Re: Starcluster - Taking advantage of multiple cores on EC2

From: Rayson Ho <no email>
Date: Wed, 31 Aug 2011 10:57:11 -0700 (PDT)

Bill,

1) What do you get when you run "qhost" on the EC2 cluster??

2) If you run your application outside of SGE on your EC2 cluster, do you get the same behavior??

3) Intel MKL uses OpenMP internally, did you set the env. var. OMP_NUM_THREADS on the laptop??

Rayson

=================================
Grid Engine / Open Grid Scheduler
http://gridscheduler.sourceforge.net



--- On Wed, 8/31/11, Chris Dagdigian <dag_at_bioteam.net> wrote:
> Grid Engine just executes jobs and manages resources.
>
> It's up to your code to use more than one core.
>
> Maybe there is a config difference between your local
> scipy/numpy etc.
> install and how StarCluster deploys it's version?
>
> Grid Engine assumes by default a  1:1 ratio between
> job and CPU core
> unless you are explicitly submitting to a parallel
> environment.
>
> If you are the only user on a small cluster you probably
> don't have to
> do much, the worst that could happen would be that SGE
> queues up and
> runs more than one of your threaded app job on the same
> host and they
> end up competing for CPU/memory resources to the detriment
> of all.
>
> One way around that would be to configure exclusive job
> access and
> submit your job with the "exclusive" request. That will
> ensure that your
> job when it runs will get an entire execution host.
>
> Another way is to fake up a parallel environment. For your
> situation it
> is very common for people to build a parallel environment
> called
> "Threaded" or "SMP" so that they can run threaded apps
> without
> oversubscribing an execution host.
>
> With a threaded PE set up you'd submit your job:
>
>   $ qsub -pe threaded=<# CPU> my-job-script.sh
>
> ... and SGE would account for your single job using more
> than one CPU on
> a single host.
>
>
> FYI Grid Engine has recently picked up some Linux core
> binding
> enhancements that make it easier to pin jobs and tasks to
> specific
> cores. I'm not sure if the version of GE that is built into
> StarCluster
> today has those features yet but it should gain them
> eventually.
>
> Regards,
> Chris
>
>
>
>
>
>
>
> Bill Lennon wrote:
> > Dear Starcluster Gurus,
> >
> > I’ve successfully loaded the Starcluster AMI onto a
> single high-memory
> > quadruple extra large instance and am performing an
> SVD on a large
> > sparse matrix and then performing k-means on the
> result.  However, I’m
> > only taking advantage of one core when I do
> this?  On my laptop (using
> > scipy numpy, intel MKL), on a small version of this,
> all cores are taken
> > advantage of automagically.  Is there an easy way
> to do this with a
> > single starcluster instance with Atlas? Or do I need
> to explicitly write
> > my code to multithread?
> >
> > My thanks,
> >
> > Bill
> >
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Received on Wed Aug 31 2011 - 13:57:13 EDT