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Subject: Re: [OMPI users] Over committing?
From: Rushton Martin (JMRUSHTON_at_[hidden])
Date: 2011-04-13 11:09:27


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

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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 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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