[jira] [Commented] (BEAM-748) Issues with local processes in MongoDbIO and JdbcIO

2016-11-01 Thread JIRA 

[ 
https://issues.apache.org/jira/browse/BEAM-748?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=15625456#comment-15625456
 ] 

Jean-Baptiste Onofré commented on BEAM-748:
---

It could be related to BEAM-856 (when several jobs are running on the same 
machine). Let's try to see if BEAM-856 (and related) helps.

> Issues with local processes in MongoDbIO and JdbcIO
> ---
>
> Key: BEAM-748
> URL: https://issues.apache.org/jira/browse/BEAM-748
> Project: Beam
>  Issue Type: Bug
>  Components: testing
>Affects Versions: Not applicable
>Reporter: Daniel Halperin
>Assignee: Jean-Baptiste Onofré
>
> Hey JB, Can you take a look at these issues? Causing flakes in precommit 
> testing.
> https://builds.apache.org/job/beam_PreCommit_MavenVerify/3931/
> A few different types, likely due to issues setting up databases and reusing 
> them across tests?
> {code}
> java.net.ConnectException : Error connecting to server localhost on port 
> 1,527 with message Connection refused.
> {code}
> {code}
> A lock could not be obtained due to a deadlock, cycle of locks and waiters is:
> Lock : ROW, SYSCOLUMNS, (4,42)
>   Waiting XID : {187, S} , APP, insert into BEAM values (?,?)
>   Granted XID : {185, S} 
> Lock : ROW, SYSTABLES, (1,30)
>   Waiting XID : {185, X} , APP, drop table BEAM
>   Granted XID : {185, S} , {187, S} 
> . The selected victim is XID : 187.
> Stacktrace
> java.sql.SQLTransactionRollbackException: 
> A lock could not be obtained due to a deadlock, cycle of locks and waiters is:
> Lock : ROW, SYSCOLUMNS, (4,42)
>   Waiting XID : {187, S} , APP, insert into BEAM values (?,?)
>   Granted XID : {185, S} 
> Lock : ROW, SYSTABLES, (1,30)
>   Waiting XID : {185, X} , APP, drop table BEAM
>   Granted XID : {185, S} , {187, S} 
> . The selected victim is XID : 187.
>   at 
> org.apache.derby.client.am.SQLExceptionFactory.getSQLException(Unknown Source)
>   at org.apache.derby.client.am.SqlException.getSQLException(Unknown 
> Source)
>   at org.apache.derby.client.am.ClientConnection.prepareStatement(Unknown 
> Source)
>   at org.apache.beam.sdk.io.jdbc.JdbcIOTest.initTable(JdbcIOTest.java:106)
>   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>   at 
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>   at 
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>   at java.lang.reflect.Method.invoke(Method.java:498)
>   at 
> org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
>   at 
> org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
>   at 
> org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
>   at 
> org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
>   at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271)
>   at 
> org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70)
>   at 
> org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
>   at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
>   at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
>   at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
>   at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
>   at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
>   at 
> org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
>   at 
> org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
>   at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
>   at org.junit.runners.Suite.runChild(Suite.java:127)
>   at org.junit.runners.Suite.runChild(Suite.java:26)
>   at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
>   at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
>   at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
>   at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
>   at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
>   at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
>   at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:55)
>   at 
> org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:137)
>   at 
> org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:107)
>   at 
> org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:83)
>   at 
>

[jira] [Commented] (BEAM-748) Issues with local processes in MongoDbIO and JdbcIO

2016-10-14 Thread JIRA 

[ 
https://issues.apache.org/jira/browse/BEAM-748?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=15575269#comment-15575269
 ] 

Jean-Baptiste Onofré commented on BEAM-748:
---

By the way, it could also be caused by no space left on filesystem.

> Issues with local processes in MongoDbIO and JdbcIO
> ---
>
> Key: BEAM-748
> URL: https://issues.apache.org/jira/browse/BEAM-748
> Project: Beam
>  Issue Type: Bug
>  Components: testing
>Affects Versions: Not applicable
>Reporter: Daniel Halperin
>Assignee: Jean-Baptiste Onofré
>
> Hey JB, Can you take a look at these issues? Causing flakes in precommit 
> testing.
> https://builds.apache.org/job/beam_PreCommit_MavenVerify/3931/
> A few different types, likely due to issues setting up databases and reusing 
> them across tests?
> {code}
> java.net.ConnectException : Error connecting to server localhost on port 
> 1,527 with message Connection refused.
> {code}
> {code}
> A lock could not be obtained due to a deadlock, cycle of locks and waiters is:
> Lock : ROW, SYSCOLUMNS, (4,42)
>   Waiting XID : {187, S} , APP, insert into BEAM values (?,?)
>   Granted XID : {185, S} 
> Lock : ROW, SYSTABLES, (1,30)
>   Waiting XID : {185, X} , APP, drop table BEAM
>   Granted XID : {185, S} , {187, S} 
> . The selected victim is XID : 187.
> Stacktrace
> java.sql.SQLTransactionRollbackException: 
> A lock could not be obtained due to a deadlock, cycle of locks and waiters is:
> Lock : ROW, SYSCOLUMNS, (4,42)
>   Waiting XID : {187, S} , APP, insert into BEAM values (?,?)
>   Granted XID : {185, S} 
> Lock : ROW, SYSTABLES, (1,30)
>   Waiting XID : {185, X} , APP, drop table BEAM
>   Granted XID : {185, S} , {187, S} 
> . The selected victim is XID : 187.
>   at 
> org.apache.derby.client.am.SQLExceptionFactory.getSQLException(Unknown Source)
>   at org.apache.derby.client.am.SqlException.getSQLException(Unknown 
> Source)
>   at org.apache.derby.client.am.ClientConnection.prepareStatement(Unknown 
> Source)
>   at org.apache.beam.sdk.io.jdbc.JdbcIOTest.initTable(JdbcIOTest.java:106)
>   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>   at 
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>   at 
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>   at java.lang.reflect.Method.invoke(Method.java:498)
>   at 
> org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
>   at 
> org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
>   at 
> org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
>   at 
> org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
>   at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271)
>   at 
> org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70)
>   at 
> org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
>   at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
>   at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
>   at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
>   at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
>   at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
>   at 
> org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
>   at 
> org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
>   at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
>   at org.junit.runners.Suite.runChild(Suite.java:127)
>   at org.junit.runners.Suite.runChild(Suite.java:26)
>   at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
>   at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
>   at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
>   at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
>   at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
>   at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
>   at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:55)
>   at 
> org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:137)
>   at 
> org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:107)
>   at 
> org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:83)
>   at 
> org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
>   at 
>

[jira] [Commented] (BEAM-748) Issues with local processes in MongoDbIO and JdbcIO

2016-10-13 Thread JIRA 

[ 
https://issues.apache.org/jira/browse/BEAM-748?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=15573247#comment-15573247
 ] 

Jean-Baptiste Onofré commented on BEAM-748:
---

Yup, let me take a look.

> Issues with local processes in MongoDbIO and JdbcIO
> ---
>
> Key: BEAM-748
> URL: https://issues.apache.org/jira/browse/BEAM-748
> Project: Beam
>  Issue Type: Bug
>  Components: testing
>Affects Versions: Not applicable
>Reporter: Daniel Halperin
>Assignee: Jean-Baptiste Onofré
>
> Hey JB, Can you take a look at these issues? Causing flakes in precommit 
> testing.
> https://builds.apache.org/job/beam_PreCommit_MavenVerify/3931/
> A few different types, likely due to issues setting up databases and reusing 
> them across tests?
> {code}
> java.net.ConnectException : Error connecting to server localhost on port 
> 1,527 with message Connection refused.
> {code}
> {code}
> A lock could not be obtained due to a deadlock, cycle of locks and waiters is:
> Lock : ROW, SYSCOLUMNS, (4,42)
>   Waiting XID : {187, S} , APP, insert into BEAM values (?,?)
>   Granted XID : {185, S} 
> Lock : ROW, SYSTABLES, (1,30)
>   Waiting XID : {185, X} , APP, drop table BEAM
>   Granted XID : {185, S} , {187, S} 
> . The selected victim is XID : 187.
> Stacktrace
> java.sql.SQLTransactionRollbackException: 
> A lock could not be obtained due to a deadlock, cycle of locks and waiters is:
> Lock : ROW, SYSCOLUMNS, (4,42)
>   Waiting XID : {187, S} , APP, insert into BEAM values (?,?)
>   Granted XID : {185, S} 
> Lock : ROW, SYSTABLES, (1,30)
>   Waiting XID : {185, X} , APP, drop table BEAM
>   Granted XID : {185, S} , {187, S} 
> . The selected victim is XID : 187.
>   at 
> org.apache.derby.client.am.SQLExceptionFactory.getSQLException(Unknown Source)
>   at org.apache.derby.client.am.SqlException.getSQLException(Unknown 
> Source)
>   at org.apache.derby.client.am.ClientConnection.prepareStatement(Unknown 
> Source)
>   at org.apache.beam.sdk.io.jdbc.JdbcIOTest.initTable(JdbcIOTest.java:106)
>   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>   at 
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>   at 
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>   at java.lang.reflect.Method.invoke(Method.java:498)
>   at 
> org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
>   at 
> org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
>   at 
> org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
>   at 
> org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
>   at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271)
>   at 
> org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70)
>   at 
> org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
>   at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
>   at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
>   at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
>   at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
>   at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
>   at 
> org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
>   at 
> org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
>   at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
>   at org.junit.runners.Suite.runChild(Suite.java:127)
>   at org.junit.runners.Suite.runChild(Suite.java:26)
>   at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
>   at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
>   at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
>   at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
>   at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
>   at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
>   at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:55)
>   at 
> org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:137)
>   at 
> org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:107)
>   at 
> org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:83)
>   at 
> org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
>   at 
> org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:161)
>