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

Guille guillermo.marco at gmail.com
Thu Nov 11 07:11:54 MST 2010


What i've found is that i can't run the script from any of the 5 nodes.
Because all my scripts are in /usr/local/bin/ and those can't be accesed if
the script is launched from any of the 5 nodes... What can i do to view my
/usr/local/bin from any of my clusters? i've tried with a symbolic link but
it doesn't work.

2010/11/11 Kevin Van Workum <vanw at sabalcore.com>

>
>
> 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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