Upgrading from 4.3.4 to 4.4.1 - reindex completes at 99% with a system crash

[Lori Wermske]

We are trying to upgrade from 4.3.4 to 4.4.1. We finished the install and restarted JIRA. A reindex starts and gets to 99%, then it crashes with no error messages. Not sure what to do at this point. Cannot bring JIRA back up.

here is the log file

****************
JIRA starting...
****************

2011-09-16 12:27:50,940 main INFO [atlassian.jira.startup.JiraStartupLogger]

___ Environment _____________________________

JIRA Build : 4.4.1#660-r161644
Build Date : Tue Aug 30 00:00:00 CDT 2011
JIRA Installation Type : Standalone
Application Server : Apache Tomcat/6.0.32 - Servlet API 2.5
Java Version : 1.6.0_26 - Sun Microsystems Inc.
Current Working Directory : E:\atlassian\JIRA 4.3.4\Install
Maximum Allowable Memory : 742MB
Total Memory : 247MB
Free Memory : 185MB
Used Memory : 62MB
Memory Pool: Code Cache : Code Cache: init = 2359296(2304K) used = 788096(769K) committed = 2359296(2304K) max = 50331648(49152K)
Memory Pool: Eden Space : Eden Space: init = 71630848(69952K) used = 64658304(63142K) committed = 71630848(69952K) max = 214827008(209792K)
Memory Pool: Survivor Space : Survivor Space: init = 8912896(8704K) used = 0(0K) committed = 8912896(8704K) max = 26804224(26176K)
Memory Pool: Tenured Gen : Tenured Gen: init = 178978816(174784K) used = 0(0K) committed = 178978816(174784K) max = 536870912(524288K)
Memory Pool: Perm Gen : Perm Gen: init = 16777216(16384K) used = 11211440(10948K) committed = 16777216(16384K) max = 268435456(262144K)
JVM Input Arguments : -XX:MaxPermSize=256m -Xms256m -Xmx768m -Djava.awt.headless=true -Datlassian.standalone=JIRA -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true -Dmail.mime.decodeparameters=true -Djava.util.logging.config.file=E:\atlassian\JIRA 4.3.4\Install\conf\logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djava.endorsed.dirs=E:\atlassian\JIRA 4.3.4\Install\endorsed -Dcatalina.base=E:\atlassian\JIRA 4.3.4\Install -Dcatalina.home=E:\atlassian\JIRA 4.3.4\Install -Djava.io.tmpdir=E:\atlassian\JIRA 4.3.4\Install\temp

___ Java System Properties ________________

atlassian.standalone : JIRA
awt.toolkit : sun.awt.windows.WToolkit
catalina.base : E:\atlassian\JIRA 4.3.4\Install
catalina.home : E:\atlassian\JIRA 4.3.4\Install
catalina.useNaming : true
common.loader : ${catalina.base}/lib,
${catalina.base}/lib/*.jar,
${catalina.home}/lib,
${catalina.home}/lib/*.jar
file.encoding : Cp1252
file.encoding.pkg : sun.io
java.awt.graphicsenv : sun.awt.Win32GraphicsEnvironment
java.awt.headless : true
java.awt.printerjob : sun.awt.windows.WPrinterJob
java.class.version : 50.0
java.home : E:\atlassian\JIRA 4.3.4\Install\jre
java.io.tmpdir : E:\atlassian\JIRA 4.3.4\Install\temp
java.naming.factory.initial : org.apache.naming.java.javaURLContextFactory
java.naming.factory.url.pkgs : org.apache.naming
java.runtime.name : Java(TM) SE Runtime Environment
java.runtime.version : 1.6.0_26-b03
java.specification.name : Java Platform API Specification
java.specification.vendor : Sun Microsystems Inc.
java.specification.version : 1.6
java.util.logging.config.file : E:\atlassian\JIRA 4.3.4\Install\conf\logging.properties
java.util.logging.manager : org.apache.juli.ClassLoaderLogManager
java.vendor : Sun Microsystems Inc.
java.vendor.url : http://java.sun.com/<br< a=""> /> java.vendor.url.bug : http://java.sun.com/cgi-bin/bugreport.cgi<br< a=""> /> java.version : 1.6.0_26
java.vm.info : mixed mode
java.vm.name : Java HotSpot(TM) Server VM
java.vm.specification.name : Java Virtual Machine Specification
java.vm.specification.vendor : Sun Microsystems Inc.
java.vm.specification.version : 1.0
java.vm.vendor ...










































































































































































































https://itcoe.snapon.com<br< a=""> /> Default Language : English (United States)
External User Management : OFF
CROWD Integration : ON

___ Application Properties ________________

com.atlassian.bonfire.plugin:build : 2
com.atlassian.jira.ext.calendar:build : 2000
com.atlassian.jira.ext.charting:build : 1500
com.atlassian.sal.jira:build : 2
com.at...


















https://itcoe.snapon.com<br< a=""> /> jira.browser.unsupported.warnings.disabled : false
jira.bulk.edit.limit.issue.count : 1000
jira.chart.days.previous.limit.daily : 300
jira.chart.days.previous.limit.hourly : 10
jira.chart.days.previous.limit.monthly : 7500
jira.chart.days.previous.limit.quarterly : 22500
jira.chart.days.previous.limit.weekly : 1750
jira.chart.days.previous.limit.yearly : 36500
ji...















































































































































































































































































































































































































































































http://www.aQute.biz<br< a=""> /> Description : JAR Processing Library for creating and verifying OSGi manifest headers

Crowd REST API : crowd-rest-application-management
Version : 1.0
Status : enabled
Vendor : Atlassian Software Systems
Description ...























































































































































































































































http://confluence.snapon.com:8090<br< a=""> /> Matching URLs : /sr/jira.issueviews:searchrequest
/secure/RunPortlet
Matching IP : 10.0.13.33

___ Java Class Paths ______________________

sun.boot.class.path : E:\atlassian\JIRA 4.3.4\Install\jre\lib\resources.jar;
E:\atlassian\JIRA 4.3.4\Install\jre\lib\rt.jar;
...

[Carsten Beck-Astrup]

We also had some issues with memory when upgrading on a 32 bit server. Increasing memory also gave problems if we increased too much. We found that setting memory to 1024 MB worked for us (use the tomcat6w //ES//SERVICENAME command)

Another way is to set the following in java options (also with the above command)

-XX:+HeapDumpOnOutOfMemoryError

This way you get a dump if Out Of Memory and that maybe will give you some answers (or answers to Atlassian support)

[Jeremy Largman]

Often these can be solved by either increasing JIRA memory or by figuring out if indexing is getting blocked by a lock timeout.