Troubleshooting Tomcat Issues With Java 1.6

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Article Information

This article applies to the following ZCS versions.

ZCS 4.5 Article ZCS 4.5


To troubleshoot mailbox server tomcat OutOfMemory (OOME), or hang/unresponsive issues, Zimbra Support usually requests for stacktrace (catalina.out), mailbox.log and zimbrastats.csv files from customers. When these files do *not* review any useful information, Zimbra will need java heap dumps to pinpoint the issue. Until Zimbra ships Java 1.6 starting in ZCS 4.5.7, you'll be requested to follow the instructions in this article to install Java 1.6 manually, and collect all the necessary information.

1. Zimbra currently ships with Java 1.5 on non-Mac platforms.
2. Java 1.6 is not going to fix the issue. It'll only help us gather the heap dumps so that we can find out the root cause of the problem.
3. Before upgrading to the next version, you should revert back to Java 1.5.

Procedures to Install and Configure Java 1.6

1. Download JDK 6u1 from
(Note: The procedures here were verified against 6u1, but should be applicable to 6u2 as well, except for the path name).

2. Follow the instructions included with the download to install Java 1.6.

3. As the zimbra user, run:

zmcontrol stop

4. As root, run:

mv /opt/zimbra/jdk1.5.0_08 /opt/zimbra/jdk1.5.0_08_orig
cp -a /usr/java/jdk1.6.0_01 /opt/zimbra/jdk1.5.0_08
cd /opt/zimbra/libexec
mv zmtomcatmgr zmtomcatmgr.orig
ln -s zmtomcatmgr.unrestricted zmtomcatmgr

5. As the zimbra user, run:

zmlocalconfig -e tomcat_java_options="-client -XX:NewRatio=2 -Djava.awt.headless=true -verbose:gc
-XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:+HeapDumpOnOutOfMemoryError
-XX:HeapDumpPath=/opt/zimbra/log -XX:ErrorFile=/opt/zimbra/log/java_error%p.log"
zmcontrol start

7. To verify that everything starts OK, as the zimbra user, run:

zmcontrol status  

As root, run:


which should show an output similar to the following:

12221 TomcatLauncher 
12313 TransformationSomething

The above means that two JVM processes are alive.

Issues after Upgrade

1. If you see something like:

Error occurred: Untrusted Server Certificate Chain

please look at SSL Certificate Problems.

2. If all the shared folders disappear and you get the following error while trying to view them:

msg - system failure: IOException
code - service.FAILURE
method - ZmCsfeCommand.prototype.invoke
detail - soap:Receiver

please restart Zimbra and try again.

Procedures to Install the zmstat Scripts

1. Download the tarball and transfer it to your Zimbra server.
2. As the zimbra user, run the following commands:

mkdir -p /opt/zimbra/log/zmstat/bin
cd /opt/zimbra/log/zmstat/bin
tar xvfz

3. As the zimbra user, run zmstat:

/opt/zimbra/log/zmstat/bin/zmstat start

This will run several processes that capture stats every 10 seconds. They are saved in various /opt/zimbra/log/zmstat/*.csv files, and they rotate at midnight to 2007-mm-dd subdirectory.

Data to Collect

1. Set up a cron job to run the following two commands, as the zimbra user, every 30 (or 60) minutes, and redirect the output to a file. This will give us some trend data.

jmap -histo:live <tomcat_pid>
jmap -histo <tomcat_pid>

where <tomcat_pid> is the PID of TomcatLauncher from the jps command.

2. When the problem occurs again, run these commands as root:

/opt/zimbra/java/bin/jmap -heap <tomcat_pid>
/opt/zimbra/java/bin/jmap -permstat <tomcat_pid>
/opt/zimbra/java/bin/jmap -finalizerinfo <tomcat_pid> 

Also, run these commands as the zimbra user:

jmap -histo:live <tomcat_pid> 
jmap -histo <tomcat_pid> 
jmap -dump:live,format=b,file=/opt/zimbra/log/heap_dump.dat <tomcat_pid>
kill -3 <tomcat_pid>

Note: All the jmap commands (except for the dump) write to stdout. The jmap -permstat command may take several minutes to run.

3. Also, send the followings:

/opt/zimbra/log/zmstat/*.csv (including previous day's subdir)
/opt/zimbra/tomcat/logs/catalina.out (need previous day’s file as well)
/opt/zimbra/log/mailbox.log (need previous day’s file as well)
output of "df –h"
Verified Against: Zimbra Collaboration Suite 4.5.4 on RHEL4 32-bit Date Created: 7/12/2007
Article ID: Date Modified: 2015-03-24

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