JIRA Unable to esablish a connection with the database.

Our company has use JIRA for nearly two years, and it helps a lot in bug tracing. But recently our testers find it has a problem which makes them can not work. We will really appreciate it if anyone can solve this problem.

1.Problem: end users can not connect to JIRA, once them type the url it will report errors like below:

HTTP Status 500 - org.ofbiz.core.entity.GenericDataSourceException: Unable to esablish a connection with the database. (File input/output error: /var/atlassian/application-data/jira/database/jiradb.log)
type Exception report
message org.ofbiz.core.entity.GenericDataSourceException: Unable to esablish a connection with the database. (File input/output error: /var/atlassian/application-data/jira/database/jiradb.log)
description The server encountered an internal error (org.ofbiz.core.entity.GenericDataSourceException: Unable to esablish a connection with the database. (File input/output error: /var/atlassian/application-data/jira/database/jiradb.log)) that prevented it from fulfilling this request.
exception
com.atlassian.jira.crowd.embedded.ofbiz.db.DataAccessException: org.ofbiz.core.entity.GenericDataSourceException: Unable to esablish a connection with the database. (File input/output error: /var/atlassian/application-data/jira/database/jiradb.log)
	com.atlassian.jira.crowd.embedded.ofbiz.db.OfBizHelper.findByAnd(OfBizHelper.java:51)
	com.atlassian.jira.crowd.embedded.ofbiz.OfBizUserDao.findAttributesGenericValues(OfBizUserDao.java:335)
	com.atlassian.jira.crowd.embedded.ofbiz.OfBizUserDao.findByNameWithAttributes(OfBizUserDao.java:108)
	com.atlassian.crowd.directory.AbstractInternalDirectory.findUserWithAttributesByName(AbstractInternalDirectory.java:148)
	com.atlassian.crowd.manager.directory.DirectoryManagerGeneric.findUserWithAttributesByName(DirectoryManagerGeneric.java:291)
	com.atlassian.crowd.manager.application.ApplicationServiceGeneric.findUserWithAttributesByName(ApplicationServiceGeneric.java:332)
	com.atlassian.crowd.embedded.core.CrowdServiceImpl.getUserWithAttributes(CrowdServiceImpl.java:109)
	com.atlassian.crowd.embedded.core.DelegatingCrowdService.getUserWithAttributes(DelegatingCrowdService.java:45)
	com.atlassian.crowd.embedded.core.FilteredCrowdServiceImpl.getUserWithAttributes(FilteredCrowdServiceImpl.java:50)
	com.atlassian.jira.security.login.LoginStoreImpl.getLoginInfo(LoginStoreImpl.java:108)
	com.atlassian.jira.security.login.LoginManagerImpl.getLoginInfo(LoginManagerImpl.java:92)
	com.atlassian.jira.security.login.LoginManagerImpl.performElevatedSecurityCheck(LoginManagerImpl.java:101)
	com.atlassian.jira.security.login.JiraElevatedSecurityGuard.performElevatedSecurityCheck(JiraElevatedSecurityGuard.java:25)
	com.atlassian.seraph.filter.PasswordBasedLoginFilter.runAuthentication(PasswordBasedLoginFilter.java:111)
	com.atlassian.seraph.filter.PasswordBasedLoginFilter.login(PasswordBasedLoginFilter.java:72)
	com.atlassian.seraph.filter.BaseLoginFilter.doFilter(BaseLoginFilter.java:131)
	com.atlassian.jira.web.filters.JiraLoginFilter.doFilter(JiraLoginFilter.java:70)
	com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	com.atlassian.oauth.serviceprovider.internal.servlet.OAuthFilter.doFilter(OAuthFilter.java:55)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	com.atlassian.prettyurls.filter.PrettyUrlsCombinedMatchDispatcherFilter.doFilter(PrettyUrlsCombinedMatchDispatcherFilter.java:61)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
	com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
	com.atlassian.util.profiling.filters.ProfilingFilter.doFilter(ProfilingFilter.java:99)
	com.atlassian.jira.web.filters.JIRAProfilingFilter.doFilter(JIRAProfilingFilter.java:19)
	com.atlassian.johnson.filters.AbstractJohnsonFilter.doFilter(AbstractJohnsonFilter.java:71)
	org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:176)
	org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:145)
	org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:92)
	org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:394)
	com.atlassian.gzipfilter.GzipFilter.doFilterInternal(GzipFilter.java:74)
	com.atlassian.gzipfilter.GzipFilter.doFilter(GzipFilter.java:51)
	com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	com.atlassian.plugin.remotable.plugin.module.oauth.OAuth2LOFilter.doFilter(OAuth2LOFilter.java:70)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	com.atlassian.plugin.remotable.host.common.service.http.bigpipe.BigPipeRequestIdFilter.doFilter(BigPipeRequestIdFilter.java:33)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	com.atlassian.prettyurls.filter.PrettyUrlsCombinedMatchDispatcherFilter.doFilter(PrettyUrlsCombinedMatchDispatcherFilter.java:61)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	com.sysbliss.jira.plugins.workflow.servlet.JWDSendRedirectFilter.doFilter(JWDSendRedirectFilter.java:25)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
	com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
	com.atlassian.jira.web.filters.steps.ChainedFilterStepRunner.doFilter(ChainedFilterStepRunner.java:84)
	com.atlassian.core.filters.cache.AbstractCachingFilter.doFilter(AbstractCachingFilter.java:33)
	com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31)
	com.atlassian.core.filters.encoding.AbstractEncodingFilter.doFilter(AbstractEncodingFilter.java:41)
	com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31)
	com.atlassian.jira.web.filters.PathMatchingEncodingFilter.doFilter(PathMatchingEncodingFilter.java:49)
	com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31)
	com.atlassian.jira.startup.JiraStartupChecklistFilter.doFilter(JiraStartupChecklistFilter.java:74)
	com.atlassian.jira.web.filters.steps.ChainedFilterStepRunner.doFilter(ChainedFilterStepRunner.java:84)
	com.atlassian.jira.web.filters.JiraFirstFilter.doFilter(JiraFirstFilter.java:57)

root cause
org.ofbiz.core.entity.GenericDataSourceException: Unable to esablish a connection with the database. (File input/output error: /var/atlassian/application-data/jira/database/jiradb.log)
	org.ofbiz.core.entity.jdbc.SQLProcessor.getConnection(SQLProcessor.java:371)
	org.ofbiz.core.entity.jdbc.SQLProcessor.prepareStatement(SQLProcessor.java:515)
	org.ofbiz.core.entity.GenericDAO.selectListIteratorByCondition(GenericDAO.java:1040)
	org.ofbiz.core.entity.GenericDAO.selectByAnd(GenericDAO.java:608)
	org.ofbiz.core.entity.GenericHelperDAO.findByAnd(GenericHelperDAO.java:131)
	org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:788)
	org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:773)
	org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:750)
	com.atlassian.jira.crowd.embedded.ofbiz.db.OfBizHelper.findByAnd(OfBizHelper.java:47)
	com.atlassian.jira.crowd.embedded.ofbiz.OfBizUserDao.findAttributesGenericValues(OfBizUserDao.java:335)
	com.atlassian.jira.crowd.embedded.ofbiz.OfBizUserDao.findByNameWithAttributes(OfBizUserDao.java:108)
	com.atlassian.crowd.directory.AbstractInternalDirectory.findUserWithAttributesByName(AbstractInternalDirectory.java:148)
	com.atlassian.crowd.manager.directory.DirectoryManagerGeneric.findUserWithAttributesByName(DirectoryManagerGeneric.java:291)
	com.atlassian.crowd.manager.application.ApplicationServiceGeneric.findUserWithAttributesByName(ApplicationServiceGeneric.java:332)
	com.atlassian.crowd.embedded.core.CrowdServiceImpl.getUserWithAttributes(CrowdServiceImpl.java:109)
	com.atlassian.crowd.embedded.core.DelegatingCrowdService.getUserWithAttributes(DelegatingCrowdService.java:45)
	com.atlassian.crowd.embedded.core.FilteredCrowdServiceImpl.getUserWithAttributes(FilteredCrowdServiceImpl.java:50)
	com.atlassian.jira.security.login.LoginStoreImpl.getLoginInfo(LoginStoreImpl.java:108)
	com.atlassian.jira.security.login.LoginManagerImpl.getLoginInfo(LoginManagerImpl.java:92)
	com.atlassian.jira.security.login.LoginManagerImpl.performElevatedSecurityCheck(LoginManagerImpl.java:101)
	com.atlassian.jira.security.login.JiraElevatedSecurityGuard.performElevatedSecurityCheck(JiraElevatedSecurityGuard.java:25)
	com.atlassian.seraph.filter.PasswordBasedLoginFilter.runAuthentication(PasswordBasedLoginFilter.java:111)
	com.atlassian.seraph.filter.PasswordBasedLoginFilter.login(PasswordBasedLoginFilter.java:72)
	com.atlassian.seraph.filter.BaseLoginFilter.doFilter(BaseLoginFilter.java:131)
	com.atlassian.jira.web.filters.JiraLoginFilter.doFilter(JiraLoginFilter.java:70)
	com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	com.atlassian.oauth.serviceprovider.internal.servlet.OAuthFilter.doFilter(OAuthFilter.java:55)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	com.atlassian.prettyurls.filter.PrettyUrlsCombinedMatchDispatcherFilter.doFilter(PrettyUrlsCombinedMatchDispatcherFilter.java:61)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
	com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
	com.atlassian.util.profiling.filters.ProfilingFilter.doFilter(ProfilingFilter.java:99)
	com.atlassian.jira.web.filters.JIRAProfilingFilter.doFilter(JIRAProfilingFilter.java:19)
	com.atlassian.johnson.filters.AbstractJohnsonFilter.doFilter(AbstractJohnsonFilter.java:71)
	org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:176)
	org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:145)
	org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:92)
	org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:394)
	com.atlassian.gzipfilter.GzipFilter.doFilterInternal(GzipFilter.java:74)
	com.atlassian.gzipfilter.GzipFilter.doFilter(GzipFilter.java:51)
	com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	com.atlassian.plugin.remotable.plugin.module.oauth.OAuth2LOFilter.doFilter(OAuth2LOFilter.java:70)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	com.atlassian.plugin.remotable.host.common.service.http.bigpipe.BigPipeRequestIdFilter.doFilter(BigPipeRequestIdFilter.java:33)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	com.atlassian.prettyurls.filter.PrettyUrlsCombinedMatchDispatcherFilter.doFilter(PrettyUrlsCombinedMatchDispatcherFilter.java:61)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	com.sysbliss.jira.plugins.workflow.servlet.JWDSendRedirectFilter.doFilter(JWDSendRedirectFilter.java:25)
	com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
	com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
	com.atlassian.jira.web.filters.steps.ChainedFilterStepRunner.doFilter(ChainedFilterStepRunner.java:84)
	com.atlassian.core.filters.cache.AbstractCachingFilter.doFilter(AbstractCachingFilter.java:33)
	com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31)
	com.atlassian.core.filters.encoding.AbstractEncodingFilter.doFilter(AbstractEncodingFilter.java:41)
	com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31)
	com.atlassian.jira.web.filters.PathMatchingEncodingFilter.doFilter(PathMatchingEncodingFilter.java:49)
	com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31)
	com.atlassian.jira.startup.JiraStartupChecklistFilter.doFilter(JiraStartupChecklistFilter.java:74)
	com.atlassian.jira.web.filters.steps.ChainedFilterStepRunner.doFilter(ChainedFilterStepRunner.java:84)
	com.atlassian.jira.web.filters.JiraFirstFilter.doFilter(JiraFirstFilter.java:57)

note The full stack trace of the root cause is available in the Apache Tomcat/7.0.29 logs.
Apache Tomcat/7.0.29

2.Environment: JIRA is installed in CentOS with CONFLUENCE (which work fluently without problem).

3.Solution: restart server may work for a while, but the next day this error will happen again.

 

1 answer

Hi Rachel,

Please check if the user account with which you are starting the JIRA service, has read/write permission to the folders in /var/atlassian/application-data

Thank you for answering. I found it's probably because lack of memory space.

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