[GE users] permissions on directories...

Robert Griffiths Robert.Griffiths at int.sc.mufg.jp
Wed May 17 15:55:29 BST 2006


Hi Davide,
 
Do you pass the "-cwd" flag when you submit your job? I seem to recall that
the current working directory was not passed through to the job unless
"-cwd" is also specified on the command line.
 
If this is not the case, is your directory visible on all of your nodes? It
could be that the example SGE script runs from wherever because it doesn't
require any data from the current working directory...
 
We've had some errors similar to this in the past, but mostly it's because
some volume from NFS hasn't been exported to a recently-introduced machine.
 
Hope that helps!
 
Rob
 
-----Original Message-----
From: davide cittaro [mailto:daweonline at gmail.com] 
Sent: 17 May 2006 15:19
To: users at gridengine.sunsource.net
Subject: Re: [GE users] permissions on directories...



Hi there, I'm still investigating on the permission error... It seems that
permission mode doesn't explain the error... what I can say now is:
1- I launch the script from a directory X it goes in Eqw state
2- I copy that script in my home it runs 
3- I copy a SGE example script in directory X it runs
4- I run the script from directory X but on another cluster grid (that
shares the directory X)... it runs...

the messages:

05/17/2006 16:13:48|execd|ia32|E|shepherd of job 430.1 exited with exit
status = 27
05/17/2006 16:13:48|execd|ia32|W|reaping job "430" ptf complains: Job does
not exist
05/17/2006 16:13:48|execd|ia32|E|can't open usage file
"active_jobs/430.1/usage" for job 430.1: No such file or directory
05/17/2006 16:13:48|execd|ia32|E|05/17/2006 16:13:48 [2486:4613]:
execvp(/opt/sge6/bioinfo/spool/ia32/job_scripts/430,
"/opt/sge6/bioinfo/spool/ia32/job_scripts/430") failed: No such file or
directory 

Any hint?

d


On 5/10/06, Reuti <reuti at staff.uni-marburg.de
<mailto:reuti at staff.uni-marburg.de> > wrote: 

Am 10.05.2006 um 11:48 schrieb davide cittaro:

> Okay, now the question: is the directory /opt/sge6/bioinfo/spool/
> alpha2 readable/executable by all users on the execution host(s)? The
> scripts are run directly from this location. 
>
> Well, the permissions are 755 and other users (with 775, 771) on
> their homes can run stuff... The users are stored in a LDAP server
> that runs remotely... can be this a problem?

Are you sure that this is the only difference - can you try to change 
the permission settings and see the result? My users also have
different protection settings (700 or 755) and I don't face any
problems with this setup.

What Linux are you using? In Debian AFAIK the default is that each 
user is his own group, in contrast to SuSE, where all are in one
default group. So, what are the detailed protection settings of opt/
sge6/bioinfo/spool/alpha2? How is your primary/secondary group setup
of your users? I have access to a Debian cluster with an external 
LDAP and all is working smoothly.

-- Reuti

> d
>
>
>
> -- Reuti
>
>
> > the -cwd option should save him from such errors, shouldn't it?
> >
> > d 
> >
> > On 5/10/06, Reuti <reuti at staff.uni-marburg.de
<mailto:reuti at staff.uni-marburg.de>  > wrote:Hi,
> >
> > Am 10.05.2006 um 10:50 schrieb davide cittaro:
> > 
> > > Hi all, I've seen that some users cannot run GE and the jobs
> are in
> > > Eqw state, but qstat -j doesn't say anything at all...
> > > I don't know which permissions they have on the cwd, where they 
> > > launch jobs, but they have 700 on their /home... Is it possible
> > > that this somehow interferes with GE?
> >
> >
> > no, this should work. Is there any hint in any of the messages files 
> > $SGE_ROOT/spool/qmaster/messages or the one from the node where the
> > job tried to start? Anything in the standard-out/-err files?
> >
> > -- Reuti
> >
> >
> > > Thanks 
> > >
> > > d
> >
> >
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