[GE users] core duo systems not accepting jobs

flengyel flengyel at gc.cuny.edu
Mon Jul 13 02:56:38 BST 2009


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No, that's not the issue. That would not explain why
the jobs are waiting, since if it were incorrect some
kind of error output would be generated.


I've tried rewriting the script as the following less
flexible one:

!/bin/bash
if [ $# -lt 1 ]; then
  echo "Usage: gsub gaussianfile"
  exit
fi
qsub -pe gauss 2 -cwd -q x86_64.q@@coreduos  <<__HereDocument__
#!/bin/bash
#$ -S /bin/bash
#$ -N $1

export g03root=/usr/local/gaussian
. /usr/local/gaussian/g03/bsd/g03.profile
export SGE_ROOT=/usr/local/sge
.  /usr/local/sge/default/common/settings.sh
export GAUSS_SCRDIR=/tmp

g03 $1
__HereDocument__


Now this "should not" make a difference, but now jobs seem to be
running when I use this one. (The scare quotes are present because
the modal operator "should" in computer science usually means that
the person who uttered it is wrong...)

FL



-----Original Message-----
From: Anand Vaidya [mailto:anandvaidya.ml at gmail.com]
Sent: Sun 7/12/2009 9:40 PM
To: users; Lengyel, Florian
Subject: Re: [GE users] core duo systems not accepting jobs

On 13 July 2009 am 07:29:58 flengyel wrote:
> -----Original Message-----
> I wonder if the trouble is with the job submission script gsub
>
> [flengyel at nept strange]$ more /usr/local/bin/gsub
> #!/bin/bash
> if [ $# -lt 1 ]; then
>   echo "Usage: gsub gaussianfile [qsub options]"
>   exit
> fi
> ARGS=("$@")
> QOPTS=${ARGS[@]:1}
> qsub $QOPTS <<__HereDocument__
> #!/bin/bash
> #$ -S /bin/bash
> #$ -cwd
> #$ -N $1
> #$ -pe gauss 2
> #$ -q x86_64.q
>
> export g03root=/usr/local/gaussian
> . /usr/local/gaussian/g03/bsd/g03.profile
> export SGE_ROOT=/usr/local/sge
> .  /usr/local/sge/default/common/settings.sh
> export GAUSS_SCRDIR=/tmp
>
> g03 $1
> __HereDocument__

Hi,

I think you should invoke Gaussian as

g03 < $1

and not g03 $1

Right?

Regards
Anand




>
>
>
>
> You've probably already done this but it's time to move beyond qstat
> and qconf output, do you see anything in your SGE spool logs for the
> qmaster host, the scheduler process or even the execd messages file
> for some of the 2-way systems?
>
>
> -Chris
>
>
> I have local spool logs in $SGE_ROOT/spool on each execution host.
> Not certain where to look for these...nothing in
> /usr/local/sge/spool/messages for today on m35, for example...
>
> Thanks again.
>
> FL
>
> On Jul 12, 2009, at 6:40 PM, flengyel wrote:
> > -----Original Message-----
> > From: craffi [mailto:dag at sonsorol.org]
> > Sent: Sun 7/12/2009 6:39 PM
> > To: users at gridengine.sunsource.net
> > Subject: Re: [GE users] core duo systems not accepting jobs
> >
> > Things look pretty good, a few queue instances down in 'au' state and
> > one of your x86_64 hosts in load alarm state 'a' with some insane load
> > average. Your quad.q hosts are almost totally maxed out.
> >
> > Indeed.
> >
> > And you do have a bunch of x86_64.q hosts with free job slots that are
> > totally idle.
> >
> > Right
> >
> > Commenting only now on the "qstat -j" data you posted I'd zero in on
> >
> > this report from the scheduler:
> > >                             cannot run because no access to pe
> >
> > "gauss"
> >
> > >                             cannot run in PE "gauss" because it only
> > > offers 0 slot
> >
> > This brings to mind a few guesses:
> >
> > - Have you run out of "gauss" PE slots? How many are configured in the
> > PE object?
> >
> > 9999
> >
> > - Is your user allowed to access that PE or is there a quota or ACL
> > list that may be blocking them?
> >
> > Yes. No quota that I am aware of.
> >
> >
> > - Is your user part of the "Research" group? You have access control
> > configured on that queue via the "user_lists" parameter in the queue
> > config
> >
> > Yes.
> >
> > -Chris
>
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