[Swift-devel] RE: [Swift-user] Execution error

Thu Apr 30 18:08:26 CDT 2009

Odd. Try "gt2:gt2:pbs" instead of "gt2:gt2:PBS".

On Thu, 2009-04-30 at 17:57 -0500, Yue, Chen - BMD wrote:
> Hi Mihael,
>  
> The error message is different after I change from gt2:PBS to
> gt2:gt2:PBS on TACC LoneStar. I attached the trace as following. I
> don't know if there is still setup problem. Thank you very much!
>  
> /////////////////////////
> [yuechen at communicado PTMap2]$ swift PTMap2-unmod.swift -sites.file
> sites.xml -tc.file tc.data
> Swift 0.9rc2 swift-r2860 cog-r2388
> RunID: 20090430-1742-tfabq6q4
> Progress:
> Progress:  Stage in:1
> Progress:  Stage in:1
> Progress:  Stage in:1
> Progress:  Submitting:1
> Progress:  Submitted:1
> Progress:  Active:1
> Failed to transfer wrapper log from
> PTMap2-unmod-20090430-1742-tfabq6q4/info/r on TACC_LoneStar
> Progress:  Active:1
> Failed to transfer wrapper log from
> PTMap2-unmod-20090430-1742-tfabq6q4/info/t on TACC_LoneStar
> Progress:  Stage in:1
> Progress:  Active:1
> Failed to transfer wrapper log from
> PTMap2-unmod-20090430-1742-tfabq6q4/info/v on TACC_LoneStar
> Progress:  Failed:1
> Execution failed:
>         Exception in PTMap2:
> Arguments: [e04.mzXML, ./seqs-ecolik12/fasta02, inputs-unmod.txt,
> parameters.txt]
> Host: TACC_LoneStar
> Directory: PTMap2-unmod-20090430-1742-tfabq6q4/jobs/v/PTMap2-v7baq5aj
> stderr.txt:
> stdout.txt:
> ----
> Caused by:
>         Cannot submit job
> org.globus.cog.abstraction.impl.common.task.TaskSubmissionException:
> Cannot submit job
>         at
> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.submitSingleJob(JobSubmissionTaskHandler.java:145)
>         at
> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.submit(JobSubmissionTaskHandler.java:99)
>         at
> org.globus.cog.abstraction.impl.common.AbstractTaskHandler.submit(AbstractTaskHandler.java:46)
>         at
> org.globus.cog.abstraction.impl.common.task.ExecutionTaskHandler.submit(ExecutionTaskHandler.java:43)
>         at
> org.globus.cog.abstraction.coaster.service.job.manager.WorkerManager.startWorker(WorkerManager.java:221)
>         at
> org.globus.cog.abstraction.coaster.service.job.manager.WorkerManager.run(WorkerManager.java:145)
> Caused by: org.globus.gram.GramException: The gatekeeper failed to
> find the requested service
>         at org.globus.gram.Gram.checkHttpReply(Gram.java:137)
>         at org.globus.gram.Gram.request(Gram.java:342)
>         at org.globus.gram.GramJob.request(GramJob.java:262)
>         at
> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.submitSingleJob(JobSubmissionTaskHandler.java:133)
>         ... 5 more
> Cleaning up...
> Shutting down service at https://129.114.50.32:35257
> Got channel MetaChannel: 13391897 -> GSSSChannel-null(1)
> - Done
> ////////////////////////
>  
> Chen, Yue
> 
> 
> ______________________________________________________________________
> From: Mihael Hategan [mailto:hategan at mcs.anl.gov]
> Sent: Thu 4/30/2009 5:37 PM
> To: Yue, Chen - BMD
> Cc: Michael Wilde; swift-devel
> Subject: RE: [Swift-devel] RE: [Swift-user] Execution error
> 
> 
> On Thu, 2009-04-30 at 17:32 -0500, Yue, Chen - BMD wrote:
> > Hi Michael,
> > 
> > I already have +osg-client-1.0.0-r1 in my .soft file. But I change
> it
> > to +osg-client and tried again. "ranger" gave me the same error
> > message. In the meantime, I tested one job on both Abe and Lonestar
> > and they both gave me qsub error.
> 
> Can you try "gt2:gt2:PBS" instead of "gt2:PBS" on all sites?
> 
> >  I attached as following:
> > 
> > ////////////////////////////////////
> > [yuechen at communicado PTMap2]$ swift PTMap2-unmod.swift -sites.file
> > sites.xml -tc.file tc.data
> > Swift 0.9rc2 swift-r2860 cog-r2388
> > RunID: 20090430-1722-oncfdolb
> > Progress:
> > Progress:  Stage in:1
> > Progress:  Stage in:1
> > Progress:  Stage in:1
> > Progress:  Submitting:1
> > Progress:  Submitted:1
> > Failed to transfer wrapper log from
> > PTMap2-unmod-20090430-1722-oncfdolb/info/3 on TACC_LoneStar
> > Progress:  Active:1
> > Failed to transfer wrapper log from
> > PTMap2-unmod-20090430-1722-oncfdolb/info/5 on TACC_LoneStar
> > Progress:  Stage in:1
> > Progress:  Active:1
> > Failed to transfer wrapper log from
> > PTMap2-unmod-20090430-1722-oncfdolb/info/7 on TACC_LoneStar
> > Progress:  Failed:1
> > Execution failed:
> >         Exception in PTMap2:
> > Arguments: [e04.mzXML, ./seqs-ecolik12/fasta02, inputs-unmod.txt,
> > parameters.txt]
> > Host: TACC_LoneStar
> > Directory:
> PTMap2-unmod-20090430-1722-oncfdolb/jobs/7/PTMap2-7uagp5aj
> > stderr.txt:
> > stdout.txt:
> > ----
> > Caused by:
> >         Cannot submit job: Could not submit job (qsub reported an
> exit
> > code of -1). no error output
> > org.globus.cog.abstraction.impl.common.task.TaskSubmissionException:
> > Cannot submit job: Could not submit job (qsub reported an exit code
> of
> > -1). no error output
> >         at
> >
> org.globus.cog.abstraction.impl.scheduler.common.AbstractJobSubmissionTaskHandler.submit(AbstractJobSubmissionTaskHandler.java:63)
> >         at
> >
> org.globus.cog.abstraction.impl.common.AbstractTaskHandler.submit(AbstractTaskHandler.java:46)
> >         at
> >
> org.globus.cog.abstraction.impl.common.task.ExecutionTaskHandler.submit(ExecutionTaskHandler.java:43)
> >         at
> >
> org.globus.cog.abstraction.coaster.service.job.manager.WorkerManager.startWorker(WorkerManager.java:221)
> >         at
> >
> org.globus.cog.abstraction.coaster.service.job.manager.WorkerManager.run(WorkerManager.java:145)
> > Caused by:
> > org.globus.cog.abstraction.impl.scheduler.common.ProcessException:
> > Could not submit job (qsub reported an exit code of -1). no error
> > output
> >         at
> >
> org.globus.cog.abstraction.impl.scheduler.common.AbstractExecutor.start(AbstractExecutor.java:94)
> >         at
> >
> org.globus.cog.abstraction.impl.scheduler.common.AbstractJobSubmissionTaskHandler.submit(AbstractJobSubmissionTaskHandler.java:53)
> >         ... 4 more
> > Cleaning up...
> > Shutting down service at https://129.114.50.32:34704
> > Got channel MetaChannel: 2013263 -> GSSSChannel-null(1)
> > - Done
> > /////////////////////////////////////////
> > 
> > My sites.xml is at : /home/yuechen/PTMap2/sites.xml. I'm wondering
> if
> > this still relates to my setup. Thanks!
> > 
> > Chen, Yue
> > 
> > 
> >
> >
> 
> 
> 
>  
> 
> 
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