[GE users] permissions on directories...

davide cittaro daweonline at gmail.com
Wed May 17 16:45:04 BST 2006


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Hi. Well, actually the script should process <2Mb files... By the way I
could launch them from my home directory and everything seems working...

$ mount
/home type nfs (rw,nosuid,rsize=16384,wsize=16384,addr=85.239.175.2) <= here
works
/data type nfs (rw,nosuid,rsize=16384,wsize=16384,addr=85.239.175.2)  <=
here doesn't

Also, another GE cluster, mounting the same directories in the same way
works.

d

On 5/17/06, Reuti <reuti at staff.uni-marburg.de> wrote:
>
> Am 17.05.2006 um 16:18 schrieb davide cittaro:
>
> > 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
>
> Are you on Linux? Error 27 means file too large. Is it a big file? -
> Reuti
>
> > 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> 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 > 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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