[gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS
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.
> 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.
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
More information about the gromacs.org_gmx-users