Changing issue level security scheme throws IndexException

I tried to associate a new issue level security scheme to a project with 380 issues. The first time I tried this, Jira immediately crashed with an HotSpot error shown below. The second time I tried to validate the problem wasn't just a random fluke, I got the stack traces following the SIGSEGV report.

It seems that when I start the security level assigning, Lucene creates two separate lock files into the temp directory but only one of them is referred to in the traces below.

1. An unexpected error has been detected by HotSpot Virtual Machine:
   #
2. SIGSEGV (0xb) at pc=0xb7a0ac41, pid=7603, tid=1839385520
   #
3. Java VM: Java HotSpot(TM) Server VM (1.5.0_05-b05 mixed mode)
4. Problematic frame:
5. V [libjvm.so+0x39ec41]
   #
6. An error report file with more information is saved as /tmp/hs_err_pid7603.log
   #
7. If you would like to submit a bug report, please visit:
8. http://java.sun.com/webapps/bugreport/crash.jsp

2006-01-17 11:48:32,339 [webwork.dispatcher.ServletDispatcher] Could not execute action
com.atlassian.jira.issue.index.IndexException: Exception caught whilst deIndexing.
at com.atlassian.jira.issue.index.DefaultIndexManager.deIndexIssuesAndComments(DefaultIndexManager.java:367)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:247)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:211)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndex(DefaultIndexManager.java:391)
at com.atlassian.jira.web.action.admin.issuesecurity.SelectProjectSecuritySchemeStep2.changeLevels(SelectProjectSecuritySchemeStep2.java:71)
at com.atlassian.jira.web.action.admin.issuesecurity.SelectProjectSecuritySchemeStep2.doExecute(SelectProjectSecuritySchemeStep2.java:40)
at webwork.action.ActionSupport.execute(ActionSupport.java:153)
at com.atlassian.jira.action.JiraActionSupport.execute(JiraActionSupport.java:51)
at webwork.dispatcher.GenericDispatcher.executeAction(GenericDispatcher.java:132)
at com.atlassian.jira.web.dispatcher.JiraServletDispatcher.service(JiraServletDispatcher.java:178)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.jira.web.filters.AccessLogFilter.doFilter(AccessLogFilter.java:51)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119)
at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55)
at com.atlassian.jira.web.filters.SitemeshExcludePathFilter.doFilter(SitemeshExcludePathFilter.java:38)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.seraph.filter.SecurityFilter.doFilter(SecurityFilter.java:182)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.seraph.filter.LoginFilter.doFilter(LoginFilter.java:177)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.util.profiling.filters.ProfilingFilter.doFilter(ProfilingFilter.java:132)
at com.atlassian.jira.web.filters.ProfilingAndErrorFilter.doFilter(ProfilingAndErrorFilter.java:25)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.jira.web.filters.ActionCleanupDelayFilter.doFilter(ActionCleanupDelayFilter.java:37)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.johnson.filters.JohnsonFilter.doFilter(JohnsonFilter.java:91)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.jira.web.filters.gzip.GzipFilter.doFilter(GzipFilter.java:64)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.core.filters.AbstractEncodingFilter.doFilter(AbstractEncodingFilter.java:37)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
at org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:307)
at org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:385)
at org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:748)
at org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:678)
at org.apache.jk.common.SocketConnection.runIt(ChannelSocket.java:871)
at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
at java.lang.Thread.run(Thread.java:595)
Caused by: java.io.IOException: Lock obtain timed out: Lock@/home/jira/jira/temp/lucene-c2f2d05a807581e6d8ca495ffc70727c-write.lock
at org.apache.lucene.store.Lock.obtain(Lock.java:58)
at org.apache.lucene.index.IndexReader.aquireWriteLock(IndexReader.java:408)
at org.apache.lucene.index.IndexReader.delete(IndexReader.java:432)
at org.apache.lucene.index.IndexReader.delete(IndexReader.java:454)
at com.atlassian.jira.issue.index.DefaultIndexManager.deIndexIssue(DefaultIndexManager.java:224)
at com.atlassian.jira.issue.index.DefaultIndexManager.deIndexIssuesAndComments(DefaultIndexManager.java:361)
... 55 more
2006-01-17 11:48:32,348 ERROR [[Catalina].[localhost].[/].[action]] Servlet.service() for servlet action threw exception
com.atlassian.jira.issue.index.IndexException: Exception caught whilst deIndexing.
at com.atlassian.jira.issue.index.DefaultIndexManager.deIndexIssuesAndComments(DefaultIndexManager.java:367)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:247)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:211)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndex(DefaultIndexManager.java:391)
at com.atlassian.jira.web.action.admin.issuesecurity.SelectProjectSecuritySchemeStep2.changeLevels(SelectProjectSecuritySchemeStep2.java:71)
at com.atlassian.jira.web.action.admin.issuesecurity.SelectProjectSecuritySchemeStep2.doExecute(SelectProjectSecuritySchemeStep2.java:40)
at webwork.action.ActionSupport.execute(ActionSupport.java:153)
at com.atlassian.jira.action.JiraActionSupport.execute(JiraActionSupport.java:51)
at webwork.dispatcher.GenericDispatcher.executeAction(GenericDispatcher.java:132)
at com.atlassian.jira.web.dispatcher.JiraServletDispatcher.service(JiraServletDispatcher.java:178)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.jira.web.filters.AccessLogFilter.doFilter(AccessLogFilter.java:51)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119)
at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55)
at com.atlassian.jira.web.filters.SitemeshExcludePathFilter.doFilter(SitemeshExcludePathFilter.java:38)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.seraph.filter.SecurityFilter.doFilter(SecurityFilter.java:182)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.seraph.filter.LoginFilter.doFilter(LoginFilter.java:177)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.util.profiling.filters.ProfilingFilter.doFilter(ProfilingFilter.java:132)
at com.atlassian.jira.web.filters.ProfilingAndErrorFilter.doFilter(ProfilingAndErrorFilter.java:25)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.jira.web.filters.ActionCleanupDelayFilter.doFilter(ActionCleanupDelayFilter.java:37)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.johnson.filters.JohnsonFilter.doFilter(JohnsonFilter.java:91)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.jira.web.filters.gzip.GzipFilter.doFilter(GzipFilter.java:64)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.core.filters.AbstractEncodingFilter.doFilter(AbstractEncodingFilter.java:37)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
at org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:307)
at org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:385)
at org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:748)
at org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:678)
at org.apache.jk.common.SocketConnection.runIt(ChannelSocket.java:871)
at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
at java.lang.Thread.run(Thread.java:595)
Caused by: java.io.IOException: Lock obtain timed out: Lock@/home/jira/jira/temp/lucene-c2f2d05a807581e6d8ca495ffc70727c-write.lock
at org.apache.lucene.store.Lock.obtain(Lock.java:58)
at org.apache.lucene.index.IndexReader.aquireWriteLock(IndexReader.java:408)
at org.apache.lucene.index.IndexReader.delete(IndexReader.java:432)
at org.apache.lucene.index.IndexReader.delete(IndexReader.java:454)
at com.atlassian.jira.issue.index.DefaultIndexManager.deIndexIssue(DefaultIndexManager.java:224)
at com.atlassian.jira.issue.index.DefaultIndexManager.deIndexIssuesAndComments(DefaultIndexManager.java:361)
... 55 more
2006-01-17 11:48:33,688 ERROR [500ErrorPage] Exception caught in 500 page Exception caught whilst deIndexing.
com.atlassian.jira.issue.index.IndexException: Exception caught whilst deIndexing.
at com.atlassian.jira.issue.index.DefaultIndexManager.deIndexIssuesAndComments(DefaultIndexManager.java:367)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:247)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:211)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndex(DefaultIndexManager.java:391)
at com.atlassian.jira.web.action.admin.issuesecurity.SelectProjectSecuritySchemeStep2.changeLevels(SelectProjectSecuritySchemeStep2.java:71)
at com.atlassian.jira.web.action.admin.issuesecurity.SelectProjectSecuritySchemeStep2.doExecute(SelectProjectSecuritySchemeStep2.java:40)
at webwork.action.ActionSupport.execute(ActionSupport.java:153)
at com.atlassian.jira.action.JiraActionSupport.execute(JiraActionSupport.java:51)
at webwork.dispatcher.GenericDispatcher.executeAction(GenericDispatcher.java:132)
at com.atlassian.jira.web.dispatcher.JiraServletDispatcher.service(JiraServletDispatcher.java:178)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.jira.web.filters.AccessLogFilter.doFilter(AccessLogFilter.java:51)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119)
at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55)
at com.atlassian.jira.web.filters.SitemeshExcludePathFilter.doFilter(SitemeshExcludePathFilter.java:38)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.seraph.filter.SecurityFilter.doFilter(SecurityFilter.java:182)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.seraph.filter.LoginFilter.doFilter(LoginFilter.java:177)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.util.profiling.filters.ProfilingFilter.doFilter(ProfilingFilter.java:132)
at com.atlassian.jira.web.filters.ProfilingAndErrorFilter.doFilter(ProfilingAndErrorFilter.java:25)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.jira.web.filters.ActionCleanupDelayFilter.doFilter(ActionCleanupDelayFilter.java:37)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.johnson.filters.JohnsonFilter.doFilter(JohnsonFilter.java:91)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.jira.web.filters.gzip.GzipFilter.doFilter(GzipFilter.java:64)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.atlassian.core.filters.AbstractEncodingFilter.doFilter(AbstractEncodingFilter.java:37)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
at org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:307)
at org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:385)
at org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:748)
at org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:678)
at org.apache.jk.common.SocketConnection.runIt(ChannelSocket.java:871)
at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
at java.lang.Thread.run(Thread.java:595)
Caused by: java.io.IOException: Lock obtain timed out: Lock@/home/jira/jira/temp/lucene-c2f2d05a807581e6d8ca495ffc70727c-write.lock
at org.apache.lucene.store.Lock.obtain(Lock.java:58)
at org.apache.lucene.index.IndexReader.aquireWriteLock(IndexReader.java:408)
at org.apache.lucene.index.IndexReader.delete(IndexReader.java:432)
at org.apache.lucene.index.IndexReader.delete(IndexReader.java:454)
at com.atlassian.jira.issue.index.DefaultIndexManager.deIndexIssue(DefaultIndexManager.java:224)
at com.atlassian.jira.issue.index.DefaultIndexManager.deIndexIssuesAndComments(DefaultIndexManager.java:361)
... 55 more