[torqueusers] confused by mpiexec/mpirun with PBS

Garrick Staples garrick at usc.edu
Fri Feb 11 11:14:39 MST 2005


PBS gives you a machine list to use.  The name of the file is in $PBS_NODEFILE.
So in your pbs script, you can do something like:
   $np=$(wc -l $PBS_NODEFILE)
   mpirun -np $np -machinefile $PBS_NODEFILE

On Fri, Feb 11, 2005 at 10:36:10AM +0100, Salvatore Di Nardo alleged:
> 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. 
> > 
> > where i'm wrong?
> > 
> > Salvatore Di Nardo 
> > 
> > ______________________________________________________________________
> > 
> > _______________________________________________
> > torqueusers mailing list
> > torqueusers at supercluster.org
> > http://supercluster.org/mailman/listinfo/torqueusers

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-- 
Garrick Staples, Linux/HPCC Administrator
University of Southern California
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