[torquedev] [Bug 217] New: Multiple job array dependencies are not honored

bugzilla-daemon at supercluster.org bugzilla-daemon at supercluster.org
Thu Sep 20 14:32:29 MDT 2012


           Summary: Multiple job array dependencies are not honored
           Product: TORQUE
           Version: 3.0.x
          Platform: All
        OS/Version: Linux
            Status: NEW
          Severity: major
          Priority: P5
         Component: pbs_server
        AssignedTo: dbeer at adaptivecomputing.com
        ReportedBy: tasbu at aol.com
                CC: torquedev at supercluster.org
   Estimated Hours: 0.0

I've boiled down a significant job dependency array bug to a simple test
The problem is that job array dependencies are not honored when you have
more than one array dependency.

The script below creates 2 small sleep jobs of different lengths and submits
each as an array. A final wrap-up job is submitted as depending upon both
of the job arrays successfully finishing. However, the dependent job does not
wait for both arrays to exit successfully before starting, rather,
it starts early after the first array job finishes:

   sleep30_array           sleep15_array
        |                       |
        |                       |
        |                       -
        |                     done
        |                dep job starts
        |                    *bug*
dep job should start here

cat << EOF > sleeper15
sleep 15
cat << EOF > sleeper30
sleep 30

JOB1=`cat sleeper30 | qsub -t 1-2`
JOB2=`cat sleeper15 | qsub -t 1-2`
echo "cat sleeper15 | qsub -W depend=afterokarray:${JOB1}:${JOB2}"
cat sleeper15 | qsub -W depend=afterokarray:${JOB1}:${JOB2}

Running the script above will give the something like the following:

cat sleeper15 | qsub -W depend=afterokarray:55349[].madrid:55350[].madrid

-- after 20 seconds --

> qstat
55349[].madrid             STDIN            tasbu                  0 R batch
55350[].madrid             STDIN            tasbu                  0 C batch
55351.madrid               STDIN            tasbu                  0 R batch

55351.madrid should not be running!

Torque version: 3.0.5

A solution to this problem is crucial to our pipeline and I would
appreciate any fixes / workarounds.

Thanks -

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