[Bioclusters] Submitting SGE jobs as nobody

Joseph Landman bioclusters@bioinformatics.org
Wed, 29 Oct 2003 06:14:15 -0500

On Wed, 2003-10-29 at 06:53, david speed (RI) wrote:

> We have encountered a strange problem when testing our prototype, the
> web interface will fail with this error message
> Can't exec "/local/SGE/bin/glinux/qsub": Input/output error

Could we see

	ls -alF /local/SGE/bin/glinux/qsub

Also, what user is running the apache daemon?  I presume that the CGI is
not an SUID code and dropping permissions to the other user.

Also, does

	su - `id apache`

(assuming apache is the user running the web server daemon) work?

Usually the permissions on qsub are set somewhat restrictive.  I would

	chown root:root /local/SGE/bin/glinux/qsub
	chmod 4755 /local/SGE/bin/glinux/qsub

It seems that you have 2 or more issues that are interacting.  First, it
appears that you might not have read or write permissions in the
directory where the script runs initially.  It would be worthwhile to
know what that directory is.  Second, it appears that the q* commands
may have somewhat more restrictive permission than needed.  You might be
able to fix the second problem in a different manner, though I would be
cautious and reluctant about adding te apache group to the system or
root group. 

The changing nature of the error messages seems to indicate something
like an automount.  

> However if we try to run again the error message changes to ( and
> stays the same for subsequent attempts)
> Can't exec "/local/SGE/bin/glinux/qsub": Permission denied
> I've been able to able to temporarily fix this problem by running qsub
> on the command line while logged into my own account on the machine.  
> After I do this the web interface submits jobs as expected (even
> typing qsub then ctrl-c to escape while its waiting for stdin works)
> for the remainder of the working day,  however the fix 'wears off'
> sometime between when I go home at night and get back here in the
> morning when I have to use my qsub command line fix to get things
> working again.
> Has anyone seem this problem before?
> Any help in identifying / resolving the problem so that user nobody
> jobs are submitted as expected without any weirdness will be
> appreciated
> Thanks for your time.
> David
> David Speed
> Programmer
> Roslin Institute
> Bioinformatics Group
> Roslin, 
> Midlothian, 
> EH25 9PS, 
> UK
> Telephone: +44 (0)131 527 4200 (switchboard) 
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Joseph Landman, Ph.D
Scalable Informatics LLC
email: landman@scalableinformatics.com
  web: http://scalableinformatics.com
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