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

Nate Woody nate.a.woody at gmail.com
Thu Nov 11 07:30:41 MST 2010


When you ssh to a compute node and execute:

/usr/local/bin/tophat  <args>

What do you see?  Copy the error into an email.

Nate


On Thu, Nov 11, 2010 at 9:11 AM, Guille <guillermo.marco at gmail.com> wrote:
> 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.
>> Run your code on 500 processors.
>> Sign up for a free trial account.
>> www.sabalcore.com
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>>
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>
>
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