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

himanshu khandelia hkhandelia at gmail.com
Sun Nov 4 20:12:19 CET 2007

My apologies for not reading the reference properly. Thanks, Mark

However, the --byslot option is not being able to do the needful. I
will update if I learn something new.

On Nov 2, 2007 11:50 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> himanshu khandelia wrote:
> > 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
> When describing material like this, you'd do well to separate your
> speculation from your knowledge in your description, and limit the
> former. If your speculation was so hot, you'd have probably fixed the
> problem by now :-)
> http://www.open-mpi.org/faq/?category=running#mpirun-scheduling suggests
> that the interplay of --byslot and --bynode with your machine will
> depend how the hostfile is set up. You need to find out what the
> defaults for the machine are and how to tweak them to what you want
> under PBS.
> hostfile:
> node0 slots=4 max_slots=4
> node1 slots=4 max_slots=4
> and then two "mpirun -np 4 --byslot --hostfile hostfile mdrun" look
> right to me.
> Mark
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