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From Pedro da Silveira <pedro...@gmail.com>
Subject Phonon task
Date Tue, 29 Jan 2013 21:03:10 GMT
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

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