I've boiled down a significant job dependency array bug to a simple test
script.
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*
        |
       ---
       done
dep job should start here


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

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}
--------SCRIPT_END------

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

> sh SCRIPT
cat sleeper15 | qsub -W depend=afterokarray:55349[].madrid:55350[].madrid
55351.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 -
Tom