Since upgrading from 4.5.4 to 4.5.6, the zimbra services (all of them) shut down every morning at 3:01.

Could be the same issue as this forum post

The server stays up and is accessible via SSH. Uptime shows that it didn't reboot. I issue a simple zmcontrol start and everything comes back online like normal and functions without error all day long.

I saw in the zimbra user crontab that zmpurgemessages was running at 3am so I changed it to run later to determine if it was the problem - the services still shut down at 3am.

It's a pretty new machine - Dual Xeon quad cores, 8GB RAM, 925GB RAID.

This server was running 4.5.4 for several months without any issues. Issue appeared a couple days after the upgrade to 4.5.6.

The catalina.out log is small.
Code:
[root@mailhost log]# ls -lah /opt/zimbra/tomcat/logs/catalina.out
-rw-rw-rw-  1 zimbra zimbra 259K Jul 20 09:12 /opt/zimbra/tomcat/logs/catalina.out
/opt/zimbra/tomcat/logs/catalina.out
Code:
[tomcat launcher] got signal SIGTERM invoking stop
Jul 20, 2007 3:01:58 AM org.apache.coyote.http11.Http11BaseProtocol pause
INFO: Pausing Coyote HTTP/1.1 on http-80
Jul 20, 2007 3:01:58 AM org.apache.coyote.http11.Http11BaseProtocol pause
INFO: Pausing Coyote HTTP/1.1 on http-443
Jul 20, 2007 3:01:58 AM org.apache.coyote.http11.Http11BaseProtocol pause
INFO: Pausing Coyote HTTP/1.1 on http-7071
Jul 20, 2007 3:01:59 AM org.apache.catalina.core.StandardService stop
INFO: Stopping service Catalina
Jul 20, 2007 3:02:10 AM org.apache.catalina.core.StandardWrapper unload
INFO: Waiting for 39 instance(s) to be deallocated
Jul 20, 2007 3:02:11 AM org.apache.catalina.core.StandardWrapper unload
INFO: Waiting for 39 instance(s) to be deallocated
Jul 20, 2007 3:02:12 AM org.apache.catalina.core.StandardWrapper unload
INFO: Waiting for 39 instance(s) to be deallocated
Jul 20, 2007 3:02:12 AM org.apache.catalina.core.StandardWrapper unload
INFO: Waiting for 8 instance(s) to be deallocated
Jul 20, 2007 3:02:13 AM org.apache.catalina.core.StandardWrapper unload
INFO: Waiting for 8 instance(s) to be deallocated
Jul 20, 2007 3:02:14 AM org.apache.catalina.core.StandardWrapper unload
INFO: Waiting for 8 instance(s) to be deallocated
Jul 20, 2007 3:02:14 AM org.apache.catalina.core.StandardWrapper unload
INFO: Waiting for 2 instance(s) to be deallocated
Jul 20, 2007 3:02:15 AM org.apache.catalina.core.StandardWrapper unload
INFO: Waiting for 2 instance(s) to be deallocated
Jul 20, 2007 3:02:16 AM org.apache.catalina.core.StandardWrapper unload
INFO: Waiting for 2 instance(s) to be deallocated
Jul 20, 2007 3:02:17 AM org.apache.catalina.core.StandardWrapper unload
INFO: Waiting for 8 instance(s) to be deallocated
log4j:ERROR Error occured while converting date.
java.lang.NullPointerException
        at java.lang.System.arraycopy(Native Method)
        at java.lang.AbstractStringBuilder.getChars(AbstractStringBuilder.java:331)
        at java.lang.StringBuffer.getChars(StringBuffer.java:202)
        at org.apache.log4j.helpers.ISO8601DateFormat.format(ISO8601DateFormat.java:120)
        at java.text.DateFormat.format(DateFormat.java:314)
        at org.apache.log4j.helpers.PatternParser$DatePatternConverter.convert(PatternParser.java:436)
        at org.apache.log4j.helpers.PatternConverter.format(PatternConverter.java:56)
        at org.apache.log4j.PatternLayout.format(PatternLayout.java:495)
        at org.apache.log4j.WriterAppender.subAppend(WriterAppender.java:292)
        at org.apache.log4j.DailyRollingFileAppender.subAppend(DailyRollingFileAppender.java:349)
        at org.apache.log4j.WriterAppender.append(WriterAppender.java:150)
        at org.apache.log4j.AppenderSkeleton.doAppend(AppenderSkeleton.java:221)
        at org.apache.log4j.helpers.AppenderAttachableImpl.appendLoopOnAppenders(AppenderAttachableImpl.java:57)
        at org.apache.log4j.Category.callAppenders(Category.java:187)
        at org.apache.log4j.Category.forcedLog(Category.java:372)
        at org.apache.log4j.Category.log(Category.java:864)
        at org.apache.commons.logging.impl.Log4JLogger.error(Log4JLogger.java:192)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:260)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:541)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
        at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)
        at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:667)
        at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
        at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
        at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
        at java.lang.Thread.run(Thread.java:595)
Jul 20, 2007 3:02:18 AM org.apache.catalina.core.StandardWrapper unload
INFO: Waiting for 8 instance(s) to be deallocated
Jul 20, 2007 3:02:19 AM org.apache.catalina.core.StandardWrapper unload
INFO: Waiting for 8 instance(s) to be deallocated
/var/log/zimbra.log
Code:
Jul 20 03:01:02 mailhost slapd[4555]: is_entry_objectclass("", "2.5.6.1") no objectClass attribute
Jul 20 03:01:48 mailhost saslauthd[6786]: server_exit     : master exited: 6786
Jul 20 03:01:48 mailhost slapd[4555]: daemon: shutdown requested and initiated.
Jul 20 03:01:48 mailhost slapd[4555]: slapd shutdown: waiting for 0 threads to terminate
Jul 20 03:01:48 mailhost slapd[4555]: slapd stopped.
Jul 20 03:01:53 mailhost amavis[7338]: Net::Server: 2007/07/20-03:01:53 Server closing!
Jul 20 03:01:56 mailhost zmtomcatmgr[10209]: threaddump requested
Jul 20 03:01:56 mailhost zmtomcatmgr[6263]: sending SIQUIT to tomcat/JVM process 6264
Jul 20 03:01:58 mailhost zmtomcatmgr[10216]: stop requested
Jul 20 03:01:58 mailhost zmtomcatmgr[10216]: waiting for manager process 6263 to die
Jul 20 03:01:58 mailhost zmtomcatmgr[6263]: shutdown requested, sending TERM signal to 6264
Jul 20 03:02:22 mailhost zmtomcatmgr[6263]: tomcat/JVM process exited (waitpid expected 6264 got 6264)
Jul 20 03:02:22 mailhost zmtomcatmgr[6263]: manager woke up from wait on tomcat/JVM with pid 6264
Jul 20 03:02:23 mailhost zmtomcatmgr[10216]: manager process 6263 died, shutdown completed
Jul 20 03:02:28 mailhost zmtomcatmgr[10277]: status requested
Jul 20 03:02:28 mailhost zmtomcatmgr[10277]: file /opt/zimbra/log/zmtomcatmgr.pid does not exist
Jul 20 03:02:28 mailhost zmtomcatmgr[10277]: assuming no other instance is running
Jul 20 03:02:28 mailhost zmtomcatmgr[10277]: no manager process is running
Jul 20 03:02:28 mailhost zmtomcatmgr[10278]: status requested
Jul 20 03:02:28 mailhost zmtomcatmgr[10278]: file /opt/zimbra/log/zmtomcatmgr.pid does not exist
Jul 20 03:02:28 mailhost zmtomcatmgr[10278]: assuming no other instance is running
Jul 20 03:02:28 mailhost zmtomcatmgr[10278]: no manager process is running
Jul 20 03:02:28 mailhost postfix/postfix-script: stopping the Postfix mail system
Jul 20 03:02:28 mailhost postfix/master[6740]: terminating on signal 15
Jul 20 03:02:33 mailhost zmtomcatmgr[10432]: threaddump requested
Jul 20 03:02:33 mailhost zmtomcatmgr[10432]: file /opt/zimbra/log/zmtomcatmgr.pid does not exist
Jul 20 03:02:33 mailhost zmtomcatmgr[10432]: assuming no other instance is running
Jul 20 03:02:33 mailhost zmtomcatmgr[10432]: no manager process is running
Jul 20 03:02:35 mailhost zmtomcatmgr[10440]: stop requested
Jul 20 03:02:35 mailhost zmtomcatmgr[10440]: file /opt/zimbra/log/zmtomcatmgr.pid does not exist
Jul 20 03:02:35 mailhost zmtomcatmgr[10440]: assuming no other instance is running
Jul 20 03:02:35 mailhost zmtomcatmgr[10440]: no manager process is running
Jul 20 03:02:40 mailhost zmtomcatmgr[10442]: status requested
Jul 20 03:02:40 mailhost zmtomcatmgr[10442]: file /opt/zimbra/log/zmtomcatmgr.pid does not exist
Jul 20 03:02:40 mailhost zmtomcatmgr[10442]: assuming no other instance is running
Jul 20 03:02:40 mailhost zmtomcatmgr[10442]: no manager process is running
Jul 20 03:02:40 mailhost zmtomcatmgr[10443]: status requested
Jul 20 03:02:40 mailhost zmtomcatmgr[10443]: file /opt/zimbra/log/zmtomcatmgr.pid does not exist
Jul 20 03:02:40 mailhost zmtomcatmgr[10443]: assuming no other instance is running
Jul 20 03:02:40 mailhost zmtomcatmgr[10443]: no manager process is running
Jul 20 03:02:43 mailhost zimbramon[10219]: 10219:info: 2007-07-20 03:02:01, STATUS: : Cannot: determine
Jul 20 03:02:43 mailhost sendmail[10248]: l6KA2bdR010248: from=zimbra, size=869, class=0, nrcpts=1, msgid=<200707201002.l6KA2bdR010248@mailhost.fhi.net>, rel
ay=zimbra@localhost
Jul 20 03:02:43 mailhost sendmail[10248]: l6KA2bdR010248: to=zimbra, ctladdr=zimbra (502/502), delay=00:00:06, xdelay=00:00:00, mailer=relay, pri=30869, rela
y=[127.0.0.1] [127.0.0.1], dsn=4.0.0, stat=Deferred: Connection refused by [127.0.0.1]
/var/log/secure
Code:
Jul 20 02:50:03 mailhost sudo:   zimbra : TTY=unknown ; PWD=/opt/zimbra ; USER=root ; COMMAND=/opt/zimbra/libexec/zmtomcatmgr status
Jul 20 02:52:03 mailhost sudo:   zimbra : TTY=unknown ; PWD=/opt/zimbra ; USER=root ; COMMAND=/opt/zimbra/libexec/zmtomcatmgr status
Jul 20 02:54:04 mailhost sudo:   zimbra : TTY=unknown ; PWD=/opt/zimbra ; USER=root ; COMMAND=/opt/zimbra/libexec/zmtomcatmgr status
Jul 20 02:56:03 mailhost sudo:   zimbra : TTY=unknown ; PWD=/opt/zimbra ; USER=root ; COMMAND=/opt/zimbra/libexec/zmtomcatmgr status
Jul 20 02:58:04 mailhost sudo:   zimbra : TTY=unknown ; PWD=/opt/zimbra ; USER=root ; COMMAND=/opt/zimbra/libexec/zmtomcatmgr status
Jul 20 03:00:03 mailhost sudo:   zimbra : TTY=unknown ; PWD=/opt/zimbra ; USER=root ; COMMAND=/opt/zimbra/libexec/zmtomcatmgr status
Jul 20 03:01:56 mailhost sudo:   zimbra : TTY=unknown ; PWD=/ ; USER=root ; COMMAND=/opt/zimbra/libexec/zmtomcatmgr threaddump
Jul 20 03:01:58 mailhost sudo:   zimbra : TTY=unknown ; PWD=/ ; USER=root ; COMMAND=/opt/zimbra/libexec/zmtomcatmgr stop
Jul 20 03:02:28 mailhost sudo:   zimbra : TTY=unknown ; PWD=/ ; USER=root ; COMMAND=/opt/zimbra/libexec/zmtomcatmgr status
Jul 20 03:02:28 mailhost sudo:   zimbra : TTY=unknown ; PWD=/ ; USER=root ; COMMAND=/opt/zimbra/libexec/zmtomcatmgr status
Jul 20 03:02:28 mailhost sudo:   zimbra : TTY=unknown ; PWD=/ ; USER=root ; COMMAND=/opt/zimbra/postfix-2.2.9/sbin/postalias /etc/aliases
Jul 20 03:02:28 mailhost sudo:   zimbra : TTY=unknown ; PWD=/ ; USER=root ; COMMAND=/opt/zimbra/postfix-2.2.9/sbin/postfix stop norewrite
Jul 20 03:02:33 mailhost sudo:   zimbra : TTY=unknown ; PWD=/ ; USER=root ; COMMAND=/opt/zimbra/libexec/zmtomcatmgr threaddump
Jul 20 03:02:35 mailhost sudo:   zimbra : TTY=unknown ; PWD=/ ; USER=root ; COMMAND=/opt/zimbra/libexec/zmtomcatmgr stop
Jul 20 03:02:40 mailhost sudo:   zimbra : TTY=unknown ; PWD=/ ; USER=root ; COMMAND=/opt/zimbra/libexec/zmtomcatmgr status
Jul 20 03:02:40 mailhost sudo:   zimbra : TTY=unknown ; PWD=/ ; USER=root ; COMMAND=/opt/zimbra/libexec/zmtomcatmgr status
/var/log/messages
Code:
Jul 20 03:01:48 mailhost saslauthd[6786]: server_exit     : master exited: 6786
Jul 20 03:01:53 mailhost amavis[7338]: Net::Server: 2007/07/20-03:01:53 Server closing!
Jul 20 03:02:43 mailhost zimbramon[10219]: 10219:info: 2007-07-20 03:02:01, STATUS: : Cannot: determine
Jul 20 03:04:02 mailhost zimbramon[10445]: 10445:info: 2007-07-20 03:04:01, STATUS: : Cannot: determine
Jul 20 03:06:03 mailhost zimbramon[10498]: 10498:info: 2007-07-20 03:06:01, STATUS: : Cannot: determine
Jul 20 03:08:02 mailhost zimbramon[10551]: 10551:info: 2007-07-20 03:08:01, STATUS: : Cannot: determine
I'm getting tired of jumping out of bed at 3am to restart the services. Any help is warmly welcome.