[torqueusers] PBS_NODEFILE order question

Brock Palen brockp at umich.edu
Tue Feb 17 18:44:42 MST 2009


Try this is using Open MPI  1.2.x  series

mpirun -bynode app

-bynode places cpus like you have in your listing.

You just have to be careful, that you always have 2 cpus per node, or  
something similar.

the tpn option and gemoetry option if using moab with toruque should  
be a big help.

For example:

I want 2 nodes, 2 cpus per machine, I don't want 4 ever,  and I want  
Open MPI to put rank 0 and 2 on node 1, and rank, 1 and 3 on node 2.

#PBS -l nodes=2:ppn=2,tpn=2

mpirun -bynode myapp

Your not mixing threads with with MPI are you that you want that kind  
of layout?

Brock Palen
www.umich.edu/~brockp
Center for Advanced Computing
brockp at umich.edu
(734)936-1985



On Feb 17, 2009, at 8:38 PM, Garrick Staples wrote:

> On Tue, Feb 17, 2009 at 04:43:04PM -0800, Jackie Scoggins alleged:
>> torque - version 2.1.8
>> maui version 3.2.6p19
>>
>> Is there a way to make the PBS_NODEFILE order the nodes as follows:
>>
>> n0000
>> n0001
>> n0000
>> n0001
>> n0000
>> n0001
>
> Nope.
>
>
>> I have tried chopping up the PBS_NODEFILE and using a different
>> hostfile for mpirun but I get an orted error from mpirun because it
>> does not look like it is selecting the nodes in the order in which I
>> specify in my hostfile.
>
> Probably best for whatever tool to have options for whatever sort  
> orders you
> like.  I'm sure this would fit nicely into openmpi.
>
> -- 
> Garrick Staples, GNU/Linux HPCC SysAdmin
> University of Southern California
>
> See the Prop 8 Dishonor Roll at http:// 
> www.californiansagainsthate.com/
>
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