[GE users] No job scripts - Job submission from cmd line only

reuti reuti at staff.uni-marburg.de
Wed Sep 16 10:26:40 BST 2009


Am 16.09.2009 um 08:53 schrieb sangamesh:

> Thanks Reuti. its working fine
>
> If, there are two commands for single application, then how they  
> can be used on command line
> For eg: qsub -b y -cwd -V grompp mdrun
> doesn't working.
>
> But in script, these commands can be mentioned in two separate  
> lines which works fine.

You can use the same technique as you would to put them in one  
command line or in one line in a script. As with the environment  
variables, you have to escape any special character.

man bash => section "Lists"

-- Reuti


>  Thanks,
> Sangamesh
>
> On Mon, Sep 14, 2009 at 3:25 PM, reuti <reuti at staff.uni-marburg.de>  
> wrote:
> Hi,
>
> Am 14.09.2009 um 07:48 schrieb sangamesh:
>
> > Dear SGE users,
> >
> >      Is it possible to submit serial and parallel jobs to SGE from
> > command line only, instead of using a script?
> >
> > For eg:
> > qsub  -N Prl_Job -cwd -pe mvapi 16 mpirun -machinefile $TMPDIR/
> > machines -np $NSLOTS sander.MPI
>
> in principle: yes. But you will need to submit it with "-b y" and
> proper quoting, as $TMPDIR isn't known at submission time:
>
> $ qsub -b y -N Prl_Job -cwd -pe mvapi 16 mpirun -machinefile '$TMPDIR/
> machines' -np '$NSLOTS' sander.MPI
>
> -- Reuti
>
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