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Subject: Re: [OMPI users] Oversubscription of nodes with Torque and OpenMPI
From: Lloyd Brown (lloyd_brown_at_[hidden])
Date: 2013-11-22 13:18:33


As far as I understand, the mpirun will assign processes to hosts in the
hostlist ($PBS_NODEFILE) sequentially, and if it runs out of hosts in
the list, it starts over at the top of the file.

Theoretically, you should be able to request specific hostnames, and the
processor counts per hostname, in your torque submit request. I'm not
sure if this is correct (we don't use Torque here anymore, and I'm going
off memory), but it should be approximately correct:

> qsub -l nodes=n0000:2+n0001:2+n0002:8+n0003:8+n0004:2+n0005:2+n0006:2+n0007:4 ...

Granted, that's awkward, but I'm not sure if there's another way in
Torque to request different numbers of processors per node. You might
ask on the Torque Users list. They might tell you to change the nodes
file to reflect the number of actual processes you want on each node,
rather than the number of physical processors on the hosts. Whether
this works for you, depends on whether you want this type of
oversubscription to happen all the time, or on a per-job basis, etc.

Lloyd Brown
Systems Administrator
Fulton Supercomputing Lab
Brigham Young University
http://marylou.byu.edu

On 11/22/2013 11:11 AM, Gans, Jason D wrote:
> I have tried the 1.7 series (specifically 1.7.3) and I get the same
> behavior.
>
> When I run "mpirun -oversubscribe -np 24 hostname", three instances of
> "hostname" are run on each node.
>
> The contents of the $PBS_NODEFILE are:
> n0007
> n0006
> n0005
> n0004
> n0003
> n0002
> n0001
> n0000
>
> but, since I have compiled OpenMPI using the "--with-tm", it appears
> that OpenMPI is not using the $PBS_NODEFILE (which I tested by modifying
> the torque pbs_mom to write a $PBS_NODEFILE that contained "slot=xx"
> information for each node. mpirun complained when I did this).
>
> Regards,
>
> Jason
>
> ------------------------------------------------------------------------
> *From:* users [users-bounces_at_[hidden]] on behalf of Ralph Castain
> [rhc_at_[hidden]]
> *Sent:* Friday, November 22, 2013 11:04 AM
> *To:* Open MPI Users
> *Subject:* Re: [OMPI users] Oversubscription of nodes with Torque and
> OpenMPI
>
> Really shouldn't matter - this is clearly a bug in OMPI if it is doing
> mapping as you describe. Out of curiosity, have you tried the 1.7
> series? Does it behave the same?
>
> I can take a look at the code later today and try to figure out what
> happened.
>
> On Nov 22, 2013, at 9:56 AM, Jason Gans <jgans_at_[hidden]
> <mailto:jgans_at_[hidden]>> wrote:
>
>> On 11/22/13 10:47 AM, Reuti wrote:
>>> Hi,
>>>
>>> Am 22.11.2013 um 17:32 schrieb Gans, Jason D:
>>>
>>>> I would like to run an instance of my application on every *core* of
>>>> a small cluster. I am using Torque 2.5.12 to run jobs on the
>>>> cluster. The cluster in question is a heterogeneous collection of
>>>> machines that are all past their prime. Specifically, the number of
>>>> cores ranges from 2-8. Here is the Torque "nodes" file:
>>>>
>>>> n0000 np=2
>>>> n0001 np=2
>>>> n0002 np=8
>>>> n0003 np=8
>>>> n0004 np=2
>>>> n0005 np=2
>>>> n0006 np=2
>>>> n0007 np=4
>>>>
>>>> When I use openmpi-1.6.3, I can oversubscribe nodes but the tasks
>>>> are allocated to nodes without regard to the number of cores on each
>>>> node (specified by the "np=xx" in the nodes file). For example, when
>>>> I run "mpirun -np 24 hostname", mpirun places three instances of
>>>> "hostname" on each node, despite the fact that some nodes only have
>>>> two processors and some have more.
>>> You submitted the job itself by requesting 24 cores for it too?
>>>
>>> -- Reuti
>> Since there are only 8 Torque nodes in the cluster, I submitted the
>> job by requesting 8 nodes, i.e. "qsub -I -l nodes=8".
>>>
>>>
>>>> Is there a way to have OpenMPI "gracefully" oversubscribe nodes by
>>>> allocating instances based on the "np=xx" information in the Torque
>>>> nodes file? It this a Torque problem?
>>>>
>>>> p.s. I do get the desired behavior when I run *without* Torque and
>>>> specify the following machine file to mpirun:
>>>>
>>>> n0000 slots=2
>>>> n0001 slots=2
>>>> n0002 slots=8
>>>> n0003 slots=8
>>>> n0004 slots=2
>>>> n0005 slots=2
>>>> n0006 slots=2
>>>> n0007 slots=4
>>>>
>>>> Regards,
>>>>
>>>> Jason
>>>>
>>>>
>>>>
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