[GE users] Altering array task range does not work

iadzhubey iadzhubey at rics.bwh.harvard.edu
Tue Mar 23 16:09:44 GMT 2010


Hi,

On Tuesday 23 March 2010 03:56:05 am dougalb wrote:
> Can you provide the full command you are using?

Assuming that we already have an array job 3456 awaiting execution while 
sitting in a queue, that has been submitted like this:

$ qsub -cwd -b y -t 1-100 ./array_wrapper.sh

One example I tried would be:

$ qalter -t 10-20 3456

Which gives the error message:

"found lonely '-t 10-20' option (The -t option needs a leading job name)"

Presumably because qalter's command line parser takes the first '-t 10-20' as a 
part of a specification of the job *which* to alter instead of the *option* to 
be altered for the 3456 command.

--Ivan

>   $ qalter 4562 -t 1000-2000 -h s
> 
> That should work.
> 
> On Mon, Mar 22, 2010 at 10:37 PM, iadzhubey
> 
> <iadzhubey at rics.bwh.harvard.edu> wrote:
> > Any suggestions at all? Anyone, please?
> > 
> > --Ivan
> > 
> > On Monday 22 March 2010 10:48:53 am iadzhubey wrote:
> >> Hi Reuti,
> >> 
> >> On Monday 22 March 2010 08:42:44 am reuti wrote:
> >> > Hi,
> >> > 
> >> > Am 20.03.2010 um 08:57 schrieb iadzhubey:
> >> > > I am trying to adjust the task range of an already submitted and
> >> > > pending array job but cannot figure out how to do this (and if it's
> >> > > even supported). Qalter manpage lists '-t' as supported option but
> >> > > when specified with qalter command it is recognised as an
> >> > > (incomplete) wc_job_range_list specification instead, which results
> >> > > in a syntax error message.
> >> > 
> >> > you mean the error message like:
> >> > 
> >> > found lonely '-t 15-20' option (The -t option needs a leading job
> >> > name)'?
> >> 
> >> Yep, this is the error message. I've also tried every other combination
> >> of command-line switches to qalter I can think of but to no avail.
> >> 
> >> Any hope this may actually work? For now, I am using a crude workaround
> >> by submitting array jobs with the fixed maximum range (e.g., -t
> >> 1-75000) and then letting the first dispatched task of each array qdel
> >> all extraneous tasks at runtime. This works but is not an elegant
> >> solution.
> >> 
> >> Best,
> >> Ivan
> > 
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