[GE users] SGEfy a job

Chris Dagdigian dag at sonsorol.org
Wed Sep 17 12:41:40 BST 2008


A good first test would be to take a few of your SSH-driven commands  
and just replace SSH with a call to SGE 'qrsh' to see if that works.  
The qrsh command will try to execute your task ASAP on the least busy  
node in the system. It only works if there are job slots free so this  
is not something you can assume will be functional all the time.

A second test would be to look in $SGE_ROOT/examples/job/ and take a  
peek at sleeper.sh and simple.sh -- those scripts are the bare bones  
basic scripts that you would submit to SGE via "qsub ./path-to- 
simple.sh". Just put your application commands including the output to  
the NFS location into a shell script and qsub that script in to SGE.    
Pay careful attention to the neat "#$ <sge arg>" syntax that lets you  
embed things in your shell script that are interpreted as arguments to  
qsub. This makes it really easy to bake in all your SGE job commands  
into the script so that you can just "qsub ./my-script.sh" and let it  
go.

qsub can also directly support running your binary "(qsub -b y ...)"  
but most people submit jobs via shell scripts.

Once you are familiar with qrsh and qsub the next more "advanced"  
thing would involve taking all your jobs N pieces and submitting them  
as an SGE job array. The job array allows you to submit your N tasks  
to the cluster via a single qsub command and you get back a single  
jobID for all N of your work units.

-Chris




On Sep 17, 2008, at 7:33 AM, Mag Gam wrote:

> Hello,
>
> I have a job which does a reactive fluid flow simulation and it
> outputs several result files onto  a shared NFS filesystem. The way I
> am doing it now is, splitting the job into n pieces and SSHing it over
> to x servers and having each server run a small portion of the job.
> This is the "poor" man's way of doing it. I was wondering if there is
> a document or procedure I can follow to make my job run with SGE.
>
> I am curious about any environment variabes, weighting, and things of
> that nature.
>
> TIA
>
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