[SQOOP-1177] Sqoop Export Upsert Query for MySQL fails with Deadlock exception

• Type: Bug
• Status: Open
• Priority: Major
• Resolution: Unresolved
• Affects Version/s: 1.4.3

Environment

Sqoop 1.4.3, MySQL 5.5.27

• Assignee: Unassigned
• Reporter: Sarath Rachakonda
• Created: 21/Aug/13 13:07
• Updated: 22/Aug/13 05:18

Description

When Sqoop Export upsert query tries to update data in MySQL table by the 2 default mappers it failed with following MySQL deadlock exception.

013-08-17 21:29:23,753 DEBUG org.apache.sqoop.mapreduce.mysql.MySQLUpsertOutputFormat: Using upsert query: INSERT INTO `AGG_SOCIALMENTION`(datedm_id, externalindividual_type, topicdm_id, topicclassdm_id, companydm_id, locationdm_id, gender_type, media_id, mention_type_id, mentions_count, qualificationscore_avg, positive_sentiment_count, negative_sentiment_count, neutral_sentiment_count, agg_sm_id) VALUES(?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?) ON DUPLICATE KEY UPDATE datedm_id=VALUES(datedm_id), externalindividual_type=VALUES(externalindividual_type), topicdm_id=VALUES(topicdm_id), topicclassdm_id=VALUES(topicclassdm_id), companydm_id=VALUES(companydm_id), locationdm_id=VALUES(locationdm_id), gender_type=VALUES(gender_type), media_id=VALUES(media_id), mention_type_id=VALUES(mention_type_id), mentions_count=VALUES(mentions_count), qualificationscore_avg=VALUES(qualificationscore_avg), positive_sentiment_count=VALUES(positive_sentiment_count), negative_sentiment_count=VALUES(negative_sentiment_count), neutral_sentiment_count=VALUES(neutral_sentiment_count), agg_sm_id=VALUES(agg_sm_id)
2013-08-17 21:29:28,546 ERROR org.apache.sqoop.mapreduce.AsyncSqlOutputFormat: Got exception in update thread: java.sql.BatchUpdateException: Deadlock found when trying to get lock; try restarting transaction
	at com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:2013)
	at com.mysql.jdbc.PreparedStatement.executeBatch(PreparedStatement.java:1449)
	at org.apache.sqoop.mapreduce.AsyncSqlOutputFormat$AsyncSqlExecThread.run(AsyncSqlOutputFormat.java:231)
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLTransactionRollbackException: Deadlock found when trying to get lock; try restarting transaction
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:407)
	at com.mysql.jdbc.Util.getInstance(Util.java:382)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1064)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3603)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3535)
	at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1989)
	at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2150)
	at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2626)
	at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2119)
	at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2415)
	at com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:1976)
	... 2 more

2013-08-17 21:29:28,546 DEBUG org.apache.sqoop.mapreduce.mysql.MySQLUpsertOutputFormat: Using upsert query: INSERT INTO `AGG_SOCIALMENTION`(datedm_id, externalindividual_type, topicdm_id, topicclassdm_id, companydm_id, locationdm_id, gender_type, media_id, mention_type_id, mentions_count, qualificationscore_avg, positive_sentiment_count, negative_sentiment_count, neutral_sentiment_count, agg_sm_id) VALUES(?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?) ON DUPLICATE KEY UPDATE datedm_id=VALUES(datedm_id), externalindividual_type=VALUES(externalindividual_type), topicdm_id=VALUES(topicdm_id), topicclassdm_id=VALUES(topicclassdm_id), companydm_id=VALUES(companydm_id), locationdm_id=VALUES(locationdm_id), gender_type=VALUES(gender_type), media_id=VALUES(media_id), mention_type_id=VALUES(mention_type_id), mentions_count=VALUES(mentions_count), qualificationscore_avg=VALUES(qualificationscore_avg), positive_sentiment_count=VALUES(positive_sentiment_count), negative_sentiment_count=VALUES(negative_sentiment_count), neutral_sentiment_count=VALUES(neutral_sentiment_count), agg_sm_id=VALUES(agg_sm_id)
2013-08-17 21:29:28,551 ERROR org.apache.sqoop.mapreduce.AsyncSqlRecordWriter: Top level exception: 
java.sql.BatchUpdateException: Deadlock found when trying to get lock; try restarting transaction
	at com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:2013)
	at com.mysql.jdbc.PreparedStatement.executeBatch(PreparedStatement.java:1449)
	at org.apache.sqoop.mapreduce.AsyncSqlOutputFormat$AsyncSqlExecThread.run(AsyncSqlOutputFormat.java:231)
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLTransactionRollbackException: Deadlock found when trying to get lock; try restarting transaction
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:407)
	at com.mysql.jdbc.Util.getInstance(Util.java:382)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1064)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3603)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3535)
	at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1989)
	at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2150)
	at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2626)
	at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2119)
	at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2415)
	at com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:1976)
	... 2 more
2013-08-17 21:29:28,552 ERROR org.apache.sqoop.mapreduce.TextExportMapper: 
2013-08-17 21:29:28,552 ERROR org.apache.sqoop.mapreduce.TextExportMapper: Exception raised during data export
2013-08-17 21:29:28,552 ERROR org.apache.sqoop.mapreduce.TextExportMapper: 
2013-08-17 21:29:28,553 ERROR org.apache.sqoop.mapreduce.TextExportMapper: Exception: 
java.io.IOException: java.sql.BatchUpdateException: Deadlock found when trying to get lock; try restarting transaction
	at org.apache.sqoop.mapreduce.AsyncSqlRecordWriter.write(AsyncSqlRecordWriter.java:220)
	at org.apache.sqoop.mapreduce.AsyncSqlRecordWriter.write(AsyncSqlRecordWriter.java:46)
	at org.apache.hadoop.mapred.MapTask$NewDirectOutputCollector.write(MapTask.java:558)
	at org.apache.hadoop.mapreduce.task.TaskInputOutputContextImpl.write(TaskInputOutputContextImpl.java:85)
	at org.apache.hadoop.mapreduce.lib.map.WrappedMapper$Context.write(WrappedMapper.java:106)
	at org.apache.sqoop.mapreduce.TextExportMapper.map(TextExportMapper.java:84)
	at org.apache.sqoop.mapreduce.TextExportMapper.map(TextExportMapper.java:39)
	at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:140)
	at org.apache.sqoop.mapreduce.AutoProgressMapper.run(AutoProgressMapper.java:64)
	at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:672)
	at org.apache.hadoop.mapred.MapTask.run(MapTask.java:330)
	at org.apache.hadoop.mapred.Child$4.run(Child.java:268)
	at java.security.AccessController.doPrivileged(Native Method)
	at javax.security.auth.Subject.doAs(Subject.java:396)
	at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1408)
	at org.apache.hadoop.mapred.Child.main(Child.java:262)
Caused by: java.sql.BatchUpdateException: Deadlock found when trying to get lock; try restarting transaction
	at com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:2013)
	at com.mysql.jdbc.PreparedStatement.executeBatch(PreparedStatement.java:1449)
	at org.apache.sqoop.mapreduce.AsyncSqlOutputFormat$AsyncSqlExecThread.run(AsyncSqlOutputFormat.java:231)
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLTransactionRollbackException: Deadlock found when trying to get lock; try restarting transaction
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:407)
	at com.mysql.jdbc.Util.getInstance(Util.java:382)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1064)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3603)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3535)
	at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1989)
	at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2150)
	at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2626)
	at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2119)
	at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2415)
	at com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:1976)
	... 2 more
2013-08-17 21:29:28,553 ERROR org.apache.sqoop.mapreduce.TextExportMapper: On input: 20130715|4|285|10|18|37523|3|1|1|1|90.0|0|0|1|null