[torqueusers] submitting a job, then modify script and resubmit

Mahmood Naderan nt_mahmood at yahoo.com
Mon Feb 13 07:48:50 MST 2012


Thanks for your answer. I got that.

Another question is about modification of other config files. Does qsub copy all files or it does only copy the script?

In this case, I have a scr.sh which is:
#PBS ...
./run config.ini


the config.ini file looks like:
exe = bin1
args = 8

The first qsub is:
qsub scr.sh

After submitting that, I modify the config.ini to 

exe = bin1
args = 64

Then I resubmit scr.sh again

qsub scr.sh

Please note that the scr.sh doesn't change in this case. However the config.ini is modified.
 

Does your answer apply to this case? 

Regards
// Naderan *Mahmood;


________________________________
From: Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu>
To: Mahmood Naderan <nt_mahmood at yahoo.com>; Torque Users Mailing List <torqueusers at supercluster.org> 
Sent: Monday, February 13, 2012 5:33 PM
Subject: Re: [torqueusers] submitting a job, then modify script and resubmit

On Mon, Feb 13, 2012 at 8:15 AM, Mahmood Naderan <nt_mahmood at yahoo.com> wrote:
> Dear all,
> 1- Assume I have a script (named scr.sh) like this:
>
> #PBS -N run1
> #PBS -V
> #PBS -l nodes=1
> #PBS -q long
> #PBS -o /home/mahmood/run1.out
> #PBS -j oe
> cd $PBS_O_WORKDIR
> ./run1 config1
>
> 2- Then I run
> qsub scr.sh
>
> 3- the jobs state is 'Q' since all cores are busy. That is fine...
> 4- while run1 is in 'Q', I reopen scr.sh and change it to
>
> #PBS -N run2
> #PBS -V
> #PBS -l nodes=1
> #PBS -q long
> #PBS -o /home/mahmood/run2.out
> #PBS -j oe
> cd $PBS_O_WORKDIR
> ./run1 config2
>
>
> 5- Then I run
> qsub scr.sh
>
> 6- this job also is in 'Q' until some cores become free.
> 7- After some hours, two cores become free and both "run1" and "run2" change to 'R'.
>
> The question is, when run1 change to 'R', will it read its own scr.sh (which contain "./run config1")?
> Since the latest modification to scr.sh belongs to run2, I wonder what happen to run1?

qsub makes a copy of the submit script and the batch system will
execute that. that is the only way how it can consistently feeding
submission from standard input.

axel.


> You may say that I can test that myself to see the result, but since they stay in 'Q' for long time, I want to be sure about what I am doing.
> Hope that I state the problem correctly.
>
>
> // Naderan *Mahmood;
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> torqueusers at supercluster.org
> http://www.supercluster.org/mailman/listinfo/torqueusers



-- 
Dr. Axel Kohlmeyer    akohlmey at gmail.com
http://sites.google.com/site/akohlmey/

Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.


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