SQ 5.1.1 - Sonar Scan hangs at "Store results in database"

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Vara Prasad

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Jun 23, 2015, 5:36:22 AM6/23/15

to sona...@googlegroups.com

Hi,

We are seeing a hang in sonar analysis on Sonar 5.1.1 (With sonar xml plugin 1.2) after the below line in sonar-runner console output

14:05:57.370 INFO - Store results in database

From the thread dump, found that below is the call stack
"main" prio=10 tid=0x0000000006930000 nid=0x1225 runnable [0x00002b501940c000]
   java.lang.Thread.State: RUNNABLE
    at org.sonar.xml.XmlStartElementTokenizer.consumeAttributeValueUntilQuoteOrEol(XmlStartElementTokenizer.java:142)
    at org.sonar.xml.XmlStartElementTokenizer.consumeStartElement(XmlStartElementTokenizer.java:102)
    at org.sonar.xml.XmlStartElementTokenizer.consume(XmlStartElementTokenizer.java:70)
    at org.sonar.xml.XmlStartElementTokenizer.consume(XmlStartElementTokenizer.java:33)
    at org.sonar.colorizer.TokenizerDispatcher.colorize(TokenizerDispatcher.java:50)
    at org.sonar.batch.source.HighlightingRenderer.render(HighlightingRenderer.java:40)
    at org.sonar.batch.source.CodeColorizers.toSyntaxHighlighting(CodeColorizers.java:86)
    at org.sonar.batch.index.SourceDataFactory.applyHighlighting(SourceDataFactory.java:200)
    at org.sonar.batch.index.SourceDataFactory.consolidateData(SourceDataFactory.java:78)
    at org.sonar.batch.index.SourcePersister.computeData(SourcePersister.java:152)
    at org.sonar.batch.index.SourcePersister.persist(SourcePersister.java:93)
    at org.sonar.batch.index.SourcePersister.persist(SourcePersister.java:81)
---
---
---

Upon further debugging we found that the issue with a file with xml extension which is having binary data.
The run hangs only on 5.1.1, however on 4.5.1 (with sonar xml plugin 1.2.) even though the same file is in the source, the run succeeds.

On 4.5.1 and 5.1.1 we are seeing a message like below for this file.
13:41:21.967 WARN - Unable to anayle file <some_dir>/test.xml 13:41:21.967 WARN - Cause: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.

Is there any changes in 5.1.1 which is causing this hang ?

With Regards,
Vara Prasad.

Julien HENRY

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Jun 25, 2015, 3:43:24 AM6/25/15

to sona...@googlegroups.com, varapra...@gmail.com, Linda Martin

Hi Vara,

Is there any changes in 5.1.1 which is causing this hang ?

Yes. Previously the code colorization was dynamically applied on server side each time the file was displayed. In 5.1 we decided to compute the colorization once for all during the batch analysis. So I think the issue you are facing was already present in 4.5 but only when trying to display the file in SQ server.

Anyway this looks like a bug in XML plugin (I'll let Linda confirm). Would you be able to share the offending file as a reproducer?

Thanks

Julien

talk2d...@gmail.com

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Aug 24, 2015, 3:27:49 AM8/24/15

to SonarQube

I am facing similar issue with sonar version 4.5.1. Is there any solution or workaround for this issue?

Sonar analysis is hung at "Store results in database" . However, I do not have sonar xml plugin installed in my sonarQube. I have java, javascript and web plugins (+ pmd, checkstyle and cobertura)

Regards,

Darshan

Freddy Mallet

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Aug 24, 2015, 9:47:06 AM8/24/15

to talk2d...@gmail.com, SonarQube

Hi Darshan and Vara,

To help us clearly understanding what happens and so to fix this issue, would it be possible for you to use for instance "Visual VM" (https://visualvm.java.net/) or similar profiling tool to perfectly understand where the time is spent ? In worth case Darshan, could you also do a thread dump ?

Thanks

Freddy MALLET | SonarSource

Product Director & Co-Founder
http://sonarsource.com

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Darshan Thakkar

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Aug 24, 2015, 3:16:21 PM8/24/15

to Freddy Mallet, SonarQube

Hi Freddy,

Here is the Thread dump as requested...

[INFO] [14:02:12.646] Store results in database
2015-08-24 14:07:35
Full thread dump Java HotSpot(TM) 64-Bit Server VM (20.4-b02 mixed mode):

"pool-2-thread-1" prio=10 tid=0x00007fd1e50e0000 nid=0x4a84 waiting on condition [0x00007fd1ba6c3000]
   java.lang.Thread.State: TIMED_WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x000000070e4619c0> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:196)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2025)
	at java.util.concurrent.DelayQueue.take(DelayQueue.java:164)
	at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:609)
	at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:602)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"CLEANUP_MANAGER" prio=10 tid=0x00007fd1e4e38800 nid=0x4a73 in Object.wait() [0x00007fd1b98b1000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at com.persistit.IOTaskRunnable.run(IOTaskRunnable.java:173)
	- locked <0x000000070e309da8> (a com.persistit.CleanupManager)
	at java.lang.Thread.run(Thread.java:662)

"CHECKPOINT_WRITER" prio=10 tid=0x00007fd1e4eda000 nid=0x4a72 in Object.wait() [0x00007fd1b99b2000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at com.persistit.IOTaskRunnable.run(IOTaskRunnable.java:173)
	- locked <0x000000070e31dff8> (a com.persistit.CheckpointManager)
	at java.lang.Thread.run(Thread.java:662)

"TXN_UPDATE" prio=10 tid=0x00007fd1e50d6800 nid=0x4a71 in Object.wait() [0x00007fd1b9ab3000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at com.persistit.IOTaskRunnable.run(IOTaskRunnable.java:173)
	- locked <0x000000070e45ce70> (a com.persistit.TransactionIndex$ActiveTransactionCachePollTask)
	at java.lang.Thread.run(Thread.java:662)

"PAGE_WRITER:8192" prio=10 tid=0x00007fd1e50bf000 nid=0x4a70 in Object.wait() [0x00007fd1b9bb4000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at com.persistit.IOTaskRunnable.run(IOTaskRunnable.java:173)
	- locked <0x000000070e49b0d8> (a com.persistit.BufferPool$PageWriter)
	at java.lang.Thread.run(Thread.java:662)

"JOURNAL_FLUSHER" prio=10 tid=0x00007fd1e4e2e800 nid=0x4a6f in Object.wait() [0x00007fd1b9cb5000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at com.persistit.IOTaskRunnable.run(IOTaskRunnable.java:173)
	- locked <0x000000070e4abe28> (a com.persistit.JournalManager$JournalFlusher)
	at java.lang.Thread.run(Thread.java:662)

"JOURNAL_COPIER" prio=10 tid=0x00007fd1e4ef1000 nid=0x4a6e in Object.wait() [0x00007fd1b9db6000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at com.persistit.IOTaskRunnable.run(IOTaskRunnable.java:173)
	- locked <0x000000070e36bfe0> (a com.persistit.JournalManager$JournalCopier)
	at java.lang.Thread.run(Thread.java:662)

"LOG_FLUSHER" daemon prio=10 tid=0x00007fd1e45eb800 nid=0x4a65 waiting on condition [0x00007fd1b9eb7000]
   java.lang.Thread.State: TIMED_WAITING (sleeping)
	at java.lang.Thread.sleep(Native Method)
	at com.persistit.util.Util.sleep(Util.java:558)
	at com.persistit.Persistit$LogFlusher.run(Persistit.java:188)

"Abandoned connection cleanup thread" daemon prio=10 tid=0x00007fd1e4d44800 nid=0x4a44 in Object.wait() [0x00007fd1ba19a000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
	- locked <0x000000070dc996f0> (a java.lang.ref.ReferenceQueue$Lock)
	at com.mysql.jdbc.AbandonedConnectionCleanupThread.run(AbandonedConnectionCleanupThread.java:40)

"Low Memory Detector" daemon prio=10 tid=0x00007fd1e4222000 nid=0x4989 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread1" daemon prio=10 tid=0x00007fd1e421f800 nid=0x4988 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread0" daemon prio=10 tid=0x00007fd1e421d800 nid=0x4987 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Signal Dispatcher" daemon prio=10 tid=0x00007fd1e421b000 nid=0x4986 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Surrogate Locker Thread (Concurrent GC)" daemon prio=10 tid=0x00007fd1e4219000 nid=0x4985 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Finalizer" daemon prio=10 tid=0x00007fd1e41fc800 nid=0x4984 in Object.wait() [0x00007fd1bae5e000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
	- locked <0x000000070a062200> (a java.lang.ref.ReferenceQueue$Lock)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
	at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)

"Reference Handler" daemon prio=10 tid=0x00007fd1e41fa800 nid=0x4983 in Object.wait() [0x00007fd1baf5f000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:485)
	at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
	- locked <0x000000070a062380> (a java.lang.ref.Reference$Lock)

"main" prio=10 tid=0x00007fd1e4007800 nid=0x496e waiting on condition [0x00007fd1ebb86000]
   java.lang.Thread.State: RUNNABLE
	at java.util.HashMap.<init>(HashMap.java:209)
	at org.apache.ibatis.executor.resultset.DefaultResultSetHandler.<init>(DefaultResultSetHandler.java:80)
	at org.apache.ibatis.session.Configuration.newResultSetHandler(Configuration.java:462)
	at org.apache.ibatis.executor.statement.BaseStatementHandler.<init>(BaseStatementHandler.java:70)
	at org.apache.ibatis.executor.statement.PreparedStatementHandler.<init>(PreparedStatementHandler.java:39)
	at org.apache.ibatis.executor.statement.RoutingStatementHandler.<init>(RoutingStatementHandler.java:45)
	at org.apache.ibatis.session.Configuration.newStatementHandler(Configuration.java:468)
	at org.apache.ibatis.executor.BatchExecutor.doUpdate(BatchExecutor.java:55)
	at org.apache.ibatis.executor.BaseExecutor.update(BaseExecutor.java:105)
	at org.apache.ibatis.executor.CachingExecutor.update(CachingExecutor.java:71)
	at org.apache.ibatis.session.defaults.DefaultSqlSession.update(DefaultSqlSession.java:152)
	at org.apache.ibatis.session.defaults.DefaultSqlSession.insert(DefaultSqlSession.java:141)
	at org.sonar.core.persistence.DbSession.insert(DbSession.java:137)
	at org.sonar.core.persistence.BatchSession.insert(BatchSession.java:128)
	at org.apache.ibatis.binding.MapperMethod.execute(MapperMethod.java:51)
	at org.apache.ibatis.binding.MapperProxy.invoke(MapperProxy.java:52)
	at $Proxy80.insert(Unknown Source)
	at org.sonar.batch.index.MeasurePersister.persist(MeasurePersister.java:71)
	at org.sonar.batch.phases.PhaseExecutor.executePersisters(PhaseExecutor.java:145)
	at org.sonar.batch.phases.PhaseExecutor.execute(PhaseExecutor.java:129)
	at org.sonar.batch.scan.ModuleScanContainer.doAfterStart(ModuleScanContainer.java:194)
	at org.sonar.api.platform.ComponentContainer.startComponents(ComponentContainer.java:92)
	at org.sonar.api.platform.ComponentContainer.execute(ComponentContainer.java:77)
	at org.sonar.batch.scan.ProjectScanContainer.scan(ProjectScanContainer.java:233)
	at org.sonar.batch.scan.ProjectScanContainer.scanRecursively(ProjectScanContainer.java:228)
	at org.sonar.batch.scan.ProjectScanContainer.doAfterStart(ProjectScanContainer.java:221)
	at org.sonar.api.platform.ComponentContainer.startComponents(ComponentContainer.java:92)
	at org.sonar.api.platform.ComponentContainer.execute(ComponentContainer.java:77)
	at org.sonar.batch.scan.ScanTask.scan(ScanTask.java:64)
	at org.sonar.batch.scan.ScanTask.execute(ScanTask.java:51)
	at org.sonar.batch.bootstrap.TaskContainer.doAfterStart(TaskContainer.java:125)
	at org.sonar.api.platform.ComponentContainer.startComponents(ComponentContainer.java:92)
	at org.sonar.api.platform.ComponentContainer.execute(ComponentContainer.java:77)
	at org.sonar.batch.bootstrap.BootstrapContainer.executeTask(BootstrapContainer.java:173)
	at org.sonar.batch.bootstrapper.Batch.executeTask(Batch.java:95)
	at org.sonar.batch.bootstrapper.Batch.execute(Batch.java:67)
	- locked <0x000000070d8aec28> (a org.sonar.batch.bootstrapper.Batch)
	at org.sonar.runner.batch.IsolatedLauncher.execute(IsolatedLauncher.java:48)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.sonar.runner.impl.BatchLauncher$1.delegateExecution(BatchLauncher.java:87)
	at org.sonar.runner.impl.BatchLauncher$1.run(BatchLauncher.java:75)
	at java.security.AccessController.doPrivileged(Native Method)
	at org.sonar.runner.impl.BatchLauncher.doExecute(BatchLauncher.java:69)
	at org.sonar.runner.impl.BatchLauncher.execute(BatchLauncher.java:50)
	at org.sonar.runner.api.EmbeddedRunner.doExecute(EmbeddedRunner.java:102)
	at org.sonar.runner.api.Runner.execute(Runner.java:100)
	at org.sonar.maven.SonarMojo.execute(SonarMojo.java:173)
	at org.codehaus.mojo.sonar.Bootstraper.executeMojo(Bootstraper.java:104)
	at org.codehaus.mojo.sonar.Bootstraper.start(Bootstraper.java:67)
	at org.codehaus.mojo.sonar.SonarMojo.execute(SonarMojo.java:109)
	at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:84)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59)
	at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183)
	at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:320)
	at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156)
	at org.apache.maven.cli.MavenCli.execute(MavenCli.java:537)
	at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:196)
	at org.apache.maven.cli.MavenCli.main(MavenCli.java:141)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:290)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:230)
	at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:409)
	at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:352)

"VM Thread" prio=10 tid=0x00007fd1e41f4000 nid=0x4982 runnable 

"Gang worker#0 (Parallel GC Threads)" prio=10 tid=0x00007fd1e4016000 nid=0x4977 runnable 

"Gang worker#1 (Parallel GC Threads)" prio=10 tid=0x00007fd1e4018000 nid=0x4978 runnable 

"Gang worker#2 (Parallel GC Threads)" prio=10 tid=0x00007fd1e4019800 nid=0x4979 runnable 

"Gang worker#3 (Parallel GC Threads)" prio=10 tid=0x00007fd1e401b800 nid=0x497a runnable 

"Gang worker#4 (Parallel GC Threads)" prio=10 tid=0x00007fd1e401d000 nid=0x497b runnable 

"Gang worker#5 (Parallel GC Threads)" prio=10 tid=0x00007fd1e401f000 nid=0x497c runnable 

"Gang worker#6 (Parallel GC Threads)" prio=10 tid=0x00007fd1e4021000 nid=0x497d runnable 

"Gang worker#7 (Parallel GC Threads)" prio=10 tid=0x00007fd1e4022800 nid=0x497e runnable 

"Concurrent Mark-Sweep GC Thread" prio=10 tid=0x00007fd1e4116800 nid=0x4981 runnable 
"Gang worker#0 (Parallel CMS Threads)" prio=10 tid=0x00007fd1e4112800 nid=0x497f runnable 

"Gang worker#1 (Parallel CMS Threads)" prio=10 tid=0x00007fd1e4114800 nid=0x4980 runnable 

"VM Periodic Task Thread" prio=10 tid=0x00007fd1e422d000 nid=0x498a waiting on condition 

JNI global references: 1393

Heap
 par new generation   total 153344K, used 2829K [0x00000006ffa00000, 0x000000070a060000, 0x000000070a060000)
  eden space 136320K,   1% used [0x00000006ffa00000, 0x00000006ffca06d0, 0x0000000707f20000)
  from space 17024K,   0% used [0x0000000707f20000, 0x0000000707f42e40, 0x0000000708fc0000)
  to   space 17024K,   0% used [0x0000000708fc0000, 0x0000000708fc0000, 0x000000070a060000)
 concurrent mark-sweep generation total 2981504K, used 961128K [0x000000070a060000, 0x00000007c0000000, 0x00000007c0000000)
 concurrent-mark-sweep perm gen total 224612K, used 130306K [0x00000007c0000000, 0x00000007cdb59000, 0x0000000800000000)

Regards,

Darshan

ronny....@googlemail.com

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Aug 28, 2015, 6:00:17 AM8/28/15

to SonarQube

Hi,

we're having the same issue with SonarQube 5.1.2 and XML plugin 1.3. SonarRunner enters an infinite loop drawing 100% CPU time after reaching "Execute org.sonar.batch.index.SourcePersister" in the debug log

11:16:00.810 INFO - Store results in database
11:16:00.810 DEBUG - Execute org.sonar.batch.phases.GraphPersister
11:16:00.845 DEBUG - Execute org.sonar.batch.index.SourcePersister
11:16:02.346 DEBUG - Updating semaphore batch-rsz:website::main
11:16:12.358 DEBUG - Updating semaphore batch-rsz:website::main
11:16:22.363 DEBUG - Updating semaphore batch-rsz:website::main
11:16:32.367 DEBUG - Updating semaphore batch-rsz:website::main
11:16:42.372 DEBUG - Updating semaphore batch-rsz:website::main
11:16:52.376 DEBUG - Updating semaphore batch-rsz:website::main
11:17:02.381 DEBUG - Updating semaphore batch-rsz:website::main
... [endless repetitions] ...

I generated multiple thread dumps. Each of them shows the main thread at the following place:

"main" prio=10 tid=0x00007f175c00a000 nid=0x5ef0 runnable [0x00007f1763978000]

java.lang.Thread.State: RUNNABLE
at org.sonar.xml.XmlStartElementTokenizer.consumeAttributeValueUntilQuoteOrEol(XmlStartElementTokenizer.java:142)

at org.sonar.xml.XmlStartElementTokenizer.consumeStartElement(XmlStartElementTokenizer.java:110)

    at org.sonar.xml.XmlStartElementTokenizer.consume(XmlStartElementTokenizer.java:70)
    at org.sonar.xml.XmlStartElementTokenizer.consume(XmlStartElementTokenizer.java:33)
    at org.sonar.colorizer.TokenizerDispatcher.colorize(TokenizerDispatcher.java:50)
    at org.sonar.batch.source.HighlightingRenderer.render(HighlightingRenderer.java:40)
    at org.sonar.batch.source.CodeColorizers.toSyntaxHighlighting(CodeColorizers.java:86)
    at org.sonar.batch.index.SourceDataFactory.applyHighlighting(SourceDataFactory.java:200)
    at org.sonar.batch.index.SourceDataFactory.consolidateData(SourceDataFactory.java:78)
    at org.sonar.batch.index.SourcePersister.computeData(SourcePersister.java:152)
    at org.sonar.batch.index.SourcePersister.persist(SourcePersister.java:93)
    at org.sonar.batch.index.SourcePersister.persist(SourcePersister.java:81)

    at org.sonar.batch.phases.DatabaseModePhaseExecutor.executePersisters(DatabaseModePhaseExecutor.java:165)
    at org.sonar.batch.phases.DatabaseModePhaseExecutor.execute(DatabaseModePhaseExecutor.java:133)
    at org.sonar.batch.scan.ModuleScanContainer.doAfterStart(ModuleScanContainer.java:264)

at org.sonar.api.platform.ComponentContainer.startComponents(ComponentContainer.java:92)
at org.sonar.api.platform.ComponentContainer.execute(ComponentContainer.java:77)

    at org.sonar.batch.scan.ProjectScanContainer.scan(ProjectScanContainer.java:235)
    at org.sonar.batch.scan.ProjectScanContainer.scanRecursively(ProjectScanContainer.java:230)
    at org.sonar.batch.scan.ProjectScanContainer.doAfterStart(ProjectScanContainer.java:220)

at org.sonar.api.platform.ComponentContainer.startComponents(ComponentContainer.java:92)
at org.sonar.api.platform.ComponentContainer.execute(ComponentContainer.java:77)

    at org.sonar.batch.scan.ScanTask.scan(ScanTask.java:57)
    at org.sonar.batch.scan.ScanTask.execute(ScanTask.java:45)
    at org.sonar.batch.bootstrap.TaskContainer.doAfterStart(TaskContainer.java:135)

at org.sonar.api.platform.ComponentContainer.startComponents(ComponentContainer.java:92)
at org.sonar.api.platform.ComponentContainer.execute(ComponentContainer.java:77)

at org.sonar.batch.bootstrap.GlobalContainer.executeTask(GlobalContainer.java:158)

at org.sonar.batch.bootstrapper.Batch.executeTask(Batch.java:95)
at org.sonar.batch.bootstrapper.Batch.execute(Batch.java:67)

- locked <0x0000000785433b28> (a org.sonar.batch.bootstrapper.Batch)

at org.sonar.runner.batch.IsolatedLauncher.execute(IsolatedLauncher.java:48)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)

    at org.sonar.runner.impl.BatchLauncher$1.delegateExecution(BatchLauncher.java:87)
    at org.sonar.runner.impl.BatchLauncher$1.run(BatchLauncher.java:75)
    at java.security.AccessController.doPrivileged(Native Method)
    at org.sonar.runner.impl.BatchLauncher.doExecute(BatchLauncher.java:69)
    at org.sonar.runner.impl.BatchLauncher.execute(BatchLauncher.java:50)
    at org.sonar.runner.api.EmbeddedRunner.doExecute(EmbeddedRunner.java:102)
    at org.sonar.runner.api.Runner.execute(Runner.java:100)

    at org.sonar.runner.Main.executeTask(Main.java:70)
    at org.sonar.runner.Main.execute(Main.java:59)
    at org.sonar.runner.Main.main(Main.java:53)

Full dumps:

2015-08-28 09:11:13
Full thread dump Java HotSpot(TM) 64-Bit Server VM (24.76-b04 mixed mode):

"pool-2-thread-1" prio=10 tid=0x00007f175ca12000 nid=0x616d waiting on condition [0x00007f174b404000]

java.lang.Thread.State: TIMED_WAITING (parking)
at sun.misc.Unsafe.park(Native Method)

    - parking to wait for <0x0000000788c48df0> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
    at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:226)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2082)
    at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1090)
    at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:807)
    at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1068)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1130)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)

"CLEANUP_MANAGER" prio=10 tid=0x00007f175cd24800 nid=0x5fc5 in Object.wait() [0x00007f174a277000]

   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    at com.persistit.IOTaskRunnable.run(IOTaskRunnable.java:173)

- locked <0x0000000785e522e0> (a com.persistit.CleanupManager)
at java.lang.Thread.run(Thread.java:745)

"CHECKPOINT_WRITER" prio=10 tid=0x00007f175cd47000 nid=0x5fc4 in Object.wait() [0x00007f174a378000]

   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    at com.persistit.IOTaskRunnable.run(IOTaskRunnable.java:173)

- locked <0x0000000785f0a7d0> (a com.persistit.CheckpointManager)
at java.lang.Thread.run(Thread.java:745)

"TXN_UPDATE" prio=10 tid=0x00007f175cd44000 nid=0x5fc3 in Object.wait() [0x00007f174a479000]

   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    at com.persistit.IOTaskRunnable.run(IOTaskRunnable.java:173)

- locked <0x0000000785f0aa50> (a com.persistit.TransactionIndex$ActiveTransactionCachePollTask)
at java.lang.Thread.run(Thread.java:745)

"PAGE_WRITER:8192" prio=10 tid=0x00007f175cd3b800 nid=0x5fc2 in Object.wait() [0x00007f174a57a000]

   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    at com.persistit.IOTaskRunnable.run(IOTaskRunnable.java:173)

- locked <0x0000000785f28ef0> (a com.persistit.BufferPool$PageWriter)
at java.lang.Thread.run(Thread.java:745)

"JOURNAL_FLUSHER" prio=10 tid=0x00007f175cd3a000 nid=0x5fc1 in Object.wait() [0x00007f174a67b000]

   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    at com.persistit.IOTaskRunnable.run(IOTaskRunnable.java:173)

- locked <0x0000000785f25ad8> (a com.persistit.JournalManager$JournalFlusher)
at java.lang.Thread.run(Thread.java:745)

"JOURNAL_COPIER" prio=10 tid=0x00007f175cd35800 nid=0x5fc0 in Object.wait() [0x00007f174a77c000]

   java.lang.Thread.State: TIMED_WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    at com.persistit.IOTaskRunnable.run(IOTaskRunnable.java:173)

- locked <0x0000000785f3d8a0> (a com.persistit.JournalManager$JournalCopier)
at java.lang.Thread.run(Thread.java:745)

"LOG_FLUSHER" daemon prio=10 tid=0x00007f175ccf3000 nid=0x5fbf waiting on condition [0x00007f174a87d000]

   java.lang.Thread.State: TIMED_WAITING (sleeping)
    at java.lang.Thread.sleep(Native Method)
    at com.persistit.util.Util.sleep(Util.java:558)
    at com.persistit.Persistit$LogFlusher.run(Persistit.java:188)

"Abandoned connection cleanup thread" daemon prio=10 tid=0x00007f175c83f800 nid=0x5f6e in Object.wait() [0x00007f174afb7000]

java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(Native Method)

    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:135)
    - locked <0x00000007854335d0> (a java.lang.ref.ReferenceQueue$Lock)
    at com.mysql.jdbc.AbandonedConnectionCleanupThread.run(AbandonedConnectionCleanupThread.java:43)

"Service Thread" daemon prio=10 tid=0x00007f175c0ae800 nid=0x5f01 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread1" daemon prio=10 tid=0x00007f175c0ac800 nid=0x5f00 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread0" daemon prio=10 tid=0x00007f175c0a9800 nid=0x5eff waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Signal Dispatcher" daemon prio=10 tid=0x00007f175c0a7000 nid=0x5efe waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Finalizer" daemon prio=10 tid=0x00007f175c07d000 nid=0x5efd in Object.wait() [0x00007f175814a000]

java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)

    - waiting on <0x00000007854337a8> (a java.lang.ref.ReferenceQueue$Lock)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:135)
    - locked <0x00000007854337a8> (a java.lang.ref.ReferenceQueue$Lock)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:151)
    at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:209)

"Reference Handler" daemon prio=10 tid=0x00007f175c07b000 nid=0x5efc in Object.wait() [0x00007f175824b000]

java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)

    - waiting on <0x0000000785433850> (a java.lang.ref.Reference$Lock)
    at java.lang.Object.wait(Object.java:503)
    at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:133)
    - locked <0x0000000785433850> (a java.lang.ref.Reference$Lock)

"main" prio=10 tid=0x00007f175c00a000 nid=0x5ef0 runnable [0x00007f1763978000]

java.lang.Thread.State: RUNNABLE
at org.sonar.xml.XmlStartElementTokenizer.consumeAttributeValueUntilQuoteOrEol(XmlStartElementTokenizer.java:142)

at org.sonar.xml.XmlStartElementTokenizer.consumeStartElement(XmlStartElementTokenizer.java:110)

at org.sonar.api.platform.ComponentContainer.startComponents(ComponentContainer.java:92)
at org.sonar.api.platform.ComponentContainer.execute(ComponentContainer.java:77)

at org.sonar.batch.bootstrap.GlobalContainer.executeTask(GlobalContainer.java:158)

at org.sonar.batch.bootstrapper.Batch.executeTask(Batch.java:95)
at org.sonar.batch.bootstrapper.Batch.execute(Batch.java:67)

- locked <0x0000000785433b28> (a org.sonar.batch.bootstrapper.Batch)

at org.sonar.runner.batch.IsolatedLauncher.execute(IsolatedLauncher.java:48)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

    at org.sonar.runner.Main.executeTask(Main.java:70)
    at org.sonar.runner.Main.execute(Main.java:59)
    at org.sonar.runner.Main.main(Main.java:53)

"VM Thread" prio=10 tid=0x00007f175c076800 nid=0x5efb runnable

"GC task thread#0 (ParallelGC)" prio=10 tid=0x00007f175c01f800 nid=0x5ef1 runnable

"GC task thread#1 (ParallelGC)" prio=10 tid=0x00007f175c021800 nid=0x5ef2 runnable

"GC task thread#2 (ParallelGC)" prio=10 tid=0x00007f175c023800 nid=0x5ef3 runnable

"GC task thread#3 (ParallelGC)" prio=10 tid=0x00007f175c025000 nid=0x5ef4 runnable

"GC task thread#4 (ParallelGC)" prio=10 tid=0x00007f175c027000 nid=0x5ef5 runnable

"GC task thread#5 (ParallelGC)" prio=10 tid=0x00007f175c029000 nid=0x5ef6 runnable

"GC task thread#6 (ParallelGC)" prio=10 tid=0x00007f175c02b000 nid=0x5ef7 runnable

"GC task thread#7 (ParallelGC)" prio=10 tid=0x00007f175c02c800 nid=0x5ef8 runnable

"GC task thread#8 (ParallelGC)" prio=10 tid=0x00007f175c02e800 nid=0x5ef9 runnable

"GC task thread#9 (ParallelGC)" prio=10 tid=0x00007f175c030800 nid=0x5efa runnable

"VM Periodic Task Thread" prio=10 tid=0x00007f175c0b9800 nid=0x5f02 waiting on condition

JNI global references: 197

Heap
PSYoungGen      total 458752K, used 106393K [0x00000007d5500000, 0x00000007f8380000, 0x0000000800000000)
eden space 457216K, 22% used [0x00000007d5500000,0x00000007dbb7d220,0x00000007f1380000)
from space 1536K, 94% used [0x00000007f2680000,0x00000007f27e93e0,0x00000007f2800000)
to   space 57344K, 0% used [0x00000007f4b80000,0x00000007f4b80000,0x00000007f8380000)
ParOldGen       total 255488K, used 228105K [0x0000000780000000, 0x000000078f980000, 0x00000007d5500000)
object space 255488K, 89% used [0x0000000780000000,0x000000078dec27b0,0x000000078f980000)
PSPermGen       total 51712K, used 51481K [0x0000000770000000, 0x0000000773280000, 0x0000000780000000)
object space 51712K, 99% used [0x0000000770000000,0x00000007732466e8,0x0000000773280000)

2015-08-28 09:12:07
Full thread dump Java HotSpot(TM) 64-Bit Server VM (24.76-b04 mixed mode):

"pool-2-thread-1" prio=10 tid=0x00007f175ca12000 nid=0x616d waiting on condition [0x00007f174b404000]