Re: [gridsam-discuss] JobStatus not complete when running PBS jobs

[Justin B. <jb...@ec...>]

Hi Pawel,

Which version of PBS are you using?
And are the PBS server and scheduler on the same machine as GridSAM?

	Justin

On 20 May 2009, at 13:51, Pawel Sztromwasser wrote:

> Hello,
>
> I guess similar issue has been mentioned once on the mailing list, but
> doesn't look like solved:
>
> http://sourceforge.net/mailarchive/forum.php?thread_name=002701c64d08%2449efd790%24db421080%40cs.ucl.ac.uk&forum_name=gridsam-discuss
>
> This also looks relevant, but I think it has been included into  
> version
> of GridSAM I am using (2.1.4):
>
> http://sourceforge.net/mailarchive/forum.php?thread_name=20080617145418.605536413%40soton.ac.uk&forum_name=gridsam-developer
>
> So what is the problem? I configured GridSAM to run jobs using PBS and
> then I am submitting them using GridSAM's Web Services. Jobs start OK,
> but their status freezes at state 'active' (response from getJobStatus
> method below). I checked jobs on the cluster and they had finished, so
> it seems like GridSAM doesn't check properly job's status on the
> cluster. It worked properly while running simple POSIX programs like  
> cat
> and echo, so it is something with PBS.
>
> I double checked  pbs.PBSJobStatusCommand in jobmanager-pbs.xml file  
> and
> it is correct. Is there anything additional that GridSAM uses to check
> if job completed on the cluster? maybe something is wrong with my  
> setup,
> like directories with wrong permissions it can't access?
>
> I am using GridSAM 2.1.4 with OMII toolkit 3.4.4.
>
> Thank you in advance for help,
> Pawel
>
>
> ------------------------
> <getJobStatusResponse xmlns="http://www.icenigrid.org/service/ 
> gridsam">
> 	<JobStatus>
> 		<JobIdentifier>
> 		<ID>urn:gridsam:0131f86a215956de01215965031d000b</ID>
> 		</JobIdentifier>
> 		<Stage>
> 			<State>pending</State>
> 			<Description>job is being scheduled</Description>
> 			<Time>2009-05-19T17:02:20.701+02:00</Time>
> 		</Stage>
> 		<Stage><State>staging-in</State><Description>staging
> files...</Description><Time>2009-05-19T17:02:20.803+02:00</Time></ 
> Stage><Stage><State>staged-in</State><Description>no
> file needs to be staged
> in</Description><Time>2009-05-19T17:02:20.807+02:00</Time></Stage>
> 		<Stage>
> 			<State>active</State>
> 			<Description>job is being launched through PBS</Description>
> 			<Time>2009-05-19T17:02:20.933+02:00</Time>
> 		</Stage>
> 		<Property name="urn:pbs:script">
>
> #! /bin/sh
> # PBS batch job script built by Globus job manager
> #
> #PBS -S /bin/sh
> #PBS -Wx=NODESET:ONEOF:FEATURE:switch10:switch11:ecs
>
> #PBS -o /work/pawels/blast-runs/blast1.out
>
> #PBS -e /work/pawels/blast-runs/blast1.err
>
> cd ${PBS_O_WORKDIR}
>
> /local/blast-2.2.18/bin/blastall \
>      -i /work/pawels/blast-runs/seq/batch0.fasta -o
> /work/pawels/blast-runs/seq/batch0.fasta.blast -p blastp -d
> /net/compute-2-23.local/scratch/andersl/uniref90 -m7
> touch .complete
> 		</Property>
> 		<Property name="urn:pbs:launched">true</Property>
> 		<Property name="urn:gridsam:principal">OU=BCCS, O=UiB,
> EMA...@bc..., C=Norway, ST=Hordaland,
> CN=gridsam_certificate</Property>
> 		<Property
> name="urn:gridsam:pbs:jobid">2116221.hpcmaster.bccs.uib.no</Property>
> 	</JobStatus>
> </getJobStatusResponse>
>
>
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--
Justin Bradley
Design & Development Team Leader
j.b...@om...
OMII-UK
Bay 23, 4067, B32
University of Southampton