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Subject: Re: [OMPI users] shm unlinking
From: Rushton Martin (JMRUSHTON_at_[hidden])
Date: 2011-04-14 09:46:43


A typical file is called
/dev/shm/psm_shm.41e04667-f3ba-e503-8464-db6c209b3430

I had assumed that these were from OMPI, but clearly I could be wrong.
They vary in size, but are typically 42MiB, only 0.2% of our small
diskless nodes' memory, but put a dozen in there and they start to be
noticed. lsof shows all the processes in a particular job have the same
one open, the other files are associated chronologically with failed
jobs.

HTH

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 Jeff Squyres
Sent: 14 April 2011 14:33
To: Open MPI Users
Subject: Re: [OMPI users] shm unlinking

On Apr 14, 2011, at 9:22 AM, Rushton Martin wrote:

> For your information: we were supplied with a script when we bought
> the cluster, but the original script made the assumption that all
> processes and shm files belonging to a specific user ought to be
> deleted. This is a problem if users submit jobs which only half fill
> a node and the second job starts on the same node as the first one.
> The first job to finish causes the continuing job to stop dead. We
> therefore had to disable any cleanup to allow jobs to run. Now we are

> finding a slow fill up with the shm files and I need to do something;
> at least now I have a way forward.

Note that Open MPI v1.4.x is likely using mmap files by default -- these
should be under /tmp/ somewhere. If they get left around, they can
cause shared memory to be filled up, but they should also be unrelated
in /dev/shm kinds of things. If you're seeing /dev/shm fill up, that
might be due to something else.

Also, I'm a little confused by your reference to psm_shm... are you
talking about the QLogic PSM device? If that does some tomfoolery with
/dev/shm somewhere, I'm unaware of it (i.e., I don't know much/anything
about what that device does internally).

--
Jeff Squyres
jsquyres_at_[hidden]
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