[torqueusers] qsub and mpiexec -f machinefile

Tiago Silva (Cefas) tiago.silva at cefas.co.uk
Thu Feb 20 06:32:48 MST 2014


Sure, I will want to stick to the exact same nodes. In my case I don't need to worry about free slots on the nodes I am specifying exclusive usage with -W x="NACCESSPOLICY:SINGLEJOB".
I actually oversubscribe the cores as some processes have very little to do, that is part of the performance optimisation I want to retain

Thanks again
tiago

> -----Original Message-----
> From: torqueusers-bounces at supercluster.org [mailto:torqueusers-
> bounces at supercluster.org] On Behalf Of Michel Béland
> Sent: 20 February 2014 13:10
> To: torqueusers at supercluster.org
> Subject: Re: [torqueusers] qsub and mpiexec -f machinefile
> 
> Tiago Silva (Cefas) wrote:
> 
> > Thanks, this seems promising. Before I try building with openmpi, if
> I
> > parse PBS_NODEFILE to produce my own machinefile for mpiexec, for
> > instance following my previous example:
> >
> > n100
> > n100
> > n101
> > n101
> > n101
> > n101
> >
> > won't mpiexec start mpi processes with ranks 0-1 onto n100 and with
> > rank 2-5 on n101? That what I think it does when I don't use qsub.
> 
> Yes, but you should not change the nodes inside the $PBS_NODEFILE. You
> can change the order but do not delete machines and add new ones,
> otherwise your MPI code will try to run on nodes belonging to other
> jobs.
> 
> If you want to have exactly the nodes above, you can ask for -
> lnodes=n100:ppn=2+n101:ppn=4. If you only want two cores on the first
> node and four on the second but the specific nodes are irrelevant, you
> can ask for -lnodes=1:ppn=2+1:ppn=4 instead.
> 
> Michel Béland
> Calcul Québec
> 
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