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.<br>The real problem is that my 5 nodes can't acces my /usr/local/bin/ scripts.<br><br>
<div class="gmail_quote">2010/11/11 Nate Woody <span dir="ltr"><<a href="mailto:nate.a.woody@gmail.com">nate.a.woody@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
The easy check is to ssh over to one of your nodes and see if the<br>
script executes OK from the node. I bet it doesn't.<br>
<br>
When I'm confused I usually start adding pwd and ls lines to my batch<br>
script. Verify that you are in the directory that you think you're in<br>
and that the directory contains what you thing it does.<br>
<font color="#888888"><br>
Nate<br>
</font><div><div></div><div class="h5"><br>
<br>
On Thu, Nov 11, 2010 at 8:50 AM, Kevin Van Workum <<a href="mailto:vanw@sabalcore.com">vanw@sabalcore.com</a>> wrote:<br>
><br>
><br>
> On Thu, Nov 11, 2010 at 6:42 AM, Guille <<a href="mailto:guillermo.marco@gmail.com">guillermo.marco@gmail.com</a>> wrote:<br>
>><br>
>> Hi guys i've made a PBS script to launch another program called "tophat"<br>
>><br>
>> tophat is located at /usr/local/bin/tophat<br>
>><br>
>> Here's my pbs script located in /home/PBS_scripts/<br>
>><br>
>> #!/bin/sh<br>
>> #PBS -l walltime=00:05:00<br>
>> #PBS -N tophat_script<br>
>> #PBS -o tophat_script.out<br>
>> #PBS -e tophat_scriptb.err<br>
>><br>
>> echo Script starts..<br>
>> cd /usr/local/bin/<br>
>> ./tophat -r 150 /data/results/Sl65/reference_genome/GRch37.58/hg19 1_1.fa<br>
>> 1_2.fa<br>
>> echo Script ends..<br>
>><br>
>> This job script never uses any node or procesor, (1 node and 1 procesor by<br>
>> default) and apears in queue as "C" state.<br>
>><br>
>> The tophat_scriptb.err looks like this:<br>
>><br>
>> /opt/torque/mom_priv/jobs/<a href="http://22825.sistemas-genom8.sistemas.local.SC" target="_blank">22825.sistemas-genom8.sistemas.local.SC</a>: line 9:<br>
>> ./tophat: No such file or directory<br>
>><br>
>> How the hell i can specify the path to my script location because i've<br>
>> tried doing cd like the script above and using PBS_O_PATH but nothing seems<br>
>> to work..<br>
>><br>
>> Thanks for help :)<br>
><br>
> Perhaps 'tophat' is on your submitting machine only, and not on your<br>
> execution node?<br>
><br>
>><br>
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>><br>
><br>
><br>
><br>
> --<br>
> Kevin Van Workum, PhD<br>
> Sabalcore Computing Inc.<br>
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