[gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS

[himanshu khandelia]

I get bad scaling with 8 cpus.
http://www.gromacs.org/index.php?option=com_wrapper&Itemid=84


> I'm not seeing how openmpi (the implementation) can be
> allocating cpus "depending on what options gromacs was originally
> compiled with".

I do not see immediately how either, but just seemed logical to me. I
may be wrong


On Nov 2, 2007 4:28 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> himanshu khandelia wrote:
> > Hi Mark,
> >
> > I do not want to request two separate 1-node jobs, so that I can make
> > maximum use of the MAUI queue algorithm on our local cluster, which
> > sometimes favors jobs which utilize more resources.
>
> So what about using 8-cpu jobs?
>
> > I posted on this list, because someone here might have faced a similar
> > problem before, and because how openmpi allocates cpus also depends on
> > what options gromacs was originally compiled with (in connection to
> > MPI). So its not strictly a 100% openmpi question.
>
> GROMACS is using the MPI protocol in a manner independent of the
> implementation. I'm not seeing how openmpi (the implementation) can be
> allocating cpus "depending on what options gromacs was originally
> compiled with".
>
>
> Mark
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