Connection timed out

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Connection timed out

Pengcheng Yang
Dear InterMiners,

The integrating steps have been interrupted by "Connection timed out"
error for several times. Each time I re-run the integrating work,
sometimes success to the end, sometimes interrupted by the same
"Connection timed out" at later integrating step. After dumping at each
step and re-run the integrating several times, the loading process
succeed at the end.

I am sure this problem has not been reported previously by searching
"ConnectException: Connection timed out" in the mail list archive.

Thank you and best,

Pengcheng

============= error messages ==================

starting command: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew
--stacktrace --no-daemon --stacktrace integrate
-Psource=faw-gene-expression-PRJNA408280


FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:buildTgtItems'.
 > org.apache.torque.engine.EngineException: java.net.ConnectException:
Connection timed out (Connection timed out)

* Try:
Run with --info or --debug option to get more log output.

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task
':dbmodel:buildTgtItems'.
         at
org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100)
         at
org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
         at
org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:63)
         at
org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
         at
org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
         at
org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
         at
org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
         at
org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
         at
org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
         at
org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
         at
org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
         at
org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
         at
org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
         at
org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
         at
org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
         at
org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
         at
org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
         at
org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
         at
org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:124)
         at
org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:80)
         at
org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:105)
         at
org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:99)
         at
org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:625)
         at
org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:580)
         at
org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:99)
         at
org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
         at
org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
         at
org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
Caused by: : org.apache.torque.engine.EngineException:
java.net.ConnectException: Connection timed out (Connection timed out)
         at
org.apache.torque.task.TorqueDataModelTask.initControlContext(TorqueDataModelTask.java:277)
         at
org.apache.torque.task.TorqueSQLTask.initControlContext(TorqueSQLTask.java:188)
         at
org.apache.velocity.texen.ant.TexenTask.execute(TexenTask.java:480)
         at org.intermine.task.BuildDbTask.execute(BuildDbTask.java:183)
         at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
         at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
         at
org.intermine.plugin.dbmodel.DBModelUtils$_closure5.doCall(DBModelUtils.groovy:88)
         at
org.intermine.plugin.integrate.IntegratePlugin$_apply_closure8$_closure22.doCall(IntegratePlugin.groovy:205)
         at
org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:681)
         at
org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:656)
         at
org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:122)
         at
org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
         at
org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
         at
org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
         at
org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
         at
org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:111)
         at
org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
         ... 27 more
Caused by: org.apache.torque.engine.EngineException:
java.net.ConnectException: Connection timed out (Connection timed out)
         at
org.apache.torque.engine.database.transform.XmlToAppData.parseFile(XmlToAppData.java:170)
         at
org.apache.torque.task.TorqueDataModelTask.initControlContext(TorqueDataModelTask.java:234)
         ... 43 more
Caused by: java.net.ConnectException: Connection timed out (Connection
timed out)
         at
org.apache.torque.engine.database.transform.DTDResolver.getInputSource(DTDResolver.java:120)
         at
org.apache.torque.engine.database.transform.DTDResolver.resolveEntity(DTDResolver.java:106)
         at
org.apache.torque.engine.database.transform.XmlToAppData.resolveEntity(XmlToAppData.java:193)
         at
com.sun.org.apache.xerces.internal.util.EntityResolverWrapper.resolveEntity(EntityResolverWrapper.java:110)
         at
com.sun.org.apache.xerces.internal.impl.XMLEntityManager.resolveEntityAsPerStax(XMLEntityManager.java:997)
         at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.dispatch(XMLDocumentScannerImpl.java:1151)
         at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.next(XMLDocumentScannerImpl.java:1045)
         at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:959)
         at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
         at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)
         at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:842)
         at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:771)
         at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
         at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213)
         at
com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:643)
         at
com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(SAXParserImpl.java:327)
         at
org.apache.torque.engine.database.transform.XmlToAppData.parseFile(XmlToAppData.java:161)
         ... 44 more


* Get more help at https://help.gradle.org

BUILD FAILED in 2m 46s
Wed Feb 12 15:02:28 CST 2020

finished


ERROR: 256
failed with exit code 0:
/home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace
--no-daemon --stacktrace integrate -Psource=faw-gene-expression-PRJNA408280


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Re: Connection timed out

Daniela Butano-2

Hi Pengcheng,

I suggest that you run the build when tomcat is not running. Please check that you have set the gradle daemon to false. Here the doc

Daniela

On 12/02/2020 07:22, Pengcheng Yang wrote:
Dear InterMiners,

The integrating steps have been interrupted by "Connection timed out" error for several times. Each time I re-run the integrating work, sometimes success to the end, sometimes interrupted by the same "Connection timed out" at later integrating step. After dumping at each step and re-run the integrating several times, the loading process succeed at the end.

I am sure this problem has not been reported previously by searching "ConnectException: Connection timed out" in the mail list archive.

Thank you and best,

Pengcheng

============= error messages ==================

starting command: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=faw-gene-expression-PRJNA408280


FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:buildTgtItems'.
> org.apache.torque.engine.EngineException: java.net.ConnectException: Connection timed out (Connection timed out)

* Try:
Run with --info or --debug option to get more log output.

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:buildTgtItems'.
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
        at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:63)
        at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
        at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
        at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
        at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
        at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
        at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
        at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
        at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:124)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:80)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:105)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:99)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:625)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:580)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:99)
        at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
        at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
        at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
Caused by: : org.apache.torque.engine.EngineException: java.net.ConnectException: Connection timed out (Connection timed out)
        at org.apache.torque.task.TorqueDataModelTask.initControlContext(TorqueDataModelTask.java:277)
        at org.apache.torque.task.TorqueSQLTask.initControlContext(TorqueSQLTask.java:188)
        at org.apache.velocity.texen.ant.TexenTask.execute(TexenTask.java:480)
        at org.intermine.task.BuildDbTask.execute(BuildDbTask.java:183)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
        at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
        at org.intermine.plugin.dbmodel.DBModelUtils$_closure5.doCall(DBModelUtils.groovy:88)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure8$_closure22.doCall(IntegratePlugin.groovy:205)
        at org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:681)
        at org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:656)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:122)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:111)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
        ... 27 more
Caused by: org.apache.torque.engine.EngineException: java.net.ConnectException: Connection timed out (Connection timed out)
        at org.apache.torque.engine.database.transform.XmlToAppData.parseFile(XmlToAppData.java:170)
        at org.apache.torque.task.TorqueDataModelTask.initControlContext(TorqueDataModelTask.java:234)
        ... 43 more
Caused by: java.net.ConnectException: Connection timed out (Connection timed out)
        at org.apache.torque.engine.database.transform.DTDResolver.getInputSource(DTDResolver.java:120)
        at org.apache.torque.engine.database.transform.DTDResolver.resolveEntity(DTDResolver.java:106)
        at org.apache.torque.engine.database.transform.XmlToAppData.resolveEntity(XmlToAppData.java:193)
        at com.sun.org.apache.xerces.internal.util.EntityResolverWrapper.resolveEntity(EntityResolverWrapper.java:110)
        at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.resolveEntityAsPerStax(XMLEntityManager.java:997)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.dispatch(XMLDocumentScannerImpl.java:1151)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.next(XMLDocumentScannerImpl.java:1045)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:959)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)
        at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:842)
        at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:771)
        at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
        at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213)
        at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:643)
        at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(SAXParserImpl.java:327)
        at org.apache.torque.engine.database.transform.XmlToAppData.parseFile(XmlToAppData.java:161)
        ... 44 more


* Get more help at https://help.gradle.org

BUILD FAILED in 2m 46s
Wed Feb 12 15:02:28 CST 2020

finished


ERROR: 256
failed with exit code 0: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=faw-gene-expression-PRJNA408280


_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
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Re: Connection timed out

Pengcheng Yang

Hi Daniela,

I have set the GRADLE_OPTS as below:

export GRADLE_OPTS="-server -Xmx10g -XX:+UseParallelGC -Xms2g -XX:SoftRefLRUPolicyMSPerMB=1 -XX:MaxHeapFreeRatio=99 -Dorg.gradle.daemon=false"

I will test stop tomcat in the next building work.

Thanks!

Pengcheng


On 2020-2-12 17:55, Daniela Butano wrote:

Hi Pengcheng,

I suggest that you run the build when tomcat is not running. Please check that you have set the gradle daemon to false. Here the doc

Daniela

On 12/02/2020 07:22, Pengcheng Yang wrote:
Dear InterMiners,

The integrating steps have been interrupted by "Connection timed out" error for several times. Each time I re-run the integrating work, sometimes success to the end, sometimes interrupted by the same "Connection timed out" at later integrating step. After dumping at each step and re-run the integrating several times, the loading process succeed at the end.

I am sure this problem has not been reported previously by searching "ConnectException: Connection timed out" in the mail list archive.

Thank you and best,

Pengcheng

============= error messages ==================

starting command: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=faw-gene-expression-PRJNA408280


FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:buildTgtItems'.
> org.apache.torque.engine.EngineException: java.net.ConnectException: Connection timed out (Connection timed out)

* Try:
Run with --info or --debug option to get more log output.

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:buildTgtItems'.
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
        at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:63)
        at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
        at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
        at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
        at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
        at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
        at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
        at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
        at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:124)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:80)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:105)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:99)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:625)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:580)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:99)
        at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
        at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
        at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
Caused by: : org.apache.torque.engine.EngineException: java.net.ConnectException: Connection timed out (Connection timed out)
        at org.apache.torque.task.TorqueDataModelTask.initControlContext(TorqueDataModelTask.java:277)
        at org.apache.torque.task.TorqueSQLTask.initControlContext(TorqueSQLTask.java:188)
        at org.apache.velocity.texen.ant.TexenTask.execute(TexenTask.java:480)
        at org.intermine.task.BuildDbTask.execute(BuildDbTask.java:183)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
        at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
        at org.intermine.plugin.dbmodel.DBModelUtils$_closure5.doCall(DBModelUtils.groovy:88)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure8$_closure22.doCall(IntegratePlugin.groovy:205)
        at org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:681)
        at org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:656)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:122)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:111)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
        ... 27 more
Caused by: org.apache.torque.engine.EngineException: java.net.ConnectException: Connection timed out (Connection timed out)
        at org.apache.torque.engine.database.transform.XmlToAppData.parseFile(XmlToAppData.java:170)
        at org.apache.torque.task.TorqueDataModelTask.initControlContext(TorqueDataModelTask.java:234)
        ... 43 more
Caused by: java.net.ConnectException: Connection timed out (Connection timed out)
        at org.apache.torque.engine.database.transform.DTDResolver.getInputSource(DTDResolver.java:120)
        at org.apache.torque.engine.database.transform.DTDResolver.resolveEntity(DTDResolver.java:106)
        at org.apache.torque.engine.database.transform.XmlToAppData.resolveEntity(XmlToAppData.java:193)
        at com.sun.org.apache.xerces.internal.util.EntityResolverWrapper.resolveEntity(EntityResolverWrapper.java:110)
        at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.resolveEntityAsPerStax(XMLEntityManager.java:997)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.dispatch(XMLDocumentScannerImpl.java:1151)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.next(XMLDocumentScannerImpl.java:1045)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:959)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)
        at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:842)
        at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:771)
        at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
        at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213)
        at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:643)
        at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(SAXParserImpl.java:327)
        at org.apache.torque.engine.database.transform.XmlToAppData.parseFile(XmlToAppData.java:161)
        ... 44 more


* Get more help at https://help.gradle.org

BUILD FAILED in 2m 46s
Wed Feb 12 15:02:28 CST 2020

finished


ERROR: 256
failed with exit code 0: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=faw-gene-expression-PRJNA408280


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Re: Connection timed out

Pengcheng Yang

Hi Daniela,

Recently, I have tested building FAWMine with tomcat stopped, but the "Connection timed out" error appeared again.

Just for your information.

Best,

Pengcheng


On 2020-2-12 20:11, Pengcheng Yang wrote:

Hi Daniela,

I have set the GRADLE_OPTS as below:

export GRADLE_OPTS="-server -Xmx10g -XX:+UseParallelGC -Xms2g -XX:SoftRefLRUPolicyMSPerMB=1 -XX:MaxHeapFreeRatio=99 -Dorg.gradle.daemon=false"

I will test stop tomcat in the next building work.

Thanks!

Pengcheng


On 2020-2-12 17:55, Daniela Butano wrote:

Hi Pengcheng,

I suggest that you run the build when tomcat is not running. Please check that you have set the gradle daemon to false. Here the doc

Daniela

On 12/02/2020 07:22, Pengcheng Yang wrote:
Dear InterMiners,

The integrating steps have been interrupted by "Connection timed out" error for several times. Each time I re-run the integrating work, sometimes success to the end, sometimes interrupted by the same "Connection timed out" at later integrating step. After dumping at each step and re-run the integrating several times, the loading process succeed at the end.

I am sure this problem has not been reported previously by searching "ConnectException: Connection timed out" in the mail list archive.

Thank you and best,

Pengcheng

============= error messages ==================

starting command: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=faw-gene-expression-PRJNA408280


FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':dbmodel:buildTgtItems'.
> org.apache.torque.engine.EngineException: java.net.ConnectException: Connection timed out (Connection timed out)

* Try:
Run with --info or --debug option to get more log output.

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:buildTgtItems'.
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
        at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:63)
        at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
        at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
        at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
        at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
        at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
        at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
        at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
        at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:124)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:80)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:105)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:99)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:625)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:580)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:99)
        at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
        at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
        at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
Caused by: : org.apache.torque.engine.EngineException: java.net.ConnectException: Connection timed out (Connection timed out)
        at org.apache.torque.task.TorqueDataModelTask.initControlContext(TorqueDataModelTask.java:277)
        at org.apache.torque.task.TorqueSQLTask.initControlContext(TorqueSQLTask.java:188)
        at org.apache.velocity.texen.ant.TexenTask.execute(TexenTask.java:480)
        at org.intermine.task.BuildDbTask.execute(BuildDbTask.java:183)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
        at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
        at org.intermine.plugin.dbmodel.DBModelUtils$_closure5.doCall(DBModelUtils.groovy:88)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure8$_closure22.doCall(IntegratePlugin.groovy:205)
        at org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:681)
        at org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:656)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:122)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:111)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
        ... 27 more
Caused by: org.apache.torque.engine.EngineException: java.net.ConnectException: Connection timed out (Connection timed out)
        at org.apache.torque.engine.database.transform.XmlToAppData.parseFile(XmlToAppData.java:170)
        at org.apache.torque.task.TorqueDataModelTask.initControlContext(TorqueDataModelTask.java:234)
        ... 43 more
Caused by: java.net.ConnectException: Connection timed out (Connection timed out)
        at org.apache.torque.engine.database.transform.DTDResolver.getInputSource(DTDResolver.java:120)
        at org.apache.torque.engine.database.transform.DTDResolver.resolveEntity(DTDResolver.java:106)
        at org.apache.torque.engine.database.transform.XmlToAppData.resolveEntity(XmlToAppData.java:193)
        at com.sun.org.apache.xerces.internal.util.EntityResolverWrapper.resolveEntity(EntityResolverWrapper.java:110)
        at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.resolveEntityAsPerStax(XMLEntityManager.java:997)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.dispatch(XMLDocumentScannerImpl.java:1151)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.next(XMLDocumentScannerImpl.java:1045)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:959)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)
        at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:842)
        at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:771)
        at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
        at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213)
        at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:643)
        at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(SAXParserImpl.java:327)
        at org.apache.torque.engine.database.transform.XmlToAppData.parseFile(XmlToAppData.java:161)
        ... 44 more


* Get more help at https://help.gradle.org

BUILD FAILED in 2m 46s
Wed Feb 12 15:02:28 CST 2020

finished


ERROR: 256
failed with exit code 0: /home/pengchy/soft/intermine.4.0/git/fawmine/gradlew --stacktrace --no-daemon --stacktrace integrate -Psource=faw-gene-expression-PRJNA408280


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