[gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS
Mark.Abraham at anu.edu.au
Fri Nov 2 23:50:37 CET 2007
himanshu khandelia wrote:
> I get bad scaling with 8 cpus.
>> 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 :-)
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
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.
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