[GE users] qsub does not run my bash file

Charu Chaubal Charu.Chaubal at Sun.COM
Thu Apr 20 23:37:43 BST 2006


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Hi Massimo,

Although you have #!/bin/bash on the first line of your script, probably 
a different shell is being used to interpret the script when you submit 
this job.  This is likely due to the queue config 
shell_start_mode=posix_compliant.

You can change this parameter to shell_start_mode=unix_behavior, or you 
could explicitly indicate the use of bash for this job.  One way to do 
this is to add this line to your script (doesn't matter where -- usually 
it's put near the top)

#$ -S /bin/bash

This says to use the specified shell when running the job.

Regards,
    Charu


Massimo Canonico wrote On 04/20/06 15:08,:

> Hi,
> I'm trying to see how qsub work with bash files that use variable.
>
> I have a very simple bash file:
> #!/bin/bash
> basepath=/export/home/mex/BoTSched
> echo $basepath
>
> if I run it, I get the correct output:
> [mex at clusun subfile]$ ./prova.sh
> /export/home/mex/BoTSched
>
> but if I try to submit it to SGE:
> [mex at clusun subfile]$ qsub ./prova.sh
> Your job 20056 ("prova.sh") has been submitted.
>
> I got an error:
> [mex at clusun subfile]$ more ~/prova.sh.e20056
> basepath=/export/home/mex/BoTSched: Command not found.
> basepath: Undefined variable.
>
> [mex at clusun subfile]$ more ~/prova.sh.o20056
> Warning: no access to tty (Bad file descriptor).
> Thus no job control in this shell.
>
> Any ideas?
>
> Thanks,
>  Massimo.
>
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