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[farmshare-discuss] How to submit batch jobs on barley?

David Gabriel Simas dsimas at stanford.edu
Mon Mar 12 12:33:09 PDT 2012



----- Original Message -----
> Hello,
> 
> Follow-up to this question. I submitted some jobs two days ago, with
> the command
> 
> qsub -cwd -M mbaryakh at stanford.edu ./jobs_barley.sh
> 

Could you post your job script here?

> They were queued up with code qw every time I checked, and now they
> are gone from the list. It looks like the jobs never started: there
> is
> no output, I have received no emails, and the error files are blank.
> Is there any way to tell why the wait time is so long and why its
> failing?

The wait time is long because the cluster is in heavy use.
Unfortunately, as the system is currently configured, a
single user or small number of users can dominate the cluster.
We intend to fix that with a fair-share job scheduling system,
but that requires some more work and testing on our part.

DGS


> 
> Thanks for your help,
> Masha
> 
> 
> On Tue, Mar 6, 2012 at 3:38 PM, Alex Chekholko <chekh at stanford.edu>
> wrote:
> > On 03/06/2012 03:29 PM, Ken Van Tilburg wrote:
> >>
> >>  I know you cannot submit an executable with "qsub", so I tried
> >>  running
> >> a script that executes this "generate_events" executable, but when
> >> I
> >> type "qstat -j <JOBID>", I get a bunch of output that says the job
> >> was
> >> never queued up because all the clusters were overloaded/full.
> >
> >
> > You definitely can submit an executable to qsub, just use the -b
> > flag, e.g.:
> >
> > [chekh at corn22.stanford.edu] ~ [0]
> > $ qsub hostname
> > Unable to read script file because of error: error opening
> > hostname: No such
> > file or directory
> > [chekh at corn22.stanford.edu] ~ [14]
> > $ qsub -b y hostname
> > Your job 116705 ("hostname") has been submitted
> >
> > Your jobs are queued up but not yet running because the cluster is
> > full.
> >  Just like my job 116705.  It's in state 'qw'.
> >
> > Regards,
> > --
> > Alex Chekholko chekh at stanford.edu 347-401-4860
> > _______________________________________________
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> > farmshare-discuss at lists.stanford.edu
> > https://mailman.stanford.edu/mailman/listinfo/farmshare-discuss
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