[GE users] SGE questions

john.li at mindspeed.com john.li at mindspeed.com
Thu Mar 1 18:12:15 GMT 2007


I assume 'spooling the jobscript' means copying the script to a spooling 
area
first, before the execution.   This is a new concept to me,  I don't think 
LSF does this at all.

There is no distinction betweeen a binary executable and a script.   In 
LSF, I don't worry
about it.  I submit either a binary or a script, as long as it is in my 
search path, LSF
will have no problem of running it.






Reuti <reuti at staff.uni-marburg.de> 
03/01/07 10:05 AM
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Subject
Re: [GE users] SGE questions






Am 01.03.2007 um 18:29 schrieb john.li at mindspeed.com:

>
> Hi Rayson,
>
> Thanks for the reply.   And thanks for correct my mistake on the 
> description.
>
> The reason that I brought this behavior up is due to the umask 
> issue that I mentioned
> in my original email.   The umask seems to inherit user shell umask 
> when a job is
> submitted as a script.  (Inherit environment umask is what I 
> want)   but not as a binary.
> But SGE doesn't use $PATH to search for a script, which is not good 
> as far as I concern.
> I don't have this problem in LSF at all.

You mean something like:

qsub `which myscript.sh`

Is LSF spooling the jobscript, or using the original during the later 
execution?

-- Reuti


> Thanks,
>
>
>
>
> "Rayson Ho" <rayrayson at gmail.com>
> 02/28/07 03:07 PM
> Please respond to
> users at gridengine.sunsource.net
>
>
> To
> users at gridengine.sunsource.net
> cc
> Subject
> Re: [GE users] SGE questions
>
>
>
>
>
> On 2/28/07, john.li at mindspeed.com <john.li at mindspeed.com> wrote:
> > I'm new to SGE and trying to deploy SGE to replace LSF.
>
> Good :)
>
> > 3.  It seems that if I use -b y in the qsub  command, I MUST 
> specify the
> > full path
> > for the binary executable or it is in the current working 
> directory.   SGE
> > doesn't
> > use the $PATH variable to locate the binary executable.   But SGE 
> will use
> > $PATH
> > to locate a script if I use -b n for a script.   Is there a 
> reason for this
> > behavior?
>
> Shouldn't it be the other way around??
>
> "-b n" tells qsub that the job is a script, and SGE will look for the
> job script in the current directory or the location specified at qsub
> time.
>
> "-b y" tells qsub that the job is a binary program, and SGE will not
> spool the binary to the master machine. Since the location of the
> binary can be different with different OSes/architectures, recording
> the path does not make sense.
>
> I've just tested on my cluster and that's the behavior... and I
> believe it has something to do with POSIX 1003.2d (standard for batch
> queuing systems).
>
> * also note that LSF does not spool the job script or the binary at 
> bsub time.
>
> Rayson
>
>
>
>
> >
> > I have more questions, but this is good for now.  :-) 
> Someone,  please
> > help...
> >
> > Best regards,
> >
> > John,
> >
> >
> >
> >
>
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