[GE users] Scripting help

Reuti reuti at staff.uni-marburg.de
Mon Apr 11 15:37:54 BST 2005


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Dale,

if I got you in the correct way, you want to submit the script vqcib.csh 
with some fixed parameters option1, option2,... Then your (submitted) 
script will call <path>/vqcib.exe $*? So you can't make a qsub for now 
because of the "Unknown option" error message?

Reuti

Schmitz Dale M Contr 20 IS/INPTG wrote:
> -----Original Message-----
> From: Reuti [mailto:reuti at staff.uni-marburg.de]
> Sent: Monday, April 11, 2005 9:08 AM
> To: users at gridengine.sunsource.net
> Subject: Re: [GE users] Scripting help
> 
>  
> 
> Schmitz Dale M Contr 20 IS/INPTG wrote:
> 
>>  I've done that...and I still get the "Unknown option" error.
> 
>>
> 
>>  Originally, the whole thing went like this:  an application called a
> 
>>  script, vqcib, which contained the line:
> 
>>
> 
>>  <path>/vqcib.exe $*
> 
>>
> 
>>  ...and away the job went.  Now with the grid engine, I can't merely
> 
>>  insert a qsub into that script because I can't qsub an executable.  So I
> 
>>  rewrote vqcib to read:
> 
>  
> 
> What is an:
> 
>  
> 
> echo $*
> 
>  
> 
> telling you in the script before the .exe call?
> 
>  
> 
> It?s giving me all the parameters that need to be submitted with the 
> vqcib.exe job.
> 
>  
> 
>>
> 
>>  <path>/qsub <path>vqcib.csh $*
> 
>  
> 
> I don't know the details, but did you gave additional parameters in the
> 
> original call to the .exe? And you just add them like:
> 
>  
> 
> <path>/qsub <path>vqcib.csh option1 option2
> 
>  
> 
> and they should go the script. And for this qsub you get the error?
> 
> Which SGE? Or is the error coming from the application? - Reuti
> 
>  
> 
> The original call to the .exe used ?$*?, as in ?vqcib.exe $*? passing 
> all parameters to vqcib.exe.  qsub doesn?t like that for some reason.
> 
>  
> 
>>
> 
>>  ...and now vqcib.csh contains the line:
> 
>>
> 
>>  <path>/vqcib.exe $*
> 
>>
> 
>>  ...but evidently something's getting lost in translation somewhere
> 
>>  because either the grid engine or the executable is returning an
> 
>>  "Unknown option" error, possibly meaning that vqcib.exe is not receiving
> 
>>  the full list of parameters or they've been corrupted somehow.  First
> 
>>  things first though: do I understand the qsub man page and grid engine
> 
>>  documentation enough to assume that my implementation should work, or am
> 
>>  I missing something?  Are there better ways to pass along parameters in
> 
>>  the grid engine?
> 
>>
> 
>>  Thanks,
> 
>>  Dale
> 
>>
> 
>>
> 
>>
> 
>>  -----Original Message-----
> 
>>  From: Reuti [mailto:reuti at staff.uni-marburg.de]
> 
>>  Sent: Monday, April 11, 2005 8:44 AM
> 
>>  To: users at gridengine.sunsource.net
> 
>>  Subject: Re: [GE users] Scripting help
> 
>>
> 
>>  It's $1, $2 ... in the script and $* for all parameters. Details you
> 
>>  find in "man csh". - Reuti
> 
>>
> 
>>  Schmitz Dale M Contr 20 IS/INPTG wrote:
> 
>>
> 
>> >Either way I go with that, with or without the "--", the trick seems
> 
>>
> 
>>  to
> 
>>
> 
>> >be getting the parameters identified in the vqcib.csh script.  Within
> 
>> >vqcib.csh, what variable identifies the parameters and what's the
> 
>>
> 
>>  syntax
> 
>>
> 
>> >for using that variable?
> 
>> > 
> 
>> >Dale
> 
>> > 
> 
>> >-----Original Message-----
> 
>> >From: Reuti [mailto:reuti at staff.uni-marburg.de]
> 
>> >Sent: Monday, April 11, 2005 8:29 AM
> 
>> >To: users at gridengine.sunsource.net
> 
>> >Subject: Re: [GE users] Scripting help
> 
>> > 
> 
>> >Hi,
> 
>> > 
> 
>> >what do you mean in detail: your submit script is submitting:
> 
>> > 
> 
>> >qsub vqcib.csh $*
> 
>> > 
> 
>> >and you need
> 
>> > 
> 
>> >qsub vqcib.csh -- $*
> 
>> > 
> 
>> > 
> 
>> >Depending on the parmeters, the -- is not always necessary as I found.
> 
>> > 
> 
>> >CU - Reuti
> 
>> > 
> 
>> > 
> 
>> >Schmitz Dale M Contr 20 IS/INPTG wrote:
> 
>> > 
> 
>> > 
> 
>> >>I can't seem to find (or maybe interpret) the info I need to send
> 
>> >>command line parameters to a script that I'm qsub'ing.  I read from
> 
>> > 
> 
>> >the
> 
>> > 
> 
>> > 
> 
>> >>qsub man page that I should be able to:
> 
>> >> 
> 
>> >> 
> 
>> >> 
> 
>> >>qsub <scriptfile> -- <options>
> 
>> >> 
> 
>> >> 
> 
>> >> 
> 
>> >>However, I don't quite understand how to receive the options in the
> 
>> >><scriptfile> so that they can be passed along to the executable.
> 
>> >> 
> 
>> >> 
> 
>> >> 
> 
>> >>As it stands, I have a process that submits a job thusly:
> 
>> >> 
> 
>> >> 
> 
>> >> 
> 
>> >>vqcib.csh $*
> 
>> >> 
> 
>> >> 
> 
>> >> 
> 
>> >>...in a tcsh environment.  "vqcib" is a script that executes
> 
>> > 
> 
>> >"vqcib.exe
> 
>> > 
> 
>> > 
> 
>> >>$*".  My question is how can I rewrite vqcib.csh to allow me to qsub
> 
>> > 
> 
>> >it
> 
>> > 
> 
>> > 
> 
>> >>and pass the parameters ($*) along to the executable.  I don't see any
> 
>> > 
> 
>> > 
> 
>> >>method in the qsub man page or the Administration and Users's Guide
> 
>> > 
> 
>> >for
> 
>> > 
> 
>> > 
> 
>> >>using the #$ script prefix for doing this.
> 
>> >> 
> 
>> >> 
> 
>> >> 
> 
>> >>Thanks
> 
>> >> 
> 
>> >>Dale
> 
>> >> 
> 
>> >> 
> 
>> >> 
> 
>> >> 
> 
>> >> 
> 
>> > 
> 
>> > 
> 
>> > 
> 
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>>
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>>
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>>
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