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

Mark Abraham Mark.Abraham at anu.edu.au
Fri Nov 2 16:28:15 CET 2007

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".


More information about the gromacs.org_gmx-users mailing list