Create
cancel
Turn on suggestions
Auto-suggest helps you quickly narrow down your search results by suggesting possible matches as you type.
Showing results for 
Search instead for 
Did you mean: 
Sign up Log in
Product Q&A
See all
Community resources
Top groups
Explore all groups
Community resources
Learn
Community resources
Events
Community resources

Cannot rebuild indexes, Hibernate error

joshua kugler
joshua kugler
Contributor
August 27, 2012

We're in the process of upgrading from Confluence 3.3 to Confluence 4.2.13. We first did the upgrade to 3.5, and that went well. The upgrade to 4.2.13 is working, but the indexes are not rebuilding. The error int he log is below.

Java 1.6.0_34

MySQL 5.5.25

Java Mysql Connector 5.1.21

This is the search index. The "Did you mean" index rebuilds with no issue. Everything else with the site seems to be working. Any ideas?

2012-08-27 17:48:52,540 WARN [confluence-interactive-reindexing-thread] [v2.c3p0.impl.DefaultConnectionTester] statusOnException SQL State '08007' of Exception tested by statusOnException() implies that the database is invalid, and the pool should refill itself with fresh Connections.
 -- referer: http://wiki-up.lab.whamcloud.com/admin/search-indexes.action | url: /admin/reindex.action | userName: joshua | action: reindex
com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: Communications link failure during commit(). Transaction resolution unknown.
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
	at java.lang.reflect.Constructor.newInstance(Unknown Source)
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
	at com.mysql.jdbc.Util.getInstance(Util.java:381)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1012)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:986)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:981)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:926)
	at com.mysql.jdbc.ConnectionImpl.commit(ConnectionImpl.java:1660)
	at com.mchange.v2.c3p0.impl.NewProxyConnection.commit(NewProxyConnection.java:803)
	at net.sf.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:63)
	at org.springframework.orm.hibernate.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:510)
	at org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:732)
	at org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:701)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.commitTransactionAfterReturning(TransactionAspectSupport.java:321)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:116)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
	at $Proxy87.indexEntities(Unknown Source)
	at com.atlassian.confluence.search.IndexingTask.runInternal(IndexingTask.java:35)
	at com.atlassian.confluence.util.longrunning.ConfluenceAbstractLongRunningTask.run(ConfluenceAbstractLongRunningTask.java:26)
	at java.lang.Thread.run(Unknown Source)
2012-08-27 17:48:52,544 WARN [confluence-interactive-reindexing-thread] [v2.c3p0.impl.C3P0PooledConnectionPool] doMarkPoolStatus A ConnectionTest has failed, reporting that all previously acquired Connections are likely invalid. The pool will be reset.
 -- referer: http://wiki-up.lab.whamcloud.com/admin/search-indexes.action | url: /admin/reindex.action | userName: joshua | action: reindex
2012-08-27 17:48:52,545 ERROR [confluence-interactive-reindexing-thread] [sf.hibernate.transaction.JDBCTransaction] commit Commit failed
 -- referer: http://wiki-up.lab.whamcloud.com/admin/search-indexes.action | url: /admin/reindex.action | userName: joshua | action: reindex
com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: Communications link failure during commit(). Transaction resolution unknown.
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
	at java.lang.reflect.Constructor.newInstance(Unknown Source)
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
	at com.mysql.jdbc.Util.getInstance(Util.java:381)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1012)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:986)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:981)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:926)
	at com.mysql.jdbc.ConnectionImpl.commit(ConnectionImpl.java:1660)
	at com.mchange.v2.c3p0.impl.NewProxyConnection.commit(NewProxyConnection.java:803)
	at net.sf.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:63)
	at org.springframework.orm.hibernate.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:510)
	at org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:732)
	at org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:701)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.commitTransactionAfterReturning(TransactionAspectSupport.java:321)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:116)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
	at $Proxy87.indexEntities(Unknown Source)
	at com.atlassian.confluence.search.IndexingTask.runInternal(IndexingTask.java:35)
	at com.atlassian.confluence.util.longrunning.ConfluenceAbstractLongRunningTask.run(ConfluenceAbstractLongRunningTask.java:26)
	at java.lang.Thread.run(Unknown Source)
2012-08-27 17:48:52,549 ERROR [confluence-interactive-reindexing-thread] [confluence.util.longrunning.ConfluenceAbstractLongRunningTask] run Long running task "Rebuilding Search Index" failed to run.
 -- referer: http://wiki-up.lab.whamcloud.com/admin/search-indexes.action | url: /admin/reindex.action | userName: joshua | action: reindex
org.springframework.transaction.TransactionSystemException: Could not commit Hibernate transaction; nested exception is net.sf.hibernate.TransactionException: Commit failed with SQL exception: 
	at org.springframework.orm.hibernate.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:514)
	at org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:732)
	at org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:701)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.commitTransactionAfterReturning(TransactionAspectSupport.java:321)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:116)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
	at $Proxy87.indexEntities(Unknown Source)
	at com.atlassian.confluence.search.IndexingTask.runInternal(IndexingTask.java:35)
	at com.atlassian.confluence.util.longrunning.ConfluenceAbstractLongRunningTask.run(ConfluenceAbstractLongRunningTask.java:26)
	at java.lang.Thread.run(Unknown Source)
Caused by: net.sf.hibernate.TransactionException: Commit failed with SQL exception: 
	at net.sf.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:71)
	at org.springframework.orm.hibernate.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:510)
	... 10 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: Communications link failure during commit(). Transaction resolution unknown.
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
	at java.lang.reflect.Constructor.newInstance(Unknown Source)
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
	at com.mysql.jdbc.Util.getInstance(Util.java:381)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1012)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:986)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:981)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:926)
	at com.mysql.jdbc.ConnectionImpl.commit(ConnectionImpl.java:1660)
	at com.mchange.v2.c3p0.impl.NewProxyConnection.commit(NewProxyConnection.java:803)
	at net.sf.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:63)
	... 11 more

Answer
Watch
Like Vanishree kumari likes this
2463 views

1 answer

1 accepted

6 votes
Answer accepted
Harry Chan5
Harry Chan
Rising Star
Rising Star
Rising Stars are recognized for providing high-quality answers to other users. Rising Stars receive a certificate of achievement and are on the path to becoming Community Leaders.
Get recognized
August 27, 2012

Hi, please try to add ?autoReconnect=true to the end of your database's JDBC URL and add the validationQuery parameter.

Follow this guide here https://confluence.atlassian.com/pages/viewpage.action?pageId=104300792 for more information.

View More Comments
joshua kugler
joshua kugler
Contributor
August 27, 2012

I don't seem to have a config file as referenced by the above page. I have <HOMEDIR>/conf/confluence.cfg.xml. I'll paste it below. From the URL you pasted, I'm not 100% sure how to add the validations query. And I already do have the autoreconnect=true in the URL. Snipping the irrelevant parts.

&lt;?xml version="1.0" encoding="UTF-8"?&gt;

&lt;confluence-configuration&gt;
    &lt;property name="hibernate.c3p0.acquire_increment"&gt;1&lt;/property&gt;
    &lt;property name="hibernate.c3p0.idle_test_period"&gt;100&lt;/property&gt;
    &lt;property name="hibernate.c3p0.max_size"&gt;30&lt;/property&gt;
    &lt;property name="hibernate.c3p0.max_statements"&gt;0&lt;/property&gt;
    &lt;property name="hibernate.c3p0.min_size"&gt;0&lt;/property&gt;
    &lt;property name="hibernate.c3p0.timeout"&gt;30&lt;/property&gt;
    &lt;property name="hibernate.connection.driver_class"&gt;com.mysql.jdbc.Driver&lt;/property&gt;
    &lt;property name="hibernate.connection.password"&gt;...&lt;/property&gt;
    &lt;property name="hibernate.connection.url"&gt;jdbc:mysql://localhost/confluence?autoReconnect=true&amp;amp;sessionVariables=storage_engine%3DInnoDB&lt;/property&gt;
    &lt;property name="hibernate.connection.username"&gt;confluence&lt;/property&gt;
    &lt;property name="hibernate.database.lower_non_ascii_supported"&gt;true&lt;/property&gt;
    &lt;property name="hibernate.dialect"&gt;com.atlassian.hibernate.dialect.MySQLDialect&lt;/property&gt;
    &lt;property name="hibernate.setup"&gt;true&lt;/property&gt;
  &lt;/properties&gt;
&lt;/confluence-configuration&gt;

Like • pinoccs serge likes this
joshua kugler
joshua kugler
Contributor
August 27, 2012

Found it here: https://confluence.atlassian.com/display/DOC/Surviving+Database+Connection+Closures Will add it, and report back.

Like • pinoccs serge likes this
joshua kugler
joshua kugler
Contributor
August 27, 2012

Tried rebuilding the index again, and had the same issue. This was after adding the validation query, and restarting confluence.

Like
Harry Chan5
Harry Chan
Rising Star
Rising Star
Rising Stars are recognized for providing high-quality answers to other users. Rising Stars receive a certificate of achievement and are on the path to becoming Community Leaders.
Get recognized
August 27, 2012

Can you try to increase the lock wait_timeout on MySQL server? Instructions on how to do it can be found here https://confluence.atlassian.com/display/JIRAKB/Reindexing+JIRA+Results+in+Communications+Link+Failure+During+Commit

If that doesn't fix it, try to increase the global interactive timeout as documented here https://confluence.atlassian.com/display/CONFKB/Attachment+Upload+Failed+with+'Communications+link+failure+during+commit()'+Error.

It's definitely timing out before it can commit. That is the problem.

Like
Harry Chan5
Harry Chan
Rising Star
Rising Star
Rising Stars are recognized for providing high-quality answers to other users. Rising Stars receive a certificate of achievement and are on the path to becoming Community Leaders.
Get recognized
August 27, 2012

Did you also add ?autoReconnect=true to the end of the JDBC connection URL?

Like
joshua kugler
joshua kugler
Contributor
August 27, 2012

As shown in the config file pasted above, I already had that in the URL.

Like
joshua kugler
joshua kugler
Contributor
August 27, 2012

That was it. Thanks. It was 180, and I increased it to 600.

Thank you!

Like
Reply

Suggest an answer

Log in or Sign up to answer
Confluence
Confluence
TAGS
AUG Leaders

Atlassian Community Events

    See all events