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Subject: Re: [OMPI users] Over committing?
From: Rushton Martin (JMRUSHTON_at_[hidden])
Date: 2011-04-13 11:29:02


I'm afraid I can't comment on how OMPI was configured, "as supplied by
the suppliers"! The users experiencing these problems use the Intel
bindings, loaded via the modules command. We are running CentOS 5.3.

Martin Rushton
HPC System Manager, Weapons Technologies
Tel: 01959 514777, Mobile: 07939 219057
email: jmrushton_at_[hidden]
www.QinetiQ.com
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-----Original Message-----
From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]] On
Behalf Of Ralph Castain
Sent: 13 April 2011 16:21
To: Open MPI Users
Subject: Re: [OMPI users] Over committing?

Afraid I have no idea - we regularly run on Torque machines with the
nodes fully populated. While most runs are only for a few hours, some
runs go for days.

How was OMPI configured? What OS version?

On Apr 13, 2011, at 9:09 AM, Rushton Martin wrote:

> Version 1.3.2
>
> Consider a job that will run with 28 processes. The user submits it
> with:
>
> $ qsub -l nodes=4:ppn=7 ...
>
> which reserves 7 cores on (in this case) each of x3550x014 x3550x015
> and
> x3550x016 x3550x020. Torque generates a file (PBS_NODEFILE) which
> lists each node 7 times.
>
> The mpirun command given within the batch script is:
>
> $ mpirun -np 28 -machinefile $PBS_NODEFILE <executable>
>
> This is what I would refer to as 7+7+7+7, and it runs fine.
>
> The problem occurs if, for instance, a 24 core job is attempted. qsub

> gets nodes=3:ppn=8 and mpirun has -np 24. The job is now running on
> three nodes, using all eight cores on each node - 8+8+8. This sort of

> job will eventually hang and has to be killed off.
>
> Cores Nodes Ppn Result
> ----- ----- --- ------
> 8 1 any works
> 8 >1 1-7 works
> 8 >1 8 hangs
> 16 1 any works
> 16 >1 1-15 works
> 16 >1 16 hangs
>
> We have also tried test jobs on 8+7 (or 7+8) with inconclusive
results.
> Some of the live jobs run for a month or more and cut down versions do

> not model well.
>
> Martin Rushton
> HPC System Manager, Weapons Technologies
> Tel: 01959 514777, Mobile: 07939 219057
> email: jmrushton_at_[hidden]
> www.QinetiQ.com
> QinetiQ - Delivering customer-focused solutions
>
> Please consider the environment before printing this email.
> -----Original Message-----
> From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]]
> On Behalf Of Ralph Castain
> Sent: 13 April 2011 15:34
> To: Open MPI Users
> Subject: Re: [OMPI users] Over committing?
>
>
> On Apr 13, 2011, at 8:13 AM, Rushton Martin wrote:
>
>> The bulk of our compute nodes are 8 cores (twin 4-core IBM x3550-m2).
>> Jobs are submitted by Torque/MOAB. When run with up to np=8 there is

>> good performance. Attempting to run with more processors brings
>> problems, specifically if any one node of a group of nodes has all 8
>> cores in use the job hangs. For instance running with 14 cores (7+7)

>> is fine, but running with 16 (8+8) hangs.
>>
>>> From the FAQs I note the issues of over committing and aggressive
>> scheduling. Is it possible for mpirun (or orted on the remote nodes)

>> to be blocked from progressing by a fully committed node? We have a
>> few
>> x3755-m2 machines with 16 cores, and we have detected a similar issue

>> with 16+16.
>
> I'm not entirely sure I understand your notation, but we have never
> seen an issue when running with fully loaded nodes (i.e., where the
> number of MPI procs on the node = the number of cores).
>
> What version of OMPI are you using? Are you binding the procs?
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