Generating a thread dump

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Occasionally, JIRA may appear to 'freeze' during execution of an operation. During these times, it is helpful to retrieve a thread dump — a log containing information about currently running threads and processes within the Java Virtual Machine. Taking thread-dumps is a non-destructive process that can be run on live systems. This document describes the steps necessary to retrieve a thread dump.

The steps necessary to retrieve the thread dump are dependant on the operating system JIRA is running in — please follow the appropriate steps below.

Windows environment

JIRA running from startup.bat

  1. In the Command Console window where JIRA is running, open the properties dialog box by right clicking on the title bar and select "Properties".
  2. Select the Layout tab.
  3. Under Screen Buffer Size, set the Height to 3000.
  4. Click OK.
  5. With the same command console in focus, press CTRL-BREAK. This will output the thread dump to the command console.
  6. Scroll back in the command console until you reach the line containing "Full thread dump".
  7. Right click the title bar and select Edit -> Mark. Highlight the entire text of the thread dump.
  8. Right click the title bar and select Edit -> Copy. The thread dump can then be pasted into a text file.

JIRA running as a Windows service

Using jstack

The JDK ships with a tool named jstack for generating thread dumps.

  1. Identify the process. Launch the task manager by, pressing Ctrl + Shift + Esc and find the Process ID of the Java (JIRA) process. You may need to add the PID column using View -> Select Columns ...
  2. Run jstack <pid> to Capture a Single Thread Dump. This command will take one thread dump of the process id <pid>, in this case the pid is 22668:
C:\Users\Administrator>jstack.exe -l 22668 > threaddump.txt

This will output a file called threaddump.txt to your current directory.

Common issues with jstack:

  • You must run jstack as the same user that is running JIRA.
  • If you get the error "Not enough storage is available to process this command", download the 'psexec' utility from here, then run the following command using it:
    psexec -s jstack <pid> >> threaddumps.txt
  • If the jstack executable is not in your $PATH, then please look for it in your <JDK_HOME>/bin directory
  • If you receive java.lang.NoClassDefFoundError: sun/tools/jstack/JStack check that tools.jar is present in your JDK's lib directory. If it is not, download a full version of the JDK.

Linux/Unix/OS X environment

Linux/Unix command line

  1. Identify the java process that JIRA is running in. This can be achieved by running a command similar to:

    ps -ef | grep java

    The process will appear similarly as follows:

    keithb     910   873  1 17:01 pts/3    00:00:18 /usr/java/jdk/bin/java -Xms128m -Xmx256m
-Xms128m -Xmx256m -Djava.awt.headless=true -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
-Djava.awt.headless=true -Djava.endorsed.dirs=/tmp/atlassian-jira-enterprise-3.6-standalone/common/endorsed
-classpath :

  2. In order to retrieve the thread dump, execute the command

    kill -3 <pid>

    where pid is the process id — in this case, 910.

  3. The thread dump will be written to the Tomcat console output. The console output is redirected to the logs/catalina.out file, which can be found in the JIRA application installation directory for JIRA Standalone / Installer.

Linux/Unix Alternative: Generating thread dumps using jstack

If you have trouble using kill -3 <pid> to obtain a thread dump, try using jstack a java utility that will output stack traces of Java threads for a given process.

  1. Identify the javaprocess that JIRA is running in. This can be achieved by running a command similar to:

    ps -ef | grep java

  2. The process will appear similarly as follows:

    adam 22668 0.3 14.9 1691788 903928 ? Sl Jan27 9:36 /usr/lib/jvm/java-6-sun-1.6.0.14/bin/java -Djava.util.logging.config.file=/home/adam/Products/installs/atlassian-jira-enterprise-4.0.1-standalone/conf/logging.properties -XX:MaxPermSize=256m -Xms128m -Xmx1048m -Djava.awt.headless=true -Datlassian.standalone=JIRA -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true -Dmail.mime.decodeparameters=true -Datlassian.mail.senddisabled=false -Datlassian.mail.fetchdisabled=false -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djava.endorsed.dirs=/home/adam/Products/installs/atlassian-jira-enterprise-4.0.1-standalone/common/endorsed -classpath /home/adam/Products/installs/atlassian-jira-enterprise-4.0.1-standalone/bin/bootstrap.jar -Dcatalina.base=/home/adam/Products/installs/atlassian-jira-enterprise-4.0.1-standalone -Dcatalina.home=/home/adam/Products/installs/atlassian-jira-enterprise-4.0.1-standalone -Djava.io.tmpdir=/home/adam/Products/installs/atlassian-jira-enterprise-4.0.1-standalone/temp org.apache.catalina.startup.Bootstrap start

  3. Run jstack <pid> to capture a single thread dump
    This command will take one thread dump of the process id <pid>, in this case the pid is 22668, and log output to the file JIRAthreaddump.txt

    adam@jiratrack:~$ jstack 22668 > JIRAthreaddump.txt

  4. Take multiple thread dumps
    Typically you'll want to take several dumps about 10 seconds apart, in which case you can generate several dumps and output the stack traces to a single file as follows:

    adam@jiratrack:~$ jstack 22668 >> JIRAthreaddump.txt
adam@jiratrack:~$ jstack 22668 >> JIRAthreaddump.txt
adam@jiratrack:~$ jstack 22668 >> JIRAthreaddump.txt

    If you are connecting to the server through RDP, jstack might fail with following error:

    Not enough storage is available to process this command 

    You will need to open a RDP session in console mode: mstsc /admin

Analysis tools

Try TDA or Samurai to inspect your thread dump.

TDA

  1. Download TDA.
  2. CD to the directory where the JAR exists.

  3. Run:

    java -jar -Xmx512M ~/tda-bin-1.6/tda.jar
  4. Open your catalina.out file, containing the thread dump.

Issue processing thread dump with TDA (NumberFormatException)

Should you get an error on TDA console like:

Exception in thread "AWT-EventQueue-0" java.lang.NumberFormatException: For input string: "5 os_prio=0"
        at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
        at java.lang.Long.parseLong(Long.java:441)
        at java.lang.Long.<init>(Long.java:702)
        at com.pironet.tda.utils.ThreadsTableModel.getValueAt(ThreadsTableModel.java:80)
        at com.pironet.tda.utils.TableSorter.getValueAt(TableSorter.java:285)
        at javax.swing.JTable.getValueAt(JTable.java:2717)
        at javax.swing.JTable.prepareRenderer(JTable.java:5719)
        at javax.swing.plaf.basic.BasicTableUI.paintCell(BasicTableUI.java:2114)
        at javax.swing.plaf.basic.BasicTableUI.paintCells(BasicTableUI.java:2016)
        at javax.swing.plaf.basic.BasicTableUI.paint(BasicTableUI.java:1812)
        at javax.swing.plaf.ComponentUI.update(ComponentUI.java:161)
        at javax.swing.JComponent.paintComponent(JComponent.java:778)
        at javax.swing.JComponent.paint(JComponent.java:1054)
        at javax.swing.JComponent.paintChildren(JComponent.java:887)
        at javax.swing.JComponent.paint(JComponent.java:1063)
        at javax.swing.JViewport.paint(JViewport.java:731)
        at javax.swing.JComponent.paintChildren(JComponent.java:887)
        at javax.swing.JComponent.paint(JComponent.java:1063)
        at javax.swing.JComponent.paintChildren(JComponent.java:887)
        at javax.swing.JSplitPane.paintChildren(JSplitPane.java:1047)
        at javax.swing.JComponent.paint(JComponent.java:1063)
        at javax.swing.JComponent.paintToOffscreen(JComponent.java:5230)
        at javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:295)
        at javax.swing.RepaintManager.paint(RepaintManager.java:1249)
        at javax.swing.JComponent._paintImmediately(JComponent.java:5178)
        at javax.swing.JComponent.paintImmediately(JComponent.java:4989)
        at javax.swing.RepaintManager$3.run(RepaintManager.java:808)
        at javax.swing.RepaintManager$3.run(RepaintManager.java:796)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
        at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:796)
        at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:769)
        at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:718)
        at javax.swing.RepaintManager.access$1100(RepaintManager.java:62)
        at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1677)
        at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:312)
        at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:733)
        at java.awt.EventQueue.access$200(EventQueue.java:103)
        at java.awt.EventQueue$3.run(EventQueue.java:694)
        at java.awt.EventQueue$3.run(EventQueue.java:692)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:703)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
        at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)

Apply the following command on the thread dump(s) to fix the thread header format to make it processable:
sed -i 's/prio=[0-9]\{1,2\} os_prio=[0-9]\{1,2\}/prio=5/g' <filename>

For Mac:

sed -i '' 's/prio=[0-9]\{1,2\} os_prio=[0-9]\{1,2\}/prio=5/g' <filename>

Check the known thread dump knowledge base articles:

Last modified on Jan 30, 2018

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