotext.com? Also please mention which version of GrahpDB you have.

Your logs should be located by default at ~/.aduna/openrdf-sesame/logs (Linux) or %HOMEPATH%.adunaopenrdf-sesamelogs

link

answered 28 Mar '16, 11:23

Venelin%20Kotsev's gravatar image

Venelin Kotsev
4212
accept rate: 20%

may be I have to apply the matter in another forum, because I did not install GraphDB and my problem is with the sesame Worbench

link

answered 29 Mar '16, 04:38

hajar's gravatar image

hajar
1111
accept rate: 0%

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Asked: 01 Mar '16, 15:01

Seen: 1,570 times

Last updated: 18 Aug '16, 03:28

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