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Thread: Zimbra 6.0.12: sometimes mysql does not start

  1. #1
    fabrica64 is offline Starter Member
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    Default Zimbra 6.0.12: sometimes mysql does not start

    Zimbra 6.0.12 on Ubuntu 10.04 LTS in a KVM virtual machine hosted by a Ubuntu 10.04 LTS server.

    Sometimes (approx. 1 out of 10 boots), when starting Zimbra server (thus starting zimbra automatically at boot), mysql does not start preventing zimbra from working correctly.

    If I shutdown and restart zimbra everything works fine.

    The error from mailbox.log file is:

    ...
    ...
    2011-05-23 02:23:48,702 INFO [main] [] system - Setting mysql connector property: maxActive=100
    2011-05-23 02:23:48,714 INFO [main] [] system - Setting mysql connector property: maxActive=100
    2011-05-23 02:23:48,725 INFO [main] [] dbconn - instantiating DB connection factory class com.zimbra.cs.db.ZimbraConnectionFactory
    2011-05-23 02:23:52,898 WARN [main] [] misc - Could not establish a connection to the database. Retrying in 5 seconds.
    com.zimbra.common.service.ServiceException: system failure: getting database connection
    ExceptionId:main:1306110232894:54198d5de2583136
    Code:service.FAILURE
    at com.zimbra.common.service.ServiceException.FAILURE (ServiceException.java:248)
    at com.zimbra.cs.db.DbPool.getConnection(DbPool.java: 313)
    at com.zimbra.cs.db.DbPool.getConnection(DbPool.java: 277)
    at com.zimbra.cs.db.DbPool.waitForDatabase(DbPool.jav a:199)
    at com.zimbra.cs.db.DbPool.startup(DbPool.java:190)
    at com.zimbra.cs.util.Zimbra.startup(Zimbra.java:156)
    at com.zimbra.cs.util.Zimbra.startup(Zimbra.java:123)
    at com.zimbra.soap.SoapServlet.init(SoapServlet.java: 125)
    at javax.servlet.GenericServlet.init(GenericServlet.j ava:241)
    at org.mortbay.jetty.servlet.ServletHolder.initServle t(ServletHolder.java:440)
    at org.mortbay.jetty.servlet.ServletHolder.doStart(Se rvletHolder.java:263)
    at org.mortbay.component.AbstractLifeCycle.start(Abst ractLifeCycle.java:50)
    at org.mortbay.jetty.servlet.ServletHandler.initializ e(ServletHandler.java:685)
    at org.mortbay.jetty.servlet.Context.startContext(Con text.java:140)
    at org.mortbay.jetty.webapp.WebAppContext.startContex t(WebAppContext.java:1254)
    at org.mortbay.jetty.handler.ContextHandler.doStart(C ontextHandler.java:517)
    at org.mortbay.jetty.webapp.WebAppContext.doStart(Web AppContext.java:471)
    at org.mortbay.component.AbstractLifeCycle.start(Abst ractLifeCycle.java:50)
    at org.mortbay.jetty.handler.HandlerCollection.doStar t(HandlerCollection.java:152)
    at org.mortbay.jetty.handler.ContextHandlerCollection .doStart(ContextHandlerCollection.java:156)
    at org.mortbay.component.AbstractLifeCycle.start(Abst ractLifeCycle.java:50)
    at org.mortbay.jetty.handler.HandlerCollection.doStar t(HandlerCollection.java:152)
    at org.mortbay.component.AbstractLifeCycle.start(Abst ractLifeCycle.java:50)
    at org.mortbay.jetty.handler.HandlerWrapper.doStart(H andlerWrapper.java:130)
    at org.mortbay.component.AbstractLifeCycle.start(Abst ractLifeCycle.java:50)
    at org.mortbay.jetty.handler.HandlerWrapper.doStart(H andlerWrapper.java:130)
    at org.mortbay.jetty.handler.DebugHandler.doStart(Deb ugHandler.java:127)
    at org.mortbay.component.AbstractLifeCycle.start(Abst ractLifeCycle.java:50)
    at org.mortbay.jetty.handler.HandlerWrapper.doStart(H andlerWrapper.java:130)
    at org.mortbay.jetty.Server.doStart(Server.java:224)
    at org.mortbay.setuid.SetUIDServer.doStart(SetUIDServ er.java:158)
    at org.mortbay.component.AbstractLifeCycle.start(Abst ractLifeCycle.java:50)
    at org.mortbay.xml.XmlConfiguration.main(XmlConfigura tion.java:985)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Nativ e Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Native MethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(De legatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at org.mortbay.start.Main.invokeMain(Main.java:194)
    at org.mortbay.start.Main.start(Main.java:534)
    at org.mortbay.start.Main.start(Main.java:441)
    at org.mortbay.start.Main.main(Main.java:119)
    Caused by: com.mysql.jdbc.exceptions.MySQLNonTransientConnect ionException: Server connection failure during transaction. Due to underlying exception: 'java.net.ConnectException: Connection refused'.

    ** BEGIN NESTED EXCEPTION **


    java.net.ConnectException
    MESSAGE: Connection refused

    STACKTRACE:

    java.net.ConnectException: Connection refused
    at java.net.PlainSocketImpl.socketConnect(Native Method)
    at java.net.PlainSocketImpl.doConnect(PlainSocketImpl .java:351)
    at java.net.PlainSocketImpl.connectToAddress(PlainSoc ketImpl.java:213)
    at java.net.PlainSocketImpl.connect(PlainSocketImpl.j ava:200)
    at java.net.SocksSocketImpl.connect(SocksSocketImpl.j ava:366)
    at java.net.Socket.connect(Socket.java:529)
    at java.net.Socket.connect(Socket.java:478)
    at java.net.Socket.<init>(Socket.java:375)
    at java.net.Socket.<init>(Socket.java:218)
    at com.mysql.jdbc.StandardSocketFactory.connect(Stand ardSocketFactory.java:256)
    at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:271)
    at com.mysql.jdbc.Connection.createNewIO(Connection.j ava:2921)
    at com.mysql.jdbc.Connection.<init>(Connection.java:1 555)
    at com.mysql.jdbc.NonRegisteringDriver.connect(NonReg isteringDriver.java:285)
    at java.sql.DriverManager.getConnection(DriverManager .java:582)
    at java.sql.DriverManager.getConnection(DriverManager .java:154)
    at org.apache.commons.dbcp.DriverManagerConnectionFac tory.createConnection(DriverManagerConnectionFacto ry.java:68)
    at com.zimbra.cs.db.ZimbraConnectionFactory.createCon nection(ZimbraConnectionFactory.java:50)
    at org.apache.commons.dbcp.PoolableConnectionFactory. makeObject(PoolableConnectionFactory.java:294)
    at org.apache.commons.pool.impl.GenericObjectPool.bor rowObject(GenericObjectPool.java:1148)
    at org.apache.commons.dbcp.PoolingDataSource.getConne ction(PoolingDataSource.java:96)
    at com.zimbra.cs.db.DbPool.getConnection(DbPool.java: 294)
    at com.zimbra.cs.db.DbPool.getConnection(DbPool.java: 277)
    at com.zimbra.cs.db.DbPool.waitForDatabase(DbPool.jav a:199)
    at com.zimbra.cs.db.DbPool.startup(DbPool.java:190)
    at com.zimbra.cs.util.Zimbra.startup(Zimbra.java:156)
    at com.zimbra.cs.util.Zimbra.startup(Zimbra.java:123)
    at com.zimbra.soap.SoapServlet.init(SoapServlet.java: 125)
    at javax.servlet.GenericServlet.init(GenericServlet.j ava:241)
    at org.mortbay.jetty.servlet.ServletHolder.initServle t(ServletHolder.java:440)
    at org.mortbay.jetty.servlet.ServletHolder.doStart(Se rvletHolder.java:263)
    at org.mortbay.component.AbstractLifeCycle.start(Abst ractLifeCycle.java:50)
    at org.mortbay.jetty.servlet.ServletHandler.initializ e(ServletHandler.java:685)
    at org.mortbay.jetty.servlet.Context.startContext(Con text.java:140)
    at org.mortbay.jetty.webapp.WebAppContext.startContex t(WebAppContext.java:1254)
    at org.mortbay.jetty.handler.ContextHandler.doStart(C ontextHandler.java:517)
    at org.mortbay.jetty.webapp.WebAppContext.doStart(Web AppContext.java:471)
    at org.mortbay.component.AbstractLifeCycle.start(Abst ractLifeCycle.java:50)
    at org.mortbay.jetty.handler.HandlerCollection.doStar t(HandlerCollection.java:152)
    at org.mortbay.jetty.handler.ContextHandlerCollection .doStart(ContextHandlerCollection.java:156)
    at org.mortbay.component.AbstractLifeCycle.start(Abst ractLifeCycle.java:50)
    at org.mortbay.jetty.handler.HandlerCollection.doStar t(HandlerCollection.java:152)
    at org.mortbay.component.AbstractLifeCycle.start(Abst ractLifeCycle.java:50)
    at org.mortbay.jetty.handler.HandlerWrapper.doStart(H andlerWrapper.java:130)
    at org.mortbay.component.AbstractLifeCycle.start(Abst ractLifeCycle.java:50)

    at org.mortbay.jetty.handler.HandlerWrapper.doStart(H andlerWrapper.java:130)
    at org.mortbay.jetty.handler.DebugHandler.doStart(Deb ugHandler.java:127)
    at org.mortbay.component.AbstractLifeCycle.start(Abst ractLifeCycle.java:50)
    at org.mortbay.jetty.handler.HandlerWrapper.doStart(H andlerWrapper.java:130)
    at org.mortbay.jetty.Server.doStart(Server.java:224)
    at org.mortbay.setuid.SetUIDServer.doStart(SetUIDServ er.java:158)
    at org.mortbay.component.AbstractLifeCycle.start(Abst ractLifeCycle.java:50)
    at org.mortbay.xml.XmlConfiguration.main(XmlConfigura tion.java:985)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Nativ e Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Native MethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(De legatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at org.mortbay.start.Main.invokeMain(Main.java:194)
    at org.mortbay.start.Main.start(Main.java:534)
    at org.mortbay.start.Main.start(Main.java:441)
    at org.mortbay.start.Main.main(Main.java:119)


    ** END NESTED EXCEPTION **


    Attempted reconnect 3 times. Giving up.

    at com.mysql.jdbc.SQLError.createSQLException(SQLErro r.java:888)
    at com.mysql.jdbc.Connection.createNewIO(Connection.j ava:2997)
    at com.mysql.jdbc.Connection.<init>(Connection.java:1 555)
    at com.mysql.jdbc.NonRegisteringDriver.connect(NonReg isteringDriver.java:285)
    at java.sql.DriverManager.getConnection(DriverManager .java:582)
    at java.sql.DriverManager.getConnection(DriverManager .java:154)
    at org.apache.commons.dbcp.DriverManagerConnectionFac tory.createConnection(DriverManagerConnectionFacto ry.java:68)
    at com.zimbra.cs.db.ZimbraConnectionFactory.createCon nection(ZimbraConnectionFactory.java:50)
    at org.apache.commons.dbcp.PoolableConnectionFactory. makeObject(PoolableConnectionFactory.java:294)
    at org.apache.commons.pool.impl.GenericObjectPool.bor rowObject(GenericObjectPool.java:1148)
    at org.apache.commons.dbcp.PoolingDataSource.getConne ction(PoolingDataSource.java:96)
    at com.zimbra.cs.db.DbPool.getConnection(DbPool.java: 294)
    ... 39 more
    2011-05-23 02:24:01,915 WARN [main] [] misc - Could not establish a connection to the database. Retrying in 5 seconds.
    ...
    ...

    Then continuing this way until restart...

    No other error is listed in any log file. The system does an automatic shutdown at 2:01 and, after being backed up (it;s a virtual machine) it is restarted at 2:23.

    In the mysql_error.log you may see at 2011-05-23 02:23 that there is no "mysql started" statement, there is another start later at 8:30, forced by hand after detecting that something was not working.


    ...
    ...
    110522 18:48:04 mysqld started
    110522 18:48:05 InnoDB: Started; log sequence number 0 327492748
    110522 18:48:05 [Note] /opt/zimbra/mysql/libexec/mysqld: ready for connections.
    Version: '5.0.90-log' socket: '/opt/zimbra/db/mysql.sock' port: 7306 Source distribution
    110522 18:51:16 [Note] /opt/zimbra/mysql/libexec/mysqld: Normal shutdown

    110522 18:51:16 InnoDB: Starting shutdown...
    110522 18:51:18 InnoDB: Shutdown completed; log sequence number 0 327552135
    110522 18:51:18 [Note] /opt/zimbra/mysql/libexec/mysqld: Shutdown complete

    110522 18:51:18 mysqld ended

    110522 18:52:37 mysqld started
    110522 18:52:38 InnoDB: Started; log sequence number 0 327552135
    110522 18:52:38 [Note] /opt/zimbra/mysql/libexec/mysqld: ready for connections.
    Version: '5.0.90-log' socket: '/opt/zimbra/db/mysql.sock' port: 7306 Source distribution
    110523 2:01:02 [Note] /opt/zimbra/mysql/libexec/mysqld: Normal shutdown

    110523 2:01:05 InnoDB: Starting shutdown...
    110523 2:01:07 InnoDB: Shutdown completed; log sequence number 0 327727300
    110523 2:01:07 [Note] /opt/zimbra/mysql/libexec/mysqld: Shutdown complete

    110523 02:01:07 mysqld ended

    110523 08:30:30 mysqld started
    110523 8:30:31 InnoDB: Started; log sequence number 0 327727300
    110523 8:30:31 [Note] /opt/zimbra/mysql/libexec/mysqld: ready for connections.
    Version: '5.0.90-log' socket: '/opt/zimbra/db/mysql.sock' port: 7306 Source distribution
    110524 2:01:02 [Note] /opt/zimbra/mysql/libexec/mysqld: Normal shutdown

    110524 2:01:04 InnoDB: Starting shutdown...
    110524 2:01:07 InnoDB: Shutdown completed; log sequence number 0 329872614
    110524 2:01:07 [Note] /opt/zimbra/mysql/libexec/mysqld: Shutdown complete
    ...
    ...

    Thanks and regards
    - Paolo

  2. #2
    dik23 is offline Advanced Member
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    Default

    How are you closing Zimbra down ?

    Do you use zmcontrol stop or are you just stopping the vm ?

  3. #3
    fabrica64 is offline Starter Member
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    Default

    I am closing the VM, but executing all shutdown steps. KVM send an ACPI shutdown request and the VM executes a shutdown, which should execute:

    /etc/init.d/zimbra stop

    I don't know if the stop is executed correctly. From the logs it seems that it is executed, but the shutdown takes a lot less than executing

    # /etc/init.d/zimbra stop

    from a terminal, so it may be that some part of the system is taken down abruptly during a shutdown

    Do you have any experience about it?

  4. #4
    dik23 is offline Advanced Member
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    I am running Zimbra in OpenVZ and had problems with the database not starting after automated backups of the vm.

    Now I just have zmcontrol stop in the Zimbra crontab one minute (it currently takes just over 30s on my setup) before the backup is scheduled and all works fine. For good measure I have another crontab entry one minute after the backup is scheduled to start, zmcontrol start, just in case.

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