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

[Pawel S. <Paw...@bc...>]

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, 
EMAILADDRESS=paw...@bc..., C=Norway, ST=Hordaland, 
CN=gridsam_certificate</Property>
		<Property 
name="urn:gridsam:pbs:jobid">2116221.hpcmaster.bccs.uib.no</Property>
	</JobStatus>
</getJobStatusResponse>