[torqueusers] confused by mpiexec/mpirun with PBS

Troy Baer troy at osc.edu
Fri Feb 11 11:37:41 MST 2005


On Fri, 2005-02-11 at 04:36, Salvatore Di Nardo wrote:
> hem ... no one can enlight me about that?
> 
> On Wed, 2005-02-09 at 12:28, Salvatore Di Nardo wrote: 
> > Hi all,
> > i have a little cluster with a master and 8 nodes ( master and nodes
> > have 2 AMDx64 procs). We use this cluster to run several standard
> > tools (non mpi) and mpiblast.
> > 
> > Since now we ran mpiblast outside pbs ( using lamboot and mpirun ),
> > but this have the issue that lambboot do not consider nodes already
> > busy by pbs ( and vice-versa) so i tryed to run mpiblast subliting
> > it with qsub, but i'm a bit confused.
> > 
> > If i run mpiblast with mpirun i still to launch lamboot with hes own
> > config file, and this mean that mpiblast will be ran on nodes
> > already busy from other jobs.
> > 
> > If i use mpiexec i must give a "machine list" where tu run it, so i
> > must give free nodes.
> > 
> > There is any way to tell pbs to use ( as example) 8 procs on free
> > nodes, avoiding to specify directly what nodes are free? PBS is
> > supposed to do this work so i expect that lauching mpiblast ( using
> > 8 processors) via pbs mean that pbs will automatically schedule it
> > on free nodes ( or at least with 1 proc free) and not that i need to
> > give a lamboot file ( for mpirun ) or "machine list" to mpiexec that
> > contains only free nodes. 

Whose mpiexec are you using, one that came with MPICH2 or the one from
OSC?  If it's the one from OSC, it automagically gets the hostlist from
PBS.

	--Troy
-- 
Troy Baer                       email:  troy at osc.edu
Science & Technology Support    phone:  614-292-9701
Ohio Supercomputer Center       web:  http://oscinfo.osc.edu





More information about the torqueusers mailing list