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From Raminder Singh <raminderjsi...@gmail.com>
Subject Re: Submit task to Lonestar using my Xsede account instead of using ogce
Date Wed, 06 Feb 2013 22:08:52 GMT
According to Gram user guide [1], executable file permission does not allow execution. This
guide can help you with gram error codes. 

Thanks
Raminder

1. http://www.globus.org/toolkit/docs/4.0/execution/prewsgram/user-index.html


On Feb 6, 2013, at 4:52 PM, Pedro da Silveira wrote:

> Hi Raminder,
> 
> I tested the task submission again. My workflow has 2 application services
> and 4 inputs total. Those 2 tasks run in less than 5 minutes, it is a just
> a test.
> The first application services ran successfully (File transfer and job),
> but the second application services didn't. The second application services
> got the files transfer correctly, but did not submit the task to PBS. The
> Airavata server was constantly printing "Job Error Code: 72".
> Do you know what could possibly cause this message?
> 
> This is the Airavata-Server log messages:
> 
> [INFO] -----END DATA-----
> [INFO] Status is zero
> [INFO] Status of job
> https://gridftp1.ls4.tacc.utexas.edu:50383/16289984330111623786/8943296923859958664/isFAILED
> [INFO] -----DATA-----
> [INFO] Status of job
> https://gridftp1.ls4.tacc.utexas.edu:50383/16289984330111623786/8943296923859958664/isFAILED
> [INFO] -----END DATA-----
> [INFO] Job Error Code: 72
> [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.provider.impl.GramProvider.executeApplication(GramProvider.java:225)
> 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] Job Protocol    : https
> Host name   : gridftp1.ls4.tacc.utexas.edu
> Port number : 50383
> Url path    : 16289984330111623786/8943296923859958664/
> User        : null
> Pwd         : null
> on host lonestar4.tacc.teragrid.org Job Exit Code = 72
> [INFO] -----END DATA-----
> [ERROR] Job Protocol    : https
> Host name   : gridftp1.ls4.tacc.utexas.edu
> Port number : 50383
> Url path    : 16289984330111623786/8943296923859958664/
> User        : null
> Pwd         : null
> on host lonestar4.tacc.teragrid.org Job Exit Code = 72
> org.apache.airavata.core.gfac.exception.JobSubmissionFault: Job Protocol
> : https
> Host name   : gridftp1.ls4.tacc.utexas.edu
> Port number : 50383
> Url path    : 16289984330111623786/8943296923859958664/
> User        : null
> Pwd         : null
> on host lonestar4.tacc.teragrid.org Job Exit Code = 72
> at
> org.apache.airavata.core.gfac.provider.impl.GramProvider.executeApplication(GramProvider.java:222)
> 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: java.lang.Exception: Job Protocol    : https
> Host name   : gridftp1.ls4.tacc.utexas.edu
> Port number : 50383
> Url path    : 16289984330111623786/8943296923859958664/
> User        : null
> Pwd         : null
> on host lonestar4.tacc.teragrid.org Job Exit Code = 72
> ... 12 more
> Exception in thread "Thread-67"
> org.apache.airavata.workflow.model.exceptions.WorkflowRuntimeException:
> org.apache.airavata.workflow.model.exceptions.WorkflowException: Job
> Protocol    : https
> Host name   : gridftp1.ls4.tacc.utexas.edu
> Port number : 50383
> Url path    : 16289984330111623786/8943296923859958664/
> User        : null
> Pwd         : null
> on host lonestar4.tacc.teragrid.org Job Exit Code = 72
> 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:
> Job Protocol    : https
> Host name   : gridftp1.ls4.tacc.utexas.edu
> Port number : 50383
> Url path    : 16289984330111623786/8943296923859958664/
> User        : null
> Pwd         : null
> on host lonestar4.tacc.teragrid.org Job Exit Code = 72
> 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: Job
> Protocol    : https
> Host name   : gridftp1.ls4.tacc.utexas.edu
> Port number : 50383
> Url path    : 16289984330111623786/8943296923859958664/
> User        : null
> Pwd         : null
> on host lonestar4.tacc.teragrid.org Job Exit Code = 72
> at
> org.apache.airavata.core.gfac.provider.impl.GramProvider.executeApplication(GramProvider.java:222)
> 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: java.lang.Exception: Job Protocol    : https
> Host name   : gridftp1.ls4.tacc.utexas.edu
> Port number : 50383
> Url path    : 16289984330111623786/8943296923859958664/
> User        : null
> Pwd         : null
> on host lonestar4.tacc.teragrid.org Job Exit Code = 72
> ... 12 more
> 
> 
> Thank you,
> 
> 
> 
> 
> 
> On Wed, Feb 6, 2013 at 9:23 AM, Raminder Singh <raminderjsingh@gmail.com>wrote:
> 
>> Hi Pedro,
>> 
>> Can you check space in home directory of your account on Lonestar? I have
>> seen such problem if you cross disk quota.  Gram does not give any error
>> and job does not go into queue. If quota is fine then we need to debug more.
>> 
>> Thanks
>> Raminder
>> 
>> On Feb 5, 2013, at 7:49 PM, Pedro da Silveira wrote:
>> 
>>> Hi Dev,
>>> 
>>> I am trying to submit a workflow using my Xsede account using Xbaya. It
>> has
>>> worked successfully using "ogce" account.
>>> I changed the file "airavata-server.properties" to use my Xsede portal
>>> account.
>>> 
>>> myproxy.user=pedrorcs
>>> myproxy.pass=******
>>> 
>>> I also changed the Application Service to use a different settings like
>> my
>>> user $SCRATCH directory.
>>> 
>>> Executable path:
>>> /scratch/00091/tg458470/executePwscf.sh
>>> 
>>> Scratch Working directory:
>>> /scratch/00091/tg458470/Phonon
>>> 
>>> I set the workflow to run then I setup correctly the local path to input
>>> files on my desktop.
>>> All input files got transferred correctly, but the job were never not
>>> submitted to PBS.
>>> Can someone please clarify if I am doing something wrong?
>>> 
>>> This is the log on Airavata-Server:
>>> 
>>> 
>> =================================================================================================================
>>> [INFO] Experiment launched
>>> :SimplePhonon_01a4d374-486f-4948-937f-a9de4b2b45eb
>>> [INFO] -----DATA-----
>>> [INFO] Start scheduling
>>> [INFO] -----END DATA-----
>>> [INFO] Searching registry for some deployed application hosts
>>> [INFO] Found service on: lonestar4.tacc.teragrid.org
>>> [INFO] Found service on: lonestar4.tacc.teragrid.org
>>> [INFO] -----DATA-----
>>> [INFO] Finish scheduling
>>> [INFO] -----END DATA-----
>>> null
>>> [INFO] Proxy file renewed to
>>> /tmp/x509up_upedrorcsed4c4290-90e6-40a6-bfe7-3c5239da1b7c for the user
>>> pedrorcs with 3600 lifetime.
>>> [INFO] Creating Directory = gridftp1.ls4.tacc.utexas.edu:2811
>>> =//scratch/00091/tg458470/Phonon
>>> [INFO] Creating Directory = gridftp1.ls4.tacc.utexas.edu:2811
>>> 
>> =//scratch/00091/tg458470/Phonon/AppSimplePhonon_Tue_Feb_05_18_30_22_CST_2013_7a7dded8-e058-4be2-ad43-cacf77b3138d
>>> [INFO] Creating Directory = gridftp1.ls4.tacc.utexas.edu:2811
>>> 
>> =//scratch/00091/tg458470/Phonon/AppSimplePhonon_Tue_Feb_05_18_30_22_CST_2013_7a7dded8-e058-4be2-ad43-cacf77b3138d/inputData
>>> [INFO] Creating Directory = gridftp1.ls4.tacc.utexas.edu:2811
>>> 
>> =//scratch/00091/tg458470/Phonon/AppSimplePhonon_Tue_Feb_05_18_30_22_CST_2013_7a7dded8-e058-4be2-ad43-cacf77b3138d/outputData
>>> org.globus.gsi.gssapi.GlobusGSSCredentialImpl@2161df1f
>>> [INFO] The remote file is
>>> 
>> ///scratch/00091/tg458470/Phonon/AppSimplePhonon_Tue_Feb_05_18_30_22_CST_2013_7a7dded8-e058-4be2-ad43-cacf77b3138d/inputData/Pwscf_Input
>>> [INFO] Uploading file
>>> [INFO] Upload file
>>> 
>> to:///scratch/00091/tg458470/Phonon/AppSimplePhonon_Tue_Feb_05_18_30_22_CST_2013_7a7dded8-e058-4be2-ad43-cacf77b3138d/inputData/Pwscf_Input
>>> is done
>>> org.globus.gsi.gssapi.GlobusGSSCredentialImpl@2161df1f
>>> [INFO] The remote file is
>>> 
>> ///scratch/00091/tg458470/Phonon/AppSimplePhonon_Tue_Feb_05_18_30_22_CST_2013_7a7dded8-e058-4be2-ad43-cacf77b3138d/inputData/Mg.vbc3
>>> [INFO] Uploading file
>>> [INFO] Upload file
>>> 
>> to:///scratch/00091/tg458470/Phonon/AppSimplePhonon_Tue_Feb_05_18_30_22_CST_2013_7a7dded8-e058-4be2-ad43-cacf77b3138d/inputData/Mg.vbc3
>>> is done
>>> org.globus.gsi.gssapi.GlobusGSSCredentialImpl@2161df1f
>>> [INFO] The remote file is
>>> 
>> ///scratch/00091/tg458470/Phonon/AppSimplePhonon_Tue_Feb_05_18_30_22_CST_2013_7a7dded8-e058-4be2-ad43-cacf77b3138d/inputData/008Ocabm3.vdb
>>> [INFO] Uploading file
>>> [INFO] Upload file
>>> 
>> to:///scratch/00091/tg458470/Phonon/AppSimplePhonon_Tue_Feb_05_18_30_22_CST_2013_7a7dded8-e058-4be2-ad43-cacf77b3138d/inputData/008Ocabm3.vdb
>>> is done
>>> [INFO] -----DATA-----
>>> [INFO] Start execution
>>> [INFO] -----END DATA-----
>>> org.globus.gsi.gssapi.GlobusGSSCredentialImpl@2161df1f
>>> [INFO] -----DATA-----
>>> [INFO] Finished launching job, Host = lonestar4.tacc.teragrid.org RSL =
>> &(
>>> queue = "development" )( stdout =
>>> 
>> "/scratch/00091/tg458470/Phonon/AppSimplePhonon_Tue_Feb_05_18_30_22_CST_2013_7a7dded8-e058-4be2-ad43-cacf77b3138d/lonestar_application.stdout"
>>> )( count = "12" )( executable = "/scratch/00091/tg458470/executePwscf.sh"
>>> )( stderr =
>>> 
>> "/scratch/00091/tg458470/Phonon/AppSimplePhonon_Tue_Feb_05_18_30_22_CST_2013_7a7dded8-e058-4be2-ad43-cacf77b3138d/lonestar_application.stderr"
>>> )( maxwalltime = "20" )( hostCount = "1" )( minmemory = "1024" )(
>> project =
>>> "TG-TRA120030" )( jobtype = "mpi" )( environment = ( "inputData"
>>> 
>> "/scratch/00091/tg458470/Phonon/AppSimplePhonon_Tue_Feb_05_18_30_22_CST_2013_7a7dded8-e058-4be2-ad43-cacf77b3138d/inputData"
>>> ) ( "outputData"
>>> 
>> "/scratch/00091/tg458470/Phonon/AppSimplePhonon_Tue_Feb_05_18_30_22_CST_2013_7a7dded8-e058-4be2-ad43-cacf77b3138d/outputData"
>>> ) )( proxy_timeout = "1" )( arguments =
>>> 
>> "///scratch/00091/tg458470/Phonon/AppSimplePhonon_Tue_Feb_05_18_30_22_CST_2013_7a7dded8-e058-4be2-ad43-cacf77b3138d/inputData/Pwscf_Input"
>>> 
>> "///scratch/00091/tg458470/Phonon/AppSimplePhonon_Tue_Feb_05_18_30_22_CST_2013_7a7dded8-e058-4be2-ad43-cacf77b3138d/inputData/Mg.vbc3"
>>> 
>> "///scratch/00091/tg458470/Phonon/AppSimplePhonon_Tue_Feb_05_18_30_22_CST_2013_7a7dded8-e058-4be2-ad43-cacf77b3138d/inputData/008Ocabm3.vdb"
>>> )( directory =
>>> 
>> "/scratch/00091/tg458470/Phonon/AppSimplePhonon_Tue_Feb_05_18_30_22_CST_2013_7a7dded8-e058-4be2-ad43-cacf77b3138d"
>>> )( maxmemory = "2048" ) working directory =
>>> 
>> /scratch/00091/tg458470/Phonon/AppSimplePhonon_Tue_Feb_05_18_30_22_CST_2013_7a7dded8-e058-4be2-ad43-cacf77b3138d
>>> temp directory = /scratch/00091/tg458470/Phonon Globus GateKeeper
>> Endpoint
>>> = gridftp1.ls4.tacc.utexas.edu:2119/jobmanager-sge
>>> [INFO] -----END DATA-----
>>> 
>> =================================================================================================================
>>> 
>>> 
>>> Thank you so much,
>>> 
>>> 
>>> Pedro da Silveira
>> 
>> 


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