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JIRA filling up logfiles with endless JNDI exceptions

Patrick Toma
Patrick Toma April 20, 2012

We're running JIRA 5.0, with JDK 1.6.0_24, running on a 64 bit linux VM (Linux 2.6.18-274.18.1.0.1.el5). The app is running on Apache Tomcat/6.0.35.

The application appears to be running normally but in the catalina.out and atlassian-jira.log files, it continuously spews out exceptions as shown below.

This makes the logfiles unusable (its impossible to find anything), also they are constantly filling up, which is also a nuisance.

We are planning to go live in production with JIRA 5.0 (migrating our teams over from v3.6) on April 27. We'd like to go into Production with this issue resolved.

Thanks.

2012-04-20 02:49:31,819 http-8080-13 WARN anonymous 169x12957x1 115kvla 172.19.107.69 /rest/usermanagement/1/user/group/nested core.entity.transaction.JNDIFactory JNDIFactory.getUserTransaction Failed to find UserTransaction named java:comp/env/UserTransaction in JNDI.

2012-04-20 02:49:31,821 http-8080-13 WARN anonymous 169x12957x1 115kvla 172.19.107.69 /rest/usermanagement/1/user/group/nested core.entity.transaction.JNDIFactory NamingException while finding UserTransaction named java:comp/env/UserTransaction in JNDI.

javax.naming.NameNotFoundException: Name UserTransaction is not bound in this Context

at org.apache.naming.NamingContext.lookup(NamingContext.java:770)

at org.apache.naming.NamingContext.lookup(NamingContext.java:140)

at org.apache.naming.NamingContext.lookup(NamingContext.java:781)

at org.apache.naming.NamingContext.lookup(NamingContext.java:140)

at org.apache.naming.NamingContext.lookup(NamingContext.java:781)

at org.apache.naming.NamingContext.lookup(NamingContext.java:153)

at org.apache.naming.SelectorContext.lookup(SelectorContext.java:152)

at javax.naming.InitialContext.lookup(InitialContext.java:392)

at org.ofbiz.core.entity.transaction.JNDIFactory.getUserTransaction(JNDIFactory.java:113)

at org.ofbiz.core.entity.TransactionFactory.getUserTransaction(TransactionFactory.java:93)

at org.ofbiz.core.entity.TransactionUtil.getStatus(TransactionUtil.java:81)

at org.ofbiz.core.entity.jdbc.SQLProcessor.getConnection(SQLProcessor.java:412)

at org.ofbiz.core.entity.GenericDAO.insert(GenericDAO.java:98)

at org.ofbiz.core.entity.GenericHelperDAO.create(GenericHelperDAO.java:64)

at org.ofbiz.core.entity.GenericDelegator.create(GenericDelegator.java:487)

at org.ofbiz.core.entity.GenericDelegator.create(GenericDelegator.java:467)

at org.ofbiz.core.entity.GenericValue.create(GenericValue.java:98)

at com.atlassian.crowd.embedded.ofbiz.db.OfBizHelper.createValue(OfBizHelper.java:162)

at com.atlassian.crowd.embedded.ofbiz.OfBizUserDao.storeAttributeValue(OfBizUserDao.java:277)

at com.atlassian.crowd.embedded.ofbiz.OfBizUserDao.storeAttributeValues(OfBizUserDao.java:254)

at com.atlassian.crowd.embedded.ofbiz.OfBizUserDao.storeAttributes(OfBizUserDao.java:237)

at com.atlassian.crowd.directory.AbstractInternalDirectory.processAuthentication(AbstractInternalDirectory.java:196)

at com.atlassian.crowd.directory.AbstractInternalDirectory.authenticate(AbstractInternalDirectory.java:148)

at com.atlassian.crowd.manager.directory.DirectoryManagerGeneric.authenticateUser(DirectoryManagerGeneric.java:277)

at com.atlassian.crowd.manager.application.ApplicationServiceGeneric.authenticateUser(ApplicationServiceGeneric.java:122)

at com.atlassian.crowd.embedded.core.CrowdServiceImpl.authenticate(CrowdServiceImpl.java:67)

at com.atlassian.crowd.embedded.core.DelegatingCrowdService.authenticate(DelegatingCrowdService.java:35)

at com.atlassian.crowd.embedded.core.FilteredCrowdServiceImpl.authenticate(FilteredCrowdServiceImpl.java:43)

at com.atlassian.jira.security.login.JiraSeraphAuthenticator.crowdServiceAuthenticate(JiraSeraphAuthenticator.java:75)

at com.atlassian.jira.security.login.JiraSeraphAuthenticator.authenticate(JiraSeraphAuthenticator.java:40)

at com.atlassian.seraph.auth.DefaultAuthenticator.login(DefaultAuthenticator.java:94)

at com.atlassian.seraph.filter.PasswordBasedLoginFilter.runAuthentication(PasswordBasedLoginFilter.java:127)

at com.atlassian.seraph.filter.PasswordBasedLoginFilter.login(PasswordBasedLoginFilter.java:72)

at com.atlassian.seraph.filter.BaseLoginFilter.doFilter(BaseLoginFilter.java:130)

at com.atlassian.jira.web.filters.JiraLoginFilter.doFilter(JiraLoginFilter.java:70)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)

at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)

at com.atlassian.oauth.serviceprovider.internal.servlet.OAuthFilter.doFilter(OAuthFilter.java:71)

at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)

at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)

at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)

at com.atlassian.plugins.rest.module.servlet.RestSeraphFilter.doFilter(RestSeraphFilter.java:40)

at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)

at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)

at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)

at com.atlassian.crowd.plugin.rest.filter.BasicApplicationAuthenticationFilter.doFilter(BasicApplicationAuthenticationFilter.java:67)

at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)

at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)

at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)

at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

at com.atlassian.johnson.filters.AbstractJohnsonFilter.doFilter(AbstractJohnsonFilter.java:71)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:350)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

at com.atlassian.gzipfilter.GzipFilter.doFilterInternal(GzipFilter.java:81)

at com.atlassian.gzipfilter.GzipFilter.doFilter(GzipFilter.java:51)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)

at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)

at com.atlassian.crowd.plugin.rest.filter.RestServiceVersionFilter.doFilter(RestServiceVersionFilter.java:56)

at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)

at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)

at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)

at com.sysbliss.jira.plugins.workflow.servlet.JWDSendRedirectFilter.doFilter(JWDSendRedirectFilter.java:25)

at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)

at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)

at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)

at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

at com.atlassian.jira.web.filters.steps.ChainedFilterStepRunner.doFilter(ChainedFilterStepRunner.java:78)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

at com.atlassian.core.filters.cache.AbstractCachingFilter.doFilter(AbstractCachingFilter.java:33)

at com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

at com.atlassian.core.filters.encoding.AbstractEncodingFilter.doFilter(AbstractEncodingFilter.java:41)

at com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31)

at com.atlassian.jira.web.filters.PathMatchingEncodingFilter.doFilter(PathMatchingEncodingFilter.java:45)

at com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

at com.atlassian.jira.web.monitor.ActiveRequestsFilter$PassToChainFilterFunc.doFilter(ActiveRequestsFilter.java:346)

at com.atlassian.jira.web.monitor.ActiveRequestsFilter$DebugLogFilterFunc.doFilter(ActiveRequestsFilter.java:463)

at com.atlassian.jira.web.monitor.ActiveRequestsFilter.doFilter(ActiveRequestsFilter.java:173)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

at com.atlassian.jira.startup.JiraStartupChecklistFilter.doFilter(JiraStartupChecklistFilter.java:75)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

at com.atlassian.multitenant.servlet.MultiTenantServletFilter.doFilter(MultiTenantServletFilter.java:91)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

at com.atlassian.jira.web.filters.steps.ChainedFilterStepRunner.doFilter(ChainedFilterStepRunner.java:78)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)

at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)

at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)

at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)

at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)

at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)

at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859)

at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:602)

at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)

at java.lang.Thread.run(Thread.java:662)

2012-04-20 02:49:31,822 http-8080-13 WARN anonymous 169x12957x1 115kvla 172.19.107.69 /rest/usermanagement/1/user/group/nested core.entity.transaction.JNDIFactory JNDIFactory.getUserTransaction Failed to find UserTransaction named java:comp/env/UserTransaction in JNDI.

2012-04-20 02:49:31,829 http-8080-13 WARN anonymous 169x12957x1 115kvla 172.19.107.69 /rest/usermanagement/1/user/group/nested core.entity.transaction.JNDIFactory NamingException while finding UserTransaction named java:comp/env/UserTransaction in JNDI.

javax.naming.NameNotFoundException: Name UserTransaction is not bound in this Context

at org.apache.naming.NamingContext.lookup(NamingContext.java:770)

at org.apache.naming.NamingContext.lookup(NamingContext.java:140)

at org.apache.naming.NamingContext.lookup(NamingContext.java:781)

at org.apache.naming.NamingContext.lookup(NamingContext.java:140)

at org.apache.naming.NamingContext.lookup(NamingContext.java:781)

at org.apache.naming.NamingContext.lookup(NamingContext.java:153)

at org.apache.naming.SelectorContext.lookup(SelectorContext.java:152)

at javax.naming.InitialContext.lookup(InitialContext.java:392)

at org.ofbiz.core.entity.transaction.JNDIFactory.getUserTransaction(JNDIFactory.java:113)

at org.ofbiz.core.entity.TransactionFactory.getUserTransaction(TransactionFactory.java:93)

at org.ofbiz.core.entity.TransactionUtil.getStatus(TransactionUtil.java:81)

at org.ofbiz.core.entity.jdbc.SQLProcessor.getConnection(SQLProcessor.java:412)

at org.ofbiz.core.entity.jdbc.SQLProcessor.prepareStatement(SQLProcessor.java:515)

at org.ofbiz.core.entity.GenericDAO.selectListIteratorByCondition(GenericDAO.java:1034)

at org.ofbiz.core.entity.GenericDAO.selectByAnd(GenericDAO.java:605)

at org.ofbiz.core.entity.GenericHelperDAO.findByAnd(GenericHelperDAO.java:131)

at org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:788)

at org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:773)

at org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:750)

at sun.reflect.GeneratedMethodAccessor32.invoke(Unknown Source)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at com.atlassian.multitenant.impl.MultiTenantComponentFactoryImpl$AbstractMultiTenantAwareInvocationHandler.invokeInternal(MultiTenantComponentFactoryImpl.java:181)

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2 answers

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Colin Goudie
Colin Goudie
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April 20, 2012

It sounds like you have done a custom war/ear installation but haven't configured the Context file properly.

See the UserTransaction resource that is needed. It is documented here

http://confluence.atlassian.com/display/JIRA042/Installing+JIRA+on+Tomcat+6.0#InstallingJIRAonTomcat60-5ConfigureTomcat

Specifically adding this part into your ROOT.xml or jira.xml

<Resource name="UserTransaction" auth="Container" type="javax.transaction.UserTransaction"
    factory="org.objectweb.jotm.UserTransactionFactory" jotm.timeout="60"/>
  <Manager pathname=""/>

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Michael Demey
Michael Demey May 28, 2012

Hi,

piggybacking on this question and your comment:

I have this same error (4.4) and the config file has the exact same configuration as you posted, is there any other solution to this problem? Or any known causes that I can look into so that I can solve thel or exclude them as sources of this issue?

Thanks in advance!

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erik chen2
erik chen
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November 15, 2014

just cp dist-tomcat/tomat-6/jira.xml to tomcat/conf/Catalina/locahost

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erik chen2
erik chen
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November 15, 2014

just cp dist-tomcat/tomat-6/jira.xml to tomcat/conf/Catalina/locahost

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