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Thread: [SOLVED] OS upgrade from 4.5.6 to 4.5.10 fails - tomcat/mailbox

  1. #1
    cmattogno is offline New Member
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    Default [SOLVED] OS upgrade from 4.5.6 to 4.5.10 fails - tomcat/mailbox

    Upgrade from 4.5.6 to 4.5.10 OpenSource on Ubuntu 6.06

    Full off-line backup before upgrade.

    I have reverted back to the backup three times and verified that it it works, then I upgrade and not so good.

    No errors at time of update, or at boot. Just no web interface, admin interface and IMAP from Thunderbird times out.

    zimbra@zimbra:~$ zmcontrol start
    Host zimbra.collaborative.org
    Starting ldap...Done.
    Starting logger...Done.
    Starting mailbox...Done.
    Starting imapproxy...Done.
    Starting antispam...Done.
    Starting antivirus...Done.
    Starting snmp...Done.
    Starting spell...Done.
    Starting mta...Done.
    Starting stats...Done.

    Everything looks good, except ...

    zimbra@zimbra:~$ zmcontrol status
    Host zimbra.collaborative.org
    antispam Running
    antivirus Running
    imapproxy Running
    ldap Running
    logger Running
    mailbox Stopped
    tomcat is not running
    mta Running
    snmp Running
    spell Running
    stats Running

    Catalin says:
    zimbra@zimbra:~$ cat /opt/zimbra/tomcat/logs/catalina.out
    Dec 4, 2007 5:13:45 PM org.apache.coyote.http11.Http11BaseProtocol init
    INFO: Initializing Coyote HTTP/1.1 on http-80
    Dec 4, 2007 5:13:46 PM org.apache.coyote.http11.Http11BaseProtocol init
    INFO: Initializing Coyote HTTP/1.1 on http-443
    Dec 4, 2007 5:13:46 PM org.apache.coyote.http11.Http11BaseProtocol init
    INFO: Initializing Coyote HTTP/1.1 on http-7071
    Dec 4, 2007 5:13:46 PM org.apache.catalina.startup.Catalina load
    INFO: Initialization processed in 2204 ms
    Dec 4, 2007 5:13:46 PM org.apache.catalina.core.StandardService start
    INFO: Starting service Catalina
    Dec 4, 2007 5:13:46 PM org.apache.catalina.core.StandardEngine start
    INFO: Starting Servlet Engine: Apache Tomcat/5.5.15
    Dec 4, 2007 5:13:46 PM org.apache.catalina.core.StandardHost start
    INFO: XML validation disabled
    log4j:WARN No appenders could be found for logger (org.apache.catalina.startup.T ldConfig).
    log4j:WARN Please initialize the log4j system properly.
    Dec 4, 2007 5:13:47 PM org.apache.catalina.core.StandardContext resourcesStart
    SEVERE: Error starting static Resources
    java.lang.IllegalArgumentException: Document base /opt/zimbra/apache-tomcat-5.5. 15/server/webapps/host-manager does not exist or is not a readable directory
    at org.apache.naming.resources.FileDirContext.setDocB ase(FileDirContext. java:140)
    at org.apache.catalina.core.StandardContext.resources Start(StandardConte xt.java:3812)
    at org.apache.catalina.core.StandardContext.start(Sta ndardContext.java:3 983)
    at org.apache.catalina.core.ContainerBase.addChildInt ernal(ContainerBase .java:759)
    at org.apache.catalina.core.ContainerBase.addChild(Co ntainerBase.java:73 9)
    at org.apache.catalina.core.StandardHost.addChild(Sta ndardHost.java:524)
    at org.apache.catalina.startup.HostConfig.deployDescr iptor(HostConfig.ja va:603)
    at org.apache.catalina.startup.HostConfig.deployDescr iptors(HostConfig.j ava:535)
    at org.apache.catalina.startup.HostConfig.deployApps( HostConfig.java:470 )
    at org.apache.catalina.startup.HostConfig.start(HostC onfig.java:1118)
    at org.apache.catalina.startup.HostConfig.lifecycleEv ent(HostConfig.java :310)
    at org.apache.catalina.util.LifecycleSupport.fireLife cycleEvent(Lifecycl eSupport.java:119)
    at org.apache.catalina.core.ContainerBase.start(Conta inerBase.java:1020)
    at org.apache.catalina.core.StandardHost.start(Standa rdHost.java:718)
    at org.apache.catalina.core.ContainerBase.start(Conta inerBase.java:1012)
    at org.apache.catalina.core.StandardEngine.start(Stan dardEngine.java:442 )
    at org.apache.catalina.core.StandardService.start(Sta ndardService.java:4 50)
    at org.apache.catalina.core.StandardServer.start(Stan dardServer.java:700 )
    at org.apache.catalina.startup.Catalina.start(Catalin a.java:551)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Nativ e Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Native MethodAccessorImpl. java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(De legatingMethodAcces sorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at org.apache.catalina.startup.Bootstrap.start(Bootst rap.java:275)
    at org.apache.catalina.startup.Bootstrap.main(Bootstr ap.java:406)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Nativ e Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Native MethodAccessorImpl. java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(De legatingMethodAcces sorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at com.zimbra.cs.launcher.TomcatLauncher.start(Tomcat Launcher.java:42)
    at com.zimbra.cs.launcher.TomcatLauncher.main(TomcatL auncher.java:64)
    Dec 4, 2007 5:13:47 PM org.apache.catalina.core.StandardContext start
    SEVERE: Error in resourceStart()
    Dec 4, 2007 5:13:47 PM org.apache.catalina.core.StandardContext start
    SEVERE: Error getConfigured
    Dec 4, 2007 5:13:47 PM org.apache.catalina.core.StandardContext start
    SEVERE: Context [/host-manager] startup failed due to previous errors
    Dec 4, 2007 5:13:47 PM org.apache.catalina.core.StandardContext stop
    INFO: Container org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/ host-manager] has not been started
    Dec 4, 2007 5:13:47 PM org.apache.catalina.startup.HostConfig deployDescriptor
    WARNING: A docBase /opt/zimbra/apache-tomcat-5.5.15/webapps/zimbra inside the ho st appBase has been specified, and will be ignored
    log4j:WARN No appenders could be found for logger (org.apache.catalina.session.M anagerBase).
    log4j:WARN Please initialize the log4j system properly.
    Dec 4, 2007 5:13:48 PM org.apache.catalina.core.StandardContext resourcesStart
    SEVERE: Error starting static Resources
    j
    at org.apache.catalina.startup.Bootstrap.main(Bootstr ap.java:406)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Nativ e Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Native MethodAccessorImpl. java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(De legatingMethodAcces sorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at com.zimbra.cs.launcher.TomcatLauncher.start(Tomcat Launcher.java:42)
    at com.zimbra.cs.launcher.TomcatLauncher.main(TomcatL auncher.java:64)
    Dec 4, 2007 5:13:48 PM org.apache.catalina.core.StandardContext start
    SEVERE: Error in resourceStart()
    Dec 4, 2007 5:13:48 PM org.apache.catalina.core.StandardContext start
    SEVERE: Error getConfigured
    Dec 4, 2007 5:13:48 PM org.apache.catalina.core.StandardContext start
    SEVERE: Context [/manager] startup failed due to previous errors
    Dec 4, 2007 5:13:48 PM org.apache.catalina.core.StandardContext stop
    INFO: Container org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/ manager] has not been started
    log4j:WARN No appenders could be found for logger (org.apache.catalina.session.M anagerBase).
    log4j:WARN Please initialize the log4j system properly.
    Zimbra server reserving server socket port=995 bindaddr=null ssl=true
    Fatal error: terminating: PrivilegedServlet init failed




    Any help at all is appreciated. I have gone through the forum and tried many fixes, but none work.

    Thank you.

    'topher

  2. #2
    jholder's Avatar
    jholder is offline Former Zimbran
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    Default

    Something's running on port 995

    lsof | grep TCP

  3. #3
    cmattogno is offline New Member
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    Default

    with zimbra started up...

    cleanup 312 postfix 12u IPv4 93846 TCP zimbra.collaborative.org:40074->zimbra.collaborative.org:ldap (ESTABLISHED)
    smtpd 318 postfix 6u IPv4 17633 TCP *:smtp (LISTEN)
    smtpd 318 postfix 16u IPv4 94299 TCP zimbra.collaborative.org:40099->zimbra.collaborative.org:ldap (ESTABLISHED)
    cleanup 319 postfix 12u IPv4 93959 TCP zimbra.collaborative.org:40082->zimbra.collaborative.org:ldap (ESTABLISHED)
    smtpd 321 postfix 6u IPv4 17633 TCP *:smtp (LISTEN)
    smtpd 321 postfix 16u IPv4 94225 TCP zimbra.collaborative.org:40092->zimbra.collaborative.org:ldap (ESTABLISHED)
    smtpd 332 postfix 6u IPv4 17633 TCP *:smtp (LISTEN)
    smtpd 332 postfix 16u IPv4 94332 TCP zimbra.collaborative.org:40102->zimbra.collaborative.org:ldap (ESTABLISHED)
    smtpd 335 postfix 6u IPv4 17633 TCP *:smtp (LISTEN)
    smtpd 335 postfix 16u IPv4 94264 TCP zimbra.collaborative.org:40096->zimbra.collaborative.org:ldap (ESTABLISHED)
    cleanup 338 postfix 12u IPv4 94285 TCP zimbra.collaborative.org:40097->zimbra.collaborative.org:ldap (ESTABLISHED)
    smtpd 368 postfix 6u IPv4 17633 TCP *:smtp (LISTEN)
    smtpd 368 postfix 16u IPv4 94836 TCP zimbra.collaborative.org:40127->zimbra.collaborative.org:ldap (ESTABLISHED)
    amavisd 436 zimbra 7u IPv4 17317 TCP localhost:10024 (LISTEN)
    amavisd 436 zimbra 15u IPv4 95930 TCP zimbra.collaborative.org:53361->zimbra.collaborative.org:ldap (ESTABLISHED)
    amavisd 683 zimbra 7u IPv4 17317 TCP localhost:10024 (LISTEN)
    amavisd 683 zimbra 15u IPv4 95950 TCP zimbra.collaborative.org:53364->zimbra.collaborative.org:ldap (ESTABLISHED)
    smtpd 697 postfix 6u IPv4 17750 TCP localhost:10025 (LISTEN)
    sshd 3553 root 3u IPv6 8355 TCP *:ssh (LISTEN)
    miniserv. 3618 root 6u IPv4 8456 TCP *:10000 (LISTEN)
    sshd 5301 root 3u IPv6 12645 TCP zimbra.collaborative.org:ssh->159.250.29.246:34422 (ESTABLISHED)
    sshd 5312 adnim1 3u IPv6 12645 TCP zimbra.collaborative.org:ssh->159.250.29.246:34422 (ESTABLISHED)
    sshd 6259 root 3u IPv6 107292 TCP zimbra.collaborative.org:ssh->c-71-192-30-191.hsd1.ma.comcast.net:62969 (ESTABLISHED)
    sshd 6605 adnim1 3u IPv6 107292 TCP zimbra.collaborative.org:ssh->c-71-192-30-191.hsd1.ma.comcast.net:62969 (ESTABLISHED)
    sshd 6649 root 3u IPv6 15709 TCP zimbra.collaborative.org:ssh->159.250.29.246:60160 (ESTABLISHED)
    sshd 6661 adnim1 3u IPv6 15709 TCP zimbra.collaborative.org:ssh->159.250.29.246:60160 (ESTABLISHED)
    slapd 6960 zimbra 7u IPv4 16333 TCP zimbra.collaborative.org:ldap (LISTEN)
    slapd 6960 zimbra 11u IPv4 17781 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:35627 (ESTABLISHED)
    slapd 6960 zimbra 17u IPv4 80312 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:53157 (ESTABLISHED)
    slapd 6960 zimbra 19u IPv4 114699 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:60077 (ESTABLISHED)
    slapd 6960 zimbra 23u IPv4 95931 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:53361 (ESTABLISHED)
    slapd 6960 zimbra 24u IPv4 88775 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:48692 (ESTABLISHED)
    slapd 6960 zimbra 25u IPv4 95951 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:53364 (ESTABLISHED)
    slapd 6960 zimbra 26u IPv4 89356 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:48710 (ESTABLISHED)
    slapd 6960 zimbra 27u IPv4 83398 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:46879 (ESTABLISHED)
    slapd 6960 zimbra 28u IPv4 84164 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:41576 (ESTABLISHED)
    slapd 6960 zimbra 30u IPv4 81544 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:46810 (ESTABLISHED)
    slapd 6960 zimbra 31u IPv4 22293 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:46681 (ESTABLISHED)
    slapd 6960 zimbra 32u IPv4 84799 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:41597 (ESTABLISHED)
    slapd 6960 zimbra 33u IPv4 91532 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:40896 (ESTABLISHED)
    slapd 6960 zimbra 39u IPv4 93847 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:40074 (ESTABLISHED)
    slapd 6960 zimbra 45u IPv4 93960 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:40082 (ESTABLISHED)
    slapd 6960 zimbra 51u IPv4 94226 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:40092 (ESTABLISHED)
    slapd 6960 zimbra 53u IPv4 94265 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:40096 (ESTABLISHED)
    slapd 6960 zimbra 54u IPv4 94286 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:40097 (ESTABLISHED)
    slapd 6960 zimbra 55u IPv4 94300 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:40099 (ESTABLISHED)
    slapd 6960 zimbra 56u IPv4 94333 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:40102 (ESTABLISHED)
    slapd 6960 zimbra 57u IPv4 94837 TCP zimbra.collaborative.org:ldap->zimbra.collaborative.org:40127 (ESTABLISHED)
    mysqld 7353 zimbra 11u IPv4 16846 TCP localhost:7307 (LISTEN)
    mysqld 7449 zimbra 11u IPv4 17002 TCP *:7306 (LISTEN)
    perdition 7612 zimbra 3u IPv4 17207 TCP *:imap2 (LISTEN)
    perdition 7615 zimbra 3u IPv4 17228 TCP *:imaps (LISTEN)
    perdition 7618 zimbra 3u IPv4 17248 TCP *:pop3 (LISTEN)
    perdition 7621 zimbra 3u IPv4 17267 TCP *:pop3s (LISTEN)
    amavisd 7650 zimbra 7u IPv4 17317 TCP localhost:10024 (LISTEN)
    clamd 7691 zimbra 5u IPv4 17401 TCP *:3310 (LISTEN)
    httpd 7710 zimbra 3u IPv6 17423 TCP *:7780 (LISTEN)
    httpd 7711 zimbra 3u IPv6 17423 TCP *:7780 (LISTEN)
    httpd 7713 zimbra 3u IPv6 17423 TCP *:7780 (LISTEN)
    httpd 7715 zimbra 3u IPv6 17423 TCP *:7780 (LISTEN)
    httpd 7716 zimbra 3u IPv6 17423 TCP *:7780 (LISTEN)
    httpd 7717 zimbra 3u IPv6 17423 TCP *:7780 (LISTEN)
    master 7794 root 11u IPv4 17633 TCP *:smtp (LISTEN)
    master 7794 root 14u IPv4 17636 TCP *:ssmtp (LISTEN)
    master 7794 root 101u IPv4 17750 TCP localhost:10025 (LISTEN)
    trivial-r 7800 postfix 8u IPv4 17780 TCP zimbra.collaborative.org:35627->zimbra.collaborative.org:ldap (ESTABLISHED)
    trivial-r 8829 postfix 8u IPv4 22292 TCP zimbra.collaborative.org:46681->zimbra.collaborative.org:ldap (ESTABLISHED)
    amavisd 9116 zimbra 7u IPv4 17317 TCP localhost:10024 (LISTEN)
    amavisd 9116 zimbra 15u IPv4 114698 TCP zimbra.collaborative.org:60077->zimbra.collaborative.org:ldap (ESTABLISHED)
    amavisd 27467 zimbra 7u IPv4 17317 TCP localhost:10024 (LISTEN)
    amavisd 27467 zimbra 15u IPv4 80311 TCP zimbra.collaborative.org:53157->zimbra.collaborative.org:ldap (ESTABLISHED)
    amavisd 27705 zimbra 7u IPv4 17317 TCP localhost:10024 (LISTEN)
    amavisd 27705 zimbra 15u IPv4 84163 TCP zimbra.collaborative.org:41576->zimbra.collaborative.org:ldap (ESTABLISHED)
    amavisd 28109 zimbra 7u IPv4 17317 TCP localhost:10024 (LISTEN)
    amavisd 28109 zimbra 15u IPv4 81543 TCP zimbra.collaborative.org:46810->zimbra.collaborative.org:ldap (ESTABLISHED)
    amavisd 28516 zimbra 7u IPv4 17317 TCP localhost:10024 (LISTEN)
    amavisd 28516 zimbra 15u IPv4 84798 TCP zimbra.collaborative.org:41597->zimbra.collaborative.org:ldap (ESTABLISHED)
    amavisd 28884 zimbra 7u IPv4 17317 TCP localhost:10024 (LISTEN)
    amavisd 28884 zimbra 15u IPv4 83392 TCP zimbra.collaborative.org:46879->zimbra.collaborative.org:ldap (ESTABLISHED)
    amavisd 30599 zimbra 7u IPv4 17317 TCP localhost:10024 (LISTEN)
    amavisd 30599 zimbra 15u IPv4 88774 TCP zimbra.collaborative.org:48692->zimbra.collaborative.org:ldap (ESTABLISHED)
    amavisd 30886 zimbra 7u IPv4 17317 TCP localhost:10024 (LISTEN)
    amavisd 30886 zimbra 15u IPv4 89355 TCP zimbra.collaborative.org:48710->zimbra.collaborative.org:ldap (ESTABLISHED)
    smtpd 31869 postfix 6u IPv4 17633 TCP *:smtp (LISTEN)
    smtpd 31869 postfix 16u IPv4 91531 TCP zimbra.collaborative.org:40896->zimbra.collaborative.org:ldap (ESTABLISHED)


    and after zmcomtrol stop...

    sshd 3553 root 3u IPv6 8355 TCP *:ssh (LISTEN)
    miniserv. 3618 root 6u IPv4 8456 TCP *:10000 (LISTEN)
    sshd 5301 root 3u IPv6 12645 TCP zimbra.collaborative.org:ssh->159.250.29.246:34422 (ESTABLISHED)
    sshd 5312 adnim1 3u IPv6 12645 TCP zimbra.collaborative.org:ssh->159.250.29.246:34422 (ESTABLISHED)
    sshd 6259 root 3u IPv6 107292 TCP zimbra.collaborative.org:ssh->c-71-192-30-191.hsd1.ma.comcast.net:62969 (ESTABLISHED)
    sshd 6605 adnim1 3u IPv6 107292 TCP zimbra.collaborative.org:ssh->c-71-192-30-191.hsd1.ma.comcast.net:62969 (ESTABLISHED)
    sshd 6649 root 3u IPv6 15709 TCP zimbra.collaborative.org:ssh->159.250.29.246:60160 (ESTABLISHED)
    sshd 6661 adnim1 3u IPv6 15709 TCP zimbra.collaborative.org:ssh->159.250.29.246:60160 (ESTABLISHED)


    I would assume perdition is listening on 995 ... am I right?

  4. #4
    cmattogno is offline New Member
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    JACKPOT!

    Thank you.
    Right as I hit submit, I had an epiphany ... I wan't running the IMAP/POP Proxy before? was I? ... I started all the services, killed perdition (zmperditionctl stop) then started tomcat (tomcat start), adnd then I was able to disable in the web admin interface. I then shutdown everything (zmcontrol stop) and the started everything up (zmcontrol start) and all is god again.

    Thank you for that direction.

    'topher

  5. #5
    mmorse's Avatar
    mmorse is offline Moderator
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    Default

    should be pop ssl
    Is this a single server install? any reason you have perdition enabled?
    zmprov -l modifyServer server.domain.com -zimbraServiceEnabled imapproxy
    zmprov gs server.domain.com | grep Pop and let us know what you have.

  6. #6
    mmorse's Avatar
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