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Subject: Re: [OMPI users] Oversubscription of nodes with Torque and OpenMPI
From: Reuti (reuti_at_[hidden])
Date: 2013-11-22 13:03:33


Am 22.11.2013 um 18:56 schrieb Jason Gans:

> 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".

No, AFAICT it's necessary to request there 24 too. To investigate it further it would also be good to copy the $PBS_NODEFILE in your job script for later inspection to your home directory. I.e. whether you are getting the correct values there already.

-- Reuti

>>
>>
>>> 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
>>>
>>>
>>>
>>> _______________________________________________
>>> users mailing list
>>> users_at_[hidden]
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
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