After installing secsign plugin Jira crashed and not opening

Question

Using Jira 8.2.0. To enable 2FA i installed secsign plugin and configured user ids. Later when logged out and tried to login, Jira is not working. Jira crashed and unable to start it again

Find below catalina.log

12-May-2020 17:21:57.807 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version: Apache Tomcat/8.5.35
12-May-2020 17:21:57.808 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Nov 3 2018 17:39:20 UTC
12-May-2020 17:21:57.809 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server number: 8.5.35.0
12-May-2020 17:21:57.809 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Windows 7
12-May-2020 17:21:57.809 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 6.1
12-May-2020 17:21:57.809 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
12-May-2020 17:21:57.809 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: C:\Program Files\Atlassian\JIRA\jre
12-May-2020 17:21:57.810 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_181-b13
12-May-2020 17:21:57.810 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
12-May-2020 17:21:57.810 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: C:\Program Files\Atlassian\JIRA
12-May-2020 17:21:57.810 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: C:\Program Files\Atlassian\JIRA
12-May-2020 17:21:57.810 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=C:\Program Files\Atlassian\JIRA\conf\logging.properties
12-May-2020 17:21:57.811 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
12-May-2020 17:21:57.812 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms384m
12-May-2020 17:21:57.812 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx768m
12-May-2020 17:21:57.813 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:InitialCodeCacheSize=32m
12-May-2020 17:21:57.813 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:ReservedCodeCacheSize=512m
12-May-2020 17:21:57.814 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.awt.headless=true
12-May-2020 17:21:57.814 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.standalone=JIRA
12-May-2020 17:21:57.815 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true
12-May-2020 17:21:57.816 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dmail.mime.decodeparameters=true
12-May-2020 17:21:57.816 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory
12-May-2020 17:21:57.817 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:-OmitStackTraceInFastThrow
12-May-2020 17:21:57.817 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.locale.providers=COMPAT
12-May-2020 17:21:57.818 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
12-May-2020 17:21:57.818 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
12-May-2020 17:21:57.819 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xloggc:C:\Program Files\Atlassian\JIRA\bin\..\logs\atlassian-jira-gc-%t.log
12-May-2020 17:21:57.820 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+UseGCLogFileRotation
12-May-2020 17:21:57.820 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:NumberOfGCLogFiles=5
12-May-2020 17:21:57.825 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:GCLogFileSize=20M
12-May-2020 17:21:57.826 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDetails
12-May-2020 17:21:57.826 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDateStamps
12-May-2020 17:21:57.827 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCTimeStamps
12-May-2020 17:21:57.827 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCCause
12-May-2020 17:21:57.827 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dignore.endorsed.dirs=
12-May-2020 17:21:57.828 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=C:\Program Files\Atlassian\JIRA
12-May-2020 17:21:57.829 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=C:\Program Files\Atlassian\JIRA
12-May-2020 17:21:57.829 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=C:\Program Files\Atlassian\JIRA	emp
12-May-2020 17:21:57.830 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: [C:\Program Files\Atlassian\JIRA\jre\bin;C:\Windows\Sun\Java\bin;C:\Windows\system32;C:\Windows;C:\ProgramData\Oracle\Java\javapath;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\Kaspersky Lab\Kaspersky Endpoint Security 10 for Windows SP1\;C:\Program Files\Java\jdk1.8.0_65\bin;C:\Program Files (x86)\Kaspersky Lab\Kaspersky Endpoint Security 10 for Windows SP2\;.]
12-May-2020 17:21:58.061 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["https-jsse-nio-8443"]
12-May-2020 17:21:59.122 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
12-May-2020 17:21:59.126 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 1811 ms
12-May-2020 17:21:59.139 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
12-May-2020 17:21:59.144 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.35
12-May-2020 17:22:42.659 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["https-jsse-nio-8443"]
12-May-2020 17:22:42.681 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 43553 ms

Tuncay Senturk _Snapbytes_ · Answer

Please raise a ticket to the plugin vendor (details are in my comment above) with the entire atlassian-jira.log file

Saravanaperumal I C · Answer

Hi Please let me know how can i share the logs with you.

Saravanaperumal I C · Answer

2020-05-12 17:03:32 Commons Daemon procrun stderr initialized

12-May-2020 17:03:49.782 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version:        Apache Tomcat/8.5.35

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built:          Nov 3 2018 17:39:20 UTC

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server number:         8.5.35.0

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name:               Windows 7

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version:            6.1

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture:          amd64

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home:             C:\PROGRA~1\ATLASS~1\JIRA\jre

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version:           1.8.0_181-b13

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor:            Oracle Corporation

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE:         C:\Program Files\Atlassian\JIRA

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME:         C:\Program Files\Atlassian\JIRA

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.awt.headless=true

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.standalone=JIRA

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dmail.mime.decodeparameters=true

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:-OmitStackTraceInFastThrow

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDetails

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDateStamps

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCTimeStamps

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCCause

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+UseGCLogFileRotation

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:NumberOfGCLogFiles=5

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:GCLogFileSize=20M

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xloggc:C:\Program Files\Atlassian\JIRA\logs\atlassian-jira-gc-%t.log

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:InitialCodeCacheSize=32m

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:ReservedCodeCacheSize=512m

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=C:\Program Files\Atlassian\JIRA

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=C:\Program Files\Atlassian\JIRA

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dignore.endorsed.dirs=C:\Program Files\Atlassian\JIRA\endorsed

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=C:\Program Files\Atlassian\JIRA	emp

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=C:\Program Files\Atlassian\JIRA\conf\logging.properties

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: exit

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: abort

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms384m

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx2048m

12-May-2020 17:03:49.876 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: [C:\Program Files\Atlassian\JIRA\bin;C:\Windows\Sun\Java\bin;C:\Windows\system32;C:\Windows;C:\ProgramData\Oracle\Java\javapath;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\Kaspersky Lab\Kaspersky Endpoint Security 10 for Windows SP1\;C:\Program Files\Java\jdk1.8.0_65\bin;C:\Program Files (x86)\Kaspersky Lab\Kaspersky Endpoint Security 10 for Windows SP2\;;.]

12-May-2020 16:57:18.406 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["https-jsse-nio-8443"]

12-May-2020 16:57:20.356 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read

12-May-2020 16:57:20.387 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 12949 ms

12-May-2020 16:57:20.465 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]

12-May-2020 16:57:20.465 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.35

12-May-2020 16:59:07.028 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["https-jsse-nio-8443"]

12-May-2020 16:59:07.060 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 106680 ms

12-May-2020 17:18:25.191 INFO [Thread-42] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["https-jsse-nio-8443"]

12-May-2020 17:18:25.575 INFO [Thread-42] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]

12-May-2020 17:19:53.249 WARNING [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [JonasBatch] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:

java.lang.Object.wait(Native Method)

java.lang.Object.wait(Object.java:502)

org.objectweb.jonas_timer.TimerManager.batch(TimerManager.java:193)

org.objectweb.jonas_timer.Batch.run(TimerManager.java:65)

12-May-2020 17:19:53.250 WARNING [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [JonasClock] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:

java.lang.Thread.sleep(Native Method)

org.objectweb.jonas_timer.TimerManager.clock(TimerManager.java:142)

org.objectweb.jonas_timer.Clock.run(TimerManager.java:46)

12-May-2020 17:19:53.250 WARNING [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [jira-monitoring-plugin] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:

java.lang.Object.wait(Native Method)

java.util.TimerThread.mainLoop(Timer.java:552)

java.util.TimerThread.run(Timer.java:505)

12-May-2020 17:19:53.251 WARNING [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [pool-23-thread-1] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:

sun.misc.Unsafe.park(Native Method)

java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)

java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)

java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:442)

java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1074)

java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)

java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

java.lang.Thread.run(Thread.java:748)

12-May-2020 17:19:53.251 WARNING [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [pool-26-thread-1] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:

sun.misc.Unsafe.park(Native Method)

java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)

java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)

java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:442)

java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1074)

java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)

java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

java.lang.Thread.run(Thread.java:748)

12-May-2020 17:19:53.252 WARNING [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [Analytics] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:

sun.misc.Unsafe.park(Native Method)

java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)

java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)

java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:442)

com.segment.analytics.internal.AnalyticsClient$Looper.run(AnalyticsClient.java:106)

java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

java.util.concurrent.FutureTask.run(FutureTask.java:266)

java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

com.segment.analytics.Platform$1$1.run(Platform.java:45)

java.lang.Thread.run(Thread.java:748)

12-May-2020 17:19:53.252 WARNING [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [Analytics] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:

sun.misc.Unsafe.park(Native Method)

java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)

java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)

java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1093)

java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:809)

java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1074)

java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)

java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

com.segment.analytics.Platform$1$1.run(Platform.java:45)

java.lang.Thread.run(Thread.java:748)