[torqueusers] Script problem (can't find executable)

Guille guillermo.marco at gmail.com
Thu Nov 11 07:13:43 MST 2010


I just can execute the script from 1 specific node if i copy it form my
/usr/local/bin to the /bin/ directory in that specific node.
The real problem is that my 5 nodes can't acces my /usr/local/bin/ scripts.

2010/11/11 Nate Woody <nate.a.woody at gmail.com>

> The easy check is to ssh over to one of your nodes and see if the
> script executes OK from the node.  I bet it doesn't.
>
> When I'm confused I usually start adding pwd and ls lines to my batch
> script.  Verify that you are in the directory that you think you're in
> and that the directory contains what you thing it does.
>
> Nate
>
>
> On Thu, Nov 11, 2010 at 8:50 AM, Kevin Van Workum <vanw at sabalcore.com>
> wrote:
> >
> >
> > On Thu, Nov 11, 2010 at 6:42 AM, Guille <guillermo.marco at gmail.com>
> wrote:
> >>
> >> Hi guys i've made a PBS script to launch another program called "tophat"
> >>
> >> tophat is located at /usr/local/bin/tophat
> >>
> >> Here's my pbs script located in /home/PBS_scripts/
> >>
> >> #!/bin/sh
> >> #PBS -l walltime=00:05:00
> >> #PBS -N tophat_script
> >> #PBS -o tophat_script.out
> >> #PBS -e tophat_scriptb.err
> >>
> >> echo Script starts..
> >> cd /usr/local/bin/
> >> ./tophat -r 150 /data/results/Sl65/reference_genome/GRch37.58/hg19
> 1_1.fa
> >> 1_2.fa
> >> echo Script ends..
> >>
> >> This job script never uses any node or procesor, (1 node and 1 procesor
> by
> >> default) and apears in queue as "C" state.
> >>
> >> The tophat_scriptb.err looks like this:
> >>
> >> /opt/torque/mom_priv/jobs/22825.sistemas-genom8.sistemas.local.SC: line
> 9:
> >> ./tophat: No such file or directory
> >>
> >> How the hell i can specify the path to my script location because i've
> >> tried doing cd like the script above and using PBS_O_PATH but nothing
> seems
> >> to work..
> >>
> >> Thanks for help :)
> >
> > Perhaps 'tophat' is on your submitting machine only, and not on your
> > execution node?
> >
> >>
> >> _______________________________________________
> >> torqueusers mailing list
> >> torqueusers at supercluster.org
> >> http://www.supercluster.org/mailman/listinfo/torqueusers
> >>
> >
> >
> >
> > --
> > Kevin Van Workum, PhD
> > Sabalcore Computing Inc.
> > Run your code on 500 processors.
> > Sign up for a free trial account.
> > www.sabalcore.com
> > 877-492-8027 ext. 11
> >
> > _______________________________________________
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> > torqueusers at supercluster.org
> > http://www.supercluster.org/mailman/listinfo/torqueusers
> >
> >
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