Communication packets error with MySQL

Hi,
I'm having a problem with executing a query on MySQL. It seems that I'm getting the communication packets error once in a while and I'm not sure whether the query is bad or the settings on the database server is bad. Could anyone give me an insight where to look after?
Thank you,
852825
MySQL: 5.1.41-3ubuntu12.7
JDBC: 5.1.12
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: Got an error writing communication packets
     at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
     at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
     at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
     at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
     at com.mysql.jdbc.Util.handleNewInstance(Util.java:409)
     at com.mysql.jdbc.Util.getInstance(Util.java:384)
     at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1015)
     at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3562)
     at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3494)
     at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1960)
     at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2114)
     at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2696)
     at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2105)
     at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2264)

I've tried the community but no response so far. Any tips on where to look?

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    When I want to record on an attendance code without clock times then the above works fine. The SAP system in which CATS resides looks into table PTIMEOV1. So far so good.
    However, when I want to record hours WITH clock times then I cannot save the data. The error message HRTIM00CATS667 shows up:
    "Communication error with the LOCAL_EXEC Function BAPI_PTMGREXTATTABS_CHECK is no t available  system"
    Diagnosis
    An error has occured during communication with the HR System. The HR data in the time sheet cannot be validated.
    From the error message description it seems that it wants to check the SAP HR system instead of looking for the check in the SAP system in which CATS resides.....
    When I change the value from LOCAL_EXEC to the system in which HR resides then the error disappears, but then it really checks into the SAP HR system (synchronous check with that SAP HR system) and that is not what the customer wants. The check should be local on the PTIMEOV1 table (in case the SAP HR system is down).
    I did not find any OSS notes on the topic....or other info on SDN.
    Can anyone help me out concerning this starnge error message, at least for me?
    Thanks very much in advance,
    Kind regards,
    Mirko

    "A point to add"
    I just noticed that following message is being continously receiving in the database alert_log:
    Sat Oct 9 16:04:52 2010
    WARNING: inbound connection timed out (ORA-3136)
    Sat Oct 9 16:05:32 2010
    WARNING: inbound connection timed out (ORA-3136)
    Sat Oct 9 16:06:30 2010
    WARNING: inbound connection timed out (ORA-3136)
    Sat Oct 9 16:07:10 2010
    WARNING: inbound connection timed out (ORA-3136)
    Sat Oct 9 16:09:35 2010
    Incremental checkpoint up to RBA [0x1d.1f9928.0], current log tail at RBA [0x1d.1f9a79.0]
    Sat Oct 9 16:11:52 2010
    WARNING: inbound connection timed out (ORA-3136)
    Sat Oct 9 16:29:40 2010
    Incremental checkpoint up to RBA [0x1d.1f9b87.0], current log tail at RBA [0x1d.1f9bf4.0]
    ~
    Please help.

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