[torqueusers] specifying nodes for MPI jobs on small cluster

Gus Correa gus at ldeo.columbia.edu
Thu Feb 7 12:28:22 MST 2013


Hi Andrew

Not sure I understood what exactly you want to do,
but have you tried this?

#PBS -l nodes=1:ppn=8


It will request one node with 8 processors.

I hope this helps,
Gus Correa

On 02/07/2013 11:38 AM, Andrew Dawson wrote:
> Nodes file looks like this:
>
> cirrus np=1
> cirrus1 np=8
> cirrus2 np=8
> cirrus3 np=8
> cirrus4 np=8
>
> On 7 Feb 2013 16:25, "Ricardo Román Brenes" <roman.ricardo at gmail.com
> <mailto:roman.ricardo at gmail.com>> wrote:
>
>     hi!
>
>     How does your node config file looks like?
>
>     On Thu, Feb 7, 2013 at 3:10 AM, Andrew Dawson <dawson at atm.ox.ac.uk
>     <mailto:dawson at atm.ox.ac.uk>> wrote:
>
>         Hi all,
>
>         I'm configuring a recent torque/maui installation and I'm having
>         trouble with submitting MPI jobs. I would like for MPI jobs to
>         specify the number of processors they require and have those
>         come from any available physical machine, the users shouldn't
>         need to specify processors per node etc.
>
>         The torque manual says that the nodes option is mapped to
>         virtual processors, so for example:
>
>              #PBS -l nodes=8
>
>         should request 8 virtual processors. The problem I'm having is
>         that our cluster currently has only 5 physical machines (nodes),
>         and setting nodes to anything greater than 5 gives the error:
>
>              qsub: Job exceeds queue resource limits MSG=cannot locate
>         feasible nodes (nodes file is empty or all systems are busy)
>
>         I'm confused by this, we have 33 virtual processors available
>         across the 5 nodes (4 8-core machines and one single core) so my
>         interpretation of the manual is that I should be able to request
>         8 nodes, since these should be understood as virtual processors?
>         Am I doing something wrong?
>
>         I tried setting
>
>         #PBS -l procs=8
>
>         but that doesn't seem to do anything, MPI stops due to having
>         only 1 worker available (single core allocated to the job).
>
>         Thanks,
>         Andrew
>
>         p.s.
>
>         The queue I'm submitting jobs to is defined as:
>
>         create queue normal
>         set queue normal queue_type = Execution
>         set queue normal resources_min.cput = 12:00:00
>         set queue normal resources_default.cput = 24:00:00
>         set queue normal disallowed_types = interactive
>         set queue normal enabled = True
>         set queue normal started = True
>
>         and we are using torque version 2.5.12 and we are using maui
>         3.3.1 for scheduling
>
>
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>
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