[GE users] SGE questions

john.li at mindspeed.com john.li at mindspeed.com
Thu Mar 1 17:29:28 GMT 2007

Hi Rayson,

Thanks for the reply.   And thanks for correct my mistake on the 

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.


"Rayson Ho" <rayrayson at gmail.com> 
02/28/07 03:07 PM
Please respond to
users at gridengine.sunsource.net

users at gridengine.sunsource.net

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 
> to locate a script if I use -b n for a script.   Is there a reason for 
> 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

"-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 


> I have more questions, but this is good for now.  :-)    Someone, please
> help...
> Best regards,
> John,

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