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Posted to dev@manifoldcf.apache.org by "Karl Wright (JIRA)" <ji...@apache.org> on 2012/11/28 09:19:00 UTC
[jira] [Created] (CONNECTORS-571) MySQL operations time out when
long transaction undertaken and need to be restarted
Karl Wright created CONNECTORS-571:
--------------------------------------
Summary: MySQL operations time out when long transaction undertaken and need to be restarted
Key: CONNECTORS-571
URL: https://issues.apache.org/jira/browse/CONNECTORS-571
Project: ManifoldCF
Issue Type: Bug
Components: Framework core
Affects Versions: ManifoldCF 1.0.1, ManifoldCF 1.0
Reporter: Karl Wright
Fix For: ManifoldCF 1.1
If a transaction takes too long, MySQL handles this by aborting other threads that are trying to get locks on the resources being held. When it does this ManifoldCF does not handle the situation properly, and does not retry the aborted threads.
The SQLException that is thrown is:
ERROR 1205 (HY000): Lock wait timeout exceeded; try restarting transaction
The context that this happens in is varied:
{code}
2012/11/22 23:39:28 ERROR (Job start thread) - Job start thread aborting and restarting due to database connection reset: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
at org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
at org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
at org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
at org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
at org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performQuery(DBInterfaceMySQL.java:852)
at org.apache.manifoldcf.crawler.jobs.JobManager.startJobs(JobManager.java:4711)
at org.apache.manifoldcf.crawler.system.JobStartThread.run(JobStartThread.java:68)
Caused by: java.sql.SQLException: Lock wait timeout exceeded; try restarting transaction
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
at com.mysql.jdbc.MysqlIO.nextRowFast(MysqlIO.java:1578)
at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1434)
at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:2925)
at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:477)
at com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:2631)
at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:1800)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2221)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2293)
at org.apache.manifoldcf.core.database.Database.execute(Database.java:826)
at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
2012/11/22 23:39:28 ERROR (Finisher thread) - Finisher thread aborting and restarting due to database connection reset: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
at org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
at org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
at org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
at org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
at org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performQuery(DBInterfaceMySQL.java:852)
at org.apache.manifoldcf.crawler.jobs.JobManager.finishJobs(JobManager.java:6469)
at org.apache.manifoldcf.crawler.system.FinisherThread.run(FinisherThread.java:64)
Caused by: java.sql.SQLException: Lock wait timeout exceeded; try restarting transaction
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
at com.mysql.jdbc.MysqlIO.nextRowFast(MysqlIO.java:1578)
at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1434)
at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:2925)
at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:477)
at com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:2631)
at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:1800)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2221)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2293)
at org.apache.manifoldcf.core.database.Database.execute(Database.java:826)
at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
2012/11/22 23:39:30 ERROR (Worker thread '253') - Worker thread aborting and restarting due to database connection reset: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
at org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
at org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
at org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
at org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
at org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performModification(DBInterfaceMySQL.java:678)
at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performUpdate(DBInterfaceMySQL.java:275)
at org.apache.manifoldcf.core.database.BaseTable.performUpdate(BaseTable.java:80)
at org.apache.manifoldcf.crawler.jobs.JobQueue.updateCompletedRecord(JobQueue.java:722)
at org.apache.manifoldcf.crawler.jobs.JobManager.markDocumentCompletedMultiple(JobManager.java:2435)
at org.apache.manifoldcf.crawler.system.WorkerThread.run(WorkerThread.java:765)
Caused by: java.sql.SQLException: Lock wait timeout exceeded; try restarting transaction
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3541)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2002)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2163)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2427)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2345)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2330)
at org.apache.manifoldcf.core.database.Database.execute(Database.java:840)
at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
{code}
and
{code}
ERROR 2012-11-22 19:36:28,593 (Worker thread '16') - Worker thread aborting and restarting due to database connection reset: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
at org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
at org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
at org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
at org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
at org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performModification(DBInterfaceMySQL.java:678)
at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performUpdate(DBInterfaceMySQL.java:275)
at org.apache.manifoldcf.core.database.BaseTable.performUpdate(BaseTable.java:80)
at org.apache.manifoldcf.crawler.jobs.HopCount.markForDelete(HopCount.java:1426)
at org.apache.manifoldcf.crawler.jobs.HopCount.doDeleteInvalidation(HopCount.java:1356)
at org.apache.manifoldcf.crawler.jobs.HopCount.doFinish(HopCount.java:1057)
at org.apache.manifoldcf.crawler.jobs.HopCount.finishParents(HopCount.java:389)
at org.apache.manifoldcf.crawler.jobs.JobManager.finishDocuments(JobManager.java:4309)
at org.apache.manifoldcf.crawler.system.WorkerThread.run(WorkerThread.java:557)
Caused by: java.sql.SQLException: Lock wait timeout exceeded; try restarting transaction
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3541)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2002)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2163)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2427)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2345)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2330)
at org.apache.manifoldcf.core.database.Database.execute(Database.java:840)
at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
{code}
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[jira] [Resolved] (CONNECTORS-571) MySQL operations time out when
long transaction undertaken and need to be restarted
Posted by "Karl Wright (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/CONNECTORS-571?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Karl Wright resolved CONNECTORS-571.
------------------------------------
Resolution: Fixed
> MySQL operations time out when long transaction undertaken and need to be restarted
> -----------------------------------------------------------------------------------
>
> Key: CONNECTORS-571
> URL: https://issues.apache.org/jira/browse/CONNECTORS-571
> Project: ManifoldCF
> Issue Type: Bug
> Components: Framework core
> Affects Versions: ManifoldCF 1.0, ManifoldCF 1.0.1
> Reporter: Karl Wright
> Assignee: Karl Wright
> Fix For: ManifoldCF 1.1
>
>
> If a transaction takes too long, MySQL handles this by aborting other threads that are trying to get locks on the resources being held. When it does this ManifoldCF does not handle the situation properly, and does not retry the aborted threads.
> The SQLException that is thrown is:
> ERROR 1205 (HY000): Lock wait timeout exceeded; try restarting transaction
> The context that this happens in is varied:
> {code}
> 2012/11/22 23:39:28 ERROR (Job start thread) - Job start thread aborting and restarting due to database connection reset: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> at org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
> at org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
> at org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
> at org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
> at org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
> at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performQuery(DBInterfaceMySQL.java:852)
> at org.apache.manifoldcf.crawler.jobs.JobManager.startJobs(JobManager.java:4711)
> at org.apache.manifoldcf.crawler.system.JobStartThread.run(JobStartThread.java:68)
> Caused by: java.sql.SQLException: Lock wait timeout exceeded; try restarting transaction
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
> at com.mysql.jdbc.MysqlIO.nextRowFast(MysqlIO.java:1578)
> at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1434)
> at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:2925)
> at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:477)
> at com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:2631)
> at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:1800)
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2221)
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
> at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
> at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2293)
> at org.apache.manifoldcf.core.database.Database.execute(Database.java:826)
> at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
> 2012/11/22 23:39:28 ERROR (Finisher thread) - Finisher thread aborting and restarting due to database connection reset: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> at org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
> at org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
> at org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
> at org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
> at org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
> at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performQuery(DBInterfaceMySQL.java:852)
> at org.apache.manifoldcf.crawler.jobs.JobManager.finishJobs(JobManager.java:6469)
> at org.apache.manifoldcf.crawler.system.FinisherThread.run(FinisherThread.java:64)
> Caused by: java.sql.SQLException: Lock wait timeout exceeded; try restarting transaction
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
> at com.mysql.jdbc.MysqlIO.nextRowFast(MysqlIO.java:1578)
> at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1434)
> at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:2925)
> at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:477)
> at com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:2631)
> at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:1800)
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2221)
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
> at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
> at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2293)
> at org.apache.manifoldcf.core.database.Database.execute(Database.java:826)
> at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
> 2012/11/22 23:39:30 ERROR (Worker thread '253') - Worker thread aborting and restarting due to database connection reset: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> at org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
> at org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
> at org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
> at org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
> at org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
> at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performModification(DBInterfaceMySQL.java:678)
> at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performUpdate(DBInterfaceMySQL.java:275)
> at org.apache.manifoldcf.core.database.BaseTable.performUpdate(BaseTable.java:80)
> at org.apache.manifoldcf.crawler.jobs.JobQueue.updateCompletedRecord(JobQueue.java:722)
> at org.apache.manifoldcf.crawler.jobs.JobManager.markDocumentCompletedMultiple(JobManager.java:2435)
> at org.apache.manifoldcf.crawler.system.WorkerThread.run(WorkerThread.java:765)
> Caused by: java.sql.SQLException: Lock wait timeout exceeded; try restarting transaction
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3541)
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2002)
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2163)
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
> at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
> at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2427)
> at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2345)
> at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2330)
> at org.apache.manifoldcf.core.database.Database.execute(Database.java:840)
> at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
> {code}
> and
> {code}
> ERROR 2012-11-22 19:36:28,593 (Worker thread '16') - Worker thread aborting and restarting due to database connection reset: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> at org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
> at org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
> at org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
> at org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
> at org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
> at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performModification(DBInterfaceMySQL.java:678)
> at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performUpdate(DBInterfaceMySQL.java:275)
> at org.apache.manifoldcf.core.database.BaseTable.performUpdate(BaseTable.java:80)
> at org.apache.manifoldcf.crawler.jobs.HopCount.markForDelete(HopCount.java:1426)
> at org.apache.manifoldcf.crawler.jobs.HopCount.doDeleteInvalidation(HopCount.java:1356)
> at org.apache.manifoldcf.crawler.jobs.HopCount.doFinish(HopCount.java:1057)
> at org.apache.manifoldcf.crawler.jobs.HopCount.finishParents(HopCount.java:389)
> at org.apache.manifoldcf.crawler.jobs.JobManager.finishDocuments(JobManager.java:4309)
> at org.apache.manifoldcf.crawler.system.WorkerThread.run(WorkerThread.java:557)
> Caused by: java.sql.SQLException: Lock wait timeout exceeded; try restarting transaction
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3541)
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2002)
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2163)
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
> at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
> at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2427)
> at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2345)
> at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2330)
> at org.apache.manifoldcf.core.database.Database.execute(Database.java:840)
> at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
> {code}
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[jira] [Assigned] (CONNECTORS-571) MySQL operations time out when
long transaction undertaken and need to be restarted
Posted by "Karl Wright (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/CONNECTORS-571?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Karl Wright reassigned CONNECTORS-571:
--------------------------------------
Assignee: Karl Wright
> MySQL operations time out when long transaction undertaken and need to be restarted
> -----------------------------------------------------------------------------------
>
> Key: CONNECTORS-571
> URL: https://issues.apache.org/jira/browse/CONNECTORS-571
> Project: ManifoldCF
> Issue Type: Bug
> Components: Framework core
> Affects Versions: ManifoldCF 1.0, ManifoldCF 1.0.1
> Reporter: Karl Wright
> Assignee: Karl Wright
> Fix For: ManifoldCF 1.1
>
>
> If a transaction takes too long, MySQL handles this by aborting other threads that are trying to get locks on the resources being held. When it does this ManifoldCF does not handle the situation properly, and does not retry the aborted threads.
> The SQLException that is thrown is:
> ERROR 1205 (HY000): Lock wait timeout exceeded; try restarting transaction
> The context that this happens in is varied:
> {code}
> 2012/11/22 23:39:28 ERROR (Job start thread) - Job start thread aborting and restarting due to database connection reset: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> at org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
> at org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
> at org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
> at org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
> at org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
> at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performQuery(DBInterfaceMySQL.java:852)
> at org.apache.manifoldcf.crawler.jobs.JobManager.startJobs(JobManager.java:4711)
> at org.apache.manifoldcf.crawler.system.JobStartThread.run(JobStartThread.java:68)
> Caused by: java.sql.SQLException: Lock wait timeout exceeded; try restarting transaction
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
> at com.mysql.jdbc.MysqlIO.nextRowFast(MysqlIO.java:1578)
> at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1434)
> at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:2925)
> at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:477)
> at com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:2631)
> at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:1800)
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2221)
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
> at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
> at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2293)
> at org.apache.manifoldcf.core.database.Database.execute(Database.java:826)
> at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
> 2012/11/22 23:39:28 ERROR (Finisher thread) - Finisher thread aborting and restarting due to database connection reset: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> at org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
> at org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
> at org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
> at org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
> at org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
> at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performQuery(DBInterfaceMySQL.java:852)
> at org.apache.manifoldcf.crawler.jobs.JobManager.finishJobs(JobManager.java:6469)
> at org.apache.manifoldcf.crawler.system.FinisherThread.run(FinisherThread.java:64)
> Caused by: java.sql.SQLException: Lock wait timeout exceeded; try restarting transaction
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
> at com.mysql.jdbc.MysqlIO.nextRowFast(MysqlIO.java:1578)
> at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1434)
> at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:2925)
> at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:477)
> at com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:2631)
> at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:1800)
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2221)
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
> at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
> at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2293)
> at org.apache.manifoldcf.core.database.Database.execute(Database.java:826)
> at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
> 2012/11/22 23:39:30 ERROR (Worker thread '253') - Worker thread aborting and restarting due to database connection reset: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> at org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
> at org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
> at org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
> at org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
> at org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
> at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performModification(DBInterfaceMySQL.java:678)
> at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performUpdate(DBInterfaceMySQL.java:275)
> at org.apache.manifoldcf.core.database.BaseTable.performUpdate(BaseTable.java:80)
> at org.apache.manifoldcf.crawler.jobs.JobQueue.updateCompletedRecord(JobQueue.java:722)
> at org.apache.manifoldcf.crawler.jobs.JobManager.markDocumentCompletedMultiple(JobManager.java:2435)
> at org.apache.manifoldcf.crawler.system.WorkerThread.run(WorkerThread.java:765)
> Caused by: java.sql.SQLException: Lock wait timeout exceeded; try restarting transaction
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3541)
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2002)
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2163)
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
> at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
> at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2427)
> at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2345)
> at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2330)
> at org.apache.manifoldcf.core.database.Database.execute(Database.java:840)
> at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
> {code}
> and
> {code}
> ERROR 2012-11-22 19:36:28,593 (Worker thread '16') - Worker thread aborting and restarting due to database connection reset: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> at org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
> at org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
> at org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
> at org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
> at org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
> at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performModification(DBInterfaceMySQL.java:678)
> at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performUpdate(DBInterfaceMySQL.java:275)
> at org.apache.manifoldcf.core.database.BaseTable.performUpdate(BaseTable.java:80)
> at org.apache.manifoldcf.crawler.jobs.HopCount.markForDelete(HopCount.java:1426)
> at org.apache.manifoldcf.crawler.jobs.HopCount.doDeleteInvalidation(HopCount.java:1356)
> at org.apache.manifoldcf.crawler.jobs.HopCount.doFinish(HopCount.java:1057)
> at org.apache.manifoldcf.crawler.jobs.HopCount.finishParents(HopCount.java:389)
> at org.apache.manifoldcf.crawler.jobs.JobManager.finishDocuments(JobManager.java:4309)
> at org.apache.manifoldcf.crawler.system.WorkerThread.run(WorkerThread.java:557)
> Caused by: java.sql.SQLException: Lock wait timeout exceeded; try restarting transaction
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3541)
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2002)
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2163)
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
> at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
> at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2427)
> at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2345)
> at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2330)
> at org.apache.manifoldcf.core.database.Database.execute(Database.java:840)
> at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
> {code}
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[jira] [Commented] (CONNECTORS-571) MySQL operations time out when
long transaction undertaken and need to be restarted
Posted by "Karl Wright (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/CONNECTORS-571?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13505303#comment-13505303 ]
Karl Wright commented on CONNECTORS-571:
----------------------------------------
r1414575
> MySQL operations time out when long transaction undertaken and need to be restarted
> -----------------------------------------------------------------------------------
>
> Key: CONNECTORS-571
> URL: https://issues.apache.org/jira/browse/CONNECTORS-571
> Project: ManifoldCF
> Issue Type: Bug
> Components: Framework core
> Affects Versions: ManifoldCF 1.0, ManifoldCF 1.0.1
> Reporter: Karl Wright
> Assignee: Karl Wright
> Fix For: ManifoldCF 1.1
>
>
> If a transaction takes too long, MySQL handles this by aborting other threads that are trying to get locks on the resources being held. When it does this ManifoldCF does not handle the situation properly, and does not retry the aborted threads.
> The SQLException that is thrown is:
> ERROR 1205 (HY000): Lock wait timeout exceeded; try restarting transaction
> The context that this happens in is varied:
> {code}
> 2012/11/22 23:39:28 ERROR (Job start thread) - Job start thread aborting and restarting due to database connection reset: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> at org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
> at org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
> at org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
> at org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
> at org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
> at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performQuery(DBInterfaceMySQL.java:852)
> at org.apache.manifoldcf.crawler.jobs.JobManager.startJobs(JobManager.java:4711)
> at org.apache.manifoldcf.crawler.system.JobStartThread.run(JobStartThread.java:68)
> Caused by: java.sql.SQLException: Lock wait timeout exceeded; try restarting transaction
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
> at com.mysql.jdbc.MysqlIO.nextRowFast(MysqlIO.java:1578)
> at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1434)
> at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:2925)
> at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:477)
> at com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:2631)
> at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:1800)
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2221)
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
> at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
> at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2293)
> at org.apache.manifoldcf.core.database.Database.execute(Database.java:826)
> at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
> 2012/11/22 23:39:28 ERROR (Finisher thread) - Finisher thread aborting and restarting due to database connection reset: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> at org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
> at org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
> at org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
> at org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
> at org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
> at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performQuery(DBInterfaceMySQL.java:852)
> at org.apache.manifoldcf.crawler.jobs.JobManager.finishJobs(JobManager.java:6469)
> at org.apache.manifoldcf.crawler.system.FinisherThread.run(FinisherThread.java:64)
> Caused by: java.sql.SQLException: Lock wait timeout exceeded; try restarting transaction
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
> at com.mysql.jdbc.MysqlIO.nextRowFast(MysqlIO.java:1578)
> at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1434)
> at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:2925)
> at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:477)
> at com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:2631)
> at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:1800)
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2221)
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
> at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
> at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2293)
> at org.apache.manifoldcf.core.database.Database.execute(Database.java:826)
> at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
> 2012/11/22 23:39:30 ERROR (Worker thread '253') - Worker thread aborting and restarting due to database connection reset: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> at org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
> at org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
> at org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
> at org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
> at org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
> at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performModification(DBInterfaceMySQL.java:678)
> at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performUpdate(DBInterfaceMySQL.java:275)
> at org.apache.manifoldcf.core.database.BaseTable.performUpdate(BaseTable.java:80)
> at org.apache.manifoldcf.crawler.jobs.JobQueue.updateCompletedRecord(JobQueue.java:722)
> at org.apache.manifoldcf.crawler.jobs.JobManager.markDocumentCompletedMultiple(JobManager.java:2435)
> at org.apache.manifoldcf.crawler.system.WorkerThread.run(WorkerThread.java:765)
> Caused by: java.sql.SQLException: Lock wait timeout exceeded; try restarting transaction
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3541)
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2002)
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2163)
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
> at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
> at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2427)
> at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2345)
> at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2330)
> at org.apache.manifoldcf.core.database.Database.execute(Database.java:840)
> at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
> {code}
> and
> {code}
> ERROR 2012-11-22 19:36:28,593 (Worker thread '16') - Worker thread aborting and restarting due to database connection reset: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database exception: Exception doing query: Lock wait timeout exceeded; try restarting transaction
> at org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:681)
> at org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:709)
> at org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1394)
> at org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:144)
> at org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:186)
> at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performModification(DBInterfaceMySQL.java:678)
> at org.apache.manifoldcf.core.database.DBInterfaceMySQL.performUpdate(DBInterfaceMySQL.java:275)
> at org.apache.manifoldcf.core.database.BaseTable.performUpdate(BaseTable.java:80)
> at org.apache.manifoldcf.crawler.jobs.HopCount.markForDelete(HopCount.java:1426)
> at org.apache.manifoldcf.crawler.jobs.HopCount.doDeleteInvalidation(HopCount.java:1356)
> at org.apache.manifoldcf.crawler.jobs.HopCount.doFinish(HopCount.java:1057)
> at org.apache.manifoldcf.crawler.jobs.HopCount.finishParents(HopCount.java:389)
> at org.apache.manifoldcf.crawler.jobs.JobManager.finishDocuments(JobManager.java:4309)
> at org.apache.manifoldcf.crawler.system.WorkerThread.run(WorkerThread.java:557)
> Caused by: java.sql.SQLException: Lock wait timeout exceeded; try restarting transaction
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3609)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3541)
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2002)
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2163)
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
> at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
> at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2427)
> at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2345)
> at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2330)
> at org.apache.manifoldcf.core.database.Database.execute(Database.java:840)
> at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:641)
> {code}
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