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Details

Type: Bug
Resolution: Fixed
Priority: Medium
Fix Version/s: 3.0.7, 3.1.4, 3.2.2
Affects Version/s: 2.5.0, 2.12.0
Component/s: Database - MySQL
Labels:
- da-db
- da-db-mysql

Bug Fix Policy:
View Atlassian Server bug fix policy

Description

Symptoms

This issue might cause Pull Requests to misbehave as well as a number of performance issues on your instance. As an example of PRs misbehaviour, it's been reported:

(...) the following error more and more frequently when trying to merge a PR from the Stash UI (happening on multiple repos): "New changes were pushed to master in project/repo while the merge was being performed. Please retry the merge.

You will find similar stack traces in your logs:

atlassian.log

2014-01-24 01:48:07,044 WARN  [rescope-details:thread-2] nj9312 108x272810x0 j74y32 10.1.52.24 SSH - git-receive-pack '/consumer/yp.git' c.a.s.i.p.r.DefaultRescopeProcessor 345: Could not delete empty rescope with ID 1471
org.hibernate.exception.LockAcquisitionException: could not execute statement
	at org.hibernate.dialect.MySQLDialect$1.convert(MySQLDialect.java:411) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final]
	at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:49) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final]
	at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:125) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final]
	at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:110) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final]
	at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:136) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final]
	at org.hibernate.hql.spi.TableBasedDeleteHandlerImpl.execute(TableBasedDeleteHandlerImpl.java:163) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final]
	at org.hibernate.hql.internal.ast.exec.MultiTableDeleteExecutor.execute(MultiTableDeleteExecutor.java:63) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final]
	at org.hibernate.hql.internal.ast.QueryTranslatorImpl.executeUpdate(QueryTranslatorImpl.java:414) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final]
	at org.hibernate.engine.query.spi.HQLQueryPlan.performExecuteUpdate(HQLQueryPlan.java:282) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final]
	at org.hibernate.internal.SessionImpl.executeUpdate(SessionImpl.java:1290) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final]
	at org.hibernate.internal.QueryImpl.executeUpdate(QueryImpl.java:116) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final]
	at com.atlassian.stash.internal.AbstractHibernateDao.deleteById(AbstractHibernateDao.java:53) ~[stash-dao-impl-2.9.2.jar:na]
	at com.atlassian.stash.internal.AbstractHibernateDao.deleteById(AbstractHibernateDao.java:22) ~[stash-dao-impl-2.9.2.jar:na]
	at com.sun.proxy.$Proxy156.deleteById(Unknown Source) ~[na:na]
	at com.atlassian.stash.internal.pull.rescope.DefaultRescopeProcessor$3.doInTransactionWithoutResult(DefaultRescopeProcessor.java:139) ~[stash-service-impl-2.9.2.jar:na]
	at org.springframework.transaction.support.TransactionCallbackWithoutResult.doInTransaction(TransactionCallbackWithoutResult.java:33) ~[spring-tx-3.2.4.RELEASE.jar:3.2.4.RELEASE]
	at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:131) ~[spring-tx-3.2.4.RELEASE.jar:3.2.4.RELEASE]
	at com.atlassian.stash.internal.pull.rescope.DefaultRescopeProcessor.deleteActivity(DefaultRescopeProcessor.java:130) [stash-service-impl-2.9.2.jar:na]
	at com.atlassian.stash.internal.pull.rescope.DefaultRescopeProcessor.processAll(DefaultRescopeProcessor.java:100) [stash-service-impl-2.9.2.jar:na]
	at com.atlassian.stash.internal.pull.rescope.DefaultRescopeProcessor.process(DefaultRescopeProcessor.java:77) [stash-service-impl-2.9.2.jar:na]
	at com.atlassian.stash.internal.pull.rescope.DefaultRescopeProcessor$RescopeCalculator.run(DefaultRescopeProcessor.java:219) ~[stash-service-impl-2.9.2.jar:na]
	at com.atlassian.stash.internal.concurrent.StateTransferringExecutor$StateTransferringRunnable.run(StateTransferringExecutor.java:69) ~[stash-platform-2.9.2.jar:na]
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) ~[na:1.7.0_25]
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) ~[na:1.7.0_25]
	at java.util.concurrent.FutureTask.run(FutureTask.java:166) ~[na:1.7.0_25]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) ~[na:1.7.0_25]
	at java.lang.Thread.run(Thread.java:724) ~[na:1.7.0_25]
	... 10 frames trimmed
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) ~[na:1.7.0_25]
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:411) ~[mysql-connector-java-5.1.22-bin.jar:na]
	at com.mysql.jdbc.Util.getInstance(Util.java:386) ~[mysql-connector-java-5.1.22-bin.jar:na]
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1065) ~[mysql-connector-java-5.1.22-bin.jar:na]
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4096) ~[mysql-connector-java-5.1.22-bin.jar:na]
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4028) ~[mysql-connector-java-5.1.22-bin.jar:na]
	at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2490) ~[mysql-connector-java-5.1.22-bin.jar:na]
	at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2651) ~[mysql-connector-java-5.1.22-bin.jar:na]
	at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2734) ~[mysql-connector-java-5.1.22-bin.jar:na]
	at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2155) ~[mysql-connector-java-5.1.22-bin.jar:na]
	at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2458) ~[mysql-connector-java-5.1.22-bin.jar:na]
	at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2375) ~[mysql-connector-java-5.1.22-bin.jar:na]
	at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2359) ~[mysql-connector-java-5.1.22-bin.jar:na]
	at com.jolbox.bonecp.PreparedStatementHandle.executeUpdate(PreparedStatementHandle.java:203) ~[bonecp-0.7.1.RELEASE.jar:0.7.1.RELEASE]
	at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:133) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final]
	... 23 common frames omitted

Cause

This issue affects all versions of Stash from 2.5.0 through the just released 2.12.0. It is 100% MySQL-specific, and should not affect customers using any other database.

Solution

Upgrade to the indicated fix releases.

Workaround

Exactly because of this issue and STASH-4701, we recommend that customers with larger instances (you can consider that 500+ licenses) move off MySQL (you can see the warning we placed on Connecting Stash to MySQL). Therefore, if you can move to an alternative database (for example, PostgreSQL) in case you don't want to upgrade now, that'd also solve this issue for you.

Leaving as-is will cause you performance issues as well as Pull Requests misbehaviour while merging. For instance:

(...)the following error more and more frequently when trying to merge a PR from the Stash UI (happening on multiple repos): "New changes were pushed to master in project/repo while the merge was being performed. Please retry the merge."

The good news is that Stash makes it really easy for you to migrate databases. All you have to do is:

Preparation: configure a PostgreSQL db (it can be any other supported databases) as described on Connecting Stash to PostgreSQL
Migration: migrate your instance data over to PostgreSQL as described on Connecting Stash to an external database
To run the Database Migration Wizard:
1. Log in to Stash.
2. In the administration area, click Database (under 'Settings').
3. Click Migrate database and follow the instructions for running the migration.

Attachments

Issue Links

causes

BSERV-4701 Performance empty pull request rescope activities is very poor on MySQL

Closed

BSERV-4126 MergeException: New changes were pushed to master in PROJECT/repo while the merge was being performed

Closed

is duplicated by

BSERV-4354 Database on high load extremly bugly

Closed

BSERV-4125 Deadlock found when trying to get lock; try restarting transaction

Closed

mentioned in: Page Loading...; Page Loading...; Page Loading...; Page Loading...; Page Loading...; Page Loading...

(5 mentioned in)

Empty activity deletion deadlocks on MySQL