JIRA access problem

[Rick Lupori]

Hello, I'm having trouble launching Jira on my local machine, http://localhost:8081. I get the following errors below but they appear to :be only warnings and not the root cause of the problem. I would be happy to submit my logs.

An unexpected error has occured during startup.: We couldn't start JIRA

An error occurred while trying to start JIRA. We can't give you any more detail right now, we suggest checking the logs for more detail and contacting our support team.
See our documentation for more information on contacting our support team and creating a support zip.

Thank you,

Rick

[Fazila Ashraf · Accepted solution]

Hi @Rick Lupori

Please share the logs 

[Rick Lupori]

Hi thanks for your response. I read there is a way to do this once you log into Jira but I cannot log into Jira. Where should I upload the logs?

Thanks,

Rick

[Nic Brough -Adaptavist-]

Here really - we're not looking for the whole log, just the bit where your login fails.

[Rick Lupori]

ok got it thank you. These are error logs from the jirasoftware230418180204-stderr.2018-12-12.log and jirasoftware230418180204-stdout.2018-12-12.log log files. Please let me know if I'm missing a log event?

--------------------------------------------------
-- FROM LOG
--jirasoftware230418180204-stderr.2018-12-12.log
--------------------------------------------------
12-Dec-2018 06:20:14.347 INFO [Thread-32] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8081"]
12-Dec-2018 06:20:14.427 INFO [Thread-32] org.apache.catalina.core.StandardService.stopInternal Stopping service Catalina
12-Dec-2018 06:20:26.004 WARNING [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [ROOT] registered the JDBC driver [org.h2.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
12-Dec-2018 06:20:26.004 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-Dec-2018 06:20:26.004 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-Dec-2018 06:20:26.020 INFO [Thread-32] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8081"]
12-Dec-2018 06:20:26.020 INFO [Thread-33] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [StandardServer[8006]] after stop() had already been called. The second call will be ignored.

--------------------------------------------------
-- FROM LOG
-- jirasoftware230418180204-stdout.2018-12-12.log
--------------------------------------------------
**************************************************************************************
h2 is an in-memory database, and susceptible to corruption when abnormally terminated.
DO NOT USE IN PRODUCTION, please switch to a regular database.
**************************************************************************************

2018-12-12 07:56:22,312 JIRA-Bootstrap INFO [c.a.jira.startup.DatabaseLauncher] Database transactions enabled: true
2018-12-12 07:56:22,315 JIRA-Bootstrap INFO [c.a.jira.startup.DatabaseLauncher] Using JIRA's default for database transaction isolation level: 2
2018-12-12 07:56:22,320 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger]

Database configuration OK

___ Database Configuration ________________

Loading entityengine.xml from : file:/C:/Program%20Files/Atlassian/JIRA/atlassian-jira/WEB-INF/classes/entityengine.xml
Entity model field type name : h2
Entity model schema name : PUBLIC
Database Version : H2 - 1.4.185 (2015-01-16)
Database Driver : H2 JDBC Driver - 1.4.185 (2015-01-16)
Database URL : jdbc:h2:file:C:\Program Files\Atlassian\Application Data\JIRA/database/h2db
Database JDBC config : h2 jdbc:h2:file:C:\Program Files\Atlassian\Application Data\JIRA/database/h2db

2018-12-12 07:57:25,520 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (5): [com.atlassian.jira.plugins.jira-development-integration-plugin, com.radiantminds.roadmaps-jira, com.atlassian.jpo, com.atlassian.gadgets.directory, com.pyxis.greenhopper.jira], 286 seconds remaining
2018-12-12 07:57:26,264 ThreadPoolAsyncTaskExecutor::Thread 3 ERROR [c.a.p.osgi.factory.OsgiPlugin] Unable to start the plugin container for plugin 'com.atlassian.jira.plugins.jira-development-integration-plugin'
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'devSummaryUpdateJob': Invocation of init method failed; nested exception is com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericDataSourceException: Generic Entity Exception occurred in deleteByAnd (SQL Exception while executing the following:DELETE FROM PUBLIC.clusteredjob WHERE JOB_ID=? (General error: "java.lang.IllegalArgumentException"; SQL statement:
DELETE FROM PUBLIC.clusteredjob WHERE JOB_ID=? [50000-185]))
at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:136)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:408)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1570)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:545)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:482)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:772)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:839)
at org.eclipse.gemini.blueprint.context.support.AbstractDelegatedExecutionApplicationContext.access$1600(AbstractDelegatedExecutionApplicationContext.java:60)
at org.eclipse.gemini.blueprint.context.support.AbstractDelegatedExecutionApplicationContext$4.run(AbstractDelegatedExecutionApplicationContext.java:325)
at org.eclipse.gemini.blueprint.util.internal.PrivilegedUtils.executeWithCustomTCCL(PrivilegedUtils.java:85)
at org.eclipse.gemini.blueprint.context.support.AbstractDelegatedExecutionApplicationContext.completeRefresh(AbstractDelegatedExecutionApplicationContext.java:290)
at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$CompleteRefreshTask.run(DependencyWaiterApplicationContextExecutor.java:137)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericDataSourceException: Generic Entity Exception occurred in deleteByAnd (SQL Exception while executing the following:DELETE FROM PUBLIC.clusteredjob WHERE JOB_ID=? (General error: "java.lang.IllegalArgumentException"; SQL statement:

...
...
...
2018-12-12 07:57:26,585 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 285 seconds remaining
2018-12-12 07:57:27,717 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 284 seconds remaining
2018-12-12 07:57:28,736 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 283 seconds remaining
2018-12-12 07:57:29,773 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 282 seconds remaining
2018-12-12 07:57:30,810 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 281 seconds remaining
2018-12-12 07:57:31,866 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 280 seconds remaining
2018-12-12 07:57:32,878 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 279 seconds remaining
2018-12-12 07:57:34,030 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 278 seconds remaining
2018-12-12 07:57:34,458 ThreadPoolAsyncTaskExecutor::Thread 10 INFO [c.atlassian.agile.support]

*********************************************************************************
Atlassian GreenHopper v7.9.0-DAILY20180326142825 #926d98943e28d1b1 built 2018-03-26T07:35:44.582-07:00 - plugin starting...
*********************************************************************************

2018-12-12 07:57:35,052 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 277 seconds remaining
2018-12-12 07:57:36,058 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 276 seconds remaining
2018-12-12 07:57:36,347 ThreadPoolAsyncTaskExecutor::Thread 3 ERROR [o.e.g.b.e.i.util.concurrent.RunnableTimedExecution] Closing runnable for context NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.jira.plugins.jira-development-integration-plugin, config=osgibundle:/META-INF/spring/*.xml) did not finish in 10000ms; consider taking a snapshot and then shutdown the VM in case the thread still hangs
2018-12-12 07:57:36,350 ThreadPoolAsyncTaskExecutor::Thread 3 ERROR [o.e.g.b.e.internal.support.ExtenderConfiguration] Application context refresh failed (NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.jira.plugins.jira-development-integration-plugin, config=osgibundle:/META-INF/spring/*.xml))
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'devSummaryUpdateJob': Invocation of init method failed; nested exception is com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericDataSourceException: Generic Entity Exception occurred in deleteByAnd (SQL Exception while executing the following:DELETE FROM PUBLIC.clusteredjob WHERE JOB_ID=? (General error: "java.lang.IllegalArgumentException"; SQL statement:

...
...
...

2018-12-12 07:57:46,752 JIRA-Bootstrap ERROR [c.a.jira.health.HealthChecks] We couldn't start JIRA
2018-12-12 07:57:46,752 JIRA-Bootstrap ERROR [c.a.jira.health.HealthChecks] An error occurred while trying to start JIRA. We can't give you any more detail right now, we suggest checking the logs for more detail and contacting our support team.
See our documentation for more information on contacting our support team and creating a support zip.
2018-12-12 07:57:46,915 JIRA-Bootstrap ERROR [c.a.jira.startup.DefaultJiraLauncher] JIRA has failed to start because of the following errors: [(Event: Level = (EventLevel: fatal) , Key = (EventType: startup-unexpected) , Desc = We couldn't start JIRA , Exception = An error occurred while trying to start JIRA. We can't give you any more detail right now, we suggest checking the logs for more detail and contacting our support team.<br/>See our documentation for more information on contacting our support team and creating a support zip.)]
2018-12-12 07:57:46,960 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Memory Usage:
---------------------------------------------------------------------------------
Heap memory : Used: 485 MiB. Committed: 999 MiB. Max: 1002 MiB
Non-heap memory : Used: 253 MiB. Committed: 274 MiB. Max: 1264 MiB
---------------------------------------------------------------------------------
TOTAL : Used: 738 MiB. Committed: 1273 MiB. Max: 2266 MiB
---------------------------------------------------------------------------------
2018-12-12 07:59:21,158 hipchat-plugin-tasks-executor-0 DEBUG [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] getService bundle [com.atlassian.plugins.base-hipchat-integration-plugin-api]

[Rick Lupori]

Hello, I'm wondering if my logs were deleted from this post. I uploaded them but now I don't see them. Let me try again.

[Rick Lupori]

Here are the errors from my log files.

--------------------------------------------------
-- FROM LOG
--jirasoftware230418180204-stderr.2018-12-12.log
--------------------------------------------------
12-Dec-2018 06:20:14.347 INFO [Thread-32] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8081"]
12-Dec-2018 06:20:14.427 INFO [Thread-32] org.apache.catalina.core.StandardService.stopInternal Stopping service Catalina
12-Dec-2018 06:20:26.004 WARNING [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [ROOT] registered the JDBC driver [org.h2.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
12-Dec-2018 06:20:26.004 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-Dec-2018 06:20:26.004 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-Dec-2018 06:20:26.020 INFO [Thread-32] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8081"]
12-Dec-2018 06:20:26.020 INFO [Thread-33] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [StandardServer[8006]] after stop() had already been called. The second call will be ignored.

--------------------------------------------------
-- FROM LOG
-- jirasoftware230418180204-stdout.2018-12-12.log
--------------------------------------------------
**************************************************************************************
h2 is an in-memory database, and susceptible to corruption when abnormally terminated.
DO NOT USE IN PRODUCTION, please switch to a regular database.
**************************************************************************************

2018-12-12 07:56:22,312 JIRA-Bootstrap INFO [c.a.jira.startup.DatabaseLauncher] Database transactions enabled: true
2018-12-12 07:56:22,315 JIRA-Bootstrap INFO [c.a.jira.startup.DatabaseLauncher] Using JIRA's default for database transaction isolation level: 2
2018-12-12 07:56:22,320 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger]

Database configuration OK

___ Database Configuration ________________

Loading entityengine.xml from : file:/C:/Program%20Files/Atlassian/JIRA/atlassian-jira/WEB-INF/classes/entityengine.xml
Entity model field type name : h2
Entity model schema name : PUBLIC
Database Version : H2 - 1.4.185 (2015-01-16)
Database Driver : H2 JDBC Driver - 1.4.185 (2015-01-16)
Database URL : jdbc:h2:file:C:\Program Files\Atlassian\Application Data\JIRA/database/h2db
Database JDBC config : h2 jdbc:h2:file:C:\Program Files\Atlassian\Application Data\JIRA/database/h2db

2018-12-12 07:57:25,520 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (5): [com.atlassian.jira.plugins.jira-development-integration-plugin, com.radiantminds.roadmaps-jira, com.atlassian.jpo, com.atlassian.gadgets.directory, com.pyxis.greenhopper.jira], 286 seconds remaining
2018-12-12 07:57:26,264 ThreadPoolAsyncTaskExecutor::Thread 3 ERROR [c.a.p.osgi.factory.OsgiPlugin] Unable to start the plugin container for plugin 'com.atlassian.jira.plugins.jira-development-integration-plugin'
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'devSummaryUpdateJob': Invocation of init method failed; nested exception is com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericDataSourceException: Generic Entity Exception occurred in deleteByAnd (SQL Exception while executing the following:DELETE FROM PUBLIC.clusteredjob WHERE JOB_ID=? (General error: "java.lang.IllegalArgumentException"; SQL statement:
DELETE FROM PUBLIC.clusteredjob WHERE JOB_ID=? [50000-185]))
at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:136)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:408)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1570)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:545)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:482)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:772)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:839)
at org.eclipse.gemini.blueprint.context.support.AbstractDelegatedExecutionApplicationContext.access$1600(AbstractDelegatedExecutionApplicationContext.java:60)
at org.eclipse.gemini.blueprint.context.support.AbstractDelegatedExecutionApplicationContext$4.run(AbstractDelegatedExecutionApplicationContext.java:325)
at org.eclipse.gemini.blueprint.util.internal.PrivilegedUtils.executeWithCustomTCCL(PrivilegedUtils.java:85)
at org.eclipse.gemini.blueprint.context.support.AbstractDelegatedExecutionApplicationContext.completeRefresh(AbstractDelegatedExecutionApplicationContext.java:290)
at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$CompleteRefreshTask.run(DependencyWaiterApplicationContextExecutor.java:137)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericDataSourceException: Generic Entity Exception occurred in deleteByAnd (SQL Exception while executing the following:DELETE FROM PUBLIC.clusteredjob WHERE JOB_ID=? (General error: "java.lang.IllegalArgumentException"; SQL statement:

...
...
...
2018-12-12 07:57:26,585 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 285 seconds remaining
2018-12-12 07:57:27,717 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 284 seconds remaining
2018-12-12 07:57:28,736 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 283 seconds remaining
2018-12-12 07:57:29,773 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 282 seconds remaining
2018-12-12 07:57:30,810 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 281 seconds remaining
2018-12-12 07:57:31,866 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 280 seconds remaining
2018-12-12 07:57:32,878 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 279 seconds remaining
2018-12-12 07:57:34,030 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 278 seconds remaining
2018-12-12 07:57:34,458 ThreadPoolAsyncTaskExecutor::Thread 10 INFO [c.atlassian.agile.support]

*********************************************************************************
Atlassian GreenHopper v7.9.0-DAILY20180326142825 #926d98943e28d1b1 built 2018-03-26T07:35:44.582-07:00 - plugin starting...
*********************************************************************************

2018-12-12 07:57:35,052 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 277 seconds remaining
2018-12-12 07:57:36,058 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 276 seconds remaining
2018-12-12 07:57:36,347 ThreadPoolAsyncTaskExecutor::Thread 3 ERROR [o.e.g.b.e.i.util.concurrent.RunnableTimedExecution] Closing runnable for context NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.jira.plugins.jira-development-integration-plugin, config=osgibundle:/META-INF/spring/*.xml) did not finish in 10000ms; consider taking a snapshot and then shutdown the VM in case the thread still hangs
2018-12-12 07:57:36,350 ThreadPoolAsyncTaskExecutor::Thread 3 ERROR [o.e.g.b.e.internal.support.ExtenderConfiguration] Application context refresh failed (NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.jira.plugins.jira-development-integration-plugin, config=osgibundle:/META-INF/spring/*.xml))
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'devSummaryUpdateJob': Invocation of init method failed; nested exception is com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericDataSourceException: Generic Entity Exception occurred in deleteByAnd (SQL Exception while executing the following:DELETE FROM PUBLIC.clusteredjob WHERE JOB_ID=? (General error: "java.lang.IllegalArgumentException"; SQL statement:

...
...
...

2018-12-12 07:57:46,752 JIRA-Bootstrap ERROR [c.a.jira.health.HealthChecks] We couldn't start JIRA
2018-12-12 07:57:46,752 JIRA-Bootstrap ERROR [c.a.jira.health.HealthChecks] An error occurred while trying to start JIRA. We can't give you any more detail right now, we suggest checking the logs for more detail and contacting our support team.
See our documentation for more information on contacting our support team and creating a support zip.
2018-12-12 07:57:46,915 JIRA-Bootstrap ERROR [c.a.jira.startup.DefaultJiraLauncher] JIRA has failed to start because of the following errors: [(Event: Level = (EventLevel: fatal) , Key = (EventType: startup-unexpected) , Desc = We couldn't start JIRA , Exception = An error occurred while trying to start JIRA. We can't give you any more detail right now, we suggest checking the logs for more detail and contacting our support team.<br/>See our documentation for more information on contacting our support team and creating a support zip.)]
2018-12-12 07:57:46,960 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Memory Usage:
---------------------------------------------------------------------------------
Heap memory : Used: 485 MiB. Committed: 999 MiB. Max: 1002 MiB
Non-heap memory : Used: 253 MiB. Committed: 274 MiB. Max: 1264 MiB
---------------------------------------------------------------------------------
TOTAL : Used: 738 MiB. Committed: 1273 MiB. Max: 2266 MiB
---------------------------------------------------------------------------------
2018-12-12 07:59:21,158 hipchat-plugin-tasks-executor-0 DEBUG [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] getService bundle [com.atlassian.plugins.base-hipchat-integration-plugin-api]

[Rick Lupori]

Let me try in chunks...

--------------------------------------------------
-- FROM LOG
--jirasoftware230418180204-stderr.2018-12-12.log
--------------------------------------------------
12-Dec-2018 06:20:14.347 INFO [Thread-32] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8081"]
12-Dec-2018 06:20:14.427 INFO [Thread-32] org.apache.catalina.core.StandardService.stopInternal Stopping service Catalina
12-Dec-2018 06:20:26.004 WARNING [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [ROOT] registered the JDBC driver [org.h2.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
12-Dec-2018 06:20:26.004 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-Dec-2018 06:20:26.004 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-Dec-2018 06:20:26.020 INFO [Thread-32] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8081"]
12-Dec-2018 06:20:26.020 INFO [Thread-33] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [StandardServer[8006]] after stop() had already been called. The second call will be ignored.

[Rick Lupori]

-------------------------------------------------
-- FROM LOG
-- jirasoftware230418180204-stdout.2018-12-12.log
--------------------------------------------------
**************************************************************************************
h2 is an in-memory database, and susceptible to corruption when abnormally terminated.
DO NOT USE IN PRODUCTION, please switch to a regular database.
**************************************************************************************

2018-12-12 07:56:22,312 JIRA-Bootstrap INFO [c.a.jira.startup.DatabaseLauncher] Database transactions enabled: true
2018-12-12 07:56:22,315 JIRA-Bootstrap INFO [c.a.jira.startup.DatabaseLauncher] Using JIRA's default for database transaction isolation level: 2
2018-12-12 07:56:22,320 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger]

Database configuration OK

___ Database Configuration ________________

Loading entityengine.xml from : file:/C:/Program%20Files/Atlassian/JIRA/atlassian-jira/WEB-INF/classes/entityengine.xml
Entity model field type name : h2
Entity model schema name : PUBLIC
Database Version : H2 - 1.4.185 (2015-01-16)
Database Driver : H2 JDBC Driver - 1.4.185 (2015-01-16)
Database URL : jdbc:h2:file:C:\Program Files\Atlassian\Application Data\JIRA/database/h2db
Database JDBC config : h2 jdbc:h2:file:C:\Program Files\Atlassian\Application Data\JIRA/database/h2db

[Rick Lupori]

...
...
...
2018-12-12 07:57:26,585 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 285 seconds remaining
2018-12-12 07:57:27,717 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 284 seconds remaining
2018-12-12 07:57:28,736 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 283 seconds remaining
2018-12-12 07:57:29,773 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 282 seconds remaining
2018-12-12 07:57:30,810 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 281 seconds remaining
2018-12-12 07:57:31,866 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 280 seconds remaining
2018-12-12 07:57:32,878 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 279 seconds remaining
2018-12-12 07:57:34,030 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 278 seconds remaining
2018-12-12 07:57:34,458 ThreadPoolAsyncTaskExecutor::Thread 10 INFO [c.atlassian.agile.support]

*********************************************************************************
Atlassian GreenHopper v7.9.0-DAILY20180326142825 #926d98943e28d1b1 built 2018-03-26T07:35:44.582-07:00 - plugin starting...
*********************************************************************************

2018-12-12 07:57:35,052 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 277 seconds remaining
2018-12-12 07:57:36,058 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 276 seconds remaining
2018-12-12 07:57:36,347 ThreadPoolAsyncTaskExecutor::Thread 3 ERROR [o.e.g.b.e.i.util.concurrent.RunnableTimedExecution] Closing runnable for context NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.jira.plugins.jira-development-integration-plugin, config=osgibundle:/META-INF/spring/*.xml) did not finish in 10000ms; consider taking a snapshot and then shutdown the VM in case the thread still hangs
2018-12-12 07:57:36,350 ThreadPoolAsyncTaskExecutor::Thread 3 ERROR [o.e.g.b.e.internal.support.ExtenderConfiguration] Application context refresh failed (NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.jira.plugins.jira-development-integration-plugin, config=osgibundle:/META-INF/spring/*.xml))
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'devSummaryUpdateJob': Invocation of init method failed; nested exception is com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericDataSourceException: Generic Entity Exception occurred in deleteByAnd (SQL Exception while executing the following:DELETE FROM PUBLIC.clusteredjob WHERE JOB_ID=? (General error: "java.lang.IllegalArgumentException"; SQL statement:

[Rick Lupori]

...
...
...

2018-12-12 07:57:46,752 JIRA-Bootstrap ERROR [c.a.jira.health.HealthChecks] We couldn't start JIRA
2018-12-12 07:57:46,752 JIRA-Bootstrap ERROR [c.a.jira.health.HealthChecks] An error occurred while trying to start JIRA. We can't give you any more detail right now, we suggest checking the logs for more detail and contacting our support team.
See our documentation for more information on contacting our support team and creating a support zip.
2018-12-12 07:57:46,915 JIRA-Bootstrap ERROR [c.a.jira.startup.DefaultJiraLauncher] JIRA has failed to start because of the following errors: [(Event: Level = (EventLevel: fatal) , Key = (EventType: startup-unexpected) , Desc = We couldn't start JIRA , Exception = An error occurred while trying to start JIRA. We can't give you any more detail right now, we suggest checking the logs for more detail and contacting our support team.<br/>See our documentation for more information on contacting our support team and creating a support zip.)]
2018-12-12 07:57:46,960 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Memory Usage:
---------------------------------------------------------------------------------
Heap memory : Used: 485 MiB. Committed: 999 MiB. Max: 1002 MiB
Non-heap memory : Used: 253 MiB. Committed: 274 MiB. Max: 1264 MiB
---------------------------------------------------------------------------------
TOTAL : Used: 738 MiB. Committed: 1273 MiB. Max: 2266 MiB
---------------------------------------------------------------------------------
2018-12-12 07:59:21,158 hipchat-plugin-tasks-executor-0 DEBUG [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] getService bundle [com.atlassian.plugins.base-hipchat-integration-plugin-api]

[Rick Lupori]

I hope those went through.... Thank you, Rick

[Nic Brough -Adaptavist- · Accepted solution]

Ok, that looks like you are having SQL errors, which suggest you may have a damaged database.  This is not unexpected for the internal database (there's good reasons for the warning about the database type not being suitable for production)

The next thing I would try is restoring from the last backup you took - if this has the same errors, we know it's data or config, if it works, we know the database is corrupt.  If you didn't do one manually, check <jira home>/export for the newest file.

[Rick Lupori]

Thank you very much again. The problem is all the articles I've found that explains how to restore from the activeobjects.xml and entities.xml file in the <jira home>/export folders requires that I restore through the system which won't load for me....https://confluence.atlassian.com/adminjiraserver073/restoring-data-from-an-xml-backup-861253849.html#Restoringdatafromanxmlbackup-restorexmldata . Is there another way? I tried to also do a search for these files in <jira home> folders and could not find them. Can you please point me to an article that could help me restore them?

Thanks, Rick

[Nic Brough -Adaptavist-]

There's not much we can point you at, it sounds like you are looking at the right docs to do a restore, but you're actually blocked before you get there.

Is this Jira install you're working with a completely clean empty Jira?

[Rick Lupori]

No it's not. I had a lot of project data information is like to try to restore.

Rick

[Rick Lupori]

With those activeobjects.xml and entities.xml file backups, can I do a complete reinstall of jira and then restore from those backups? Would all my project data information be restored?

Thanks,

Rick

[Nic Brough -Adaptavist-]

The full xml import will destroy everything you have in the target Jira.  I wouldn't ever try that on anything other than an empty Jira.

To do that, I'd start again - grab the installer for the version you want, run it, and let it install.  Tell it to use new directories and an empty database you've set up for it.  After install, login and check the basics are there, then use "import"

[Rick Lupori]

Hi Nic, I started a new thread because I didn't want to keep bothering you. I was referred back to this one. 

I'm not sure what you mean by the target Jira. When you say empty Jira do you mean uninstall it first? So if I uninstall Jira and all of the components I installed including:

Jira Software (Server) 10 Users: Starter License, and Portfolio for Jira (Server) for JIRA (Server) 10 Users: Starter License. 

...would I be able to reinstall Jira Software, and Portfolio for Jira, and then re-import all the project data I had from the most recent activeobjects.xml and entities.xml files?

Thank you again.

Rick 

[Rick Lupori]

Whoops almost forgot...and also link back up to the licenses I had before? Or would I have to re-purchase those licenses?

Thanks,

Rick

[Nic Brough -Adaptavist-]

Yes, "empty" does mean a new installation.  If you want it on the same machine with the same settings as the old one, you will need to uninstall it.  Also you'll need to clear out the database it is using.

The licences are done by keys - you can paste those keys into the new installation, no new purchase or rebuilding needed.

[Rick Lupori]

OK you have been extremely helpful. Thank you again. Before I begin I wanted to mention the version I installed back in January was 7.9.0 and now the new installation package I downloaded is 7.13.0. After I uninstall 7.9.0 through Add/Remove files and delete all the files in the C:\Program Files\Atlassian folder which I'm assuming will also delete the database, will I have any issues installing the newer version and restoring from my backup files? Or should I install the one I installed back in January ?

Thanks,

Rick

[Nic Brough -Adaptavist-]

In theory, you can often import an older version of a backup into a more recent Jira.  This is not recommended, as if you have any problems with it, you're going to have to go back to where you started.

I would very strongly recommend that you install an "empty" 7.9.0 and restore the data into that.

>delete all the files in the C:\Program Files\Atlassian folder which I'm assuming will also delete the database

No, it will not - the database is a separate service (it may be running on the same server as Jira).  You will need to nip into to there and ideally create a new empty database for Jira to use.

[Rick Lupori]

I did a complete uninstall. I reinstalled the 7.9.0 install and the same error happened. When I originally installed Jira I installed it with all the defaults. I connected it to the original database it came with. 

So I'm not sure what you mean by "nip into there and ideally create a new empty database".

I can't be the only person running into this. There must be a series of documented steps on how to reinstall Jira from scratch?

Thanks,

Rick

[Nic Brough -Adaptavist-]

It's not about "reinstall", it's more simple than that.  You install a new Jira.  That's all.  It doesn't matter if the machine had an old Jira on it as long as you've deleted the install and home directories for the last install.

The important thing here seems to be that you're connecting to the old database.  Do not do that, we already know it was broken.  Create a new, clean, empty database as it says in the standard install guide.

[Rick Lupori]

Thank you for the quick response. Correct me if I'm wrong but in order to create a new database you have to do that within the Jira software running on your browser, correct? I can't get that far. As soon as I launch the new installed version of Jira I get the Atlassian JIRA is starting up... Loading Jira add-ons ..." initialization setup screen with the juggling balls. After about 2 to 3 minutes I get the error. How do I create a new, clean, empty database if I can't get Jira to launch?

Thanks,

Rick

[Rick Lupori]

I didn't delete the old directories from the old install. I'm in now. I lpan to do the "I'll set it up myself" option correct? Or should I choose the "Set it up for me"? I guess it doesn't matter since now I know how to reinstall from scratch. I hope it's smooth sailing from here on out.

Thank you again,

Rick

[Rick Lupori]

HI Nic, I'm all set now. Or at least I think I am. I am now linked to a SQL Server database. My only question I have remaining is during the restore I entered the entitites.xml file. I never did anything with the activeobjects.xml file? What is that file and how do I restore it?

thanks,

Rick

[Rick Lupori]

So I now have the option to create my own database now in the Database Setup screen. Can I select SQL Server and then restore from my backup instead of going through and selecting the "Built In (for evaluation or demonstration)" which created this mess?

Thanks,

Rick