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From Lahiru Gunathilake <glah...@gmail.com>
Subject Re: Phonon task
Date Tue, 29 Jan 2013 21:16:19 GMT
Hi Pedro,

I think this is due to connection to the server has lost, if you get the
same error again this could be an issue, but I think this is due to some
connection failure to lonestar .. can you try again.

Lahiru

On Tue, Jan 29, 2013 at 4:03 PM, Pedro da Silveira <pedrorcs@gmail.com>wrote:

> Hi All,
>
> I ran a task on Lonestar using Apache Airavata that took approximately 15
> hour to finish. In the end it finishes successfully.
>
> I noticed on the log of Apache Airavata that it was constantly printing,
> while I was hanging waiting the task to finish. It looks fine, since the
> job was taking some time to finish.
>
> =============================
> [INFO] Status is zero
> [INFO] Status is zero
> [INFO] Job proxy expired. Trying to renew proxy
> org.globus.gsi.gssapi.GlobusGSSCredentialImpl@19d00552
> [INFO] Proxy file renewed to
> /tmp/x509up_uogce8653d6c7-7eed-4628-abf3-816fb122c8d6 for the user ogce
> with 3600 lifetime.
> [INFO] Myproxy renewed
> [INFO] Status is zero
> [INFO] Status is zero
> ============================================
>
> In the end, my task completed nicely, but at the Xbaya I had this screen:
>
> http://i50.tinypic.com/208h08p.jpg
>
> <ns:description>The connection to the server failed (check host and port)
> [Caused by: Connection refused]:
> org.apache.airavata.core.gfac.exception.JobSubmissionFault: The connection
> to the server failed (check host and port) [Caused by: Connection
> refused]</ns:description>
>
>
> At the Airavata-Server log, I had:
>
> =================================================================
>
> [INFO] Job proxy expired. Trying to renew proxy
> org.globus.gsi.gssapi.GlobusGSSCredentialImpl@ef61e4a
> [INFO] Proxy file renewed to
> /tmp/x509up_uogce6ce97bd7-650c-46fb-8dea-b6f537fecd13 for the user ogce
> with 3600 lifetime.
> [ERROR] Context passed was NULL.
> java.lang.RuntimeException: Context passed was NULL.
> at
>
> org.apache.airavata.workflow.tracking.impl.ProvenanceNotifierImpl.sendingFault(ProvenanceNotifierImpl.java:496)
> at
>
> org.apache.airavata.workflow.tracking.impl.ProvenanceNotifierImpl.sendingFault(ProvenanceNotifierImpl.java:485)
> at
>
> org.apache.airavata.core.gfac.notification.impl.WorkflowTrackingNotification.executionFail(WorkflowTrackingNotification.java:108)
> at
>
> org.apache.airavata.core.gfac.notification.impl.DefaultNotifier.executionFail(DefaultNotifier.java:135)
> at
>
> org.apache.airavata.core.gfac.exception.JobSubmissionFault.sendFaultNotification(JobSubmissionFault.java:52)
> at
>
> org.apache.airavata.core.gfac.provider.impl.GramProvider.executeApplication(GramProvider.java:231)
> at
>
> org.apache.airavata.core.gfac.provider.AbstractProvider.execute(AbstractProvider.java:69)
> at
>
> org.apache.airavata.core.gfac.services.impl.AbstractSimpleService.execute(AbstractSimpleService.java:118)
> at org.apache.airavata.core.gfac.GfacAPI.gridJobSubmit(GfacAPI.java:140)
> at
>
> org.apache.airavata.xbaya.invoker.EmbeddedGFacInvoker.invoke(EmbeddedGFacInvoker.java:256)
> at
>
> org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.handleWSComponent(WorkflowInterpreter.java:749)
> at
>
> org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.executeDynamically(WorkflowInterpreter.java:533)
> at
>
> org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.scheduleDynamically(WorkflowInterpreter.java:218)
> at
>
> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.executeWorkflow(WorkflowInterpretorSkeleton.java:389)
> at
>
> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.access$400(WorkflowInterpretorSkeleton.java:87)
> at
>
> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton$2.run(WorkflowInterpretorSkeleton.java:382)
> at java.lang.Thread.run(Thread.java:680)
> [INFO] -----DATA-----
> [INFO] lonestar4.tacc.teragrid.org,&( queue = "normal" )( stdout =
>
> "/scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/lonestar_application.stdout"
> )( count = "64" )( executable =
> "/scratch/01437/ogce/Vlab/Phonon/executePhonon.sh" )( stderr =
>
> "/scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/lonestar_application.stderr"
> )( maxwalltime = "1440" )( hostCount = "8" )( minmemory = "10240" )(
> project = "TG-STA110014S" )( jobtype = "mpi" )( environment = ( "inputData"
>
> "/scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/inputData"
> ) ( "outputData"
>
> "/scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/outputData"
> ) )( proxy_timeout = "1" )( arguments =
>
> "///scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/inputData/Pwscf_Input"
>
> "///scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/inputData/Cd_PON_sp_LDA.vdb"
>
> "///scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/inputData/Te_PON_LDA.vdb"
>
> "///scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/inputData/Phonon_Input"
> )( directory =
>
> "/scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4"
> )( maxmemory = "15360" )
> [INFO] -----END DATA-----
> [ERROR] The connection to the server failed (check host and port) [Caused
> by: Connection refused]
> org.apache.airavata.core.gfac.exception.JobSubmissionFault: The connection
> to the server failed (check host and port) [Caused by: Connection refused]
> at
>
> org.apache.airavata.core.gfac.provider.impl.GramProvider.executeApplication(GramProvider.java:229)
> at
>
> org.apache.airavata.core.gfac.provider.AbstractProvider.execute(AbstractProvider.java:69)
> at
>
> org.apache.airavata.core.gfac.services.impl.AbstractSimpleService.execute(AbstractSimpleService.java:118)
> at org.apache.airavata.core.gfac.GfacAPI.gridJobSubmit(GfacAPI.java:140)
> at
>
> org.apache.airavata.xbaya.invoker.EmbeddedGFacInvoker.invoke(EmbeddedGFacInvoker.java:256)
> at
>
> org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.handleWSComponent(WorkflowInterpreter.java:749)
> at
>
> org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.executeDynamically(WorkflowInterpreter.java:533)
> at
>
> org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.scheduleDynamically(WorkflowInterpreter.java:218)
> at
>
> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.executeWorkflow(WorkflowInterpretorSkeleton.java:389)
> at
>
> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.access$400(WorkflowInterpretorSkeleton.java:87)
> at
>
> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton$2.run(WorkflowInterpretorSkeleton.java:382)
> at java.lang.Thread.run(Thread.java:680)
> Caused by: org.globus.gram.GramException: The connection to the server
> failed (check host and port) [Caused by: Connection refused]
> at org.globus.gram.Gram.renew(Gram.java:595)
> at org.globus.gram.GramJob.renew(GramJob.java:329)
> at org.globus.gram.GramJob.renew(GramJob.java:315)
> at
>
> org.apache.airavata.core.gfac.provider.utils.JobSubmissionListener.waitFor(JobSubmissionListener.java:72)
> at
>
> org.apache.airavata.core.gfac.provider.impl.GramProvider.executeApplication(GramProvider.java:206)
> ... 11 more
> Exception in thread "Thread-42"
> org.apache.airavata.workflow.model.exceptions.WorkflowRuntimeException:
> org.apache.airavata.workflow.model.exceptions.WorkflowException: The
> connection to the server failed (check host and port) [Caused by:
> Connection refused]
> at
>
> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.executeWorkflow(WorkflowInterpretorSkeleton.java:392)
> at
>
> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.access$400(WorkflowInterpretorSkeleton.java:87)
> at
>
> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton$2.run(WorkflowInterpretorSkeleton.java:382)
> at java.lang.Thread.run(Thread.java:680)
> Caused by: org.apache.airavata.workflow.model.exceptions.WorkflowException:
> The connection to the server failed (check host and port) [Caused by:
> Connection refused]
> at
>
> org.apache.airavata.xbaya.invoker.EmbeddedGFacInvoker.invoke(EmbeddedGFacInvoker.java:321)
> at
>
> org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.handleWSComponent(WorkflowInterpreter.java:749)
> at
>
> org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.executeDynamically(WorkflowInterpreter.java:533)
> at
>
> org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.scheduleDynamically(WorkflowInterpreter.java:218)
> at
>
> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.executeWorkflow(WorkflowInterpretorSkeleton.java:389)
> ... 3 more
> Caused by: org.apache.airavata.core.gfac.exception.JobSubmissionFault: The
> connection to the server failed (check host and port) [Caused by:
> Connection refused]
> at
>
> org.apache.airavata.core.gfac.provider.impl.GramProvider.executeApplication(GramProvider.java:229)
> at
>
> org.apache.airavata.core.gfac.provider.AbstractProvider.execute(AbstractProvider.java:69)
> at
>
> org.apache.airavata.core.gfac.services.impl.AbstractSimpleService.execute(AbstractSimpleService.java:118)
> at org.apache.airavata.core.gfac.GfacAPI.gridJobSubmit(GfacAPI.java:140)
> at
>
> org.apache.airavata.xbaya.invoker.EmbeddedGFacInvoker.invoke(EmbeddedGFacInvoker.java:256)
> ... 7 more
> Caused by: org.globus.gram.GramException: The connection to the server
> failed (check host and port) [Caused by: Connection refused]
> at org.globus.gram.Gram.renew(Gram.java:595)
> at org.globus.gram.GramJob.renew(GramJob.java:329)
> at org.globus.gram.GramJob.renew(GramJob.java:315)
> at
>
> org.apache.airavata.core.gfac.provider.utils.JobSubmissionListener.waitFor(JobSubmissionListener.java:72)
> at
>
> org.apache.airavata.core.gfac.provider.impl.GramProvider.executeApplication(GramProvider.java:206)
> ... 11 more
>
> =================================================================
>
> My questions:
>
> Is there anything that I should do to avoid this error to happen?
> What do I have to do transfer one output file "Text File" from Lonestar
> back to my Desktop?
>
> Thank you,
>
> Pedro da Silveira
>



-- 
System Analyst Programmer
PTI Lab
Indiana University

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