[GE users] sge with perl

Joe Landman landman at scalableinformatics.com
Tue Sep 16 00:53:52 BST 2008


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Mag Gam wrote:
> Yes. They depend on each other. Actually, I will open a new thread of
> discussion on MPI and scheduling. Thanks again for your help!
> 
> On Mon, Sep 15, 2008 at 12:33 PM, Rayson Ho <rayrayson at gmail.com> wrote:
>> A simpiler way to speed things up is is to run multiple jobs on the
>> cluster... Are those 2-hr jobs independent of each other??
>>

Hi Mag:

  Something worth considering (and relatively standard optimization 
practice) is to explore which are the time expensive routines, and see 
if they can be recoded (rewritten or parallelized).

  Have you profiled your code, so that you know where the time expensive 
portion is?  I ask, as often times we see optimization/parallelization 
projects commence in advance of an understanding of what the specific 
computational rate limiting step is.  For example, MPI parallel 
operations won't necessarily help an I/O bound code.

Joe

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Joseph Landman, Ph.D
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Scalable Informatics LLC,
email: landman at scalableinformatics.com
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