[gmx-developers] Trying to understand performance issue - due to all threads pinning to first core?

[Roland Schulz]

Hi,

depending on the jobs scheduler you use, you can get get the slot number
you got assigned for the shared node, so that your jobscript an set the
correct pinoffset.

Roland


On Wed, Dec 19, 2012 at 1:55 PM, Shirts, Michael (mrs5pt) <
mrs5pt at eservices.virginia.edu> wrote:

> > you can use -nopin but you will get slightly lower performance.
>
> Ah, great!  I'll try this.  I didn't see this documented on the page --
> perhaps it should be added -- if, of course, I didn't just miss it.
>
> > You can
> > also use pinoffset and number the different gromacs instances you are
> > running any way you wish. Most programs don't pin so it is unlikely that
> it
> > going to conflict with other programs if you are running both Gromacs and
> > other programs.
>
> But that doesn't solve situations where I have four students plus myself
> all
> submitting Gromacs runs to the same cluster :)
>
> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821
>
>
>
>
>
>
>
>


-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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