Easier fix that sleeping was to add system wide semaphore which puts all
concurrent requests to single queue.
So the problem is in the way how Fuseki handles situation where
(concurrent) requests are coming in faster that it can process it.
Usually there are 2 ways to handle that: return error to client or sleep
until there is more space in request queue.
Br
On 2.8.2018 17:18, Andy Seaborne wrote:
On 02/08/18 12:56, Mikael Pesonen wrote:
I dont have any configuration, so it's default?
Command line:
/usr/bin/java -Dlog4j.configuration=file:...log4j.properties
-Xmx5600M -jar fuseki-server.jar --update --port 3030
--loc=...jena_data_test/ /ds
log4j.properties is default except couple of INFO -> WARN
On 2.8.2018 12:56, Andy Seaborne wrote:
Fuseki configuration?
The stacktrace isn't GSP.
Im only calling /ds endpoint with php+curl
It says "SPARQL_Update.perform" so it is not GSP.
https://www.w3.org/TR/sparql11-http-rdf-update/
>>> I'm not able to produce a sendable script that
>>> would case these errors.
It (still) looks like there is an environment factor.
Andy
On 02/08/18 10:41, Mikael Pesonen wrote:
3.7.0.
On 2.8.2018 12:40, Andy Seaborne wrote:
version?
On 02/08/18 10:06, Mikael Pesonen wrote:
It does happen in our test environment on high load quite often.
More sleep I put in the test script, less frequently error happens.
Most of the time transactions are executed after the error, but
not always. Fuseki never returns error. Rarely below error
happens, don't know if it's related.
I'm not able to produce a sendable script that would case these
errors.
So as a fix I'm planning just to add enough sleep between every
Fuseki call. 50-100ms seems to work.
org.apache.jena.query.QueryException: Secondary index duplicate:
GSPO->GPOS -> [[0000000000A9D430], [0000000015AFB422],
[0000000000002602], [04007E280A6A5DC0]]
at
org.apache.jena.sparql.lang.ParserARQUpdate._parse(ParserARQUpdate.java:78)
at
org.apache.jena.sparql.lang.ParserARQUpdate.parse$(ParserARQUpdate.java:45)
at
org.apache.jena.sparql.lang.UpdateParser.parse(UpdateParser.java:48)
at
org.apache.jena.update.UpdateAction.parseExecute(UpdateAction.java:421)
at
org.apache.jena.update.UpdateAction.parseExecute(UpdateAction.java:380)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.execute(SPARQL_Update.java:234)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.executeBody(SPARQL_Update.java:189)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.perform(SPARQL_Update.java:106)
at
org.apache.jena.fuseki.servlets.ActionService.executeLifecycle(ActionService.java:192)
at
org.apache.jena.fuseki.servlets.ActionService.execCommonWorker(ActionService.java:106)
at
org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java:73)
at
org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:73)
at
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1637)
at
org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61)
at
org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
at
org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
at
org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
at
org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
at
org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449)
at
org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365)
at
org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)
at
org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)
at
org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383)
at
org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362)
at
org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
at
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1637)
at
org.apache.jena.fuseki.servlets.CrossOriginFilter.handle(CrossOriginFilter.java:285)
at
org.apache.jena.fuseki.servlets.CrossOriginFilter.doFilter(CrossOriginFilter.java:248)
at
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1629)
at
org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:533)
at
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
at
org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548)
at
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
at
org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:190)
at
org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1595)
at
org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:188)
at
org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1253)
at
org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:168)
at
org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:473)
at
org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1564)
at
org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:166)
at
org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1155)
at
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
at
org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:455)
at
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
at org.eclipse.jetty.server.Server.handle(Server.java:561)
at
org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:334)
at
org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:251)
at
org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:279)
at
org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:104)
at
org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:124)
at
org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:247)
at
org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.produce(EatWhatYouKill.java:140)
at
org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131)
at
org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:243)
at
org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:679)
at
org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:597)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.jena.tdb.TDBException: Secondary index
duplicate: GSPO->GPOS -> [[0000000000A9D430], [0000000015AFB422],
[0000000000002602], [04007E280A6A5DC0]]
at
org.apache.jena.tdb.store.tupletable.TupleTable.add(TupleTable.java:103)
at
org.apache.jena.tdb.store.nodetupletable.NodeTupleTableConcrete.addRow(NodeTupleTableConcrete.java:88)
at
org.apache.jena.tdb.store.QuadTable.add(QuadTable.java:60)
at
org.apache.jena.tdb.store.DatasetGraphTDB.addToNamedGraph(DatasetGraphTDB.java:97)
at
org.apache.jena.sparql.core.DatasetGraphTriplesQuads.add(DatasetGraphTriplesQuads.java:44)
at
org.apache.jena.sparql.core.DatasetGraphTriplesQuads.add(DatasetGraphTriplesQuads.java:31)
at
org.apache.jena.sparql.core.DatasetGraphWrapper.add(DatasetGraphWrapper.java:116)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.addToDatasetGraph(UpdateEngineWorker.java:539)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.lambda$execInsert$4(UpdateEngineWorker.java:532)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.execInsert(UpdateEngineWorker.java:532)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.execInsert(UpdateEngineWorker.java:521)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.visit(UpdateEngineWorker.java:418)
at
org.apache.jena.sparql.modify.request.UpdateModify.visit(UpdateModify.java:100)
at
org.apache.jena.sparql.modify.UpdateVisitorSink.send(UpdateVisitorSink.java:46)
at
org.apache.jena.sparql.modify.UpdateVisitorSink.send(UpdateVisitorSink.java:26)
at
org.apache.jena.sparql.modify.UsingUpdateSink.send(UsingUpdateSink.java:61)
at
org.apache.jena.sparql.modify.UsingUpdateSink.send(UsingUpdateSink.java:31)
at
org.apache.jena.sparql.lang.SPARQLParserBase.emitUpdate(SPARQLParserBase.java:189)
at
org.apache.jena.sparql.lang.arq.ARQParser.Update1(ARQParser.java:1491)
at
org.apache.jena.sparql.lang.arq.ARQParser.Update(ARQParser.java:1419)
at
org.apache.jena.sparql.lang.arq.ARQParser.UpdateUnit(ARQParser.java:52)
at
org.apache.jena.sparql.lang.ParserARQUpdate._parse(ParserARQUpdate.java:62)
... 57 more
org.apache.jena.query.QueryException: Secondary index duplicate:
GSPO->GPOS -> [[0000000000A9D430], [0000000015AFB422],
[0000000000002602], [04007E280A6A5DC0]]
at
org.apache.jena.sparql.lang.ParserARQUpdate._parse(ParserARQUpdate.java:78)
at
org.apache.jena.sparql.lang.ParserARQUpdate.parse$(ParserARQUpdate.java:45)
at
org.apache.jena.sparql.lang.UpdateParser.parse(UpdateParser.java:48)
at
org.apache.jena.update.UpdateAction.parseExecute(UpdateAction.java:421)
at
org.apache.jena.update.UpdateAction.parseExecute(UpdateAction.java:380)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.execute(SPARQL_Update.java:234)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.executeBody(SPARQL_Update.java:189)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.perform(SPARQL_Update.java:106)
at
org.apache.jena.fuseki.servlets.ActionService.executeLifecycle(ActionService.java:192)
at
org.apache.jena.fuseki.servlets.ActionService.execCommonWorker(ActionService.java:106)
at
org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java:73)
at
org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:73)
at
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1637)
at
org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61)
at
org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
at
org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
at
org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
at
org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
at
org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449)
at
org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365)
at
org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)
at
org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)
at
org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383)
at
org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362)
at
org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
at
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1637)
at
org.apache.jena.fuseki.servlets.CrossOriginFilter.handle(CrossOriginFilter.java:285)
at
org.apache.jena.fuseki.servlets.CrossOriginFilter.doFilter(CrossOriginFilter.java:248)
at
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1629)
at
org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:533)
at
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
at
org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548)
at
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
at
org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:190)
at
org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1595)
at
org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:188)
at
org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1253)
at
org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:168)
at
org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:473)
at
org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1564)
at
org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:166)
at
org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1155)
at
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
at
org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:455)
at
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
at org.eclipse.jetty.server.Server.handle(Server.java:561)
at
org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:334)
at
org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:251)
at
org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:279)
at
org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:104)
at
org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:124)
at
org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:247)
at
org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.produce(EatWhatYouKill.java:140)
at
org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131)
at
org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:243)
at
org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:679)
at
org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:597)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.jena.tdb.TDBException: Secondary index
duplicate: GSPO->GPOS -> [[0000000000A9D430], [0000000015AFB422],
[0000000000002602], [04007E280A6A5DC0]]
at
org.apache.jena.tdb.store.tupletable.TupleTable.add(TupleTable.java:103)
at
org.apache.jena.tdb.store.nodetupletable.NodeTupleTableConcrete.addRow(NodeTupleTableConcrete.java:88)
at
org.apache.jena.tdb.store.QuadTable.add(QuadTable.java:60)
at
org.apache.jena.tdb.store.DatasetGraphTDB.addToNamedGraph(DatasetGraphTDB.java:97)
at
org.apache.jena.sparql.core.DatasetGraphTriplesQuads.add(DatasetGraphTriplesQuads.java:44)
at
org.apache.jena.sparql.core.DatasetGraphTriplesQuads.add(DatasetGraphTriplesQuads.java:31)
at
org.apache.jena.sparql.core.DatasetGraphWrapper.add(DatasetGraphWrapper.java:116)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.addToDatasetGraph(UpdateEngineWorker.java:539)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.lambda$execInsert$4(UpdateEngineWorker.java:532)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.execInsert(UpdateEngineWorker.java:532)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.execInsert(UpdateEngineWorker.java:521)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.visit(UpdateEngineWorker.java:418)
at
org.apache.jena.sparql.modify.request.UpdateModify.visit(UpdateModify.java:100)
at
org.apache.jena.sparql.modify.UpdateVisitorSink.send(UpdateVisitorSink.java:46)
at
org.apache.jena.sparql.modify.UpdateVisitorSink.send(UpdateVisitorSink.java:26)
at
org.apache.jena.sparql.modify.UsingUpdateSink.send(UsingUpdateSink.java:61)
at
org.apache.jena.sparql.modify.UsingUpdateSink.send(UsingUpdateSink.java:31)
at
org.apache.jena.sparql.lang.SPARQLParserBase.emitUpdate(SPARQLParserBase.java:189)
at
org.apache.jena.sparql.lang.arq.ARQParser.Update1(ARQParser.java:1491)
at
org.apache.jena.sparql.lang.arq.ARQParser.Update(ARQParser.java:1419)
at
org.apache.jena.sparql.lang.arq.ARQParser.UpdateUnit(ARQParser.java:52)
at
org.apache.jena.sparql.lang.ParserARQUpdate._parse(ParserARQUpdate.java:62)
... 57 more
On 2.8.2018 11:03, Andy Seaborne wrote:
(subject line changed - this is not the original thread report)
On 01/08/18 10:32, Mikael Pesonen wrote:
Hi,
is it somehow possible to get this error (TransactionManager
ERROR There are now active transactions ) from Fuseki GSP so
that client could sleep and retry later allowing db to finish
the transaction?
No - it's an internal consistency check.
Does the transaction still happen?
Do you have a reproducible script to make this happen? I've
never seen it occur.
Andy
On 19.6.2018 23:56, Andy Seaborne wrote:
On 18/06/18 11:36, Mikael Pesonen wrote:
On 18.6.2018 13:30, Andy Seaborne wrote:
On 18/06/18 10:55, Mikael Pesonen wrote:
Hi Andy,
On 18.6.2018 12:05, Andy Seaborne wrote:
>>> errors occur less than before.
which errors?
TransactionManager ERROR There are now active transactions
This occurs when Im inserting new data and trying to read it
right away (get empty result), or deleting data and trying to
read it to make sure it's deleted (get data that should be
deleted). There are no other errors in the log.
From looking at the code, I can't see how that happens - is it
now possible to provide a reproducible script so that I can
run it on machine?
Andy
-ku
FINLAND
--
Lingsoft - 30 years of Leading Language Management
www.lingsoft.fi
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Mikael Pesonen
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e-mail: mikael.peso...@lingsoft.fi
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