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

Nate Woody nate.a.woody at gmail.com
Thu Nov 11 07:11:24 MST 2010


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.
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