With in-memory db everything works. Ran ~50000 operations x10 (10
scripts in parallel) and no problems. Mem usage was 3g-5,5g (java
xmx4000) and vm 10g.
So what does this tell? System is upcloud server so there shouldn't be
any issues with disk there...
Br,
On 3.8.2018 16:33, ajs6f wrote:
That seems a bit strange. I would think that the single dataset lock and
multiple-reader-or-single-writer policy would guard against this-- only one
thread (request) can mutate the dataset at a time. Or is this a problem with
TDB? Do you see this occurring with in-memory datasets?
ajs6f
On Aug 3, 2018, at 8:01 AM, Mikael Pesonen <mikael.peso...@lingsoft.fi> wrote:
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
Speech Applications - Language Management - Translation - Reader's and Writer's
Tools - Text Tools - E-books and M-books
Mikael Pesonen
System Engineer
e-mail: mikael.peso...@lingsoft.fi
Tel. +358 2 279 3300
Time zone: GMT+2
Helsinki Office
Eteläranta 10
FI-00130 Helsinki
FINLAND
Turku Office
Kauppiaskatu 5 A
FI-20100 Turku
FINLAND
--
Lingsoft - 30 years of Leading Language Management
www.lingsoft.fi
Speech Applications - Language Management - Translation - Reader's and Writer's
Tools - Text Tools - E-books and M-books
Mikael Pesonen
System Engineer
e-mail: mikael.peso...@lingsoft.fi
Tel. +358 2 279 3300
Time zone: GMT+2
Helsinki Office
Eteläranta 10
FI-00130 Helsinki
FINLAND
Turku Office
Kauppiaskatu 5 A
FI-20100 Turku
FINLAND
