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https://issues.apache.org/jira/browse/JENA-515?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13743620#comment-13743620
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Andy Seaborne commented on JENA-515:
------------------------------------
The issue is that the one request isn't the sole cause of the problem. Heap is
a global resource for the whole JVM and it can be that no one single part of
the system is responsible for running out of memory; it's the combination of
uses of heap together being too much for the heap provided. When heap runs
out, all active threads in the system are damaged. The validity of the system
is not known.
What would better address your requirement for running with a small heap is to
tune down some of the internal parameters which are currently fixed (it can be
done but only in java currently).
BTW as part of JENA-516, doPost has been rewritten.
> Incorrectly error message "Currently in a transaction" when querying SPARQL
> ---------------------------------------------------------------------------
>
> Key: JENA-515
> URL: https://issues.apache.org/jira/browse/JENA-515
> Project: Apache Jena
> Issue Type: Bug
> Components: Fuseki, TDB
> Affects Versions: TDB 0.10.1
> Reporter: Knut-Olav Hoven
> Assignee: Stephen Allen
>
> This has happened after a OutOfMemoryError during import (batched import of
> 1000 resources per request).
> Fetching entire database with curl works OK:
> http://localhost:3030/ds/data?graph=sift-tprogram
> When querying with SPARQL I get an 500 error "Currently in a transaction".
> No other clients are active.
> Log output:
> {code}
> 15:27:01 INFO Fuseki :: [73] GET
> http://localhost:3030/ds/query?query=PREFIX+sift%3A+%3Chttp%3A%2F%2Fgluon.nrk.no%2F2013%2Fsift%23%3E%0D%0APREFIX+prog%3A+%3Chttp%3A%2F%2Fgluon.nrk.no%2F2013%2Fsift-program%23%3E%0D%0A%0D%0ASELECT+*%0D%0AFROM+%3Chttp%3A%2F%2Flocalhost%3A3030%2Fds%2Fdata%2Fsift-tprogram%3E%0D%0A%7B%0D%0A%3Fs+sift%3Akeys+%222005%2F02952%22+.%0D%0A%3Fs+%3Fp+%3Fo%0D%0A%7D%0D%0ALIMIT+1000&output=text&stylesheet=%2Fxml-to-html.xsl&force-accept=text%2Fplain
> 15:27:01 INFO Fuseki :: [73] Query = PREFIX sift:
> <http://gluon.nrk.no/2013/sift#> PREFIX prog:
> <http://gluon.nrk.no/2013/sift-program#> SELECT * FROM
> <http://localhost:3030/ds/data/sift-tprogram> { ?s sift:keys "2005/02952" .
> ?s ?p ?o } LIMIT 1000
> 15:27:02 WARN Fuseki :: [73] RC = 500 : Currently in a
> transaction (location:/home/n21759/var/jena-fuseki/db/)
> com.hp.hpl.jena.sparql.JenaTransactionException: Currently in a transaction
> (location:/home/n21759/var/jena-fuseki/db/)
> at
> com.hp.hpl.jena.tdb.transaction.DatasetGraphTransaction.checkNotActive(DatasetGraphTransaction.java:125)
> at
> com.hp.hpl.jena.sparql.core.DatasetGraphTrackActive.begin(DatasetGraphTrackActive.java:44)
> at
> org.apache.jena.fuseki.servlets.HttpAction.beginRead(HttpAction.java:118)
> at
> org.apache.jena.fuseki.servlets.SPARQL_Query.execute(SPARQL_Query.java:234)
> at
> org.apache.jena.fuseki.servlets.SPARQL_Query.executeWithParameter(SPARQL_Query.java:193)
> at
> org.apache.jena.fuseki.servlets.SPARQL_Query.perform(SPARQL_Query.java:78)
> at
> org.apache.jena.fuseki.servlets.SPARQL_ServletBase.executeLifecycle(SPARQL_ServletBase.java:185)
> at
> org.apache.jena.fuseki.servlets.SPARQL_ServletBase.executeAction(SPARQL_ServletBase.java:166)
> at
> org.apache.jena.fuseki.servlets.SPARQL_ServletBase.execCommonWorker(SPARQL_ServletBase.java:154)
> at
> org.apache.jena.fuseki.servlets.SPARQL_ServletBase.doCommon(SPARQL_ServletBase.java:73)
> at
> org.apache.jena.fuseki.servlets.SPARQL_Query.doGet(SPARQL_Query.java:59)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:735)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
> at
> org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
> at
> org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1448)
> at
> org.eclipse.jetty.servlets.UserAgentFilter.doFilter(UserAgentFilter.java:82)
> at org.eclipse.jetty.servlets.GzipFilter.doFilter(GzipFilter.java:294)
> at
> org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1419)
> at
> org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:455)
> at
> org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:229)
> at
> org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1075)
> at
> org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:384)
> at
> org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
> at
> org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1009)
> at
> org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
> at
> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
> at org.eclipse.jetty.server.Server.handle(Server.java:370)
> at
> org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:489)
> at
> org.eclipse.jetty.server.BlockingHttpConnection.handleRequest(BlockingHttpConnection.java:53)
> at
> org.eclipse.jetty.server.AbstractHttpConnection.headerComplete(AbstractHttpConnection.java:949)
> at
> org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.headerComplete(AbstractHttpConnection.java:1011)
> at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:644)
> at
> org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235)
> at
> org.eclipse.jetty.server.BlockingHttpConnection.handle(BlockingHttpConnection.java:72)
> at
> org.eclipse.jetty.server.nio.BlockingChannelConnector$BlockingChannelEndPoint.run(BlockingChannelConnector.java:298)
> at
> org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
> at
> org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
> at java.lang.Thread.run(Thread.java:722)
> 15:27:02 INFO Fuseki :: [73] 500 Currently in a transaction
> (location:/home/n21759/var/jena-fuseki/db/) (601 ms)
> {code}
> Log message of the OutOfMemoryError:
> {code}
> java.lang.OutOfMemoryError: Java heap space
> Dumping heap to java_pid28296.hprof ...
> Heap dump file created [280365745 bytes in 2.986 secs]
> 15:10:27 WARN HttpAction :: Transaction still active in endWriter
> - no commit or abort seen (forced abort)
> 15:10:28 WARN HttpAction :: Exception in forced abort (trying to
> continue)
> 15:10:40 WARN Fuseki :: [66] RC = 500 : Java heap space
> java.lang.OutOfMemoryError: Java heap space
> at java.util.Arrays.copyOf(Arrays.java:2367)
> at
> java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:130)
> at
> java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:114)
> at
> java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:415)
> at java.lang.StringBuffer.append(StringBuffer.java:237)
> at java.io.StringWriter.write(StringWriter.java:112)
> at java.io.PrintWriter.write(PrintWriter.java:456)
> at java.io.PrintWriter.write(PrintWriter.java:473)
> at java.io.PrintWriter.print(PrintWriter.java:603)
> at java.io.PrintWriter.println(PrintWriter.java:756)
> at java.lang.Throwable$WrappedPrintWriter.println(Throwable.java:763)
> at java.lang.Throwable.printStackTrace(Throwable.java:657)
> at java.lang.Throwable.printStackTrace(Throwable.java:720)
> at
> org.apache.log4j.DefaultThrowableRenderer.render(DefaultThrowableRenderer.java:60)
> at
> org.apache.log4j.spi.ThrowableInformation.getThrowableStrRep(ThrowableInformation.java:87)
> at
> org.apache.log4j.spi.LoggingEvent.getThrowableStrRep(LoggingEvent.java:413)
> at org.apache.log4j.WriterAppender.subAppend(WriterAppender.java:313)
> at org.apache.log4j.WriterAppender.append(WriterAppender.java:162)
> at
> org.apache.log4j.AppenderSkeleton.doAppend(AppenderSkeleton.java:251)
> at
> org.apache.log4j.helpers.AppenderAttachableImpl.appendLoopOnAppenders(AppenderAttachableImpl.java:66)
> at org.apache.log4j.Category.callAppenders(Category.java:206)
> at org.apache.log4j.Category.forcedLog(Category.java:391)
> at org.apache.log4j.Category.log(Category.java:856)
> at org.slf4j.impl.Log4jLoggerAdapter.warn(Log4jLoggerAdapter.java:479)
> at org.apache.jena.atlas.logging.Log.warn(Log.java:160)
> at org.apache.jena.atlas.logging.Log.warn(Log.java:155)
> at
> org.apache.jena.fuseki.servlets.HttpAction.endWrite(HttpAction.java:156)
> at
> org.apache.jena.fuseki.servlets.SPARQL_REST_RW.doPost(SPARQL_REST_RW.java:97)
> at
> org.apache.jena.fuseki.servlets.SPARQL_REST.doPost$(SPARQL_REST.java:246)
> at
> org.apache.jena.fuseki.servlets.SPARQL_REST.dispatch(SPARQL_REST.java:203)
> at
> org.apache.jena.fuseki.servlets.SPARQL_REST.perform(SPARQL_REST.java:190)
> at
> org.apache.jena.fuseki.servlets.SPARQL_ServletBase.executeLifecycle(SPARQL_ServletBase.java:185)
> 15:10:41 INFO Fuseki :: [66] 500 Java heap space (73.238 s)
> 15:10:41 INFO Fuseki :: [67] POST
> http://localhost:3030/ds/data?graph=sift-tprogram
> 15:11:06 WARN Fuseki :: [67] RC = 500 : Java heap space
> java.lang.OutOfMemoryError: Java heap space
> at java.util.Arrays.copyOfRange(Arrays.java:2694)
> at java.lang.String.<init>(String.java:203)
> at java.lang.StringBuilder.toString(StringBuilder.java:405)
> at
> org.apache.jena.riot.tokens.TokenizerText.readIRI(TokenizerText.java:477)
> at
> org.apache.jena.riot.tokens.TokenizerText.parseToken(TokenizerText.java:192)
> at
> org.apache.jena.riot.tokens.TokenizerText.hasNext(TokenizerText.java:89)
> at
> org.apache.jena.atlas.iterator.PeekIterator.fill(PeekIterator.java:50)
> at
> org.apache.jena.atlas.iterator.PeekIterator.next(PeekIterator.java:92)
> at org.apache.jena.riot.lang.LangEngine.nextToken(LangEngine.java:99)
> at org.apache.jena.riot.lang.LangEngine.expect(LangEngine.java:143)
> at
> org.apache.jena.riot.lang.LangEngine.expectOrEOF(LangEngine.java:128)
> at
> org.apache.jena.riot.lang.LangTurtleBase.expectEndOfTriplesTurtle(LangTurtleBase.java:258)
> at
> org.apache.jena.riot.lang.LangTurtle.expectEndOfTriples(LangTurtle.java:49)
> at
> org.apache.jena.riot.lang.LangTurtleBase.triples(LangTurtleBase.java:243)
> at
> org.apache.jena.riot.lang.LangTurtleBase.triplesSameSubject(LangTurtleBase.java:186)
> at
> org.apache.jena.riot.lang.LangTurtle.oneTopLevelElement(LangTurtle.java:44)
> at
> org.apache.jena.riot.lang.LangTurtleBase.runParser(LangTurtleBase.java:90)
> at org.apache.jena.riot.lang.LangBase.parse(LangBase.java:42)
> at
> org.apache.jena.fuseki.servlets.SPARQL_REST.parse(SPARQL_REST.java:417)
> at
> org.apache.jena.fuseki.servlets.SPARQL_REST.parseBody(SPARQL_REST.java:406)
> at
> org.apache.jena.fuseki.servlets.SPARQL_REST_RW.doPost(SPARQL_REST_RW.java:87)
> at
> org.apache.jena.fuseki.servlets.SPARQL_REST.doPost$(SPARQL_REST.java:246)
> at
> org.apache.jena.fuseki.servlets.SPARQL_REST.dispatch(SPARQL_REST.java:203)
> at
> org.apache.jena.fuseki.servlets.SPARQL_REST.perform(SPARQL_REST.java:190)
> at
> org.apache.jena.fuseki.servlets.SPARQL_ServletBase.executeLifecycle(SPARQL_ServletBase.java:185)
> at
> org.apache.jena.fuseki.servlets.SPARQL_ServletBase.executeAction(SPARQL_ServletBase.java:166)
> at
> org.apache.jena.fuseki.servlets.SPARQL_ServletBase.execCommonWorker(SPARQL_ServletBase.java:154)
> at
> org.apache.jena.fuseki.servlets.SPARQL_ServletBase.doCommon(SPARQL_ServletBase.java:73)
> at
> org.apache.jena.fuseki.servlets.SPARQL_REST.service(SPARQL_REST.java:180)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
> at
> org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
> at
> org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1448)
> 15:11:06 INFO Fuseki :: [67] 500 Java heap space (25.723 s)
> {code}
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