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 <[EMAIL PROTECTED]> 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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
