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Communications link failure with MySQL

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I am getting this error near the end of a long transformation. Can someone give some ideas on what the problem might be? I have searched the forum and found similar "Communications link failure" issues but the suggested fix doesn't make a difference in this case. I increased net_write_timeout = 600 from 100.

2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Unexpected error
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : org.pentaho.di.core.exception.KettleStepException:
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Error in step, asking everyone to stop because of:
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) :
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Error looking up row in database
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Communications link failure
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) :
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : The last packet successfully received from the server was 1,290,343 milliseconds ago. The last packet sent successfully to the server was 1,290,448 milliseconds ago.
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) :
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) :
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at org.pentaho.di.trans.steps.insertupdate.InsertUpdate.processRow(InsertUpdate.java:318)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at org.pentaho.di.trans.step.RunThread.run(RunThread.java:50)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at java.lang.Thread.run(Thread.java:695)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Caused by: org.pentaho.di.core.exception.KettleDatabaseException:
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Error looking up row in database
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Communications link failure
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) :
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : The last packet successfully received from the server was 1,290,343 milliseconds ago. The last packet sent successfully to the server was 1,290,448 milliseconds ago.
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) :
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at org.pentaho.di.core.database.Database.getLookup(Database.java:3082)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at org.pentaho.di.core.database.Database.getLookup(Database.java:3055)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at org.pentaho.di.trans.steps.insertupdate.InsertUpdate.lookupValues(InsertUpdate.java:91)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at org.pentaho.di.trans.steps.insertupdate.InsertUpdate.processRow(InsertUpdate.java:301)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : ... 2 more
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) :
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : The last packet successfully received from the server was 1,290,343 milliseconds ago. The last packet sent successfully to the server was 1,290,448 milliseconds ago.
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1121)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3938)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2551)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2731)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2815)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2155)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2322)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at org.pentaho.di.core.database.Database.getLookup(Database.java:3063)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : ... 5 more
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Caused by: java.net.SocketException: Broken pipe
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at java.net.SocketOutputStream.socketWrite0(Native Method)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:92)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at java.net.SocketOutputStream.write(SocketOutputStream.java:136)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:65)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:123)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3919)
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : ... 11 more
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Unable to commit connection(s) :org.pentaho.di.core.exception.KettleDatabaseException:
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Unable to get database metadata from this database connection
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : No operations allowed after connection closed.
2014/01/17 16:17:43 - Insert / Update Availabilities.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Unable to commit connection(s) :org.pentaho.di.core.exception.KettleDatabaseException:
2014/01/17 16:17:43 - Insert / Update Availabilities.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Error comitting connection
2014/01/17 16:17:43 - Insert / Update Availabilities.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Communications link failure during commit(). Transaction resolution unknown.
2014/01/17 16:17:43 - Insert / Update curriculum prefs.0 - Finished processing (I=0, O=0, R=1, W=0, U=0, E=1)
2014/01/17 16:17:43 - Insert / Update grade levels.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Unable to commit connection(s) :org.pentaho.di.core.exception.KettleDatabaseException:
2014/01/17 16:17:43 - Insert / Update grade levels.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Error comitting connection
2014/01/17 16:17:43 - Insert / Update grade levels.0 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Communications link failure during commit(). Transaction resolution unknown.
2014/01/17 16:17:43 - Insert / Update grade levels.0 - Finished processing (I=0, O=0, R=0, W=0, U=0, E=1)
2014/01/17 16:17:43 - Insert / Update Availabilities.0 - Finished processing (I=0, O=0, R=0, W=0, U=0, E=1)
2014/01/17 16:17:43 - psPeopleToCivi-step2 - psPeopleToCivi-step2
2014/01/17 16:17:43 - psPeopleToCivi-step2 - psPeopleToCivi-step2
2014/01/17 16:17:44 - psPeopleToCivi-step2 - psPeopleToCivi-step2
2014/01/17 16:17:44 - psPeopleToCivi-step2 - psPeopleToCivi-step2
2014/01/17 16:17:46 - Spoon - The transformation has finished!!
2014/01/17 16:17:46 - psPeopleToCivi-step2 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Errors detected!
2014/01/17 16:17:46 - psPeopleToCivi-step2 - ERROR (version 4.4.0-stable, build 17588 from 2012-11-21 16.02.21 by buildguy) : Errors detected!
2014/01/17 16:17:46 - psPeopleToCivi-step2 - psPeopleToCivi-step2
2014/01/17 16:17:46 - psPeopleToCivi-step2 - psPeopleToCivi-step2

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