[Rocks-Discuss] qsub: illegal -j value

[Jonas Baltrusaitis]

Haven't seen that one before:

[jbaltrus@mr9540 siesta]$ qsub siesta
qsub: illegal -j value
[jbaltrus@mr9540 siesta]$

Couldn't google it, either. Any help?

thanks

Jonas

[Anoop Rajendra]

What are the contents of "siesta" script?

-a

[Jonas Baltrusaitis]

#!/bin/bash
#PBS -l nodes=1:ppn=4
#PBS -S /bin/bash
#PBS -j siesta.err
#PBS -V

echo "Node file: $PBS_NODEFILE :"
echo "---------------------"
cat $PBS_NODEFILE
echo "---------------------"

echo "Starting run at: `date`"

echo "PBS Working Directory: $PBS_O_WORKDIR"

echo "Filename is: $PBS_JOBNAME"

export PATH=${PATH}:/share/apps/siesta-2.0.2/Src

mkdir /share/apps/scratch/$PBS_JOBNAME

cp /$PBS_O_WORKDIR/$PBS_JOBNAME.fdf /share/apps/scratch/$PBS_JOBNAME

cd /share/apps/scratch/$PBS_JOBNAME

mpirun -n 4 -machinefile $PBS_NODEFILE /share/apps/siesta-2.0.2/Src/siesta $PBS_JOBNAME.fdf | $PBS_JOBNAME.out

mv /share/apps/scratch/$PBS_JOBNAME/*.* $PBS_O_WORKDIR

rm -rf /share/apps/scratch/$PBS_JOBNAME

echo "Job finished at: `date`"

--- On Thu, 5/14/09, Anoop Rajendra <anoop.r...@gmail.com> wrote:

[Gus Correa]

Hi Jonas

I haven't used the -j option in quite a while, so I may be wrong.

However, the Torque/PBS
qsub option -j doesn't seem to take a file name argument,
but one of these three keywords:
"oe" (to join the stdout and stderr streams onto the stdout),
"eo" (to join the stdout and stderr streams onto the stderr), or
"n" (to cancel the request to join stdout and stderr).

If you want to declare a filename to dump stdout use the -o option,
and the -e option for stderr.

"man qsub" is your friend!

For instance:

#PBS -j eo
#PBS -e siesta.err

dumps stdout and stderr to siesta.err

#PBS -j oe
#PBS -o siesta.out

dumps stdout and stderr to siesta.out

#PBS -o siesta.out
#PBS -e siesta.err

doesn't merge the streams, dumping stdout to siesta.out,
and stderr to siesta.err.

I hope this helps.

Gus Correa
---------------------------------------------------------------------
Gustavo Correa
Lamont-Doherty Earth Observatory - Columbia University
Palisades, NY, 10964-8000 - USA
---------------------------------------------------------------------

[Jonas Baltrusaitis]

useful, fix it. learning slowly

--- On Thu, 5/14/09, Gus Correa <g...@ldeo.columbia.edu> wrote:

[Bart Brashers]

Just a hint regarding mpirun: if you substitute mpiexec instead, you don't have to use the "-n 4 -machinefile $PBS_NODEFILE". mpiexec is smarter than mpirun, and is PBS-aware. It just knows how many nodes to use, and which nodes to use. It's part of the Torque roll...

Bart

________________________________

echo "Filename is: $PBS_JOBNAME"

export PATH=${PATH}:/share/apps/siesta-2.0.2/Src

mkdir /share/apps/scratch/$PBS_JOBNAME

cp /$PBS_O_WORKDIR/$PBS_JOBNAME.fdf /share/apps/scratch/$PBS_JOBNAME

cd /share/apps/scratch/$PBS_JOBNAME

mv /share/apps/scratch/$PBS_JOBNAME/*.* $PBS_O_WORKDIR

rm -rf /share/apps/scratch/$PBS_JOBNAME

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