Hello,
after a hard reboot because of a problem we cannot start Jira.
Log:
23-Jul-2018 13:42:12.128 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version: Apache Tomcat/8.5.6
23-Jul-2018 13:42:12.129 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Oct 6 2016 20:15:31 UTC
23-Jul-2018 13:42:12.129 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server number: 8.5.6.0
23-Jul-2018 13:42:12.129 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
23-Jul-2018 13:42:12.129 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 3.16.0-4-amd64
23-Jul-2018 13:42:12.130 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
23-Jul-2018 13:42:12.130 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /opt/atlassian/jira/jre
23-Jul-2018 13:42:12.130 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_102-b14
23-Jul-2018 13:42:12.130 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
23-Jul-2018 13:42:12.130 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /opt/atlassian/jira
23-Jul-2018 13:42:12.130 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /opt/atlassian/jira
23-Jul-2018 13:42:12.130 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/opt/atlassian/jira/conf/logging.properties
23-Jul-2018 13:42:12.130 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
23-Jul-2018 13:42:12.130 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms384m
23-Jul-2018 13:42:12.130 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx768m
23-Jul-2018 13:42:12.130 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.awt.headless=true
23-Jul-2018 13:42:12.130 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.standalone=JIRA
23-Jul-2018 13:42:12.130 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true
23-Jul-2018 13:42:12.130 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dmail.mime.decodeparameters=true
23-Jul-2018 13:42:12.131 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory
23-Jul-2018 13:42:12.131 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:-OmitStackTraceInFastThrow
23-Jul-2018 13:42:12.131 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.plugins.startup.options=
23-Jul-2018 13:42:12.131 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
23-Jul-2018 13:42:12.131 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
23-Jul-2018 13:42:12.131 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xloggc:/opt/atlassian/jira/logs/atlassian-jira-gc-%t.log
23-Jul-2018 13:42:12.131 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+UseGCLogFileRotation
23-Jul-2018 13:42:12.131 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:NumberOfGCLogFiles=5
23-Jul-2018 13:42:12.131 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:GCLogFileSize=20M
23-Jul-2018 13:42:12.131 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDetails
23-Jul-2018 13:42:12.131 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDateStamps
23-Jul-2018 13:42:12.131 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCTimeStamps
23-Jul-2018 13:42:12.131 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCCause
23-Jul-2018 13:42:12.131 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/opt/atlassian/jira
23-Jul-2018 13:42:12.131 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/opt/atlassian/jira
23-Jul-2018 13:42:12.131 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/opt/atlassian/jira/temp
23-Jul-2018 13:42:12.131 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: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
23-Jul-2018 13:42:12.240 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8081"]
23-Jul-2018 13:42:12.246 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
23-Jul-2018 13:42:12.252 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
23-Jul-2018 13:42:12.253 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8081"]
23-Jul-2018 13:42:12.254 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
23-Jul-2018 13:42:12.257 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 383 ms
23-Jul-2018 13:42:12.264 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service Catalina
23-Jul-2018 13:42:12.264 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.6
23-Jul-2018 13:42:12.272 SEVERE [Catalina-startStop-1] org.apache.catalina.startup.HostConfig.beforeStart Unable to create directory for deployment: /opt/atlassian/jira/conf/Catalina/localhost
23-Jul-2018 13:42:14.967 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler [http-nio-8081]
23-Jul-2018 13:42:14.968 SEVERE [main] org.apache.coyote.AbstractProtocol.start Failed to start end point associated with ProtocolHandler [http-nio-8081]
java.net.BindException: Address already in use
at sun.nio.ch.Net.bind0(Native Method)
at sun.nio.ch.Net.bind(Net.java:433)
at sun.nio.ch.Net.bind(Net.java:425)
at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223)
at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74)
at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:228)
at org.apache.tomcat.util.net.AbstractEndpoint.start(AbstractEndpoint.java:874)
at org.apache.coyote.AbstractProtocol.start(AbstractProtocol.java:590)
at org.apache.catalina.connector.Connector.startInternal(Connector.java:969)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.StandardService.startInternal(StandardService.java:440)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:791)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.startup.Catalina.start(Catalina.java:655)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:355)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)
23-Jul-2018 13:42:14.969 SEVERE [main] org.apache.catalina.core.StandardService.startInternal Failed to start connector [Connector[HTTP/1.1-8081]]
org.apache.catalina.LifecycleException: Failed to start component [Connector[HTTP/1.1-8081]]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:167)
at org.apache.catalina.core.StandardService.startInternal(StandardService.java:440)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:791)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.startup.Catalina.start(Catalina.java:655)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:355)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)
Caused by: org.apache.catalina.LifecycleException: service.getName(): "Catalina"; Protocol handler start failed
at org.apache.catalina.connector.Connector.startInternal(Connector.java:976)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
... 11 more
Caused by: java.net.BindException: Address already in use
at sun.nio.ch.Net.bind0(Native Method)
at sun.nio.ch.Net.bind(Net.java:433)
at sun.nio.ch.Net.bind(Net.java:425)
at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:223)
at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:74)
at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:228)
at org.apache.tomcat.util.net.AbstractEndpoint.start(AbstractEndpoint.java:874)
at org.apache.coyote.AbstractProtocol.start(AbstractProtocol.java:590)
at org.apache.catalina.connector.Connector.startInternal(Connector.java:969)
... 12 more
23-Jul-2018 13:42:14.970 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler [http-nio-8080]
23-Jul-2018 13:42:14.989 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler [http-nio-8081]
23-Jul-2018 13:42:14.991 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 2733 ms
23-Jul-2018 13:42:14.992 SEVERE [main] org.apache.catalina.core.StandardServer.await StandardServer.await: create[localhost:8005]:
java.net.BindException: Address already in use
at java.net.PlainSocketImpl.socketBind(Native Method)
at java.net.AbstractPlainSocketImpl.bind(AbstractPlainSocketImpl.java:387)
at java.net.ServerSocket.bind(ServerSocket.java:375)
at java.net.ServerSocket.<init>(ServerSocket.java:237)
at org.apache.catalina.core.StandardServer.await(StandardServer.java:440)
at org.apache.catalina.startup.Catalina.await(Catalina.java:743)
at org.apache.catalina.startup.Catalina.start(Catalina.java:689)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:355)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)
23-Jul-2018 13:42:14.992 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8081"]
23-Jul-2018 13:42:14.992 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
23-Jul-2018 13:42:14.995 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8081"]
23-Jul-2018 13:42:15.045 INFO [main] org.apache.catalina.core.StandardService.stopInternal Stopping service Catalina
23-Jul-2018 13:42:19.053 WARNING [localhost-startStop-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [Abandoned connection cleanup thread] 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.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
com.mysql.jdbc.AbandonedConnectionCleanupThread.run(AbandonedConnectionCleanupThread.java:43)
23-Jul-2018 13:42:19.053 WARNING [localhost-startStop-1] 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)
23-Jul-2018 13:42:19.053 WARNING [localhost-startStop-1] 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)
23-Jul-2018 13:42:19.061 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
23-Jul-2018 13:42:19.062 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8081"]
23-Jul-2018 13:42:19.063 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8081"]
23-Jul-2018 13:42:19.063 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8081"]
23-Jul-2018 13:42:19.063 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]
23-Jul-2018 13:42:19.063 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8081"]
23-Jul-2018 13:42:19.064 INFO [main] org.apache.coyote.AbstractProtocol.destroy Failed to deregister MBean named [Catalina:type=ProtocolHandler,port=8081] from MBean server [com.sun.jmx.mbeanserver.JmxMBeanServer@1055e4af]
23-Jul-2018 13:42:19.064 WARNING [main] org.apache.catalina.util.LifecycleMBeanBase.unregister Failed to unregister MBean with name [Catalina:type=Connector,port=8081] during component destruction
javax.management.InstanceNotFoundException: Catalina:type=Connector,port=8081
at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.getMBean(DefaultMBeanServerInterceptor.java:1095)
at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.exclusiveUnregisterMBean(DefaultMBeanServerInterceptor.java:427)
at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.unregisterMBean(DefaultMBeanServerInterceptor.java:415)
at com.sun.jmx.mbeanserver.JmxMBeanServer.unregisterMBean(JmxMBeanServer.java:546)
at org.apache.catalina.util.LifecycleMBeanBase.unregister(LifecycleMBeanBase.java:197)
at org.apache.catalina.util.LifecycleMBeanBase.destroyInternal(LifecycleMBeanBase.java:73)
at org.apache.catalina.connector.Connector.destroyInternal(Connector.java:1017)
at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
at org.apache.catalina.core.StandardService.destroyInternal(StandardService.java:571)
at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
at org.apache.catalina.core.StandardServer.destroyInternal(StandardServer.java:881)
at org.apache.catalina.util.LifecycleBase.destroy(LifecycleBase.java:297)
at org.apache.catalina.startup.Catalina.stop(Catalina.java:729)
at org.apache.catalina.startup.Catalina.start(Catalina.java:690)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:355)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:495)