nav[aria-label="Primary Navigation"] { padding: 0; & ul { list-style: none; width: 100%; display: flex; flex-direction: row; justify-content: start; align-items: start; gap: 30px; padding: 0; & li { margin: 0; } & ul li { list-style: none; } } }

JIRA is crashing after "Starting Plugin System"

taisto_jbiz

A fresh installed JIRA Software 8.7.1 is crashing randomly under start.

A few time it starts OK , but mostly kills the server during "Starting the JIRA Plugin System ", sometimes logging Warnings but mostly not.

I have tried with builtin Java 1.8 but there was Errors in GC logs so I have also tried with

OpenJdk 8 and OpenJDK 11.

Running on:

-ubuntu 18.04

-mysql 5.7

- 8G RAM

Any suggestions ?

regs

Taisto

================FROM STARTUP "Starting the JIRA Plugin System "

WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.felix.framework.ext.ClassPathExtenderFactory$DefaultClassLoaderExtender (file:/opt/atlassian/jira/atlassian-jira/WEB-INF/lib/org.apache.felix.framework-5.6.12.jar) to method java.net.URLClassLoader.addURL(java.net.URL)
WARNING: Please consider reporting this to the maintainers of org.apache.felix.framework.ext.ClassPathExtenderFactory$DefaultClassLoaderExtender
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
2020-03-12 12:04:37,057+0000 ThreadPoolAsyncTaskExecutor::Thread 9 INFO [c.a.ratelimiting.internal.RateLimitingConfiguration] Rate Limited Request Handler ENABLED

=============Catalina out

12-Mar-2020 12:03:51.883 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version: Apache Tomcat/8.5.42
12-Mar-2020 12:03:51.887 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Jun 4 2019 20:29:04 UTC
12-Mar-2020 12:03:51.888 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server number: 8.5.42.0
12-Mar-2020 12:03:51.888 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
12-Mar-2020 12:03:51.888 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 4.15.0-88-generic
12-Mar-2020 12:03:51.888 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
12-Mar-2020 12:03:51.889 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /usr/lib/jvm/java-11-openjdk-amd64
12-Mar-2020 12:03:51.889 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 11.0.6+10-post-Ubuntu-1ubuntu118.04.1
12-Mar-2020 12:03:51.889 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Ubuntu
12-Mar-2020 12:03:51.889 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /opt/atlassian/jira
12-Mar-2020 12:03:51.889 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /opt/atlassian/jira
12-Mar-2020 12:03:51.890 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.lang=ALL-UNNAMED
12-Mar-2020 12:03:51.891 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.io=ALL-UNNAMED
12-Mar-2020 12:03:51.891 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED
12-Mar-2020 12:03:51.891 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/opt/atlassian/jira/conf/logging.properties
12-Mar-2020 12:03:51.891 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
12-Mar-2020 12:03:51.891 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms512m
12-Mar-2020 12:03:51.892 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx2048m
12-Mar-2020 12:03:51.892 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:InitialCodeCacheSize=32m
12-Mar-2020 12:03:51.892 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:ReservedCodeCacheSize=512m
12-Mar-2020 12:03:51.892 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.awt.headless=true
12-Mar-2020 12:03:51.892 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.standalone=JIRA
12-Mar-2020 12:03:51.892 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true
12-Mar-2020 12:03:51.893 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dmail.mime.decodeparameters=true
12-Mar-2020 12:03:51.893 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory
12-Mar-2020 12:03:51.893 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:-OmitStackTraceInFastThrow
12-Mar-2020 12:03:51.893 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.locale.providers=COMPAT
12-Mar-2020 12:03:51.893 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.plugins.startup.options=-fg
12-Mar-2020 12:03:51.893 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
12-Mar-2020 12:03:51.894 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
12-Mar-2020 12:03:51.894 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=0027
12-Mar-2020 12:03:51.894 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xlog:gc*:file=/opt/atlassian/jira/logs/atlassian-jira-gc-%t.log:time,uptime:filecount=5,filesize=20M
12-Mar-2020 12:03:51.894 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+UseParallelGC
12-Mar-2020 12:03:51.894 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dignore.endorsed.dirs=
12-Mar-2020 12:03:51.894 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/opt/atlassian/jira
12-Mar-2020 12:03:51.895 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/opt/atlassian/jira
12-Mar-2020 12:03:51.895 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/opt/atlassian/jira/temp
12-Mar-2020 12:03:51.895 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:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib]
12-Mar-2020 12:03:51.985 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-7070"]
12-Mar-2020 12:03:52.006 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 805 ms
12-Mar-2020 12:03:52.054 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
12-Mar-2020 12:03:52.054 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.42
12-Mar-2020 12:03:52.068 SEVERE [Catalina-startStop-1] org.apache.catalina.startup.HostConfig.beforeStart Unable to create directory for deployment: [/opt/atlassian/jira/conf/Catalina/localhost]
12-Mar-2020 12:03:58.696 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-7070"]
12-Mar-2020 12:03:58.712 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
12-Mar-2020 12:03:58.741 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 6733 ms

Accepted answers

Moses Thomas_08kyb0

@taisto_jbiz This log is not enough, could you give this log <jira-home-dir>/logs/atlassian-jira.log

Kind regards,

All comments

Moses Thomas_08kyb0

@taisto_jbiz This log is not enough, could you give this log <jira-home-dir>/logs/atlassian-jira.log

Kind regards,

taisto_jbiz

2020-03-12 12:04:06,770+0000 JIRA-Bootstrap INFO [c.a.jira.upgrade.PluginUpgradeListener] [plugin-upgrade-listener] Created
2020-03-12 12:04:06,770+0000 JIRA-Bootstrap INFO [c.a.j.c.cache.pauser.NonClusteredReplicationPauserManager] Non-clustered mode: ReplicationPauserManager implemented by NonClusteredReplicationPauserManager
2020-03-12 12:04:06,771+0000 JIRA-Bootstrap INFO [c.a.jira.plugin.JiraCacheResetter] [jira-cache-reseter] Created and registered for events
2020-03-12 12:04:06,774+0000 JIRA-Bootstrap INFO [c.a.jira.plugin.PluginTransactionListener] [plugin-transaction] Created, registered for events and schedulled stats job
2020-03-12 12:04:06,792+0000 JIRA-Bootstrap INFO [c.a.jira.i18n.CachingI18nFactory] [i18n-caching-factory] Registering for events
2020-03-12 12:04:06,808+0000 JIRA-Bootstrap INFO [c.a.jira.plugin.JiraCacheResetter] [jira-cache-reseter] Initialized.
2020-03-12 12:04:06,808+0000 JIRA-Bootstrap INFO [c.a.jira.plugin.PluginTransactionListener] [plugin-transaction] Initialized.
2020-03-12 12:04:06,927+0000 JIRA-Bootstrap INFO [c.a.jira.startup.DatabaseLauncher] Database transactions enabled: true
2020-03-12 12:04:06,927+0000 JIRA-Bootstrap INFO [c.a.jira.startup.DatabaseLauncher] Using JIRA's default for database transaction isolation level: 2
2020-03-12 12:04:06,933+0000 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger]

Database configuration OK

___ Database Configuration _________________

Loading entityengine.xml from : file:/opt/atlassian/jira/atlassian-jira/WEB-INF/classes/entityengine.xml
Entity model field type name : mysql
Entity model schema name :
Database Version : MySQL - 5.7.29-0ubuntu0.18.04.1
Database Driver : MySQL Connector Java - mysql-connector-java-5.1.48 ( Revision: 29734982609c32d3ab7e5cac2e6acee69ff6b4aa )
Database URL : jdbc:mysql://address=(protocol=tcp)(host=db01)(port=3306)/jira_carbiz?sessionVariables=default_storage_engine=InnoDB
Database JDBC config : mysql57 jdbc:mysql://address=(protocol=tcp)(host=db01)(port=3306)/jira_carbiz?sessionVariables=default_storage_engine=InnoDB

2020-03-12 12:04:07,001+0000 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger]

___ Starting the JIRA Plugin System _________________

============== atlassian-jira.log
2020-03-12 12:04:07,003+0000 JIRA-Bootstrap INFO [c.a.plugin.manager.DefaultPluginManager] Plugin system earlyStartup begun
2020-03-12 12:04:10,651+0000 FelixStartLevel WARN [o.e.g.b.e.internal.support.ExtenderConfiguration] Gemini Blueprint extensions bundle not present, annotation processing disabled.
2020-03-12 12:04:18,282+0000 JIRA-Bootstrap WARN [c.a.p.osgi.util.OsgiHeaderUtil] removing duplicate import package com.atlassian.jira.blueprint.api~ for plugin com.atlassian.jira-core-project-templates - it is likely that a duplicate package was supplied in the OSGi instructions in the plugin's MANIFEST.MF
2020-03-12 12:04:18,283+0000 JIRA-Bootstrap WARN [c.a.p.osgi.util.OsgiHeaderUtil] removing duplicate import package com.atlassian.jira.projects.shortcuts~ for plugin com.atlassian.jira-core-project-templates - it is likely that a duplicate package was supplied in the OSGi instructions in the plugin's MANIFEST.MF
2020-03-12 12:04:23,786+0000 JIRA-Bootstrap WARN [c.a.p.osgi.util.OsgiHeaderUtil] removing duplicate import package com.atlassian.webresource.api.data~ for plugin com.pyxis.greenhopper.jira - it is likely that a duplicate package was supplied in the OSGi instructions in the plugin's MANIFEST.MF
2020-03-12 12:04:26,703+0000 ThreadPoolAsyncTaskExecutor::Thread 8 WARN [o.s.b.factory.support.DefaultListableBeanFactory] Overriding user-defined bean definition for bean 'pluginAccessor' with a framework-generated bean definition: replacing [Generic bean: class [com.atlassian.plugin.osgi.bridge.external.HostComponentFactoryBean]; scope=; abstract=false; lazyInit=true; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [bundle://32.0:0/META-INF/spring/atlassian-plugins-host-components.xml]] with [Root bean: class [org.eclipse.gemini.blueprint.service.importer.support.OsgiServiceProxyFactoryBean]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null]
2020-03-12 12:04:26,704+0000 ThreadPoolAsyncTaskExecutor::Thread 8 WARN [o.s.b.factory.support.DefaultListableBeanFactory] Overriding user-defined bean definition for bean 'pageBuilderService' with a framework-generated bean definition: replacing [Generic bean: class [com.atlassian.plugin.osgi.bridge.external.HostComponentFactoryBean]; scope=; abstract=false; lazyInit=true; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [bundle://32.0:0/META-INF/spring/atlassian-plugins-host-components.xml]] with [Root bean: class [org.eclipse.gemini.blueprint.service.importer.support.OsgiServiceProxyFactoryBean]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null]

taisto_jbiz

Hi Mo, pasted the tail from atlassian-jira.log

best regs

taisto

taisto_jbiz

it looks like it stops in the this place when I try to restart

___ Starting the JIRA Plugin System _________________

2020-03-12 14:49:19,556+0000 JIRA-Bootstrap INFO [c.a.plugin.manager.DefaultPluginManager] Plugin system earlyStartup begun
2020-03-12 14:49:23,147+0000 FelixStartLevel WARN [o.e.g.b.e.internal.support.ExtenderConfiguration] Gemini Blueprint extensions bundle not present, annotation processing disabled.
2020-03-12 14:49:31,174+0000 JIRA-Bootstrap WARN [c.a.p.osgi.util.OsgiHeaderUtil] removing duplicate import package com.atlassian.jira.blueprint.api~ for plugin com.atlassian.jira-core-project-templates - it is likely that a duplicate package was supplied in the OSGi instructions in the plugin's MANIFEST.MF
2020-03-12 14:49:31,174+0000 JIRA-Bootstrap WARN [c.a.p.osgi.util.OsgiHeaderUtil] removing duplicate import package com.atlassian.jira.projects.shortcuts~ for plugin com.atlassian.jira-core-project-templates - it is likely that a duplicate package was supplied in the OSGi instructions in the plugin's MANIFEST.MF
2020-03-12 14:49:36,859+0000 JIRA-Bootstrap WARN [c.a.p.osgi.util.OsgiHeaderUtil] removing duplicate import package com.atlassian.webresource.api.data~ for plugin com.pyxis.greenhopper.jira - it is likely that a duplicate package was supplied in the OSGi instructions in the plugin's MANIFEST.MF
2020-03-12 14:49:39,718+0000 ThreadPoolAsyncTaskExecutor::Thread 10 WARN [o.s.b.factory.support.DefaultListableBeanFactory] Overriding user-defined bean definition for bean 'pluginAccessor' with a framework-generated bean definition: replacing [Generic bean: class [com.atlassian.plugin.osgi.bridge.external.HostComponentFactoryBean]; scope=; abstract=false; lazyInit=true; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [bundle://32.0:0/META-INF/spring/atlassian-plugins-host-components.xml]] with [Root bean: class [org.eclipse.gemini.blueprint.service.importer.support.OsgiServiceProxyFactoryBean]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null]
2020-03-12 14:49:39,718+0000 ThreadPoolAsyncTaskExecutor::Thread 10 WARN [o.s.b.factory.support.DefaultListableBeanFactory] Overriding user-defined bean definition for bean 'pageBuilderService' with a framework-generated bean definition: replacing [Generic bean: class [com.atlassian.plugin.osgi.bridge.external.HostComponentFactoryBean]; scope=; abstract=false; lazyInit=true; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in URL [bundle://32.0:0/META-INF/spring/atlassian-plugins-host-components.xml]] with [Root bean: class [org.eclipse.gemini.blueprint.service.importer.support.OsgiServiceProxyFactoryBean]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null]

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